title: Detection of Acute Radiation Sickness: A Feasibility Study in Non-human Primates Circulating miRNAs for triage in Radiological Events

status: Public on Nov 04 2016

city: Monrovia

first: Claude

last: Rogers

address: 1225 S. Shamrock Ave.

institute: ChromoLogic

summary: Development of biomarkers capable of estimating absorbed dose is critical for effective triage of affected individuals after radiological events. Levels of cell-free circulating miRNAs in plasma were compared for dose-response analysis in non-human primates (NHP) exposed to lethal (6.5 Gy) and sub-lethal (1 and 3 Gy) doses over a 7 day period. The doses and test time points were selected to mimic triage needs in the event of a mass casualty radiological event. Changes in miRNA abundance in irradiated animals were compared to a non-irradiated cohort and a cohort experiencing acute inflammation response from exposure to lipopolysaccharide (LPS). An amplification-free, hybridization-based direct digital counting method was used for evaluation of changes in microRNAs in plasma from all animals. Consistent with previous murine studies, circulating levels of miR-150-5p exhibited a dose- and time-dependent decrease in plasma. Furthermore, plasma miR-150-5p levels were found to correlate well with lymphocyte and neutrophil depletion kinetics. Additionally, plasma levels of several other evolutionarily and functionally conserved miRNAs were found altered as a function of dose and time. Interestingly, miR-574-5p exhibited a distinct, dose-dependent increase 24 h post irradiation in NHPs with lethal versus sub-lethal exposure before returning to the baseline level by day 3.  This particular miRNA response was not detected in previous murine studies but was observed in animals exposed to LPS, indicating distinct molecular and inflammatory responses. Furthermore, an increase in low-abundant miR-126, miR-144, and miR-21 as well as high-abundant miR-1-3p and miR-206 was observed in irradiated animals on day 3 and/or day 7. The data from this study could be used to develop a multi-marker panel with known tissue-specific origin that could be used for developing rapid assays for dose assessment and evaluation of radiation injury on multiple organs. Furthermore this approach may be utilized to screen for tissue toxicity in patients who receive myeloablative and therapeutic radiation.

overall_design: Radiation Treatment: Male and female rhesus macaques (Macaca mulatta) NHPs were exposed to 1 (N = 6), 3 (N = 8), or 6.5 Gy (N = 5). The day of irradiation was defined as Day 0. At the time of irradiation, the age of the animals ranged from approximately 2 to 5 years. On the day prior to irradiation (Day −1), the body weights ranged from 3.4 to 5.9 kg and from 3.8 to 6.5 kg, for males and females, respectively. All animals were declared healthy before inclusion and were evaluated for mortality and clinical signs (twice daily). Detailed examinations, including body weight and temperature, were performed, prior to animal assignment, during the week prior to irradiation, and on Days 1, 3, and 7. On day 0, the animals were subjected to a single uniform total body dose of gamma radiation from a 60Co source (Theratron 1000), with a targeted dose rate of 50 cGy/min. Sequential anteroposterior and posteroanterior exposures with whole body irradiation were used. Animals were not sedated during the irradiation and were breathing ambient air. Dosimeters (nanoDot™; Landuer Glenwood, IL) were placed on the animals for confirmation of exposure, however there was no real-time dosimetry performed via Farmer's chamber. In this study, all animals reached scheduled termination on Day 7.  LPS Treatment: In order to assess the specificity of miRNA biomarkers to ionizing radiation and to rule out or distinguish common systemic inflammation response indicators, 4 cohorts of 2 rhesus macaques (M. mulatta) NHPs each, with a body weight between 4.0–4.9 kg, were subjected to lipopolysaccharide (LPS) injections, known to induce a systemic cellular immune response. Intravenous injection of LPS mimics inflammation and is used to assess marker specificity to irradiation. Briefly, on Day 1 of the study, an intravenous injection of LPS (Sigma Aldrich, Catalog number: 020m4062, serotype 0127:B8) reconstituted in sterile saline (0.9% sodium chloride) was administered (0.0, (vehicle-only sham), 0.7, 2.1, 2.8 mg/kg), without sedation or anesthesia. Blood samples were collected by venipuncture, without sedation or anesthesia,   into a Vacutainer® containing lithium heparin as an anti-coagulant for hematology once during the week prior to dosing and on Days 2 and 3. Blood samples for immunological assessment were processed to plasma. Plasma was prepared and frozen (−80°C) for miRNA analysis. Blood samples were collected, without sedation or anesthesia, by venipuncture into a Vacutainer® containing lithium heparin as an anti-coagulant for hematology three occasions prior to irradiation (within 2 weeks prior to irradiation) and daily for the first seven days after irradiation. Plasma was isolated and frozen (−80°C) prior to miRNA analysis.  An amplification-free, hybridization based direct digital counting method developed by NanoString Technologies was used for evaluation of changes in circulating miRNAs. However, in this assay, available human probes were used as miRNAs are evolutionarily conserved between human and NHPs. RNA was extracted from 200 µL plasma using Qiagen miRNeasy kit. After lysis, three synthetic oligonucleotides (spike-in oligos) were added. Purified RNA was eluted in 100 µL water and concentrated to 20 µL. The digital multiplexed nanoString nCounter miRNA expression assay was performed with RNA present in 3 µL (10–20 ng cell free RNA).

first: Naresh

last: Menon

first: Agnes

last: Lukaszewicz

first: James

last: Axtelle

first: Marshleen

last: Yadav

first: Feifei

last: Song

first: Arnab

last: Chakravarti

first: Naduparambil

last: Jacob


title: High altitude adaptation of Tibetans

status: Public on Nov 08 2016

city: Beijing

first: Yong-Biao

last: Zhang

state: Select a State or Province

address: Beichen west road 1#

country: China

institute: Beijing Institute of Genomics

summary:
Since their arrival in the Tibetan Plateau during the Neolithic Age, Tibetans have been well-adapted to extreme  environmental conditions and possess genetic variation that reflect their living environment and migratory history. To  investigate the origin of Tibetans and the genetic basis of adaptation in a rigorous environment, we genotyped 30 Tibetan  individuals with more than one million SNP markers. Our findings suggested that Tibetans, together with the Yi people,  were descendants of Tibeto-Burmans who diverged from ancient settlers of East Asia. The valleys of the Hengduan  Mountain range may be a major migration route. We also identified a set of positively-selected genes that belong to  functional classes of the embryonic, female gonad, and blood vessel developments, as well as response to hypoxia. Most of  these genes were highly correlated with population-specific and beneficial phenotypes, such as high infant survival rate and  the absence of chronic mountain sickness.
Genetic features of Tibetans have been broadly investigated, but the properties of copy number variation (CNV) have not  been well examined. To get a preliminary view of CNV in Tibetans, we scanned 29 Tibetan genomes with the Illumina  Human-1 M high-resolution genotyping microarray and identified 139 putative copy number variable regions (CNVRs),  consisting of 70 deletions, 61 duplications, and 8 multi-allelic loci. Thirty-four of the 139 CNVRs showed differential allele  frequencies versus other East-Asian populations, with P values ,0.0001. These results indicated a distinct pattern of CNVR  allele frequency distribution in Tibetans. The Tibetan CNVRs are enriched for genes in the disease class of human  reproduction (such as genes from the DAZ, BPY2, CDY, and HLA-DQ and -DR gene clusters) and biological process categories  of ‘‘response to DNA damage stimulus’’ and ‘‘DNA repair’’ (such as RAD51, RAD52, and MRE11A). These genes are related to  the adaptive traits of high infant birth weight and darker skin tone of Tibetans, and may be attributed to recent local  adaptation. Our results provide a different view of genetic diversity in Tibetans and new insights into their high-altitude  adaptation.

overall_design: 30 samples were investigate


title: Microarrays of Maize Recombinant Inbred Lines inoculated with Cercospora zeina, which causes  grey leaf spot (GLS) disease

city: Cape Town

first: Shane

last: Murray

address: University Avenue North

department: Dept of Molecular and Cell Biology

country: South Africa

institute: University of Cape Town

summary: Global transcriptome profiling of leaf tissue from 100 RILs.  All plants were field-grown and infected with GLS.  Objective was to carry out systems genetics of the transcriptional responses to GLS, by overlaying results obtained from co-expression correlation analysis,  eQTL analysis and QTL analysis.

overall_design: Plants were grown at Baynesfield Estate (KwaZulu-Natal, South Africa) as three replicated, randomised blocks. Each replicate of a RIL was a row of 10 plants. RILs were inoculated at the six leaf stage by placing into the whorls 50 g per plant of dry powdered maize leaf material collected from GLS infected maize.   RNA was extracted from three biological repeats of 100 selected maize RILs at 103 DAP, sampled at Baynesfield in March 2009. The RNA from the three biological repeats was pooled to create 100 samples. Each biological repeat consisted of 10 cm X 10 cm leaf pieces from two different plants in a RIL row. Fifty RIL microarrays were processed according to the “distant pair” experimental design. RNA was amplified from each of the 100 RIL samples using the Amino Allyl MessageAmpII aRNA Amplification kit (Ambion, Dallas, USA), labeled with either Cy3 or Cy5 (100 pmol each), and hybridized to Agilent-016047 maize 4×44 K microarrays .

middle: L

first: Dave

middle: K

last: Berger

first: Bridget

middle: G

last: Crampton

first: Nanette

last: Christie


title: Expression profile for higA mutant of Pseudomonas aeruginosa PA14

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

country: USA

institute: Pennsylvania State University

summary:
The previously uncharacterized proteins HigB (unannotated) and HigA (PA4674) of Pseudomonas aeruginosa PA14 were found to form a type II TA system in which antitoxin HigA masks the RNase activity of toxin HigB through direct binding.
To determine the physiological role of HigB/HigA in P. aeruginosa, a whole-transcriptome experiment was performed for the higA antitoxin deletion mutant of the PA14 strain compared to the wild-type PA14 strain. The rationale was that for the strain that lacks the antitoxin, the effect of the toxin could be discerned due to enhanced activity of the toxin.
Furthermore, toxin HigB reduces production of the virulence factors pyochelin, pyocyanin, swarming, and biofilm formation.

overall_design: The higA mutant of Pseudomonas aeruginosa PA14 compared to the P. aeruginosa PA14 wild-type

first: Thammajun


title: Targeting PI3K/mTOR signaling exerts potent antitumor activity in pheochromocytoma in vivo

status: Public on Nov 03 2016

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

summary:
Pheochromocytomas (PCC) are mostly benign tumors, amenable to complete surgical resection. However, 10–17% of cases can become malignant, and once metastasized, there is no curative treatment for this disease. Given the need to identify effective therapeutic approaches for PCC, we evaluated the antitumor potential of the dual PI3K/mTOR inhibitor BEZ235 against these tumors. We employed an in vivo model of endogenous PCCs (MENX mutant rats), which closely recapitulate the human tumors. Mutant rats with PCCs were treated with 2 doses of BEZ235 (20 and 30 mg/kg), or with placebo, for 2 weeks. Treatment with BEZ235 induced cytostatic and cytotoxic effects on rat PCCs, which could be appreciated by both staining the tumors ex vivo with appropriate markers, and non-invasively by functional imaging (diffusion weighted-DW-MRI) in vivo.
Transcriptomic analyses of tumors from rats treated with BEZ235 or placebo identified potential mediators of therapy response. Slc6a2, encoding the norepinephrine transporter (NET), was downregulated in a dose-dependent manner by BEZ235 in rat PCCs. Moreover, BEZ235 reduced Slc6a2/NET expression also in PCC cell lines (PC12, MPC, MTT). Studies of a BEZ235-resistant derivative of the MPC cell line (MPCR) confirmed that the reduction of NET expression associates with the response to the drug. Reduction of NET expression following BEZ235 treatment in vivo could be monitored by Positron Emission Tomography (PET) using a tracer targeting NET. Altogether, we demonstrate the efficacy of BEZ235 against PCC in vivo, and show that functional imaging can be employed to monitor the response of PCC to PI3K/mTOR inhibition therapy.

overall_design: We compared pituitary adenomas from heterozygous p27Kip1/Cdknb1 mutant rats treated with NVP-BEZ235 and control animals

first: Misu

last: Lee

first: Ninelia

last: Minaskan

first: Tobias

last: Wiedemann

first: Martin

last: Irmler

first: Behrooz

middle: H

last: Yousefi

first: Rickmer

last: Braren

first: Iina

last: Laitinen

first: Natalia

last: Pellegata


title: Conversion of terminally committed hepatocytes to culturable bipotent progenitor cells with regenerative capacity

status: Public on Nov 15 2016

city: Philadelphia

first: Takeshi

last: Katsuda

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

summary:
A challenge for advancing approaches to liver regeneration is loss of functional differentiation capacity when hepatocyte progenitors are maintained in culture. Recent lineage-tracing studies have shown that mature hepatocytes (MHs) convert to an immature state during chronic liver injury, and we investigated whether this conversion could be recapitulated in vitro and if such converted cells could represent a source of expandable hepatocytes. We report that a cocktail of small molecules, Y-27632, A-83-01 and CHIR99021, can convert rat and mouse MHs in vitro into proliferative bipotent cells, which we term chemically induced liver progenitors (CLiPs). CLiPs can differentiate into both MHs and biliary epithelial cells that can form functional ductal structures. CLiPs in long-term culture did not lose their proliferative capacity or their hepatic differentiation ability, and rat CLiPs were shown to extensively repopulate chronically injured liver tissue. Thus our study advances the goals of liver regenerative medicine.
Transcriptomic analyses for freshly isolated MHs and cells cultured for the designated periods with or without YAC stimulation (Matrix 1). Transcriptomic analysis for  CLiPs which underwent hepatic induction (Matrix 2). Transcriptomic comparison of hepatic inducibility between CLiPs at early passage and those at late passages (Matrix 3). Transcriptomic comparison between chimera-derived rat cells (designated as “2nd”) and primary rat MH-derived cells (designated as “1st”) (Matrix 4).

overall_design: Freshly isolated hepatocytes were cultured in the presence or absence of YAC. Hepatic induction was performed for P1 CLiPs or clonal CLiPs.

first: Takahiro

last: Ochiya


title: Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing [total RNA]

status: Public on Oct 31 2016

city: Göteborg

first: Cecilia

last: Lässer

address: Box 424

department: Krefting Research Centre

country: Sweden

institute: University of Gothenburg

summary: Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid.  However, there are conflicting results regarding the nature of exRNA. Here, we have separated two distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not. Furthermore, the HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, snoRNA, and snRNA with little or no evidence of full-length 18S and 28S rRNA. The LD exRNA was enriched in mitochondrial rRNA, mitochondrial tRNA, tRNA, piRNA, Y RNA, and full-length 18S and 28S rRNA. The proteomes of the HD and LD exRNA-containing fractions were determined with LC-MS/MS and analysed with Gene Ontology term finder, which showed that both proteomes were associated with the term extracellular vesicles and electron microscopy suggests that at least a part of the exRNA is associated with exosome-like extracellular vesicles. Additionally, the proteins in the HD fractions tended to be associated with the nucleus and ribosomes, whereas the LD fraction proteome tended to be associated with the mitochondrion. We show that the two exRNA signatures released by a single cell type can be separated by floatation on a density gradient. These results show that cells can release multiple types of exRNA with substantial differences in RNA species content. This is important for any future studies determining the nature and function of exRNA released from different cells under different conditions.

overall_design:
Samples were analysed in three biological replicates, except for the HD exRNA samples where four biological repliates were analysed. The samples were of three typs; mast cells, and the RNA secreted my these cells into the extracelllular space isolated by ultracentrifugation and denisty gradients, were the extracellular RNA was divided into a high density and a low density fraction. Resulting in 9 samples in total, which are paired, that this the RNA in cell 1, HD 1 and LD 1 are isolated from the cell culture and so on.
Please note that the accession numbers for the associated NGS and proteomic data are PRJNA343960 (BioProject) and PXD004931 (PRIDE archive).

first: Ganesh

middle: V

last: Shelke

first: Ashish

last: Yeri

first: Dae-Kyum

last: Kim

first: Rossella

last: Crescitelli

first: Stefania

last: Raimondo

first: Margareta

last: Sjöstrand

first: Yong

middle: S

last: Gho

first: Kendall

last: Jensen

first: Jan

last: Lötvall


title: Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing [miRNA]

overall_design:
Samples were analysed in three biological replicates. The samples were of three typs; mast cells, and the RNA secreted my these cells into the extracelllular space isolated by ultracentrifugation and denisty gradients, were the extracellular RNA was divided into a high density and a low density fraction. Resulting in 9 samples in total, which are paired, that this the RNA in cell 1, HD 1 and LD 1 are isolated from the cell culture and so on.
Please note that the accession numbers for the associated NGS and proteomic data are PRJNA343960 (BioProject) and PXD004931 (PRIDE archive).


title: Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing

type:
Expression profiling by array
Non-coding RNA profiling by array

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

overall_design:
Refer to individual Series
Please note that the accession numbers for the associated NGS and proteomic data are PRJNA343960 (BioProject) and PXD004931 (PRIDE archive).


title: Expression data from Saccharomyces cerevisiae with eEF1A overexpression

status: Public on Oct 29 2016

city: Canterbury

first: Daniel

last: Tarrant

address: Stacey Building

country: United Kingdom

institute: University of Kent

summary:
The canonical role of eEF1A is to deliver the aminoacyl tRNA to the ribosome, we have used the yeast model system to investigate further roles for this protein.
We used microarray to study the transcriptomic effects of elevated levels of eEF1A on yeast cells during log phase growth

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Yeast cells were grown to log phase, the RNA extracted and hybridised to affymetrix arrays.

first: D

middle: J

first: C

middle: W

last: Gourlay


title: Deregulated expression of HDAC9 in B cells promotes development of lymphoproliferative disease and lymphoma in mice [Bcell subsets]

status: Public on Nov 17 2016

city: Stirling

first: Kevin

last: Petrie

state: Stirling

address: Stirling

department: Biological and Environmental Sciences

institute: University of Stirling

type:
Expression profiling by array
Third-party reanalysis

summary: Histone deacetylase 9 (HDAC9) is expressed in B cells, and its overexpression has been observed in B-lymphoproliferative disorders, including B-cell non-Hodgkin lymphoma (B-NHL). We examined HDAC9 protein expression and copy number alterations in primary B-NHL samples, identifying high HDAC9 expression among various lymphoma entities and HDAC9 copy number gains in 50% of diffuse large B-cell lymphoma (DLBCL). To study the role of HDAC9 in lymphomagenesis, we generated a genetically engineered mouse (GEM) model that constitutively expressed an HDAC9 transgene throughout B-cell development under the control of the immunoglobulin heavy chain (IgH) enhancer (Eμ). Here, we report that the Eμ-HDAC9 GEM model develops splenic marginal zone lymphoma and lymphoproliferative disease (LPD) with progression towards aggressive DLBCL, with gene expression profiling supporting a germinal center cell origin, as is also seen in human B-NHL tumors. Analysis of Eμ-HDAC9 tumors suggested that HDAC9 might contribute to lymphomagenesis by altering pathways involved in growth and survival, as well as modulating BCL6 activity and p53 tumor suppressor function. Epigenetic modifications play an important role in the germinal center response, and deregulation of the B-cell epigenome as a consequence of mutations and other genomic aberrations are being increasingly recognized as important steps in the pathogenesis of a variety of B-cell lymphomas. A thorough mechanistic understanding of these alterations will inform the use of targeted therapies for these malignancies. These findings strongly suggest a role for HDAC9 in B-NHL and establish a novel GEM model for the study of lymphomagenesis and, potentially, preclinical testing of therapeutic approaches based on histone deacetylase inhibitors.

overall_design:
FLAG-epitope-tagged full-length human HDAC9 cDNA was cloned into the pEμSR vector, placing the HDAC9-sequence-containing oligonucleotide cassette downstream of the immunoglobulin heavy chain (IgH) enhancer (Eμ) and the SRα potent promoter (Bodrug et al., 1994). The Eμ-HDAC9 transgenic fragment was isolated from the vector by enzymatic digestion using the NotI restriction sites and injected into B6CBAF1 pronuclei. Mice were backcrossed and maintained in a C57BL/6 background to generate three transgenic lines: 1468, 1469 and 1839. PCR genotyping was performed using SV40 primers: F: 5′-GGAACTGATGAATGGGAGCA-3′ and R: 5′-GCAGTGCAGCTTTTTCCTTT-3′. Mice were housed and maintained in accordance with UK Home Office regulations. Animals were monitored and analyzed from birth to 23 months of age and sacrificed if showing signs of illness. Statistical analysis was performed using Prism (GraphPad Software). Kaplan–Meier cumulative survival and the log-rank (Mantel–Cox) test were used to determine tumor-free survival and the χ2 test was used to compare B-NHL incidence in HDAC9 mice versus wild-type controls. P<0.05 was considered statistically significant. All experimental protocols were monitored  and approved by The Institute of Cancer Research Animal Welfare and Ethical Review Body, in compliance with guidelines specified by the UK Home Office Animals (Scientific Procedures) Act 1986 and the United Kingdom National Cancer Research Institute guidelines for the welfare of animals in cancer research (Workman et al., 2010). ARRIVE guidelines were applied when reporting in vivo experiments (Kilkenny et al., 2010).
This series contains re-analyzed samples from GSE15907 and GSE89954.


title: Analysis of mRNA from Gli1 expressing stromal cells of mice given SAG21k versus vehicle

status: Public on Oct 21 2016

city: Stanford

first: Philip

last: Beachy

state: CA

address: 265 Campus Drive

institute: Stanford University

summary: Comparison of mRNA expression from FACS isolated Gli1 expressing stromal cells from mice given SAG21k versus vehicle

overall_design: Total mRNA from FACS isolated Gli1 expressing stromal cells from mice colons were isolated from the SAG21k and Vehicle control groups

first: John

last: Lee

first: Michael

middle: E

last: Rothenberg

first: E

last: Seeley

first: Bryan

last: Zimdahl

first: Sally

last: Kawano

first: Wan-Jin

last: Lu

first: Kunyoo

last: Shin

first: Tomoyo

last: Kato

first: James

last: Chen

first: Maximilian

last: Diehn

middle: F

last: Clarke

middle: A


title: Genome-wide expression profiling after Valproic acid treatment in Saccharomyces cerevisiae

status: Public on Oct 14 2016

city: Bhopal

first: Raghuvir

middle: singh

last: Tomar

state: MP

address: ITI (Gas Rahat) Building Govindpura - Bhopal

department: Department of Biological Sciences

country: India

institute: Indian Institute of Science Education & Research

summary:
Valproic acid (VA) is a small-chain branched fatty acid, widely used as anticonvulsant, and mood stabilizer to treat psychiatric illness. Valproic acid is also known to inhibit the histone deacetylases (HDACs), which makes it as a potent antitumor agent in alone or in combination with other cytotoxic drugs. Beside its conventional activities, valproic acid reported to have much broader, complicated effects and affect many complex physiological processes. However the molecular mechanisms of valproic acid are unclear.
So, we used budding yeast transcriptome analysis to better understand the molecular mechanism of action of valproic acid. The clusters of differentially expressed genes in microarray after VA (6mM) treatment and their functional enrichment analysis revealed its overall effects on various biological processes such as cell cycle, signal transduction, metabolism, transcription, ubiquitination, transporter activities and many more. The microarray data were validated by quantitative real-time PCR.

overall_design: Wild-type yeast (W1588-4c) cells were grown to exponential phase and the cells were left untreated (Control) or treated with a dose of 6mM Valproic acid (VA) for 3h. Two independent experiments were performed for each experiment (Control or VA). Total RNAs were extracted and hybridized on Affymetrix microarrays.

first: Upendarrao

last: Golla


title: Comparative transcriptome analysis of basal gene expression in Wild-type and Sen1ΔN mutant of Saccharomyces cerevisiae

status: Public on Oct 12 2016

summary:
In Saccharomyces cerevisiae, Sen1 is a 252-kDa, nuclear superfamily-1 RNA/DNA helicase that encoded by an essential gene SEN1 (Senataxin). It is an important component of the Nrd1p-Nab3p-Sen1p (NRD1) complex that regulates the transcriptional termination of most non-coding and some coding transcripts at RNA polymerase pause sites. Sen1 specifically interacts with Rnt1p (RNase III), an endoribonuclease, and with Rpb1p (Rpo21p), a subunit of RNA polymerase II, through its N-terminal domain (NTD), which is a critical element of the RNA-processing machinery. Moreover, mutations in the N-terminal tail of SETX, a human ortholog of yeast Senataxin (Sen1) reported in neurological disorders.
In one of the earlier studies, we have reported that the loss of dispensable NTD in yeast Sen1 resulted in flocculation and slow growing phenotypes along with defective DNA damage repair mechanisms. So, we attempted to explore the molecular basis of functional impairment associated with the loss of Sen1 N-terminal domain through global oligonucleotide microarray analysis. Also, we investigated for functionally enriched pathways based on the altered basal level gene expression profiles upon NTD loss of Sen1. The microarray data were validated by quantitative real-time PCR wherever necessary.

overall_design: Wild-type (BY4741) and Sen1ΔN mutant yeast cells were inoculated to an OD600 of 0.4 in fresh synthetic complete liquid media and then the cells were further allowed to grow until reaches to exponential phase (OD600-1.5). Two independent experiments were performed for each experiment (WT or Sen1ΔN). Total RNAs were extracted and hybridized on Affymetrix microarrays.


title: Identification of miRNA, lncRNA and mRNA-associated ceRNA networks and potential biomarker for MELAS with mitochondrial DNA A3243G mutation [array]

status: Public on Oct 23 2016

city: Jinan

first: Wei

last: Wang

state: Shandong

address: West Wenhua Road

department: Department of Neurology

institute: Qilu Hospital, Shandong University

summary: To elucidate the regulating networks of dysregulated ncRNAs in Mitochondrial myopathy, Encephalopathy, Lactic Acidosis, and Stroke-like episodes (MELAS) with m.A3243G mutation.

overall_design: The MELAS sample consisted of a muscle pool from 20 MELAS patients with m.A3243G mutation, and the Control sample consisted of a muscle pool from 20 healthy controls. LncRNA sequencing and miRNA array of muscle pools were performed by the service provider (LC Sciences). The secondary qRT-PCR validation of the most promising miRNAs and lncRNAs using individual samples were from the same group. The findings were all consistent with results from our high-throughput data.


title: Comparison of gene expression changes following knockdown of KMT2A and MSK1 in mouse embryonic fibroblasts

status: Public on Oct 26 2016

city: Birmingham

last: Halsall

address: Medical School, Vincent Drive

department: Cancer and Genomic Sciences

institute: University of Birmingham

summary:
The KMT2A/MLL1 lysine methyltransferase complex is an epigenetic regulator of selected developmental genes, in part through the SET-domain-catalyzed methylation of H3K4. It is essential for normal embryonic development and haematopoiesis and frequently mutated in cancer. The catalytic properties and targeting of KMT2A/MLL1 depend on the proteins with which it complexes and the post-translational protein modifications which some of these proteins put in place, though detailed mechanisms remain unclear. We have shown that KMT2A/MLL1 (both native and FLAG-tagged) and Msk1 (RPS6KA5), co-immunoprecipitated in various cell types.
This experiment showed that the great majority of genes whose activity changed on KTM2A/MLL1 knockdown responded comparably to Msk1 knockdown.

overall_design: A 10 array study in which KMT2A (Mll1) or MSK1 were knocked down in mouse embryonic fibroblasts. There were 3 control (mock transfected) samples, 4 KMT2A shRNA samples and 3 MSK1 shRNA samples.

first: Maaike

last: Wiersma

last: Turan

middle: M

last: Turner

first: Karl

middle: P

last: Nightingale


title: Analysis of mRNA from mice with colitis given SAG21k versus vehicle

last: Beachy

summary: Comparative analysis of mRNA from colons of mice that were given colitis though use of 5% dextran sulfate in the drinking water (Days 0-5)

overall_design: Colons from SAG21k treated mice were compared with colons from vehicle treated mice

last: Lee

last: Rothenberg

last: Seeley


title: Analysis of differential gene expression in NFKBIE-mutated and non-mutated primary mediastinal B-cell lymphoma (PMBL) via NanoString mRNA expression profiling.

status: Public on Oct 09 2016

city: Berlin

first: Daniel

last: Noerenberg

address: Augustenburger Platz 1

department: Hematooncology

institute: Charité University Medicine

summary: We recently reported a truncating deletion in the NFKBIE gene, which encodes IκBε, a negative feedback regulator of NF-κB, in clinically aggressive chronic lymphocytic leukemia (CLL). Preliminary data indicate enrichment of NFKBIE aberrations in other lymphoid malignancies, hence we screened a large patient cohort (n=1460) diagnosed with different lymphoid neoplasms. We observed a a remarkably high frequency of NFKBIE aberrations (46/203 cases, 22,7%) in primary mediastinal B-cell lymphoma (PMBL). The deletion was associated with a particular aggressive clinical course and reduced survival in multivariate analysis. With gene expression profiling (GEP) via the NanoString nCounter hybridization system and the NanoString GX Human PanCancer Pathway Panel including 30 additional custom genes, the aim of this analysis was to study the differential activation of various oncogenic pathways including NFKB-signaling in NFKBIE mutated vs. non-mutated PMBL.

overall_design: For mRNA profiling and gene expression analysis, RNA from paraffin-embedded primary PMBL tissue was available for 36 patients (21 wildype and 15 NFKBIE mutated samples). 29 samples (8 NFKBIE-mutated and 21 wildtype PMBL) passed RNA and data quality controls and were used for gene expression analysis. RNA was profiled using the NanoString GX Human PanCancer Pathway Panel including 30 additional custom genes.

first: Larry

last: Mansouri

first: Emma

last: Young

first: Elena

last: Mylonas

first: Maysaa

last: Abdulla

first: Mareike

last: Frick

first: Fazila

last: Asmar

first: Viktor

last: Ljungström

first: Markus

last: Schneider

first: Kenichi

last: Yoshida

first: Aron

last: Skaftason

first: Tatjana

last: Pandzic

first: Blanca

last: Gonzalez

first: Anna

last: Tasidou

first: Nils

last: Waldhueter

first: Alfredo

last: Rivas-Delgado

first: Maria

last: Angelopoulou

first: Marita

last: Ziepert

first: Christopher

last: Arends

first: Lucile

last: Couronné

first: Dido

last: Lenze

first: Claudia

last: D. Baldus

first: Christian

last: Bastard

first: Jessica

last: Okosun

first: Jude

last: Fitzgibbon

first: Bernd

last: Dörken

first: Hans

last: Drexler

first: Damien

last: Roos-Weil

first: Clemens

last: Schmitt

first: Helga

last: Duverger Munch-Petersen

first: Thorsten

last: Zenz

first: Martin-Leo

last: Hansmann

first: Jonathan

middle: C

last: Strefford

first: Gunilla

last: Enblad

first: Olivier

last: Bernard

first: Elisabeth

last: Ralfkiaer

first: Martin

last: Erlanson

first: Penelope

last: Korkolopoulou

first: Magnus

last: Hultdin

first: Theodora

last: Papadaki

first: Kirsten

last: Grønbæk

first: Armando

last: Lopez-Guillermo

first: Ralf

last: Küppers

first: Seishi


title: Expression data from SSG1 long-lived mutant

status: Public on Oct 04 2016

city: Kagamiyama, Higashi-Hiroshima

first: MUNEYOSHI

last: KANAI

country: Japan

institute: National Research Institute of Brewing

summary:
The SSG1-1 mutation was an allele of the YHR032W gene in Saccharomyces cerevisiae. The SSG1-1 mutants contained higher levels of AdoMet than wild type (WT). SSG1-1 single mutants were shown to have a long lifespan, suggesting that the Ssg1-1 protein might have a role in longevity.
We used microarrays to compare the global gene expression profiles between the wild type and SSG1-1 mutants under normal growth condition.

overall_design: WT(W303-1A) and SSG1-1 strains pre-grown in SDC(pH 6.0) medium were inoculated in SDC(pH 6.0) medium and grown until early-log phase for RNA extraction and hybridization on Affymetrix microarrays. In order to obtain more global insights into role of SSG1 for lifespan extension, we performed the genome-wide expression analysis of SSG1 mutants.

first: Takafumi

last: Ogawa

first: Muneyoshi

last: Kanai

first: Masaki

last: Mizunuma


title: RNA Expression Data from Four Isolated Bovine Ovarian Somatic Cell Types

status: Public on Sep 28 2016

city: Lincoln

first: Sarah

last: Romereim

state: NE

address: 3940 Fair Street

department: Animal Science

institute: University of Nebraska-Lincoln

summary:
After ovulation, somatic cells of the ovarian follicle (theca and granulosa cells) become the small and large luteal cells of the corpus luteum. Aside from known cell type-specific receptors and steroidogenic enzymes, little is known about the differences in the gene expression profiles of these four cell types. Analysis of the RNA present in each bovine cell type using Affymetrix microarrays yielded new cell-specific genetic markers, functional insight into the behavior of each cell type via Gene Ontology Annotations and Ingenuity Pathway Analysis, and evidence of small and large luteal cell lineages using Principle Component Analysis. Enriched expression of select genes for each cell type was validated by qPCR. This expression analysis offers insight into the lineage and differentiation process that transforms somatic follicular cells into luteal cells.
The orignal Affymetrix .CEL files and the normalized linear expression data are included in this submission.

overall_design: There are four cell types analyzed including granulosa cells (GC, n = 4), theca cells (TC, n = 3), large luteal cells (LLC, n = 3), and small luteal cells (SLC, n = 3). Each replicate is from tissue from a separate cow. There are no treatments or controls, as all the cells are collected from healthy animals at specific stages of the estrous cycle (pre-ovulation dominant follicle versus mid-luteal phase corpus luteum).

first: Adam

last: Summers

first: William

last: Pohlmeier

first: Pan

last: Zhang

first: Xiaoying

last: Hou

first: Heather

last: Talbott

first: Robert

last: Cushman

first: Jennifer

middle: R

last: Wood

first: John

last: Davis

first: Andrea

last: Cupp


title: CD8αα+MHC-II+ Cell with Capacity to Terminate Autoimmune Inflammation Is A Novel Antigen-Presenting NK-like cell in Rats

status: Public on Sep 20 2016

city: Houston

first: David

last: Loose

state: TX

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharm

institute: University of Texas

summary: Discovery of immune tolerance mechanisms, which inhibit pre-existing autoimmune inflammation, may provide us with new strategies for treating autoimmune diseases. We have identified a CD8αα+MHC-II+ cell with professional APC capacity during our investigation on spontaneous recovery from autoimmune glomerulonephritis in a rat model. This cell actively invades inflamed target tissue to terminate an on-going autoimmune inflammation by selective killing of effector autoreactive T cells. Now, we showed that this cell used a cytotoxic machinery of Ly49s+ NK cells in killing of target T cells. Thus, this CD8αα+MHC-II+ cell, which previously was thought a professional APC, is an antigen presenting-NK (AP-NK) cell. Following its coupling with target T cells through antigen presentation, killing stimulatory receptor Ly49s6 and co-receptor CD8αα on this cell used non-classic MHC-I RT1CE16 on the target T cells as a ligand to initiate killing. Thus, activated effector T cells with elevated expression of RT1CE16 were highly susceptible to the killing by the CD8αα+ AP-NK cell. Granule cytolytic perforin/granzyme C from this cell subsequently mediated cytotoxicity, and thus, inhibition of granzyme C effectively attenuated the killing. As it can recognize and eliminate effector autoreactive T cells in the inflamed target tissue, CD8αα+ AP-NK cell not only represents a new type of immune cell involved in immune tolerance, but also is a potential candidate for developing a cell-based therapy for pre-existing autoimmune diseases.

overall_design: With magnetic beads methods, CD8αα+MHC-II(RT1B)+ or CD8αα+RT1Blow populations were isolated from PBL or glomeruli of immunized Wista Kyoto (WKY) or Lewis (LEW) rats. Total RNAs were isolated immediately and used for DNA microarray or other purposes. After synthesis of cDNA, an aliquot of 750 ng of amplified products was loaded onto Illumina Sentrix Beadchip Array Rat arrays, hybridized at 58ºC in an Illumina Hybridization Oven (Illumina) for 17 hours, washed and incubated with streptavidin -Cy3 to detect biotin-labeled cRNA on the arrays. Arrays were dried and scanned with BeadArray Reader (Illumina). Data were analyzed using GenomeStudio software (Illumina). Clustering and pathway analysis were performed with GenomeStudio and Ingenuity Pathway Analysis (Ingenuity Systems, Redwood City, CA) softwares respectively.

first: Yahuan

last: Lou

first: Junbo

last: Shim

first: Colin

last: Carlock

first: Jean

last: Wu


title: Comparative genomics analysis of mononuclear phagocyte subsets confirms similarity between lymphoid tissue-resident and dermal XCR1+ DCs in mouse and human and distinguishes them from Langerhans cells.

status: Public on Feb 14 2017

city: MARSEILLE

first: Marc

last: DALOD

address: Parc Scientifique et Technologique de Luminy, 163 avenue de Luminy, Case 906, 13288 Marseille cedex 9

country: France

institute: CIML

type:
Third-party reanalysis
Expression profiling by array

summary: Dendritic cells (DC) are mononuclear phagocytes which exhibit a dendritic morphology and excel at naïve T cell activation. DC encompass several subsets initially identified by their expression of specific cell surface molecules and later shown to possess distinct functions. DC subset differentiation is guided by different transcription factors and cytokines. Identifying DC subsets is challenging as very few cell surface molecules are uniquely expressed on any one of these cell populations and conventional flow cytometry analysis using limited antigens is biased and potentially misleading. Moreover, the antigens currently used to define mononuclear phagocyte subsets vary depending on the tissue and animal species studied and even between laboratories. This has led to confusion in the definition of the identity of myeloid cell subsets across tissues and between species. Here we report a comparative genomics strategy that enables universal definition of DC subsets and other myeloid cell types across species. We have developed a novel, simple and user friendly software, BubbleGUM, which generates and integrates gene signatures for high throughput gene set enrichment analysis. We illustrate the use of BubbleGUM by re-analyzing 3 concatenated public datasets of blood/spleen and skin/cutaneous lymph node myeloid cell subsets in humans and in mice. This analysis demonstrates the equivalence between human and mouse skin XCR1+ DCs, and between mouse and human Langerhans cells.

sample_organism:
Homo sapiens
Mus musculus

overall_design:
Dendritic cells (DC) are mononuclear phagocytes which exhibit a dendritic morphology and excel at naïve T cell activation. DC encompass several subsets initially identified by their expression of specific cell surface molecules and later shown to possess distinct funcRecent studies have identified multiple DC-like populations in human skin with overlapping phenotypes but with distinct transcriptome profiles, functions, and lineage relationships with other tissue DCs in humans and mice (Haniffa et al. Immunity. 2012. PMID 22795876; Chu et al. JEM. 2012. PMID 22547651; Artyomov et al. JEM. 2015. PMID 25918340), leading to a certain level of confusion in the field. In this study, using comparative genomics, we aimed to clarify these conflicting reports and define murine and human skin mononuclear phagocyte subsets, their intra-species tissue equivalents and inter-species homologs. To achieve this goal, we performed high throughput module (gene set enrichment) meta-analyses with our newly released BubbleGUM software (Spinelli et al. BMC Genomics. 2015; PMID 26481321) on a number of independent public datasets for mononuclear phagocyte populations in the blood or spleen, skin or cutaneous lymph node of humans and in mice. This allowed us to rigorously identify DC subsets, monocytes and macrophages in these tissues and to align them across species.

The Mouse Gene 1.0 ST (GPL6246) CEL files were processed through Bioconductor in the R statistical environment (version 3.0.2). Quality control of the array hybridization (NUSE plot) and normalization of the raw Affymetrix expression data with Robust Multi-chip Analysis (Irizarry, R. and al) were performed using the oligo package (Matrix1). PCA was performed to remove the dataset effect visible on the first principal component (Matrix2), using ade4 package.  The Illumina Human WG-6 v3 (GPL10558) and Illumina Human HT12 v4.0(GPL6884) raw data files were processed through Bioconductor in the R statistical environment (version 3.0.2). Gene expression signals from GSE60317 and GSE35457 were merged by their common probes. Quantile Normalization (Bolstad, 2004) was applied on the merged expression arrays using the package lumi and then expression values were log2-transformed. Gene expression signals from GSE66355 were already background corrected and quantile normalized. Noise threshold was estimated at 5 based on the density of all gene expression signals. All values less than this threshold were replaced by this threshold. Expression values were then log2-transformed to be comparable to the 2 others datasets. The three datasets were merged by the common probes and quantile normalization was applied again (Matrix3). PCA was performed to remove the dataset effect visible on the first two principal components (Matrix4).  Human and Mouse datasets were then merged based on identification of orthologous genes using the Ensembl BioMart software with selection of “one-to-one” orthology relationships only (Matrix5).

first: Sabrina

last: Carpentier

first: Thien-Phong

last: Vu Manh

first: Rabie

last: Chelbi

first: Sandrine

last: Henri

first: Bernard

last: Malissen

first: Muzlifah

last: Haniffa

first: Florent

last: Ginhoux

last: Dalod


title: Increased expression of proenkephalin and prodynorphin mRNAs in the nucleus accumbens of compulsive methamphetamine taking rats

status: Public on Sep 02 2016

city: Baltimore

first: Jean Lud

last: Cadet

state: MD

address: 251 Bayview Blvd, Suite 200

department: Molecular Neuropsychiatry Research Branch

institute: NIDA, IRP

summary: Addiction to psychostimulants is associated with neuroadaptive changes in various brain regions.   In this experiment we use a model of methamphetamine self-administration during which we use footshocks as adverse consequences to divide rats into animals that continue to press an active lever to get the drug (shock-resistant) whereas other rats stop or significantly reduce pressing the lever (shock-sensitive) in the presence of these adverse consequences.   To investigate potential molecular bases for the divergent phenotype, we performed a whole rat transcriptome study using Affymetrix rat arrays that cover more than 24,000 coding transcripts. The array experiments revealed that there were 24 differentially expressed genes between the resistant and sensitive rats, with 15 up- and 9 downregulated transcripts. Ingenuity pathway analysis revealed that these transcripts belong in a network of genes involved in nervous system development and function, cell signaling, behavior, and disorders of the basal ganglia. These genes included proenkephalin (PENK) and prodynorphin (PDYN), among others. Because PDYN and PENK are expressed in dopamine D1- and D2-containing NAc neurons, respectively, these findings suggest that mechanisms that impact both cell types may play a role in the regulation of compulsive methamphetamine taking by rats.

overall_design: Six rats from each of the 3 groups including control, shock resistant, and shock sensitive were selected based on RNA quality and integrity for RNA extraction and hybridization on Affymetrix microarrays.

middle: L

first: Irina

middle: N

last: Krasnova

first: Donna

last: Walther

first: Christie

last: Brannock

first: Bruce

last: Ladenheim

first: Michael

middle: T

last: McCoy

first: Daniel

last: Collector

first: Ndeah

last: Terry

first: Subramaniam

last: Jayanthi


title: Deciphering a functional gene network underlying robustness to protein overproduction

status: Public on Sep 01 2016

city: Szeged

first: Zoltan

last: Farkas

state: Csongrad

address: Temesvari krt. 62.

country: Hungary

institute: Biological Research Centre

summary:
We systematically investigated the impact of genetic variation and the environment on protein overproduction costs in Saccharomyces cerevisiae
To identify genes mediating protein overproduction costs, genetic perturbations were applied. The yEVenus overexpression plasmid was crossed into gene deletion backgound. The generation of double mutant strains enabled us to investigate the transcriptional response of the cells under two different internal stress: deletion of a given gene, plus the overexpression of a gratuitous protein

overall_design: To explore the cellular response under gratuitous protein overproduction, a sensitized background was used (sse1 deletion). Our aim was to identify differentially expressed genes upon protein overproduction. 3-3 biological replicates were used for the control (single deletion strain with an empty plasmid) and for the overexpression strains (single deletion strain with yEVenus multi-copy plasmid) as well. The cellular response to overexpression was normalized to the control sse1 deletion strain, without overexpression.

first: Zoltán

last: Bódi

first: Dorottya

last: Kalapis

first: Peter

last: Horvath

first: Béla

last: Szamecz

first: Gábor

last: Boross

first: Károly

last: Kovács

first: Ferenc

last: Pal

first: Edit

last: Rutkai

first: Attila

last: Szvetnik

first: Balazs

last: Papp

first: Csaba

last: Pál


title: Gene expression analysis of human monocytes co-cultured with adipocytes

status: Public on Sep 07 2016

city: Singapore

first: Vivien

last: Koh

address: 1E Kent Ridge Road

country: Singapore

institute: National University Health System

summary: This study analyzed the differentiation and polarization of human monocytes regulated by factors released from adipocytes (termed adipokines) at the gene expression level. The hypothesis was that adipokines affect differentiation and M1/M2 polarization of human monocytes. Results revealed interesting up- and down-regulated genes related to the differentiation and M1/M2 polarization of human monocytes in response to adipokines.

overall_design: Total RNA was isolated from monocytes co-cultured for 24 or 48 h with SGBS preadipocytes or adipocytes (after 2 weeks of differentiation).

first: Shotaro

last: Nakajima


title: Nuclear mRNA quality control is bypassed for rapid export of stress responsive transcripts (Microarray)

status: Public on Jun 14 2016

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Comparative analyses of Mex67 and Npl3 binding to mRNA at normal growth condition (25°C) and upon shift to heat stress (30 min, 42°C).

overall_design: Comparative analyses of mRNA binding of Mex67, Npl3 and no tag control at normal growth condition (25°C) and upon heat stress (30 min, 42°C) via RNA Co-IP experiments. Respective co-purified mRNAs were subjected to cDNA  Microarray chips.

first: Daniel

last: Becker

first: Alexandra

last: Hackmann

first: Gesa

last: Zander

last: Salinas-Riester

first: Heike

last: Krebber

first: Thomas

last: Lingner


title: Effects of dietary forage and calf starter on ruminal pH and transcriptomic adaptation of the rumen epithelium in Holstein calves during the weaning transition

status: Public on Jun 29 2016

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

summary: We assessed the transcriptomic adaptation of the calf rumen epithelium to changes in ruminal pH caused by feeding calf starter with and without forage during weaning transition.

overall_design: The calves were divided into a gorage provision group (HAY group, n = 3) and forage non-provision group (CON group, n = 4) 3 weeks after weaning.

first: Yo-Han

last: Kim


title: Oxidative and Cytokinin Treatment of CRF6

status: Public on Sep 23 2016

city: Auburn

first: Aaron

last: Rashotte

state: Alabama

address: 101 Rouse Life Sciences, Department of Biological Sciences, Auburn University

department: Biological Sciences

institute: Auburn University

summary:
Oxidative and Cytokinin treatment of Arabidopsis wildtype, crf6 mutant, and CRF6 overexpressing seedlings
Arabidopsis seedlings were treated with oxidative stress or cytokinin to determine transcripts altered in each genotype background

overall_design: We treated plants for 6hours with oxidative stress (hydrogen peroxide (20mM)) or cytokinin (Benzyl Adenine (2microM) to determine target genes of CRF6

first: Paul

last: Zwack


title: Gene Co-Expression Network Analysis Unraveling Transcriptional Regulation of High-altitude Adaptation of Tibetan Pigs

status: Public on Jul 15 2016

city: Yangling

first: Cunling

last: Jia

state: Shaanxi

address: Xinong road 22#

department: Animal science

institute: Northwest A&F University

summary: To elucidate further  molecular mechanisms underlying the regulation of hypoxia-adaptive phenotypes in Tibetan pigs, we  used transcriptome microarrays from lung tissues of Tibetan pigs and Duroc pigs both at high and low altitude analyzed differentially expressed genes (DEGs), biological pathway and constructed co-expression regulation network. A total of 3,068 DEGs were identified which involved metabolic process, cellular process, immune biological process and angiogenesis pathway. The regulatory (RIF) and phenotypic (PIF) impact factors analysis identified several known and potentially regulators of hypoxia adaption, including IKBKG, KLF6 and RBPJ (RIF1), SF3B1, EFEMP1, HOXB6 and ATF6 (RIF2).

overall_design: We employed a complete migrant design, i.e. Tibetan pigs from Tibetan Autonomous Prefecture of Diqing (3,500 m) (TH) and Duroc pigs from lowland (Guangzhou, 40 m) (DL) were migrated to lowland (TL) or highland (DH) on 1 month old, respectively and raised until  6 month old.  Gene expression of lung tissuesfrom four groups was measured.


title: Transcription profiling of different state of Mycoplasma gallisepticum

status: Public on Aug 18 2016

city: Moscow

first: Tatiana

middle: A.

last: Semashko

address: Malaya Pirogovskaya

country: Russia

institute: RCPCM

summary: Mycoplasma gallisepticum is a convenient model object for studying the regulation of transcription because it has a reduced genome, lack of cell wall and many metabolic pathways, and also easy to culture and non-pathogenic to humans. For rapid investigation of gene expression we developed microarray design including 3 366 probes for 678 genes. They included 665 protein coding sequences and 13 antisense RNAs from 816 genes and 17 ncRNAs present in Mycoplasma gallisepticum. This work was carried out transcriptomic profiling for different types of effects on the expression of genes of Mycoplasma gallisepticum: 1) genetic knock-out mutants; 2) cell culture exposed to sublethal concentrations of antibiotics; and 3) well-characterized heat stress effect. The study was performed on Agilent one-color microarray with custom design and random-T7 polymerase primer for cDNA synthesis. Using set of different probes for each gene or ncRNA allows to increase accuracy of gene expression quality.

overall_design: Transcriptome profiling of 1) wild type Mycoplasma gallisepticum cell culture and mutants with transposone insertion to 5’ UTR of hypothetical protein GCW_03380, RBS of lactate dehydrogenase GCW_00390, helicase SNF2 GCW_03935, 1-deoxy-D-xylulose 5-phosphate reductoisomerase GCW_00495 or potential sigma factor GCW_00440 in exponential growth phase; 2) Mycoplasma gallisepticum cell culture under treatment with sublethal concentrations of carbonyl cyanide m-chlorophenylhydrazone (CCCP), novobiocin or tetracycline; and 3) Mycoplasma gallisepticum cell culture under heat stress at 46C during 15 min. All experiments were carried out in 2 biological replicates.

first: Alexander

last: Arzamasov

first: Gleb

middle: Y

last: Fisunov

first: Vadim

last: Govorun


title: Gene expression profile of Trichophyton rubrum growth on protein substrates

status: Public on Aug 01 2016

city: RIBEIRAO PRETO

first: Tamires

middle: Aparecida

last: Bitencourt

state: SP

address: AV COSTABILE ROMANO 2221

department: BIOTECNOLOGY

country: Brazil

institute: UNAERP

summary: We investigated the transcription profile of germinant conidia growth on protein substrates to widen the knowledge about relevant genes for pathogenecity, and also it was verified an encoding gene of adhesin like protein, which was modulated during the growth of T. rubrum on keratin.

overall_design: About 2.6 x 106 conidia/  mL solution was prepared from T. rubrum growth on Sabouraud for 15 days. The solution was inoculated in Cove's medium with nitrate and glucose (control), Cove's medium with 0.25% of elastin, and Cove's medium with 0.5% of keratin. These conditions were incubated for 24h, 36h and 72h.  Two independent experiments were performed for each condition.

first: Claudia

last: Macedo

first: Matheus

last: Franco

first: Amanda

last: Fassis

last: Komoto

first: Eliana

middle: G

last: Stheling

first: Iran

last: Malavazi

first: Geraldo

last: Passos

first: Rene

middle: O

last: Beleboni

first: Mozart

last: Marins

first: Ana

last: Fachin


title: WRKY43 regulates polyunsaturated fatty acid content and abiotic stress tolerance of Arabidopsis seeds

status: Public on Aug 16 2016

city: Münster

first: Maik

last: Boehmer

state: Deutschland

address: Schlossplatz 7

department: IBBP

institute: Westfälische Wilhelms Universität

summary: Loss of the seed-specific WRKY transcription factor WRKY43 confers enhanced tolerance towards high salt, high osmolarity and low temperature with respect to seed germination. wrky43 loss of function lines display increased inhibition of seed germination in response to exogenous ABA, while WRKY43 overexpression lines are more tolerant towards exogenous ABA. The opposing effect of the wrky43 mutant on salt and ABA tolerance is reminiscent of fatty acid desaturase mutants. Loss of WRKY43 enhances polyunsaturated fatty acid content, particularly 18:2 and 18:3 in TAGs and Phospholipids. Gene chip arrays show that ABA-induced regulation of FUSCA3, ZAT10 and seed storage proteins are absent in the wrky43 mutant. Promoter-Luciferase studies confirm direct regulation of ZAT10 by WRKY43 and suggest indirect regulation of FUS3 and SSPs. In summary WRKY43 acts as a positive regulator of ABA-dependent gene regulation and of fatty acid desaturation that finally results in enhanced tolerance to abiotic stress.

overall_design: 2 biological replicates of Arabidopsis thaliana Ler-0 wildtype and wrky43 muatnt seeds were compared after incubation in liquid 0.5 MS media with 2 µM ABA for 4 days

first: M

last: Böhmer

first: K

last: Geilen


title: Expression data from Arabidopsis pifq seedlings grown in short days (SD) and in free running (LL) conditions.

status: Public on Aug 31 2016

city: Barcelona

first: Elena

last: Monte

address: Campus UAB Edifici CRAG

country: Spain

institute: CRAG

summary:
Members of the PIF quartet (PIFq) (PIF1, PIF3, PIF4, and PIF5) collectively contribute to induce growth in Arabidopsis seedlings under short day (SD) conditions, specifically promoting elongation at dawn. Their action involves the direct regulation of growth-related and hormone-associated genes.
The objective of this genomic analysis was to define a comprehensive set of SD-regulated genes at dawn compared to free-running (LL) conditions in the wild type, followed by identification of those SD-regulated genes whose expression depends on the presence of PIFq. By using this sequential strategy, our aim was to identify PIF/SD-coregulated genes.

overall_design: Two genotypes [wild type Columbia (Col-0) and pifq mutant] and two treatments [SD and LL] were included. Each sample had three biological replicates. Seedlings were grown under SD (8h white light + 16 h of darkness) for 2 days and then either mantained in SD (SD samples) or kept under white light (LL) for an additional day. Samples were collected at the end of the night in SD (ZT24) or the end of the subjective night in LL (CT24).

first: Judit

last: Soy

first: Guiomar

last: Martín


title: Cell-sorting analysis with SEOR1pro::SEOR1-YFP in a novel in vitro tissue culture system, VISUAL

status: Public on May 25 2016

city: Kobe

first: Yuki

last: Kondo

address: 1-1 Rokkodai-cho, Nada-ku

department: Graduate School of Science

institute: Kobe University

summary:
We established a novel in vitro tissue culture system (named VISUAL), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons
To isolate phloem-specific genes in VISUAL, we performed GeneChip analysis after cell-sorting experiments with SEOR1pro::SEOR1-YFP.

overall_design: Arabidopsis cotyledons cultured with the induction medium were sampled at 72 hours after the induction. After protoplasts isolation, YFP-positive and YFP-negative cells were collected. YFP-positive cells are phloem cells while YFP-negative cells are non-phloem cells.

first: Yukiko

last: Sugisawa


title: A genome-wide transcriptomic analysis of radiation-responsive genes in the radiation-resistant fungus, C. neoformans

status: Public on Jun 01 2016

city: Jeongeup

first: Kwang-Woo

last: Jung

address: 29 Geumgu-gil

country: South Korea

institute: Korea Atomic Energy Research Institute

summary: The basidiomycetous fungus Cryptococcus has been known as radiation resistant fungi and is found in highly radioactive environments such as the damaged nuclear reactor at Chernobyl. Although Cryptococcus exhibits greater resistant for gamma radiation than the model yeast Saccharomyces cerevisiae, the resistant mechanism of gamma radiation remains elusive. To elucidate a unique regulatory system for radiation-resistance in C. neoformans, we performed genome-wide comparative analysis through DNA microarray analysis using C. neoformans WT strain (serotype A, H99 strain) responding gamma radiation. Based on the transcriptome analysis, genes involved in DNA damage repair systems (RAD51, RDH54, and RAD54) were significantly increased in response to gamma radiation. Actually, rad54∆ and rdh54∆ mutants exhibited sensitivity against both gamma radiation and DNA damage inducers. Furthermore, genes regarding to molecular chaperone and ubiquitination systems were strongly induced. In contrast, expression levels of genes related to protein synthesis, fatty acids/sterols synthesis, and other cellular molecules. Especially, ergosterol homeostasis is required for gamma radiation resistance. Furthermore, radiation-induced genes such as RIG4, RIG5, and RIG6 in C. neoformans play critical roles in gamma radiation resistance. Taken together, the transcriptome analysis contributes to understanding unique molecular mechanism of radiation-resistant fungus C. neoformans.

overall_design: To elucidate transcriptome change during recovery process post irrdiation, samples were taken at three time interval (30 min, 60 min, and 120 min). The three independent DNA microarry with three independent biological replicates were analyzed to obtain high reliability.

first: Dong-Hoon

last: Yang

first: Sangyong

last: Lim

first: Yong-Sun

last: Bahn


title: Comparison between WT and apl in a novel in vitro tissue culture system, VISUAL

summary:
We established a novel in vitro tissue culture system (named VISUAL), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons
To compare gene expression profiles between WT and apl during vascular development, we performed GeneChip analysis using VISUAL.

overall_design: Arabidopsis cotyledons cultured with the induction medium were sampled at 72 hours after the induction.


title: Transcriptomes of a xylose-utilizing industrial flocculating Saccharomyces cerevisiae strain cultured in media containing different sugar sources

status: Public on Apr 28 2016

city: Chengdu

first: Wei-Yi

last: Zeng

state: Sichuan

address: Chuanda Road ,Shuangliu County

department: Architecture and environment

institute: Sichuan University

summary:
The molecular basis for glucose and xylose fermentation by industrial Saccharomyces cerevisiae is of interest to promote bioethanol production
We used microarrays to investigate the transcriptional difference of a industrial strain cultured in both single sugar media and a mixed sugar medium of glucose and xylose

overall_design: In this study, microaerobic batch fermentations of KF7M-16 were carried out in both single sugar medium (either glucose or xylose) and mixed sugar medium (including the glucose fermentation phase and the xylose fermentation phase). RNA was extracted at 2h for glucose-fermenting cells and an 7h for xylose-fermenting cells. The global transcriptomes were analyzed to identify the molecular response to different fermentation states.

first: Yue-Qin

last: Tang


title: Comparative transcriptomes reveal novel evolutionary strategies adopted by Saccharomyces cerevisiae with improved xylose utilization capability

status: Public on Apr 30 2016

summary:
The xylose fermentation capability of an industrainl Saccharomyces cerevisiae strain was enhanced by adaptive evolution. Eight homozygots were generated by tetrads dissection.
The underlying molecular basis of the enhanced xylose fermentation capability was analyzed.

overall_design: The enriched transcriptional difference between the eight homozygotes generated from the evolved strain and the parental strain  revealed novel responses to xylose that were likely to contribute to the improved xylose utilization.


title: Global gene expression profiling following a dietary selenium supplementation in sheep (Ovis aries).

status: Public on Apr 26 2016

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

institute: AstraZeneca

summary: In the present study, we studied the effect of dietary selenium (Se) supplementation on the transcriptomic profile of sheep. The main objective was to evaluate the effect of Se-supplementation on the overall transcriptome of sheep, the altered pathways, and the biological processes related to it . A custom oligo microarray platform (AMADID: 070119) was designed, then used to profile gene expression from 20 samples from 10 sheep at two time points (T0; before Se-supplementation, and T40; at the end of a 40-d Se-supplementation period). Isolated and purified total RNAs were individually hybridized to the custom (4x44k) DNA microarray. The comparison of control and treated animal transcriptomes revealed a large set of differentially expressed genes. After functional analysis and qPCR validation, the result showed several pathways and biological processes that have been altered following Se-supplementation to the diet.

overall_design: Ten lactating crossbred ewes (3 to 4 y of age and 55 to 65 kg BW) were assigned to a before-and-after experimental design, where each animal served as its own control. The sheep have been acclimatized (4-wk) on a basal diet containing a maintenance level of Se (0.13 mg Se/kg DM). At the end of the 4-wk acclimatization period the sheep started to receive the supra Se-supplemented diet (0.45 mg Se/kg DM) for a 40-d period. Blood samples were collected at 2 time points [T0; one day before the supra Se-supplementation, and T40; at the end of the 40-d supra Se-supplementation phase]. Blood samples were collected from each individual animal directly into Paxgene blood collection tubes, processed and stored at -20˚C till further analyses. All samples yielded high quality RNA that was tested prior the microarray setup.

first: Mery

last: Giantin

first: Mauro

last: Dacasto

first: Federica

last: Castellani

first: Lisa

last: Grotta

first: Fiorentina

last: Palazzo

first: Giuseppe

last: Martino


title: Gata.a, Tcf7 and Zic-r.a ChIP-chip analysis in Ciona intestinalis embryo (16-cell stage)

status: Public on Apr 22 2016

city: Kyoto

first: Atsushi

last: Kubo

state: Kyoto

address: Sakyo-ku

department: Department of zoology, Graduate School of Science

institute: Kyoto University

type: Genome binding/occupancy profiling by genome tiling array

summary: DNA binding profiles of three maternal factors (Tcf7, Gata.a and Zic-r.a) in chordate 16-cell stage embryo. 16-cell stage ciona intestinalis embryos were collected from multiple batches and the extracted chromatin was immunoprecipitated by the antibodies which specifically recognize ciona Gata.a, Tcf7 and Zic-r.a, respectively.

overall_design: Three independent chromatin immunoprecipitation assay (Gata.a, Tcf7 and Zic-r.a)

first: Yutaka

last: Satou


title: Microarray gene expression study of cycling vs arrested S. Pombe minimal cells

status: Public on Apr 01 2016

city: Gothenburg

first: Zsolt

last: Szilagyi

address: Medicinaregatan 9A

institute: University of Gothenburg

summary:
A minimal cell cycle control module is driving the cell cycle in these S. Pombe cells.
During the experiment the cells are arrested or released to cycle through  the different phases of the cell cycle.

overall_design: Samples were collected at the indicated times points from arrested and cycling cells and expression of genes were measured by microarrays on an Affymetrix platform.

first: Gabor

last: Banyai

first: Damien

last: Coudrouse


title: The BTH-incuced WRKY62-dependent genes

status: Public on Mar 31 2016

city: Tsukuba

first: Hiroshi

last: Takatsuji

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Plant Sciences

institute: National Institute of Agrobiological Sciences

summary: WRKY62 is a transcriptional repressor regulated downstream of WRKY45, a central TF of the salicylic acid (SA) signaling pathway for defense response in rice. To characteraze SA signaling induced genes whose expressions were regulated by WRKY62, we analized genome-wide epression profiles in WRKY62-kd and NB rice using benzothiadiazole (BTH), SA singaling activator.

overall_design: Nipponbare rice (Oryza sativa) and WRKY62-kd rice were treated with or without 30 µM of BTH and analyzed after incubation for 0, 12 and 24h.

first: Setsuko

last: Fukushima


title: Gene expression-based investigation of a new role for the glyoxylate shunt in contributing to tolerance to oxidative stress.

status: Public on Feb 24 2016

city: Anam-Dong, Seungbuk-Ku

first: Sungeun

last: Ahn

state: Seoul

address: Anamro

department: molecular microbiology

institute: Korea university

type: Expression profiling by high throughput sequencing

summary: Transcriptional profiling in Pseudomonas aeruginosa MPAO1 and its glyoxylate shunt gens transposon insertion mutants (aceA and glcB) was perfomed using microarray analysis with or without 1mM PQ treatment. Based on the gene expression, we investigated role of glyoxylate shunt in P. aeruginosa and found out pathway related with glyoxylate shunt under oxidative stress.

overall_design: We performed a transcriptome anaylsis of WT and glyoxylate shunt knockout mutants(aceA and glcB) with or without 1mM PQ treatment. Two independent microarray analysis were done.

first: Woojun

last: Park


title: Genomic instability induced by lowered expression of POL3 in yeast

status: Public on Mar 03 2016

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

type: Genome variation profiling by genome tiling array

summary: DNA replication stress (DRS)-linked genomic instability has emerged as an important factor driving cancer development. To understand the mechanisms of DRS-associated genomic instability and phenotypic evolution, we mapped chromosomal alterations in a yeast strain with lowered expression of the replicative DNA polymerase δ. At a whole-genome level, we identified both hotspots of mitotic recombination and chromosome-specific aneuploidy dependent on decreased levels of DNA polymerase δ. The high rate of chromosome loss is likely a reflection of reduced DNA repair capacity in strains with low levels of DNA polymerase. Most recombinogenic DNA lesions were introduced during S or G2 phase, presumably as a consequence of broken replication forks.

overall_design: To reduce the expression of gene POL3, a KANMX-GAL1 cassette was inserted before the ORF of this gene in haploid strains JSC54-1 (W303-1A) and JSC20-1 (YJM789), resulting in mutants DZ1 and DZ2 (genotypes of these strains were listed in Table S1 and primers used to for strain construction were in Table S2), respectively. Mating DZ1 and DZ2 and subsequent knockout of MATalpha generated a diploid strain DZ12. We grew single cells of strain DZ12 to colonies on solid low-gal (2% yeast extract, 2% peptone and 3% raffinose, 0.005% galactose) medium and 35 colonies were selected for whole genome SNP-microarray analysis that can examine about 13,000 SNPs located throughout the genome. 6 DZ12-derived colonies (DZHG1-6) from single cycle growth on high-gal medium (0.05% galactose) were also examined. To induce reciprocal crossover events in DZ12, DZ12 cells were incubated in YPD liquid medium for 6 h to deplete polymerase δ and then plated on solid medium to form sectored colonies (S1-S60). These sectored colonies were analyzed with SNP microarray specific for chromosome 4.

first: Thomas

last: Petes


title: Influence of Nod Factors on early developmental stages of root development in Medicago truncatula

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: We would like to know how symbiotic molecules such as Nod Factors (NF) influence lateral root (LR) development in M. truncatula. We have preliminary evidence that this action is through early stages of root development. Auxin is the major phytohormone controlling LR development and we also have evidence that NF interfere with auxin for the control of LR development. This transcriptomic study aims at finding new molecular targets that would be responsive to auxin and NF treatment, even at a higher level by the combination of both auxin and NF. Such targets could be involved in the control or early development stages of LR that would be controlled both by auxin and NF treatment. - 2 day old M. truncatula (accession A17) plantlets grown on M medium were transferred for 2 days on M medium+ 10-5M NPA (1-N-Naphthylphthalamic acid, auxin transport inhibitor) then transferred for 10 h on M medium containing 10-6 M NAA (naphthalene-1-acetic acid, permeant auxin analog) or 10-7 M Nod factors (NF) or a combination of both (10-6 M NAA + 10-7 M NF). These are compared to mock treated (solvent only) plants.

overall_design: 12plex_med_2013_04 12 dye-swap - treated vs untreated comparison

first: Sandra

last: Bensmihen

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Expression data from Saccharomyces cerevisae strains overexpressing RNA-binding hnRNP Yra1

status: Public on Mar 11 2016

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

institute: CABIMER, Universidad de Sevilla

summary:
Transcription is a major obstacle for replication fork progression and a cause of genome instability. Such instability increases in mutants with an imbalance proportion of Yra1, a component of THO/TREX.
We used microarrays to the global impact of Yra1 overexpression and found that no general impact was observed.

overall_design: S. cerevisiae strains were grown in minimal medium raffinose and were shifted to galactose (2%) for four hours in liquid culture, total RNA was isolated and hybridized on Affymetrix microarrays

last: Gavaldá

first: José

last: Santos-Pereira

first: María

last: García-Rubio

first: Rosa

last: Luna


title: Expression data from Saccharomyces cerevisiae

status: Public on Jan 01 2016

city: Göteborg

first: Zihe

last: Liu

address: Kemivägen 10

institute: Chalmers University of Technology

summary:
In this study, we characterize the protein uptake and degradation pathways of S. cerevisiae to better understand its impact on protein secretion titers. We do find that S. cerevisiae can consume significant (g/L) quantities of whole proteins. Characterizing the systems with metabolomics and transcriptomics, we identify metabolic and regulatory markers that are consistent with uptake of whole proteins by endocytosis, followed by intracellular degradation and catabolism of substituent amino acids.
Uptake and degradation of recombinant protein products may be common in S. cerevisiae protein secretion systems, and the current data should help formulate strategies to mitigate product loss.

overall_design: Saccharomyces cerevisiae strains at different cultivation conditions were selected at early glucose phase in batch fermentations for RNA extraction and hybridization on Affymetrix microarrays. Biological triplicates were applied, and strains growing at normal conditions (with no BSA supplemented) were used as the control strain.

first: Keith

last: Tyo


title: Chaetocin efficacy on Dahl rat

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Transcriptional profiling of left ventricular tissues of Dahl rat with or without treatment of chaetocin

overall_design: Three-condition experiment, Control vs. failing heart, failing heart vs. treatment with chaetocin. 3 samples mixture per each group

first: Tomohiko

last: Ono


title: miR-146a Exerts Differential Effects on Melanoma Growth and Metastatization.

status: Public on Mar 18 2016

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

country: Italy

institute: University of Padova

summary: Malignant melanoma is the most aggressive form of skin cancer therefore it is crucial to disclose its underlying molecular mechanisms. MicroRNAs are small endogenous non-coding RNAs able to post-transcriptionally down-regulate the expression of direct target genes. Using a melanoma progression model, we identified miR-146a as a key double-acting player in melanoma malignancy. In fact, miR-146a is able to enhance tumor growth while it suppresses dissemination. We evidenced that melanoma cell growth is coordinated by its direct target lunatic fringe (LFNG) which operates on the NOTCH/PTEN/Akt pathway. Instead, metastasis formation inhibition is linked to decreased expression of ITGAV and ROCK1. Relevantly, miR-146a expression correlates with melanoma recurrence and it is enriched both in patients-derived melanoma and cutaneous metastasis samples, while its direct targets are depleted. However, miR-146a levels drop in Circulating Tumor Cells, suggesting the necessity for miR-146a expression to fluctuate during tumor progression in order to favor tumor growth and allow dissemination. This study reconciles the contradictory biological functions of miR-146a in melanoma progression and unravels distinct molecular mechanisms that need to be considered for therapeutic interventions.

overall_design: To identify microRNAs involved in malignant melanoma progression, miR profilings have been performed in our lab taking advantage of a human melanoma cellular model consisting of a poorly aggressive B-RAF V600E-mutated parental cell line (A375P) and its four variants MA-1, MC-1, MA-2 and MC-2, derived from one (MA-1 and MC-1) or two (MA-2 and MC-2) subsequent rounds of injections in mice and showing progressively increased metastatic potential.

first: Monica

last: Raimo

first: Francesca

last: Orso

first: Elena

last: Grassi

first: Daniela

last: Cimino

first: Elisa

last: Penna

first: Michael

last: Stadler

first: Luca

last: Primo

first: Enzo

last: Calautti

first: Pietro

last: Quaglino

first: Paolo

last: Provero

last: Taverna


title: YRA1 overexpression microarray and ChIP-chip

first: Andrés

last: Aguilera

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

overall_design: Refer to individual Series


title: Gene expression data of the Arabidopsis thaliana mutant aladin

status: Public on Dec 30 2015

city: Vienna

first: Guillaume

last: Queval

address: Dr Bohr Gasse 3

country: Austria

institute: GMI-Gregor Mendel Institute of Molecular Plant Biology GmbH

summary:
The ALADIN protein is a component of the nuclear pore complex in higher eukaryotes. Alteration in ALADIN is the basis for the human disease called triple A syndrome (Achalasia-Addisonianism-Alacrima Syndrome). A recent report showed that ALADIN deficiency decreases the tolerance to oxidative stress in human cells and impairs their ability to proliferate. An ALADIN homologue exists in plants, but its functions are still unknown. Therefore, the role of ALADIN was investigated in Arabidopsis thaliana in link with the regulation of the cell cycle.
Transcriptome profiling of the roots and shoots of the aladin mutant showed the induction of numerous transcripts linked to stress response and hormone signalling.

overall_design: Roots and shoots from the aladin mutant and the respective wild type ecotype: Wassilewskija-4 were harvested separatly in triplicates, amounting for a total of 12 samples. RNA was extracted and gene expression was measured using Affymetrix Arabidopsis Gene 1.0 ST Array.

first: Christine

middle: H

last: Foyer


title: Transcriptomic response of Saccharomyces cerevisiae in mixed-culture wine fermentation with Hanseniaspora guilliermondii

status: Public on Dec 24 2015

city: Vila Real

first: Ana

last: Mendes-Ferreira

address: Quinta de Prados

country: Portugal

institute: Universidade de Trás-os-Montes e Alto Douro

summary: Natural grape-juice fermentations involve the sequential development of different yeast species which strongly influence the chemical and sensorial traits of the final product.   In the present study,we aimed to examine the transcriptomic response of Saccharomyces cerevisiae to the presence of Hanseniaspora guilliermondii wine fermentation.

overall_design: Paralell fermentations  were carried out in natural grape-juice using S. cerevisiae for  both single and mixed culture with a H. guilliermondii strain. For RNA extraction, cells were collected at 24h, 48h and 96 h from both fermentations

first: C

last: Barbosa

first: P

last: Lage

first: N

last: Mira

first: A

last: Mendes-Faia


title: Expression data from Arabidopsis thaliana senescent leaves treated with cytokinins

status: Public on Dec 11 2015

city: Olomouc

first: Maria

last: Majeska Cudejkova

address: Slechtitelu 27

department: Centre of Region Hana for Biotechnological and Agricultural Research

country: Czech Republic

institute: Palacky University

summary:
Cytokinins are plant hormones with biological functions ranging from coordination of plant growth and development to the regulation of senescence. A series of 2-chloro-N6-(halogenobenzylamino)purine ribosides was prepared and tested for cytokinin activity in selected bioassays. Several compounds showed significant activity, especially in delaying senescence in detached wheat leaves.
We used microarrays to gather information about the reprogramming of gene transcription when senescent Arabidopsis leaves were treated with selected C2-substituted aromatic cytokinin ribosides that showed high activity in the senescence bioassay.

overall_design: Arabidopsis senescent leaves were treated with cytokinins and subsequently used for RNA extraction and hybridization on Affymetrix microarrays. 21-days old Arabidopsis leaves were treated with the appropriate cytokinin or left untreated (DMSO only).

first: Lenka

last: Radova

first: Ondrej

last: Plihal


title: Maize cytolines provide key nuclear genes that are under the control of retrograde signaling pathways in plants

status: Public on Oct 17 2015

city: Cluj-Napoca

first: Simona

last: Visan

state: Cluj

address: 34-36 Republicii

department: Functional Genomics, Proteomics and Experimental Pathology

country: Romania

institute: The Oncology Institute “Prof Dr. Ion Chiricuta”,

summary: By comparing data from the three cytolines (two cytoplsm donors and one nucleus donor) we identified key nuclear genes whose expression is modulated through the retrograde signaling pathways.

overall_design: One-color microarray study was performed to measure differences in gene expression between maize cytolines TC208(cytTC316), TC208(cytW633) and their nucleus donor line TC208. Three biological replicates for each genotype were used.

first: Mihai

last: Miclaus

first: Ovidiu

last: Balacescu

first: Ioan

last: Has

first: Loredana

first: Voichita

first: Dana

last: Suteu

first: Samuel

last: Neuenschwander

first: Irene

last: Keller

first: Rémy

last: Bruggmann


title: Yeast response to TFM exposure: time course

status: Public on Oct 23 2015

city: Northfield

first: Darlene

last: Olsen

state: VT

address: 158 Harmon Drive

department: Mathematics

country: USA

institute: Norwich University

summary: Microarray analysis was used for a global investigation of the cellular effects of acute 3-trifluoromethyl-4-nitrophenol (TFM) exposure on Saccharomyces cerevisiae over time. TFM is used to control sea lamprey (Petromyzon marinus) populations in the Lake Champlain and Great Lakes regions. Little is known about the changes in gene expression due to TFM exposure so this time course microarray study was performed to reveal significantly altered patterns of gene expression when yeast cultures were exposed to 0.05mM TFM over four hours.

overall_design: Cultures of BY4741 yeast were grown in non-fermentable yeast peptone glycerol ethanol (YPGE) media at 30°C to saturation and treated for 1, 2, or 4 hours with 2% isopropanol (untreated) or 0.05mM TFM (treated). Samples taken immediately before treatment represented “time zero” samples. For each treatment and time point, two independent RNA samples were isolated (except at 2h for untreated yeast due to poor RNA quality of one of the samples).

first: Karen

last: Hinkle


title: Gene expression changes in a histone sprocket arginine mutant in histone H2A R78A

status: Public on Aug 05 2015

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

summary: Examined gene expression changes in a histone H2A R78A mutant in Saccharomyces cerevisiae relative to wild-type cells. THe overall goal of this study was to determine the functions of histone 'sprocket' arginine residues, which insert into the DNA minor groove in the nucleosome. We examined the roles of sprocket arginine mutants in gene expression, histone incorporation, and DNA repair.

overall_design: Three wild-type control replicate samples and three experimental (H2A R78A) replicates

middle: J

first: Isaura

last: Gallegos


title: Atf1 overexpression gene expression changesS. pombe

status: Public on Aug 31 2015

city: Kolkata

first: Geetanjali

last: Sundaram

address: 35 Ballugunje circular road

department: Biochemistry

institute: University of Calcutta

summary: Atf1 was overexpressed in wt S. pombe cells for 24 hours and gene expression changes were analysed

overall_design: all samples were processed in duplicates.  Gene expression in cells overexpressing ATf1 was compared with respect to the levels in control cells transformed with the empty vector.

first: Sushobhana

last: Bandyopadhyay


title: Expression data of S. pombe wild-type and sgo2-deleted strains

status: Public on Oct 01 2015

city: Suita

first: Junko

last: Kanoh

state: Osaka

address: 3-1 Yamadaoka

department: Institute for Protein Research

institute: Osaka University

summary: Gene expression is regulated by various mechanisms. One is gene silencing, which is caused by highly condensed chromatin structure. S. pombe Sgo2 is a protein involved in the spindle assembly checkpoint at centromere. In order to investigate the other functions of Sgo2, we analyzed the effect of Sgo2 deletion  in global gene expressions.

overall_design: S. pombe cultures (wild-type and sgo2-deletion strains) at log phase were collected and global mRNAs were analyzed.

first: Sanki

last: Tashiro

first: Kazuto

last: Kugou

first: Kunihiro

last: Ohta


title: Expression data from S. cerevisiae

status: Public on Dec 31 2015

city: Taipei

first: Wan-Sheng

last: Lo

state: Taiwan

address: 128 Academia Road, Section 2, Nankang

department: IPMB

country: Taiwan

institute: Academia Sinica

summary: Low level of H3 Lys4 tri-methylation is a signature feature of silenced chromatin regions.  We used microarray to analyze the contribution of S. cerevisiae H3 Lys4 demethylase Jhd2p in silenced chromatin formation process.

overall_design: Total RNA from two JHD2 gene altered strains : jhd2 deletion and JHD2 over-expression, together with a set1 deletion strain (Set1p: H3 Lys4 methlase) were analyzed with Affymetrix Yeast 2.0 array.  We sought to dissect Jhd2p functions into H3 Lys4 methylation related and unrelated parts by comparing microarry results of JHD2 and SET1 gene altered strains.

first: Chia-yi

last: Chien

first: Pu-Yeh

last: Kan

first: Chun-Yi

last: Chiu


title: Effects of Lrf (encoded by Zbtb7a) deletion on gene expression in mouse embryonic fibroblast (MEF)

status: Public on Jul 10 2015

city: Shanghai

first: Xue-Song

last: Liu

address: 333 Haike Road

department: School of Life Science and Technology

country: China

institute: ShanghaiTech University

summary:
LRF is reported as a transcription repressor, but its transcription target genes are not completely known
We compared the gene expression difference between control and Lrf deleted MEF by microarray

overall_design: Lrfflox/flox MEFs were transduced with MSCV-PIG-Cre or empty control vector retroviruses for 2 days at passage 2. After selection with puromycin for 2 days, total RNAs were purified using the RNAeasy Mini Kit (Qiagen) and treated with RNase-free DNase set (Qiagen). RNAs from two independent experiments were labelled and hybridized using Affymetrix GeneChip® HT Mouse Genome 430 arrays by the Beth Israel Deaconess Medical Center Genomics and Proteomics

first: Pier

last: Pandolfi


title: Spc1/ Spc1K49R overexpression - gene expression changes in S. pombe

country: India

summary: Spc1/ Spc1K49R was overexpressed in wt S. pombe cells for 24 hours and gene expression changes were analysed

overall_design: All samples were processed in duplicates.  Gene expression in cells overexpressing Spc1 / Spc1K49R was compared with respect to the levels in control cells transformed with the empty vector.

first: Madhurima

last: Paul

first: Sanchari

last: Sanyal


title: Expression profile in Overexpression of GST,GST-Med3

status: Public on Aug 06 2015

city: Gothenburg

first: Claes

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

country: Sweden

institute: Gothenburg University

summary: We have used microarrays to study the gene expression changes in Overexpression of GST,GST-Med3  of yeast cells to detect how the overexpressioin may affect global  gene expression.

overall_design: RNA samples were taken from yeast cells overexpressed GST or GST-med3 and hybridized to affymetrix microarrays: GST and GST-Med3

first: Xuefeng

last: Zhu


title: Identification of targets genes of PRDM2 in G0 arrested myoblasts of C2C12

status: Public on Jun 30 2015

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

type: Genome binding/occupancy profiling by array

summary: PRDM2 directly associates with the Myogenin promoter and repress its transcription. This led to the hypothesis that PRDM2 could potentially associate directly with other promoters and regulate their expression.To gain further insight into the pathways and genes controlled by PRDM2, ChIP-on-Chip analysis was performed using mouse 44K promoter array. Since PRDM2 represses transcription by H3K9 dimethylation, we were interested in determining which targets were occupied by PRDM2 as well as showed enrichment for H3K9me2. Hence ChIP-on-Chip analysis for H3K9me2 was performed to find the overlap between PRDM2 and H3K9me2 marked promoters.

overall_design: Agilent two-color ChIP-on-Chip experiment, Organism: Mus musculus ,Genotypic Technology designed Custom Mouse Promoter 244k ChIP-on-chip Array (AMADID-019046)

first: Sirisha

last: Cheedipudi

first: Deepika

last: Puri

first: Amena

last: Saleh

first: Hardik

last: Gala

first: Mohammed

last: Rumman

first: Malini

middle: S

last: Pillai

first: Prethish

last: Sreenivas

first: Reety

last: Arora

first: Jeeva

last: Sellathurai

first: Henrik

middle: D

last: Schroeder

first: Rakesh

last: Mishra

first: Jyotsna

last: Dhawan


title: Expression analysis of RPA12Δ in Saccharomyces cerevisiae (BY4741)

city: Mysore

first: Ram

last: Rajasekharan

address: Mysore

department: Lipid Science Department

institute: Central Food Technological Research Institute

summary:
RPA12 is a subunit of RNA polymerase I.
We used microarrays to know the effect RPA12 deltion in lipid metabolism and identified distinct classes of up-regulated genes during this process.

overall_design: Stationary phase cells were taken for RNA extraction and hybridization on Affymetric microarrays

first: Kamlesh

middle: K

last: Yadav


title: Expression data of MYB36 mutants

city: Aberdeen

first: David

middle: E

last: Salt

address: St Machar Drive

department: Institute of Biological and Environmental Sciences

country: United Kingdom

institute: University of Aberdeen

summary:
We have identified the causal genes, which is MYB36, of ionome mutants.
To identify the genes regulated by MYB36, RNAs prepared from two alleles were applied for the micoarray analysis.

overall_design: Two-weeks old roots grown under normal conditions were applied for the microarray analysis

first: Takehiro

last: Kamiya


title: Genome-wide expression profiling after Allyl Alcohol treatment in Saccharomyces cerevisiae

status: Public on Apr 30 2015

city: Bhopal

first: Raghuvir

middle: singh

last: Tomar

state: MP

address: ITI (Gas Rahat) Building Govindpura - Bhopal

department: Department of Biological Sciences

institute: Indian Institute of Science Education & Research

summary:
Allyl alcohol is a highly toxic industrial chemical used as a synthetic substrate, and as an herbicide in agriculture. It is evident that Allyl alcohol is metabolized by alcohol dehydrogenases (ADH) to the highly toxic Acrolein. Acrolein is a simple unsaturated aldehyde, ubiquitous environmental pollutant, endogenous metabolite and major constituent of cigarette smoke. Acrolein is highly electrophilic in nature and has strong reactivity towards nucleophiles present in cell such as amino acids, proteins and DNA.
Several studies have tried to explore the molecular mechanisms of acrolein cytotoxicity. In continuation, we attempted to investigate the global transcriptional response of yeast cells upon treatment with 0.4mM Allyl alcohol (Acrolein) using oligonucleotide microarray assay. Also, we investigated for functionally enriched pathways based on the altered gene expression profiles after Allyl alcohol treatment. The microarray data were validated by quantitative real-time PCR.

overall_design: Wild-type yeast (W1588-4c) cells were grown to exponential phase and the cells were left untreated (Control) or treated with a dose of 0.4mM Allyl Alcohol (AA) for 3h. Two independent experiments were performed for each experiment (Control or AA). Total RNAs were extracted and hybridized on Affymetrix microarrays.

first: Upendarrao

last: Golla


title: Yeast m6A methylated mRNAs are enriched on translating ribosomes during meiosis, and under Rapamycin treatment

status: Public on Aug 12 2015

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

institute: University of Nottingham

summary:
Interest in mRNA methylation has exploded in recent years.  The sudden interest in a 40 year old discovery was due in part to the recent finding of FTO?s (Fat Mass Obesity) N6-methyl-adenosine (m6A) deaminase activity, thus suggested a link between obesity-associated diseases and the presence of m6A in mRNA. Another catalyst of the sudden rise in mRNA methylation research was the release of mRNA methylomes for human, mouse and Saccharomyces cerevisiae. However, the molecular function, or functions of this mRNA ?epimark? remain to be discovered. There is supportive evidence that m6A could be a mark for mRNA degradation due to its binding to YTH domain proteins, and consequently being chaperoned to P bodies. Nonetheless, only a subpopulation of the methylome was found binding to YTHDF2 in HeLa cells.
The model organism Saccharomyces cerevisiae, has only one YTH domain protein (Pho92, Mrb1), which targets PHO4 transcripts for degradation under phosphate starvation. However, mRNA methylation is only found under meiosis inducing conditions, and PHO4 transcripts are apparently non-methylated.  In this paper we set out to investigate if m6A could function alternatively to being a degradation mark in S. cerevisiae, we also sought to test whether it can be induced under non-standard sporulation conditions. We find associations between the presence of m6A and message translatability. We also find m6A induction following prolonged rapamycin treatment.

overall_design: GeneChip analyses were performed to investigate the distribution of early meiotic transcripts (3hours) on different polysome and monosome fractions

first: Zsuzsanna

last: Bodi

first: Andrew

last: Bottley

first: Nathan

last: Archer

first: Sean

last: May

first: Rupert

last: Fray


title: Transcriptional profiling of PRDM2 Knock down vs.controlGFPsh proliferating C2C12 Myoblasts

city: Bad nauheim

first: Sirisha

last: Cheedipudi

state: Hessen

department: cardiac origin cell lines

country: Germany

institute: Max-planck institue for heart and lung research

summary:
Knockdown of PRDM2 led to precocious differentiation. To understand the molecular basis for this phenotype, we performed microaary analysis of growing myoblasts.
Genes differentially regulated by PRDM2 knock down were reveraled by microarray analysis  using NIA15K mouse chips.

overall_design: Control and knock down cells were grown in proliferating conditions

first: Deepika

last: Puri

first: Amena

last: Saleh

first: Hardik

last: Gala

first: Prethish

last: Sreenivas

first: Mohammed

last: Rumman

first: Malini

last: Pillai

first: Reety

last: Arora