|
| 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 |
| E-mail(s) |
cristina.leoni@irb.usi.ch
|
| 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 |
|
| Relations |
| BioSample |
SAMN09005301 |
| SRA |
SRX4015347 |
