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| Status |
Public on Oct 12, 2019 |
| Title |
SF12017_snATAC |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Homo sapiens |
| Characteristics |
tissue: glioma
progression: Primary
genotype/variation: IDH1 Mutant astrocytoma G2
age: 55
gender: Male
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| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclei were extracted from frozen tissues following the “Frakenstein” protocol developed by Luciano Martelotto, Ph.D., Melbourne, Centre for Cancer Research, Victorian Comprehensive Cancer Centre, and available from 10X Genomics
For fresh tissues, 10.2 μL of live cells, at a concentration of 1700 live-cells/μL,were loaded into the10X Chromium Single Cell capture chip. For frozen tissues, ~15,000 nuclei were loaded per capture. Single-cell/nucleus capture, reverse transcription, cell lysis, and library preparation were performed per manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq using apaired-end 100bp protocol.
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| Library strategy |
ATAC-seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Single nuclei ATAC-Seq Bin Matrix
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| Data processing |
The CellRanger ATAC software (version 1.1.0) was used for read alignment, deduplication, and identifying transposase cut sites.
genome build: hg38
processed data files format and content: Matrix file (mtx) includes sparse matrix of read counts, unique cell barcode files (tsv), and feature file (tsv)
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| Submission date |
Oct 11, 2019 |
| Last update date |
Mar 30, 2025 |
| 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) |
| GSE138794 |
A single cell atlas of human glioma |
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| Relations |
| BioSample |
SAMN13020371 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4119514_SF12017_snATAC_barcodes.tsv.gz |
842 b |
(ftp)(http) |
TSV |
| GSM4119514_SF12017_snATAC_matrix.mtx.gz |
11.6 Kb |
(ftp)(http) |
MTX |
| GSM4119514_SF12017_snATAC_peaks.bed.gz |
10.1 Kb |
(ftp)(http) |
BED |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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