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Sample GSM1324083 Query DataSets for GSM1324083
Status Public on Apr 14, 2014
Title MGG8TPC_3
Sample type SRA
 
Source name MGG8 human glioblastoma stem cell line
Organism Homo sapiens
Characteristics tissue: glioblastoma
Treatment protocol None
Growth protocol MGG4 TPC and iTPC, MGG8 TPC and iTPC were cultured and passaged using standard neural stem cell conditions as described in Wakimoto et al, 2009 (PMID: 19351838) and Conti et al, 2005 (PMID: 16086633) MGG 4 FCS and MGG8 FCS were cultured in DMEM + 10% FCS and 1X P/S
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from cells using RNeasy Kit (Qiagen). 2 ug of total RNA were used to fragment and polyA isolate the 3’ends of mRNA transcripts.
Illumina sequencing libraries were constructed as described in Yoon and Brem, 2010.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description MGG8 TPC
Data processing Reads were aligned to the human genome assembly hg19 with TopHat version 1.4.1.
Briefly, to calculate expression values for each gene we scanned 500 basepair window within 10 kb of the annotated 3’ end of all genes, and counted reads that fell in the highest 500 basepair window across all libraries. To normalize across libraries we fit each individual libraries distribution of gene expression values into the same negative binomial distribution.
For comparative analyses, we used the edgeR R package with general linear model (GLM) to identify expressed genes, annotate and collapse multiple values for each gene and identify differentially expressed genes between the three matched TPC/DGC pairs, and the MGG8 DGC empty (two replicates) and MGG8 POU3F2+SOX2+SALL2+OLIG2 iTPCs.
Density maps were generated with IGVTools
Genome_build: hg19
Supplementary_files_format_and_content: BIGWIG, density maps, value of gene expression values
 
Submission date Feb 07, 2014
Last update date Apr 14, 2014
Contact name Esther Rheinbay
E-mail(s) esther@broadinstitute.org
Organization name Broad Institute
Street address 7 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL11154
Series (2)
GSE54791 Reconstructing and reprogramming the tumor propagating potential of glioblastoma stem-like cells: RNA-seq
GSE54792 Epigenomic profiling of stemness, differentiation and primary tissues in human glioblastoma
Relations
BioSample SAMN02630912

Supplementary file Size Download File type/resource
GSM1324083_MGG8TPC_3.bw 16.2 Mb (ftp)(http) BW
Raw data not provided for this record
Processed data provided as supplementary file

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