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Sample GSM1904420 Query DataSets for GSM1904420
Status Public on May 12, 2016
Title RNA-Seq_MGG4_KD [Sample 4]
Sample type SRA
Source name MGH4 Glioma stem-like cells
Organism Homo sapiens
Characteristics cell line: MGG4
cell type: Glioma cell line
cell subtype: Cancer stem-like cells
infected with: shRNA sequence targeting Imp2
genotype/variation: IMP2 knockdown
Treatment protocol MGH4 cell line infected with shRNA sequence targeting Imp2
Growth protocol Neurobasal medium (Invitrogen) supplemented with L-glutamine (Glutamax, Gibco), B27 supplement (Invitrogen), N2 supplement (Invitrogen), 20 ng/mL recombinant human EGF (R&D Systems), 20 ng/ml recombinant human FGF2 (R&D Systems). Puromycin selection for 5 days
Extracted molecule polyA RNA
Extraction protocol Total RNA extraction kit Exiqon, on colum DNASE treatment (Qiagen)
Illumina polyA stranded
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description processed data: RNA_IMP2s_KD.txt
Data processing Genomic alignment with TopHat 2.0.12, --b2-very-sensitive --library-type fr-firststrand --b2-N 1
Differential expression calling with edgeR 3.10.2 and R 3.2.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited textfile containing the raw readcounts, normalized cpm and gene fold-changes
Submission date Oct 08, 2015
Last update date May 15, 2019
Contact name Tommy Beat Schlumpf
Organization name ETH Z├╝rich
Department D-BSSE
Lab Paro
Street address Mattenstrasse 26
City Basel
State/province Basel-Stadt
ZIP/Postal code 4058
Country Switzerland
Platform ID GPL18573
Series (2)
GSE73845 Functional characterization of RNA-binding protein IMP2 in primary Glioma cell lines [HTS]
GSE73847 Functional characterization of RNA-binding protein IMP2 in primary Glioma cell lines
BioSample SAMN04156651
SRA SRX1317318

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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