|
| Status |
Public on Feb 15, 2013 |
| Title |
input genomic DNA_brain |
| Sample type |
SRA |
| |
|
| Source name |
Mouse adult hybrid brain
|
| Organism |
Mus musculus x Mus spretus |
| Characteristics |
tissue: Adult whole brain
strain: BL6/spretus
chip antibody: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed using fixed chromatin from mouse brain or cell lines. DNA from ChIP pull-down chromatin fractions were de-crosslinked and purified using QIAquick PCR purification kit. Genomic DNA was prepared from an aliquot of the same batch of nuclei from F1 brain
Sequencing libraries were prepared each from four pooled independent PolII-S5p ChIP samples from Patski cells or from Xist mutant F1 brain, using the Illumina seq sample prep kit. Size selection of the library was done by gel excision and purification of DNA in the 200-600bp range. Control sequencing library was prepared from genomic DNA prepared from F1 brain.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Brains were collected from female F1 hybrid (BL6/spretus) carring an Xist mutation (B6.Cg-Xist<tm5Sado>) and thus having complete skewing of inactivation of the spretus X chromosome.
|
| Data processing |
Basecalls performed using CASAVA version 1.4
A pseudo-spretus genome was assembled by replacing available SNPs between C57BL/6J and M. spretus (Sanger Center) into the BL6 reference genome. Reads were aligned to the C57BL/6J reference sequence (mm9, UCSC) and to the pseudo-spretus genome separately using BWA (Burrows-Wheeler Aligner).
Only high-quality uniquely-mapped reads were used for assignment to each haploid genome based on available SNPs.
PolII-S5p peak regions in brain were selected using all uniquely mapped reads by both CisGenome (FDR=1e-5 as the cutoff) and MACS (Model-based Analysis of ChIP-Seq) (p=1e-5 as the cutoff).
The SNP-associated read counts were used to assess average allelic enrichment at the 5’ end and 3’ end of genes.
Genome_build: mm9
|
| |
|
| Submission date |
Feb 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Xinxian Deng |
| E-mail(s) |
dengx2@u.washington.edu
|
| Organization name |
University of Washington
|
| Department |
Laboratory Medicine and Pathology
|
| Lab |
HSB C526
|
| Street address |
1959 NE Pacific St.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
|
| Platform ID |
GPL16616 |
| Series (2) |
| GSE30761 |
Mammalian X upregulation |
| GSE44255 |
Allele-specific maps of RNA polymerase II phosphorylated at serine 5 in mouse cultured hybrid cells and mouse hybrid brain |
|
| Relations |
| SRA |
SRX236086 |
| BioSample |
SAMN01919789 |
| Named Annotation |
GSM1081375_brain.gDNA.100.BL6.bigWig |
| Named Annotation |
GSM1081375_brain.gDNA.100.spretus.bigWig |
