|
| Status |
Public on Oct 13, 2011 |
| Title |
H3K4me3 forebrain ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Forebrain cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6CBAF1/J
age: E10.5
cell type: forebrain cells
chip antibody: H3K4me3
chip antibody manufacturer: Millipore
chip antibody catalog #: 17-614
chip antibody lot #: NG1794844
|
| Treatment protocol |
Tissue samples were isolated in PBS supplemented with 10% Fetal Calf Serum and made single cell by collagenase treatment and applying a cell-strainer cap (BD Biosciences). Nuclei were sonicated to generate fragments with average length around 300 bp.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Chromatin IP against H3K4me3
|
| Data processing |
Reads were mapped to the mm9 (NCBI m37, July 2007) Mouse genome assembly with bowtie version 0.12.5 (Langmead et al, 2009) with parameters -n 2 --best -strata -m 5. Duplicated reads (reads mapping at exactly the same genomic position in the same orientation) were removed as probable PCR artifacts. Genome coverage densities were calculated for each strand separately, then shifted downstream by 70 bp, averaged and normalized by the total number of mapped reads (times 10^-7). Enriched regions were detected using MACS version 1.4.0beta (Zhang et al., 2008) and selected for a p-value<0.001 and an FDR<0.05. Signal on chromosomes not containing Hox clusters was removed.
|
| |
|
| Submission date |
Aug 22, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Marion LELEU |
| Organization name |
EPFL
|
| Department |
School of Life Sciences
|
| Lab |
Laboratory of developmental genomics
|
| Street address |
EPFL-SV-ISREC-UPDUB- Station 19
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE31570 |
The Dynamic Architecture of Hox Gene Clusters |
|
| Relations |
| SRA |
SRX093315 |
| BioSample |
SAMN00714235 |
