|
Status |
Public on Aug 15, 2018 |
Title |
RNAseq amphioxus 10h replicate 2 |
Sample type |
SRA |
|
|
Source name |
whole embryo
|
Organism |
Branchiostoma lanceolatum |
Characteristics |
developmental stage: 10h
|
Growth protocol |
Embryos were cultivated at 19°C in filtered seawater until desired developmental stage, and fixed in RNAlater (Thermo Fisher Scientific)
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted using RNeasy Mini Kit (Qiagen)
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
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 |
GPL20177 |
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 |
SAMN07966287 |
SRA |
SRX3353162 |