Browse
Submit Data
Databases
Help
Login

Dataset Information

137 Views

8 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 161

Single cell analysis reveals cancer cell heterogeneities in hepatocellular carcinoma [SMART-seq]

ABSTRACT: Combined transcriptomic and functional analyses of HCC cells at single-cell level were performed to assess CSC heterogeneity. Overall design: Single-cell transcriptome analyses of two HCC cell lines (HuH-1 and HuH-7) and one patient-derived circulating tumor cells by using SMART-Seq protocol ***Due to patient privacy concerns, the submitter declares that patient data will be submitted to dbGaP.***

INSTRUMENT(S): Illumina HiSeq 2500 (Homo sapiens)

SUBMITTER: Xin Wei Wang

PROVIDER: GSE103866 | GEO | 2018-06-11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Publications

Single-cell analysis reveals cancer stem cell heterogeneity in hepatocellular carcinoma.

Zheng Hongping H Pomyen Yotsawat Y Hernandez Maria Olga MO Li Caiyi C Livak Ferenc F Tang Wei W Dang Hien H Greten Tim F TF Davis Jeremy L JL Zhao Yongmei Y Mehta Monika M Levin Yelena Y Shetty Jyoti J Tran Bao B Budhu Anuradha A Wang Xin Wei XW

Hepatology (Baltimore, Md.) 20180509 1

Intratumor molecular heterogeneity of hepatocellular carcinoma is partly attributed to the presence of hepatic cancer stem cells (CSCs). Different CSC populations defined by various cell surface markers may contain different oncogenic drivers, posing a challenge in defining molecularly targeted therapeutics. We combined transcriptomic and functional analyses of hepatocellular carcinoma cells at the single-cell level to assess the degree of CSC heterogeneity. We provide evidence that hepatic CSCs ...[more]

PMID: 29315726

Similar Datasets

Single cell analysis reveals cancer cell heterogeneities in hepatocellular carcinoma [Chromium 10X]

Project description:Combined transcriptomic and functional analyses of HCC cells at single-cell level were performed to assess CSC heterogeneity. Overall design: Single-cell transcriptome analyses of two HCC cell lines (HuH-1 and HuH-7) and one patient-derived circulating tumor cells by using Chromium 10X protocol. ***Due to patient privacy concerns, the submitter declares that patient data will be submitted to dbGaP.***

| GSE103867 | GEO

RNA-seq of pre-treatment and post-relapse matched samples from melanoma patients

Project description:RNA-seq of pre-treatment and post-relapse matched samples from melanoma patients RNA-seq was performed for matched samples before treatment and after relapse from six patients that have been treated with RAF or RAF+MEK inhibitors. Submitter declares that raw sequence data will be submitted to dbGaP due to patient privacy concerns.

2016-02-25 | E-GEOD-77940 | ArrayExpress

Single cell RNA-seq analysis of oligodendroglioma

Project description:To understand the diversity of expression states within oligodendroglioma tumors, we obtained six freshly resected samples, profiled ~1000 cells from each tumor and examined their diversity. Overall design: Tumors were disaggregated, sorted into single cells, and profiled by Smart-seq2. **GSM1812084 to GSM1815456: Submitter declares reads will be made available through dbGaP.** **Sample records after GSM1815456: Submitter declares reads will be submitted to controlled access SRA and/or dbGaP. The sample records that follow GSM1815456 are incomplete.**

| GSE70630 | GEO

Single cell RNA-seq analysis of melanoma

Project description:To understand the diversity of expression states within melanoma tumors, we obtained freshly resected samples, dissagregated the samples, sorted into single cells and profiled them by single-cell RNA-seq. Tumors were disaggregated, sorted into single cells, and profiled by Smart-seq2. *Raw data files absent for samples GSM1851356 and GSM1851494.* **Submitter declares reads will be made available through dbGaP.**

2016-04-05 | E-GEOD-72056 | ArrayExpress

Single cell RNA-seq analysis of IDH-mutant astrocytoma

Project description:To understand the diversity of expression states within IDH-mutant astrocytoma tumors, we profiled 6341 cells from 10 tumors by single cell RNA-seq Overall design: Tumors were disaggregated, sorted into single cells, and profiled by Smart-seq2. ---------------------------------------------------------------------------- **Submitter declares reads will be made available through controlled access SRA and/or dbGaP.**

| GSE89567 | GEO

A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers (MBD-Seq)

Project description:The incidence of HPV-related oropharyngeal squamous cell carcinoma (OPSCC) has increased more than 200% in the past 20 years. Recent genetic sequencing efforts have elucidated relevant genes in head and neck cancer, but HPV-related tumors have consistently shown few DNA mutations. In this study, we sought to analyze alternative splicing events (ASE) that could alter gene function independent of mutations. To identify ASE unique to HPV-related tumors, RNA sequencing was performed on 46 HPV-positive OPSCC and 25 normal tissue samples. A novel algorithm using outlier statistics on RNA-sequencing junction expression identified 109 splicing events, which were confirmed in a validation set from The Cancer Genome Atlas. Overall design: MBD-sequencing data for 50 HPV+ HNSCC tumors, 25 normal UPPP, 2 HPV+ HNSCC patient derived xenografts, and 2 HPV+ HNSCC cell lines (SCC-090, SCC-047) ---------------------------------------------- Submitter declares that the raw data will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.

| GSE112023 | GEO

A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers (RNA-Seq)

Project description:The incidence of HPV-related oropharyngeal squamous cell carcinoma (OPSCC) has increased more than 200% in the past 20 years. Recent genetic sequencing efforts have elucidated relevant genes in head and neck cancer, but HPV-related tumors have consistently shown few DNA mutations. In this study, we sought to analyze alternative splicing events (ASE) that could alter gene function independent of mutations. To identify ASE unique to HPV-related tumors, RNA sequencing was performed on 46 HPV-positive OPSCC and 25 normal tissue samples. A novel algorithm using outlier statistics on RNA-sequencing junction expression identified 109 splicing events, which were confirmed in a validation set from The Cancer Genome Atlas. Overall design: RNA-sequencing data for 47 HPV+ HNSCC tumors, 25 normal UPPP, 2 HPV+ HNSCC patient derived xenografts, and 2 HPV+ HNSCC cell lines (SCC-090, SCC-047) ---------------------------------------------- Submitter declares that the raw data will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.

| GSE112026 | GEO

Comprehensive Epigenetic Landscape of Rheumatoid Arthritis Fibroblast-like Synoviocytes [WGBS]

Project description:Epigenetics is important in the pathogenesis of immune-mediated diseases like rheumatoid arthritis (RA). Here we show the first complete epigenomic characterization of RA fibroblast-like synoviocytes (FLS) by profiling histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3, H3K9me3), open chromatin, RNA expression and whole genome DNA methylation. To address the complex multidimensional relationship and reveal the epigenetic regulation of RA, we perform integrative analyses using a novel unbiased method to identify genomic regions with similar profiles. Epigenomically similar regions exist in RA cells are particularly associated with active enhancers and promoters as well as specific transcription factor binding motifs. Differentially marked genes are enriched for immunological and unexpected pathways, with “Huntington's Disease Signaling” identified as particularly prominent. We validate the relevance of this pathway to RA by showing that Huntingtin-interacting protein-1 regulates FLS invasion into matrix. This work establishes a high-resolution epigenomic landscape of RA and demonstrates the potential for integrative analyses to identify unanticipated therapeutic targets. Overall design: Establishing a high-resolution epigenomic landscape of RA FLS by integrating diverse epigenomic data. This series includes WGBS data on Fibroblast-like synoviocytes from RA or OA patients. The submitter declares that the raw data will be made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap) due to patient privacy concerns.

| GSE112657 | GEO

Defining T cell states associated with response to checkpoint immunotherapy in melanoma

Project description:we profiled 16,291 immune cells from 48 tumor samples of melanoma patients treated with checkpoint inhibitors, using single-cell transcriptomics. Overall design: Tumors were disaggregated, sorted into CD45+ single cells, and profiled by Smart-seq2 ----------------------------------------------------- Submitter states "As this is human data, raw sequencing files are submitted via dbGap." dbGaP accession code: phs001680.v1.p1

2018-10-05 | GSE120575 | GEO

Comprehensive Epigenetic Landscape of Rheumatoid Arthritis Fibroblast-like Synoviocytes [ChIP-seq]

Project description:Epigenetics is important in the pathogenesis of immune-mediated diseases like rheumatoid arthritis (RA). Here we show the first complete epigenomic characterization of RA fibroblast-like synoviocytes (FLS) by profiling histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3, H3K9me3), open chromatin, RNA expression and whole genome DNA methylation. To address the complex multidimensional relationship and reveal the epigenetic regulation of RA, we perform integrative analyses using a novel unbiased method to identify genomic regions with similar profiles. Epigenomically similar regions exist in RA cells are particularly associated with active enhancers and promoters as well as specific transcription factor binding motifs. Differentially marked genes are enriched for immunological and unexpected pathways, with “Huntington's Disease Signaling” identified as particularly prominent. We validate the relevance of this pathway to RA by showing that Huntingtin-interacting protein-1 regulates FLS invasion into matrix. This work establishes a high-resolution epigenomic landscape of RA and demonstrates the potential for integrative analyses to identify unanticipated therapeutic targets. Overall design: Establishing a high-resolution epigenomic landscape of RA FLS by integrating diverse epigenomic data. This series contains ChIP-seq data for H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3, H3K9me3 on fibroblast-like synoviocytes from RA or OA patients. The submitter declares that the raw data will be made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap) due to patient privacy concerns.

| GSE112655 | GEO

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
GPMDB
JPOST Repository

EGA
EVA
ENA
LINCS
PAXDB

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data