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Sample GSM1465118 Query DataSets for GSM1465118
Status Public on Mar 16, 2015
Title Sample_5_D
Sample type SRA
Source name CD8+ T cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: mediastinal lymph node
developmental expsoure: vehicle
infectious status: infected with influenza virus
replicate: 2
Extracted molecule genomic DNA
Extraction protocol CD8+ T cels were enriched from tissue using negative selection magnetic beads. DNA were extracted using QIAGEN Dneasy, as per manufacturer's recommendations. Following enzymatic digestion and sonication, immunoprecipitation was performed using anti-5meC (Eurogentek, BI-MECY-0100, lot 081103).
Methyl-seq library construction was performed with NEXTflex Methyl-seq kit (Biooscientific, Austin, TA) per manufacturer’s recommendations. Briefly, 1200 ng of genomic DNA was sheared to an average size of 200-400bp with the Covaris S2 (Covaris, Woburn, MA). Sheared DNA sizing was confirmed with a Bioanlayzer 2100 (Agilent, Santa Clara, CA) and subsequent end repair, adenylation, and adaptor ligation was performed. DNA was heated to 95°C, and incubated with anti-5methylcytosine antibody (Epigentek, Farmingdale, NY). Methylated DNA was immunoprecipitated with Dynabeads (Life Technologies, Grand Island, NY), and released from the beads using Proteinase K digestion. DNA was purified using the MinElute PCR Purification Kit (QIAGEN), followed by library PCR amplification and gel size selection.
Library strategy MeDIP-Seq
Library source genomic
Library selection 5-methylcytidine antibody
Instrument model Illumina Genome Analyzer IIx
Data processing MeDIP-seq reads were aligned to mouse reference genome (mm9) using Bowtie (version 0.12.7 parameter set -n 2 -k 1 -m 1) allowing up to 2 nucleotide mismatches to the reference genome and considering only uniquely mappable reads for downstream analyses using MEDIPS package in R and other custom perl, R scripts. Aligned reads were extended in the sequencing direction to a length of 400 nucleotides. The short read coverage of the extended reads was calculated at genome wide 50 bp bins and wiggle files were generated using MEDIPS.exportWIG function in MEDIPS R package.
Genome_build: mm9
Supplementary_files_format_and_content: WIG
Submission date Aug 05, 2014
Last update date May 15, 2019
Contact name B Paige Lawrence
Organization name University of Rochester Medical Center
Department Environmental Medicine
Street address 575 Elmwood Ave.
City Rochester
State/province NY
ZIP/Postal code 14642
Country USA
Platform ID GPL11002
Series (2)
GSE60113 Linking the aryl hydrocarbon receptor with altered DNA methylation patterns and developmentally induced aberrant antiviral T cell responses [MeDIP-Seq]
GSE60115 Linking the aryl hydrocarbon receptor with altered DNA methylation patterns and developmentally induced aberrant antiviral T cell responses
BioSample SAMN02952543
SRA SRX669730

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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