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Sample GSM1533393 Query DataSets for GSM1533393
Status Public on Aug 27, 2015
Title WT_RNA-seq
Sample type SRA
 
Source name mouse optic cups_WT
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: optic cups
Stage: 10.5E Embryos
Extracted molecule total RNA
Extraction protocol total RNA was purified from 200 optic cups of 10.5 days mouse embryos
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description wildtype
Data processing libraries sequenced usign Illumina GAIIx single end 75nt
base-calling was produced by Illumina RTA Software v 1.13.48
demultiplexed fastq files were generated using CASAVAv1.7
sequencing adaptor contaminations were removed using cutadapt
reads were mapped and gene expression quantified using rsem v1.17
counts were normalized using TMM from edgeR package
Processed_data_file_format_and_content: tab separated file. Contains normalized counts. Samples in columns, Genes in rows
Genome_build: mm10
 
Submission date Oct 28, 2014
Last update date May 15, 2019
Contact name Carlos Torroja
E-mail(s) ctorroja@cnic.es
Phone (+34) 91 4531200
Organization name Centro Nacional de Investigaciones Cardiovasculares (CNIC)
Department Bioinformatics Unit
Street address Melchor Fernandez Almagro, 3
City Madrid
State/province Madrid
ZIP/Postal code 28029
Country Spain
 
Platform ID GPL11002
Series (1)
GSE62786 Meis1 coordinates a network of genes implicated in eye development and microphthalmia
Relations
BioSample SAMN03145630
SRA SRX745812

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

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