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Sample GSM8279073 Query DataSets for GSM8279073
Status Public on May 22, 2024
Title JN-DSRCT-1, siCTRL, R2, RNA-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: control non-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’) 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. The experiment was performed in triplicate.
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 polyA RNA
Extraction protocol Cells were collected at 4°C in PBS after 48-hour silencing. Cell pellets were lyzed and RNA extracted using Qiagen RNEasy kit according to manufacturer's instructions. RNA quality control was performed before library construction based on RNA Integrity Number (RIN) evaluated on Agilent 2100 Bioanalyzer.
After the QC procedure, rRNA was removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs(dUTP, dATP, dGTP and dCTP), RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Then followed by purification by AMPure XP beads, terminal repair, polyadenylation, sequencing adapter ligation, size selection and degradation of second-strand U-contained cDNA by the USER enzyme. The strand-specific cDNA library was generated after the final PCR enrichment.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description column H48_siCTRL_R2
Data processing RNA-seq data were analyzed according to nf-core/rnaseq pipeline
Raw reads quality control (QC) was performed using FastQC
Adapter trimming was done with Trim Galore!
Pseudoalignment to the reference genome and transcript quatification were performed using Salmon
Assembly: hg19 (GENCODE version 19)
Supplementary files format and content: Count matrix in transcript per million
 
Submission date May 18, 2024
Last update date May 24, 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
GSE267804 Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in Desmoplastic Small Round Cell Tumors [Cell_line_RNA-seq]
Relations
BioSample SAMN41447697
SRA SRX24681655

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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