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Series GSE233993 Query DataSets for GSE233993
Status Public on Sep 11, 2024
Title Determining the chromatin accessibility profiles of functionally distinct SHH-medulloblastoma sub-populations
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Using FACS sorting on SOX2-eGFP and MKi67-RFP mice on a Ptch1+/- background, we identified cycling& non-cycling stem cells and tumor bulk subpopulations in endpoint mouse SHH-subgroup medulloblastoma tumors, and determined their chromatin accessibility progiles to identify unique regulators of cell state.
 
Overall design We sorted SHH-subgroup medulloblastoma cells from endpoint mouse tumors into SOX2+ and SOX2- based on presence of eGFP signal to distinguish the stem-like and bulk tumor compartments. We also sorted the SOX2+ stem cells into cycling (MKI67+) and non-cycling (MKI67-) sub-compartments based on presence of RFP. We then performed sequencing on ATAC libraries generated from these cells.
 
Contributor(s) Desai K, Dirks P
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Submission date Jun 02, 2023
Last update date Sep 12, 2024
Contact name Kinjal Desai
E-mail(s) kinjal.desai@sickkids.ca
Organization name The Hospital for Sick Children
Department Developmental and Stem Cell
Lab Dr. Peter Dirks
Street address 686 Bay Street, PGCRL 16-14
City Toronto
State/province ON
ZIP/Postal code M5G 0A4
Country Canada
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (12)
GSM7440257 Primary mouse SHH MB SOX2- tumor cells replicate 1
GSM7440258 Primary mouse SHH MB SOX2- tumor cells replicate 2
GSM7440259 Primary mouse SHH MB SOX2- tumor cells replicate 3
Relations
BioProject PRJNA979167

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

Supplementary file Size Download File type/resource
GSE233993_RAW.tar 5.5 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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