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| Status |
Public on Jul 06, 2023 |
| Title |
Dysfunction of 5-methylcytosine oxidases and the Polycomb protein RYBP leads to widespread DNA hypermethylation and cell transformation [RNA-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To investigate the function of RYBP, YAF2, TET1, TET2, TET3 or the cooperative function in the human bronchial cells, we established defective clone cell lines in which each target gene has been knocked out by guide RNA
We then performed gene expression profiling analysis from mRNA-seq.
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| Overall design |
Comparative gene expression profiling analysis of mRNA-seq data in HBEC3 defective cell (Control cells, RYBP KO, YAF2 KO, RYBP/YAF2 DKO , TET1/2/3 TKO and TET1/2/3/RYBP QKO ).
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| Web link |
https://aacrjournals.org/cancerres/article/83/15/2480/728088/Deficiency-of-the-Polycomb-Protein-RYBP-and-TET
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| Contributor(s) |
Cui W, Huang Z, Pfeifer G |
| Citation(s) |
37272752 |
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| Submission date |
Jul 20, 2022 |
| Last update date |
Oct 05, 2023 |
| Contact name |
Gerd Pfeifer |
| E-mail(s) |
gerd.pfeifer@vai.org
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| Organization name |
Van Andel Research Institute
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| Street address |
333 Bostwick Ave. NE
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| City |
Grand Rapids |
| State/province |
MI |
| ZIP/Postal code |
49503 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (26)
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| GSM6364244 |
HBEC3 cells, Scr2, batch1 |
| GSM6364245 |
HBEC3 cells, Scr3, batch1 |
| GSM6364246 |
HBEC3 cells, RKO1, batch1 |
| GSM6364247 |
HBEC3 cells, RKO2, batch1 |
| GSM6364248 |
HBEC3 cells, RKO3, batch1 |
| GSM6364249 |
HBEC3 cells, YKO1, batch1 |
| GSM6364250 |
HBEC3 cells, YKO2, batch1 |
| GSM6364251 |
HBEC3 cells, YKO3, batch1 |
| GSM6364252 |
HBEC3 cells, R/Y DKO1, batch1 |
| GSM6364253 |
HBEC3 cells, R/Y DKO2, batch1 |
| GSM6364254 |
HBEC3 cells, R/Y DKO3, batch1 |
| GSM6364255 |
HBEC3 cells, WT, batch2 |
| GSM6364256 |
HBEC3 cells, EmpV, batch2 |
| GSM6364257 |
HBEC3 cells, Scr3, batch2 |
| GSM6364258 |
HBEC3 cells, RKO1, batch2 |
| GSM6364259 |
HBEC3 cells, RKO2, batch2 |
| GSM6364260 |
HBEC3 cells, RKO3, batch2 |
| GSM6364261 |
HBEC3 cells, TET123 TKO1, batch2 |
| GSM6364262 |
HBEC3 cells, TET123 TKO2, batch2 |
| GSM6364263 |
HBEC3 cells, TET123 TKO3, batch2 |
| GSM6364264 |
HBEC3 cells, QKO1, batch2 |
| GSM6364265 |
HBEC3 cells, QKO2, batch2 |
| GSM6364266 |
HBEC3 cells, QKO3, batch2 |
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| This SubSeries is part of SuperSeries: |
| GSE208689 |
Dysfunction of 5-methylcytosine oxidases and the Polycomb protein RYBP leads to widespread DNA hypermethylation and cell transformation |
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| Relations |
| BioProject |
PRJNA860609 |
| SRA |
SRP387317 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE208686_RAW.tar |
2.0 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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