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Sample GSM1143424 Query DataSets for GSM1143424
Status Public on Mar 25, 2014
Title RNAseq_E10.5_rep1
Sample type SRA
 
Source name whole organism, E10.5
Organism Mus musculus
Characteristics strain/background: CBA/Ca×C57Bl/10
developmental stage: E10.5
tissue: whole body
Treatment protocol No treatment. Normal embryonic development.
Growth protocol CBA/Ca×C57Bl/10 crosses. Embryos taken at 10.5dpc, taking the day in which the plug was found as 0.5dpc.
Extracted molecule total RNA
Extraction protocol TRI-reagent followed by chloroform extraction, phenol:chloroform:methyl-butanol (25:24:1) extraction and propanol precipitation.
RNA libraries were prepared for Illumina sequencing using the standard protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Replicate 1.
Data processing Mapping: reads were mapped to the mouse genome (mm9 assembly) using Tophat software (http://tophat.cbcb.umd.edu/).
Assigning reads to transcripts: total counts and RPKM for each transcript were calculated using the RSeQC package (v2.3.3, http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html).
Genome_build: MGSCv37
Supplementary_files_format_and_content: Plain text files with raw counts and RPKM values for each transcript.
 
Submission date May 16, 2013
Last update date May 15, 2019
Contact name Juan J. Tena
E-mail(s) jjtenagu@upo.es
Organization name CABD/CSIC
Street address Univ. Pablo Olavide, Ctra. Utrera km1
City Sevilla
ZIP/Postal code 41013
Country Spain
 
Platform ID GPL13112
Series (1)
GSE47033 RNA-seq in whole mouse embryos at stage E10.5
Relations
BioSample SAMN02146467
SRA SRX278615

Supplementary file Size Download File type/resource
GSM1143424_RNAseq_E10.5_rep1.rpkm.gz 745.7 Kb (ftp)(http) RPKM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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