|
| Status |
Public on Jun 01, 2016 |
| Title |
Treated_2 caudal_fin_0dpa |
| Sample type |
SRA |
| |
|
| Source name |
caudal fin, cortisol, 0dpa
|
| Organism |
Danio rerio |
| Characteristics |
strain/background: AB
tissue: caudal fin
age: adult
embryonic treatment: cortisol
days post amputation: 0dpa
|
| Treatment protocol |
DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development, and then maintained to 4.5 months under normal conditions.
|
| Growth protocol |
AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-EZplus kit from Qiagen.
Illumina TruSeq PolyA+ mRNA libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Zebrafish mRNA.
Processed data file: fin_CPM.txt
|
| Data processing |
Sequence quality was assessed using Fastqc QC (v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were trimmed using Trimmomatic (v 0.3; Bolger et al., 2014).
Trimmed reads were aligned to the zebrafish (Danio rerio) transcriptome annotated by Ensembl (version 83) of the GRCz10 genome assembly using RSEM version 1.2.25 (Li and Dewey, 2011) and Bowtie 1.1.2 (Langmead et al., 2009).
Differentially expressed transcripts were determined using R/edgeR version 3.10.2 (Robinson et al., 2010).
Genome_build: Danio rerio GRCz10
Supplementary_files_format_and_content: Tab-delimited text files with read counts (counts per million) per sample.
|
| |
|
| Submission date |
Apr 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Benjamin L King |
| E-mail(s) |
benjamin.l.king@maine.edu
|
| Phone |
207-581-2803
|
| Organization name |
University of Maine
|
| Department |
Molecular and Biomedical Sciences
|
| Street address |
5735 Hitchner Hall
|
| City |
Orono |
| State/province |
ME |
| ZIP/Postal code |
04469 |
| Country |
USA |
| |
|
| Platform ID |
GPL18413 |
| Series (2) |
| GSE80260 |
Cortisol-treated zebrafish embryos develop into pro-inflammatory adults with aberrant immune gene regulation [adults] |
| GSE80286 |
Cortisol-treated zebrafish embryos develop into pro-inflammatory adults with aberrant immune gene regulation |
|
| Relations |
| BioSample |
SAMN04851153 |
| SRA |
SRX1704261 |
