|
| Status |
Public on Mar 02, 2017 |
| Title |
RNA-seq of Vehicle treated HSC rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Hepatic stellate cells (HSC) with vehicle treatment
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: adult HSC myofibroblasts
passage: passage 7-8
treatment: ethanol vehicle for 48 hours
|
| Treatment protocol |
HSC myofibroblasts were treated with either ethanol vehicle or nortriptyline (27 uM) for 48 hours prior to RNA extraction. Prior to TGF-beta stimulation, HSCs were serum starved in media containing DMEM with 0.2% bovine serum albumin (BSA) for 48 hours. Cells were then treated with TGF-β (2.5ng/ml) and either ethanol vehicle or nortriptyline (27 uM) for 16 hours prior to harvest.
|
| Growth protocol |
HSC myofibroblasts were cultured ex vivo in DMEM with 10% FCS.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol reagent, treated with DNAse I and cleaned using an acid-phenol:chloroform extraction. RNA quality was checked using an Agilent TapeStation 2200. All samples had a RIN score greater than 9.
RNA-seq libraries were prepared from 600 ng of total RNA according to the manufacturer’s instructions for the Illumina TruSeq Stranded mRNA Kit and barcoded for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw RNA-seq data were mapped into human reference genome (hg19) with bowtie2 (v2.1.0). Furthermore, HTSeq (v0.6.1) was used to quantify expression of coding genes in HSCs under different conditions. The mapped reads in bam format were converted into BigWig.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig; text fileswith the number of reads mappped into the coding and noncoding genes from the RNA-seq
|
| |
|
| Submission date |
Mar 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Chan Zhou |
| E-mail(s) |
zhou.chan@mgh.harvard.edu
|
| Phone |
7062543741
|
| Organization name |
Mass General Hospital, Harvard Medical School
|
| Department |
gastroenterology
|
| Lab |
Alan Mullen
|
| Street address |
55 Fruit Street
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE78853 |
Tricyclic Antidepressants Induce Inactivation of Hepatic Stellate Cell (HSC) Myofibroblasts |
|
| Relations |
| BioSample |
SAMN04529452 |
| SRA |
SRX1610956 |
