NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1121877 Query DataSets for GSM1121877
Status Public on May 28, 2013
Title MGG8CSC ASCL1
Sample type SRA
 
Source name MGG8 human glioblastoma stem cell line
Organism Homo sapiens
Characteristics cell line: MGG8
cell type: human glioblastoma stem cells
chip-antibody: ASCL1
chip-antibody vendor: Epitomics
chip-antibody cat. #: T091
Treatment protocol None
Growth protocol MGG and NS cells 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)
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 gel extraction. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer or Illumina Hiseq 2000 following the manufacturer's protocols.
After IP and adapter ligation, library fragments of 200-600 bp were isolated by gel extraction. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer or Illumina Hiseq 2000 following the manufacturer's protocols.
 
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: wig, density maps
 
Submission date Apr 12, 2013
Last update date May 29, 2013
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)
GSE46014 Histone modification and TF ChIP-Seq for glioblastoma cell lines and neural stem cells
GSE46016 Epigenomic profiling of glioblastoma stem cells
Relations
BioSample SAMN02051362

Supplementary file Size Download File type/resource
GSM1121877_MGG8CSC.ASCL1.wig.gz 120.9 Mb (ftp)(http) WIG
Raw data not provided for this record
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap