|
| Status |
Public on Sep 14, 2023 |
| Title |
RCMB56-ht snRNA+ATAC-seq (ATAC) |
| Sample type |
SRA |
| |
|
| Source name |
medulloblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: medulloblastoma
cell type: medulloblastoma
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Disassociated cryopreserved cells stored in 10%DMSO/FBS were used. At least 50mg of tissue (1M cells) was used for both samples. Disassociated cells were prepared for Single Cell Multiome ATAC + Gene Expression sequencing (10X Genomics) according to the manufacturer’s instructions
Sequencing was performed on an Illumina NovaSeq S4 200 to a depth of at least 250M reads for snATAC-seq and 200M reads for snRNA-seq
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
MM_614 files are snATAC-seq sequenced over 2 lanes (technical replicate).
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
|
| Data processing |
Sequencing data were uniformly processed using CellRanger ARC v2.0.0 with default parameters.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx are standard outputs from 10X single-cell pipelines. Mtx file is a table indexed by barcode on rows, and features on columns.
|
| |
|
| Submission date |
Aug 16, 2023 |
| Last update date |
Sep 14, 2023 |
| Contact name |
Lukas Chavez |
| E-mail(s) |
lchavez@sbpdiscovery.org
|
| Phone |
(858)952-3775
|
| Organization name |
Sanford Burnham Prebys Medical Discovery Institute
|
| Department |
Cancer Genome and Epigenetics Program, NCI-Designated Cancer Center
|
| Street address |
10901 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE240984 |
Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastomas [scRNA+ATAC-seq] |
| GSE240985 |
Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastomas |
|
| Relations |
| BioSample |
SAMN37007933 |
| SRA |
SRX21383207 |
