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Sample GSM3122695 Query DataSets for GSM3122695
Status Public on May 01, 2019
Title TN D0_A09
Sample type SRA
Source name Naïve T lymophocyte_resting
Organism Homo sapiens
Characteristics cell type: primary T lymphocytes derived from human periferal blood mononuclear cells (PBMC)
cell type: Naive T lymophocyte
cell status: resting
Treatment protocol Resting naïve T lymphocytes collected after isolation and directly used for genomic DNA extraction
Growth protocol sample preparation: Human perferal blood mononuclear cells were separated from peripheral blood using Ficoll-Paque Plus (GE Healthcare). CD4+ T lymphocytes were further isolated by positive selection using magnetic microbeads (Miltenyi Biotec). Naive T cell subsets were then sorted based on the expression of the following surface markers: CD4+CD25–CD45RA+CCR7+.
Primary human T lymphocytes were isolated from human periferal blood mononuclear cells and were either left resting or were stimulated for 3 days with anti-CD3 and anti-CD28 antibodies
sample preparation:
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was purified using the DNeasy Blood & Tissue Kit (Qiagen)
Premium RRBS Kit (Diagenode)
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina HiSeq 3000
Description Sample 1
Data processing Sequencing was carried out on an Illumina HiSeq 3000
reads were aligned to hg19 human reference genome using Bismark v0.16.1 (PMID: 21493656 )
Genome-wide methylation call report was obtained using Bismark methylation extractor
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab delimited methylation file with .cov2cyt_detected.txt extension. Each line has 6 fields: chromosome - start and end position - covering methylated reads - covering unmethylated reads - CpG context type and actual CpG sequence.
Submission date Apr 30, 2018
Last update date May 01, 2019
Contact name Cristina Leoni
Organization name Institute For Research in Biomedicine
Department Molecular Immunology
Lab Silvia Monticelli
Street address Via Vincenzo Vela 6
City Bellinzona
State/province Ticino
ZIP/Postal code 6500
Country Switzerland
Platform ID GPL21290
Series (1)
GSE113884 Active and passive mechanisms of 5mC and 5hmC removal in human T lymphocytes
BioSample SAMN09005301
SRA SRX4015347

Supplementary file Size Download File type/resource
GSM3122695_A09.cov2cyt_detected.txt.gz 94.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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