|
| Status |
Public on Aug 15, 2018 |
| Title |
RNAseq zebrafish 72 hpf |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Danio rerio |
| Characteristics |
developmental stage: 72 hpf
|
| Growth protocol |
Embryos were cultivated at 28°C in E3 medium until desired developmental stage
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryos were fixed in RNAlater (Thermo Fisher Scientific) and RNA extracted using RNeasy Mini Kit (Qiagen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNA_seq
|
| Data processing |
Reads were aligned against reference genome using Tophat2 software, and gene models were built using Cufflinks.
Genome_build: Amphioxus Bl71nemr (Genomic sequencing data was submitted to ENA under the master PRJEB13665 accession), Zebrafish September 2014 (GRCz10/danRer10), Medaka October 2005 (oryLat2).
Supplementary_files_format_and_content: Individual RPKM files (reads per kilobase per million mapped reads) for amphioxus and zebrafish. Complete table of TPM (transcripts per million) for medaka.
|
| |
|
| Submission date |
Nov 02, 2017 |
| 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 |
GPL18413 |
| Series (2) |
| GSE106430 |
Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [RNA-Seq] |
| GSE106431 |
Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits |
|
| Relations |
| BioSample |
SAMN07966337 |
| SRA |
SRX3353222 |
