 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 01, 2024 |
| Title |
CTRL JUN20 r2 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Danio rerio |
| Characteristics |
tissue: whole embryo
genotype: wild type
developmental stage: 5 dpf larvae
treatment: CTRL
|
| Treatment protocol |
The exposure of the larvae took place from 4dpf to 5dpf and was driven through the water: SEC extracts were dissolved in fish water, to a final concentration of 20x.
|
| Growth protocol |
Zebrafish (Danio rerio) embryos were obtained by natural mating following standard procedures. At 2 hours post fertilization (hpf), eggs were collected, rinsed and fertilized viable eggs were transferred to embryo water (90 µg/ml of Instant Ocean -Aquarium Systems, Sarrebourg, France-, 0.58 mM CaSO4·2H2O, dissolved in reverse osmosis purified water) and kept under standard conditions (28.5 ºC and 12L:12D photoperiod).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ZF embryos were taken in an Eppendorf (10 larvae per replicate) and flash frozen on dry ice. Total RNA was extracted using AllPrep DNA/RNA Mini Kit (Qiagen, CA, USA). Then, total RNA was assayed for quantity and quality using Qubit® RNA BR Assay kit (Thermo Fisher Scientific) and RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent Technologies).
Library construction and RNA-sequencing (RNA-seq) was performed by the National Center for Genomic Analysis (CNAG, Barcelona, Spain). The RNA-Seq library was prepared with KAPA Stranded mRNA-Seq Illumina Platforms Kit (Roche) following manufacturer recommendations using Illumina platform compatible adaptors with unique dual indexes and unique molecular identifiers (Integrated DNA Technologies). The final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on NovaSeq 6000 (Illumina) with a read length of 2x51bp following the manufacturer’s protocol for dual indexing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
AS8978
|
| Data processing |
Real Time Analysis (RTA v3.4.4) software was used for basecalling and the quality scoring of the run.
Generation of FASTQ sequence files was carried out with CASAVA software.
RNA-seq reads were aligned to the GRCz11 genome reference using STAR software version 2.7.8a (Dobin et al., 2013) with ENCODE parameters. The total sequencing output was 60 million paired end reads for each sample and 100% mapped properly to the reference genome. Quality control of the mapping was performed with Samtools and Gemtools.
Differential expression analysis between CTRL and SEC treated larvae was performed with the DESeq2 (3.17) R package with the Likelihood ratio test option (Li and Dewey, 2011; Love et al., 2014).
Assembly: GRCz11
Supplementary files format and content: *.txt: Tab-delimited text files include absolute reads values (counts).
Supplementary files format and content: COUNTS_genes_WWTP.xlsx: Excel file includes absolute reads values (counts) for each sample.
|
| |
|
| Submission date |
Aug 07, 2023 |
| Last update date |
Nov 01, 2024 |
| Contact name |
Claudia Sanz Lanzas |
| E-mail(s) |
claudiasanzlanzas@gmail.com
|
| Organization name |
IDAEA-CSIC
|
| Department |
Environmental Toxicology
|
| Street address |
Jordi Girona 18-26
|
| City |
Barcelona |
| ZIP/Postal code |
08014 |
| Country |
Spain |
| |
|
| Platform ID |
GPL24995 |
| Series (1) |
| GSE240250 |
Detoxification of wastewater treatment plant effluents by enhanced soil aquifer treatment |
|
| Relations |
| BioSample |
SAMN36873405 |
| SRA |
SRX21282140 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7688882_AS8978.txt.gz |
348.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
