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Sample GSM5455576 Query DataSets for GSM5455576
Status Public on Jun 07, 2023
Title M2_Het_A4W_4
Sample type SRA
 
Source name single M2 egg
Organism Mus musculus
Characteristics strain: B6D2F1
developmental stage: M2
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 SAMN20251568
SRA SRX11472360

Supplementary file Size Download File type/resource
GSM5455576_A4W_4_gene_abundances.tsv.gz 1.2 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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