title: Gene expression profile of human bone marrow MSCs in an early osteoinductive stage (e-MSCs)

status: Public on Nov 27 2015

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Early osteoinductive bone marrow MSCs (e-MSCs) acquire enhanced hematopoiesis-supportive ability.  We performed microarray analysis on e-MSCs. Cell chemotaxis-assosiated genes were positively enriched and cell adhesion-associated genes were negatively enriched compared with control MSCs. The expression of CXCL12 and VCAM1 extremely decreased.

overall_design: Microarray analysis was performed on human bone marrow MSCs stimulated with osteogenesis-inducing cocktails (OICS) for 2 days (e2-MSCs) or 5 days (e5-MSCs). Human bone marrow MSCs without the treatment were used for control.

first: Noriko

last: Sugino

first: Yasuo

last: Miura

first: Hisayuki

last: Yao


title: Essential Roles of the Smc5/6 complex in Replication through Pausing Sites and Endogenous DNA Damage Tolerance

status: Public on Nov 19 2015

city: Milan

first: Demis

last: Menolfi

address: via Adamello 16

country: Italy

institute: IFOM

type: Genome binding/occupancy profiling by genome tiling array

summary: The essential functions of the conserved Smc5/6 complex remain elusive. To uncover its roles in genome maintenance, we established Saccharomyces cerevisiae cell cycle-regulated alleles that enable restriction of Smc5/6 components to S or G2/M. Unexpectedly, the essential functions of Smc5/6 segregated fully and selectively to G2/M. Genetic screens that became possible with generated alleles identified processes that crucially rely on Smc5/6 specifically in G2/M: metabolism of DNA recombination structures triggered by endogenous replication stress, and replication through natural pausing sites located in late-replicating regions. In the first process, Smc5/6 modulates remodeling of recombination intermediates, cooperating with dissolution activities. In the second, Smc5/6 prevents chromosome fragility and toxic recombination instigated by prolonged pausing and the fork protection complex, Tof1-Csm3. Our results thus dissect Smc5/6 essential roles, and reveal that combined defects in DNA damage tolerance and pausing site-replication cause recombination-mediated DNA lesions, which we propose to drive developmental and cancer-prone disorders.

overall_design: BrdU incorporation profiles by ssDNA-BrdU IP on chip have been generated as described (Katou et al., 2003). Protein binding profiles by ChIP-chip  analysis were generated as described (Bermejo et al., 2009). Labeled probes were hybridized to Affymetrix S.cerevisiae Tiling 1.0 (P/N 900645) arrays and processed with TAS software.

first: Axel

last: Delamarre

first: Armelle

last: Lengronne

first: Philippe

last: Pasero

first: Dana

last: Branzei


title: Honey bee "Apis mellifera intermissa"

status: Public on Feb 01 2016

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: Apis mellifera intermissa (Buttel-Reepen, 1906) is the native honeybee subspecies of Algeria. A.m.intermissa occurs in Tunisia, Algeria and Morocco, between the Atlas and the Mediterranean and Atlantic coasts (Ruttner, 1988), in an area of more than 2500 km long. Intermissa indicates the position through this bee races between tropical Africa and European breeds (Peyvel, 1994). The settlement area of the Tellian extends from Tunisia to Morocco.  Ruttner  et al (1978) describes the pure Tellian. It is a black hair of his coat poverty brings out the black color. It is a small size, there are some times light illumination on the tergites.   This bee is very aggressive, nervous, sick to take part, as swarms huge fall and even produced many brood and can build up to one hundred queen cells (Le Conte, 2002).  A.m.intermissa is prone to swarming, shows an aggressive behaviour and an abundant use of propolis (Ruttner 1988).  This study is part of the project funded by the USAID Grant No. TA-MOU-08-M29-075.

overall_design: Agilent two-color CGH experiment, Organism: Apis mellifera, Agilent Custom Apis mellifera aCGH, 2X400K (AMADID:035669) designed by Genotypic Technology Private Limited Labeling kit:  Agilent Genomic DNA labeling Kit (Part Number: 5190-0453)

first: Nizar

middle: J

last: haddad

first: Loucif-Ayad

last: Wahida

first: Adjlane

last: Noureddine


title: Epigenetic regulation of the homeobox gene MSX1 associates with platinum resistant disease in high grade serous epithelial ovarian cancer

status: Public on Nov 26 2015

city: London

first: Robert

last: Brown

address: Du Cane Road, The Hammersmith Hospital-4th floor

country: United Kingdom

institute: Imperial College London

summary: Introduction: Although High Grade Serous Ovarian Cancer (HGSOC) is considered a chemo-responsive disease, a proportion of patients do not respond to platinum-based chemotherapy at presentation or have progression-free survival of <6 months. Validated biomarkers of lack of response would enable alternative treatment stratification for these patients and identify novel mechanisms of resistance. Methods: Differential DNA methylation was investigated in independent tumour sets using Illumina 27K HumanMethylation arrays and validated by bisulphite pyrosequencing. Gene expression was by Affymetrix arrays and qRT-PCR. The role of Msh homeobox 1 (MSX1) in drug sensitivity was investigated by gene reintroduction into ovarian cancer cell lines. Results: CpG sites at contiguous genomic locations within the MSX1 gene have significantly lower levels of methylation in HGSOC which recur by 6 months compared to after 12 months and/or with RECIST response (p<0.05, q<0.05). A decrease in methylation at these intragenic CpG sites was significantly correlated with decreased MSX1 gene expression. Low expression of MSX1 was associated with poor progression-free survival independent of known clinical prognostic features (p=0.014). Three mutant or wild-type TP53 expressing ovarian cancer cell lines, resistant to cisplatin, have reduced MSX1 expression compared to matched parental, platinum sensitive, lines. Re-expression of MSX1 in resistant lines led to cisplatin sensitisation, increased apoptosis, increased p21 and BAX expression. However, in two TP53-null cell lines, MSX1 failed to change cisplatin sensitivity. Conclusion: Hypomethylation of MSX1 is a biomarker of resistant HGSOC disease at presentation and identifies a novel mechanism of platinum drug resistance.

overall_design: Bisulphite converted DNA from the 86 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Charlotte

last: Wilhelm-Benartzi


title: Self-maintenance of rat C6 glioma stem cells (GSCs) by their non-GSC progenies

status: Public on Jan 01 2016

city: Tokyo

first: Kouichi

last: Tabu

address: 1-5-45, Yushima, Bunkyo-ku

country: Japan

institute: Tokyo Medical and Dental University

summary: Analysis of Hoechst 33342 dye-effluxing side population cells (SP cells defined as glioma stem cells, GSCs) and dye-retaining main population cells (MP cells defined as non-GSCs) that were FACS-sorted from the C6 glioma cell line stably expressing EGFP (C6-eGFP). ECM-related genes, such as Col4a1 and Col4a2, and the iron carrier gene Tf are upregulated in MP cells. Results provide the insight into molecular basis underlying the maintenance of GSCs by non-GSCs.

overall_design: Gene expression profiles were compared between SP and MP cells just after FACS-sorting from the whole C6-eGFP cells based on their Hoechst-effluxing abilities.

first: Tetsuya

last: Taga


title: RNA-protein interaction screening for SNORD50A and SNORD50B

status: Public on Nov 23 2015

city: Stanford

first: Paul

last: Khavari

state: CA

address: 269 Campus Drive

country: USA

institute: Stanford University

type:
Protein profiling by protein array
Other

summary: Putative RNA-protein interactions with selected snoRNAs were screened using labaled RNA hybridized to a human protein microarray

overall_design: snoRNAs SNORD50A and SNORD50B were in vitro transcribed, labeled with Cy5 and independently hybridized on human protein microarrays. The labeling process was optimized in order to achieve ~ 3 pmol dye per every microgram RNA while maintaining signal intensities that were readily visualized.

first: Dan

middle: E

last: Webster


title: Comparative genomic analyses of the human NPHP1 locus reveal complex genomic architecture and its regional evolution in primates

status: Public on Nov 30 2015

city: Houston

first: Bo

last: Yuan

address: One Baylor Plaza

institute: Baylor College of Medicine

type: Genome variation profiling by genome tiling array

summary: Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM# 256100) is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs) are abundant. Loss of function of NPHP1 is responsible for approximately 85% of the NPHP1 cases - about 80% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via non-allelic homologous recombination (NAHR) between two flanking directly oriented ~45 kb LCRs. Published data revealed a non-pathogenic inversion polymorphism involving the NPHP1 gene flanked by two inverted ~358 kb LCRs. Using optical mapping and array-comparative genomic hybridization, we identified three potential novel structural variant (SV) haplotypes at the NPHP1 locus that may protect a haploid genome from genomic instability and NPHP1 deletion. Inter-species comparative genomic analyses among primate genomes revealed massive genomic changes during evolution. The aggregated data suggest that dynamic genomic rearrangements occurred historically within the NPHP1 locus and generated SV haplotypes observed in the human population today, which may have differential susceptibility to the NPHP1 deletion within a personal genome. Our study documents diverse SV haplotypes at a complex LCR-laden human genomic region. Comparative analyses provide a model for how this complex region arose during primate evolution, and studies among humans reflect the possibility that intra-species polymorphism may potentially modulate an individual’s susceptibility to acquiring disease-associated alleles.

sample_organism:
Macaca mulatta
Papio anubis
Gorilla gorilla
Pan troglodytes
Pongo abelii
Homo sapiens

overall_design: aCGH experiments were performed on DNA samples from human subjects without NPHP1 (N=10), DNA samples from human subjects affected with NPHP1 (N=8), and nonhuman primate DNA samples of baboon (N=1), rhesus macaque (N=2), orangutan (N=1), gorilla (N=3) and chimpanzee (N=7). Human DNA sample of NA10851 were used as the universal reference for the aCGH experiment.

first: James

middle: R

last: Lupski


title: Expression data from chicken Pectoralis major

status: Public on Nov 20 2015

city: Village-Neuf

first: Jérôme

last: Schmeisser

address: 1, Boulevard d'Alsace

department: CRNA

country: France

institute: DSM Nutritional Products

summary:
Development of Pectoralis major has been investigated through gene expression analysis in comparing animals receiving a restricted diet in P and Ca (NC), a normal diet with sufficient level of P and Ca (PC), and a restricted diet supplemented with phytase (Phy1000).
We used microarrays (ChiGene-1_0-st) to evaluate gene expression underlying pathways affectd by the diet and/or the phytase supplementation and to identify classes of differentially expressed genes.

overall_design: Pectoralis major from chicken were sampled at day 36 for RNA extraction and hybridization on Affymetrix microarrays. 4 pools of 4 samples per treatment were used to identify potentially affected pathway related to the diet.

first: J


title: A 5-gene signature predicts outcome in women with hormone receptor-negative early breast cancer treated with chemoterapy.

city: Madrid

first: Juan Ángel

last: Fresno Vara

state: Madrid

address: Paseo de la castellana 261

department: INGEMM

country: Spain

institute: Hospital La Paz

summary: Hormone-receptor negative (HR-) breast cancer accounts for approximately one third of all breast tumors and has a worse prognosis compared with hormone receptor-positive disease. Their unfavorable outcome and the lack of hormonal receptors determine the use of adjuvant chemotherapy as part of the standard treatment for these tumors. However, a significant proportion of patients relapse after receiving adjuvant chemotherapy. Classical prognostic factors such as tumor size, lymph node status and grade of differentiation do not suffice to identify patients with a higher risk of relapse.   In the last decade, gene profiling has allowed the description of signatures with prognostic value in hormone receptor-positive tumors, but similar information is scarce in HR- disease. Reliable identification of poor-prognosis patients would be important to offer participation in clinical trials with new drugs and to modify follow-up schedules. In this study, we assessed gene expression with quantitative polymerase-chain reaction (RT-qPCR) in HR- early stage breast cancer. RNA was isolated from formalin-fixed paraffin-embedded (FFPE) tissue. Our purpose was to identify a gene signature related to outcome.

overall_design: RNA expression profiles from 65 ffpe tumor samples from patients diagnosed of invasive ductal carcinoma of the breast and at least 5 years of follow-up were determined with the goal of developing a gene expression-based model predictive of recurrence

first: Juan

middle: A

first: Iker

last: Sanchez-Navarro

first: Enrique

last: Espinosa

first: Angelo

last: Gámez-Pozo


title: Epithelial mesenchymal-like transition occurs in a subset of cells in castration resistant prostate cancer bone metastases

status: Public on Dec 18 2015

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: TGF-beta is a known driver of epithelial-mesenchymal transition (EMT) which is associated with tumor aggressiveness and metastasis. However, EMT has not been fully explored in clinical specimens of castration-resistant prostate cancer (CRPC) metastases. To assess EMT in CRPC, gene expression analysis was performed on 149 visceral and bone metastases from 62 CRPC patients and immunohistochemical analysis was performed on 185 CRPC bone and visceral metastases from 42 CRPC patients. In addition, to assess the potential of metastases to seed further metastases the mitochondrial genome was sequenced at different metastatic sites in one patient. TGF-beta was increased in bone versus visceral metastases. While primarily cytoplasmic; nuclear and cytoplasmic Twist were significantly higher in bone than in visceral metastases. Slug and Zeb1 were unchanged, with the exception of nuclear Zeb1 being significantly higher in visceral metastases. Importantly, nuclear Twist, Slug, and Zeb1 were only present in a subset of epithelial cells that had an EMT-like phenotype. Underscoring the relevance of EMT-like cells, mitochondrial sequencing revealed that metastases could seed additional metastases in the same patient. In conclusion, while TGF-beta expression and EMT-associated protein expression is present in a considerable number of CRPC visceral and bone metastases, nuclear Twist, Slug, and Zeb1 localization and an EMT-like phenotype (elongated nuclei and cytoplasmic compartment) was only present in a small subset of CRPC bone metastases. Mitochondrial sequencing from different metastases in a CRPC patient provided evidence for the seeding of metastases from previously established metastases, highlighting the biological relevance of EMT-like behavior in CRPC metastases.

overall_design: Custom Agilent 44K whole human genome expression oligonucleotide microarrays were used to profile 149 CRPC tumors from 63 patients. RNA was amplified prior to hybridization against a common reference pool of prostate tumor cell lines.

first: Maahum

last: Haider

first: Xiaotun

last: Zhang

first: Ericson

last: Nolan

first: Lawrence

middle: D

last: True

first: Hung-Ming

last: Lam

first: Lisha

middle: G

first: Melanie

last: Ketchanji

first: Nghiem

last: Belinda

first: Bryce

last: Lakely

first: Roger

first: Bruce

last: Montgomery

middle: H

last: Lange

first: Martine

middle: P

last: Roudier

first: Celestia

last: Higano

last: Bielas

first: Peter

middle: S

last: Nelson

middle: L

last: Vessella

first: Colm

last: Morrissey


title: miRNA profile of WI-38 cells and their progressively transformed derivatives

status: Public on Jan 29 2016

city: Rehovot

first: Yonit

last: Hoffman

address: Herzel

country: Israel

institute: Weizmann Institute of Science

summary: microRNA array of 4 cell lines: WI-38 primary fibroblasts (“Control”), slow growers (early passage after immortalization, Slow), fast growers (extensive passaging after immortalization) and fast growers transformed by constitutively activated mutant H-RasV12 (“Ras”)

overall_design: WI-38 cells were grown in 37° in MEM supplemented with 10% non-heat-inactivated fetal bovine serum (Sigma), pen-strep, sodium pyruvate, L-glutamine solution (Beit HaEmek). RNA was extracted using Nucleospin miRNA kit (Macherey-Nagel), according to manufacturer’s instructions. microRNA array analysis was done in duplicates, using the miRNA Complete Labeling and Hyb Kit (Agilent, 5190-0456) according to the manufacturer's instructions. Briefly, for each sample 100ng RNA was dephosphorylated, denatured, labeled with Cyanine 3-pCp and purified using Micro Bio-Spin 6 Columns. Hybridization was done for 20h with Agilent SurePrint G3 Unrestricted miRNA 8x60K (Release 19.0) arrays. Arrays were scanned using an Agilent DNA microarray scanner, and analyzed using the AgiMicroRna package in R  with the RMA algorithm. The function filterMicroRna was applied with the following parameters: control = TRUE, IsGeneDetected = TRUE, wellaboveNEG = TRUE, limIsGeneDetected = 50 and limNEG = 25.

first: Debora

last: Bublik

first: Alejandro

last: P. Ugalde

first: Ran

last: Elkon

first: Tammy

last: Biniashvili

first: Reuven

last: Agami

first: Moshe

last: Oren

first: Yitzhak

last: Pilpel


title: Population structure shapes copy number variation in malaria parasites

city: San Antonio

first: Ian

middle: Harry

last: Cheeseman

state: TX

department: Genetics

institute: Texas Biomedical Research Institute

summary: If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in 7 countries in Africa, SE Asia and S. America using a high density SNP/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500bp to 59kb, as well as 10,107 flanking, biallelic SNPs. Overall, CNVs were rare, small and skewed towards low frequency variants, consistent with the deleterious model. Relative to African and SE Asian populations, CNVs were significantly more common in S. America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g. DNA helicase, and 3 conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen.

overall_design: SNP/CGH hybridisation of 175 malaria parasite samples


title: SSEA4 is a marker for chemotherapy resistance [miRNA]

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

country: Germany

institute: Miltenyi Biotec GmbH

summary: By coupling PDX and cell surface marker screening technologies, we have identified distinct tumor cell sub-populations that are associated  with tumor resistance to chemotherapy. In the majority of relapsed tumors, the percentage of the marker-positive cells shifted back to pretreatment  levels. SSEA4 is one of the cell surface molecules tested that could distinguish enriched residual tumor cells in all the different TNBC PDX  models analyzed. The expression of SSEA4 is associated with tumor resistance to chemotherapy and SSEA4+ cells show increased gene expression of  genes involved in response to toxins, cellular import/export, cell migration and EMT.

overall_design: The dataset comprises four different sample groups including SSEA4- and SSEA4+ cell fractions isolated from mouse xenografts of human breast cancer cells. Two technical replicates were generated for each cell fraction. Microarray analysis was performed on the Agilent Whole Human Genome Oligo Microarray 8x60K (v2) platform.

first: Andrea

last: Aloia

first: Evgeniya

last: Petrova

first: Stefano

last: Cairo

first: Silvia

last: Rüberg

first: Olivier

last: Deas

first: David

last: Agorku

first: Andreas

last: Bosio

first: Jean-Gabriel

last: Judde

first: Olaf

last: Hardt


title: Study of the impact of G9a on DNA methylation in mouse embryonic cells [array]

status: Public on Nov 13 2015

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

institute: CNRS

type: Methylation profiling by genome tiling array

summary: We explored the role of the lysine-methyltrasferase G9a in the control of DNA methylation during mouse embryogenesis. We provide maps of cytosine methylation by MeDIP and RRBS in G9a-deficient mouse embryos and ES cells, as well as ChIP-Seq profiles for H3K9me2 in embryos and RNA-Seq expression profiles in G9a-deficient embryos.

overall_design: We mapped DNA methylation by MeDIP in WT and G9aKO E9.5 embryos. Experiments were performed in triplicates, and MeDIP and Input samples were hybridized to Nimblegen HD2 mm9 promoter deluxe arrays covering 12 kb of all gene promoters.

first: Sylvain

last: Guibert


title: Genome-wide transcriptional Responses to Fusarium oxysporum and Tomato mosaic virus in Tomato

status: Public on Nov 12 2015

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

institute: University of Verona

summary: The aim of this study was to compare the tomato global transcriptional profiles in response to host attack by ToMV and Fol in order to identify genomic differences and similarities in incompatible interactions between a foliar and a vascular pathogen.

overall_design: In order to identify a set of genes of interest in tomato plants infected with F. oxysporum f. sp. lycopersici (Fol) and Tomato Mosaic Virus (ToMV) a transcriptional analysis was performed. Tomato genes differentially expressed upon inoculation with Fol and ToMV were identified at 2 days post-inoculation, using an un-inoculated sample as reference.

first: G

last: Andolfo

first: F

last: Ferriello

first: L

last: Tardella

first: A

last: Sigillo

last: Frusciante

first: M

last: Ercolano


title: Mouse T-cell lymphomas induced by irradiation at different ages

city: Chiba

first: Masaaki

last: Sunaoshi

state: Chiba

address: 4-9-1 Anagawa, Inage-ku

department: Department of Radiation Effects Research, Institute for Radiological Science

institute: National Institutes for Quantum Science and Technology

summary: Children are considered more sensitive to radiation-induced cancer than adults, yet any differences in genomic alterations associated with age at exposure and their underlying mechanisms remain unclear. We analyzed the mutation of key tumor suppressor genes in T-cell lymphomas arising after weekly irradiation of female B6C3F1 mice with 1.2 Gy X-rays for 4 consecutive weeks starting during infancy (1 week old), adolescence (4 weeks old) or as young adults (8 weeks old). T-cell lymphoma incidence did not show any statistical differences among three irradiated groups; however, the frequency of loss of heterozygosity on chromosomes 11 and 19 showed opposing correlations with age at exposure. Ikaros on chromosome 11 was mutated frequently in the young adult–irradiation group (63%; 5/8), frequently incurring multiple independent hits (including deletions and mutations) or suffering a single hit predicted to result in a dominant negative protein (such as those lacking exon 4, an isoform we have designated Ik11, which lacks two of the four zinc–finger domains important for DNA binding). Pten on chromosome 19 was mutated more frequently in tumors from infant- (67%; 10/15) compared with young adult-irradiated mice (13%; 1/8, P = 0.041). Despite the presence of homozygous Pten mutations, DNA copy number was unchanged in the infant-irradiation group, suggesting duplication of the mutated allele by chromosome mis-segregation or mitotic recombination. Taken together, our findings demonstrate that while deletions on chromosome 11 affecting the Ikaros locus are a prominent feature of young adult irradiation-induced T-cell lymphoma, tumors arising after infant irradiation suffer a second hit in the Pten gene by chromosome mis-segregation or recombination. This is the first report showing age-at-exposure associated radiation-induced genomic alterations in two key tumor suppressor genes linked to T-cell lymphomagenesis. These data are important for considering the risks associated with childhood exposure to radiation.

overall_design: 38 T-cell lymphomas arising after weekly irradiation of female B6C3F1 mice with 1.2 Gy X-rays for 4 consecutive weeks starting at different ages (Infant: 1 week old (15 tumors), Adolescent: 4 weeks old (13 tumors), Young adult: 8 weeks old (10 tumors)) were analyzed.

first: Shizuko

last: Kakinuma


title: The expression profiles of miRNAs in the heart with glucose fluctuation compared with sustained hyperglycemia.

status: Public on Nov 17 2015

city: Oita

first: Yasushi

last: Teshima

address: 1-1 Idaigaoka, Yufu

institute: Oita University

summary: We examined miRNAs expression profiles in rat hearts. The expression of five of 350 scanned miRNAs significantly differed between rat hearts exposed to vehicle and diabetic rat hearts. The expression of 31 miRNAs significantly differed between vehicle and diabetes with fluctuations in glucose levels, and that of 22 miRNAs significantly differed between diabetic hearts and diabetic hearts with glucose fluctuations.

overall_design: Diabetes mellitus was induced with an intravenous injection of streptozotocin (60 mg/kg) and glucose fluctuation was induced by a 24-h- fast and an insulin injection (0.5 IU/kg).

first: Luong

middle: C

last: Thuc

first: Shotaro

last: Saito


title: A Microarray-Based Analysis Reveals That A Short Photoperiod Promotes Hair Growth in the Arbas Cashmere Goat

status: Public on Nov 11 2015

city: Hohhot

first: cunfa

last: zhao

address: zhaojun Road

country: China

institute: Academy of Agriculture and Stockbreeding Sciences

summary: we evaluated the Arbas Cashmere goat, a species that is especially used in this type of research. The goats were exposed to an experimentally controlled short photoperiod to study the regulation of cyclical cashmere growth. Exposure to a short photoperiod extended the anagen phase of the Cashmere goat hair follicle to increase cashmere production. Based on assessments of tissue sections, it was observed that the short photoperiod significantly induced cashmere growth. A comparison of the differences in gene expression between the short photoperiod and the natural conditions using gene chip technology supported this conclusion. Using the gene chip data, we identified genes that showed altered expression under the short photoperiod compared to natural conditions, and it was found that these genes are involved in the biological processes of hair follicle growth, structural composition of the hair follicle, and the morphogenesis of the surrounding skin appendages.

overall_design: Based on their similar weights, health conditions and good reproductive performance in a group of the same strain, we chose 62-year-old female adult Arbas Cashmere goats as our research specimens and randomly divided them into a test group (T1, T2, T3) and a control group (C1, C2, C3).The goats in the test group were grazed, fed, and allowed to drink from 9:30-16:30 daily, and they were housed in a dark shed with good air conditions for the rest of the time. The temperature in the shed was 1 degree less than that outside, and the opacity was controlled at approximately 0.1 lux. The control group was grazed in natural conditions. We used regular management to care for all of the goats.

first: Bin

last: Liu

first: Yurong

last: Li

first: Cunfa

last: Zhao


title: Gene transcription, metabolite and lipid profiling in eco-indicator daphnia magna indicate diverse mechanisms of toxicity by legacy and emerging flame-retardants.

status: Public on Nov 06 2015

city: Gaithersburg

first: Leona

middle: Dance

last: Scanlan

state: MD

address: 100 Bureau Dr

institute: NIST

summary: The use of chemical flame-retardants (FR) in consumer products has steadily increased over the last 30 years. Toxicity data exist for legacy FRs such as pentabromodiphenyl ether (pentaBDE), but less is known about effects of new formulations. To address this issue, the toxicity of seven FR chemicals and formulations was assessed on the freshwater crustacean Daphnia magna. Acute 48-h nominal LC50 values for penta- and octabromodiphenyl ether (pentaBDE, octaBDE), Firemaster 550 (FM550), Firemaster BZ-54 (BZ54), bis(2-ethylhexyl) tetrabromophthalate (BEH-TEBP), triphenyl phosphate (TPhP), and nonbrominated BEH-TEBP analog bis(2-ethylhexyl) phthalate (BEHP) ranged from 0.058 mg/L (pentaBDE) to 3.96 mg/L (octaBDE). mRNA expression, (1)H NMR-based metabolomic and lipidomic profiling at 1/10 LC50 revealed distinct patterns of molecular response for each exposure, suggesting pentaPBDE affects transcription and translation, octaBDE and BEH-TEBP affect glycosphingolipid biosynthesis and BZ54 affects Wnt and Hedgehog signal pathways as well as glycosaminoglycan degradation. Brominated components of FM550 (i.e., BZ54) were significantly higher in Daphnia after 48 h following 1/10 LC50 exposure. FM550 elicited significant mRNA changes at five concentrations across a range from 1/10^6 LC50 to 1/2 LC50. Analyses suggest FM550 impairs nutrient utilization or uptake in Daphnia.

overall_design: Seven flame retardant formulations and equal volume solvent (DMSO) controls for each; four exposed and three or four biological replicates per condition.

first: Alexandre

middle: V

last: Loguinov

first: Quincy

last: Teng

first: Philipp

last: Antczak

first: Kathleen

last: Dailey

first: Daniel

middle: T

last: Nowinski

first: Jonah

last: Kornbluh

first: Xin

middle: X

last: Lin

first: Erica

last: Lachenauer

first: Audrey

last: Arai

first: Nora

middle: K

last: Douglas

first: Francesco

last: Falciani

first: Heather

middle: M

last: Stapleton

first: Chris

last: Vulpe


title: Identification of novel biomarkers and potential target molecules of human hepatocellular carcinoma using THOC5, a member of the transcription/export (TREX) complex, depleted system

status: Public on Nov 02 2015

city: Hannover

first: Doan Duy Hai

last: Tran

state: Niedersachsen

address: Carl-Neubergsstr. 1

department: Institut of physiological Chemistry

institute: Hannover Medical School

summary: Hepatocellular carcinoma (HCC) is a frequent cancer with poor prognosis and with limited possibilities for anti-cancer treatment. Evidence has recently accumulated suggesting that multiple signaling pathways are activated in human cancer. It has been recently shown by exosome sequencing of HCC  that 161 putative driver genes are associated with 11 recurrently altered pathways, suggesting that we need to inhibit these multiple pathways for HCC therapy. THOC5, a member of transcription/export (TREX) complex, that plays a role in less than 1% of mRNA processing in normal cells such as fibroblasts or macrophages, is not required for maintenance of mature hepatocytes. In this study, we have examined the role of THOC5 in human HCC.     Enhanced THOC5 expression was not observed in differentiation grading 1 (G1) human HCC, but 78% of G2 and G3 exhibited increased levels of THOC5. Furthermore, the 50% depletion of THOC5 in hepatocellular carcinoma cell lines, Huh7 and HepG2 causes lipid accumulation and apoptosis. Transcriptome analysis using THOC5 depleted Huh7 and HepG2 cells revealed that 1049 and 837 genes were downregulated upon depletion of THOC5 in Huh7 and HepG2 cells, respectively. Among these genes, 396 were commonly downregulated in both cell lines. Some of these, such as tissue inhibitor of metalloproteinase 3 (TIMP3), tripartite motif containing 24 (TRIM24), ribosomal protein S6 kinase polypeptide 3 (RPS6KA3) and transmembrane emp24-like trafficking protein 10 (TMED10) are known to be fine tuners for several signal transduction pathways. The expression of these proteins was correlated with the THOC5 expression level in HCC. To inhibit multiple signaling pathways we are currently examining the effects of a combination of siRNAs against THOC5 target genes in HCC cell lines.  Our data suggest that THOC5, which controls a set of genes that are involved in HCC malignancy can be a potential biomarker for HCC. In addition, THOC5 target gene, TMED10 may also be a novel biomarker of HCC. Furthermore, the suppression of the THOC5 gene per se or multiple THOC5 target genes may represent a novel strategy for cancer therapy.

overall_design: Huh7 and HepG2 cells were infected with lentiviral THOC5 and control shRNAs. Five days after infection, total RNAs were isolated and subjected to microarray analysis.

first: Doan

first: Teruko

last: Tamura


title: Extreme sensitivity of gene expression in human neurocytes SH-SY5Y to ultra-low doses of a medicinal plant with anxiolytic-like properties

status: Public on Nov 01 2015

first: Alberto

last: Ferrarini

summary: Gelsemium sempervirens L. (Gelsemium) is a traditional medicinal plant which at ultra-low doses is employed as anxiolytic and antidepressant, but consistent evidence is lacking and the possible mechanisms involved at the level of nervous system are largely unknown. In this study we have investigated the gene expression of a human neurocyte cell line treated in vitro with increasing dilutions of Gelsemium extract.   Starting from a crude extract containing the active principle gelsemine at the concentration of 6.5×10−4 M, six centesimal (c) dilutions of Gelsemium were prepared according to the French homeopathic pharmacopoeia: 2c, 3c, 4c, 5c, 9c and 30c. Human neuroblastoma cells SHSY5Y were exposed for 24h to Gelsemium and their transcriptome was compared with control cells treated with the corresponding vehicle solutions. RNA from cells treated with Gelsemium/controls dilutions was isolated and analyzed by microarray. Four biological replicates were tested for each condition. The exposure to the Gelsemium 2c dilution (the highest dose employed, corresponding to 6.5x10-9 M gelsemine) significantly changed the expression of 56 genes, 49 of which were down-regulated and 7 were overexpressed. These genes belong to G-protein coupled protein signalling pathways, calcium homeostasis, inflammatory response and neuropeptide receptors. Cytotoxicity was excluded by WST-1 viability test. The mean fold change of the Gelsemium-downregulated geneset was negative compared to controls in each treatment condition. Although the effect in general decreased with increasing drug dilutions, cluster analysis allowed to identify some groups with typical profile of changes with different dilutions. Among the 49 genes down regulated by Gelsemium 2c, most showed decreased expression after treatment with all dilutions of Gelsemium and comparison with respective controls (Wilcoxon test) was highly significant:  47 genes were down regulated with 3c (p<0.0001), 42 with 4c (p<0.0001), 38 with 5c (p<0.0001), 30 with 9c (p<0.0001), 27 in 30c (p<0.0001). No significant differences of gene expression due to Gelsemium were found in a randomly chosen geneset of the whole cell trascriptome.   In conclusion this study showed that Gelsemium, a medicinal plant used in traditional medicine, modulates several genes possibly involved in  neuronal function. High throughput microarray technology allowed to detect a small but statistically significant response to extremely low doses/high dilutions, thus revealing an extreme sensitivity of human genome to this kind of pharmacological regulation.

overall_design: A 54 array study that includes both SHSY5Y and IMR32  human neuroblastoma cells samples to investigate the expression changes that result in the treatment with increasing dilutions of Gelsemium sempervirens plant ethanolic extract compared to controls. Each experiment with SHSY5Y cells contained 12 samples. The neurocyte cultures were treated for 24h with 6 dilutions of the Gelsemium sempervirens extract, namely 2c, 3c, 4c, 5c, 9c, 30c (c means centesimal dilution following homeopathic Pharmacopoeia) and the corresponding 6 dilutions of the vehicle solution (controls). Four biological replicates of the experiment were analyzed. IMR32 cells were exposed to Gelsemium 2c dilution and the corresponding control in triplicate experiments.

first: Marta

last: Marzotto

first: Debora

last: Olioso

first: Paolo

last: Bellavite


city: Greifswald

first: Anke

last: Schmidt

state: MV

address: Felix-Hausdorff-Str. 2

department: Plasma Life Science

institute: INP Greifswald

summary:
Oxidative stress illustrates an imbalance between radical formation and removal. Frequent redox stress is critically involved in a variety of human pathologies including cancer, psoriasis, and chronic wounds. However, reactive species pursue a dual role being involved in signaling on the one hand and oxidative damage on the other. Using a HaCaT keratinocyte cell culture model, we here aimed at investigating the cellular and transcriptional response to periodic, low dose oxidative challenge over three months. Chronic redox stress was generated by frequent incubation with cold physical plasma treated cell culture medium. Using mRNA microarray technology, we found both acute ROS stress responses as well as numerous adaptions on the transcriptional level and over several weeks of redox challenge. This included an altered expression of 260 genes that function in inflammation and redox homeostasis, such as, signaling molecules, cytokines, and anti-oxidant enzymes. Apoptotic signaling was affected to a minor extend, especially in p53 down-stream targets. Strikingly, the anti-apoptotic heat shock protein HSP27 was strongly upregulated. These results suggest a variety of adaptive responses relating involved a number of cellular processes elicited by frequent redox stress over several months. They may help to better understand inflammatory responses in redox related diseases and possibly allow uncovering new biomarkers of ROS-stress.
Microarrays were used to analyze and investigate the biological effects of repeated exposure of cold physical plasma on human HaCaT keratinocytes. Using an argon plasma jet kinpen, regulated transcripts were analyzed and further described in Schmidt et al. (submittes): “Long-term exposure to cold plasma-generated ROS –an in vitro model for redox-related diseases of the  skin”.

overall_design: HaCaT keratinocytes exposed to plasma treated medium - time course

first: Thomas

last: von Woedtke


title: Transcriptomic effects of combined 17beta-estradiol and progesterone treatment of cultured human uterine smooth muscle cells and of the progesterone inhibitor RU486 (mifepristone)

city: Galway

first: Michael

last: Cairns

address: University Road

department: NCBES

country: Ireland

institute: NUI Galway

summary: The myometrium is an important reproductive tissue composed primarily of smooth muscle cells. Contractility of the myometrial smooth muscle cells during  pregnancy and labour is modulated by hormones. Despite much research, little is known about the molecular mechanism by which estrogen and progesterone regulate myometrial contractility. This study investigates global gene expression profile of cultured human uterine smooth muscle cells (hUtSMCs) following 17β-estradiol (E2) and/or progesterone treatments using cDNA microarray technology. Furthermore the effects of addition of the progesterone inhibitor RU486 were investigated. Many genes were regulated in the presence of P4 or E2 alone but almost six times these numbers were regulated in the presence of the combination. The majority of these genes returned to near baseline levels (control samples) on addition of RU486. In total 796 annotated genes were significantly differentially expressed in the combined presence of P4 and E2 (relative to untreated levels). Furthermore, 666 annotated genes were significantly regulated by the addition of RU486 to the P4/E2 combination (relative to P4/E2 levels). Gene ontology analysis of these differentially expressed genes revealed a strong association of P4/E2 treatment with the downregulated expression of genes involved in cell communication, signal transduction, channel activity, inflammatory response and differentiation. Upregulated processes included cell survival (anti-apoptosis), gene transcription, steroid hormone biosynthesis, muscle development, insulin receptor signaling and cell growth. Functional withdrawal of progesterone using RU486 effectively reversed the processes induced by P4/E2 treatment. The hUtSMC system is an additional useful model to investigate steroid effects on smooth muscle cells in isolation from other myometrial cell types.

overall_design:
In this study human myometrial smooth muscle cells (hUtSMCs) purchased from Lonza were cultured and treated with 17beta estradiol and progesterone either alone or in combination. In addition the 17beta estradiol  and progesterone combined treated samples were also treated with the progesterone inhibitor RU486 (mifepristone). RNA was isolated after 72h from both treated and untreated control cells. The experiment was repeated 3 times.

Please note that slides were scanned three times successively (i.e. 3 .gpr files per sample) and the median raw values were used as input raw data for GeneSpring analysis (Median_Table_InputRAW.xlsx).

first: Sreenath

last: Chandran

first: Margaret

last: O'Brien

first: Enda

last: O'Connell

first: Kaveh

last: Mashayekhi

first: Terry

middle: J

last: Smith


title: Differential expression profiling of  Arabidopsis ABHD11 knock-out mutant

status: Public on Oct 01 2015

city: Bangalore

first: Genotypic

last: technology

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

institute: Genotypic Technology

summary: ABHD11 has a acylhydrolase activity. Knock-out of abhd11 increases phospholipids in plant leaves. Wholegenome array was done to check the differential expressed genes in lipid metabolic pathway

overall_design: Organism: Arabidopsis thaliana, Agilent Custom Arabidopsis Gene Expression 8x60k Array (AMADID: 037661) designed  by Genotypic Technology Private Limited.

first: Anitha

last: Vijayakumar

first: Ram

last: Rajasekharan


title: A grapevine anthocyanin acyltransferase, transcriptionally regulated by VvMYBA, can produce most acylated anthocyanins present in grape skins

status: Public on Oct 16 2015

city: San Pietro in Cariano

first: Marianna

last: Fasoli

state: Verona

address: Via della Pieve 70

department: Biotechnology

summary: Anthocyanins are flavonoid compounds responsible for red/purple colours in the leaves, fruit and flowers of many plant species. They are produced through a multistep pathway which is controlled by MYB transcription factors. VvMYBA1 and VvMYBA2 activate anthocyanin biosynthesis in grapevine (Vitis vinifera) and are non-functional in white grapevine cultivars. In this study, transgenic grapevines with altered VvMYBA gene expression were developed, and transcript analysis was carried out on berries using a microarray technique. The results showed that VvMYBA is a positive regulator of the later stages of anthocyanin synthesis, modification and transport in Shiraz. One up-regulated gene ANTHOCYANIN 3- O-GLUCOSIDE-6”-O-ACYLTRANSFERASE (Vv3AT) encodes a BAHD acyltransferase protein,  belonging to a clade separate from most anthocyanin acyltransferases. Functional studies (in planta and in vitro) show that Vv3AT has a broad anthocyanin substrate specificity and can also utilise both aliphatic and aromatic acyl donors, a novel activity for this enzyme family found in nature. In V. vinifera cv. Pinot Noir, a red-berried grapevine mutant lacking acylated anthocyanins, Vv3AT contains a nonsense mutation encoding a truncated protein that lacks two motifs required for BAHD protein activity. Promoter activation assays confirm that Vv3AT transcription is activated by VvMYBA1, which adds to the current understanding of the regulation of the BAHD gene family. The flexibility of Vv3AT to use both classes of acyl donors will be useful in the engineering of anthocyanins in planta or in vitro.

overall_design: Transgenic Chardonnay/Shiraz and non-transformed WT controls were all grown in the same glasshouse in ambient light with a night break. Day and night temperatures were approximately 27oC and 22oC respectively. For microarray experiments, whole berries were sampled from independent transgenic lines: three from transgenic Chardonnay and four from transgenic Shiraz, resulting in three and four biological replicates respectively. Bunches were harvested close to ripeness based on average total soluble solids (TSS, measured as oBrix). This was aimed to be between 20 – 24 oBrix and was determined from TTS of a subsamples from each bunch (Table S53). A sample consisted of all remaining berries from a single bunch except when there were <100 berries in which case more than one bunch was used in the one replicate. Whole berries were immediately frozen in liquid nitrogen. For skin samples, the skins were first removed from fresh berries then frozen in liquid nitrogen. All samples were stored at -80oC.

first: Amy

middle: R

last: Rinaldo

first: Erika

last: Cavallini

first: Sarah

last: Moss

first: Giovanni

last: Tornielli

first: Sara

last: Zenoni

first: Christopher

last: Ford

first: Paul

last: Boss

first: Amanda

last: Walker

first: Yong

last: Jia

first: Debra

last: McDavid

first: Lauren

last: Hooper

first: Simon

last: Robinson


title: Analysis of the origin of parthenocarpy in Corinto Bianco grapes

city: Logrono

first: Pablo

last: Carbonell-Bejerano

state: La Rioja

address: Madre de Dios, 51

department: Instituto de las Ciencias de la Vid y del Vino

institute: CSIC

summary: Seedlessness is a highly relevant trait in grapevine berries that are intended for fresh consumption or raisin production. Corinto Bianco (CB) is a parthenocarpic somatic variant of the seeded cultivar Pedro Ximenes (PX). Both variants were compared to understand the basis of this parthenocarpic phenotype. CB berries ripened normally although their size was six times smaller than in PX. Macrogametogenesis was aborted in CB, which was also pollen sterile. Occasionally, one seed developed in 1.6% of CB berries that displayed a comparable size to that of PX berries. Microsatellite genotyping and flow cytometry analyses of seedlings generated from these seeds identified tetraploid plants recapitulating the same genotype than the mother plant and triploids likely resulting from fertilization of diploid cells by external pollen, uncovering that most CB viable gametes were unreduced gametes. Microarray and RNA-seq analyses identified 1,958 genes differentially expressed between CB and PX developing flowers. CB-upregulated and downregulated genes were enriched in sporophyte and gametophyte-preferential genes, respectively and indicated a lack of postmeiotic germline development in CB flowers. RNA-seq was also useful to identify SNP polymorphisms distinguishing both variants and parthenocarpy-responsible candidate genes including a putative deleterious substitution in the protein encoded by a HAL2-like gene.

overall_design: A total of 6 samples were hybridized. RNA from Corinto Bianco and Pedro Ximenes flower buds, collected just before anthesis (closed flowers from inflorescences with few flowers starting to open, 1 dpa), were compared. Every sample was collected simultaneously and three biological replicates were analyzed for each sample.

first: José

last: Martínez-Zapater


title: Gene expression profiles of CD4 T cells and CD45+ HLA-DR+ cells during experimental allergic rhinitis in humans.

status: Public on Sep 01 2015

city: Subiaco

first: Anthony

last: Bosco

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

summary:
Six patients with seasonal allergic rhinitis were challenged daily for 8 days with birch pollen extract. A mucosal biopsy was obtained from one nostril at basline (day 0) and from the other nostril after allergen challenge (day 9).
The mucosal biopsies were digested into single cells, and then sorted into CD4 T cells and CD45+HLA-DR+ cells. Total RNA was extracted, amplified using whole transcriptome amplification, and gene expression was profiled on microarrays.

overall_design: The study design consisted of 6 subjects, 2 cell types (CD4 T cells, CD45+ HLA-DR+ cells), and 2 conditions (baseline, allergen challenge).

first: Ralph

last: Dollner

first: Patrick

last: Holt

first: Frode

last: Jahnsen


title: Gene expression analysis of pig cumulus-oocyte complexes stimulated in vitro with follicle stimulating hormone or epidermal growth factor-like peptides

status: Public on Sep 30 2015

city: Charlestown

first: Petr

last: Vodicka

state: Massachusetts

address: 114 16th Street

department: Department of Neurology

institute: Massachusetts General Hospital

summary:
Background: The gonadotropin-induced resumption of oocyte meiosis in preovulatory follicles is preceded by expression of epidermal growth factor (EGF)-like peptides, amphiregulin (AREG) and epiregulin (EREG), in mural granulosa and cumulus cells. Both the gonadotropins and the EGF-like peptides possess the capacity to stimulate resumption of oocyte meiosis in vitro via activation of a broad signaling network in cumulus cells. To better understand the rapid genomic actions of gonadotropins (FSH) and EGF-like peptides, we analyzed transcriptomes of cumulus cells at 3 h after their stimulation.
Methods: We hybridized aRNA from cumulus cells to a pig oligonucleotide microarray and compared the transcriptomes of FSH- and AREG/EREG-stimulated cumulus cells with untreated control cells and vice versa. The identified over- and underexpressed genes were subjected to functional genomic analysis according to their molecular and cellular functions. The expression pattern of 50 selected genes with a known or potential function in ovarian development was verified by real-time qRT-PCR.
Results: Both FSH and AREG/EREG increased the expression of genes associated with regulation of cell proliferation, cell migration, blood coagulation and extracellular matrix remodeling. FSH alone induced the expression of genes involved in inflammatory response and in the response to reactive oxygen species. Moreover, FSH stimulated the expression of genes closely related to some ovulatory events either exclusively or significantly more than AREG/EREG (AREG, ADAMTS1, HAS2, TNFAIP6, PLAUR, PLAT, and HSD17B7). In contrast to AREG/EREG, FSH also increased the expression of genes coding for key transcription factors (CEBPB, FOS, ID1/3, and NR5A2), which may contribute to the differing expression profiles of FSH- and AREG/EREG-treated cumulus cells.
Conclusions: The impact of FSH on cumulus cell gene transcription was higher than the impact of EGF-like factors in terms of the number of cell functions affected as well as the number of over- and underexpressed genes. Both FSH and EGF-like factors overexpressed genes involved in the post-ovulatory switch in steroidogenesis and tissue remodelling. However, FSH was remarkably more efficient in the up-regulation of several specific genes essential for ovulation of matured oocytes and also genes that been reported to play an important role in maturation of cumulus-enclosed oocytes in vitro.

overall_design: Three different samples (FSH treated, AREG/EREG treated and control untreated cumulus cells), each represented by 3 independently prepared biological replicates were hybridized to 9 microarrays (Pigoligoarray, www.pigoligoarray.org) as follows: 1st and 3rd biological replicate: Control AlexaFluor 647 + AREG/EREG AlexaFluor 555; AREG/EREG AlexaFluor 647 + FSH AlexaFluor 555; FSH AlexaFluor 647 + Control AlexaFluor 555. 2nd biological replicate (dye swap): Control AlexaFluor 555 + AREG /EREG AlexaFluor 647; AREG/EREG AlexaFluor 555 + FSH AlexaFluor 647; FSH AlexaFluor 555 + Control AlexaFluor 647.

first: Milan

last: Blaha

first: Lucie

last: Nemcova

first: Katerina

last: Kepkova

first: Radek

last: Prochazka


title: Chromosomal microarray analysis for validation of the NGS-based CNV detection results in clinical samples

city: Hong Kong

first: Zirui

last: DONG

address: Shatin, N.T.

department: Dept. of Obstetrics and Gynaecology

institute: The Chinese University of Hong Kong

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

summary: In order to evaluate the performance of CNV detection in next-generation sequencing platform in varied sample types, we employed chromosomal microarray analysis (CMA) for validation of the samples with NGS-based detection results (NCBI Sequence Read Archive with accession number SRA296708). Besides array Comparative Genomics Hybridization (aCGH, Agilent) , we used a commerical SNP-array (Illumina) including early abortus, induced termination, prenatal samples and postnatal samples. CMA results were compared with NGS-based detection results. 100% consistency was obtained between NGS-based approach and CMA in pathogenic or likely pathogenic CNVs detection.

overall_design: SNP-array was perfomed, according to the manufacturer's protocol, in the samples with NGS-based detection result and sufficient DNA amount (>500ng). Each clinical subject was referred for chomosomal analysis because of the clinical indication.

first: Ping

last: HU

first: Jun

last: ZHANG


title: aCGH for CNV detection in clinical samples

summary: In order to evaluate the performance of CNV detection in next-generation sequencing platform in varied sample types, we employed chromosomal microarray analysis (CMA) for validation of the samples with NGS-based detection results (NCBI Sequence Read Archive with accession number SRA296708). Besides snp-array, we used a customized array Comparative Genomics Hybridization (aCGH, Agilent) approach for a cohort of clinical samples including early abortus, induced termination, prenatal samples and postnatal samples. CMA results were compared with NGS-based detection results. 100% consistency was obtained between NGS-based approach and CMA in pathogenic or likely pathogenic CNVs detection.

overall_design: aCGH was perfomed in the samples with NGS-based detection result and sufficient DNA amount (>500ng). Each clinical subject was referred for chomosomal analysis because of the clinical indication. Each case was detected by aCGH by using a healthy Chinese adult as control.

first: Kwong

middle: W

last: CHOY

first: Hoi

last: WONG


title: Overexpression Studies of SNHG1 Revealed that SNHG1 Regulated the Distal Genes Expression in Cancer

city: Beijing

first: Guifeng

last: Wei

state: Beijing

address: 15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: Many long noncoding transcripts are involved in cancer progression. Here, we utilized high-throughput microarray to compare the transcriptome alterations between the SNHG1 overexpression or control in HCT116 cell lines. Two isoforms of SNHG1 (denoted as SNHG1S and SNHG1L in the present work) were separately cloned and stably expressed in HCT116 cells with the lentivector. Moreover, GSEA analysis revealed the significant associations between SNHG1-regulated genes and plethora of gene signatures or pathways, such as process of interferon response. Collectively,the present study indicated that SNHG1 regulated the distal genes in cancer progression.

overall_design: HCT116 cells overexpressing SNHG1 isoforms (Short or Long) or control vector. Three biological replicates of each condition were analyzed on Agilent microarray.

first: Y

last: Sun

first: G

first: H

last: Luo

first: J

first: R

last: Chen


title: Male breast cancer copy number profiles

status: Public on Sep 13 2015

city: Amsterdam

first: Philip

last: Schouten

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: Exploratory study of copy number profiles of male breast cancer patients.

overall_design: The experiment contains 75 male breast cancer samples, analysed on a 135K whole genome CGH array

first: Hedde

middle: D

last: Biesma

first: Joyce

last: Sanders

first: Wim

last: Brugman

first: Ron

last: Kerkhoven

first: Ingrid

last: Mandjes

first: Miangela

last: Lacle

first: Petra

last: Van der Groep

first: Paul

last: Van Diest

first: Sabine

last: Linn


title: Preadult life history variation determines adult transcriptome expression

status: Public on Aug 21 2015

city: Las Vegas

first: Allen

middle: G.

last: Gibbs

state: Nevada

address: 4505 S Maryland Parkway

department: School of Life Sciences

institute: University of Nevada

summary: Investigation of whole genome transcription expression level changes in Drosophila mojavensis wild-type populations (Las Bocas:LB and Punta Prieta:PP). The experiment was designed to investigate preadult life history affects over adult transcriptome expression.

overall_design: A total of 137 hybridizations were performed in this entire experiment. We used 135K 12-plex NimbleGen arrays. Total RNA was recovered from each sample listed below. The experimental design consisted a total of two populations (Las Bocas:LB; Punta Prieta:PP),  two host diets (Agria:AG and Organ pipe:OP) and four "length of egg to adult development time" points, i.e. 14, 15, 16, and 17 days. (14 days:D1; 15 days:D2; 16 days:D3; 17 days:D4). Each chip measures the expression level of 14528 transcripts. One to 5 replicates were used for each type (R1, R2, R3 etc.). Fly source details are as follows: Las Bocas 2009: LB09; Punta Prieta 2008:PP08.

middle: G

first: William

last: Etges

first: Subhash

last: Rajpurohit

first: Cassia

last: de Oliveira


title: Development of gene expression signatures for TLX1 overexpression in human thymus C34+ T-cell progenitors cultured on an OP9-DLL1 feeder layer

status: Public on Aug 05 2015

city: Ghent

first: Kaat

last: Durinck

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Center for Medical Genetics

summary: The T-cell leukemia homeobox 1 (TLX1, HOX11) transcription factor is critically involved in the multistep pathogenesis of T-cell acute lymphoblastic leukemia (T-ALL) and often cooperates with NOTCH1 activation during malignant T-cell transformation. However, the exact molecular mechanisms by which these T-cell specific oncogenes cooperate during transformation remain to be established. Here, we used an integrative genomics approach to show that the oncogenic properties of TLX1 are mediated by genome-wide interference with the ETS1 and RUNX1 transcription factors. Partial disruption of ETS1 and RUNX1 activity by ectopic TLX1 expression in immature thymocytes drives repression of T-cell specific super-enhancers and mediates an unexpected transcriptional antagonism with NOTCH1 signaling. These phenomena coordinately trigger a TLX1 driven pre-leukemic phenotype in human thymic precursor cells, which corresponds with the in vivo thymic regression observed in murine TLX1 tumor models, and creates a strong genetic pressure for acquiring activating NOTCH1 mutations as a prerequisite for full leukemic transformation. In conclusion, our results uncover a functional antagonism between cooperative oncogenes during the earliest phases of tumor development and provide novel insights in the multistep pathogenesis of TLX1 driven human leukemia.

overall_design: Gene expression was measured after TLX1 overexpression in human CD34+ T-cell progenitors cultured on an OP9-DLL1 feeder layer. Cells were collected after 72h of co-culture. This was performed for 2 independent thymus CD34+ donors.

first: Wouter

last: Van Loocke

first: Pieter-Jan

last: Volders

first: Pieter

last: Mestdagh

first: Jo

last: Vandesompele

first: Inge

last: Van de Walle

first: Tom

last: Taghon

last: Van Vlierberghe


title: Development of gene expression signatures for GSI treatment of the ALL-SIL cell line.

overall_design: Gene expression was measured in the ALL-SIL T-ALL cell line after treatment with DMSO (solvent control) or GSI (γ-Secretase Inhibitor). Cells were collected 48h after treatment. This was performed for 3 replicates.

first: Frank

last: Speleman

last: van Vlierberghe


title: Development of gene expression signatures for TLX1 knockdown in the ALL-SIL cell line.

overall_design: Gene expression was measured in the ALL-SIL T-ALL cell line after electroporation with scrambled siRNA and 2 independent TLX1 targetings siRNAs. Cells were collected 24h after treatment. This was performed for 3 replicates.


title: Development of gene expression signatures for JQ1 treatment of the ALL-SIL cell line.

overall_design: Gene expression was measured in the ALL-SIL T-ALL cell line after treatment with DMSO (solvent control) or JQ1. Cells were collected 12h after treatment. This was performed for 3 replicates.


title: Development of gene expression signatures for RUNX1 knockdown in the ALL-SIL cell line.

overall_design: Gene expression was measured in the ALL-SIL T-ALL cell line after electroporation with scrambled siRNA and 2 independent RUNX1 targetings siRNAs. Cells were collected 24h after treatment. This was performed for 3 replicates.


title: Transgenic AhNF-YC-OE vs Wild type Col 0 Arabidopsis plants

status: Public on Jul 14 2015

city: Irapuato

first: John P

last: Délano-Frier

state: Guanajuato

address: Km 9.6 del Libramiento Norte Carretera Irapuato-León SN

department: Biotechnology and Biochemistry

country: Mexico

institute: CINVESTAV Irapuato

summary: Transcriptional profiling of Arabidopsis rossette leaves comparing WT Col-0 with a transgenic lines overexpressing AhNF-YC gene from Amaranthus hypochondriacus in three different conditions.

overall_design: Three-condition experiment WT vs AhNF-YC OE plant leaves. The analyzed conditions were: normal growth conditions, water stress for 5 days and 24 hrs of recovery after normal watering was reestablished to 8-day water stressed plants.

first: Paola

middle: A

last: Palmeros-Suárez

first: John

middle: P


title: Development of gene expression signatures for ETS1 knockdown in the ALL-SIL cell line.

overall_design: Gene expression was measured in the ALL-SIL T-ALL cell line after electroporation with scrambled siRNA and 2 independent ETS1 targetings siRNAs. Cells were collected 24h after treatment. This was performed for 3 replicates.


title: Development of gene expression signatures of 64 T-ALL patient samples

overall_design: Gene expression profiling of 64 T-ALL patient samples

first: Jean

last: Soulier


title: Chromosomal microarray data for validation of copy-number variants detection from a low-coverage whole-genome sequencing approach in clinical samples

first: Zirui

last: DONG

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

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

overall_design: Refer to individual Series


title: Analysis of wheat straw grown Trichoderma reesei gene expression as influenced by L-methionine in the medium

status: Public on Jun 11 2015

city: Vienna

first: Robert

last: Bischof

address: Gumpendorferstraße 1a

country: Austria

institute: ACIB GmbH

summary: Wheat straw grown cultures of T. reesei QM9414 were supplemented with 100 µM L-methionine and  the genome wide gene expression monitored in order to find novel L-Methionine repressible genes.

overall_design: Total RNA was isolated from independent duplicate shake flask cultures of T. reesei QM9414 pregrown on pretreated wheat straw. Global gene and analyzed using a 4 chip design where 2 chips each represented cultures with or without exogeneously added 100 µM L- Methionine.

first: Bernhard

last: Seiboth


title: Dynamic and coordinated expression changes of rice small RNAs in response to Xanthomonas oryzae pv. oryzae

status: Public on Aug 31 2015

city: Old Westbury

first: Ying-Tao

last: Zhao

state: NY

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: Endogenous small RNAs are newly identified players in plant immune responses, yet their roles in rice (Oryza sativa) responding to pathogens are still less understood, especially for pathogens that can cause severe yield losses. Here, we examined the small RNA expression profiles of rice leaves at 2, 6, 12, and 24 hours post infection of Xanthomonas oryzae pv. oryzae (Xoo) virulent strain PXO99, the causal agent of rice bacterial blight disease. Dynamic expression changes of some miRNAs and trans-acting siRNAs (ta-siRNAs) were identified, together with a few novel miRNA targets, including a disease resistance gene targeted by osa-miR159a.1. Coordinated expression changes were observed among some miRNA and ta-siRNAs in response to Xoo infection, with small RNAs exhibiting the same expression pattern tended to regulate genes in the same or functional correlated signaling pathways, including auxin and GA signaling pathways, nutrition and defense related pathways, etc. Highly abundant small RNAs with pathogen-responsive expression changes were identified from the exonic region of a protein-coding gene, which may present a new class of functional small RNAs. These findings reveal the dynamic and complex roles of small RNAs in rice-pathogen interactions, and identified new targets for regulating plant immune responses.

overall_design: Examination of the small RNA expression profiles of rice leaves at 2, 6, 12, and 24 hours post infection of Xanthomonas oryzae pv. oryzae (Xoo) virulent strain PXO99

first: Xiu-Jie

last: Wang

first: Yan-Tao

last: Jia


title: Steroid-dependent regulation of bovine oviductal epithelial cells: a transcriptomal analysis of mRNA and miRNA

status: Public on Mar 16 2015

city: Lexington

first: Phillip

last: Bridges

state: KY

address: 206 WP Garrigus Building

department: Animal and Food Sciences

institute: University of Kentucky

summary: Reproductive success depends on a functional oviduct for gamete storage, maturation, fertilization, and early embryonic development.  The ovarian-derived sex steroids estrogen and progesterone have been found to influence cell proliferation, differentiation and functionality of the oviduct.  The objective of this study was to investigate steroidal regulation of oviductal epithelial cell function by using the Bovine Gene 1.0 ST array (Affymetrix Inc., CA) for transcriptional profiling.  Our overall goals were to increase our understanding of known epithelial cell processes critical for fertility, and to identify novel genes and biochemical processes for future analysis.  Transcripts were annotated using NetAffx annotation database for the Bovine gene 1.0 ST array and last updated in June 2014.

overall_design: Normally cycling Angus heifers were assigned to either luteal phase (LP, high progesterone, n=3) or follicular phase (FP, high estradiol, n=3) groups.  Heifers in the LP group were killed between day 11 and 12 after ovulation.  Heifers in the FP group were treated with 25 mg PGF2α (Lutalyse, Pfizer, NY) at 8 pm on day 6 after ovulation and killed 36 h later.  Cycle stage was confirmed by ultrasonography and oviducts were collected within 20 minutes after slaughter.  Epithelial cells were isolated from the ampulla and isthmus and total RNA extracted and purified using TRIzol and RNeasy columns, respectively.

first: K

middle: L

last: Cerny

first: P


title: Gene duplication of type-B ARR transcription factors systematically extends transcriptional regulatory structures in Arabidopsis

status: Public on Feb 03 2015

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

summary: Many of duplicated genes are enriched in signaling pathways. Recently, gene duplication of kinases has been shown to provide genetic buffering and functional diversification in cellular signaling. Transcription factors (TFs) are also often duplicated. However, how duplication of TFs affects their regulatory structures and functions of target genes has not been explored at the systems level. Here, we examined regulatory and functional roles of duplication of three major ARR TFs (ARR1, 10, and 12) in Arabidopsis cytokinin signaling using wild-type and single, double, and triple deletion mutants of the TFs. Comparative analysis of gene expression profiles obtained from Arabidopsis roots in wild-type and these mutants showed that duplication of ARR TFs systematically extended their transcriptional regulatory structures, leading to enhanced robustness and diversification in functions of target genes, as well as in regulation of cellular networks of target genes. Therefore, our results suggest that duplication of TFs contributes to robustness and diversification in functions of target genes by extending transcriptional regulatory structures.

overall_design:
Duplication of TFs can confer an extension of transcriptional regulatory structures for target genes by providing new regulatory relationships between duplicated TFs and new or old target genes. To examine the nature of the extension in the regulatory structure, we performed gene expression profiling of Arabidopsis root tissues obtained from wild-type (WT) and deletion mutants of three type-B ARR1, 10, and 12.
To examine how the extended regulatory structures by the duplicated ARR TFs are utilized for the responses to external CK, we generated gene expression profiles of WT Arabidopsis roots treated with mock or exogenous CK for 1 hour. Total RNAs were isolated from two biological replicates at each condition and used to measure gene expression level.

first: Hong

last: Nam

first: Daehee

last: Hwang


title: Transcriptomic effects of the expression in Arabidopsis of a TCP15-EAR fusion controlled by its own promoter (one-color experiment)

status: Public on May 16 2015

city: Santa Fe

first: Agustin

middle: Lucas

last: Arce

state: Santa Fe

address: Ciudad Universitaria

country: Argentina

institute: Instituto de Agrobiotecnología del Litoral

summary:
TCP proteins are transcription factors that participate in plant development (Martin-Trillo ad Cubas, 2010; Uberti-Manassero et al., 2013). Previous studies demonstrated that the Arabidopsis thaliana TCP protein TCP15 affects the development of leaves, stems and flowers (Kieffer et al., 2011; Uberti-Manassero et al., 2013).
To obtain further insight into the molecular mechanisms involved in TCP15 action, we performed a transcriptional profiling of plants that express a repressor form of TCP15 under the control of the TCP15 promoter (P15::TCP15-EAR), previously described in Uberti-Manassero et al. (2012). For this purpose, gene expression was quantified in RNA extracted from complete rosettes of 25-day-old P15::TCP15-EAR plants and compared with that in RNA extracted from wild-type (Col-0) plants of the same age.

overall_design: Two genotype experiment: wild type vs. P15::TCP15-EAR plants. Biological replicates: 1 wild type replicate, 1 P15::TCP15-EAR replicate.

first: Daniel

middle: H

last: Gonzalez

first: Nora

last: Uberti-Manassero

first: Agustín

first: Leandro

middle: E

last: Lucero


title: Identification of novel long non-coding RNAs as biomarker for patients with renal cell carcinoma

status: Public on Feb 18 2015

city: Bonnn

first: Jörg

last: Ellinger

state: NRW

address: Sigmund-Freud-Straße 25

department: Urologie

institute: Universitätsklinikum Bonn

summary:
Long non-coding RNAs (lncRNA) play an important role in carcinogenesis, but knowledge  of lncRNA expression in renal cell carcinoma is rudimental. We screened 32,183 lncRNA transcripts in malignant and adjacent normal renal tissue and determined dysregulation of approximately 4% of the lncRNA transcripts in clear cell renal cell carcinoma tissue.
The distinct changes of lncRNA expression may be used to develop a non-invasive biomarker, because lncRNAs are detectable in bodily fluids.

overall_design: Microarray experiments were performed to determine the expression of 32,183 lncRNA transcripts belonging to 17,512 lncRNAs in 15 corresponding normal and malignant renal tissues

first: Jasmine

last: Blondeau

first: Doris

last: Schmidt


title: Transcriptomic analysis of bolting tolerance in six sugar beet genotypes

status: Public on Dec 31 2014

city: Reims

first: Claire

last: Hébrard

address: Camus Moulin de la Housse

institute: Unité de Recherche Vigne et Vins de Champagne

summary: The aim of this study was to identify genes that could be involved in sugar beet bolting tolerance. We focused on shoot apical meristem, the site of floral transition, from six sugar beet genotypes that were submitted to 9 weeks of vernalization treatment. This duration of cold exposure allowed bolting in the 3 sensitive genotypes but not in the 3 resistant ones. Single-copy sequences of DNA, potentially enriched in coding sequences, were isolated by Cot analysis and sequenced using Roche's GS-FLX sequencing technology in order to complete public sugar beet databases. Oligonucleotide arrays based on our single-copy sequences (about 42 000 predicted Open Reading Frames (ORFs)) and public database sequences (30 235 ESTs) were designed and used for transcriptomic and methylation analyses. We identified 1580 differentially expressed sequences (DES) and 1526 differentially methylated sequences (DMS) between bolting resistant and bolting sensitive genotypes. Using higher stringency criteria, we focused on 169 DES (with 87 up-regulated in R genotypes and 82 up-regulated in S ones) and 111 DMS (all hyper-methylated in S genotypes). In addition, 14 sequences were found to be both differentially methylated and differentially expressed, exhibiting negative correlation between their methylation and expression. We showed that bolting tolerance involved an integrated network of genes from environment perception, phytohormone signaling to flowering induction.

overall_design: Gene expression in sugar beet shoot apical meristem was measured after 9 weeks of vernalization treatment at 4°C. Experiment was performed one time using six different sugar beet genotypes named 1, 2, 3, 4, 5 and 7. Genotypes 3 and 7 were both hybridized on two different arrays to have technical replicates.

last: Peterson

first: Glenda

last: Willems

first: Alain

last: Delaunay

first: Béline

last: Jesson

first: Marc

last: Lefebvre

first: Steve

last: Barnes

first: Stéphane

last: Maury


title: Transcriptome and DNA methylation variations between six sugar beet genotypes with distinct bolting tolerance levels

type:
Expression profiling by array
Methylation profiling by array

sample_organism:
Beta vulgaris subsp. vulgaris
Beta vulgaris


title: Oligonucleotide Array CGH Profiles of Breast Cancer Patients Treated with High Dose or Conventional Chemotherapy

status: Public on Dec 22 2014

first: Philip

middle: C

last: Schouten

summary: DNA copy number profiles can identify patients with a defect in BRCA1 or BRCA2. We previously showed that patients with a BRCA1 like profile benefit from intensified alkylating chemotherapy  (IA, 4 cycles 5-fluorouracyl (5FU), epirubicin, cyclophosphamide (C) + 1 cycle carboplatin, thiotepa and cyclophosphamide with autologous stem cell transplantation (ASCT)). Presumably, this is because of the defect in error free homologous recombination DNA repair. Here we present an independent study IA chemotherapy (2 cycles induction, followed by ifosfamide, 12 g/m2; carboplatin, 900 mg/m2; and epirubicin, 180 mg/m2 with ASCT) versus anthracyclin-C (AC) or C-methothrexate-5FU  (CMF) regimens in high risk breast cancer.

overall_design: DNA isolated from untreated resection specimens of 117 patients was labeled using Enzo labeling kit for array CGH and hybridized to a custom 135k Nimblegen platform.

first: Frederik

last: Marme

first: Sebastian

last: Aulman

first: Hans-Peter

last: Sinn

first: Hendrik

last: Van Essen

first: Bauke

last: Ylstra

first: Micheal

last: Hauptmann

first: Andreas

last: Schneeweiss

first: Sabine

last: Linn


title: Cardiac mRNA profiling in mice treated with lipopolysaccharide

status: Public on Dec 06 2014

city: Philadelphia

first: Konstantinos

last: Drosatos

state: PA

address: 3500 N. Broad st

department: Pharmacology

institute: Temple University

summary: To identify the messenger RNA (mRNA) profile in the hearts of mice that were treated with lipopolysaccharide (LPS) and identify potential changes in the expression of genes that may account for inhibition of cardiac Ppara that has been observed in LPS-treated mice, 8 mouse samples were analyzed with whole genome microarrays.

overall_design: Total RNA from pieces of hearts obtained from 8 C57BL/6 mice that were treated either with saline (4 mice) or with lipopolysaccharide (4 mice).


title: DNA methylation variations between six sugar beet genotypes with distinct bolting tolerance levels

first: Claire

last: Hébrard

summary: The aim of this study was to explore epigenetic variations between sugar beet genotypes with distinct bolting tolerance levels and to identify genes that could be involved in sugar beet bolting tolerance. We focused on shoot apical meristem, the site of floral transition, from six sugar beet genotypes that were submitted to 9 weeks of vernalization treatment. This duration of cold exposure allowed bolting in the 3 sensitive genotypes but not in the 3 resistant ones. Single-copy sequences of DNA, potentially enriched in coding sequences, were isolated by Cot analysis and sequenced using Roche's GS-FLX sequencing technology in order to complete public sugar beet databases. Oligonucleotide arrays based on our single-copy sequences (about 42 000 predicted Open Reading Frames (ORFs)) and public database sequences (30 235 ESTs) were designed and used for transcriptomic and methylation analyses. We identified 1580 differentially expressed sequences (DES) and 1526 differentially methylated sequences (DMS) between bolting resistant and bolting sensitive genotypes. Using higher stringency criteria, we focused on 169 DES (with 87 up-regulated in R genotypes and 82 up-regulated in S ones) and 111 DMS (all hyper-methylated in S genotypes). In addition, 14 sequences were found to be both differentially methylated and differentially expressed, exhibiting negative correlation between their methylation and expression. We showed that bolting tolerance involved an integrated network of genes from environment perception, phytohormone signaling to flowering induction.

overall_design: Two condition experiment on sugar beet shoot apical meristems after 9 weeks of vernalization treatment at 4°C. Experiment was performed one time using six  sugar beet genotypes. Genotypes 1, 4 and 7 correspond to the group of bolting resistant genotypes and genotypes 2, 3, 5 correspond to the group of bolting sensitive genotypes. Methylated DNA was compared to the corresponding genomic DNA for each genotype.

first: Daniel

last: Peterson


title: Development of gene expression signatures with lncRNAs for T-cell subsets (CD34+ and CD4+CD8+)

status: Public on Oct 27 2014

city: Gent

first: Annelynn

last: Wallaert

address: De Pintelaan 185

institute: UGent

summary: Genetic studies in T-cell acute lymphoblastic leukemia have uncovered a remarkable complexity of oncogenic and loss-of-function mutations. Amongst this plethora of genetic changes, NOTCH1 activating mutations stand out as the most frequently occurring genetic defect, identified in more than 50% of T-cell acute lymphoblastic leukemias, supporting an essential driver role for this gene in T-cell acute lymphoblastic leukemia oncogenesis. In this study, we aimed to establish a comprehensive compendium of the long non-coding RNA transcriptome under control of Notch signaling. For this purpose, we measured the transcriptional response of all protein coding genes and long non-coding RNAs upon pharmacological Notch inhibition in the human T-cell acute lymphoblastic leukemia cell line CUTLL1 using RNA-sequencing. Similar Notch dependent profiles were established for normal human CD34+ thymic T-cell progenitors exposed to Notch signaling activity in vivo. In addition, we generated long non-coding RNA expression profiles (array data) from GSI treated T-ALL cell lines, ex vivo isolated Notch active CD34+ and Notch inactive CD4+CD8+ thymocytes and from a primary cohort of 15 T-cell acute lymphoblastic leukemia patients with known NOTCH1 mutation status. Integration of these expression datasets with publically available Notch1 ChIP-sequencing data resulted in the identification of long non-coding RNAs directly regulated by Notch activity in normal and malignant T-cell context. Given the central role of Notch in T-cell acute lymphoblastic leukemia oncogenesis, these data pave the way towards development of novel therapeutic strategies that target hyperactive Notch1 signaling in human T-cell acute lymphoblastic leukemia.

overall_design: Gene expression was measured in sorted T-cell subsets of 4 healthy donors.

first: Kaat

last: Durinck

first: Inge

last: Van de Walle

first: Wouter

last: Van Loocke

first: Pieter-Jan

last: Volders

first: Pieter

last: Mestdagh

first: Jo

last: Vandesompele

first: Tom

last: Taghon

first: Frank

last: Speleman


title: Development of gene expression signatures with lncRNAs for GSI treatment of T-ALL cell lines

overall_design: Gene expression was measured in 4 different T-ALL cell lines (HPB-ALL, DND-41, TALL-1 and ALL-SIL) after treatment with GSI or DMSO (solvent control). Cells were collected 12h and 48h after treatment.

first: Suzanne

last: Vanhauwaert


title: Differential expression of mRNA encoding cytokines and chemokines in the reproductive tract after infection of mice with Chlamydia trachomatis

status: Public on Oct 18 2014

first: Phillip

last: Bridges

summary: Chlamydia trachomatis is an obligate intracellular pathogen and the most frequently reported sexually transmitted bacteria in the United States.  Infection with Chlamydia trachomatis targets epithelial cells within the genital tract which respond by secreting chemokines and cytokines.  Persistent inflammation can lead to fibrosis, tubal infertility and/or ectopic pregnancy.  Our objective was to determine the inflammatory mediators involved in clearance of low-grade infection and the potential involvement in chronic inflammation.  Our hypothesis was that mRNA encoding pro-inflammatory cytokines and chemokines will be differentially expressed in the female reproductive tract of mice infected with C. trachomatis at both 28 and 35 days post-infection compared to controls.  Superarray analysis was performed using RT2 Profiler PCR arrays for mouse Cytokines and Chemokines (Qiagen).

overall_design: Six to eight week old female C3H/HeJ mice (Jackson Laboratories, Sacramento, CA) were pretreated with 2.5 mg medroxyprogesterone acetate (SICOR Pharmaceuticals) on Days -10 and -3 before infection.  On Day 0, mice were infected via vaginal challenge with 0 or 5 x 102 inclusion-forming units (IFUs) of C. trachomatis, serovar D in 0.01 mL of Eagle Minimal essential media (MEM, Gibco).  Mice were killed on day 28 (n = 3 for control and infected) in experiment 1 and day 35 (n = 3 for control and infected) in experiment 2.  Vaginal tissue, uterine horns and the oviducts were collected and processed for superarray analysis.

first: Katheryn

last: Cerny

first: Maranda

last: Van Fleet

first: Anatoly

last: Slepenkin

first: Ellena


title: Development of gene expression signatures with lncRNAs for GSI treatment of the CUTLL1 cell line.

overall_design: Gene expression was measured in the CUTLL1 T-ALL cell line after treatment with GSI or DMSO (solvent control). Cells were collected 12h and 48h after treatment. This was performed for 3 replicates.


title: Neonatal testis transcriptome profiles differ among calves born to cows supplemented with different forms of dietary selenium throughout gestation

status: Public on Oct 16 2014

summary: In many parts of the US, selenium (Se)-deficient soils dictate the necessity of supplementing this trace mineral directly to the diet of cattle, with the form of Se supplied known to affect tissue-level gene expression profiles and presumably function. Because a deficiency of Se will reduce fertility, including reduced biosynthesis of testosterone by the testis and an increased frequency of abnormalities in mature spermatozoa, we hypothesized that the form of Se supplemented to cows during gestation would affect the transcriptome of the neonatal bull calf testis.  Microarray analysis using the Bovine gene 1.0 ST array (GeneChip; Affymetrix, Inc., Santa Clara, CA) was conducted to determine whether gestational form of supplemental Se affected gene expression profiles in the testis. GeneChip transcript annotations were last updated in January 2013 using the annotation update release 33 from the NetAffx annotation database.

overall_design: Twenty-four Angus cross cows were assigned randomly (n=8) to individual ad libitum intake of a common vitamin-mineral mix that contained 35 ppm of Se supplied as either inorganic (ISe, sodium selenite; Prince Se Concentrate, Prince Agri Products, Inc., Quincy, IL), organic (OSe, Sel-Plex; Alltech Inc., Nicholasville, KY), or a 50/50 mix of ISe/OSe (Mix) Se for 4 months prior to breeding and throughout gestation.   Cows were managed under a fall-calving, forage-based, cow-calf production regimen at the University of Kentucky Princeton Research and Education Center.  Testis tissue (ISe n=5; OSe n=4; Mix n=4) was collected within 2 days of birth, and RNA extracted for microarray analysis.

first: K

first: W

last: Burris

first: J

last: Matthews

first: P


title: Development of gene expression signatures with lncRNAs for coculture of CD34+ T-cells with an OP9-DLL1 feeder layer

first: Annelynn

overall_design: CD34+ cells of 4 healthy donors are cultured on a OP9-GFP or OP9-DLL1 feeder layer.

first: Kaat

first: Inge


title: The phenylpropanoid pathway is controlled at different branches by a set of R2R3 MYB C2 repressors in grapevine

status: Public on Sep 30 2014

city: Verona

first: Erika

last: Cavallini

address: Strada Le Grazie, 15

country: Italy

institute: University of Verona

summary: A set of grapevine R2R3 MYB repressors negatively regulate the expression of genes involved in different branches of the phenylpropanoid pathway

overall_design: For the genetic transformation of Vitis vinifera cv Maccabeu, the in vitro plantlets were grown for 90 days under light and temperature controlled. For overexpression of VvMYBC2-L3 in Vitis vinifera cv Maccabeu hairy roots, the cDNA sequence was transferred into the binary vector pH2GW7 by site-specific recombination. The construct was then inserted into Agrobacterium tumefaciens A4 by electroporation and used for the grapevine transformation. The induction and culture of transgenic HRs in grapevine were performed as described by Torregrosa and Bouquet (1997), with modifications reported in Cutanda-Perez et al. (2009).

first: Josè

middle: T

last: Matus

first: Laura

last: Finezzo

first: Sara

last: Zenoni

first: Rodrigo

last: Loyola

first: Flavia

last: Guzzo

first: Agnès

last: Ageorges

first: Patricio

last: Arce-Johnson

first: Giovanni

middle: B

last: Tornielli


title: Transcriptome analyses of grape berry skin induced by UV irradiation.

status: Public on Dec 01 2014

city: Nagoya

first: Mami

last: Suzuki

state: Aichi

address: Chikusa hurocho

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

summary: We conducted transcript profiling and metabolome profiling induced by UV irradiation in grape berry skin. Transcriptome analysis was carried out with genome-wide microarray and two hundred thirty eight genes were more than 5-fold up-regulated by UV irradiation. The enrichment analysis showed GO terms including stilbene synthase (STS) gene. Moreover, the principal component analysis (PCA) of metabolome analysis showed a compound, identified resveratrol, accumulated in grape berry skin specifically. Our result clearly shows that UV irradiation induced only accumulation of resveratrol and its analogues but did not induce accumulation of the other phenolic compounds.

overall_design: Examination of transcriptome profile in Vitis vinifera cv Pinot noir berry skin induced by UV irradiation. 2 samples examined: Control (=dark 1h), UV treated 1h. Each data point was performed three different biological replicates for treatment.

first: Katsuhiro

last: Shiratake


title: Contrast of poly-ribosomal mRNA in germina vesicle (GV) and metaphase II (MII) bovine oocytes.

status: Public on Sep 09 2014

city: Quebec

first: Eric

last: Fournier

state: Quebec

address: 2325 Rue de l'Universite

department: Departement des sciences animales

country: Canada

institute: Universite Laval

summary: Poly-ribosomal mRNA from pools of 75 bovine oocytes at the germinal vesicle(GV) and metaphase II(MII) stages were isolated by sucrose fractionation then compared through microarray hybridization.

overall_design:
3 biological replicates from germinal vesicle(GV) and metaphase II(MII) bovine oocytes were hybridized against each other while alternating dyes. One additional technical replicate (dye-swap of one of the previous hybridizations) was added to balance dye usage.

The normalized log2 ratio (GV/MII) data is provided in the 'normalized_data.txt' file. Please note that data were scanned/extracted using a different Agilent reference file, and thus the feature extraction number for a given probe (in both normalized and raw data files) is different from that in the official Agilent-041017 platform (GPL18537). The reference file used for this study is provided as a Series supplementary file (041017_D_DNAFront_BCBottom_20120517.txt).

last: Scantland

first: Irene

last: Tessaro

first: Carolina

last: Macabelli

first: Gaël

last: Cagnone

first: Angus

last: Macaulay

first: Alberto

last: Luciano

first: Claude

last: Robert


title: Lack of genetic heterogeneity at high-resolution aCGH between primary breast cancers and their paired lymph node metastases

status: Public on Aug 01 2014

first: Philip

last: Schouten

summary: Lymph-node (LN) metastases predict for high recurrence rates in breast cancer patients. Eradication of micro-metastatic tumor cells is the primary goal of adjuvant systemic treatment. Decisions regarding systemic treatment depend largely on primary tumor characteristics rather than on characteristics of their LN metastases. However, it remains unclear to what extent LN metastases, having already metastasized locally, resemble their primary breast tumors and as such will be eradicated by the systemic therapy chosen. In this study we investigated the genetic differences between primary breast cancers and their paired LN metastases using array comparative genomic hybridization analyses on a high resolution 720K Nimblegen platform. Thus far, no metastasis-specific genomic aberrations have been identified. We hypothesized that this is due to low-resolution platforms and lack of stratification on breast cancer subtypes (specifically, triple-negative (TN) versus luminal). Furthermore, we speculated that as TN tumours are known to be more genetically unstable, their LN metastases would show an increase in random copy number aberrations (CNAs). Therefore, we studied 10 primary TN breast tumour–LN pairs and 10 luminal pairs and found that all LN metastases clustered nearest to their matched tumour except for two. These two were explained by poor hybridization quality and, interestingly, the presence of two histological components in one tumour. We found no significantly altered CNAs between pairs in the whole group, nor when subdivided over subtypes; neither did we find a CNA increase in LN metastases compared to primary tumours within the TN subgroup, suggesting most CNAs are functional and not random. Our findings suggest a strong clonal relationship between primary breast tumours and its LN metastases and support the use of the primary tumor characteristics to guide adjuvant systemic chemotherapy in breast cancer patients, since primary tumors and their subsequent LN metastases seem remarkably similar, at least prior to treatment.

overall_design: The experiment contains 27 paired primary breast cancer samples with their lymph node metastases, analysed on a 135K whole genome CGH array

first: Marieke

last: Vollebergh

first: Chris

last: Klijn


title: Effect of solar ultraviolet radiation on grape berry skin transcriptome

city: Logrono

first: Pablo

last: Carbonell-Bejerano

address: Madre de Dios, 51

institute: CSIC

summary: UV radiation (UV) alters secondary metabolism in the skin of Vitis vinifera L. berries, which may affect on the final composition of both, grapes and wines. We compared berry skin transcriptome and phenolic composition between Tempranillo berries grown in the presence or absence of solar UV in a mid-altitude Tempranillo vineyard. By analysing two different ripening degrees, expression of 121 genes was significantly altered. Functional enrichment identified that, principally, secondary metabolism-related transcripts were induced by UV, including VvFLS1, VvGT5 and VvGT6 flavonol biosynthetic genes induction. Concurrently, flavonol accumulation was the most evident impact of UV on the berry skin phenolic composition. Monoterpenoid biosynthetic transcripts were also up-regulated by UV, whereas induction of stilbenoid biosynthetic transcripts and stilbenes accumulation was probably induced by the joint action of UV and other condition under the UV-blocking filter, likely higher temperature. Among regulatory genes, VvMYBF1, VvMYB24 and three bHLH transcription factors were up-regulated by UV. Homologs to Arabidopsis UVR8-dependent UV-B-induced genes were also induced, including VvHY5-1, VvHY5-2 and VvRUP UV-B signalling genes. This suggests that the UV-B-specific signalling pathway is activated in the skin of grapes grown at low-medium altitudes. The biosynthesis and accumulation of UV-absorbing compounds that are appreciated for winemaking were almost specifically triggered, which indicates that viticultural practices increasing solar UV incidence may improve grape features important to wine production.

overall_design: A total of 12 samples were hybridized. Grape skin RNA from berries ripening under a UV-transmitting filter (FUV+) and a UV-blocking filter (FUV-) was compared. Berry skin of two different ripening stages was analysed on each UV treatment. All samples were harvested simultaneously and a NaCl series was used to select the ripening degree in a non-invasive way. Three biological replicates were analyzed for each sample.

first: José

last: Martínez-Zapater


title: Development of gene expression signatures with lncRNAs for 15 T-ALL patients

first: Annelynn

last: Wallaert

overall_design: Gene expression was measured 15 patients diagnosed with T-ALL. 8 patients were NOTCH1 wild type, 7 patients were NOTCH1 mutant.

first: Kaat

last: Durinck

first: Wouter

last: Van Loocke

first: Pieter-Jan

last: Volders

first: Yves

last: Benoit

first: Nadine

last: Van Roy

first: Bruce

last: Poppe

first: Pieter

last: Mestdagh

first: Jo

last: Vandesompele

first: Frank

last: Speleman


title: Development of gene expression signatures with lncRNAs for 64 T-ALL patient samples

overall_design: Gene expression profiling of 64 T-ALL patient samples

first: Jean

last: Soulier


title: Ssn6, a new regulator of white-opaque switching in Candida albicans

status: Public on Jun 30 2014

city: San Francisco

first: Aaron

last: Hernday

state: Ca

institute: UC San Francisco

summary:
The human fungal pathogen Candida albicans can switch between two phenotypic cell types, termed “white” and “opaque.” Both cell types are heritable for many generations, and the switch between the two types occurs epigenetically, that is, without a change in the DNA sequence of the genome. In this work we describe that SSN6,  the C. albicans functional homolog of Saccharomyces cerevisiae Cyc8, is a regulator of the white-opaque switch.
Chromatin IP's were performed using the protocol described by Hernday et al (Methods Enzymol. 2010;470:737-58. ).  Briefly, log phase cultures were crosslinked with formaldehyde prior to cell lysis, chromatin shearing, and transcription-factor immunoprecipitation.  Recovered DNA was amplified, dye-coupled, and competitively hybridized to a 244k-probe tiling array with a non-enriched genomic DNA reference.

overall_design: Immunoprecipitated chromatin was hybridized against a non-enriched genomic DNA reference to identify transcription-factor binding sites