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| Status |
Public on Oct 08, 2017 |
| Title |
Input_GDF15 |
| Sample type |
SRA |
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| Source name |
Human tracheobronchial epithelial cells (hTBEs)
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Human tracheobronchial epithelial cells
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| Treatment protocol |
We chose 2 h of GDF15 stimulation for ChIP-seq analysis since the maximal activation of Smad1 pathway was observed at this time-point after rhGDF15 (25 ng/ml) stimulation in hTBEs as reported in our previous study (PMID: 27093475).
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| Growth protocol |
Normal human tracheobronchial epithelial cells at passage 2 were seeded onto collagen-coated 60 mm tissue culture dishes (4 x 10^5 cells) in bronchial epithelial cell growth medium (BEGM) with SingleQuots™ supplements (Lonza, Walkersville, MD) at 37°C, 5% CO2. At 80-90% confluence, cells were treated with 0.1% BSA-HCl (control) or 25 ng/ml of recombinant human GDF15 (rhGDF15, R&D Systems, Minneapolis, MN) for 2 h.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was sheared using the isothermal Covaris S2 to produce approximately 100-300bp fragments for Ion Proton ChIP-seq. DNA-protein complexes were immunoprecipitated with an anti-pSMAD antibody (#11971, Cell Signaling), captured by magnetic beads, cross-links reversed, and the genomic DNA purified (Invitrogen Magnify ChIP Kit #49-2024).
Libraries were made according to the instructions using the Ion Xpress Plus Fragment Library Kit- 4471252
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Ion Torrent Proton |
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| Data processing |
ChIP-seq sequencing reads were aligned to the human reference genome using the Ion Torrent Suite software, version 4.0.2 and version 4.4
Peak-calling from aligned reads will be performed using the Model-based Analysis for ChIP-Sequencing (MACS2) software (Zhang, 2008), comparing pSmad IPs to their respective total input controls. Peak significance was determined with a false discovery rate (FDR) cutoff of 0.001.
Peaks found by ChIP-seq will be associated with the nearest gene by genomic location, using both the RefSeq, refGene, and UCSC known gene models. A gene lists based on closest called peaks was generated.
Genome_build: HG19
Supplementary_files_format_and_content: peak.bed files were generated using MACS2 as described above
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| Submission date |
Jun 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Patrick OConnor |
| E-mail(s) |
[email protected]
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| Organization name |
National Jewish Health
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| Department |
Center for Genes, Environment and Health
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| Lab |
OConnor
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| Street address |
1400 Jackson St
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| City |
Denver |
| State/province |
Colorado |
| ZIP/Postal code |
80206 |
| Country |
USA |
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| Platform ID |
GPL17303 |
| Series (1) |
| GSE100625 |
Growth differentiation factor 15 (GDF15) promotes human rhinovirus infection and inflammation |
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| Relations |
| BioSample |
SAMN07290563 |
| SRA |
SRX2965767 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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