title: Fibroblast cells immediate-early after human cytomegalovirus infection

status: Public on Jul 16 2003

city: Bern

first: Marc

last: Kenzelmann

address: Friedbuhlstrasse 51

department: Molecular Genome Analysis

country: Switzerland

institute: Institute of Medical Microbiology, University of Bern

summary:
Human cytomegalovirus (HCMV) has been shown to have the potential to alter cellular gene expression early after infection. However, one-gene approaches and the use of closed system gene expression technologies have identified only few cellular genes whose activity changed immediate-early. We therefore used serial analysis of gene expression (SAGE) to investigate the transcriptional program of human fibroblasts in response to HCMV in the immediate-early phase of infection. Differential expression of various cellular genes was monitored. Transcriptional expression changes of genes coding for ribosomal proteins reflected a general cellular response to starvation and stress. But differential regulation of genes coding for transcription factors and proteins associated with cellular metabolism, homeostasis and cell structure may represent transcriptional alterations in response to HCMV infection. Expression kinetics by 5' nuclease fluorigenic real-time PCR of selected genes revealed partial protection of infected cells against initial stress-associated alterations of gene expression and indicated fluctuations of transcriptional levels over time. Additionally, agreement with the quantitative results obtained by SAGE was observed only for genes up-regulated in HCMV-infected cells. This finding pointed to various technical and statistical parameters that all may be critical for quantitative transcriptome studies using global approaches, especially when exploring biological systems in a critical phase of cellular physiology.
Keywords: other

first: M

first: K

last: Muhlemann


title: Identification of microRNA as novel circulating markers for presence of intracranial aneurysms

status: Public on Sep 14 2013

city: Jinan

first: Fan

last: Jiang

state: Shandong

address: 107 Wen Hua Xi Road

country: China

institute: Shandong University

summary: We carried out a case control study in an attempt to identify changes in circulating microRNAs in patients with intracranial aneurysms (IAs). We selected 40 cases (20 ruptured and 20 unruptured) and 20 healthy controls. We randomly selected 5 samples from each group and combined them into a sample pool. In this way we obtained 12 sample pools and one pool was used for a single microarray. Changes in microRNA levels in the plasma were surveyed with Agilent Human microRNA Microarray (Release 14.0, 8x15K). We identified 20 microRNAs that were unanimously changed in both ruptured and unruptured patients.

overall_design: We included 40 cases (20 ruptured and 20 unruptured) and 20 healthy controls. We randomly selected 5 plasma samples from each group and combined them into a sample pool. In this way we obtained 12 sample pools and one pool was used for a single microarray. Total RNA was isolated from 1 ml plasma from each sample pool and resuspended in the same volume of buffer. A fixed volume of RNA sample was used for microarray detection.

first: Peng-Xiang

last: Li

first: Qunye

last: Zhang

first: Xiao

last: Wu

first: Xinjian

last: Yang


title: Clostridium difficile CD630E: growth with 10 mM cysteine in PY vs growth in PY

status: Public on Dec 31 2013

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

summary:
Comparison of Clostridium difficile transcriptome of strain CD630E grown for 10 hours in PY (supplemented with mild concentration of cysteine) versus PYC (PY supplemented with 10 mM of cysteine).
Experimental procedure was designed to investigate the influence of cysteine on toxins production and the regulatory network involved.

overall_design:
two-conditions experiments, excess of cysteine vs mild concentration of cysteine, 4 biological replicates for each condition

Description of the supplementary files:
Main - Short description of the experiment
Result_all - All significative genes
Result_Gold* - High quality significative gene
Result_Silver** - Medium quality significative gene
All_Raw_data - All genes results significative and non significative
Design_Genes-OUT - Genes not present in the platform
Design_Genes-Oligos - Number of oligos design per gene

* Gold : Nbr significative oligos = Nbr oligos designed for this gene
** Silver : Nbr significative oligos = Nbr oligos designed for this gene -1

first: Marie

middle: B

last: Dancer-Thibonnier

last: Monot


status: Public on Jan 27 2003

city: Cambridge

first: Scott

middle: A

last: Rifkin

state: MA

address: 16 Divinity Ave

department: OEB

country: USA

institute: Harvard University

summary:
Drosophila yakuba white prepupae vs. blue gut larvae
Keywords: repeat sample

first: Junhyong

last: Kim

first: Kevin

middle: P

last: White


title: Evolution of gene expression in the Drosophila melanogaster subgroup

status: Public on Mar 05 2003

summary:
Little is known about broad patterns of variation and evolution of gene expression during any developmental process. Here we investigate variation in genome-wide gene expression among Drosophila simulans, Drosophila yakuba and four strains of Drosophila melanogaster during a major developmental transition-the start of metamorphosis. Differences in gene activity between these lineages follow a phylogenetic pattern, and 27% of all of the genes in these genomes differ in their developmental gene expression between at least two strains or species. We identify, on a gene-by-gene basis, the evolutionary forces that shape this variation and show that, both within the transcriptional network that controls metamorphosis and across the whole genome, the expression changes of transcription factor genes are relatively stable, whereas those of their downstream targets are more likely to have evolved. Our results demonstrate extensive evolution of developmental gene expression among closely related species.
Keywords: other

sample_organism:
Drosophila melanogaster
Drosophila simulans
Drosophila yakuba

first: S

first: J


title: Ebola-infected non-human primates - PBMCs

status: Public on Jun 28 2007

first: Kate

last: Rubins

address: Nine Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary:
Infection with Ebola virus (EBOV) causes a fulminant and often fatal hemorrhagic fever.  In order to improve our understanding of EBOV pathogenesis and EBOV-host interactions we have examined the molecular features of EBOV infection in vivo.   Using self-spotted cDNA microarrays, we analyzed genome-wide host expression patterns in sequential blood samples from nonhuman primates (NHP) infected with EBOV.
A reference experiement design type is where all samples are compared to a common reference.
Keywords: reference_design

sample_organism:
Macaca fascicularis
Homo sapiens

overall_design:
Ebola infection of non-human primates (cynomolgus macaques).  We took sequential samples of peripheral blood mononuclear cells (PBMC) from 15 cynomolgus macaques infected intramuscularly with 1000 plaque forming units (PFUs) of EBOV, Zaire strain. Peripheral blood samples (2.5mL) were collected on days 1, 4, or 6 prior to infection, in order to define a robust baseline, and then on successive days after infection, until death (immediately prior to euthanasia).  Animals were euthanized at days 1, 2, 3, 4, 5, and 6 postinfection.  PBMC's were collected at days post-infection as noted, preserved in Trizol, Trizol-extracted total RNA, 1 round amplified (Ambion MessageAmp I), directly labeled by Cy5 incorporation during reverse transcription of amplified RNA. Each blood sample was hybridized versus a common reference.  The same reference is used for all samples - Stratagene Universal Human Reference RNA, 1 round of amplification (Ambion MessageAmp I), directly labeled by Cy3 incorporation during reverse transcription of amplified reference RNA.  Two to three biological replicates of pre-infection samples were taken for each animal, as well as two to nine biological replicates (from different animals) at each day post-infection.  A total of 50 arrays, representing 15 animals is included in this dataset.
Using regression correlation


title: Profiling of MCF-7 cells treated with proteasome inhibitor MG132 and either dexamethasone or 17b-estradiol

status: Public on May 09 2008

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
The objective of the study was to investigate the effect of proteasome inhibition on glucocorticoid and estrogen receptor regulated gene expression.
Keywords: Transcriptional profiling, Proteasome inhibitors, gene expression, steroid receptor

overall_design: MCF-7 cells were treated with proteasome inhibitor (MG132), dexamethasone, 17b-estradiol or MG132 plus dexamethasone or MG132 plus 7b-estardiol.  Control cells were not treated.  RNA was collected from 2 biological experiments.

first: H

middle: K

last: Kinyamu

first: T

last: Archer


title: Stunned silence: gene expression programs in human cells infected with Monkeypox or Vaccinia virus

status: Public on Apr 14 2011

city: Stanford

first: Patrick

middle: O

last: Brown

state: CA

address: Beckman Center b439

department: Department of biochemistry

institute: Stanford university school of medicine

summary:
Three experiments, corresponding to the three figures in the article, are represented in this set. Each experiment was an ex vivo treatment time course as described in the paper. For each of the experiments, mRNA was isolated at the indicated time points, cDNA was directly prepared by reverse transcription in the presence of Cy5-labeled dUTP, and the expression profiled using Cy3-labeled cDNA prepared by reverse transcription of Stratagene Universal Human Reference RNA as a control.

One experiment, corresponding to Figure 1 in the paper, is a set of infection, or mock-infection time courses, in which each of three cell types: primary human dermal fibroblasts, primary human macrophages, or HELA cells were respectively infected with Monkeypox virus, Vaccinia virus, or Ebola virus, or mock-infected. Infected cells or mock-infected cells were harvested and lysed at the indicated times after infection and mRNA isolated for analysis following the protocol described above.

The second experiment, corresponding to Figure 2 in the paper, is a set of treatments of human dermal fibroblasts, each in 24-well plates with either: PBS only (mock), interferon alpha (IFN-alpha) at 0.6 pM final concentration (Sigma, St. Louis, MO), tumor necrosis factor alpha (TNF-alpha) at 0.6 pM final concentration (Sigma), PMA at 25ng/mL final concentration plus ionomycin at 1micromolar final concentration, polyinosinic-polycytidylic acid as potassium salt (poly(I-C)) at 100 microg/mL final concentration (Sigma), Escherichia coli 055:B5 lipopolysaccharide (LPS) at 1microg/mL final concentration (Sigma), or dexamethasone at 1 micromolar final concentration (Sigma). Cells were harvested and lysed at the indicated times and mRNA isolated for analysis following the protocol described above.

The third experiment, corresponding to Figure 3 in the paper, is a set of infections or mock-infections of human dermal fibroblasts, or human primary macrophages, with Monkeypox virus or Vaccinia virus, respectively, followed by treatment with either ionomycin + phorbol myristic acid (PMA) or with poly(I-C). The intention of the experiment was to investigate whether prior infection altered the response of the cells to the chemical agents. Cells were harvested and lysed at the indicated times and mRNA isolated for analysis following the protocol described above.

Description of sample characteristics:
Time: Time after infection or Mock infection
Infection: Ebola-Zaire/killed Monkeypox Virus/Mock infection/Monkaypox Virus/None/Pre infection/Vaccinia NY/Vaccinia WR
Compound Based Treatment: Dexamethasone/Interferon-alpha/Ionomycin + PMA/LPS/PBS/polyinosinic-polycytidylic acid/TNF-alpha
Cell Type: Primary Human Dermal Fibroblast/Primary Human Macrophage/HeLa
Figure in article: Numbers group slides that are represented in the same figure of the article.

overall_design: A stimulus or stress experiment design type is where that tests response of an organism(s) to stress/stimulus. e.g. osmotic stress, behavioral treatment


title: Pre-symptomatic diagnosis of Ebola virus infection

status: Public on Jun 14 2016

city: Seattle

first: Krupa

middle: Arun

last: Navalkar

state: WA

address: 401 Terry Avenue North

institute: Institute for Systems Biology

type:
Expression profiling by array
Third-party reanalysis

summary: Normalized Gene expression data used for meta-analysis from studies: GSE31747, GSE8317, GSE24943, GSE24125. We studied the changes in macaque and human peripheral blood cell gene expression after infection with Ebola Zaire virus (EBZ) to identify host responses that occur before the emergence of symptoms. We integrated data from in vivo and in vitro infection studies of macaque or human peripheral blood. We identified mRNAs that were differentially expressed at early, middle, and late times after infection. The EBZ early genes showing increased or decreased expression were then compared to literature-derived host responses to malaria, rhinovirus and influenza virus which identified the patterns unique to each pathogen. From the group of EBZ-specific genes, we next predicted those that encoded secreted or membrane-associated proteins. Pairs of these host response mRNAs or proteins could become candidates for differential diagnosis of an early EBZ infection, before the emergence of conventional symptoms. Four key immune response pathways that were activated early showed profoundly decreased expression at late times.

sample_organism:
Macaca fascicularis
Macaca mulatta
Homo sapiens

overall_design:
GSE8317: The ‘VALUE’ column in .txt files which is the log2 ratio of Cy5-Treatment/Cy3-Control is imported into the analysis software after median baselining.
GSE24943: Lowess normalization was applied to the ratio of Cy5-Treatment/Cy3-Control samples and imported into the analysis software after median baselining.
GSE31747: Affymetrix Human Genome U95 Version 2 Array .CEL datafiles were RMA summarized, quantile normalized and median baselined for import into the analysis software.
GSE24125: Lowess normalization was applied to the ratio of Cy5-Treatment/Cy3-Control samples and imported into the analysis software after median baselining.

first: Taek-Kyun

first: Richard

last: Gelinas


title: Early transcriptional responses of Arabidopsis thaliana to ammonium and nitrate deprivation

status: Public on May 31 2016

city: Stuttgart

first: Jochen

last: Menz

address: Fruwirthstr. 20

department: Institute of Crop Science

country: Germany

institute: University of Hohenheim

summary: Identification of the earliest transcriptional responses of adult Arabidopsis plant roots towards N-deprivation. Hydroponically grown Plants (35 days old) were 5 days adapted to nitrate or ammonium,respectively, as sole N-source to detect N-form specific transcripts.

overall_design: 24 Samples: 2 Pre-Treatments (5 Day adaptation to 3mM Ammonium/Nitrate) x 3 sampling time-points (0min, 15 min, 180 min) x 3 independent replications per time-point + 6 additional controls (2 x 15min, 1x 180min per Pre-Treatment)

first: Uwe

last: Ludewig


title: Liver Pharmacology and Xenobiotic Response Repertoire

status: Public on Mar 28 2008

city: Mountain View

first: Jeremy

last: Gollub

address: 325 E. Middlefield Rd.

institute: Iconix Biosciences

summary:
A definition of RNA expression changes that correlate with liver response programs and an understanding of the similarities and differences in responses to different classes of chemicals would aid in new chemical or drug characterization and add to our understanding of liver biology. We have used a supervised classification approach to systematically mine a large microarray database derived from livers of compound-treated rats.  Thirty-four distinct signatures (classifiers) for pharmacological and toxicological endpoints resolvable by gene expression can be identified. The contribution of genes to signatures is not correlated to average expression or amplitude of regulation, and pre-selection of genes can significantly reduce signature performance. Just 200 genes are sufficient to classify all endpoints and can form the basis of a small diagnostic array useful in toxicogenomics.  Signature genes were enriched in xenobiotic and acute phase response genes as well as un-annotated genes, suggesting that not all key genes in liver xenobiotic responses have been identified. Individual signatures can be re-derived up to 25 times from a gene set cyclically .stripped. of the signature genes. The union of these non-overlapping sets was used to describe the biological mechanisms of liver fibrosis.

Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf
Keywords: dose response, time course, compound treatment

overall_design: Treatment of male Sprague-Dawley rats with 344 compounds at various doses and durations, in biological triplicate, along with vehicle-matched control animals.  Liver samples were assayed for gene expression.  A total of 1695 samples were hybridized to single-channel CodeLink RU1 arrays.  Biological triplicates were combined with matched control samples to calculate log ratios.  Classifiers were generated and evaluated for 2112 biological questions, resulting in 34 distinct, high-performance "signatures."

first: Georges

last: Natsoulis

first: Cecelia

middle: I

last: Pearson

first: Barray

last: Eynon

first: Joe

last: Ferng

first: Ramesh

last: Nair

first: Radha

last: Idury

first: May

last: Lee

first: Mark

last: Fielden

last: Brennan

first: Alan

last: Roter

first: Kurt

last: Jarnagin