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Sample GSM4476421 Query DataSets for GSM4476421
Status Public on Oct 28, 2020
Title 2cell_early_total_RNA_rep1
Sample type SRA
 
Source name Preimplantation embryo
Organism Mus musculus
Characteristics tissue: Preimplantation embryo
genotype: wild-type
developmental stage: early 2-cell
Extracted molecule total RNA
Extraction protocol 8-week-old female mice were intraperitoneally injected with PMSG and hCG. Embryos were harvested in M2 medium 36 h after hCG
Total RNA-seq libraries were prepared as previously described (Brind'Amour, J., et al. 2018). Total RNA was isolated from about 100 mouse embryos using TRIzol (Thermo, 10296028), and ribosomal RNA was depleted using the NEB Next rRNA Depletion Kit (NEB, E6310S) according to the manufacturer’s instruction. Double-stranded cDNA was synthesized using NEB Next first-strand (NEB, E7771S) and second-strand synthesis modules (NEB, E7550S). Library preparation was performed using NEBNext UltraTM II DNA Library Prep Kit (NEB, E7645S) according to the manufacturer’s instruction. All libraries were sequenced by Illumina Hi-Seq Xten platform according to manufacturer’s instruction.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Basecalls performed using CASAVA version 1.8
RNA-Seq reads were aligned to the mm9 genome assembly using tophat 2.1.1, transcript abundance (FPKM) were calculated based on Reflat annotation using cufflinks version 2.1.1
Genome_build: mm9
 
Submission date Apr 14, 2020
Last update date Oct 29, 2020
Contact name Bofeng Liu
E-mail(s) lbf12thu@gmail.com
Organization name Tsinghua University
Department School of Life Science
Lab Xie Wei Lab
Street address Haidian District
City Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL21273
Series (1)
GSE135457 The landscape of RNA Pol II binding reveals a step-wise transition during ZGA
Relations
BioSample SAMN14598136
SRA SRX8115744

Supplementary file Size Download File type/resource
GSM4476421_2cell_early_total_RNA_FPKM.txt.gz 178.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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