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Sample GSM2861062 Query DataSets for GSM2861062
Status Public on Dec 11, 2018
Title EB45_RNA(F4)
Sample type SRA
 
Source name whole organism
Organism Daphnia pulex
Characteristics strain: Eloise Butler (45)
clone: Clone 45
tissue: whole organism
exposure: control
gender: female
replicate: rep1
age: Mix of ages of 3, 8 and 15 days
Treatment protocol Maintained under standard condition with normal levels of oxygen (6 mg/L) for 3, 8 and 15 days
Growth protocol Daphnia pulex Eloise Butler strains were maintained in standard COMBO.
Extracted molecule polyA RNA
Extraction protocol Control samples of Daphnia pulex EB clones of 3, 8 and 15 days old were pooled and RNA was extracted using RNeasy micro kit (Qiagen) according to the manufactures protocol.
Libraries were prepared and sequenced using Illumina NextSeq 500 platform at the Centre for Genomics and Bioinformatics, Indiana University.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Illumina adapters (using core sequence: AGATCGGAAGAGC) and nucleotides with low quality (Phred score<20) were removed with cutadapt (v.1.11).
The filtered reads were mapped to the reference genome (GCA_900092285.1) using tophat2 (v.2.1.0).
The read counts for genes were extracted with HTSeq (v.0.9.1) using unstranded union mode for genes. The read counts were converted to FPKM values for expression analysis.
Genome_build: GCA_900092285.1
Supplementary_files_format_and_content: txt (gene expression count and FPKM values from RNA-seq mapping: GSF1035-F.expression.txt)
 
Submission date Nov 17, 2017
Last update date May 15, 2019
Contact name Jouni Antero Kvist
Organization name University of Helsinki
Department Research Program for Molecular Neurology
Lab Med­ical Neuro­gen­et­ics group
Street address Haartmaninkatu 8
City Helsinki
State/province Uusimaa
ZIP/Postal code 00014
Country Finland
 
Platform ID GPL24021
Series (1)
GSE103939 DNA methylation profiling of Daphnia species.
Relations
Reanalyzed by GSM3533034
SRA SRX3405479
BioSample SAMN08044848

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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