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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
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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.
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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.
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Contributor(s) |
Desai K, Dirks P |
Citation missing |
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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
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Organization name |
The Hospital for Sick Children
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Department |
Developmental and Stem Cell
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Lab |
Dr. Peter Dirks
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Street address |
686 Bay Street, PGCRL 16-14
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City |
Toronto |
State/province |
ON |
ZIP/Postal code |
M5G 0A4 |
Country |
Canada |
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Platforms (1) |
GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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Samples (12)
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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 |
GSM7440260 |
Primary mouse SHH MB SOX2- tumor cells replicate 4 |
GSM7440261 |
Primary mouse SHH MB SOX2+ tumor cells replicate 1 |
GSM7440262 |
Primary mouse SHH MB SOX2+ tumor cells replicate 2 |
GSM7440263 |
Primary mouse SHH MB SOX2+ tumor cells replicate 3 |
GSM7440264 |
Primary mouse SHH MB SOX2+ tumor cells replicate 4 |
GSM7440265 |
Primary mouse SHH MB SOX2+/MKI67- tumor cells replicate 1 |
GSM7440266 |
Primary mouse SHH MB SOX2+/MKI67- tumor cells replicate 2 |
GSM7440267 |
Primary mouse SHH MB SOX2+/MKI67+ tumor cells replicate 1 |
GSM7440268 |
Primary mouse SHH MB SOX2+/MKI67+ tumor cells replicate 2 |
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Relations |
BioProject |
PRJNA979167 |