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Homo sapiens
8 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The aim of the study was to identify in vivo spermatogonial gene expression within the context of their biological niche.
Publication Title
Screening for biomarkers of spermatogonia within the human testis: a whole genome approach.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
The neuronal ceroid lipofuscinoses (NCL) are a group of childhood inherited neurodegenerative disorders characterized by blindness, early dementia and pronounced cortical atrophy. The similar pathological and clinical profiles of different forms of NCL suggest that common disease mechanisms may be involved. Here, we have performed quantitative gene expression profiling of cortex from targeted knock out mice produced for Cln1 and Cln5 to explore NCL-associated molecular pathways. Combined microarray datasets from both mouse models exposed a common affected pathway: genes regulating cytoskeletal dynamics and neuronal growth cone stabilization display similar aberrations. We analyzed locus specific gene expression and showed regional clustering of Cln1 and three major genes of this pathway, further supporting a close functional relationship between the corresponding gene products, Cap1, Ptprf and Ptp4a2. The evidence from the gene expression data was substantiated by immunohistochemical staining data of Cln1-/- and Cln5-/- cortical neurons. These primary neurons displayed abnormalities in beta-tubulin and actin as well as abnormal intracellular distribution of growth cone associated proteins GAP-43, synapsin and Rab3. Our data provide the first evidence for a common molecular pathogenesis behind neuronal degeneration in CLN1 and CLN5. Since CLN1 and CLN5 code for proteins with distinct functional roles these data may have implications for other forms of NCL.
Publication Title
Brain gene expression profiles of Cln1 and Cln5 deficient mice unravels common molecular pathways underlying neuronal degeneration in NCL diseases.
Sample Metadata Fields
Sex, Age, Specimen part, Disease
View Samples- Mus musculus
- 8 Downloadable Samples
Illumina HiSeq 2500
Description
Injured skeletal muscle regenerates, but with age or in muscular dystrophies, muscle is replaced by fat. Upon injury, muscle-resident fibro/adipogenic progenitors (FAPs) proliferated and gave rise to adipocytes. These FAPs dynamically produced primary cilia, structures that transduce intercellular cues such as Hedgehog (Hh) signals. Genetically removing cilia from FAPs inhibited intramuscular adipogenesis, both after injury and in a mouse model of Duchenne muscular dystrophy. Blocking FAP ciliation also enhanced myofiber regeneration after injury and reduced myofiber size decline in the muscular dystrophy model. Hh signaling through FAP cilia regulated the expression of TIMP3, a secreted metalloproteinase inhibitor, that inhibited MMP14 to block adipogenesis. A pharmacological mimetic of TIMP3 blocked the conversion of FAPs into adipocytes, pointing to a strategy to combat fatty degeneration of skeletal muscle. We conclude that ciliary Hh signaling by FAPs orchestrates the regenerative response to skeletal muscle injury. Overall design: Transcriptomic profiling using RNAseq was performed on RNA derived from a bipotent, progenitor cell population, called fibro/adipogenic progenitors (FAPs), purified from tibialis anterior muscle 3 days post glycerol injury. Two populations of cells were sequenced, one from wild type muscle (FAP-ctrl) and another from cells in which cilia, using a floxed Ift88 allele, were conditionally deleted (FAP-no cilia). A total of five FAP-ctrl and 3 FAP-no cilia samples were used. The TruSeq Stranded Total RNA Library Prep Kit (Ilumina) was used to generate the library, which was subsequently sequenced using an Illumina 2500 SE 50bp platform and aligned to the GRCm38.78 whole genome using STAR RNAseq aligner. Individual read counts were normalized to the geometric mean read count across all samples using DEseq. Sequencing yielded ~314 million total reads with an average read depth of ~34.9 million reads per sample.
Publication Title
Ciliary Hedgehog Signaling Restricts Injury-Induced Adipogenesis.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples
GSE27568- Mus musculus
- 16 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Analysis of Ubb knockout mouse testes at 7, 4, 21, and 28 dpp. Ubiquitin (Ub) is an essential protein found in all eukaryotic cells and plays important roles in a variety of cellular functions including germ cell development. Targeted disruption of the polyubiquitin gene Ubb results in male and female infertility in mice with germ cells arrested at meiotic prophase I.
Publication Title
Altered testicular gene expression patterns in mice lacking the polyubiquitin gene Ubb.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
This study examined the gene expression effects of treating androgen-deprived C4-2 prostate cancer cells with the ACLY inhibitor BMS-303141 and the AR antagonist enzalutamide. Overall design: Cells were treated with vehicle control, ACLY inhibitor alone, Enzalutamide alone, and ACLY-inhibitor and Enzalutamide combined together for 24 hours under androgen-depleted conditions (RPMI + 5% charcoal stripped serum). Biological triplicate samples were prepared.
Publication Title
Targeting ACLY sensitizes castration-resistant prostate cancer cells to AR antagonism by impinging on an ACLY-AMPK-AR feedback mechanism.
Sample Metadata Fields
Subject
View Samples- Mus musculus
- 13 Downloadable Samples
- Illumina HiSeq 2500
Description
The goals of this study is to test whether NICD presence protects the RBPjk-null Hair Follicles by altering gene expression via association with other DNA binding proteins at P3, just before the conversion to TSLP-producing keratin cysts. Overall design: Methods: Skin samples were embedded in OCT. Sectioned at 20µm thickness. Dehydrated in EtOH, and equilibrated to Xylene before the LCM procedure. Laser capture was performed with Arcturus Veritas. Methods: ~100 hair follicles from Notch-null, PS-null, RBPjk-null and wild-type samples were pooled into 3 biological replicates for each genotype and subjected to RNA isolation followed by RNA-Seq. Conclusions: A total of 2047 genes were differentially expressed (=1.5 fold) in three or more biological replicates of Notch mutant hair follicles compared to wild-type controls (p-value<0.05). Unsupervised hierarchical clustering analysis failed to distinguish between the mutants.
Publication Title
The Notch Intracellular Domain Has an RBPj-Independent Role during Mouse Hair Follicular Development.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Notch1 deficient hair matrix keratinocytes have lower mitotic rates, resulting in smaller follicles with fewer cells. In addition, the ratio of melanocytes to keratinocytes is greatly reduced. Microarray was performed to study downstream mechanism of Notch1-deficiency
Publication Title
Bi-compartmental communication contributes to the opposite proliferative behavior of Notch1-deficient hair follicle and epidermal keratinocytes.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
To determine if RU-486 would be effective as a chemopreventive agent, microarrays were used to analyse global gene expression changes in wild-type vs. MMTV-PAX8PPARg mice to determine their differential response to RU486
Publication Title
The chemopreventive effect of mifepristone on mammary tumorigenesis is associated with an anti-invasive and anti-inflammatory gene signature.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Danio rerio
- 18 Downloadable Samples
- NextSeq 500
Description
Low incubation temperature during early development negatively affects survival and related innate immune processes in zebrafish larvae exposed to lipopolysaccharide Overall design: Zebrafish embryos were collected from 28 °C, and divided into three temperature groups (24 °C, 28 °C, 32 °C) for incubation. At the first-feeding stage, larvae from each incubation temperature group were further split into three temperature groups in a full-factorial way for LPS challenge. In total, nine temperature groups (three incubation temperatures x three challenge temperatures) were generated. At 24 h post LPS challenge, mortality of larvae were recorded. Larvae originating from 24 °C incubation temperature group had higher mortality rate than larvae from the other two temperature groups. LPS-treated larvae from three temperature groups, incubation 24 °C x challenge 24 °C, incubation 24 °C x challenge 32 °C, and incubation 32 °C x challenge 24 °C, together with their respective control were chosen for transcriptomic analyses using mRNA sequencing. A total of 722 genes were determined differentially expressed (DEGs) by DESeq2 (adjusted p-value < 0.05) in LPS-challenged larvae compared to control, and 605 of them had a fold change greater than 1.5, including 294 DEGs (144 up-/150 down-regulated) in larvae incubated and challenged with LPS at 24 °C; 33 DEGs (20 up-/13 down-regulated) in larvae incubated at 32 °C and challenged at 24 °C; and 278 DEGs (190 up-/88 down-regulated) in larvae incubated at 24 °C and challenged at 32 °C. Larvae incubated and challenged with LPS at 24 °C had stimulated innate immune response compared to control, while they also showed down-regulated innate immune processes and genes. In larvae incubated at 32 °C and challenged at 24 °C, the innate immune processes were up-regulated in larvae exposed to LPS compared to control, and theses processes were even much stronger (with higher enrichment values) than larvae from incubation and challenge temperature of 24 °C. In larvae incubated at 24 °C and challenged with LPS at 32 °C, limited innate immune response were up-regulated, and additional hypoxia and oxidative processes were observed. Genes annexin A2a, S100 calcium binding protein A10b, and lymphocyte antigen-6, epidermis were identified as promising candidates for LPS recognition and signal transduction.
Publication Title
Low incubation temperature during early development negatively affects survival and related innate immune processes in zebrafish larvae exposed to lipopolysaccharide.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Lacciac Acid A was indentified as an inhibitor of DMNT1. MCF-7 cells were treated with Lacciac Acid A (200 uM) for 5 days. Changes in gene expression were identified by using Affymetrix Human gene ST1.0 arrays. We used microarrays to determine global changes in gene expression upon treatment with Lacciac Acid A an inhibitor of DMNT1.
Publication Title
Laccaic acid A is a direct, DNA-competitive inhibitor of DNA methyltransferase 1.
Sample Metadata Fields
Specimen part
View Samples