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| Status |
Public on Jan 01, 2018 |
| Title |
zfish_0ppm_R2 |
| Sample type |
SRA |
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| Source name |
ovary
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| Organism |
Danio rerio |
| Characteristics |
tissue: ovary
strain: EK
mehg exposure: 0 ppm
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| Treatment protocol |
Ovaries were flash frozen in RNA-later and placed on dry ice immediately after dissection until proper storage at -80C.
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| Growth protocol |
Adult EK female zebrafish were exposed to MeHg (0, 1, 3, or 10 ppm with ethanol as the vehicle) for an entire life cycle, starting with maternal exposure. Fish were exposed until euthanized.
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| Extracted molecule |
total RNA |
| Extraction protocol |
High quality total RNA was extracted from the ovary using Direct-zol* RNA MiniPrep kit (Zymo Research). Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance.
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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| 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
The cleaned reads for each sample were independently aligned to the reference zebrafish genome (Zv9, UCSC) using TopHat
The alignment output from TopHat was converted into a transcriptome using Cufflinks (v. 2.2.1), and alignment data was confirmed using RNAseQC against the Zv9 reference transcriptome of zebrafish
Sample specific transcriptomes were assembled using Cufflinks with the Zv9 transcriptome as a reference to correct fragment biases by better identifying the start/end point of each exon
Transcriptomes from each sample were merged into an ovary specific transcriptome using Cuffmerge
Differential expression was conducted with Cuffdiff using pooled dispersion, geometric normalization, and the merged ovary transcriptome.
Genome_build: UCSC Zv9
Supplementary_files_format_and_content: Cuffdiff outputs FPKM files, which show expression values. Included in ovary.zip
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| Submission date |
Sep 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Carvan |
| E-mail(s) |
carvanmj@uwm.edu
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| Organization name |
University of Wisconsin-Milwaukee
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| Department |
School of Freshwater Sciences
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| Street address |
600 E. Greenfield
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| City |
Milwaukee |
| State/province |
WI |
| ZIP/Postal code |
53204 |
| Country |
USA |
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| Platform ID |
GPL14875 |
| Series (1) |
| GSE73615 |
Female Reproductive Impacts of Dietary Methylmercury in Yellow Perch (Perca flavescens) and Zebrafish (Danio rerio) |
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| Relations |
| BioSample |
SAMN04123951 |
| SRA |
SRX1297638 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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