GEO DataSets

(Submitter supplied) Mutations in the Huntingtin (HTT) gene cause Huntington disease (HD), a neurodegenerative disorder. While HTT is known to be involved, as a scaffold protein, in several cellular functions, its normal and pathogenic functions during the development of the human forebrain remain poorly understood. To investigate the roles of wild-type and mutant HTT alleles during human neural and striatal development we inactivated HTT alleles in a series of isogenic clones of a human induced pluripotent stem cell (iPSC) line derived from a patient with HD. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

31 Samples

Download data: TXT

(Submitter supplied) Varicella-zoster virus (VZV), an alphaherpesvirus, causes chickenpox (varicella) in young children with an annual minimum of 140 million new cases and herpes zoster in senior, a painful and debilitating disease with 3-5‰ incidence. A complex structural transcriptome of VZV, which numerous novel transcripts, transcript isoforms, and unknown splice events are found during cell infection. Circular RNA (circRNA), a newly important component of the transcriptome, is increasing discoveries of circRNA function in mammalian cells. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17303

1 Sample

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

22 Samples

Download data

(Submitter supplied) To incorporate Kupffer cells into hiPSC-LOs, we differentiated erythro-myeloid progenitors (EMPs) from hiPSCs. We compares the gene expression profiles of hiPSC-EMPs with cord-blood hematopoietic stem and progenitor cells (CB-HSPCs); and EMP-generated Kupffer cells (EMP-KC) with human primary Kupffer cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

12 Samples

Download data: XLSX

(Submitter supplied) To recapitulate the pathology of human septic liver, we established hiPSC-derived liver organoids containing Kupffer cells (KuLOs). We performed gene expression profiling analysis using data obtained from RNA-seq of KuLOs with/without LPS/IFNr stimulation and the KuLOs during recovery after endotoxin elimination.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

10 Samples

Download data: TXT

(Submitter supplied) Searching for the new molecular signatures of Duchenne muscular dystrophy (DMD)-associated cardiomyopathy development

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

8 Samples

Download data: TXT

(Submitter supplied) The Golgi stress response is an important cytoprotective system that enhances Golgi function in response to cellular demand, while cells damaged by prolonged Golgi stress undergo cell death. OSW-1, a natural compound with anticancer activity, potently inhibits OSBP that transports cholesterol and phosphatidylinositol-4-phosphate (PI4P) at contact sites between the endoplasmic reticulum and the Golgi apparatus. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL17303

4 Samples

Download data: CSV

(Submitter supplied) The Golgi stress response is an important cytoprotective system that enhances Golgi function in response to cellular demand, while cells damaged by prolonged Golgi stress undergo cell death. OSW-1, a natural compound with anticancer activity, potently inhibits OSBP that transports cholesterol and phosphatidylinositol-4-phosphate (PI4P) at contact sites between the endoplasmic reticulum and the Golgi apparatus. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

6 Samples

Download data: TXT

(Submitter supplied) Strict regulation of RNA helicase activity, often accomplished by protein cofactors, is essential to ensure target specify within the complex cellular environment. The largest family of RNA helicase cofactors are the G-patch proteins, but the cognate RNA helicases and cellular functions of numerous human G-patch proteins remain elusive. Here, we discover that GPATCH4 is a stimulatory cofactor of DHX15 that interacts with the helicase in the nucleolus via residues in its G-patch domain. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL17303

12 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17303 GPL20301

26 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) We carried out the analysis using human skin fibrobllast HCA2 (MJ90) cells dox-inducible shLuciferase or shFbxo22. Cells were indcued to be senescent cells by treatment with 10 Gy. As a result, Gene set enrichment analysis revealed a significant increase in the expression of lysomal-related and autophagosomal genes in control cells, whereas this gene ontology was not increased in cells depleted of Fbxo22

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

12 Samples

Download data: XLSX

(Submitter supplied) HIV-1 latency results from tightly regulated molecular processes that act at distinct steps of HIV-1 gene expression. To elucidate the molecular players that govern latency, we previously performed a dCas9-chromatin immunoprecipitation coupled with mass spectrometry (Catchet-MS) and identified the interactome of the latent HIV-1 LTR. Here we characterize the Catchet-MS-identified PCI domain-containing 2 (PCID2) protein, a component of the TREX2 complex, to play a dual role in promoting HIV-1 latency by enforcing both transcriptional repression and post-transcriptional blocks to HIV-1 gene expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

4 Samples

Download data: TXT

(Submitter supplied) The aim of this study was to obtain a better understanding of the molecular background of hidradenitis suppurativa (HS). Global transcriptome analysis of lesional and perilesional skin identifies numerous differentially expressed genes that display unique expression pattern in HS. Genes, whose expression is dysregulated in the skin of patients suffering from HS are novel biomarker candidates and potential therapeutic targets for HS.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

16 Samples

Download data: FASTA, TXT

(Submitter supplied) The aggressiveness of pancreatic ductal adenocarcinoma (PDAC) is affected by a tumor microenvironment (TME). In this study, to recapitulate PDAC TME ex vivo, we cocultured patient-derived PDAC cells with mesenchymal and vascular endothelial cells derived from human induced-pluripotent stem cells (hiPSCs) to create a fused pancreatic cancer organoid (FPCO) in air–liquid interface. FPCOs were further induced to resemble two distinct parts of a PDAC tissue. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

31 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17303 GPL24676

33 Samples

Download data: MTX, TSV

(Submitter supplied) To investigate the alterations that occur in the TGF-B signalling pathway in Alström syndrome, we established by lentiviral transduction with CRISPR an hTERT-BJ-5ta cell line with the ALMS1 gene inhibited. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells (WT and KO) after 24h of TGF-β stimulation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

6 Samples

Download data: TXT

(Submitter supplied) Immunomodulatory Drugs (IMiDs) are a backbone therapy for multiple myeloma (MM). Despite their efficacy, most patients develop resistance and the mechanism(s) are not fully defined. Here, we show that IMiD responses are directed by IMiD-dependent degradation of IKZF1 and IKZF3 that bind to enhancers necessary to sustain the expression of MYC and other myeloma oncogenes. IMiD treatment universally depleted chromatin-bound IKZF1, but eviction of P300 and BRD4 co-activators only occurred in IMiD-sensitive cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

12 Samples

Download data: CSV

(Submitter supplied) Immunomodulatory Drugs (IMiDs) are a backbone therapy for multiple myeloma (MM). Despite their efficacy, most patients develop resistance and the mechanism(s) are not fully defined. Here, we show that IMiD responses are directed by IMiD-dependent degradation of IKZF1 and IKZF3 that bind to enhancers necessary to sustain the expression of MYC and other myeloma oncogenes. IMiD treatment universally depleted chromatin-bound IKZF1, but eviction of P300 and BRD4 co-activators only occurred in IMiD-sensitive cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17303

20 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17303 GPL24676

48 Samples

Download data: BW

(Submitter supplied) S-adenosylmethionine represents a potent inhibitor of cancer cell proliferation, migration and invasion in vitro. The reason remains unclear. Here, we examined if treatment with exogenous SAM is capable of causing alterations in the methylation of the histone markers H3K4me3 and H3K27me3, which are both known to be important in the initiation and progression of prostate cancer.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17303

17 Samples

Download data: BW