|
| Status |
Public on Dec 05, 2016 |
| Title |
Global transcriptional profiling of HEK293 cells transfected with ATFs, mouse embryonic fibroblasts, and mouse iPS cells derived with artificial transcription factors |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We tested various architectures of artificial transcription factors (ATFs) in HEK293 cells to test the contribution of the interaction domain, nuclear localization domain, size of DNA-binding domain, and activation domain. Then we made a genome-scale ATF library and tested it in reprogramming mouse embryonic fibroblasts to induced pluripotent stem (iPS) cells. Three combinations of ATFs (C2, C3, and C4) could induce pluripotency when expressed with Sox2, Klf4, and c-Myc. We harvested polyadenylated RNAs from 11 cell types derived with different sets of factors. The transcriptional profiles of ATF-induced iPS cells are similar to that of iPS cells induced with Oct4, Sox2, Klf4, and c-Myc and mouse embryonic stem cells, exhibiting up-regulation of pluripotency markers and down-regulation of fibroblast markers. Comparisons of cells undergoing reprogramming at an intermediate stage before becoming fully reprogrammed suggest that ATFs activate a different set of genes than the set activated by Oct4. This study provides a proof-of-principle that a gene-activating ATF library can be used to identify cell fate-defining transcriptional networks in an unbiased manner.
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| |
|
| Overall design |
Total RNA was collected from HEK293 cells from 5 different conditions (n=1), and poly-adenylated transcripts were sequenced. Total RNA was collected from 11 different mouse conditions (n=3 or 4), and poly-adenylated transcripts were sequenced.
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| |
|
| Contributor(s) |
Ansari AZ, Eguchi A |
| Citation(s) |
27930301 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| U01 HL099773 |
Midwest Progenitor Cell Consortium |
MORGRIDGE INSTITUTE FOR RESEARCH |
James Alexander Thomson |
|
| |
| Submission date |
Oct 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Aseem Ansari |
| Organization name |
University of Wisconsin-Madison
|
| Department |
Biochemistry and The Genome Center
|
| Lab |
Ansari
|
| Street address |
440 Henry Mall
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
|
| Samples (43)
|
|
| This SubSeries is part of SuperSeries: |
| GSE89221 |
Functional genomics of artificial transcription factor-induced iPS cells |
|
| Relations |
| BioProject |
PRJNA350708 |
| SRA |
SRP092125 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE89219_C2_SKM_early_genes_fpkm.txt.gz |
651.6 Kb |
(ftp)(http) |
TXT |
| GSE89219_C2_SKM_genes_fpkm.txt.gz |
678.2 Kb |
(ftp)(http) |
TXT |
| GSE89219_C3_SKM_early_genes_fpkm.txt.gz |
655.7 Kb |
(ftp)(http) |
TXT |
| GSE89219_C3_SKM_genes_fpkm.txt.gz |
665.9 Kb |
(ftp)(http) |
TXT |
| GSE89219_C4_SKM_early_genes_fpkm.txt.gz |
653.8 Kb |
(ftp)(http) |
TXT |
| GSE89219_C4_SKM_genes_fpkm.txt.gz |
673.4 Kb |
(ftp)(http) |
TXT |
| GSE89219_ES_genes_fpkm.txt.gz |
678.0 Kb |
(ftp)(http) |
TXT |
| GSE89219_Empty_SKM_genes_fpkm.txt.gz |
652.8 Kb |
(ftp)(http) |
TXT |
| GSE89219_MEF_genes_fpkm.txt.gz |
669.9 Kb |
(ftp)(http) |
TXT |
| GSE89219_OSKM_early_genes_fpkm.txt.gz |
661.1 Kb |
(ftp)(http) |
TXT |
| GSE89219_OSKM_genes_fpkm.txt.gz |
675.5 Kb |
(ftp)(http) |
TXT |
| GSE89219_human_gene_exp_diff.txt.gz |
15.4 Mb |
(ftp)(http) |
TXT |
| GSE89219_minus2_fpkm_tracking.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSE89219_minus3_fpkm_tracking.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSE89219_mock_fpkm_tracking.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSE89219_mouse_gene_exp_diff.txt.gz |
63.6 Mb |
(ftp)(http) |
TXT |
| GSE89219_plus2_fpkm_tracking.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSE89219_plus3_fpkm_tracking.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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