GPL11154[RGSE] - GEO DataSets

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Select item 2000644611.

Endothelial MMP14 is required for endothelial dependant growth support of human airway basal cells

(Submitter supplied) Human airway basal cells (BC) are the stem/progenitor population of the airway epithelium, and play a central role in anchoring the epithelium to the basement membrane. The anatomic position of BC allows for potential paracrine signaling between BC and the underlying non-epithelial stromal cells. In support of this, we previously demonstrated endothelial cells (EC) support growth of BC during co-culture via vascular endothelial growth factor A (VEGFA)-mediated signaling. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
10 Samples

Download data: FPKM_TRACKING

Series

Accession:: GSE64461

ID:: 200064461

SRA Run Selector

Select item 2002669122.

RNA sequencing of 15 patient derived cSCC cell lines

(Submitter supplied) 15 patient derived cscc cell lines were subjected to RNA sequencing to determine the RNA landscape of cutaneous squamous cell carcinoma (cSCC) tumour cells only.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
15 Samples

Download data: TXT

Series

Accession:: GSE266912

ID:: 200266912

Select item 2002354013.

Effect of Palbociclib on gene expression of two gastric cancer cell lines(including AGS and SNU1)

(Submitter supplied) Palbociclib, a kind of CDK4/6 inhibitor, was proved to be able to induce senescence in several cancer cell lines. After treated with Palbociclib, two GC cell lines (including AGS and SNU1) exhibited senescence-associated features, such as enlarged cell size, formation of heterochromatin foci in the nucleus, and increased activity of SA-β-Gal.Many senescence-related genes, such as CDKN1A, CDKN2A and TP53, were evaluated in the Palbociclib-treated GC cells, while proliferation-related genes, such as TOP2A and MKI67, were decreased. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
8 Samples

Download data: TXT

Series

Accession:: GSE235401

ID:: 200235401

Select item 2002328874.

A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival

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

Organism:: Homo sapiens; Mus musculus

Type:: Other; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:: GPL20301 GPL21103 GPL11154
17 Samples

Download data: BED, BW, COOL, HIC, NARROWPEAK

Series

Accession:: GSE232887

ID:: 200232887

Select item 2002328835.

A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival [ChIP-seq]

(Submitter supplied) Gene deserts spanning more than 500kb of non-protein coding genomic sequence are considered evolutionarily ancient and stable and are enriched in the vicinity of developmental regulator genes (Ovcharenko 2005). These extensive genomic regions typically harbor numerous conserved elements with predicted gene regulatory potential pointing to critical tissue-specific functions during development. Nevertheless, the biological necessity and underlying funtional enhancer landscapes of most gene deserts near developmental transcription factors (TFs) remain unknown, and it is unclear how precise pleiotropic expression patterns emerge from gene desert sequence. more...

Organism:: Homo sapiens

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

Platform:: GPL11154
8 Samples

Download data: BED, BW

Series

Accession:: GSE232883

ID:: 200232883

Select item 2002682486.

RNAseq of gingival fibroblasts exposed to PRF membranes and PRF serum.

(Submitter supplied) Platelet-rich fibrin (PRF) is prepared from the coagulated plasma of fractionated blood. When squeezing between two plates, PRF is separated into the solid PRF membranes and a liquid exudate, the PRF serum. The question arises regarding the extent to which the overall PRF activity remains in the membranes and what is lost in the serum. To this aim, we have exposed gingival fibroblasts to lysates prepared from PRF membranes and PRF serum, followed by bulk RNA sequencing. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
9 Samples

Download data: TXT

Series

Accession:: GSE268248

ID:: 200268248

Select item 2002531107.

The SW480 cell line as a model of resident and migrating colon cancer stem cells

(Submitter supplied) Gene expression profiling of the SW480 sphere and bulk subpopulations.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
8 Samples

Download data: XLSX

Series

Accession:: GSE253110

ID:: 200253110

Select item 2001512068.

RNA-Sequencing of LBH transcriptomes in human breast cancer cell lines

(Submitter supplied) Purpose: Gene expression analysis of knockdown and overexpression of LBH (Limb-Bud-and-Heart) in human breast cancer cell lines using RNA-Seq Methods: RNA was collected and analyzed from three biological replicates of each condition (LBH vs vector) for LBH overexpression (OE) in two human breast cancer cell lines (BT549, MCF7). Additionally, RNA was collected and analyzed from three biological replicates of each condition (siLBH vs non-target/NT siRNA) for LBH knockdown (KD) in two human triple negative breast cancer cells lines (HCC1395, MDA-MB-231). more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
24 Samples

Download data: CSV

Series

Accession:: GSE151206

ID:: 200151206

SRA Run Selector

Select item 2002321389.

In vitro organoid-based assays reveal SMAD4 tumor-suppressive mechanisms for serrated colorectal cancer invasion

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

Organism:: Homo sapiens; Mus musculus

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

Platforms:: GPL11154 GPL23479
14 Samples

Download data

Series

Accession:: GSE232138

ID:: 200232138

Select item 20023213610.

In vitro organoid-based assays reveal SMAD4 tumor-suppressive mechanisms for serrated colorectal cancer invasion [ChIP-seq]

(Submitter supplied) We establish a model system where organoids derived from tumors found in the Smad4KO BRAFV600E/+ mouse model present multiple phenotypes characteristic of invasion both in ex vivo and in vivo systems. Additionally, Smad4KO BRAFV600E/+ tumor organoids have the ability to infiltrate a transwell and initiate colonies on the culture plate below. This invasive behavior can be suppressed when SMAD4 is re-expressed in the tumor organoids. more...

Organism:: Homo sapiens

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

Platform:: GPL11154
2 Samples

Download data: BED

Series

Accession:: GSE232136

ID:: 200232136

Select item 20024307811.

Genome-wide analysis of long noncoding RNAs as cis-acting regulators of transcription factor-encoding genes in IgA nephropathy

(Submitter supplied) IgA nephropathy (IgAN) is the most common form of primary glomerulonephritis in the world, but the disease pathogenesis noncoding is yet to be elucidated.Previous studies have revealed regulatory functions for long noncoding RNA (lncRNA) in various diseases; however, the roles of lncRNA in IgAN and regulation of transcription factors (TFs) have been scarcely investigated.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
9 Samples

Download data: TXT

Series

Accession:: GSE243078

ID:: 200243078

Select item 20023674312.

Pharmacological inhibition of LIFR impairs ovarian cancer progression by blocking LIF/LIFR autocrine loop

(Submitter supplied) We examined the transcriptional chagnes modulated by LIFR inhibitory compound EC359 by perfroming global transcriptome analysis. ES2 cells were treated with vehicle or EC359 for 12 h and the RNA was isolated and utilized for RNA-seq analysis. Our results demonstrated that EC359 modulated unique pathways including oxidative phosphorylation, Glutathione signaling, JNK signaling, NRF2 signaling, ovarian cancer signaling, hypoxia signaling and apoptotic pathways.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
4 Samples

Download data: TXT

Series

Accession:: GSE236743

ID:: 200236743

Select item 20023342913.

Effect of ARL11 overexpression on gene expression of MDA-MB-231 cells during olaparib treatment

(Submitter supplied) To investigate the function ARL11 in the regulation of PARPi resistance, we established MDA-MB-231 cells overexpressing ARL11. We then performed gene expression profiling analysis using data obtained from RNA-seq of ARL11 overexpression or vector control MDA-MB-231 cells treated with or without Olaparib.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
4 Samples

Download data: CSV

Series

Accession:: GSE233429

ID:: 200233429

Analyze with GEO2R

Select item 20023476514.

Effects of chemical in vitro activation versus fragmentation on human ovarian tissue and follicle growth in culture

(Submitter supplied) Abstract STUDY QUESTION What is the effect of the chemical in vitro activation (cIVA) protocol compared with fragmentation only (Frag, also known as mechanical IVA) on gene expression, follicle activation, and growth in human ovarian tissue in vitro? SUMMARY ANSWER Although histological assessment shows that cIVA significantly increases follicle survival and growth compared to Frag, both protocols stimulate extensive and nearly identical transcriptomic changes in cultured tissue compared to freshly collected ovarian tissue, including marked changes in energy metabolism and inflammatory responses. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
27 Samples

Download data: TXT

Series

Accession:: GSE234765

ID:: 200234765

Select item 20021055515.

Impaired signaling pathways on Berardinelli–Seip congenital lipodystrophy macrophages during Leishmania infantum infection

(Submitter supplied) This was an in vitro experimental study of monocytes-derived macrophages from blood samples of BSCL individuals (type I - AGPAT2, type II - BSCL2, and heterozygous - BSCL2), and healthy controls (WT). Samples were infected with L. infantum. In the control group, there are monocytes-derived macrophages from individuals WT with and without a history of visceral leishmaniasis (VL). RNA-seq was done to identify the different group responses to the infection.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
36 Samples

Download data: TXT

Series

Accession:: GSE210555

ID:: 200210555

Analyze with GEO2R

Select item 20023267816.

Gene expression profiling of RKO cells with or without SQLE knockdown.

(Submitter supplied) RKO cells (WT or SQLE knockdown) were harvested and mRNA were extracted for high-throughput sequencing.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
6 Samples

Download data: XLS

Series

Accession:: GSE232678

ID:: 200232678

Analyze with GEO2R

Select item 20026778117.

Transcriptional outcome of telomere elongation in human fibrosarcoma model

(Submitter supplied) The study focuses on understanding the transcriptional changes and the pathways altered when human cancer (fibrosarcoma ) cells are subjected to telomere elongation.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
6 Samples

Download data: TXT

Series

Accession:: GSE267781

ID:: 200267781

Analyze with GEO2R

Select item 20026775918.

AP-1 regulates heterogeneous cellular dormancy in TNBC II

(Submitter supplied) Slow-cycling cells (SCCs) are a heterogeneous subpopulation of tumor cells. They pre-exist in tumor tissues and evade killing by chemotherapeutics that target mitosis due to their dormant nature. We here utilized PKH26 retaining method to label and isolate SCCs, and RNA-seq was performed to understand the gene expression characteristics of SCCs. Here we reported that up-regulations of AP-1 subunits regulate triple negative breast cancer (TNBC) dormancy by up-regulating the expression of CDKN1A and GADD45 family as transcription factors.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
6 Samples

Download data: TXT

Series

Accession:: GSE267759

ID:: 200267759

Analyze with GEO2R

Select item 20026775719.

AP-1 regulates heterogeneous cellular dormancy in TNBC

(Submitter supplied) Slow-cycling cells (SCCs) are a heterogeneous subpopulation of tumor cells. They pre-exist in tumor tissues and evade killing by chemotherapeutics that target mitosis due to their dormant nature. We here utilized varieties of fluorescent dyes or proteins (Claret, H2BeGFP, and Violet) retaining method to label and isolate SCCs, and RNA-seq was performed to understand the gene expression characteristics of subpopulations of SCCs.