|
| Status |
Public on Nov 16, 2012 |
| Title |
Th1_Tbet |
| Sample type |
SRA |
| |
|
| Source name |
Th1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: T-bet; Antibody vendor: Lab produced (Szabo et al., Nature 2000).
cell type: Th1
cell number: 100000000
|
| Growth protocol |
Naive human CD4+ T-cells (CD4+CD45RA+CD45RO-HLADR-CD62L+) were isolated from healthy donors by negative immunomagnetic selection (Miltenyi Biotec) and activated for 72 hours by plate bound anti-CD3 and anti-CD28 antibodies (2 ug/ml, BD Pharmingen). Cells were then cultured for 10 days with rhIL-2 (NCI, 100 U/ml) in the presence of rhIL-12 (10 ng/ml, R&D Systems) and anti-IL-4 (10 ug/ml, BD Pharmingen) for Th1 polarisation or rhIL-4 (10 ng/ml, R&D Systems) and anti-IFN-g (10 ug/ml, BD Pharmingen) for Th2 polarisation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIPs were performed according to Jenner lab protocol (see Jenner et al., PNAS 2009 or Kanhere et al., Mol Cell 2010). Libraries were constructed from half of the ChIP DNA sample or 200ng of input sample using the standard Illumina protocol and reagents, except that DNA in the range 150-350bp was gel-purified after PCR-amplification. Libraries were quantified using by Qubit and Agilent bioanalyzer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Chromatin IP against T-bet in Th1 cells
Th1_Tbet.bed: alignment (bed format)
Th1_Tbet_06_peaks.bed: MACS peaks (pvalue cut-off <= 1e-6)
Th1_Tbet.bw: bigwig
|
| Data processing |
Image analysis and base calling were performed using the solexa pipeline. Reads were aligned to the human genome build hg18 using Eland. Only reads with zero to two mismatches were aligned. Uniquely aligned reads passing quality threshold were retained. When multiple reads matched to same position only a single read was considered for further analysis. Aligned sequences were extended by 150bp . Counts were background corrected and normalized to reads per million. Bigwig files were generated using 10bp windows. Peaks were called using MACS algorithm (http://liulab.dfci.harvard.edu/MACS/).
|
| |
|
| Submission date |
Aug 10, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Aditi Kanhere |
| E-mail(s) |
a.kanhere@liverpool.ac.uk
|
| Organization name |
University of Liverpool
|
| Lab |
Kanhere Lab
|
| Street address |
Institute of Systems, Molecular and Integrative Biology
|
| City |
Liverpool |
| ZIP/Postal code |
L69 3GE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE31320 |
Genome-wide identification of functional elements regulated by T-bet and GATA3 in human T-cells |
|
| Relations |
| SRA |
SRX092313 |
| BioSample |
SAMN00710327 |
