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Sample GSM6674418 Query DataSets for GSM6674418
Status Public on Dec 01, 2023
Title GOF E15.5 WT_3
Sample type SRA
 
Source name Heart ventricles
Organism Mus musculus
Characteristics tissue: Heart ventricles
genotype: WT
Extracted molecule polyA RNA
Extraction protocol RNA was harvested using Rneasy mini plus kit (Qiagen)
Total RNA (100 ng) was used to generate barcoded RNA-seq libraries using the NEBNext Ultra II Directional RNA Library preparation kit (New England Biolabs) according to manufacturer’s instructions. First, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and first and second cDNA strand synthesis. Next, cDNA ends were repaired and adenylated. The NEBNext adaptor was then ligated followed by second strand removal, uracile excision from the adaptor and PCR amplification. The size of the libraries was checked using the Agilent 2100 Bioanalyzer and the concentration was determined using the Qubit® fluorometer (ThermoFisher)
Libraries were sequenced on a HiSeq4000 (Illumina) to generate 60 bases single reads.FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description WT_3
Data processing Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Sequencing adapter contaminations were removed with cutadapt, discarding those reads that were shorter than 30 nt after trimming.
Resulting reads were aligned against the GRCm38.91 mouse transcriptome, with RSEM v1.3.1, to obtain expression estimates at gene level.
Assembly: GRCm38.91
Supplementary files format and content: Ensembl gene and transcript IDs, and RSEM-estimated raw counts for 53,465 annotated genes, in each sample.
 
Submission date Oct 24, 2022
Last update date Dec 01, 2023
Contact name Jose Luis de la Pompa
E-mail(s) jlpompa@cnic.es
Phone +34620936633
Organization name Centro Nacional de Investigaciones Cardiovasculares (CNIC)
Lab Intercellular Signaling in Cardiovascular Development & Disease
Street address Melchor Fernández Almagro 3
City Madrid
State/province MADRID
ZIP/Postal code 28029
Country Spain
 
Platform ID GPL21103
Series (2)
GSE216467 Characterization of the effect of overexpressing the Nrg-1 (neuregulin-1) gene, using the cardiac driver line Nkx2.5-Cre, in E (embryonic day) 15.5 heart venticles
GSE216471 Role of Nrg-1 in the development of heart ventricular chamber in mice.
Relations
BioSample SAMN31430894
SRA SRX18006977

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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