|
| Status |
Public on May 22, 2024 |
| Title |
JN-DSRCT-1, no_si, R2, ATAC |
| Sample type |
SRA |
| |
|
| Source name |
JN-DSRCT-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: JN-DSRCT-1
cell type: Desmoplastic Small Round Cell Tumor
treatment: no siRNA
|
| Treatment protocol |
JN-DSRCT-1 cell line was transfected with a custom siRNA targeting EWSR1::WT1 (3’ GAT CTT GAT CTA GGT GAG A 5’), CCND1 (Horizon Discovery «on»-TARGETplus Human CCND1 siRNA-smart pool, reference L-003210–00-0005) or non-targeting siRNA (Horizon Discovery «on»-TARGETplus Non-targeting siRNA#1, reference D-001810-01-05), according to manufacturer’s instructions. After cell seeding and obtention of 50% confluency, transfection was performed using LipofectamineTM RNAiMAX (InvitrogenTM reference 13778150), and the medium was replaced the day after. A 48-hour silencing time point was used for each described experiment.
|
| Growth protocol |
JN-DSRCT-1 cell line was maintained in 2D adherent culture within DMEM/F-12 (GibcoTM) supplemented with 10% FBS, 1% Penicillin-Streptomycin (GibcoTM), 1% Sodium Pyruvate (GibcoTM), 1% Sodium Bicarbonate (GibcoTM), 1% Non-Essential Amino Acids (GibcoTM) and 1% HEPES (GibcoTM). Cell passaging was performed at 1/10 twice a week. Used cells were controlled for mycoplasma-free status.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC was performed according to Omni-ATAC protocol (Corces et al., Nat Methods, 2017). DNA purification was then performed using the Qiagen MinElute Reaction Cleanup kit.
NebNextUltra II Library prep kit for DNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
genomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
ATAC-seq data were analyzed according to nf-core/atacseq pipeline
Raw reads quality control (QC) was performed using FastQC
Adapter trimming was done with Trim Galore!
Read mapping to the reference genome (GRCh38) was done using BWA
Duplicate reads were discarded using picard
BigWig files were generated using BEDTools for IGV visualization
Assembly: GRCh38
Supplementary files format and content: BigWig files
|
| |
|
| Submission date |
May 18, 2024 |
| Last update date |
May 22, 2024 |
| Contact name |
Clémence Henon |
| E-mail(s) |
clemence.henon@gustaveroussy.fr
|
| Organization name |
Gustave Roussy
|
| Street address |
114 rue Edouard Vaillant
|
| City |
Villejuif |
| ZIP/Postal code |
94800 |
| Country |
France |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE263523 |
Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in Desmoplastic Small Round Cell Tumors |
| GSE267807 |
Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in Desmoplastic Small Round Cell Tumors [ATAC-seq] |
|
| Relations |
| BioSample |
SAMN41447720 |
| SRA |
SRX24600827 |
