|
Status |
Public on Apr 06, 2016 |
Title |
5Aug10_Ctrl |
Sample type |
SRA |
|
|
Source name |
primary hepatocyte_vehicle
|
Organism |
Homo sapiens |
Characteristics |
treatment: vehicle cell type: primary hepatocyte cells
|
Treatment protocol |
In vitro studies were performed within 72 to 120 hours from the time of hepatocyte isolation. The primary human hepatocytes were grown on collagen coated plates and treated with rifampin (10 µM) or vehicle (methanol, 0.01%) for 24 hours.
|
Growth protocol |
Human hepatocytes from seven different subjects were obtained from CellzDirect (Durham, NC). The primary human hepatocytes were grown on collagen coated , cultured in Williams' E medium without phenol red containing Primary Hepatocyte Maintenance Supplements (Life Technologies Corporation, Carlsbad, CA). Each culture from a different individual subject was treated as a biologic replicate (n = 7).
|
Extracted molecule |
total RNA |
Extraction protocol |
Trizol per manufacturer's (Invitrogen) protocol RNA was fragmented with RNAaseIII, cDNA libraries constructed with SOLiD adaptors by reverse transcription
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
AB SOLiD 4 System |
|
|
Data processing |
Sequence reads were aligned with BFAST (v.0.6.4e) towards reference genome and junction library. Details refers to Breese and Liu, Bioinformatics, 2013, PMID: 23314324 Aligned reads were fitered with NGSUtils (Breese and Liu, Bioinformatics 2013), only unique mapped reads with no more than 2 mismatchs were kept. Read counts and RPKM was calculated with NGSUtils based on RefSeq annotation. Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files include raw counts and RPKM values
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|
|
Submission date |
Apr 05, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Hai Lin |
E-mail(s) |
linhai@iupui.edu
|
Organization name |
IUPUI
|
Street address |
410 W 10th St
|
City |
Indianapolis |
ZIP/Postal code |
46202 |
Country |
USA |
|
|
Platform ID |
GPL13393 |
Series (1) |
GSE79933 |
Regulation of microRNA expression by rifampin in human hepatocytes |
|
Relations |
BioSample |
SAMN04613400 |
SRA |
SRX1680995 |