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SRP136107
Mus musculus
9 Downloadable Samples
Illumina HiSeq 2500
Description
Purpose: The goal of this study is to evaluate the transcriptome profiling (RNA-seq) of dormant and proliferating breast cancer cells using an in vitro 3D model Methods: mRNA profiles of D2.0R cells growing either on basal membrane extracts (BME) (dormant phase) or BME + Collagen (COL) (proliferative phase) at days 1 or 5 of culture were generated by deep sequencing in triplicate with Ilumina HiSeq2500 using Illumina TruSeq V4. Aligned reads (BAM files) were analysed using PartekFlow software for differential expression and gene enrichment analysis. Comparisons used Partek Gene Specific Analysis (GSA) algorithm and multiple comparisons were corrected using False Discovery Rate (FDR), which was set at 0.05 Results: Using an optimized data analysis workflow, we mapped about 118 – 133 million reads per sample to the mouse genome (build mm9). Total alignment with reference genome is between 81-90%. RNA-seq identified 5,524 transcripts showing differential expression between the D2.0R cells cultured on BME + COL vs D2.0R cells cultured on BME matrices at day 5, with a fold change =1.5 or =-1.5 and p value <0.05. On the other hand, only 1,097 were found to be differentially expressed between D2.0R cells growing on BME matrices at day 5 and day 1, with a fold change =1.5 or =-1.5 and p value <0.05. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to breast cancer dormancy and identifies autophagy as a top biological process activated in dormant D2.0R cells. Conclusions: Our study represents a detailed analysis of the transcriptomes of dormant and proliferating D2.0R cells, with three biologic replicates, generated by RNA-seq technology. RNA-seq based transcriptome characterization identifies autophagy as the most prevalent upregulated pathway in dormant breast cancer cells. Overall design: mRNA profiles of D2.0R cells after culture on BME or BME + COL matrices for 1 or 5 days were generated by deep sequencing in triplicate with Ilumina HiSeq2500 using Illumina TruSeq V4.
Publication Title
Autophagy promotes the survival of dormant breast cancer cells and metastatic tumour recurrence.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 88 Downloadable Samples
- IlluminaHiSeq2000
Description
Bariatric surgery is the most effective therapy of severe human obesity. It is associated with improvements in metabolic and non metabolic co-morbidities which are thought to be mediated by a decrease of adipose tissue inflammation. However, the molecular mechanisms behind these beneficial effects are poorly understood. We analyzed expression profiles in subcutaneous adipose tissue from 22 obese women before and 3 months after surgery using the RNA-seq technology. Of 15,972 detected genes, 1214 were differentially expressed after surgery. Upregulated genes were mostly involved in the basal cellular machinery. Downregulated genes were enriched in metabolic functions of adipose tissue. At baseline, we identified 26 modules of coexpressed genes. The four most stable modules reflected the innate and adaptive immune responses of adipose tissue, including a general signature of innate immune cells, an adaptive immune response elicited by T lymphocytes, a neutrophil-mediated inflammatory signature and an interferon-signaling pathway, respectively. After surgery, a few crucial molecules involved in chemotaxis and activation of immune cells were disconnected from their respective networks. These molecules may represent therapeutic targets against adipose inflammation. Overall design: mRNA sequencing of subcutaneous adipose tissue (SAT) samples from 22 obese women before and 3 months after bariatric surgery
Publication Title
Bariatric Surgery Induces Disruption in Inflammatory Signaling Pathways Mediated by Immune Cells in Adipose Tissue: A RNA-Seq Study.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 16 Downloadable Samples
Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
Adiponectin is an adipose-derived hormone with anti-inflammatory activity. Following subacute ozone exposure (0.3 ppm for 24-72 h), pulmonary neutrophilic inflammation is augmented in adiponectin deficient mice. The purpose of this study was to use microarrays to examine the impact of adiponectin deficiency on changes in pulmonary gene expression induced by ozone, a common air pollutant.
Publication Title
Pivotal role of IL-6 in the hyperinflammatory responses to subacute ozone in adiponectin-deficient mice.
Sample Metadata Fields
Sex, Specimen part
View Samples- Arabidopsis thaliana
- 9 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
We performed microarray experiments with RNAs from dissected immature anthers (stages 4-7) from wild-type, dyt1 and ams mutant plants, using the Affymetrix ATH1 chip.
Publication Title
Regulation of the Arabidopsis anther transcriptome by DYT1 for pollen development.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
We used microarray analysis to examine transcriptomic changes in cdm1 mutant, identifying genes potentially regulated by CDM1 by comparing gene expression between cdm1 and wild type young floral buds. Among 375 genes that showed differential expression (P-value <0.05) with >1.5-fold changes between wild type and cdm1, 185 genes were down-regulated by 1.5 to 7.10-folds, whereas 190 genes were up-regulated by 1.5 to 5.82-folds.
Publication Title
The Arabidopsis CALLOSE DEFECTIVE MICROSPORE1 gene is required for male fertility through regulating callose metabolism during microsporogenesis.
Sample Metadata Fields
Specimen part
View Samples- Oryza sativa
- 12 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
KMD is genetically engenered to be highly resistant to lepidopteran pests through expressing a synthetic cry1Ab gene and its parent non-transgenic rice is Xiushui 11.The developmental duration of BPH feeding on KMD2 was significantly delayed. And moreover, the fecundity of BPH was significantly lower when fed on Bt rice than on the non-Bt parental plants.To investigate unintended effects in KMD2 that causes changes in BPH performance, we performed microarray (GeneChip) analysis to compare the gene expression profiles between Bt rice and non-transgenic parental plants in response to BPH infestation.
Publication Title
Comparing Gene Expression Profiles Between Bt and non-Bt Rice in Response to Brown Planthopper Infestation.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 8 Downloadable Samples
- IlluminaHiSeq2000
Description
MicroRNAs have been implicated in various skin cancers, including melanoma, squamous cell carcinoma, and basal cell carcinoma; however, the expression of microRNAs and their role in Merkel cell carcinoma (MCC) have yet to be explored in depth. To identify microRNAs specific to MCC (MCC-miRs), next-generation sequencing (NGS) of small RNA libraries was performed on different tissue samples including MCCs, other cutaneous tumors, and normal skin. Comparison of the profiles identified several microRNAs upregulated and downregulated in MCC. For validation, their expression was measured via qRT-PCR in a larger group of MCC and in a comparison group of non-MCC cutaneous tumors and normal skin. Eight microRNAs were upregulated in MCC: miR-502-3p, miR-9, miR-7, miR-340, miR-182, miR-190b, miR-873, and miR-183. Three microRNAs were downregulated: miR-3170, miR-125b, and miR-374c. Many of these MCC-miRs, with the miR-183/182/96a cistron in particular, have connections to tumorigenic pathways implicated in MCC pathogenesis. In situ hybridization confirmed that the highly expressed MCC-miR, miR-182, is localized within tumor cells. Furthermore, NGS and qRT-PCR reveals that several of these MCC-miRs are highly expressed in the patient-derived MCC cell line, MS-1. These data indicate that we have identified a set of MCC-miRs with high implications for MCC research. Overall design: To identify microRNAs specific to Merkel cell carcinoma (MCC) next-generation sequencing (NGS) of small RNA libraries was performed on different tissue samples including MCCs, other cutaneous tumors, and normal skin
Publication Title
Characterization of the Merkel Cell Carcinoma miRNome.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We used microarrays to compare the expression profiles between brains of BCAS1 knockout and wild type mice
Publication Title
Mice lacking BCAS1, a novel myelin-associated protein, display hypomyelination, schizophrenia-like abnormal behaviors, and upregulation of inflammatory genes in the brain.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 19 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Type 1 diabetes mellitus (T1D) is a common autoimmune disease mediated by autoimmune attack against pancreatic b cells.Dys-regualtion of the component of peripheral blood mononuclear cells (PBMCs), including T-cells and B-cells, and smaller amounts of NK cells and dendritic cells, have all been implicated in this process
Publication Title
Decreased miR-146 expression in peripheral blood mononuclear cells is correlated with ongoing islet autoimmunity in type 1 diabetes patients 1miR-146.
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples- Homo sapiens
- 17 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Autologous nonmyeloablative hematopoietic stem cell transplantation (AHST) was the first therapeutic approaches that can improvecell function in type 1 diabetic (T1D) patients. This study was designed to investigate the potential mechanisms involved.We applied AHST to nine T1D patients diagnosed within six months and analyzed the acute response in peripheral blood genomic expression profiling at the six-month follow-up.
Publication Title
Acute response of peripheral blood cell to autologous hematopoietic stem cell transplantation in type 1 diabetic patient.
Sample Metadata Fields
Specimen part, Time
View Samples