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| Status |
Public on Apr 14, 2014 |
| Title |
MGG4TPC_1 |
| Sample type |
SRA |
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| Source name |
MGG4 human glioblastoma stem cell line
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| Organism |
Homo sapiens |
| Characteristics |
tissue: glioblastoma
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| Treatment protocol |
None
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| 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
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
MGG4 TPC
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| 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
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| Submission date |
Feb 07, 2014 |
| Last update date |
Apr 14, 2014 |
| Contact name |
Esther Rheinbay |
| E-mail(s) |
esther@broadinstitute.org
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| Organization name |
Broad Institute
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| Street address |
7 Cambridge Center
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN02630934 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1324075_MGG4TPC_1.bw |
11.6 Mb |
(ftp)(http) |
BW |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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