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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
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
BioSample SAMN05215789
SRA SRX1830783

Supplementary file Size Download File type/resource 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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