|
| Status |
Public on Mar 21, 2018 |
| Title |
postnbCreERT2_7dpi_3 |
| Sample type |
SRA |
| |
|
| Source name |
Heart
|
| Organism |
Danio rerio |
| Characteristics |
treatment: 7 dpi
|
| Treatment protocol |
postnb:CreERT2;ubb:loxP-GFP-loxP-mCherry fish were treated over night with 4-OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.
|
| Growth protocol |
All experiments were conducted with adult zebrafish between 3 and 9 months of age, raised at a density of 3 fish/l.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Ventricular apex were dissotiated using pronase, elastase, DNase and liberase TH. mCherry-positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure (Thermofisher) following manufacturer instructions.0.2-0.6 ng of total RNA was used to generate barcoded RNA-seq libraries using the Ovation Single Cell RNA-Seq System (NuGEN) with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer (ThermoFisher Scientific). 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). 3-5 pooled hearts were used per sample.
Index-tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit (Illumina, San Diego, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Sequencing adaptor contaminations were removed from reads using cutadapt.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25.
Genome_build: Ensembl genebuild 10, release 82 (Danio rerio assembly Zv9).
Supplementary_files_format_and_content: Matrix_table.xlsx file contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.
|
| |
|
| Submission date |
Jul 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Manuel J Gomez |
| E-mail(s) |
mjgomezr@cnic.es
|
| Organization name |
CNIC
|
| Lab |
Bioinformatics Unit
|
| Street address |
Melchor Fernández Almagro, 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL18413 |
| Series (1) |
| GSE101199 |
postnb lineage traced cells at 7 and 60 days post cryoinjury (dpi) during adult zebrafish cardiac ventricle regeneration |
|
| Relations |
| BioSample |
SAMN07346450 |
| SRA |
SRX2997959 |
