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Status |
Public on Dec 15, 2021 |
Title |
RRBS-DMSO-Rep5 |
Sample type |
SRA |
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Source name |
testis
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Organism |
Danio rerio |
Characteristics |
tissue: testis developmental stage: Adult treatment: DMSO
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Treatment protocol |
Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant-free water for 7 days prior to sampling the testis tissue.
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Extracted molecule |
genomic DNA |
Extraction protocol |
Total RNA and DNA were isolated using the ZR-Duet™ DNA/RNA Mini Prep kit (Zymo Research, CA). Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single-ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT-Dx, a Diagenode company (Ghent, Belgium). Briefly, libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI (New England Biolabs, MA), followed by end repair and A-tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor-ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end (PE) sequencing was performed on an Illumina HiSeq2500 platform.
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Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
Reduced Representation |
Instrument model |
Illumina HiSeq 2000 |
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Data processing |
DNA methylation analysis was carried out following Bisulfite Analysis Toolkit (BAT). The details are provided in this website: https://www.bioinf.uni-leipzig.de/Software/BAT/. This contains 4 different modules - Mapping, Calling, Analysis and DMRs RNAseq - pre-processing using FASTQC RNAseq - mapping the reads to the genome using STAR RNAseq - counting the reads using HT-seq count RNAseq - statistical analysis using edgeR Genome_build: GRCz10 Supplementary_files_format_and_content: Text format; RNAseq data files (Htseq-count) contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary_files_format_and_content: P0_3.metilene_qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary_files_format_and_content: P10.metilene_qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary_files_format_and_content: P0_3-overlap-P10.txt: Common DMRs between 3 and 10nM PCB126 groups
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Submission date |
Dec 12, 2021 |
Last update date |
Dec 15, 2021 |
Contact name |
Neelakanteswar Aluru |
E-mail(s) |
naluru@whoi.edu
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Phone |
508-289-3607
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Organization name |
Woods Hole Oceanographic Institution
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Department |
Biology
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Lab |
Aluru Lab
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Street address |
45 Water Street
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City |
Woods Hole |
State/province |
MA |
ZIP/Postal code |
02543 |
Country |
USA |
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Platform ID |
GPL14875 |
Series (1) |
GSE190741 |
PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis |
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Relations |
BioSample |
SAMN23960937 |
SRA |
SRX13390817 |
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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