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Sample GSM8279063 Query DataSets for GSM8279063
Status Public on May 22, 2024
Title JN-DSRCT, assay_1, isotype, R2, ChIP-seq
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: NA
Treatment protocol No treatment was performed on JN-DSRCT-1 cells for assay 1. For assay 2, JN-DSRCT-1 cell line was transfected with a custom siRNA targeting EWSR1::WT1 (3’ GAT CTT GAT CTA GGT GAG A 5’), 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. For ChIP assay, JN-DSRCT-1 cells were grown to ~80% confluence in 15 cm dishes.
Extracted molecule genomic DNA
Extraction protocol Chromatin was crosslinked for 15 minutes at room temperature (RT) by adding methanol-free formaldehyde (1% final) in the dishes culture media. Then, formaldehyde was quenched by adding a glycine solution, and cells were scraped and centrifuged before freezing for subsequent utilization. After thawing on ince, cells were resuspended in FL buffer before nuclei extraction according to the NEXSON protocol (Arrigoni et al., Nucleic Acids Res, 2016). Immunoprecipitation was performed on sheared chromatin using H3K9ac, H3K27ac, WT1 C-terminal (GTX15249), or rabbit isotype antibodies overnight and immune complexes were captured the next day using Dynabeads Protein G beads. Crosslink was reverted with Proteinase K and DNA was purified on Qiagen PCR purification columns.
NebNextUltra II Library prep kit for DNA
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing ChIP-seq data analyses were performed according to nf-core/chipseq pipeline
Raw reads quality control (QC) was performed using FastQC
Adapter trimming was done with Trim Galore!
Reads were further mapped to the reference genome (GRCh38) using BWA
Duplicate reads were discarded using picard
BigWig files were generated using BEDTools to allow IGV visualization of fragments
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
GSE267803 Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in Desmoplastic Small Round Cell Tumors [ChIP-seq]
Relations
BioSample SAMN41447730
SRA SRX24600814

Supplementary file Size Download File type/resource
GSM8279063_JN1_isoR_R2.bigWig 610.9 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA

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