|
| Status |
Public on Jun 07, 2023 |
| Title |
Early_2cell_KI_IP_S16 |
| Sample type |
SRA |
| |
|
| Source name |
Early 2-cell embryos
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6D2F1
developmental stage: Early 2-cell
female mouse donor genotype: Eif4e1b FLAGHA knock-in
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
200-250 M2 eggs or early 2-cell embryos were collected from Eif4e1b with C terminal FLAGHA knock-in female or WT female mice as one sample. After removing the zona pellucida, washed with PBS, embryos for a same sample were transferred into a 1 ml nuclease free centrifuge tube with a minimal volume of PBS.
EZ-Manga RIP kit and anti-HA beads were used to perform RIP experiment. RNA in supernatant after IP was purified with RNAclean XP beads and used as input. Smart-Seq2 protocol was used to process RNA bound by anti-HA bead or RNAclean XP beads and finally finish the 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 GRCm38 reference genome using STAR ver. 2.7.6a.
StringTie ver. 2.1.4 was used to generate counts of genes in the GTF reference (release 101) downloaded from ENSEMBL.
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) |
| GSE180217 |
Germ-cell specific eIF4E1b regulates maternal mRNA translation to ensure zygotic genome activation [RIP-seq] |
| GSE180218 |
Germ cell-specific eIF4E1b regulates maternal mRNA translation to ensure zygotic genome activation |
|
| Relations |
| BioSample |
SAMN20253231 |
| SRA |
SRX11475671 |
