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| Status |
Public on May 04, 2019 |
| Title |
GA1_15°C |
| Sample type |
SRA |
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| Source name |
pool of 3 whole specimen
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| Organism |
Daphnia magna |
| Characteristics |
strain: P132.85
developmental stage: mothers reproducing parthenogenetically, carrying the first clutch of eggs
treatment: GA
temperature: 15°C
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| Treatment protocol |
Juvenile D. magna for experiments originated from mothers that carried the third clutch of parthenogenetic offspring. Neonates (within 8 h after release from the mothers’ brood pouch) were randomly distributed to jars containing 600 ml tap water, the respective food and if scheduled, supplements. In total we analysed 5 treatments with RNAseq: GA, GA+ EPA, CY, Cy + EPA, and CRY. All D. magna individuals were raised until they deposited the first clutch of eggs into their brood pouch (reaching maturity) before sampling. Daphnia were rinsed twice with deionized water before blotting them dry with lint-free tissue. Whole animal samples were shock-frozen in liquid nitrogen and stored at -80°C thereafter until further experimentation.
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| Growth protocol |
Daphnia magna clone P132.85 originating from the pond Driehoek in Heusden (The Netherlands; N51°44'01", E5°08'17") were cultured at 15°C in aged, aerated and sterile-filtered (45 µm) tap water under dim light conditions. The animals were kept at a maximum density of 15 individuals per L under non-limiting food conditions by feeding them 2 mg carbon per L of Acutodesmus obliquus (formerly: Scenedesmus obliquus) during pre-culture every second day by transferring them into fresh glasses with food.
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| Extracted molecule |
total RNA |
| Extraction protocol |
In total, 5 treatment groups were prepared for sequencing with 3 replicates each. Replicate sample pools consisted of 5 specimens to ensure appropriate amounts for RNA extraction and comparability. Total RNA was extracted using the NucleoSpin RNA extraction kit (Machery und Nagel, Düren/Germany) according to the manufacturer´s instructions. In addition, traces of remaining genomic DNA were removed using the Turbo DNA-free Kit (Invitrogen, Karlsruhe/Germany) in line with the manufacturer´s manual. The quality of the isolated RNA was monitored using capillary electrophoresis on a Bioanalyzer (Agilent Technologies, Santa Clara/USA). Only samples with OD280/OD260≤ 2.0, OD280/OD230 ≤ 2.0 and RIN ≤ 8.0 were used for sequencing.
Clean-up of mRNA, cDNA library construction as well as sequencing was conducted at the University of Cologne’s Cologne Centre for Genomics (CCG)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Raw sequencing data were clipped and trimmed using Trimmomatic (Bolger, Lohse, & Usadel, 2014) to remove bias of sequencing adapters and low quality regions at the beginning and end of sequences.
Reads were mapped to the Daphnia magna genome assembly version 2.4 (NCBI BioProject accession No. PRJNA298946), containing 26.646 translations (open access since April 2016). Mapping was conducted using RSEM v.1.2.31 (Li & Dewey, 2011) connected to bowtie2 (Langdon, 2015) to generate FPKM outputs for transcript analysis.
MeV software v. 4.8.1 (Howe, Sinha, Schlauch, & Quackenbush, 2011) connected to edgeR (Robinson, McCarthy, & Smyth, 2010) was used for the analysis and clustering of differential gene expression. One-Way ANOVA was used on the basis of normalized FPKM values generated with RSEM (Li & Dewey, 2011) to identify differently expressed genes among all treatments.
The available annotation from the Daphnia magna genome was enriched through assignments from the artNOG (EggNOG 4.0) database. COG categories as well as functional descriptions were added to the existing annotation.
Genome_build: NCBI BioProject accession No. PRJNA298946
Supplementary_files_format_and_content: txt files were generated using RSEM. FPKM values were used for the analysis of DGE in MeV
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| Submission date |
May 03, 2019 |
| Last update date |
May 04, 2019 |
| Contact name |
Heidrun Sigrid Windisch |
| E-mail(s) |
Heidrun.Windisch@hhu.de
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| Phone |
+49 211 81 - 1 35 66
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| Organization name |
Heinrich-Heine-University
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| Department |
Cell Biology and Zoology
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| Street address |
Universitätsstrasse 1
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| City |
Düsseldorf |
| State/province |
NRW |
| ZIP/Postal code |
40225 |
| Country |
Germany |
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| Platform ID |
GPL24325 |
| Series (2) |
| GSE130673 |
Transcriptome sequencing of a keystone aquatic herbivore yields insights on the temperature-dependent metabolism of essential lipids [15°C] |
| GSE130674 |
Transcriptome sequencing of a keystone aquatic herbivore yields insights on the temperature-dependent metabolism of essential lipids |
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| Relations |
| BioSample |
SAMN08523325 |
| SRA |
SRX3687900 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3747538_48616.genes.results.txt.gz |
487.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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