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GSE16014
Homo sapiens
6 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
In order to identify patterns of gene expression associated with biological effects in THP-1 cells induced by F3, we performed a transcriptomic analysis on the THP-1 control and F3-treated THP-1 cells by oligonucleotide microarray
Publication Title
Ganoderma lucidum polysaccharides in human monocytic leukemia cells: from gene expression to network construction.
Sample Metadata Fields
Cell line
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
Illumina HiSeq 2500
Description
The correlation coefficient (R) for the expression profile of all transcripts between WT and asr3-1, and between WT and OX9 without flg22 treatment is close to linear, suggesting that ASR3 does not affect general gene transcription. Hierarchical clustering analysis flg22-induced genes in any of the three genotypes suggested that the asr3-1 mutant displayed overall enhanced flg22 response whereas OX9 displayed overall reduced responses compared to WT plants. Overall design: RNA-seq analysis was performed with 10-day-old seedlings of WT, asr3-1 and 35S:ASR3-HA transgenic line OX9 with or without 100 nM flg22 treatment for 30 min. Two independent repeats were performed for RNA-seq analysis. For each repeat, equal amount of RNA from two biological replicates was pooled for RNA-seq library construction. RNA-seq library preparation and sequencing were carried out on an Illumina HiSeq 2500 platform with 100 nt single end reads.
Publication Title
Phosphorylation of trihelix transcriptional repressor ASR3 by MAP KINASE4 negatively regulates Arabidopsis immunity.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 14 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Macrophages in tumor microenvironment have been characterized as M1- and M2-polarized subtypes. This study sought to investigate the effects of different macrophage subtypes on the biological behavior and global gene expression profiles of lung cancer cells. Expression microarray and bioinformatics analyses indicated that the different macrophage subtypes mainly regulated genes involved in cell cycle, cytoskeletal remodeling, coagulation, cell adhesion and apoptosis pathways in A549 cells, a pattern that correlated with the altered behavior of A549 cells observed after coculture with macrophage subtypes.
Publication Title
Opposite Effects of M1 and M2 Macrophage Subtypes on Lung Cancer Progression.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Deficiency of the microRNA-31-microRNA-720 pathway in the plasma and endothelial progenitor cells from patients with coronary artery disease.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Homo sapiens
- 3 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Early EPCs (eEPCs) appear at less than 1 week in culture dishes, whereas late EPCs (LEPCs) appear late at 2-4 weeks. Distinct angiogenic properties between these two EPC subpopulations have been disclosed by the angiogenesis assay: late EPCs, but not eEPCs, form vascular networks de novo and are able to incorporate into vascular networks. On the contrary, eEPCs, but not late ones, indirectly augment tubulogenesis even when physically separated by a Transwell membrane, implying the involvement of a cytokine-based paracrine mechanism.
Publication Title
Deficiency of the microRNA-31-microRNA-720 pathway in the plasma and endothelial progenitor cells from patients with coronary artery disease.
Sample Metadata Fields
Specimen part, Time
View Samples- Homo sapiens
- 2 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
High glucose impairs the angiogenic activities of late endothelial precursor cells (EPC). We found that far infrared (FIR) treatment restored partially the activity of late EPC. However, the mechanisms are unclear. We performed gene expression microarray analysis to assess the expression profiles of high glucose-treated late EPC with or without FIR treatment.
Publication Title
Deficiency of the microRNA-31-microRNA-720 pathway in the plasma and endothelial progenitor cells from patients with coronary artery disease.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 2 Downloadable Samples
- IlluminaHiSeq2000
Description
We show that PSPC1 is required for cancer cell motilities and stemness properties in vitro and lung metastasis in vivo. We used high throughput sequencing to analyze the PSPC1 regulated gene expression. Loss of PSPC1 results in significant gene expression level changes in thousands of individual transcripts in key regulators of the EMT, CSCs and TGFb signaling. Overall design: Methods: Gene expression profiles of A549 shPSPC1 knockdown cells were generated by Illumna RNA sequencing and compared to profiles derived from control cells (shLacZ knockdown).
Publication Title
PSPC1 mediates TGF-β1 autocrine signalling and Smad2/3 target switching to promote EMT, stemness and metastasis.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 167 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
We used microarray gene expression analyses to unveil the mechanisms underlying NT-3-chitosan-induced spinal cord regeneration.
Publication Title
Transcriptome analyses reveal molecular mechanisms underlying functional recovery after spinal cord injury.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 11 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The CLS1/CAF co-culture maintained the cancer stemness. This cancer stemness was lost when the CAF feeder cells were removed during passaging.
Publication Title
Cancer-associated fibroblasts regulate the plasticity of lung cancer stemness via paracrine signalling.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 4 Downloadable Samples
- IlluminaHiSeq2000
Description
In order to explore the status of DNA methylation in hypoxia response, we show that TET1, a DNA dioxygenase converting 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), regulates hypoxia-responsive gene expression. Hypoxia/HIF-2a regulates the expression of TET1. Knockdown of TET1 mitigated hypoxia-induced EMT. RNA sequencing and 5hmC sequencing identified the set of TET1-regulated genes. Overall design: Four samples (Four samples, Hypoxia (scrambled control), Hypoxia (TET1-si), Normoxia (scrambled control) and Normoxia (TET1-si), are performed by RNA-Seq and hMeDIP-Seq RNA-Seq and hMeDIP-Seq
Publication Title
TET1 regulates hypoxia-induced epithelial-mesenchymal transition by acting as a co-activator.
Sample Metadata Fields
No sample metadata fields
View Samples