|
| Status |
Public on Jun 07, 2023 |
| Title |
Late2Cell_KO_J6K_5 |
| Sample type |
SRA |
| |
|
| Source name |
single embryo
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6D2F1
developmental stage: Late 2-cell
female mouse donor genotype: Eif4e1b-/-
|
| Extracted molecule |
polyA RNA |
| 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. M2 eggs were collected from hormone simulated females without mating. M2 eggs or embryos were washed in PBS and transferred into acidic Tyrodes solution to remove zonae pellucidae. Single zona-free eggs or embryos were finally lysed and processed following the scNMT-seq protocol.
G&T-Seq protocol was used to construct single embryo RNA-Seq libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Base calling was finished with RTA2.
Sequenced reads were trimmed using Trimmomatic ver. 0.39 by indicating “NexteraPE-PE.fa” as the adapter sequence file, then mapped to the reference genome using STAR ver. 2.7.6a. The reference genome contains sequences of GRCm38 and ERCC spike-ins.
StringTie ver. 2.1.4 was used to generate counts of genes in the GTF reference downloaded from ENSEMBL(release 101) and from ERCC spike-in product page.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM, TPM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jul 15, 2021 |
| 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) |
| GSE180206 |
Germ-cell specific eIF4E1b regulates maternal mRNA translation to ensure zygotic genome activation [RNA-seq] |
| GSE180218 |
Germ cell-specific eIF4E1b regulates maternal mRNA translation to ensure zygotic genome activation |
|
| Relations |
| BioSample |
SAMN20251588 |
| SRA |
SRX11472684 |
