|
| Status |
Public on Jun 28, 2022 |
| Title |
A673_CHLA10_pooled_data |
| Sample type |
SRA |
| |
|
| Source name |
A673 and CHLA10 cells pooled
|
| Organism |
Homo sapiens |
| Characteristics |
disease: Ewing sarcoma
cell line: HTO labeled by cell type (HTO1- A673, HTO2- CHLA10)
|
| Growth protocol |
A673 was maintained in RPMI 1640 media (Gibco) supplemented with 10% FBS (Atlas Biologicals) and 2mmol/L-glutamine (Life Technologies). CHLA10 was maintained in IMDM media (Fisher scientific) supplemented with 20% FBS, 2mmol/L-glutamine, and 1X Insulin-Transferrin-Selenium (Gibco). Cells were cultured at 37°C with 5% CO2 and were split according to ATCC and COG recommendations.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries generated using the 3’ V3 10X Genomics Chromium Controller following the manufacturer’s protocol (CG000183)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RNA data
|
| Data processing |
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files
CellRanger (3.1) Pipeline (10X Genomics) was used to align reads and generate count matrices
Supplementary_files_format_and_content: tar.gz containing .mtx.gz, and .tsv.gz files for the mRNA, ADT, and HTO data to be read into R for use in the Seurat/monocle3 pipeline.
|
| |
|
| Submission date |
Feb 02, 2021 |
| Last update date |
Jun 28, 2022 |
| Contact name |
April Apfelbaum |
| E-mail(s) |
[email protected]
|
| Organization name |
Dana-farber Cancer Institute
|
| Department |
Pediatric Oncology
|
| Lab |
Bandopadhayay Lab
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE165973 |
EWS-FLI1 and HOXD13 control tumor cell plasticity in Ewing sarcoma [CITE-seq] |
|
| Relations |
| BioSample |
SAMN17761147 |
| SRA |
SRX10004024 |
