|
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 |