|
| Status |
Public on Dec 03, 2019 |
| Title |
Epb2_KO3 |
| Sample type |
SRA |
| |
|
| Source name |
Heart
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Heart ventricles
genotype: Efnb2Flox;Nfatc1-Cre
developmental stage: E16.5
|
| Growth protocol |
Experiments were conducted with WT and mutant mouse embryos at E12.5, E15.5 and E16.5.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA from whole hearts, collected at E12.5 from WT and Jag1Flox;Nfatc1-Cre and from WT and Delta4Flox;Nfatc1-Cre embryos, was isolated with the Arcturus Picopure RNA isolation kit (Applied Biosystems). RNA from ventricles, collected at E15.5 from WT and D4Cdh5-CreER, from WT and Delta4GOF;Tie2-Cre and from E16.6 WT and Efnb2Flox;Nfatc1-Cre embryos was isolated with RNA Isolation Kit: RNeasy.
Libraries were prepared using the NEBNext Ultra RNA Library preparation kit (New England Biolabs)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Epb2_matrix_table.xls
|
| Data processing |
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Reads were pre-processed with a pipeline that used cutadapt v1.6 to remove Illumina adaptors, and FastQC to perform quality controls after each step.
Processed reads were mapped on the transcriptome and quantified using RSEM v1.2.3.
Genome_build: GRCm38, Ensembl genebuild 76
Supplementary_files_format_and_content: matrix_table.xls files contain ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.
|
| |
|
| Submission date |
Feb 14, 2018 |
| 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 |
GPL17021 |
| Series (1) |
| GSE110614 |
Coronary arterial development is regulated by a Dll4-Jag1-EphrinB2 signaling cascade |
|
| Relations |
| BioSample |
SAMN08536504 |
| SRA |
SRX3699663 |
