|
| Status |
Public on Mar 31, 2017 |
| Title |
DMSO_Control_2 |
| Sample type |
SRA |
| |
|
| Source name |
apex of 3 hearts
|
| Organism |
Danio rerio |
| Characteristics |
developmental stage: adult
strain: AB
stress: cryoinjury
treatment: control
tissue: Heart
|
| Treatment protocol |
Adult fish were injected with peritoneal RO or DMSO carrier 24h and 48h after cryoinjury of the heart
|
| Growth protocol |
Standard protocols were used to maintain the zebrafish to adulthood
|
| 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 TruSeq RNA Sample Preparation Kit v2 standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Cryoinjured heart treated with DMSO
DMSO2
|
| 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 zebrafish transcriptome (Ensembl gene-build GRCZv9.v75; ftp://ftp.ensembl.org/pub/release-75/gtf/danio_rerio/Danio_rerio.Zv9.75.gtf.gz) and gene expression quantified using RSEM v1.2.3 and Bowtie2 v2.0.6.
Data were normalized using TMM with the Bioconductor package EdgeR
Differential expression were tested using GLM with the Bioconductor package EdgeR
Genome_build: GRCZv9.v75
Supplementary_files_format_and_content: ROvsControl.NormCounts.csv reports TMM-normalized counts per million reads sequenced
|
| |
|
| Submission date |
May 07, 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 |
GPL15583 |
| Series (1) |
| GSE68650 |
Injury-activated endocardium plays structural and signalling roles in zebrafish heart regeneration |
|
| Relations |
| BioSample |
SAMN03611822 |
| SRA |
SRX1021205 |
