|
| Status |
Public on Apr 01, 2014 |
| Title |
RUNX1_TregRA+ S030b |
| Sample type |
SRA |
| |
|
| Source name |
CD4+CD25+CD45RA+ expanded naive regulatory T cells
|
| Organism |
Homo sapiens |
| Characteristics |
donor: S030b
cell type: CD4+CD25+CD45RA+ expanded naive regulatory T cells
chip antibody: RUNX1 (abcam ab 23980)
chip antibody manufacturer: abcam
chip antibody catalog #: ab 23980
|
| Growth protocol |
cells were isolated according to: Hoffmann P, Eder R, Boeld TJ, et al. Only the CD45RA(+) subpopulation of CD4(+)CD25(high) T cells gives rise to homogeneous regulatory T-cell lines upon in vitro expansion. Blood. 2006;108:4260-4267; cell populations were expanded according to: Hoffmann P, Eder R, Kunz-Schughart LA, Andreesen R, Edinger M. Large-scale in vitro expansion of polyclonal human CD4(+)CD25(high) regulatory T cells. Blood. 2004;104:895-903.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
DNA from chromatin immunoprecipitation was adapter-ligated and PCR amplified using NEBNext DNA Sample Prep Reagent Set1 (NEB E6000L) and Adapter Oligo Mix and PCR primers from Illumina following the manufacturer’s protocol. Barcoded Libraries were generated with the Bioo Nextflex barcoding materials. ChIP fragments were sequenced for 36 or 50 cycles on Illumina Genome Analyzers I, II, HiScanSQ or HiSeq 1000 according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
Chromatin IP against RUNX1
|
| Data processing |
Sequence tags were mapped to the human reference sequence (GRCh27/hg19) using Bowtie1 and only uniquely mapped tags were used for downstream analyses. Parameters: -q --best -m 1
Genome_build: hg19
Supplementary_files_format_and_content: alignment files produced with bowtie
|
| |
|
| Submission date |
Dec 21, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Rehli |
| E-mail(s) |
[email protected]
|
| Organization name |
University Hospital Regensburg
|
| Department |
Internal Med III
|
| Street address |
F.-J.-Strauss-Allee 11
|
| City |
Regensburg |
| ZIP/Postal code |
93042 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15456 |
| Series (1) |
| GSE43119 |
The enhancer and promoter landscape of human regulatory and conventional T cell subpopulations |
|
| Relations |
| SRA |
SRX212442 |
| BioSample |
SAMN01845581 |
