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| Status |
Public on Oct 20, 2021 |
| Title |
SF10207 (snATAC) |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Homo sapiens |
| Characteristics |
age: 43
Sex: M
disease state: Oligodendroglioma Anaplastic (WHO gr. 3)
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| Treatment protocol |
Following euthanasia, mice were perfused with PBS, tumor tissue was harvested and snap frozen.
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| Growth protocol |
All surgical procedures were conducted according to our Institutional Animal Care and Use Committee and NIH ethical guidelines. ATRX-KO and wildtype SB28 cells expressing IDH1R132H and a luciferase reporter were used to establish intracranial tumors in C57BL/6j mice, using 6 mice per cohort. Animals were anesthetized using isoflurane, each surgical procedure was performed after placing the animal in a stereotactic frame. An aliquot of 5 × 104 SB28 cells was injected into the right parietal region of the brain. The injection site was 2 mm to the right of the central suture and 0.5 mm anterior to the lambda junction; depth of injection was 2-3 mm. The rate of injection was 1 l/min.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue processing, tagmentation, nuclei capture and library prep was performed by the 10X Genomics platform.
Single-cell/nucleus capture, reverse transcription, cell lysis, and library preparation were performed per manufacturer’s protocol.
Sequencing was performed according to 10X Genomics recommended protocols on an Illumina NovaSeq 6000.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
We used CellRanger (version 3.0.2) to pre-process the sc/snRNA-seq data from the 10X Genomics platform.
The CellRanger ATAC software (version 1.1.0) was used for read alignment, deduplication, and identifying transposase cut sites.
The output matrix of CellRanger was further filtered for quality based on two criteria: 1) number of fragments > 1000; 2) fragments in promoter ratio > 0.2.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: Filtered peak matrix (.mtx) files. Bed files, peaks (TSV).
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| Submission date |
Jul 30, 2020 |
| Last update date |
May 16, 2022 |
| Contact name |
Aaron Diaz |
| E-mail(s) |
aaron.diaz@ucsf.edu
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| Organization name |
University of California, San Francisco
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| Department |
Neurological Surgery
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| Lab |
Diaz Lab
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| Street address |
1450 3rd St
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE155430 |
A single-cell epigenetic atlas of human IDH-mutant glioma |
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| Relations |
| BioSample |
SAMN15678095 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4704295_SF10207_barcodes.tsv.gz |
204 b |
(ftp)(http) |
TSV |
| GSM4704295_SF10207_matrix.mtx.gz |
2.9 Kb |
(ftp)(http) |
MTX |
| GSM4704295_SF10207_peaks.bed.gz |
12.1 Kb |
(ftp)(http) |
BED |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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