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Status |
Public on Apr 29, 2021 |
Title |
D1IL2 |
Sample type |
SRA |
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Source name |
regulatory T cells
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Organism |
Homo sapiens |
Characteristics |
individual: donor1 treatment: IL-2 chip antibody: H3K27Ac (ab4729, abcam) cell type: CD4 T cell
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Growth protocol |
Naïve CD4+ T cells were expanded with L-cells (as described above) for 22 days with either TGF-β, or Hp-TGM
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2500 |
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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
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Submission date |
Jan 11, 2021 |
Last update date |
Apr 29, 2021 |
Contact name |
Shigeru Tanaka |
E-mail(s) |
stanaka@chiba-u.jp
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Organization name |
Chiba University
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Department |
Allergy and Clinical Immunology
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Street address |
1-8-1 Inohana
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City |
Chiba |
ZIP/Postal code |
2608670 |
Country |
Japan |
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Platform ID |
GPL16791 |
Series (1) |
GSE164548 |
Induction of stable human FOXP3+ Tregs by a parasite-derived TGF-β mimic |
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Relations |
BioSample |
SAMN17283234 |
SRA |
SRX9820593 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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