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| Status |
Public on Oct 01, 2014 |
| Title |
Female1 |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Danio rerio |
| Characteristics |
tissue: Whole Brain
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| Treatment protocol |
NA
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| Growth protocol |
NA
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| 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.
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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 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.
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| Submission date |
Jul 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Aniruddha Chatterjee |
| E-mail(s) |
aniruddha.chatterjee@otago.ac.nz
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| Phone |
+64-210701558
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| Organization name |
University of Otago
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| Department |
Pathology
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| Lab |
Epigenetics and Disease
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| Street address |
270 Great king Street
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| City |
Dunedin |
| State/province |
Otago |
| ZIP/Postal code |
9054 |
| Country |
New Zealand |
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| Platform ID |
GPL14875 |
| Series (1) |
| GSE59916 |
Genome-wide DNA methylation map of Zebrafish male and female brain |
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| Relations |
| BioSample |
SAMN02947262 |
| SRA |
SRX666319 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1456411_Female_1_CpG.txt.gz |
2.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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