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Sample GSM5013775 Query DataSets for GSM5013775
Status Public on Apr 29, 2021
Title D1IL2
Sample type SRA
 
Source name regulatory T cells
Organism Homo sapiens
Characteristics individual: donor1
treatment: IL-2
chip antibody: H3K27Ac (ab4729, abcam)
cell type: CD4 T cell
Growth protocol Naïve CD4+ T cells were expanded with L-cells (as described above) for 22 days with either TGF-β, or Hp-TGM
Extracted molecule genomic DNA
Extraction protocol Nuclear lysates were sonicated and histone-DNA complexes were isolated with antibody.
Libraries were prepared by using DNA SMART ChIP-Seq kit (Clontech) according to the protocol. 150-400bp products were selected and subjected to the analysis.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing First three bases of sequenced reads were trimmed according to the library protocol and low quality sequences were removed. Rest of the reads were aligned to hg19 by using Bowtie2 (ver.2.2.9) in a default setting.
Uniquely mapped reads were selected and the duplicated reads were discarded by using Picard Tools (ver.2.1.1)
Peaks were called using SICER (ver.1.1.1) with the threshold of FDR less than 0.000000001.
Genome_build: hg19
Supplementary_files_format_and_content: bed (chromosome name, the starting position, the ending position, control read count, normalized control read count, case read count, normalized case read count, fold change case vs control, pvalue case vs control, FDR case vs control, fold change control vs case, pvalue control vs case, FDR case vs control)
case is TGM condition, control is TGF condition
 
Submission date Jan 11, 2021
Last update date Apr 29, 2021
Contact name Shigeru Tanaka
E-mail(s) stanaka@chiba-u.jp
Organization name Chiba University
Department Allergy and Clinical Immunology
Street address 1-8-1 Inohana
City Chiba
ZIP/Postal code 2608670
Country Japan
 
Platform ID GPL16791
Series (1)
GSE164548 Induction of stable human FOXP3+ Tregs by a parasite-derived TGF-β mimic
Relations
BioSample SAMN17283234
SRA SRX9820593

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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