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| Status |
Public on Mar 16, 2015 |
| Title |
Sample_8_D |
| Sample type |
SRA |
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| Source name |
CD8+ T cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: peripheral lymph nodes
developmental expsoure: TCDD
infectious status: naïve
replicate: 1
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| 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.
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| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina Genome Analyzer IIx |
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| 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
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| Submission date |
Aug 05, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
B Paige Lawrence |
| Organization name |
University of Rochester Medical Center
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| Department |
Environmental Medicine
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| Street address |
575 Elmwood Ave.
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| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN02952545 |
| SRA |
SRX669732 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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