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Sample GSM2837517 Query DataSets for GSM2837517
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

Supplementary file Size Download File type/resource
GSM2837517_RNAseq_amphioxus_Embr_10h_rep2.cRPKM.txt.gz 200.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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