|
| Status |
Public on Jul 06, 2018 |
| Title |
Cast/Ei_oocyte_RNAseq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
GVO
|
| Organism |
Mus musculus |
| Characteristics |
strain: Cast/EiJ
tissue: oocyte
developmental stage: GV
chip antibody: n/a
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq: total RNA was isolated from 100-200 mouse or rat oocytes using TriReagent, and ribosomal RNA was depleted using NEB Next rRNA Depletion kit according to manufacturer’s instruction. Double stranded cDNA was synthesized using NEB Next first strand and second strand synthesis modules.
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 |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
RNA-seq: Paired-end reads were trimmed using Trimmomatic v.0.32, and aligned to the mm10 (mouse), hg19 (human) and rn6 (rat) assemblies using STAR v.2.4.0.i. 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 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 |
SAMN08848931 |
| SRA |
SRX3875400 |
