|
| Status |
Public on Aug 31, 2017 |
| Title |
GR Dex+GFP_3D |
| Sample type |
SRA |
| |
|
| Source name |
Human airway smooth muscle 2 (HASM2)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Human airway smooth muscle 2 (HASM2)
transduction: Ad-GFP
treatment: Dex
chip antibody: GR (gift of Miles Pufall)
|
| Treatment protocol |
Anti GR antibody is a gift of Miles Pufall and was custom-made by Covance. It was raised against in rabbits against the epitope QPDLSKAVSLSMGLYMGETETKVMGNDLG and affinity purified. RNAPII ChIP antibody came from Biolegend, Clone 8WG16, Catalog #920102
|
| Growth protocol |
Human ASM cells were derived from a normal deceased donor (PMID: 27371733) as described (PMID:20670427) and cultured in Ham’s F-12 medium with L-glutamine (Corning) supplemented with 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation (ChIP) was performed as described previously (PMID: 23508109, 27371733), with the following modifications: cross-linking was performed by adding methanol-free 16% formaldehyde directly to the culture media to a final concentration of 1% and incubating for 5 minutes at room temperature with gentle rocking; samples were subsequently sonicated with a Diagenode Bioruptor at high power in 30-second bursts separated by 30-second incubations in ice water for a total of 25 cycles.
A minimum of 1 ng DNA from ChIP samples were used to prepare libraries using the Nugen Ovation Ultralow System V2 1-16 Part No. 0344 according to the manufacturer’s instructions. Samples were run on an Illumina HiSeq using 1X50 bp end reads
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Barcode: AAGCCT
|
| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 2 with the default setting.
Mapped reads were compressed, sorted and indexed using Samtools
Peaks were called using MACS version 2 with the default setting
Genome_build: mm9
Supplementary_files_format_and_content: .narrowPeak (BED file)
|
| |
|
| Submission date |
Mar 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Tzu Lip Phang |
| E-mail(s) |
tzu.phang@ucdenver.edu
|
| Phone |
(303) 724-6057
|
| Organization name |
University of Colorado, Denver
|
| Department |
Medicine
|
| Street address |
12700 East 19th Avenue
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE95632 |
Effects of dexamethasone and KLF15 on genome-wide occupancy of the glucocorticoid receptor (NR3C1) and RNA polymerase II (RNAPII) in human airway smooth muscle |
|
| Relations |
| BioSample |
SAMN06469674 |
| SRA |
SRX2609665 |
