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Series GSE68108 Query DataSets for GSE68108
Status Public on Mar 23, 2016
Title Genome wide mapping of long noncoding (lnc) RNAs in hepatic stellate cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Hepatic stellate cells are the primary cell type responsible for development of fibrosis in chronic liver disease. We used directional RNA sequencing (RNA-seq) and chromatin immunoprecipitation and sequencing (ChIP-seq) to identify the lncRNAs expressed in human HSCs. We also identified the lncRNAs that change in expression with differentiation of nonfibrotic quiescent HSCs into fibrotic HSC myofibroblasts and those that are regulated by TGF-beta signaling. ChIP-seq was also performed to identify DNA regions occupied by H3K27ac to define super-enhancers in HSC myofibroblasts. This study identified lncRNAs expressed HSCs that may regulate fibrosis.
 
Overall design Analysis of genome-wide lncRNA expression using RNA-seq and ChiP-seq in human HSCs under four different conditions
 
Contributor(s) Zhou C, York SR, Mullen AC
Citation(s) 27007663
Submission date Apr 21, 2015
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
 
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (22)
GSM1663079 RNA-seq HSC myofibroblasts rep 1A
GSM1663080 RNA-seq HSC myofibroblasts rep 1B
GSM1663081 RNA-seq HSC myofibroblasts rep 2A
Relations
BioProject PRJNA281757
SRA SRP057513

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE68108_H3K27_nomodel_SPMR_logLR.bw 218.7 Mb (ftp)(http) BW
GSE68108_MFB_BC.minus.bw 253.8 Mb (ftp)(http) BW
GSE68108_MFB_BC.plus.bw 262.4 Mb (ftp)(http) BW
GSE68108_MFB_H3K4me3_SPMR_logLR.bw 430.3 Mb (ftp)(http) BW
GSE68108_RAW.tar 732.8 Mb (http)(custom) TAR (of BW)
GSE68108_TGF.minus.bw 146.6 Mb (ftp)(http) BW
GSE68108_TGF.plus.bw 151.1 Mb (ftp)(http) BW
GSE68108_TGFb_H3K4me3_logLR.bw 162.3 Mb (ftp)(http) BW
GSE68108_noTGF.minus.bw 162.9 Mb (ftp)(http) BW
GSE68108_noTGF.plus.bw 167.9 Mb (ftp)(http) BW
GSE68108_noTGFb_H3K4me3_logLR.bw 189.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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