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| Status |
Public on May 13, 2016 |
| Title |
Th17_ATAC_rep1 |
| Sample type |
SRA |
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| Source name |
Tonsils
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Th17
markers: CD4+CCR6+
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP Samples: Preparation of samples for ChIP was carried out as described (Brind'Amour et al, 2015). Pre-cleared chromatin was subjected to immunoprecipitation overnight at 4°C with acetylated H3K27 antibody or trimethylated H3K4 antibody, conjugated to Dynabeads coated with Protein-A. Samples were washed as described (Brind'Amour et al, 2015) and DNA was purified with phenol:chloroform:isoamylalcohol (25:24:1, pH 8) using Maxtract tubes (Qiagen), then precipitated overnight. ATAC Samples. Preparation of samples for ATAC was carried out as described (Buenrostro et al, 2015). Aliquots of 25,000 cells were lysed (10mM Tris-Cl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40), pellets were resuspended in 50µl of transposition mix (Tagment DNA buffer, Tagment DNA enzyme, Illumina), and incubated at 37oC (30 min). Samples were purified using MinElute spin columns (Qiagen).
ChIP Samples: ChIP or input DNA was used for indexed library preparation, pooled (4-6 samples), and subjected to 50 bp single-end sequencing per manufacturer’s protocol (Illumina HiSeq2500). ATAC Samples. Nextera index adapters (i7 and i5) were used to amplify transposed DNA fragments (Illumina). Libraries were purified using AMPure XP beans (Beckman-Coulter), pooled (2-3 samples) and subjected to PE50 sequencing on an Illumina HiSeq2500.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
ATAC DNA
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| Data processing |
Library strategy: ATAC-Seq
Basecalls performed using CASAVA.
Sequencing tags from FAIRE- and ChIP-Seq were aligned to the reference genome (build GRCh37/hg19) with Novoalign.
ChIP: MACS was used to identify ChIP peaks by comparison of matched treatment to input samples using the following changes to the default settings: --nomodel --shiftsize=150 (H3K27ac), --nomodel --shiftsize=100 (H3K4me3). ATAC: Samples were processed with MACS using the following changes to default settings, --nomodel --shiftsize=50.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using MACS.
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| Submission date |
Jan 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Eugene M Oltz |
| E-mail(s) |
eoltz@wustl.edu
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| Organization name |
Washington University in St Louis
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| Department |
Pathology & Immumonolgy
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| Street address |
660 Euclid Ave, Campus Box 8118
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| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE77299 |
Distinct Gene Regulatory Pathways for Human Innate Versus Adaptive Lymphoid Cells [ChIP-seq & ATAC-seq] |
| GSE78897 |
Distinct Gene Regulatory Pathways for Human Innate Versus Adaptive Lymphoid Cells |
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| Relations |
| BioSample |
SAMN04444300 |
| SRA |
SRX1549379 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2048321_Th17_ATAC_rep1.wig.gz |
490.8 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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