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Sample GSM8279118 Query DataSets for GSM8279118
Status Public on May 22, 2024
Title JN-DSRCT-1, siCCND1, 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: CCND1-targeting 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 SAMN41447716
SRA SRX24600831

Supplementary file Size Download File type/resource
GSM8279118_ATAC_JN1_si_CTRL_R2.mLb.clN.bigWig 1.0 Gb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA

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