title: Identifying conserved and novel miRNAs in germinating seeds of Glycine max using deep sequencing

status: Public on May 25 2015

city: Porto Alegre

first: Rogerio

last: Margis

state: RS

address: Av. Bento Goncalves 9500

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development. In soybean (Glycine max), an important edible oil crop, valuable lipids are synthesized and stored in the cotyledons during embryogenesis .This storage lipids are used as energy source of the emerging seeds, during the germination procces. Until now, there are no microRNAs related to lipid metabolism in soybean or any other plant. This work aims to describe the miRNAome of germinating seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus germinating seeds. A total of 183 familes were detected through a computational analysis of a large number of reads obtained from deep sequencing from  two small RNA libraries of (i) pooled germintaing seeds stages and (ii) mature soybean seeds. We have found 39 new mirna precursors which produce 41 new mature forms. The present work also have identified isomiRNAs and mirnas offset (moRNAs). This work presents a comprehensive study of the miRNA transcriptome of soybean germinating seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in lipid consumption in development soybean seeds.

overall_design: MicroRNA profiles in 2 different seed libraries (mature seeds and a pool of germinating seed stages) of Glycine max by deep sequencing (Illumina GAII).

first: Guilherme

middle: L

last: de Morais

first: Rogério

middle: R


title: Genomic polymorphism is genotyped to determine the association between genotypes and treatment outcomes

status: Public on May 30 2015

city: Seoul

first: Hee-Jun

last: Kim

address: Heukseok-Ro, Dongjak-gu

country: South Korea

institute: Chung-Ang University Hospital

summary: The Illumina GoldenGate Genotyping Assay is a flexible, pre-optimized assay that uses a discriminatory DNA polymerase and ligase to interrogate 96 SNP loci simultaneously. This Assay utilizes the BeadArray Reader. Using this assay, we examined the distribution of the patients` genotypes to determine which genotype tends to have a better outcomes for cancer treatment.

overall_design: To investigate genomic polymorphism, we collected whole blood samples from breast cancer patients before the neoadjuvant chemotherapy. Genomic DNA was isolated from mononuclear cells and specific polymorphisms were analyzed by the GoldenGate assay was consisted of 96 custom selected SNPs within 34 genes. The labeled DNA were amplified and immobilized onto paramagnetic particles, and hybridized. BeadArray Reader was used to detect the data.

first: Seock-Ah

last: Im


title: Escherichia coli K-12: 0%, 10% and 30% hydrogen peroxide (H2O2) treatments, in wild type and luxS mutants

status: Public on May 19 2015

city: Singapore

first: Aram

last: Kang

state: Singapore

address: 62 Nanyang Drive

department: School of Chemical and Biomedical Engineering

country: Singapore

institute: Nanyang Technological University

summary: Transcripitonal profiling of Escherichia coli K-12 W3110 comparing wild type and luxS mutants without or with 10%, 30% H2O2 treatments, two biological replicates for each condition

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: two-variables experiments: samples without or with treatment of 10% or 30% H2O2 for 30min; wild type and luxS mutants

first: Hua

last: Ling

first: Matthew

middle: W

last: Chang


title: Differentially expressed gene profiles before and after the ethanol sclerotherapy in patients with ovarian endometriomas

status: Public on May 28 2015

city: Harbin

first: xiaoqiu

last: dong

address: Yiyuan Str 37, Harbin, Heilongjiang Province

department: Ultrasonography

country: China

institute: the Fourth Hospital of Harbin Medical University

summary: To detect the differentially expressed genes and subsequently identify disease-related signatures and potential biomarkers for patients with ovarian endometriomas in the serum before and 3 months after the ultrasound-guided ethanol sclerotherapy in patients with ovarian endometriomas. we have employed the KangChen Bio-technology Corp. NimbleGen Human Gene Expression Microarray 12x135K. Among these, six genes showed statistical significance including IL6, CD36, JUNB, B4GALT1, HES1, and NR4A1, which were also validated by qPCR analysis.

overall_design: The gene expression in human blood was measured before and 3 months after the ultrasound-guided ethanol sclerotherapy in the same patients with ovarian endometriomas.

first: Lu-Lu

last: Wang

first: Huai-Qiu

last: Cai

first: Xiao-Qiu

last: Dong

first: Li-Wei

last: Zhang

first: Shan-Shan

last: Jiang

first: Ning

last: Zhao

first: Xiao-Hui

last: Shao

first: Si-Ming

first: Li

last: Zhu

first: Tong


title: Agilent 244K aCGH data for 10 human gastric cancers

status: Public on May 29 2015

city: Suwon

first: Dongho

address: #300 Chunchun-dong, Jangan-Ku, Suwon, Kyungggi-do

department: Samsung Biomedical Research Institute

institute: Sungkyunkwan University School of Medicine

summary: Copy number alteration (CNA) is a good signpost to identify cancer related genes. CNAs were analyzed using the Agilent 244K array comparative genomic hybridization (aCGH) in fresh-frozen tumor and matched normal tissues from 10 gastric cancer patients.

overall_design: Whole genomic CNAs in 10  human gastric cancers were analyzed using the Agilent aCGH-244K arrays. Matched normal tissues were used as the reference.

first: Dong-Hao

last: Jin

first: Seong-Eun

last: Park

first: Jeeyun

last: Lee

first: Kyung-Mi

first: Sung

first: Duk-Hwan

first: Joobae


title: Agilent 400K aCGH data for 30 human gastric cancers

last: Kim

type: Genome variation profiling by genome tiling array

summary: Copy number alteration (CNA) is a good signpost to identify cancer related genes. CNAs were analyzed using the Agilent 400K array comparative genomic hybridization (aCGH) in fresh-frozen tumor and matched normal tissues from 30 gastric cancer patients.

overall_design: Whole genomic CNAs in 30 human gastric cancers were analyzed using the Agilent aCGH-400K arrays. Matched normal tissues were used as the reference.


title: Effect of oxidative stress on the association of long noncoding RNA and mRNA with ribosomes

first: Igor

middle: V

last: Kurochkin

address: 30 Biopolis street, #07-01 Matrix

institute: Bioinformatics Institute, A*STAR

summary: In this study we analysed the association of long noncoding RNAs (lncRNAs) and mRNAs with ribosomes in control and oxidatively stressed (2hr treatment with H2O2) MRC5 fibroblasts. A custom microarray was used to analyze the stress-induced distribution changes of transcripts between the non-translating (free RNP and 80S), low-translating (two, three and four ribosomes), and highly-translating (five and more ribosomes) pools in three experiments.  The finding suggests that stress-induced lncRNAs showed a higher polysome occupancy as compared to the transcripts of coding genes in response to oxidative stress.

overall_design: Samples from 23 polysome fractions were divided into 3 pools: untranslated (fractions 1-9,representing free RNPs and 80S ribosomes); low-translated (fractions 10-14, representing 2-4 ribosomes) and highly-translated (fractions 15-23 representing 5 and more ribosomes). The procedure was carried out three times, each with an independent RNA preparation and each analyzed with 3 microarrays, both in control and OS condition (2 hours) together with whole-cell RNA for each condition.

first: Aliaksandr

middle: A

last: Yarmishyn

first: Candida

last: Vaz

first: Antonis

last: Giannakakis

first: Leah

last: Vardy

first: Vladimir

last: Kuznetsov

first: Ernesto

last: Guccione


title: Evaluating microRNA profiles reveals discriminative responses following genotoxic or non-genotoxic carcinogen exposure in primary mouse hepatocytes [Exiqon]

status: Public on May 18 2015

city: Maastricht

first: Linda

last: Rieswijk

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

summary: The study investigated differential miRNA changes in primary mouse hepatocyte following 24 and 48 hours of exposure to aflatoxin B1, cisplatin, benzo(a)pyrene,  2,3,7,8-tetrachloordibenzo-p-dioxine, cyclosporin A or Wy-14,643 or their responsive solvent. Three (four for Wy-14,643) biological replicates per compound/solvent.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In total 60 arrays

first: L


title: Differential in vivo tumorigenicity of distinct subpopulations from a luminal-like breast cancer model (SNP)

status: Public on May 26 2015

city: Oslo

first: Nirma

last: Skrbo

address: Ullernchauseen 70

department: Dep of Genetics

country: Norway

institute: Oslo University Hospital

summary: The cellular heterogeneity of one patient derived orthotopic breast cancer xenograft model PDX was investigated using flow cytometry, combined with assessment of in vivo tumorigenicity and SNP genotyping array for copy number analysis. Epithelial cell adhesion molecule (EpCAM) was revealed as a highly specific cell surface marker of the human tumor cell population in both xenografts.  Based on expression patterns observed in primary tumor tissue, SSEA-4 and CD24 were chosen as markers to further subdivide the luminal tumor cells into four subpopulations. FACS sorting was used to isolate four cell subpopulations.  Results: In vivo tumorigenicity assay showed that SSEA-4+/CD24+ cells were non-tumorigenic, while the three other subpopulations were tumorigenic. Tumors resulting from the SSEA-4+/CD24- subpopulation of luminal cancer cells, did not express CD24, while tumors arising from the SSEA-4-/CD24-, and SSEA-4-/CD24+ populations both recapitulated the original tumor containing all four subpopulations. Copy number analysis comparing the four subpopulations between eachother, did reveal high similarity. Although there were some minor differencies between the subpopulations, no differences in genome aberrations could explain their difference in tumorigenicity.  Discussion: Our results imply that subpopulations from one primary tumor can give rise to dissimilar daughter tumors. These tumors may not necessarily respond to the same targeted treatment, and thereby represent a therapy escape mechanism. This study highlights that to remove the risk of breast cancer recurrence, inhibition of the molecules critical for driving the tumor progression in several tumor cell subpopulations might be essential

overall_design: Four subpopulations were analysed using Infinium HumanOmniExpressExome BeadChip array. Replicates are not included, the HumanOmniExpressExome-8v1-2_A.egt  file was used as a reference.

first: Geir-Olav

last: Hjortland

first: Alexandr

last: Kristian

first: Ruth

last: Holm

first: Silje

last: Nord

first: Lina

last: Prasmickaite

first: Olav

last: Engebråten

first: Therese

last: Sørlie

first: Gunhild

middle: M

last: Mælandsmo

first: Kristin

last: Andersen


title: Evaluating microRNA profiles reveals discriminative responses following genotoxic or non-genotoxic carcinogen exposure in primary mouse hepatocytes [Affymetrix]

summary: The study investigated differential gene expression in primary mouse hepatocyte mRNA following 24 and 48 hours of exposure to aflatoxin B1, cisplatin, benzo(a)pyrene,  2,3,7,8-tetrachloordibenzo-p-dioxine, cyclosporin A or Wy-14,643 or their responsive solvent. Three (four for Wy-14,643) biological replicates per compound/solvent.


title: DK010: FOXO target gene CTDSP2 inhibits cell cycle progression through regulation of p21-Cip1/Waf1

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

summary: Activity of Forkhead box O (FOXO) transcription factors is inhibited by PI3K-PKB/Akt signalling to control a variety of cellular processes including cell cycle progression. Through comparative analysis of a number of microarray datasets, we identified a set of genes commonly regulated by FOXO and PI3K/PKB, which includes Carboxyl-Terminal Domain Small Phosphatase 2 (CTDSP2). We validated CTDSP2 as a genuine FOXO target gene and show that ectopic CTDSP2 can induce cell cycle arrest. We analysed transcriptional regulation after CTDSP2 expression and identified extensive regulation of genes involved in cell cycle progression, which depends on the phosphatase activity of CTDSP2. Most notably regulated genes are p21Cip1/Waf1 and E2F1, both implicated in S-phase entry. We show that p21Cip1/Waf1 is regulated by CTDSP2 in a p53-independent manner and that p21Cip1/Waf1 upregulation results in decreased cyclin/CDK2 and cyclin/CDK6 activity. Thus, we identify FOXO-dependent CTDSP2 regulation as a novel regulatory mechanism for inhibiting proliferation in the absence of growth factor/PI3K signalling.

overall_design: U2OS cells stably expressing tetracycline-activatable CTDSP2 or CTDSP2(dead) were compared to parental cells in a common reference design on dual-channel Human V2 GE microarrays (Agilent). 48 hrs after doxycycline treatment, RNA samples were isolated. 4 biological replicates per sample group, as common reference U2OS untreated cells were used. Dye-swaps were done on half of the samples. As a control, untransfected U2OS cells were treated with doxycycline.

first: David

middle: E

last: Kloet

first: Paulien

last: Polderman

first: Astrid

last: Eijkelenboom

first: Lydia

last: Smits

first: Miranda

middle: H

last: van Triest

first: Maaike

middle: C

last: van den Berg

middle: J

first: Dik

last: van Leenen

first: Philip

last: Lijnzaad

first: Frank

last: Holstege

first: Boudewijn

last: Burgering


title: LncRNA expression analysis of Clostridium butyricum-induced cell apoptosis in colon cancer SW480 cells

city: Chongqing

first: Xiaorong

last: Yang

address: 1#, Yuzhong Road

institute: Chongqing Medical University

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

summary: To compare lncRNAs and mRNAs expression profiles in colon cancer after co-cultured with CB  and without CB, we extracted total RNA of colon cancer cell line(SW480) after co-cultured with CB(SW480/CB) and paired control without CB(SW480/ctr), and identified the dysregulated lncRNAs and mRNAs using Agilent Human lncRNAs/mRNAs microarrays.

overall_design: Totally, this study includes 2 samples. 1 samples is CB treatment group and another 1 sample is control group.

first: Liuyang

last: Zhao


title: Expression profiling of long non-coding and coding gene expression of gastric cancer cell lines

city: Luoyang

first: Ying

last: Wang

address: 24 Jinghua Road

institute: the First Affiliated Hospital of Henan University of Science and Technology

summary: The high throghput lncRNA and mRNA microarray data showed a total of 27,883 lncRNAs and 19,644 mRNAs expressed in gastric cancer cell line, SGC7901 and two multidrug-resistance sublines, SGC7901/ADR and SGC7901/VCR

overall_design:
Expression profiling of long non-coding and coding gene expression of gastric cancer cell line, SGC7901 and two multidrug-resistance subllines of SGC7901, SGC7901/VCR and SGC7901/ADR
GC cell line, SGC7901, and two MDR sublines, SGC7901/VCR and SGC7901/ADR were subjected to an lncRNA microarray analysis. Bioinformatics and verification experiments were performed to investigate the potential lncRNAs involved in the development of MDR.

first: Daiming

last: Fan


title: Expression profiling of EvgSc and ompR mutants

status: Public on May 20 2015

city: Liverpool

first: Kim

last: Clarke

address: Crown Street

country: United Kingdom

institute: University of Liverpool

summary: In order to explore the transcriptional reprogramming in EvgSc, ompR and EvgSc/ompR mutants we have used whole genome microarray profiling.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: EvgSc, ompR and EvgSc/ompR mutants were developed. Each mutant was profiled in duplicate.

first: Pete

last: Lund


title: Meg3 regulated genes in pancreatic beta cells

status: Public on May 21 2015

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

country: USA

institute: NIDDK/NIH

summary: Meg3 is a long non-coding RNA. It's target genes are unknown. The mouse pancreatic beta cell line MIN6-4N was used to assess the expression of genes upon stable Meg3 overexpression

overall_design: Stable cell lines were isolated that have integated pcDNA3.1 or pcDNA3.1-mMeg3.The cells were processed for RNA isolation.  The level of Meg3 expression  was assessed by RT-PCR. RNA preps  were used for microarray analysis.

first: Sita

middle: D

last: Modali

first: Sunita

middle: K

last: Agarwal


title: Myelodysplastic syndrome marrow stroma shows widespread aberrant hypermethylation that is abrogated by treatment with DNMT inhibitors

city: Bronx

first: Yiting

last: Yu

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

type: Methylation profiling by genome tiling array

summary: The marrow microenvironment contributes to the pathogenesis of ineffective hematopoiesis in Myelodysplastic Syndromes (MDS). Since mutations and cytogenetic alterations are generally not present in marrow stromal cells, we hypothesized that epigenetic alterations may be responsible for altered stroma functionin MDS. Global DNA methylation of MDS marrow-derived stroma was analyzed by HELP assay and compared to healthy controls. MDS stroma showed aberrant hypermethylation that preferentially occurred outside of CpG islands and involved important signaling pathways.Comparison with stroma derived from 5-Azacytidine (5-Aza) treated MDS patients revealed abrogation of aberrant methylation in treated samples. Integrative expression analysis revealed that the WNT pathway was epigenetically dysregulated in MDS stroma, and the WNT antagonists FRZB and SFRP1 were aberrantly hypermethylated and underexpressed. These epigenetic changes were validated ina co-culture model of stroma and leukemic cells and in an independent set of MDS samples. Importantly, 5-Aza treatment of MDS stroma enhanced hematopoietic activity and erythroid differentiationfrom co-cultured healthy CD34+ cells. These results reveal widespread aberrant epigenetic changes in the MDS marrow microenvironment and demonstrate that DNA methyl transferase inhibitors alter the epigenomic profiles of stromal cells, potentiallycontributing to theirtherapeutic efficacy.

overall_design: The study population consisted of 6 MDS patients and 3 healthy controls. Individual HpaII restriction digest profiles were compared to an internal MspI digest control, to yield differentially methylated fragments for every sample.

first: T

last: Bhagat

first: A

last: Verma


title: DK003: FOXO target gene CTDSP2 inhibits cell cycle progression through regulation of p21-Cip1/Waf1

first: Marian

last: Groot Koerkamp

overall_design: DL23 cells, containing FoxO3.A3-ER, stimulated with 4OHT for 8 hrs were compared to unstimulated cells in a direct comparison on dual-channel spotted expression microarrays. 4 biological replicates each were used. RNA samples were isolated and dye-swaps were done on half of the samples.

first: David

last: Kloet

first: Paulien

last: Polderman

first: Astrid

last: Eijkelenboom

first: Lydia

last: Smits

first: Miranda

last: van Triest

first: Maaike

last: van den Berg


title: Genome-wide Definition of Promoter and Enhancer Usage During Neural Induction of Human Embryonic Stem Cells [gene expression profile]

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: Genome-wide mapping of transcriptional regulatory elements are essential tools for the understanding of the molecular events orchestrating self-renewal, commitment and differentiation of stem cells. We combined high-throughput identification of nascent, Pol-II-transcribed RNAs by Cap Analysis of Gene Expression (CAGE-Seq) with genome-wide profiling of histones modifications by chromatin immunoprecipitation (ChIP-seq) to map active promoters and enhancers in a model of human neural commitment, represented by embryonic stem cells (ESCs) induced to differentiate into self-renewing neuroepithelial-like stem cells (NESC). We integrated CAGE-seq, ChIP-seq and gene expression profiles to discover shared or cell-specific regulatory elements, transcription start sites and transcripts associated to the transition from pluripotent to neural-restricted stem cell. Our analysis showed that >90% of the promoters are in common between the two cell types, while approximately half of the enhancers are cell-specific and account for most of the epigenetic changes occurring during neural induction, and most likely for the modulation of the promoters to generate cell-specific gene expression programs. Interestingly, the majority of the promoters activated or up-regulated during neural induction have a “bivalent” histone modification signature in ESCs, suggesting that developmentally-regulated promoters are already poised for transcription in ESCs, which are apparently pre-committed to neuroectodermal differentiation. Overall, our study provide a collection of differentially used enhancers, promoters, transcription starts sites, protein-coding and non-coding RNAs in human ESCs and ESC-derived NESCs, and a broad, genome-wide description of promoter and enhancer usage and gene expression programs occurring in the transition from a pluripotent to a neural-restricted cell fate.

overall_design: ESCs (H9 NIH code WA09, ISL1 Ds-Red) were kindly provided by the group of K.R. Chien. Neural differentiation was induced by the method of embryoid bodies following a published protocol [1]. Briefly, 4-days embryoid bodies were transferred to polyornithine-coated dishes and propagated in N2-supplemented DMEM/F12 (Invitrogen). Total RNA was extracted from 1-2x10^6 cells from three different cultures of ESCs and NESCs, transcribed into biotinylatedcRNA and hybridized onto GeneChip® HG-U133 Plus 2.0 Arrays (Affymetrix)  according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA).

first: Valentina

last: Poletti

first: Alessia

last: Carri

first: Guidantonio

last: Tagliazucchi

first: Luca

last: Petiti

first: Emilia

last: Mazza

first: Clelia

last: Peano

first: Gianluca

last: De Bellis

first: Annarita

last: Miccio

first: Elena

last: Cattaneo

first: Fulvio

last: Mavilio


title: Exosomal natural antisense transcripts released from colorectal cancer SW480 cells into culture supernatants

city: Hirosaki

first: Mitsuru

last: Chiba

state: Aomori

address: 66-1 Hon-cho

department: Graduate School of Health Sciences

country: Japan

institute: Hirosaki University

summary: In the present study, natural antisense transcripts (NATs), transcribed from reverse strand deoxynucleic acids (DNAs) of genes, into exosomes released from colorectal cancer SW480 cells were searched using an sense/antisense-custom microarray.

overall_design: SW480 cells were cultured with serum-free RPMI1640 for 48 h. Then, culture media were collected, centrifugated, and filtrated using 0.22-um filters. Exosomes from culture media were collected by ultracentrifugation.


title: Transcriptional effect of the luteinizing hormone surge in bovine granulosa cells during the peri-ovulation period

status: Public on May 27 2015

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

summary: Granulosa cells from three different stages were used to assess the short- and long-term effects of luteinizing hormone (LH) on follicle differentiation: 1) 2 h before induction of the LH surge, 2) 6 h and 3) 22 h after the LH surge.

overall_design: Three time points experiment: 2h pre-LH, 6h post-LH and 22h post-LH. Granulosa cells from the 6h post-LH and 22h post-LH were compared to the 2h pre-LH. Biological replicates: 4 from each time point. One replicate per array. Dye-swaps were performed.

first: Isabelle

last: Gilbert

first: Marc


title: AS001: FOXO target gene CTDSP2 inhibits cell cycle progression through regulation of p21-Cip1/Waf1

first: Marian

last: Groot Koerkamp

overall_design: HEK293T cells were transiently transfected with expression vector for FOXO4 and compared with Empty vector-transfected controls after 48 hrs. 4 biological replicates each, refpool= HEK293T untreated. RNA samples were isolated and put on dual-channel spotted microarrays. Dye-swaps were done on half of the samples.

first: David

last: Kloet

first: Paulien

last: Polderman

first: Astrid

last: Eijkelenboom

first: Lydia

last: Smits

first: Miranda

first: Dik

last: van Leenen

first: Philip

last: Lijnzaad

first: Frank

last: Holstege

first: Boudewijn

last: Burgering


title: Identification of genes differentially expressed in lung cancer cells after the transfection of miR-221 or miR-222.

status: Public on May 22 2015

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: To evaluate involvement of miR-221 and miR-222 in lung cancer, we investigated the effects of miR-221 and miR-222 overexpression on six lung cancer cell lines as well as one immortalized normal human bronchial epithelial cell line.

overall_design: Two cell lines, H3255 and H1299 with no replicates were studied.  Cells were transfected with miR-221, miR-222, or miR control.  Microarray analysis was done to identify genes differentially expressed in lung cancer cells after the transfection of miR-221 or miR-222.

first: Ryo

last: Yamashita

first: Mitsuo

last: Sato


title: DK009: FOXO target gene CTDSP2 inhibits cell cycle progression through regulation of p21-Cip1/Waf1

overall_design: DL23 cells, containing FoxO3.A3-ER, stimulated with 4OHT for 24hrs were compared to unstimulated cells in a common reference design on dual-channel spotted expression microarrays. 4 biological replicates each were used. RNA samples were isolated and dye-swaps were done on half of the samples. As refpool, DLD1 parental cell line was used.

last: van Triest

first: Maaike

last: van den Berg


title: ΔMAT1-1-1 (Pc20g07800) vs. P2niaD18 (wild type)

city: Bochum

first: Kordula

last: Becker

address: Universitätsstr 150

country: Germany

institute: Ruhr-Universität Bochum

summary: Identification of differentially expressed genes in a deletion strain of α-domain mating-type transcription factor MAT1-1-1 compared to wild type P2niaD18

overall_design: Analysis of total RNA from P. chrysogenum strains grown for 36, 60, and 96 h on solid M322 medium under light conditions at 27°C

first: Wolfers

last: Simon


title: Gene expression signatures of rice floral organs before and after pollination under heat and combined drought and heat stress

status: Public on May 31 2015

city: Potsdam

first: Xia

last: Li

address: Am Mühlenberg 1

institute: Max-Planck-Institute of Molecular Plant Physiology

summary:
Floral organs are extremely sensitive to stress during anthesis and lead to severe yield loss. Rice anthers and pollinated pistils of two cultivars with contrasting tolerance to heat and drought stress under variable conditions, including control, heat, combined heat and drought stress, were used to explore gene expression pattern in male and female reproductive organs during anthesis under control and stress conditions. More gene regulation was induced by combined drought and heat stress than heat in anthers of both cultivars. N22 showed less regulation under combined stress than Moroberekan. The overlap of regulated genes between two cultivars was rather low, indicated the distinct molecular stress responses.
We used whole genome microarrays to explore gene expression pattern and molecular mechanisms in male and female reproductive organs during anthesis under control and stress conditions in two rice cultivars, sought to identify the key transcripts that play roles in inducing heat and drought tolerance during reproduction in rice.

overall_design: Rice anthers and pollinated pistils from two cultivars N22 and Moroberekan at different conditions were collected for RNA extraction and hybridization on Affymetrix rice microarrays. We tried to explore temporal transcriptome changes and molecular mechanisms in male and female reproductive organs during anthesis under control, heat, or combined drought and heat stress in two contrasting rice cultivars.

first: Lovely

last: Lawas

first: Richard

last: Malo

first: Ulrike

last: Glaubitz

first: Ellen

last: Zuther

first: Alexander

last: Erban

first: Ramil

last: Mauleon

first: Sigrid

last: Heuer

first: Joachim

last: Kopka

first: Dirk

last: Hincha

first: Krishna

middle: S

last: Jagadish


title: Hemin and Iron transcriptome of Porphyromonas gingivalis

city: Richmond

first: Janina

middle: P

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

institute: Virginia Commonwealth University

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

overall_design: Refer to individual Series


title: Generation of murine stem cells by small molecule

city: beijing

first: chun

last: liu

state: beijing

address: beijing

institute: Peking University

summary: Transcriptional profiling of stem cells and parental cells

overall_design: Two samples were analyzed: PEG cells and parental cells. Each sample have three replicates.

first: Pingping

last: Hou

first: Yanqin

first: Xu

last: Zhang

first: Chun

last: Liu

first: Jingyang

last: Guan

first: Honggang

first: Yang

last: Zhao

first: Hongkui

last: Deng


title: Evaluating mRNA and microRNA profiles reveals discriminative and compound-specific responses following genotoxic or non-genotoxic carcinogen exposure in primary mouse hepatocytes

first: Linda

last: Rieswijk


title: FOXO target gene CTDSP2 inhibits cell cycle progression through regulation of p21-Cip1/Waf1

first: Marian

last: Groot Koerkamp


title: Hemin and iron transcriptome of Porphyromonas gingivalis (part 1)

summary: Transcriptional profiling of P. gingivalis cells comparing cells grown under hemin replete conditions to that grown under hemin depleted conditions

overall_design: Two-condition experiment, hemin replete vs. hemin deplete grown cells. Biological replicates: 3 independently grown and harvested bacterial cells. Four technical replicates (four replicates per array).


title: The molecular phenotype of endocapillary proliferation in IgA nephropathy and potential modulation by bioactive small molecules

city: Ann Arbor

first: Celine

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

summary: Endocapillary proliferation is associated with higher risk of progressive disease in IgAN. To better understand molecular pathways involved in the development of endocapillary proliferation and to identify novel specific therapeutic targets, we evaluated the glomerular transcriptome of microdissected kidney biopsies from 22 patients with IgAN.  Endocapillary proliferation was defined according to the Oxford scoring system by 3 nephropathologists.  We analyzed mRNA expression using microarrays and identified transcripts differentially expressed in patients with endocapillary proliferation.   Next, we employed both transcription factor analysis and in silico drug screening and confirmed that the endocapillary proliferation transcriptome is significantly enriched with pathways modulated by corticosteroid exposure.  With this approach we also identified novel therapeutic targets and bioactive small molecules that may be considered for therapeutic trials for treatment of IgAN.

overall_design: RNA from glomerular compartment was extracted and processed for hybridization on Affymetrix microarrays.

first: Jeff

last: Hodgin

first: Rohan

last: John

first: Elisabeth

last: Grone

first: Stefan

last: Porubsky

first: Hermann-Josef

first: Matthias

last: Kretzler

first: Heather

middle: N

last: Reich


title: Transcriptomic effects of the expression in Arabidopsis of a TCP15-EAR fusion controlled by its own promoter (two-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: 2 wild type replicates, 2 P15::TCP15-EAR replicates.

first: Daniel

last: Gonzalez

first: Nora

last: Uberti-Manassero

first: Agustín

first: Leandro

last: Lucero


title: miRNA expression studies in uveal melanoma (South Asian-Indian population).

status: Public on May 14 2015

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: To predict differentially expressed miRNAs between monosomy 3 and disomy 3, and to associate these miRNAs with the clinico-pathological parameters in South Asian Indian population with uveal melanoma (UM). The study consists of six uveal melanoma primary tumour tissues of South Asian-Indian population. These six tumours have been screened for chromosome 3 aberration using Chromogenic in-situ hybridisation (CISH). Thus, sample under the study includes, three each of monosomy 3 and disomy 3. The miRNA profiling was carried out from the tumor sections of formalin-fixed paraffin embedded eyeball samples. miRNA expression profile was obtained in monosomy 3 and disomy 3  samples, analysed by unsupervised analysis (Principal Component Analysis) and supervised analysis (Significance analysis of microarray). The select up-regulated and candidate miRNAs associated with monosomy 3 uveal melanoma tumors were validated further with qRT-PCR (n=86). Thus, this study indicates the role of miRNAs in UM tumor progression and their implication in predetermining the liver metastasis.

overall_design:
The study consists of six uveal melanoma  primary tumour tissues of South Asian-Indian population. These six tumours have been screened for chromosome 3 abberation using chromogenic in-situ hybridisation (CISH). Thus, samples under the study includes three each of  monosomy 3 and disomy 3. The miRNA profiling were carried out from the tumor sections of  formalin-fixed paraffin embedded eyeball samples. The up-regulated miRNAs associated with monosomy 3 uveal melanoma tumors were short listed and the candidate miRNAs were validated further with qRT-PCR.
Agilent one-color experiment, Organism: Homo sapiens, Agilent Human miRNA 8x15k Arrays AMADID: 021827 [Agilent miRNA labeling reagent and Hybridization Kit Cat # 5190-0408]

first: Nalini

last: Venkatesan

first: Subramanian

last: Krishnakumar

first: Vikas

last: Khetan

first: Perinkulam

last: Deepa


title: ZNF217 is an oncogene that promotes a basal phenotype and expansion of a progenitor cell population during breast cancer progression

city: San Francisco

first: Laurie

last: Littlepage

state: CA

address: 513 Parnassus Avenue, Box 0452

department: Anatomy

institute: University of California, San Francisco

summary: Amplification of 20q13 occurs in 20-30% of primary human breast cancers and correlates with poor prognosis. The transcription factor ZNF217 is a candidate oncogene in 20q13. Patients with breast tumors expressing high ZNF217 had reduced survival and increased resistance to chemotherapy. Inducible Znf217 expression in the mammary epithelium of our transgenic mouse resulted in premalignant and invasive lesions. Znf217 overexpression in a mouse luminal breast cancer model generated primary tumors with heterogeneous epithelial and progenitor cell marker expression and promoted metastasis. The AKT inhibitor triciribine inhibited growth and restored sensitivity to a cytotoxic drug in cells expressing high ZNF217. Triciribine reduced tumor burden in vivo, suggesting that ZNF217 may be a novel drug target.

overall_design: Total RNA was isolated from samples overexpressing ZNF217 (4 NMuMG). RNA was also harvested from each cell line expressing a vector control to use as a reference for each microarray sample analyzed. Total RNA was hybridized to mouse MEEBO arrays as described (http://www.microarray.org/sfgf/meebo.do). Samples were verified to have strong overexpression of ZNF217 by qRT-PCR or Western analysis.

first: Adam

last: Adler


title: Transcriptomic effects of the expression in Arabidopsis of a TCP15-EAR fusion controlled by its own promoter


title: Gene expression profiles of nasopharyngeal carcinoma cell line HNE2 following TP53 overexpression

city: Changsha

first: Wei

last: Xiong

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

summary: Recent studies have revealed that long non-coding RNAs (lncRNAs) participate in all steps of cancer initiation and progression by regulating protein coding genes at the epigenetic, transcriptional and post-transcriptional levels. LncRNAs are in turn regulated by other genes, forming a complex regulatory network. The regulation networks between the p53 tumor suppressor and lncRNAs in nasopharyngeal carcinoma (NPC) remain unclear. The aim of this study was to investigate the regulatory roles of the TP53 gene in regulating lncRNA and mRNA expression profiles in NPC cell line HNE2.

overall_design: p53 induced gene expression in human nasopharyngeal carcinoma cell line HNE2 was measured at 0, 12, 24 and 48 hours after transfected by pCMV-p53 plasmid.

first: Zhaoyang

last: Zeng

first: Zhaojian

last: Gong

first: Shanshan

last: Zhang

first: Fang

first: Yong

first: Xiaoling

last: Li

first: Guiyuan


title: Identification of time-dependent biomarkers and effects of exposure to volatile organic compounds using high-throughput analysis (methylation)

status: Public on May 15 2015

city: Ansan

first: jiyoung

last: hong

address: Hanyang Univ.,55, Hanyangdaehak-ro, Sangrok-Gu

institute: hanyang university

summary: Methylation of DNA is one of the common epigenetic signaling tools that cells use to lock the expression of various genes. In this study, we examined the effects of VOCs exposure in humans on methylation using microarray analysis. We recruited participants who had short-term exposure, long-term exposure, or no exposure. We then analyzed changes in methylation in blood samples from these participants. We found that 1178 genes were hypermethylated and 402 genes were hypomethylated compared with the control group in time-dependent manner. Further research is required to determine the time-dependent effects of VOCs on epigenetic regulation of gene expression.

overall_design: Methylation of DNA in human blood samples (IRB #AS 14039) divided into three groups: control (unexposed workers; n = 12), short-term exposure (workers exposed to VOCs for less than 10 years; n = 12), and long-term exposure (workers exposed to VOCs for more than 10 years; n = 12) was experimented by methylation microarray analysis after exposure to VOCs

first: Ji-Young

last: Hong

first: So-Yeon

last: Yu

first: Gi-Won

last: Kim

first: Jeong-Jin

last: Ahn

first: Youngjoo

first: Seri

last: Lim

first: Sang-Wook

last: Son

first: Seung-Yong

last: Hwang


title: Towards understanding the biological function of the unusual chaperonin GroEL1 of Mycobacterium tuberculosis

city: RENTON

first: Tige

last: Rustad

state: WASHINGTON

address: 1700 DAYTON AVE NE

institute: Seattle BioMed

type: Expression profiling by genome tiling array

summary:
Expression data from wild type (H37Rv) and GroEL1(H37RvΔgroEL1::Hyg) mutant strains under a range of environmental stresses
The 60 kDa heat shock proteins, also known as GroELs are components of the essential protein folding machinery of the cell, but are also dominant antigens in many infectious diseases. Although generally essential for cellular survival, in some organisms such as Mycobacterium tuberculosis, one or more paralogous GroELs are known to be dispensable. In M. tuberculosis, groEL2 is essential for cell survival, but the biological role of the non-essential GroEL1 is still elusive. To understand the relevance of GroEL1 in M. tuberculosis physiology, detailed transcriptomic analyses for the wild type H37Rv and groEL1 knockout (groEL1 KO) were performed under in vitro stress conditions: stationary phase, cold shock, low aeration, mild cold shock and low pH. Additionally, the survival of the groEL1 KO was assessed in macrophages at multiplicity of infection (MOI) of 1:1 and 1:5. We observed that survival under low aeration was significantly compromised in the groEL1 KO. Further, the gene expression analyses under low aeration showed change in expression of several key virulence factors like two component system PhoP/R and MprA/B, sigma factors sigG, M and H and adversely affected known hypoxia response regulators Rv0081, Rv0023 and DosR.  Our work is therefore suggestive of an important role of GroEL1 for survival under low aeration by affecting the expression of genes known for hypoxia response.

overall_design: Expression data from wild type and GroEL1 mutant strains in response to 8 environmental stresses plus log phase growth, with at least three biological replicates of each.

first: Sharma

last: Aditi

first: Mahajan

last: Gaurang

first: Rao

last: Kanury

first: Banerjee

last: Sharmistha

first: Mande

last: Shekhar

first: David

last: Sherman


title: Comparative transcriptomic analysis between a high and a low sulfite producers wine yeast strains

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

country: France

institute: INRA

summary: The goal of this study was to compare the expression level of the whole genome of two wine yeast strains highly differing in their sulfite production (High producer strain: 10281A; Low producer strain: 1764A). Conditions maximizing SO2 production were selected: nitrogen rich media (425 mg/l assimilable nitrogen) and low temperature (16°C). This transcriptomic analysis was performed during the sulfite production phase, just after the entry in stationary phase. This analysis is part of a global work, aiming at the identification of the molecular basis of sulfite production by wine yeasts through physiologic, transcriptomic and genetic studies.

overall_design: Two strains compared in the same conditions with biological replicates following a dye-swap design.

first: Jessica

last: Noble

first: Isabelle

last: Sanchez


title: caArray_gray-00298: Genomic and transcriptional aberrations linked to breast cancer pathophysiologies - Genome Copy Number (Scanning and OncoBAC)

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary: This study explores the roles of genome copy number abnormalities (CNAs) in breast cancer pathophysiology by identifying associations between recurrent CNAs, gene expression, and clinical outcome in a set of aggressively treated early-stage breast tumors. It shows that the recurrent CNAs differ between tumor subtypes defined by expression pattern and that stratification of patients according to outcome can be improved by measuring both expression and copy number, especially high-level amplification. Sixty-six genes deregulated by the high-level amplifications are potential therapeutic targets. Nine of these (FGFR1, IKBKB, ERBB2, PROCC, ADAM9, FNTA, ACACA, PNMT, and NR1D1) are considered druggable. Low-level CNAs appear to contribute to cancer progression by altering RNA and cellular metabolism.

overall_design:
gray-00298
Assay Type: aCGH
Provider: UCSF Spot
Organism: Homo sapiens (ncbitax)


title: Validation experiment of copy number variations identified by next-generation sequencing in chickens (part 1)

city: Shenzhen

first: Guoqiang

last: Yi

state: Guangdong

address: No 7,Pengfei Road,Dapeng District,Shenzhen

institute: Agricultural Genome Institute at Shenzhen

summary: Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we perform a genome-wide analysis of CNVs in the 12 diversified chicken genomes based on next-generation sequencing. We apply aCGH experiments to confirm our predicted CNVs. Results from aCGH agree well with our findings and the Pearson’s correlation values between the test and reference samples range from 0.395 to 0.740.

overall_design: The whole blood samples were collected from Beijing You (BY), Dongxiang (DX), Luxi Game (LX),  Red Jungle Fowl (RJF), Shouguang (SG), Silkie (SK), Tibetan (TB), Wenchang (WC), and White Plymouth Rock (WR),  and genomic DNA was isolated using standard phenol/chloroform extraction methods. Each test sample labeled with Cy3 was mixed with Red Jungle Fowl as reference sample labeled with Cy5. All process and analysis was performed in terms of standard NimbleGen procedure. However, due to some uncontrollable factors, none of results were obtained in three consecutive trials for CS, RIR and WL, so we had to choose a similar Agilent custom-designed 1*1.0 M array.

first: Lujiang

last: Qu

first: Jianfeng

last: Liu

first: Yiyuan

last: Yan

first: Ning

last: Yang


title: Identification and characterization of cold responsive microRNAs in tea plant (Camellia sinensis) based on high-throughput sequencing and their targets using degradome analysis [microarray]

city: Nanjing

first: Yue

last: Zhang

state: Jiangsu

address: Weigang No.1

department: Tea Science Research Institute

institute: Nanjing Agricultural University

summary: Solexa sequencing technology was used to perform high throughput sequencing of the small RNA library from the cold treatment of tea leaves. Subsequently, aligning these sequencing date with plant known miRNAs, we characterized 112 C. sinensis conserved miRNAs. In addition, 215 potential candidate miRNAs were found; among them, 131 candidates with star sequence were chosen as novel miRNAs. There are both congruously and differently regulated miRNAs, and line-specific miRNAs were identified by microarray-based hybridization in response to cold stress. The miRNA chip included 3228 miRNA probes corresponding to miRNA transcripts listed in Sanger miRBase release 19.0 and 283 novel miRNAs probes founding in tea plant.

overall_design: In the study presented here, two tea plant cultivars, ‘Yingshuang’ (YS, a cold-tolerant tea plant cultivar) and ‘Baiye 1’ (BY, a cold-sensitive tea plant cultivar), were kept at 4°C for 4,12, 24 h, respectively, and 28°C for as control. These samples were used to acquire expression profiles of a total of 3,511 unique genes, leading to the successful construction of supervised

first: Xujun

last: Zhu

first: Mingle

last: Wang

first: Changnian

last: Song

first: Zhongwei

last: Zou

first: Wanping

last: Fang

first: Xinghui

last: Li


title: LNCaP cells: shRNA library with bicalutamide

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

summary: Short hairpin RNA library-based functional screening identified ribosomal protein L31 that modulates prostate cancer cell growth

overall_design: Vehicle vs. bicalutamide treated LNCaP cells infected with lentiviral shRNA library. Biological replicates: 2 vehicle treatments, 2 bicalutamide treatments.

first: Satoshi

last: Inoue


title: Validation experiment of copy number variations identified by next-generation sequencing in chickens (part 2)

summary: Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we perform a genome-wide analysis of CNVs in the 12 diversified chicken genomes based on next-generation sequencing. We apply aCGH experiments to confirm our predicted CNVs. Results from aCGH agree well with our findings and the Pearson’s correlation values between the test and reference samples range from 0.644 to 0.722.

overall_design: The whole blood samples from Cornish, Rhode Island Red, and White Leghorn


title: DNA methylation profiling in pheochromocytoma and paraganglioma reveals diagnostic and prognostic markers

status: Public on May 11 2015

city: Paris

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

institute: Ligue Nationale contre le Cancer

summary: A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net):we explored DNA methylation patterns associated with PPGL malignancy using two large and well characterized cohorts of PPGL collected through a multi-institutional collaboration through the European Network for the Study of Adrenal Tumors (ENS@T).

overall_design: Bisulfite converted DNA from fresh frozen paragangliomas and adrenal medulla samples were hybridized to Illumina Infinium 27k Human Methylation

first: Aguirre

last: de Cubas

first: Esther

last: Koepershoek

first: Lucia

last: Inglada-Pérez

first: Eric

last: Letouzé

first: Maria

last: Currás-Freixes

first: Agustin

middle: F

last: Fernández

first: Iñaki

last: Comino-Méndez

first: Francesca

last: Schiavi

first: Veronika

last: Mancikova

first: Graeme

last: Eisenhofer

first: Massimo

last: Mannelli

first: Guiseppe

last: Opocher

first: Henri

last: Timmers

first: Felix

last: Beuschlein

first: Ronald

last: de Krijger

first: Alberto

last: Cascon

first: Mario

last: Fraga

first: Judith

last: Favier

first: Anne-Paule

last: Gimenez-Roqueplo

first: Mercedes

last: Robledo


title: The functional study of zebrafish rig1 gene in NNV infection

status: Public on May 12 2015

city: Taipei

first: gen

middle: hwa

last: lin

state: Nankang

address: 128,section2,academia road

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

summary: Transcriptional profiling of ZF-4 cells comparing controle morpholino-infection cells with rig1 morpholino-infection cells. This assay is used for determination of gene expression profiling at 6 hpi under NNV infection in rig1 knockdown cells.

overall_design: Two-condition experiment, controle morpholino-NNV infection cells vs. rig1 morpholino-NNV infection cells (5 MOI).

first: Gen-Hwa

last: Lin

first: Hsu-Yu

last: Chen

first: Jen-Leih

last: Wu


title: caArray_EXP-550: TCGA (READ):  Analysis of DNA Methylation for rectal adenocarcinoma (READ) Using Illumina Infinium Human DNA Methylation 27 platform (HumanMethylation27)(jhu-usc)

first: Mervi

last: Heiskanen

state: MD

summary: TCGA Analysis of DNA Methylation for rectal adenocarcinoma (READ) Using Illumina Infinium Human DNA Methylation 27 platform

overall_design:
EXP-550
Assay Type: Methylation
Provider: Illumina
Array Designs: jhu-usc.edu_OV.HumanMethylation27.v2
Organism: home sapiens (ncbitax)
Tissue Sites: rectal
Material Types: Primary solid_tumor, Control Cell Line, organism_part, Solid normal_tissue
Disease States: Rectal Adenocarcinoma, NOT SPECIFIED, [Not Available], Rectal Mucinous Adenocarcinoma

first: Peter

last: Laird


title: Global gene expression analysis of Bacillus cereus to proanthocyanidin exposure

city: Tokyo

first: Tomoko

last: TAMURA

address: 1-1-1 Sakuragaoka Setagaya-ku

department: Nutritional Science and Food Safety

institute: Tokyo University of Agriculture

summary: B. cereus RNA isolation were taken at OD 0.5 just before addition of 0.02 mg/mL EEC, and at 30 min of exposure. Water was added instead of EEC for control. Total RNA was isolated and we performed DNA microarray for genome-wide transcriptional analysis of B. cereus ATCC 14579 in the presence or absence of EEC. The microarray used in this study was custom-made B. cereus ATCC 14579 developed by Agilent Technologies (https://earray.chem.agilent.com/earray/). The B. cereus microarray design was based on the predicted chromosomal open reading frames (NCBI Accession No. AE016877). It targets the 5234 annotated CDS, three non-overlapping probes were designed, low-quality probes were eliminated, and finally 15242 could be spotted. Microarray data was normalized to 75th percentile and the difference was found to be significant by unpaired T-test (P = 0.05). Next, ratio changes of 2-fold (for up-regulated genes in the EEC stress condition) and 0.5-fold (for down-regulated genes in the EEC stress condition) were regarded as biologically significant. 596 were up-regulated and 495 were down-regulated.

overall_design: Bacillus cereus was selected at 0, 30 min exposure for RNA extraction and hybridization on Agilent microarrays.

last: Tamura

first: Kiyoshi

last: Mura


title: caArray_EXP-576: TCGA (LUAD): Gene Expression Analysis of TCGA samples using Agilent Expression 244K microarrays (UNC)

status: Public on May 13 2015

summary: Gene Expression Analysis of TCGA  samples using Agilent Expression 244K microarrays.

overall_design:
EXP-576
Assay Type: Gene Expression
Provider: Agilent
Array Designs: AgilentG4502A_07_3
Organism: Homo sapiens (ncbitax)
Tissue Sites: Lung
Material Types: Control Analyte, organism_part, Primary solid_tumor, genomic_DNA
Disease States: Lung Adenocarcinoma, NOT SPECIFIED

first: Michael

last: Topal

first: Katherine

last: Hoadley


title: caArray_EXP-574: TCGA(Kirc): Gene Expression Analysis of TCGA samples using Agilent Expression 244K microarrays (UNC)

overall_design:
EXP-574
Assay Type: Gene Expression
Provider: Agilent
Array Designs: AgilentG4502A_07_3
Organism: Homo sapiens (ncbitax)
Tissue Sites: Kidney
Material Types: Control Analyte, organism_part, Primary solid_tumor, genomic_DNA
Disease States: Kidney Clear Cell Renal Carcinoma, NOT SPECIFIED


title: Gene expression profile in NNV infected ZF-4 cells

summary: Transcriptional profiling of ZF-4 cells comparing mock infection cells with cells infected with NNV. This assay is used for determination of gene expression profiling at 6 hpi under NNV infection.

overall_design: Two-condition experiment, Mock infection vs. NNV infection (5 MOI).


title: Validation experiment of copy number variations identified by next-generation sequencing in chickens

first: Guoqiang

last: Yi

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

overall_design: Refer to individual Series


title: The transcriptome of TRPV1-positive sensory neurons revealed by subgroup-elimination transcriptomics

city: Cologne

first: Joerg

last: Isensee

address: Robert Koch Str. 10

department: Department of Anesthesiology and Intensive Care Medicine

institute: University Hospital of Cologne

summary: We developed an approach to rapidly eliminate the subgroup of sensory neurons expressing the heat-gated cation channel TRPV1 from dissociated rat sensory ganglia using agonist treatment followed by density centrifugation. To identify transcripts predomintly expressed in TRPV1-positive neurons, we compared the transcriptome of all cells within sensory ganglia versus all cells without TRPV1 expressing neurons using RNA-Seq.

overall_design: Four replicate experiments with  RNA from DRG neurons of one rat per experiment were performed. Dissociated neurons were split up in three parts, treated with solvent DMSO (0.1%), casaicin (10 µM), or RTX (100 nM) for 30 min followed by gradient centrifugation. RNA was extracted from the remaining pellet containing either all cells or all cells without TRPV1-positive neurons.

first: Carsten

last: Wenzel

first: Rene

last: Buschow

first: Robert

last: Weissmann

first: Christine

last: Andres

first: Andreas

last: Kuss

first: Tim

last: Hucho


title: Replacement diets in gilthead sea bream

status: Public on May 09 2015

city: Castellón

first: Josep

last: Calduch-Giner

address: Ribera de Cabanes

country: Spain

institute: Institute of Aquaculture Torre de la Sal (CSIC)

summary: Transcriptional profiling of adipose tissue comparing three diets with different levels of replacement of fish oil for vegetable oils.

overall_design:
Juvenile gilthead sea bream (Sparus aurata L.) of 16 g initial mean body weight were distributed into 9 fibreglass tanks (500 l) in groups of 60 fish at the research experimental facilities of IATS. Each group received (from May 23rd to September 19th) one of the three experimental diets nominally CTRL, 66VO and VO. All diets were based on plant proteins and dietary oil was either Scandinavian FO (CTRL diet) or a blend of vegetable oils, replacing the 66% (66VO diet) and 100% (VO diet) of FO.
Four samples, using a control diet (CTRL) as reference and double color hybridization and dye swap with the other two (66VO, VO)

first: Jaume

last: Pérez-Sánchez


title: Coordinated epigenetic remodelling occurs during early breast carcinogenesis [Human promoter ChIP-chip]

city: Darlinghurst

first: Warwick

middle: James

last: Locke

state: NSW

address: 384 Victoria St

department: Cancer Deparment

country: Australia

institute: The Garvan Institute of Medical Research

type: Genome binding/occupancy profiling by array

summary: Dysregulation of the epigenome is a common event in malignancy. However, deciphering the earliest cancer associated epigenetic events remains a challenge. Cancer epigenome studies to date have primarily utilised cancer cell lines or clinical samples, where it is difficult to identify the initial epigenetic lesions from those that occur over time. Here, we analysed the epigenome of normal Human Mammary Epithelial Cells (HMEC) and a matched variant cell population (vHMEC) that has escaped senescence and undergone partial carcinogenic transformation. Using this model system we sought to identify the earliest epigenetic changes that potentially occur during carcinogenesis. First we show that the transcriptome of vHMEC resembles that of basal-like breast cancer. Moreover, in vHMEC there is significant deregulation of MYC, p53, EZH2/polycomb, the Aryl Hydrocarbon Receptor (AHR) and miRNAs-143, 145, 199a and 519a at the transcriptional level. Second, we find that vHMEC exhibit genome-wide changes in DNA methylation affecting key cancer-associated pathways. Hypermethylation predominately impacted gene promoters (particularly those targeted by AHR and TP53) and polycomb associated loci, whereas hypomethylation frequently affected enhancers. Next we show that long range epigenetic deregulation occurred in vHMEC involving concordant change in chromatin modification and gene expression across ~0.5-1Mb regions. Finally, we demonstrate that the DNA methylation changes we observe in vHMECs, occur in basal-like breast cancer (notably FOXA1 hypermethylation).. Overall our results suggest that the first steps of carcinogenesis are associated with a co-ordinated deregulation of DNA methylation and chromatin modification spanning a range of genomic loci potentially targeted by key transcription factors and a corresponding deregulation of transcriptional networks.

overall_design: H3K27me3 ChIP-chip was performed on HMEC and vHMEC from 4 donors, H3K9ac was performed on cells from 2 donors. Both H3K27me3 and H3K9ac ChIP was performed on two time points for vHMEC and used the same input materia.


title: miRNA Real-time quantitative PCR analysis of EAE CD4+T cells

status: Public on May 08 2015

city: Shanghai

last: Shen

address: 145 Shan  Dong  Middle Road

institute: Renji Hospital, JiaoTong University School of Medicine

summary: EAE is a mouse model of human multiple sclerosis. We used miRNA low density array to screen abnormally expressed miRNAs in autoimmune CD4+T cells.Generally, splenic CD4+T cells were isolated from three groups: healthy C57BL/6 mice, C57BL/6 mice with the induction of EAE for 16 days, and C57BL/6 mice with the induction of EAE for 32 days. Then we did miRNA profilings on these samples.

overall_design: Splenic CD4+T cells were isolated from the above three groups. Each group consist of six mice.  Equal amount total RNA from each mouse was pooled prior to miRNA expression analysis.

first: Wen

last: Pan


title: caArray_carpt-00469: Copy Number and Targeted Mutational Analysis Reveals Novel Somatic Events in Metastatic Prostate Tumors

status: Public on May 07 2015

first: Mervi

last: Heiskanen

summary: A comprehensive genomic survey for somatic events in systemic metastatic prostate tumors.

overall_design:
carpt-00469
Assay Type: aCGH
Provider: Agilent
Array Designs:
Organism: Homo sapiens (ncbitax)
Material Types: genomic_DNA, synthetic_DNA, organism_part, whole_organism, genomic DNA
Disease States: Prostate Cancer


title: A mutation of RNA polymerase β’ subunit (RpoC) converts heterogeneously vancomycin-intermediate S. aureus (hVISA) into ‘slow-VISA’ (sVISA)

city: Bunkyo-Ku

first: tomomi

last: hishinuma

state: Tokyo

institute: juntendo university

summary: Various mutations in the rpoB gene, which encodes the RNA polymerase beta subunit, are associated with increased vancomycin (VAN) resistance in vancomycin-intermediate S. aureus (VISA) and hetero-VISA (hVISA) strains. We reported that rpoB mutations are also linked to the expression of the recently found slow VISA (sVISA) phenotype (Saito et al 2014 AAC). Because RpoC and RpoB are components of RNA polymerase, we examined the effect of rpoC(P440L) mutation on the expression of the sVISA phenotype in the Mu3fdh2*V6-5 strain (V6-5), which was derived from a previously reported hVISA strain with the VISA phenotype. V6-5 had an extremely prolonged doubling time (72.2 min) and high vncomycin MIC (16 mg/L). However, the phenotype of V6-5 was unstable, and the strain frequently reverted to hVISA with concomitant loss of slow growth rate, cell wall thickness, and reduced autolysis. Whole genome sequencing of phenotypic revertant strain V6-5-L1 and comparison with V6-5 revealed a second mutation F562L in rpoC. Introduction of the wild-type rpoC gene using multi-copy plasmid resolved the sVISA phenotype of V6-5, indicating that rpoC(P440L) mutation expressed the sVISA phenotype in hVISA. To investigate the mechanisms of resistance in the sVISA strain, we independently isolated additional 10 revertants to hVISA and VISA. In subsequent whole genome analysis, we identified compensatory mutations in the genes of three distinct functional categories; rpoC gene itself as regulatory mutations, peptidoglycan biosynthesis genes, and relQ which is involved in stringent response. It appears that rpoC(P440L) mutation causes sVISA phenotype by augmenting cell-wall peptidoglycan synthesis, and through the control of stringent response.

overall_design: 9 analysis using 60 mer-oligo microarray, 4 rpoC mutant, 2 relQ mutant, 2 mutations associated with the peptidoglycan, 1 wild-type strain

first: Miki

last: MATSUO

first: Tomomi

last: HISHINUMA

first: Yuki

last: KATAYAMA

first: Keiichi

last: HIRAMATSU


title: Early depletion of primordial germ cells in zebrafish promotes testis formation

city: Singapore

first: Keh-Weei

last: Tzung

address: 1 Research Link National University of Singapore

institute: Temasek Life Sciences Laboratory

summary: The requirement for primordial germ cells (PGCs) during sexual differentiation is variable among vertebrates. It has been shown that in zebrafish complete loss of PGCs in the embryos causes exclusive male development. Further, transplantation of a single PGC into a germline deficient zebrafish embryos generates male exclusively, suggesting PGC number might be important for the ovarian fate.To explore how PGC number might regulate sexual development in zebrafish, we experimentally manipulated its number by injecting dnd MO into embryos to generate fish containing a spectrum of PGC number. The experiment was designed to compare transcriptomes between the developing trunk regions of wild type and dnd morphants at different developmental stages.

overall_design: The dnd MO was microinjected into one cell stage embryos to generate zebrafish with a range of PGC numbers. Transcriptomes of developing trunk regions of wild type and dnd morphants at 14 dpf and 22 dpf were analyzed.

first: Laszlo

last: Orban


title: A genomic landscape of enhanced bovine pluripotency

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

institute: Princess Maxima Center for Pediatric Oncology


title: Early transcriptional response to phytopathogen Xanthomonas campestris pv. campestris by susceptible cabbage host

city: Lincoln

first: Dhairyasheel

last: Desai

state: Canterbury

address: Ellesmere Junction Road/Spring Road

department: Bio-Protection Research Centre

country: New Zealand

institute: Lincoln University

summary: Black rot, caused by Xanthomonas campestris pv. campestris (Xcc) is one of the most devastating diseases of cruciferous crops worldwide. The pathogen infects and multiplies in plant vascular tissues and, as the disease progresses, the veins of infected tissues turn black and characteristic V-shaped lesions appear along the margins of leaves.The aim of this work is to identify differentially expressed genes from Brassica oleracea during early infection by Xcc, in an attempt to identify proteins related to resistance.

overall_design: Cabbge seedlings were inoculated with Xanthomonas campestris pv campestris (Xcc) suspension and cabbage gene expression at 6h., 24h. And 48h. After inoculation was assessed with help of Brassica 95k EST microarray chip.

first: Robert

last: Braun

first: Sandra

last: Visnovsky

first: Andrew

last: Pitman

first: John

last: Hampton

first: Mary

last: Christey


title: Transcriptome of accumbens nuclei from mice having low scores of cocaine-dependent conditioned place preference

status: Public on May 10 2015

city: PARIS

first: Gilles

last: Maussion

address: 16 rue Henri Huchard

institute: INSERM U675

summary: Molecular basis of transition to addiction in vulnerable individuals is largely unknown. We hypothesized that human susceptibility genes can be identified on the basis of conserved molecular mechanisms in rodent brains. We used a short-term cocaine-dependent conditioned place preference (CPP) to identify genetic hallmarks of early steps of reward memory in basal ganglia including accumbens nucleus (NAc), globus pallidus (GP) and subthalamic nucleus (STN). Using genome-wide microarray analysis and CPP as a quantitative trait, we found that synaptic plasticity-related genes are deregulated in these three structures. A significant enrichment in bona fide transcripts involved in dendritic spine local translation was evidenced. mGluR5 is transcriptionally deregulated in Acc and GP of cocaine-treated animals. Grin3a that encodes a NMDA receptor subunit involved in Ca++ permeability is deregulated in NAc. Furthermore, Orexin/Hcrt transcript level is decreased in STN, a region known to be involved in discriminating addictive drugs and natural rewards. We also found that mGluR5 and Grin3a expression deregulation is sufficient to induce changes in synaptic plasticity-related genes. Altogether, these results suggest that a combined deregulation of mGluR5 and Grin3A pathway in NAc, mGluR5 in GP and orexin system in STN may generate an incentive memory contrasted between addictive drugs and natural rewards. Such pathways may include clusters of genes that are potential susceptibility genes for transition to addiction.

overall_design: Agilent Whole Mouse Genome oligomicroarrays (GEO accession no. GPL2872, Agilent Technologies, Palo Alto, CA) were used. They contain 60-mer DNA probes synthesized in situ in a 44k format. Of 44,290 spots, 2756 are controls. The remaining 41,534 spots represent 33,661 unique transcripts which correspond to 20,202 unique human genes. Five independent (five accumbens nuclei from mice treated with cocaine and having a low score of conditioned place preference compared to five accumbens nuclei from mice treated with saline solution) measurements were carried out for each group of biological conditions using exchanged dye-labeled RNA targets (i.e., Cy3 and Cy5 dyeswapping experiments).

first: Sabah

last: Kelai

first: Aude-Marie

last: Lepagnol-Bestel

first: Evangelos

last: Chortis

first: Sandrine

last: Imbeaud

first: Florence

last: Noble

first: Jean-Marie

last: Moalic

first: Philip

last: Gorwood

first: Michel

last: Simonneau


title: BBr002: A genomic landscape of enhanced bovine pluripotency

department: Research

summary: Genes and signaling pathways involved in pluripotency have been studied extensively in mouse and human pre-implantation embryos and embryonic stem (ES) cells. The unsuccessful attempts to generate ES cell lines from other species including cattle suggests that other genes and pathways are involved in maintaining pluripotency in these species. To investigate which genes are involved in bovine pluripotency, expression profiles were generated from morula, blastocyst, trophectoderm and inner cell mass (ICM) samples using microarray analysis. As MAPK inhibition can increase the NANOG/GATA6 ratio in the inner cell mass, additionally blastocysts were cultured in the presence of a MAPK inhibitor and changes in gene expression in the inner cell mass were analyzed.                              Between morula and blastocyst 3,774 genes were differentially expressed and the largest differences were found in blastocyst up-regulated genes. Gene ontology (GO) analysis shows lipid metabolic process as the term most enriched with genes expressed at higher levels in blastocysts. Genes with higher expression levels in morulae were enriched in the RNA processing GO term. Of the 497 differentially expressed genes comparing ICM and TE the expression of NANOG, SOX2 and POU5F1 was indeed increased in the ICM confirming their evolutionary preserved role in pluripotency. Several genes implicated to be involved in differentiation or fate determination were also  expressed at higher levels in the ICM. Genes expressed at higher levels in the ICM were enriched in the RNA splicing and regulation of gene expression GO term.  Although NANOG expression was elevated upon MAPK inhibition, SOX2 and POU5F1 expression showed little increase. Expression of other genes in the MAPK pathway including DUSP4 and SPRY4, or influenced by MAPK inhibition such as IFNT, was affected.                                                                                The data obtained from the microarray studies provide further insight in gene expression during bovine embryonic development. They show an expression profile in pluripotent cells that indicates a pluripotent but epiblast-like state. These data indicate that MAPK inhibition alone is not sufficient to maintain a pluripotent character in bovine cells.

overall_design: Microarrays used were bovine whole genome gene expression microarrays V2 (Agilent Technologies) representing 43,653 Bos taurus 60-mer oligos in a 4x44K layout.    RNA samples from ERK-inhibited ICM and control-treated ICM were compared in a common reference experiment design using 4 dual channel microarrays with each sample hybridized against an identical sample consisting of a pool of blastocysts total RNA. Within each group of two microarrays for each treatment, sample versus common reference hybridizations were performed in balanced dye-swap.

first: Bas

last: Brinkhof

first: Helena

middle: T

last: van Tol

first: Sascha

middle: G

last: Ijzer

first: Kaveh

last: Mashayekhi

first: Henk

last: Haagsman

first: Bernard

last: Roelen


title: Transcriptomes of accumbens nuclei from mice submitted to a short-term cocaine-dependent conditioned place preference

overall_design: Agilent Whole Mouse Genome oligomicroarrays (GEO accession no. GPL2872, Agilent Technologies, Palo Alto, CA) were used. They contain 60-mer DNA probes synthesized in situ in a 44k format. Of 44,290 spots, 2756 are controls. The remaining 41,534 spots represent 33,661 unique transcripts which correspond to 20,202 unique human genes. Five independent (four accumbens nuclei from mice treated with cocaine compared to four accumbens nuclei from mice treated with saline solution) measurements were carried out for each group of biological conditions using exchanged dye-labeled RNA targets (i.e., Cy3 and Cy5 dyeswapping experiments). Each hybridization was numerized hybridization by a GenePix 4000B Microarray Scanner and an Agilent G6525 Microarray Scanner.


title: Transcriptomes of subthalamic nuclei from mice submitted to a short-term cocaine-dependent conditioned place preference

overall_design: Agilent Whole Mouse Genome oligomicroarrays (GEO accession no. GPL2872, Agilent Technologies, Palo Alto, CA) were used. They contain 60-mer DNA probes synthesized in situ in a 44k format. Of 44,290 spots, 2756 are controls. The remaining 41,534 spots represent 33,661 unique transcripts which correspond to 20,202 unique human genes. Five  independent (five subthalamic nuclei from mice treated with cocaine compared to five subthalamic nuclei from mice treated with saline solution) hybridizations were carried out for each group of biological conditions using exchanged dye-labeled RNA targets (i.e., Cy3 and Cy5 dyeswapping experiments). Each hybridization was numerized hybridization by a GenePix 4000B Microarray Scanner and an Agilent G6525 Microarray Scanner

first: Chortis

last: Evangelos

last: Simmoneau


title: BBr001: A genomic landscape of enhanced bovine pluripotency

first: Marian

last: Groot Koerkamp

summary: Genes and signaling pathways involved in pluripotency have been studied extensively in mouse and human pre-implantation embryos and embryonic stem (ES) cells. The unsuccessful attempts to generate ES cell lines from other species including cattle suggests that other genes and pathways are involved in maintaining pluripotency in these species. To investigate which genes are involved in bovine pluripotency, expression profiles were generated from morula, blastocyst, trophectoderm and inner cell mass (ICM) samples using microarray analysis. As MAPK inhibition can increase the NANOG/GATA6 ratio in the inner cell mass, additionally blastocysts were cultured in the presence of a MAPK inhibitor and changes in gene expression in the inner cell mass were analyzed.                Between morula and blastocyst 3,774 genes were differentially expressed and the largest differences were found in blastocyst up-regulated genes. Gene ontology (GO) analysis shows lipid metabolic process as the term most enriched with genes expressed at higher levels in blastocysts. Genes with higher expression levels in morulae were enriched in the RNA processing GO term. Of the 497 differentially expressed genes comparing ICM and TE the expression of NANOG, SOX2 and POU5F1 was indeed increased in the ICM confirming their evolutionary preserved role in pluripotency. Several genes implicated to be involved in differentiation or fate determination were also  expressed at higher levels in the ICM. Genes expressed at higher levels in the ICM were enriched in the RNA splicing and regulation of gene expression GO term.  Although NANOG expression was elevated upon MAPK inhibition, SOX2 and POU5F1 expression showed little increase. Expression of other genes in the MAPK pathway including DUSP4 and SPRY4, or influenced by MAPK inhibition such as IFNT, was affected.                                           The data obtained from the microarray studies provide further insight in gene expression during bovine embryonic development. They show an expression profile in pluripotent cells that indicates a pluripotent but epiblast-like state. These data indicate that MAPK inhibition alone is not sufficient to maintain a pluripotent character in bovine cells.

overall_design: Microarrays used were bovine whole genome gene expression microarrays V2 (Agilent Technologies) representing 43,653 Bos taurus 60-mer oligos in a 4x44K layout.  RNA samples from morula, blastocyst and dissected inner cell mass (ICM) and trophectoderm (TE) were compared in a common reference experiment design using 8 dual channel microarrays with each sample hybridized against an identical sample consisting of a pool of blastocysts total RNA. Within each group of two microarrays for each  stage/tissue type, sample versus common reference hybridizations were performed in balanced dye-swap.

middle: A


title: Overexpression of ENOD40 in Arabidopsis thaliana plants reveals a role of the gene in cell wall turnover and glucosinolate accumulation.

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

institute: University of Verona

summary: The transcriptional and metabolic profiles of rosettes of three independent Arabidopsis thaliana ecotype Wassiliewska lines overexpressing the soybean early noduline GmENOD40 gene were compared to those of wt, and a biomarker analysis was performed. ENOD40 overexpression resulted in 382 modulated genes, 142 of which upregulated and 165 downregulated in all the three transformed lines. Cell wall, membrane, hydrolase activity on glycosidic bonds, defense response and response to stimulus gene categories were overrepresented in the modulated genes compared to TAIR complete database. Metabolomics analysis (through liquid chromatography-mass spectrometry) allowed to putatively identify 13 different glucosinolates, some flavonoids, sinapic and ferulic acid derivatives, hydroxybenzoic acid derivatives, non aromatic organic acids, amino acids. Positive genes biomarkers of the transformed plants were mainly involved in cell wall turnover, whereas positive metabolite biomarkers were the methylthioalkyl-glucosinolates.

overall_design: The transcriptional profile of rosettes of three independent Arabidopsis thaliana ecotype Wassiliewska lines overexpressing the soybean early noduline GmENOD40 gene were compared to those of wt, and a biomarker analysis was performed.

first: Chiara

last: Guarnerio

first: Flavia

last: Guzzo

first: Marisa

last: Levi


title: caArray_brown-00173: Molecular portraits of human breast tumours

status: Public on May 06 2015

city: Rockville

first: Mervi

last: Heiskanen

institute: NCI

summary: Human breast tumours are diverse in their natural history and in their responsiveness to treatments. Variation in transcriptional programs accounts for much of the biological diversity of human cells and tumours. In each cell, signal transduction and regulatory systems transduce information from the cell's identity to its environmental status, thereby controlling the level of expression of every gene in the genome. Here we have characterized variation in gene expression patterns in a set of 65 surgical specimens of human breast tumours from 42 different individuals, using complementary DNA microarrays representing 8,102 human genes. These patterns provided a distinctive molecular portrait of each tumour. Twenty of the tumours were sampled twice, before and after a 16-week course of doxorubicin chemotherapy, and two tumours were paired with a lymph node metastasis from the same patient. Gene expression patterns in two tumour samples from the same individual were almost always more similar to each other than either was to any other sample. Sets of co-expressed genes were identified for which variation in messenger RNA levels could be related to specific features of physiological variation. The tumours could be classified into subtypes distinguished by pervasive differences in their gene expression patterns.

overall_design:
brown-00173
Assay Type: Gene Expression
Provider: UCSF Spot
Organism: Homo sapiens (ncbitax)


title: caArray_becic-00229: Gene expression analysis of prostate cancers

summary: Prostate cancer is a biologically heterogeneous disease with considerable variation in clinical aggressiveness. The behavior of prostate cancer can be considered a direct or indirect result of aberrant alterations of gene expression in prostate epithelial cells. Identification of the patterns of gene-expression alterations that are related to the aggressiveness of prostate cancers will greatly assist the development of tools for early detection of prostate cancers with poor clinical outcome and identification of targets for future therapeutic intervention. To detect the patterns of gene-expression alterations of prostate cancers, we performed a comprehensive gene-expression analysis on 30 prostate tissues of various levels of invasiveness (ranging from those confined to the organ to distant metastases) and Gleason grades (combined scores 4-9), using the Affymetrix chip set Hu35k (A-D) and U95a. Following three sequential selection screens, we identified 84 largely novel genes and expressed sequence tag (EST) sequences whose expression levels were altered significantly in prostate cancer samples compared with control normal tissues. In addition, the expression levels of a group of 12 genes and EST sequences was found to be altered significantly in aggressive type of prostate cancers but not in organ-confined prostate cancers. Cluster analysis using the 84-gene list showed that the highly aggressive prostate cancers contained gene-expression patterns that were distinct from organ-confined prostate cancers ( Molecular Carcinogenesis 33:25-35, 2002).

overall_design:
becic-00229
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: Hu35KsubA
Organism: Homo sapiens (ncbitax)
Tissue Sites: Prostate
Material Types: synthetic_DNA, synthetic_RNA, organism_part
Disease States: Normal, Prostate_Adenocarcinoma


title: Differential expression of genes in Streptococcus sanguinis nox mutant and its complemented strain

status: Public on May 04 2015

city: Richmond

first: Xiuchun

last: Ge

state: VA

address: 521 North 11th Street

institute: Virginia Commonwealth University

summary: Transcriptional profiling of Streptococcus sanguinis nox mutant and its complemented strain compared to the wild-type SK36.

overall_design: Two experiments:nox mutant vs. SK36, nox complemeted strain vs. SK36. Biological replicates: triplicates, independently grown and harvested. Four replicate per array.

first: Ping

last: Xu


title: The cellular origin and malignant transformation of Waldenström's Macroglobulinemia [copy number variation]

city: Pamplona

first: Bruno

last: Paiva

address: Av. Pio XII, 55

institute: Clinica Universidad de Navarra

summary: Although information on the molecular pathogenesis of Waldenström’s Macroglobulinemia (WM) has greatly improved in recent years, the exact cellular origin and the mechanisms behind WM transformation from IgM MGUS remain undetermined. Here, we undertook an integrative phenotypic, molecular and genomic approach to study clonal B-cells from newly-diagnosed patients with IgM MGUS (n=22), smoldering (n=17), and symptomatic WM (n=10). Through principal-component-analysis of multidimensional flow cytometry data, we demonstrated overlapping phenotypic profiles between clonal B-cells from IgM MGUS, smoldering and symptomatic WM patients. Similarly, virtually no genes were significantly deregulated between FACS-sorted clonal B-cells from the three disease stages. Interestingly, while the transcriptome of the Waldenström’s clone was highly deregulated as compared to CD25-CD22+ normal B-cells, significantly less genes were differentially expressed and specific WM pathways down-regulated while comparing the transcriptome of the Waldenström’s clone vs. its normal phenotypic counterpart: CD25+CD22+dim B-cells. The frequency of specific copy number abnormalities [+4, del(6q23.3-6q25.3), +12, and +18q11-18q23] progressively increased from  IgM MGUS and smoldering WM vs. symptomatic WM (18% vs. 20% and 73%, respectively; P =.008), suggesting a multistep transformation of clonal B-cells that albeit benign (i.e.: IgM MGUS and smoldering WM), already harbor the phenotypic and molecular signatures of the malignant Waldenström’s clone.

overall_design: Copy number analysis using the Affymetrix CytoScan 750K Array to study clonal B-cells from newly-diagnosed patients with IgM MGUS, smoldering, and symptomatic WM. Peripheral T-cells from paired and unpaired controls were also assessed.

first: Luis

last: Corchete

first: Maria-Belen

last: Vidriales

first: Ramón

last: García-Sanz

first: Jose

last: Perez

first: Maria

middle: L

last: Sánchez

first: Paloma

last: Barcena

first: Cristina

last: Jimenez

last: Sarasquete

first: Maria-Victoria

last: Mateos

first: Enrique

middle: M

last: Ocio

first: Noemi

last: Puig

first: Fernando

last: Escalante

first: José

last: Hernández

first: Rebeca

last: Cuello

first: Alfonso

last: de Coca

first: Magdalena

last: Sierra

first: Maria-Carmen

last: Montes

first: Tomás

last: González-López

first: Josefina

last: Galende

first: Abelardo

last: Bárez

last: Alonso

first: Emilia

last: Pardal

last: Orfao

first: Norma

last: Gutierrez

first: Jesús

last: San Miguel


title: miRNA expression profiling in rhabdomyosarcoma cell lines

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

summary: Rhabdomyosarcomas (RMS) are rare but very aggressive tumours of childhood that arise as a consequence of regulatory disruption of the growth and differentiation pathways of myogenic precursor cells. Based on morphology, two major RMS subtypes can be identified: embryonal RMS (ERMS) and alveolar (ARMS). To better understand the global function of miRNA in RMS, we analyzed the expression profile of 8 different RMS cell lines (3 PAX3/FOXO1 positive and 5 PAX3/FOXO1 negative RMS) using the mirVana miRNA Probe Set V1 (Ambion). The miRNA microarray platform was able to distinguish PAX3/FOXO1 positive (RH4, RH30, RH28) and negative RMS (RD, CCA, SMS-CTR, RH36, RH18) cell lines through the expression pattern of about 90 miRNAs. Since the translocation positive RMS patients fared worse than the negative counterpart our results demonstrated the potential of miRNA expression profiling to classify different RMS subtypes, in agreement to previous gene expression studies, and set the basis for a further functional characterization of selected miRNAs implicated in RMS pathogenesis and in the different clinical behaviour and aggressiveness of the two RMS subtypes. We decided to study miRNAs with the greatest difference in expression between PAX3/FOXO1 positive and negative RMS:miR-23a, miR-27a and miR-199a.

overall_design: microRNA expression profiling was carried out using the mirVana Probe Set V1 (Ambion) that is a collection of about 400 amine-modified DNA oligonucleotides representing a panel of the human, mouse and rat microRNAome in the miRNA Registry (miRBase - Release 9). We analyzed the expression profiles of 8 different rhabdomyosarcoma cell lines: three PAX3/FOXO1 positive (RH4, RH30, RH28) and five negative (RD, CCA, SMS-CTR, RH36, RH18). The miRNA population from each cell  line was compared to a reference sample consisting of a pool of the 8 total RNA samples mixed in equal amounts. Two replicates of each experiment were performed using  different microarray slides, in which sample and reference RNAs, labeled either with Cy3 or Cy5 fluorochromes, were crossed in both combinations (dye-swapping procedure).

first: Lucia

last: Tombolan

first: Silvia

last: Casara

first: Matteo

last: Zampini

first: Angelica

last: Zin

first: Chiara

last: Romualdi

first: Angelo

last: Rosolen

first: Cristiano

last: De Pittà


title: Molecular alterations in areas generating fast ripples in an animal model of temporal lobe epilepsy

status: Public on May 01 2015

city: Boston

first: Kellen

last: Winden

state: MA

address: 300 Longwood Ave

department: Neurology

institute: Boston Children's Hospital

summary: The molecular basis of epileptogenesis is poorly characterized. Studies in humans and animal models have identified an electrophysiological signature that precedes the onset of epilepsy, which has been termed fast ripples (FRs) based on its frequency. Multiple lines of evidence implicate regions generating FRs in epileptogenesis, and FRs appear to demarcate the seizure onset zone, suggesting a role in ictogenesis as well. We performed gene expression analysis comparing areas of the dentate gyrus that generate FRs to those that do not generate FRs in a well-characterized rat model of epilepsy. We identified a small cohort of genes that are differentially expressed in FR versus non-FR brain tissue and used quantitative PCR to validate some of those that modulate neuronal excitability. Gene expression network analysis demonstrated conservation of gene co-expression between non-FR and FR samples, but examination of gene connectivity revealed changes that were most pronounced in the cm-40 module, which contains several genes associated with synaptic function and the differentially expressed genes Kcna4, Kcnv1, and Npy1r that are down-regulated in FRs. We then demonstrate that the genes within the cm-40 module are regulated by seizure activity and enriched for the targets of the RNA binding protein Elavl4. Our data suggest that seizure activity induces co-expression of genes associated with synaptic transmission and that this pattern is attenuated in areas displaying FRs, implicating the failure of this mechanism in the generation of FRs.

overall_design: 21 samples, 10 fast ripple areas and 11 paired non-fast ripples areas


title: Affymetrix profile of human liver progenitor cells

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

institute: University of Stirling

summary: Human liver progenitor cells (LPCs) show therapeutic potential, however, their in vitro culture results in inadequate function and phenotypic instability reflecting incomplete understanding of in vivo processes. Foetal LPCs capable of differentiation to a hepatocyte phenotype were isolated and mRNA expression profiling carried out using Affymetrix HGU133plus2 microarrays. This was compared to profiles from mature human hepatocytes and human embryonic stem cells undergoing hepatocytic differentiation. Foetal LPCs exhibit a distinct molecular profile consistent with a stem cell signature, cell division, and some liver-specific functions.

overall_design: 9 independent samples of second trimester liver progenitor cells were profiled along with 3 independent mature hepatocyte samples and 3 each of embryonic stem cells at day 9 and day 17 of differentiation to hepatocyte like cells.


title: MicroRNA Expression profiles of mature hepatocytes and foetal liver progenitor cells

summary: Human liver progenitor cells (LPCs) show therapeutic potential, however, their in vitro culture results in inadequate function and phenotypic instability reflecting incomplete understanding of in vivo processes. Foetal LPCs capable of differentiation to a hepatocyte phenotype were isolated and mRNA expression profiling carried out using Exiqon miRCURY microarrays. This was compared to profiles from mature human hepatocytes. Foetal LPCs exhibit a distinct miRNA profile consistent with a stem cell signature, cell division, and some liver-specific functions.

overall_design: 3 independent samples of second trimester liver progenitor cells were prolfiled along with 3 independent mature hepatocyte samples.


title: Profile of human liver progenitor cells

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

overall_design: Refer to individual Series


title: Differentiation of fiber initials on cotton ovules

city: Fort Collins

first: Kathleen

last: Yeater

state: CO

address: 2150 Centre Avenue

institute: USDA-ARS

summary: Transcriptional profiling of cotton ovule cells.  Comparison of expression of genes in cultured ovules (-1 DPA) treated with or without phytohormones (5um IAA and 1um GA) and over a time-course from 0 to 12 hours.

platform_organism:
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design: The phytohormone incubation periods for unfertilized ovules were 0, 1, 3, 6, and 12 hours (H) with two biological replicates at each time-point.

first: Hee

last: Kim

first: Doug

last: Hinchliffe

first: Barbara

last: Triplett

first: Z

last: Chen

first: David

last: Stelly

first: Hong

last: Moon

first: Matthew

last: Gilbert

first: Gregory

last: Thyssen

first: Rickie

middle: B

last: Turley

last: Fang


title: Comparative anterior pituitary miRNA and mRNA expression profiles of Bama minipigs and Landrace pigs reveal potential molecular network involved in animal postnatal growth [miRNA array]

status: Public on May 05 2015

city: Guangzhou

first: Ruisong

last: Ye

address: 483 Wushan Tianhe

institute: South China Agricultural University

summary: The anterior pituitary is the most important endocrine organ modulating animal postnatal growth, mainly by controlling growth hormone (GH) gene transcription, synthesis, and secretion. As an ideal model for animal postnatal growth studies, the Bama minipig is characterized as having a lower growth performance and fewer individual differences compared with larger pig breeds. In this study, anterior pituitaries from Bama minipig and Landrace pig were used for miRNA and mRNA expression profile analysis using miRNA microarrays and mRNA-seq. Consequently, a total of 222 miRNAs and 12,909 transcripts were detected, and both miRNAs and mRNAs in the two breeds showed high correlation (r > 0.97). Additionally, 41 differentially expressed miRNAs and 2,254 transcripts were identified. Pathways analysis indicated that 32 pathways significantly differed in the two breeds. Importantly, two GH-regulation-signalling pathways, cAMP and inositol 1, 4, 5-triphosphate (IP3), and multiple GH-secretion-related transcripts were significantly down-regulated in Bama minipigs. Moreover, target prediction by two algorithms (TargetScan and RNAhybrid) indicated that most miRNA–mRNA target pairs (63.68–71.33%) presented a negatively correlated expression pattern. A possible network among miRNAs, mRNAs, and GH-regulation pathways was also proposed. These data will be helpful in understanding the possible molecular mechanisms involved in animal postnatal growth.

overall_design: 2 pooled samples were analyzed. A pool of 3 pig anterior pituitary was used for Bama minpigs and Landrace pigs,respectively.

first: Rui-Song

first: Yong-Liang

last: Zhang


title: transcript modification by myb1 interactants-MYB1’s partners

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: au13-14_myb1 - transcript modification by myb1 interactants - Transcription modification produced by transgenes - We produced 5 transgenic lines, overexpressing Eg MYB1,Eg MYB1+ EgOVATE, EgMYB1+EgHISTONE, EgHISTONE, EgOVATE and the CONTROL with the empty vectors. We have 2 lines of each construction. Plants were grown in short day conditions and we sampled the inflorescence stem.

overall_design: 10 dye-swap - normal vs transgenic comparaison

first: Jacqueline

last: Grima-Pettenati

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Marie-Laure

last: Martin-Magniette


title: Profiling of Salivary Exosomal microRNAs in Oral Lichen Planus Patients [set 2]

status: Public on Apr 30 2015

city: Daegu

first: Heon-Jin

last: Lee

address: 2177 Dalgubeol Daero

department: School of Dentistry, Microbiology and Immunology

country: South Korea

institute: Kyungpook National University

summary: In this study, we compared microRNA (miRNA) profiles of salivary exosomes of patients with oral lichen planus with those of healthy controls. Saliva samples from 16 patients with oral lichen planus and 8 healthy controls were divided into 2 sets and were examined by performing miRNA microarray analysis.

overall_design:
Examination of 8 oral lichen planus patients and 4 healthy controls.  Each patient and control represent pooled RNAs from salivary exosomes of 8 patients and 4 healthy controls, respectively.
Please note that each set (i.e. set1 and set2) was analysed independently.


title: MAQC-III/SEQC Main Study ABCD titration experiment, ERCC spike-in profiles and gene-level estimates for a selected test set

status: Public on Apr 03 2015

city: Vienna

first: Pawel

middle: P.

last: Labaj

address: Muthgasse 18

department: Department of Biotechnology

country: Austria

institute: Boku University Vienna

summary:
Comparison to RNA-Seq showed different strengths and weaknesses for different regimes of expression strength. At sufficient read-depth, both platforms seemed comparable for gene-level expression profiling.
Comparison to RNA-Seq showed comparable accuracy and precision with microarrays for ERCC spike-ins at medium to high expression levels. At low expression levels, the array showed signal attenuation but better precision, while RNA-Seq maintained accuracy albeit with highly inflated variance. In summary, both platforms can be meaningfully applied in a similar range of expression strength.

overall_design: Assessment of (precision, accuracy, reproducibility, mutual information, titration order consistency, and known mixing ratio recovery) by measurement of known-ratio mixtures of two RNA reference samples. The array probes 776 complex genes representative of the AceView gene model annotation, as well as 92 ERCC spike-in controls.

first: Nancy

last: Stralis-Pavese

first: Paweł

last: Łabaj

first: Djork-Arné

last: Clevert

first: Mario

last: Fasold

first: Sepp

last: Hochreiter

first: Hans

last: Binder

last: Kreil