title: Kinesin-associated RNA: RNA co-immunoprecipitated with Kinesin IP vs RNA from Aplysia CNS

summary:
Whole genome transcriptional profiling is used to identify ESTs found in RNA co-immunoprecipitated from Aplysia CNS with antibodies against Aplysia Kinesin Heavy Chain (ApKHC)
RNA derived from Aplysia CNS served as control in the opposite channel. Custom Aplysia EST array to probe the samples was designed and ordered from Agilent.

last: Puthanveettil


title: Toward synaptic transcriptomes: Direct sequencing and identification of RNAs actively transported by the kinesin complex from the cell body to synapses in Aplysia neurons

status: Public on Apr 24 2013

city: St Augustine

first: Andrea

middle: B

last: Kohn

state: FL

address: 9505 Ocean Shore Blvd

department: Whitney lab

country: USA

institute: University of Florida

summary: Specific mRNAs are transported from the cell body to synapses where their translation can modify communication of pre-existing synapses and induce formation of new synaptic connections in response to learning.  Little is known, however, about the identity of the RNAs that are actively transported and when and how these RNAs are utilized during learning. By focusing on RNAs that are associated with kinesin, a motor protein that transports gene products from the cell body to synapses, we have now applied microarrays and 454 sequencing to identify actively transported RNAs from the Aplysia central nervous system. Using a library prepared from the kinesin complex immunoprecipitated from the central nervous system (CNS), we have identified thousands of unique transcripts, of which ~600 mRNAs were annotated.

overall_design: Two sample comparison: kinesin IP vs. control.

first: Sathyanarayanan

middle: V

first: Eric

middle: R

last: Kandel

first: Leonid

middle: L

last: Moroz


title: Imatinib Disrupts Lymphoma Angiogenesis by Targeting Vascular Pericytes

status: Public on Apr 22 2013

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

summary: Pericytes/vascular smooth muscle cells (VSMCs), regulated by platelet-derived growth factor receptor β (PDGFRβ) signaling, play important roles in endothelial survival and vascular stability. Here we report that treatment with imatinib, an inhibitor of PDGFRβ, led to significant tumor growth impairment associated with increased apoptosis in human lymphoma xenografts including Farage, Karpas422 and OCI-Ly7 in SCID mice. Confocal analysis of the tumor tissue showed decreased microvessel density, decreased vascular flow, and increased vascular leak in the imatinib-treated cohorts. Imatinib targeted tumor-associated PDGFRβ+ pericytes in vivo by inducing apoptosis and disruption of the PDGFRβ+ perivascular network, and PDGFRβ+ VSMC in vitro by inhibition of proliferation. FACS analysis of mononuclear cell suspension of tumor tissues revealed decreased mature pericytes and endothelial cells, as well as their progenitors with imatinib treatment. Compared to imatinib, treatment with anti-PDGFRβ monoclonal antibody partially inhibited the growth of Farage lymphomas. Lastly, microarray analysis of differentially expressed genes in PDGFRβ+ VSMC following imatinib treatment showed significant down-regulation of genes implicated in proliferation, survival and angiogenesis, including those within PI3K/AKT and MAPK/ERK1/2 pathways downstream of PDGFRβ signaling. Taken together, targeting PDGFRβ+ pericytes in lymphoma presents a novel and complementary target to endothelial cells for efficacious antiangiogenic therapy.

overall_design: PDGFRb+ murine vascular smooth muscle cells (VSMCs) were treated in 10 uM imatinib for 24 or 48 hours. Gene expression changes in response to imatinib treatment were examined using NimbleGen MM8_60mer gene expression microarrays by comparing expression patterns at 24- and 48-hours treatment to the baseline level (0 hours).

first: Jia

last: Ruan

first: Chunjie

last: Wang

first: Lei

last: Fan

first: Shao-ning

last: Yang

first: Humin

first: Juqun

last: Shen

first: John

middle: P

last: Leonard

first: Ari

last: Melnick

first: Leandro

last: Cerchietti

first: Katherine

middle: A

last: Hajjar


title: DNA methylome signature in rheumatoid arthritis

status: Public on Apr 25 2013

city: San Diego

middle: William

last: Whitaker

state: Ca

address: Gliam Drive

institute: UCSD

summary:
Objectives: Epigenetics can influence disease susceptibility and severity. While DNA methylation of individual genes has been explored in autoimmunity, no unbiased systematic analyses have been reported. Therefore, a genome-wide evaluation of DNA methylation loci in fibroblast-like synoviocytes (FLS) isolated from the site of disease in rheumatoid arthritis (RA) was performed.

Methods: Genomic DNA was isolated from six RA and five osteoarthritis (OA) FLS lines and evaluated using the Illumina HumanMethylation450 chip. Cluster analysis of data was performed and corrected using Benjamini–Hochberg adjustment for multiple comparisons. Methylation was confirmed by pyrosequencing and gene expression was determined by qPCR. Pathway analysis was performed using the Kyoto Encyclopedia of Genes and Genomes.

Results: RA and control FLS segregated based on DNA methylation, with 1859 differentially methylated loci. Hypomethylated loci were identified in key genes relevant to RA, such as CHI3L1, CASP1, STAT3, MAP3K5, MEFV and WISP3. Hypermethylation was also observed, including TGFBR2 and FOXO1. Hypomethylation of individual genes was associated with increased gene expression. Grouped analysis identified 207 hypermethylated or hypomethylated genes with multiple differentially methylated loci, including COL1A1, MEFV and TNF. Hypomethylation was increased in multiple pathways related to cell migration, including focal adhesion, cell adhesion, transendothelial migration and extracellular matrix interactions. Confirmatory studies with OA and normal FLS also demonstrated segregation of RA from control FLS based on methylation pattern.

Conclusions: Differentially methylated genes could alter FLS gene expression and contribute to the pathogenesis of RA. DNA methylation of critical genes suggests that RA FLS are imprinted and implicate epigenetic contributions to inflammatory arthritis.

overall_design: Fibroblast-like synoviocyte cell-lines from osteoarthritis (OA) and rheumatoid arthritis (RA) patients.

middle: W

first: Kazuhisa

last: Nakano

first: David

last: Boyle

first: Wei

first: Gary

middle: S

last: Firestein


title: Gene expression in cellular compartments of Aplysia motor neurons

status: Public on Apr 26 2013

city: New York

first: Sergey

last: Kalachikov

state: NY

address: NWC Bld, 550 West 120th Street Rm 1002

department: Chemical Engineering

institute: Columbia University

summary:
Whole genome transcriptional profiling is used to compare ESTs found in cell bodies and processes of Aplysia motor neurons
RNA samples derived from cell bodies or processes of Aplysia single cultured motor neurons were hybridized to custom Aplysia EST microarrays.

overall_design: Two-condition experiment; four biological replicates for each condition were reciprocally hybridized on each two-color array

first: Sathyaramayanan

last: Puthanveetil

first: Irina

last: Morozova


title: Genomic analysis of diffuse pediatric low-grade gliomas identifies recurrent, oncogenic MYBL1-truncating rearrangements

status: Public on Apr 23 2013

city: Boston

first: Peleg

middle: Moshe

last: Horowitz

state: MA

address: 44 Binney St. SM1010

department: Cancer Biology

institute: Dana-Farber Cancer Institute

type: Genome variation profiling by genome tiling array

summary: Pediatric low-grade gliomas (PLGGs) are among the most common solid tumors in children but apart from BRAF mutations or duplications in specific subclasses, few genetic driver events are known. Diffuse PLGGs comprise a set of uncommon subtypes that exhibit invasive growth and are therefore especially challenging clinically.  These tumors are particularly poorly understood. We performed high-resolution copy-number analysis of 44 diffuse PLGGs to identify recurrent alterations. Diffuse PLGGs exhibited fewer such alterations than adult low-grade gliomas, but we identified several significantly recurrent events. The most significant event, 8q13.1 gains, were observed in 28% of diffuse astrocytomas grade II (DA2s) and resulted in partial duplication of the transcription factor MYBL1 with truncation of its C-terminal negative-regulatory domain. A similar recurrent deletion-truncation breakpoint was identified in two angiocentric gliomas in the related gene MYB on 6q23.3. Whole-genome sequencing of a MYBL1-rearranged DA2 demonstrated MYBL1 tandem duplication, and few other events. Two novel, truncated MYBL1 transcripts identified in this tumor induced anchorage-independent growth when expressed in 3T3 cells and tumor formation in nude mice. Truncated transcripts were also expressed in two additional tumors with MYBL1 partial duplication. Our results define clinically relevant molecular subclasses of diffuse PLGGs and highlight a potential role for the MYB family in the biology of low-grade gliomas.

overall_design: IRB approval from all institutions was obtained, and all samples were from patients who provided informed consent or were studied with waiver of the requirement for informed consent by the appropriate IRB. Samples of various histologic subtypes were identified and collected at multiple institutions (Boston Children’s Hospital, Boston, MA, The University of Texas School of Medicine Southwestern, Dallas, TX, Children’s Cancer Hospital, Egypt, Cairo, Johns Hopkins University School of Medicine, Baltimore, MD, Children’s National Medical Center, Washington, DC, The Hospital for Sick Children, Toronto, Canada, Mayo Clinic, Rochester, MN). Central histopathologic review was performed by at least three board-certified neuropathologists using WHO criteria. DNA extraction from archival FFPE samples and Array CGH were performed as previously described (Craig, et al., 2012 PLoS One). GC-normalized copy-number data for the samples were then cleaned of known germline CNVs. Circular Binary Segmentation was used to segment the copy-number data, using parameters [alpha=0.001, undo.splits=sdundo, undo.SD=1.5, min.width=5]. Forty-four samples passed QC metrics (based on aCGH quality metrics for DNA integrity) for inclusion in the GISTIC analysis. Segmented data were analyzed with GISTIC 2.0 to determine statistically significant recurrent broad and focal CNAs. The following parameters were used: minimum segment size = 8, lesion amplitude threshold = 0.2, focal/broad cutoff = 0.9x chromosome arm length, q-value threshold 0.10, and gene confidence level 0.95.

first: Lori

last: Ramkissoon

middle: M

first: Justin

last: Craig

first: Shakti

middle: H

first: Benjamin

middle: E

last: Rich

first: Steve

last: Schumacher

first: Aaron

last: McKenna

first: Mike

last: Lawrence

first: Guillaume

last: Bergthold

first: Priscilla

middle: K

last: Brastianos

first: Barbara

last: Tabak

first: Matthew

middle: D

last: Ducar

first: Paul

last: vanHummelen

first: Laura

last: MacConaill

first: Tina

last: Pouissant-Young

first: Yoon-Jae

last: Cho

first: Hala

last: Taha

first: Madeha

last: Mahmoud

first: Daniel

middle: C

last: Bowers

first: Linda

last: Margraf

first: Uri

last: Tabori

first: Cynthia

last: Hawkins

first: Roger

middle: J

last: Packer

first: Dana

last: Hill

first: Scott

last: Pomeroy

first: Charles

middle: G

last: Eberhart

first: Ian

middle: F

last: Dunn

first: Liliana

last: Goumnerova

first: Gad

last: Getz

first: Jennifer

last: Chan

first: Sandro

last: Santagata

first: William

last: Hahn

last: Stiles

first: Azra

last: Ligon

first: Mark

last: Kieran


title: Fis occupancy along the Salmonella enterica serovar Typhimurium SL1344 fis::3XFlag strain grown in different aeration regimes.

status: Public on May 01 2013

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

type: Genome binding/occupancy profiling by genome tiling array

summary: The regulatory role of the Fis protein in fis and in the transcription of several gene regions during mid-exponential and late-stationary phase, and during different growth aeration regimes, has been investigated. Studies were done during those two growth phases and in aerated and non-aerated (microaerobic) conditions, to measure Fis enrichment and binding peaks in strategic gene regions by genome-wide microarray analysis ChIP-chip. This research investigation points to central roles for SPI-1, SPI-2, DNA gyrase and topoisomerase I, the elements of the stringent response, and the regulatory function of Fis-binding patterns, in setting and re-setting the activity of the fis gene and other involved promoters as a function of the growth conditions and aeration regimes experienced by Salmonella.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: One sample with four different treatments. Three biological replicates per sample. The Aerated 2 hour sample was set as the control condition for all samples.

first: Seratna

last: Guadarrama

first: Shane

last: Dillon

last: Dorman


title: Diel growth of Thalassiosira pseudonana

status: Public on Apr 18 2013

city: Seattle

first: Justin

last: Ashworth

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Transcript levels of all T. pseudonana genes was measured every twelve hours throughout the batch (non-chemostatic) growth of axenic cells grown in large glass bioreactors on a 12hr:12hr dark:light cycle for five days. The data were analyzed to reveal the physiological and regulatory changes that recurred in this diatom when transitioning between dark and light conditions, as well as from exponential phase to stationary, nutrient limited conditions. The longitudinal experiment was performed with two replicates, at 400 and 800ppm CO2.

overall_design: Two growth experiments were conducted, with 10 and 9 longitudinal samples collected from each experiment, respectively. Two-color arrays were used with dye flips for labeling. A common internal reference sample was used for one channel on each array. Expression changes for longitudinal analysis were calculated as the difference from the mean log2 expression ratio for each to the common reference sample, for each gene, over all samples within an experiment. For the analysis of diel states in T. pseudonana, samples from the two series were matched according to the time from innoculation, and divided into four classes: dawn samples (taken at the end of each dark phase), dusk samples (taken at the end of each light phase), exponential samples (the first five samples in each series prior to a drop in growth rate on Day 3), and stationary samples (all samples including following the drop in growth rate on Day 3).

first: Mónica

middle: V

last: Orellana

first: Nitin

last: Baliga


title: Transcriptional profiling of ptc6 and ptc1ptc6 mutant yeast cells and the effects of Rapamycin

status: Public on Apr 19 2013

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

country: Spain

institute: Universitat Autonoma de Barcelona

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

overall_design: Refer to individual Series

first: Asier

last: Gonzalez

first: Carlos

last: Casado

first: Joaquin

last: Arino


title: Doxorubicin enhances nucleosome turnover around promoters

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

type: Expression profiling by genome tiling array

summary:
We use a metabolic labeling strategy for directly measuring nucleosome turnover to examine the effect of doxorubicin on chromatin dynamics in squamous cell carcinoma cell lines derived from genetically defined mice. We find that doxorubicin enhances nucleosome turnover around gene promoters, and turnover correlates with gene expression level.

Keywords: Chromatin affinity-purification on microarray

overall_design: 26 CATCH-IT arrays and 8 expression arrays.

first: Fan

last: Yang

first: Christopher

last: Kemp

first: Steven


title: Gene Expression Changes in the Spinal Cords of Lewis Rats with Myelin Basic Protein-Induced Experimental Autoimmune Encephalomyelitis (EAE)

status: Public on Apr 03 2013

city: Brisbane

first: Hayley

middle: Ruth

last: Inglis

state: Queensland

address: Building 71/918, Royal Brisbane & Women’s Hospital Campus,Herston, QLD, 4029

department: Clinical Neurosciences

country: Australia

institute: University of Queensland , Centre for Clinical Research

summary:
Myelin Basic Protein (MBP) induced experimental autoimmune encephalomyelitis (EAE) in the Lewis rat, produces an an acute weakness, or paralysis of the tail and hind limb ataxia ,weakness or paralysis associated with increased permiability of the blood brain barrier, inflammation and demyelination in central nervous system (CNS).  Clinical symptoms , ascending weakness or paralysis of the tail followed by the hind limbs and in rare cases the fore limbs occurs 8 and 14 days post immunisation (dpi) and is generally resolved completely by day 20  dpi.  We have carried out transcriptome analysis of total RNA from the spinal cords of female Lewis rats at the peak of disease (EAE)  and age matched  healthy controls to identify gene expression changes associated with the disease.
In these data sets we include the exon and gene expression data obtained from total RNA preparations from the spinal cords of female Lewis  rats sacrificed at the clinical peak of MBP induced EAE and age matched , untreated, healthy controls.  This data was used to obtain 2265 mapped IDS wich identified 1190 known genes which were differentially expressed in the spinal cord in EAE compared to healthy animals.

overall_design: 8 total RNA samples were prepared.  A two way ANOVA comparison carried out in Partek Genomics Suite was used to detect gene transcripts for which the expression levels varied significantly (un-adjusted p-values ≤ 0.05) from the healthy controls.  2265 mapped IDs were uploaded to the Ingenuity pathway analysis suite (IPA)  where 1190 known genes were identified as being differentially regulated between groups.  An FDR ≤ 5% and fold change limit of +/- 4.0 further refined the data set to identify the 72 most highly and significantly differentially regulated genes in the spinal cord at the clinical peak of disease in MBP induced EAE in the Lewis rat.

middle: R

first: Judith

last: Greer

first: Pamela

last: McCombe


title: Expression data from subcutaneous adipose tissue of barrows and boars

status: Public on Apr 08 2013

city: Beijing

first: Yuchang

last: Yao

address: College of Animal Science and Technology, China Agricultural University, 2 Yuanmingyuan Xilu, Haidian District

country: China

institute: China Agricultural University

summary:
The male hypogonadism is closely associated with adipose tissue metabolism. Domestic pig has been a widely used experimental animal in biomedical research because of their similarity to humans in body size and other physiological/anatomical features.  However, the transcriptional responses of pigs to male hypogonadism in subcutaneous adipose tissue remain unclear so far.
We used microarrays to detail the transcriptional profiles of barrows and boars, and determined the gene networks regulated by castration-induced sex hormone deficiency. This study will help to provide a significant addition to knowledge about fat accumulation and lipid metabolism in hypogonadal man.

overall_design: The subcutaneous adipose tissue of barrows and boars were acquired at 175 d of age for RNA extraction and hybridization on Affymetrix microarrays. All the fifteen pairs of full sibs were divided into six subgroups. An equal amount of total RNA from 5 boars was pooled in a subgroup, and RNA from 5 barrows in each pair of full sibs was pooled in another subgroup. Each pooled RNA sample was hybridized to a separate array. A total of 6 gene chips were used in this study, resulting in three biological duplicates.

first: Yu-Chang

first: Chun-Jiang

last: Zhao


title: Identifying chromatin associations with promyelocytic leukemia nuclear bodies using immunoTRAP

status: Public on Mar 28 2013

city: Toronto

first: Paul

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

summary: Studies using fluorescence in situ hybridization (FISH) have attempted to determine whether specific gene loci associate with promyelocytic leukemia nuclear bodies (PML NBs).  Two drawbacks accompany this approach; the lack of spatial resolution inherent with the technique, and the a priori basis for selecting which genes to probe.  To overcome these limitations, we developed a technique, which we call immunoTRAP, which purifies the DNA contacting PML NBs at molecular dimensions.  When we combined the immunoTRAP technique with immunoFISH and microarray analysis, not only did we verify a TP53-PML NB association, but were able also to identify novel locus associations such as PML, ABCA7, and TFF1.  In addition, we observed that these associations are cell type specific, and induction of significantly higher levels of PML gene expression, as well as other physiological changes brought about by interferon treatment, can lead to a physical association of the PML gene with PML NBs in normal human fibroblasts. Thus, immunoTRAP is a technique capable of identifying the chromatin associations around nuclear subcompartments and is amenable for further downstream applications such as microarray analysis or deep sequencing.

overall_design: Identification of binding (Cy5) to PML vs. to non-specific binding in Jurkat cells (n=5)

first: Reagan

last: Ching

first: Kashif

last: Ahmed

first: Linda

middle: Z

last: Penn

first: David

middle: P

last: Bazett-Jones


title: Identification of a prognostic gene expression-based signature for patients with prostate cancer treated with radical prostatectomy

status: Public on Apr 01 2013

first: Yi

last: Zhang

address: 9640 Towne Centre Drive, Suite 200

institute: bioTheranostics

summary: Gene expression profiling was performed on tissue samples via a complementary DNA-mediated annealing, selection, extension, and ligation (DASL) assay (Illumina).  1536 were selected for profiling. 210 prostate cancer samples were used.Random forests classifcation was applied to the DASL data, and a set of genes was selected for further development.

overall_design: Total RNA was isolated from prostate cancer prostatecomy samples, purified,  cDNA generated, and DASL performed.

first: Mark

last: Erlander


title: Marker gene discovery for Staphylococcus epidermidis infection in zebrafish embryos (Agilent)

city: Leiden

first: Wouter

last: Veneman

state: Zuid-Holland

address: Einsteinweg 55

department: Institute Biology Leiden

country: Netherlands

institute: Leiden University

summary: We use the zebrafish embryo model to study the innate immune response against Staphylococcus epidermidis. Therefore, we injected S. epidermidis (and three controls groups) into the yolk at 2 hpf and samples at mutiple timepoints. Gene expression profiles were obtained at 6, 30, 54, 78, 102 and 126 hpi by microarrays. The results show that the gram-positive bacterium S. epidermidis induces a late immune response with a strong response at 102 hpi.

overall_design: This microarray study was designed to determine the gene expression profile during infection with Staphylococcus epidermidis. RNA was isolated from groups of embryos (20) at 6 timepoints during the infection. Wildtypes zebrafish embryos were micro-injected into the yolk (2hpf) with (1) 20 CFU of S. epidermdis O-47 mCherry bacteria suspended in PVP (Polyvinylpyrrolidone), (2)  mock-injected with PVP as a control, (3) Needle insertion as control, (4) Non-injected as a control. After injections embryos were transferred into fresh egg water and incubated at 28°C. At 8 hpf (6 h post infection), 32 hpf (30 h post infection), 56 hpf (54 h post infection),  80 hpf (78 h post infection),  104 hpf (102 h post infection) or  128 hpf (126 h post infection) twenty embryos per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.  All treatment groups were analyzed using a common reference approach.

first: W

first: H

last: Spaink

first: A

last: Meijer

first: O

middle: W

last: Stockhammer


title: Differential expression of skeletal muscle genes between normal and pale, soft and exudative (PSE) turkey meat.

status: Public on Mar 20 2013

city: East Lansing

first: Yuwares

last: Malila

state: Michigan

address: 3340 Anthony Hall

department: Food Science and Human Nutrition

institute: Michigan State University

summary: The objective of this study was to determine differential gene expression of turkey breast muscle regarding development of PSE meat defect. Genetically unimproved, random-bred (RBC2) turkeys representing turkeys from 1966, which are smaller and grow slower than modern turkeys, were raised at the Michigan State University (MSU) Poultry farm and harvested at 22 week of age. Breast meat was collected and snap frozen in liquid nitrogen. Percent marinade uptake at 24h post-slaughter of each sample was determined. The highest (n=6) and the lowest (n=6) marinade uptake were classified as normal and PSE, respectively. Differentially expressed genes between normal and PSE was identified using TSMLO microarray and confirmed by qRT-PCR. Forty-one oligos were differentially expressed (false discovery rate, FDR<0.1). Candidate genes and pathways associated with development of PSE in turkey were suggested for further experiment to gain greater comprehension about this meat quality defect.

overall_design: Two-condition experiment: normal vs PSE; Biological replicate: n=6 for each condition; Birds were randomly assigned to an array and hybridizations were performed in random order.

first: Kelly

last: Sporer

first: Rob

last: Tempelman

first: Gale

last: Strasburg


title: Expression data of Nodule Cysteine-Rich (NCR) Defensin-Like (DEFL) genes in different stages of nodule development in Medicago truncatula

status: Public on Mar 05 2013

city: Minneapolis

first: Kevin

middle: A

last: Silverstein

state: MN

address: 599 Walter Library, 117 Pleasant St SE

department: Minnesota Supercomuting Institute

institute: Universtiy of Minnesota

summary: We have undertaken a detailed study to identify mechanisms regulating expression of NCRs. We used a custom Affymetrix oligonucleotide microarray to examine the expression changes of 566 NCRs in different stages of nodule development. Additionally, rhizobial mutants were used to understand the importance of the rhizobial components in induction of NCRs. Early NCRs were detected during the initial infection of rhizobia in nodules and continue to be expressed into the late stages of nodule development. Late NCRs were induced concomittant with bacteroid development in the nodules. The induction of these groups of genes was correlated with the number and morphology of rhizobia in the nodule.

overall_design: We used a custom Affymetrix chip containing 684 probe sequences of Medicago DEFLs to explore the expression patterns of NCRs in nodules inoculated with Sinorhizobium meliloti 1021(Sm1021) at marked developmental stages and nodules inoculated with various mutants derived from Sm1021 totalling 14 different treatments. Each treatment was supported by three biological replicates giving a grand total of 42 samples.

first: Sumitha

last: Nallu

first: Kathryn

last: VandenBosch

first: Deborah

last: Samac

first: Bruna

last: Bucciarelli

first: Carroll

last: Vance


title: Legionella pneumophila transcriptomic response to CuO nanoparticles

status: Public on Mar 04 2013

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

institute: McGill University

summary: Legionella pneumophila was exposed for 3h to 160 ug/ml of CuO nanoparticle. Untreated samples are used as the control condition.

platform_organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

overall_design: Two conditions: CuO (treated) and UN (untreated control. Three bioilogical repliucates. Genomic DNA is used as a reference channel. (Talaat, 2002, NAR).

first: Jingrang

last: Lu

first: Ian

last: Struewing

first: Helen

middle: Y

last: Buse

first: Jiahui

last: Kou

first: Howard

last: Shuman

first: Nicholas

last: Ashbolt


title: Transcriptional profiling of yeast cells lacking either the protein phosphatase Ptc6 or Ptc1 and Ptc6, members of the 2C family of protein phosphatases in Saccharomyces cerevisiae.

first: Antonio

last: Casamayor

summary: Type 2C protein phosphatases are encoded in Saccharomyces cerevisiae by several related genes (PTC1-7). To gain insight into the functions attributable to a specific member of this gene family, we have investigated the transcriptional profile of ptc6 mutants under standard growth conditions. We have found that lack of Ptc6 did not alter the transcriptional profile when cells were in log phase in YPD medium. Only one gene, involved in iron transport (FIT3), in addition to PTC6 itself, was considered down-regulated. We also identified the transcriptional changes induced by the simultaneous lack of Ptc1 and Ptc6 proteins.

overall_design:
* In a first set of experiments we compared the expression profile of ptc6 mutant cells with that of wt cells. We performed 2 biological replicates, and for each experiment we performed two chips (dye swap). Overall we analyzed 4 chips:

Biological replicate 1: GSM937247, GSM937248

Biological replicate 2: GSM937251, GSM937252

* In the second set of data we compared the expression profile of ptc1ptc6 double mutant cells with that of wt cells. We performed 2 biological replicates, and for each experiment we performed two chips (dye swap). Overall we analyzed 4 chips:

Biological replicate 1: GSM937312, GSM937316

Biological replicate 2: GSM937319, GSM937320

first: Asier

last: Gonzalez

first: Carlos

last: Casado

first: Joaquin

last: Arino


title: Transcriptional profiling of Rapamycin-treated ptc6 and ptc1ptc6 mutant yeast cells

summary: We are interested in the study of the sensitivity of yeast cells lacking either the type 1 protein phosphatase Ptc6 or Ptc1 and Ptc6 to the drug rapamycin. In order to carry out our studies, we analyzed the changes in the transcription profile that a short-term incubation with rapamycin (200 ng/mL) has in wild type, ptc6 mutant and ptc1 ptc6 double mutant cells. It has been shown that inhibition of the TOR pathway by treatment with rapamycin has profound effects on the global transcriptional profile. We confirmed the previously described transcription changes induced by the drug in wild type cells and characterized an notable attenuation of the transcriptional response in cells lacking either PTC6 or PTC1 and PTC6 genes.

overall_design:
* First we compared the expression profile of Rapamycin-treated wild type with that of mock-treated cells. There is one biological replicate with two chips (dye swap).

Techical replicate: GSM937443, GSM937444

* In the second set of experiments we compared the expression profile of Rapamycin-treated ptc6 mutant cells with that of mock-treated ptc6 mutant cells. We performed one biological replicate in two chips (dye swap).

Techical replicate: GSM937471, GSM937472

* In the third set of data we compared the expression profile of Rapamycin-treated ptc1ptc6 double mutant cells with that of mock-treated ptc1 ptc6 mutant cells. There is one biological replicate with two chips (dye swap).

Techical replicate: GSM9373476, GSM9373495


title: Transcriptional analysis of Bos taurus and AlHV-1 in MDBK infected cells and in lymph nodes of infected calves

status: Public on Mar 21 2013

city: Liege

first: Leonor

last: Palmeira

address: Bd Colonster 20

department: Faculty of Veterinary Medicine

country: Belgium

institute: University of Liege

summary:
Wildebeests carry asymptomatically Alcelaphine herpesvirus 1 (AlHV-1), a γ-herpesvirus inducing a lethal lymphoproliferative disease named malignant catarrhal fever (MCF) in a number of susceptible species of the Artiodactyla order, including cattle. The local population welfare in eastern Africa is directly endangered by the important but underestimated impact of this disease on their livelihood. Although AlHV-1 genomic DNA is detected in abundance in tissues during MCF, no infectious viral particles and very low viral protein expression levels are observed. This suggests that AlHV-1 might be latent during MCF. Here, we studied the implication of AlHV-1 latency during MCF.

We first examined the expression of poly-adenylated RNA from infected (multiplicity of infection, moi = 0.01) MDBK cells at 72h pi. This late time point was chosen as we expect the majority of viral genes to be expressed. The expression was obtained from two-color dye-swap analyses of 4 independent biological repeats.

To determine cellular and viral gene expression during MCF, we extracted RNA from the inguinal LN (iLN) of each calf for analysis on a custom designed array. The arbitrary choice of the iLN as the selected tissue was based on the fact that AlHV-1 viral genomic load are the highest in the LN. Cellular and viral RNA transcription profiles were analyzed with two-color dye-swap analyses of 4 independent biological repeats.

platform_organism:
Bos taurus
Alcelaphine gammaherpesvirus 1

overall_design: Cellular and viral gene expression were analysed in Mock- and AlHV-1-infected MDBK cells (in vitro) as well as in the inguinal lymphnodes of Mock- and AlHV-1-infected calves (in vivo). Each experiment (in vitro and in vivo) was carried out with 4 biological replicates for each conditon (mock- and AlHV-1-infected). The 4 samples for each experiment were hybridized in a one-to-one dye-swap design without pooling the Mock-infected samples, and yielding 8 arrays per experiment.


title: The human Gut Chip “HuGChip”, an explorative phylogenetic microarray for determining gut microbiome diversity at Family level

status: Public on Mar 01 2013

city: Clermont-Ferrand

first: Nicolas

last: Parisot

address: 28 place Henri Dunant

country: France

institute: EA 4678 CIDAM

summary:
A phylogenetic microarray targeting 66 families described in the human gut microbiota has been developped aud used to monitor the gut microbiota's structure and diversity. The microarray format provided by Agilent and used in this study is 8x15K.
A study with a total of 4 chips was realized.

sample_organism:
Escherichia coli
Bacteroides fragilis
[Clostridium] leptum
Lactobacillus acidophilus
Blautia producta
uncultured bacterium

overall_design:
Arrays 1 and 2: Hybridization with 100ng of labelled 16S rRNA gene amplicons from a mock community sample and 250ng of labelled 16S rRNA gene amplicons from 1 faecal sample. Each Agilent-030618 array probe (4441) was synthetized in three replicates.
Arrays 3 and 4: Hybridization with 250ng of labelled 16S rRNA gene amplicons from 2 faecal samples. Each Agilent-40558 array probe (4441) was synthetized in three replicates.

first: William

last: Tottey

first: Jérémie

last: Denonfoux

first: Faouzi

last: Jaziri

first: Mohiedine

last: Missaoui

first: Eric

last: Peyretaillade

first: Monique

last: Alric

first: Pierre

last: Peyret

first: Jean-François

last: Brugère


title: Gene expression profiles during seed development and maturation in Brassica napus

city: Saskatoon

first: Adrian

last: Cutler

address: 110 Gymnasium Place

institute: National Research Council of Canada

summary: Time course of gene expression profiles during seed development and maturation in Brassica napus were studied using Combimatrix Brassica microarray.

overall_design: The time course expression of 90K Brassica napus EST contigs were measured at 8 developing seed stages of 10, 15, 20, 25, 30, 35, 40 and 45 DAF (days after flowering) using single color microarray

first: Daiqing

last: Huang

first: Chushin

last: Koh

first: J

last: Feurtado

first: Edward

last: Tsang


title: Transcriptional profiling of nhr-114 vs. glp-1 animals, and wild type + Trp vs. wild type animals.

city: Cambridge

first: Xicotencatl

last: Gracida

address: 52 Oxford St.

institute: Harvard University

summary: Animals can thrive on variable food resources as a result of autonomous processes and beneficial relationships with their gut microbes. Food intake elicits major physiological changes, which are compensated with transient systemic responses that maintain homeostasis in the organism. This integration of external information occurs through cellular sensory elements, such as nuclear receptors, which modulate gene expression in response to specific cues. Given the importance of the germline stem cells (GSCs) for the development of the germ line and the continuity of the species, it is reasonable to assume that GSCs might be shielded from the negative influence of environmental perturbations. To our knowledge, however, there are no mechanisms reported that protect proliferating germ cells from harmful dietary metabolites. Using Caenorhabditis elegans as a model, we report that the somatic activity of the conserved nuclear receptor nhr-114/HNF4 protects GSC divisions and GSC integrity from dietary metabolites. In the absence of nhr-114 and on certain bacterial diets, otherwise somatically normal animals accumulate germ cell division defects during development and become sterile. We find that in nhr-114(-) animals the induction of germline defects and sterility depends on the bacterial metabolic status with respect to the essential amino acid tryptophan. This illustrates an animal-microbe interaction in which somatic nuclear receptor activity preserves the germline by buffering against dietary metabolites, likely through a somatic detoxifying response. Overall, our findings uncover an unprecedented and presumably evolutionary conserved soma-to-germline axis of communication that maintains reproductive robustness on variable food resources.

overall_design: Trasncriptional profiles of adult sterile nhr-114(RNAi) animals were compared to those of sterile glp-1(q224ts) animals. Independently, the transcriptional profiles of wild type animals fed an OP50 diet supplemented with Tryptophan was compared to wild type animals fed a standard OP50 diet.

first: Christian

last: Eckmann


title: Gene expression profiling of the hyperplastic growth zones of the late trout embryo myotome using laser capture microdissection and microarray analysis.

city: Rennes

first: Pierre-Yves

last: Rescan

address: Campus de Beaulieu

department: Phase

institute: INRA

summary: Background A unique feature of fish is that new muscle fibres continue to be produced throughout much of the life cycle; a process termed muscle hyperplasia. In trout, this process begins in the late embryo stage and occurs in both a discrete, continuous layer at the surface of the primary myotome (stratified hyperplasia) and between existing muscle fibres throughout the myotome (mosaic hyperplasia). In post-larval stages, muscle hyperplasia is only of the mosaic type and persists until 40% of the maximum body length is reached. To characterise the genetic basis of myotube neoformation in trout, we combined laser capture microdissection and microarray analysis to compare the gene expression profile of hyperplastic areas of the late embryo myotome with that of adult myotomal muscle which displays only limited muscle hyperplasia.   Results. Gene expression was analysed using Agilent trout oligo microarrays. Our analysis identified more than 6800 transcripts that were significantly up-regulated in the superficial hyperplastic zones of the late embryonic myotome compared to adult myotomal muscle. In addition to Pax3, Pax7 and the fundamental myogenic basic helix-loop-helix regulators, we identified a large set of up-regulated transcriptional factors, including Myc paralogs, members of Hes family and many homeobox-containing transcriptional regulators. Other cell-autonomous regulators overexpressed in hyperplastic zones included a large set of cell surface proteins belonging to the Ig superfamily. Among the secreted molecules found to be overexpressed in hyperplastic area, we noted growth factors as well as signalling molecules. A novel finding in our study is that many genes that regulate planar cell polarity (PCP) were overexpressed in superficial hyperplastic zones, suggesting that the PCP pathway is involved in the oriented elongation of the neofibres. Our microarray results were validated by in situ hybridisation of transcripts overexpressed in laser captured growth zones.   Conclusion. The results obtained in this study provide a valuable resource for further analysis of novel genes potentially involved in hyperplastic muscle growth in fish. Ultimately, this study could yield insights into particular genes, pathways or cellular processes that may potentially regulate muscle regeneration in other vertebrates.

overall_design: To characterise the genetic basis of myotube neoformation in trout, we combined laser capture microdissection and microarray analysis to compare the gene expression profile of hyperplastic areas of the late embryo myotome (peripheral and deep domains)  with that of adult myotomal muscle which displays only limited muscle hyperplasia.

first: Jerome

last: Montfort

first: Alain

last: Fautrel

first: Cecile

last: Ralliere

first: Veronique

last: Lebret


title: Expression response of Brucella melitensis strain 16M (ATCC23456) to erythritol

city: Madison

first: Erik

last: Petersen

state: WI

address: 1656 Linden Dr.

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

summary:
The four-carbon sugar erythritol is an important component of B. melitensis pathogenesis.
To determine the transcriptional response to erythritol, B. melitensis strain 16M was grown in the presence of either glucose or erythritol as a sole carbon source.

overall_design: Two control samples (glucose) and two experimental samples (erythritol) were analyzed on Nimblegen B. melitensis microarray chips.

first: Petersen

last: Erik

first: Rajashekara

last: Gireesh

first: Neelima

last: Sanakkayala

first: Eskra

last: Linda

first: Harms

last: Jerome

first: Splitter

last: Gary


title: Dysregulated deltaNp63alpha negatively regulates p73-mediated maspin expression

status: Public on Feb 26 2013

city: Bethesda

first: Kathryn

last: King

state: MD

address: 29 Lincoln Drive, HFD-123

department: Division of Monoclonal Antibodies

institute: FDA/CDER

summary: The p53 homologue, p63, is critical for normal epidermal development. While overexpression of deltaNp63alpha has been reported in squamous cell cancers, the contribution of p63 to cancer pathogenesis remains unclear. We previously demonstrated that overexpressed deltaNp63alpha aberrantly maintains proliferation of primary epidermal keratinocytes under conditions that normally induce growth arrest and differentiation. To identify target genes impacted by dysregulated deltaNp63alpha that may contribute to squamous cancer development and progression, microarray analyses were performed. Herein we report that elevated deltaNp63alpha differentially regulates genes in primary mouse keratinocytes involved in a variety of cellular functions, including cell cycle regulation, differentiation, skin barrier formation and function, apoptosis, host defense/inflammation, adhesion, migration and invasion. Of note, multiple protease inhibitor mRNAs were coordinately downregulated under both proliferating and differentiating culture conditions. These downregulated genes include two serine protease inhibitors: maspin (serpinB5) and plasminogen activator inhibitor-2 (PAI-2; serpinB2), as well as a tissue inhibitor of metalloproteinase-3 (TIMP-3). Correspondingly, secreted levels of TIMP-3 and PAI-2 protein declined in the presence of dysregulated deltaNp63alpha, while secreted maspin protein levels remained stable. Intracellular maspin protein expression decreased in response to overexpressed deltaNp63alpha, as did intracellular PAI-2. Unlike PAI-2 and maspin, TIMP-3 protein was not detected intracellularly in control or deltaNp63alpha-overexpressing keratinocytes, supporting a solely extracellular function for TIMP-3. Electrophoretic mobility shift assays using a p53/p63 consensus DNA binding sequence from the maspin promoter revealed binding of an endogenous transcription factor(s) to the consensus sequence in normal keratinocytes that was disrupted by overexpressed deltaNp63alpha. This binding was also interrupted by the addition of a p73 antibody, but not antibodies to p63 or p53, and was absent in samples derived from p73(-/-) keratinocytes, confirming p73 as a constituent of the endogenous transcription factor complex. These data suggest protease inhibitors as novel targets of dysregulated deltaNp63alpha in cancer pathogenesis.

overall_design: Keratinocytes were transduced with adenoviruses encoding deltaNp63alpha. Keratinocytes were either maintained in low calcium conditions (0.05 mM for 24 hours) (n=6) or high calcium conditions (0.12 mM for 24 hours) (n=6). Control samples consisted of keratinocytes transduced with adenoviruses encoding beta-galactosidase also treated with low calcium (n=6) and high calcium (n=6) conditions. Twelve technical repeat microarray experiments were conducted, pairing high-calcium deltaNp63alpha samples with high-calcium beta-galactosidase samples (n=6) and low-calcium deltaNp63alpha samples with low-calcium beta-galactosidase samples (n=6). Six of the technical repeats were conducted as reverse-fluoro experiments.


title: Cav3.2 T-type calcium channel-dependent gene expression after retrieval of context-associated memory

status: Public on Feb 28 2013

city: Hualien

first: Ingrid

last: Liu

address: E411, 701, Section 3 Chung Yang Road

department: Molecular Biology and Human Genetics

country: Taiwan

institute: Tzu Chi University

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

overall_design: Refer to individual Series


title: Pheromone-induced biofilm arrays in the planktonic and pheromone-induced biofilm growth conditions

status: Public on Feb 22 2013

city: Taipei

first: Ching-Hsuan

last: Lin

state: Taiwan

address: National Taiwan University, 1 Roosevelt Rd. Sec. 4

department: Department of Biochemical Science and Technology

institute: National Taiwan University

summary: Candida albicans can stochastically switch between two phenotypes, white and opaque.  Opaque cells are the sexually competent form of C. albicans and therefore undergo efficient polarized growth and mating in the presence of pheromone.  In contrast, white cells cannot mate, but are induced - under a specialized set of conditions - to form biofilms in response to pheromone.  In this work, we compare the genetic regulation of such "pheromone-stimulated" biofilms with that of "conventional" C. albicans biofilms.  In particular, we examined a network of six transcriptional regulators (Bcr1, Brg1, Efg1, Tec1, Ndt80, and Rob1) that mediate conventional biofilm formation for their potential roles in pheromone-stimulated biofilm formation.  We show that four of the six transcription factors (Bcr1, Brg1, Rob1, and Tec1) promote formation of both conventional and pheromone-stimulated biofilms, indicating they play general roles in cell cohesion and biofilm development.  In addition, we identify the master transcriptional regulator of pheromone-stimulated biofilms as C. albicans Cph1, ortholog of Saccharomyces cerevisiae Ste12.  Cph1 regulates mating in C. albicans opaque cells, and here we show that Cph1 is also essential for pheromone-stimulated biofilm formation in white cells.  In contrast, Cph1 is dispensable for the formation of conventional biofilms.  The regulation of pheromone- stimulated biofilm formation was further investigated by transcriptional profiling and genetic analyses.  These studies identified 206 genes that are induced by pheromone signaling during biofilm formation.  One of these genes, HGC1, is shown to be required for both conventional and pheromone-stimulated biofilm formation.  Taken together, these observations compare and contrast the regulation of conventional and pheromone-stimulated biofilm formation in C. albicans, and demonstrate that Cph1 is required for the latter, but not the former.

overall_design:
4 condition experiment: white and opaque cells in planktonic and pheromone-induced biofilm conditions with and without alpha pheromone.

WT strain (P37005), the tec1 mutant strain and the cph1 mutant strain

first: Richard

last: Bennett


title: Expression data of Defensin-like genes (DEFLs) from different parts and treatments of Arabidopsis thaliana

status: Public on Feb 23 2013

first: Kevin

last: Silverstein

summary: Since most of the DEFLs were recently discovered and many are not well represented on standard microarrays, little is known about their expression pattterns. To address this gap, we have designed a custom Affymetrix microarray (AtMtDEFL array) with known and predicted Arabidopsis and Medicago DEFL genes and the closely related maternally expressed gene family. The custom array was utilized for hybridizations of mRNAs from a wide range of conditions and tissues from both plant species, enabling a comparative analysis in the two model plant species.  The custom chip transcript analysis provided the first expression evidence for many of the computationally identified DEFLs previously lacking gene expression evidence, and indicated both common and unique patterns of DEFL gene expression between the two model plant species.

overall_design: The custom designed Affymetrix chip consisting of nearly all DEFLs from Arabidopsis thaliana was used for transcript profiling study in a variety of plant organs, developmental stages, and pathogenic associations totalling 16 different treatments. Each treatment was supported by three biological replicates giving a grand total of 48 samples.

first: Mesfin

last: Tesfaye

first: Sumitha

last: Nallu

last: VandenBosch

first: Deborah

last: Samac


title: Expression data of Defensin-like genes (DEFLs) from different parts and treatments of Medicago truncatula

overall_design: The custom designed Affymetrix chip consisting of nearly all DEFLs from Medicago truncatula was used for transcript profiling study in a variety of plant organs, developmental stages, and during symbiotic and pathogenic associations totalling 13 different treatments. Each treatment was supported by three biological replicates giving a grand total of 39 samples.


title: A. borkumensis cells: control vs. 1-octanol-stressed cells

status: Public on Feb 27 2013

city: Frankfurt

first: Daniela

middle: Jasmin

last: Näther

address: Max-von-Laue-Str. 9

department: Molecular Biosciences

country: Germany

institute: Goethe University Frankfurt

summary: Transcriptional profiling of Alcanivorax borkumensis cells, grown on either pyruvate or hexadecane as carbon source, that were stressed with 1- octanol. The gene expression was measured 15 min, 30 min, 60 min and 90 min after 1-octanol addition.

overall_design: Two-condition experiment, 1-octanol-stressed vs. unstressed cells; different time points were investigated after 1-octanol was spiked in (15 min, 30 min, 60 min, 90 min); for each condition 3 replicates were used, for the control condition 4 replicates (pyruvate cultures) and 3 replicates (hexadecane cultures) were used for analysis

first: Hermann

last: Heipieper


title: Chip-chip investigation of the effcts of phthalate plastisizers on fetal rat testes

city: Newort on tay

first: Simon

last: Plummer

address: 23 Wellgate Street

country: United Kingdom

institute: Micromatrices Associates ltd

summary: ChIP microarrays were used to investigate whether dibutylphthalate (DBP)-mediated repression of SF1-regulated genes was associated with changes in transcription factor binding to genes involved in DBP-induced testicular maldevelopment. The repressive effect of DBP on SF1 regulated gene expression in fetal testes correlates with inhibition of SF1 binding to steroidogenic gene promoters.

overall_design: Comparison of control- and DBP- in utero 500mg/Kg treated fetal rat testes

first: Dhritiman

last: Dan


title: Genome expression profile of early response to photobacteriosis in gilthead sea bream (Sparus aurata)

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

summary: Analysis of the gene expression profiles of Sparus aurata head kidney after infection with Photobaterium damselae piscicida. The expression levels of 21,497 sea bream transcripts, on both directions, 24 and 48 hours post-infection, were compared with the levels detected in uninfected individuals.

overall_design: Sea bream individuals were exposed by immersion in 100 l of aereated sea water containing 2.89x108 CFU of a virulent Photobacterium damselae piscidida strain (249/ittio99) for 30 min. After pathogen exposure, all fish were returned to one tank. A challenge in the absence of pathogen was carried out with the same experimental procedure. For both infected and uninfected group, four (4) fish were collected at 24h and 48h post challenge and euthanized by over anesthetization, for a total of 16 individuals. Samples of head kidney were taken and stored in RNA later at -20°C until RNA extraction. Gene expression profiling was then performed using the Agilent-027679 Sparus aurata Oligo Microarray platform  based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.6 used XDR ID to link the pairs of scans together automatically when extracting data.

first: Caterina

last: Pellizzari

first: Aleksei

last: Krasnov

first: Luca

last: Bargelloni


title: van Kessel STR415 v JV54

status: Public on Feb 20 2013

city: Bloomington

first: Julia

last: van Kessel

state: IN

address: 1001 E 3rd Street, Biology Building

department: Biology

institute: Indiana University

summary: Microarray data for study "The master regulators AphA and LuxR control the Vibrio harveyi quorum-sensing regulon: analysis of their individual and combined effects". Bacteria use a chemical communication process called quorum sensing to control transitions between individual and group behaviors. In the Vibrio harveyi quorum-sensing circuit, two master transcription factors AphA and LuxR coordinate the quorum-sensing response. Here we show that AphA regulates 167 genes, LuxR regulates 625 genes, and they co-regulate 77 genes. LuxR strongly controls genes both at low-cell-density and high-cell-density, suggesting it is the major quorum-sensing regulator. By contrast, AphA is absent at high-cell-density, and acts to fine-tune quorum-sensing gene expression at low-cell-density. We examined two loci as case studies of co-regulation by AphA and LuxR. First, AphA and LuxR directly regulate expression of the genes encoding the quorum regulatory small RNAs Qrr2, Qrr3, and Qrr4, the consequence of which is a specifically timed transition between the individual and the group lifestyle. Second, AphA and LuxR repress type III secretion system genes but at different times and to different extents. The consequence of this regulation is that type III secretion is restricted to a peak at mid-cell-density. Thus, asymmetric production of AphA and LuxR coupled with differences in their strength and timing of target gene regulation generates a precise temporal pattern of gene expression.

overall_design: Triplicate biological samples of Vibrio harveyi strains STR415 and JV54 were hybridized to Agilent arrays (Amadid design ID: 021087), and one experiment was a control dye-swap, for a total of four experiments in this array set.

first: Steven

last: Rutherford

last: Van Kessel


title: van Kessel BB120 v JV48 timecourse

overall_design: Samples from eight time points along a growth curve from strains BB120 and JV48 were hybridized to Agilent arrays (Amadid design ID: 037644). Time points were collected at the following optical densities (OD600): 1 = 0.001, 2 = 0.08, 3 = 0.03, 4 = 0.07, 5 = 0.16, 6 = 0.4, 7 = 1.0, and 8 = 2.4.


title: Expression data of Defensin-like genes (DEFLs) from different parts and treatments of Medicago truncatula and Arabidopsis thaliana

sample_organism:
Arabidopsis thaliana
Medicago truncatula


title: van Kessel STR416 v JV55

overall_design: Triplicate biological samples of Vibrio harveyi strains STR416 and JV55 were hybridized to Agilent arrays (Amadid design ID: 021087), and one experiment was a control dye-swap, for a total of four experiments in this array set.


title: van Kessel KM810 v JV55

overall_design: Triplicate biological samples of Vibrio harveyi strains KM810 and JV55 were hybridized to Agilent arrays (Amadid design ID: 021087), and one experiment was a control dye-swap, for a total of four experiments in this array set. KM810 contains a luxO D47E phosphomimic allele and a deletion in luxR; JV55 contains a luxO D47E phosphomimic allele and deletions in luxR and aphA.


title: RNA expression analysis in a multigeneration feeding study of OF1 outbred mice

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

summary: To analyze the effect of different aliments, male OF1 mice were fed ad libitum with a custom-made diet containing 33% maize derived from three cultivars containing comparable nutritional values for multiple generations. To evaluate possible effects on the gene expression in the small intestine,  the jejunum of nine randomly chosen males of the F3 was sampled at the age of 7 weeks. Note that the lack of information on the time of sampling or its randomization between the experimental groups limited the value of the internal microarray data set for the context originally addressed (diet).

overall_design: 3 feed groups, 3 replicates per group

first: Claudia

last: Binter

first: Christian

last: Guelly


title: van Kessel BB120 v KM669 timecourse

overall_design: Samples from eight time points along a growth curve from strains BB120 and KM669 were hybridized to Agilent arrays (Amadid design ID: 037644). Time points were collected at the following optical densities (OD600): 1 = 0.001, 2 = 0.08, 3 = 0.03, 4 = 0.07, 5 = 0.16, 6 = 0.4, 7 = 1.0, and 8 = 2.4.


title: van Kessel BB120 v STR417 timecourse

overall_design: Samples from eight time points along a growth curve from strains BB120 and STR417 were hybridized to Agilent arrays (Amadid design ID: 037644). Time points were collected at the following optical densities (OD600): 1 = 0.001, 2 = 0.08, 3 = 0.03, 4 = 0.07, 5 = 0.16, 6 = 0.4, 7 = 1.0, and 8 = 2.4.


title: Single Cell Transcriptomic Analysis of Prostate Cancer Cells

status: Public on Feb 19 2013

city: Seattle

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: The ability to interrogate circulating tumor cells (CTC) and disseminated tumor cells (DTC) is restricted by the small number detected and isolated (typically <10).  We wanted to determine if a commercially available technology could provide a transcriptomic profile of a single prostate cancer (PCa) cell.  We clonally selected and cultured a single passage of cell cycle synchronized C4-2B PCa cells.  Ten sets of single, 5-, or 10-cells were isolated using a micromanipulator under direct visualization with an inverted microscope.  Additionally, we analyzed 10 individual DTC isolated from each of 2 patients with metastatic PCa.  We have shown that a transcriptomic profile can be obtained from a single cell using commercially available technology.  As expected, fewer amplified genes are detected from a single-cell sample than from pooled cell samples, but this method can be used to obtain a transcriptomic profile from DTC isolated from the bone marrow of patients with PCa.

overall_design:
Custom Agilent 44K whole human genome expression oligonucleotide microarrays were used to profile clonally selected and cultured single passage of cell cycle synchronized C4-2B PCa cells isolated using a micromanipulator under direct visualization with an inverted microscope into ten sets of single, 5-, or 10-cells.  Single disseminated tumor cells were isolated from bone marrow (BM) samples of two advanced prostate cancer patients. Essentially, a two-step selection process was employed, in which anti-CD45 and anti-CD61 conjugated to immunomagnetic beads were used for negative selection, and anti-HEA was used for positive selection. Cells were then fluorescently stained for BerEP4, counter stained with RPE anti-CD45, and individually selected (10 single cells each per patient) under fluorescent light using a micropipette system for further analysis. RNA was amplified using the WT-Oviation one-direct system and hybridization against a common reference pool of prostate tumor cell lines.
Data from C42B cell data and data from single cells isolated from the bone marrow of patients were normalized and analyzed separately.

first: Christopher

last: Welty

first: Roger

first: Bryce

last: Lakely

first: Jing

last: Xia

first: Shu

last: Chen

first: Roman

last: Gulati

first: Sandy

last: Larson

first: Paul

last: Lange

first: Bruce

last: Montgomery

first: Peter

middle: S

last: Nelson

first: Robert

middle: L

last: Vessella

first: Colm

last: Morrissey


title: The effect of deficiency of two ATF6 homologues at early developmental stage

city: Kyoto

first: Tokiro

last: Ishikawa

address: Kitashirakawa-oiwake, Sakyo-ku

department: Biophysics

country: Japan

institute: Graduate School of Science, Kyoto University

summary: Mammalian ATF6α/β are membrane-bound transcription factors which are activated by endoplasmic reticulum (ER) stress-induced proteolysis to upregulate various ER quality control proteins to maintain the homeostasis of the ER. ATF6α- and ATF6β-single knockout mice develop normally but ATF6α/β-double knockout causes embryonic lethality, the reason for which remains unknown. Here, we showed that medaka fish exhibits the same phenotype regarding the effects of deleting ATF6α, ATF6β, and both. Analyses revealed that ER stress occurred physiologically during early embryonic development, particularly in the brain, otic vesicle and notochord. The absence of transcriptional induction of ER chaperones in ATF6α/β-double knockout blocked notochord development, which was partially rescued by microinjection-mediated overexpression of the major ER chaperone BiP. Thus, ATF6α/β-mediated adjustment of chaperones to the increased demands in the ER is essential for development of the notochord, which synthesizes and secretes large amounts of extracellular matrix proteins to serve as the body axis.

overall_design: Gene expression profile at stage 24 of DKO fish (ATF6a -/-b-/-) and control fish (ATF6a+/- b+/-) was determined. Two independent experiments were performed.

first: Kazutoshi

last: Mori


title: MiRNA analysis during hepatitis C virus infection

status: Public on Feb 17 2013

city: Nantes

first: Cyrille

last: Féray

address: 1 rue Gaston Veil

institute: Faculté de médecine de Nantes

summary: This study is complementary to the "Genome-wide analysis of host mRNA translation during hepatitis C virus infection" study (GSE44210), for which sucrose gradient ultracentrifugation followed by microarray analysis was used to identify translationally-regulated mRNAs (mRNAs associated with ribosomes) from JFH1-infected and uninfected Huh-7.5.1 cells. MicroRNA arrays have been conducted in parallel on total RNA from infected and uninfected cells, in order to determine if microRNA regulation could explain some of the mRNA translation regulations.

overall_design: Huh7 cells were infected with HCV JFH-1 strain. Controls consisted in non-infected cells. 3 days after infection, total RNAs were extracted from cell lysate and subjected to miRNA microarray analysis.

first: Hélène

last: Colman

first: Catherine

last: Le Berre-Scoul

first: Céline

last: Hernandez

first: Sandra

last: Pierredon

first: Audrey

last: Bihouée

first: Rémi

last: Houlgatte

first: Stephan

last: Vagner

first: Arielle

last: Rosenberg


title: van Kessel KM808 v JV54

first: Julia

last: van Kessel

overall_design: Triplicate biological samples of Vibrio harveyi strains KM808 and JV54 were hybridized to Agilent arrays (Amadid design ID: 021087), and one experiment was a control dye-swap, for a total of four experiments in this array set.

first: Steven

last: Rutherford

last: Van Kessel


title: Gene Expression analysis of transgenic RAS heatshock zebrafish embryos at 30 hpf

status: Public on Feb 16 2013

city: Boston

first: Anthony

middle: Dominc

last: DiBiase

address: KFRB, 1 Blackfan St, Suite 8216

department: Hem/Onc

institute: Children's Hospital Boston

summary: Heterogeneous Tg(hsp70-hRASG12V) embryos were obtained by mating the male homozygous transgenic fish to wildtype females. They were raised to 24 hour-post fertilization (hpf) stage and received heatshock at 37°C in waterbath for one hour, and kept in 28.5°C till 30hpf for RNA extraction. Wildtype embryos receiving the same heatshock treatment were used as controls. Each microarray sample was prepared by pooling 50 embryos and biological duplication was used.

overall_design: The zebrafish has been established as a powerful vertebrate model organism for large-scale genetic screens and chemical screens. Here, we seek to establish that zebrafish embryos can be utilized as an in vivo system to dissect crucial pathways for oncogenesis. A microarray analysis was performed by comparing transcription profile of heterogeneous Tg(hsp70-hRASG12V) embryos with heatshock to wildtype embryos with heatshock. Both groups of embryos received heatshock at 37°C for one hour at 24 hour-post fertilization (hpf) stage, and kept in 28.5°C till 30hpf for RNA extraction. Each microarray sample was prepared by pooling 50 embryos and biological triplicate was used. Ingenuity Pathway Analysis (IPA) was performed using the upregulated lists. “Cancer “ was the top diseases and disorders, with “Developmental disorder” and “Organismal Injury and Abnormalities” as the second and third diseases and disorders, validating that transient heatshock induction of oncogenic RAS in embryos activates major pathways in oncogenesis.

first: Le

last: Xiuning

first: Yi

last: Zhou


title: Transcription dependent dynamic supercoiling in Raji human B cells in vivo

first: Damian

last: Wojtowicz

address: 8600 Rockville Pike; Rm 8N811N

institute: NCBI/NLM/NIH

summary: Transcription has the capacity to modify mechanically DNA topology, DNA structure, and nucleosome arrangement. Resulting from ongoing transcription, these modifications in turn, may provide instant feedback to the transcription machinery. To substantiate the connection between transcription and DNA dynamics, we charted an ENCODE map of transcription-dependent dynamic supercoiling in human Burkitt lymphoma cells using psoralen photobinding to probe DNA topology in vivo. Dynamic supercoils spread ~1.5 kb upstream of the start sites of active genes. Low and high output promoters handle this torsional stress differently as shown using inhibitors of transcription and topoisomerases, and by chromatin immunoprecipation of RNA polymerase and topoisomerases I and II. Whereas lower outputs are managed adequately by topoisomerase I, high output promoters additionally require topoisomerase II. The genome-wide coupling between transcription and DNA topology emphasizes the importance of dynamic supercoiling for gene regulation.

overall_design: Raji cells: untreated and treated with DRB, CPT and BLAP.  Three biological replicates per treatment, each hybridized to new array. Total: 12 samples (4 treatments x 3 replicates).

first: Fedor

last: Kouzine

first: Ashutosh

last: Gupta

first: Laura

last: Baranello

first: Khadija

last: Ben-Aissa

first: Juhong

last: Liu

first: Teresa

middle: M

last: Przytycka

first: David

last: Levens


title: Transcription dependent dynamic supercoiling is a short-range genomic force

overall_design: Refer to individual Series


title: Individual and Combined Roles of the Master Regulators AphA and LuxR in Control of the Vibrio harveyi Quorum-Sensing Regulon


title: Gene expression assay from Raji human B cells

summary: Nuclear RNA from Raji human B cells was hybridized to NimbleGen arrays to quantify gene expression levels.

overall_design: Three biological replicates, each hybridized to new array.


title: Chip-chip from THP1 cells with H3K4me3, H3K9me2 , H3K27me3, JARIDIA, LSD1, JHDM1A, JHDM2A, JHDM3A, SIN3A, SNF2H, BRG1

status: Public on Feb 15 2013

city: Duarte

first: Nancy

last: Chen

state: CA

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

summary: THP1 cells  were ChIPed with indicated antibodies.

overall_design: Comparison  of selected chromatin marks in THP1 cells

first: Rama

last: Natarajan

first: Feng

last: Miao

first: Zhuo


title: Gene expression profiling of a nisin-sensitive Listeria monocytogenes Scott A ctsR deletion mutant

status: Public on Feb 14 2013

city: Wyndmoor

first: yanhong

state: PA

address: 600 E. Mermaid Lane

institute: ERRS-ARS-USDA

summary: Transcriptional profling of a Listeria monocytogenes under nisin treatment comparing ctsR mutant and wild type

overall_design: one condition (nisin treament 20ug/ml, 24 hours) experiment,  ctsR mutant vs. wild type Listeria monocytogenes Scott A, 2 biological replicates, 4 technical replicates

first: Yanhong


title: Transcriptome Profiling of Hippocampal CA1 After Early Life Seizure-Induced Preconditioning May Elucidate New Genetic Therapies for Epilepsy

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: Injury of the CA1 subregion induced by a single injection of kainic acid (1×KA) is attenuated when juvenile animals (P20) have a history of two sustained neonatal seizures on P6 and P9. To identify gene candidates involved in the spatially protective effects produced by early life conditioning seizures, we profiled and compared the transcriptomes of CA1 subregions from control, 1×KA, and 3×KA treated animals. More genes were regulated following 3×KA (9.6%) than after 1×KA (7.1%). Following 1×KA, genes supporting oxidative stress, growth, development, inflammation, and neurotransmission were upregulated (e.g., Cacng1, Nadsyn1, Kcng1, Aven, S100a4, GFAP, Vim, Hrsp12, Grik1). After 3×KA, protective genes were differentially over-expressed (e.g., Cat, Gpx7, GAD1, Hspa12A, Foxn1, adenosine A1 receptor, Ca2+ adaptor and homeostatic proteins, Cacnb4, Atp2b2, anti-apoptotic Bcl-2 gene members, intracellular trafficking protein, Grasp, suppressor of cytokine signaling (Socs3)). Distinct anti-inflammatory interleukins not observed in adult tissues (e.g., IL6 transducer, IL23 and IL33 or their receptors (ILF2)) were also over-expressed. Several transcripts were validated by real-time polymerase chain reaction (QPCR) and immunohistochemistry. QPCR showed that casp 6 was increased after 1×KA but reduced after 3×KA; pro-inflammatory gene cox1 was either upregulated or unchanged after 1×KA but reduced by ~70% after 3×KA. Enhanced GFAP immunostaining following 1×KA was selectively attenuated in the CA1 subregion after 3×KA. The observed differential transcriptional responses may contribute to early life seizure-induced pre-conditioning and neuroprotection by reducing glutamate receptor-mediated Ca2+ permeability of the hippocampus and redirecting inflammatory and apoptotic pathways which could lead to new genetic therapies for epilepsy.

overall_design: The transcriptomes of the hippocampal CA1 region of Sprague Dawley 23-day-old male rats after 1 or 3 seizures induced by kainic acid injection were compared to the corresponding controls (injected with PBS) using Duke 27k oligonucleotide arrays.

first: Linda

middle: K

last: Friedman

first: Joey

last: Mancuso

first: Ayan

last: Patel

first: Vinay

last: Kudur

first: Joerg

last: Leheste

first: Sanda

first: Julian

last: Botta

middle: C

last: Spray


title: L. monocytogenes ctsR mutant 2-1 cells response to pressure

summary:
transcriptional profiling of L. monocytogenes ctsR mutant under pressure treatment
SUBMITTER_CITATION: Liu, Y., Huang, L., Joerger, R.D., Gunther, N.W. 2012. Genes that are involved in high hydrostatic pressure treatments in a Listeria monocytogenes Scott A ctsR deletion mutant. Journal of Microbial and Biochemical Technology. 4:050-056.

overall_design: Two-condition experiment: mutant under pressure (450Mpa, 3min)  vs. normal condition, two biological replicates.


title: Chip-chip from THP1 cells with H3K56Ac

summary: THP1 cells  were ChIPed with H3K56Ac


title: Expression data from clinical S. aureus strains

status: Public on Feb 13 2013

city: Yongin

first: yuna

middle: sophia

last: yun

address: Yonggu St. 1920

country: South Korea

institute: AmorePacific Co.

summary:
Microarray hybridization analysis was conducted to identify genes that may affect biofilm formation.
Isolates from the 50 clinical isolates, two from LSG (strain number 2 and 7) and two from HSG donors (strain number 10 and 33) were selected.

overall_design: We monitored relative mRNA abundance in the four clinical S. aureus isolates using the Genechip S. aureus Genome Array (GeneChip Expression, Affymetrix, Inc., USA) to study the patterns of gene expression. The arrays contain probe sets corresponding to more than 3,300 S. aureus ORFs. Additionally, they contain probes to detect RNA of either forward or reverse orientation from more than 4,800 intergenic regions. In total, 107 were used as a control to verify the test results. A total of 432 probes on the microarrays overlapped between ORFs and intergenic regions. Two samples from each strains were used for the microarray and two independent experiments were performed.

first: Yuna

last: Yun

first: Kyeho

last: Shin


title: Comparative gene expression analysis in fruits of a tomato introgression line performing higher level of total phenolics

city: Portici (NA)

first: Antonio

last: Di Matteo

address: Via Universita' 100 - Parco Gussone - Edificio 75

department: DiSSPAPA

institute: University of Naples Federico II

summary: Tomatoes are one of the valuable sources of antioxidants such as carotenes, ascorbic acid (AsA), and phenolic compounds (flavonoids and hydroxycinnamic acid derivatives). These secondary metabolites have been proved to be beneficial for humans and animals because their involvement in the prevention of many proliferative and degenerative diseases. The aim of this work is to gain greater insights in the genetic control of phenylpropanoid accumulation in tomato fruit  by using genomics-based strategies.  In order to identify QTLs controlling antioxidant accumulation in tomato fruit we carried out a comparative analysis of Solanum pennellii x S. lycopersicum cv. M82 introgression lines (ILs) over three year trials in greenhouse environment. Among all, IL7-3 showed higher fruit content of total phenolics and the HPLC-UV profile revealed that chlorogenic acid mainly accounted for the higher performance of this line.  To investigate in details genetic mechanisms and candidate genes controlling phenols synthesis and accumulation in IL7-3 fruit we performed a comparative transcriptomic analysis in tomato pericarp. In particular, RNA was extracted from percarp of IL7-3 and M82 parental line and hybridized on a 90k Combimatrix TomatArray 1.0. The experiment was repeated over two consecutive years. The transcriptomic approach allowed to identify 291 differentially expressed transcripts, 149 showing up-rgulation and 142 down-regulation. The ethylene signaling pathway has been involved in the modulation of the level of total phenolics in ripe fruit. In particular, an Ethilene Responsive Factor 1 (ERF1) was functionally characterized by TILLING (Targeting Local Lesion IN Genomes) approach. The mutant line expressed lower accumulation of phenolics in the fruit and additional insights on the regulation of phenolics in tomato ripe fruit were provided.

overall_design: Comparative microarray analysis between a tomato introgression line (IL7-3) expressing higher level of fruit total phenolics and its parental cultivar M82 (reference) was performed. In particular, samples were generated by pooling red-ripe fruit from the same plant and discarding the seeds, jelly parenchyma, columella and placenta tissues. Three plant replica were used for each line (IL7-3 and M82) and the experiment was replicated over two consecutive years.


title: Developing endosperm: Nipponbare vs NIL(TGW6)

status: Public on Feb 12 2013

city: Itakura

first: Naoki

last: Hirotsu

state: Gunma

address: 1-1-1 Izumino

department: Life Sciences

institute: Toyo University

summary: Gene expression profoling of developping endosperm at 3 and 6 days after flowering (DAH): Nipponbare vs NIL(TGW6)

overall_design: We used two rice varieties, NIL(TGW6) and Nipponbare.NIL(TGW6) is a nearly isogenic line containing the thousand grain weight qTGW6. For samples used three stages: 3 and 6 DAH endosperm in both Nipponbare and NIL(TGW6). Two dye swapped experiments were performed.

first: K

last: Ishimaru

last: Ujiie

first: N

last: Murakami


title: Behavioural and functional characterization of Kv10.1 (Eag1) knockout mice

status: Public on Feb 11 2013

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Kv10.1 (Eag1), member of the Kv10 family of voltage-gated potassium channels, is preferentially expressed in adult brain. The aim of the present study was to unravel the functional role of Kv10.1 in the brain by generating knockout mice, where the voltage sensor and pore region of Kv10.1 was removed to render non-functional proteins through deletion of exon 7 of the KCNH1 gene using the “3 Lox P strategy”. Kv10.1-deficient mice show no obvious alterations during embryogenesis and develop normally to adulthood; cortex, hippocampus and cerebellum appear anatomically normal. Other tests, including general health screen, sensorimotor functioning and gating, anxiety, social behaviour, learning and memory did not show any functional aberrations in Kv10.1 null mice. Kv10.1 null mice display mild hyperactivity and longer-lasting haloperidol-induced catalepsy, but there was no difference between genotypes in amphetamine sensitisation and withdrawal, reactivity to apomorphine and haloperidol in the prepulse inhibition tests or to antidepressants in the haloperidol-induced catalepsy. Furthermore, electrical properties of Kv10.1 in cerebellar Purkinje cells did not show any difference between genotypes. Bearing in mind that Kv10.1 is overexpressed in over 70% of all human tumours and that its inhibition leads to a reduced tumour cell proliferation, the fact that deletion of Kv10.1 does not show a marked phenotype is a prerequisite for utilising Kv10.1 blocking and/or reduction techniques, such as siRNA, to treat cancer.

overall_design: 4 mice each for control wildtype and knockout mice

first: Roser

last: Ufartes

first: Tomasz

last: Schneider

first: Lena

last: Mortensen

first: C

last: de Juan Romero

first: Klaus

last: Hentrich

first: Hendrik

last: Knoetgen

first: Vadim

last: Beilinson

first: Wiebke

last: Moebius

first: Victor

last: Tarabykin

first: Frauke

last: Alves

first: Luis

last: Pardo

first: J

middle: N

last: Rawlins

first: Walter

last: Stuehmer


title: To map a potential locus corresponding to the CD23low phenotype

city: Gothenburg

first: Weicheng

last: Ren

address: Guldhedsgatan 10A

country: Sweden

institute: Gothenburg University

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary:
CD23, the low affinity receptor for IgE, has been proposed to play a critical role in the regulation of IgE production, based on altered IgE levels in CD23-deficient mice and transgenic mouse models, as well as in mouse strains with mutations in the CD23 gene, e.g. 129 substrains. Here, we have investigated a mouse line termed LxT1 that expresses reduced CD23 surface levels on B cells, and its influence on IgE production. Extensive phenotypic analyses showed that CD23 surface expression was reduced in LxT1 compared to the control, without affecting B cell development in general. We linked the CD23low surface level in LxT1 mice to a recessive locus, a 129-derived region spanning 28Mb on chromosome 8, which includes the CD23 gene. Sequence analysis confirmed the five mutations within the CD23 coding region in LxT1 mice, the same as those present in NZB and 129 substrains. However, this CD23low phenotype was not observed in all 129 substrains despite carrying these same CD23 mutations in the coding region.
Affymetrix Mouse Diversity Genotyping Array was performed according to the manufacturer's directions on DNA extracted from crossed mice samples. The array can interrogate more than 623,000SNPs, yielding an average SNP density of one marker per 4.3kb. Genetic linkage analysis was performed to exploit the co-segregation of chromosomal regions with the CD23 phenotype to identify the location of causative genes.

overall_design: To map a potential mutation, male LxT1 mice were crossed to female BALB/c mice to generate F1 mice. Two females from the F1 litters were backcrossed to the parental male LxT1 to generate N2 mice for analysis of phenotype and genetic mapping. N2 mice with (n=6) and without (n=5) CD23low surface level and (n=1) BALB/c were used to map putative genetic alteration that may cause the CD23low phenotype.

first: Kristina

last: Lagerstedt

first: Inga-Lill

last: Mårtensson


title: van Kessel BB721 v JAF548

status: Public on Feb 08 2013

first: Julia

last: van Kessel

country: USA

summary: Microarray data for study "The master regulators AphA and LuxR control the Vibrio harveyi quorum-sensing regulon: analysis of their individual and combined effects". Bacteria use a chemical communication process called quorum sensing to control transitions between individual and group behaviors. In the Vibrio harveyi quorum-sensing circuit, two master transcription factors AphA and LuxR coordinate the quorum-sensing response. Here we show that AphA regulates 167 genes, LuxR regulates 625 genes, and they co-regulate 77 genes. LuxR strongly controls genes both at low-cell-density and high-cell-density, suggesting it is the major quorum-sensing regulator. By contrast, AphA is absent at high-cell-density, and acts to fine-tune quorum-sensing gene expression at low-cell-density. We examined two loci as case studies of co-regulation by AphA and LuxR. First, AphA and LuxR directly regulate expression of the genes encoding the quorum regulatory small RNAs Qrr2, Qrr3, and Qrr4, the consequence of which is a specifically timed transition between the individual and the group lifestyle. Second, AphA and LuxR repress type III secretion system genes but at different times and to different extents. The consequence of this regulation is that type III secretion is restricted to a peak at mid-cell-density. Thus, asymmetric production of AphA and LuxR coupled with differences in their strength and timing of target gene regulation generates a precise temporal pattern of gene expression.

overall_design: Triplicate biological samples of Vibrio harveyi strains BB721 and JAF548 were hybridized to Agilent arrays (Amadid design ID: 021087), and one experiment was a control dye-swap, for a total of four experiments in this array set.

first: Steven

last: Rutherford

last: Van Kessel


title: Fur regulation in nontyepable Haemophilus influenzae

status: Public on Feb 05 2013

city: Columbus

first: Alistair

last: Harrison

state: OH

address: 700 Children's Drive

department: Center for Microbial Pathogenesis

institute: The Research Institute at Nationwide Children's Hospital

summary: Nontypeable Haemophilus influenzae (NTHi) is a commensal microorganism of the normal human nasopharyngeal flora, yet also an opportunistic pathogen of the upper and lower respiratory tracts.  Changes in gene expression patterns in response to host microenvironments are likely critical for persistence.  One such system of gene regulation is the ability to carefully regulate iron uptake.  A central regulatory system that controls iron uptake, mediated by the ferric uptake regulator Fur, is present in multiple bacteria, including NTHi.  To understand the regulation of iron homeostasis in NTHi, fur was deleted in the prototypic NTHi clinical isolate, 86-028NP.  Using an NTHi-specific microarray, we identified genes whose expression was repressed or activated by Fur.

overall_design: These data comprise transcriptional anaylses of a pediatric isolate of NTHi (86-028NP) an rpsL mutant of 86-028NP, a fur mutant of 86-028NP and a fur mutant of 86-028NPrpsL.  NTHi parent and fur mutant strains were grown in defined medium containing 10 µg /ml human hemoglobin to mid-log phase.  Cells were then harvested and RNA extracted.  A total of four biological replicates were generated for these analyses.

first: Estevan

last: Santana

first: Blake

last: Szelestey

first: David

middle: E

last: Newsom

first: Peter

last: White

first: Kevin

last: Mason


title: Profiling of genes expressed in cultured human keratinocytes established from the bulge region of hair follicles.

city: Nishinomiya

first: Yoshie

last: Yoshikawa

state: Hyogo

address: 1-1 Mukogawa-cho

department: Genetics

institute: Hyogo College of Medicine

summary:
We established a culture method of human keratinocytes from the bulge region of a plucked hair follicle, that contains multipotent epithelial stem cells with high proliferative potential. Using our method, keratinocyte cultures were successfully obtained from all subjects without invasive skin biopsies. We compared the gene expression profiles between the cultured keratinocytes derived from human hair-follicle-bulge (bulge–derived keratinocytes; BDKs) and neonatal human epidermal keratinocytes (NHEKs), and between BDKs from donors with atopic dermatitis and non-atopic controls using microarray analysis.

Keywords: expressin profiling

overall_design: Two cell cultures, BDK vs. NHEK cells. 18 BDKs; derived from eighteen healthy volunteers , 6 NHEKs; purchased from Kurabo (Osaka, Japan). One replicate per array.

first: Yusuke

last: Sasahara

first: Katsuyuki

last: Takeuchi

first: Yoshimasa

last: Tsujimoto

first: Takashi

last: Hashida-Okado

first: Yukio

last: Kitano

first: Tomoko

last: Hashimoto-Tamaoki


title: Inferring the in vivo cellular program of developing bovine muscle from expression data

status: Public on Feb 03 2013

city: Brisbane

first: Nicholas

middle: James

last: Hudson

address: 306 Carmody Road

department: Animal, Food and Health Sciences

institute: CSIRO

summary: We outline an in vivo cellular program of bovine longissimus muscle development inferred from expression data from 60 days post conception to 3 months postnatal. Analytic challenges included changes in cellular composition, ambiguous ‘diagnostic’ markers of cell type and contrasts between cattle human and mouse myogenesis. Nevertheless, the expression profiles of the myosin isoforms support slow and fast muscle fibres emanating from primary and secondary myogenesis respectively, while expression of the prenatal myosin subunits is down regulated prior to birth. Of the canonical pro-myogenic Transcription Factors (TF), MYF6 and MYF5 are negatively co-expressed, with MYF6 displaying higher expression in the post-natal samples and MYF5, MYOG, HES6 and PAX7 displaying higher expression in early development. A set of TFs (SIX1, EYA2 and DACH2) considered important in undifferentiated murine cells were equally abundant in differentiated bovine cells. An examination of mammalian regulators of fibre composition, muscle mass and muscle metabolism, underscored the roles of PPARGC1A, TGF-β signalling and the NHR4 Nuclear Hormone Receptors on bovine muscle development. Enriched among the most variably expressed genes from the entire data set were molecules regulating mitochondrial metabolism of carbohydrate (PDK4), fat (UCP3), protein (AGXT2L1) and high energy phosphate (CKMT2). The dramatic increase in the expression of these transcripts, which may enable the peri-natal transition to metabolic independence critical for new-born herbivores, provides surprising evidence for substantial developmental remodelling of muscle mitochondria and reflects changes in nutrient availability. Overall, despite differences in size, metabolism and physiology, the muscle structural subunit expression program appears very similar in ruminants, rodents and humans.

overall_design: 2 treatment groups (Piedmontese by Hereford and Wagyu by Hereford cattle) across 10 LD muscle developmental time points, with 3 or 4 individuals per cell

middle: J


title: miRNA in human lung fibroblasts

status: Public on Feb 01 2013

city: Birmingham

first: Gang

last: Liu

state: Alabama

address: 901 19TH ST S

department: Medicine

institute: University of Alabama at Birmingham

summary: By employing miRCURY™ LNA array, we have identified a subset (79) of the total number of miRNAs that are differentially expressed in TGF beta1-treated human lung fibroblasts MRC-5 cells, as compared to untreated control cells

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: To know the differential expression of miRNA in human lung fibroblasts after treatment of TGF beta1


title: Chip-chip for H3K27me3 and H3K4me3 in DNA methylation deficient mouse embryonic fibroblasts

status: Public on Feb 09 2013

city: Heidelberg

first: James

middle: P

last: Reddington

address: Meyerhofstrasse 1

institute: EMBL

summary: DNA methylation and the Polycomb Repression System are epigenetic mechanisms that play important roles in maintaining transcriptional repression. Recent evidence suggests that DNA methylation can attenuate the binding of Polycomb protein components to chromatin and thus plays a role in determining their genomic targeting. However, whether this role of DNA methylation is important in the context of transcriptional regulation is unclear. By genome-wide mapping of the Polycomb Repressive Complex 2 (PRC2)-signature histone mark, H3K27me3, in severely DNA hypomethylated mouse somatic cells, we show that hypomethylation leads to widespread H3K27me3 redistribution, in a manner that reflects the local DNA methylation status in wild-type cells. Unexpectedly, we observe striking loss of H3K27me3 and PRC2 from Polycomb-target gene promoters in DNA hypomethylated cells, including Hox gene clusters. Importantly, we show that many of these genes become ectopically expressed in DNA hypomethylated cells, consistent with loss of Polycomb-mediated repression. An intact DNA methylome is required for appropriate Polycomb-mediated gene repression by constraining PRC2 targeting. These observations identify a previously unappreciated role for DNA methylation in gene regulation and therefore influence our understanding of how this epigenetic mechanism contributes to normal development and disease.

overall_design: comparison of Dnmt1+/+ vs Dnmt1-/- mouse embryonic fibroblasts

first: Richard

middle: R

last: Meehan


title: Studies of target genes for signal transduction pathways (using a Ras1-, a Cdc42- and a Gap1-mutant) in the basidiomycete Schizophyllum commune.

city: Jena

first: Erika

last: Kothe

address: Neugasse 25

department: Microbial Communication, Institute of Microbiology

institute: Friedrich-Schiller-University

summary: Transcriptome changes associated with signal transduction mutants were analysed in order to identify targets of the distinct pathways of Ras1, Cdc42 and Gap1. Two monokaryons (12-43 and 4-39), a dikaryon (W22 x 12-43), a constitutive active Ras1 mutant (T2G12V, monokaryon), a Cdc42 mutant (G12V, monokaryon) and a ∆gap1 x ∆gap1 dikaryon (F15 x F28, deletion of Gap1) were analyzed for that purpose.

overall_design: With microarray analysis mRNA expression in different mutants of the basidiomycete S. commune was analyzed. Genes which show regulation in the comparison either of the two monokaryons 12-43 and 4-39 (for Ras2 and Cdc42 mutant) or the dikaryon W22 x 12-43 (for Gap1 x Gap1 dikaryon) have been eliminated from other comparisons as stage-specific (mono- or dikaryon) differences. Two biological replicate samples were analyzed for each condition.

first: Nicole

last: Knabe

first: Daniela

last: Freihorst

first: Susann

last: Erdmann


title: Sockeye salmon (Oncorhynchus nerka) from Aniakchak National Monument and Preserve muscle transcriptome

city: King Salmon

first: Scott

middle: A

last: Pavey

state: Alaska

address: PO Box 7

department: Natural Resources

institute: Katmai National Park

summary: This dataset was gene expression from natural sockeye salmon populations used to test the preservation of coexpression networks that were found in lake whitefish. Here is the abstract of the manuscript:Background : A functional understanding of processes involved in adaptive divergence is one of the awaiting opportunities afforded by high throughput transcriptomic technologies. Functional analysis of co-expressed genes has succeeded in the biomedical field in identifying key drivers of disease pathways. However, in ecology and evolutionary biology, functional interpretation of transcriptomic data is still limited.  Results : Here we used Weighted Gene Co-Expression Network Analysis (WGCNA) to identify modules of co-expressed genes in muscle and brain tissue of a lake whitefish backcross progeny. Modules were connected to gradients of known adaptive traits involved in the ecological speciation process between benthic and limnetic ecotypes. Key drivers, i.e. hub genes of functional modules related to reproduction, growth, and behavior were identified, and module preservation was assessed in natural populations. Using this approach, we identified modules of co-expressed genes involved in phenotypic divergence and their key drivers, and further characterized the underlying regulatory structure governing these complex traits.   Conclusions : Functional analysis of transcriptomic data can significantly contribute to the understanding of the mechanisms underlying ecological speciation. Our findings point to BMP and Calcium signaling as common pathways involved in coordinated evolution of trophic behavior, trophic morphology (gill rakers), and reproduction. Results also point to housekeeping pathways implicating hemoglobins and constitutive stress response (HSP70) governing growth in lake whitefish.

overall_design: Here are 49 female sockeye salmon transcriptomes as measured by the 16k cGRASP microarray.

first: Marie

last: Filteau

first: Jérôme

last: St-Cyr

first: Louis

last: Bernatchez


title: myb52-2 t-dna -Transcriptome analysis of atmyb52 mutant vs wild-type

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: rs11-11_myb52 - myb52-2 t-dna  - What are the structural and regulator genes regulated by MYB52 transcription factor? - Plants grew in short-day growth chamber until they reached 20 cm height. Ten centimeter-stem from the rosette were collected. Samples are pools of 8 wild-type (Col0) or (atmyb52) mutant plants. Two biological repeats were conducted.

overall_design: 2 dye-swap - normal vs transgenic comparaison

first: Deborah

last: Goffner

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Marie-Laure

last: Martin-Magniette