|
| Status |
Public on Jan 01, 2018 |
| Title |
T6R |
| Sample type |
SRA |
| |
|
| Source name |
Retina
|
| Organism |
Danio rerio |
| Characteristics |
tissue: Retina
generation: F3
strain: EK
mehg conc: 0.03µM MeHg
|
| Treatment protocol |
The F1 generation embryos were exposed to MeHg. Retina of F3 generation was used for isolating RNA.
|
| Growth protocol |
Eggs of EK strain zebrafish were exposed to methylmercury (0.0 and 0.03μM with ethanol as the vehicle) for 24 hours, then raised normally. This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage. The F2 and F3 generations were never exposed to exogenous MeHg.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
High quality total RNA was extracted from the retina using RNeasy Micro Kit (QIAGEN, Valencia, CA, USA).
Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin-Madison.
Each library was generated using a paired-end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, CA, USA). Samples were run with 12 samples per lane, with 100 base pair, paired-end reads. Sequencing depth was 14-32 million reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalling was performed using CASAVA 1.8.2.
Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt
FastQC was used to ensure that cleaned reads were of higher quality than initial raw reads supplied by the sequencer
The cleaned reads for each sample were independently aligned to the reference zebrafish genome (Zv9, UCSC) using TopHat
Aligned reads were used to generate count and fpkm data using Cuffnorm against Zv9 trainscriptome
Genome_build: UCSC Zv9
Supplementary_files_format_and_content: Tab delimited matrix of gene counts and FPKM normalized counts
|
| |
|
| Submission date |
Oct 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael J Carvan III |
| E-mail(s) |
carvanmj@uwm.edu
|
| Phone |
(414)382-1706
|
| Organization name |
University of Wisconsin-Milwaukee
|
| Department |
School of Freshwater Sciences
|
| Lab |
Carvan Lab
|
| Street address |
600 E. Greenfield Ave.
|
| City |
Milwaukee |
| State/province |
WI |
| ZIP/Postal code |
53204 |
| Country |
USA |
| |
|
| Platform ID |
GPL14875 |
| Series (2) |
| GSE73795 |
Methylmercury (MeHg) induced Transgenerational Inheritance of Retinal Transcriptome in Zebrafish (Danio rerio) [retina] |
| GSE73797 |
Methylmercury (MeHg) induced Transgenerational Inheritance of Brain Transcriptome in Zebrafish (Danio rerio) |
|
| Relations |
| BioSample |
SAMN04147961 |
| SRA |
SRX1309259 |
