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| Status |
Public on Aug 05, 2011 |
| Title |
input DNA_Th1_2 |
| Sample type |
SRA |
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| Source name |
input DNA
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: spleen
cell type: primary CD4 T cells
culture condition: Th1
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| Growth protocol |
Splenic CD4 T cells were prepared using a magnetic cell sorter (AutoMACS; Miltenyi Biotec) yielding a purity of >98%. Where indicated, cells from C57BL/6 mice were stimulated with immobilized anti-TCR mAb (H57â597; 3 mg/ml) and anti-CD28 mAb under Th1- or Th2-culture conditions for 2 days in vitro. Th1 conditions; 25 U/ml IL-2, 10 U/ml IL-12, and antiï¾IL-4 mAb. Th2 conditions; 25 U/ml IL-2, 100 U/ml IL-4. After culturing under Th1- or Th2-culture conditions for 3 more days, the cells were harvested.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-Seq analysis, IP and input samples were prepared using ChIP-Seq Sample Prep kit (Illumina). Adaptor-ligated DNA fragments were size fractionated by 12% acrylamide gel, and the 170- to 250-bp fraction was recovered. DNA thus obtained was amplified by 18 cycles of PCR. One nanogram of DNA was used for the sequencing reaction of the Illumina GAIIx, according to the manufacturerâs instructions.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
control input DNA for H3K27me3-, H3K9ac-, and H3K4me3-ChIP (Th1) experiment
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| Data processing |
A total of 170,000â250,000 clusters was generated per tile, and 36 cycles of the sequencing reactions were performed. Short-read sequences were aligned to the mouse genome sequences (mm9 from University of California, Santa Cruz Genome Browser; http://genome.ucsc.edu/) using the Eland program. Sequences allowing no more than two mismatches per sequence were used for the analysis.
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| Submission date |
Aug 04, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Atsushi Onodera |
| Organization name |
Chiba University
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| Department |
Immunology
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| Street address |
Chuo-ku Inohana 1-8-1
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| City |
Chiba |
| ZIP/Postal code |
260-8670 |
| Country |
Japan |
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| Platform ID |
GPL11002 |
| Series (1) |
| GSE28292 |
Genome-wide analysis reveals unique regulation of transcription of Th2-specific genes by GATA3 |
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| Relations |
| SRA |
SRX092588 |
| BioSample |
SAMN00710533 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM773487_Th1_WT_input.bed.gz |
66.7 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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