title: Expression analysis of seeds and seedlings of tomato growing on regular MS medium or MS medium supplemented with Helical multi-walled carbon nanotubes (Helical MWCNTs) in concentration 25 ug/ml

status: Public on May 30 2016

city: Little Rock

first: Mariya

last: Khodakovskaya

state: AR

address: 2801 S. University Avenue

department: Biology

country: USA

institute: University of Arkansas at Little Rock

summary:
To investigate effects of Helical multi-walled carbon nanotubes (Helical MWCNTs) on total expression profile of tomato seeds and young sedlings we introduced Helical MWCNTs in MS agar medium in concentrationd of 25 ug/ml.
Objectives for this study included the identification of genes that were up or down-regulated at the transcriptional level in tomato seeds and seedlings in response to application of Helical MWCNTs

overall_design: Tomato seeds (1 day after placement of medium) and 11-days old seedlings growing on regular MS agar medium or MS medium supplemented with Helical MWCNTs (25 ug/ml) were selected for RNA extraction and hybridization on Affymetrix microarrays.


title: The human decapping scavenger enzyme DcpS modulates microRNA turnover

status: Public on May 23 2016

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

summary: The decapping scavenger enzyme DcpS is known for its role in hydrolyzing the cap structure following mRNA degradation. Recently, we discovered a new function in miRNA degradation activation for the ortholog of DcpS in C. elegans. Here we show that human DcpS conserves its role in miRNA turnover. In human cells, DcpS is a nucleocytoplasmic shuttling protein and that DcpS activates miRNA degradation independently of its scavenger decapping activity in the cytoplasmic compartment. We also demonstrate that this new function for DcpS requires the contribution of the 5’-3’ exonuclease Xrn2. Our findings support a conserved role of DcpS as a modulator of miRNA turnover in animals.

overall_design: Profiling of microRNAs expression from human cultured cells treated with DcpS inhibitor

first: Oussama

last: Meziane

first: Sandra

last: Piquet

first: Gabriel

middle: D

last: Bossé

first: Dominic

last: Gagné

first: Claude

last: Robert

first: Michael

middle: A

last: Tones

first: Martin

middle: J

last: Simard


title: Tumor Cell Survival Dependence on the DExH-Box Helicase DHX9

status: Public on May 19 2016

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

summary: The ATP-dependent DExH/D-box helicase DHX9 is a key participant in a number of gene regulatory steps, including transcriptional, translational, microRNA-mediated control, DNA replication, and maintenance of genomic stability. DHX9 has also been implicated in maintenance of the tumorigenic process and in drug response. Here, we report that inhibition of DHX9 expression is lethal to multiple human and mouse cancer cell lines. In contrast, using a novel conditional shDHX9 mouse model, we demonstrate that sustained and prolonged suppression of DHX9 is well tolerated at the organismal level. Our results demonstrate a robust tolerance for DHX9 knockdown in non-transformed cells and supports the targeting of DHX9 as an effective and specific chemotherapeutic approach.

overall_design: Comparison of gene expression in large intestine of mice with or without reduced expression of DHX9.


title: Microenvironment-driven IGF-1R/PI3K signaling underlies acquired resistance to CSF1R inhibition in gliomas (CGH)

status: Public on May 20 2016

city: Philadelphia

first: Robert

middle: L

last: Bowman

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania School of Medicine

type: Genome variation profiling by genome tiling array

summary: Macrophages accumulate with glioblastoma multiforme (GBM) progression, and can be acutely targeted via inhibition of colony stimulating factor-1 receptor (CSF-1R) to regress high-grade tumors in animal models. However, whether and how resistance emerges in response to sustained CSF-1R blockade is unknown. Here, we investigate whether long-term CSF-1R inhibition can stably regress GBM in preclinical trials. We show that while overall survival is significantly prolonged, tumors recur eventually in >50% of mice. Upon isolation and transplantation of recurrent tumor cells into naïve animals, gliomas re-establish sensitivity to CSF-1R inhibition, indicating that resistance is microenvironment-driven. PI3K pathway activity was elevated in recurrent GBM, driven by macrophage-derived IGF-1 and tumor cell IGF-1R. Consequently, combining IGF-1R or PI3K blockade with continuous CSF-1R inhibition in recurrent tumors significantly prolonged overall survival. By contrast, monotherapy with IGF-1R or PI3K inhibitors in rebound or treatment-naïve tumors was less effective, indicating the necessity of combination therapy to expose PI3K signaling-dependency in recurrent disease. Our findings thus reveal a potential therapeutic approach for treating resistance to CSF-1R inhibitors in the clinical setting.

overall_design: 3 rebound neurosphere cell lines were assayed against 3 references to normal mouse liver

first: Daniela

middle: F

last: Quail

first: Alberto

last: Schuhmacher

first: Johanna

last: Joyce


title: E. coli cells: Control vs. P. aeruginosa spent-media treated

status: Public on May 24 2016

city: New York

first: Anupama

last: Khare

state: NY

address: 1150 St. Nicholas Ave., Room 406

institute: Columbia University

summary: Transcriptional profiling of E. coli cells comparing control untreated cells with cells treated with P. aeruginosa spent media. The goal was to identify the effects of P. aeruginosa spent media on E. coli cells.

overall_design: Two-condition experiment. 2 biological replicates

first: Khare

last: Anupama

first: Tavazoie

last: Saeed


title: Reducing sampling bias in molecular studies of grapevine fruit ripening: transcriptomic assessment of the density sorting method

status: Public on May 22 2016

city: Logrono

first: Pablo

last: Carbonell-Bejerano

state: La Rioja

address: Madre de Dios, 51

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

country: Spain

institute: CSIC

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

The interplay between environmental and genetic factors conditions the fruit ripening program in plants. Transcriptome analysis of grapevine fruits can help understanding these interactions to consciously cope with conditions leading to detrimental effects for viticultural purposes. However, considering the grapevine characteristic ripening asynchrony, which can be intensified by contrasting conditions, accurate grape sampling may be essential for molecular comparisons. In this study, berry density sorting according to floatability in NaCl solutions was assessed as a grape ripening staging strategy. Total sugar content was more correlated with berry density than with other non-invasive ripening parameters. The transcriptome was compared between three density classes collected near commercial maturity using grapevine whole-genome NimbleGen microarrays. Expression profiles clearly related with ripening progression were detected in a density series simultaneously collected from a vineyard of Albariño. By contrast, considerable differences were detected when the same density series was sampled on two different dates from the same vineyard of Tempranillo. Functional analysis indicated that environmental differences between both sampling moments determined most of these expression differences. Ripening degree-dependent responses to the environment were also detected. Finally, the effect of the sorting procedures on the grape transcriptome showed negligible when it was directly tested. Altogether, these findings evidence the convenience of homogenizing the developmental stage and the sampling time conditions for transcriptome comparisons. Berry density sorting proved useful to this end, although this method could be limited when the berry sugar concentration is not determined by the ripening developmental program.

overall_design: Refer to individual Series


title: Hyperglycemia induced microRNAs in endothelial dysfunction

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

summary: Hyperglycemia is a hallmark in prediabetes and type 2 diabetes mellitus (T2DM) which increases risk of micro and macrovascular complications such as diabetic retinopathy, diabetic nephropathy (microvascular complications), and peripheral vascular disease, cerebrovascular disease and cardiovascular diseases (macrovascular complications). Endothelial cells are affected in both cases. In this study, we investigated the miRNA expression changes in HUVECs during different glucose treatment (5mM, 10mM, 25mM and 40mM glucose) at various time intervals (6, 12, 24 and 48hrs). The results of miRNA microarray showed there is a correlation between hyperglycemia induced endothelial dysfunction and miRNA expression. In silico prediction showed that the following pathways: Regulation of actin cytoskeleton, PI3K-Akt signaling pathway, Apoptosis, Neurotrophin signaling pathway, and Insulin signaling pathway, were dysregulated during hyperglycemia. Majority of the pathways are related to apoptosis. 10 miRNAs (miR-26a-5p, -26b-5p, 29b-3p, 29c-3p, 125b-1-3p, -130b-3p, - 140-5p, -221-3p, -192-5p, and -320a,) showed increased expression with increasing concentration of glucose treatment. miR-26a-5p, -29b-3p, - 140-5p, -221-3p, and -192-5p are involves in endothelial apoptosis. Our study revealed miRNAs (miR-29b-3p and – 192-5p) with known mRNA targets (BCL2 and MCL1) showed expression pattern inversely correlating with their respective target mRNAs. Therefore these miRNAs could involve in the endothelial dysfunction due to hyperglycemia.

overall_design: HUVECs subjected to 0mM to 40mM glucose treatment at different time intervals (6, 12, 24 and 48hrs)

first: Silambarasan

last: Maskomani

first: Jun

last: Tan

first: Arunmozhiarasi

last: Armugam

first: Jeyaseelan

last: Kandiah


title: Transcriptomic study of the sex differentiation process in turbot

city: Santiago de Compostela

first: Diego

last: Robledo

address: Rúa Lope Gómez de Marzoa s/n CIBUS building

department: Genetics

institute: University of Santiago de Compostela

summary: Gonad is a bipotential tissue that depending on the genetic and environmental inputs its final phenotype will be determined. Gonadal development is a very complex process because from an undifferentiated gonad the future testis or ovary will be formed. To better understand the complexity of the gonad plasticity throughout development we explored the transcriptomic landscape of gonads from undifferentiated to juvenile fish. For this study we have used turbot (Scophthalmus maximus) that presents one of the most remarkable sexual dimorphism in cultured fish species. With the aim of identifying gene patterns for each gonad developmental stages a microarray species-specific enriched by reproduction- and immune-related genes was assessed. Further genes with sex-differential mRNA expression were mapped in the sex- and growth-QTL (quantitative trait loci) markers. Data revealed that gonadal transcriptome prevail in front of fish biometry as it was possible to classify gonads according to sexual development status by using gene expression profiles rather than their age or size. The same classification was observed with a selection of a subset of reproduction-related genes showing the importance of gene profiles for each of the developing gonadal stage. Overall microarray data showed the importance of the level of expression (intensity) rather than the number of genes found in each development period. Larger numbers of differentially expressed genes (DEG) were found in the differentiating gonads when compared to ovaries and much smaller number resulted when compared to testis. However, more number of DEG was found in testis when compared to ovaries. The earliest presence of cyp19a1a, the key female sex differentiation gene, was found at 90 dpf together with its transcription factor foxl2 showing at the same time a positive correlation with other genes related to extracellular matrix (ecm2), immune system (irf5) or methylation (sall1). The presence of male-related genes like sox9 was evidenced at early developmental stages (70 and 90 dpf) while expression of dmrt3 started not earlier than 150 dpf, coinciding when larger number of male-related genes were found. All developmental stages presented genes related to immune system and epigenetic mechanisms revealing their importance during gonadal development. Sex-QTLs showed larger amount of sex-differential transcripts in the linkage group 6 and 21 both in males and females but transcripts mapped near growth-QTLs were only found in females. Here it is presented the first assessment of the expression profiles observed in the gonads at different developmental stages by identifying genes responsible for male or female traits. It has been identified gene clusters for each developmental stages and gene network interactions for each sexual phenotype. The expression of known male and female-related genes were precisely described throughout gonadal development as well as the expression of other genes with an unknown reproduction function which have been identified for the first time during sexual development process. In addition, it was possible to localize some of these genes on the sex- and growth-QTLs. The data presented here can help to better understand the reproduction system in cultured fish species and improved selection breeding programs to increase their productivity.

overall_design: 30 turbot gonad samples were analyzed belonging to five different gonad development stages: pre-undifferentiated (4), undifferentiated (7), differentiating (8) and juveniles (11). Juveniles were also divided by sex in male juveniles (5) and female juveniles (6)

first: Laia

last: Ribas

first: Ana

last: Viñas

first: Antonio

last: Gómez-Tato

first: Paulino

last: Martínez

first: Francesc

last: Piferrer


title: Pharmacogenetic profiling of human embryonic stem cells

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

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

summary: Predicting response to drug or xenobiotic exposure is vital to risk assessment and clinical response rates.  Primary human hepatocytes are commonly used to evaluate liver drug metabolism and toxicity.  They are the most physiologically relevant in vitro model, retaining expression of most ADME-relevant genes.  However, human hepatocytes are source limited, have high donor variability, only survive short term in culture, and lack selection for specific genetic profiles.  To overcome the limitations associated with primary hepatocytes we and others are investigating the potential of pluripotent stem cells as an alternative or complementary source for generating hepatocytes.  Pluripotent stem cells offer advantages over primary hepatocytes because stem cells have high replicative capacity, potentially providing a limitless source of hepatocytes.  Stem cell derived hepatocytes (SCDHs) may also provide an improved in vitro system for evaluating pharmacogenetic relationships, e.g. cytochrome P450 (CYP) enzymes and their impact on drug metabolism and toxicity.  To demonstrate the utility of SCDHs in pharmacogenetic screening, we genotyped the five commonly used WiCell® human embryonic stem cell lines (hESC), H1, H7, H9, H13 and H14.

overall_design: Testing the utility of stem cell derived hepatocytes for pharmacogenic screening

first: Jenna

last: Voellinger

first: Edward

last: Kelly


title: Mitochondrial-derived Oxidative Stress Alters Gene Expression and DNA Methylation in the Heart [methylation]

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: Mitochondrial dysfunction causes oxidative stress and cardiomyopathy. Oxidative stress also is a side effect of dideoxynucleoside antiretrovirals (NRTI) and NRTI-induced cardiomyopathy. We show here that treatment with the NRTI AZT (1-[(2R,4S,5S)-4-azido-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione) modulates cardiac gene expression epigenetically through production of mitochondrially-derived reactive oxygen species (ROS). Transgenic mice with ubitquitous expression of mitochondrially-targeted catalase (MCAT) and C57BL/6 wild-type mice littermates (WT) were administered AZT (p.o., 0.22 mg/d; 35 days), and cardiac DNA and mRNA were isolated. In AZT-treated WT, 95 cardiac genes were differentially expressed compared to vehicle-treated WTs. When MCAT mice were treated with AZT, each of those 95 genes reverted to the pattern of vehicle-treated WTs. In AZT-treated WT hearts, Mthfr (5,10-methylenetetrahydrofolate reductase; a critical enzyme in synthesis of methionine cycle intermediates including S-adenosylmethionine (SAM)), was overexpressed. AZT caused hypermethylation (47%) and hypomethylation (53%) of differentially methylated DNA regions in WT cardiac DNA. AZT-treated MCAT heart DNA exhibited greater hypermethylation (91%) and less hypomethylation (9%) compared to vehicle-treated controls. Results show that mitochondrially-derived oxidative stress in the heart that is caused by AZT hinders cardiac DNA methylation, alters cardiac gene expression, and promotes characteristic pathophysiological changes of cardiomyopathy. This mechanism for NRTI toxicity offers insight into long-term side effects from these commonly used antiviral agents.

overall_design: 16 left ventricle cardiac samples [4 vehicle (1%CMC)-treated wild-type C57BL/6, 4 AZT-treated wild-type C57BL/6, 4 vehicle-treated MCAT overexpressing, and 4 AZT-treated MCAT overexpressing) were collected, and genomic DNA was extracted from each sample and hybridized to a 2.1M deluxe mouse promoter array. Results were normalized and compared to gene expression array results from similar mouse groups. Each array represents a single mouse. All mice were of C57BL/6 background.

first: Christopher

last: Koczor


title: Methamphetamine and HIV-Tat Alter Murine Cardiac DNA Methylation and Gene Expression

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


title: Genome-wide profiling of long noncoding RNA expression patterns in chemoresistant breast cancer cells

status: Public on May 28 2016

city: Wu Xi

first: Dong-Xu

last: He

address: Jiangnan University

department: Jiangnan University

country: China

institute: National Engineering Laboratory for Cereal Fermentation Technology

summary: Long non-coding RNAs (lncRNAs) are involved in cancer progression. In this study, the lncRNA profiling were analyzed in chemoresistant and sensitive breast cancer cells. We found a group of dysregulated lncRNAs in chemoresistant cells. Expression of dysregulated lncRNAs are correlated with dysregulated mRNAs, and enriched in GO and KEGG pathways related with cancer progression and chemoresistance development. Within those lncRNA-mRNA interactions, some lncRNAs may cis-regulate neighboring protein coding genes and involved in chemoresistance. The lncRNA NONHSAT028712 was then validated to regulate nearby CDK2 and interfere with cell cycle and chemoresistance. Furthermore, we identified another group of lncRNAs trans-regulated gene expression via interacting with different transcription factors (TF). Whereby NONHSAT057282 and NONHSAG023333 was found to modulate chemoresistance and most likely interacted with ELF1 and E2F1 respectively. In conclusion, this study reported for the first time the lncRNA expression patterns in chemoresistant breast cancer cells, and provided a group of novel lncRNA targets in mediating chemoresistance development in both cis- and trans- action mode.

overall_design: MCF-7/ADM replication 3 times, MCF-7/WT replication 3 times

first: Xiao-Ting

last: Gu

first: Guang-yuan

last: Zhang

first: Ai-Qin

last: Mao

first: Chun-Xiao

last: Lu

first: Jian

last: Jin

first: Xin

last: Ma


title: caArray_liu-00258: Gene expression profiles of BRCA1-linked, BRCA2-linked, and sporadic ovarian cancers

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary: We used complementary DNA (cDNA) microarrays to compare gene expression patterns in ovarian cancers associated with BRCA1 or BRCA2 mutations with gene expression patterns in sporadic epithelial ovarian cancers and to identify patterns common to both hereditary and sporadic tumors.

overall_design:
liu-00258
Assay Type: Gene Expression
Provider: GenePix
Array Designs: Hs-ATC7.6k-v5px_16Bx22Cx22R
Organism: Homo sapiens (ncbitax)
Material Types: total RNA, cell, synthetic DNA, organism_part, whole_organism
Disease States: Ovarian Adenocarcinoma, Normal


title: MiRNA signatures in cell cycle sorted cells [HDFa_miRNA_array]

city: Budapest

first: Vince

middle: Kornél

last: Grolmusz

address: Szentkirályi 46.

country: Hungary

institute: Semmelweis University

summary: For the further examination of cell cycle dependent miRNA expression profile, DNA content based fluorescence activated cell sorting (cell cycle sort) was performed on human transformed cancer cell lines and primary, untransformed fibroblasts. Phase-dependent miRNA expression profiling was performed on G1, S and G2 phases. Results were validated by quantitative real-time PCR.

overall_design:
Phase-dependent miRNA expression profiling was performed on sorted human cancer (adrenocortical - NCI-H295R) cells and primary untransformed fibroblasts (HDFa). G1, S and G2 phases were successfully sorted and analyzed.
HDFa_miRNA dataset

middle: K

first: Attila

last: Patocs


title: MiRNA signatures in cell cycle sorted cells [H295R_miRNA_array]

overall_design:
Phase-dependent miRNA expression profiling was performed on sorted human cancer (adrenocortical - NCI-H295R) cells and primary untransformed fibroblasts (HDFa). G1, S and G2 phases were successfully sorted and analyzed.
H295R_miRNA dataset


title: Expression data from preadipocytes isolated from laying hen II

city: Winnipeg

first: Alemu

middle: Regassa

last: Hunde

state: Manitoba

address: 12 Dafoe Road

department: Animal Science

country: Canada

institute: University of Manitoba

summary: Adipogenesis is one of the most intensively studied models of cellular differentiation, and transcriptional activities involved in the process have been extensively investigated. We analyzed transcripts differentially expressed between hen preadipocytes treated with adipogenic cocktail containing 500 nM dexamethasone, 0.5 mM 3-isobutyl-1-methylxanthine, 20 µg/mL insulin and 300 μM OA (DMIOA) and non-treated control cells and transcripts differentially expressed between preadipocytes treated with DMIOA alone and those treated with a combination of DMIOA and 20(S)-hydroxycholesterol (DMIOA + 20(S)) using Affymetrix GeneChip® Chicken Genome Array containing 28,000 transcripts.

overall_design: Preadipocytes were isolated from hen abdominal tissue, cultured and treated with DMIOA, DMIOA+Retinoic Acid

last: Regassa

first: WooKyun

last: Kim


title: Methamphetamine and HIV-Tat Alter Murine Cardiac DNA Methylation and Gene Expression [Gene Expression]

summary:
This study addresses the individual and combined effects of HIV-1 and methamphetamine (N-methyl-1-phenylpropan-2-amine, METH) on cardiac dysfunction in a transgenic mouse model of HIV/AIDS.  METH is abused epidemically and is frequently associated with acquisition of HIV-1 infection or AIDS. We employed microarrays to identify mRNA differences in cardiac left ventricle (LV) gene expression following METH administration (10d, 3mg/kg/d, subcutaneously) in C57Bl/6 wild-type littermates (WT) and Tat-expressing transgenic (TG) mice.  Arrays identified 880 differentially expressed genes (expression fold change>1.5, p<0.05) following METH exposure, Tat expression, or both.  Using pathway enrichment analysis, mRNAs encoding polypeptides for calcium signaling and contractility were altered in the LV samples. Correlative DNA methylation analysis revealed significant LV DNA methylation changes following METH exposure and Tat expression.  By combining these data sets, 38 gene promoters (27 related to METH, 11 related to Tat) exhibited differences by both methods of analysis.  Among those, only the promoter for CACNA1C that encodes L-type calcium channel Cav1.2 displayed DNA methylation changes concordant with its gene expression change.  Quantitative PCR verified that Cav1.2 LV mRNA abundance doubled following METH. Correlative immunoblots specific for Cav1.2 revealed a 3.5-fold increase in protein abundance in METH LVs.  Data implicate Cav1.2 in calcium dysregulation and hypercontractility in the murine LV exposed to METH.  They suggest a pathogenetic role for METH exposure to promote LV dysfunction that outweighs Tat-induced effects.
This study addresses how HIV-1 and methamphetamine comorbidities affect cardiac (left ventricle) gene expression and epigenetic nuclear DNA methylation.

overall_design: Each sample was fluorescently labeled and hybridized to Roche Nimblegen 12X135kb MM9 Gene Expression Arrays.


title: microRNA profiling of different adipose tissues and muscles

city: Shanghai

first: Hao

last: Ying

address: 320 YUEYANG ROAD

department: INS

institute: SIBS,CAS

summary: Purpose: The goals of this study are to compare microRNA profiling in different adipose tissues and muscles using microRNA arrays. Methods: Tissue microRNA profiles of 2-3-month old mice were generated by using miRCURY™ LNA microRNA Array. The samples were hybridized on a hybridization station following the scheme you outlined in the sample submission. Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image. The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been calculated the median. We use Median Normalization Method to obtain “Normalized Data”, Normalized Data = (Foreground-Background) / median, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction. Results and conclusion: The miRNA expression profiling was completed on our samples. The profiling identified a subset of the total number of miRNAs analyzed by the miRCURY™ array that are differentially expressed in brown adipose tissue, inguinal adipose tissue, epidydimal adipose tissue, gastrocnemius muscle, and soleus muscle.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Tissue microRNA profiles of 2-3-month old mice were generated by microarray, using miRCURY™ LNA Array.

first: Ying

last: Hao

first: Xia

last: Hongfeng


title: Methamphetamine and HIV-Tat Alter Murine Cardiac DNA Methylation and Gene Expression [Methylation]

first: William

last: Lewis

overall_design: Each sample was fluorescently labeled and hybridized to Roche Nimblegen 2.1M Deluxe Promoter Arrays.

last: Koczor


title: Expression data of cultured organoids derived from human colorectal tumors and normal samples.

status: Public on May 26 2016

city: Tokyo

first: Mariko

last: Shimokawa

address: 35, Shinanomachi, Shinjuku-Ku

country: Japan

institute: Keio University

summary: We analyzed gene expression of 58 line patinet-derived colorectal tumors and normal organoids.

overall_design: mRNA from 58 cultured organoids were extracted and hybridized to GeneChip PrimeView Human Gene Expression Array, and scanned using GeneChip Scanner 3000 7G.

first: Masayuki

last: Fujii


title: caArray_lau-00212: Expression profiles of osteosarcoma that can predict response to chemotherapy

summary: Use of expression profiles of osteosarcoma to predict response to chemotherapy

overall_design:
lau-00212
Assay Type: Gene Expression
Provider: GenePix
Array Designs: GP_KKWONG UniGem10K
Organism: Homo sapiens (ncbitax)
Material Types: synthetic_DNA, organism_part, whole_organism, total_RNA
Disease States: Osteoblastoma, normal


title: The microbial functional diversity in response to altered precipitation on Tibet Plateau as characterized by GeoChip

city: Beijing

first: Haowei

last: Yue

address: School of Environment

institute: Tsinghua University

summary: Global warming substantially changes precipitation patterns in the Tibetan plateau, with projection of increased precipitation in southern and northern Tibet but decreased precipitation in the center. Understanding mechanisms of such changes in greenhouse gas emissions is of vital importance in predicting ecosystem feedbacks to climate changes. Nonetheless, it has been hampered by limited knowledge in soil microbial communities, one of the major drivers of greenhouse gas emission. Here, we report a field experiment simulating drying and wetting conditions in the Tibetan grassland. Our field site is located at the Haibei Alpine Grassland Ecosystem Research Station in the northeast of Tibet Plateau, China, and we employed GeoChip 5.0 180K to analyze microbial responses.

overall_design: 18 samples were collected from 3 plots in Haibei Station, with 6 replicates in each plot

first: Yunfeng

last: Yang

first: Jizhong

last: Zhou


title: Xylose induced dynamic effects on metabolism and gene expression in engineered Saccharomyces cerevisiae in anaerobic glucose-xylose cultures

city: VTT, Espoo

first: Merja

last: Oja

address: Tietotie 2

country: Finland

institute: VTT Technical Research Centre of Finland

summary:
Xylose induced effects on metabolism and gene expression during anaerobic growth of an engineered Saccharomyces cerevisiae on mixed glucose-xylose medium were quantified. Gene expression of S. cerevisiae harbouring an XR-XDH pathway for xylose utilisation was analysed from early cultivation when mainly glucose was metabolised, to times when xylose was co-consumed in the presence of low glucose concentrations, and finally, to glucose depletion and solely xylose being consumed. Cultivations on glucose as a sole carbon source were used as a control. Genome-scale dynamic flux balance analysis models were developed and simulated to analyse the metabolic dynamics of S. cerevisiae in the cultivations. Model simulations quantitatively estimated xylose dependent dynamics of fluxes and challenges to the metabolic network utilisation. Increased relative xylose utilisation was predicted to induce two-directionality of glycolytic flux and a redox challenge already at low glucose concentrations. Xylose effects on gene expression were observed also when glucose was still abundant. Remarkably, xylose was observed to specifically delay the glucose-dependent repression of particular genes in mixed glucose-xylose cultures compared to glucose cultures. The delay occurred during similar metabolic flux activities in the both cultures.
Xylose is abundantly present together with glucose in lignocellulosic streams that would be available for the valorisation to biochemicals or biofuels. Yeast S. cerevisiae has superior characteristics for a host of the bioconversion except that it strongly prefers glucose and the co-consumption of xylose is yet a challenge. Further, since xylose is not a natural substrate of S. cerevisiae, the regulatory response it induces in an engineered yeast strain cannot be expected to have evolved for its utilisation. Dynamic cultivation experiments on mixed glucose-xylose medium having glucose cultures as control integrated with mathematical modelling allowed to resolve specific effects of xylose on the gene expression and metabolism of engineered S. cerevisiae in the presence of varying amounts of glucose.

overall_design: S. cerevisiae harbouring an XR-XDH pathway for xylose is grown in two conditions, growth on D-glucose vs growth on both D-glucose and D-xylose. The strains were grown in bioreactors and samples for microarrays were taken from 5 time points during the cultivation (3.5h, 6.5h, 9.5h, 12.5h, and 24.5h). Three replicate cultures were performed for each strain. The total number of microarrays is 30. Each arrays measures 5,777 genes from Saccharomyces cerevisiae with eight 60-mer probes per gene, with three-fold technical redundancy.

first: Susanne

last: Alff-Tuomala

first: Laura

last: Salusjärvi

first: Dorothee

last: Barth

last: Penttilä

first: Juha-Pekka

last: Pitkänen

last: Ruohonen

first: Paula

last: Jouhten


title: Identification of the genes regulated by maternal Ovo-B in PGCs in Drosophila melanogaster.

city: Tsukuba

first: Yuko

last: Shinozuka

state: Ibaraki-ken

address: Tennoudai 1-1-1

department: Life Science Center of TARA

institute: University of Tsukuba

summary: To identify downstream genes which was regulated by maternal Ovo-B in PGCs, we compared the transcriptomes between OvoA-expressing PGCs and control PGCs by microarry analysis in Drosophila melanogaster. We used fluorescence-activated cell sorting (FACS) to isolate PGCs from the stage 16 embryos carrying the transgene, EGFP-vasa, which expresses GFP specifically and continuously in the germline throughout the life cycle.

overall_design: RNAs from FACS-sorted OvoA-expressing PGCs and control PGCs from the stage 16 embryos were hybridized to microarray after Cy3 labling.

first: Masanao

last: Sato

first: Chiyo

last: Noda

first: Satoru

last: Kobayashi


title: Multifactorial competition and resistance in a two-species bacterial system

first: Anupama

last: Khare

overall_design: Refer to individual Series


title: The functional benefits of cardiac progenitor cells can be equaled by their secreted extracellular vesicles

status: Public on May 29 2016

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

summary:
Introduction: Cell-derived extracellular vesicles ([EVs], i.e., exosomes and microparticles) have been reported to mediate the cardioprotective effects of stem cells. However, a head-to-head comparison of their effects with those of the cells from which they derive has not been reported.
Hypothesis: The effects of the EV content of human embryonic stem cell (hESC)-derived cardiac progenitors may be equivalent to those of the parent cells.
Methods: Two series of immunodeficient (nude) mice underwent permanent coronary artery ligation. Three weeks later, those with an echocardiographically-determined LV ejection fraction ≤ 50% were randomly allocated to receive transcutaneous echo-guided peri-infarct injections of alpha-MEM media (controls), hESC-derived SSEA-1+ cardiac progenitors (500000 cells in 30 μL), or total EV secreted by those 500000 cells in 48 hours in an equivalent volume. The second series also included sham-operated animals for which the needle was inserted into the myocardium in three places without injection. EVs were collected from the cell-secreted medium by ultracentrifugation and characterized by flow cytometry, and nanosight NTS. Outcomes were assessed after 6 weeks by echocardiography, taking LV end-systolic volume (ESV) as the primary end point. Hearts were processed for the assessment of fibrosis and angiogenesis. Total RNA was extracted from carefully selected animals for gene expression analysis by Affymetrix chip. Only animals with similar VTS at baseline were used for this analysis. All data were collected and analyzed blindly.
Results: Cardiac progenitors were successfully generated by exposure of the pluripotent ESC to bone morphogenetic protein-2, purified by anti-CD15 immunomagnetic sorting and then cultured on vitronectin for 48 hours, after which cells or EVs derived from the same cell batch were injected. After 6 weeks in the first series, LVESV [m±SEM] in controls did not significantly differ from the pre-injection value (difference: -2.64 ± 1.54 µL, p=0.12, n= 12). Conversely, in the cell-treated group, LVESV significantly decreased by -4.20 ± 0.96 µL (p=0.0007, n=16). A similar decrease was seen in the EV-treated group: -5.73 ± 1.21 µL (p=0.0003, n=15). Similar patterns were seen for LV end-diastolic volumes: controls (-2.46 ± 1.19 µL, p=NS), cells (-4.48 ± 1.47 µL, p=0.009), EV (-4.29 ± 1.31 µL, p=0.005). For the second series, the VTD of cell- and EV-treated animals remained stable (cell: -1.85 ± 3.27 µL, p=NS, n= 4; EV: +0.05 ± 1.53 µL, p=NS, n = 4), whereas sham- and control-treated animals deteriorated significantly (sham: +2.20 ± 0.35 µL, p = 0.003, n = 5; control: +3.27 ± 0.87 µL, p = 0.03, n = 4). The trend held for VTS, though differences were not significant. Analysis of gene expression data revealed interesting pathways that were more highly expressed in cell- and EV-treated animals than in controls and sham-operated animals.
Conclusions: These data support the hypothesis that EVs may be critical mediators of the paracrine effects of cell therapy, and for the sake of streamlining translational processes, deserve to be considered as potential alternatives to stem cell transplantation.

overall_design: Gene expression levels were compared between mouse hearts.

first: Anaïs

last: Kervadec

first: Philippe

last: Menasché

first: Nisa

last: Renault


title: Total RNA Sequencing reveals microbial communities in human blood and disease specific effects

status: Public on May 25 2016

city: Los Angeles

first: Harry

middle: Taegyun

last: Yang

state: CA

address: Engineering VI 286

department: Computer Science

institute: University of California, Los Angeles

summary: An increasing body of evidence suggests an important role of the human microbiome in health and disease. We propose a ‘lost and found’ pipeline, which examines high quality unmapped sequence reads for microbial taxonomic classification. Using this pipeline, we are able to detect bacterial and archaeal phyla in blood using RNA sequencing (RNA-Seq) data. Careful analyses, including the use of positive and negative control datasets, suggest that these detected phyla represent true microbial communities in whole blood and are not due to contaminants. We applied our pipeline to study the composition of microbial communities present in blood across 192 individuals from four subject groups: schizophrenia (n=48), amyotrophic lateral sclerosis (n=47), bipolar disorder (n=48) and healthy controls (n=49). We observe a significantly increased microbial diversity in schizophrenia compared to the three other groups and replicate this finding in an independent schizophrenia case-control study. Our results demonstrate the potential use of total RNA to study microbes that inhabit the human body.

first: Serghei

last: Mangul

first: Loes

middle: M

last: Olde Loohuis

first: Anil

middle: P

last: Ori

first: Guillaume

last: Jospin

first: David

last: Koslicki

first: Timothy

last: Wu

first: Marco

last: Boks

first: Catherine

last: Lomen-Hoerth

first: Martina

last: Wiedau-Pazos

first: Rita

last: Cantor

first: Williem

last: de Vos

first: Rene

middle: S

last: Kahn

first: Jonathan

last: Eisen

first: Eleazar

last: Eskin

first: Roel

last: Ophoff


title: Mitochondrial-derived Oxidative Stress Alters Gene Expression and DNA Methylation in the Heart

first: William

last: Lewis


title: E. coli cells: Control vs. iron-supplemented P. aeruginosa spent-media treated

city: New York

first: Anupama

last: Khare

address: 1150 St. Nicholas Ave., Room 406

institute: Columbia University

summary: Transcriptional profiling of E. coli cells comparing control untreated cells with cells treated with iron-supplemented P. aeruginosa spent media. The goal was to identify the effects of P. aeruginosa spent media on E. coli cells, while neutralizing any effects of the P. aeruginosa siderophores

overall_design: Two-condition experiment. 2 biological replicates

first: Khare

last: Anupama

first: Tavazoie

last: Saeed


title: Mitochondrial-derived Oxidative Stress Alters Gene Expression and DNA Methylation in the Heart [expression]

overall_design: 15 left ventricle cardiac samples [4 vehicle (1%CMC)-treated wild-type C57BL/6, 3 AZT-treated wild-type C57BL/6, 4 vehicle-treated MCAT overexpressing, and 4 AZT-treated MCAT overexpressing) were collected, and RNA was extracted from each sample. Double-stranded cDNA was synthesized and hybridized to a 12X135 mouse expression array. Results were normalized and compared to DNA methylation array results from similar mouse groups. Each array represents a single mouse. All mice were of C57BL/6 background.

first: Christopher

last: Koczor


title: The role of long noncoding RNAs in T-cell acute lymphoblastic leukemia

status: Public on May 17 2016

city: Gent

first: Annelynn

last: Wallaert

address: De Pintelaan 185

country: Belgium

institute: UGent

summary: T-cell acute lymphoblastic leukemia (T-ALL) is genetically heterogeneous and can be classified into genetic subclasses based on protein coding gene expression profiles. Thus far, long noncoding RNAs (lncRNAs), representing one of the largest fractions of the human transcriptome, remained unexplored as genetics markers for distinct T-ALL subtypes. Therefore, we here determined, for the first time, lncRNA expression profiles in lymphoblasts of 64 T-ALL patients and identified a robust set of lncRNAs that discriminate previously established genetic subtypes of human T-ALL. Half of these lncRNAs were positively correlated with the expression levels of neighboring protein coding genes located in their immediate vicinity, hinting towards cis-regulatory functions. In addition, gene set enrichment analysis showed that these lncRNA signatures were also recapitulated in human T-ALL cell lines representative for the different genetic subclasses, suggesting that these tumor lines could serve as valuable in vitro cellular model systems for further functional lncRNA studies. Finally, comparison of T-ALL lncRNA signatures with those from stage-specific normal developing human thymocytes revealed multiple ectopically expressed, putative oncogenic lncRNAs. Our data identify lncRNAs novel genetic markers in T-ALL biology and warrant further in depth investigations towards landscaping of their specific role in thymopoiesis and leukemogenesis.

overall_design: Gene expression profiles of 10 different T-ALL cell lines

first: Kaat

last: Durinck

first: Wouter

last: Van Loocke

first: Pieter-Jan

last: Volders

first: Pieter

last: Mestdagh

first: Jo

last: Vandesompele

last: Van Vlierberghe

first: Frank

last: Speleman


title: Cytoplasmic polyadenylation is a major regulator of mRNA fate during oogenesis and egg activation.

status: Public on May 18 2016

city: Ithaca

first: Jeffrey

last: Pleiss

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

summary: The GLD-2 class of poly(A) polymerases regulate the timing of translation of stored transcripts by elongating the poly(A) tails of target mRNAs in the cytoplasm. WISPY is a GLD-2 enzyme that acts in the Drosophila female germline and is required for the completion of the egg-to-embryo transition. Though a handful of WISPY target mRNAs have been identified during both oogenesis and early embryogenesis, we aimed to discover the full range of WISPY targets at each stage. To globally identify these targets, we carried out microarray analysis to look for maternal mRNAs whose poly(A) tails fail to elongate in the absence of WISP function. We examined the polyadenylated portion of the maternal transcriptome in both stage 14 (mature) oocytes and in early embryos that had completed egg activation. Our analysis shows that the poly(A) tails of thousands of maternal mRNAs fail to elongate in wisp-deficient oocytes and embryos. Furthermore, we have identified specific classes of genes that are highly regulated in this manner at each stage. Our study shows that cytoplasmic polyadenylation is a major regulatory mechanism during oocyte maturation and egg activation.

overall_design: Four groups of comparisons: WT vs. wisp total RNA from stage 14 oocytes, WT vs. wisp total RNA from fertilized eggs, WT vs. wisp poly(A)+ RNA from stage 14 oocytes, WT vs. wisp poly(A)+ RNA from fertilized eggs. Each comparison consisted of three independent RNA extractions and each experiment was done with dye-swap pairs as two technical replicates.

first: Jun

last: Cui

first: Caroline

middle: V

last: Sartain

first: Mariana

last: Wolfner


title: DNA methylation profiling of blood monocytes in obstructive sleep apnea (OSA) patients: Effect of positive airway pressure (PAP) treatment.

status: Public on May 11 2016

city: SYRACUSE

first: Mira

last: Krendel

state: New York

address: 505 Irving Ave

institute: Upstate Medical University

summary: Background: Obstructive sleep apnea (OSA) is a highly prevalent condition that is associated with a wide range of long-term morbidities including metabolic, cardiovascular, and cognitive alterations, possibly via activation of systemic inflammatory and oxidative stress pathways. Implementation of positive airway pressure (PAP) is the first line treatment for OSA. However, the molecular and cellular mechanisms underlying OSA-induced morbidities and their response to PAP treatment remain unclear. Methods And Results: DNA methylation profiles were examined in blood monocytes of OSA patients before and after PAP treatment. We identified 1,847 regions showing significant differential DNA methylation (p<0.001 and MAT score >4) between the groups. Analysis of biochemical pathways and gene networks demonstrated that differentially methylated regions (DMRs) were associated with immune responses, and particularly with mechanisms governing gene regulation by peroxisome proliferation-activated receptors (PPAR). Single locus quantitative PCR analysis revealed that DNA methylation was increased at the PPAR responsive elements (PPAREs) of 8 genes in the post-treatment samples, suggesting that PAP treatment leads to an increase in DNA methylation at PPAREs, possibly affecting the binding of the PPARG complex and downstream gene expression. Conclusions: Our work provides initial evidence of epigenetic regulation particularly involving metabolic pathways in OSA patients that are responsive to PAP treatment. We postulate that differentially methylated regions in blood monocytes may serve as potential biomarkers in clinical practice.

overall_design: Blood monocyte samples from 6 OSA patients were analyzed by MeDIP coupled to microarray analysis: Blood monocytes were collected from the same group of patients before (PRE group, n=6) and after (POST group, n=6) CPAP treatment.

first: Rene

last: Cortese

first: Chunling

last: Zhang

first: Riyue

last: Bao

first: Jorge

last: Andrade

first: Abdelnaby

last: Khalyfa

first: Babak

last: Mokhlesi

first: David

last: Gozal


title: Oviductal transcriptome is modified after insemination during spontaneous ovulation in the sow

city: Murcia

first: Pilar

last: Coy

state: Murcia

address: Campus de Espinardo.Facultad de Veterinaria

department: Physiology

institute: University of Murcia

summary: Gene Expression Microarray technology was used to compare oviduct transcriptome between inseminated and non-inseminated pigs during spontaneous oestrus. We used an in vivo model approaching the study from a physiological point of view in which no hormonal treatment (animals were in natural oestrus) and no artificial sperm selection (selection was performed within the female genital) were imposed. It is therefore emphasised that no surgical introduction of spermatozoa and no insemination at a site other than the physiological one were used. This approach revealed 17 genes that were two-fold or more up-regulated in oviducts exposed to spermatozoa and/or developing embryos and 9 genes that were two-fold or more down-regulated. These changes would indicate a modification of the environment preparing the oviduct for a successful fertilization and for an adequate embryo early development. The objective of this study was to investigate differences in oviductal transcriptome between inseminated and non-inseminated pigs during spontaneous oestrus in a specific area of the oviduct (ampullary-isthmic junction). We decided to analyse this specific part of the oviduct where spermatozoa released from sperm reservoir arrive close to the time of ovulation because it is where fertilization and zygote formation occurs.

overall_design: We used 5 artificially inseminated and 5 non-inseminated pigs during spontaneous oestrus. Inseminations were performed with seminal doses at a concentration of 3 x 107 spermatozoa/ml. Complete oviductal tissue samples from the ampullary-isthmic junction (sample size >1cm including the end of the ampulla) were taken from each animal and immediately frozen in liquid nitrogen for mRNA extraction.

first: Rebeca

last: López-Úbeda

first: Francisco

last: García-Vázquez

first: Raquel

last: Romar

first: Joaquín

last: Gadea

first: Marta

last: Muñoz

first: Ronald

middle: H

last: Hunter


title: miRNA profiling of mature C2C12 myotubes using modified (COS) vs standard (STD) tissue culture conditions

city: Montreal

first: R. Thomas

last: Jagoe

state: Quebec

address: Jewish General Hospital, 3755 Cote Ste Catherine

department: Medicine

institute: McGill University

summary:
miRNA profiling comparing modified (COS = Cytokine (low dose), Oxygen (physiological), Stimulation (low frequency electrical)) or standard (STD) culture condtions for 72hrs prior to harvest at day 8 post differentiation.  Secondary experiment to assess additional impact of dexamethasone when given in COS conditions.
5 arrays were labeled with same RNA in each channel (self-self hybridisations) to establish parameters for detecting real change for each probe on the arrays.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Main experiment: two-conditions; 6 biological replicates; 1 replicate per array.  Secondary experiment: two conditions: 2 biological replicates; 1 replicate per array

first: R

middle: T


title: MDAH-041 Spontaneous Immortalization

status: Public on May 12 2016

city: Detroit

first: Joshua

last: Stevens

state: MICHIGAN (MI)

address: 540 E. Canfield St.

department: Center for Molecular Medicine and Genetics

institute: Wayne State University School of Medicine

summary: Gene expression at various stages of immortalization

overall_design: 6 samples with two independent replicates each and two commercial RNA controls were included

first: Heng

last: Henry


title: Effects of halogenated boroxine on expression of human cancer drug targets in melanoma cell line

city: Sarajevo

first: Lejla

last: Pojskic

address: Zmaja od Bosne 8

country: Bosnia and Herzegovina

institute: Institute for Genetic Engineering and Biotechnology

summary: Recently it was found that dipotassium-trioxohydroxytetrafluorotriborate, K2(B3O3F4OH), is a  potent and highly specific inhibitor of precancerous cell processes. We conducted gene  expression profiling of human melanoma cells before and after treatment with two  concentrations (0.1 and 1 mM) of this boron inorganic derivative in order to assess its effects  on deregulation of genes associated with tumor pathways. Parallel trypan blue exclusion assay  was performed to assess the cytotoxicity effects of this chemical. Treatment with K2(B3O3F4OH)  induced a significant decrease of cell viability in melanoma cellline at both tested  concentrations. Furthermore, these treatments caused deregulation of more than 30 genes  known as common anti-tumor drug targets. IGF-1 and hTERT were found to be significantly  downregulated and this result may imply potential use of K2(B3O3F4OH) as an inhibitor or  human telomerase and insulin-like growth factor 1, both of which are associated with various  tumor pathways.

overall_design: Upon the treatment of melanoma cells by K2(B3O3F4OH) in the  above-mentioned manner, total RNA was extracted from harvested  cells using RNA isolation kit (QIAGEN GmbH, Hilden,  Germany).Human Cancer Drug Targets RT2 Profiler PCR  method is used according to manufacturer’s instructions (RT2  Profiler PCR Array Handbook, Qiagen N. V., Venlo, Limburg,  Netherlands) for a multigene profiling of expression of 84 genes  (Table 2) on ABI 7300 real-time PCR apparatus (Applied  Biosystems, Foster City, CA). The three cell populations used in  the experiment (cell culture control sample and two cell cultures  treated with K2(B3O3F4OH) in concentrations of 0.1mM and  1mM) were subsequently analyzed in three identical 96 wells array  formats. The quality check up (false positive and false negative  signals evaluation) was based on positive and negative controls  included on arrays, as well as gDNA contamination probes.

first: Sanin

last: Haveric

first: Naida

last: Lojo-Kadric

first: Maida

last: Hadzic

first: Anja

first: Zoran

last: Galic

first: Borivoj

first: Daniella

last: Vullo

first: Claudiu

last: Supuran

first: Mladen

last: Milos


title: Transcriptome analysis of as1-1, tfl2-1 and as1-1 tfl2-1 mutants in comparison with wild type.

status: Public on May 10 2016

city: shanghai

first: Zhongfei

last: Li

address: songhu road 2005

institute: fudan university

summary: ASYMMETRIC LEAVES 1 (AS1) is an important transcription factor for leaf development in Arabidopsis. But how it regulates downstream genes is largely unknown. We found a co-factor of AS1, LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), also named as TERMINAL FLOWER 2 (TFL2), a PcG protein in Arabidopsis. To further investigate how AS1 and LHP1 co-regulate downstream genes at the genome level, we perform the transcriptome analysis of as1-1, tfl2-1, and as1-1 tfl2-1 in comparison with wild type (WT).

overall_design: 12-day-old seedlings of wild-type (WT), as1-1, tfl2-1 and as1-1 tfl2-1 grown in normal growth condition were used for RNA extraction and microarray. Duplicate samples were analyzed.

first: Bin


title: Gene Expression Based Characterization of B7H3 In Prostate Cancer

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St #430

institute: GenomeDx

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


title: Aflatoxin B1 induces persistent epigenomic effects in primary human hepatocytes associated with hepatocellular carcinoma [DNA methylation]

city: Maastricht

first: Linda

last: Rieswijk

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

summary: Chronic exposure to aflatoxin B1 (AFB1) has, in certain regions in the world, been strongly associated with the development of hepatocellular carcinoma (HCC). AFB1 is a very potent hepatotoxic and carcinogenic mycotoxin which is frequently reported as a food contaminant.  Epigenetic modifications provoked by environmental exposures, such as AFB1, may create a so called persistent "epigenetic memory" or "footprint". Deregulation of epigenetic mechanisms has actually been reported in HCC patients following AFB1 exposure; however no attempts have yet been made to investigate early effects on the epigenome level which may be persistent on longer term thereby possibly initiating carcinogenic events. In this study, we aim to identify methyl DNA-mRNA-interactions representative for a persistent epigenetic "footprint" associated with the early onset of AFB1-induced HCC. For this, primary human hepatocytes were exposed to 0.3 µM of AFB1 for 5 days. Persistent epigenetic effects were m  easured 3 days after terminating the carcinogenic treatment. Whole genome DNA methylation changes and whole genome transcriptomic analysis were analyzed applying microarray technologies, and cross-omics interactions were evaluated. Upon combining transcriptomics data with results on DNA methylation, a range of persistent hyper- and hypomethylated genes was identified which appeared also affected on the transcriptome level. For six of the hypomethylated and upregulated genes, namely TXNRD1, PCNA, CCNK, DIAPH3, RAB27A and HIST1H2BF, a clear role in carcinogenic events could be identified. This study is the first to report on a carcinogen-induced persistent impact on the "epigenetic footprint" in relation with the transcriptome which could be indicative for the early onset of AFB1-related development of HCC.

overall_design:
The study investigated differential gene expression, microRNA expression and DNA methylation changes in a pool of primary human hepatocyte RNA after 3 days of wash out following 5 days of repetative exposure to 0.3 uM of aflatoxin B1 or DMSO. Three biological replicates per compound/solvent. In total 6 arrays.
The references 27, 28, 29, 30 and 32 are:

27. Eijssen LM, Jaillard M, Adriaens ME, Gaj S, de Groot PJ, Muller M, et al. User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org. Nucleic Acids Res. 2013;41(Web Server issue):W71-6.
28. Gautier L, Cope L, Bolstad BM, Irizarry RA. affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 2004;20(3):307-15.
29. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5(10):R80.
30. Rieswijk L, Lizarraga D, Brauers KJ, Kleinjans JC, van Delft JH. Characterisation of cisplatin-induced transcriptomics responses in primary mouse hepatocytes, HepG2 cells and mouse embryonic stem cells shows conservation of regulating transcription factor networks. Mutagenesis. 2014;29(1):17-26.
32. Coonen M, Theunissen DH, Kleinjans JC, Jennen DG. MagiCMicroRna: a web implementation of AgiMicroRna using shiny. Source code for biology and medicine. 2015;10:4

first: L


title: Aflatoxin B1 induces persistent epigenomic effects in primary human hepatocytes associated with hepatocellular carcinoma [mRNA]


title: Prior Knowledge-based Approach for Associating Emerging Contaminants with Effects in Fish Exposed In Situ:  A Case Study in the St. Croix River Basin, MN, WI, USA.

city: St Paul

first: Anthony

last: Schroeder

address: 1985 Lower Buford Cir # 173

institute: University of Minnesota

summary: Evaluating the potential human health and ecological risks associated with exposures to complex chemical mixtures in the environment is one of the main challenges of chemical safety assessment and environmental protection.  There is a need for approaches that can help to integrate chemical monitoring and biological effects data to evaluate risks associated with specific chemicals present in the environment.  In the present study water samples from five locations near two wastewater treatment plants in the St. Croix River basin on the border of MN and WI, USA were analyzed for 127 contaminants including wastewater indicators, pharmaceuticals, and a number of natural and synthetic steroids. Prior knowledge about chemical-gene interactions was used to develop site-specific knowledge assembly models (KAMs) that were used to formulate hypothesis concerning possible biological effects of exposure to the chemicals detected at each location and suggest assays and endpoints for follow-up investigation. Additionally empirical hepatic gene expression data were collected for fathead minnows (Pimephales promelas) exposed in situ, for 12 d, at each location using a high density oligonucleotide microarray. Empirical gene expression data were analyzed to identify functional annotation terms enriched among the lists of differentially-expressed probes. However, the general nature of many of the terms made hypothesis formulation on the basis of the transcriptome-level response alone difficult. However, integrated analysis of the transcriptome data in the context of the site-specific KAMs allowed for evaluation of the likelihood of specific chemicals contributing to observed biological responses, based on prior knowledge.

overall_design: Adult male fathead minnows were exposed in situ to treated wastewater effluent, or water upstream or downstream of two wastewater treatment plants along the St. Croix River in MN and WI.  Two replicates of ten fish (20 fish total) were placed into mini-mobile environmental monitoring units and exposed to continually flowing water from the appropriate treatment.  Fish were exposed for 12 days and then sampled.  Livers from 6-7 randomly chosen fathead minnows were isolated and RNA was extracted for hepatic transciptome analysis using microarray. The transcriptomic profiles were compared to control fish exposed to well water for 12 days.

first: Dalma

last: Martinović-Weigelt

first: Gerald

last: Ankley

first: Kathy

middle: E

last: Lee

first: Natalia

last: Garcia-Reyero

first: Edward

last: Perkins

first: Heiko

last: Schoenfuss

first: Daniel

last: Villeneuve


title: Half-Half experiments

first: Joshua

last: Stevens

summary: Various cell lines including clones of MDAH-041 cells were karyotypically defined by SKY. Two replicates of each line was harvested from one flask of cells.

overall_design: Replicate from 1/2 of a flask was compared to the replicate from the other half of the flask

first: Henry

last: Heng


title: Aflatoxin B1 exposure induces epigenetic mechanisms in primary human hepatocytes revealing novel biological processes associated with hepatocellular carcinoma (MeDIP)

type: Genome binding/occupancy profiling by genome tiling array

summary: The study investigated differential gene expression, microRNA expression and DNA methylation changes in a pool of primary human hepatocyte RNA and DNA following 5 days of repetitive exposure to a low or moderate dose of aflatoxin B1 or DMSO. Three biological replicates per compound/solvent. In total 9 arrays.

overall_design: In total 9 arrays.


title: Aflatoxin B1 exposure induces epigenetic mechanisms in primary human hepatocytes revealing novel biological processes associated with hepatocellular carcinoma (miRNA)

summary: The study investigated differential gene expression, microRNA expression and DNA methylation changes in a pool of primary human hepatocyte RNA and DNA following 5 days of repetitive exposure to a low or moderate dose of aflatoxin B1 or DMSO. Three biological replicates per compound/solvent.

overall_design: In total 9 arrays. The PHH_5D_MD_control and PHH_LD_5D_control Samples are the same Samples just processed differently. The raw data files for these Samples are on the Series record.


title: Streptomyces coelicolor M145 scbRDM vs WT and scbR2DM vs WT

city: Beijing

first: Xiao

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: To help understand the functions of GBL receptor ScbR and antibiotic receptor ScbR2, the global transcriptional profiles of scbRDM and scbR2DM compared to WT were studied.

overall_design: Transcprits of mutants scbRDM and scbR2DM were compared to WT at corresponded time points: WT and  scbRDM at 30h, WT and  scbR2DM at 42h mycelium were collected, and subjected to microarray hybridization and analysis. Three duplicated were conducted.

first: Weishan

last: Wang


title: Diatom phytochromes reveal the existence of far-red light based sensing in the ocean

status: Public on May 09 2016

city: Paris

first: Angela

last: Falciatore

address: 15 rue de l'ecole de Medicine

department: UMR 7238, LCQB

institute: CNRS

summary: The absorption of visible light in aquatic environments has led to the common assumption that aquatic organisms sense and adapt to penetrative blue/green light wavelengths, but show little or no response to the more attenuated red/far-red wavelengths. Here we show that two marine diatom species, Phaeodactylum tricornutum and Thalassiosira pseudonana, possess a bona fide red/far-red light sensing phytochrome (DPH) that uses biliverdin as a chromophore and displays accentuated red-shifted absorbance peaks compared to other characterized plant and algal phytochromes. Exposure to both red and far-red light causes changes in gene expression in P. tricornutum and the responses to far-red light disappear in DPH knockout cells, demonstrating that P. tricornutum DPH mediates far-red light signaling. The identification of DPH genes in diverse diatom species widely distributed along the water column further emphasizes the ecological significance of far-red light sensing, raising questions about the sources of far-red light. Our analyses indicate that, although far-red wavelengths from sunlight are only detectable at the ocean surface, chlorophyll fluorescence and Raman scattering can generate red/far-red photons in deeper layers. This study opens up novel perspectives on phytochrome-mediated far-red light signaling in the ocean and on the light sensing and adaptive capabilities of marine phototrophs.

overall_design: Phaeodactylum tricornutum cultures growing in 12L/12D cycles were exposed, at the end of the 12 h dark period, to 30 minutes of low fluence of red or far-red light and harvested immediately after the light treatment. Cells were also collected before the light treatment as reference point and, culture kept in dark for 30 minutes represented the control condition. Two biological replicates were sampled for each condition.

first: Marianne

last: Jaubert

first: Antonio Emidio

last: Fortunato


title: Aflatoxin B1 exposure induces epigenetic mechanisms in primary human hepatocytes revealing novel biological processes associated with hepatocellular carcinoma

first: Linda

overall_design: Refer to individual Series


title: Genomic landscape of somatic alterations in esophageal squamous cell carcinoma and gastric cancer

city: Bethesda

first: Maxwell

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

summary: Gastric cancer and esophageal cancer are the 2nd and 6th leading causes of cancer death worldwide. We analyzed DNA copy numbers for 73 ESCC (43 SNP5.0 and 30 500K SNP) with the Affymetrix SNP arrays .  Our analyses implicated potential driver mutations involving the following genes: mutations in TP53, BRCA2, NOTCH2, CTNNB1, and LEPREL2; amplification of CCND1, FGF3/4/19, and MYC; and deletion of CDKN2A/B.

overall_design: Copy number analysis of Affymetrix SNP5.0 arrays

last: Hu

first: Mitsutaka

last: Kadota

first: Huaitian

last: Liu

first: Hailong

last: Wu

first: Hua

last: Su

first: Christian

middle: C

last: Abnet

first: Neal

middle: D

last: Freedman

first: Howard

last: Yang

first: Chaoyu

first: Chunhua

last: Yan

first: Lemin

first: Sheryl

last: Gere

first: Amy

last: Hutchinson

first: Kevin

middle: B

last: Jacobs

first: Guohong

last: Song

first: Quan

first: Ti

last: Ding

first: You

last: Qiao

first: Jill

last: Koshiol

first: Sanford

last: Dawsey

first: Carol

last: Giffen

first: Alisa

last: Goldstein

first: Philip

middle: R

last: Taylor


title: Baseline Expression of Inflammatory Cytokines and Receptors in the T47D Human Breast Cancer Cell Line

status: Public on May 06 2016

city: Springfield

first: Sophia

last: Ran

state: IL

address: 801 N. Rutledge St.

department: MMICB

institute: Southern Illinois University - School of Medicine

summary: Immortalized human breast cancer cell line, T47D, was analyzed via RT-qPCR for transcript expression of selected inflammatory cytokines and cytokine receptors associated with promotion of tumor vasculature and breast cancer metastasis

overall_design: An array of inflammatory cytokines and matching receptors that have been associated with the promotion of tumor vasculature and breast cancer metastasis were identified based on literature and clinical data. Using this array, we screened normal breast tissue and seven breast cancer cell lines (T47D, MCF7, ZR-75, HCC1806, MDA-MB-231, HCC1954, SUM149), representing a range of breast cancer types. These results can be analyzed individually or used to compare the expression differences in normal breast tissue to breast cancer cell lines to identify potential mediators of autocrine or paracrine promotion of tumor angiogenesis, lymphangiogenesis and metastasis. Each cell line is published separately in GEO.

first: Vineela

last: Sunkepalli

first: Kelly

last: Hall

first: Lisa

last: Volk-Draper


title: Aflatoxin B1 induces persistent epigenomic effects in primary human hepatocytes associated with hepatocellular carcinoma [miRNA]

first: Linda

last: Rieswijk

first: L


title: Baseline Expression of Inflammatory Cytokines and Receptors in the SUM149 Human Breast Cancer Cell Line

summary: Immortalized human breast cancer cell line, SUM149, was analyzed via RT-qPCR for transcript expression of selected cytokines and cytokine receptors associated with promotion of tumor vasculature and breast cancer metastasis


title: Aflatoxin B1 induces persistent epigenomic effects in primary human hepatocytes associated with hepatocellular carcinoma


title: Baseline Expression of Inflammatory Cytokines and Receptors in the MDA-MB-231 Human Breast Cancer Cell Line

summary: Immortalized human breast cancer cell line, MDA-MB-231, was analyzed via RT-qPCR for transcript expression of selected cytokines and cytokine receptors associated with promotion of tumor vasculature and breast cancer metastasis


title: Baseline Expression of Inflammatory Cytokines and Receptors in the ZR-75 Human Breast Cancer Cell Line

summary: Immortalized human breast cancer cell line,  ZR-75, was analyzed via RT-qPCR for transcript expression of selected cytokines and cytokine receptors associated with promotion of tumor vasculature and breast cancer metastasis


title: Gene Expression Based Characterization of B7H3 In Prostate Cancer [BCR]

first: Elai

last: Davicioni

summary: B7-H3 (CD276), part of the B7 superfamily, has been shown to play an immunomodulatory role, however its regulation, receptor, and mechanism of action remain unclear.  Protein levels of B7-H3 have been previously shown to relate to prostate cancer outcomes and currently, humanized monoclonal antibodies are being investigated for clinical therapeutic use (enoblituzumab, MGA271, Macrogenics).  Here we use genomic expression data to examine the relationship of B7-H3 to prostate cancer clinical characteristics and molecular profile.

overall_design: Retrospective case-cohort design for 294 men (genomic data available for 211) initially diagnosed with intermediate or high risk localized prostate cancer who had no neo-adjuvant treatment, underwent RP between 1992 and 2010, and subsequently experienced BCR. These men received no post-RP secondary therapy prior to metastasis.

first: Benjamin

last: Benzon

first: George

last: Zhao

first: Michael

last: Haffner

first: Mandeep

last: Takhar

first: Nicholas

last: Erho

first: Kasra

last: Yousefi

first: Paula

last: Hurley

first: Jennifer

last: Bishop

first: Jeffrey

last: Tosoian

first: Kamyar

last: Ghabili

first: Mohammed

last: Alshalalfa

first: Stephanie

last: Glavaris

first: Brian

last: Simons

first: Phuoc

last: Tran

first: R

middle: J

last: Karnes

first: Emmanuel

last: Antonarakis

first: Edward

last: Schaeffer

first: Charles

middle: G

last: Drake

first: Felix

last: Feng

first: Ashley

last: Ross


title: Embryo thermal manipulation: muscle transcriptional profile in chickens submitted or not to heat challenge 34d posthach

city: Nouzilly

first: Anne

last: Collin

address: UR83 Recherches Avicoles

institute: INRA

summary: Meat type chickens have limited capacities to cope with high environmental temperatures, sometimes leading to important mortality in farms and subsequent economic loss. One of the strategies to increase the sustainability of broiler chicken production is to enhance their adaptive capacities to face heat exposure using heat conditioning (C) during embryogenesis. This strategy was shown to improve thermotolerance in later life. The aim of this study was to determine the effect of C (39.5°C, 12h/24 vs 37.8°C from d7 to d16 of embryogenesis) and of a subsequent heat challenge (32°C for 5h, CH) applied on d34, on global gene expression in the Pectoralis major muscle (PM). Chicken Genome Array (60 K) was used to compare muscle gene expression profiles of Control (T) and heat-conditioned C chickens (characterized by low body temperature) reared at 21°C, and reared at 32°C (TCH and CCH respectively) in a dye-swap design with four comparisons and 8 broilers per condition. Real-time RT-PCR was subsequently performed to validate differential expressions in each comparison. Gene ontology, clustering and network building strategies were used. This study was performed with the financial support of the French Agence Nationale de la Recherche, Project «Jeunes Chercheuses et Jeunes Chercheurs», ANR-09-JCJC-0015-01, THERMOCHICK.

overall_design: Four-condition experiment on chicken breast muscle samples, Controls at 32°C  (TCH) vs.  Controls at 21°C  (T), heat-conditioned at 21°C (C) vs. Controls at 21°C  (T), heat-conditioned at 32°C (CCH) vs. heat-conditioned at 21°C (C), heat-conditioned at 32°C (CCH) vs.  Controls at 32°C  (TCH). Biological replicates: 8 per treatment characterized by low body temperatures in C and CCH treatments and high body temperatures in T and TCH treatments.

first: Thomas

last: Loyau

first: Christelle

last: Hennequet-Antier

first: Marie

last: Leduc

first: Sabine

last: Crochet

first: Mélanie

last: Sannier

first: Vincent

last: Coustham

first: Michel

last: Duclos

first: Cécile

last: Berri

first: Sandrine

last: Mignon-Grasteau

first: Sophie

last: Tesseraud

first: Aurélien

last: Brionne

first: Sonia

last: Métayer-Coustard

first: Marco

last: Moroldo

first: Jérôme

last: Lecardonnel

first: Patrice

last: Martin

last: Lagarrigue

first: Shlomo

last: Yahav


title: Aflatoxin B1 exposure induces epigenetic mechanisms in primary human hepatocytes revealing novel biological processes associated with hepatocellular carcinoma (Affymetrix)

first: Linda

last: Rieswijk

summary: The study investigated differential gene expression, microRNA expression and DNA methylation changes in a pool of primary human hepatocyte RNA and DNA following 5 days of repetitive exposure to a low (LD) or moderate (MD) dose of aflatoxin B1 or DMSO. Three biological replicates per compound/solvent.

overall_design: In total 8 arrays. The PHH_5D_MD_control and PHH_LD_5D_control Samples are the same Samples just processed differently. The CEL files for these Samples are on the Series record.

first: L


title: Validation of a genomic classifier for prediction of metastasis following postoperative radiation therapy.

city: San Diego

first: Elai

last: Davicioni

address: 10355 Science Center Dr

institute: GenomeDx Biosciences

summary: To test the hypothesis that a genomic classifier (GC) would predict biochemical failure (BF) and distant metastasis (DM) in men receiving radiation therapy (RT) after radical prostatectomy (RP).

overall_design: 139 primary prostate cancer tumor (radical prostatectomy, FFPE) specimins from patients at TJU who recieved post-RP radiation therapy.

first: Robert

last: Den

first: Felix

middle: Y

last: Feng

first: Timothy

middle: N

last: Showalter

first: Mark

last: Mishra

first: Edouard

last: Trabulsi

first: Costas

last: Lallas

first: Leonard

last: Gomella

first: W

last: Kelly

first: Ruth

last: Birbe

first: Peter

middle: A

last: McCue

first: Mercedeh

last: Ghadessi

first: Kasra

last: Yousefi

first: Karen

last: Knudsen

first: Adam

last: Dicker


title: Baseline Expression of Inflammatory Cytokines and Receptors in Normal Breast Tissue and Seven Breast Cancer Cell Lines

first: Sophia

last: Ran

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


title: Baseline Expression of Inflammatory Cytokines and Receptors in the MCF7 Human Breast Cancer Cell Line

summary: Immortalized human breast cancer cell line, MCF7, was analyzed via RT-qPCR for transcript expression of selected cytokines and cytokine receptors associated with promotion of tumor vasculature and breast cancer metastasis

first: Vineela

last: Sunkepalli

first: Kelly

last: Hall

first: Lisa

last: Volk-Draper


title: Baseline Expression of Inflammatory Cytokines and Receptors in the HCC1954 Human Breast Cancer Cell Line

summary: Immortalized human breast cancer cell line, HCC1954, was analyzed via RT-qPCR for transcript expression of selected cytokines and cytokine receptors associated with promotion of tumor vasculature and breast cancer metastasis


title: Baseline Expression of Inflammatory Cytokines and Receptors in the Normal Human Breast

summary: Immortalized human breast cancer cell line, Normal, was analyzed via RT-qPCR for transcript expression of selected cytokines and cytokine receptors associated with promotion of tumor vasculature and breast cancer metastasis

overall_design: An array of inflammatory cytokines and matching receptors that have been associated with the promotion of tumor vasculature and breast cancer metastasis were identified based on literature and clinical data. Using this array, we screened normal breast tissue, procured from the Simmons Cancer Instititute Tissue Bank at Southern Illinois University School of Medicine, along with seven breast cancer cell lines (T47D, MCF7, ZR-75, HCC1806, MDA-MB-231, HCC1954, SUM149), representing a range of breast cancer types. These results can be analyzed individually or used to compare the expression differences in normal breast tissue to breast cancer cell lines to identify potential mediators of autocrine or paracrine promotion of tumor angiogenesis, lymphangiogenesis and metastasis. Each cell line is published separately in GEO.


title: Baseline Expression of Inflammatory Cytokines and Receptors in the HCC1806 Human Breast Cancer Cell Line

summary: Immortalized human breast cancer cell line, HCC1806, was analyzed via RT-qPCR for transcript expression of selected cytokines and cytokine receptors associated with promotion of tumor vasculature and breast cancer metastasis


title: Mitochondrial Polymerase Gamma Dysfunction and Aging Cause Cardiac Nuclear DNA Methylation Changes [100718_MM9_EXP]

city: Atlanta

first: William

last: Lewis

address: 101 Woodruff Circle

institute: Emory University

summary:
Cardiomyopathy (CM) is an intrinsic weakening of the myocardium with contractile dysfunction and congestive heart failure (CHF).  CHF has been postulated to result from decreased mitochondrial energy production and oxidative stress.  The effects of decreased mitochondrial oxygen consumption can also accelerate with aging, with the mitochondrial theory of aging forming the basis of this knowledge.  We previously showed DNA methylation changes in human hearts with CM.  This was associated with mitochondrial DNA depletion, being another molecular marker of CM.  We examined the relationship between mitochondrial dysfunction and cardiac epigenetic DNA methylation changes in both young and old mice.  We used genetically engineered C57Bl/6 mice transgenic for a cardiac-specific mutant of the mitochondrial polymerase (termed Y955C).  Y955C mice undergo left ventricular hypertrophy (LVH) at a young age (~94 days old), and LVH decompensated to CHF at old age (~255 days old).  In Y955C hearts, 95 differentially expressed genes were found, while 4,452 genes were differentially expressed in aged hearts.  Moreover, cardiac DNA methylation patterns differed between Y955C (4,506 peaks with 68.5% hypomethylation) and aged hearts (73,286 peaks with 80.2% hypomethylated). Correlatively, of the 95 Y955C-dependent differentially expressed genes, 30 genes (31.6%) also displayed differential DNA methylation; in the 4,452 age dependent differentially expressed genes, 342 gene (7.7%) displayed associated DNA methylation changes.  Both Y955C and aging demonstrated significant enrichment of CACGTG-associated E-box motifs in differentially methylated regions.  Cardiac mitochondrial polymerase dysfunction alters nuclear DNA methylation. Furthermore, aging causes a robust change in cardiac DNA methylation that is partially associated with mitochondrial polymerase dysfunction.
This study addresses how Y955C-mutated mitochondrial DNA polymerase g  and aging affect cardiac (left ventricle) gene expression and epigenetic nuclear DNA methylation.

overall_design: Each sample was fluorescently labeled and hybridized to Roche Nimblegen 12X135kb MM9 Gene Expression Arrays.

first: Christopher

last: Koczor


title: Mitochondrial Polymerase Gamma Dysfunction and Aging Cause Cardiac Nuclear DNA Methylation Changes


title: Mitochondrial Polymerase Gamma Dysfunction and Aging Cause Cardiac Nuclear DNA Methylation Changes [100929_MM9_Deluxe_Prom_Meth_HX1]

overall_design: Each sample was fluorescently labeled and hybridized to Roche Nimblegen 2.1M Deluxe Promoter Arrays.


title: Genome-wide epigenetic alteration in adult T-cell leukemia cells and HTLV-1-mediated immortalized cells

city: Tokyo

first: Makoto

last: Yamagishi

address: 4-6-1, Shirokanedai, Minatoku

department: Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences

institute: The University of Tokyo

summary: We performed ChIP-on-chip analysis of primary ATL patient cells, normal CD4+ T cells, and Tax-transduced cells to decipher the ATL-specific ‘epigenetic-code’ that was critical in ATL pathogenesis.

overall_design: Comparison of histone H3K27me3 and H3K4me3 marks in normal, Tax-transduced, and ATL cells. Investigation of the biological effects of HTLV-1 Tax on the host epigenome in HTLV-1 infected cells.

first: Dai

last: Fujikawa

last: Hori

first: Kazumi

last: Nakano

first: Toshiki

last: Watanabe


title: spatially- and tempospatially-stressed spider mites (Tetranychus urticae) vs control spider mites (Tetranychus urticae)

status: Public on May 02 2016

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

institute: University of Ghent

summary: In this study, we profiled the transcriptional changes in a polyphagous spider mite, Tetranychus urticae, after adaptation to spatial and tempospatial stress. We show heritable down-regulation of genes encoding for core enzymes involved in the citric acid and gluconeogenesis/glycolyse pathways (glucose 6-phosphatase among others). Additionally, we observe heritable transcriptional changes in amino acid pathways (methionine, tyrosine and phenylalanine) and in laterally acquired genes from bacteria (cobalamin-independent methionine synthase). By similiar study results in other organisms, we argue that these heritable transcriptional changes (partially) underpin the changed life history traits observed in our experimental evolution set-up.

overall_design: We have two comparisons, first; spatially-stressed mites (SPA) vs control mites (HOM), in 3 biological replications and second; tempospatially-stressed mites (TEM) vs control mites (HOM) in 3 biological replications. The labeled cRNA samples were pooled and hybdrized to a custom Sureprint genome wide G3 Gene Expression 8x60K microarray. Data was extracted by Agilent Feature Extraction software (using protocol GE2_107_SEP09). Limma was used for the pre-processing and final statistical analysis of the data.

first: Annelies

last: De Roissart

first: Dries

last: Bonte

first: Thomas

last: Van Leeuwen


title: Heterotrophy can save corals from oxidative stress and bleaching

status: Public on May 04 2016

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

summary: Scleractinian corals acquire autotrophic nutrients via the photosynthetic activity of their symbionts and the subsequent transfer of photosynthates. Zooplankton predation by the animal (heterotrophy) is an additional food source. Under stress events, corals loose their symbionts, a phenomena known as bleaching, which eventually leads to starvation, unless corals increase their heterotrophic capacities. Molecular mechanisms by which heterotrophy sustains metabolism in stressed corals remain elusive. Here for the first time, we identify specific genes expressed in heterotrophically fed and unfed corals maintained under normal and light-stress conditions inducing bleaching. Physiological parameters and gene expression profiling showed ominously that fed corals better resisted the stress than unfed corals, by presenting less oxidative damage and protein/DNA degradation. Light stressed and unfed/starved corals (HLS) up-regulated by 140 and 13 times two genes (CP2U1 and CP1A2), which belong to the Cytochrome P450 superfamily, while these genes remained almost unchanged in fed corals (HLF). Other genes of redox regulation, DNA damage response, molecular chaperones, and protein degradation were also up-regulated in HLS corals, presenting higher bleaching, and strong decrease of the photosynthesis performance compared to HLF corals. Several pivotal genes associated with the calcification apparatus such as carbonic anhydrases, calcium-transporting ATPase, calcium channel subunit, and bone morphogenetic proteins (BMPs), were significantly down-regulated only in HLS corals. A parallel decrease in the calcification rates of these later corals was also observed. All together, these results show clearly that heterotrophy helps preventing oxidative stress in corals, and thus avoid the cascade of metabolic problems downstream this stress.

overall_design: 4-condition experiment: low light-unfed/starved (LLS), low light fed (LLF), high light unfed/starved (HLS) and high light fed (HLF) treatments on Red Sea coral Stylophora pistillata. Data from four to six biological replicates and one to two technical replicates for each biological one, were used for each treatment.

first: Oren

last: Levy

first: Sarit

last: Karako-Lampert

first: Didier

last: Zoccola

first: Christine

last: Ferrier-Pages


title: Profile of gene expression with HCV infection in Huh7.5 cells

status: Public on May 01 2016

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

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

summary: Differential expression study of lncRNAs (long non-coding RNAs) and mRNAs in HCV infection. For this we infected Huh7.5 cells with HCV (JFH-1) virus and control cells were mock infected. 48h post infection we isolated total RNA using qiagen RNeasy kit as per manufacturer's protocol. The total RNA was then subjected to microarray for both lncRNAs and mRNAs. The resultant profile can be used to compare gene expression in HCV infection versus mock infected cells.

overall_design:
Agilent Human Whole Genome Microarray Gene expression 8X60K (AMADID: 039494) , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)
Huh7.5 cells were infected with HCV (JFH-1) virus and control cells were mock infected.

first: Geetika

last: Sharma

first: Ranajoy

last: Mullick

first: Saumitra

last: Das


title: Expression data obtained from  primary dermal papilla cell cultures and human hair follicle organ culture from occipital scalp

city: Bradford

first: Val

last: Randall

address: Richmond Road

country: United Kingdom

institute: University of Bradford

summary: In this dataset, we include the expression data obtained from  primary dermal papilla cell cultures and human hair follicle organ culture from occipital scalp

overall_design: 6 Total samples were analyzed.  We compare  the expression data obtained from  primary dermal papilla cell cultures and human hair follicle organ culture from occipital scalp. Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

first: Heero

last: Rahman


title: Expression profiling of cia-cGAS knockout LT-HSC cells

first: Pengyan

last: Xia

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of biophysics, Chinese Academy of Sciences

summary: Investigation of global gene expression levels between circular RNA cia-cGAS knockout LT-HSCs and cia-cGAS WT cells.

overall_design: Gene expression profiling using sorted LT-HSC cells from WT and cia-cGAS knockout mice. Total RNA extracted from WT and cia-cGAS knockout cells were quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. The sample preparation and microarray hybridization were performed based on the NimbleGen’s standard protocols.

first: Shuo

last: Wang

first: Zusen

last: Fan


title: Identification of genes differentially expressed upon knockdown of CRISP-3 in human prostate cancer cells

city: Mumbai

first: Bhakti

middle: Rajesh

last: Pathak

address: Jehangir Merwanji Street

department: Structural Biology

institute: National Institute for research in Reproductive Health

summary: Human prostate cancer cell line LNCaP was stably transfected with a construct expressing shRNA against CRISP-3 gene. Knockdown of CRISP-3 was confirmed at RNA and protein level in the selected stable clones at three different passages. In order to identify the possible signalling pathways regulated by CRISP-3, one of the knockdown clones was subjected to microarray analysis. Global gene expression profile of the CRISP-3 knockdown clone was compared to that of the emprty vector clone. It was observed that Kallikrein 3 was significantly downregulated upon CRISP-3 knockdown whereas Annexin A1 and Vimentin were one of the highly upregulated genes.

overall_design: Agilent one-color experiment,Organism: Homo sapiens, Agilent SurePrint G3 Human Exon 4x180K Microarray (AMADID -028679)

first: Ananya

last: Breed

first: Smita

last: Mahale


title: Gene expression profiles of various CSB mutant cell lines

status: Public on May 05 2016

city: London

first: Yuming

address: South Mimms

department: Mechanisms of Transcription Laboratory

institute: Cancer Research UK

summary:
A new ubiquitination site of CSB was identified and proved to play roles in oxidative stress repair. This study characterizes the gene expression signatures affected by CSB-K991R as compared to wild type and UBD mutant.
Using Nimblegen microarray we identified differentially expressed genes in human fibroblasts derived from CS patients as compared to CSB reconstituted cell lines (wild type), also we found the similar gene expression patterns between K991R and UBD mutant derivatives.

overall_design: The Nimblegen human 12 x 135K gene expression array was used to define gene expression profiles in human fibroblasts either lacking CSB or expressing exogenous CSB wild type or mutants.

first: Probir

last: Chakravarty

first: Jesper

last: Svejstrup


title: NapM, a new nucleoid-associated protein, broadly regulates gene expression and affects mycobacterialresistance to anti-tuberculosis drugs

status: Public on Apr 30 2016

city: Wuhan

first: liu

last: yu

state: Hubei Province

address: Shizishan Street

institute: Huazhong Agricultural University

summary: To identify the genes with napM-dependent differential expression, the gene expression profiles of the wild-type M. smegmatis strain and the napM-deleted strains were compared. For this case, the genes with fold changes exceeding 2 (P < 0.05) were considered significant. Strikingly, 156 genes were found to be differentially expressed in the absence of napM. Among these genes,121 were upregulated and 35 were downregulated.

overall_design: For microarray studies, all M. smegmatis and M. smegmatis napM::hyg strains were prepared in triplicate (OD600 = 1.2). RNAs were isolated as described previously (Yang et al., 2012), purified using an RNeasy mini kit (Cat#74106, QIAGEN, GmBH) according to the manufacturer’s instructions, and checked for an RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Total RNAs were processed in microarray facilities affiliated with Sangon Biotech (Shanghai) Co., Ltd. and hybridized to arrays that consisted of 665060-mer probes in situ synthesized by Agilent Technologies. The probes were designed in accordance with the genome sequences of Mycobacterium smegmatis mc2 155(GenBank accession numbers: NC_008596.1), which include 6938 open reading frames. The scanned output files were analyzed with the Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) and Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US). The genes that showed significant differences in expression levels (P ≤ 0.05) and fold changes exceeding 2.0 between M. smegmatis and the M. smegmatis napM::hyg strain were identified and noted as marked gene-expression changes for further analysis.

first: Y

last: Liu

first: H

first: T

last: Cui

first: X

last: Zhou

last: Jia

last: Zhang

first: Z

last: He


title: Affymetrix SNP array data for Genetic Structure of the Newfoundland Population samples

city: St. John's

first: Guangju

last: Zhai

state: NL

address: 300 Prince Philip Drive

department: Genetics, Medicine

institute: Memorial University of Newfoundland

summary: the data was used to investigate genetic structure of the Newfoundland population.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted fromperipheral blood samples.
Customized Axiom Array was used to genotype 442 samples collected from Newfoundland and Labrador

first: Jiayi

first: Michael

middle: O

last: Woods

first: Jane

last: Green

first: Patrick

last: Parfrey

first: Proton

first: Roger


title: Segmental chromosomal imbalances arise at high frequency in human fibroblasts (BAC array)

city: Leuven

first: Eftychia

last: Dimitriadou

address: Herestraat 49, ON1, bus 602

institute: KU Leuven

summary: Preservation of chromosome integrity is key for the survival of any organism. To assure segregation of intact chromosomes, cell division is presumed to be under strict control of cell-cycle checkpoints. Estimates of chromosomal mutation rates per generation based on cytogenetic analyses of newborns and products of conception, range between 4.57x10-5 and 3.42x10-4. In contrast, the high incidence of segmental imbalances detected by single-cell genome-wide copy number profiling indicates that the error rate per cell division might be more than an order of magnitude higher. To directly measure the de novo incidence of segmental chromosomal imbalances, we plated a single fibroblast and analyzed the genomes of the two sister cells following a single cell division. Analysis of 89 pairs of sister cells (178 single cells in total) from 5 different cell lines revealed megabase-sized chromosomal imbalances in 21 fibroblasts, 14 of which derived from 7 mitoses with complementary segmental aneuploidies in the two daughter cells. The mutation rate of segmental imbalances is thus at least 7.9%, indicating that compared to the per generation chromosome stability is at least 100 times lower in vitro and likely underestimated in vivo.

overall_design: The genome of 78 single fibroblasts deriving from 3 different cell lines was amplified using the Sureplex amplification system. These test samples were hybridized comparatively to commercial male or female reference DNA on 24Sure+ BAC arrays.

first: Masoud

last: ZamaniEsteki

first: Thierry

last: Voet

first: Joris

last: Vermeesch


title: Transcriptome analysis associated with MDV infection in leghorn SPF chicken

city: Tian'an

first: XIANYAO

last: LI

address: No. 61  Daizong Street,

department: Department of Animal Science

institute: Shandong Agricultural University

summary: Using global transcriptome analysis and specific pathogen free chicken CEF, we try to identify genes, pathways involving in the response to MDV infection.

overall_design: Primary chicken CEF cells were isolated from 10-day-old specific-pathogen free (SPF) white leghorn chicken embryos. Primary chicken CEF cell collected from one embryo was seeded onto two individual flasks with the density of 5×106/flask. Cells in one of flask were infected by MDV and the other were mock infected, in total, four chicken embryos was used in the current study. The cells were collected at 56 hours post inoculation. Total RNA was isolated using Rneasy Mini Kit (Qiagen) from MDV infected chicken CEF cell. A custom chicken 4×44K Agilent microarray was used to identify the gene expression profile in the response to MDV infection.

first: Xianyao

last: li

first: Shuai

last: Su

first: Zhizhong


title: Global Gene expression profile of Phorone exposed to Chemically Transformed C3H10T1/2 cells.

city: Lucknow

first: Dr Sushil

last: Kumar

state: Uttar Pradesh

address: M G Marg

department: Environmental Carcinogenesis

institute: Indian Institute of Toxicology Research

summary: In this study, we have investigated the changes in transformed cells that occur after GSH depletion and may be critical to accentuate the attenuation of carcinogenesis. The in vitro carcinogenesis method and GSH depletor Phorone (PHO) were used. We found that exposure of transformed C3H10T1/2 cells to PHO (2mM) caused attenuation of transformed cell growth as seen in soft agar assay. Loss of cellular GSH content, increase in intracellular ROS generation, and DNA strand break formation also occurred. A microarray based study using 8x60k oligonucleotide array in duplicate revealed changes in global gene expression profile. Our study has identified changes in expression of many genes that may contribute in abatement of carcinogenesis.

overall_design: Agilent one-color experiment,Organism: Mus musculus, Agilent Custom Mouse Whole Genome Mouse 8x60k Gene expression designed by Genotypic Technology Private Limited, Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Sushil

first: Shivam

last: Priya