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Sample GSM3462536 Query DataSets for GSM3462536
Status Public on Jan 01, 2020
Title Ctrl_late_3h_2
Sample type SRA
 
Source name Mix of whole embryos
Organism Branchiostoma lanceolatum
Characteristics treatment: DMSO 0.1percent
time of treatment: 15.5hpf
developmental stage: 18.5hpf
Treatment protocol Embryos were treated with 0,1% DMSO or 50µM SU5402.
Growth protocol Embryos were grown in 6cm Petri dishes filled with 6mL of filtered sea water with DMSO or SU5402.
Extracted molecule total RNA
Extraction protocol Embryos were frozen in liquid nitrogen after getting rid of the filtered sea water by centrifugation. Total RNA was extracted using the RNeasy Mini Plus Kit from QIAGEN following manufacturer's instructions. Disruption and homogenization were undertaken using TissueLyzer from QIAGEN.
A library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “Truseq RNA sample preparation low throughput” protocol with some modifications. Briefly, mRNA was purified from 2 µg total RNA using oligo-dT magnetic beads and fragmented using divalent cations at 94°C for 8 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers, then the second strand of the cDNA was synthesized using Polymerase I and RNase H. The next steps of RNA-Seq library preparation were performed in an automated system using SPRIworks Fragment Library System I kit (ref A84801, Beckman Coulter, Inc) with the SPRI-TE instrument (Beckman Coulter, Inc). Briefly, in this system double stranded cDNA fragments were blunted, phosphorylated and ligated to indexed adapter dimers, and fragments in the range of ~200-400 bp were size selected. The automated steps were followed by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 15 cycles (6 hpt libraries) or 12 cycles (3 and 9 hpt libraries); 5 min at 72°C), then surplus PCR primers were removed by purification using AMPure XP beads (Agencourt Biosciences Corporation). DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description DMSO 0.1%
Data processing The first 50 bases of pass-filter reads were retained, in order to be comparable between the different samples.
These reads were mapped onto the reference transcriptome (https://wwwphp.obs-banyuls.fr/repository/transcriptome_B_lanceolatum/TotalMergeAssembliesGenbankRenomme.fasta.gz) using bwa v0.6.1 29 and the following set of parameters : -l 27 -n 4 -e 4. Only uniquely aligned reads were then retained. The number of reads aligned to each contig was computed using R.
Genome_build: Reference transcriptome constructed using data from Oulion et al (PLoS One. 2012; 7(5): e36554) and the data obtained in this study, available on the following URL : https://wwwphp.obs-banyuls.fr/repository/transcriptome_B_lanceolatum/TotalMergeAssembliesGenbankRenomme.fasta.gz
Supplementary_files_format_and_content: Tabulated text file containing raw read counts in each sample.
 
Submission date Nov 07, 2018
Last update date Jan 01, 2020
Contact name Stephanie Bertrand
E-mail(s) stephanie.bertrand@obs-banyuls.fr
Organization name CNRS/SU UMR7232
Street address AVENUE PIERRE FABRE
City BANYULS SUR MER
ZIP/Postal code 66650
Country France
 
Platform ID GPL20177
Series (1)
GSE122245 Comparative RNA-seq analysis between control and SU5402 treated amphioxus (Branchiostoma lanceolatum) embryos
Relations
BioSample SAMN10390890
SRA SRX4990351

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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