|
| Status |
Public on Jan 01, 2023 |
| Title |
4 mGy/h, 4 days, rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole organism
|
| Organism |
Daphnia magna |
| Characteristics |
tissue: Whole organism
Sex: Female
developmental stage: Juvenile, 4 days old
genotype: WT
treatment: 4 mGy/h gamma radiation
time point: 4 days exposure
|
| Treatment protocol |
Daphnia magna were exposed to 7 dose-rates (0, 0.4, 1, 4, 10, 40, 100 mGy/h) of gamma radiation in a static system (50 mL plastic beaker filled with 45 mL culture medium) for 8 days. Samples were taken after 4 and 8 days exposure for RNA-seq.
|
| Growth protocol |
Daphnia magna were cultured in the M7 medium, pH 7.8-8.2, dissolved oxygen >8 mg/L and temperature 19-21, according to the standard toxicity testing guideline OECD TG211
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Zymo Tissue & Insect Micro Prep kit. The quantity and purity of the RNA were measured using an ND-1000 Nanodrop and integrity assessed using an Agilent Bioanalyzer.
Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
D41
Processed file_raw_counts_4d_mRNAGene.txt
|
| Data processing |
Sequence reads filtering: the BGI software SOAPnuke to filter the low quality reads
Genome mapping: HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts)
Dose-responsive gene identification: Dromics R package
Assembly: NCBI genome assembly: ASM399081v1
Supplementary files format and content: tab-delimited files with counts and annotations for each gene in the files
|
| |
|
| Submission date |
Jun 30, 2022 |
| Last update date |
Jan 01, 2023 |
| Contact name |
You Song |
| E-mail(s) |
you.song@niva.no
|
| Organization name |
Norwegian Institute for Water Research (NIVA)
|
| Department |
Ecotoxicology and Risk Assessment
|
| Street address |
Økernveien 94
|
| City |
Oslo |
| ZIP/Postal code |
0579 |
| Country |
Norway |
| |
|
| Platform ID |
GPL32412 |
| Series (1) |
| GSE207246 |
Multiomics Point of Departure (moPOD) Modeling Supports an Adverse Outcome Pathway Network for Ionizing Radiation |
|
| Relations |
| BioSample |
SAMN29438934 |
| SRA |
SRX15950518 |
