|
| Status |
Public on Jul 22, 2014 |
| Title |
PHH-DMSO-FXR |
| Sample type |
SRA |
| |
|
| Source name |
primary human hepatocytes
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Liver
chip antibody: FXR (1:1 mixture of sc-1204x and sc-13063x, ChIP grade, Santa Cruz)
|
| Treatment protocol |
cells were treated with 0.1% DMSO control for 1 hour
|
| Growth protocol |
Primary human hepatocytes were cultured in 37 °C, 5% CO2 upon arrival. Three hours later, medium were refreshed with serum-free HMM Hepatocyte Maintenance Medium supplemented with dexamethasone, insulin, and GA-1000 (Lonza, Switzerland)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed, lysed, sonicated. Chromatin were pulled down by antibody
Illumina TrueSeqTM DNA Sample Prep Kit (San Diego, CA)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
PHH_DMSO_FXR_NC_rIgG_paired.bedgraph
|
| Data processing |
After sequencing, raw data files were processed through Genome Analyzer Pipeline Software (Illumina)
For ChIP-seq, all sequenced paired-end reads were aligned to Homo sapiens version 19 (hg19) reference genome using bowtie (version 0.12.7).
Regions with read enrichment were detected using Model-based Analysis of ChIP-Seq (MACS v 1.4.1) method
By comparing with the rIgG background, non-specific peaks with false discovery rate (FDR) greater than 0.1 were eliminated.
Identified peaks were further split by Mali Salmon's Peak Splitter (http://www.ebi.ac.uk/bertone/software.html) and filtered by p-value of Poisson distribution lower than 10-5.
Peaks were annotated using R packages (http://www.r-project.org) based on the ENSEMBL version 65 human genes.
Genome_build: hg19, ENSEMBL version 65 human genes
Supplementary_files_format_and_content: processed files are in BEDGRAPH format; scores represent FXR antibody pull down normalized to rIgG control antibody
|
| |
|
| Submission date |
May 01, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Le Zhan |
| E-mail(s) |
zhanle999@gmail.com
|
| Phone |
9135530042
|
| Organization name |
Rutgers University
|
| Department |
Pharmacology and Toxicology
|
| Lab |
EOHSI 332
|
| Street address |
170 Frelinghuysen Rd
|
| City |
Piscataway |
| State/province |
NJ |
| ZIP/Postal code |
08854 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE57227 |
Genome wide binding and transcriptome analysis of human FXR in primary human hepatocytes [HTS] |
| GSE57312 |
ChIP-seq and RNA-seq study of human FXR in primary human hepatocytes and microarray analysis of GW4064 versus vehicle treated wild type mouse livers |
|
| Relations |
| BioSample |
SAMN02741834 |
| SRA |
SRX530184 |
