Search

Your search keyword '"Czajkowsky, Daniel M"' showing total 345 results
Start Over Author "Czajkowsky, Daniel M"
345 results on '"Czajkowsky, Daniel M"'

3. Specific pupylation as IDEntity reporter (SPIDER) for the identification of protein-biomolecule interactions

Author

Jiang, He-Wei, Chen, Hong, Zheng, Yun-Xiao, Wang, Xue-Ning, Meng, Qingfeng, Xie, Jin, Zhang, Jiong, Zhang, ChangSheng, Xu, Zhao-Wei, Chen, Zi-Qing, Wang, Lei, Kong, Wei-Sha, Zhou, Kuan, Ma, Ming-Liang, Zhang, Hai-Nan, Guo, Shu-Juan, Xue, Jun-Biao, Hou, Jing-Li, Liu, Zhe-Yi, Niu, Wen-Xue, Wang, Fang-Jun, Wang, Tao, Li, Wei, Wang, Rui-Na, Dang, Yong-Jun, Czajkowsky, Daniel M., Pei, JianFeng, Dong, Jia-Jia, and Tao, Sheng-Ce

Published
2023
Full Text
View/download PDF

34. Time‐resolved transcriptomics of mouse gastric pit cells during postnatal development reveals features distinct from whole stomach development.

Author

Wei, Ying, Xu, Zeqian, Hu, Miaomiao, Wu, Zhongqin, Liu, Axian, Czajkowsky, Daniel M., Guo, Yan, and Shao, Zhifeng

Subjects
STOMACH, MICE, TRANSCRIPTOMES, MICRODISSECTION, PHENOTYPES
Abstract

Whole‐organ transcriptomic analyses have emerged as a common method for characterizing developmental transitions in mammalian organs. However, it is unclear if all cell types in an organ follow the whole‐organ defined developmental trajectory. Recently, a postnatal two‐stage developmental process was described for the mouse stomach. Here, using laser capture microdissection to obtain in situ transcriptomic data, we show that mouse gastric pit cells exhibit four postnatal developmental stages. Interestingly, early stages are characterized by the up‐regulation of genes associated with metabolism, a functionality not typically associated with pit cells. Hence, beyond revealing that not all constituent cells develop according to the whole‐organ determined pathway, these results broaden our understanding of the pit cell phenotypic landscape during stomach development. [ABSTRACT FROM AUTHOR]

Published
2023
Full Text
View/download PDF

38. Additional file 6 of Monocytic THP-1 cells diverge significantly from their primary counterparts: a comparative examination of the chromosomal conformations and transcriptomes

Author

Liu, Yulong, Li, Hua, Czajkowsky, Daniel M., and Shao, Zhifeng

Abstract

Additional file 6 : Supplementary Figure S1. Comparison of gene expression levels in different compartments. Supplementary Figure S2. Similarities/differences of compartments between primary cells and THP-1 cells. Supplementary Figure S3. Example of differentially expressed genes whose changed expression is associated with the changes of compartment. Supplementary Figure S4. Compartments identified with different software yield similar results at loci of immune-related genes. Supplementary Figure S5. Comparison of gene expression levels at regions that switched compartments. Supplementary Figure S6. Relationship between gene expression levels and compartment changes in primary, GM-CSF-induced macrophages and macrophagic THP-1 cells. Supplementary Figure S7. Similarity of TAD locations between the primary and down-sampled THP-1 datasets. Supplementary Figure S8. Numbers of loops in the down-sampled datasets in the monocytic and macrophagic THP-1 cells. Supplementary Figure S9. Hi-C heatmap showing loop-scale chromosomal structural differences. Supplementary Figure S10. Correlation between chromosomal structural changes and gene expression. Supplementary Figure S11. A/B compartments identified by different software exhibit high congruence.

Published
2021
Full Text
View/download PDF

48. Measurement of the electron-phonon coupling factor dependence on film thickness and grain size in Au, Cr, and Al

Author

Hostetler, John L., Smith, Andrew N., Czajkowsky, Daniel M., and Norris, Pamela M.

Subjects
Thin films -- Optical properties, Phonons -- Research, Thermal diffusivity -- Measurement, Astronomy, Physics
Abstract

Femtosecond thermoreflectance data for thin films and bulk quantities of Au, Cr, and Al are compared with the parabolic two-step thermal diffusion model for the purpose of determining the electron-phonon coupling factor. The thin films were evaporated and sputtered onto different substrates to produce films that vary structurally. The measurement of the electron-phonon coupling factor is shown to be sensitive to grain size and film thickness. The thin-film thermoreflectance data are compared with that of the corresponding bulk material and to a theoretical model relating the coupling rate to the grain-boundary scattering and size effects on the mean free path of the relevant energy carrier.

Published
1999

50. High-Resolution Single-Cell Models of Ensemble Chromatin Structures during Drosophila Embryogenesis from Population Hi-C

Author

Sun, Qiu, Perez-Rathke, Alan, Czajkowsky, Daniel M., Shao, Zhifeng, and Liang, Jie

Abstract

We describe a computational method for reconstruction of large 3D ensemble of single-cell chromatin conformations from population Hi-C. Our method identifies specific interactions constituting a small fraction (5–6% in Drosophila ) of measured Hi-C frequencies. Yet, surprisingly, they are sufficient to drive chromatin folding, giving rise to much of observed Hi- C topological features. Our models reveal dramatic changes in chromatin compaction across three developmental stages of Drosophila , with > 50% of single cells likely maintaining TAD-like structures, possibly even in early embryos when no population TADs are discernable. Our models reveal details on how varying single-cell domain boundaries become fixated through-out development, with strong preferred-positioning at binding sites of insulator complexes during and after midblastula transition. Overall, our method can be used to re-interpret population Hi-C by generating ensembles of single-cell chromatin conformations at high resolution, facilitating better understanding of genome organization.

Published
2019
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results