|
| Status |
Public on May 31, 2022 |
| Title |
MAT2A-inhibited_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
bovine morulae
|
| Organism |
Bos taurus |
| Characteristics |
sourse: in vitro produced, inhibitor (FIDAS-5) treated from the 8-16 cell stage
day after ivf: day 6
chip antibody: Diagenode C15410069
|
| Treatment protocol |
The culture was chemically semi-defined (bovine serum albumin was added) and performed under low oxygen tension (5%). The 8-16 cell stage embryos at 72 hpi (day 3 of IVF) were allocated to control (0.1% (v/v) DMSO, a vehicle of FIDAS-5) or MAT2A-inhibited (20 µM FIDAS-5) groups and further cultured up to day6 (144 hpi).
|
| Growth protocol |
Bovine morulae were in vitro produced by in vitro fertilization (IVF) and further cultured in mSOF up to day 6 (IVF = day 0).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Morula-stage embryos at 144 h post IVF were collected as approximately 50 embryos per biological replicate for ChIP. ChIP for small cell numbers was performed with a Low Cell ChIP-Seq Kit (Active Motif) according to the manufacturer’s manual (version A3) with some modifications. The morulae were freed from the zona pellucida by using pronase before crosslinking with formaldehyde. After crosslink-quenching, the sample was sonicated to shear chromatin using a Bioruptor UCD-250 (Cosmo Bio) for 30 x 30 s with 30-s pauses in ice-water. The sample was centrifuged for 2 min at 18,000 x g and the supernatant (200 μL) was transferred to a new tube. The 200-µL sample of sheared chromatin was processed for ChIP using 3.2 µg anti-H3K27me3 antibody (C15410069, Diagenode). For the normalization of sequencing read count, Drosophila-derived chromatin (0.17 ng, Active Motif) and corresponding antibody (1 µg, Active Motif) were added as spike-in. The ChIPed DNA was decrosslinked, purified, and resuspended in 40 µL low-EDTA TE buffer.
Sequencing libraries of the ChIPed DNA were constructed by using Next Gen DNA Library Kit and Next Gen Indexing Kit (Active Motif) following the manufacturer’s instruction.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing reads were aligned to the bovine genome (Bos_taurus_UMD_3.1.1/bosTau8, Jun. 2014) using Bowtie (version 1.1.1). The peaks were called in the ChIP samples relative to the baseline using Model-based Analysis of ChIP-Seq (MACS, version 1.4.2) with following options; --nomodel --nolambda --shiftsize=300.
Assembly: bosTau8
Supplementary files format and content: wig.gz files of called peaks
|
| |
|
| Submission date |
Mar 10, 2022 |
| Last update date |
Jun 01, 2022 |
| Contact name |
Shuntaro Ikeda |
| Organization name |
Kyoto University
|
| Department |
Graduate School of Agriculture
|
| Street address |
Kitashirakawa Oiwake-cho, Sakyo-ku
|
| City |
Kyoto |
| ZIP/Postal code |
6068502 |
| Country |
Japan |
| |
|
| Platform ID |
GPL23055 |
| Series (2) |
| GSE198293 |
Genome-wide H3K27me3 profile in in vitro produced bovine morula treated with MAT2A inhibitor |
| GSE198295 |
Profile in in vitro produced bovine morulae treated with MAT2A inhibitor |
|
| Relations |
| BioSample |
SAMN26558925 |
| SRA |
SRX14426946 |
