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| Status |
Public on May 03, 2024 |
| Title |
PNC single cell multiome ATAC |
| Sample type |
SRA |
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| Source name |
primary
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| Organism |
Mus musculus |
| Characteristics |
tissue: primary
cell type: preneoplastic cells
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
GNPs, PNCs, and tumor cells were isolated from the cerebellum of Ptch1- Atoh1EGFP mice at P7, 6 weeks, and adulthood using percoll gradient centrifugation, respectively. Nuclei isolation was performed according to the manufacturer’s protocol (CG000366 Rev C, 10x Genomics). Of note, the incubation with the lysis buffer was optimized to 3 minutes. Targeted Nuclei Recovery was 5000 or 10000, depending on the number of isolated nuclei.
Single Cell Multiome ATAC + Gene Expression; Library preparation was performed according to the manufacturer’s protocol (CG000338 RevE, 10x Genomics).
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| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Description |
10x Genomics
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| Data processing |
All analysises were performed using Cell Ranger Arc software 2.0.1
Assembly: mm10
Supplementary files format and content: h5 matrix and tab-separated fragment files
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| Submission date |
Sep 20, 2023 |
| Last update date |
May 03, 2024 |
| Contact name |
Kohei Kumegawa |
| E-mail(s) |
kohei.kumegawa@gmail.com
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| Organization name |
Japanese Foundation for Cancer Research
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| Street address |
3-8-31 Ariake, Koto-ku
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| City |
Tokyo |
| ZIP/Postal code |
135-8550 |
| Country |
Japan |
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| Platform ID |
GPL21626 |
| Series (2) |
| GSE240362 |
Cancer-Specific Epigenome Identifies Oncogenic Hijacking by Nuclear Factor I Family Proteins for Medulloblastoma Progression |
| GSE243609 |
Dynamic Chromatin Alteration Induces Oncogenic Hijacking by Essential Transcriptional Factors during Medulloblastoma Tumorigenesis [Multiome] |
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| Relations |
| BioSample |
SAMN37475073 |
| SRA |
SRX21829911 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7791841_RS03056_fragments.tsv.gz |
940.5 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
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