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Sample GSM2387399 Query DataSets for GSM2387399
Status Public on Jul 05, 2017
Title tw18/+
Sample type SRA
 
Source name tw18 heterozygote epiblast
Organism Mus musculus
Characteristics strain: 129/SvEv
developmental stage: E6.5
genotype: tw18/+
tissue: epiblast
Extracted molecule total RNA
Extraction protocol RNA was extracted embryo epiblasts using the RNeasy Micro Kit (Qiagen).
Total RNA-Seq were generated using the TotalScript RNA-Seq-Seq Kit (Epicentre) with random hexamers according to manufacturer’s instructions with slight modifications. Briefly, all reagents during the cDNA synthesis steps were scaled down in order to achieve a total volume of 39µl, allowing all of the material to be used in the subsequent tagmentation procedure. To further improve strand-specificity of the libraries, Actinomycin D was added to the first strand cDNA synthesis reaction at 5ng/µl final concentration and the libraries were finally amplified using 14 PCR cycles. Quantification was performed using the Qubit high sensitivity DNA assay (Invitrogen) and the libraries were verified using the DNA HS Bioanalyzer chips (Agilent).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description embryos obtained from matings of tw18/+ mice
Data processing Reads were mapped to the mm10 genome (containing chromosomes 1-19, X, Y and M) with TopHat2 (version 2..0.8b) using bowtie (version 1.0.0) and providing refSeq annotations in gtf format (UCSC) and the options -g1 --library-type fr-firststrand.
For calculation of FPKM’s, we used Cuffdiff, part of Cufflinks (version 2.2.1) with the options -u --no-effective-length-correction -b.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-seperated file containing gene symbols and the corresponding FPKM values.
 
Submission date Nov 09, 2016
Last update date May 15, 2019
Contact name Jinhua Liu
Organization name Max Planck Institute for Molecular Genetics
Street address Ihnestra§e 73
City Berlin
ZIP/Postal code 14159
Country Germany
 
Platform ID GPL13112
Series (1)
GSE89734 Patterning and gastrulation defects caused by the tw18 lethal are due to loss of Ppp2r1a
Relations
BioSample SAMN06008219
SRA SRX2340885

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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