|
| Status |
Public on Mar 25, 2014 |
| Title |
RNAseq_ICabE24_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Oryzias latipes |
| Characteristics |
developmental stage: stage 24
tissue: embryo
|
| Growth protocol |
Embryos were raised at 26ºC untill they reached the desired developmental stage. They were dechorionated manually before RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
60 embryos per sample were suspended in Trizol reagent (Intron Biotechnology) with chloroform. RNA was isolated from the aqueous phase, purified by isopropanol precipitation and cleaned using RNeasy MinElute Cleanup kit (Qiagen).
RNA libraries were prepared for Illumina sequencing using standard protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Mapping: reads were mapped to the O. latipes genome (oryLat2 assembly) using Tophat software (http://tophat.cbcb.umd.edu/).
Assigning reads to transcripts: total counts and RPKM for each transcript were calculated using RSeQC package (v2.3.3, http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html)
Genome_build: oryLat2
Supplementary_files_format_and_content: Plain text files with raw counts and RPKM values for each transcript.
|
| |
|
| Submission date |
Apr 29, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Juan J. Tena |
| E-mail(s) |
jjtenagu@upo.es
|
| Organization name |
CABD/CSIC
|
| Street address |
Univ. Pablo Olavide, Ctra. Utrera km1
|
| City |
Sevilla |
| ZIP/Postal code |
41013 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17089 |
| Series (1) |
| GSE46484 |
RNA-seq in Oryzias latipes at stage 24 |
|
| Relations |
| BioSample |
SAMN02086419 |
| SRA |
SRX272492 |
