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Sample GSM2545859 Query DataSets for GSM2545859
Status Public on Aug 20, 2017
Title 24h_28psu_203_Amill
Sample type SRA
 
Source name juveniles coral
Organism Acropora millepora
Characteristics Stage: Juvenile
treatment: 28 PSU
time: 24h
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using 3ml TRIzol Reagent for the coral adults and using RNAaqueous-Micro total RNA isolation kit (AMBION) for the juveniles.
Libraries were constructed using the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420S) following the manufacturers recommended protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description processed data file column: B4
Data processing Reads were mapped onto the Acropora millepora genome using TopHat2 --read-mismatches 5 --read-gap-length 4 --read-edit-dist 6 --read-realign-edit-dist 5 --min-intron-length 30 --min-segment-intron 30 --library-type fr-firststrand --GTF --b2-very-sensitive
Counts were generated using htseq-count
Differentially gene expression analysis was done using DESeq2
gene annotations for the processed data files are located at: http://dna.anu.edu.au/~huaying/amil_v1.0/
 
Submission date Mar 22, 2017
Last update date May 15, 2019
Contact name Catalina Aguilar
E-mail(s) catalina.aguilarhurtado@my.jcu.edu.au
Organization name James Cook University
Department Collegue of Public Health, Medical and Veterinary Sciences
Lab Coral Genomics
Street address 1 James Cook Dr.
City Townsville
State/province Queensland
ZIP/Postal code 4811
Country Australia
 
Platform ID GPL23215
Series (1)
GSE96916 Transcriptomic analysis of the response of Acropora millepora to hypo-osmotic stress provides insights into DMSP biosynthesis by corals
Relations
BioSample SAMN06639218
SRA SRX2669932

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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