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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 [WGBS] |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
We inactivated RYBP, YAF2, TET1, TET2, and TET3 in bronchial cells, individually and in combination, and observed widespread DNA methylation by performing whole genome bisulfite sequencing.
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| Overall design |
Comparative DNA methylation analysis of WGBS data in HBEC3 defective cell (Control cells, RKO, YKO, TET2 KO, TET3KO, TET2/TET3 DKO, TET123 TKO and TET123/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 (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (24)
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| GSM6364297 |
HBEC3 cells, RYBP KO1 |
| GSM6364298 |
HBEC3 cells, RYBP KO2 |
| GSM6364299 |
HBEC3 cells, RYBP KO3 |
| GSM6364300 |
HBEC3 cells, YAF2 KO1 |
| GSM6364301 |
HBEC3 cells, YAF2 KO2 |
| GSM6364302 |
HBEC3 cells, YAF2 KO3 |
| GSM6364303 |
HBEC3 cells, TET2 KO1 |
| GSM6364304 |
HBEC3 cells, TET2 KO2 |
| GSM6364305 |
HBEC3 cells, TET2 KO3 |
| GSM6364306 |
HBEC3 cells, TET2/3 DKO1 |
| GSM6364307 |
HBEC3 cells, TET2/3 DKO2 |
| GSM6364308 |
HBEC3 cells, TET2/3 DKO3 |
| GSM6364309 |
HBEC3 cells, TET123 TKO1 |
| GSM6364310 |
HBEC3 cells, TET123 TKO2 |
| GSM6364311 |
HBEC3 cells, TET123 TKO3 |
| GSM6364312 |
HBEC3 cells, RYBP/T123 QKO1 |
| GSM6364313 |
HBEC3 cells, RYBP/T123 QKO2 |
| GSM6364314 |
HBEC3 cells, RYBP/T123 QKO3 |
| GSM6364315 |
HBEC3 cells, TET3KO1 |
| GSM6364316 |
HBEC3 cells, TET3KO2 |
| GSM6364317 |
HBEC3 cells, TET3KO3 |
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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 |
PRJNA860621 |
| SRA |
SRP387319 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE208688_RAW.tar |
4.3 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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