title: Transcriptome profiling in human primary mitochondrial respiratory chain disease

status: Public on Jul 01 2013

city: Philadelphia

first: Marni

middle: J

last: Falk

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics/ Human Genetics

institute: CHOP

summary:
Primary mitochondrial respiratory chain (RC) diseases are heterogeneous in etiology and manifestations but collectively impair cellular energy metabolism.  To identify a common cellular response to RC disease, systems biology level transcriptome investigations were performed in human RC disease skeletal muscle and fibroblasts.  Global transcriptional and post-transcriptional dysregulation in a tissue-specific fashion was identified across diverse RC complex and genetic etiologies.  RC disease muscle was characterized by decreased transcription of cytosolic ribosomal proteins to reduce energy-intensive anabolic processes, increased transcription of mitochondrial ribosomal proteins, shortened 5'-UTRs to improve translational efficiency, and stabilization of 3'-UTRs containing AU-rich elements.  These same modifications in a reversed direction typified RC disease fibroblasts.  RC disease also dysregulated transcriptional networks related to basic nutrient-sensing signaling pathways, which collectively mediate many aspects of tissue-specific cellular responses to primary RC disease.  These findings support the utility of a systems biology approach to improve mechanistic understanding of mitochondrial RC disease.
To identify a common cellular response to primary RC that might improve mechanistic understanding and lead to targeted therapies for human RC disease, we performed collective transcriptome profiling in skeletal muscle biopsy specimens and fibroblast cell lines (FCLs) of a diverse cohort of human mitochondrial disease subjects relative to controls.  Systems biology investigations of common cellular responses to primary RC disease revealed a collective pattern of transcriptional, post-transcriptional and translational dysregulation occurring in a highly tissue-specific fashion.

overall_design: Affymetrix Human Exon 1.0ST microarray analysis was performed on 29 skeletal muscle samples and Fibroblast cell lines from mitochondrial disease patients and age- and gender-matched controls.

first: Zhe

last: Zhang


title: Expression data from wildtype and mec-3 mutant PVD/OLL sensory neurons in C. elegans

status: Public on May 02 2013

city: Nashville

first: William

middle: Clay

last: Spencer

state: TN

address: 465 21st Ave S

department: Cell & Developmental Biology

country: USA

institute: Vanderbilt University

type: Expression profiling by genome tiling array

summary: Nociceptive neurons develop a complex dendritic arbor to sense noxious stimuli, which enables animals to react to environmental insults and perform self-protective behaviours. The genetic programs controlling neuronal dendritic morphogenesis are poorly understood. In C. elegans, the PVD sensory neuron generates a complex dendritic arbor that envelops the body of the animal. This nociceptive neuron enables study of dendrite formation in vivo. MEC-3 is a transcription factor expressed in the PVD neuron (Chatzigeorgiou et al., 2010; Li et al., 2011; Way and Chalfie, 1989). mec-  3 mutant PVD neurons fail to elaborate lateral branches and show defective function  (Smith et al., 2010; Tsalik et al., 2003) (Husson et al., 2012).

overall_design: We used tiling arrays to identify genes regulated by the mec-3 transcription factor in PVD sensory neurons.  We employ the mRNA-tagging method to isolate poly(A) RNA from the PVD and OLL neurons in wildtype and mec-3 mutants (3 replicates each) by expressing a 3X FLAG-tagged poly(A) binding protein PAB-1 in PVD and OLL under control of the ser-2prom3B promoter. The enriched poly(A) RNA is amplified using the NuGEN WT-Pico amplification system and applied to Affymetrix C. elegans tiling microarrays. Whole animal reference samples were obtained by isolating total RNA at the L2/L3 stages in wildtype and mec-3 mutants (2 replicates each) and processed as above.

first: Cody

last: Smith

first: Timothy

last: O'Brien

middle: C

first: Marios

last: Chatzigeorgiou

first: Elana

last: Feingold-Link

first: Steven

last: Husson

first: Sayaka

last: Hori

first: Shohei

last: Mitani

first: Alexander

last: Gottschalk

middle: R

last: Schafer

first: David

middle: M

last: Miller


title: Influenza peptide reactivity within a cohort of age-stratified individuals pre and post vaccination with the 2008/2009 trivalent influenza vaccine

status: Public on May 01 2013

city: Oberlin

first: Jordan

last: Price

state: OH

address: 119 Woodland St

institute: Oberlin College

summary:
The aim of the study was to test the hypothesis that peptide array reactivity will reveal patterns that can be associated with poor or effective neutralization response to seasonal influenza vaccine
We diluted patient sera 1:80 and incubated dilutions on a streptavidin-coated glass surface that was printed with biotinylated peptides derived from seasonal strains of influenza hemagglutinin included in the 2008/2009 trivalent influenza vaccine

platform_organism:
Influenza B virus
H1N1 subtype
H3N2 subtype

overall_design: In this study, serum from 76 study participants, subsetted into young (≤30 years old) and elderly (≥60 years old) categories were profiled for IgG/IgM antibody reactivity to influenza hemagglutinin peptudes. Using multivariate linear regression and correcting for multiple hypothesis testing by cross-validation, ee found that patterns of peptide reactivity associated with a poor or effective neutralization response to H1N1 and B strains of influenza.

middle: V

first: Justin

middle: A

last: Jarrell

last: Furman

first: Nicole

middle: H

last: Kattah

first: Evan

last: Newell

first: Cornelia

middle: L

last: Dekker

first: Mark

last: Davis

first: Paul

last: Utz


title: The response of Streptococcus pneumoniae to replication stress on the transcriptome of a wild-type strain

status: Public on Apr 23 2013

city: Groningen

first: Jelle

last: Slager

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

summary: The aim of this study is to identify the response of S. pneumoniae to HPUra-induced replication stress on transcriptional level in a wild type strain.

overall_design: Two cultures were compared to each other. One treated with HPUra and one untreated. A dye-swap was included, and both the dye-swap and original labeling were repeated once as a technical replicate. The slide configuration also contained 3 replicate spots for each gene. This makes a total of 4 slides with 3 replicate spots per slide.

first: Morten

last: Kjos

first: Laetitia

last: Attaiech

first: Edwin

last: de Jong

first: Matthijs

last: Schokker

first: Jan-Willem

last: Veening


title: Autoimmune antigen and serum factor antigen reactivity in a cohort of patients with autoimmune polyendocrinopathy syndrome type 1(APS-1) and healthy controls.

status: Public on Sep 24 2013

summary:
The aim of the study was to test the hypothesis that APS-1 patient sera contains IgG reactivity to serum factor antigens concomitant with prototypical autoimmne antigens.
We diluted patient sera 1:250 and incubated dilutions on a nitrocellulose-platform array printed with whole protein antigens.

platform_organism:
Gallus gallus
Homo sapiens
Bos taurus

overall_design: In this study, serum from 14 ndividuals (subsetted into APS-1 patient and healthy control categories) was profiled for IgG autoantibody reactivity to whole protein autoimmune and serum factor antigens. APS-1 patient sera was found using the significance analysis of microarrays (SAM) algorithm to be significantly more reactive with prototypical cytokine antigens previously identified as targets of autoantibodies.


title: Microarray analysis to identify differentially expressed genes of intracellular Brucella abortus in RAW264.7 cells

status: Public on Apr 30 2013

city: Shanghai

first: Mingxing

last: Tian

address: NO.518, Ziyue Road, Minhang District

country: China

institute: Shanghai Veterinary Research Institute

summary: Microarray analysis determined that 7.82% (244/3334) of Brucella abortus genes were up-regulated and 5.4% (180/3334) were down-regulated in RAW264.7 macrophages, compared to free-living bacteria in TSB

overall_design: In the study, Brucela abortus was isolated from infected macrophages at 24 post-infection, DNA microarray was used to analysis the differentially expressed genes between intracellular bacteria and free-living ones in TSB

first: Shengqing

last: Yu

first: Jing

last: Qu

first: Xiangan

last: Han

first: Min

last: Zhang

first: Chan

last: Ding

first: Jiabo

first: Guanghua

last: Chen


title: A transcriptomic analysis of American lobster (Homarus americanus) immune response during infection with the bumper car parasite Anophryoides haemophila

status: Public on Mar 27 2013

city: Charlottetown

first: Fraser

last: Clark

state: PEI

address: 550 University Ave

department: Pathology and Microbiology

country: Canada

institute: University of Prince Edward Island

summary: Transcriptomic profiling of Homarus americanus after in vivo infection with scuticocilliate parasite Anophryoides haemophila

overall_design: Two condition (control and infected) time series experiment; Biological replicates: 3 x 24 h control, 3 x 8 week control, 4 x 10 week control, 4 x 24 h infected, 4 x 48 h infected, 4 x 1 week infected, 5 x 3-4 week infected, 11 x 5-7 week infected, 4 x 8 week infected and 5 x 10 week infected.

first: K

middle: F

first: Spencer

last: Greenwood

first: Adam

last: Acorn


title: Mutations in GlnA, NifA and NifK enabling photosynthetic growth of Rhodobacter sphaeroides in the absence of CO2 fixation

status: Public on May 22 2013

city: Madison

first: Oleg

last: Moskvin

state: WI

address: 1220 Capitol Court

institute: University of Wisconsin-Madison

summary: Previously isolated spontaneous mutants of Rhodobacter sphaeroides, which were initially compromised in their ability to assimilate carbon dioxide through the reductive pentose phosphate pathway, were found to exhibit abnormal nitrogenase gene regulation as well as altered patterns of nitrogenase enzymatic activity. The genomes of these strains were studied by whole genome pyrosequencing and whole genome microarray analysis to identify possible loci responsible for the observed phenotypes.

overall_design: 3 R.sphaeroides strains were grown in matching conditions to reveal strain-specific gene expression

first: F

last: Tabita

first: Mark

last: Gomelsky


title: Tobacco smoking transcriptional imprinting contributes to urothelial cancer

status: Public on Mar 20 2013

city: Mannheim

first: Li

last: Li

address: Theodor-Kutzer-Ufer

country: Germany

institute: University Heidelberg

summary:
Smoking is a major risk factor for Urothelial carcinoma (UC).  However the complex mechanisms, how smoking promotes carcinogenesis and tumour progression, remain obscure. A microarray based approached was therefore performed to detect the smoking derived gene expression alteration in non-malignant and malignant urothelial tissues from patients with superficial or invasive UC. Smoking enhanced cell migration and response to tissue damages. In non-malignant tissues smoking induced immune response and altered the cytoskeleton. In urothelial carcinoma, smoking altered extracellular and chromosome structures.  Smoking affected tissues from patients with invasive carcinomamore strongly,  up-regulating particularly growth factors and oncogenes in non-malignant  tissue  of patients with invasive but not with superficial carcinoma. In former smokers, comparable changes were seen in tissues form patients with invasive disease while they were minor or reversed in tissue of patients with superficial disease. Best but not complete tissue repair was suggestedfor non-malignant tissue from patients with superficial tumours.
we used microarray techniques to define gene expression profile which may explain the contribution of smoking to urothelial carcinoma.

overall_design: Gene expression profiling using GeneChip HG-U133A Plus 2.0 (Affymetrix) was performed on non-malignant and carcinogenic urothelium from six patients with superficial and six with invasive urothelial carcinoma, each group including two current, former, and non-smokers.

first: Ute

last: Gabriel


title: Passage through the mammalian gut triggers a phenotypic switch required for Candida albicans commensalism

status: Public on Jul 28 2013

city: San Francisco

first: Changbin

state: California

address: HSE450, 513 Parnassus Avenue

department: Department of Microbiology & Immunology

institute: University of California, San Francisco

summary: Among ~5,000,000 fungal species on Earth, Candida albicans is exceptional in its lifelong association with humans, where it exists either as a benign component of the gastrointestinal microbiome or as an invasive pathogen.  Although it is generally assumed that invasiveness results from a breakdown of host immunity , it is also possible that specific fungal programs control the transition between these divergent lifestyles.  Here, we report that exposure of C. albicans to the mammalian gut triggers a developmental switch, driven by the Wor1 transcription factor, to a commensal cell type.  Wor1 has been thought to occur only in unique genetic backgrounds, but we show that WOR1 expression is triggered when wild-type cells are propagated in a murine gastrointestinal infection model.  Similar to Wor1’s role in a white-opaque switch for mating, WOR1 overexpression within the host induces a novel switch affecting cell and colony morphology and conferring commensal fitness.  However, these hyperfit GUT (Gastrointestinally-IndUced Transition) cells lack the functional hallmarks of opaque cells, which they resemble morphologically, whereas bona fide opaque cells are defective for commensalism.   Instead, the GUT cell transcriptome is optimized for the environment of the distal mammalian digestive tract.  The GUT cell type switch illuminates how a single organism can utilize distinct genetic programs to transition between commensalism and invasive tissue pathogenesis

overall_design: Candida albicans strains including the Wild type strain (SN425),  WOR1OE -White (a/a, SN1044), WOR1OE -GUT (a/a, SN1045),  White (a/a, SN966) and Opaque (a/a, SN967) were grown at room temperature in SC medium supplemented with 100ug/ml adenine; 2-4 biological replicates were performed per strain. RNA was prepared from these strains and samples were hybridized on custom Agilent C. albicans ORF arrays (15,000 spots/array, 70-mer probes).

first: Kalyan

last: Pande

first: Suzanne

last: Noble


title: Expression profiles of wildtype and Shox2 knockout embryonic limbs

status: Public on Feb 15 2013

first: Carsten

last: Sticht

department: ZMF

summary: The development of vertebrate extremities is a complex process which requires a highly coordinated network of different transcriptional activities. The homeodomain transcription factor Shox2 is a key player in limb formation controlling neural, muscular and skeletal development. Here, we compared gene expression profiles of wildtype and Shox2 knockout limbs using microarray experiments to identify Shox2 target genes.

overall_design: Limbs of E12.5 mouse embryos were dissected, fore- and hindlimbs were pooled and genotyped for RNA extraction. RNA from 3 embryos of 2 different pregnancies (in total 6 embryos) was pooled per genotype (Wildtype and Shox2 Knockout) and compared.

first: Anne

last: Glaser

first: Norbert

last: Gretz


title: Gene expression profiling of a hypoxic seizure model of epileptogenesis in the rat.

status: Public on Mar 06 2013

city: Cambridge

first: Joachim

last: Theilhaber

state: MA

address: 270 Albany Street

department: Translational Medicine

institute: Sanofi

summary:
Microarray profiling was used to investigate gene expression in the hypoxic seizure model of acquired epilepsy in the rat, with the aim of characterizing functional pathways which are persistently activated or repressed during epileptogenesis. Hippocampal and cortical tissues were transcriptionally profiled over a one week period following an initial series of seizures induced by mild hypoxia at post-natal day 10 (P10), and the gene expression data was then analyzed with a focus on gene set enrichment analysis, an approach which emphasizes regulation of entire pathways rather than of individual genes.  Animals were subjected to one of three conditions, control condition with no exposure to hypoxia, hypoxic seizures, and hypoxic seizures followed by treatment with the AMPAR antagonist NBQX, a compound tentatively proposed to be a modulator of epileptogenesis.
Gene expression in the control samples was found to be consistent with known processes of neuronal maturation in the rat for the given time window. The hypoxic seizure response was found to be saliently enriched for components of the PI3K/mTOR and Wnt signaling pathways, alongside gene sets representative of glutamatergic, synaptic and axonal processes, perhaps regulated as a downstream consequence of activation of these pathways.  Wnt signaling components were also found enriched in the more specifically epileptogenic NBQX-responsive gene set.  While activation of the mTOR pathway is consistent with its known role in epileptogenesis and strengthens the case for mTOR or PI3K pathway inhibitors as potential anti-epileptogenic drugs, investigation of the role of Wnt signaling and the effect of cognate inhibitors offers a parallel avenue of research toward anti-epileptogenic treatment.

overall_design:
Cohorts of ten days old (P10) rat pups were subjected to one of three experimental conditions: 1) a control sham treatment inducing no hypoxic seizures (noHS), 2) a treatment under hypoxia inducing hypoxic seizures (HS), in which each animal underwent a 15 minutes passage at 5% O2, and 3) a treatment with hypoxia inducing hypoxic seizures, followed by four intra-peritoneal injections of NBQX over a 48 h period, starting at 30 minutes post-hypoxia (HS+NBQX). Control vehicle injections of DMSO were performed for the animals under the noHS and HS conditions. Time of occurrence and number of seizures for the animals undergoing hypoxia were recorded and analyzed.  Times to the first seizure were found to be exponentially distributed, with mean time to first seizure of 114 seconds, and total count of seizures occurring in the 15 minute hypoxic interval was found to be approximately normally distributed, with mean count 10.6 and standard deviation 2.9. For each treatment condition, cohorts of 4 to 6 rat pups were killed at five sampling times spanning 1 hour to 1 week post-hypoxia  (1h, 6h, 12h, 48h, 168h post-hypoxia), for a total of 75 animals sacrificed. Whole cortex and hippocampi were extracted from the sacrificed animals and separately profiled on two Affymetrix high-throughput plate microarrays after RNA quality control, resulting in a total of 144 CEL files encapsulating the gene expression data.
The 144 CEL files, generated from scans of the individual microarrays on the two 96-well Affymetrix HT Rat Focus Arrays, were processed according to the MAS5 algorithm, resulting for each input CEL file in output of 24,249 probeset-level intensities and corresponding absent/present calls. For each processed scan, two summary statistics, consisting of the total number of present calls on the chip, and the 75th percentile of present call intensities, were then computed. A quality control step was performed by inspecting for outlier scans in the space of these two statistics (no outliers were found). Additional visual inspection of a heat map of clustered profiles identified a potential tissue assignment swap between two samples, which were conservatively eliminated from further analysis. The resulting 142 quality-controlled profiles were then assembled into a single data matrix, and normalized to each other by linear rescaling of all probeset intensities so as to bring the 75th percentile of present call intensities on all chips to a single common value.  These processing steps, and most of the subsequent analyses discussed here, were done using the Gecko gene expression analysis platform (Theilhaber et al., 2004). Additional analyses were performed using the R statistical tools framework (R Development Core Team 2008).

first: Sanjay

last: Rakhade


title: Transcriptional override: a regulatory network model of indirect responses to modulations in microRNA expression (miRNA)

status: Public on Nov 19 2013

city: Atlanta

first: Christopher

middle: G

last: Hill

state: GA

address: 315 Ferst Dr

department: Biology

institute: Georgia Institute of Technology

type:
Third-party reanalysis
Non-coding RNA profiling by array

summary: MicroRNAs are small non-coding molecules that have been shown to repress the translation of thousands of genes. Changes in microRNA expression in a variety of diseases, including cancer, are leading to the development of microRNAs as early indicators of disease, and to their potential use as therapeutic agents. A significant hurdle to the use of microRNAs as therapeutics is our inability to predict the molecular and cellular consequences of perturbations in the levels of specific microRNAs on targeted cells. While the direct gene (mRNA) targets of individual microRNAs can be computationally predicted and are often experimentally validated, assessing the indirect effects of microRNA variation remains a major challenge in molecular systems biology. We present experimental evidence for a computational model that quantifies the extent to which down-regulated transcriptional repressors contribute to the unanticipated upregulation of putative microRNA targets. An appreciation of the effects of these repressors may provide a more complete understanding of the indirect effects of microRNA dysregulation in diseases such as cancer, and to their successful clinical application. This is a re-analysis of GSE23383, as described below in “overall design”.

overall_design:
mRNA were collected from the surface epithelial cells of 3 normal ovaries and from laser capture microdisection of 3 ovarian tumors. microRNA expression was captured on Affymetrix Ambion mirCHIP 14K chips. All signals were then log2 normalized. This is a re-analysis of GSE23383 but using both probe sets, labelled A and B,  for each of the six original samples (3 normal + 3 cancer) to determine the signals of human (hsa-*) microRNAs. The associated samples are GSM573599, GSM573600, GSM573601, GSM573602, GSM573603, GSM573604.
Data processing: For each probe, an estimated background value is subtracted that is derived from the median signal of a set of G-C-matched anti-genomic controls. Arrays within a specific analysis experiment were normalized together according to the variance stabilization method described by Huber et al. (Huber et al., 2002). Detection calls were based on a Wilcoxon rank-sum test of the miRNA probe signal compared to the distribution of signals from GC-content matched anti-genomic probes. A two-sample t-Test, with assumption of equal variance, was applied for statistical hypothesis testing. This test defined which probes are considered to be significantly differentially expressed based on a p-value of 0.01 and log2 difference ≥ 1. Processed data uploaded as CHP files.

first: C

first: L

last: Matyunina

middle: D

last: Walker

first: J

last: McDonald


title: Expression profiling of mouse liver after treatment with Vascular Endothelial Growth Factor  (VEGF) inhibitor aflibercept

status: Public on Sep 01 2013

city: Stanford

first: Kevin

last: Wei

state: CA

address: CCSR 3105a  269 Campus Drive

department: Hematology Division

institute: Stanford University School of Medicine

summary: Transcriptional profiling of mouse liver was compared between VEGF inhibitor aflibercept and control treatment after 9 weeks.

overall_design: 8-10 week-old SCID mice received VEGF Trap protein (aflibercept) subcutaneously twice per week at 25mg per kg body weight for 9 weeks.   For control groups, mice were treated with humanized Fc (Regeneron).  5 biological replicates were performed for the control group and 4 biological replicates were performed for the treatment group

first: Calvin

last: Kuo


title: EXPRESSION QTL MAPPING ACROSS SOIL MOISTURE ENVIRONMENTS REVEALS CONTRASTING ASSOCIATIONS WITH GENOMIC FEATURES IN ARABIDOPSIS THALIANA

status: Public on Mar 02 2013

city: Austin

first: David

middle: Bryant

last: Lowry

state: TX

address: 1 University Station #C0930

department: Integrative Biology

institute: University of Texas at Austin

summary:
Understanding the patterns and processes driving natural genetic variation in gene expression is of fundamental importance to biology. In this study, we examined genetic variation in gene transcription through expression QTL (eQTL) analysis in the Tsu-1 x Kas-1 recombinant inbred line (RIL) mapping population of Arabidopsis thaliana. To understand how natural variation in transcription responds to abiotic stress, we conducted eQTL in both well watered and soil drying conditions. Further, we evaluated whether elements of genome structure were associated with eQTL occurance and genes responding to treatment conditions. Overall, we identified thousands of genes that responded to soil moisture availability and hundreds of eQTLs. However, we identified very few interactions between eQTLs and environmental conditions, and both treatment conditions were enriched for similar gene ontology (GO) categories. We did find strong evidence for associations between genome structure and natural variation in transcription. In general, genes with eQTLs were positively associated with local recombination rates and levels of polymorphism while genes responding to the treatment were negatively correlated with these factors. Our study provides further insight into the origin and maintenance of natural variation in transcription and how that variation responds to environmental conditions.
Expression analysis by hybridization to atSNPTILE array (Affymetrix).

overall_design: Seed of the 104 RILs from reciprocal crosses between A. thaliana (L.) Heynh. accessions Kas-1 (CS903) and Tsu-1 (CS1640) were sown on fritted clay (Profile Products LLC, Buffalo Grove, IL) in 2.5-inch pots. Plants were arranged in a randomized complete block design consisting of 4 blocks, and then the pots were refrigerated at 4°C in darkness for 6 d to cold-stratify the seeds prior to commencement of a 12 h photoperiod in Conviron ATC60 growth chambers (Controlled Environments, Winnipeg, MB), at 23°C and 40% humidity during the day and 20°C and 50% humidity during the dark period. Light intensity was approximately 330 µmol m-2 s-1. After four weeks of growth, half of the plants were given a drought treatment, while the others remained fully watered. The drought treatment was randomly assigned to 2 of the 4 blocks and consisted of a slow decrease in soil moisture content over the course of one week. Each day, all pots assigned to the drought treatment were weighed, and water was added to individual pots to bring them to the target gravimetric water content. The target water content decreased each day, in the following series:  100%, 90%, 80%, 70%, 60%, 45%, and 40% of field capacity. At the end of the treatment, leaf tissue was collected from both treatments for RNA extraction.

middle: B

first: Tierney

last: Logan

first: Luca

last: Santuari

first: Christian

middle: S

last: Hardtke

first: James

last: Richards

first: John

middle: K

last: McKay

first: Saunak

last: Sen

first: Thomas

middle: E

last: Juenger

first: Leah

last: DeRose-Wilson


title: Bacillus subtilis Rnase Y activity in vivo analysed by tiling microarrays

status: Public on Jan 15 2013

city: Paris

first: Harald

last: Putzer

address: 13, rue P. et M. Curie

department: UPR9073, IBPC

country: France

institute: CNRS

summary: RNase Y is an essential endoribonuclease affecting global mRNA stability in Bacillus subtilis. We used high-resolution tiling arrays to analyze the effect of RNase Y depletion on RNA abundance covering the entire genome. The data confirm that this endoribonuclease plays a key role in initiating the decay of a large number of mRNAs as well as non coding RNAs. Comparison of the data with that of two other recent studies revealed very significant differences. About two thirds of the mRNAs upregulated following RNase Y depletion were different when compared to either one of these studies and only about 10% of were in common in all three studies.Our data confirmed already known RNase Y substrates and due to the precision and reproducibility of the profiles allows an exceptionally detailed view of the turnover of hundreds of new RNA substrates.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: A four arrays study of the transcriptome profiles of the B. subtilis RNase Y depletion strain SSB447 (Shahbabian et al., 2009) in which the gene rny is under the control of an IPTG inducible promoter. Rnase Y depleted cells (IPTG-) are compared to the transcript profiles of non depleted cells (IPTG+). As the rny gene is essential, depletion can only be partial. Here we carefully selected the time point for taking the sample in order to minimize growth rate effects and to obtain an highly reproducible data set.

first: Soumaya

last: Laalami

first: Pierre

last: Nicolas


title: Investigation of the methylation changes occurring during breast cancer pathology

status: Public on Dec 22 2012

city: Aarhus

first: Tomasz

last: Wojdacz

address: Wilhelm Meyers Alle 230

department: Department of Biomedicine

country: Denmark

institute: University of Aarhus

type: Methylation profiling by genome tiling array

summary: The experiment was designed to discover deferentially methylated regions between DNA extracted from breast cancer tissues and DNA samples extracted from tissue obtained form breast reduction surgeries. The study involved 20 breast cancer samples and 5 tissue samples from breast reductions. Each of the samples was processed by the arrays and collected data were used to compare the genome wide methylation pattern cancer samples (cases) and breast reduction samples (controls).

overall_design: The methylation pattern of 5 DNA samples from breast reduction was compared with the methylation pattern of 20 DNA samples from breast cancer tumors

first: Johanne

last: Windeløv

first: Britta

last: Thestrup

first: Jens

last: Overgaard

first: Lise

last: Hansen


title: yeast wt-matA pool - plate reader

status: Public on Nov 14 2012

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

institute: UMC Utrecht

summary: Contains a collection of wildtype matA Saccharomyces cerevisiae strains grown using a Tecan platereader for estimating the biological variation.

overall_design: Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. Two independent cultures were hybridized on two separate microarrays.

first: Dik

last: van Leenen

first: Marian

last: Groot Koerkamp

first: Sander

last: van Hooff

first: Philip

last: Lijnzaad

first: Frank

last: Holstege


title: yeast wt-matA pool

summary: Contains a collection of wildtype matA Saccharomyces cerevisiae strains for estimating the biological variation.


title: Transcriptome response to nitrosative stress in Rhodobacter sphaeroides 2.4.1

status: Public on Nov 11 2012

city: Bunkyo-ku

first: Hiroyuki

last: Arai

state: Tokyo

address: Yayoi 1-1-1

department: Department of Biotechnology

country: Japan

institute: The University of Tokyo

summary:
DNA microarray analysis was employed to investigate the transcriptome response to nitrosative stress in a non-denitrifying facultative photosynthetic bacterium Rhodobacter sphaeroides 2.4.1. We focused on the role played by a nitric oxide-response transcriptional regulator NnrR in the response.
The transcriptome profiles of R. sphaeroides 2.4.1 and its nnrR mutant before and after exposure to nitrosating agents S-nitrosoglutathione (GSNO) or sodium nitroprusside (SNP) under semiaerobic conditions were analyzed.

overall_design: R. sphaeroides 2.4.1 and its nnrR mutant were cultivated in glass bottles under semiaerobic growth conditions. When the optical density at 600 nm reached approximately 0.15-0.2, 1 mM GSNO or SNP was added to the medium. RNA was isolated from a 50 ml aliquot of the culture prior to the addition of GSNO or SNP and at 15 min after the addition. The experiment was performed in duplicate independent cultures.

first: Jung

last: Roh

first: Jesus

last: Eraso

first: Samuel

last: Kaplan


title: yeast wt pool - plate reader

summary: Contains a collection of wildtype Saccharomyces cerevisiae strains for estimating the biological variation. Wildtypes are obtained from the yeast wildtypes – platereader, wt pool background set HybSet, by randomly taking 100 wt vs. refpool (pooled wts) and 100 refpool vs. wt hybridizations


title: Streptococcus mutans UA159 with or without 8.4% oxygen vs. nox mutant strain. pH7

status: Public on Oct 04 2012

city: Rochester

first: Roberta

last: Faustoferri

state: NY

address: 601 Elmwood Ave. Box 611

department: Center for Oral Biology

institute: University of Rochester Medical Center

summary: Transcriptional analysis of the effects of oxygen concentraion in S. mutans

overall_design: RNA was extracted from 3 or 4 replicate samples of S. mutans UA159, UA159 grown in 8.4 % oxygen concentration and MU1020 (∆nox) grown in continuous culture to steady-state pH values of 7.  RNA was labeled with Cy3.  For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from S. mutans UA159 cultures grown to mid-log.

first: Jonathon

last: Baker

first: Adam

last: Derr

first: Kannan

last: Karuppaiah

first: Matthew

last: MacGilvray

first: Jessica

last: Kajfasz

first: Isamar

last: Ramos

first: Jacob

middle: P

last: Bitoun

first: Jose

last: Lemos

first: Zezhang

middle: T

last: Wen

first: Robert

last: Quivey


title: The regulon of the pleiotropic transcription factor Spx in Bacillus subtilis

status: Public on Sep 06 2012

city: Jouy-en-Josas

first: Pierre

last: Nicolas

address: INRAE - Domaine de Vilvert

institute: INRAE - Université Paris-Saclay

type: Genome binding/occupancy profiling by genome tiling array

summary:
The transcriptional regulator Spx plays a key role in maintaining the redox homeostasis of Bacillus subtilis cells exposed to disulfide stress.
Defects in Spx were previously shown to lead to differential expression of numerous genes but direct and indirect regulatory effects could not be distinguished.
Wild-type strain and spx mutant cells exposed or not to diamide stress were subjected to tiling array gene expression analysis.
To distinguish direct and indirect effects, the genomic sites bound by the Spx-RNAP complex were mapped using a chromatine immunoprecipitation approach.
This allowed the identification of 144 transcription units comprising 275 genes under direct Spx regulation.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: This data set contains 4 samples. Immunoprecipitated (IP) DNA from Bacillus subtilis Bas044 strain (BSB1, a tryptophan-prototrophic derivative 168 strain expressing a SPA-tagged Spx protein) were extracted from bacterial cultures in absence or presence of diamide. IP and whole cell extract DNA were hybridized on tiling array to generate ChIP-on-chip profiles. Two biological replicates were analyzed.

first: Tatiana

last: Rochat

first: Philippe

last: Noirot


title: Microbial communities in the gut of the beetle Odontotaenius disjunctus

status: Public on Aug 14 2012

city: Berkeley

first: Nhu

last: Nguyen

address: 111 Koshland Hall

department: Plant and Microbial Biology

institute: University of California, Berkeley

summary:
16S amplicon pool analyses of the four gut sections of the wood-feeding beetle, Odontotaenius disjunctus
The beetle is purely wood feeding, and we aim to first characterize the community that exist within the gut sections

platform_organism: Bacteria Archaea

overall_design: 4 beetles, four gut sections per beetle, one PhyloChip per gut section, total = 16 chips

first: Eoin

last: Brodie


title: RpoHI and RpoHII regulons in Rhodobacter sphaeroides 2.4.1

status: Public on Aug 03 2012

first: Yann

last: Dufour

address: 1550 Linden Drive

department: Bacteriology

institute: University of Wisconsin - Madison

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: RpoHI and RpoHII regulons in Rhodobacter sphaeroides 2.4.1 from gene expression profiling

summary: In this study, we performed expression profiling experiments to determine the respective regulons of RpoHI and RpoHII in Rhodobacter sphaeroides. We grew R. sphaeroides in aerobic conditions and induced either proteins ectopically and compared the global gene expression profiles.

overall_design: The expression profiles of R. sphaeroides strains lacking either RpoHI or RpoHII were compered to strains expressing RpoHI or RpoHII ectopically from a plasmid to detect gene differentially expressed. Three biological replicates were performed for each strain.

first: Timothy

middle: J

last: Donohue


title: MicroRNA expression profile in GlycophorinA positive cells of severe and intermedia Eb thalassemia

status: Public on Jul 30 2012

city: Kolkata

first: Uma

last: Dasgupta

address: 92, APC Road

department: Biophysics, Molecular Biology & Bioinformatics

country: India

institute: Calcutta University

summary: To investigate whether the microRNA expression profile changes with modulation of severity, GlycophorinA positive cells were isolated by immunomagnetic procedure from peripheral blood of two Eb thalassemia patients with same b globin gene mutation but differing in transfusion requirment. MicroRNA expression profile of the two samples were monitored.

overall_design: Agilent one-color experiment,Organism: Human ,Agilent-019118 Human miRNA Microarray  Labeling kit: Agilent miRNA labeling reagent and Hybridization Kit Cat # 5190-0408

first: Papai

last: Roy

first: Mohammed

last: Aiyaz


title: HCMV infection of human neural precursor cells: HCMV expression

status: Public on Jul 22 2012

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

summary: HCMV treated and control human primary adult neural precursor cells (isolated from hippocampus) were used at passages 2-4 for infection with HCMV and RNA was harvested at indicated times

sample_organism:
Human betaherpesvirus 5
unidentified

overall_design: Primary adult neural precursor cells were infected with HCMV strains Towne and TR (O.1MOI) and RNA was extracted at 72 hrs postinfection for expression profiling on both HCMV and Affymetrix DNA arrays

first: Liliana

last: Soroceanu


title: Patterns of aberrant DNA methylation after toxicant-induced malignant transformation (MeDIP-chip dataset 1)

status: Public on Jun 26 2012

city: Tucson

first: Paul

last: Severson

state: AZ

address: 1515 N Campbell Ave

department: Pharmacology and Toxicology

institute: University of Arizona

summary: Aberrant DNA methylation is frequently observed in cancer. The aim of this study was to determine how DNA methylation is changed after toxicant-induced malignant transformation. This study also puts the DNA methylation changes into context with respect to the aberrant DNA methylation events that occur in bladder and prostate carcinogenesis not associated with toxicant exposure.

overall_design: Immortalized UROtsa (n=3) and RWPE-1 (n=2) are compared to normal HUC (n=2) and PrEC (n=2), respectively. Arsenite (n=1), monomethylarsonous acid (n=2) or cadmium (n=1) transformed UROtsa are compared to parental UROtsa (n=3). Arsenite (n=2), cadmium (n=1) or MNU (n=1) transformed RWPE-1 cells are compared to parental RWPE-1 cells (n=2). Clinical bladder tumor biopsies (n=6), urothelial carcinoma cell lines (n=2) and prostate cancer cell lines (n=3) are compared to thier normal tissue counterparts HUC (n=2) and PrEC (n=2). Immunoprecipitation using anti-methylcytosine (5MeC) antibody.

first: Lukas

last: Vrba

first: Erik

last: Tokar

first: Michael

last: Waalkes

first: Bernard

middle: W

last: Futscher


title: Patterns of aberrant DNA methylation after toxicant-induced malignant transformation (miRNA dataset)

summary: Aberrant DNA methylation is frequently observed in cancer. The aim of this study was to determine how DNA methylation is changed after arsenic-induced malignant transformation.

overall_design: Arsenite-transformed RWPE-1 cells (n=2) are compared to parental RWPE-1 cells (n=2). Normal PrEC (n=2) are included for comparison. Immunoprecipitation using anti-methylcytosine (5MeC) antibody.


title: Patterns of aberrant DNA methylation after toxicant-induced malignant transformation (MeDIP-chip dataset 2)


title: Identifying the signaling cascades and regulatory mechanisms that control osmotic stress response

status: Public on Jul 10 2012

city: Pittsburgh

first: Anthony

last: Gitter

address: 5000 Forbes Ave

department: Computer Science Department

institute: Carnegie Mellon University

summary: We performed knockout and wild type expression experiments in yeast grown in soribtol to identify genes invovled in controling osmotic stress response.

overall_design: Soribitol experiments were performed by growing to logarithmic phase in synthetic complete (SC) medium and then washing and resuspending in SC medium with 1M sorbitol for 30 minutes.  Two replicates were performed per knockout strain and compared with two or four control replicates depending on the platform.

first: Miri

last: Carmi

first: Ziv

last: Bar-Joseph


title: Patterns of aberrant DNA methylation after toxicant-induced malignant transformation


title: Tiling array hybridizations of genomic DNA from Bacillus subtilis 168.

status: Public on Mar 07 2012

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

institute: University Medicine Greifswald

summary:
Genomic DNA prepared from B. subtilis 168 cells grown to stationary phase was hybridized to tiling arrays. The data are used in transcriptome studies to compute expression intensities from raw intensity data using a model of shift and drift
and correcting for probe affinity variations as described in (Nicolas et al., 2009, Bioinformatics 25, 2341-2347).

overall_design: B. subtilis 168 was grown in LB medium to stationary phase. Genomic DNA was prepared from four independent cultures. After sonication, DNA was labeled with Cy3 and hybridized to tiling arrays.

first: Etienne

last: Dervyn

first: Pierre

last: Nicolas


title: Microarray analysis on spleens and livers of mice inoculated subcutaneously with J558 myeloma cells and supplemented with oil palm phenolics (OPP)

status: Public on Mar 17 2012

city: Kajang

first: Soon-Sen

last: Leow

state: Selangor

address: No. 6, Persiaran Institusi, Bandar Baru Bangi

country: Malaysia

institute: Malaysian Palm Oil Board

summary: OPP (1500 ppm gallic acid equivalent (GAE)) was supplemented to BALB/c mice inoculated subcutaneously with J558 myeloma cells at the dorsum of the neck in order to observe possible immune responses in cancer suppression. Spleens and livers were harvested at three designated time points, eighteen hours, one week and four weeks after inoculation of the cells for gene expression studies. Results show that the expression of immune-related genes in the spleen was delayed, while those related to inflammation in the liver were down-regulated across time, thus suggesting that OPP may have anti-inflammatory properties in suppressing cancer.

overall_design: Total RNA obtained from spleens and livers of BALB/c mice given OPP (four weeks after subcutaneous inoculation of J558 myeloma cells) were compared to controls given distilled water at three time points, eighteen hours, one week and four weeks after inoculation of the cells (three replicates per group per time point)

first: Shamala

last: Sekaran

first: Ravigadevi

last: Sambanthamurthi


title: Transcriptomic analyses of Staphylococcus epidermidis in mixed-species biofilms with Candida albicans

status: Public on Feb 28 2012

city: Houston

first: Mohan

last: Pammi Venkatesh

address: One Baylor Plaza

department: Pediatrics

institute: Baylor College of Medicine

summary: To explain enhanced biofilm formation and increased dissemination of S. epidermidis in mixed-species biofilms, microarrays were used to explore differential gene expression of S. epidermidis in mixed-species biofilms. One sample from single species biofilm (S1) and mixed-species biofilm (SC2) were excluded from analyses for outliers. We observed upregulation (2.7%) and down regulation (6%) of S. epidermidis genes in mixed-species biofilms. Autolysis repressors lrgA and lrgB were down regulated 36-fold and 27-fold respectively and was associated with increased eDNA possibly due to enhanced autolysis in mixed-species biofilms. These data suggest that bacterial autolysis and release of eDNA in the biofilm matrix may be responsible for enhancement and dissemination of mixed-species biofilms of S. epidermidis and C. albicans.

sample_organism:
Staphylococcus epidermidis
Candida albicans

overall_design: Staphylococcal gene expression in mixed-species biofilms with Candida and in single species biofilms of S. epidermidis were analyzed. The experiment was repeated thrice on 3 different days (3 biological replicates each for single species biofilms of S. epidermidis and mixed-species biofilms). Only 2 biological replicates were analyzed and one biological replicate was not analyzed (S1 and SC1 - raw data files are provided on the Series record). Single species biofilms of S. epidermidis (strain 1457) and C. albicans (strain 32354) and mixed-species biofilms were formed on 6-well tissue culture plates. Five ml of organism suspensions (O.D. 0.3, S. epidermidis 107 CFU/ml or C. albicans 105 CFU/ml)  or 2.5 ml each for mixed-species biofilms for 24 hr. RNA was harvested from single species and mixed-species biofilms.

last: Pammi


title: The condition-dependent transcriptome of Bacillus subtilis 168

summary: Recent studies revealed the unsuspected complexity of the bacterial transcriptome but its systematic analysis across many diverse conditions remains a challenge. Here we report the condition-dependent transcriptome of the prototype strain B. subtilis 168 across 104 conditions reflecting the bacterium's life-styles. This data set composed of 269 tiling array hybridizations allowed to observe ~85% of the annotated CDSs expressed in the higher 30% in at least one hybridization and thus provide an excellent coverage of the transcriptome of this bacterium. In addition to the Genbank annotation 1583 new segments of the chromosome were identified as transcribed and have transcription levels reported in the data matrix.

overall_design: RNA samples prepared from B. subtilis 168 grown under 104 experimental conditions were reverse transcribed, labeled and hybridized to tiling arrays. Most hybridizations were performed in duplicate or triplicate using RNA isolated from independent cultures. All experiments were performed with strain BSB1 which is a tryptophan-prototrophic (trp+) derivative of the 168 trpC2 strain.

first: Eric

last: Botella

first: Elisabeth

last: Härtig

first: Ludovic

last: Le Chat

first: Jules

last: Matthieu

first: Susanne

last: Pohl

first: Tatiana

last: Rochat

first: Praveen

last: Sappa

first: Marc

last: Schaffer


title: Stage-specific transcriptional changes during zygotic embryogenesis in maritime pine (Pinus pinaster Ait.)

status: Public on Jan 30 2012

city: Oeiras

first: Marta

last: Simões

address: Quinta do Marquês - EAN

country: Portugal

institute: IBET

summary: The significant morphological differences observed during embryo development in angiosperms and gymnosperms are expected to be the result of a differential control of gene expression. We used a loblolly pine (Pinus taeda) cDNA microarray to analyze global transcriptional changes along zygotic embryogenesis in maritime pine (Pinus pinaster). A time-course analysis of the data obtained from the five embryo developmental groups used in this study led to the identification of 4,645 genes whose expression varied along P. pinaster embryogenesis. These transcripts were clustered into six distinct expression profiles. The grouping of these profiles in early, mid-embryogenesis and embryo maturation, according to the developmental period where most of the sequences were up-regulated, evidenced that characteristic transcriptional changes are associated to each developmental period. The application of a cut-off value of 1.95-fold change led to the identification of 1,838 differentially expressed transcripts that were categorized by biological process. Metabolism, interaction with the environment, oxidation-reduction and transport were some of the most represented categories. During early embryogenesis genes putatively involved in phytohormone-mediated signaling were identified, whereas in middle stages the overrepresented genes could be associated with cotyledon formation and induction of somatic embryogenesis. Genes associated with the synthesis of storage products were up-regulated in the latest stages of pine embryo development. It was also during this developmental period that the largest number of sequences putatively encoding transcription factors was identified.

overall_design: Pine immature zygotic embryos were pooled into five different developmental groups according to the collection date (Day0; Day5; Day11; Day15 and Day25). A common reference design was used. Total RNA was extracted from each sample. Three extractions were prepared per sample (biological replicates). A defined ammount from each RNA sample was pooled to use as reference. Messenger RNA was amplified for both test samples and reference. These were hybridized together in two separate experiments (technical replicates). In total, 30 slides were analyzed.

first: W

last: Lorenz

first: João

last: Maroco

first: Rob

last: Alba

first: Jeffrey

last: Dean

first: Célia

last: Miguel


title: evolution of genotypes and differences - affy_gnp07_regeneome_cotton

status: Public on Jun 01 2012

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

department: URGV

institute: INRA

summary: affy_gnp07_regeneome_cotton - evolution of genotypes and differences  - Genes involved in somatic embryogenesis

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design:
24 arrays - Cotton; genotype and ecotype comparison,time course
The samples are from the following varieties of Gossypium hirsutum (wild type):
- Irma  from variety NEmb
- 1a and B2 are two independent batch of seeds from the variety Coker310.
They were selected for their ability to perform embryogenesis. Irma does not embryogenesis after the formation of callus. 1a and b2 have respectively a low and a high capacity for embryogenesis.

first: D

first: J

last: Faure

first: M

last: Obellianne

last: Hervé

first: R

last: Berthomé

first: S

last: Balzergue

last: Martin-Magniette

first: C

last: Pannetier


title: Bacillus subtilis SigA ChIP-chip (BsubT2 array)

status: Public on Jan 01 2012

city: Jouy en Josas

first: Nathalie

last: Pigeonneau

address: domaine de Vilvert

department: Micalis

summary: Identification of the specific SigA binding regions on the B. subtilis chromosome during exponential, transition and stationary growth phases. The data served to help the analysis of the repertoire of B. subtilis promoters established from transcriptome profiles.

overall_design: 3 growth phases (exponential, transition, stationary) x 2 biological replicates were analysed on the BsubT2 tiling array.

first: François

last: Lecointe

first: Pierre

last: Nicolas


title: Bacillus subtilis SigA ChIP-chip (BsubT1 array)

overall_design: 3 growth phases (exponential, transition, stationary) x 2 biological replicates were analysed on the BsubT1 tiling array.


title: Transcriptome analysis of a Bacillus subtilis mutant defective in the transcription termination factor Rho.

first: Ulrike

last: Mäder

summary: This analysis is part of the study GSE27219, The condition-dependent transcriptome of Bacillus subtilis 168. In this study, 120 transcription units where identified for which transcription did not terminate at any specific site, leading to mRNA extension over long distances with slowly decreasing signal intensity. In most cases, lack of termination and read-through generated antisense transcripts. These findings together with the lack of intrinsic terminators suggested that transcription termination of the 120 transcription units could be mediated by the transcription termination factor Rho. In order to investigate the impact of Rho-mediated termination, tiling array hybridizations using RNA samples of a B. subtilis rho-null mutant and its parental strain were performed.

overall_design: B. subtilis 1012 wild-type and rho-mutant cells were grown in LB medium. Samples for tiling array analysis were taken during exponential growth phase. Hybridizations were performed in triplicate using RNA isolated from independent cultures.

first: Elena

last: Bidnenko

first: Thomas

last: Wiegert


title: Characterization of the transcriptional heterogeneity present within the rat lymphatic and blood vasculatures

status: Public on Jun 23 2012

city: Temple

first: David

middle: C.

last: Zawieja

address: 702 SW HK Dodgen Loop

department: Dept. of Systems Biology and Translational Medicine

institute: Texas A&M Health Science Center

summary: The goal and objective of this study was to identify the transcriptional profiles differentiating the artery, vein, and lymphatic lineages in the adult rat vasculature with particular emphasis on the unique elements of the collecting lymphatic vessel transcriptome. A 2 x 3 experimental design was utilized in which parallel arteries, veins, and lymphatics from two different tissue beds were examined. The rat thoracic duct was selected as a large, post-nodal collecting lymphatic vessel that exhibits excellent conduit-type behavior while the rat mesenteric lymphatic was selected as a smaller, pre-nodal collecting lymphatic vessel that exhibits excellent pump behavior (see Gashev AA, et al. Microcirculation. 2004 Sep;11(6):477-92. [PMID: 15371129]). The axillary artery and vein were selected for comparison to the thoracic duct due to their similar anatomical position distal to the common junction of the lymphatic and venous vascular trees and represent a large artery and large vein, respectively. The mesentery artery and vein were selected for comparison to the mesenteric lymphatic vessels due to their parallel position within the mesenteric vasculature and represent a small atery and small vein, respectively.

overall_design: A 2 x 3, reference-based, experimental design was utilized consisting of both large (thoracic) and small (mesenteric) arteries, veins, and collecting lymphatic vessels for a total of 6 sample groups with n=6 biological replicates present in each group. All vessels acquired from the same donor animal have the same numerical label and were handled in parallel through all experimental steps. Each vessel sample RNA sample was amplified, labeled with Cy5, and compared to the same Rat Universal Reference RNA sample (Stratagene, La Jolla, CA) that was amplified and labeled with Cy3 dye. No dye swaps were utilized.

first: Eric

last: Bridenbaugh

first: Daniel

middle: C

last: Jupiter

first: Hung-Chung

last: Huang

first: Vincent

last: VanBuren


title: Bacillus subtilis SigA ChIP-chip

overall_design: Refer to individual Series


title: Chip-chip from mouse diffuse large B cell lymphoma cell lines with PU.1

status: Public on Oct 15 2011

city: Seoul

first: Dong-Mi

last: Shin

address: 1 gwanak-ro

country: South Korea

institute: seoul national university

summary: PU.1, a transcriptional factor, is expressed in wide range of B cells from early to mature stage. To identify PU.1 direct targets in germinal center B cells, ChIP-chip ananlysis was done in three different GC-origin diffuse large B cell lymphoma cell lines.

overall_design: PU.1 ChIP in two different cell lines (NFS201 and NFS202:high level of PU.1) and in one negative control cell lines(NFS205:negatvie for PU.1). Total three different samples. One sample per a set of two arrays (promoter1 and promoter2).

first: Chang-Hoon

last: Lee

first: Herbert

last: Morse


title: Chip-chip from mouse diffuse large B cell lymphoma cell lines with IRF8

summary: IRF8, a transcriptional factor, has the heightened expression in germinal center(GC) B cell and GC-origin B cell lymphoma. To identify IRF8 direct targets in GC B cells, ChIP-chip ananlysis was done in three different GC-origin diffuse large B cell lymphoma cell lines. IRF8-negative cell lines, MPC11, was also used as a negatvie control.

overall_design: IRF8 ChIP in three different cell lines (NFS201, NFS202 and NFS205:high level of IRF8) and in one negative control cell lines(MPC11:negatvie for IRF8). Total four different samples. One sample per a set of two arrays (promoter1 and promoter2).


title: Chip-chip from human diffuse large B cell lymphoma cell lines with IRF8

summary: IRF8, a transcriptional factor, has the heightened expression in germinal center(GC) B cell and GC-origin B cell lymphoma. To identify IRF8 direct targets in GC B cells, ChIP-chip ananlysis was done in three different GC-origin diffuse large B cell lymphoma cell lines. IRF8-negative cell lines, MMS1, was also used as a negatvie control.

overall_design: IRF8 ChIP in three different cell lines (ODH1, VAL and LY1:high level of IRF8) and in one negative control cell lines (MMS1:negatvie for IRF8). Total four different samples. One sample per a set of two arrays (promoter1 and promoter2).


title: Transcriptional network governed by IRF8 and/or PU.1 in germinal center B cells

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Mouse B cell lymphoma cell lines:IRF8 knockdown cells vs. Control

summary: Expression profiling of NFS202 mouse B cell lymphoma cell lines comparing cells stably expressing siIRF8 vector with cells expressing control vector only

overall_design: six technical replicates of siIRF8 expressing cells. Six technical replicates of controls; one replicate per array

first: Zoreh

last: Naghashfar


title: Expression data from H2-producing Rhodobacter sphaeroides cultures fed different organic substrates

status: Public on Aug 22 2011

city: Madison

first: Timothy

last: Donohue

state: Wisconsin

department: Department of Bacteriology

institute: University of Wisconsin-Madison

summary:
Rhodobacter sphaeroides produces hydrogen gas (H2) via its nitrogenase enzyme during photoheterotrophic growth under nitrogen-limited conditions.  We find that cells produce different amounts of H2 and show different growth rates, depending on the organic substrate provided (lactate, succinate, glucose, xylose, or glycerol).
We used global transcript analyses to determine what genes are involved in the onset of H2 production, and those that lead to different H2 production capacities in cells fed different organic substrates.

overall_design: Growth and real-time H2 production were followed for photoheterotrophically grown Rhodobacter sphaeroides cultures (19 mL test tube cultures) fed one of five different organic substrates (lactate, succinate, glucose, xylose, or glycerol) and provided glutamate as the sole nitrogen source.  Cells were harvested for RNA extraction during early post-exponential growth, at points near the maximum H2 production rates of the cultures.  Non-H2-producing cells (500 mL cultures) fed succinate and provided NH4+ as nitrogen source were also harvested for RNA extraction as reference samples.  At least two samples for every given set of conditions were analyzed.

first: Wayne

last: Kontur

first: Eva

last: Ziegelhoffer

first: Melanie

middle: A

last: Spero

first: Saheed

last: Imam

middle: R

last: Noguera


title: Global methylation in normal and malignant urothelial cells

status: Public on Sep 20 2011

city: Sheffield

first: Ewa

last: Dudziec

address: Beech Hill Road

department: ICS

country: United Kingdom

institute: The University of Sheffield

summary: We have created 5-methylcytosine profiles for normal and malignant urothelial cells.

overall_design: Competitive hybridization of background and 5-methylcytosine enriched immunoprecipiated DNA fractions

first: Andreas

last: Gogol-Döring

first: Victoria

last: Cookson

first: Wei

last: Chen

first: James

last: Catto


title: Cell envelope metabolism in phosphate limited Bacillus subtilis cells

status: Public on Jul 13 2011

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary:
Investigation of the whole genome expression level changes in phosphate limited Bacillus subtilis wild-type and delta-phoPR cells
Investigation of the whole genome expression level changes of wild-type and delta-phoPR Bacills subtilis cells comparing high and low phosphate medium

overall_design: For each sample analyzed in this study 3 technical replicates were performed. 3 different samples were taken for wild-type cell and delta-phoPR cell, respectively. Samples were taken from exponentially growing cells in high and low phosphate medium as well as from phosphate-limited cells.

first: Eric

last: Botella

first: Sebastian

last: Hubner

first: Paola

last: Bisicchia

first: Annette

last: Hansen

first: David

last: Noone

first: Letal

last: Salzberg

first: Leagh

last: Powell

first: Kevin

last: Devine


title: Zebrafish embryos: exposure to 3,4-dichloraniline, 2,4-dichlorophenol, pentachlorophenol, and cadmium chloride

status: Public on May 06 2010

city: Liverpool

first: Ashley

last: Sawle

address: Crown Street

department: Biosciences

institute: University of Liverpool

summary: Large-scale toxicogenomic screening approaches offer great promise for generating a bias-free, system-wide view of toxicological effects and modes-of-action of chemicals and ecotoxicants. Early applications of microarray technology have identified relatively small groups of responding genes with which to define new targets for analysis by conventional means. We have trialled a more intensive approach to the design and interpretation of array experiments incorporating a balanced interwoven ANOVA design with higher levels of biological replication, a more thorough analysis of errors and false discovery rates, and an analysis of response patterns using gene networks. Zebrafish embryos were exposed to ecotoxicants representing different classes - 2,4-dichlorophenol (DCP), 3,4-dichloroaniline (DCA), pentachlorophenol (PCP), and cadmium chloride - at low concentrations producing a developmental disturbance to 10% of embryos, and half of this dose. Extracted RNA was then analysed on microarrays. Analysis revealed responses of 3000–5000 genes, which is 10–1000 times greater than previously reported, with significance at lower levels of fold-change. Some gene responses were common to multiple toxicants and others that were restricted to just one or two toxicants. The gene expression profiles for the different toxicants were distinctive, and analysis using network-based packages provides a high level of detail of affected processes, some of which were novel. This approach provides a more highly refined view of toxic effects, from which meaningful patterns of response can be discerned and related to functional deficits, and from which more reliable indicators of toxicological effect can be predicted.

overall_design: Interwoven loop design consisting of 12 separate conditions - two exposure concentrations plus control for each of the four toxicants - using six replicates for each conditions, each array was hybridised with independent replicates from each of two conditions resulting in 72 samples on 36 arrays

first: Andrew

last: Cossins

first: Graham

last: Whale

first: Ernst

last: Wit


title: Expression profiling of BORIS knockout mice testis

status: Public on Mar 31 2010

first: Dong-Mi

last: Shin

summary: To identify differentially expressed genes in Boris KO testis, gene expression profilings were performed with NIAID mouse customized arrays. Gene expressions of five biological replicates of Boris KO testis were compared to those of wild type testis.

overall_design: Total RNAs from WT and BORIS KO testes prepared from P14 mice were labelled with Cy5 and Cy3, respectively. Five sets of each genotype were studied.

first: Teruhiko

last: Suzuki

first: Natsuki

last: Kosaka-Suzuki

first: Jeong-Heon

last: Yoon

first: Ziedulla

last: Abdullaev

first: Elena

last: Pugacheva

first: Svetlana

last: Park

first: Herbert

last: Morse

first: Dmitri

last: Loukinov

first: Victor

last: Lobanenkov


title: Role of the global transcriptional regulator PrrA in R. sphaeroides 2.4.1

status: Public on Feb 19 2010

first: Jung Hyeob

last: Roh

address: 6431 Fannin St.

department: Microbiology & Molecular Genetics

institute: The University of Texas

summary:
We performed microarray analyses to investigate the extent of genes regulated by the Prr system.
We compared the transcriptome and proteome profiles of the wild type (WT) and mutant PrrA2 cells grown anaerobically, in the dark, with DMSO as electron acceptor.  Approximately 25% of the genes present in the genome are PrrA-regulated, at the transcriptional level, either directly or indirectly, by ≥ 2-fold relative to wild type.  The genes affected are widespread throughout all COG functional categories, with previously unsuspected “metabolic” genes affected when in the PrrA mutant background.  PrrA was found to act both as an activator and a repressor of transcription, with more genes being repressed in the presence of PrrA (9:5 ratio).  An analysis of the genes encoding the 1,536 peptides detected through our chromatographic study, which corresponds to 36% coverage of the genome, revealed that approximately 20% of the genes encoding these proteins were positively regulated, whereas approximately 32% were negatively regulated by PrrA, which is in excellent agreement with the percentages obtained for the whole genomic transcriptome profile.  In addition, comparison of the transcriptome and proteome mean parameter values chosen between WT and PrrA2 showed good qualitative agreement, indicating that transcript regulation paralleled the corresponding protein abundance.  The microarray analysis was validated by direct mRNA measurement of randomly selected, both positively and negatively regulated genes.  lacZ transcriptional and kan translational fusions enabled us to map putative PrrA binding sites, as well as revealing gene targets for indirect regulation by PrrA.

overall_design: WT R. sphaeroides 2.4.1 and the PrrA2 mutant were grown in 800 ml of medium in 1-liter glass bottles under anaerobic conditions until the optical density at 600 nm (OD600) reached approximately 0.4. RNA was isolated from a 50-ml aliquot of the culture. The experiment was performed in quadruplicate independent cultures, and three cultures were subsequently selected.

first: Jesus

middle: M

last: Eraso

first: Jung

middle: H

first: Xiaohua

last: Zeng

first: Stephen

last: Callister

first: Mary

last: Lipton

first: Samuel

last: Kaplan


title: Human carcinoma-associated fibroblasts (CAF): co-culture with cancer cells vs. CAF only

status: Public on Oct 14 2009

city: Gwangju

first: Da-Woon

last: jung

address: 1 Oryong-Dong

department: Life Science

institute: Gwangju Institute of Science and Technology

summary: Gene expression profiling of CAF co-cultured with human oral squamous cell carcinoma (OSCC) cells compared with mono-cultured CAF. To identify key molecular regulators expressed by carcinoma-associated fibroblasts (CAF) that promote cancer cell invasion, microarrays were performed by comparing co-cultured OSCC cells and CAF with monoculture controls.

overall_design:
comparison 1: CAF co-cultured with OSCC vs. mono-cultured CAF
comparison 2: OSCC co-cultured with CAF vs. mono-cultured OSCC

1.7X10(5) YD-10B OSCC cells and 1.7X10(5) CAF were seeded in the upper chamber and lower chamber, respectively, of 6-transwell plates containing collagen-coated 1 micrometer pore transmembrane filters (Becton Dickinson, Franklin Lakes, NJ, USA). Monoculture control samples were generated by culturing only CAF or OSCC on the same side of the filter as in the co-culture design.

first: Jin

last: Kim

last: Jung


title: Expression profiling of IL6 and Myc TG mouse plasmacytoma

status: Public on Feb 01 2010

first: Dong-Mi

last: Shin

summary: To identify differentially expressed genes in mouse IL6 and Myc double TG plasmacytoma, total RNAs from mouse plasmacytoma generated from IL6 + Myc TG mice were applied to NIAID mouse gene expression arrays. The transcriptome in IL6+ Myc TG mouse PCT was compared to transcriptome in IL6 TG mouse PCT

overall_design: Eleven set of IL6+Myc TG PCTs and ten set of IL6 TG PCTs were used. Total RNAs from each mouse labelled with Cy3, and reference RNAs labeled with Cy5 were hybridzed to spotted oligomicroarray.

first: Sebastian

last: Rutsch

first: Vishala

last: Neppalli

first: Wendy

last: DuBois

last: Morse 3rd

first: Hartmut

last: Goldschmidt

first: Siegfried

last: Janz


title: Transcriptional responses of Rhaodobacter sphaeroides to Tungsten

status: Public on Jun 03 2010

city: Laramie

first: Mark

last: Gomelsky

state: WY

department: Molecular Biology

institute: University of Wyoming

summary: Cultures were grown photosynthetically in the media supplemented with either Molibdenium (control), Tungsten instead of Molibdenium or conbination of the both metal ions.

overall_design: photosynthetic cultures were grown in sealed bottles at 10 W/m2 illumination.

first: Elizabeth

last: Sockett

first: Oleg

last: Moskvin


title: Leukemia inhibitory factor regulates timing of oligodendrocyte development and myelination in postnatal optic nerve

status: Public on Jul 01 2009

city: Bethesda

first: Philip

last: Lee

state: MD

address: 35 Lincoln Drive

institute: NIH/NICHD

summary: Oligodendrocyte precursor cells from postnatal day 10 optic nerve remained in a developmentally immature state in LIF-/- mice.  Partial recovery of myelin genes is seen in LIF-/- mice by postnatal day 14 in the optic nerve.  Very little difference in myelin genes in the optic nerve is seen by postnatal day 35 (adult).

overall_design: Optic nerves from male mice postnatal day 10, day 14 and day 35 (adult)

first: R

last: Fields


title: Digging deeper into the PpsR regulon of Rhodobacter sphaeroides

status: Public on Aug 31 2008

first: patrice

last: bruscella

address: 6431 Fannin

department: Microbiology and Molecular Genetics

institute: University of Texas Health Science Center

summary:
The expression of genes involved in photosystem development in Rhodobacter sphaeroides is dependent upon three major regulatory networks: FnrL, the PrrBA two-component system and the AppA-PpsR pathway. A PrrA- mutant strain of R. sphaeroides is unable to develop under photosynthetic conditions, but when combined with a ppsR mutation, is able to resume growth. In an effort to better characterize the ppsR regulon and to unravel the relationship between the PrrBA and the AppA-PpsR networks, we compared transcriptome profiles from the wild type, PrrA- and PrrA-PpsR- strains under a permissive, common, growth condition: anaerobic-dark-DMSO. Here is stored the microarray data for the PrrA-PpsR- double mutant strain grown under this condition.
Keywords: transcriptome profile

overall_design:
Rhodobacter sphaeroides PrrA-PpsR- grown under anaerobic dark DMSO conditions. Sparged with 95% N2, 5% CO2 in sistrom minimal medium A supplemented with final concentration 0.1% YE, 0.5% DMSO.

The total RNA from three independent cultures of R. sphaeroides PrrA-PpsR- grown under anaerobic-dark-DMSO conditions was used. cDNA synthesis, fragmentation, labeling and hybridization are described elsewhere (Roh et al., 2004).

first: Patrice

last: Bruscella


title: Investigation of the physiological functions of PRDM6

status: Public on Apr 01 2008

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

summary:
PRDM6 belongs to the PRDM family of transcriptional repressors that all contain a PR domain and Zinc finger domains. Prdm6 has transcriptional repressor activity. Prdm6 may regulate factors that are involved in the differentiation / proliferation of smooth muscle cells, promoting proliferation. PRDM6 knockouts are embryonic lethal around 12.0 dpc
 knockout embryos eventually develop edema: cardiovascular defect
 vascularization defect in the yolk sac: dysorganized angiogenesis
Keywords: cDNA array, yolk sac, murine embryo E10.5

overall_design: 6 homozygote samples (yolk sacs), age 10.5 days, hybridized against a pool of of 6 wildtype samples in 12 replicates including 6 dye swap experiments.

first: Johannes

last: Beckers

first: Marion

last: Horsch

first: Andreas

last: Gewies


title: Transcriptome dynamics during the transition from anaerobic photosynthesis to aerobic respiration in R. sphaeroides

status: Public on Jul 29 2008

first: Jung Hyeob

last: Roh

summary:
we performed time series microarray analyses to investigate transcriptome dynamics during the transition from anaerobic photosynthesis to aerobic respiration. Published on J. Bacteriol., 190 (1), 286-299, 2008.
Major changes in gene expression profiles occurred in the initial 15 min after the shift from anaerobic-light to aerobic-dark conditions, with changes continuing to occur up to 4 hours postshift. Those genes whose expression levels changed significantly during the time series were grouped into three major classes by clustering analysis. Class I contained genes, such as that for the aa3 cytochrome oxidase, whose expression levels increased after the shift. Class II contained genes, such as those for the photosynthetic apparatus and Calvin cycle enzymes, whose expression levels decreased after the shift. Class III contained genes whose expression levels temporarily increased during the time series.

Keywords: time course

overall_design: R. sphaeroides 2.4.1 was grown in 800 ml of medium in 1-liter glass bottles under anaerobic photosynthesis conditions. When the optical density at 600 nm (OD600) reached approximately 0.2 to 0.3, the light was turned off and the composition of the gas mixture was abruptly changed for aerobic growth conditions. RNA was isolated from a 50-ml aliquot of the culture prior to the shift to aerobic conditions (0 min) and at 15 min, 30 min, 1 h, 2 h, and 4 h after the shift. The final OD600 at 4 h was approximately 0.3 to 0.4, representing not quite a culture doubling. The experiment was performed in quadruplicate independent cultures.

first: Hiroyuki

last: Arai

first: Jung

first: Samuel

last: Kaplan


title: PCT and normal

status: Public on Sep 30 2008

first: Dong-Mi

last: Shin

summary: A hallmark feature of mature B cell tumors in humans is the occurrence of balanced chromosomal translocations, most often involving immunoglobulin (Ig) genes and a wide range of partner genes. Ig/oncogene translocations also occur in mice. However, they are regularly associated with a specific tumor type only for plasmacytomas (PCT), a neoplasm that features Ig/Myc translocations in over 95% of cases. In addition to the contribution of Myc signaling to mouse B cell lymphomagenesis, to identify any other oncogenic pathway in mouse PCT, expression profiling of mouse PCT was performed.

overall_design: six biological replicates of mouse PCT from IL-6 TG mice vs. five biological replicates of normal spleen.

first: Daniel

last: Shaffer

first: Hongsheng

last: Wang

first: Derry

last: Roopenian

first: Herbert

last: Morse


title: Regulation of hydrogen peroxide-dependent gene expression in Rhodobacter sphaeroides: Regulatory functions of OxyR

status: Public on Jun 22 2005

first: Mark

last: Gomelsky

summary:
Transcriptome profiling of Rhodobacter sphaeroides cells (WT and delta-oxyR mutant) grown in semiaerobic conditions, 7 and 30 min after addition of H2O2 up to 1 mM
Keywords: time series

overall_design: semiaerobic cultures grown in flasks; addition of hydrogen peroxide 7 and 30 min prior to cell collection

first: Tanja

last: Zeller

first: Oleg

last: Moskvin

first: Kuanyu

last: Li

first: Gabriele

last: Klug


title: The Transcriptionally Active Regions in the Genome of Bacillus subtilis

status: Public on Jun 10 2009

city: Kongens Lyngby

first: Simon

last: Rasmussen

address: Kemitorvet, Building 208

department: Department of Systems Biology

institute: Technical University of Denmark

summary: The majority of all genes have so far been identified and annotated systematically through in silico gene finding.  Here we report the finding of 3,217 strand-specific Transcriptionally Active Regions (TARs) in the genome of Bacillus subtilis by the use of tiling arrays. We have measured the genome-wide expression during mid-exponential growth on rich (LB) and minimal  (M9) medium. The identified TARs account for 81.5% of the genes as they are currently annotated and additionally we find 44 novel protein-coding genes, 85 putative non-coding RNAs (ncRNAs) and 184 antisense transcripts. Hybridization of labeled genomic DNA (gDNA) has revealed a few thousand regions giving rise to very low signals. These are mostly caused by sequence errors, as is observed in the highly degenerate trp operon and the folding of stable structures such as the regions containing Rho-independent terminators. Through this work we have discovered a group of membrane-associated genes, among these having a long conserved 3’ UnTranslated Region (UTR) predicted to fold into a large and highly stable structure. Among these are YwbN, a target of the twin-arginine translocase (Tat) protein translocation system.

overall_design:
The transcriptionally active regions were determined at two different conditions, rich medium (Luria Broth) and minimal medium (M9). Cells were harvested at mid-exponential phase (OD600 = 0.5) and each condition were replicated three times.
From each replicate RNA was extracted using FastRNA pro blue kit (Qbiogene) and labelled with Cy3 using a strand-specific protocol. The cDNA was hybridized to 385K NimbleGen tiling arrays 'BaSysBio Bsub T1' covering the entire genome with 45-65 nt isothermal probes, spaced by 22 nt on each strand.
Additionally genomic DNA was extracted from 4 replicates at OD600 = 0.5, labelled and hybridized to the tiling arrays. These serve as a reference for the mRNA hybridizations.

The normalized RNA hybridization signals were used to create segments using a structural change model (Huber et al, 2006) and transcriptionally active regions were identified by a segment joining-scheme.

first: Hanne

last: Jarmer

first: Henrik

last: Nielsen


title: PpsR regulon in Rhodobacter sphaeroides

status: Public on Jul 03 2004

summary:
mRNA levels were measured in  Rhodobacter sphaeroides 2.4.1 at 20% O2 and 0.5% O2, Rhodobacter sphaeroides 2.4.1 App11 (AppA-null), Rhodobacter sphaeroides 2.4.1 (pPNs) and PpsR mutant PPS2-4.   The mRNA samples were prepared from cultures supplied with 20% O2, 1% CO2, and 79% N2, and grown in the dark to an OD of 0.18.   The mRNA levels for each strain was measured three times.
Keywords: repeat sample


title: 4 growth modes - RNA from Laramie & Houston RNA

status: Public on Jul 19 2003

summary:
aerobic, semiaerobic (3% O2),photosynthetic and DMSO growth conditions, 2.4.1 strain. Growth and RNA isolation were done independently in 2 laboratories (Laramie and Houston). Genechip sample preparation - in Laramie.
Keywords: ordered

sample_organism:
Cereibacter sphaeroides
Cereibacter sphaeroides 2.4.1


title: CT01 vs wild-type at 3% O2

status: Public on Apr 01 2005

first: Timothy

last: Donohue

address: 1552 University Avenue

department: Bacteriology

institute: University of Wisconsin - Madison

summary:
Comparison of wild-type (2.4.1) and CT01 (contains an omega Spr/Smr insertion in RSP4157) gene expression; growth condition is (3% O2 + 96%N2 + 1%CO2) semi-aerobic growth in the dark.  Manuscript in preparation.

The below normalized data was generated using GeneSpring software with the following settings:

A data:
Data Transformation: set all values less than 0.01 to 0.01
Per Chip: normalize to 50th percentile, and then
Per Gene: normalize to median

B data:
Data Transformation:  set all values less than 0.01 to 0.01
Per Chip: normalize to 50th percentile
Values from independent replicates were averaged
Keywords = Rhodobacter sphaeroides
Keywords = photosynthesis
Keywords = semi-aerobic
Keywords = purple bacteria
Keywords: other

first: Christine

middle: L

last: Tavano


title: 30% O2 vs PS 10W/m2

summary:
Comparison of wild-type (2.4.1) R. sphaeroides gene expression in 30% O2 aerobic respiration vs. photosynthesis 10W/m2 light, to identify candidate photosynthesis genes.
RNA preparation:  pellet cells from exponential phase cultures using 5% phenol in ethanol stop solution; lysozyme + SDS to lyse; phenol/chloroform extraction + DNase treatment + RNeasy kit clean up.  Manuscript in preparation.

The below normalized data was generated using GeneSpring software with the following settings:

A data:
Data Transformation: set all values less than 0.01 to 0.01
Per Chip: normalize to 50th percentile, and then
Per Gene: normalize to median

B data:
Data Transformation: set all values less than 0.01 to 0.01
Per Chip: normalize to 50th percentile
Values from independent replicates were averaged
Keywords = Rhodobacter sphaeroides
Keywords = photosynthesis
Keywords = purple bacteria
Keywords: other

first: Jennifer

last: Anthony


title: Rhodobacter sphaeroides respiration and photosynthesis

summary:
This series contains two subsets of samples not being directly compared. The two subsets are:

GSE2145: 30% O2 vs PS 10W/m2
GSE2146: CT01 vs wild-type at 3% O2

Below results represent the K-means (K=4) clustering analysis using GeneSpring software.
The list contains genes/ORFs contained in each of the 4 clusters.
Keywords: other


title: Rhodobacter sphaeroides salt stress response

status: Public on Jun 22 2007

summary:
Two excessive NaCl concentrations (0.25%  and 1.5%) and two periods of treatment (7 min and 45 min) were used as moderate- and high-salt sress conditions at early and later stages of response, respectively. As a baseline, samples from cells grown on a standard SIS medium in the same growing system and same illumination were used.
Keywords: time course and dose response

overall_design: Cells were grown photosynthetically (10W/m2 illumination) in 60-ml tubes bubbled with 2% CO2, 98% N2. NaCl (dissolved in anoxic buffer) was added at OD600=0.4

first: Minoru

last: Tsuzuki

first: Jill

last: Zeilstra


title: Oxygen-dependent transcriptome profiling in R.sphaeroides 2.4.1 in the dark

status: Public on Feb 14 2007

summary:
Wild type (2.4.1) strain, dark conditions, controlled oxtgen concentration in the growth medium (achieved by constant sparging with a gas mixture containing 1% CO2, variable - indicated for every sample - concentration O2 and balance N2).
Keywords: dose response

overall_design: Cells were harvested at OD 0.16-0.18 after rapid addition of rifampicin, spun down and frozen for subsequent RNA isolation. RNA was isolated using bead beater and RNeasy kit. Traces of DNA were removed by DNAse I treatment until level non-detectable by 33-36 cycles of real-time PCR. Further sample preparaton -according Affymetrix protocols. Data processing: MAS 5.0 values are deposited here (for compatability with other submitted samples), values used in the publications are obtained with RMA and may be recreated using the supplied CEL files.


title: Wild type versus Delta ChrR

summary:
Comparing wild type to strain lacking anti sigma factor ChrR.  Aerobic conditions (30% oxygen).
Keywords = SigmaE
Keywords = ChrR
Keywords = Oxygen stress
Keywords: other


status: Public on Jun 17 2004

summary:
Data used in "Responses of the Rhodobacter sphaeroides Transcriptome to Blue Light Under Semiaerobic Conditions" paper. Cells are grown at 10% O2 (see detailed description in the paper and in the sample info).
Keywords: time-course

first: Stephan

last: Braatsch