|
| Status |
Public on Dec 01, 2023 |
| Title |
LOF E9.5 KO_2 |
| Sample type |
SRA |
| |
|
| Source name |
Heart ventricles
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Heart ventricles
genotype: Nrg-1flox;Tie2-Cre
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Arcturus PicoPure RNA isolation kit (Thermo Fisher Scientific)
200 ng of total RNA were used to generate barcoded RNA-seq libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs). Briefly, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and then first and second cDNA strand synthesis. Next, cDNA 3’ ends were adenylated and the adapters were ligated followed by PCR library amplification. Finally, the size of the libraries was checked using the Agilent 2100 Bioanalyzer DNA 1000 chip and their concentration was determined using the Qubit® fluorometer (Life Technologies)
Libraries were sequenced on a HiSeq2500 (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 2500 |
| |
|
| Description |
KO_2
|
| 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 |
GPL17021 |
| Series (2) |
| GSE216470 |
Characterization of the effect of deleting the Nrg-1(neuregulin-1) gene, using the endothelial driver line Tie2-Cre in E (embryonic day) 9.5 hearts |
| GSE216471 |
Role of Nrg-1 in the development of heart ventricular chamber in mice. |
|
| Relations |
| BioSample |
SAMN31430843 |
| SRA |
SRX18010821 |
