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15 results on '"healthy cats"'

1. Mean abundance and standard deviation of the miRNAs detected in the urinary miRNAome of the final 35 feline samples included in RNAseq analyses

Author

Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, Cirera, Susanna, Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, and Cirera, Susanna

Abstract

This includes information from their source (database/study/de novo) and their genomic coordinates. CPM: Counts Per Million.

Published
2022

2. S7 Table - Dataset of Urinary microRNAome in healthy cats and cats with pyelonephritis or other urological conditions

Author

Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, Cirera, Susanna, Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, and Cirera, Susanna

Abstract

A. List of differentially abundant (DA) miRNAs between the Control group (healthy) and the different uropathological conditions and between PN and the other uropathological conditions using RNAseq data. B. List of all miRNAs comparisons (without q-value and log2FC filters). The values of log2FC are calculated using the Controls as baseline and therefore a positive log2FC implies an upregulation of the specific miRNA in the pathological state and vice versa. Accordingly, in the comparison PN vs Other pathologies, the PN group was set as baseline, and a negative log2FC thus indicates up-regulation in PN compared to other pathologies. log2FC: log2 of the fold-change in expression. CKD: Chronic Kidney Disease; SB/C: Subclinical Bacteriuria/Cystitis; PN: Pylonephritis; UO: Ureteral Obstruction.

Published
2022

3. Pathway enrichment analysis of putative mRNA target genes of non-redundant differentially abundant (DA) miRNAs seeds surviving the criteria |log2FC| ≥ 1.5 and q-value < 0.05 in qPCR analyses and which were also DA in the small RNAseq dataset

Author

Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, Cirera, Susanna, Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, and Cirera, Susanna

Abstract

Pathway enrichment of the KEGG and Reactome terms are shown if they gathered significant false discovery rate (FDR) and corrected p-values (q-value < 0.05); their associated mRNA genes found are also shown.

Published
2022

4. Detailed list of known and putative de novo miRNAs that passed the defined quality control filters in the feline urine datasets

Author

Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, Cirera, Susanna, Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, and Cirera, Susanna

Abstract

Including the miRNA ID name based on sequence homology with other species (blastn), miRNA coordinates, strand, closest homology miRNA with their percentage of identity and probability (E-value) and consensus mature, star and precursor sequences.

Published
2022

5. List of differentially abundant (DA) miRNAs between the healthy control group and the different uropathological conditions and between PN and the other uropathological conditions using qPCR data

Author

Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, Cirera, Susanna, Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, and Cirera, Susanna

Abstract

The values of log2FC are calculated using the Control cats as baseline, and, therefore, a positive log2FC implies an up-regulation of the specific miRNA in the pathological state and vice versa. Accordingly, in the comparison PN vs. other pathologies, the PN group was set as baseline, and a negative log2FC thus indicates up-regulation in PN compared to other pathologies. In dark grey DA miRNA surviving the criteria |log2FC| ≥ 1.5 and q-value < 0.05; in light grey DA miRNAs surviving the criteria |log2FC| ≥ 1.5 and p-value < 0.05; CKD: Chronic kidney disease; SB/C: Subclinical bacteriuria/Cystitis; PN: Pyelonephritis; UO: Ureteral obstruction, FDR: False discovery rate.

Published
2022

6. Pearson correlation analysis between abundance profiles of small RNAseq and qPCR data from selected miRNAs that were DA (|log2FC| ≥ 1.5 for qPCR and ≥ 2 for small RNAseq; q-value < 0.05) using both methodologies

Author

Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, Cirera, Susanna, Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, and Cirera, Susanna

Abstract

CKD: Chronic kidney disease; PN: Pyelonephritis; SB/C: Subclinical bacteriuria/Cystitis; UO: Ureteral obstruction, CPM: Counts per million, Rq: Relative quantities.

Published
2022

7. Principal component analysis (PCA) of samples profiled by small RNAseq technique

Author

Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, Cirera, Susanna, Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, and Cirera, Susanna

Abstract

A. PCA of urine samples on the basis of normalized read counts of the known and putative novel miRNAs for the 38 samples initially processed. The red arrows indicate the outlier Control samples (C5, C6 and C7). B. PCA excluding the high outlier samples. CKD: Chronic kidney disease; PN: Pyelonephritis; SB/C: Subclinical bacteriuria/Cystitis; UO: Ureteral obstruction.

Published
2022

8. miRNAs selected for qPCR verification

Author

Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, Cirera, Susanna, Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, and Cirera, Susanna

Abstract

The table includes for each miRNA the arguments for its selection for further validation, the forward and reverse sequence, the miRBase sequence used as template for primer design, if successful miRNA amplification was obtained with qPCR and qPCR amplification efficiency.

Published
2022

9. Bland-Altman plots of abundance profiles of small RNAseq and qPCR

Author

Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, Cirera, Susanna, Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, and Cirera, Susanna

Abstract

The data presented is from selected miRNAs that were DA (|log2FC| ≥ 1.5 for qPCR and |log2FC| ≥ 2 for small RNAseq; q-value < 0.05) using both methodologies. CKD: Chronic kidney disease; PN: Pyelonephritis; SB/C: Subclinical bacteriuria/Cystitis; UO: Ureteral obstruction, CPM: Counts per million, Rq: Relative quantities.

Published
2022

10. Sequencing and mapping statistics

Author

Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, Cirera, Susanna, Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, and Cirera, Susanna

Abstract

Reads mapped to the different gene biotypes in the genome are included. SD: standard deviation; rRNA: ribosomal RNA; tRNA: transfer RNA; snoRNA: small nucleolar RNA; snRNA: small nuclear RNA; RE: repeat elements; miRNA: microRNA.

Published
2022

11. miRDeep2 results

Author

Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, Cirera, Susanna, Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, and Cirera, Susanna

Abstract

mirDeep2 output of the 996 miRNAs identified with information from their sequences, scores and probabilities of being a true positive miRNA, among others.

Published
2022

12. Stacked bar plot reporting the fraction of small RNAseq reads assigned to the annotated Felis catus miRNAs (fca-miRNAs) from Ensembl v.99 (blue), feline genome (orange) or that were not mapped (red)

Author

Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, Cirera, Susanna, Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, and Cirera, Susanna

Abstract

CKD: Chronic kidney disease; PN: Pyelonephritis; SB/C: Subclinical bacteriuria/Cystitis; UO: Ureteral obstruction

Published
2022

13. Detailed characteristics of the known and putative novel miRNAs in cat urine for the 35 samples based on RNAseq data

Author

Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, Cirera, Susanna, Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, and Cirera, Susanna

Abstract

A. Proportion of samples for which each of the known miRNAs across the different groups were detected. B. Cumulative abundance of the known feline miRNAs. The dots indicate the log10 of the miRNA abundance for each miRNA. miRNAs are sorted in each group in a decreasing order by their miRNA abundance on the x-axis, independently for each group. C. Proportion of samples for which each of the putative novel miRNA candidates across the different groups were detected. D. Cumulative abundance of the putative novel miRNAs. The dots indicate the log10 of the miRNA abundance for each miRNA. miRNAs are sorted in each group in a decreasing order by their miRNA abundance on the x-axis, independently for each group. CKD: Chronic kidney disease; PN: Pyelonephritis; SB/C: Subclinical bacteriuria/Cystitis; UO: Ureteral obstruction, CPM: Counts per million.

Published
2022

14. Principal component analysis (PCA) of urine samples (N = 38) on the basis of log2 normalized relative quantities (Rq) of profiled miRNAs using qPCR

Author

Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, Cirera, Susanna, Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, and Cirera, Susanna

Abstract

All samples together (all groups), as well as each one of the contrasts considered (Controls vs. PN; Control vs. SB/C; Control vs. UO; Control vs. CKD; PN vs. SB/C; PN vs. UO; PN vs. CKD and PN vs. other Pathologies) are shown. CKD: Chronic kidney disease; PN: Pyelonephritis; SB/C: Subclinical bacteriuria/Cystitis; UO: Ureteral obstruction.

Published
2022

15. Flowchart outlining the pipeline for small RNAseq analysis

Author

Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, Cirera, Susanna, Gòdia, Marta, Brogaard, Louise, Mármol-Sánchez, Emilio, Langhorn, Rebecca, Nordang Kieler, Ida, Reezigt, Bert Jan, Nielsen, Lise Nikolic, Jessen, Lisbeth Rem, and Cirera, Susanna

Abstract

Including the identification of known and putative novel miRNAs, miRNA abundance profiling and differential abundance analysis. rRNA: ribosomal RNA; tRNA: transfer RNA; snoRNA: small nucleolar RNA; snRNA: small nuclear RNA; RE: repeat elements; qPCR: quantitative real-time PCR.

Published
2022

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