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Bevacizumab or Avastin® (Av), the recombinant antibody targeting VEGF, improves progression-free but not overall survival of metastatic breast cancer patients due to development of Av resistance. We showed that Av-therapy-induced inflammatory microenvironment contributes to the refractoriness to Av treatment. Here we present data regarding the effect of Av treatment on migration of a non-invasive breast cancer cell line, MCF-7. The data presented hereis related to the research article “Bevacizumab induces inflammation in MDA-MB-231 breast cancer cell line and in a mouse model” (Hajjar et al., 2018). Keywords: Bevacizumab, MCF-7, Migration, RTCA

The data presented in this article are related to the research paper entitled “Intensified mitophagy in skeletal muscle with aging is downregulated by PGC-1alpha overexpression in vivo” (Yeo et al., 2019). The data explained the surgical procedure of in vivo local transfection by electroporation method in aged mouse tibialis anterior muscle, and plasmid DNA preparation and verification protocol. The data also showed the transfection efficiency levels of GFP or GFP-tagged PGC-1alpha through immunohistochemistry method for frozen muscle cross-sections.

In this article, using human pancreatic cancer cell lines and tumor specimens, we analyze the expression and localization of the invadopodia-related proteins TKS5 and Cortactin. Specifically, we present data on: a) TKS5 expression and localization by immunofluorescence in human pancreatic tumors, b) Cortactin expression by western blotting in various human pancreatic adenocarcinoma cell lines, c) TKS5 and Cortactin localization at invadopodia in BxPC-3 pancreatic adenocarcinoma cells, and d) TKS5 and Cortactin localization by co-immunofluorescence in human pancreatic cancer specimens. Data presented here is related to and supportive of the research article by Chen et al., "TKS5-positive invadopodia-like structures in human tumor surgical specimens" (Chen et al., 2019), where interpretation of the research data presented here is available.

Graphical abstract Abstract The development of gene editing technologies, especially the CRISPR-Cas9 system, has been pivotal for understanding the functional role of proteins. Rapid and efficient genotyping methods are necessary to screen for generated mutations and streamline the isolation of homozygotes. CRISPR-Cas9 system targeting a single site in the gene typically results in small indels. Many genotyping methods utilize the heteroduplex that is formed when wild-type and mutant amplicons with small indels anneal during PCR creating a bubble due to mismatched strands. These methods include T7 endonuclease/Cel-I assay, high resolution melting (HRM) analysis, and heteroduplex mobility assay (HMA). Our protocol explains a simple, two step method of a mixing HMA (mHMA) to identify homozygous mutants, a modification of the previously published HMA. We have utilized the mHMA for screening and genotyping numerous CRISPR generated models. The mHMA method to differentiate homozygous wild type from homozygous mutant animals eliminates - • DNA sequencing, even with small indels that can be difficult to discern on a gel. • additional enzymatic reaction steps, such as with the T7EI/Cel-I assay. • specialized equipment and analysis tools, such as with HRM analysis.

Graphical abstract, Cellular migration plays a crucial role within multicellular organisms enabling organ development, wound healing and efficient immune responses, but also metastasis. Therefore, it is crucial to dissect the underlying mechanisms. Directed migration and invasion are most efficient in response to chemotactic signals. To study cell migration and chemotactic responses, current experimental setups use either simplified 2D, tissue-mimetic 3D (e.g. collagen matrices) or in vivo environments. While the in vivo experiments are closest to the real physiological situation, they require animal experiments and are thus ill-suited for screening purposes. 3D matrices, on the other hand, can mimic in vivo conditions in many respects thus serving as instructive settings for the initial dissection of cell migration and chemotaxis. However, performing 3D chemotaxis assays has its limitations due to the delicate nature of most available setups and the tedious and time-consuming manual quantification process. Here, we present • A method for the easy construction of a chemotaxis chamber suitable for the analysis of large cell numbers. • A procedure to quantify their migration automatically with minimal input required by the experimenter. • Both successfully validated by analyzing the 3D chemotaxis of highly migratory primary dendritic cells and the invasive MDA-MB-231 cancer cells.

Molecular Interaction Network Approach (MINA) was used to elucidate candidate disease genes. The approach was implemented to identify novel gene association with commonly known autoimmune diseases [1]. In MINA, we evaluated the hypothesis that “network proximity” within a whole genome molecular interaction network can be used to inform the search for multigene inheritance. There are now numerous examples of gene discoveries based upon network proximity between novel and previously identified disease genes (Yin et al., 2017 [2], Wang et al., 2011 [3], and Barrenas et al., 2009 [4]). This study extends the application of interaction networks to the interrogation of Genome Wide Association studies: first, by showing that a group of nine autoimmune diseases (AuD) genes “seed genes”, are connected in a highly non-random manner within a whole genome network; and second, by showing that the minimal number of connecting genes required to connect a maximal number of AuD candidate genes are highly enriched as candidate genes for AuD predisposing mutations. The findings imply that a threshold number of candidate genes for any heritable disorder can be used to “seed” a molecular interaction network that • Serves to validate the disease status of closely associated seed genes • Identifies genes that are highly enriched as novel candidate disease genes • Provides a strategy for elucidation of epistatic gene x gene interactionsThe method could provide a critical toll for understanding the genetic architecture of common traits and disorders. Method name: MINA, Molecular Interaction Network Approach, Keywords: Autoimmune diseases, Crohn’s disease (CD), Systemic lupus erythematosus (SLE), Rheumatoid arthritis (RA), Psoriasis (PSO), Type-1 diabetes (T1D), Type-2 diabetes (T2D), Celiac disease (CeD), Multiple sclerosis (MS), Association, Molecular network

The interaction of lipids (entry mechanism) with respect to both oxy- and deoxy-myoglobin was explored using unrestrained Molecular Dynamics simulations. The results indicated a spontaneous entry of both palmitic and palmitoylcarnitine molecules into the oxy-Mb structure at the main binding site, whereas in deoxy-Mb, both the lipid ligands move away from the protein surface. For the alternative binding locations, entry of the ligands was independent of the oxygenation state. Presented here are the tables with the myoglobin binding energies for palmitic acid and palmitoylcarnitine estimated using Alchemical Free Energy Perturbation approach for the key structures obtained in unrestrained Molecular Dynamics simulations. These data are referenced in the original article "Exploring the entry route of palmitic acid and palmitoylcarnitine into myoglobin", reference number YABBI7787.

This article contains microbiome data from the upper respiratory tract of patients living with HIV/TB, HIV and TB from Meiktila, a town in Myanmar where there is a high incidence of HIV and TB. Microbiomes were compared for HIV/TB infected and healthy adults from the same population. We collected nasopharyngeal and oropharyngeal swabs from a total of 33 participants (Healthy {5}, HIV/TB {8}, HIV {14}, and TB {6}). DNA was extracted from the swabs and subjected to custom single step 16s rRNA sequencing on an Illumina MiSeq platform. The sequencing data is available via http://www.ncbi.nlm.nih.gov/bioproject/ PRJNA432583.

The data provided in this article are related to the research article entitled “Effect of Super Magnetic Nanoparticles Coated with Various Electric Charges on α-Synuclein Protein Fibrillation Process” (Javdani et al.). This article describes how electrically different charged and concentrated iron oxide nanoparticles synthesized using reverse co-precipitation method affects the fibrillation of albumin protein. Keywords: Nanoparticle, Iron Oxide, Albumin, Fibrillation

The data presented here pertain to a research article entitled “Structural characterization and dynamics of globotetraosylceramide in vascular endothelial cells under TNF-α stimulation” (Okuda et al., 2010). The present article provides additional structural and gene expression data for the characterization of a TNF-α–inducible glycosphingolipid, globotetraosylceramide (Gb4), in vascular endothelial cells. (i) Structural details of Gb4 in lipid raft–enriched cell membranes were determined by MALDI-TOF MS. These analyses identified Gb4 with very-long-chain fatty acids as the major molecular species in this fraction, and the expression levels of whole molecular species of Gb4 with different fatty acid structures in the membrane are uniformly upregulated by TNF-α stimulation. (ii) The expression levels of genes encoding enzymes for synthesis of the ceramide portion of Gb4 were analyzed by real-time PCR. These assays revealed that TNF-α stimulation promotes transcription of the Elovl1 and Cers5 genes, which are involving in the synthesis of Gb4 with very-long-chain fatty acids. Collectively, these results indicate that TNF-α regulates glycosphingolipid synthesis and lipid raft formation in vascular endothelial cells via transcriptional up-regulation of related genes. These data thus provide new insights useful for understanding the molecular basis of inflammation-associated pathology in vascular endothelia.

Retinal vein occlusion (RVO) is a common vascular disease of the retina; however, the pathogenesis of RVO is still unclear. Branch RVO (BRVO) commonly occurs at the arteriovenous crossing and it was formerly believed that the diseased artery mechanically compresses the vein. However, it has been reported that the retinal vein runs deep beneath the artery at the arteriovenous crossing in eyes with an arterial overcrossing, and the venous lumen often appears to be preserved, even at the arteriovenous crossing, as shown by optical coherence tomography. Paques et al. [1] found venous nicking without arteriovenous contact using adaptive optics imaging. Thus, we investigated the potential role of a dysregulation of the retinal vein. While the pathogenesis of retinal vein occlusion (RVO) is still unclear, systemic hypertension and increased level of endothelin-1 (ET-1) are known risk factors (Flammer and Konieczka, 2015) [2]. We focused on the behavior of retinal veins in spontaneous hypertensive rats (SHR). Then, one of the retinal veins became exceptionally constricted and was nearly occluded (Fig. 1), and the chorioretinal blood flow significantly decreased in the retinas of SHRs following the intravenous injection of ET-1. In addition, immunoreactivity to ET-A receptor was higher in SHR retinas than in control (WKY; Wistar Kyoto rat) retinas (Fig. 2). The protein levels of ET-A receptor and HIF-1 were also significantly higher in SHR retinas than in WKY retinas (Fig. 3). We observed vasoactivity of retinal veins; a retinal venous constriction (Kida et al., 2018) [3]. This supports the hypothesis that ET-1 can constrict retinal veins, thus increasing retinal venous pressure, and that ET-1 may even contribute to the pathogenesis of RVO.

This data article indicates the in vitro cytotoxicity of kaempferol and gallic acid across different cancer cell lines including A2780 (ovarian), H460 (lung), A431 (skin), MIA PaCa-2 (pancreas), Du145 (prostate), HT29 (colon), MCF-7 (breast), BE2-C (neuroblastoma), SJ-G2, U87 and SMA (glioblastoma). The dataset showed that the inhibitory activity of kaempferol was comparatively stronger than gallic acid. Thereby, kaempferol is offered as a potent anticancer agent for further investigation and beneficial as a dietary supplement. The data within this article relates to the research article entitled “Screening phytochemical content, antioxidant, antimicrobial and cytotoxic activities of Catharanthus roseus (L.) G. Don stem extract and its fractions” (Pham et al., 2018).

The data described here support the research article “4-HNE carbonylation induces local conformational changes on bovine serum albumin and thioredoxin. A molecular dynamics study” (Alviz-Amador et al., 2018) . Dataset on Gaff force field parameters of AMBER is provided for assembled three non-standard amino acids resulting of the 4-HNE Michael addition, the main end product of lipids peroxidation. Data include a framework for derivation of missing bonds, angles and dihedral parameters for Cys, His, and Lys modified amino acids, alongside optimized partial charges derived with Restrained Electrostatic Potential (RESP) method and the new force field parameters obtained by quantic mechanical (QM) using HF/6-31G** level of theory. Benchmark as a graphics tutorial summary steps to obtained new parameters and the validation of non-standard amino acids is presented. The new residues constructed are put available to the scientific community to perform molecular dynamics simulations of modified 4-HNE proteins. Keywords: AMBER, Gaff, Force field parameterization, Mechanical quantic, Molecular dynamics, Geometry optimization, Validation

Human embryonic stem cells (hESCs) were used as a model of embryonic neurogenesis to identify the effect of excess fat uptake on neurodevelopment (Ardah et al., 2018). Herein, by directed differentiation of hESCs into neurons using established protocols, this data was generated for expression profiles of select lncRNAs during in vitro embryonic neurogenesis and their differential expression due to excess fat (palmitate) uptake. The undifferentiated hESCs were treated with 250 µM palmitate after identifying it as the highest concentration which is non-toxic to these cells. The palmitate treated hESCs were differentiated towards neurons keeping the levels of palmitate consistent throughout the differentiation process and fat uptake was confirmed by Oil Red O staining. The expression analysis of lncRNAs was performed by RT-qPCR on vehicle control and palmitate treated cells from 4 stages of differentiation, D0 (undifferentiated hESCs), D12 (neural stem cells), D44 (neural progenitors) and D70 (neurons) using lncRNAs array plates from Arraystar Inc. which contains 372 functionally identified lncRNAs found to be associated with lipid metabolism and other pathways (Cat# AS-NR-004).

Cerebrospinal fluid (CSF) is a key body fluid that maintains the homeostasis in central nervous system (CNS). As a biofluid whose content reflects the brain metabolic activity, the CSF is analyzed in the context of neurological diseases and is rarely collected from healthy subjects. For this reason, the metabolite variation associated with general phenotypic characteristics such as gender and age have hardly ever been studied. Here we present the hydrophilic interaction liquid chromatography-high resolution mass spectrometry (HILIC-HRMS) data as a result of untargeted metabolomics analysis of a cohort of elderly cognitively healthy volunteers ( n = 32). 146 unambiguously identified water soluble metabolites (using accurate mass, retention time and MS/MS matching against spectral libraries) were measured and their abundances across all the subjects depending on their gender are provided in this article. Data tables are available at https://data.mendeley.com/datasets/c73xtsd4s5/1. it's published on mendeley, the DOI is DOI:10.17632/c73xtsd4s5.1. The data presented in this article are related to the research article entitled "A global HILIC-MS approach to measure polar human cerebrospinal fluid metabolome: Exploring gender-associated variation in a cohort of elderly cognitively healthy subjects" (Gallart-Ayala et al., 2018, In press).

These data and analyses support the research article “Re-evaluating the LD50 requirements in the codified potency testing of veterinary vaccines containing Leptospira serogroups Icterohaemorrhagiae and Canicola in the United States” (Walker et al., 2018). Validity and disposition requirements submitted to the Center for Veterinary Biologics (CVB) are provided for serials (numbered lots) of commercial product potency tested for serogroups Canicola and Icterohaemorrhagiae in support of the Virus-Serum-Toxin Act (VSTA). Time course data for hamster loss after challenge with various concentrations of Leptospira during codified potency testing are also presented. The dose of Leptospira lethal to 50% of hamsters (LD50) was calculated by the Dragstedt-Behrens method for the in vivo data collected, and the equation is described here.

Animal nutrition and toxin deterrence rely on the ability to taste, which occurs through columnar taste cells clustered within taste buds. Taste buds in mammals are located within specialized tissues, called papillae. However, taste buds in fish and amphibians, such as axolotls (Ambystoma mexicanum), are not housed in papillae, rather they are embedded within the pharyngeal epithelium. This simplified tissue level organization, along with the ability of cultured oropharyngeal explants from early embryos to produce taste buds on the same time-line as embryos, make the axolotl an excellent model to identify molecules specifically involved in taste bud cell differentiation. We performed de novo transcriptomic analysis on RNA sequences from three different stages of oropharyngeal explants: stages 37/38, 39, and 41. RNA-seq data from 17 total samples representing these stages were pooled to generate a de novo assembly of the transcriptome using a Trinity pipeline. From 27.9Gb of raw sequences, we identified 21,244 transcripts. To our knowledge, this is the first published assembly of axolotl oropharyngeal endoderm explants. This data and transcriptome assembly relate to the research article “Transcriptome Analysis of Axolotl Oropharyngeal Explants During Taste Bud Differentiation Stages” (Kohli et al. 2020). This RNA-seq data and transcriptome assembly provide information on genes expressed in the oropharyngeal endoderm and will be valuable in the identification of taste bud development genes.

Paenibacillus curdlanolyticus B-6 is a facultative anaerobic bacterium that efficiently produces a lignocellulolytic multienzyme complex. The whole genome of P. curdlanolyticus B-6 was sequenced on an Ion GeneStudio S5 system, which yielded 74 contigs with a total size of 4,875,097 bp, 4,473 protein-coding sequences, and a G+C content of 49.7%. The genome data have been deposited in DDBJ/ENA/GenBank under accession numbers BLWM01000001–BLWM01000074. Analyses of average nucleotide identities and phylogenetic relationships of 16S rRNA sequences of Paenibacillus species revealed that strain B-6 is most closely related to Paenibacillus xylaniclasticus TW1. P. curdlanolyticus B-6 should thus be reclassified as a strain of P. xylaniclasticus.

Here we report the whole genome sequence of Lactobacillus fermentum HFD1 strain, the producer of antibacterial peptides. The genome consists of one circular chromosome with 2101878 bp in length and GC-content of 51.8%, and includes linear DNA with 5386 bp in length with 100% identity to bacteriophage phiX174. The analysis of the genome has revealed 2049 genes encoding for proteins including 867 proteins without known function and 70 genes encoding for RNAs (10 rRNAs, 59 tRNAs and 1 tmRNA). Putative genes responsible for the biosynthesis of 4 antimicrobial peptides were identified. The NCBI Bioproject has been deposited at NCBI under the accession number PRJNA615901 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA615901/) and consist of full annotated genome and raw sequence data.

Spectral libraries generated by data dependent acquisition (DDA) are a useful tool for the analysis of data created by data independent acquisition (DIA) in mass spectrometry. The quality of DIA analysis is dependent on the quality of the spectral library. We used cerebrospinal fluid (CSF) of patients with Parkinson's disease and healthy controls to create a spectral library of human CSF proteome. To this date, there is no validated CSF biomarker for Parkinson's disease. This data set may therefore be valuable for the future analysis of CSF proteins. Part of the samples consisted of fractions that were separated by gel electrophoresis. After tryptic digestion, all samples were spiked with indexed retention time (iRT) peptides and were measured using a DDA mass spectrometry approach. The here provided data set can be used as a CSF-specific spectral library. Data files generated from the described workflow are hosted in the public repository ProteomeXchange under the identifier PXD013487.

The nanometer spacing between nucleosomes throughout global chromatin organisation modulates local DNA template access, and through continuous dynamic rearrangements, regulates genome function [1]. However, given that nucleosome packaging occurs on a spatial scale well below the diffraction limit, real time observation of chromatin structure in live cells by optical microscopy has proved technically difficult, despite recent advances in live cell super resolution imaging [2]. One alternative solution to quantify chromatin structure in a living cell at the level of nucleosome proximity is to measure and spatially map Förster resonance energy transfer (FRET) between fluorescently labelled histones – the core protein of a nucleosome [3]. In recent work we established that the phasor approach to fluorescence lifetime imaging microscopy (FLIM) is a robust method for the detection of histone FRET which can quantify nuclear wide chromatin compaction in the presence of cellular autofluorescence [4]. Here we share FLIM data recording histone FRET in live cells co-expressing H2B-eGFP and H2B-mCherry. The data was acquired in the frequency domain [5] and processed by the phasor approach to lifetime analysis [6]. The data can be valuable to researchers interested in using the histone FRET assay since it highlights the impact of cellular autofluorescence and acceptor-donor ratio on quantifying chromatin compaction. The data is related to the research article “Phasor histone FLIM-FRET microscopy quantifies spatiotemporal rearrangement of chromatin architecture during the DNA damage response” [4].

Human linker histones (H1s) are important in chromatin packaging and condensation. The central globular domain of H1 anchors the protein to the nucleosome. The nucleosomal binding modes of different H1 globular domains may affect nucleosomal DNA accessibility in distinct ways. The globular domain structures of human linker histones H1.0 (GH1.0), H1.4 (GH1.4), H1t (GH1t) and H1oo (GH1oo) were homology modelled and energy minimized. A docking algorithm [validated by re-docking GH5 from the GH5-chromatosome crystal structure (PDB: 4QLC) to the nucleosome] was used to dock the modelled domains to the same nucleosome template. In addition, GH1 (PDB: 1GHC) and a protein consisting of the N-terminal and globular domains of H1x (NGH1x) were also docked using this algorithm. Models of these docked structures are presented here in the form of PDB files. The models can be used to gain more insight with regards to the nucleosomal binding modes of H1s and their individual influence on chromatin compaction.

Marine sponges are acknowledged as a bacterial hotspot and resource of novel natural products or genetic material with industrial or commercial potential. However, sponge-associated bacteria are difficult to be cultivated and the production of their desirable metabolites is inadequate in terms of rate and quantity, yet bioinformatics and metagenomics tools are steadily progressing. Bacterial diversity profiles of high-microbial-abundance wild tropical marine sponges Aaptos aaptos and Xestospongia muta were obtained by sample collection at Pulau Bidong and Pulau Redang islands, 16S rRNA amplicon sequencing on Illumina HiSeq2500 platform (250 bp paired-end) and metagenomics analysis using Ribosomal Database Project (RDP) classifier. Raw sequencing data in fastq format and relative abundance histograms of the dominant 10 species are available in the public repository Discover Mendeley Data (http://dx.doi.org/10.17632/zrcks5s8xp). Filtered sequencing data of operational taxonomic unit (OTU) with chimera removed is available in NCBI accession numbers from MT464469 to MT465036.

Metal-deficient Cu,Zn-superoxide dismutase (apo-SOD1) is associated with the formation of SOD1 aggregates that accumulate in ALS disease. The data supplied in this article support the accompanying publication showing SOD1 modification and aggregation induced by lipid aldehydes [1]. Here, we present the LC-MS/MS dataset on apo-SOD1 modification induced by seven different lipid aldehydes: 4-hydroxy-2-hexenal (HHE), 4-hydroxy-2-nonenal (HNE), 2-hexen-1-al (HEX), 2,4-nonadienal (NON), 2,4-decadienal (DEC) or secosterol aldehydes (SECO-A or SECO-B). Modified protein samples were digested with trypsin and sequenced by a LC coupled to a Q-TOF instrument. Protein sequencing and peptide modification analysis was performed by Mascot 2.6 (Matrix Science) and further validated by manual inspection. Mass spectrometry data (RAW files) obtained in this study have been deposited to MassIVE and the observed peptide-aldehyde adducts can be used in further studies exploring SOD1 modifications in vivo.

The research paper linked to this data paper is available in Munin at https://hdl.handle.net/10037/20588. A previous investigation showed that the endometrium normalized in women with endometrial hyperplasia after three months treatment with high dose levonorgestrel IUS (intrauterine system). The effect was maintained even if immunohistochemical analyses of the endometrium showed that nuclear progesterone receptors (nPRs) were completely downregulated. These observations indicated that some type of non-genomic effect existed. We conducted new investigations of endometrial hyperplasia, now with 6 months low dose levonorgestrel IUS treatment. Again, the growth disturbances were reversed with normalization of the endometrium. In the context of these studies, RT-qPCR analyses of the endometrium were performed before and after treatment, to determine expression of nuclear progesterone receptors (nPRA+B and nPRB), membrane progesterone receptors (mPR, α-, β- and γ-subtypes) and progesterone receptor membrane components (PGRMC1and PGRMC2). The human cervical cell line (C-4 I) with no detectable nPRs, was included in the investigation as biological control .The gene expression of nPRs, mPRs and PGRMCs was determined in the logarithmic growth phase. Tissue and cellular mRNA was determined with RT-qPCR and used as a surrogate marker for receptor (protein) expression. The present data are connected to the related article entitled “Expression of nuclear progesterone receptors (nPRs), membrane progesterone receptors (mPRs) and progesterone receptor membrane components (PGRMCs) in the human endometrium after 6 months levonorgestrel low dose intrauterine therapy”.

Mycoplasma gallisepticum (MG) is one of the smallest free-living and self-replicating organisms, it is characterized by lack of cell wall and reduced genome size. As a result of genome reduction, MG has a limited variety of DNA-binding proteins and transcription factors. To investigate the dynamic changes of the proteomic profile of MG nucleoid, that may assist in revealing its mechanisms of functioning, regulation of chromosome organization and stress adaptation, a quantitative proteomic study was performed on MG nucleoids obtained from the cell culture in logarithmic and stationary phases of synchronous growth. MG cells were grown on a liquid medium with a 9 h starvation period. Nucleoids were obtained from the cell culture at the 26th and the 50th hour (logarithmic and stationary growth phases respectively) by sucrose density gradient centrifugation. LC-MS analysis was carried out on an Ultimate 3000 RSLCnano HPLC system connected to a Fusion Lumos mass spectrometer, controlled by XCalibur software (Thermo Fisher Scientific) via a nanoelectrospray source (Thermo Fisher Scientific). For comprehensive peptide library generation one sample from each biological replicate was run in DDA mode. Then, all the samples were run in a single LC-MS DIA run. Identification of DDA files and DIA quantitation was performed with MaxQuant and Skyline software, correspondingly. All raw data generated from IDA and DDA acquisitions are presented in the PRIDE database with identifier PXD019077.

Mycoplasma hominis is an opportunistic bacterium that can cause acute and chronic infections of the urogenital tract. This bacterium, like all other Mycoplasma species, is characterized by the reduced genome size, and, consequently, reduction of the main metabolic pathways. M. hominis cells cannot effectively use glucose as a carbon and energy source. Therefore, the main pathway of energy metabolism is the arginine dihydrolase pathway. However, several bacteria can use nucleosides as the sole energy source. Biochemical studies using Salmonella typhimurium have shown that three enzymes (thymidine phosphorylase, phosphopentose mutase and deoxyribose-phosphate aldolase) are involved in the thymidine catabolic pathway. All these enzymes are present in M. hominis. For understanding changes in the energy metabolism of M. hominis we performed shotgun proteome analysis of M. hominis cells in liquid medium with arginine or thymidine as a carbon source. LC-MS analysis was performed with an Ultimate 3000 Nano LC System (Thermo Fisher Scientific) coupled to a Q Exactive HF benchtop Orbitrap mass spectrometer (Thermo Fisher Scientific) via a nanoelectrospray source (Thermo Fisher Scientific). Data are available via ProteomeXchange with identifier PXD018714 (https://www.ebi.ac.uk/pride/archive/projects/PXD018714).

This article provides a reusable dataset describing detailed phenotypic and associated clinical parameters in n=303 clinical isolates of urinary Escherichia coli collected at Vanderbilt University Medical Center. De-identified clinical data collected with each isolate are detailed here and correlated to biofilm abundance and metabolomics data. Biofilm-abundance data were collected for each isolate under different in vitro conditions along with datasets quantifying biofilm abundance of each isolate under different conditions. Metabolomics data were collected from a subset of bacterial strains isolated from uncomplicated cases of cystitis or cases with no apparent symptoms accompanying colonization. For more insight, please see “Defining a Molecular Signature for Uropathogenic versus Urocolonizing Escherichia coli: The Status of the Field and New Clinical Opportunities” [1].

Myrciaria dubia “camu-camu” is a native shrub of the Amazon that is commonly found in areas that are flooded for three to four months during the annual hydrological cycle. This plant species is exceptional for its capacity to biosynthesize and accumulate important quantities of a variety of health-promoting phytochemicals, especially vitamin C [1], yet few genomic resources are available [2]. Here we provide the dataset of a de novo assembly and functional annotation of the transcriptome from a pool of samples obtained from seeds during the germination process and seedlings during the initial growth (until one month after germination). Total RNA/mRNA was purified from different types of plant materials (i.e., imbibited seeds, germinated seeds, and seedlings of one, two, three, and four weeks old), pooled in equimolar ratio to generate the cDNA library and RNA paired-end sequencing was conducted on an Illumina HiSeq™2500 platform. The transcriptome was de novo assembled using Trinity v2.9.1 and SuperTranscripts v2.9.1. A total of 21,161 transcripts were assembled ranging in size from 500 to 10,001 bp with a N50 value of 1,485 bp. Completeness of the assembly dataset was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) software v2/v3. Finally, the assembled transcripts were functionally annotated using TransDecoder v3.0.1 and the web-based platforms Kyoto Encyclopedia of Genes and Genomes (KEGG) Automatic Annotation Server (KAAS), and FunctionAnnotator. The raw reads were deposited into NCBI and are accessible via BioProject accession number PRJNA615000 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA615000) and Sequence Read Archive (SRA) with accession number SRX7990430 (https://www.ncbi.nlm.nih.gov/sra/SRX7990430). Additionally, transcriptome shotgun assembly sequences and functional annotations are available via Discover Mendeley Data (https://data.mendeley.com/datasets/2csj3h29fr/1).

The complete genome of the thraustochytrid Aurantiochytrium limacinum strain CCAP_4062/1 was sequenced using both Illumina Novaseq 6000 and third generation sequencing technology PacBio RSII in order to obtain trustworthy assembly and annotation. The reads from both platforms were combined at multiple levels in order to obtain a reliable assembly, then compared to the A. limacinum ATCCⓇ MYA1381™ reference genome. The final assembly was annotated with the help of strain CCAP_4062/1 RNAseq data. A. limacinum strain CCAP_4062/1 is an industrial strain used for the production of very long chain polyunsaturated fatty acids, like the docosahexaenoic acid that is an essential fatty acid synthesised only at very low pace in humans and vertebrates . Thraustochytrids in general and Aurantiochytrium more specifically, are used for carotenoid and squalene production as well. Beside their biotechnological interest, thraustochytrids play a crucial role in both inshore and oceanic basins ecosystems. Genome sequences will foster biotechnological as well as ecological studies.

Linker histone H1 plays a vital role in the packaging of DNA. H1 has a tripartite structure: a conserved central globular domain that adopts a winged-helix fold, flanked by highly variable and intrinsically unstructured N- and C-terminal domains. The datasets presented in this article include raw 2D and 3D BEST-TROSY NMR data [1H-15 N HSQC; 15 N and 13C HNCO, HN(CO)CACB, HNCACB, HN(CA)CO] recorded for NGH1x, a truncated version of H1x containing the N-terminal and globular domains, but lacking the C-terminal domain. Experiments were conducted on double-labelled (15 N and 13C) NGH1x in 'low' and 'high salt,' to investigate the secondary structure content of the N-terminal domain of H1x under these conditions. We provide modelled structures of NGH1x (in low and high salt) based on the assigned chemical shifts in PDB format. The high salt structure of NGH1x (globular domain of H1x [GH1x; PDB: 2LSO ] with the H1x NTD) was docked to the nucleosome to generate NGH1x- and GH1x-chromatosomes. The GH1x-chromatosome was generated for comparative purposes to elucidate the role of the N-terminal domain. We present raw data trajectories of molecular dynamics simulations of these chromatosomes in this article. The MD dataset provides nanosecond resolution data on the dynamics of GH1x- vs NGH1x-chromatosomes, which is useful to elucidate the DNA binding properties of the N-terminal domain of H1x in chromatin, as well as the dynamic behaviour of linker DNA in these chromatosomes.

From April to December 2017, the case-control data were collected in the Department of Ophthalmology & Visual Science, Eye & ENT Hospital, Fudan University. One hundred primary angle closure glaucoma (PACG), one hundred primary open angle glaucoma (POAG) patients and two hundred control participants were consecutively recruited. The serum nitrotyrosine (NT) levels was not significant different in PACG or POAG patients stratified by gender (1,868.17±427.13 nmol/L vs. 1,768.77±410.17 nmol/L, p>0.05; 1,734.04±460.74 vs. 1,696.46±405.73 nmol/L, p>0.05). Serum NT level was not significantly associated with glaucoma severity in either PACG group or POAG group based on mean deviation (MD) (mild, n=30; moderate, n=24; sever, n=19; blinding, n=27, p>0.05, in Table 3 for PACG; mild, n=9; moderate, n=20; sever, n=21; blinding, n=40; p>0.05, in Table 4 for POAG). Multivariable logistic regression analysis indicated that the risk of developing PACG were significantly associated with serum total triglyceride (TG) and uric acid (UA) levels (OR=1.638, 95%CI: 1.059-2.531, p=0.026 for TG, OR=0.003, 95%CI: 0-0.461, p=0.024 for UA). Serum TG, gamma-glutamyl transferase (GGT) and total bilirubin (TB) levels were significantly associated with POAG (OR=2.00, 95%CI: 1.363-2.934, p

Freshwater catfish of the genus Clarias, known as the airbreathing catfish, are widespread and important for food security through small scale inland fisheries and aquaculture. Limited genomic data are available for this important group of fishes. The bighead catfish (Clarias macrocephalus) is a commercial aquaculture species in southeast Asia used for aquaculture and threatened in its natural environment through habitat destruction, over-exploitation and competition from other introduced species of Clarias. Despite its commercial importance and threats to natural populations, public databases do not include any genomic data for C. macrocephalus. We present the first genomic data for the bighead catfish from Illumina sequencing. A total of 128 Gb of sequence data in paired-end 150 bp reads were assembled de novo, generating a final assembly of 883 Mbp contained in 27,833 scaffolds (N50 length: 80.8 kbp) with BUSCO completeness assessments of 96.3% and 87.6% based on metazoan and Actinopterygii ortholog datasets, respectively. Annotation of the genome predicted 21,124 gene sequences, which were assigned putative functions based on homology to existing protein sequences in public databases. Raw fastq reads and the final version of the genome assembly have been deposited in the NCBI (BioProject: PRJNA604477, WGS: JAAGKR000000000, SRA: SRR11188453). The complete C. macrocephalus mitochondrial genome was also recovered from the same sequence read dataset and is available on NCBI (accession: MT109097), representing the first mitogenome for this species. Lastly, we find an expansion of the mb and ora1 genes thought to be associated with adaptations to air-breathing and a semi-terrestrial life style in this genus of catfish.

Traumatic optic neuropathy (TON) is a degenerative process that occurs in a subset of patients following blunt force trauma to the head. This condition is characterized by retinal ganglion cell (RGC) death and axon degeneration within the optic nerve [1]. At the cellular level, mitochondrial changes are associated with many optic neuropathies [2, 3]. Here, we provide a dataset demonstrating changes in the optic nerve mitochondrial lipid profile of a sonication-induced traumatic optic neuropathy (SI-TON) mouse model at 1, 7, and 14 days after injury. 32 C57BL/6J mice were separated into 4 groups (control, 1, 7, and 14 days) of 8, with 4 males and 4 females in each. Mice were exposed to sonication-induced trauma as described previously (by Tao et al) and optic nerves were harvested at 1, 7, or 14 days following injury [4]. Mitochondria were isolated from homogenized optic nerves and lipids were extracted. Extracted mitochondrial lipids were analysed with a Q-Exactive Orbitrap Liquid Chromatography-Mass Spectrometer (LC MS-MS). Further analysis of raw data was conducted with LipidSearch 4.1.3 and Metaboanalyst 4.0. This data is publicly available at the Metabolomics Workbench, http://www.metabolomicsworkbench.org (Project ID: PR000905).

In this work we present three-dimensional (3D) measurements of Brillouin scattering spectra of the in-vivo zebrafish larvae eye. This dataset was obtained by Brillouin microscopy, an emerging all-optical and non-contact technique that gives access to material properties through the process of Brillouin scattering. Herein, we share a representative 3D dataset of spectral properties of 48–52 h post-fertilization (hpf) zebrafish embryos. These spectral properties can be related to a complex longitudinal modulus and thus elastic and viscous properties given knowledge of refractive index and material density. The dataset encompasses the crystalline lens as well as several different retinal layers. This data provides a valuable resource as well as a starting point for researchers interested in the mechanobiology of vertebrate eye development.

Measurement of background radiations (BRs) as the sources of cancer risk, is important. The aim of this study was to measure the BR, as well as its cancer risk and mortalities in Kohgiluyeh and Boyer-Ahmad province (KBAp). Indoors and outdoors BRs were measured in eight cities utilizing a Geiger-Muller detector. Five main locations (north, east, west, south, and center) were chosen for measuring outdoor and indoor BRs in each city of KBAp. The BEIR VII-Phase 2 model was used to calculate the BRs induced cancer risks and mortalities of various cancer types at different ages. The average dose rates of outdoor and indoor were 136.9 ± 12.5 and 149.3 ± 19.8 nSv.h−1, respectively. The average annual effective doses (AEDs) for adults, children, and infants were 0.17, 0.19, and 0.22 mSv.y−1 due to the outdoor, and 0.73, 0.84, and 0.94 mSv.y−1 resulting from the indoor exposure, respectively. The average lifetime risk for one year BRs induced cancers was 164.8 ± 15.7 and 307.1 ± 32.3 (in 100,000 people) for new-borns male and female, in that order. This risk decreased with age and reached 11.2 ± 1.6 and 13.8 ± 1.6 (in 100,000 people) for men and women at the age of 80, respectively. The average lifetime risk of mortality due to cancers induced by annual BRs was 70.7 ± 8.3 and 113.8 ± 10.6 (incidence probability in 100,000 people) for new-borns male and female respectively. This risk decreased with age and reached 9.8 ± 1.3 and 12.2 ± 1.3 (in 100,000 people) for men and women at the age of 80 years, respectively.

In enteric bacteria, DNA supercoiling is highly responsive to environmental conditions. Host specific features of environment serve as cues for the expression of genes required for colonization of host niches via changing supercoiling [1]. It has been shown that substitution at position 87 of GyrA of Salmonella enterica str. SL1344 influences global supercoiling and results in an altered transcriptome with increased expression of stress response pathways [2]. Aminocoumarin antibiotics, such as novobiocin, can be used to relax supercoiling and alter the expression of supercoiling-sensitive genes. Meanwhile, Salmonella enterica demonstrates a significant resistance to this antibiotic and relatively small variability of supercoiling in response to the growth phase, osmotic pressure, and novobiocin treatment. Here we present for the first time transcriptome data of Salmonella enterica subsp. Enterica serovar Typhimurium str. 14028S grown in the presence of novobiocin. These data will help identify genes involved in novobiocin resistance and adaptation processes associated with torsion perturbations in S. enterica. Cleaned FASTQ files for the RNA-seq libraries are deposited in the NCBI Sequence Read Archive (SRA, Identifier: SRP239815) and have been assigned BioProject accession PRJNA599397.

Bacillus amyloliquefaciens KCTC18343P(=MBE1283) isolated from Makgeolli, Korean traditional rice wine, strongly inhibits the growth of food and plant pathogens. A complete genome sequence of B. amyloliquefaciens KCTC18343P is presented in this report. The genome is 3,979,925 bp in size and harbors 3856 genes. The BioProject has been deposited at DDBJ/EMBL/GenBank. The GenBank accession numbers are PRJNA301202 for the BioProject, NZ_CP013727 for the chromosome, and NZ_CP013728 for the plasmid. Keywords: Complete genome, Bacillus amyloliquefaciens, Antipathogenic activity, Rice wine

Single-molecule fluorescent in situ hybridization (smFISH) has emerged as a powerful technique that allows one to localize and quantify the absolute number of mRNAs in single cells. In combination with immunofluorescence (IF), smFISH can be used to correlate the expression of an mRNA and a protein of interest in single cells. Here, we provide and quantify an smFISH-IF dataset in S. cerevisiae. We measured the expression of the cell cycle-controlled mRNA CLN2 and the cell cycle marker alpha-tubulin. The smFISH-IF protocol describing the dataset generation is published in the accompanying article “Simultaneous detection of mRNA and protein in S. cerevisiae by single-molecule FISH and Immunofluorescence” [1]. Here, we analyze the smFISH data using the freely available software FISH-quant [2]. The provided datasets are intended to assist scientists interested in setting up smFISH-IF protocol in their laboratory. Furthermore, scientists interested in the generation of imaging analysis tools for single-cell approaches may find the provided dataset useful. To this end, we provide the differential interference contrast (DIC) channel, as well as multicolor, raw Z-stacks for smFISH, IF and DAPI.

The data presented here are related to the research article, entitled Genetic linkage of oxidative stress with cardiometabolic traits in an intercross derived from hyperlipidemic mouse strains, published in Atherosclerosis 2019 Dec 3;293:1–10 (D. Fuller, A.T. Grainger, A. Manichaikul, W. Shi). The supporting materials include original genotypic and phenotypic data obtained from 266 female F2 mice derived from an intercross between C57BL/6 (B6) and BALB/cJ (BALB) Apoe−/- mice. F2 mice were fed 12 weeks of Western diet, starting at 6 weeks of age. Plasma levels of HDL, LDL cholesterol, triglycerides, glucose and malondialdehyde (MDA) and atherosclerosis in the aortic root and the left carotid artery were measured. 127 microsatellite markers across the entire genome were genotyped. The data is provided in the format ready for QTL analysis with J/qtl and MapManager QTX. Keywords: Genetic linkage, Oxidative stress, Cardiometabolic trait, Atherosclerosis, Mouse

Graphical abstract, Many studies require the detection and relative quantitation of proteins from cell culture samples using immunoblotting. Limiting factors are the cost of protease inhibitors, the time required to break cells and generate samples, as well as the high risk of protein loss during cell breakage procedures. In addition, a common problem is the viscosity of lysed samples due to the released genomic DNA. As a consequence, the DNA needs to be broken down prior to denaturing polyacrylamide protein gel electrophoresis (SDS-PAGE), e.g. by passing the sample through a syringe gauge needle, sonication, or DNase treatment. In a quest to find a more cost-effective, fast, and yet robust procedure, we found that cell lysis, protein denaturation, and DNA fragmentation can be done in only two steps: harvesting followed by a simple non-laborious 2nd step. Similarly to many pre-existing cell breakage procedures, in our Rapid Protein Extraction (RPE) method, proteins liberated from cells are immediately exposed to a denaturing environment. However, advantages of our method are: • No breaking buffer is needed, instead proteins are liberated directly into the denaturing protein loading buffer used for SDS-PAGE. Consequently, our RPE method does not require any expensive inhibitors. • The RPE method does not involve post-lysis centrifugation steps; instead all cell material is dissolved during the 2nd step, the mixing-heat-treatment step which is new to this method. This prevents potential protein loss that may occur during centrifugation. In addition, this 2nd step simultaneously shears the genomic DNA, making an additional step for DNA fragmentation unnecessary. • The generated samples are suitable for high-quality quantitative immunoblotting. With our RPE method we successfully quantified the phosphorylated forms of protein kinase GCN2 and its substrate eIF2α. In fact, the western signals were stronger and with less background, as compared to samples generated with a pre-existing method.

Graphical abstract, We tested three types of medical-grade buccal swabs against standard cotton swabs for differences in DNA yield. A panel of swab types – one drugstore (Q-tips®) and three medical-grade – was used for buccal cell collection from three different individuals. DNA was extracted from all swabs using a QIAcube robot; quantitation values were measured by an Alu-based qPCR assay; and differences were compared through a 2-way ANOVA. Our results demonstrate that cotton swabs recover as much DNA as medical-grade swabs, but at a tremendously lower cost. Cotton swabs also display the greatest consistency of DNA yield, as indicated by the lowest coefficient of variation among the four tested swab types. These findings suggest that the use of standard cotton swabs for buccal cell collection offers not only a significant cost savings, but a more consistent method compared to the use of medical-grade swabs.

Graphical abstract, Highlights • Insertion of a Cys4 sequence and single Cys motif allowedsite-specific labeling with FlAsH and Alexa568 of a protein. • FRET is a well-known technique useful for analysis of structural changes of proteins labeled with donor and accepter fluorophores. • Inter-fluorophore distances and proximity ratios of the peakintensities are used to understand structural changes., Fluorescence Resonance Energy Transfer (FRET) is a well-known methodology for detection and quantitation of structural changes of proteins in solution. FRET requires site-specific protein labeling with two fluorophores, one of which functions as an energy donor and the other one as an energy acceptor. However, the site-specific labeling of protein is often complex and difficult, particularly when inserting two fluorophores in specific sites. We have examined several protein labeling approaches with a varying degree of success. Described here is a dual labeling strategy that worked reproducibly in a number of protein targets and we believe will be applicable to a variety of proteins, which have few or no native cysteine (Cys) residues. We have successfully double-labeled DnaA protein of Bacillus anthracis, which lacks intrinsic Cys residues. A cysteine residue was inserted at the N-terminus by in vitro mutagenesis and a Cys-Cys-Phe-Gly-Cys-Cys (CCPGCC) sequence at the C-terminus by PCR. This protein was labeled site-specifically with a fluorescein derivative, FlAsH, at the CCPGCC sequence followed by Alexa568 maleimide at the N-terminus Cys residue. Structural changes of the protein with nucleotide, DNA and an inhibitor protein binding were determined by FRET analysis of the double-labeled protein. This comprehensive novel methodology for site-specific protein labeling with different fluorophores is applicable for understanding different in vitro proteomic structural studies. Here, we describe a verified technique used for FRET spectral analysis and quantitative evaluation of structural changes using fluorophore labeled DnaA protein constructs as an example.

Graphical abstract, Pediatric high grade glioma (pHGG) and diffuse intrinsic pontine glioma (DIPG) are rare, but rapidly fatal malignancies of the central nervous system (CNS), and the leading cause of cancer-related death in children. Besides the scarcity of available biological material for research, the study of these diseases has been hampered by methodological problems. One of the major obstacles is the difficulty with which these cells can be genetically modified by conventional laboratory methods, such as lentiviral transduction. As a result, only very few successful stable modifications have been reported. As pHGG and DIPG cells are most often cultured as neurospheres, and therefore retain stem cell-like characteristics, we hypothesized that this culture method is also responsible for their resistance to transduction. We therefore developed a protocol in which pHGG and DIPG cells are temporarily forced to form an adherent monolayer by exposure to serum, to create a window-of-opportunity for lentiviral transduction. We here demonstrate that this protocol reliably and reproducibly introduces stable genetic modifications in primary DIPG and pHGG cells. • Short-term serum exposure enables lentiviral transduction of primary pediatric glioma neurospheres.

Graphical abstract, In vitro generation of red blood cells has become a goal for scientists globally. Directly, in vitro-generated red blood cells (RBCs) may close the gap between blood supply obtained through blood donation and high demand for therapeutic uses. In addition, the cells obtained can be used as a model for haematologic disorders to allow the study of their pathophysiology and novel treatment discovery. For those reasons, a number of RBC culture systems have been established and shown to be successful; however, the cost of each millilitre of packed RBC is still extremely high. In order to reduce the cost, we aim to see if we can reduce the number of factors used in the existing culture system. In this study, we examined how well haematopoietic stem cells proliferate and differentiate into mature red blood cells with modified culture system. • Absence of extra heparin or insulin or both from the erythroid differentiation media did not affect haematopoietic stem cell proliferation and differentiation. Therefore, we show that the cost and complexity of erythroid culture can be reduced, which may improve the feasibility of in vitro generation of red blood cells.

Graphical abstract, Direct cloning of metagenomes has proven to be a powerful tool for the exploration of the diverse sequence space of a microbial community leading to gene discovery and biocatalyst development. The key to such approach is the development of rapid, sensitive, and reliable functional screening of libraries. The majority of library screen have relied on the use of agar plates in petri dishes incorporating the target enzyme substrate for activity detection of positive clones (Iqbal et al. [1], Knietsch et al. [2], Popovic et al. [3]). In this article, a novel method is described consisting of: (1) formulation and application of substrate gel microtiter assay plates, (2) screening of libraries of clones in split pools in the wells of the assay plate, and (3) progressive enrichment and isolation of individual positive clones. The method has been successfully used in the rapid discovery of novel genes and enzymes from rumen microbial metagenome with high efficacy. • Novel substrate gel assay plates for activity screening with localized and intensified signals. • Rapid and complete screening of library clones in split pools. • Progressive enrichment scheme as a refining step for isolating target gene.

Graphical abstract, Immunofluorescence staining is used extensively to examine various types of cellular events. However, even when an antibody can detect its epitopes in western blotting, it sometimes fails to detect its epitopes when used for immunofluorescence staining. One example is the antiparallel microtubule overlaps in the anaphase and telophase spindle midzone, which functions as a signaling scaffold for cleavage furrow specification. It has been believed that it cannot be visualized by immunofluorescence staining due to the highly dense structure of microtubule overlaps (Ifuji et al., 2017). Here, we show a simple method for visualization of antiparallel microtubule overlaps in the anaphase and telophase spindle midzone. • Air-drying cells before fixation enables visualization of antiparallel microtubule overlaps in the anaphase and telophase spindle midzone, which cannot be visualized by the conventional method. • Simple method that requires minimal usage of equipment. • Commonly used anti-tubulin antibodies can be used in this method.

Bighead carp (Aristichthys nobilis) and silver carp (Hypophthalmichthys molitrix) are closely related species in the subfamily Xenocypridinae within Cyprinidae, and they are also two of the four most important pond-cultured fish species in China. The ability to resist some diseases often differs significantly in silver carp and bighead carp during fishery production. However, the evolutionary divergence of the immune defense functions in these two species is still not understood at the molecular level. The data presented in this article are related to the research article entitled “Comparative analysis of spleen transcriptome detects differences in evolutionary adaptation of immune defense functions in bighead carp and silver carp” (Li et al., 2018). Please refer to this data article for interpretation of the data. Data provided in this submission comprise the Ka/Ks ratios of orthologs as well as adaptive evolution genes, expression levels of orthologs, and TPM value of genes expressed only in spleen of bighead carp or silver carp. These data provide a better understanding of the differences in evolutionary adaptation of immune defense functions in bighead carp and silver carp.

Graphical abstract A noisy image of fluorescently-labeled mRNA transcripts can be analyzed by Cell-by-Cell Relative Integrated Transcript (CCRIT) Quantification to automatically identify cells and cell clusters and quantify each cell’s mRNA expression level., Advanced molecular probing techniques such as single molecule fluorescence in situ hybridization (smFISH) or RNAscope can be used to assess the quantity and spatial location of mRNA transcripts within cells. Quantifying mRNA expression in large image sets usually involves automated counting of fluorescent spots. Though conventional spot counting algorithms may suffice, they often lack high-throughput capacity and accuracy in cases of crowded signal or excessive noise. Automatic identification of cells and processing of many images is still a challenge. We have developed a method to perform automatic cell boundary identification while providing quantitative data about mRNA transcript levels across many images. Comparisons of mRNA transcript levels identified by the method highly correlate to qPCR measurements of mRNA expression in Drosophila genotypes with different levels of Rhodopsin 1 transcript. We also introduce a graphical user interface to facilitate analysis of large data sets. We expect these methods to translate to model systems where automated image processing can be harnessed to obtain single-cell data. The described method: • Provides relative intensity measurements that scale directly with the number of labeled transcript probes within individual cells. • Allows quantitative assessment of single molecule data from images with crowded signal and moderate signal to noise ratios.

IS1548, a 1316-bp element of the ISAs1 family affects the expression of several genes of the opportunistic pathogen Streptococcus agalactiae. Furthermore, certain lineages of S. agalactiae are more frequently associated to particular diseases than other [1, 2]. We took advantage of the release of the genome sequences of a huge number of epidemiologically unrelated S. agalactiae strains of various origin to analyze the prevalence of IS1548 among S. agalactiae strains. To this end, S. agalactiae genome available at the National Center for Biotechnology Information (NCBI) database were blasted with IS1548 DNA sequences. A sequence type (ST), based on the allelic profile of seven housekeeping genes, was assigned to each strain possessing IS1548. These strains were then grouped into clonal complexes (CCs). The data obtained will give the opportunity to compare the sequenced genomes of S. agalactiae based on their lineage and/or possession of IS1548, and to select the corresponding strains for comparative experimental studies. The data is related to the research article « Dual and divergent transcriptional impact of IS1548 insertion upstream of the peptidoglycan biosynthesis murB gene of Streptococcus agalactiae” [2].