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Sample GSM1657599 Query DataSets for GSM1657599
Status Public on Feb 12, 2016
Title Dll4KO-Tie2_2
Sample type SRA
 
Source name whole hearts of 8 embryos
Organism Mus musculus
Characteristics developmental stage: embryo
age: E9.5
genotype/variation: Dll4flox; Tie2-Cre
tissue: Heart
Growth protocol Standard protocols were used to maintain the mice
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted using Trizol (Invitrogen) And then purified on Rneasy spin columns (Qiagen). RNA integrity (RNA Integrity Score ≥ 7.9) And quantity were determined on the Agilent 2100 Bioanalyzer.
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 Dll4 KO in Tie2 domain
Data processing Illumina RTA software v 1.13.48.0
Fastq files extracted with CASAVA 1.8
Reads were pre-processed with Cutadapt 1.6.1, To remove TruSeq adaptor.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build GRCm38.v70) And genome, Using RSEM v1.2.3 and Bowtie2 v2.0.6.
Data were normalized using TMM with the Bioconductor package EdgeR
Data were batch corrected with Bioconductor package ComBat.R
Differential expression were tested using GLM with the Bioconductor package EdgeR
Genome_build: GRCm38.v70
Supplementary_files_format_and_content: D4NFKOvsWT.D4T2KOvsWT.NormCounts.csv. TMM Normalised counts per million reads sequenced
Supplementary_files_format_and_content: NINFKOvsWT.NormCounts.csv. TMM Normalised counts per million reads sequenced
 
Submission date Apr 14, 2015
Last update date Sep 08, 2022
Contact name Jose Luis de la Pompa
E-mail(s) jlpompa@cnic.es
Organization name Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC).
Lab Intercellular Signalling in Cardiovascular Development & Disease
Street address Melchor Fernández Almagro 3
City Madrid
ZIP/Postal code 28029
Country Spain
 
Platform ID GPL11002
Series (1)
GSE67889 Sequential Notch activation regulates ventricular chamber development
Relations
BioSample SAMN03483034
SRA SRX995261

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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