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Sample GSM1625880 Query DataSets for GSM1625880
Status Public on Jun 15, 2016
Title RNA-Seq blastocyst KD Gata4 rep3
Sample type SRA
 
Source name Preimplantation embryo
Organism Mus musculus
Characteristics strain: C57BL/6N x DBA/2N
developmental stage: Blastocyst
Growth protocol Knockdown siRNA injected embryos were cultured in CZB medium containing glutamine at 37℃ under 5% CO2 in air.
Extracted molecule polyA RNA
Extraction protocol After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer.
RNA-Seq libraries were prepared using Smart-Seq2 protocol with slightly modification
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description FPKM_blastocyst.txt.gz
Data processing Basecalls performed using CASAVA version 1.8
RNA-Seq reads were aligned to the mm9 genome assembly using STAR version 2.4.0, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: The wig files counted by the number of reads falling into 100bp bin in the genome. Tab-delimited text files include RPKM values for each sample
 
Submission date Mar 05, 2015
Last update date May 15, 2019
Contact name Wei Xie
E-mail(s) xiewei121@tsinghua.edu.cn
Organization name Tsinghua University
Street address zhongguancun beidajie
City Beijing
ZIP/Postal code 100086
Country China
 
Platform ID GPL18480
Series (2)
GSE66390 The landscape of accessible chromatin in mammalian pre-implantation embryos
GSE66582 The landscape of accessible chromatin in mammalian pre-implantation embryos (RNA-Seq)
Relations
BioSample SAMN03389637
SRA SRX902569

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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