|
| Status |
Public on Jun 17, 2013 |
| Title |
Dre_48h_control |
| Sample type |
SRA |
| |
|
| Source name |
Dre_48h_control
|
| Organism |
Danio rerio |
| Characteristics |
strain: wild-type WIK strain
tissue: whole embryos
developmental stage: 48 hpf
treatment: control
barcode: GCTT
|
| Treatment protocol |
Stock solutions for Ag NP, Ag Bulk and silver nitrate were made up in ultrapure water, and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers, at 28+/- 1°C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures, glass chambers received 400 mL of ISO water, prepared according to OECD guidelines for zebrafish embryo experiments (http://www.oecd.org/), containing 5 µg/L of 10nm Ag NP, 5 µg/L of Ag Bulk or 0.25 µg/L of silver nitrate. A control chamber was set up containing water alone. Solutions were replaced every 12h during the exposure period, and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h, 3 pools of 50 embryos were removed from each exposure tank, immediately frozen in liquid nitrogen and stored at -80°C for analysis of gene expression. The experiment was terminated at 48 hpf.
|
| Growth protocol |
Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al., 2008 Aquat Toxicol. 87(2):115-26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers, approximately 1 hour post-fertilisation (hpf). Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
High throughput (HT)-SuperSAGE libraries were prepared as described in Matsumura et al 2010, PLoS ONE 5(8):e12010. Samples were multiplexed on each lane of the Illumina flow-cell.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
FASTQ/A Barcode splitter from the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/download.html) was used to separate the samples from each lane using the 4 base barcode.
FASTQ-to-FASTA from the FASTX-Toolkit was used to convert the fastq files to fasta files.
FASTQ/A trimmer from the FASTX-Toolkit was used to remove the barcodes (the first 4 bases) from the sequence.
A Perl script was used to remove all bases after the last occurence of CATG (NlaIII restriction site, used for sequence tag preparation) in each of the sequences
FASTX_collapser was used to collapse the sequences and calculate the frequency of unique sequence tags (unitags) in each library
Supplementary_files_format_and_content: tabulated text files include frequency of all unitags in the treatment library
|
| |
|
| Submission date |
May 22, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Ronny van Aerle |
| E-mail(s) |
r.van-aerle@exeter.ac.uk
|
| Organization name |
University of Exeter
|
| Department |
Biosciences, College of Life and Environmental Sciences
|
| Lab |
van Aerle Lab
|
| Street address |
Stocker Road
|
| City |
Exeter |
| State/province |
Devon |
| ZIP/Postal code |
EX4 4QD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9319 |
| Series (1) |
| GSE38125 |
Transcriptomic profiles of zebrafish embryos exposed to silver (nanoparticles, bulk and ions) using HT-SuperSAGE in a Illumina GA2 platform |
|
| Relations |
| SRA |
SRX148958 |
| BioSample |
SAMN00997683 |
