title: Bone morphogenetic protein 4 induced miRNA expression in breast cancer cell lines

city: Tampere

first: Emma-Leena

last: Alarmo

address: Biokatu 6

institute: Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere

summary: Bone morphogenetic protein 4 (BMP4) is a remarkably powerful inhibitor of breast cancer cell proliferation, but is also able to induce breast cancer cell migration in certain cellular contexts. Previous data demonstrate that BMP4 controls the transcription of a variety of protein coding genes, but not much is known about microRNAs (miRNA) regulated by BMP4. In this study, miRNA expression patterns following BMP4 treatment were determined in one mammary epithelial and seven breast cancer cell lines using microarrays. The analysis identified 20 to 128 differentially expressed miRNAs in individual cell lines with emphasis on upregulation over downregulation. Four miRNAs (miR-16-5p, miR-106b-5p, miR-23a-3p and miR-23b-3p) were commonly induced in a subset of breast cancer cells upon BMP4 treatment and inhibition of their expression resulted in an increase in BT-474 cell number, indicating that they possess tumor suppressive properties. Yet no major change was detected when the cells were simultaneously treated with BMP4, and thus these miRNAs do not act as the main mediators of BMP4-induced growth reduction. MiR-16-5p and miR-106b-5p were elevated in MDA-MB-231 cells that respond to BMP4 with increased migration. Their inhibition, in combination with BMP4 treatment, resulted in enhanced MDA-MB-231 cell migration, suggesting that miR-16-5p and miR-106b-5p are engaged in BMP4-induced motility. Taken together, we have shown for the first time that in breast cancer cells BMP4 induces variable miRNA expression patterns.

overall_design: Seven breast cancer cell lines and one mammary epithelial cell line were treated with 100 ng/ml BMP4 or vehicle control for four hours. Total of 16 labeled samples were hybridized to Agilent microarrays.

first: Riikka

last: Havunen

first: Sergei

last: Häyrynen

first: Sanna

last: Penkki

first: Johanna

last: Ketolainen

first: Matti

last: Nykter

first: Anne

last: Kallioniemi


title: Selective glucocorticoid-induced attenuation of the inflammatory response in zebrafish

status: Public on Dec 01 2015

city: Leiden

first: Marcel

last: Schaaf

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

summary: In the present study, we have used the zebrafish to investigate the anti-inflammatory effects of glucocorticoids. An inflammatory response was induced by amputation of the tail fin of 3dpf zebrafish larvae, and the effect of treatment with the glucocorticoid beclomethasone was investigated. A microarray study was performed to study transcriptional changes 4 hours after amputation and the beclomethasone-induced effects on these changes. Our results show that beclomethasone attenuates almost the entire transcriptional response to amputation. Interestingly, the amputation-induced expression of genes involved in leukotriene biosynthesis appears to be resistant to beclomethasone treatment.

overall_design: This microarray study was designed to determine the effect of glucocorticoid treatment on amputation-induced transcriptional changes. For this purpose, the tail fin of 3dpf zebrafish larvae was amputated and 4 hours later larvae were collected. Glucocorticoid treament (25 microM beclomethasone) started two hours before the amputation. This resulted in 4 treament groups: con/veh, amp/veh, con/beclo, amp/beclo. RNA was isolated from 20 larvae per treatment group. Four individual experiments were performed, and the resulting quadruplicate samples were analyzed by microarray, using a common reference approach.

first: A

last: Chatzopoulou

first: J

last: Heijmans

first: H

last: Spaink

middle: H

last: Meijer

first: M

middle: J


title: affy_med_2013_05-Comparison between nodules of WT, NF737 and MS240 lines

city: evry

first: labrune

last: cecile

address: 2 rue gaston cremieux

country: France

institute: INRA

summary: affy_med_2013_05 - affy_med_2013_05 - The experiment is designed to detect transcriptome differences between wild type and two fix minus (NF737 and MS240) mutant lines.-Medicago truncatula WT (R108) and two mutant lines (NF737 and MS240/dnf2) were nodulated using WSM419 Sinorhizobium medicae symbiotic bacteria. Plants were grown in vitro on BN medium and the nodules harvested 14 days post inoculation (dpi). RNA was extracted using the plant RNA extraction kit from Thermo Scientific followed by a DNAse I treatment (TurbO DNAse I Ambion).

overall_design: 9 arrays - Medgene -1.0stv1; gene knock out

first: Stephanie

last: Huguet

first: Benjamin

last: Gourion

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Fip1 regulates mRNA alternative polyadenylation to promote embryonic stem cell self-renewal and somatic cell reprogramming.

city: Research Triangle Park

first: Georgette

middle: Mona

last: Charles

state: NC

address: 111 T.W. Alexander Drive

department: Laboratory of Molecular Carcinogenesis

country: USA

institute: National Institutes of Environmental Health Sciences

summary: Expression profiling of mESCs after Fip1 depletion, 4 days post-transfection with siRNAs

overall_design: Examination of mRNA levels after Fip1 depletion in Mouse ESCs (E14Tg2a.4 cells)

first: G

middle: M

first: C

last: Yao

first: B

last: Lackford

first: L

last: Wang

first: X

last: Zheng

first: E

last: Choi

last: Xie

first: Ji

last: Wan

first: Yi

last: Xing

last: Freudenberg

first: R

last: Jothi

last: Hu

first: Y

last: Shi


title: Microarray analysis profiling of the effect of cowpea phenolic extract on gene expression in bovine peripheral blood in vitro

status: Public on Nov 21 2015

city: Greensboro

first: Mulumebet

last: Worku

state: North Carolina

address: 1601 E market Street

department: Animal Sciences

institute: North Carolina Agricultural and Technical State University

summary: Plant-derived secondary metabolites found in animal feed sources are beneficial for nutrition and health. Cowpea is a protein and phenolic-rich forage used as feed resource in animal system. The objective of this study was to understand the effect of cowpea secondary metabolites on gene expression in cows blood in vitro. Whole blood collected from Holstein Friesian cows were treated with 10 ug/ml of cowpea leaf phenolic extract and untreated samples served as control. Total RNA was isolated and pooled together for microarray analysis. The Agilent one color bovine (v2) 4x44K array was used and preliminary gene expression profiles generated using Cy3 labeled cDNA from CPE-stimulated and untreated samples. Gene expression analysis revealed a total of 3170 differentially expressed genes- 1716 up regulated and 1454 down regulated genes respectively. Pathway analysis identified CPE treatment association with innate immune response pathways including Toll-like receptor (TLR) signaling pathway, the Wnt signaling pathway, inflammation response pathway, and increased expression of the transcription factor NFKB1 were observed. Treatment with CPE decreased the expression of proinflammatory cytokines IL1A, IL1B and IL21. Quantitative real time PCR was performed to validate some gene members of the Toll-like receptor, inflammation response and Wnt signaling pathways. In vitro treatment with CPE impacted global gene expression profile in cow blood and results obtained in this study shows the potential immuno-modulatory properties of cowpea feed phenolic in cows.

overall_design: The global gene expression of the effect of cowpea phenolic extract (CPE) was measured in bovine peripheral blood.The experiment involved two groups; cowpea phenolic extract (CPE) treated samples vs untreated control group. Pooled RNA samples from each group was hybridized on Agilent one color bovine (v2) 4x44K microarray slides. Two slides were prepared each with 4 array compartment.

first: Sarah

last: Adjei-Fremah

first: Louis

last: Jackai

first: Hamid

last: Ismail


title: Kiwifruit response to armoured scale insect feeding

status: Public on Oct 13 2015

city: Lincoln

first: Michael

middle: Garry

last: Hill

address: Gerald St

department: Applied Entomology

country: New Zealand

institute: NZ Institute of Plant & Food Research

summary: The response of kiwifruit vine (Actinidia chinensis 'Hort16A') canes to feeding by the armoured scale insect Hemiberlesia lataniae was tested by screening RNA extracted from bark against a cDNA library of 17,512 unigenes. Substantial transcriptional changes were noted after 7 days for approximately 30% of the ESTs. Transcripts associated with photosynthesis were down-regulated and those associated with secondary metabolism up-regulated. A large number of transcripts orthologous with defence-related genes were differentially expressed including several orthologous with resistance and pathogenesis. This is the first such analysis of  changes to transcript expression in  a plant challenged by feeding by insects from the family diaspididae.

overall_design: RNA was extracted from cane bark taken from treatment and control plants 2 days and 7 days after the insects were applied. Direct comparisons were made with six biological and 2 technical replicates.

first: Garry

first: Kirstin

last: Wurms

first: Marcus

last: Davy

first: Roy

last: Storey


title: Mycobacterium tuberculosis H37Rv transcriptional response to antibacterial agents

status: Public on Nov 11 2015

city: Seattle

first: Shuyi

last: Ma

state: Washington

address: 1900 9th Avenue

department: Department of Pediatrics

institute: University of Washington

summary: Bacteria commonly adapt to stresses by altering gene expression.  To understand the response of M. tuberculosis (MTB) to various antibacterial agents, we performed transcriptomics on MTB bacilli exposed to several test compounds as well as known drugs (capreomycin, cycloserine, ethionamide, isoniazid, kanamycin, moxifloxacin, PA-824, rifampicin, streptomycin).

overall_design: Bacteria were exposed for 16 hrs to various concentrations of each drug (different multiples of the compound's MIC), as noted in the title of each sample. RNA was isolated and applied to arrays provided by TIGR under the NIAID contract N01-AI-15447

first: Tige

middle: R

last: Rustad

first: Reiling

middle: P

last: Liao

first: Mark

last: Hickey

first: David

last: Sherman


title: FOXO regulates RNA interference in Drosophila and protects from RNA virus infection

status: Public on Oct 08 2015

city: Waltham

last: Marr

state: Massachusetts

address: 415 South St

department: Biology

institute: Brandeis University

type: Genome binding/occupancy profiling by genome tiling array

summary: Determination of dFOXO binding sites genomewide identified RNAi  genes as direct targets

overall_design: 2 biological replicates of DNA precipitated with antibodies to Drosophila FOXO were compared to 3 replicates of input DNA for enrichment.

last: Spellberg


title: Transcriptome analysis of HepG2 cell with QD655 and QD705 treatments

city: Miaoli County

first: Chieh Hua

last: Lin

address: 35, Keyan Road, Zhunan Town

department: Division of Biostatistics and Bioinformatics

country: Taiwan

institute: National Health Research Institutes

summary: Discovery time-course genome-wide expression profiles in HepG2 cell with QD655 and QD705 treatments to reveal genotoxicity and chronological regulatory pathway

overall_design: Time-course gene expression profiles of HepG2 cell cline with QD655 and QD705 treatments were analyzed. Total RNA were harvested from 4, 8, 12, 24 and 48 hr QD-treated and untreated cells. Human universal reference RNA was used as the reference for all the array experiments. The customized microarrays used were consisted of 49152 probes. Experiments were conducted as two replicates (different cluture).

first: Cheih-Hua

first: Hsin-Ying

last: Huang

first: Yu-Chieh

first: Chih-Yu

last: Chen

first: Chu-Li

last: Weng

first: Ying-Lan

last: Liu

first: Jyh-Lyh

last: Juang

first: Chung-Shi

last: Yang

first: Chao

middle: A

last: Hsiung


title: Molecular aspects of the role of root hairs during water stress in barley

city: Katowice

first: Miroslaw

last: Kwasniewski

state: silesia district

address: Jagiellonska 28

country: Poland

institute: University of Silesia in Katowice

summary: The important parts of the root system are root hairs, which play a role in mineral and water uptake. Here, we present an analysis of the transcriptomic response to water deficiency of the wild-type (WT) barley cultivar ‘Karat’ and its root hairless mutant rhl1.a. A comparison of the transcriptional changes induced by water stress resulted in the identification of genes whose expression was specifically affected in each genotype. At the onset of water stress, more genes were modulated by water shortage in the roots of the WT plants than in the roots of the rhl1.a. The roots of the WT plants, but not of the rhl1.a, specifically responded with the induction of genes that are related to the ABA biosynthesis, stomata closure and cell wall biogenesis, thus indicating the specific activation of processes that are related to water stress signalling and protection. On the other hand, the processes of further response to abiotic stimuli, including hydrogen peroxide, heat and high light intensity, were specifically up-regulated in the leaves of the rhl1.a. An extended period of severe stress caused more drastic transcriptome changes in the roots and leaves of the rhl1.a mutant than in those of the WT. These results are in agreement with the much stronger damage to photosystem II in the rhl1.a mutant than in its parent cultivar after ten days of water stress. Taking into account the putative stress sensing and signalling features of the root hair transcriptome, we discuss the role of root hairs as sensors of environmental conditions.

overall_design: Water-deficiency conditions related gene expression analysis was performed in barley in two genotypes: the wild-type (WT) barley cultivar ‘Karat’ and its root hairless mutant rhl1.a; in three time points: (1) control conditions, (2) onset of water stress and (3) after 10 days of severe water stress; in two organs: roots and leaves no. 2; analyses were performed in three biological replicates. Moreover an analysis of the root hair formation transcriptome was performed in the 1 cm-long root tip fragments of the wild-type (WT) barley cultivar ‘Karat’ and its root hairless mutant rhl1.a grown in aeroponic conditions; analyses were performed in four biological replicates; for each biological replicate root tip fragments from three plants were pooled together.


title: Transcriptome Profiling in NHP-HCT recipients

status: Public on Nov 29 2015

city: Pittsburgh

first: Warren

middle: David

last: Shlomchik

state: PA

address: 3550 Terrace Street

department: Medicine

institute: University of Pittsburgh

summary: Graft versus host disease (GVHD) is the most common complication of hematopoietic stem cell transplant (HCT). However, our understanding of the molecular pathways that cause this disease remains incomplete, leading to inadequate treatment strategies. To address this, we measured the gene expression profile of non-human primate (NHP) T cells during acute GVHD.  This transcriptome analysis enables an unsupervised approach to the identification of targets for disease control using a model with an immune system that closely overlaps with the human and has a high degree of cross-reactivity with human antibody-based therapeutics.

overall_design: Series of HCT performed on n=27 animals with n=47 arrays from the post transplant period including arrays from n=34 untransplanted healthy controls

first: Scott

middle: N

last: Furlan

first: Leslie

middle: S

last: Kean


title: ST3GAL1-Associated Transcriptomic Program in Glioblastoma Tumor Growth, Invasion, and Prognosis

status: Public on Nov 09 2015

city: Singapore

first: Edwin

last: Sandanaraj

address: 11 Jalan Tan Tock Seng

department: Research

country: Singapore

institute: NNI

summary: Cell surface sialylation confers many roles in cancer biology including cell proliferation, invasiveness, metastasis and angiogenesis. We show here that ST3Gal1 sialyltransferase marks a self-renewing cellular fraction. Depletion of ST3GAL1 abrogates glioma cell growth and tumorigenicity. In contrast, TGFb induces ST3GAL1 expression and correlates with the pattern of ST3Gal1 activation in patient tumors of the mesenchymal molecular subtype. To delineate the downstream events of ST3Gal1 signaling, we utilized a bioinformatical approach that leveraged on the greater statistical power of large patient databases, and subsequently verified our predictions in patient-derived glioma cells. We identify FoxM1, a major stem cell regulatory gene, as a downstream effector, and show that ST3Gal1 mediates the glioma phenotype through control of FoxM1 protein degradation

overall_design: Total RNA from primary neurosphere culture of brain tumor specimens were flow-sorted to identify Peanut Agglutinin(PNA) affinity. The fractions of different degress of PNA bound GPCs were hybridized on Illumina Human Ref-8v2 bead chips to study the impact of transcriptome pattern of PNA affinity.  Specimens were obtained from 4 patients and replicate arrays were performed for all 4 neurosphere cultures.

first: Yuk

middle: K

last: Chong

first: Tan

middle: B

last: Toh

first: Moogaambikai

last: Thangaveloo

first: Melanie

last: Tan

first: Lynnette

middle: W

last: Koh

first: Grace

middle: G

last: Lim

first: Joanna

middle: D

last: Holbrook

first: Oi

middle: L

last: Kon

first: Mahendran

last: Nadarajah

first: Ivan

last: Ng

first: Wai

first: Kah

first: Carol

last: Tang

first: Beng

middle: T

last: Ang


title: Signatures of post-zygotic structural genetic aberrations in the cells of histologically normal breast tissue that can predispose to sporadic breast cancer [SET 15]

status: Public on Oct 01 2015

city: Uppsala

first: Chiara

last: Rasi

state: Sweden

address: Husargatan 3

department: Department of Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

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

summary: Sporadic breast cancer (SBC) is a common and heterogeneous disease. There is no reliable way of early  prediction of risk for SBC in the general population. We studied 282 females with SBC concentrating on copy  number aberrations in tumor-free breast tissue (uninvolved margin, UM) outside the area of primary tumor  (PT). Totally 1162 UMs (1-14 per breast) were studied. PT and blood/skin as control was also analyzed.  Comparative analysis between genetic profiles for UM(s), PT(s) and blood/skin from the same patient is the  core of study design. We identified 108 patients with at least one aberrant UM specimen, representing 38.3%  of all cases. Gains were the dominating mutations in microscopically normal breast cells and gain of ERBB2,  with overexpression of HER2 protein, was the most common aberration in normal cells. Five additional  receptor genes (EGFR, FGFR1, IGF1R, LIFR and NGFR) also showed gains, and these were occasionally  present in combination with the gain of ERBB2. Up to 67.6% of patients showed gain of one or more of these  genes in normal cells. The aberrations found in normal cells from UMs were previously described in cancer  literature, which suggest their causative, driving role in this disease. We demonstrate that analysis of normal  cells from cancer-bearing patients leads to identification of genetic signatures that may predispose to SBC.  Early detection of signals suggesting a predisposition towards development of SBC, long before detectable  tumors are formed, is a key to the anticipated shift into a preventive paradigm of personalized medicine of  breast cancer.

overall_design:
We studied 282 female breast cancer patients that were assessed as affected by sporadic disease at the time of diagnosis and all underwent mastectomy. In total, 1162 UMs (uninvolved margin tissues), ranging from 1 to 14 UMs per patient, taken outside the location of clinically characterized index primary tumor, were analyzed on Illumina arrays. For each subject, DNA from at least one control tissue was also analyzed, which was predominantly blood DNA, alternatively skin-derived DNA. We also studied primary tumor (PT), or up to 3 primary tumor foci from patients with diagnosis of multifocal disease. This GEO project contains the genotyping profiles (processed and normalized data including Log R Ratio and B allele frequency) for these 1162 UMs used in the study. Information on phenotypes (age at diagnosis, tumor focality, tumor grade, tumor molecular phenotype) is also provided, whenever available.   This subSeries represents 133 tumor samples (genotype data from primary tumor tissue) from subject showing at least one UM sample with aberration.
[29_PrimaryTumors_GPL6984.txt]  29 tumors samples genotyped on the platform GPL6984 (Human1M-Duov3_B)
[2_PrimaryTumors_GPL13135.txt]  2 tumors samples genotyped on the platform GPL13135 (HumanOmniExpress BeadChip).
[4_PrimaryTumors_GPL18636.txt]  4 tumors samples genotyped on the platform GPL18636 (Illumina Human660W-Quad v1.0). Please note that GPL18636 on GEO has chromosome coordinates in genome buid 36. In the matrix table I'm maintaining the same IDs as on GEO, but the chromosomal positions (“Position_hg19”) is reported in chromosomal build 37. I did this to provide with experiments which can be directly compared with all the others, which are run on platforms that already support chromosome build 37.
[98_PrimaryTumors_GPL18224.txt]  98 tumors samples genotyped on the platform GPL18224 (Infinium HumanOmniExpressExome).


title: Oviduct-Embryo Interactions in Cattle: Two-Way Traffic or a One-Way Street? [Affymetrix]

status: Public on Nov 04 2015

city: Dublin

first: Peadar

last: O'Gaora

address: Belfield

country: Ireland

institute: UCD

summary: The objective of this study was to examine the effect of the presence of a single or multiple embryo(s) on the transcriptome of the bovine oviduct. In Experiment 1, cyclic (non-bred, n = 6) and pregnant (artificially inseminated, n = 11) heifers were slaughtered on Day 3 after estrus, and the ampulla and isthmic regions of the oviduct ipsilateral to the corpus luteum were separately flushed. Oviductal epithelial cells from the isthmus region, in which all oocytes/embryos were located, were snap-frozen for microarray analysis. In Experiment 2, heifers were divided into cyclic (non-bred, n = 6) or pregnant (multiple embryo transfer, n = 10) groups. In vitro-produced presumptive zygotes were transferred endoscopically to the ipsilateral oviduct on Day 1.5 post estrus (n = 50 zygotes per heifer). Heifers were slaughtered on Day 3 and oviductal isthmus epithelial cells were recovered for RNA sequencing. Microarray analysis in Experiment 1 failed to detect any difference in the transcriptome of the oviductal isthmus induced by the presence of a single embryo. In Experiment 2, following multiple embryo transfer, RNA sequencing revealed 278 differentially expressed genes of which 123 were up- and 155 were down-regulated in pregnant heifers. Most of the down-regulated genes were related to immune function.

overall_design: Five samples from pregnant heifers and five control, cyclic heifers were analysed

first: Niamh

last: Forde

last: Ó Gaora

first: Pat

last: Lonergan

first: Thomas

last: Spencer

first: Dimitrios

last: Rizos


title: MicroRNA 19a replacement partially rescues fin and cardiac defects in zebrafish model of Holt Oram syndrome [array]

city: Pisa

first: Romina

last: D'Aurizio

state: PI

address: via Moruzzi 1

department: IIT

country: Italy

institute: CNR

summary: The regulative role of miRNAs in Holt-Oram Syndrome is investigated in a zebrafish model.

overall_design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO-Tbx5a against the Tbx5a translational start site. 1,5 ng of MO-Tbx5a were co-injected in 1-cell stage embryos with 0,25 ng of miR-Ct (hts phenotype) or with 0,25 ng of miR-19a mimics (rescue phenotype). Embryos coinjected with 1,5ng of MO-CT and 0,25 ng of miR-Ct mimic were used as controls. At 24 hpf total RNA was extracted from 50 embryos for each thesis. The Zebrafish wild-type AB strain line was used.

first: Letizia

last: Pitto

first: Elena

last: Chiavacci

first: Mara

last: D'Onofrio

last: Arisi


title: Systems pharmacology of adiposity reveals inhibition of EP300 as a common therapeutic mechanism of caloric restriction and resveratrol in obesity

status: Public on Nov 17 2015

city: Tsu

first: Yuhei

last: Nishimura

state: Mie

address: 2-174 Edobashi

department: Integrative Pharmacology

country: Japan

institute: Mie University Graduate School of Medicine

summary: Both caloric restriction (CR) and resveratrol (RSV) have beneficial effects on obesity. However, the biochemical pathways that mediate the beneficial effects of CR and RSV can be highly interconnected and have not been fully elucidated. To reveal the common therapeutic mechanism of CR and RSV, we performed comparative transcriptome analysis of adipose tissues from diet-induced obese (DIO) zebrafish and obese human. We identified 9 and 7 genes whose expressions were regulated in common by CR and RSV in DIO zebrafish and obese human, respectively. Although the gene lists were not overlapped except for one gene, the gene ontologies enriched in the gene lists were highly overlapped, including adipocyte differentiation, lipid storage and lipid metabolism. Bioinformatic analysis of cis-regulatory sequence of these genes revealed that their transcriptional regulators were also well overlapped, including EP300, HDAC2, CEBPB, CEBPD, FOXA1 and FOXA2. We also identified 15 and 46 genes dysregulated in adipose tissue of DIO zebrafish and obese human, respectively. The bioinformatics analysis identified EP300, HDAC2, and CEBPB as common transcriptional regulators for these genes. EP300 is a histone and lysyl acetyltransferase that modulate the function of histone and various proteins including CEBPB, CEBPD, FOXA1 and FOXA2. We were able to demonstrate that the adiposity in larval zebrafish were significantly reduced by C646, an inhibitor of EP300 that antagonizes acetyl-CoA. The reduction of adiposity by C646 was not significantly different to those by RSV or co-treatment of C646 and RSV. These results suggest that inhibition of EP300 may be a common therapeutic mechanism between CR and RSV in adipose tissue of obese individuals.

overall_design: Gene expression regulated by resveratrol in visceral adipose tissue from diet-induced obese zebrafish (OF+RSV) was measured. Gene expression in visceral adipose tissue from diet-induced obese zebrafish not treated with resveratrol (OF) and from control zebrafish were also measured. Three independent experiments were performed for each group.

first: Takaaki

last: Yanai

first: Toshio

last: Tanaka


title: Genome-wide identification and analysis of microRNA expression in  MEFs, ESCs, and iPSCs

city: Minneapolis

first: Nobuaki Kikyo

email: kikyo001@umn.edu, hiraih@umich.edu

state: MN

address: 2001 6th St SE

department: Genetics, Cell Biology and Development

institute: University of Minnesota

summary: Microarray analysis of miRNA—Two micrograms of total RNA was extended at the 3′ terminus with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining. Hybridization was performed overnight on a µParaflo microfluidic chip using a microcirculation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to the target microRNA (miRBase, http://mirbase.org) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using photogenerated reagent chemistry.  The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 µl 6× SSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34°C. After RNA hybridization, tag-conjugating Cy5 dye was circulated through the microfluidic chip for dye staining. Fluorescence images were collected by using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics). Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).

overall_design: In the study presented here, compared the genome-wide expression patterns of miRNAs in MEFs, ESCs, and various iPSCs to identify miRNAs that were potentially involved in the LIF-independence. iPSCs in this study: O-retro-iPSCs-LIF(+), O-lenti-iPSCs-LIF(+), M3O-lenti-iPSCs-LIF(+), and M3O-lenti-iPSCs-LIF(-). O-retro-iPSCs-LIF(+) was established by transduction of the OSKM genes into MEFs with the pMXs-IP retroviral vector and maintained with LIF. O-lenti-iPSCs-LIF(+) was prepared with lentiviral Oct4 and retroviral Sox2, Klf4, and c-Myc (SKM) to maintain the expression of the Oct4 transgene in iPSCs as a control for the two M3O-based iPSC types. M3O-lenti-iPSCs-LIF(+) was the same as O-lenti-iPSCs-LIF(+) except that M3O was used instead of Oct4. M3O-lenti-iPSCs-LIF(-) was the same as M3O-lenti-iPSCs-LIF(+) except that LIF was omitted during establishment and maintenance.

first: Hiroyuki

last: Hirai

first: Nobuaki

last: Kikyo


title: Post-zygotic structural variants in histologically normal breast tissue may predispose to sporadic breast cancer [SET 13]

last: Rasi

summary: Sporadic breast cancer (SBC) is a common and heterogeneous disease. There is no reliable way of early prediction of risk for SBC in the general population. We studied 282 females with SBC concentrating on copy number aberrations in tumor-free breast tissue (uninvolved margin, UM) outside the area of primary tumor (PT). Totally 1162 UMs (1-14 per breast) were studied. PT and blood/skin as control was also analyzed. Comparative analysis between genetic profiles for UM(s), PT(s) and blood/skin from the same patient is the core of study design. We identified 108 patients with at least one aberrant UM specimen, representing 38.3% of all cases. Gains were the dominating mutations in microscopically normal breast cells and gain of ERBB2, with overexpression of HER2 protein, was the most common aberration in normal cells. Five additional receptor genes (EGFR, FGFR1, IGF1R, LIFR and NGFR) also showed gains, and these were occasionally present in combination with the gain of ERBB2. Up to 67.6% of patients showed gain of one or more of these genes in normal cells. The aberrations found in normal cells from UMs were previously described in cancer literature, which suggest their causative, driving role in this disease. We demonstrate that analysis of normal cells from cancer-bearing patients leads to identification of genetic signatures that may predispose to SBC. Early detection of signals suggesting a predisposition towards development of SBC, long before detectable tumors are formed, is a key to the anticipated shift into a preventive paradigm of personalized medicine of breast cancer.

overall_design:
We studied 282 female breast cancer patients that were assessed as affected by sporadic disease at the time of diagnosis and all underwent mastectomy. In total, 1162 UMs (uninvolved margin tissues), ranging from 1 to 14 UMs per patient, taken outside the location of clinically characterized index primary tumor, were analyzed on Illumina arrays. For each subject, DNA from at least one control tissue was also analyzed, which was predominantly blood DNA, alternatively skin-derived DNA. We also studied primary tumor (PT), or up to 3 primary tumor foci from patients with diagnosis of multifocal disease. This GEO project contains the genotyping profiles (processed and normalized data including Log R Ratio and B allele frequency) for these 1162 UMs used in the study. Information on phenotypes (age at diagnosis, tumor focality, tumor grade, tumor molecular phenotype) is also provided, whenever available.
92 experiments runned on platform GPL6984 (Human1M-Duov3_B)


title: Rare CNVs in Lynch Syndrome patients negative for mutations in mismatch repair genes [Agilent]

status: Public on Nov 30 2015

city: Brasília

first: Rolando

middle: Andre Rios

last: Villacis

state: DF

address: Asa Norte

department: Genetics and Morphology

country: Brazil

institute: University of Brasília - UnB

type: Genome variation profiling by genome tiling array

summary: Only a small proportion of cases suspected to have Lynch Syndrome (LS) can be explained by mutation in the mismatch repair (MMR) genes. This study aimed to identify rare CNVs that may contribute to an increased risk for hereditary colorectal cancer in patients with MMR proficiency.

overall_design: Genomic DNA was extracted from the blood of 54 unrelated patients who met criteria for LS (Amsterdam or Bethesda). Genomic alterations were evaluated using the Agilent-022060 4x180K microarray platform. The reference was a pool of normal male DNA (Promega, cat. no. G1471) or normal female DNA (Promega, cat.no. G1521).


title: Post-zygotic structural variants in histologically normal breast tissue may predispose to sporadic breast cancer [SET 12]

first: Chiara

overall_design:
We studied 282 female breast cancer patients that were assessed as affected by sporadic disease at the time of diagnosis and all underwent mastectomy. In total, 1162 UMs (uninvolved margin tissues), ranging from 1 to 14 UMs per patient, taken outside the location of clinically characterized index primary tumor, were analyzed on Illumina arrays. For each subject, DNA from at least one control tissue was also analyzed, which was predominantly blood DNA, alternatively skin-derived DNA. We also studied primary tumor (PT), or up to 3 primary tumor foci from patients with diagnosis of multifocal disease. This GEO project contains the genotyping profiles (processed and normalized data including Log R Ratio and B allele frequency) for these 1162 UMs used in the study. Information on phenotypes (age at diagnosis, tumor focality, tumor grade, tumor molecular phenotype) is also provided, whenever available.
The experiements 201-238 out of 238 experiments runned on platform GPL13135 (HumanOmniExpress BeadChip)


title: Signatures of post-zygotic structural genetic aberrations in the cells of histologically normal breast tissue that can predispose to sporadic breast cancer  [SET 14]

overall_design:
We studied 282 female breast cancer patients that were assessed as affected by sporadic disease at the time of diagnosis and all underwent mastectomy. In total, 1162 UMs (uninvolved margin tissues), ranging from 1 to 14 UMs per patient, taken outside the location of clinically characterized index primary tumor, were analyzed on Illumina arrays. For each subject, DNA from at least one control tissue was also analyzed, which was predominantly blood DNA, alternatively skin-derived DNA. We also studied primary tumor (PT), or up to 3 primary tumor foci from patients with diagnosis of multifocal disease. This GEO project contains the genotyping profiles (processed and normalized data including Log R Ratio and B allele frequency) for these 1162 UMs used in the study. Information on phenotypes (age at diagnosis, tumor focality, tumor grade, tumor molecular phenotype) is also provided, whenever available.   This subSeries represents 108 controls (genotype data from whool blood/skin ) from subject showing at least one UM sample with aberration.
[23_controls_GPL6984.txt]  23 control experiments (blood/skin tissue) run on the platform GPL6984 (Human1M-Duov3_B)
[2_controls_GPL13135.txt]  2 control experiments (blood/skin tissue) run on the platform GPL13135 (HumanOmniExpress BeadChip).
[5_controls_GPL18636.txt]  5 control experiments (blood/skin tissue) run on the platform GPL18636 (Illumina Human660W-Quad v1.0). Please note that GPL18636 on GEO has chromosome coordinates in genome buid 36. In the matrix table I'm maintaining the same IDs as on GEO, but the chromosomal positions (“Position_hg19”) is reported in chromosomal build 37. I did this to provide with experiments which can be directly compared with all the others, which are run on platforms that already support chromosome build 37.
[78_controls_GPL18224.txt]  78 control experiments (blood/skin tissue) run on the platform GPL18224 (Infinium HumanOmniExpressExome).


title: HDAC inhibition impedes epithelial–mesenchymal plasticity and suppresses metastatic, castration-resistant prostate cancer

status: Public on Oct 12 2015

city: Los Angeles

first: Yu-Ting

last: Tseng

state: California

address: 650 Charles E. Young Drive South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: University of California, Los Angeles

summary: PI3K (phosphoinositide 3-kinase)/AKT and RAS/MAPK (mitogen-activated protein kinase) pathway coactivation in the prostate epithelium promotes both epithelial–mesenchymal transition (EMT) and metastatic castration-resistant prostate cancer (mCRPC), which is currently incurable. To study the dynamic regulation of the EMT process, we developed novel genetically defined cellular and in vivo model systems from which epithelial, EMT and mesenchymal-like tumor cells with Pten deletion and Kras activation can be isolated. When cultured individually, each population has the capacity to regenerate all three tumor cell populations, indicative of epithelial–mesenchymal plasticity. Despite harboring the same genetic alterations, mesenchymal-like tumor cells are resistant to PI3K and MAPK pathway inhibitors, suggesting that epigenetic mechanisms may regulate the EMT process, as well as dictate the heterogeneous responses of cancer cells to therapy. Among differentially expressed epigenetic regulators, the chromatin remodeling protein HMGA2 is significantly upregulated in EMT and mesenchymal-like tumors cells, as well as in human mCRPC. Knockdown of HMGA2, or suppressing HMGA2 expression with the histone deacetylase inhibitor LBH589, inhibits epithelial–mesenchymal plasticity and stemness activities in vitro and markedly reduces tumor growth and metastasis in vivo through successful targeting of EMT and mesenchymal-like tumor cells. Importantly, LBH589 treatment in combination with castration prevents mCRPC development and significantly prolongs survival following castration by enhancing p53 and androgen receptor acetylation and in turn sensitizing castration-resistant mesenchymal-like tumor cells to androgen deprivation therapy. Taken together, these findings demonstrate that cellular plasticity is regulated epigenetically, and that mesenchymal-like tumor cell populations in mCRPC that are resistant to conventional and targeted therapies can be effectively treated with the epigenetic inhibitor LBH589.

overall_design: Pb-Cre+/-;PtenL/L;KrasG12D/+ mice with prostate specific loss of Pten and K-ras activation develop high grade, invasive prostate cancer and metastatic lesions in the lungs and liver. Laser-capture microdissection was used to extract tumor cells from different histopathological lesions in prostate and metastatic lesions in the lungs. Their transcript levels were measured by custom Agilent 4x44K whole mouse genome expression oligonucleotide microarrays. Each cohort, except for the poor-differentiated lesions, had three biological replicates.

first: Marcus

last: Ruscetti

first: Eman

last: Dadashian

first: Weilong

last: Guo

first: Bill

last: Quach

first: David

middle: J

last: Mulholland

first: Juw

last: Park

first: Linh

last: Tran

first: Naoko

last: Kobayashi

first: Daniella

last: Bianchi-Frias

first: Yi

last: Xing

first: Pete

last: Nelson

first: Hong

last: Wu


title: Post-zygotic structural variants in histologically normal breast tissue may predispose to sporadic breast cancer [SET 10]

overall_design:
We studied 282 female breast cancer patients that were assessed as affected by sporadic disease at the time of diagnosis and all underwent mastectomy. In total, 1162 UMs (uninvolved margin tissues), ranging from 1 to 14 UMs per patient, taken outside the location of clinically characterized index primary tumor, were analyzed on Illumina arrays. For each subject, DNA from at least one control tissue was also analyzed, which was predominantly blood DNA, alternatively skin-derived DNA. We also studied primary tumor (PT), or up to 3 primary tumor foci from patients with diagnosis of multifocal disease. This GEO project contains the genotyping profiles (processed and normalized data including Log R Ratio and B allele frequency) for these 1162 UMs used in the study. Information on phenotypes (age at diagnosis, tumor focality, tumor grade, tumor molecular phenotype) is also provided, whenever available.
The experiements 1-100 out of 238 experiments runned on platform GPL13135 (HumanOmniExpress BeadChip)


title: Post-zygotic structural variants in histologically normal breast tissue may predispose to sporadic breast cancer [SET 9]

overall_design:
We studied 282 female breast cancer patients that were assessed as affected by sporadic disease at the time of diagnosis and all underwent mastectomy. In total, 1162 UMs (uninvolved margin tissues), ranging from 1 to 14 UMs per patient, taken outside the location of clinically characterized index primary tumor, were analyzed on Illumina arrays. For each subject, DNA from at least one control tissue was also analyzed, which was predominantly blood DNA, alternatively skin-derived DNA. We also studied primary tumor (PT), or up to 3 primary tumor foci from patients with diagnosis of multifocal disease. This GEO project contains the genotyping profiles (processed and normalized data including Log R Ratio and B allele frequency) for these 1162 UMs used in the study. Information on phenotypes (age at diagnosis, tumor focality, tumor grade, tumor molecular phenotype) is also provided, whenever available.
The 701-811 samples out of 811 experiments runned on platform GPL18224 (Infinium HumanOmniExpressExome)


title: Post-zygotic structural variants in histologically normal breast tissue may predispose to sporadic breast cancer [SET 11]

overall_design:
We studied 282 female breast cancer patients that were assessed as affected by sporadic disease at the time of diagnosis and all underwent mastectomy. In total, 1162 UMs (uninvolved margin tissues), ranging from 1 to 14 UMs per patient, taken outside the location of clinically characterized index primary tumor, were analyzed on Illumina arrays. For each subject, DNA from at least one control tissue was also analyzed, which was predominantly blood DNA, alternatively skin-derived DNA. We also studied primary tumor (PT), or up to 3 primary tumor foci from patients with diagnosis of multifocal disease. This GEO project contains the genotyping profiles (processed and normalized data including Log R Ratio and B allele frequency) for these 1162 UMs used in the study. Information on phenotypes (age at diagnosis, tumor focality, tumor grade, tumor molecular phenotype) is also provided, whenever available.
The experiements 101-200 out of 238 experiments runned on platform GPL13135 (HumanOmniExpress BeadChip)


title: Post-zygotic structural variants in histologically normal breast tissue may predispose to sporadic breast cancer [SET 8]

overall_design:
We studied 282 female breast cancer patients that were assessed as affected by sporadic disease at the time of diagnosis and all underwent mastectomy. In total, 1162 UMs (uninvolved margin tissues), ranging from 1 to 14 UMs per patient, taken outside the location of clinically characterized index primary tumor, were analyzed on Illumina arrays. For each subject, DNA from at least one control tissue was also analyzed, which was predominantly blood DNA, alternatively skin-derived DNA. We also studied primary tumor (PT), or up to 3 primary tumor foci from patients with diagnosis of multifocal disease. This GEO project contains the genotyping profiles (processed and normalized data including Log R Ratio and B allele frequency) for these 1162 UMs used in the study. Information on phenotypes (age at diagnosis, tumor focality, tumor grade, tumor molecular phenotype) is also provided, whenever available.
The sixth 100 samples out of 811 experiments runned on platform GPL18224 (Infinium HumanOmniExpressExome)


title: Expression data from the mammary gland of ovariectomized (ovx) rats treated for three days with E2, 3-MC, E2+3-MC

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary:
Crosstalk between Aryl hydrocarbonreceptor (AHR) and Estrogen receptor (ER) is poorly understood, but seems to play a major role in female reproductive organs.
The study was designed to see the overall gene-expression change in the mammary gland induced by AHR ligand 3-MC alone and in combination with E2.

overall_design: Rats were treated with vehicle control (DMSO), 17β-Estradiol (E2), 3-Methylcholanthrene (3-MC) or E2+3-MC for 48 h.  Mammary glands were obtained 24 h after the last treatment. 3 biological samples from three rats were analyzed for each treatment group .

first: Janina

last: Helle

first: Georg

last: Kretzschmar


title: Post-zygotic structural variants in histologically normal breast tissue may predispose to sporadic breast cancer [SET 7]

first: Chiara

last: Rasi


title: JNK2 inhibits mammary luminal cell commitment

city: Chapel Hill

first: Charles

middle: M.

last: Perou

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

overall_design: referenceXsample

first: Michael

last: Cantrell

first: Nancy

last: Ebelt

first: Adam

last: Pfefferle

first: Chuck

middle: M

first: Carla

last: Berg


title: Expression data of ileal mucosa in developing piglets

status: Public on Sep 30 2015

city: Kyoto

first: Ryo

last: Inoue

address: 1-5, Hangi-cho, shimogamo

institute: Kyoto Prefectural University

summary:
The transcriptome changes of the ileal mucosa in suckling piglets during early postnatal life were analysed to contribute to the knowledge of a pig’s gut development. In addition, the ileal transcriptome of suckling piglets was compared with that of age-matched weaned piglets (weaned at the age of 21 days) to elucidate the effect of weaning on the developing gut.
DNA microarray was used to analyse the change of transcriptome profiles and biological pathways in porcine ileum that occurred during the developmental or the weaning process.

overall_design: Ileal mucosa was collected from thirty piglets from two littermates. Seven of the piglets were segregated and weaned at the age of 21 days (weaned group), while the others remained with their own sow as the intensive suckling piglets (suckling group) and were prohibited access to the sow’s diet to ensure that they solely consumed breast milk.  The piglets in the suckling group were killed and dissected at the age of 1 day (S1D), 7 days (S7D), 14 days (S14D), 21 days (S21D), 28 days (S28D) and 35 days (S35D). At each time point, four piglets (two from each litter) were used except in the case of 35-day-old piglets, three of them were used. Four piglets in the weaning group were killed and dissected at the age of 28 days (7 days post-weaning; 21W28D) and the remaining three were killed and dissected at the age of 35 days (14 days post-weaning; 21W35D).

first: R

first: D

last: Kelly


title: Gene expression profiling of Foxi3 deficient embryonic molar tooth epithelium

city: Helsinki

first: Maria

last: Jussila

state: Helsinki

address: Viikinkaari 9

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

summary: Foxi3 is a transcription factor expressed in the epithelium during tooth development. In this study we used a microarray analysis to indentify differentially expressed genes in bud stage (E13.5 ) mandibular molar epithelium of conditional Foxi3 knock-out embryos compared to control littermates.

overall_design: Dispase-dissociated molar epithelia of 5 conditional Foxi3 knock-out (K14-cre43;Foxi3-/floxed) or wild-type E13.5 mouse embryos were pooled together and altogether 4 biologial replicates of both genotypes were analyzed. Array and data analysis were performed in the Biomedicum Functional Genomics Unit (University of Helsinki, Finland).

first: Irma

last: Thesleff


title: Comparative genome hybridization of Enteropathogenic Yersinia

city: University of Helsinki

first: Kaisa

middle: Aulikki

last: Jaakkola

address: Agnes Sjöbergin katu 2

department: The Department of Food Hygiene and Environmental Health

institute: University of Helsinki, Faculty of veterinary medicine

summary: Enteropathogenic Yersinia enterocolitica and Yersinia pseudotuberculosis share many traits in terms of infections they cause, but their epidemiology and ecology seem to differ in many ways. Pigs are the only known reservoir for Y. enterocolitica 4/O:3 strains while Y. pseudotuberculosis strains have been isolated from variety of sources including fresh vegetables and wild animals. A comparative genomic hybridization (CGH) analysis with a DNA microarray based on three Yersinia enterocolitica and four Yersinia pseudotuberculosis genomes was conducted to shed light on genomic differences between the enteropathogenic Yersinia. In total 99 strains isolated from various sources were hybridized and analyzed.

sample_organism:
Yersinia enterocolitica
Yersinia pseudotuberculosis
Yersinia pekkanenii

platform_organism: Yersinia enterocolitica subsp. enterocolitica 8081

platform_organism: Yersinia enterocolitica subsp. palearctica Y11

platform_organism: Yersinia enterocolitica subsp. palearctica 105.5R(r)

overall_design: Array CGH. Two-color hybridizations on 8x15K Agilent arrays. Eleven reference strain (Y. enterocolitica strain 8081, Y. enterocolitica strain DSM 130 30 and Y. pseudotuberculosis IP32953) hybridizations and four replicate hybridizations of strain HV.

first: Hannu

last: Korkeala

first: Panu

last: Somervuo


title: Intra-tumor Genetic Heterogeneity in Rectal Canger

status: Public on Sep 24 2015

city: Ann Arbor

first: Ana

middle: Rodrigues

last: Grant

state: MI

address: 100 Washtenaw Avenue

department: Computational Medicine & Bioinformatics

institute: University of Michigan

summary:
Colorectal cancer arises in part from the cumulative effects of multiple gene lesions. Recent studies in selected cancer types have revealed significant intra-tumor genetic heterogeneity and highlighted its potential role in disease progression and resistance to therapy. We hypothesized the existence of significant intra-tumor genetic heterogeneity in rectal cancers involving variations in localized somatic mutations and copy number abnormalities.
Two or three spatially disparate areas from each of six rectal tumors were dissected and subjected to next-generation whole exome DNA sequencing, Oncoscan SNP arrays, and targeted confirmatory sequencing and analysis. The resulting data were integrated to define subclones using SciClone. Mutant-allele tumor heterogeneity (MATH) scores, mutant allele frequency correlation, and mutation percent concordance were calculated, and Copy number analysis including measurement of correlation between samples was performed.

overall_design: Affymetrix OncoScan V3 arrays were run on all tumor samples. The OncoScan array platform consists of a set of 217k probes designed specifically for profiling tumors. The overall resolution of the assay for detecting copy number change generates data at 50-100kb resolution across a set of 891 cancer genes, and 300-400kb across the rest of the genome.  Raw array florescence intensity data generated on the Affymetrix scanners in the form of CEL files were loaded into the OncoScan Console software v.1.1.0 (Affymetrix, Santa Clara, California). Quality control statistics as well as integrated OSCHP files were generated by OncoScan Console. The standard Affymetrix reference control file for OncoScan data was used for processing the arrays.

first: Karin

last: Hardiman

first: Peter

last: Ulintz

middle: R


title: Targeted Sequencing identifies patients with pre-clinical MDS at high risk of disease progression

status: Public on Sep 17 2015

city: Leeds

first: Catherine

last: Cargo

address: Beckett Street

department: HMDS

country: United Kingdom

institute: Leeds Cancer Centre

summary: The diagnosis of myelodysplastic syndromes (MDS) remains problematic due to the subjective nature of morphological assessment.  The reported high frequency of somatic mutations and increased structural variants by array-based cytogenetics have provided potential objective markers of disease however this has been complicated by reports of similar abnormalities in the healthy population.  We aimed to identify distinguishing features between those with early MDS and reported healthy individuals by characterising 69 patients who, following a non-diagnostic marrow, developed progressive dysplasia or acute myeloid leukaemia (AML).  Targeted sequencing and array based cytogenetics identified a driver mutation and/or structural variant in 91% (63/69) of pre-diagnostic samples with the mutational spectrum mirroring that in the MDS population.  When compared with the reported healthy population the mutations detected had significantly greater median variant allele fraction (40% vs 9-10%) and occurred more commonly with additional mutations (≥2 mutations 64% vs. 8%).    Furthermore mutational analysis identified a high-risk group of patients with shorter time to disease progression and poorer overall survival.  The mutational features in our cohort are distinct from those seen in the healthy population and, even in the absence of definitive disease, can predict outcome.  Early detection may allow consideration of intervention in poor risk patients.

overall_design: We performed array based cytogenetics using HumanCytoSNP-12 (Illumina) on 69 patients diagnosed with acute myeloid leukaemia or myelodysplastic syndrome who had a previously non-diagnostic sample.  SNP array analysis was performed on all diagnostic samples.  In those with a documented abnormality, SNP-A was performed on the corresponding pre-diagnostic sample (n=32).

middle: A

first: Nicola

last: Rowbotham

first: Paul

last: Evans

first: Sharon

last: Barrans

first: David

last: Bowen

first: Simon

last: Crouch

first: Andrew

last: Jack


title: Transcriptome analysis reveals regulatory networks underlying differential susceptibility to Botrytis cinerea in response to nitrogen availability in Solanum lycopersicum.

status: Public on Sep 16 2015

city: Santiago

first: Andrea

last: Vega

address: Vicuña Mackenna 4860

department: Ciencias Vegetales

country: Chile

institute: Pontificia Universidad Catolica de Chile

summary:
Transcriptomic analysis in response to Botrytis cinerea infections under conrasting nitrate regime
Nitrogen (N) is one of the main limiting nutrients for plant growth and crop yield. It is well documented that changes in nitrate availability, the main N source found in agricultural soils, influences a myriad of developmental programs and processes including the plant defense response. Indeed, many agronomical reports indicate that the plant N nutritional status influences their ability to respond effectively when challenged by different pathogens. However, the molecular mechanisms involved in N-modulation of plant susceptibility to pathogens are poorly characterized. In this work, we show that Solanum lycopersicum defense response to the necrotrophic fungus Botrytis cinerea is affected by plant N availability, with higher susceptibility in nitrate-limiting conditions. Global gene expression responses of tomato against B. cinerea under contrasting nitrate conditions reveals that plant primary metabolism is affected by the fungal infection regardless of N regimes. This result suggests that differential susceptibility to pathogen attack under contrasting N conditions is not only explained by a metabolic alteration. We used a systems biology approach to identify the transcriptional regulatory network implicated in plant response to the fungus infection under contrasting nitrate conditions. Interestingly, hub genes in this network are known key transcription factors involved in ethylene and jasmonic acid signaling. This result positions these hormones as key integrators of nitrate and defense against B. cinerea in tomato plants. Our results provide insights into potential crosstalk mechanisms between necrotrophic defense response and N status in plants.

overall_design: To better understand the molecular changes underlying the impact of nitrate availability on plant susceptibility to B. cinerea, we performed plant transcriptome profiling assays on mock-treated (3 biological replicates) and infected plants ( 3 biological replicates) grown under three N conditions, using GeneChip Tomato Genome Arrays (Affymetrix).

first: A

first: P

last: Canessa

first: G

last: Hoppe

first: I

last: Retamal

first: T

last: Moyano

first: J

last: Canales

first: R

last: Gutiérrez

last: Rubilar


title: Post-zygotic structural variants in histologically normal breast tissue may predispose to sporadic breast cancer [SET 6]

first: Chiara

last: Rasi

overall_design:
We studied 282 female breast cancer patients that were assessed as affected by sporadic disease at the time of diagnosis and all underwent mastectomy. In total, 1162 UMs (uninvolved margin tissues), ranging from 1 to 14 UMs per patient, taken outside the location of clinically characterized index primary tumor, were analyzed on Illumina arrays. For each subject, DNA from at least one control tissue was also analyzed, which was predominantly blood DNA, alternatively skin-derived DNA. We also studied primary tumor (PT), or up to 3 primary tumor foci from patients with diagnosis of multifocal disease. This GEO project contains the genotyping profiles (processed and normalized data including Log R Ratio and B allele frequency) for these 1162 UMs used in the study. Information on phenotypes (age at diagnosis, tumor focality, tumor grade, tumor molecular phenotype) is also provided, whenever available.
The 401-500 samples out of 811 experiments runned on platform GPL18224 (Infinium HumanOmniExpressExome)


title: Proteomic and transcriptomic analyses of Dhh1 complexes reveals mitochondrial RNP complex association with yeast P-bodies

city: Pittsburgh

first: Gregory

last: Cary

address: 4400 Fifth Ave

department: Biological Sciences

institute: Carnegie Mellon University

summary: P-bodies (PB) are cytoplasmic RNP complexes that aggregate into foci when cells are exposed to stress.  While the core components and stress response of PB and related RNP granules are conserved, it remains unclear how and why cells assemble mRNP complexes into granule foci during stress. We use mass spectrometry and antibody-based microarray to analyze proteins and RNA, respectively, that are immunoisolated with the core PB protein Dhh1-GFP. Analysis of the RNA associated with Dhh1-GFP immunoisolate reveals an enrichment of mitochondrial catalytic RNPs complex, suggesting a role for PB in mitochondrial RNA processing.

overall_design: RNA from 7 anti-GFP immunoisolations as well as total (input) RNA  for each experiment was prepared. The seven samples include one mock IP from a strain containing GFP alone as well as 6 from Dhh1-GFP strains, two replicates from a (+) glucose condition and four replicates from a (-) glucose condition in which Dhh1-GFP forms cytoplasmic foci. 5ug of total RNA and 200ng IP RNA was hybridized to cutsom Agilent microarrays and detected using the S9.6 monoclonal antibody to RNA:DNA hybrids (ATCC clone ) and a Cy3 labeled anti-mouse secondary antibody.

first: Dani

last: Vinh

first: Patrick

last: May

first: Rolf

last: Kuestner

first: Aimee

last: Dudley


title: The role of recent admixture in forming the contemporary West Eurasian genomic landscape

city: Oxford

first: George

last: Busby

state: OXON

address: Roosevelt Drive

institute: Wellcome Trust Centre for Human Genetics

summary: Over the past few years, studies of DNA isolated from human fossils and archaeological remains have generated considerable novel insight into the history of our species. Several landmark papers have described the genomes of ancient human ancestors and have demonstrated that contemporary humans harbour genetic material from ancient close relatives, the Neanderthals and Denisovans, and that ancient human individuals are often genetically distinct from nearby extant populations whilst also showing affinities with populations from further afield. Across West Eurasia, there is growing genetic evidence of large-scale, dynamic population movements over the period between 10,000 to 2,000 years ago, such that the ancestry across present-day populations is likely to be a mixture of several ancient groups. Whilst these efforts are bringing the details of West Eurasian prehistory into increasing focus, studies aimed at understanding the processes behind the generation of the current West Eurasian genetic landscape have been limited by the number of populations sampled, or have been either too regional or global in their outlook. Here, using recently described haplotype-based techniques, we present the results of a systematic survey of recent admixture history across Western Eurasia and show that admixture is a universal property across almost all groups. Admixture in all regions except North Western Europe involved the influx of genetic material from outside of West Eurasia, which we date to specific time periods. Within Northern, Western, and Central Europe, admixture tended to occur between local groups during the period 300 to 1200CE. Comparisons of the genetic profiles of West Eurasians before and after admixture show that population movements within the last 1500 years are likely to have maintained differentiation amongst groups. Our analysis provides a timeline of the gene flow events that have generated the contemporary genetic landscape of West Eurasia.

overall_design: 20 individuals from Croatia included as part of an analysis of admixture in West Eurasia

first: Sena

last: Karanchanak

first: Igor

last: Rudan


title: Fibrinogen promotes autoimmunity and demyelination via chemokine release and antigen presentation [Rn]

city: San Francisco

first: Katerina

last: Akassoglou

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

summary:
Determination of the mechanism by which fibrinogen, a central blood coagulation protein drives immunological responses targeted to the CNS. Results identify the factors involved in the regulation and provide mechanistic basis.
We subjected fibrin-stimulated microglia to microarray to determine the genes involved in innate and adaptive immune responses by fibrinogen deposited in the CNS after blood-brain barrier disruption.

overall_design: Rat microglia were stimulated with fibrin for 6 hr and subjected for RNA extraction and hybridization on Affymatrix microarrays. Two unstimulated and two fibrin-stimulated samples were generated.

first: Jae

last: Ryu


title: ECSTASY (MDMA) ALTERS CARDIAC GENE EXPRESSION AND DNA METHYLATION: IMPLICATIONS FOR CIRCADIAN RHYTHM DYSFUNCTION IN THE HEART

status: Public on Dec 11 2015

city: Atlanta

first: William

last: Lewis

state: Georgia

address: 101 Woodruff Circle

department: Pathology

institute: Emory University

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Affymetrix SNP array data for myelodysplastic syndromes (MDS) samples

status: Public on Sep 15 2015

city: Shanghai

first: Feng

last: Xu

state: Shanghai

address: 600 Yishan Road

department: Hematology

country: China

institute: Shanghai Jiaotong University Affiliated Sixth People's Hospital

summary: The progressive mechanism of myelodysplastic syndrome (MDS) remains unknown. We report that ROBO1 and ROBO2 are identified as novel progression-related somatic mutations using whole-exome and targeted sequencing in six of 16 (37.5%) paired MDS patients undergoing disease progression. To investigated the effect of ROBO1 or ROBO2 on ROBO1/2 CN number and LOH, we employed a Cytosan 750K chip to analyze the copy-number variations (CNVs) and loss of heterogeneity (LOH) in MDS patients with ROBO1&2 mutations.

overall_design: Copy number and LOH analysis of Affymetrix CytoScan 750K array was performed for 14 MDS patients with ROBO1 or ROBO2 mutations

first: Xiao

last: Li


title: Expression of miRNA in Embryonic Stem Cells-Derived Cardiomyocytes after coculture with Endothelial Cells

status: Public on Sep 11 2015

city: Tainan

first: Desy

middle: S

last: Lee

address: University Road

institute: NCKU

summary:
To identify the miRNA that potentially promote the maturation of Embryonic Stem Cells-Derived Cardiomyocytes, we performed miRNA assay profiling to  further know the miRNA expression that differentially expressed after coculture with endothelial cells
To further know the miRNA expression that differentially expressed after coculture with endothelial cells, we performed miRNA assay profiling to identify the miRNA that potentially promote the maturation of Embryonic Stem Cells-Derived Cardiomyocytes

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Embryonic Stem Cells-Derived Cardiomyocytes were re-sorted from coculture system with GFP promoter

middle: C

last: Hsieh


title: Intra-amniotic Balloon Inflation Induces an Inflammatory “Pulse” and Labor in Nonhuman Primates

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Uterine stretch is thought to induce preterm labor in women with twin and higher order pregnancies, but the pathophysiology remains unclear. We investigated the pathogenesis of stretch-induced preterm birth for the first time in a pregnant nonhuman primate model.

overall_design: Eleven chronically catheterized pregnant monkeys (Macaca nemestrina) at 118-125 days gestation (term=172 days) received either: 1) inflation of intra-amniotic balloons (N=6) or 2) saline inoculation (N=5). Cesarean section and fetal necropsy was performed due to preterm labor or to collect tissues, except in one case where the animal delivered spontaneously, reducing samples for microarray analysis to ten (five stretch and five control animals). Amniotic fluid and maternal plasma were analyzed for multiple cytokines and prostaglandins using Luminex, enzyme-linked immunosorbent assay and Analysis of Covariance. Ribonucleic acid was extracted from the myometrium in the lower uterus at Cesarean section and analyzed by microarray and quantitative reverse transcriptase polymerase chain reaction.

first: Kristina

last: Adams Waldorf

first: Aarthi

last: Mohan

first: Roger

last: Young

first: Lisa

last: Ngo

first: Ananya

last: Das

first: Jesse

last: Tsai

first: Aasthaa

last: Bansal

first: Louis

last: Paolella

first: Suren

last: Soorana

first: Michael

last: Gough

first: Cliff

last: Astley

first: Keith

last: Vogel

first: Audrey

middle: E

last: Baldessari

first: Theodor

middle: K

last: Bammler

last: Gravett

first: Lakshmi

last: Rajagopal

first: Mark

last: Johnson


title: Amyloid protein-mediated differential DNA methylation status regulates gene expression in Alzheimer’s disease model cell line.

status: Public on Sep 06 2015

city: Seoul

first: Hye Youn

last: Sung

address: 911-1 Mok-dong

department: Biochemistry

country: South Korea

institute: Ewha Womens University

summary: Genome wide DNA methylation profiling of human neuroglioma cell line (H4) and the Swedish double mutant-harboring H4 cell line (H4-sw). The Illumina Infinium 27k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 27,000 CpGs in 2 cell lines, H4 and H4-sw.

overall_design: Bisulphite converted DNA from the H4 and H4-sw cells were hybridised to the Illumina Infinium 27k Human Methylation Beadchip

first: Jung-Hyuck

last: Ahn

first: Hye

middle: Y


title: Prostate cancer stratification using molecular profiles [CamCap genotype third set]

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: Background   Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease.  As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome.    Methods  In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behavior, and compared with either CNA or transcriptomics alone.      Findings  We identified five separate patient subgroups with distinct genomic alterations and expression profiles based on 100 discriminating genes in our separate discovery and validation sets of 125 and 99 men. These subgroups were able to consistently predict biochemical relapse (p=0.0017 and p=0.016 respectively)  and were further validated in a third cohort with long-term follow-up (p=0.027). We show the relative contributions of gene expression and copy number data on phenotype, and demonstrate the improved power gained from integrative analyses. We confirm alterations in six genes previously associated with prostate cancer (MAP3K7, MELK, RCBTB2, ELAC2, TPD52, ZBTB4) in prostate cancer, and also identify 94 genes not previously linked to prostate cancer progression that would not have been detected using either transcript or copy number data alone. We confirm a number of previously published molecular changes associated with high risk disease, including MYC amplification, and NKX3-1, RB1 and PTEN deletions, as well as over-expression of PCA3 and AMACR, and loss of MSMB in tumour tissue. A subset of the 100 genes  outperforms established clinical predictors of poor prognosis (PSA, Gleason score), as well as previously published gene signatures (p=0•0001). We further show how our molecular profiles can be used for the early detection  of aggressive cases in a clinical setting, and inform treatment decisions.      Interpretation  For the first time this study demonstrates the importance of integrated genomic analyses incorporating both benign and tumour tissue data in identifying molecular alterations leading to generation of robust gene sets that are predictive of clinical outcome in independent patient cohorts.

overall_design: A total of 482 samples from 289 men with prostate cancer from two cohorts were included in this study.  The discovery cohort comprised 125 tumour samples from radical prostatectomy (RP) with 118 matched benign samples, and 85 matched blood samples.  An additional 4 benign samples from men undergoing Holmium laser enucleation of the prostate (HoLEP) and 16 radical prostatectomy samples from men with castrate-resistant prostate cancer, with 13 matched blood samples were also included.  These were assayed on several platforms, including Illumina HT12v4 gene expression arrays, Illumina OMNI2.5M genotyping arrays and Affymetrix SNP6 genotyping arrays.  The validation cohort comprised 103 tumour tissue samples from men with prostate cancer, with 99 matched benign tissue samples and 103 matched blood samples.  This datasheet describes samples in the DISCOVERY COHORT only, with complete, QCd Illumina HT12v4 data for 13 CRPC samples, 113 tumour samples and 73 matched benign samples.

first: Helen

last: Ross-Adams

first: Alastair

last: Lamb

first: Silvia

last: Halim

last: Dunning


title: Temperature-dependent regulation of gene expression in Japanese flounder Paralichthys olivaceus treated with poly (I:C)

status: Public on Sep 08 2015

city: Tokyo

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

institute: Tokyo University of Marine Science and Technology

summary: 253 genes showed more than 4-fold up- or down-regulated expressions by poly (I:C) at 15 ºC and 25 ºC.

overall_design: Fish were treated with poly(I:C) and reared at 15 ºC and 25 ºC and isolation of total RNA from spleen of the fish at 3 and 24 hours after the treatment.

first: Kittipong

last: Thanasaksiri

first: Ikuo

last: Hirono


title: Genomic and transcriptomic analysis of aroma synthesis in two hybrids between Saccharomyces cerevisiae and S. kudriavzevii in winemaking conditions

status: Public on Sep 05 2015

city: Paterna

first: Amparo

last: Gamero

state: Valencia

address: Avda. Agustín Escardino 7

department: Food Biotechnology

country: Spain

institute: IATA-CSIC

summary: This research work investigates the expression of the genes involved in flavor compound production in two hybrids between Saccharomyces cerevisiae and S. kudriavzevii under low (12°C) and moderate fermentation temperatures (28°C).

sample_organism: Saccharomyces cerevisiae x Saccharomyces kudriavzevii

overall_design: RNA samples taken from wine fermentations at 12ºC and 28ºC at the beginning of stationary phase. Three biological replicates. S. cerevisiae Lalvin T.73 used as reference strain.

first: Carmela

last: Belloch

last: Querol


title: Prostate cancer stratification using molecular profiles [CamCap genotype second set]


title: MvaT family proteins encoded on IncP-7 plasmid pCAR1 and the host chromosome regulate host transcriptome cooperatively but differently (pCAR1)

status: Public on Sep 03 2015

first: Hideaki

last: Nojiri

address: 1-1-1 Yayoi, Bunkyo-ku

department: Biotechnology Research Center

institute: The University of Tokyo

type: Expression profiling by genome tiling array

summary: MvaT proteins are recognized as a member of H-NS family proteins in pseudomonads. IncP-7 conjugative plasmid pCAR1, which was originally found in Pseudomonas resinovorans, carries an mvaT homologous gene, pmr. In Pseudomonas putida KT2440 bearing pCAR1, it was previously reported that pmr and chromosomally-encoded homologous genes, turA and turB, are majorly transcribed, and that Pmr interacts with TurA and TurB in vitro (Yun et al. J. Bacteriol. 192:4720-4731, 2010). In the present study, we clarified how the three MvaT proteins regulate the transcriptome of P. putida KT2440(pCAR1). Modified ChIP-chip analyses suggested that the binding sites of Pmr, TurA, and TurB in P. putida KT2440(pCAR1) genome were almost identical; nevertheless, transcriptome analyses using deletion mutants of each MvaT protein gene at the log and early-stationary growth phases clearly suggested that their regulons were different with one another. Especially, significant dissimilarity of regulons was found between Pmr and other two proteins. Transcriptions of the larger number of genes were affected by Pmr deletion at the early-stationary phase than at the log phase, suggesting that Pmr minimizes the pCAR1 effects on host fitness more effectively at the early-stationary phase. On the other hand, similarity found between the regulons of TurA and TurB implied that they may have complementary roles as global transcriptional regulators in response to the plasmid carriage.

overall_design: ChIP-chip: Pseudomonas putida KT2440 harboring plasmid pCAR1 cells were ChIPed with His-tag (C-terminus of each MvaT homologs) and compared with input control. Transcriptome analysis: pCAR1 RNA maps of mvaT deletion mutants were compared with those of wild-type cells.

first: Choong-Soo

last: Yun

first: Yurika

last: Takahashi

first: Masaki

last: Shintani

first: Toshiharu

last: Takeda

first: Chiho

last: Suzuki-Minakuchi

first: Kazunori

last: Okada

first: Hisakazu

last: Yamane


title: MvaT family proteins encoded on IncP-7 plasmid pCAR1 and the host chromosome regulate host transcriptome cooperatively but differently (KT2440)

overall_design: ChIP-chip: Pseudomonas putida KT2440 harboring plasmid pCAR1 cells were ChIPed with His-tag (C-terminus of each MvaT homologs) and compared with input control. Transcriptome analysis: Chromosomal RNA maps of mvaT deletion mutants were compared with those of wild-type cells.


title: MvaT family proteins encoded on IncP-7 plasmid pCAR1 and the host chromosome regulate host transcriptome cooperatively but differently

platform_organism:
Pseudomonas
Pseudomonas putida KT2440


title: Homo sapiens PBMCs: pre-vaccination (stimulation  vs. no stimulation with EV71 antigen) vs. post-vaccination (stimulation  vs. no stimulation with EV71 antigen)

city: Beijing

first: Jun

last: Zhang

address: No.2,Tiantan Xili

institute: National Institute for Food and Drug Control

summary: To characterize the primary and recall responses to EV71 vaccines, PBMCs from 19 recipients before and after vaccination with EV71 vaccine were collected. 14 samples pre-vaccination and 16 samples post-vaccination were detected by microarray and their gene expression signatures after stimulation with EV71 antigen were compared.

overall_design: Four-condition experiment,pre-vaccination PBMCs (stimulation  vs. no stimulation with EV71 antigen) vs. post-vaccination PBMCs (stimulation  vs. no stimulation with EV71 antigen)

first: Jie

last: Shao

first: Junnan


title: Time-dependent global gene expression profile of J774A.1 cells treated with ManLAM in the absence or presence of GW9662

status: Public on Sep 02 2015

city: Kolkata

first: Joyoti

last: Basu

address: A.P.C. Road

department: Chemistry

country: India

institute: Bose Institute

summary: Transcriptional profiling of J7774A.1  cells treated with ManLAM ( 5ug/ml) for 6 h in the absence or presence of GW9662

overall_design: J774A.1 cells were treated wit ManLAM either in the absence or presence of GW9662 for 6 h followed by total RNA isolation. Total RNA was labelled with Agilent’s quick-Amp labelling kit (p/n: 5190-0444) to generate fluorescent complementary RNA by using T7 promoter based linear amplification. The control sample was labelled with Cy3 while the infected samples were labelled with Cy5 and hybridized to an  Agilent oligo microarray kit.

first: Manikuntala

last: Kundu

first: Zhumur

last: Ghosh


title: MicroRNAs in Serum and Bile of Patients with Primary Sclerosing Cholangitis and/or Cholangiocarcinoma

city: Hannnover

first: Shashi

middle: Kumar

last: Gupta

address: Carl-Neuberg Strasse 1

department: IMTTS

country: Germany

institute: Hannover Medical School


title: A BRCA1 interacting lncRNA regulates homologous recombination

status: Public on Sep 01 2015

city: Bethesda

first: Vivek

last: Sharma

state: MD

address: 41 Library Drive

department: CCR

country: USA

institute: NCI

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


title: Affymetrix CytoScan 750K array data for a parthenogenetic SMA human embryonic stem cell line

city: Jerusalem

first: Ephrat

last: Levy-Lahad

address: Shmu'el Bait 12

country: Israel

institute: Shaare Zedek Medical Center

summary: A diploid 46(XX) human embryonic stem cell (HESC) line affected by Spinal muscular atrophy type 1 (SMA) due to homozygosity for a common deletion in the SMN1 gene was derived. By characterizing the methylation status of three different imprinted loci (MEST, SNRPN and H19) and carrying out genome-wide SNP analysis, we provide evidence that this cell line was established from the activation of a mutant haploid oocyte through parthenogenesis, resulting in homozygote diploidization of the entire genome.

overall_design:
Affymetrix CytoScan 750K array analysis was performed according to the manufacturer's directions on DNA extracted from tissue culture.
Copy number and LOH analysis of the Affymetrix CytoScan 750K array was performed for the SMA HESC line.

first: Silvina

last: Epsztejn-Litman

first: Rachel

last: Eiges

first: Sharon

last: Zeligson


title: Gene Expression Profiling of Chronically Inflamed FFPE Placental Tissue

city: Hamilton

first: Jefferson

last: Terry

state: Ontario

address: 1280 Main St West

country: Canada

institute: McMaster Universtiy

summary: The aim of this research was to explore gene expression changes in chronically inflammed placental tissue

overall_design: This study compared FFPE tissue with and without chronic placental inflammation, manifested as overlapping chronic chorioamnionitis, chronic villitis of unknown etiology, and chronic deciduitis. RNA expression profiling was conducted on formalin fixed, paraffin embedded placental tissue using Illumina microarrays. To further explore and validate gene expression findings, we conducted immunohistochemical assessment of protein level expression.

first: Raman

last: Kripa

first: Pare

last: Guillaume

first: Terry

last: Jefferson


title: Effect of photoperiod during late gestation on bovine mammary trancriptome

city: Columbia

first: Thomas

middle: B

last: McFadden

state: MO

address: S108 Animal Science Research Center

department: Animal Sciences

institute: University of Missouri

summary:
Cows exposed to short day photoperiod (SD, 8L:16D) during the 60-day non-lactating period prior to parturition produce more milk in their subsequent lactation compared to cows exposed to long day photoperiod (LD,16L:8D).  Although this response is well-established in dairy cows, the underlying mechanisms are not understood.  We hypothesized that differential gene expression in cows exposed to SD or LD photoperiods during the dry period could be used to identify the functional basis for the subsequent increase in milk production during lactation.  Pregnant, multiparous cows were maintained on a SD or LD photoperiod for 60-days prior to parturition.  Mammary biopsies were obtained on days -24 and -9 relative to parturition and Affymetrix GeneChip® Bovine Genome Arrays were used to quantify gene expression.  Sixty-four genes were differentially expressed (p ≤ 0.05 and fold-change ≥ |1.5|) between SD and LD treatments.  Many of these genes were associated with cell growth and proliferation, or immune function.  Ingenuity Pathway Analysis predicted upstream regulators to include TNF, TGFβ1, interferon γ and several interleukins.  In addition, expression of 125 genes was significantly different between day -24 and day -9; those genes were associated with milk component metabolism and immune function.  The interaction of photoperiod and time affected 32 genes associated with insulin-like growth factor (IGF-I) signaling.  Genes differentially expressed in response to photoperiod were associated with mammary development and immune function consistent with the enhancement of milk yield in the ensuing lactation.  Our results provide insight into the mechanisms by which photoperiod affects the mammary gland and subsequently lactation.
Data were analyzed for the effect of photoperiod treatment (LD minus SD), time relative to parturition (day -24 minus day -9) and the interaction of photoperiod treatment and time ((LD minus SD day -9) minus (LD minus SD day -24))

overall_design: Total Samples: n = 14, SD day -24 n=3, LD day -24 n=3,  SD day -9 n=4, LD day -9 n=4

first: Pamela

last: Bentley

first: Emma

middle: H

last: Wall

first: Geoffrey

last: Dahl


title: miRNA Expession Changes with Cofilin-2 Deficiency

city: Boston

first: Sarah

last: Morton

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: miRNA Expression in Quadriceps Muscle from Cofilin-2 Null Mice Compared to WT Littermates on Day 7

overall_design: Quadriceps muscle resected on day 7 from cofilin-2 deficient mice and wildtype littermates were collected and mIRNA was isolated.  Expression changes were analyzed by microarray.

first: Pankaj

last: Agrawal


title: Zebrafish larvae response to AgNPs and AgNO3

city: Belvaux

first: Sebastien

last: Cambier

state: - select a state -

address: 41 rue du brill

department: ERIN

country: Luxembourg

institute: LIST - Luxembourg Institute of Science and Technology

summary: Transcriptional profiling of zebrafish larvae comparing control with AgNO3 or AgNPs exposed zebrafish larvae.

overall_design: Three-condition experiment, Control vs. AgNO3 and Control vs. AgNPs exposed zebrafish. Biological replicates: 6 control replicates, 6 AgNO3 replicates and 6 AgNPs replicates.

first: Marthe

last: Røgeberg

first: Camilla

last: Karlsson

first: Anastasia

last: Georgantzopoulou

first: Steven

last: Verhaegen

first: Tore-Geir

last: Iversen

first: Cédric

last: Guignard

first: Marcin

last: Kruszewski

first: Lucien

last: Hoffmann

first: Jean-Nicolas

last: Audinot

first: Erik

last: Ropstad

first: Arno

last: Gutleb


title: Analysis of therapeutic miRNA against KRAS mutant colorectal cancer

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary:
We compared the profile of miRNAs expressed in HEK293 and MRC5 cells that overexpressed KRASG12V to those expressed in parental cells that harbored wild-type KRAS.
The results indicated that a subset of miRNAs was significantly down-regulated in KRASG12V transfected two cells.

overall_design: To address the functional relevance of miRNAs in KRAS mutant cancers, we transfected exogenous KRASG12V into HEK293 and MRC5 cells with wild type KRAS genes, and we comprehensively profiled the dysregulated miRNAs.

first: M

last: Hiraki

first: H

last: Yamamoto


title: Identification of diffrentially expressed genes upon DDSR1 knockdown

first: Vivek

last: Sharma

summary:
Upon DNA damage, the DNA damage response (DDR) elicits a complex signaling cascade, which includes the induction of multiple non-coding RNA species. Recently long non-coding RNAs (lncRNAs) have been shown to contribute to DDR by regulating gene expression. However, very little is known about the role that lncRNAs play in regulating DNA Repair. Using a genome-wide microarray screen we identified a novel ubiquitously expressed lncRNA, DDSR1 (DNA damage-sensitive RNA 1), which is induced upon DNA damage by several DNA double-strand break (DSB) agents. DDSR1 induction upon DNA damage is dependent on the ATM-NF-kB pathway but p53 independent. However, DDSR1 acts in the p53 network by negatively regulating p53 mediated gene expression. Loss of DDSR1 impairs cell proliferation, DDR signaling and reduces DNA repair capacity by homologous recombination (HR). The HR defect upon DDSR1 knockdown is due to reduced end resection caused by aberrant BRCA1 and RAP80 accumulation at DSB sites. In line with dual role of DDSR1 in gene regulation and HR, DDSR1 interacts with hnRNPUL1, an RNA-binding protein involved in transcription and HR. Our results reveal a previously unknown lncRNA involved in regulation of DDR by contributing to gene regulation and DNA repair by HR. Our findings highlight the importance of DDSR1 in maintaining genome stability and suggest that the DDR is even more complex than currently assumed.
We used microarrays to identify  gene expression changes upon DDSR1 knockdown

overall_design: hTERT immortalised Human Fibroblast cells were transfected a non specific siRNA or siRNA against DDSR1,72 hours post transfection RNA was isolated and process for Microarray. 3 Biological Replicates

first: Tom

last: Misteli


title: Expression data from porcine kidney cell (PK15) transfected by the plasmids

status: Public on Aug 12 2015

city: Nanjing

first: libin

last: wen

address: zhongling street 50

institute: Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences

summary:
Several recombinat viruses of porcine circovirus type 2 (PCV2),including P1, P2, ZJ-R, VL258, and VL264, have been found. The PK15 cells were transfected by the molecular clones of the abovementioned viruses, where specific sets of genes are up-regulated or down-regulated.
We used microarrays to detail the global programme of gene expression and identified distinct functions of viruses or viral proteins.

overall_design: PK15 cells were selected at 12 hours post-transfection for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the gene expression patterns of PK15 cells transfected with different molecular clones of the viruses.

first: Libin

last: Wen

first: Kongwang

last: He


title: Integration analysis of three omics data using penalized regression methods: An application to bladder cancer (Methylation)

status: Public on Aug 04 2015

city: Madrid

first: Nuria

last: Malats

state: Madrid

address: C/ Melchor Fernández Almagro 3

institute: CNIO

summary: Omics data integration is becoming necessary to investigate the still unknown genomic mechanisms of complex diseases. During the integration process, many challenges arise such as data heterogeneity, the smaller number of individuals in comparison to the number of parameters, multicollinearity, and interpretation and validation of results due to their complexity and lack of knowledge about biological mechanisms. To overcome some of these issues, innovative statistical approaches are being developed. In this work, we applied penalized regression methods (LASSO and ENET) to explore relationships between common genetic variants, DNA methylation and gene expression measured in bladder tumor samples and have proposed a permutation-based method to concomitantly assess significance and correct by multiple testing with the MaxT algorithm. The overall analysis flow consisted of three steps: (1) SNPs/CpGs were selected per each gene probe within 1Mb window upstream and downstream the gene; (2) LASSO and ENET were applied to assess the association between each expression probe and the selected SNPs/CpGs in three multivariable models (SNP, CPG, and Global models, the latter integrating SNPs and CPGs); and (3) the significance of each model was assessed using the permutation-based MaxT method. We identified 48 genes whom expression levels were associated with both SNPs and GPGs. Importantly, we replicated results for 36 (75%) of them in an independent data set (TCGA). We checked the performance of the proposed method with a simulation study and further supported our results with a biological interpretation based on an enrichment analysis. The approach we propose allows reducing computational time and is flexibly and easy to implement when analyzing several omics data. Our results highlight the importance of integrating omics data by applying appropriate statistical strategies to discover new insights into the complexity of disease genetic mechanisms.

overall_design: Bisulphite modification of 46 tumor DNA samples using EZ-96 DNA METHYLATIONGOLD KIT (Zymo Research, Irvin, CA, USA), CpG methylation data was generated using the Infinum Human Methylation 27 BeadChip Kit that detected the CpG sites with two probes, one designed against the unmethylated site (signal U) and the other against the methylated site (signal M).

first: Silvia

last: Pineda

first: Francisco

middle: X

last: Real

first: Manolis

last: Kogevinas

first: Alfredo

last: Carrato

first: Stephen

middle: J

last: Chanock

first: Núria

first: Kristel

last: Van Steen


title: Pathogen-associated molecular patterns activate expression of genes involved in cell proliferation, immunity and detoxification in the amebocyte-producing organ of the snail Biomphalaria glabrata

status: Public on Aug 01 2015

city: Albuquerque

first: Si-Ming

last: Zhang

state: NM

address: Castetter Hall

department: Biology

institute: University of New Mexico

summary: In order to understanding the transcriptome responses of the amebocyte-producing organ (APO) of the snails Biomphalaria glabrata after exposure to pathogen associated molecular patterns (PAMPs), we investigated transcriptomic responses of the APO dissected from the snails at 24 hours post-injection with bacterial pathogen-associated molecular patterns (PAMPs). Three PAMPs that include lipopolysaccharide (LPS), peptidoglycan, and fucoidan that may mimic fucosyl-rich glycan PAMPs on sporocysts of Schistosoma mansoni, were tested. Based upon the number of genes differentially expressed, LPS exhibited the strongest activity, relative to saline-injected controls. A concurrent activation of genes involved in cell proliferation, immune response and detoxification metabolism was observed.

overall_design: Three PAMPs, lipopolysaccharide (LPS),  peptidoglycan (PGN), and fucoidan (FUC) was tested. Phosphate buffered saline (PBS) was used as control. The APO was dissected after 24 hours post-injection with indiividual PAMPs or PBS. For each treatment, 4 biological replicates were used. Since APO is very small, 20 APO were pooled as a biological sample. So a total of 80 APOs (from 80 snails) were used for one treatment. A total of 320 APOs from 320 snails (80 x 4) were used for the four treatments (3 PAMPs plus 1 PBS control).


title: Identifying long non-coding RNAs in triple-negative breast cancer

city: Taizhou

first: Feilin

last: Cao

state: Zhejiang

address: No.150 Ximen Road

department: Department of Surgical Oncology, Taizhou Hospital,

institute: Wenzhou Medical University

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

summary: We investigated the expression patterns of lncRNAs and mRNAs from TNBC tissues and matched histological normal breast tissues with Agilent Human lncRNA array V4.0 (4 × 180 K), which include 78,243 human lncRNAs and 30,215 coding transcripts.

overall_design: We identified 1,758 lncRNAs and 1,254 mRNAs that were differentially expressed (≥ 2-fold change), indicating that many lncRNAs are significantly upregulated or downregulated in TNBC. Among these, XR_250621.1 and NONHSAT011259 were the most unregulated and down regulated lncRNAs. qRT-PCR was employed to validate the microarray analysis findings, and results were consistent with the data from the microarrays. GO analysis and KEGG pathway analysis were applied to explore the potential lncRNAs functions, and some pathways including microtubule motor activity and DNA replication were identified in TNBC pathogenesis.


title: Leucine metabolism regulates TRI6 expression and affects deoxynivalenol production and virulence in Fusarium graminearum

city: Ottawa

first: Rajagopal

last: Subramaniam

address: 960 Carling

institute: Agriculture and Agri-Food Canada

type: Expression profiling by high throughput sequencing

summary: TRI6 is a positive regulator of the trichothecene gene cluster and the production of trichothecene mycotoxins (deoxynivalenol [DON] and acetylated forms such as 15-ADON) in the cereal pathogen F. graminearum. As a global transcriptional regulator, TRI6 expression is modulated by nitrogen-limiting conditions, sources of nitrogen and carbon, pH, and light. However, the mechanism by which these diverse environmental factors affect TRI6 expression remains under-explored. In our effort to understand how nutrients affect TRI6 regulation, comparative digital expression profiling was performed with a wildtype F. graminearum and a Δtri6 mutant strain, grown in nutrient-rich conditions. Analysis showed that TRI6 negatively regulates genes of the branched-chain amino acid (BCAA) metabolic pathway. Feeding studies with deletion mutants of MCC, encoding methylcrotonyl-CoA-carboxylase, one of the key enzymes of leucine metabolism, showed that addition of leucine specifically down regulated TRI6 expression and reduced 15-ADON accumulation. Constitutive expression of TRI6 in the Δmcc mutant strain restored 15-ADON production. A combination of cellophane breach assays and pathogenicity experiments on wheat demonstrated that disrupting the leucine metabolic pathway significantly reduced disease. These findings suggest a complex interaction between one of the primary metabolic pathways with a global regulator of mycotoxin biosynthesis and virulence in F. graminearum.

overall_design:
Triplicate samples of digital gene expression profiling data for the Tri6 mutant and wildtype strains were compared.

**Please note that the raw data files for the current study are no longer available, and therefore are not included in the submission.

first: Swara

last: Narayanan

first: Sean

last: Walkowiak

first: Li

last: Wang

first: Manisha

last: Joshi

first: Hélène

last: Rocheleau

first: Thérèse

last: Ouellet

first: Linda

last: Harris