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E-MEXP-70
Homo sapiens
6 Downloadable Samples
Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
Gene expression profile of primary human CD34+/CD38lo cells differentiating along the megakaryocyte lineage.
Publication Title
Gene expression profile of primary human CD34+CD38lo cells differentiating along the megakaryocyte lineage.
Sample Metadata Fields
Specimen part, Time
View Samples- Homo sapiens
- 24 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
To identify epigenetically silenced genes in multiple myeloma (MM) cell lines and to determine the effects of 5-aza-2-deoxycytidine and trichostatin A on gene expression. We treated 3 multiple myeloma cell lines (MM1, NCI-H929, U266) with 5-aza-2-deoxycytidine and/or trichostatin A.
Publication Title
Genome-wide transcriptional response to 5-aza-2'-deoxycytidine and trichostatin a in multiple myeloma cells.
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples- Homo sapiens
- 107 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Tobacco smoking is responsible for over 90% of lung cancer cases, and yet the precise molecular alterations induced by smoking in lung that develop into cancer and impact survival have remained obscure. We performed gene expression analysis using HG-U133A Affymetrix chips on 135 fresh frozen tissue samples of adenocarcinoma and paired noninvolved lung tissue from current, former and never smokers, with biochemically validated smoking information. ANOVA analysis adjusted for potential confounders, multiple testing procedure, Gene Set Enrichment Analysis, and GO-functional classification were conducted for gene selection. Results were confirmed in independent adenocarcinoma and non-tumor tissues from two studies. We identified a gene expression signature characteristic of smoking that includes cell cycle genes, particularly those involved in the mitotic spindle formation (e.g., NEK2, TTK, PRC1). Expression of these genes strongly differentiated both smokers from non-smokers in lung tumors and early stage tumor tissue from non-tumor tissue (p<0.001 and fold-change>1.5, for each comparison), consistent with an important role for this pathway in lung carcinogenesis induced by smoking. These changes persisted many years after smoking cessation. NEK2 (p<0.001) and TTK (p=0.002) expression in the noninvolved lung tissue was also associated with a 3-fold increased risk of mortality from lung adenocarcinoma in smokers. Our work provides insight into the smoking-related mechanisms of lung neoplasia, and shows that the very mitotic genes known to be involved in cancer development are induced by smoking and affect survival. These genes are candidate targets for chemoprevention and treatment of lung cancer in smokers.
Publication Title
Gene expression signature of cigarette smoking and its role in lung adenocarcinoma development and survival.
Sample Metadata Fields
Sex, Age
View Samples- Sus scrofa
- 79 Downloadable Samples
Illumina HiSeq 2500
Description
Boar taint (BT) is an offensive odour or taste observed in pork from a proportion of non-castrated male pigs. Surgical castration is effective in avoiding BT, but animal welfare issues have created an incentive for alternatives such as genomic selection. In order to find candidate biomarkers, gene expression profiles were analysed from tissues of non-castrated pigs grouped by their genetic merit of BT. Differential expression analysis revealed substantial changes with log-transformed fold changes of liver and testis from -3.39 to 2.96 and -7.51 to 3.53, respectively. Co-expression network analysis revealed one module with a correlation of -0.27 in liver and three modules with correlations of 0.31, -0.44 and -0.49 in testis. Differential expression and co-expression analysis revealed candidate biomarkers with varying biological functions: phase I (COQ3, COX6C, CYP2J2, CYP2B6, ACOX2) and phase II metabolism (GSTO1, GSR, FMO3) of skatole and androstenone in liver to steroidgenesis (HSD17B7, HSD17B8, CYP27A1), regulation of steroidgenesis (STARD10, CYB5R3) and GnRH signalling (MAPK3, MAP2K2, MAP3K2) in testis. Overrepresented pathways included “Ribosome”, “Protein export” and “Oxidative phosphorylation” in liver and “Steroid hormone biosynthesis” and “Gap junction” in testis. Future work should evaluate the biomarkers in large populations to ensure their usefulness in genomic selection programs. Overall design: Total RNA was extracted from liver and testis of 48 Danish Landrace pigs with low- medium and high genetic merit of boar taint and sequenced by Illumina HiSeq 2500.
Publication Title
Systems genomics study reveals expression quantitative trait loci, regulator genes and pathways associated with boar taint in pigs.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 30 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Numerous studies have established a critical role for BMP signaling in skeletal development. In the developing axial skeleton, sequential SHH and BMP signals are required for specification of a chondrogenic fate in somitic tissue. A similar paradigm is thought to operate in the limb, but the signals involved are unclear. To investigate the nature of these signals we examined BMP action in mesenchymal populations derived from the early murine limb bud (~ E10.5). These populations exhibited a graded response to BMPs, in which early limb mesenchymal (EL) cells (from the distal hind limb) displayed an anti-chondrogenic response, whereas BMPs promoted chondrogenesis in older cell populations. To better understand the molecular basis of disparate BMP action in these various populations, gene expression profiling with Affymetrix microarrays was employed to identify BMP-regulated genes. These analyses showed that BMPs induced a distinct gene expression pattern in the EL cultures versus later mesenchymal limb populations (IM and LT).
Publication Title
Regulation of BMP-dependent chondrogenesis in early limb mesenchyme by TGFbeta signals.
Sample Metadata Fields
Specimen part
View Samples- Bos taurus
- 40 Downloadable Samples
- Illumina Genome Analyzer II
Description
Rift Valley Fever Virus (RVFV), a negative-stranded RNA virus, is the etiological agent of the vector-borne zoonotic disease, Rift Valley Fever (RVF). In both humans and livestock, protective immunity can be achieved through vaccination. Earlier and more recent vaccine trials in cattle and sheep demonstrated a strong neutralizing antibody and total IgG response induced by the RVFV vaccine, MP-12. From previous work, protective immunity in sheep and cattle vaccinates normally occurs from 7 to 21 days after inoculation with MP-12. While the serology and protective response induced by MP-12 has been studied, little attention has been paid to the underlying molecular and genetic events occurring prior to the serologic immune response. To address this, we isolated RNA from whole blood from vaccinates over a time course of 21 days before and after inoculation during a recent vaccine trial with MP-12. This RNA time course was deeply sequenced by RNASeq and bioinformatically analyzed. Our results revealed time-dependent activation or repression of numerous gene ontologies and pathways related to immune response and regulation. Additional analyses identified a correlative relationship between specific genes related to immune activity and protective immunity prior to serologic detection of antibody response. These data provide an important proof of concept for identifying molecular and genetic components underlying the immune response to vaccination and protection prior to serologic detection. Overall design: Experimental Animals: Healthy, 4 – 6 month old Bos taurus heifer and steer calves were used in the present study. The calves were seronegative to both bovine viral diarrhea and bovine leukemia virus by antigen capture enzyme-linked immunosorbent assay (ELISA) analyses done at the Texas Veterinary Medical Diagnostic Laboratory, College Station, Texas and had no detectable neutralizing antibodies to RVFV by PRNT80 at the time of vaccination. The animal experiments were performed under an Institutional Animal Care and Use Committee approved protocol #2010-192. Vaccines: The authentic recombinant MP-12 (MP12) is an attenuated RVFV vaccine prepared for use in humans by the U. S. Army Medical Research Institute of Infectious Diseases. Vaccines were propagated and prepared at University of Texas Medical Branch in Galveston, TX. Experimental Design: The calves were housed in an ABSL2 Ag biocontainment facility where they were randomized into test groups and acclimated to the facility for 14 days. Animals were inoculated either subcutaneously (s.c.) or intramuscularly (i.m.) with 1x105 PFU of MP-12 (3 animals in each group). Whole blood was collected prior to inoculation on Days 0 through 7, 10, 14, 21 and preserved for serum neutralization studies (PRNT) or total RNA purification for RNASeq analysis. Experimentally determined PRNT values were used to determine the “serologic response status” for animals “unvaccinated”, “vaccinated, not protected”, or “vaccinated, protected” with animals having a serum dilution ration of >1:80 being considered protected. Only RNA samples that met the minimum quality and quantity thresholds were used for the sequencing analysis. Rectal temperatures were recorded each time blood was collected and their health status was documented daily. At the end of the respective studies, the calves were euthanized with pentobarbital sodium (120 mg/kg i.v.). All calves were healthy and clinically normal at the termination of the respective studies. Morrill, John C., Richard C. Laughlin, Nandadeva Lokugamage, Jing Wu, Roberta Pugh, Pooja Kanani, L. Garry Adams, Shinji Makino, C. J. Peters. Immunogenicity of a Recombinant Rift Valley Fever MP-12 Vaccine Candidate in Calves. Vaccine. 2013. doi:10.1016/j.vaccine.2013.08.003. 238. Morrill, John C., Richard C. Laughlin, Nandadeva Lokugamage, Roberta Pugh, Elena Sbrana, William J. Weise, L. Garry Adams, Shinji Makino and C. J. Peters.. Safety and Immunogenicity of Recombinant Rift Valley Fever MP-12 Vaccine Candidates in Sheep. Vaccine 10.1016/j.vaccine.2012.10.118, 2012.
Publication Title
Correlative Gene Expression to Protective Seroconversion in Rift Valley Fever Vaccinates.
Sample Metadata Fields
Specimen part, Subject, Time
View Samples- Mus musculus
- 18 Downloadable Samples
- Illumina HiSeq 2500
Description
We characterize the gene expression changes which occur in the mouse glomerular podocyte, mesangial, and endothelial cells between control mice and mutant mice which are missing two copies of Fyn-proto oncogene (Fyn) and one copy of CD2-associated protein (CD2AP) in a mouse model of FSGS. Overall design: The glomeruli are purified by digestion with Collagenase A and sieving, a single cell suspension is generated via enzymatic dissociation; the single cell suspension is then FACS sorted based on GFP-fluorescence (targeting the glomerular endothelial, mesangial, and podocyte cells). Total RNA was purified using a column-based system. RNA was then quantitatively and qualitatively analyzed using an agilent bioanalynzer, cDNA libraries were generated using Nugen Ovation RNA-Seq V2, and the resulting libraries were ran on an Illumina HiSeq 2500. Data was analyzed using Strand NGS version 2.6.
Publication Title
A bigenic mouse model of FSGS reveals perturbed pathways in podocytes, mesangial cells and endothelial cells.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 16 Downloadable Samples
- IlluminaHiSeq1000
Description
We hypothesize that the observed differences in incidences of pleural and peritoneal malignant mesothelioma (MM) are the result of differences in the direct response of these cell types to asbestos rather than to differences mediated by the in vivo microenvironment. To test this hypothesis, we characterized cellular responses to asbestos in a controlled environment using high-throughput RNA sequence and other assays. Overall design: Examination of asbestos-treated versus untreated mesothelial cells from four cell lines representing two tissue types in culture.
Publication Title
Differential Susceptibility of Human Pleural and Peritoneal Mesothelial Cells to Asbestos Exposure.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 15 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
We generated whole genome expression profiles from a homogeneous population of purified pacemaker neurons (ventral Lateral Neurons, LNvs) from wild type and clock mutant Drosophila. The study identifes a group of genes whose expression is highly enriched in LNvs compared to other neurons; and a second group of genes rhythmically expressed in LNvs in a clock-dependent manner.
Publication Title
A mechanism for circadian control of pacemaker neuron excitability.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Interleukin (IL)-17 plays an important and protective role in host defence and has been demonstrated to orchestrate airway inflammation by cooperating with and inducing proinflammatory cytokines. Mircoarrays were used to identify immediate-early/ primary response IL-17A-dependent gene transcripts in primary human bronchial ASM cells from mild asthmatic and healthy individuals.
Publication Title
IL-17A mediates a selective gene expression profile in asthmatic human airway smooth muscle cells.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment, Subject, Time
View Samples