|
| Status |
Public on Jul 06, 2018 |
| Title |
Cast/Ei_oocyte_H3K36me3_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
GVO
|
| Organism |
Mus musculus |
| Characteristics |
strain: Cast/EiJ
tissue: oocyte
developmental stage: GV
chip antibody: anti-H3K36me3 (Abcam ab9050)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq: purified ChIP DNA was extracted with Phenol:chloroform followed by ethanol precipitation.
Libraries were constructed using a custom protocol (Brind’Amour et al. 2015) and amplified for 10-12 PCR cycles (RNA) or 15 PCR cycles (ChIP). 75 bp or 100bp paired-end libraries were sequenced on the NextSeq 500 or HiSeq 2500 platform an according to manufacturer’s protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
H3K36me3
|
| Data processing |
ChIP-seq: Paired-end reads were trimmed using Trimmomatic v.0.32, and aligned to the mm10 (mouse), hg19 (human) and rn6 (rat) assemblies using Bowtie2 v.2.2.3 with soft-clipping enabled. Library technical quality was assessed using Picard-tools (http://broadinstitute.github.io/picard) v.1.92 and Samtools (http://www.htslib.org/) v.1.1. PCR duplicates and alignments with mapping quality less than 10 were filtered out. Sequence alignment maps were converted to bedGraph and wiggle formats using Bedtools v2.22.1 and UCSC binary bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Apr 03, 2018 |
| Last update date |
Jul 06, 2018 |
| Contact name |
Matthew C Lorincz |
| Organization name |
University of British Columbia
|
| Department |
Medical Genetics
|
| Street address |
2350 Health Sciences Mall
|
| City |
Vancouver |
| State/province |
British Columbia |
| ZIP/Postal code |
V6T 1Z3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE112622 |
LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation |
|
| Relations |
| BioSample |
SAMN08848934 |
| SRA |
SRX3875397 |
