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Sample GSM2193313 Query DataSets for GSM2193313
Status Public on Feb 03, 2017
Title PEER_100nMGSK2879552_48h_rep1
Sample type SRA
 
Source name PEER cells
Organism Homo sapiens
Characteristics type: T-ALL
gender: female
treatment: GSK2879552
Treatment protocol Cells were treated with DMSO or 100nM GSK2879552 for 48h
Growth protocol Cells were seeded at 0.7 x 10^6 cells/ml. Cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 100 U/ml penicillin, 100 µg/ml streptomycin, 100 µg/ml kanamycin sulfate and 2 mM L-glutamine at 37°C with 5% CO2.
Extracted molecule total RNA
Extraction protocol RNA was isolated using the miRNeasy mini kit (Qiagen) with on-column DNase digestion. The RNA quality was checked by the Experion RNA StdSens analysis kit (Bio-Rad).
For each sample, 1µg of input material (measured with Ribogreen (Invitrogen)) was used. Libraries were constructed with the Truseq stranded mRNA protocol on the IP-star robot. During the library prep, mRNA was isolated via poly-A capture and cDNA was generated. Next, fragmentation, A-tailing, adaptor ligation and a PCR (13 cycli) were performed on them. The libraries were on average 300bp long. As quality control of the library, analysis on a bioanalyzer chip and a qPCR were done. Libraries were equimolary pooled and 2.4pM of this pool was loaded on the Nextseq500, SR75.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description RNA-sequencing of PEER cells treated with 100nM GSK2879552 for 48h
Data processing basecalling with bcl2fastq
Alignment and gene quantification on Gencode_v23 were done with STAR v2.4.2a.
DESeq2 was used for differential expression analisis, using a multifactorial design
Genome_build: hg38
Supplementary_files_format_and_content: STAR raw count data, tdt
 
Submission date Jun 08, 2016
Last update date May 15, 2019
Contact name Sofie Peirs
E-mail(s) sofie.peirs@ugent.be
Organization name Ghent University
Street address De Pintelaan 185
City Gent
ZIP/Postal code 9000
Country Belgium
 
Platform ID GPL18573
Series (2)
GSE83126 Effect of 48h treatment with 100nM GSK2879552 on T-ALL cell lines LOUCY and PEER
GSE83128 Oncogenic ZEB2 activation drives sensitivity towards LSD1 inhibition in T-cell acute lymphoblastic leukemia
Relations
BioSample SAMN05215789
SRA SRX1830783

Supplementary file Size Download File type/resource
GSM2193313_sample_42093_ReadsPerGene.out.tab.gz 356.0 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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