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Sample GSM1306339 Query DataSets for GSM1306339
Status Public on Apr 10, 2014
Title MGG4TPC H3K27ac
Sample type SRA
 
Source name MGG4 human glioblastoma stem cell line
Organism Homo sapiens
Characteristics chip antibody: H3K27ac (Active Motif)
Treatment protocol MGG4 and MGG 8 FCS were infected with lentiviral constructs containing individual ORFs of developmental transcription factors. Cells infected with various combinations of TF were subsequently switched to neural stem conditions for a period of roughly one month and then subjected to ChIP-seq analysis.
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 genomic DNA
Extraction protocol As described in Mikkelsen et al., Nature 2007. Chromatin was fixed and sheared to 200-1000 bp using Branson Sonifer. After IP and adapter ligation, library fragments of 200-600 bp were isolated by Ampure XP bead purification. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hiseq 2500 following the manufacturer's protocols.
Single read, Illumina
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing ChIP-Seq reads were aligned with Bowtie1; reads longer than 36 bases were truncated to 36 bases before alignment.
A filter to remove duplicate reads (identical starting position and direction) was applied
Peaks were identified as described in Rheinbay, Suva et al, Cell Reports 2013
Density maps were generated with IGVTools
Genome_build: hg19
Supplementary_files_format_and_content: BIGWIG, density maps.
Supplementary_files_format_and_content: BED: tab-delimited text file with the following columns: chr, start, end. ChIP-Seq peak calls.
 
Submission date Jan 13, 2014
Last update date Aug 26, 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)
GSE54047 Reconstructing and reprogramming the tumor propagating potential of glioblastoma stem-like cells: ChIP-seq
GSE54792 Epigenomic profiling of stemness, differentiation and primary tissues in human glioblastoma
Relations
BioSample SAMN02584186
Named Annotation GSM1306339_MGG4TPC.H3K27ac.bigWig

Supplementary file Size Download File type/resource
GSM1306339_MGG4TPC.H3K27ac.bed.gz 310.9 Kb (ftp)(http) BED
GSM1306339_MGG4TPC.H3K27ac.bigWig 166.7 Mb (ftp)(http) BIGWIG
Raw data not provided for this record
Processed data provided as supplementary file

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