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GSE101587
Homo sapiens
11 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
To investigate the genes differentially induced by c-FLIP up-regulation by lentivirus infection in monocytes from healthy donors
Publication Title
Induction of immunosuppressive functions and NF-κB by FLIP in monocytes.
Sample Metadata Fields
Disease
View Samples- Homo sapiens
- 1 Downloadable Sample
IlluminaGenomeAnalyzer
Description
We deep sequenced chromatin-associated RNAs (CARs) from human fibroblast (HF) cells. This resulted in the identification of 141 intronic regions and 74 intergenic regions harbouring CARS. Overall design: We purified CARs from normal HFs by isolating soluble chromatin after MNase treatment, followed by separation of chromatin fragments of different lengths on a sucrose gradient. CARs were converted into double-stranded cDNAs and sequenced using the Illumina Genome Analyzer I.
Publication Title
Characterization of the RNA content of chromatin.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 4 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Upon pathogenic infection, drosophila larval host mounts an immune response. Parasitic wasps inject venom that contain virulence factors during oviposition, which can elicit host immune response, and in some cases, suppress host immune responses altogether. Several microarray experiments have been performed on different classes of parasitic wasps. We wanted to compare how Ganaspis xanthopoda-infected hosts respond compared to other classes of parasitic wasps.
Publication Title
A database for the analysis of immunity genes in Drosophila: PADMA database.
Sample Metadata Fields
Time
View Samples- Homo sapiens
- 500 Downloadable Samples
Description
Age-related macular degeneration (AMD) is a complex multifactorial disease with at least 34 loci contributing to genetic susceptibility. To gain functional understanding of AMD genetics, we generated transcriptional profiles of retina from 453 individuals including both controls and cases at distinct stages of AMD. We integrated retinal transcriptomes, covering 13,662 protein-coding and 1,462 noncoding genes, with genotypes at over 9 million common single nucleotide polymorphisms (SNPs) for expression quantitative trait loci (eQTL) analysis of a tissue not included in Genotype-Tissue Expression (GTEx) and other large datasets. Cis-eQTL analysis revealed 10,474 genes under genetic regulation, including 4,541 eQTLs detected only in the retina. We then integrated the AMD-genome-wide association studies (GWAS) data with eQTLs and ascertained target genes at six loci. Furthermore, using transcriptome wide association analysis (TWAS), we identified 23 additional AMD-associated genes, including RLBP1, HIC1 and PARP12. Our studies expand the genetic landscape of AMD leading to direct targets for biological evaluation and establish the Genotype-Retina Expression (GREx) database as a resource for post-GWAS interpretation of retina-associated traits including glaucoma and diabetic retinopathy. Overall design: Retinal samples from 523 aged post-mortem human subjects from a spectrum of age-related macular degeneration (AMD) were RNA-seq profiled.
Publication Title
Improved Retinal Organoid Differentiation by Modulating Signaling Pathways Revealed by Comparative Transcriptome Analyses with Development In Vivo.
Sample Metadata Fields
No sample metadata fields
View Samples- Bos taurus
- 30 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Despite much investigation, mechanisms conferring stage specific responsiveness of the corpus luteum (CL) to prostaglandin F2 (PG) are unknown. The objective of this study was to identify PG- induced changes in transcriptome of bovine CL specific to d 11 ( PG responsive) but not d 4 (PG refractory) CL associated with luteolysis. CL were collected from heifers at 0, 4 and 24 h following PG injection on d 4 and 11 of the estrous cycle (n = 5 animals/treatment) and isolated RNA labeled and hybridized to Affymetrix GeneChip Bovine Genome Arrays. At 4 and 24 h post PG respectively, 221 (d 4) and 661 (d 11) and 248 (d 4) and 1419 (d 11) regulated genes were identified.
Publication Title
Regulation of angiogenesis-related prostaglandin f2alpha-induced genes in the bovine corpus luteum.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 140 Downloadable Samples
- Affymetrix Human Gene 1.1 ST Array (hugene11st)
Description
Fibromyalgia (FM) is a common pain disorder characterized by dysregulation in the processing of pain. Although FM has similarities with other rheumatologic pain disorders, the search for objective markers has not been successful. In the current study we analyzed gene expression in the whole blood of 70 fibromyalgia patients and 70 healthy matched controls. Global molecular profiling revealed an upregulation of several inflammatory molecules in FM patients and downregulation of specific pathways related to hypersensitivity and allergy. There was a differential expression of genes in known pathways for pain processing, such as glutamine/glutamate signaling and axonal development. We also identified a panel of candidate gene expression-based classifiers that could establish an objective blood-based molecular diagnostic to objectively identify FM patients and guide design and testing of new therapies. Ten classifier probesets (CPA3, C11orf83, LOC100131943, RGS17, PARD3B, ANKRD20A9P, TTLL7, C8orf12, KAT2B and RIOK3) provided a diagnostic sensitivity of 95% and a specificity of 96%. Molecular scores developed from these classifiers were able to clearly distinguish FM patients from healthy controls. An understanding of molecular dysregulation in fibromyalgia is in its infancy; however the results described herein indicate blood global gene expression profiling provides many testable hypotheses that deserve further exploration.
Publication Title
Genome-wide expression profiling in the peripheral blood of patients with fibromyalgia.
Sample Metadata Fields
Specimen part, Disease
View Samples- Homo sapiens
- 16 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Differential expression was used to access gene differences after Entamoeba histolytica infection.
Publication Title
The expression of REG 1A and REG 1B is increased during acute amebic colitis.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 42 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Identification of genes and pathways relevant to Cervical cancer pathogenesis. The study also aimed at identifying probable mechanistic differences in the low and high HOTAIR expressing cervical cancers patients .
Publication Title
Bridging Links between Long Noncoding RNA HOTAIR and HPV Oncoprotein E7 in Cervical Cancer Pathogenesis.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 62 Downloadable Samples
- Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
We used DNA microarrays (HG-U95Av2 GeneChips) to determine gene expression profiles for kidney biopsies and peripheral blood lymphocytes (PBLs) in transplant patients. Sample classes include kidney biopsies and PBLs from patients with 1) healthy normal donor kidneys, 2) well-functioning transplants with no clinical evidence of rejection, 3) kidneys undergoing acute rejection, and 4) transplants with renal dysfunction without rejection. Nomenclature for samples is as follows: 1) all sample names include either BX or PBL to indicate that they were derived from biopsies or PBLs respectively, 2) C indicates samples from healthy normal donors, 3) TX indicates samples from patients with well-functioning transplants with no clinical evidence of rejection, 3) AR indicates samples from transplant patients with kidneys undergoing acute rejection, 4) NR indicates samples from transplant patients with renal dysfunction without rejection.
Publication Title
Kidney transplant rejection and tissue injury by gene profiling of biopsies and peripheral blood lymphocytes.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Original patient tumor is directly implanted in mice xenografts. Tumor is propagated to multiple mice for conduct of 6 arm treatment trials and control. Therapies are selected based on T0 and F0 genomic profiles.
Publication Title
Using a rhabdomyosarcoma patient-derived xenograft to examine precision medicine approaches and model acquired resistance.
Sample Metadata Fields
No sample metadata fields
View Samples