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GSE2835
Homo sapiens
12 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
Purpose. How vitamin A contributes to the maintenance of the wet-surfaced phenotype at the ocular surface is not well understood. We sought to identify vitamin A responsive genes in ocular surface epithelia using gene microarray analysis of cultures of a human conjunctival epithelial cell line (HCjE) grown with all-trans-retinoic acid (RA). The analysis showed that the membrane-associated mucin MUC16 was induced by RA and that secretory phospholipase A2 Group IIA (sPLA2-IIA), the gene most upregulated by RA, was induced earlier. Since eicosanoids, metabolites of arachidonic acid, which is produced by sPLA2 catalysis of membrane phospholipids, have been demonstrated to affect mucin production, we sought to determine if the sPLA2 induction in HCjE cells was associated with RA induction of MUC16.
Publication Title
Effect of retinoic acid on gene expression in human conjunctival epithelium: secretory phospholipase A2 mediates retinoic acid induction of MUC16.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 24 Downloadable Samples
Illumina HiSeq 2000
Description
The heat shock response (HSR) is a mechanism to cope with proteotoxic stress by inducing the expression of molecular chaperones and other heat shock response genes. The HSR is evolutionarily well conserved and has been widely studied in bacteria, cell lines and lower eukaryotic model organisms. However, mechanistic insights into the HSR in higher eukaryotes, in particular in mammals, are limited. We have developed an in vivo heat shock protocol to analyze the HSR in mice and dissected heat shock factor 1 (HSF1)-dependent and -independent pathways. Whilst the induction of proteostasis-related genes was dependent on HSF1, the regulation of circadian function related genes, indicating that the circadian clock oscillators have been reset, was independent of its presence. Furthermore, we demonstrate that the in vivo HSR is impaired in mouse models of Huntington's disease but we were unable to corroborate the general repression of transcription after a heat shock found in lower eukaryotes. Overall design: RNA-Seq was performed on mRNA isolated from quadriceps femoris muscle of 24 mice. These mice were of wild type, R6/2, and Hsf1-/- genotypes. Two mice of each genotype were tested in four conditions: (1) heat shock, (2) control heat shock, (3) HSP90 inhibition (NVP-HSP990), and (4) HSP90 inhibition vehicle.
Publication Title
HSF1-dependent and -independent regulation of the mammalian in vivo heat shock response and its impairment in Huntington's disease mouse models.
Sample Metadata Fields
Age, Specimen part, Treatment, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
Examining changes in expression in a mouse model of SBMA compared to WT littermates. Overall design: Mice sacrificed at 14wks of age had LABC isolated and cDNA generated and sequenced on an illumina platform.
Publication Title
Androgen receptor polyglutamine expansion drives age-dependent quality control defects and muscle dysfunction.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 33 Downloadable Samples
- IlluminaHiSeq2500
Description
There is a need for reliable prognostic markers that can guide therapeutic intervention in Crohn’s disease (CD). We examined whether different behavioral phenotypes in CD can be classified based on colonic miRNA or mRNA expression and if miRNAs have prognostic utility for CD. We perform high-throughput sequencing of small RNA and mRNA isolated from colon tissue from CD patients and non-IBD (NIBD) controls. To identify miRNA and genes associated with specific behavioral phenotypes of CD, patients were stratified according to disease behavior (non-stricturing, non-penetrating; stricturing; penetrating) and compared miRNA profiles in each class with those of the NIBD group. Using a novel statistical simulation approach applied to colonic RNA-seq data for CD patients and NIBD controls, we identify at drivers of gene expression profiles associated with CD. Overall design: Macroscopically non-inflamed colon tissue from well-characterized Crohn''s disease patients and normal controls were obtained. Small RNA-seq and RNA-seq were performed on these samples. Additionally, we investigated the effect of inflammation on miRNA expression by performing small RNA-seq on matched colon samples obtained from macroscopically inflamed regions from a subset (six) of these patients with Crohn''s Disease.
Publication Title
MicroRNAs Classify Different Disease Behavior Phenotypes of Crohn's Disease and May Have Prognostic Utility.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 24 Downloadable Samples
- Illumina Genome Analyzer IIx, Illumina HiSeq 2000
Description
Transcriptional dysregulation is an early feature of Huntington''s disease (HD). We observed gene-specific changes in H3K4me3 at transcriptionally repressed promoters in R6/2 mouse and human HD brain. Genome-wide analysis showed a novel chromatin signature for this mark. Reducing the levels of the H3K4 demethylase SMCX/Jarid1c in primary neurons reversed down-regulation of key neuronal genes caused by mutant Huntingtin (Htt) expression. Finally, reduction of SMCX/Jarid1c in primary neurons from BACHD mice or the single Jarid1 in a Drosophila HD model was protective. Therefore, targeting this epigenetic signature may be an effective strategy to ameliorate the consequences of HD. Overall design: mRNA-seq in wild type and R6/2 cortex and striatum at 8 and 12 weeks.
Publication Title
Targeting H3K4 trimethylation in Huntington disease.
Sample Metadata Fields
Age, Specimen part, Subject
View Samples- Homo sapiens
- 74 Downloadable Samples
- NextSeq 500
Description
In a cross-site study we evaluated the performance of ribosomal RNA removal kits from Illumina, Takara/Clontech, Kapa Biosystems, Lexogen, New England Biolabs and Qiagen on intact and degraded RNA samples. We found that all of the kits were capable of performing significant ribosomal depletion, though there were differences in their ease of use. All kits were able to remove ribosomal RNA to below 20% with intact RNA and identify ~14,000 protein coding genes from the Universal Human Reference RNA sample at >1FPKM. Analysis of differentially detected genes among kits suggested that transcript length may be a key factor in library production efficiency. These results provide a roadmap for labs on the strengths of each of these methods and how best to utilize them. Overall design: The Universal Human Reference RNA (Agilent) was diluted to 500 ng/ul in 200ul of RNase-free water and 3.94ul of the Spike-in RNA Variant Control E2 Mix (Lexogen) were added. The sample was split into two aliquots, one of which was then heated at 94° C for 1 hour and 27 minutes. 1ul of ERCC RNA Spike-In Mix 1 was added to both the intact and degraded samples. The final intact and degraded RNA samples were then diluted to 25 ng/uL and were distributed to each of the ten genomics core facilities (members of ABRF) for ribo-depletion and library preparation following vendor protocol. Each site prepared between one and four library types. Indices were assigned by the group to prevent overlapping among libraries. Libraries were pooled at an equimolar concentration from each kit using site-specific quantification and pooling SOPs and return each pool along with individual un-pooled libraries to the designated sequencing site. The sequencing site quantified each pool, multiplexed and sequenced over three high output paired-end 75bp runs on the Illumina NextSeq 500. contributor: The Association of Biomolecular Resource Facilities (ABRF) DNA Sequencing Research Group (DSRG) members
Publication Title
Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 95 Downloadable Samples
- Affymetrix Human Gene 2.1 ST Array (hugene21st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Integrative Genomics Identifies Novel Associations with APOL1 Risk Genotypes in Black NEPTUNE Subjects.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 41 Downloadable Samples
- Affymetrix Human Gene 2.1 ST Array (hugene21st)
Description
Glomerular expression data from human kidney biopsy in African American subjects with glomerulopathies
Publication Title
Integrative Genomics Identifies Novel Associations with APOL1 Risk Genotypes in Black NEPTUNE Subjects.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 42 Downloadable Samples
- Affymetrix Human Gene 2.1 ST Array (hugene21st)
Description
Tubulointersitial expression data from human kidney biopsy in African American subjects with glomerulopathies
Publication Title
Integrative Genomics Identifies Novel Associations with APOL1 Risk Genotypes in Black NEPTUNE Subjects.
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 60 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
To gain insight in the kinetics and interplay of the predominant transcriptional responses of DNA damage signalling pathways in undifferentiated cells, mouse embryonic stem cells were exposed to cisplatin at four different time points (2, 4, 8 and 24 hr) and concentrations (1, 2, 5 and 10 uM). RNA was isolated and subjected to genome-wide expression profiling.
Publication Title
A portrait of cisplatin-induced transcriptional changes in mouse embryonic stem cells reveals a dominant p53-like response.
Sample Metadata Fields
Specimen part, Compound, Time
View Samples