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Sample GSM5730203 Query DataSets for GSM5730203
Status Public on Dec 15, 2021
Title RRBS-PCB126-3nM-Rep4
Sample type SRA
 
Source name testis
Organism Danio rerio
Characteristics tissue: testis
developmental stage: Adult
treatment: PCB126-3nM
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.
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.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina HiSeq 2000
 
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
 
Submission date Dec 12, 2021
Last update date Dec 15, 2021
Contact name Neelakanteswar Aluru
E-mail(s) naluru@whoi.edu
Phone 508-289-3607
Organization name Woods Hole Oceanographic Institution
Department Biology
Lab Aluru Lab
Street address 45 Water Street
City Woods Hole
State/province MA
ZIP/Postal code 02543
Country USA
 
Platform ID GPL14875
Series (1)
GSE190741 PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis
Relations
BioSample SAMN23960941
SRA SRX13390821

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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