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| Status |
Public on Sep 23, 2022 |
| Title |
Loss of tight junctions disrupts gastrulation patterning and increases differentiation towards the germ cell lineage in human pluripotent stem cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To investigate the role of tight junctions in BMP4 signaling and differentiation, we knocked down TJP1 in human pluripotent stem cells using CRISPRi, and examined gene expression via RNA sequencing of TWT (no KD) and TKD (TJP1 KD) cells in the untreated pluripotent (P) state and after BMP4 differentiation (B).
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| Overall design |
Comparative gene expression profiling analysis of RNA-seq data for TWT and TKD cells cultured on standard plates (S) and transwells (T), in the pluripotent (P) and BMP4 differentiated (B) conditions.
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| Contributor(s) |
Vasic I |
| Citation(s) |
37354899 |
| Submission date |
Sep 21, 2022 |
| Last update date |
Jun 28, 2023 |
| Contact name |
Ivana Vasic |
| E-mail(s) |
ivana.vasic@gladstone.ucsf.edu
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| Organization name |
Gladstone Institute
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| Street address |
1650 Owens St
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| City |
San Francisco |
| State/province |
CALIFORNIA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platforms (2) |
| GPL15433 |
Illumina HiSeq 1000 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (24)
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| GSM6596395 |
TWT, Standard Culture, Untreated, Biol Rep 1 (TWT_S_P_1) |
| GSM6596396 |
TWT, Standard Culture, Untreated, Biol Rep 2 (TWT_S_P_2) |
| GSM6596397 |
TWT, Standard Culture, Untreated, Biol Rep 3 (TWT_S_P_3) |
| GSM6596398 |
TWT, Standard Culture, BMP4 treated, Biol Rep 1 (TWT_S_B_1) |
| GSM6596399 |
TWT, Standard Culture, BMP4 treated, Biol Rep 2 (TWT_S_B_2) |
| GSM6596400 |
TWT, Standard Culture, BMP4 treated, Biol Rep 3 (TWT_S_B_3) |
| GSM6596401 |
TKD, Standard Culture, Untreated, Biol Rep 1 (TKD_S_P_1) |
| GSM6596402 |
TKD, Standard Culture, Untreated, Biol Rep 2 (TKD_S_P_2) |
| GSM6596403 |
TKD, Standard Culture, Untreated, Biol Rep 3 (TKD_S_P_3) |
| GSM6596404 |
TKD, Standard Culture, BMP4 treated, Biol Rep 1 (TKD_S_B_1) |
| GSM6596405 |
TKD, Standard Culture, BMP4 treated, Biol Rep 2 (TKD_S_B_2) |
| GSM6596406 |
TKD, Standard Culture, BMP4 treated, Biol Rep 3 (TKD_S_B_3) |
| GSM6596407 |
TWT, Transwell Culture, Untreated, Biol Rep 1 (TWT_T_P_1) |
| GSM6596408 |
TWT, Transwell Culture, Untreated, Biol Rep 2 (TWT_T_P_2) |
| GSM6596409 |
TWT, Transwell Culture, Untreated, Biol Rep 3 (TWT_T_P_3) |
| GSM6596410 |
TWT, Transwell Culture, BMP4 treated, Biol Rep 1 (TWT_T_B_1) |
| GSM6596411 |
TWT, Transwell Culture, BMP4 treated, Biol Rep 2 (TWT_T_B_2) |
| GSM6596412 |
TWT, Transwell Culture, BMP4 treated, Biol Rep 3 (TWT_T_B_3) |
| GSM6596413 |
TKD, Transwell Culture, Untreated, Biol Rep 1 (TKD_T_P_1) |
| GSM6596414 |
TKD, Transwell Culture, Untreated, Biol Rep 2 (TKD_T_P_2) |
| GSM6596415 |
TKD, Transwell Culture, Untreated, Biol Rep 3 (TKD_T_P_3) |
| GSM6596416 |
TKD, Transwell Culture, BMP4 treated, Biol Rep 1 (TKD_T_B_1) |
| GSM6596417 |
TKD, Transwell Culture, BMP4 treated, Biol Rep 2 (TKD_T_B_2) |
| GSM6596418 |
TKD, Transwell Culture, BMP4 treated, Biol Rep 3 (TKD_T_B_3) |
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| Relations |
| BioProject |
PRJNA883000 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE213911_RAW.tar |
11.3 Mb |
(http)(custom) |
TAR (of CSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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