|
| Status |
Public on Aug 30, 2022 |
| Title |
RNA_L2C_DMSO rep2 |
| Sample type |
SRA |
| |
|
| Source name |
late 2-cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6D2F1/J (female) X B6D2F1/J (male)
cell type: late 2-cell
genotype: WT
treatment: treated with DMSO
|
| Treatment protocol |
To transiently inhibit CBP/p300, embryos were cultured in KSOM containing 10μM A-485 (Tocris) between 4 and 20hpi. For transient inhibition of HDACs, embryos were cultured in KSOM containing 50nM TSA (Sigma) between 0-20 or 8-28hpi. Embryos were washed at least six times when they were transferred between different culture conditions.
|
| Growth protocol |
All animal experiments were performed in accordance with the guidelines of the Institutional Animal Care and Use Committee at Harvard Medical School. Collection of oocytes and in vitro fertilized embryos were described previously (Chen et al., 2021; Chen & Zhang, 2019). For allelic H3K27ac CUT&RUN profiling experiments, oocytes were collected from 6- to 8-week-old B6D2F1/J female mice (Jax 100006) and sperm were collected from 8- to 10-week-old PWK/PhJ male mice (Jax 003715). For CBP/p300 and HDACs inhibition experiments, both oocytes and sperm were retrieved from 6- to 8-week-old B6D2F1/J mice. The time when capacitated sperm were added to cumulus oocyte complexes in Human Tubal Fluid (HTF, Millipore) was considered as 0 hour post in vitro fertilization (0hpi). Embryos were cultured in potassium simplex optimized medium (KSOM, Milliplore) at 37°C under 5% CO2 with air.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA-seq libraries were generated using the SMART-Seq Stranded Kit (Takara) following the manufacturer protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
For the raw sequencing reads of total RNA-seq, the three leading nucleotides of read2 generated from TSO were removed. Then the adaptors were removed with Trimmomatic (v0.39) if present. The cleaned reads were mapped to GRCm38 reference genome using STAR (v2.7.8a) (Dobin et al, 2013). RSEM (v1.3.1) (Li & Dewey, 2011) was employed to quantify the genes expression levels with the transcriptome alignments generated by STAR as input. For differentially expression analysis, R package DESeq2 (v1.32.0) (Love et al, 2014) was utilized with raw counts from RSEM as input. The significantly changed genes were identified with adjusted p-value cutoff 0.05, fold change cutoff 2 and mean FPKM cutoff 1.
Assembly: mm10
Supplementary files format and content: txt files contain gene-level reads counts of RNA-seq
|
| |
|
| Submission date |
Aug 25, 2022 |
| Last update date |
Aug 31, 2022 |
| Contact name |
Yi Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
Boston Children's Hospital / Harvard Medical School
|
| Department |
PCMM
|
| Street address |
200 Longwood Avenue WAB 149
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (1) |
| GSE207222 |
Dynamic landscapes of H3K27ac in mouse preimplantation embryos |
|
| Relations |
| BioSample |
SAMN30501736 |
| SRA |
SRX17216618 |
