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Sample GSM773488 Query DataSets for GSM773488
Status Public on Aug 05, 2011
Title input DNA_Th2_2
Sample type SRA
Source name input DNA
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: spleen
cell type: primary CD4 T cells
culture condition: Th2
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 (H57−597; 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 antiミIL-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.
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 manufacturer’s instructions.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description control input DNA for H3K27me3-, H3K9ac-, and H3K4me3-ChIP (Th2) experiment
Data processing A total of 170,000–250,000 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; using the Eland program. Sequences allowing no more than two mismatches per sequence were used for the analysis.
Submission date Aug 04, 2011
Last update date May 15, 2019
Contact name Atsushi Onodera
Organization name Chiba University
Department Immunology
Street address Chuo-ku Inohana 1-8-1
City Chiba
ZIP/Postal code 260-8670
Country Japan
Platform ID GPL11002
Series (1)
GSE28292 Genome-wide analysis reveals unique regulation of transcription of Th2-specific genes by GATA3
SRA SRX092589
BioSample SAMN00710534

Supplementary file Size Download File type/resource
GSM773488_Th2_WT_input.bed.gz 69.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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