|
| Status |
Public on Sep 30, 2019 |
| Title |
Ch249 |
| Sample type |
SRA |
| |
|
| Source name |
Adult zebrafish heart_Uninjured_RFP
|
| Organism |
Danio rerio |
| Characteristics |
strain: tg(sox10:CreERT2;vmhcl:loxP-tagBFP-loxP-mCherry-NTR)
condition: Uninjured
tissue: Adult zebrafish heart
sorted cell population: RFP
|
| Extracted molecule |
total RNA |
| Extraction protocol |
0.2% RNase inhibitor in Triton X-100 plus Dilute the oligo-dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo-dT primers and 90 µl of nuclease-free water to a tube and mix well. Cells were isolated in the lowest possible volume, possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer, 1 ul of oligo dT primeres and dNTP mix. Smart-seq2 (Picelli, S., et al. Nature Protocols 2014 )
Smart-seq2 (Picelli, S., et al. Nature Protocols 2014 )
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1249
|
| Data processing |
FASTQ files were checked for quality control metrics using FastQC (version 0.11.5) and RSeqQC (version 2.6.4)
Post-Quality control, raw reads were mapped to the reference genome using Hisat2 (version 2.1.0) proceeded by exon-counting using featureCounts (version 1.6.0)
Genome_build: Ensembl GRCz11, build 94
Supplementary_files_format_and_content: Tab-delimeted files containing the Ensembl gene id and the RLE normalized counts
|
| |
|
| Submission date |
Jul 01, 2019 |
| Last update date |
Oct 01, 2019 |
| Contact name |
Nadia Mercader |
| E-mail(s) |
nmercader@cnic.es, nadia.mercader@unibe.ch
|
| Organization name |
University of Bern
|
| Street address |
Baltzerstrasse 2
|
| City |
Bern |
| ZIP/Postal code |
3012 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL23274 |
| Series (1) |
| GSE133571 |
Pre-existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish |
|
| Relations |
| BioSample |
SAMN12172052 |
| SRA |
SRX6385172 |
