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Sample GSM1956922 Query DataSets for GSM1956922
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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