|
| Status |
Public on Sep 23, 2020 |
| Title |
D3_Female_10_days |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Daphnia magna |
| Characteristics |
tissue: whole organism
strain: Bham2
gender: Female
notes: --
age: 10
treatment: Maintained under normal conditions
culturing media: High Hardness COMBO
|
| Treatment protocol |
Samples were flash frozen in liquid nitrogen when brood pouch was empty and stored in -80C until further use.
|
| Growth protocol |
Cultures of Daphnia magna, strain Bham2, were maintained in a 16:8 h light:dark photoperiod and temperature of 20 ± 1 °C, in high hardness 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. Daphnia samples were monitored every 2 hours during the light period once the appropriate age was reached.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the samples using RNeasy micro kit ((Qiagen Ltd, UK) according to the manufactures protocol.
The RNA-seq libraries were prepared using the Illumina TruSeq standard mRNA kit and sequenced (2x100bp) using Illumina Hi-Seq 4000 platform at BGI, Denmark.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The reads were mapped to reference genome of Daphnia magna (GCA_001632505.1) with TopHat2 (2.1.1) with preset b2-sensitive.
The read counts were extracted with Rsubread (1.30.9), with default settings, using the reference gene models (GCA_001632505.1).
Expression changes were analysed at gene levels using DESeq2 (1.20) with default settings. Genes with significant expression difference between males and females, chages during normal ageing or interaction with sex and age are reported in processed files.
Genome_build: GCA_001632505.1
Supplementary_files_format_and_content: csv (differential expression analysis results at gene level: RSeq_results_age only_age in days_ordered by padj.csv.gz, RSeq_results_sex-age_interaction_age in days_ordered by padj.csv.gz, RSeq_results_sex only_age in days_ordered by padj.csv.gz)
Supplementary_files_format_and_content: csv (read counts at gene level: readcounts_combined.csv.gz)
|
| |
|
| Submission date |
Jan 22, 2019 |
| Last update date |
Sep 23, 2020 |
| Contact name |
julia constantinou |
| E-mail(s) |
JKC335@student.bham.ac.uk
|
| Phone |
+441214143933
|
| Organization name |
University of Birmingham
|
| Department |
Biosciences
|
| Street address |
Edgebaston
|
| City |
Birmingham |
| ZIP/Postal code |
B15 2TT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24325 |
| Series (1) |
| GSE125466 |
RNA-sequencing analysis of genetically identical female and male Daphnia magna with age |
|
| Relations |
| BioSample |
SAMN10788779 |
| SRA |
SRX5278628 |
