|
| Status |
Public on Jun 28, 2022 |
| Title |
TC32_shHOXD13_2 |
| Sample type |
SRA |
| |
|
| Source name |
TC32
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: TC32
cell type: Ewing sarcoma
treatment: shHOXD13
genotype: HOXD13 knockdown
|
| Treatment protocol |
Cells were treated with 0.5 ug/uL for 72 hours to induce shRNA expression
|
| Growth protocol |
TC32 was maintained in RPMI 1640 media (Gibco) supplemented with 10% FBS (Atlas Biologicals) and 2mmol/L-glutamine (Life Technologies). Cells were cultured at 37°C with 5% CO2 and were split according to ATCC and COG recommendations.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the Quiagen Rneasy Kit
polyA-capture mRNA
Libraries were prepared with NEBNext Ultra II RNA Library Prep kit and Paired end 150 bp sequencing was performed on a Novaseq600
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
TC32_shHOXD13_all_reps.txt
|
| Data processing |
Adapter trimming of paired-end fastq files was performed using Trim Galore (Babraham Institute).
Trimmed reads were then aligned to GRCh38 using STAR aligner (Dobin, et al 2013) with `--quantMode GeneCounts` to count the number of reads per gene while mapping.
Differential expression analysis was performed using the default parameters from the DESeq2 package (Love et al, 2014).
Genome_build: Hg38
Supplementary_files_format_and_content: .txt files with count data
|
| |
|
| Submission date |
Jun 16, 2021 |
| Last update date |
Jun 28, 2022 |
| Contact name |
April Apfelbaum |
| E-mail(s) |
april_apfelbaum@dfci.harvard.edu
|
| 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 (2) |
| GSE148494 |
EWS-FLI1 and HOXD13 control tumor cell plasticity in Ewing sarcoma [RNA-seq] |
| GSE182513 |
EWS-FLI1 and HOXD13 control tumor cell plasticity in Ewing sarcoma |
|
| Relations |
| BioSample |
SAMN19732469 |
| SRA |
SRX11169500 |
