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| Status |
Public on Apr 30, 2022 |
| Title |
RNASeq to investigate SOX2 and SOX9 function in human fetal lung tip progenitor cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In order to understand transcription factor SOX2 and SOX9 function, we have knocked down SOX2 and SOX9 in human fetal lung tip progenitor organoids using an inducible CRISPRi system. We discovered that SOX2 knockdown didn't appear to influence organoid cell survival and led to minimal gene expression changes at transcriptome level. By contrast, SOX9 knockdown led to organoid cell self-renewal defects and we have detected hundreds of genes differentially expressed after SOX9 knockdown.
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| Overall design |
We used 2 independent organoid parental lines infected with inducible CRISPRi system. 2 different non-targeting control (NT) gRNAs, which do not bind to anywhere of the genome, 2 different gRNAs targeting for SOX2 knockdown, and 2 different gRNAs targeting for SOX9 knockdown were used to control non-specific effect from organoid lines, lentiviral infection and different gRNAs.
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| Contributor(s) |
Sun D, Tang WW, Rawlins EL |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Nov 30, 2021 |
| Last update date |
Apr 30, 2022 |
| Contact name |
Dawei Sun |
| E-mail(s) |
sundawei45232@gmail.com
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| Organization name |
University of Cambridge
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| Department |
The Gurdon Institute
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| Street address |
Tennis Court Road
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| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (12)
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| GSM5708963 |
BRC1915_human fetal lung organoid cells_CRISPRi_NT1-RNA-Seq |
| GSM5708964 |
BRC1915_human fetal lung organoid cells_CRISPRi_NT2-RNA-Seq |
| GSM5708965 |
BRC1915_human fetal lung organoid cells_CRISPRi_SOX2 g2-RNA-Seq |
| GSM5708966 |
BRC1915_human fetal lung organoid cells_CRISPRi_SOX2 g8-RNA-Seq |
| GSM5708967 |
BRC1915_human fetal lung organoid cells_CRISPRi_SOX9 g1-RNA-Seq |
| GSM5708968 |
BRC1915_human fetal lung organoid cells_CRISPRi_SOX9 g7-RNA-Seq |
| GSM5708969 |
HDBRN13393_human fetal lung organoid cells_CRISPRi_NT1-RNA-Seq |
| GSM5708970 |
HDBRN13393_human fetal lung organoid cells_CRISPRi_NT2-RNA-Seq |
| GSM5708971 |
HDBRN13393_human fetal lung organoid cells_CRISPRi_SOX2 g2-RNA-Seq |
| GSM5708972 |
HDBRN13393_human fetal lung organoid cells_CRISPRi_SOX2 g8-RNA-Seq |
| GSM5708973 |
HDBRN13393_human fetal lung organoid cells_CRISPRi_SOX9 g1-RNA-Seq |
| GSM5708974 |
HDBRN13393_human fetal lung organoid cells_CRISPRi_SOX9 g7-RNA-Seq |
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| This SubSeries is part of SuperSeries: |
| GSE189885 |
Human fetal lung tip progenitor cells |
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| Relations |
| BioProject |
PRJNA784953 |
| SRA |
SRP348656 |
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