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Sample GSM776557 Query DataSets for GSM776557
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
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

Supplementary file Size Download File type/resource
GSM776557_Th1_Tbet.bed.gz 125.3 Mb (ftp)(http) BED
GSM776557_Th1_Tbet.bw 127.7 Mb (ftp)(http) BW
GSM776557_Th1_Tbet_06_peaks.txt.gz 316.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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