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Sample GSM2108710 Query DataSets for GSM2108710
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
 
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
 
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

Supplementary file Size Download File type/resource
GSM2108710_5Aug10_Ctrl.hg19.sorted.bam.filtered.bam.rpkm.txt.gz 632.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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