|
| Status |
Public on May 14, 2023 |
| Title |
RS4.11 DMSO scRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
RS4;11
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RS4;11
disease state: B-cell acute lymphoblastic leukemia
genotype: t(4;11)
time: 10 h
agent: DMSO
|
| Treatment protocol |
Cells were treated for 10 h with 1 micromolar AZD1775(Wee1i) or DMSO.
|
| Growth protocol |
RS4;11 cell lines were maintained in RPMI 1640 (Gibco, Thermo Fisher) supplemented with 10% FBS (Gibco, Thermo Fisher), 2 mM L-glutamine (Gibco, Thermo Fisher), 10mM HEPES (Lonza), penicillin (100 U/ml), and streptomycin (100 mg/ml) (Sigma-Aldrich).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Nuclei were then isolated with 10x Genomics Nuclei Isolation protocol for Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing user guide CG000365 Rev B.
scMultiome-seq was performed using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit and Next GEM Chip J, user guide CG000338 Rev E.
Chromium Single Cell ATAC and scRNA libraries
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
scRNAseq from vehicle treated cell line, 10X Genomics multiome kit
RS411_DMSO10h_raw_feature_bc_matrix.h5
RS411_DMSO10h_filtered_feature_bc_matrix.h5
|
| Data processing |
Data was aligned with Cell Ranger Single cell Multiome ATAC + Gene expression workflow cellranger-arc-2.0.1 to human reference (GRCh38) from 10x Genomics with default parameters.
Cells were filtered with Cell Ranger 2.0.1 following alignment.
Assembly: GRCh38
Supplementary files format and content: For scRNAseq data raw and filtered CellRanger output in .h5 format. This data contains both the scRNA and scATAC count data.
Supplementary files format and content: Cellranger ATAC peak annotation in tsv format
Supplementary files format and content: Cellranger annotated ATAC peaks in bed format
|
| |
|
| Submission date |
Dec 05, 2022 |
| Last update date |
May 14, 2023 |
| Contact name |
Merja Heinäniemi |
| E-mail(s) |
merja.heinaniemi@uef.fi
|
| Organization name |
University of Eastern Finland
|
| Department |
School of Medicine, Institute of Biomedicine
|
| Lab |
Systems Genomics - Heinäniemi lab
|
| Street address |
Yliopistonranta 1E
|
| City |
Kuopio |
| ZIP/Postal code |
70211 |
| Country |
Finland |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE220112 |
Mechanistic study of Wee1 kinase inhibition with AZD1775 exposes drug targetable vulnerabilities in acute B-lymphoblastic leukemia [scMultiome] |
| GSE220114 |
Mechanistic study of Wee1 kinase inhibition with AZD1775 exposes drug targetable vulnerabilities in acute B-lymphoblastic leukemia |
|
| Relations |
| BioSample |
SAMN32045179 |
| SRA |
SRX18497845 |
