|
| Status |
Public on Mar 21, 2024 |
| Title |
SJ009_scMultiome (ATAC-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Peripheral blood
cell line: Peripheral blood leukocytes
cell type: Peripheral blood leukocytes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cryopreserved primary patient samples were thawed quickly at 37 °C water bath, followed by dead cell removal (Miltenyi Biotec,130-090-101). Then the live cells (cell viability > 90%) were collected and subjected to lysis, library construction. For PDX cells, following RBC lysis (QIAGEN, 158904), human leukemia cells were enriched by EasySep Mouse/Human Chimera Isolation kit (Stemcell Technologies, 19849)
Libraries were prepared following 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (GEX) protocol and sequenced on Illumina NovaSeq 6000 149 system (Illumina).
scMultiome
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
transcriptomic single cell |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Patient 2
10x Genomics
|
| Data processing |
Sequencing data were run on Cell Ranger version 3.1.0 to generate feature barcode matrices and information for clustering and gene expression.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Jun 26, 2023 |
| Last update date |
Mar 21, 2024 |
| Contact name |
Jun Yang |
| E-mail(s) |
jun.yang@stjude.org
|
| Phone |
901-595-2517
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Pharmaceutical Sciences
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE235787 |
Single-cell network pharmacology predicts total therapies targeting multiple developmental clones in B-cell acute lymphoblastic leukemia |
|
| Relations |
| BioSample |
SAMN35989152 |
| SRA |
SRX20784919 |
