|
| Status |
Public on Mar 23, 2016 |
| Title |
RNA-seq adult HSC serum starvation (low TGF) rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
hepatic stellate cells (HSCs)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: adult HSCs differentiated into HSC myofibroblasts
passage: passage 7-8
|
| Treatment protocol |
All HSC myofibroblasts were grown in DMEM with 10% FCS. HSC myofibroblats were grown in DMEM with 0.2% BSA for 48 hours followed by the addition of 2.5 ng/ml of TGF-beta for 16 hours for TGF-beta treatment. For serum starvation conditions (low TGF), cells were cultlures in 0.2% BSA for 48 hours and then remained in 0.2% BSA for an additiona 16 hours in parallel with cells treated with TGF-beta.
|
| Growth protocol |
All HSCs were cultured ex vivo in DMEM with 10% FCS.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For RNA-seq analysis, total RNA was extracted with Trizol reagent and cleaned using the mirVana kit by following instructions for total RNA purification. For ChIP-seq analysis, cells were crosslinked with 1% formaldehyde and sheared by sonication. Histone-DNA complexes were isolated by antibodies against H3K4me3 (Millipore 07-473, lot 2019729) and H3K27ac (Abcam Ab4729, lot GR132150-1)
RNA-seq libraries were prepared according to Iluminas instructions for the TruSeq Stranded mRNA Kit and barcoded for sequencing. ChIP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP 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 tophat (V2.1.0). The mapped reads were futher assemblied into transcirptiomes using CUFFLINK (v2.2.1) and SCRIPTURE (v.beta2) softwares. CUFFMERGE tool was used to merge the transcripts assemblied by CUFFLINK and SCRIPTURE into one list of transcripts through cuffmerge
ChIP-seq data were mapped into human reference genome (hg19) by bowtie2 and then the mapped reads were processed by using MACS2 to call peaks.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig
|
| |
|
| Submission date |
Jan 19, 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) |
| GSE68108 |
Genome wide mapping of long noncoding (lnc) RNAs in hepatic stellate cells |
|
| Relations |
| BioSample |
SAMN04422292 |
| SRA |
SRX1535263 |
