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| Status |
Public on Feb 15, 2018 |
| Title |
CpG island mediated linear and spatial gene partitioning (RNA-seq) |
| Sample organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Third-party reanalysis
|
| Summary |
We reanalyzed published RNA-seq data to study 1) the genomic landscapes near surrounding regions of transcriptional start sites with regard to the gene expression activities and 2) the gene expression change upon transcription factor (MYBL1, ATF4) depletion. Raw data were downloaded from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI) database. FASTQ files were extracted with the SRA Toolkit version 2.5.5 and aligned using STAR 2.4.2 onto the mouse and human genome (mm9 and hg19, respectively). Gene expression was calculated as RPKM values using rpkmforgenes.py (Ramsköld et al., 2009).
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| |
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| Overall design |
RNA-seq gene expression analyses in diverse mouse and human samples.
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| |
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| Contributor(s) |
Kim J, Beck S |
| Citation(s) |
29529258 |
| |
| Submission date |
Apr 28, 2016 |
| Last update date |
May 17, 2018 |
| Contact name |
Jonghwan Kim |
| E-mail(s) |
jybella@utexas.edu
|
| Phone |
512-232-8046
|
| Organization name |
University of Texas at Austin
|
| Department |
Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology
|
| Lab |
Kim Lab
|
| Street address |
2506 Speedway NMS 4.246
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
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| This SubSeries is part of SuperSeries: |
| GSE80799 |
Implications of CpG islands on chromosomal architectures and modes of global gene regulation |
|
| Relations |
| Reanalysis of |
GSM1062208 |
| Reanalysis of |
GSM1410613 |
| Reanalysis of |
GSM1088420 |
| Reanalysis of |
GSM1088421 |
| Reanalysis of |
GSM1088422 |
| Reanalysis of |
GSM1088423 |
| Reanalysis of |
GSM1088424 |
| Reanalysis of |
GSM1088425 |
| Reanalysis of |
GSM1088428 |
| Reanalysis of |
GSM1088429 |
| Reanalysis of |
GSM1123726 |
| Reanalysis of |
GSM1123732 |
| Reanalysis of |
GSM873429 |
| Reanalysis of |
GSM873433 |
| Reanalysis of |
GSM929774 |
| Reanalysis of |
GSM958729 |
| Reanalysis of |
GSM958735 |
| Reanalysis of |
GSM958736 |
| Reanalysis of |
GSM958749 |
| Reanalysis of |
GSM970853 |
| BioProject |
PRJNA319992 |
