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| Status |
Public on Aug 20, 2024 |
| Title |
ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [RNA-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
ZIC2 and ZIC3 are essential for acquisition and maintenance of primed pluripotency. In this study, we conducted next generation sequencing of polyA-enriched bulk RNA in single and compound knockouts of ZIC2, ZIC3 and ZIC5 primed hESCs, naïve hESCs lacking ZIC3 that inducibly express ZIC2, and primed hESCs that were cultured in 5iLAF medium for six days and undergoing reversion to a naive state.
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| Overall design |
Bulk RNA-seq of polyA-enriched RNA from single and compound knockout of ZIC2, ZIC3 and ZIC5 primed hESCs, naïve hESCs lacking ZIC3 that inducibly express ZIC2, and primed hESCs lacking ZIC3 that were cultured in 5iLAF medium for six days and undergoing reversion to a naive state.
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| Contributor(s) |
Hossain I, Pastor WA |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jun 25, 2024 |
| Last update date |
Aug 20, 2024 |
| Contact name |
William A. Pastor |
| E-mail(s) |
william.pastor@mcgill.ca
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| Phone |
5143988962
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| Organization name |
McGill University
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| Department |
Biochemistry
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| Street address |
3655 Promenade Sir-William-Osler
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| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3G1Y6 |
| Country |
Canada |
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| Platforms (2) |
| GPL20795 |
HiSeq X Ten (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (38)
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| GSM8352010 |
UCLA1 primed hESC, WT +sgNT, rep1 (RNA-seq) |
| GSM8352011 |
UCLA1 primed hESC, WT +sgNT, rep2 (RNA-seq) |
| GSM8352012 |
UCLA1 primed hESC, NT, rep1 (RNA-seq) |
| GSM8352013 |
UCLA1 primed hESC, NT, rep2 (RNA-seq) |
| GSM8352014 |
UCLA1 primed hESC, WT +sgZIC2, rep1 (RNA-seq) |
| GSM8352015 |
UCLA1 primed hESC, WT +sgZIC2, rep2 (RNA-seq) |
| GSM8352016 |
UCLA1 primed hESC, ZIC2-/- (RNA-seq) |
| GSM8352017 |
UCLA1 primed hESC, ZIC3-/- +sgNT, rep1 (RNA-seq) |
| GSM8352018 |
UCLA1 primed hESC, ZIC3-/- +sgNT, rep2 (RNA-seq) |
| GSM8352019 |
UCLA1 primed hESC, ZIC3-/- +sgNT, rep3 (RNA-seq) |
| GSM8352020 |
UCLA1 primed hESC, ZIC3-/- +sgNT, rep4 (RNA-seq) |
| GSM8352021 |
UCLA1 primed hESC, ZIC5-/- +sgNT, rep1 (RNA-seq) |
| GSM8352022 |
UCLA1 primed hESC, ZIC5-/- +sgNT, rep2 (RNA-seq) |
| GSM8352023 |
UCLA1 primed hESC, ZIC5-/- +sgNT, rep3 (RNA-seq) |
| GSM8352024 |
UCLA1 primed hESC, ZIC3-/- +sgZIC2, rep1 (RNA-seq) |
| GSM8352025 |
UCLA1 primed hESC, ZIC3-/- +sgZIC2, rep2 (RNA-seq) |
| GSM8352026 |
UCLA1 primed hESC, ZIC3-/- +sgZIC2, rep3 (RNA-seq) |
| GSM8352027 |
UCLA1 primed hESC, ZIC3-/- +sgZIC2, rep4 (RNA-seq) |
| GSM8352028 |
UCLA1 primed hESC, ZIC5-/- +sgZIC2, rep1 (RNA-seq) |
| GSM8352029 |
UCLA1 primed hESC, ZIC5-/- +sgZIC2, rep2 (RNA-seq) |
| GSM8352030 |
UCLA1 primed hESC, ZIC5-/- +sgZIC2, rep3 (RNA-seq) |
| GSM8352031 |
UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgNT, rep1 (RNA-seq) |
| GSM8352032 |
UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgNT, rep2 (RNA-seq) |
| GSM8352033 |
UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, rep1 (RNA-seq) |
| GSM8352034 |
UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, rep2 (RNA-seq) |
| GSM8352035 |
UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, rep3 (RNA-seq) |
| GSM8352036 |
UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DMSO, rep1 (RNA-seq) |
| GSM8352037 |
UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DMSO, rep2 (RNA-seq) |
| GSM8352038 |
UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DMSO, rep3 (RNA-seq) |
| GSM8352039 |
UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DMSO, rep4 (RNA-seq) |
| GSM8352040 |
UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, doxycycline 72h, rep1 (RNA-seq) |
| GSM8352041 |
UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, doxycycline 72h, rep2 (RNA-seq) |
| GSM8352042 |
UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, doxycycline 72h, rep3 (RNA-seq) |
| GSM8352043 |
UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, doxycycline 72h, rep4 (RNA-seq) |
| GSM8352044 |
UCLA1 reverting hESC, NT, 5iLAF d6, rep1 (RNA-seq) |
| GSM8352045 |
UCLA1 reverting hESC, NT, 5iLAF d6, rep2 (RNA-seq) |
| GSM8352046 |
UCLA1 reverting hESC, ZIC3-/-, 5iLAF d6, rep1 (RNA-seq) |
| GSM8352047 |
UCLA1 reverting hESC, ZIC3-/-, 5iLAF d6, rep2 (RNA-seq) |
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| This SubSeries is part of SuperSeries: |
| GSE270787 |
ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency |
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| Relations |
| BioProject |
PRJNA1128169 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE270786_Hossain_2024_Gene_expression_TPM_all_samples.txt.gz |
4.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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