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| Status |
Public on Apr 21, 2019 |
| Title |
Ctrl1_WGBS |
| Sample type |
SRA |
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| Source name |
hypothalamus
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: hypothalamus
gender: Male
age: postnatal day 9
treatment: control
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extracted and purified using the Qiagen Puregene kit
Five (5) μg of DNA was fragmented to ~300 bp using 28 cycles of 15 seconds on/15 seconds off on a Diagenode Bioruptor. DNA was end-repaired using 1× T4 DNA ligase buffer, 400 μM dNTPs, 15 U T4 DNA polymerase (NEB), and 50 U PNK (NEB) for 30 min at 20°C. After PCR purifying (Qiagen), adenine bases were appended to the ends using 1× NEB 2 buffer, 200 μM dATP, and 15 U Klenow Fragment (3′ to 5′ exo-, NEB) for 30 min at 37°C. After another DNA purification using the PCR MinElute kit (Qiagen), 3 μL of Illumina's methylated sequencing adapters were ligated on using 1× ligase buffer and 5 μL Quick T4 DNA Ligase (NEB) for 30 min at room temperature. After a final PCR purification, 500 ng of library was bisulfite converted using Zymo's EZ DNA Methylation-Direct kit according to the manufacturer's instructions. The library was then amplified using 2.5 U PfuTurbo Cx Hotstart DNA Polymerase (Stratagene) for 12 cycles using Illumina's standard amplification protocol.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Post-mortem brain
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| Data processing |
Filter using Illumina flag
Separate and trim reads based on adapter contamination
Align to rn6 using BSSeeker2
Combine aligned reads, both trimmed and no adapter contamination
Convert sam files to percent methylation bed files
Combine all chromosome percent methylation bed files into a single file
Genome_build: rn6
Supplementary_files_format_and_content: Percent Methylation Bed file containing single base methylation information with ranged color coding
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| Submission date |
May 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Keith Dunaway |
| E-mail(s) |
[email protected]
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| Organization name |
UC Davis
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| Department |
MMI
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| Lab |
LaSalle Lab
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| Street address |
3318 Tupper Hall
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platform ID |
GPL14844 |
| Series (2) |
| GSE99272 |
Integrative epigenomic analyses of early-life hypothalamic response to augmented maternal care [BiSulfite-seq] |
| GSE99282 |
Integrative epigenomic analyses of early-life hypothalamic response to augmented maternal care |
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| Relations |
| BioSample |
SAMN07163511 |
| SRA |
SRX2851562 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2640264_JLDY106.bed.gz |
126.5 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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