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Sample GSM1858073 Query DataSets for GSM1858073
Status Public on Feb 12, 2016
Title Jag1Jag2KO-TnT_3
Sample type SRA
Source name heart ventricles from 4 embryos
Organism Mus musculus
Characteristics developmental stage: embryo
age: E15.5
genotype/variation: Jag1flox; Jag2flox; TnT-Cre
tissue: heart venticle
Treatment protocol No treatment applied
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 NEBNext Ultra kit for Illumina
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description Double Jag1 and Jag2 KO in Tnt domain
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: MFng.NormCounts.txt. TMM Normalized counts per million reads sequenced
Supplementary_files_format_and_content: J1andJ2andJ12.NormCounts.txt. TMM Normalized counts per million reads sequenced
Submission date Aug 20, 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 GPL17021
Series (1)
GSE67889 Sequential Notch activation regulates ventricular chamber development
BioSample SAMN04002735
SRA SRX1160294

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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