title: Microarray Analysis Gene Expression Profiles in Laryngeal Muscle After Recurrent Laryngeal Nerve Injury

city: Carmel

first: Stacey

last: Halum

state: IN

address: 1185 Carmel Dr.

department: Voice Clinic of Indiana

institute: Purdue

summary: The pathophysiology of recurrent laryngeal nerve (RLN) transection injury is rare in that it is characteristically followed by a high degree of spontaneous reinnervation, with reinnervation of the laryngeal adductor complex (AC) preceding that of the abducting posterior cricoarytenoid (PCA) muscle. Here, we aim to elucidate the differentially expressed myogenic factors following RLN injury that may be at least partially responsible for the spontaneous reinnervation. F344 male rats underwent RLN injury or sham surgery (n=12).  One week after RLN injury, larynges were harvested following euthanasia. mRNA was extracted from PCA and AC muscles bilaterally, and microarray analysis was performed using a full rat genome array. Microarray analysis of denervated AC and PCA muscles demonstrated dramatic differences in gene expression profiles, with 205 individual probes that were differentially expressed between the denervated AC and PCA muscles, and only 14 genes with similar expression patterns. The differential expression patterns of the AC and PCA suggest different mechanisms of reinnervation. The PCA showed the gene patterns of Wallerian degeneration, while the AC expressed the gene patterns of reinnervation by adjacent axonal sprouting. This finding may reveal important therapeutic targets applicable to RLN and other peripheral nerve injuries.

overall_design: Compare mRNA expression from injured tissue (recurrent laryngeal nerve transection injury)  to normal tissue from two tissues laryngeal adductor complex and posterior cricoarytenoid muscles.

first: Khadijeh

last: Bijangi-Vishehsaraei

first: Kevin

last: Blum

first: Hongji

last: Zhang

first: Ahmad

middle: R

last: Safa

middle: L


title: Expressions of Cardamine amara, hirsuta and flexuorsa under wet and dry conditions

status: Public on Jul 01 2016

city: Koto

first: Jun

last: Sese

state: Tokyo

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

summary: To understand allopoyploid speciation into hydrologically fluctuating niches, we observed gene expressions of two parental species and their allotetraploid species under wet and dry conditions

sample_organism:
Cardamine amara
Cardamine flexuosa
Cardamine hirsuta

overall_design: Gene expression of leafs from control, dry and wet conditions over three Caramine species: C. amara, C. hirsuta and C. flexuosa

first: Kentaro

middle: K

last: Shimizu


title: Transcriptome analysis of male sterile maize mutants defective in somatic cell layer identities (tcl1, mtm00-06 and ms*6015) compared with fertile siblings

city: Stanford

first: John

middle: F

last: Fernandes

state: CA

address: 385 Serra Mall

department: Bio Sci

country: USA

institute: Stanford University

summary:
In order to better understand defects at the molecular level in male sterile maize mutants, we characterized 3 different mutants by microarray hybridization.
Anthers were dissected and staged to be 1000 μm in length (+/- 100 μm), allowing us to analyze changes in transcriptome between siblings relatively close to the initial observation of morphological defects.
All three of the mutants had morphological defects in the somatic layers of the anther, but only tcl1 and mtm00-06 male steriles show serial extra periclinal divisions compared to relatively minor defects in ms*6015 male steriles.

overall_design: For each mutant four biological replicates were used for both male sterile samples and fertile siblings with direct comparisons made between fertile and sterile siblings of the same mutant background.

first: Egger

last: Rachel

first: Virginia

last: Walbot


title: Rhodococcus jostii RHA1 TadA-homolog deletion mutants accumulate less polyhydroxyalkanoates (PHAs) that the parental strain

city: Vicksburg

first: Dawn

middle: E

last: Hancock

state: Mississippi

address: 3909 Halls Ferry Road

department: Engineer Research and Development Center

institute: DEPARTMENT OF DEFENSE Army Corps of Engineers

summary:
Transcriptome studies confirm the nitrogen limited physiological state of both the wild-type and mutant cells. In addition, multiple differentially expressed genes involved in the synthesis and consumption of pools of acetyl-CoA, acetoacetyl-CoA and 3-hydroxybutyryl-CoA, key metabolites for PHA and TAG synthesis, were identified.
An enrichment analysis of differentially expressed genes in the nitrogen starved wild-type versus the isogenic RHA1_ro02104 mutant strain identified genes in the mutant involved in fatty acid and lipid as well as genes involved in acyl-CoA hydrolysis and triacylglycerol degradation.

overall_design: An 8 x 15K array study using total RNA recovered from triplicate cultures of Rhodococcus jostii RHA1 under nitrogen rich and nitrogen starved conditions and triplicate cultures of Rhodococcus jostii RHA1 TadA-homolog deletion mutants (2104) under nitrogen rich and nitrogen starved conditions.

first: Karl

middle: J

last: Indest

first: Jed

middle: O

last: Eberly

first: Carina

middle: M

last: Jung

first: Matthew

last: Carr

first: Gary

middle: A

last: Blakeney


title: Muscle regeneration in fish: A temporal expression profiling and comparison with muscle fibre hyperplasia signature.

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

summary: Using an Agilent-based microarray platform we undertook a time-course analysis of transcript expression in aged trout muscle before injury (time 0) and at the site of injury 1, 8, 16 and 30 days after lesion.

overall_design: At each time points, four (time 0) or five (1, 8, 16, and 30 days post lesion) distinct individuals were sampled for histological analysis and gene expression profiling

first: Jerome

last: Montfort

last: Le Cam

first: Jean-Charles

last: Gabillard

first: Pierre-Yves

last: Rescan


title: Replication timing of control and siRNA PR-set7 cells

city: Paris

last: Cadoret

address: 15 rue hélène Brion

institute: CNRS/ Université de Paris

type: Genome variation profiling by genome tiling array

summary: Although histone modifications have been implicated in many DNA-dependent processes, their precise role in DNA replication remains poorly understood. Here, we show that the regulation of histone H4-K20 methylation states, in particular for the monomethylation, is a critical determinant of licensing and time activation of replication origins in mammalian cells.

overall_design: Two experimental condition : shRNA LUC cells (control) versus siRNA Prset-7 cells

first: Julien

last: Brustel

first: Stanimir

last: Dulev

first: Nina

last: Kirstein

first: Fanny

last: Izard

first: Charlotte

last: Grimaud

first: Chrystelle

last: Cayrou

first: Gunnar

last: Schotta

first: Marcel

last: Mechali

first: Giuseppe

last: Baldacci

first: Claude

last: Sardet

first: Nizar

middle: N

last: Batada

first: Aloys

last: Schepers

first: Eric

last: Julien


title: MaizePath: A CHG microarray for detection and identification of bacteria and viruses pathogenic on maize

city: Poznan

first: Krzysztof

last: Krawczyk

state: Greater Poland

address: Wladyslawa Wegorka 20

department: Virology and Bacteriology

country: Poland

institute: Institute of Plant Protection-National Research Institute

sample_organism:
Bacteria
Zea mays
Viruses

platform_organism:
Bacteria
Zea mays
Viruses

overall_design: Two-condition experiment, Agilent SurePrint G3 Cust. CGH Microarray 4x180K

first: Barbara

last: Uszczynska

first: Alicja

last: Majewska

first: Natasza

last: Borodynko


title: Whole organism transcriptomic analysis provides mechanistic insight into the acute toxicity of emamectin benzoate in Daphnia magna

status: Public on Jun 30 2016

city: Oslo

first: Knut Erik

last: Tollefsen

address: Gaustadallèen 21

country: Norway

institute: Norwegian Institute for Water Research (NIVA)

summary: This experiment was conducted to study the short-term (12h) transcriptional responses in Daphnia magna after exposure to the anti-sea lice chemical emamectin benzoate (EMB). The microarray results were further vefiried using qPCR. The gene exression responses were linked to adverse effects after 48h exposure, in order to supply knowledge for environmental hazard assessment of this chemical in non-target crustaceans.

overall_design: Neonatal (<24h) Daphnia magna were exposed to 7.8-2000 pM waterborne emamectin benzoate for 12h. Microarray analysis was performed using pooled whole-organism D. magna (8 individuals) and 4 biological replicates were analyzed for each treatment group.

first: You

last: Song

first: Jan

middle: T

last: Rundberget

first: Linn

last: Von Evenseth

first: Li

last: Xie

first: Tore

last: Høgåsen

first: Taisen

last: Iguchi

first: Knut

middle: D


title: Genome-wide transcriptional profiling of peripheral blood mononuclear cells challenged with Theileria annulata in crossbred and indigenous cattle of India

city: Bareilly

first: Amod

last: Kumar

address: Izatnagar

country: India

institute: Indian Veterinary Research Institute

summary: Bovine tropical theileriosis is a major haemoprotozoan disease associated with high rates of morbidity and mortality particularly in exotic and crossbred cattle. It is one of the major constraints for of the livestock development programmes in India and southern Asia. Indigenous cattle (Bos indicus) are less affected by this disease than exotic and crossbred cattle. Genetic basis of resistance to tropical theileriosis in indigenous cattle is not well studied. Recent studies gives an idea that differentially genes expressed in exotic and indigenous breeds play an important role in breed specific resistance to tropical theileriosis. The present study was designed to visualize the global gene expression profiling in PBMCs derived from indigenous (Tharparkar) and crossbred cattle with in vitro infection of T. annulata. T. annulata Parbhani strain, originally isolated from Maharashtra (India) and maintained as cryopreserved stabilates of ground-up tick tissue sporozoite (GUTS) of infected H. anatolicum anatolicum was used as infective material. Two separate microarray experiments were carried out using separately each for crossbred and Tharparkar cattle. The crossbred cattle showed 1082 differentially expressed genes (DEGs). Out of total DEGs, 597 genes were downregulated and 485 were upregulated. Their fold change varies from 2283.93 to -4816.02. Tharparkar cattle showed 875 differentially expressed genes. Out of total DEGs in Tharparkar cattle, 451 genes were downregulated and 424 genes were upregulated. Their fold change varies from 94.93 to -19.20. A subset of genes was validated by quantitative RT-PCR and results correlated well with data obtained from the microarrays indicating that the microarray results gave an accurate report of transcript level. Functional annotation study of differentially expressed genes has confirmed their involvement in various pathways including response to oxidative stress, immune system regulation, cell proliferation, cytoskeletal changes, kinases activity and apoptosis. Gene network analysis of these differentially expressed genes provided an effective way to understand the interaction among them. It is therefore, hypothesised that the dissimilar susceptibility to tropical theileriosis exhibited by indigenous and crossbred cattle is due to breed-specific differences in the interaction of infected cells with other immune cells, which ultimately influences the immune response generated against T. annulata infection.

sample_organism:
Bos indicus
Bos indicus x Bos taurus

overall_design: Global gene expression profiling in PBMCs derived from indigenous (Tharparkar) and crossbred cattle were studied after in vitro infection of T. annulata Parbhani strain at 2h time period. Two separate microarray experiments were carried out using Bovine (V2) Gene Expression Microarray, 4x44K (Agilent). Two biological replicate samples were profiled per condition (i.e. replicates samples each in crossbred and Tharparkar cattle).

first: Gyanendra

last: Gaur

first: Ravi

last: Gandham

first: Ashok

last: Tiwari


title: Establishment and Molecular Characterization of Glioblastoma Primary Cultures

city: Barretos

first: Rui

middle: Manuel

last: Reis

state: SP

address: R. Antenor Duarte Villela, 1331

department: Molecular Oncology Research Center

country: Brazil

institute: Barretos Cancer Hospital

summary: Glioblastoma, the most frequent and malignant adult brain tumor has been extensively studied; yet no effective treatment exists. To overcome this dismal scenario, it is essential to improve preclinical biological models. This study aimed to establish and molecularly characterize glioblastoma primary cultures. Additionally, it intended to assess the efficacy of molecular-targeted therapies, in the presence of putative targeting cell lines. Five glioblastoma primary cultures were established exhibiting a diversity of chromosomal alterations by aCGH, with gain of chromosome 7 and loss of chromosome 10, 13 and 17p, the most frequent alterations. Mutation profiling by Ion Torrent and Sanger sequencing showed the present of hotspot mutations in TERT (4/5), TP53 (2/5) and RB, BRAF, PTEN and EGFR (1/5). A similar chromosomal and mutation pattern was observed in the primary cultures and matched frozen tumors. The MTS cell viability assay of the p.Gly598Val EGFR mutated cell line, revealed AST1306 as the most potent EGFR inhibitor, when compared with afatinib, erlotinib, or lapatinib. Herein, glioblastoma primary cultures were successfully established and molecularly characterized. Importantly, we showed that AST1306 inhibits EGFR mutated cells, suggesting that primary cultures are suitable in vitro models for glioblastoma biology and preclinical drugs studies.

overall_design: Two-color Agilent 8x60K array CGH (aCGH) was performed in 10 glioblastoma multiforme samples (CY3) and reference DNA (CY5). The 10 glioblastoma multiforme samples were: DNA extracted from 5 primary cultured cells; DNA of 5 primary tumors (matched with the 5 primary cell lines). Gender-matched commercial DNA of each case was used as control.

first: Adriana

middle: C

last: Carloni

first: Renato

last: Oliveira

first: Raul

last: Torreiri

first: Lucas

last: Bidinotto

first: Gustavo

last: Berardinelli

first: Viviane

last: Silva

first: Carlos

last: Clara

first: Gisele

last: de Almeida

first: Jeremy

last: Squire

first: Olga

last: Martinho


title: cDNA microarray analysis revealing candidate biomineralizational genes of the pearl oyster, Pinctada fucata martensii

city: Haikou

first: Yaohua

last: Shi

address: 18 Renmin Road

department: The Ocean College

country: China

institute: Hainan University

summary: In order to screen and identify biomineralization gene, microarray technique was used to reveal tissues specific expression genes in the brunet mantle edge (ME), mantle centre (MC), and both ME and MC (ME-MC) from assembled transcriptome contigs of Pinctada fucata martensii, ideal pearl oyster for the study of biomineralization. Tissues of ME, MC, hepatopancreas, foot, gill, adductor muscle, heart and intestine were sampled from two females and one male pearl oyster. Gonad was sampled from above three individuals and another two male and one female. Equal amount RNA of each individual hepatopancreas, foot, gill, adductor muscle, heart and intestine were mixed as a composite viscera sample (CV), and equal amount gonad RNA from one male and one female were combined together as a gonad sample (GS). Hybridizations were performed with twelve samples of ME, MC, CV and GS.

overall_design: Gene expression in ME, MC, gonad and  other tissues were measured. Gonads were sampled from 6 individuals, and other tissues were sampled from above three individuals.

first: Aimin

last: Wang

first: Zhifeng

last: Gu

first: Xing

last: Zheng

first: Xin

last: Zhan


title: Transcriptional profiling of Candida albicans cells defective in glucan assembly and undergoing the Yeast to Hyphal transition

city: Milano

first: Laura

last: Popolo

address: Via Celoria 26

department: Dipartimento di Bioscienze

country: Italy

institute: Università degli Studi di Milano

summary: Wild type (CAI10) and phr1 null mutant (CAS10) were analyzed at 0, 1, 3 and 5 hours after the shift of blastospores to Hyphae inducing conditions

overall_design: For each strain, the transcriptional profiles at 3 and 5 h was obtained with respect to its own time zero.

first: Enrico

last: Ragni

first: Pedro

last: Botías


title: Identification of factors associated with high fat diet induced insulin resistance

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

institute: Genotypic Technology

summary: Whole genome expression profilling were undertaken in high fat diet (HFD)-fed obese rats to identify the genetic factors associated with metabolic dysfunction, insulin resistance and obesity.

overall_design:
Sprague dawley male rats were maintained on HFD for 12 weeks ad libitum regimen. Liver being  the principal organ for glucose homeostasis is targeted for microarray profilling. We could identify genes/factors associated with obesity induced metabolic dysfunction.
Custom Rat Whole Genome 8x60k Gene Expression Microarray (AMADID:030192 ) designed  by Genotypic Technology Private Limited.

first: Sibsankar

last: Roy

first: Nabanita

last: Das


title: SNP microarray of T-REx-293-based clones overexpressing the DNA cytosine deaminase APOBEC3B

city: London

first: Anita

last: Grigoriadis

address: Great Maze Pond

country: United Kingdom

institute: King's College London

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

summary: A conditional and isogenic system for APOBEC3B (A3B) induction in T-REx-293 cells. Cells were engineered to express doxycycline-inducible A3B-eGFP or eGFP constructs and subjected to 10 rounds of A3B-eGFP exposure causing 80-90% cell death. Control pools (eGFP) were subjected to parallel rounds of non-toxic eGFP exposure, and dilutions were done each round to mimic A3B-eGFP induced population fluctuations. DNA was extracted and subjected to SNP analyses using the Human OmniExpress-24v1-0 BeadChip (Illumina, San Diego, CA). Genotyping was performed using the humanomniexpress_24v1-0_a cluster file.

overall_design: SNP data is avaiable for a total of 16 samples, all derived from single cells mother lines A and C. For each series, each consisting of 8 samples, A3B-eGFP and eGFP daugther clones were processed on the SNP microarray, as well as 3 A3B-eGFP and 3 eGFP grand-daugther clones.

first: Jelmar

last: Quist

first: Reuben

middle: S

last: Harris

first: Andrew

last: Tutt


title: Expression data from male cynomolgus macaques exposed to 6 ppm formaldehyde

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

summary:
Exogenous formaldehyde disrupts genomic/epigenomic profiles in the rodent nose and white blood cells (WBCs) related to inflammation and immune signaling, although it does not reach the circulating blood. We aimed to compare and contrast alterations in genomic signaling in the nose and circulating blood of non-human primates exposed to formaldehyde.
We used microarrays to identify transcripts that were diffentially expressed in response to formaldehyde inhalation exposure.

platform_organism:
Macaca fascicularis
Macaca mulatta

overall_design: A total of 14 primates received two consecutive days of 6-hour whole body inhalation exposures consisting of either filtered air (n = 6) or a target of 6 ppm formaldehyde (n = 8). To assess formaldehyde-induced changes in genome-wide gene expression profiles, RNA samples extracted from the nasal epithelium and circulating WBCs were labeled and hybridized to the Affymetrix Cynomolgus Macaque Gene 1.0 ST Array.

first: S

last: Tilley

first: J

last: Rager

first: B

last: Moeller

first: D

last: Kracko

first: M

last: Doyle-Eisele

last: Swenber

first: R


title: Aspergillus oryzae gene expression with 1hr galactose, glucose, and sorbitol induction.

city: Higashihiroshima

first: Ken

last: Oda

state: Hiroshima

address: 3-7-1 Kagamiyama

department: Fundamental research division

institute: National research institute of brewing

summary: We used microarrays to find out carbon souce responsive genes of A. oryzae with 1hr induction with galactose, glucose, and sorbitol.

overall_design: The A.oryzae RIB40 was cultured for 24hr in glucose as a carbon source, then shifted to galactose, glucose, and sorbitol containing medium and cultured for 1hr. Two biological replicates in each conditions were used for the microarray analysis.

first: Kazuhiro

last: Iwashita

first: Ryoko

last: Hamada


title: Expression mRNA data from human postmortem putamen samples measured using the NanoString nCounter platform

city: New York

first: Venugopalan

last: Nair

state: NY

address: 1468 Madison Avenue

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

summary:
Background: Molecular adaptations in the striatum mediated by dopamine (DA) denervation or Levodopa (L-dopa) treatment have been implicated with the motor deficits found in Parkinson’s disease (PD). Alterations in glutamatergic neurotransmission and anti-oxidant mechanisms are reported to play important roles in mediating these changes. However, the mechanisms mediating the molecular adaptations in the striatum are not well understood. In recent years, microRNAs (miRNAs) have been recognized as potent post-transcriptional regulators of gene expression with fundamental roles in numerous biological processes. miRNAs are known to influence the development and maintenance of striatal neurons. To determine the contribution of miRNAs in molecular adaptations found in PD, we screened the expression of 800 miRNAs in postmortem striatum samples obtained from PD and neurologically normal controls. We detected the expression of approximately 250 miRNAs in postmortem human putamen samples collected from patients with PD and healthy controls. There was an abundance of a subset of 17 miRNAs (10 up- and 7 down-regulated) differing substantially between PD and the control, suggesting that miRNAs are altered in the striatum during the course of PD. Computational analysis show that  many of these miRNAs targets pro-inflammatory factors in the striatum. Therefore, we sought to detrmine the expression of experimentally validated pro-inflammatory transcripts in PD striatum.

Methods: Using a digital gene expression platform to quantify 134 gene transcripts, we compared human postmortem putamen tissues from patients with PD and neurologically normal controls.

Results: We identified deregulated expression of 10 gene transcripts (4 up- and 6 down-regulated mRNAs) in postmortem human putamen samples collected fromPD patients compared to controls. The expression of these genes negative correlates with the expression of many of the differentially epxressed miRNAs. Moreover, many of these genes are predicted targets of the differentially expressed miRNAs.

Conclusions: We identified deregulated mRNAs most likely associated with anti-oxidant mechanims in PD striatum. This approach may provide insights into pathogenesis of the disease.

overall_design: Human postmortem putamen tissues from 12 patients with PD symptoms and 12 neurologically normal controls were used in the study. Samples were obtained from the Human Brain and Spinal Fluid Resource Center, Los Angeles, CA through NIH NeuroBioBank, and stored at -80°C until RNA isolation. Total RNA was extracted using the mirVana RNA isolation kit, following the manufacturer’s instructions (Ambion). Using 225ng total RNA, mRNA levels were assayed by direct digital detection using Nanostring nCounter assay kits (Nanostring Technologies).

first: Yongchao

last: Ge


title: Transcriptional Profiling of Meq-dependent Genes in Marek’s Disease Resistant and Susceptible Inbred Chicken Lines

city: East Lansing

first: sugalesini

last: Subramaniam

state: MI

address: 3606 E Mount Hope Rd

department: CMIB

institute: Michigan State University

summary: Marek’s disease (MD) is an economically significant disease in chickens caused by the highly oncogenic Marek’s disease virus (MDV). Understanding the genes and biological pathways that confer MD genetic resistance should lead towards the development of more disease resistant commercial poultry flocks or improved MD vaccines. MDV Meq, a bZIP transcription factor, is largely attributed for viral oncogenicity though only a few host target genes have been described, which has impeded our understanding of MDV-induced tumorigenesis. Given the importance of Meq in MDV-induced pathogenesis, we explored the role of Meq in genetic resistance to MDV. Using global transcriptome analysis to compare the host response between birds challenge with either wild type MDV or a recombinant lacking Meq, we identified a number of specific genes and pathways associated with either MD resistance. Integrating prior information from ChIP-seq, microarray analysis, and SNPs exhibiting allele-specific expression (ASE) in response to MDV infection from two inbred layer lines that differ greatly in MD genetic resistance, we were able to provide a evidence for 35 genes that SNPs within transcription factor binding sites can affect transcription factor binding and gene expression in an allele-specific manner.

overall_design: Transcript profiling of CEF's (a chicken embryo fibroblast cell line) from MD susceptible and resistant lines using Affymetrix chicken GeneChips

first: Sugalesini

first: Likit

last: Preeyanon

first: Hans

middle: H

last: Cheng


title: Expression miRNA data from human postmortem putamen samples measured using the NanoString nCounter platform

summary:
Background: Molecular adaptations in the striatum mediated by dopamine (DA) denervation or Levodopa (L-dopa) treatment have been implicated with the motor deficits found in Parkinson’s disease (PD). Alterations in glutamatergic neurotransmission and anti-oxidant mechanisms are reported to play important roles in mediating these changes. However, the mechanisms mediating the molecular adaptations in the striatum are not well understood. In recent years, microRNAs (miRNAs) have been recognized as potent post-transcriptional regulators of gene expression with fundamental roles in numerous biological processes. miRNAs are known to influence the development and maintenance of striatal neurons. Therefore, we sought to determine the genome-wide expression levels of miRNAs in PD striatal tissues.

Methods: Using a digital gene expression platform to quantify miRNA levels, we compared the expression of 800 miRNAs in human postmortem putamen tissues from PD patients and controls.

Results: We detected the expression of approximately 250 miRNAs in postmortem human putamen samples collected from patients with PD and healthy controls. There was an abundance of a subset of 17 miRNAs (10 up- and 7 down-regulated) differing substantially between PD and the control tissues.

Conclusions: We identified deregulated miRNAs most likely associated with altered striatal functions found in PD. This approach may provide insight into pathogenesis and additional therapeutic targets for the development novel treatment strategies for the disease.

overall_design: Human postmortem putamen tissues from 12 patients with PD symptoms and 12 neurologically normal controls. Samples were obtained from the Human Brain and Spinal Fluid Resource Center, Los Angeles, CA through NIH NeuroBioBank, and stored at -80°C until RNA isolation. Total RNA was extracted using the miRVana RNA isolation kit, following the manufacturer’s instructions (Ambion). Using 225ng total RNA, miRNA levels were assayed by direct digital detection using Nanostring miRNA assay kits (Nanostring Technologies).


title: Genome wide microarray based expression profiles associated with BmNPV resistantance and susceptibility in Indian silkworm races of Bombyx mori

first: Genotypic

last: technology

summary: The molecular mechanism involved in BmNPV resistance was investigated using a genome wide microarray in the midgut tissues of BmNPV infected resistant (Sarupat) and susceptible (CSR-2) Indian silkworm races. In the resistant race, 735 genes were upregulated and 589 genes were down regulated at 12 hours of BmNPV post infection. Similarly in case of susceptible race, 2183 genes were up regulated and 2115 genes were down regulated.  Among the differentially expressed genes, nine upregulated and eight down regulated genes were validated using real time qPCR  analysis. In Sarupat, the significantly upregulated genes are vacuolar protein sorting associated gene, X fin like protein  and Carboxy peptidase E like protein in BmNPV infected midguts, whereas the prominent down regulated genes are glutamate receptor ionotropic kainite 2-like, BTB/POZ domain  and transferrin. In the case of CSR-2, the considerably upregulated genes are  Peptidoglycan recognition protein S6 precursor and rapamycin while the conspicuous down regulated genes are  facilitated trehalose transporter and zinc transporter  ZIP1-like gene. Our results provided a vital insights of  Bombyx mori  in reference with its molecular mechanism in immune response against the BmNPV invasion.

overall_design: Organism : Bombyx mori , Agilent Custom Silkworm Gene Expression  4x44k Array (AMADID: 066047) designed  by Genotypic Technology Private Limited.

first: Kangayam

last: Ponnuvel

first: G

last: Lekha

first: Kanika

last: Trivedy


title: Comparisons of gene expressions in zebrafish (Danio rerio) brain and gill after cold acclimation

city: Taipei

first: Ming Yi

last: Chou

state: Taiwan

address: 128 Sec. 2 Acdemia Rd.

department: Cellular and Organismic Biology

institute: Acdemia Sinica

summary:
Ambient temperature affects organisms comprehensively, however cold responses are different among tissues. Here, we adopt a transcript screening approach to explore and compare the cold responses in zebrafish gills and brain. Zebrafish were exposed to cold and the oligonucleotide-based microarray was used to identify cold-induced genes. Principle component analysis (PCA) of the gene expression profiles indicated that gills develop different strategies for the increasing of exposure period while brain relatively remained stable. Combining statistic and clustering methods, we found that gills showed higher protein metabolism and cell activity while brain showed higher stress responses and detoxification during cold acclimation. According to the microarray data sets, we extended the study on ionocyte- and isotocin neuron-related genes in gills and brain, respectively, and found these genes were broadly stimulated by cold. These data suggest that cold activates specific physiological functions in different tissues. Taken together, our results provide molecular evidences to elucidate the cold acclimation in zebrafish gills and brain.
Keywords: Time course, Tissue types

overall_design:
After the low-temperature treatment, brain and gill tissues dissected from 10 individuals were pooled as a sample and then homogenized in 0.8 ml Trizol reagent (Invitrogen, Carlsbad, CA). 120 individuals (60 for low-temperature treatment and 60 for control) were sacrificed for each microarray hybridization experiment, and another 200 individuals were used for quantitative reverse-transcription polymerase chain reaction. After chloroform extraction, RNA precipitation and ethanol washing, the RNA samples were purified and treated with DNase1 to remove the genomic DNA by using RNeasy Mini Kit (Qiagen, Huntsville, Alabama). The quantity and quality of total RNA were assessed by spectrophotometry and Bioanalyzer (Aglient Technologies, Foster City, CA).
The commercial zebrafish 14K oligonucleotides set (MWG
Biotech AG, Ebersbach, Germany) were obtained and were printed on UltraGAPS Coated slide (Corning, New York, NY ) with use of the OmniGrid 100 microarrayer (Genomic Solutions, Ann Arbor, MI) according to the manufacture’s instructions. The 14,067 oligonucleotides represent 9666 genes (7009 singlet genes and 2657 redundant genes), and the redundancy of this chip is 31 %. The detailed description of the oligonucleotides information can be obtained on the Ocimun Biosolution website.
cDNA probes were synthesized and purified by reverse transcription of 20 μg total RNA using a SuperScript indirect cDNA labeling system (Invitrogen) and MinElute PCR purification kit (Qiagen) and were labeled with Alexa 647 dye (cold treatment groups) and Alexa 555 dye (control groups)(Invitrogen), respectively. The zebrafish 14K OciChip array chip was pretreated with 1% bovine serum albumin (BSA) (fraction V), 4x saline-sodium citrate (SSC), and 1% sodium dodecylsulfate (SDS) at 42 °C for 45 min, and then hybridized overnight in a cocktail containing 5x Denhardt's solution, 6x SSC, 0.5% SDS, 50% formamide, 50 mM sodium phosphate, and 2 µg/µl yeast tRNA. Slides were washed with 2x SSC and 0.1% SDS (5 min), 1x SSC and 0.1% SDS (5 min), 0.5x SSC (5 min), and twice with 0.1x SSC (2 min each). Scanning was performed with a Genepix scanner (Molecular Devices, Sunnyvale, CA). The acquired images were analyzed using Genepix and Genespring software (Aglient Technologies, Foster City, CA). The measurements of spots were filtered by flags, and the Lowess normalization was performed after subtraction of the median background. Each experiment contained 3 biological replicates (including 1 dye swap) with different samples. The differentially expressed genes were selected from those with at least 2 of 3 significant signals (ratio > 2 or < 0.5), and then the Significant Analysis of Microarray method (SAM 3.02) was used to determine statistical significances.

first: Ming-Yi

first: Pung-Pung

last: Hwang


title: Identification of novel biomarkers associated with poor patient outcome in invasive breast carcinoma

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

institute: University of São Paulo

summary: Breast carcinoma (BC) is the leading cause of death in women worldwide, making up 23% of all cancers in women, with 1.38 million new cases worldwide annually and responsible for 460,000 deaths. Despite the significant advances in the identification of molecular markers and different modalities of treatment in primary BC, the ability to predict the metastatic behavior in breast cancer is still limited. The purpose of this study was to help identify novel molecular markers associated with clinical outcome in a cohort of Brazilian BC patients. We generated global gene expression profiles from 24 patients with invasive ductal BC followed for ≥ 5-years, including 15 samples from patients classified as presenting good prognosis based on traditional markers and clinical criteria and 9 patients that developed metastasis. We identified a set of 58 differentially expressed genes (p ≤0.01) between groups of patients with good and poor prognosis. Up-regulation of B3GNT7, PPM1D, TNKS2, PHB and GTSE1 in patients with poor prognosis was confirmed by quantitative RT-PCR in an independent sample set from patients with BC (47 with good prognosis and 8 that presented metastasis). Expression of BAD protein was investigated by immunohistochemistry in 1276 BC samples and confirmed the reduced expression levels in metastatic cases observed in the oligoarray data. These findings point to novel prognostic markers that can distinguish breast carcinoma samples according to clinical course and progression of the disease.

overall_design: Global expression profiles from 38 ductal breast tumor patient samples were used to search for molecular signatures correlated with current prognostic markers. A subset of 24 cases comprising 15 patients that remained free of disease after surgery and 9 patients that developed metastasis was used to identify candidate biomarkers associated with metastatic progression. Candidates were subsequently validated in additional independent samples by RT-qPCR or immunohistochemistry.

first: Renata

last: Canevari


title: Expression mRNA and miRNA data from human postmortem putamen samples measured using the NanoString nCounter platform

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


title: Identification of Potentially Pathogenic Variants in the Posterior Polymorphous Corneal Dystrophy 1 Locus

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

institute: Stein Eye Institute, UCLA

summary:
Purpose: To identify the genetic basis of posterior polymorphous corneal dystrophy 1 (PPCD1).

Methods: Next-generation sequencing was performed on DNA samples from 4 affected and 4 unaffected members of a previously reported family with PPCD1 linked to chromosome 20 between D20S182 and D20S195. Custom capture probes were utilized for targeted region capture of the linked interval. Single nucleotide variants (SNVs) and insertions/deletions (indels) were identified using two bioinformatics pipelines and two annotation databases. Candidate variants met the following criteria: quality score ≥20, read depth ≥5X, heterozygous, novel or rare (minor allele frequency (MAF) ≤ 0.05), present in each affected individual and absent in each unaffected individual. Structural variants were detected with two different microarray platforms to identify indels of varying sizes.

Results: Sequencing reads aligned to the linked region on chromosome 20, and high coverage was obtained across the sequenced region. The majority of identified variants were detected with both pipelines and annotation databases, although unique variants were identified. Twelve SNVs in 10 genes (2 synonymous variants and 10 noncoding variants) and 9 indels in 7 genes met the filtering criteria and were considered candidate variants for PPCD1.

Conclusions: Next-generation sequencing of the PPCD1 interval has identified 17 genes containing novel or rare SNVs and indels that segregate with the affected phenotype in an affected family previously mapped to the PPCD1 locus. We anticipate that screening of these candidate genes in other families previously mapped to the PPCD1 locus will result in the identification of the genetic basis of PPCD1.

overall_design:
Four affected and 4 unaffected individuals from a single family were analyzed for copy number variation within the PPCD1 disease locus.
Array design and analysis is based on genome build hg19.

first: Derek

last: Le

first: Ricardo

last: Frausto


title: Study of gene expression of peripheral blood T lymphocytes from age-series of monozygotic twin couples

city: Bologna

first: Daniel

last: Remondini

address: Viale Berti Pichat 6/2

department: Physics and Astronomy - DIFA

institute: Bologna University

summary:
In this study we analyse a gene expression dataset, obtained by microarray hybridization, consisting of T lymphocytes from 27 healthy monozygotic twin couples with ages ranging over whole adult lifespan (22 to 98 years).
This peculiar experimental design, combined with a ridge regression approach, allowed us to define an optimal low-dimensional gene expression signature from which chronological age can be estimated. Our work identified for the first time a group of 125 genes whose expression can be considered a signature of physiologic T cell aging. This signature has been further validated in another dataset of samples of the same cell type, but hybridized over a different platform, showing a significantly good performance that confirmed the power of the chosen analysis design. Moreover, the same signature was applied on a publicly available dataset with an analogous time series design, but hybridized on a different platform and consisting of a different cell type (human muscle cells). The lower regression performance obtained in this case indicates that the signature is cell-type specific.

overall_design: 27 couples of monozygotic twins (54 subjects in total, homogeneously distributed in an age span from 22 to 98 years) were analysed.

first: Nathan

last: Intrator

first: Stefano

last: Salvioli

first: Michela

last: Pierini

first: Paolo

last: Garagnani

first: Isabella

last: Zironi

first: Claudio

last: Franceschi

first: Gastone

last: Castellani


title: Identification of Drosophila MBF1 regulated genes in embryos

city: Taian

first: Dan

last: Wang

state: Shandong

address: No. 61 Daizong Street

institute: Shandong Agricultural University

summary:
Multiprotein bridging factor 1(MBF1), a transcriptional co-activator that can regulate transcription by forming a bridge between the TATA-box-binding protein and gene-specific transcription factors. MBF1 is required for organ development and environmental stress responses. However, the targets of MBF1 is unknown.
To identify the MBF1 regulated genes, we compared expression profiles of mRNA purified from wild-type and mbf1 mutant embryos.

overall_design: yw and mbf1 mutant embryos were selected at later stage of development for RNA extraction and hybridization on Affymetrix microarrays.

first: Marek

last: Jindra

first: Susumu

last: Hirose

first: Qing-Xin

last: Liu


title: Microarray-based gene expression of rabbit basilar artery smooth muscle cells exposed to hemodynamic insult

city: Shanghai

first: Zhaolong

last: Zhang

state: Shanghai

address: Changhai Road 168

department: Neurosurgery

institute: Changhai Hospital

summary: High-flow causes the remodeling of arteries, in which smooth muscle cells play an important role. To know the profile of smooth muscle gene expression under high-flow conditions in vivo, flow of rabbit basilar artery was increased by ligation of both common carotid arteries. Microarrays were performed to profile the gene expression of smooth muscle cells isolated from rabbit basilar artery. Expression profiles indicate 43603 differentially expressed genes in smooth muscle cells exposed to high-flow insult compared with the sham control, of which 1470 genes were upregulated and 780 genes downregulated using 2 fold-changes and P<0.05 as a cut-off.

overall_design: Bilateral common carotid arteries of female New Zealand White rabbits were ligated to increase vascular flow.The control group was performed the same procedure to expose the CCAs without ligation. Rabbits were euthanized at day 5 after ligation or exposure of bilateral CCAs in both groups (n=3 for each group). The rabbits used and all procedures in this study were approved by the local Institutional Animal Care and Use Committee. Smooth muscle cells were isolated. After  euthanization of rabbits, the whole basilar arteries were removed. The arteries were cleaned in PBS buffer,cannulated and perfused at a constant flow with a cocktail which contains PBS and 0.4 mg/ml elastase (Sigma) and 1 mg/ml collagenase (type 1A, Sigma). After an incubation time of 45 min, the tissue left was removed and stored in PBS. SMCs were released from the artery by trituration. Then Total RNA was extracted and gene chip tests were performed.

first: Z

first: Q

last: Huang

first: J


title: Long non-coding RNA expression profiling in the NCI60 cancer cell line panel using high-throughput RT-qPCR

status: Public on Jun 29 2016

city: Gent

first: Pieter

last: mestdagh

address: De Pintelaan 185

country: Belgium

institute: Center for Medical Genetics

summary: Long non-coding RNAs (lncRNAs) form a new class of RNA molecules implicated in various aspects of protein coding gene expression regulation. To study lncRNAs in cancer, we generated expression profiles for 1708 human lncRNAs in the NCI60 cancer cell line panel using a high-throughput nanowell RT-qPCR platform. We describe how qPCR assays were designed and validated and provide processed and normalized expression data for further analysis. Data quality is demonstrated by matching the lncRNA expression profiles with phenotypic and genomic characteristics of the cancer cell lines. This data set can be integrated with publicly available omics and pharmacological data sets to uncover novel associations between lncRNA expression and mRNA expression, miRNA expression, DNA copy number, protein coding gene mutation status or drug response.

overall_design: lncRNA expression profiling of 60 cancer cell lines

last: Mestdagh

first: Jo

last: Vandesompele


title: Hepatic transcriptomic changes during non-alcoholic steatohepatitis (NASH)-associated liver carcinogenesis in mice

status: Public on Jun 22 2016

city: Jefferson

first: Aline

last: de Conti

state: Arkansas

address: 3900 NCTR Road

department: Biochmical Toxicology

institute: FDA-NCTR

summary: Hepatocellular carcinoma (HCC), which accounts for 90% of all primary livers tumors, is the fourth most common cancer in the world.  The development of HCC is a long-term and complex process, and uncovering the molecular mechanisms associated with HCC development is critical for the disease diagnosis, prevention, and treatment.  Exploring these mechanisms using human HCC samples is desirable, but frequently impractical, with a number of limitations and shortcomings.  The STAMTM (Stelic Institute & Co, Tokyo, Japan) mouse model of NASH-associated liver carcinogenesis is considered a useful and relevant model for investigating the molecular pathogenesis of NASH-derived HCC. This model resembles the human HCC development associated with progression from simple steatosis to NASH, fibrosis, and HCC.  In the present study, by using high-throughput whole genome microarrays (SurePrint G3 Mouse Gene Expression v2, 8x60K; Agilent Technologies, Santa Clara, CA), we examined the transcriptomic profiles in the livers of STAMTM mice at different stages of liver carcinogenesis, including steatosis (6 week time interval), NASH (8 weeks), fibrotic stage (12 weeks), and in full-fledged HCC (20 weeks).  The results of microarray analyses showed significant progressive changes in hepatic gene expression during the development of HCC.  A total of 970, 1462, 2742, and 2857 of differentially expressed genes were identified in the livers at 6, 8, 12, and 20 weeks, respectively.  Detailed analysis of these differentially expressed genes will benefit the understanding of the underlying mechanisms of non-alcoholic fatty liver disease-derived HCC.

overall_design: Transcriptomic profile in the liver of STAM mice at 6 weeks (steatosis; n=3), 8 weeks (steatohepatitis; n=3) 12 weeks (fibrosis; n=4) and 20 weeks (HCC-stage tumor tissue, n=4) weeks. Age-matched control samples were also analyzed.

first: Volodymyr

last: Tryndyak

first: Kostiantyn

last: Dreval

first: Mekonnen

last: LemmaDechassa

first: Frederick

last: Beland

first: Igor

middle: P

last: Pogribny


title: Identification of target antigens of CSF OCB-derived monoclonal antibodies

status: Public on Jun 06 2016

city: München

first: Simone M.

last: Braendle

address: Marchioninistr. 15

country: Germany

institute: LMU München

summary: The identification of target antigens recognized by monoclonal antibodies that have been derived from oligoclonal band IgG of CSF samples from multiple sclerosis patients.

overall_design: Protoarrays were hybridized with monoclonal antibodies derived from oligoclonal band IgG of CSF samples from multiple sclerosis patients. Six individual monoclonal antibodies, derived from four different MS patients, were used. The humanized r8-18C5 with known specificity and the secondary antibody alone served as isotype and secondary antibody control, respectively.


title: Significant obesity associated gene expression changes are in the stomach but not intestines in obese mice

status: Public on Jun 15 2016

city: Cincinnati

first: Jing

last: Chen

state: OH

address: 3333 Burnet Ave

institute: CCHMC

summary: The gastrointestinal (GI) tract can have significant impact on the regulation of the whole body metabolism and may contribute to the development of obesity and diabetes. To systemically elucidate the role of the GI tract in obesity, we performed a transcriptomic analyses in different parts of the GI tract of two obese mouse models: ob/ob and high-fat diet (HFD) fed mice.  Compared to their lean controls, both obese mouse groups had significant amount of gene expression changes in the stomach (ob/ob: 959; HFD: 542), much more than the number of changes in the intestine.  Despite the difference in genetic background, the two mouse models shared 296 similar gene expression changes in the stomach.  Among those genes, some had known associations to obesity, diabetes and insulin resistance. In addition, the gene expression profile strongly suggested an increased gastric acid secretion in both obese mouse models, probably through an activation of the gastrin pathway.  In conclusion, our data reveal a previously unknown dominant connection between the stomach and obesity.

overall_design: In the genetic obesity model, samples from 6 GI tissues were collected from 6 animals of ob/ob (B6.V-Lepob/J), and 6 animals of ob lean control (Lepob, heterozygote from the colony). The gene expressions were compared between ob/ob and ob control. In the diet-induced obese model, samples from 6 GI tissues were collected from 6 animals of HFD (high fat diet), and 6 animals of normal diet. The gene expressions were compared between HFD and normal diet.

first: Lihong

first: Deepak

last: Rajpal


title: Changes of gene expression signatures in Tg(RE:HSE:EGFP) zebrafish embryos

status: Public on May 01 2016

first: Chengwen

address: No. 250 Bibo Road

institute: CHGC

summary: The WT and Tg(RE:HSE:EGFP) F2 generation embryos were heated shocked at 38°C for 1 hour at 16 hpf, then raised to 3 dpf. Total RNAs were isolated with Trizol (Invitrogen). The samples were processed and subsequently analyzed in triplicate on Zebrafish Oligo Microarrays (Agilent Technologies Italia, Italy) which contain 43,554 sets of probes. The microarrays were scanned in an Agilent DNA Microarray Scanner and the images were processed using Feature Extraction software to identify changes of gene expression signatures in Tg(RE:HSE:EGFP) zebrafish embryos.

overall_design: RUNX1-Evi-1 fusion gene was induced into wild type AB line and measured at 72 hours after  1hr heat-shock at 38°C at 16 hpf. Wild type AB line was used as the control.

first: Lijing

last: Shen


title: Human Toxome Project, comparative genomic hybridization of MCF-7 cells

status: Public on Apr 29 2016

city: Baltimore

first: Andre

last: Kleensang

state: MD

department: Center for Alternatives to Animal Testing

institute: Johns Hopkins University

summary: The central goal of the project is to define, experimentally verify, and systematically annotate pathways of endocrine disruption, as a proof of concept of mapping pathways of toxicity by systems toxicology. Experiments were designed to detect possible genomic heterogeneity and genetic drifts within MCF-7 obtained from ATCC (HTB-22, lot number 59388743, passage 147).

overall_design: 4 samples of MCF-7 genomic DNA + human female reference DNA (two with replicates, two wo replicates). Indirect CGH # 1-4. Direct CGH # 5-6. Further desciptions are given in the respective experiments.

first: Marguerite

last: Vantangoli

first: Shelly

last: Odwin-DaCosta

first: Melvin

last: Andersen

first: Kim

last: Boekelheide

first: Mounir

last: Bouhifd

first: Albert

last: Fornace

first: Carolina

middle: B

last: Livi

first: Samantha

last: Madnick

first: Alexandra

last: Maertens

first: Michael

last: Rosenberg

first: James

last: Yager

first: Thomas

last: Hartung


title: Joint-specific DNA methylation signatures in rheumatoid arthritis [methylation array]

status: Public on Jun 09 2016

city: La Jolla

first: Gary

last: Firestein

state: California

address: 9500 Gilman Dr

institute: UCSD

type: Methylation profiling by genome tiling array

summary: Stratifying patients on the basis of molecular signatures could facilitate development of therapeutics that target pathways specific to a particular disease or tissue location. Previous studies suggest that pathogenesis of rheumatoid arthritis (RA) is similar in all affected joints. Here we show that distinct DNA methylation and transcriptome signatures not only discriminate RA fibroblast-like synoviocytes (FLS) from osteoarthritis FLS, but also distinguish RA FLS isolated from knees and hips. Using genome-wide methods, we show differences between RA knee and hip FLS in the methylation of genes encoding biological pathways, such as IL-6 signaling via JAK-STAT pathway. Furthermore, differentially expressed genes are identified between knee and hip FLS using RNA-seq. Double-evidenced genes that are both differentially methylated and expressed include multiple HOX genes.  Joint-specific DNA signatures suggest that RA disease mechanisms might vary from joint to joint, thus potentially explaining some of the diversity of drug responses in RA patients.

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

first: Rizi

last: Ai

first: Deepa

last: Hammaker

first: David

middle: L

last: Boyle

first: Wei

last: Wang


title: Dam(ID)-profiling in B cells

status: Public on May 12 2016

city: Amsterdam

first: Marc

last: Hogenbirk

address: Plesmanlaan

country: Netherlands

institute: Netherlands Cancer Institute

type: Genome binding/occupancy profiling by genome tiling array

summary:
Both chromatin access, and binding of AID in B cells are of major scientific interest. Therefore DamID was setup in B cells. AID specific binding could not be identified.
In contrast to binding, DAM profiling provide a upmost useful tool in defining chromatin access in vivo.

overall_design: Ramos B cells were transduced with Dam-only or with AID-Dam lentivirus. Within the cell, Dam methylates adenines near sites where the protein of interest would interacts  (here AID) with the DNA. These methylated sequences are subsequently amplified by a methylation-specific PCR protocol as previsously described by Vogel et al (2007), and identified by hybridization to 2.1 Economy Whole Genome Nimblegen microarrays.

first: M

middle: R

last: Heideman

first: W

last: Brugman

first: H

last: Jacobs


title: Genomic profiling of Brazilian gliomas

status: Public on May 09 2016

city: Barretos

first: Lucas

middle: Tadeu

last: Bidinotto

address: Antenor Duarte Vilela, 1331

institute: Barretos Cancer Hospital

summary: The aim of this study was to perform a genomic profiling of gliomas of Brazilian origin, using array-CGH, MSI analysis and to associate the genomic alterations with TERT and IDH1 mutation status, and correlate the molecular features with clinicopathological characteristics.

overall_design: 65 frozen tissue specimen, including 7 pilocytic astrocytomas, 9 diffuse astrocytomas, 7 anaplastic astrocytomas and 42 glioblastomas, were submitted to 60K Agilent array-CGH platform in order to determine copy number aberrations (CNA)

first: Raul

last: Torrieri

first: Alan

last: Mackay

first: Marta

last: Viana-Pereira

first: Adriana

last: Carloni

first: Maria

last: Spina

first: Nathalia

last: Campanella

first: Weder

last: Menezes

first: Carlos

last: Clara

first: Aline

last: Becker

first: Gisele

last: Almeida

first: Chris

last: Jones

first: Rui

last: Reis


title: Development of a glycan microarray based method for ABO blood typing

status: Public on Apr 28 2016

city: Frederick

first: Jeff

last: Gildersleeve

address: 376 Boyles St.

institute: National Cancer Institute

summary:
Purpose:  This study uses a high-throughput glycan microarray to develop a novel method to assign ABO blood type.  The method will then be applied to samples from patients treated with PROSTVAC to determine if blood type correlates with survival
Results:  Many blood group A and B antigens correlate with blood type.  Blood typing is best achieved using a combination of 10 signals
Conclusion: ABO blood type can be determined with greater than 97% accuracy using only 4 microliters of serum.

platform_organism:
Quercus alba
Gossypium hirsutum
Rhodotorula
Trypanosoma cruzi
Pandalus borealis
Oncorhynchus nerka
Gallus gallus
Homo sapiens
Bos taurus
Ovis aries
Mus musculus
Ceratonia siliqua
Megathura crenulata
Bothrops moojeni
Frangula alnus
Senegalia senegal
Pachymenia carnosa
Dermestes lardarius

overall_design: Sera from 220 healthy subjects was divided into a training set (n=60), and test set (n=40), and a validation set (n=120).  The training set was used to evaluate various methods for assigning blood type.  The best methods were then further evaluated and refined with the test set.  Finally, the best blood typing method was applied to the validation set to more extensively assess accuracy.

first: Saddam

last: Muthana

first: James

last: Gulley

middle: W

last: Hodge

first: Jeffrey

last: Schlom


title: Determination of ABO blood type for prostate cancer patients

summary:
Purpose:  This study uses a high-throughput glycan microarray to assign ABO blood type to patients from a clinical trial on PROSTVAC.  The goal is to determine if blood type correlates with survival for patients treated with PROSTVAC
Results:  Blood types were assigned and type B and O patients were found to have longer survival than type A and AB patients
Conclusion: Blood type may serve as a convenient method to identify patients likely to respond favorably to PROSTVAC therapy

platform_organism:
Gallus gallus
Homo sapiens
Frangula alnus

overall_design: Sera from 111 patients treated with either PROSTVAC or Control vector were profiled on the array.  ABO blood type was assigned, then evaluated for correlations with overall survival


title: Delamination of neural crest cells requires transient and reversible Wnt inhibition mediated by Dact1/2

status: Public on May 21 2016

city: barcelona

first: Elisa

last: Martí

state: Not Listed

address: Baldiri i Reixac, 15-21

country: Spain

institute: IBMB-CSIC

summary:
Neural crest cells are a transient embryonic population, hence are neither present after bith and nor are they readily accesible for analysis. Therefore, little is known about the genetic networks that regulate NC especification, delamitation and migration from the dorsal neural tube  to their final destination along the embryo.
Here we have developed a novel resource for lineage tracing and for the isolation of neural crest cells in the chick embryo, enabling us to perform a genome-wide expression screen in neural crest  progenitors versus neuroepithelial cells.

overall_design: Plasmid DNA encoding the pBRE-tk-EGFP reporter construct and the pCAGGS-IRES-H2B-RFP construct were coelectroporated into HH10/11 chick embryos and the NT was dissected  out of the embryos 24 h later (HH10/11+24hpe).  Nearly 30 electroporated embryos were pooled, and a single cell suspension was obtained. GFP and RFP fluorescent cells were sorted using a MoFlo flow cytometer (DakoCytomation, Fort Collins, Colorado, USA). At least 100,000 RFP+ cells and 20,000 GFP+ cells were obtained per pool, and total RNA was extracted from the resulting cell sorted populations, 90% of RFP+/GFP+ cells or 90% of RFP+/GFP- cells, using a standard Trizol (Promega) protocol.

first: M

middle: A

last: Rabadán

first: E


title: Whole genome analysis of mouse B16 melanoma cancer cells in response to interfacial geometry

status: Public on Apr 20 2016

city: Urbana

first: Junmin

last: Lee

state: IL

address: 1304 W. Green St.

department: Materials Science and Engineering

institute: University of Illinois at Urbana-Chanpaign

summary: Analysis of the regulation of B16 gene expression in response to interfacial geometry. The hypothesis tested in the present study was that interfacial geometry modulates tumourigenicity of B16 cells. Results provide important information of the response of B16 cells to interfacial geometry especially, metastasis, MAP kinase, and STAT pathways.

overall_design: Total RNA obtained from B16 cells cultured for 5 days in different microenvironments to explore whether interfacial geometry could enhance gene expressions linked to cancer stem cells.

first: Amr

last: Abdeen

first: Kathryn

last: Wycislo

first: Timothy

middle: M

last: Fan

first: Kristopher

last: Kilian


title: Growth-rate-dependent gene expression in Bacillus subtilis

status: Public on Apr 18 2016

city: Greifswald

first: Ulrike

last: Mäder

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

department: Functional Genomics

institute: University Medicine Greifswald

summary: The B. subtilis transcriptome was analyzed under conditions of different growth rates, i.e. during growth in different cultivation media. Gene-level intensities were scaled based on the intensity values of 10 spike-in transcripts. This approach allowed to determine the total mRNA fraction out of the total RNA pool. The data revealed that the proportion of total mRNA in total RNA remained constant across samples which implies that total mRNA abundance in B. subtilis increases proportionally to the growth rate.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Total RNA was extracted from cells grown in 4 different cultivation media at growth rates from μ=0.4 h-1 to μ=1.70 h-1. Microarray hybridizations were performed with RNA from four biological replicates. Samples were labeled with Cy3 (one-color hybridizations).

first: Marc

last: Schaffer

first: Olivier

last: Borkowski

first: Anne

last: Goelzer

first: Stéphane

last: Aymerich

first: Matthieu

last: Jules

first: Vincent

last: Fromion


title: Rtr1 regulates global levels of RNA Polymerase II CTD phosphorylation during transcription elongation

status: Public on Jun 07 2016

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

summary: RNA Polymerase Serine 5 phosphorylation (H14 antibody) is examined in wt and rtr1 deletion conditions to see if deletion of rtr1 causes a redistribution of these marks across open reading frames.

overall_design: Two replicates of RNA Polymerase Serine 5 phosphorylation (H14 antibody) and H3K36me3 are examined in wt and rtr1 deletion conditions.

first: Gerald

middle: O

last: Hunter

first: Whitney

last: Smith-Kinnaman

first: Brian

last: Fleharty

first: Amber

last: Mosley


title: A Unique Rearrangement of PDGFRα and ETV6 in a new t(4;12;6) in a Patient with Acute Myeloid Leukemia (M4) Progressed from Chronic Myelomonocytic Leukemia.

status: Public on Apr 15 2016

city: Dallas

first: Jiadi

last: Wen

state: TEXAS

address: 2330 Inwood Rd

institute: UT Southwester Medical Center

summary: Objectives: Platelet derived growth factor receptor alpha (PDGFRα), which, encodes cell surface tyrosine kinase receptors for the platelet derived growth factor family undergoes different types of rearrangements creating fusion genes in myeloid neoplasms.  A cryptic deletion at 4q12 creating a fusion gene FIP1L1/ PDGFRα is the most frequent change and is associated with malignant hypereosinophilia that can lead to organ damage. The other infrequent, but consistent change involving PDGFRα seen in acute myeloid leukemia (AML) and in other myeloproliferative neoplasms with eosinophilia is a t(4;12)(q12;p13) that creates a fusion gene with ETV6.  This change activates ETV6 via the tyrosine kinase domain of the PDGFRα. In this report we cytogenetically characterized a new t(4;12;6) translocation which developed during transformation to AML in a patient with chronic myelomonocytic leukemia (CMML). Methods: The patient, a 70 year old male diagnosed with CMML; leukemic cells were JAK2- and ABL1/BCR/ABL1 negative and the karyotype was normal. Eight months from diagnosis the disease progressed to AML and concurrently had a low-grade follicular lymphoma. Standard G-band karyotype analysis and FISH analysis was performed to characterize the translocation to develop appropriate therapy based on genetic findings. Results: The patient was initially treated with hydroxyurea and allopurinoal, later it was changed to Azacytidine for CMML. At the time of transformation to AML, the BM karyotype showed a t(4;12;6)( q12;p13;p21.3). FISH with a tricolor 4q12 probe and ETV6 showed fusion between PDGFRα and ETV6.Concurentllty the patient had a low-grade non-Hodgkin lymphoma. Therefore the treatment was changed to imatinib for AML and high dose methylprednisolone and rituximab for lymphoma. Due to continued progression of the disease treatment was changed again to 5+2 (cytarabine 100mg/m2/day) for 5 days and idarubicin (13mg/m2/day for 2 days). Disease progressed further and the patient expired 11 months from diagnosis. Conclusion: This is the first report of development of a variant t(4;12;6) and fusion PDGFRα/ETV6 fusion that developed during transition from CMML to AML. Despite PDGFRα/ETV6 fusion the patient did not respond to imatinib.

overall_design: Cytogenomic microarray analysis was performed with DNA extracted from bone marrow using an Agilent CGH+SNP 180k microarray platform (Agilent GGXChip + SNP v1.0 4-plex CGH) according to the manufacturer’s protocol (Agilent Technologies). Data interpretation was performed using Genoglyphix software (Perkin Elmer).

first: Prasad

last: Koduru

first: Naga

last: Guruju

first: Prapti

last: Patel

first: Kathleen

last: Wilson

first: Sara

last: Monaghan


title: Gene expression alteration in FoxQ2 knockdown sea uchin embryos

status: Public on Apr 07 2016

city: Bethesda

first: Robert

last: Angerer

address: 30 Convent Drive

institute: NIDCR

summary: The transcription factor FoxQ2 is required for anterior pole neural development in  S. purpuratus embryos. To understand the gene regulatory network driving  neurogenesis in the anterrior pole region, it is necessary to  identify genes that depend on FoxQ2.    We carried out a microarray experiment to compare gene expression changes in FoxQ2 knockdown embryos.

overall_design: One control and one knockdown example were prepared for comparison.

first: Zheng

last: Wei

first: Shunsuke

last: Yaguchi

first: Jumko

first: Lynne


title: Gene expression evaluation of urinary bladder in mouse model of long-term ketamine injection

city: Chiayi

first: Shou-Tsung

last: Wang

address: No. 300, Syuefu Rd.

country: Taiwan

institute: National Chiayi University

summary: The aim of this cDNA array study is to search for advanced markers related to the pathogenesis of ketamine-induced cystitis. The result revealed a number of gene expressions involved in chronic wound healing response and collagen accumulation, which were closely related to fibrosis progression in the connective tissue of mice urinary bladder.

overall_design: Both four male and female Balb/c mice were separately distributed into the control (normal saline, two mice) and ketamine (two mice) groups which received ketamine hydrochloride (100 mg/kg/day) daily for a total period of 20 weeks. Subsequently, their urinary bladders were used to acquire expression profiles of 26,423 unique genes, leading to successful determination of the differentially expressed genes and pathways involved in ketamine-induced toxicity.

first: C

last: Shen

first: S

first: Y

last: Liu


title: Global gene expression of the rodent malaria parasites Plasmodium yoelii, Plasmodium berghei and Plasmodium chabaudi blood-stage parasites

status: Public on Apr 08 2016

city: Singapore

first: Regina

last: Hoo

address: 60, Nanyang Drive

department: School of Biological Science

country: Singapore

institute: Nanyang Technological University

summary: The purpose of this research is to identify and evaluate the global gene expression of the rodent malaria parasites Plasmodium yoelii, Plasmodium berghei and Plasmodium chabaudi blood-stage parasites and specifically compare the blood stage gene expression profiles of samples derived from previous studies on Plasmodium falciparum, Plasmodium vivax and Plasmodium knowlesi

sample_organism:
Plasmodium berghei
Plasmodium chabaudi
Plasmodium yoelii

overall_design:
Mice were infected by intraperitoneal injections of P. berghei ANKA, P. chabaudi AS or P. yoelii 17x parasitized erythrocytes and parasitaemia and parasite stages were monitored by thin blood smears stained with Giemsa.
Mice infected with P. chabaudi were highly synchronized and terminal bled every 2 hours under anesthesia over the course of 24 hr.
For P. berghei and P. yoelii infection, mice were terminal bleed and the stage-specific parasitized erythrocytes were separated via Nycodenz density gradient. The ring stage interface was isolated, washed and subjected to ex vivo culture, which was then collected every 2 hr over the course of 24 hr over a complete IDC life-cycle.
Samples labeled with Cy5 were hybridized against a reference RNA pool labeled with Cy3, consisting of equal amounts of P. yoelii or P. berghei or P. chabaudi RNA from each time point.

first: Lei

last: Zhu

first: Amaladoss

last: Anburaj

first: Sachel

last: Mok

first: Onguma

last: Natalang

first: Stacey

last: Lapp

first: Guangan

last: Hu

first: Ramya

last: Ramadoss

first: Kingsley

last: Liew

first: Mary

last: Galinski

first: Zybnek

last: Bozdech

first: Peter

last: Preiser


title: Transcriptomic analysis of Arabidopsis stigmatic papilla cells

status: Public on Apr 23 2016

city: Ikoma

first: Seiji

last: Takayama

state: Nara

address: 8916-5 Takayama

institute: Nara Institute of Science and Technology

summary: Microarray analysis was performed for stigmatic papilla cells isolated by laser microdissection, to discover the genes abundantly expressed in this tissue.

overall_design: Arabidopsis papillary cells were fixed and embedded in paraplast. Laser microdissection was used to separate papillary cells from the styles. Three independent experiments were performed

first: Motoko

last: Igarashi

first: Keiko

last: Ohara

first: Megumi

last: Iwano


title: Evidence for cohesin sliding along budding yeast chromosomes

status: Public on Apr 21 2016

city: London

first: Catarina

last: Samora

address: 44 Lincoln's Inn Fields

institute: The Francis Crick Institute

summary: The ring-shaped cohesin complex is thought to topologically hold sister chromatids together from their synthesis in S-phase until chromosome segregation in mitosis. How cohesin stably binds to chromosomes for extended periods, without impeding other chromosomal processes that also require access to the DNA, is poorly understood. Budding yeast cohesin is loaded onto DNA by the Scc2-Scc4 cohesin loader at centromeres and promoters of active genes, from where cohesin translocates to more permanent places of residence at transcription termination sites. Here we show that, at the GAL2 and MET17 loci, pre-existing cohesin is pushed downstream along the DNA in response to transcriptional gene activation, apparently without need for intermittent dissociation or reloading. We observe translocation intermediates and find that the distribution of most chromosomal cohesin is shaped by transcription. Our  observations support a model in which cohesin is able to slide laterally along chromosomes while maintaining topological contact with DNA. In this way, stable cohesin binding to DNA and enduring sister chromatid cohesion become compatible with simultaneous underlying chromosomal activities, including but maybe not limited to transcription.

overall_design: The Affymetrix Saccharomyces cerevisiae Chip Tiling 1.0R Arrays (catalog number 900645) and S. cerevisiae whole genome forward tiling arrays (catalog number 520286) were used to analyze the localization of Scc1 in Saccharomyces cerevisiae.  Quantitative processed data (normalized signal for IP vs input) are only available for GSM2127850 - GSM2127853.  Processed data for all other samples were temporarily created but not saved by the software that used the CEL files to generate the graphical result output files.

first: Sofía

last: Muñoz

first: Frank

last: Uhlmann


title: LIN28B is overexpressed in specific subtypes of pediatric leukemia and regulates lncRNA H19 [Oci-AML3]

city: Ghent

first: Hetty

middle: Hilde

last: Helsmoortel

address: De Pintelaan 185

department: Department of Pediatric Hematology-Oncology and Stem Cell Transplantation

institute: Ghent University

summary: The stem cell gene LIN28B was recently shown to be overexpressed in a foetal-like subgroup of juvenile myelomonocytic leukaemia. Given the involvement of LIN28B in a variety of solid paediatric cancers, we conducted a meta-analysis of LIN28B levels using publicly available gene expression data of 1361 paediatric leukaemia samples. Interestingly, this analysis revealed LIN28B overexpression in 102 childhood leukaemia patients (7.5%), suggesting oncogenic activity for LIN28B in the context of paediatric haematological diseases. As the mode of action of LIN28B during normal and malignant haematopoiesis remains largely unexplored, we subsequently analysed the transcriptional consequences of LIN28B modulation on normal and malignant haematopoietic cells and identified the long non-coding RNA (lncRNA) H19 as the first LIN28B-regulated lncRNA.

overall_design: Oci-AML3 cells were retrovirally transduced with MSCV-PIG-LIN28B and MSCV-PIG-empty vectors (gifts from Johua Mendel lab), selected with puromycin and hybridized on Agilent microarray.


title: LIN28B is overexpressed in specific subtypes of pediatric leukemia and regulates lncRNA H19

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

overall_design: Refer to individual Series


title: Maternal Whole Blood Gene Expression at 18 and 28 weeks of Gestation Associated with Spontaneous Preterm Birth in Asymptomatic Women

status: Public on Jun 01 2016

city: Toronto

first: Jan

last: Heng

state: ON

address: 25 Orde Street

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

summary:
To investigate maternal whole blood gene expression profiles associated with spontaneous preterm birth (SPTB, <37 weeks) in asymptomatic pregnant women.

The ‘All Our Babies’ (AOB) community based cohort in Calgary recruited pregnant women between May 2008 and December 2010.

overall_design:
Maternal blood at 17-23 (time point 1, T1) and 27-33 weeks of gestation (T2) were collected. Fifty-one SPTBs were matched to 114 term delivery controls.

Microarray was performed on 326 samples from 165 women. Univariate analyses determined significant clinical factors and differential gene expression associated with SPTB. Thirteen genes were validated using qRT-PCR.

Three multivariate models were constructed to identify gene expressions associated with SPTB at T1 (Model A) and T2 (Model B), and temporal gene expressions (T2-T1) associated with SPTB at T2 (Model C).

first: Yujing

middle: J

first: Craig

middle: E

last: Pennell

first: Sheila

last: McDonald

first: Angela

last: Vinturache

first: Jingxiong

last: Xu

last: Lee

first: Laurent

last: Briollais

first: Andrew

last: Lyon

first: Donna

last: Slater

first: Alan

middle: D

last: Bocking

first: Lawrence

last: de Koning

first: David

last: Olson

first: Siobhan

last: Dolan

first: Suzanne

last: Tough

first: Stephen

last: Lye


title: The transcriptomics of an evolved plant-virus gene-for-gene interaction

city: Valencia

first: Julia

last: Hillung

state: Valencia

address: Ingeniero Fausto Elio s/n

department: IBMCP

institute: CSIC-UPV

summary:
We performed threefold evolution experiment with tobacco etch potyvirus isolate At17b (TEV-At17b) in five different ecotypes of Arabidopsis thaliana L. (Di-2, Ei-2, Ler-0, St-0, and Wt-1,), that are heterogeneous in their susceptibility to TEV-At17b infection. After the evolution phase, (i) we characterized the fitness and virulence of the evolved lineages across all host ecotypes, (ii) the molecular changes fixed in the viral genomes.
Next, we analyzed the transcriptoma of the plants using Agilent Microarray tecnology (i)plants infected with local adapted viral lineage, (ii)plants infected with evolved virus vs. ancestal virus, (iii) virus evolved in new host and infecting its original host, (iv) transcriptoma of most specialized and most generalized viruses infecting all five ecotypes.

overall_design: We used at least 3 biological replicates for each sample category and as control we used mock inoculated plants. Plants of none sample category were mixed, but mantained as independent biological replicate. The data from ancestral viral strain TEV-At17b infecting A. thaliana ecotypes were taken at diferent time point (block 1) as data for evolved virus. Both sets of arrays were normalized on the whole.

first: Francisco

last: García-García

first: Joaquín

last: Dopazo

first: José

last: Cuevas

first: Santiago

middle: F

last: Elena


title: Transcriptome analyses of a pair of near-isogenic lines (NILs) from the cross Solanum lycopersicum var. cerasiforme (E9) x S. pimpinellifolium line (L5) under multistress conditions

city: Coventry

first: Miriam

last: Gifford

address: Gibbet Hill Road

department: School of Life Sciences

institute: University of Warwick

summary:
NILs were created for the detailed genetic mapping of a QTL (gFW9.1) in tomato. Residual heterozygocity in recombinant inbred lines from the cross S. lycopersicum var. cerasiforme (parental accession E9) × S. pimpinellifolium line (parental accession L5) was used for the generation of a pair of NILs of which line E9 had DNA from parent E9 on a large section of chromosome 9 (5-56 Mb), whereas line L5 had parent L5 DNA. These two lines were tested as rootstocks grafted to a common scion (cv. Boludo) in multi-stress conditions - low phosphorus and drought stress compared to high phosphorus and well-watered conditions. RNA for transcriptomic analysis was prepared from root tissues.
Secondary use of data: In a study aiming to identify genes that respond to multiple abiotic stresses, microarray data obtained from different plant species and under different stresses was analysed. A number of conserved stress-responsive genes were identified whose expression was differentially regulated in tomato roots in response to one or several stresses. 10 of these genes were validated as reliable biomarkers whose expression levels are related to different signalling pathways involved in adaptive stress responses. This dataset comprises part of the full stress dataset and is for plant roots harvested after growth under low phosphorus and drought conditions, compared to plant roots harvested after growth under sufficient phosphorus and well watered conditions.

sample_organism: Solanum lycopersicum x Solanum pimpinellifolium

overall_design: The experiment was carried out wtih 4 replicates, 2 NIL lines and 2 conditions, which resulted in 16 samples. Both “E9” and “L5” rootstock lines were grafted to Boludo scions in 30 ml modules of peat-based compost, and then transplanted into 3L pots of Perlite.  A combined low phosphorus and drought stress treatment was applied during plant growth, which resulted in significantly reduced plant development compared to the control treated lines. After 29 days of treatment, the root tissues were harvested and total RNA were isolated from all 16 samples. These RNAs (after RNA quality check) were used for Cy3 labelling and hybridization to 4 x180k Agilent microarrays containing probes designed for the genes of the S.lycopersicum cv. Heinz 1706 genome (each array contained ~5 probes for 34,619 transcripts). Data was normalised using the Robust Multichip Averaging algorithm.

first: Zoltan

last: Kevei

last: Thompson


title: A Simple, Inexpensive Strategy for Predicting Potential Beneficial Clinical Responses on Prostate Cancer Vaccine Therapy

first: Jeff

last: Gildersleeve


title: Whole blood gene expression profiling in preclinical and clinical cattle infected with atypical bovine spongiform encephalopathy.

status: Public on Apr 19 2016

city: Trieste

first: Giuseppe

last: Legname

address: Via Bonomea, 265

department: Neuroscience

institute: Sissa

summary:
The molecular events at the basis of prion diseases are characterized by the involvement of several genes which are differentially regulated during the onset and the progression of the infection. Gene expression profiling studies are a powerful tool for the development of preclinical diagnostic tests. Most of the studies performed up to date utilized tissues which are not suitable for a future perspective of a rapid analysis of the infected animals and patients.
We used microarrays to identify the differentially regulated transcripts in blood of BSE-infected cattle in both the presymtomatic and the symptomatic stage of the infection. The identified genes may be used as a signature for prion diseases.

overall_design: Cattle were intracranially inoculated with atypical BSE (H- or L- type) and the blood sampling was achived prior and after the onset of the symptoms. Not inoculated cattle were used as control. RNA was isolated from blood and processed for the hybridization on Affymetrix  microarray chips.

first: Elena

last: Xerxa

first: Maura

last: Barbisin

first: Maria

middle: N

last: Chieppa

first: Helena

last: Krmac

middle: V

last: Costassa

first: Paolo

last: Vatta

first: Marion

last: Simmons

last: Caramelli

first: Cristina

last: Casalone

first: Cristiano

last: Corona


title: LIN28B is overexpressed in specific subtypes of pediatric leukemia and regulates lncRNA H19 [K562]

first: Hetty

last: Helsmoortel

overall_design: K562 cells were retrovirally transduced with shRNA GN36578 against LIN28B and a shRNA-miR non-targeting control TRH1103 (both Transomic), selected with puromycin and hybridized on Agilent microarray.

middle: H


title: Effect of milk intake on circulating plasma miRNAs of adult humans

status: Public on Apr 06 2016

city: Baltimore

first: Kenneth

last: Witwer

state: Maryland

address: 733 N. Broadway

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University

summary: This study examines circulating plasma miRNAs of adult human subjects before and after bovine milk intake. We sought to confirm and expand findings previously reported by Baier, et al., J Nutr, 2014, PMID 25122645, using the same samples.

overall_design: Plasma samples were provided by the Zempleni lab (see Baier, et al., J Nutr, 2014, PMID 25122645) and had been taken from five healthy donors prior to milk intake (T0) and at three hours post-intake (T3). miRNA profiles were generated for each sample by OpenArray (Thermo Fisher).

first: Amanda

last: Auerbach


title: Effect of milk intake on circulating PBMC miRNAs of adult humans

summary: This study examines circulating PBMC miRNAs of adult human subjects before and after bovine milk intake. We sought to confirm and expand findings previously reported by Baier, et al., J Nutr, 2014, PMID 25122645, using the same samples.

overall_design: PBMC RNA samples were provided by the Zempleni lab (see Baier, et al., J Nutr, 2014, PMID 25122645) and had been taken from five healthy donors prior to milk intake (T0) and at six hours post-intake (T6). miRNA profiles were generated for each sample by OpenArray (Thermo Fisher).


title: GATA3 induces human T cell commitment following Notch-induced T-lineage specification (expression)

first: Inge

last: Van de Walle

address: De Pintelaan 185, blokA 4th floor

institute: UGent

summary: Here, we show that GATA3 induces T-lineage commitment following Notch-induced T-lineage specification through direct regulation of at least 3 distinct processes: repression of NK-cell fate, activation of T-lineage genes to promote further differentiation, and down modulation of Notch signalling activity.

overall_design: Gene expression was measured in RPMI8402 cells after transduction with control, shGATA3 or shTCF1 and culture for 48h. Cells were collected 48h after transduction and sorted for EGFP+. This was performed for 2 replicates.

first: Kaat

last: Durinck

first: Wouter

last: Van Loocke

first: Sagar

last: Damle

first: Pieter

last: Van Vlierberghe

first: Frank

last: Speleman

first: Ellen

last: Rothenberg

first: Tom

last: Taghon


title: Disrupted lipid homeostasis in the absence of the transcriptional activator mga2 results in a failure to activate SREBPs in Schizosaccharomyces pombe

first: Risa

last: Burr

address: 725 N Wolfe St, Physiology 107B

department: Cell Biology

institute: Johns Hopkins University School of Medicine

summary: The sre1 pathway senses molecular oxygen in the fission yeast, Schizosaccharomyces pombe. When oxygen becomes limiting, Sre1 is trafficked from the ER to the Golgi where it is cleaved through the actions of the 5-member Dsc E3 ligase complex. The released N-terminus then upregulates genes required for adaptation to hypoxia. Although the sre1 pathway is responsible for regulating a majority of the genes required for hypoxic growth, it is evident that other regulatory genes are involved in this response. To identify novel regulators of adaptation to hypoxia, we screened the S. pombe nonessential haploid deletion collection. This genome wide screen identified nine genes required for production of the membrane-bound transcription factor Sre1N. The characterization of one of these, the S. pombe transcriptional activator mga2, is presented. mga2 is the homolog of SPT23 and MGA2 in S. cerevisiae. In S. cerevisiae SPT23 and MGA2 regulate the transcription of genes involved in lipid metabolism, including the delta-9 fatty acid desaturase, OLE1. We show S. pombe mga2 also regulates lipid metabolism, and that in the absence of mga2, the lipidome is disrupted. Supplementation with unsaturated fatty acids rescued Sre1 cleavage in mga2Δ cells. However, mga2 is not simply required for activation of Sre1 as mga2Δ cells have a normoxia growth defect that is unrelated to Srel activity. Loss of mga2 results in aberrant Dsc1 glycosylation, suggesting that the Dsc complex is not properly localized to the Golgi. These results establish unsaturated fatty acids as a regulator of the SREBP pathway in fission yeast.

overall_design: 4 samples analyzed in 2 comparisons:  2 biological replicates of each WT (sre1D) and mga2D KO  (sre1D/mga2D) in a dye-swap configuration.

first: Emerson

last: Stewart

first: Wei

last: Shao

first: Hans

middle: K

last: Hannibal-Bach

first: Kwang-Lae

last: Hoe

first: Dong-Uk

last: Kim

first: Han-Oh

last: Park

first: Christer

middle: S

last: Ejsing

first: Peter

last: Espenshade


title: Cumulus cell gene expression associated with pre-ovulatory acquisition of developmental competence in bovine oocytes

status: Public on Apr 01 2016

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

summary: This study investigated the cumulus cell (CC) transcriptomic changes during the oocyte developmental competence acquisition period.

overall_design: Six dairy cows were used for 24 oocyte collections and received FSH twice daily over 3 days, followed by FSH withdrawal for 20, 44, 68 and 92 h in four different oestrous cycles for each of the six cows. Half of the cumulus–oocyte complexes were subjected to in vitro maturation, fertilisation and culture to assess blastocyst rate. The other half of the CC underwent microarray analysis and qRT-PCR.

first: Audrey

last: Bunel

first: Anne-Laure

last: Nivet

first: Patrick

last: Blondin

first: Christiant

last: Vigneault

first: François

last: Richard


title: GATA3 restrains Notch signaling activity and represses NK cell development to induce human T cell commitment following Notch-induced T-lineage specification (expression)

first: Inge

last: Van de Walle

summary: The stepwise conversion of multipotent precursors into committed T-cell progenitors depends on several transcriptional regulators, but the interplay between these factors is still obscure. This is particularly true in human since the core early Notch signalling pathway also supports NK cell development and requires tight regulation for efficient T-lineage commitment and differentiation. Here, we show that GATA3, in contrast to TCF1, induces T-lineage commitment following NOTCH1-induced T-lineage specification through direct regulation of at least 3 distinct processes: repression of NK-cell fate, activation of T-lineage genes to promote further differentiation, and downmodulation of Notch signalling activity. GATA3-mediated repression of the NOTCH1 target gene DTX1 hereby is essential to induce T-lineage commitment at the expense of NK cell differentiation. Thus, human T-lineage commitment is dependent on the precise collaboration of several transcriptional regulators that integrate through both positive and negative regulatory loops.

overall_design: Gene expression was profiled in CT CD34+ cells after transduction with control or GATA3 and coculture on OP9-DL1 for 48h. Cells were collected 48h after coculture and sorted for CD45+EGFP+. 3 independent experiments were performed on 3 different thymus donors.

first: Kaat

last: Durinck

first: Wouter

last: Van Loocke

first: Pieter

last: Van Vlierberghe

first: Frank

last: Speleman


title: Rice genes responsive to Glu

city: Tsukuba

first: Hiroshi

last: Takatsuji

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Plant Sciences

country: Japan

institute: National Institute of Agrobiological Sciences

summary: Treatment of rice roots with glutamate (Glu) induces systemic disease resistance against rice blast in leaves. To analyze the effect of Glu on the transcriptome of rice, rice roots were treated with Glu solution, and then fourth leaves were harvested and analyzed by Agilent rice microarray.

overall_design: Rice plants were treated with Glu (10 mM) or mock (water) solution and leaves were analyzed at 9 and 24 h in two biological replicates.

first: Aya

last: Akagi


title: Epigenetic assimilation in the aging human brain

status: Public on Apr 04 2016

first: Art

last: Petronis

state: Ontario

address: 250 College St

department: Campbell Family Mental Health Research Institute

institute: Centre for Addiction and Mental Health

summary: Epigenetic drift progressively increases variation in DNA modification profiles of aging cells, but the finale of such divergence remains elusive. In this study, we explored the dynamics of DNA modification and transcription in the later stages of human life. We find that brain tissues of older individuals (>75 years) become more similar to each other, both epigenetically and transcriptionally, compared with younger individuals. Inter-individual epigenetic assimilation is concurrent with increasing similarity between the cerebral cortex and the cerebellum, which points to potential brain cell dedifferentiation. DNA modification analysis of twins affected with Alzheimer's disease reveals a potential for accelerated epigenetic assimilation in neurodegenerative disease. We also observe loss of boundaries and merging of neighboring DNA modification and transcriptomic domains over time. Age-dependent epigenetic divergence, paradoxically, changes to convergence in the later stages of life. The newly described phenomena of epigenetic assimilation and tissue dedifferentiation may help us better understand the molecular mechanisms of aging and the origins of diseases for which age is a risk factor.

overall_design: We performed DNA methylome analysis on frontal cortex, cerebellum, or buccal tissues from monozygotic twins and dizygotic twins discordant for Alzheimer’s disease (AD) or disease age of onset. DNA samples were enriched for unmodified fraction of the genome using DNA-modification sensitive restriction enzyme digestion followed by adaptor-mediated PCR. The enriched fractions were labelled with a fluorescent dye (Cy3) and hybridized onto the array with a common reference pool (Cy5).

first: Gabriel

last: Oh

first: Sasha

last: Ebrahimi

first: Sun-Chong

last: Wang

first: Rene

last: Cortese

first: Zachary

last: Kaminsky

first: Irving

middle: I

last: Gottesman

first: James

last: Bruke

first: Brenda

middle: L

last: Plassman


title: Single-cell profiling of human megakaryocyte-erythroid progenitors identifies distinct megakaryocyte and erythroid differentiation pathways

status: Public on Apr 02 2016

city: Oxford

first: Adam

last: Mead

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: Background: Recent advances in single-cell techniques have provided the opportunity to finely dissect cellular heterogeneity within populations previously defined by “bulk” assays and to uncover rare cell types. In human hematopoiesis, megakaryocytes and erythroid cells differentiate from a shared precursor, the megakaryocyte-erythroid progenitor (MEP), which remains poorly defined.Results: To clarify the cellular pathway in erythro-megakaryocyte differentiation, we correlated the surface immunophenotype, transcriptional profile and differentiation potential of individual MEP cells. Highly purified, single MEP cells (n=681) were analyzed using index fluorescence-activated cell sorting with parallel targeted transcriptional profiling of the same cells performed using a specifically designed panel of 87 genes. Differentiation potential was tested in novel, single-cell differentiation assays. Our results demonstrated that immunophenotypic MEP in fact comprise three distinct subpopulations: (1) “Pre-MEP”, enriched for erythroid/megakaryocyte progenitors but with residual myeloid differentiation capacity (2) “E-MEP”, strongly biased towards erythroid differentiation, and (3) “MK-MEP”, a previously undescribed, rare population of cells that are bipotent but primarily generate megakaryocytic progeny. Therefore, conventionally-defined MEP are in fact a mixed population: a minority give rise to mixed-lineage colonies while the majority of cells are transcriptionally-primed to generate exclusively single-lineage output. Conclusions: Our study clarifies the cellular hierarchy in human megakaryocyte/erythroid lineage commitment and highlights the importance of using a combination of single-cell approaches to dissect cellular heterogeneity and identify rare cell types within a population. We present a novel immunophenotyping strategy that enables the prospective identification of specific intermediate progenitor populations in erythro-megakaryopoiesis, allowing for in-depth study of disorders including inherited cytopenias, myeloproliferative disorders and erythromegakaryocytic leukemias.

overall_design: Multiplex RT-PCR gene expression profiling of 807 human megakaryocyte-erythroid progenitor cells (MEP) isolated from three healthy donors by apheresis following G-CSF treatment. Cells were excluded if more than 70 assays did not result in amplification or displayed Ct higer than 13 for B2M or higher than 15 for GAPDH. Furthermore cells with a mean non-dropout Ct value greater than 20 were removed. This resulted in a dataset of 681 cells, which were subsequently normalised to the mean of B2M and GAPDH expression.

first: Bethan

last: Psaila

first: Nikolaos

last: Barkas

first: Deena

last: Iskander

first: Anindita

last: Roy

first: Stacie

last: Anderson

first: Neil

last: Ashley

first: Valentina

last: Caputo

first: Jens

last: Lichtenberg

first: Sandra

last: Loaiza

first: David

last: Bodine

first: Anastasios

last: Karadimitris

first: Irene

last: Roberts


title: Root development and responses are alerted by light

city: Pozuelo de Alracon

first: Juan

middle: Carlos

last: del Pozo

state: Madrid

address: Campus de Montegancedo, UPM

department: Biotechnology

institute: Centro de Biotecnología y Genómica de Plantas

summary:
Investigation of whole genome gene expression level changes in Arabidopsis roots by the effect of light.
Plant growth is sustained by a continuous cell division in meristems  followed by cell differentiation and elongation. We have found that in  Arabidopsis thaliana roots, flavonols play a key role in regulating the transition from cell division to differentiation. Using an engineered device to grow roots in darkness, but shoot in  light cycle, coupled with transcriptomic and metabolomics analysis, we deciphered that flavonols accumulation regulates proliferation-promoting levels of auxin-PLETHORA and superoxide anion (O2-). High flavonols levels restrict auxin transport and the PLETHORA gradient but also superoxide radical content, promoting an accelerated cell differentiation. Furthermore, cytokinin-SHY2 and H2O2-UPB1 pathways, which promote differentiation and, respectively, antagonize auxin and O2- activity, increase flavonols biosynthesis establishing mutual interactions among these pathways. Flavonols function as positional signals integrating hormonal and ROS pathways to determine final organ growth.
This work analyze the effect of root illumination in gene transcription. Details of how plants and roots are grown are described in Silva et al. (submitted)

overall_design: A six chip study using total RNA extracted from three independent experiments of Arabidopsis roots growing in presence of light and three  independent experiments of Arabidopsis roots growing without light.

middle: C

first: Javier

last: Silva-Navas