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Sample GSM2827679

Query DataSets for GSM2827679

Status

Public on Oct 22, 2019

Title

control C3

Sample type

SRA

Source name

pool of 7dpf larvae

Organism

Danio rerio

Characteristics

strain: AB strain
treatment: control

Treatment protocol

zebrafsih were exposed to 2 sublethal concentrations of tCS: 50 and 100 µg/L. 50% of the solution were renewed every day.

Growth protocol

zebrafish were maintained individually in 24-well microplates, at 26.5 °C under a 12:12 light/dark photoperiod cycle in a climate chamber during all the experiment.

Extracted molecule

genomic DNA

Extraction protocol

Genomic DNA from each pooled larvae sample was extracted using DNeasy Blood & Tissue Kit (Qiagen) following the manufacturer's protocol.
Reduced representation bisulfite sequencing libraries were prepared based on published protocols. Briefly, 12 RRBS libraries were prepared, 4 libraries per condition, each library containing a pool of 24 larvae. Genomic DNA was digested with MspI (New England Biolabs, Ipswich, MA) followed by end repair, addition of 3′ A overhangs and addition of methylated adaptors (Illumina, San Diego, CA) to the digested fragments. Following adaptor ligation, DNA fragments ranging from 40–220 bp (pre-ligation size) were cut from a 3% (w/v) NuSieve GTG agarose gel (Lonza, Basel, Switzerland) and subsequently bisulfite converted using the EZ DNA methylation kit (Zymo Research, Irvine, CA) with an extended incubation time of 18–20 h. Bisulfite converted libraries were amplified by PCR reactions and sequenced (100-bp single ended reads) by New Zealand Genomics Limited (University of Otago, New Zealand) on an Illumina HiSeq2000 sequencer.

Library strategy

Bisulfite-Seq

Library source

genomic

Library selection

Reduced Representation

Instrument model

Illumina HiSeq 2000

Data processing

DNA from 12 RRBS were sequenced in Illumina HiSeq Machines, Base-calling perfromed using RTA software and demultiplexed to obtain individual Fastq files.
DNA methylation analysis was perfromed using a fragment based approach using our own in house developed pipeline called DMAP (Stockwell et al Bioinformatics, 2014).
Unix scripts and Epiexplorer ( for overlapping ENCODE data) was used for further processing of data.
Genome_build: Zv9
Supplementary_files_format_and_content: Excel file contains variably methylated fragment details (excel)

Submission date

Oct 22, 2017

Last update date

Oct 22, 2019

Contact name

Elodie Falisse

E-mail(s)

elodie.falisse@unamur.be

Organization name

University of Namur

Department

Biology