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| Status |
Public on Sep 07, 2012 |
| Title |
nTreg_Foxo1_Ab_ChIPseq |
| Sample type |
SRA |
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| Source name |
nTreg cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: nTreg, Foxo1 Ab, ChIP
chip antibody: Foxo1 antibody (Abcam, Ab39670, lot#GR16346-7)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Foxo1 Ab- and Streptavidin-precipitated chromatin DNA samples were extracted with Phenol-Chloroform-Isoamyl Alcohol, and then precipitated with 1/10V 3M Sodium Acetate (pH5.2) and 2V ethanol. Lysates were clarified from sonicated nuclei and Foxo1-DNA complexes were isolated with antibody or Streptavidin. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a kit from Epicentre. The blunt, phosphorylated ends were treated with Taq DNA polymerase and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15-19 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
Basecalls performed using CASAVA v1.4
Bowtie v0.12.7 was used to identify sequences mapping uniquely to the genome
Peak calls were determined using MACS v1.4
Overlapping peaks between antibody and biotin ChIP methods were merged
Genome_build: mm9
Supplementary_files_format_and_content: BED files for uniquely mapping reads and called MACS peaks for Antibody, Biotin, and overlapping peaks are provided
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| Submission date |
Sep 06, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Willey Liao |
| Organization name |
New York Genome Center
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| Department |
Bioinformatics
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| Street address |
101 Avenue of the Americas
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10013 |
| Country |
USA |
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| Platform ID |
GPL11002 |
| Series (2) |
| GSE40656 |
Novel Foxo1-dependent Transcriptional Programs Control Treg Cell Function [ChIP-Seq] |
| GSE40657 |
Novel Foxo1-dependent Transcriptional Programs Control Treg Cell Function |
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| Relations |
| SRA |
SRX183787 |
| BioSample |
SAMN01162372 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM998924_nTreg_Ab_fdr0.01_peaks.bed.gz |
232.1 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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