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Sample GSM2027209 Query DataSets for GSM2027209
Status Public on Dec 05, 2017
Title RNA-Seq E4.0ICM rep2
Sample type SRA
 
Source name Periimplantation embryo_E4.0 Inner cell mass
Organism Mus musculus
Characteristics strain: C57BL/6N x DBA/2N
developmental stage: E4.0
tissue: Inner cell mass
Treatment protocol Embryos were collected from C57BL/6N mice induced for superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin and 5 IU of human chorionic gonadotrophin (44-48 hours apart) and mated to DBA/2N males.
Extracted molecule polyA RNA
Extraction protocol After removing the zona pellucida, ICM was isolated by immunosurgery and then directly lysed in hypotonic lysis buffer. RNA-Seq libraries were prepared using Smart-Seq2 protocol with slight modification.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description Processed data file: FPKM_stage.txt.gz
Processed data file: FPKM_replicates.txt.gz
Data processing RNA-Seq reads were aligned to the mm9 genome assembly using Tophat2 version 2.0.11. The replicates were merged together, and transcript abundance (FPKM) was calculated based on Refseq annotation using Cufflinks version 2.0.2.
Genome_build: mm9.
Bedgraph files are available in a tar archive on the series record. A tab-delimited text file includes RPKM values for each sample.
 
Submission date Jan 04, 2016
Last update date May 15, 2019
Contact name Wei Xie
E-mail(s) xiewei121@tsinghua.edu.cn
Organization name Tsinghua University
Street address Zhongguancun north street
City Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL18480
Series (1)
GSE76505 Dynamic epigenomic landscapes during early lineage specification in mouse embryos
Relations
BioSample SAMN04383625
SRA SRX1515375

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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