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| Status |
Public on Aug 04, 2022 |
| Title |
P-1764_S-1766_multiome ATAC |
| Sample type |
SRA |
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| Source name |
tumor
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| Organism |
Homo sapiens |
| Characteristics |
tissue: tumor
Sex: female
age (years): 11
location: pons
diagnosis: high-grade glioma
cellranger version(processing): cellranger-arc-2.0.0
technology: 10X Chromium Single Cell Multiome ATAC + RNA
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
scMultiome nuclei were prepared using either standard manual nuclei preparation or automated nuclei preparation. Samples subjected to automated nuclei prep were processed following the Singulator S100 protocol (S2 Genomics). Nuclei were isolated using the Nuclei Isolation kit and Singulator S100 instrument from S2 Genomics. Briefly, 5-20 mg of frozen tissue were put in a pre-cooled nuclei isolation cartridge with RNAse inhibitors. Samples were then processed on the Singulator S100 following the “extended nuclei” protocol. After nuclei prep, nuclei were centrifuged and washed twice in Diluted Nuclei Buffer (10x Genomics) and counted with the ReadyProbes Cell Viability Blue/Green kit (ThermoFisher Scientific). 20,000 nuclei/sample were loaded on the Chromium Controller (10x Genomics).
Library preparation was prepared following the manufacturer’s instructions (Next GEM Single Cell Multiome).
scMultiome (ATAC + RNA)
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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 |
Cell Ranger ARC v2.0.0 (10x Genomics) was used (‘count’ option with default parameters) to filter and align raw reads, identify transposase cut sites, detect accessible chromatin peaks, call cells and generate raw count matrices for scMultiome samples.
Sequencing reads were aligned to the hg19 genome, coupled with the Gencode v28 (Ensembl 92) gene annotation.
For visualization of chromatin accessibility in subsets of cells, BAM files from ATAC data were subsetted using the subset-bam utility from 10x Genomics (v1.1). Pseudo-bulk bigwig tracks were generated from subsetted BAMs with a bin size of 1 and RPKM normalization using the deeptools bamCoverage functionality (v3.5.0).
Assembly: hg19
Supplementary files format and content: README_scMultiome.md: markdown file containing information on the metadata, barcodes, features and matrix files.
Supplementary files format and content: *__features.tsv.gz, *__barcodes.tsv.gz, *__matrix.mtx.gz: compressed filtered features, barcodes and expression matrices generated by Cell Ranger.
Supplementary files format and content: *.metadata.NG2022.tsv: Tab-separated file containing info for each cell.
Supplementary files format and content: *.bw: bigwig files, read coverage over the human genome
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| Submission date |
Aug 04, 2022 |
| Last update date |
Aug 04, 2022 |
| Contact name |
Claudia L Kleinman |
| E-mail(s) |
claudia.kleinman@mcgill.ca
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| Phone |
514-340-8222 25139
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| Organization name |
Lady Davis Institute for Medical Research
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| Department |
Human Genetics
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| Street address |
3999 Côte Ste-Catherine Road
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| City |
Montréal |
| State/province |
Québec |
| ZIP/Postal code |
H3T 1E2 |
| Country |
Canada |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE210566 |
Multi-omic analysis of cell-of-origin and epigenomic state in pediatric H3K27M gliomas (multiome) |
| GSE210568 |
Multi-omic analysis by single-cell sequencing of epigenomic state in pediatric H3K27M gliomas |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM6432696_P-1764_S-1766_Astrocytes.ATAC.bw |
222.0 Mb |
(ftp)(http) |
BW |
| GSM6432696_P-1764_S-1766_Normal.ATAC.bw |
203.3 Mb |
(ftp)(http) |
BW |
| GSM6432696_P-1764_S-1766_OPC.ATAC.bw |
445.4 Mb |
(ftp)(http) |
BW |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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