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Sample GSM1456409 Query DataSets for GSM1456409
Status Public on Oct 01, 2014
Title Male1
Sample type SRA
Source name Brain
Organism Danio rerio
Characteristics tissue: Whole Brain
Treatment protocol NA
Growth protocol NA
Extracted molecule genomic DNA
Extraction protocol Brains were dissected from 12 male and 12 female zebrafish and were halved through the sagittal plane. 2 male and 2 female RRBS library was prepared with each library containing a pool of six halved zebrafish brain. A total of four RRBS libraries were prepared from 2 pooled male brain and 2 pooled female brain library each containing 6 halved zebrafish brain.
Genomic DNA was digested with MspI (New England Biolabs, Ipswich, MA) followed by end repair and addition of 30 A overhangs. Methylated adaptors (Illumina, San Diego, CA) with a 30 T overhang were then ligated with the generated fragments. Following adaptor ligation, DNA fragments ranging from 40 to 220 bp (preligation size) were cut from a 3% (w/v) NuSieve GTG agarose gel (Lonza, Basel, Switzerland) and subsequently bisulphite modified using the EZ DNA methylation kit (Zymo Research, Irvine, CA). The final library was amplified by PCR. The resulting library was sequenced on an Illumina platform with a single-ended, 49bp run.
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina HiSeq 2000
Data processing DNA from 4 RRBS were sequenced in Illumina HiSeq Machines, Base-calling perfromed using RTA software and demultiplexed to obtain individual Fastq files.
Single CpG site methylation calculation was perfromed using the R package methylKit.
UNIX scripts and our in house developed tool DMAP (Stockwell et al 2014, Bioinformatics) was used for post processing of the data
Genome_build: Zv9
Supplementary_files_format_and_content: .txt files describing methylation status of each filtered CpG sites.
Submission date Jul 30, 2014
Last update date May 15, 2019
Contact name Aniruddha Chatterjee
Phone +64-210701558
Organization name University of Otago
Department Pathology
Lab Epigenetics and Disease
Street address 270 Great king Street
City Dunedin
State/province Otago
ZIP/Postal code 9054
Country New Zealand
Platform ID GPL14875
Series (1)
GSE59916 Genome-wide DNA methylation map of Zebrafish male and female brain
BioSample SAMN02947260
SRA SRX666317

Supplementary file Size Download File type/resource
GSM1456409_Male_1_CpG.txt.gz 4.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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