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Sample GSM1657602 Query DataSets for GSM1657602
Status Public on Feb 12, 2016
Title Dll4WT-Nfat_2
Sample type SRA
Source name whole hearts of 9 embryos
Organism Mus musculus
Characteristics developmental stage: embryo
age: E9.5
genotype/variation: WT
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 WT sibling from Dll4 Nfat experiment
Data processing Illumina RTA software v
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
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
BioSample SAMN03483037
SRA SRX995264

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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