|
| Status |
Public on Feb 12, 2016 |
| Title |
Notch1KO-Nfat_3 |
| Sample type |
SRA |
| |
|
| Source name |
whole hearts of 8 embryos
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: embryo
age: E9.5
genotype/variation: Notch1flox; Nfatc1-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 |
Notch1 KO in Nfat 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 |
SAMN03483045 |
| SRA |
SRX995272 |
