|
| Status |
Public on May 22, 2012 |
| Title |
Anti-H3K4me3 Prdm9-/- Liver |
| Sample type |
SRA |
| |
|
| Source name |
Anti-H3K4me3 Prdm9-/-_liver_ChIP-Seq
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6;129P2-Prdm9tm1Ymat/J
genotype/variation: Prdm9-/-
tissue: liver
chip antibody: Anti-H3K4me3 Millipore (#07-473)
chip antibody vendor: Millipore
chip antibody cat. #: #07-473
sequencing technique: ChIP-Seq
|
| Growth protocol |
Cells were extracted from testis of euthanized mice and subjected to immunoprecipitation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates from mouse testis cells were crosslinked, sonicated and immunoprecipitated with anti-DMC1 or anti-RAD51 antibodies. Size selection of library fragments of 150 - 250 bp was performed after PCR amplification. SSDS samples were denatured and quickly renatured before adapter ligation.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 16
|
| Data processing |
For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected.
Peak calling was performed on pooled SSDS samples for each genetic background. Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyzer Pipeline. Reads with less than two mismatches were not aligned. MACS was used to define peaks.
The fourth column in each bedGraph file (available on Series records) represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome Build:
PRDM9_H3K4me3_Liver_peaks.bedGraph: mm9
PRDM9_H3K4Me3_Sample1_Liver.bed: mm9
|
| |
|
| Submission date |
Feb 02, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Brick |
| E-mail(s) |
[email protected], [email protected], [email protected]
|
| Organization name |
NIDDK
|
| Department |
GBB
|
| Street address |
5/205 Memorial Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE35498 |
Genetic recombination is directed away from functional genetic sites in mice. |
|
| Relations |
| SRA |
SRX118397 |
| BioSample |
SAMN00780118 |
