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Series GSE225993 Query DataSets for GSE225993
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
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
 
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)
Web link https://www.biorxiv.org/content/10.1101/2023.02.25.530019v3.full
 
Contributor(s) Prajwal B, Manoj P
Citation(s) 38521065
Submission date Feb 23, 2023
Last update date Jun 11, 2024
Contact name MANOJ PILLAI
E-mail(s) MANOJ.PILLAI@YALE.EDU
Organization name YALE UNIVERSITY
Lab PILLAI LAB
Street address 300 GEORGE STREET #786
City NEW HAVEN
State/province CT
ZIP/Postal code 06511
Country USA
 
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (16)
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
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.
Relations
BioProject PRJNA939532

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE225993_RAW.tar 23.9 Gb (http)(custom) TAR (of BW, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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