|
| Status |
Public on Jun 07, 2023 |
| Title |
Early2Cell_KO_H6G_7 |
| Sample type |
SRA |
| |
|
| Source name |
single embryo
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6D2F1
developmental stage: Early2Cell
genotype: Eif4e1b-/-
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Zygotes were collected from 6-8-week-old female mice after hormone simulation and mating. The zygotes were cultured in vitro to collect embryos at different developmental stages.The embryos were washed in PBS and transferred into acidic Tyrode’s solution to remove zonae pellucidae. Single zona-free embryos were finally lysed and processed following the scNMT-seq protocol.
Genomic DNA in the supernatant after capturing of poly-A RNA of each sample was processed following scNMT-Seq protocol to construct the single embryo bisulfite sequencing library.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Base calling was finished with RTA2.
Sequenced reads were trimmed using TrimGalore ver. 0.6.7 by indicating “--nextera” as the adapter, then mapped to the reference genome using hisat-3n version 2.2.1-3n compiled following its online tutorial. The reference genome contains sequences of GRCm38 and cl857 Sam7 Lambda DNA.
picard ver. 2.26.9 was used to remove duplicates in the aligned sam files.
Deduplicated sam files were processed by hisat-3n-table to get cytosines as well as their genomic coordinates and methylation states into .tsv files for each sample.
Cytosines in the tsv files were annotated with GRCm38 sequence to get their genomic contexts. Cytosines in GCs of from mouse chromosomes 1-19,X,Y were extracted to profile chromatin accessibility and cytosines in CGs from mouse chromosomes 1-19,X,Y were extracted to profile DNA methylation following the scNMT-seq protocol.
Assembly: GRCm38
Supplementary files format and content: Zipped tab-delimited text files including cytosines identified as well as their genomic coordinates and methylation states representing chromatin accessibility and DNA methylation profiles for each sample.
|
| |
|
| Submission date |
Apr 12, 2022 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Guanghui Yang |
| E-mail(s) |
guanghui.yang@nih.gov
|
| Organization name |
National Institutes of Health
|
| Department |
National Institute of Diabetes and Digestive and Kidney Diseases
|
| Lab |
Laboratory of Cellular and Developmental Biology
|
| Street address |
50 South Drive
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE180218 |
Germ cell-specific eIF4E1b regulates maternal mRNA translation to ensure zygotic genome activation |
| GSE200685 |
Germ-cell specific eIF4E1b regulates maternal mRNA translation to ensure zygotic genome activation [NOMe-seq] |
|
| Relations |
| BioSample |
SAMN27547706 |
| SRA |
SRX14834923 |
