|
Status |
Public on Nov 29, 2016 |
Title |
Standard-Low lipid rep4 |
Sample type |
SRA |
|
|
Source name |
Hypothalamus Tissue
|
Organism |
Psammomys obesus |
Characteristics |
Sex: male tissue: hypothalamus age: post natal 16 weeks diet: Standard Lipid
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Humane culling, hypothalamus harvest, homogenisation in PBS and trizol extraction followed by column purification. Methyl Miner enrichment Illumina ChIP-seq library prep kit
|
|
|
Library strategy |
MBD-Seq |
Library source |
genomic |
Library selection |
MBD2 protein methyl-CpG binding domain |
Instrument model |
Illumina Genome Analyzer IIx |
|
|
Description |
SL4
|
Data processing |
Basecalling with Illumina pipeline software (SCS v2.8 / RTA v1.8) 151 bp reads were checked for quality using FastQC. adapters were clipped with fastx_clipper bases with quality <30 were removed with fastq_quality_trimmer de novo assembly with ABySS reads mapped to the new assembly with BWA-MEM Reads with mapQ>=20 were counted Genome_build: de novo assembly with ABySS Supplementary_files_format_and_content: Matrix of contig methylation enrichment counts
|
|
|
Submission date |
Nov 30, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Assam El-Osta |
Organization name |
Baker Heart and Diabetes Institute
|
Lab |
Human Epigenetics
|
Street address |
75 Commercial Road
|
City |
Melbourne |
ZIP/Postal code |
3004 |
Country |
Australia |
|
|
Platform ID |
GPL21184 |
Series (1) |
GSE75483 |
Parental diet affects metabolism, obesity and hypothalamic DNA methylation in Psammomys obesus |
|
Relations |
BioSample |
SAMN04301489 |
SRA |
SRX1455831 |