|
| Status |
Public on Apr 10, 2014 |
| Title |
MGG28 primary tumor H3K27ac |
| Sample type |
SRA |
| |
|
| Source name |
Primary human tumor
|
| 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 2500 |
| |
|
| 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) |
[email protected]
|
| Organization name |
Broad Institute
|
| Street address |
7 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| 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 |
SAMN02584184 |
| Named Annotation |
GSM1306371_MGH28PT.H3K27ac.bigWig |
