|
Status |
Public on Jul 05, 2017 |
Title |
WT |
Sample type |
SRA |
|
|
Source name |
wild type epiblast
|
Organism |
Mus musculus |
Characteristics |
strain: 129/SvEv developmental stage: E6.5 genotype: wildtype 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 |
SAMN06008220 |
SRA |
SRX2340883 |