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Status |
Public on Mar 12, 2024 |
Title |
Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [ATAC-seq] |
Organisms |
Homo sapiens; Mus musculus |
Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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Summary |
To investigate changes in chromatin landscape and nucleosome positioning in response to SF3B1 mutations, we peformed ATAC seq in K562, human CD34, and murine cKit+,Sca1+,Lin- cells We then performed peak-based and nucleosome positioning analyses using data obtained from ATAC to investigate changes in chromatin accessibility and promoter nucleosome occupancy, respectively
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Overall design |
ATAC-seq in WT and SF3B1K700E K562 cells at 4 days post doxycycline induction, along with human CD34+ (isolated from healthy volunteer and MDS patient samples) and murine cKit+,Sca1+,Lin- cells (from SF3B1WT vs SF3B1K700E expressing mice)
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Web link |
https://www.biorxiv.org/content/10.1101/2023.02.25.530019v3.full
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Contributor(s) |
Prajwal B, Manoj P |
Citation(s) |
38521065 |
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Submission date |
Feb 23, 2023 |
Last update date |
Jun 11, 2024 |
Contact name |
MANOJ PILLAI |
E-mail(s) |
MANOJ.PILLAI@YALE.EDU
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Organization name |
YALE UNIVERSITY
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Lab |
PILLAI LAB
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Street address |
300 GEORGE STREET #786
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City |
NEW HAVEN |
State/province |
CT |
ZIP/Postal code |
06511 |
Country |
USA |
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Platforms (2) |
GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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Samples (16)
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GSM7061462 |
K562 cells, SF3B1 wild type, 4 days, replicate 1, ATAC-seq |
GSM7061463 |
K562 cells, SF3B1 wild type, 4 days, replicate 2, ATAC-seq |
GSM7061464 |
K562 cells, SF3B1K700E, 4 days, replicate 1, ATAC-seq |
GSM7061465 |
K562 cells, SF3B1K700E, 4 days, replicate 2, ATAC-seq |
GSM7061466 |
CD34 cells, healthy volunteer, replicate 1, ATAC-seq |
GSM7061467 |
CD34 cells, healthy volunteer, replicate 2, ATAC-seq |
GSM7061468 |
CD34 cells, healthy volunteer, replicate 3, ATAC-seq |
GSM7061469 |
CD34 cells, SF3B1-mutant MDS, replicate 1, ATAC-seq |
GSM7061470 |
CD34 cells, SF3B1-mutant MDS, replicate 2, ATAC-seq |
GSM7061471 |
CD34 cells, SF3B1-mutant MDS, replicate 3, ATAC-seq |
GSM7061472 |
CD34 cells, SF3B1-mutant MDS, replicate 4, ATAC-seq |
GSM7061473 |
CD34 cells, SF3B1-mutant MDS, replicate 5, ATAC-seq |
GSM7061474 |
CD34 cells, SF3B1-mutant MDS, replicate 6, ATAC-seq |
GSM7061475 |
cKIT+Sca1+Lin- cells, Murine Sf3b1 WT, replicate 1, ATAC-seq |
GSM7061476 |
cKIT+Sca1+Lin- cells, Murine Sf3b1 K700E, replicate 1, ATAC-seq |
GSM7061477 |
cKIT+Sca1+Lin- cells, Murine Sf3b1 K700E, replicate 2, ATAC-seq |
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This SubSeries is part of SuperSeries: |
GSE226003 |
Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape. |
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Relations |
BioProject |
PRJNA939532 |
Supplementary file |
Size |
Download |
File type/resource |
GSE225993_RAW.tar |
23.9 Gb |
(http)(custom) |
TAR (of BW, TXT) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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