|
| Status |
Public on Oct 18, 2019 |
| Title |
RNA_M_EB45.4 |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Daphnia pulex |
| Characteristics |
strain: Eloise Butler (45)
clone: Clone 45
gender: male
age: Mix of ages of 3, 8 and 15 days
tissue: whole body
exposure: control
culturing media: Standard COMBO
replicate: rep2
|
| Treatment protocol |
To induce male Daphnia, sexually matured individual female Daphnia were treated with the crustacean reproductive hormone, methyl (2E, 6E)-farnesoate (MF) at a final concentration of 400nM. This concentration is sufficient to induce male Daphnia at 100% efficiency (Olmstead & Leblanc 2002). Due to the instability of MF, media was changed daily to ensure consistent exposure. The first brood was discarded and male neonates were collected from 2nd–3rd broods. Female and male cultures were maintained separately.
Maintained under standard condition with normal levels of oxygen (6 mg/L) for 3, 8 and 15 days.
|
| Growth protocol |
Cultures of Daphnia pulex Eloise Butler strain (genotypes EB31 and EB45, originally sampled from Eloise Butler pond in Minnesota (Yampolsky et al. 2014)) were maintained in a 16:8 h light:dark photoperiod and temperature of 20 ± 1 °C, in standard COMBO medium (COMBO). Media were prepared using a protocol adapted from Kilham et al. (1998), and renewed every other day. Animals were fed every other day with Chlorella vulgaris at a concentration of ~27,550 cells of algae per individual Daphnia. Oxygen concentrations were continuously monitored using an oxygen sensor (Unisense microrespiration system, Denmark). Daphnia samples were flash frozen in liquid nitrogen and stored in -80C until further use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the samples using RNeasy micro kit ((Qiagen Ltd, UK) according to the manufacturer's protocol.
The RNA-seq libraries were prepared using the Illumina TruSeq standard mRNA kit and sequenced (1x85bp) 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 |
| |
|
| Description |
polyA RNA
processed data file: annot_daphplx17evigenes_mod.gff.gz
processed data file: expression_EBseq_gene_FvsM.txt.gz
processed data file: expression_EBseq_tr_FvsM.txt.gz
processed data file: splicing_KisSplice_reads.fa.gz
processed data file: splicing_kissDE_FvsM.txt.gz
|
| Data processing |
RNA-Seq: Illumina adapters (using core sequence: AGATCGGAAGAGC) and nucleotides with low quality (Phred score < 20) were removed with cutadapt (v.1.11).
RNA-Seq: The filtered reads were mapped to the reference genome of Daphnia pulex PA42 (GCA_900092285.1; Ye et al. 2017) using RSEM (v.1.3.0; Li & Dewey 2011) using STAR aligner (2.5.3a; Dobin et al. 2013) for the RNA-seq samples, with default settings.
RNA-Seq: The Daphnia pulex gene models used in the analysis are from November 2017 obtained from the arthropod database in eugenes (Genomic Information for Eukaryotic Organisms; http://arthropods.eugenes.org) produced by Don Gilbert using EvidentialGene (Gilbert 2016).
RNA-Seq: Expression changes were analysed at gene and transcript levels using EBSeq (v.1.20.0) (Leng et al. 2013), with default settings. Genes and transcripts with significant expression difference between males and females (with posterior probability of differential expression < 0.05) were analysed further.
Genome_build: GCA_900092285.1
Supplementary_files_format_and_content: RNA-Seq: txt (differential expression analysis results at gene level: expression_EBseq_gene_FvsM.txt.gz and transcriptome level: expression_Ebseq_tr_FvsM.txt.gz)
Supplementary_files_format_and_content: RNA-Seq: txt (de-novo differential splicing analysis results: splicing_kissDE_FvsM.txt.gz), fasta (de-novo splicing events detected by kisSplice: splicing_KisSplice_reads.fa.gz)
|
| |
|
| Submission date |
Dec 27, 2018 |
| Last update date |
Oct 18, 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) |
| GSE124427 |
A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male Daphnia pulex |
|
| Relations |
| BioSample |
SAMN10656442 |
| SRA |
SRX5185074 |
