|
| Status |
Public on Jul 22, 2014 |
| Title |
R-PHH-GW4064 |
| Sample type |
SRA |
| |
|
| Source name |
primary human hepatocytes
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Liver
|
| Treatment protocol |
cells were treated with 5 μM GW4064 compound dissolved in 0.1% DMSO for 24 hours
|
| 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 |
total RNA |
| Extraction protocol |
RNA extraced with TRIZol reagent followed by standard protocol
Illumina TrueSeqTM RNA Sample Prep Kit (San Diego, CA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
PHH_GW vs DMSO_RNA seq_gene exp.diff
|
| Data processing |
For RNA-seq, the obtained reads were aligned to the Homo sapiens reference genome (hg19) using TopHat (version 2.0.0)
The resulted alignments were then assembled into transcripts using Cufflinks (version 2.0.2).
Cuffdiff, a component of the Cufflinks package, was used to estimate FPKM (fragments per kilobase of exon model per million mapped fragments) and identify differentially expressed transcripts.
Finally the Baggerley’s test was used to perform the differential expression analysis.
Genome_build: hg19, ENSEMBL version 65 human genes
Supplementary_files_format_and_content: excel file with altered gene expression
|
| |
|
| 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 |
SAMN02741832 |
| SRA |
SRX530188 |
