|
| Status |
Public on May 28, 2013 |
| Title |
MGG4serum H3K4me1 |
| Sample type |
SRA |
| |
|
| Source name |
MGG4 human glioblastoma serum-grown cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MGG4
cell type: human glioblastoma serum-grown cells
chip-antibody: H3K4me1
chip-antibody vendor: Abcam
chip-antibody cat. #: 8895
|
| 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 |
SAMN02051349 |
