txid9606[Organism:exp] - GEO DataSets

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Select item 2002069381.

Recombinant irisin enhances the differentiation, remodeling potential, and the mechanical properties of 3D-cultured human periodontal ligament cells

(Submitter supplied) Irisin is recognized as a myokine produced by muscles, regulating metabolism and energy homeostasis, however, it may play a role in many other biological functions. Little is known about its effect on periodontal ligament cells. We employed Affymetrix to profile mRNA expression patterns between 3D human periodontal ligament cell spheroids treated with and without irisin. The mRNA expression profiling identified approximately 1000 mRNAs to be differentially expressed between the two groups, which suggests that irisin is involved in gene regulation in human periodontal ligament cells.

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL23159
6 Samples

Download data: CEL

Series

Accession:: GSE206938

ID:: 200206938

Select item 2002068612.

Adamantinomatous craniopharyngioma cyst fluid can trigger inflammatory activation of microglia to damage the hypothalamic neurons by inducing the production of β-amyloid

(Submitter supplied) Introduction: The mechanism by which adamantinomatous craniopharyngioma (ACP) damages the hypothalamus is still unclear. Cyst fuid rich in lipids and infammatory factors is a characteristic pathological manifestation of ACP and may play a very important role in hypothalamic injury caused by tumors. Objective: The objective of this study was to construct a reliable animal model of ACP cyst fuid-induced hypotha lamic injury and explore the specifc mechanism of hypothalamic injury caused by cyst fuid. more...

Organism:: Homo sapiens; Mus musculus

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL24676 GPL24247
3 Samples

Download data: MTX, TSV

Series

Accession:: GSE206861

ID:: 200206861

Select item 2002068593.

LDL delivery of microbial small RNAs drives atherosclerosis through macrophage TLR8

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

Organism:: Homo sapiens; Mus musculus

Type:: Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:: GPL24247 GPL18573 GPL24676
28 Samples

Download data: TXT

Series

Accession:: GSE206859

ID:: 200206859

Select item 2002067424.

Effect of depletion of UHRF1, DNMT1, DNMT3B during differentiation

(Submitter supplied) To investigate gene regulation by UHRF1, DNMT1, DNMT3B in THP-1 cells during differentiation, we established stable knockdown THP-1 cell lines.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
16 Samples

Download data: TXT

Series

Accession:: GSE206742

ID:: 200206742

Select item 2002067415.

Drug combination sci-Plex Data

(Submitter supplied) Recent advances in multiplexed single-cell transcriptomics experiments are facilitating the high-throughput study of drug and genetic perturbations. However, an exhaustive exploration of the combinatorial perturbation space is experimentally unfeasible, so computational methods are needed to predict, interpret, and prioritize perturbations. Here, we present the compositional perturbation autoencoder (CPA), which combines the interpretability of linear models with the flexibility of deep-learning approaches for single-cell response modeling. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
96 Samples

Download data: MTX, TSV

Series

Accession:: GSE206741

ID:: 200206741

Select item 2002067406.

A role for phase separation to prevent RNA:DNA hybrids

(Submitter supplied) The function of phase separation for many RNA-binding proteins is poorly understood, including FUS (FUSed in sarcoma). FUS binds RNA Pol II and controls phosphorylation of serine-2 (Ser2P). We uncovered a FUS activity involving no interactions with the polymerase. FUS could activate transcription of a non-eukaryote polymerase by preventing RNA invasion of DNA to form R-loops. This activity required binding to the nascent transcript and phase separation. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL24676
10 Samples

Download data: TAB

Series

Accession:: GSE206740

ID:: 200206740

Select item 2002066497.

Maggot extracts overcome cisplatin resistance of ovarian cancer cells by targeting HSP90AB1/IGF1R signaling

(Submitter supplied) To investigate the main mechanism underlying cisplatin resistance in ovarian cancer, A2780/CDDP and SKOV3/CDDP cell lines were treated with both maggot extracts and cisplatin. We then performed gene expression profiling analysis using data obtained from RNA-seq of A2780 and A2780/CDDP cells.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL23227
6 Samples

Download data: XLS

Series

Accession:: GSE206649

ID:: 200206649

Select item 2001636968.

KSHV Topologically Associating Domains in Latent Chromatin and Regulation of Reactivation

(Submitter supplied) Eukaryotic genomes are structurally organized via the formation of multiple loops that create gene expression regulatory units called topologically associating domains (TADs). Here we revealed the KSHV TAD structure at 500 base pair resolution and constructed a 3D KSHV genomic structural model. The latent KSHV genome formed very similar TAD structures among three different naturally infected PEL cell lines. more...

Organism:: Homo sapiens; Human gammaherpesvirus 8

Type:: Other

Platform:: GPL25719
10 Samples

Download data: HIC

Series

Accession:: GSE163696

ID:: 200163696

SRA Run Selector

Select item 2001333189.

Multiple Histone modifications ChIP-seq in MCF7 cells corresponding to Ctr9 KD (paper title: Ctr9, the scaffold subunit of PAFc, govens PRC2-mediated H3K27me3 domains in breast cancer cells)

(Submitter supplied) We want to examine the alternation of histone modification spectrum on chormatin in corresponding to Ctr9 loss either in an inducible KD or stable KD fashion in MCF7 breast cancer cells.

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL16791
20 Samples

Download data: BW, TSV

Series

Accession:: GSE133318

ID:: 200133318

SRA Run Selector

Select item 20020683610.

Expression profiles of lncRNAs in 3D cultures.

(Submitter supplied) Breast cancer cells reprogram the oncogenic lncRNAs/mRNAs co-expression networks in three- dimensional microenvironment To have a more functional approach, organotypic 3D cell cultures that more accurately mimic the characteristics of solid tumors in vivo and the tumor microenvironment are required. In this study, DNA microarrays were employed to deline the changes in lncRNAs expression patterns of breast cancer cells, cultured in 3D and 2D conditions from BT-474 cell line. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24539
6 Samples

Download data: CEL, CHP

Series

Accession:: GSE206836

ID:: 200206836

Select item 20020679311.

MicroRNA (miRNA) expression from blood plasma of patients with a prostate cancer

(Submitter supplied) We investigated how microRNAs' expression profile changes in blood plasma depending on a prostate cancer aggresivness.

Organism:: synthetic construct; Homo sapiens

Type:: Expression profiling by array

Platform:: GPL19117
152 Samples

Download data: CEL, TSV

Series

Accession:: GSE206793

ID:: 200206793

Analyze with GEO2R

Select item 20020672012.

The human lncRNA GOMAFU suppresses neuronal interferon response pathways affected in schizophrenia

(Submitter supplied) Long noncoding RNAs (lncRNAs) play multifaceted roles in regulating molecular networks that underlie normal brain function and the complex etiology of neuropsychiatric disorders. One example is the human neuronal lncRNA GOMAFU, which was reported to display abnormal expression in schizophrenia (SCZ) postmortem brains, regulate alternative splicing of SCZ risk gene transcripts, and harbor genetic variates contributing to the risk of SCZ. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
8 Samples

Download data: TXT

Series

Accession:: GSE206720

ID:: 200206720

Select item 20020663813.

Gene expression profile at single cell level of myeloid cells from juxta tumor (JT) and tumor (T) samples from treatment naive triple negative breast cancer (TNBC) patients

(Submitter supplied) Myeloid cell subpopulation comprises denditric cells (DC), monocytes and macrophages. We used single cell RNA sequencing (scRNA-seq) to analyze the heterogeneity of the myeloid cells, particularly to study tumor-assocaited macrophages in TNBC patients.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
7 Samples

Download data: RDS, TAR

Series

Accession:: GSE206638

ID:: 200206638

Select item 20020663714.

Gene expression profile of monocytes from healthy donor and triple negative breast cancer (TNBC) co-cultured with FAP and CD29 [bulk RNA-seq]

(Submitter supplied) These samples were either treatment naive or samples co-cultured with FAP and CD29. Myeloid cell subpopulation comprises denditric cells (DC), monocytes and macrophages. We used RNA sequencing to analyze the response of monocytes to FAP/CD29 co-culture.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
12 Samples

Download data

Series

Accession:: GSE206637

ID:: 200206637

Select item 20020662015.

Methylation array of shNC, shUHRF1, shDNMT1, shDNMT3B THP-1 cells before and after PMA treatment

(Submitter supplied) This methylation array was conducted to find out changes in genome-wide methylation pattern in THP-1 cells upon differentiation. Also, we tried to figure out the effects of knockdown of UHRF1, DNMT1 and DNMT3B in THP-1 cells in regulating genome-wide DNA methylation.

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL21145
8 Samples

Download data: IDAT, TXT

Series

Accession:: GSE206620

ID:: 200206620

Analyze with GEO2R

Select item 20020659916.

Multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in picolitre-sized droplets [dataset 3]

(Submitter supplied) K562 cells were perturbed with drug combinations for 12h in droplets. Subsequently cells were processed to generate liraries for RNA-Seq.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL18573 GPL15520
199 Samples

Download data: CSV

Series

Accession:: GSE206599

ID:: 200206599

Select item 20020659417.

Osteogenic transdifferentiation of primary human fibroblasts to osteoblast-like cells with human platelet lysate

(Submitter supplied) Inherited bone disorders account for about 10% of documented Mendelian disorders and are associated with high financial burden. Their study requires osteoblasts which play a critical role in regulating the development and maintenance of bone tissue. However, bone tissue is not always available from patients. We developed a highly efficient platelet lysate-based approach to directly transdifferentiate skin-derived human fibroblasts to osteoblast-like cells. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL20301
6 Samples

Download data: TSV

Series

Accession:: GSE206594

ID:: 200206594

Select item 20020658018.

Pro-Inflammatory Cytokines Mediate the Epithelial-to-Mesenchymal-Like Transition of Pediatric Posterior Fossa Ependymoma

(Submitter supplied) Pediatric ependymoma is a devastating brain cancer marked by its relapsing pattern and lack of effective chemotherapies. This shortage of treatments is due to limited knowledge about ependymoma tumorigenic mechanisms. By means of single-nucleus chromatin accessibility and gene expression profiling of posterior fossa primary tumors and distal metastases, we reveal key transcription factors and enhancers associated with the differentiation of ependymoma tumor cells into tumor-derived cell lineages and their transition into a mesenchymal-like state. more...