|
| Status |
Public on Aug 08, 2023 |
| Title |
H3K4me2 naive CD4+ T cell, resting (rep2) |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood
cell type: naive T cell
chip antibody: H3K4me2 (ab32356, Abcam)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
From PBMCs, untouched CD4+ T cells were isolated using the human CD4+ T Cell Isolation Kit (Miltenyi Biotec) according to manufacturer’s instructions, followed by fluorescence-activated cell sorting (FACS; using a FACSAria III, BD Biosciences) to isolate resting naive CD4+ T cells (live single CD4+ CD127+ CD25neg CD45RA+ cells), Th1 cells (live single CD4+ CD127+ CD25neg CD45RAneg CCR6neg CXCR3+ CXCR5neg CCR4- cells), Th17 cells (live single CD4+ CD127+ CD25neg CD45RAneg CCR6+ CXCR3neg CXCR5neg CCR4neg cells) and Th2 cells (live single CD4+ CD127+ CD25neg CD45RAneg CCR6neg CXCR3neg CXCR5neg CCR4+ cells).
Nextera DNA library construction (as described in Schmidl et al. Nature Methods 2015).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned using bowtie 2 using default parameters.
Sorted and indexed bam files were parsed to HOMER to creat tag directories without duplicates and bedgraphs for browser visualization.
HOMER was used to identify enriched regions ('peak calling') using findPeaks with -region -size 1000 -minDist 2500 options
Assembly: hg38
Supplementary files format and content: BedGraph genome-wide normalized signal profiles
|
| |
|
| Submission date |
Aug 11, 2022 |
| Last update date |
Aug 08, 2023 |
| Contact name |
Ralph Stadhouders |
| E-mail(s) |
stadhoudersralph@gmail.com
|
| Organization name |
Erasmus Medical Center
|
| Department |
Pulmonary Medicine
|
| Street address |
Dr. Molewaterplein 50
|
| City |
Rotterdam |
| ZIP/Postal code |
3015 GE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE211023 |
Multi-scale epigenomic priming of inflammatory genes enables rapid recall in human memory T helper cells [ChIP-seq] |
| GSE211389 |
Multi-scale epigenomic priming of inflammatory genes enables rapid recall in human memory T helper cells |
|
| Relations |
| BioSample |
SAMN30261520 |
| SRA |
SRX17029226 |
