title: Dynamic mRNA gene expression following a rapamycin treatment

summary: Dynamic mRNA gene expression from the wildtype YSBN6 during a rapamycin treatment (rapamycin-induced downshift). Rapamycin was added to yeast cells growing exponentially on glutamine as sole nitrogen source.

overall_design:
A sample was taken at steady-state 10 minutes before , and then 3, 7, 10, 14, 24, 56 and 120 minutes after rapamycin treatment. Biological triplicate gene expression was measured for samples -10, 7 and 24 minutes after shift, for a total of 14 chips. Changes were generally evaluated relative to the steady-state point (-10 minutes). Biological variability can be assessed from the replicates time points.
Other dynamic omics data are associated with this dataset. Consult the publication for more details.


title: Two contrasting genotypes of Theobroma cacao differ in their transcriptional response and in accumulation of reactive oxygen species in response to treatment with salicylic acid

status: Public on Mar 31 2015

city: University Park

first: Mark

last: Guiltinan

state: Pennsylvania

address: 422 Life Sciences Bldg.

department: Plant Molecular Biology

country: USA

institute: Penn State University

summary: In order to identify variety-specific differences in defense response induction, Scavina 6 (Sca6) and Imperial College Selection 1 (ICS1) cacao plantlets were treated with 2mM SA or water as control and leaves of three developmental stages (A,C, E) were collected. This process was repeated 3 times yielding 32 samples, (Stage E ICS1 and Stage A Sca6 were collected only twice.) Averaging across developmental stages within each genotype, ICS1 had 436 up- and 601 down-regulated genes and Sca6 had 490 up- and 447 down-regulated genes (Benjamini-Hochberg p-value < 0.05). Analysis of gene annotations and Gene Ontology terms revealed that more PR genes and genes associated with defense response were up-regulated in ICS1, the more pathogen-susceptible genotype, while Sca6 had more genes associated with photosynthesis and energy generation.

overall_design: Same 17k unigene array as described in Mejía LC, Herre EA, Sparks JP, Winter K, García MN, Van Bael SA, Stitt J, Shi Z, Zhang Y, Guiltinan MJ, Maximova SN. 2014. Pervasive effects of a dominant foliar endophytic fungus on host genetic and phenotypic expression in a tropical tree. Frontiers in Microbiology 5.

first: Andrew

last: Fister

first: Shawn

last: O’Neil

first: Zi

last: Shi

first: Yufan

last: Zhang

first: Brett

last: Tyler

first: Siela

last: Maximova


title: Rapid increase in frequency of gene copy-number variants during adaptive evolution in experimental Caenorhabditis elegans populations

status: Public on Apr 15 2015

city: Albuquerque

first: Ulfar

last: Bergthorsson

state: New Mexico

address: 219 Yale Blvd NE

department: Biology

institute: University of New Mexico

type: Genome variation profiling by genome tiling array

summary: Gene copy-number variation, which provides the raw material for the evolution of novel genes, is surprisingly widespread in natural populations.  Experimental evolution studies have demonstrated an extremely high spontaneous rate of origin of gene duplications. When organisms are suboptimally adapted to their environment, gene duplication may compensate for reduced fitness by amplifying promiscuous activity of a gene, or increasing dosage of a suboptimal gene. The overarching goal of this study is to inverstigate whether CNVs constitute a common mechanism of adaptive genetic change during compensatory evolution and to further characterize the role of natural selection in dictating their evolutionary spread at a population-genomic level. Outcrossing populations of C. elegans with low fitness were evolved for >200 generations and the frequencies of CNVs in these populations were analyzed by oligonucleotide array comparative genome hybridization, quantitative PCR, and single-worm PCR. Multiple duplications and deletions were detected in intermediate to high frequencies and several lines of evidence suggest that the changes in frequency were adaptive. 1) Many copy-number changes reached high frequency, were near fixation, or were fixed in a short time. 2) Many independent duplications and deletions in high frequency harbor overlapping regions which likely include genes that are under selection for either higher or lower rates of expression. 3) The size spectrum of deuplications and deletions in the adaptive recovery populations is significantly larger than that of spontaneous copy-number variants in mutation accumulation experiments. This is expected if larger CNVs are more likely to encompass genes that are being selected for altered gene dosage. Out results validate the great potential borne by gene copy-number changes for compensatory evolution and adaptation.

overall_design: Experimental genome evolution of copy-number variants in 25 experimental lines compared to 5 ancestral control lines.

first: James

middle: C

last: Farslow

first: Kendra

middle: J

last: Lipinski

first: Lucille

middle: B

last: Packard

middle: L

last: Edgley

first: Bin

last: Shen

first: Jon

last: Taylor

first: Stephane

last: Flibotte

first: Donald

middle: G

last: Moerman

first: Vaishali

last: Katju


title: Pathway-based integrative analysis reveals a key role for the hexosamine biosynthetic pathway in castrate resistant prostate cancer with therapeutic implications

status: Public on Apr 03 2015

city: Houston

first: Akash

middle: Kumar

last: Kaushik

state: Texas

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary:
The development and progression of castrate resistant prostate cancer (CRPC), a lethal disease, is thought to be driven by multiple events. A hallmark of CRPC is the ability to evade the cytotoxic effects of anti-androgen therapy. Importantly, persistent androgen receptor (AR) signalling is thought to play a principal role in maintaining CRPC. The precise molecular alterations driving this condition, however, are not clearly understood. Our previous studies identified specific metabolic alterations associated with localized prostate cancer (PCa) and CRPC, implicating metabolic re-programming in disease progression. Building on these findings, using a novel network-based integromics approach, here we show distinct alterations in the Hexosamine Biosynthetic Pathway (HBP) to be critical for sustaining the castrate resistant state. We found expression of the HBP enzyme glucosamine-phosphate N-acetyltransferase 1 (GNPNAT1) was regulated by androgens and elevated in androgen dependent (AD) PCa while relatively diminished in CRPC possessing either full length AR (AR-FL) or the spliced V7 variant (AR-V7). Genetic loss of function experiments for GNPNAT1 in CRPC-like cells led to increased proliferation and aggressiveness, both, in vitro and in vivo. This was mediated by specific cell cycle genes regulated by the PI3K-AKT pathway activating either AR in cells with AR-FL or SP1-ChREBP (carbohydrate response element binding protein) in cells containing AR-V7.  Strikingly, addition of HBP metabolite UDP-N-acetylglucosamine (UDP) to CRPC-like cells reduced the expression of cell cycle genes and attenuated tumor cell proliferation, both in vitro and in vivo. Furthermore, addition of UDP sensitized CRPC-like cells, inclusive of those possessing AR-V7, to enzalutamide, demonstrating the therapeutic value of targeting altered metabolic pathways in lethal PCa. We anticipate that our findings will motivate the development of novel metabolic therapeutic strategies that complement existing treatments for men with lethal prostate cancer
We used microarray analysis to determine key molecular alterations associated with inhibition of HBP pathway in CRPC by knocking down GNPNAT1 transcript level using lentiviral particle bearing shRNA in 22Rv1 and LNCaP-ABL cells

overall_design: GNPNAT1 expression was knockdown in two independent prostate cancer cells, 22Rv1 and LNCaP-ABL

middle: K

first: Arun

last: Sreekumar


title: Mice model for 15q11-13 duplication syndrome show late onset obesity and altered lipid metabolism

status: Public on May 01 2015

city: Wako

first: Xiaoxi

last: Liu

state: Saitama

address: Hirosawa 2-1

department: Brain Science Institute

country: Japan

institute: RIKEN

summary: To investigate the gene expression change in the white adipose tissue (WAT) of patDp/+ mice compared with wild type mice, the whole genome microarray profiling was performed. Total RNA from WAT of young adult stage mice (9-10 weeks old) was extracted and subject to microarray analysis. Expression change of sfrp5 gene was further validated by real-time PCR, suggesting this gene might contribute to the obesity in patDp/+ mice.

overall_design: We measured the gene expression changes in WAT of young adult stage mice. Three patDp/+ mice and three wild type mice were used in the experiment.

first: Rui

last: Kishimoto

first: Kota

last: Tamada

first: Hiroko

last: Okubo

first: Jin

last: Nakatani

first: François

last: Spitz

first: Toru

last: Takumi


title: Effect of aryl hydrocarbon receptor (Ahr) gene knockout on expression profiles of aged (18-month-old) murine hematopoietic stem cells

status: Public on Mar 28 2015

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

summary: As part of a study of the role of the aryl hydrocarbon receptor (Ahr) in maintenance and senescence of hematopoietic stem cells (HSC), global gene expression profiling was done with HSC isolated from 18-month-old Ahr-knockout and wild-type mice. HSC from aged AhR-KO mice had changes in expression of many genes related to HSC maintenance, consistent with the phenotype observed in aging Ahr-KO mice: decreased survival rate, splenomegaly, increased circulating white blood cells, hematopoietic cell accumulation in tissues, anemia, increased numbers of stem/progenitor and lineage-committed cells in bone marrow, decreased erythroid progenitor cells in bone marrow, and decreased self-renewal capacity of HSC.

overall_design: 10 samples: 5 Ahr knockout, 5 wild-type

first: Kameshwar

middle: P

last: Singh

first: Thomas

middle: A

last: Gasiewicz


title: The oncogene EVI1 enhances transcriptional and biological responses of human myeloid cells to all-trans retinoic acid [U937]

status: Public on Mar 13 2015

city: Vienna

first: Rotraud

last: Wieser

address: Waehringer Guertel 18-20

department: Clinic of Medicine I

country: Austria

institute: Medical University of Vienna

summary:
The product of the ecotropic virus integration site 1 (EVI1) gene, whose overexpression is associated with a poor prognosis in myeloid leukemias and some epithelial tumors, regulates gene transcription both through direct DNA binding and through modulation of the activity of other sequence specific transcription factors. Previous results from our laboratory have shown that EVI1 influenced transcription regulation in response to the myeloid differentiation inducing agent, all-trans retinoic acid (ATRA), in a dual manner: it enhanced ATRA induced transcription of the RARb gene, but repressed the ATRA induction of the EVI1 gene itself. In the present study, we asked whether EVI1 would modulate the ATRA regulation of a larger number of genes, as well as biological responses to this agent, in human myeloid cells. U937 and HL-60 cells ectopically expressing EVI1 through retroviral transduction were subjected to microarray based gene expression analysis, and to assays measuring cellular proliferation, differentiation, and apoptosis. These experiments showed that EVI1 modulated the ATRA response of several dozens of genes, and in fact reinforced it in the vast majority of cases. A particularly strong synergy between EVI1 and ATRA was observed for GDF15, which codes for a member of the TGF-b superfamily of cytokines. In line with the gene expression results, EVI1 enhanced cell cycle arrest, differentiation, and apoptosis in response to ATRA, and knockdown of GDF15 counteracted some of these effects.
Steinmetz B, Hackl H, Slabáková E, Schwarzinger I, Smějová M, Spittler A, Arbesu I, Shehata M, Souček K, and Wieser R: The oncogene EVI1 enhances transcriptional and biological responses of human myeloid cells to all-trans retinoic acid. Cell Cycle 13, 2931-2943 (2014).

overall_design: U937 cells transduced with an EVI1 expression vector or empty vector as a control were treated with all-trans retinoic acid (ATRA) or an equivalent amount of DMSO (solvent) for 24 h prior to gene expression microarray analysis. 3 biological replicates were performed.

first: Birgit

last: Steinmetz

first: Hubert

last: Hackl


title: Transcriptomic study on the impact of Temporomandibular joint Internal derangement in the Condylar Cartilage of Rabbits

status: Public on Mar 14 2015

city: Hangzhou

first: Angelina

middle: Shuhua

last: Wang

state: Zhejiang

address: Binwen Road No.548

department: the School of Dentistry

country: China

institute: Zhejiang Chinese Medical University

summary: Internal derangement (ID) in the temporomandibular joint (TMJ) compromises a group of clinical problems, and holds a relative high prevalence in populations. However, the temporal change in gene expression of condylar cartilage during continous ID remains unclear. The aim of current study is investigating the differential expressed gene pattern in condylar cartilage of rabbits with ID from 1 to 8 weeks. Immunohistochemical results indicated that abnormal collagen fiber arrangements, fragmentation of fibrils, inflammatory cells infiltration were detected from 1 week to 4 week in joint disc specimens, while newly formed vessels, mucoid degeneration, meniscal tears, osteoclasts and osteoblasts were observed later. The microarray analysis showed 6478 genes have more than two-fold changes among all the tested transcripts. The inflammation gene group including ACE and IL1βincreased rapidly in the early stage while decrease later. On the contrary, the bone construction related genes showed a low level at first and increased at later period in the ID progression. Besides, the current study found some genes such as HLA2G, which had never been reported, might be relevant with ID. Our findings might provide useful insights into the pathological mechanism of ID in TMJ.

overall_design: All the rabbits had free access to tap water and a standard diet for one week before the experiment. Four rabbits served as the control group (without any treatment), whereas sixteen rabbits’ left joints subjected to TMJ ID were treatment groups. The sixteen rabbits were divided randomly into four treatment groups, and each group were used for histological analysis, RNA microarray analysis and real-time PCR at 1 week, 2 weeks, 4 weeks and 8 weeks respectively.

first: Zhiyuan

last: Gu

middle: S

first: Liquan

last: Deng

first: Ye

last: Li


title: The oncogene EVI1 enhances transcriptional and biological responses of human myeloid cells to all-trans retinoic acid [HL60]

summary: The product of the ecotropic virus integration site 1 (EVI1) gene, whose overexpression is associated with a poor prognosis in myeloid leukemias and some epithelial tumors, regulates gene transcription both through direct DNA binding and through modulation of the activity of other sequence specific transcription factors. Previous results from our laboratory have shown that EVI1 influenced transcription regulation in response to the myeloid differentiation inducing agent, all-trans retinoic acid (ATRA), in a dual manner: it enhanced ATRA induced transcription of the RARb gene, but repressed the ATRA induction of the EVI1 gene itself. In the present study, we asked whether EVI1 would modulate the ATRA regulation of a larger number of genes, as well as biological responses to this agent, in human myeloid cells. U937 and HL-60 cells ectopically expressing EVI1 through retroviral transduction were subjected to microarray based gene expression analysis, and to assays measuring cellular proliferation, differentiation, and apoptosis. These experiments showed that EVI1 modulated the ATRA response of several dozens of genes, and in fact reinforced it in the vast majority of cases. A particularly strong synergy between EVI1 and ATRA was observed for GDF15, which codes for a member of the TGF-b superfamily of cytokines. In line with the gene expression results, EVI1 enhanced cell cycle arrest, differentiation, and apoptosis in response to ATRA, and knockdown of GDF15 counteracted some of these effects.

overall_design: HL60 cells transduced with an EVI1 expression vector or empty vector as a control were treated with all-trans retinoic acid (ATRA) or an equivalent amount of DMSO (solvent) for 24 h prior to gene expression microarray analysis. 3 biological replicates were performed.


title: Identification of differentially expressed microRNAs between human HCC tumors with and without vascular invasion [batch 2]

status: Public on Mar 23 2015

first: Kuang-Hsiang

last: Chuang

address: 601 Elmwood Ave

department: Wilmot Cancer Institute

summary: Non-coding microRNAs (miRNAs) mainly regulate the expression of targeted genes by regulating mRNA degradation or repressing their protein translation. Recent research has shown miRNAs to have remarkable potential as biomarkers for the diagnosis and prognosis of disease. Since vascular invasion (VI) provides a direct path for solid tumor metastasis/recurrence, in this study we investigated if miRNAs can serve as a biomarker to differentiate between VI- and VI+ tumors. MiRNA microarray profiling was then performed on 172 human HCC tumors samples with or without VI from HCC patients.

overall_design: MiRNA microarray analysis was performed on miRNA extracted from formalin-fixed paraffin-embedded (FFPE) HCC tumor specimens. The first batch of 57 HCC tumors was analyzed and the differentially expressed miRNAs were obtained between 34 VI- and 23 VI+ tumors. To avoid a potential batch effect, the second batch of 115 HCC tumor foci included 57 VI- and 58 VI+ tumors were then independently analyzed. Our study was performed with approval of the University of Rochester Research Subjects Review Board (RSRB00029467).

first: Chris

middle: T

last: Barry

first: Kuang

middle: H


title: Ageing-associated changes in DNA methylation in humans

status: Public on Mar 20 2015

city: Tampere

first: Saara

last: Marttila

address: Biokatu 6

department: School of Medicine

country: Finland

institute: University of Tampere

type: Methylation profiling by genome tiling array

summary:
Background: DNA methylation, a component of the epigenome that regulates both single genes and large sections of chromatin, is altered with ageing and is speculated to be one of the molecular mechanisms contributing to the ageing process. In our analysis, we sought to identify ageing-associated methylation changes at single- CpG-site resolution in blood leukocytes and to ensure that the observed changes were not due to differences in the proportions of leukocytes. The association of the methylation changes with gene expression levels was also investigated in the same individuals.
Results: By applying Illumina 450K array technology and a two-step analysis process, we identified 8540 high-confidence ageing-associated CpG sites, 46% of which were hypermethylated in nonagenarians. The hypermethylation-associated genes belonged to a common category, and they were predicted to be regulated by a common group of transcription factors and were enriched in a related set of GO terms and canonical pathways. On the contrary, the hypomethylation-associated genes appeared to be a more random group, as only a limited set of GO terms and canonical pathways were identified in this group. Among the 8540 CpG sites associated with ageing, there was an association with gene expression levels in 377. The genes displaying methylation-regulated expression were enriched in GO terms and canonical pathways associated with immune system functions, particularly phagocytosis.
Conclusions: According to our results, certain ageing-associated immune-system impairments may be mediated via changes in DNA methylation. The results also imply that ageing-associated hypo- and hypermethylation are distinct processes: hypermethylation could be caused by programmed changes, while hypomethylation could be the result of environmental and stochastic processes.

overall_design: Study population consisted of nonagenarians (n=122) and young controls (n=21, 19-30 years).

first: Laura

last: Kananen

first: Sergei

last: Häyrynen

first: Juulia

last: Jylhävä

first: Tapio

last: Nevalainen

first: Antti

last: Hervonen

first: Marja

last: Jylhä

first: Matti

last: Nykter

first: Mikko

last: Hurme


title: Identification of differentially expressed microRNAs between human HCC tumors with and without vascular invasion [batch 1]

first: Christopher


title: Genome-wide analysis of M1 and M2 polarized macrophages with CNI-1493 treatment

status: Public on Mar 12 2015

city: Manhasset

first: Anthony

middle: John

last: Hesketh

state: New York

address: 350 Community Dr.

institute: Feinstein Institute for Medical Research

summary:
Analysis of the effects of CNI-1493 treatment on M1 and M2 polarized macrophages.
The purpose of this microarray is to identify genes that may be differentially expressed in M1 or M2 macrophages after treatment with CNI-1493. CNI-1493 is a known inhibitor of M1 macrophages but details of its molecular mechanism are unknown. The effect of CNI-1493 on M2 macrophages has yet to be explored, but we hypothesize that CNI-1493 treatment will attenuate pro-tumor properties of M2 macrophages. We demonstrate with this array that known macrophage markers are unchanged after treatment with CNI-1493, indicating that CNI-1493 does not change the macrophage phenotype on a transcriptional level. Additionally, no candidate genes to suggest how CNI-1493 may attenuate the pro-tumor effects of M2 macrophages are readily identifiable.

overall_design: Total RNA extracted from M1 or M2 macrophages after polarization with GM-CSF (25ng/ml) or M-CSF (25ng/ml) for 7 days, followed by addition of IFN-γ (20ng/ml) and LPS (100ng/ml) or IL-4 (40ng/ml) for 18 hours, respectively, from CD14+ human PBMCs, and treated with CNI-1493 (200nM)


title: Dissection of estrogen receptor alpha signaling pathways in osteoblasts using RNA-sequencing

status: Public on Mar 11 2015

first: David

middle: George

last: Monroe

state: MN

address: 200 1st St SW

department: Endocrinology

institute: Mayo Clinic

type: Expression profiling by high throughput sequencing

summary: The goal is to identify estrogen-dependent gene expression patterns using RNAseq for 3 different ERα forms in human osteoblasts.

overall_design: We analyzed 3 different forms of estrogen receptor alpha (ERα), 1) Wild-type, 2) NERKI (DNA-binding mutant) and 3) NOER (Nuclear Only ERα, not membrane).  Each was infected into hFOB (human osteoblast) cells and treated with either vehicle or E2 (10nM) (n=3 for each group/treatment).  RNAseq was then performed.

first: Sundeep

last: Khosla


title: Expression data from mutant of RSC chromatin-remodeling complex in respiratory growth

status: Public on Mar 10 2015

city: Kagamiyama, Higashi-Hiroshima

first: MUNEYOSHI

last: KANAI

institute: National Research Institute of Brewing

summary:
RSC is a growth essential ATP-dependent chromatin-remodeling complex of Saccharomyces cerevisiae. Nps1/Sth1 is the ATPase subunit of the complex. A temperature-sensitive mutant allele of NPS1, nps1-13 and the null mutation of the RSC2 or RSC7 gene showed growth defect on a medium containing non fermentable carbon source, such as lactate or ethanol-glycerol (YPEG), suggested a possibility that RSC plays a role on mitochondria function.
We used microarrays to compare the global gene expression profiles between the wild type and nps1-13 mutant under respiratory condition.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: WT (BY4743) and nps1-13 strains pre-grown in YPD medium were inoculated in YPEG medium for RNA extraction and hybridization on Affymetrix microarrays. In order to obtain more global insights into the role of RSC under respiratory conditions, we perfomed the genome-wide expression analysis of nps1-13 in YPEG medium.

first: Yuko

last: Imamura

first: Muneyoshi

last: Kanai

first: Ryoko

last: Hamada

first: Eiko

last: Tsuchiya


title: Rice leaves in the field in 2008 with 1- or 2-min interval

city: Tsukuba

first: Takeshi

last: Izawa

state: Ibaraki

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

summary: Time-course transcriptional profiling of rice leaf in the field in 2008. This experiment was performed to evaluate the resolution of two time points by inference from gene expressions.

overall_design: Rice leaves (cv. Norin8) were collected with 1- or 2-min interval. No biological replicate.

first: Jun

last: Matsuzaki


title: Natural Variation in Fish Transcriptomes: Comparative Analysis of the Zebrafish (Danio rerio)

status: Public on Aug 01 2015

city: Cincinnati

first: Rong-Lin

last: Wang

address: 26 W MLK Dr

institute: US EPA

type:
Third-party reanalysis
Expression profiling by array

summary: Fathead minnow and zebrafish are among the most intensively studied fish species in environmental toxicogenomics.  To aid the assessment and interpretation of subtle transcriptomic effects from treatment conditions of interest, there needs to be a better characterization and understanding of the natural variation in gene expression among fish individuals within populations.  Little effort, however, has been made in this area.  Leveraging the transcriptomics data from a number of our toxicogenomics studies conducted over the years, we conducted a meta-analysis of nearly 600 microarrays generated from the ovary tissue of untreated, reproductively mature fathead minnow and zebrafish samples.  As expected, there was considerable batch-to-batch transcriptomic variation; this “batch-effect” appeared to impact the fish transcriptomes randomly.  The overall level of variation within-batch was quite low in fish ovary tissue, making it a suitable system for studying chemical stressors with subtle biological effects.  The within-batch variation, however, differed considerably among individual genes and molecular pathways.  This difference in variability is probably both technical and biological, thus suggesting a need to take into account both the expression levels and variance in evaluating and interpreting the transcriptional impact on genes and pathways by experimental conditions.  There was significant conservation of both the genomes and transcriptomes between fathead minnow and zebrafish.  The conservation to such a degree would enable not only a comparative biology approach in studying the mechanisms of action underlying environmental stressors, but also effective sharing of a large amount of existing public transcriptomics data for future development of toxicogenomics applications.

overall_design:
RNA from treated and control samples were directly hybridized on individual arrays.
This study is a reanalysis of ovary Samples from GSE38070. The data processing is different and consisted of:
Microarray image processing was performed using the latest Agilent's Feature Extraction software available at the time following the manufacturer?s protocol and recommendations.  Data processing was conducted using R package Limma in the order of backgroundCorrect("normexp"), normalizeWithinArrays("loess"), and normalizeBetweenArrays("quantile").  Various types of control probes were filtered out.  Each expression value represents the average of its duplicated probes. Only intensity data from control channel were utilized in the study after channel splitting.
The supplementary files attached contain log2 ratios(M) and log2 intensities (A) after backgroundCorrect("normexp"), normalizeWithinArrays("loess"), and normalizeBetweenArrays("quantile") in Limma; various types of control probes were filtered

last: Bencic

first: Natàlia

last: Garcia-Reyero

first: Edward

last: Perkins

first: Daniel

last: Villeneuve

first: Gerald

last: Ankley

first: Adam

middle: D

last: Biales


title: Trichophyton rubrum transcriptome in response to acriflavine

status: Public on Mar 05 2015

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

summary:
Purpose: The dermatophyte Trichophyton rubrum is an anthropophilic filamentous fungus that infects keratinized tissues and is the most common etiologic agent isolated in cases of human dermatophytoses. To better understand the molecular effects of stress responses and fungal adaptability, we evaluated the effects of acriflavine, a cytoxic drug, on T. rubrum transcriptome in a time-course assay using high-throughput RNA-seq technology.
Results: RNA-seq generated approximately 200 million short reads that were mapped to the Broad Institute’s Dermatophyte Comparative Database before differential gene expression analysis. A subset of 490 genes modulated in response to stress caused T. rubrum exposure to acriflavine were identified. These genes are involved in various cellular processes such as oxidation-reduction reactions, transmembrane transport, metal ion binding, and pathogenicity. The genes involved in pathogenicity were down-regulated, suggesting that this drug interferes with virulence factors that allow the establishment and maintenance of host infection.
Conclusion: The results obtained in this large-scale analysis provide insights into the molecular events underlying the stress responses of T. rubrum Acriflavine.

overall_design: mRNA profiling of T. rubrum grown in Sabouraud media as control (0h) and three different times of exposure to sub-inhibitory acriflavine concentrations for 3h, 12h, and 24h were used for high-throughput RNA sequencing using Applied Biosystems Solid 4 System.

first: Nalu

last: Peres

first: Tiago

middle: R

last: Jacob

first: Antonio

last: Rossi

first: Ricardo

middle: Z

last: Vêncio

first: Nilce

middle: M

last: Martinez-Rosii


title: Transcriptome of Protoplasts Reprogrammed into Stem Cells in Physcomitrella patens

status: Public on Feb 28 2015

city: Beijing

first: Lihong

last: Xiao

address: No.105 North Road of West 3rd-ring Road.Haidian District

institute: Capital Normal University

summary: We obtained genome-wide digital gene expression tag profiles within the first three days of P. patens protoplast reprogramming. At four time-points during protoplast reprogramming, the transcript levels of 4827 genes changed more than four-fold and their expression correlated with the reprogramming phase. Gene ontology (GO) and pathway enrichment analysis of differentially expressed genes (DEGs) identified a set of significantly enriched GO terms and pathways, most of which were associated with photosynthesis, protein synthesis and stress responses. DEGs were grouped into six clusters that showed specific expression patterns using a K-means clustering algorithm. An investigation of function and expression patterns of genes identified a number of key candidate genes and pathways in early stages of protoplast reprogramming, which provided important clues to reveal the molecular mechanisms responsible for protoplast reprogramming. We identified genes that show highly dynamic changes in expression during protoplast reprogramming into stem cells in P. patens. These genes are potential targets for further functional characterization and should be valuable for exploration of the mechanisms of stem cell reprogramming. In particular, our data provides evidence that protoplasts of P. patens are an ideal model system for elucidation of the molecular mechanisms underlying differentiated plant cell reprogramming.

overall_design: Examination of 4 different sampling times.


title: Identification of differently expressed miRNAs between Tamoxifen sensitive cells and Tamoxifen resistant cells

status: Public on Mar 07 2015

city: Guangzhou

first: Junjun

last: Chu

state: Guangdong

address: 426 School of Life Sciences, Sun Yat-sen Univ. East Campus, Higher Education Mega Center

department: Breast Cancer Center

institute: SUN YAT-SEN UNIVERSITY

summary:
Tamoxifen is the most widely administered adjuvant first-line hormone therapy for Estrogen receptor α (ERα) positive breast cancer patients. However, one from three patients will develop resistance, while the underlying molecular mechanisms are currently unclear.
Recent studies reported that abnormal expression of miRNAs played a role in cancer progress. To study the potential function of miRNAs in tamoxifen resistance, Affymetrix GeneChip® miRNA 3.0 microarray was employed to identify differentially expressed miRNAs between tamoxifen sensitive MCF7 parent (MCF7-Pa) cells and induced resistant (MCF7-Re) cells.

overall_design: The human breast cancer MCF7 cell line was obtained from the American Type Culture Collection (Manassas, VA, USA). MCF7 parent (MCF7-Pa) cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 40U/ml insulin. MCF7-derived tamoxifen resistant sublines (MCF7-Re) were developed by culturing in 1640 medium without phenol red (Life Technologies, USA) supplemented with 5% charcoal-stripped FBS (cFBS) (HyClone, USA) and 1 uM 4-hydroxytamoxifen (Sigma-Aldrich, MO, USA) for 1 year. After cultured in RPMI 1640 medium without phenol red supplemented with 5% cFBS and without tamoxifen for 7 days, MCF7-Pa and MCF7-Re cells total RNA was harvested using TRIzol® reagent (Life Technologies, USA) according to the manufacturer’s instructions. RNA extraction and miRNA profile detection was provided by CapitalBio Corporation (Beijing, China) as generated as the manufacturer's recommendations (Affymetrix).


title: Identification of differentially expressed microRNAs between human HCC tumors with and without vascular invasion

first: Kuang-Hsiang

last: Chuang

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

overall_design: Refer to individual Series


title: Gene expression patterns in IgG4-RD before and after steroid treatment and healthy control groups

status: Public on Mar 03 2015

city: Kahoku

first: Akio

last: Nakajima

state: Ishikawa

address: 1-1 Daigaku Uchinada

department: Immunology and Hematotology

institute: kanazawa-med

summary:
Transcriptome analysis in patients with IgG4-RD and healthy controls
IgG4-related disease (IgG4-RD) is a new emerging disease entity characterized by elevated serum IgG4 concentrations and tissue tumefaction or infiltration by IgG4-positive plasma cells. At present, however, it is not clear whether IgG4-RD is caused by abnormalities in acquired immunity, like autoimmune diseases, or whether the excess production of IgG4 is a true cause of IgG4-RD or an epiphenomenon associated with inflammatory and/or allergic reactions. We therefore attempted to identify genes related to the pathogenesis or clinicopathology of IgG4-RD. Peripheral blood mononuclear cells (PBMCs) were obtained from patients with IgG4-RD before and after steroid therapy and from healthy controls. Total RNA was extracted and DNA microarray analysis was performed to screen for genes showing changes in expression.

overall_design: To exclude any gender-related differences in gene expression, DNA microarray analysis was performed only on samples obtained from male patients and controls. Total RNA was reverse transcribed to cDNA using Ambion® WT Expression kits (Applied Biosystems, Foster City, CA), labeled with GeneChip® WT Terminal Labeling and Controls kits (Affymetrix, Santa Clara, CA), and hybridized to GeneChip® Human Gene 1.0 ST Arrays (Affymetrix), which include 28869 probes. Digitalized image data were processed using GeneChip® Operating Software (Affymetrix).

first: Yasuhito

last: Ishigaki

first: Hisanori

last: Umehara


title: Global transcriptomic changes induced by manipulate MSH1 gene in tomato using next generation sequencing

status: Public on Feb 23 2015

first: Hardik

last: Kundariya

state: PA

address: 361 N. Frear

institute: The Pennsylvania State University

summary: apical meristem tissues from 4-week-old wild type, epiF3, MSH1 gene mutant including (mild-DR and dwarf-DR) plants were used in this experiment.

overall_design: For each genotype, the transcriptome was sequenced with 3 biological replicates.

first: Xiaodong

last: Yang

first: Ying-Zhi

last: Xu

first: Jean-Jack

last: Riethoven

first: Jiantao

last: Yu

first: Sally

last: Mackenzie


title: Expression profiling of lymph nodes in tuberculosis patients reveal inflammatory milieu at site of infection

status: Public on Mar 01 2015

city: New Delhi

first: Yogendra

last: Singh

state: New Delhi

address: Mall Road

country: India

institute: CSIR-Institute of Genomics and Integrative Biology

summary: Extrapulmonary manifestations constitute 15-20% of tuberculosis cases, with lymph node as the most common site. Understanding of disease etiology is limited due to the lack of understanding patients’ infected tissue milieu. This study was designed to perform global transcriptome analysis of lymph node tissues from healthy individuals and Mycobacterium tuberculosis infected lymph nodes of patients to decipher the local response of infected tissue.

overall_design: This study was designed to elucidate gene expression signatures in the event of Lymph Node Tuberculosis. Total RNA was extracted from lymph node tissue samples of LNTB patients in BSL3 facility and together with healthy lymph node RNA samples (commercially purchased) their global transcriptome profiling was performed using Illumina HumanHT-12 V4 expression beadchip.

first: Abhijit

last: Maji

first: Richa

last: Misra

first: Anupam

last: Mondal


title: SCML2 Establishes the Male Germline Epigenome

status: Public on Feb 19 2015

first: Satoshi

last: Namekawa

state: Ohio

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Gametogenesis is dependent on the expression of germline-specific genes. However, it remains unknown how the germline epigenome is distinctly established from that of somatic lineages. Here we show that genes commonly expressed in somatic lineages and spermatogenesis-progenitor cells undergo repression in a genome-wide manner in late stages of the male germline and identify underlying mechanisms. SCML2, a germline-specific subunit of a Polycomb repressive complex 1 (PRC1), establishes the unique epigenome of the male germline through two distinct antithetical mechanisms. SCML2 works with PRC1 and promotes RNF2-dependent ubiquitination of H2A, thereby marking somatic/progenitor genes on autosomes for repression. Paradoxically, SCML2 also prevents RNF2-dependent ubiquitination of H2A on sex chromosomes during meiosis, thereby enabling unique epigenetic programming of sex chromosomes for male reproduction. Our results reveal divergent mechanisms involving a shared regulator by which the male germline epigenome is distinguished from that of the soma and progenitor cells.

overall_design: RNA-seq and ChIP-seq analyses using wild-type and Scml2-KO spermatogenic cells

first: Kazuteru

last: Hasegawa

first: Hosu

last: Sin

first: So

last: Maezawa

first: Andrey

middle: V

last: Kartashov

first: Kris

last: Alavattam

first: W

middle: C

last: Bacon

first: Artem

last: Barski


title: Self-Enforcing Feedback Activation between BCL6 and Pre-B Cell Receptor Signaling Defines a Distinct Subtype of Acute Lymphoblastic Leukemia

status: Public on Feb 08 2015

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

summary: BCL6fl/fl mouse bone marrow pre-B cells were transduced with an TCF3-PBX1 vector. The TCF3-PBX1 transduced BCL6fl/fl pre-B cells were then transduced with an empty vector (EV), or a Cre vector for Cre-mediated BCL6 deletion. Effect of BCL6 deletion in the TCF3-PBX1 pre-B cells were studied by Affymetrix GeneChip Mouse Genome 430 2.0 Arrays.

overall_design: TCF3-PBX1 transduced BCL6fl/fl mice bone marrow pre-B cells were tranduced with an empty vector (EV) or a Cre vector for BCL6 deletion

first: H

first: C

last: Hurtz

first: M

last: Muschen


title: Self-enforcing Feedback Activation between BCL6 and Pre-B Cell Receptor Signaling Defines a Distinct Subtype of Acute Lymphoblastic Leukemia

summary: We used ChIPseq in primary pre-B acute lymphomablastic leukemia (ALL) cells to identify target genes of the oncogenes TCF3-PBX1 and BCL6 that are involved in leukemogenesis of TCF3-PBX1 pre-B ALL.

overall_design: ChIP-seq using E2A (TCF3), PBX1, p300 and BCL6 antibodies in ICN12 cells (primary pre-B acute lymphomablastic leukemia)

first: Christian

first: Markus

first: Erica

last: Ballabio

first: Thomas

last: Milne


title: Genome-wide expression profiling of an in vitro model for studying esophageal epithelial differentiation

status: Public on Feb 01 2015

city: Mason

first: Joe

last: Sherrill

address: 8700 Mason-Montgomery Rd

institute: Procter and Gamble

summary: We used RNA sequencing to identify differentially expressed genes during esophageal epithelial differentiation and in the presence of interleukin 13 using an air-liquid interface culture system.

overall_design: RNA sequencing was performed on a human esophageal epithelial cell line (EPC2-hTERT) grown submerged (day 8) or at the air-liquid interface (ALI) (day 14, untreated or treated with interleukin 13 [100 ng/mL])

middle: E

last: Rothenberg

first: J


title: HOXA9 transcriptomic analysis in GBM cell lines (U87MG, U251 and primary GBML18) and in immortalized human astrocytes (hTERT/E6/E7)

status: Public on Jan 30 2015

city: Braga

first: Bruno

middle: M.

last: Costa

address: Universidade do Minho, Campus de Gualtar

department: Life and Health Sciences Research Institute (ICVS)

country: Portugal

institute: University of Minho

summary: Assess gene expression patterns upon HOXA9 ectopic expression in U87MG GBM cell line and hTERT/E6/E7 immortalized human astrocytes, and HOXA9 silencing in U251 and GBML18 GBM cell lines.

overall_design: U87MG and hTERT/E6/E7 were retrovirally-infected with an MSCV control vector (MSCV-Control) or with a construct containing the coding region of HOXA9 (MSCV-HOXA9), resulting in U87MG-Control, U87MG-HOXA9, hTERT/E6/E7-Control and hTERT/E6/E7-HOXA9 cell lines. GBML18 and U251 cells were transfected with HOXA9 gene-specific shRNA sequences (shHOXA9) or a non-efective shRNA (shControl) in pGFP-V-RS plasmid, resulting in U251-shControl, U251-shHOXA9, GBML18-shControl and GBML18-shHOXA9 cell lines. Four experimental replicates for HOXA9 overexpression cell lines, and three for HOXA9 silencing cell lines were performed.


title: IscR of Rhodobacter sphaeroides functions as repressor of genes for iron-sulphur metabolism and represents a new type of iron-sulphur binding protein

status: Public on Feb 03 2015

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

country: Germany

institute: Justus-Liebig University Gießen

summary: Iron-sulphur (Fe-S) clusters are ensembles of iron and sulphide centres. They are found in all life forms and are important components of many enzymes involved in diverse cellular processes, including respiration, DNA synthesis or gene  regulation. However, the increase in oxygen after the emergence of oxygenic photosynthesis created a threat to Fe–S proteins and, consequently, to the organisms relying on them. Therefore, bacteria have evolved mechanisms to maintain a precise intracellular iron concentration. A major role of IscR in R. sphaeroides iron dependent regulation was suggested in a bioinformatic study , which predicted a binding site in the upstream regions of several iron uptake genes. Most known IscR proteins have Fe-S clusters featuring (Cys)3(His)1 ligation. However, IscR proteins from Rhodobacteraceae harbour only one Cys residue and it was considered unlikely that they can ligate an Fe-S cluster. In this study, the role of R. sphaeroides IscR as transcriptional regulator and sensor of the Fe-S cluster status of the cell was analysed. The results provide evidence that R. sphaeroides IscR functions as transcriptional repressor of genes involved in iron metabolism by binding to the predicted DNA binding motif. Furthermore, IscR possesses a unique Fe-S cluster ligation scheme with only a single cysteine involved.

overall_design: RNA samples collected from a control strain (wild type 2.4.1) and of the iscR deletion strain (2.4.1∆iscR) were analyzed by two-color microarrays

first: Bernhard

last: Remes

first: Benjamin

last: Eisenhardt

first: Vasundara

last: Srinivasan


title: Transcriptome changes for Arabidopsis thaliana in response to lead exposure

status: Public on Jan 28 2015

city: Montpellier

first: Patrick

last: Doumas

address: Place Viala

country: France

institute: INRA

summary: Experiments were achieved on Arabidopsis thaliana. Transcriptional profiling of roots and shoots from plants treated with lead were compared to plants treated in similar conditions without lead. Four weeks old A. thaliana seedlings were treated in hydroponic cultures with Pb during 3 days, by adding or not 40 µM Pb(NO3)2.

overall_design: Two-condition experiment, lead treated vs. untreated. Biological replicates: 3

first: Florence

last: Auguy

first: Mohamed

last: El Mzibri


title: OGG1-initiated DNA base excision repair is linked to inflammatory gene expression and lung inflammation

status: Public on Feb 02 2015

city: Galveston

first: Istvan

last: Boldogh

address: 301 UNIVERSITY BLVD.

department: Microbiology & Immunology

institute: UNIVERSITY OF TEXAS MEDICAL BRANCH

summary:
Purpose: The aim of this study is to evaluate the global gene expression induced by OGG1-BER product 8-oxoG in mouse airways.

Methods: RNA extracted from individual mouse lungs (experimental group: n=5) were pooled and a total 1 μg RNA was used for Next-Generation Sequencing (NGS) analyses on an Illumina HiSeq 1000 sequencing system. Sequence analysis were performed in duplicate. First- and second-strand synthesis, adapter ligation and amplification of the library were performed using the Illumina TruSeq Sample Preparation Kit as recommended by the manufacturer (Illumina). Library quality was evaluated by using an Agilent DNA-1000 chip on an Agilent 2100 Bioanalyzer. Library DNA templates were quantitated by qPCR using known reference starndards. Cluster formation of the library of DNA templates was performed using the TruSeq PE Cluster Kit v3 (Illumina) and the Illumina cBot workstation. Paired-end, 50-base sequencing was performed with a TruSeq SBS kit v3 (Illumina) on the Illumina HiSeq 1000 by protocols defined by the manufacturer. Base call conversion to sequence reads was performed using CASAVA-1.8.2. Sequence data were analyzed with the Bowtie2, Tophat2 and GFOLD programs. Processed data are presented as reads per kilobase transcript per million (RPKM), normalized to the experimental control (RNA from saline-challenged lungs) and reported as fold change (test/control).

Results: We mapped an average of 24.76 million sequence reads per sample and identified 23,337 transcripts in total RNA extracted from lungs of Balb/cJ mice as described in Methods. Approximately 10% of the transcripts showed differential expression between the saline-challenged control and 8-oxoguanine-challeged mouse lungs, with a fold change ≥3.0. We validated the expression changes of 7 selected pro-inflammatory cytokines and chemokines of interest for our studies by qRT-PCR. Hierarchical clustering followed by Protein ANalysis THrough Evolutionary Relationships database (PANTHER) analysis of differentially expressed genes. Results showed overrepresentation of various biological functions (GO terms) including immune system process (GO:0002376; p=5.24e-12) among others. Pathway analysis (PANTHER) indicated that the most overrepresented pathway was inflammation mediated by chemokine and cytokine (P00031, p=<0.01). In addition to gene expression analysis, we confirmed OGG1•8-oxoG-dependent RAS activation in lungs by active RAS pull-down assays, airways neutrophil accumulation by bronchoalveolar lavage fluid (BALF) differential cell counts and airway inflammation by histological examination (H&E staining) of lung sections.

Conclusions: This is the first study at the whole-transcriptome level to show induction of innate immune response gene expression in mouse lungs after exposure to OGG1-BER product 8-oxoG.

overall_design: Balb/cJ mice (5 per group) were intranasally challenged with 8-oxoguanine (1 µM, 60 µl) for 30, 60 and 120 min. Control group mice were intranasally challenged with saline (60 µl). RNA from individual mice whithin the same group was pooled and subjected to deep-sequencing analysis in duplicate using NGS on an Illumina HiSeq 1000 sequencing system. After alignment and processing, the resulting RPKM from treatment groups (8-oxoG-challenged) were normalized to the control group (saline-challenged).

first: Leopoldo

last: Aguilera-Aguirre

middle: G

last: Wood

first: Steven

last: Widen


title: Helveticoside was a biologically active component of seeds extract of Descurainia Sophia.

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

summary: This study was designed to identify active component of ethanol extract of the seeds of D. sophia.

overall_design: The dose-dependent expression of genes by treatment of EEDS was measured on A549 cells. Total RNA was isolated and was subject to single channnel microarray.

first: Jun

last: Lee

first: No-Soo


title: Transcriptome changes for Hirschfeldia incana in response to lead exposure

summary: Experiments were achieved on Hirschfeldia incana, a Brassicaceae collected from metalliferous mine spoils as a Pb accumulator plant. Transcriptional profiling of roots and shoots from plants treated with lead were compared to plants treated in similar conditions without lead. Four weeks old H. incana seedlings were treated in hydroponic cultures with Pb during 3 days, by adding or not 100 µM Pb(NO3)2.


title: Transcriptional analysis of PBMCs reveals sex specific changes in the aging of the immune system

status: Public on Jan 22 2015

city: Tampere

first: Saara

last: Marttila

address: Biokatu 6

institute: University of Tampere

summary: Aging and sex have a strong influence on the functional capacity of the immune system. In general, the immune response in females is stronger than that in males, but there is little information about the effect of aging on this difference. To address this question, we performed a transcriptomic analysis of peripheral blood mononuclear cells derived from nonagenarians and young controls. We found 337 and 269 genes to be differentially expressed (p<0.05, fold change >1.5 or <-1.5) in nonagenarian females and males, respectively; 177 of these were changed in both sexes. An analysis of the affected signaling pathways revealed a clear sex bias: the number of significantly changed pathways was 43 in females and 40 in males; 23 were shared. These data show that the effects of aging on the immune system are significantly different in males and females.

overall_design: Our study population consisted of 146 nonagenarians (103 females, 43 males) and 30 young controls (19-30 years of age, 21 females, 9 males). In our study, we analyzed the gene expression difference between nonagenarian and control women as well as between nonagenarian and control males and then compared these results.

first: Taru

last: Kuparinen

first: Juulia

last: Jylhävä

first: Tapio

last: Nevalainen

first: Marja

last: Jylhä

first: Antti

last: Hervonen

first: Liina

last: Tserel

first: Pärt

last: Peterson

first: Mikko

last: Hurme


title: Transcriptome changes in response to lead exposure

first: Patrick

last: Doumas

sample_organism:
Arabidopsis thaliana
Hirschfeldia incana


title: To detect change of gene expression after knock-down of hormone receptor in hepatocellular carcinoma cell line

status: Public on Jan 19 2015

city: Shanghai

first: Hui

middle: zhen

last: Nie

address: 800 Dongchuan Road

institute: Shanghai Cancer Institute

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


title: Effect of mini-chromosome maintenance protein 2 deficiency on the locations of DNA replication origins

status: Public on Jan 14 2015

city: Buffalo

last: Pruitt

address: Elm & Carlton Streets

department: Molecular & Cellular Biology

institute: Roswell Park Cancer Institute

summary: Mini-chromosome maintenance (MCM) proteins are loaded to chromatin during G1-phase and define potential locations of DNA replication initiation. MCM protein deficiency results in genome instability and high rates of cancer in mouse models. Here we develop a method of nascent strand capture and release and show that MCM2 deficiency reduces DNA replication initiation in gene rich regions of the genome. DNA structural properties are shown to correlate with sequence motifs associated with replication origins and with locations that are preferentially affected by MCM2 deficiency. Reduced nascent strand density correlates with sites of recurrent focal CNVs in tumors arising in MCM2-deficient mice, consistent with a direct relationship between sites of reduced DNA replication initiation and genetic damage.  Between 10 and 90% of human tumors, depending on type, carry heterozygous loss or mutation of one or more Mcm2-7 genes which is expected to compromise DNA replication origin licensing and result in elevated rates of genome damage at a subset of gene rich locations.

overall_design: Mcm2 deficient vs. wild type

first: Dimiter

last: Kunnev

first: Amy

last: Freeland

first: Maochun

last: Qin

first: Robert

middle: W

last: Leach

first: Jianmin

last: Wang

first: Rajani

last: Shenoy


title: Combined inhibition of TGFβ and PDGF signaling attenuates radiation-induced pulmonary fibrosis

status: Public on Jan 15 2015

city: Heidelberg

first: Manuel

last: Roehrich

state: Baden-Württemberg

address: INF 280

department: Molecular Radiation Oncology

institute: DKFZ Heidelberg

summary: To investigate effects on mRNA expression in mouse lung tissue through treatment with Ly, Su, Imatinib, irradiation and combinations of them.

overall_design: mRNA expression was measured 24 days after irradiation. 2 biological replicates were analyzed for each treatment condition (control, Ly, Imatinib, Su, Ly+Imatinib, Ly+Su, Irradiation, Irradiation+Ly, Irradiation+Imatinib, Irradiation+Su, Irradiation+Ly+Imatinib, Irradiation+Ly+Su)

first: Monika

last: Dadrich

first: Peter

last: Huber


title: Identification of a prognostic signature for old-age mortality by integrating genome-wide transcriptomic data with the conventional predictors: the Vitality 90+ Study

first: Saara

last: Marttila

summary:
BACKGROUND: Prediction models for old-age mortality have generally relied upon conventional markers such as plasma-based factors and biophysiological characteristics. However, it is unknown whether the existing markers are able to provide the most relevant information in terms of old-age survival or whether predictions could be improved through the integration of whole-genome expression profiles.

METHODS: We assessed the predictive abilities of survival models containing only conventional markers, only gene expression data or both types of data together in a Vitality 90+ study cohort consisting of n = 151 nonagenarians. The all-cause death rate was 32.5% (49 of 151 individuals), and the median follow-up time was 2.55 years.

RESULTS: Three different feature selection models, the penalized Lasso and Ridge regressions and the C-index boosting algorithm, were used to test the genomic data. The Ridge regression model incorporating both the conventional markers and transcripts outperformed the other models. The multivariate Cox regression model was used to adjust for the conventional mortality prediction markers, i.e., the body mass index, frailty index and cell-free DNA level, revealing that 331 transcripts were independently associated with survival. The final mortality-predicting transcriptomic signature derived from the Ridge regression model was mapped to a network that identified nuclear factor kappa beta (NF-κB) as a central node.

CONCLUSIONS: Together with the loss of physiological reserves, the transcriptomic predictors centered around NF-κB underscored the role of immunoinflammatory signaling, the control of the DNA damage response and cell cycle, and mitochondrial functions as the key determinants of old-age mortality.

overall_design: The study consisted of 151 nonagenarians who were analyzed for genome-wide transcriptomic mortality predictors in a longitudinal setting.

first: Juulia

last: Jylhävä

first: Jani

last: Raitanen

last: Jylhä


title: Identification of genes enriched in the Arc, VMH, DMH and LH of adult mouse

city: St. Louis

first: Akiko

last: Satoh

state: MO

address: 660 S Euclid Avenue

institute: Washington University

summary: To identify genes selectively expressed in the DMH, we collected RNA samples from four hypothalamic nuclei, namely the Arc, VMH, DMH and LH, using laser microdissection and conducted microarray analysis to compare their gene expression profiles.

overall_design: The Arc, VMH, DMH, and LH were dissected from C57BL/6 females at 3 month of age by laser microdissection using the Leica 6000 system (n=2 each group).

first: Shin-ichiro

last: Imai


title: Identification of a plasma four-microRNA panel as a potential noninvasive biomarker for osteosarcoma

status: Public on Jan 13 2015

city: Harbin

first: Liwen

last: Wu

state: Heilongjiang

address: #37 Yiyuan Street

department: Department of Orthopedics

institute: The Fourth Affiliated Hospital of Harbin Medical University

summary:
TaqMan low density array (TLDA) was carried out to screen of the profiles of circulating miRNAs in pooled plasma samples from healthy controls and pre-operative osteosarcoma patients.
The expression changes of circulating miRNAs in osteosarcoma patients were identified.

overall_design: To select candidate plasma miRNAs for osteosarcoma detection and monitoring, we employed TLDA technique to screen expression levels of 739 miRNAs in pooled plasma samples from healthy controls and pre-operative osteosarcoma patients (each pooled from 10 individuals).

first: Feng

last: Lian


title: To detect change of gene expression after knock-down of hormone receptor in hepatocellular carcinoma cell line [RNA]

first: Hui

last: Nie

summary: Vector or shRNA was transfected into SMMC-7721 to detect effect of shRNA on gene expression

overall_design: Specific hormone receptor was knocked down by shRNA in hepatocellular carcinoma

first: Huizhen

first: Jun

last: Li


title: Comprehensive transcriptional profiling analysis reveals candidate regulators in cold-stressed seedlings of Petunia hybrida

city: wuhan

first: wei

last: zhang

institute: Huazhong Agricultural University

summary: Investigation of gene expression level changes in Petunia hybrida seedlings subjected to cold at 2°C for 0.5 h, 2 h, 24 h and 5 d, compared to the CK.

overall_design: The custom-designed four-plex microarray with 72000 features was constructed based on the EST sequences generated in Breuillin's study together with all sequences of P.hybrida and P.axillaris available at Genbank, TIGR, and the Solanaceae genomics network SGN, which was ultimately composed by a set of 24816 non-redundant unique sequences (unigenes).The probe intensity files resulting from RNA hybridization were first read into R. Background Correction, quantile normalization and summarization were then performed using the Robust Multi-array Average (RMA) method included in Bioconductor Affy package based on the home made chip description library.

first: Wei

last: Zhang


title: Pseudogene INTS6P1 regulates its cognate gene INTS6 through competitive binding of miR-17-5p in hepatocellular carcinoma

status: Public on Jan 03 2015

city: Baltimore

first: Florin

last: Selaru

address: 720 Rutland Ave Ross 950

institute: the Johns Hopkins

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

overall_design: Refer to individual Series


title: Pseudogene INTS6P1 regulates its cognate gene INTS6 through competitive binding of miR-17-5p in hepatocellular carcinoma [mRNA, lncRNA]

summary: To identify the novel tumor suppressors in hepatocellular carcinoma (HCC), we have employed whole genome microarray expression profiling as a discovery platform in HCC and paired normal liver tissues to identify genes which down-regulated in HCC. Among which, INTS6 and its pseudogene, namely INTS6P1, were found to be dramatically down-regulated in HCC. The down-regulated expression of INTS6 and INTS6P1 in HCC was further confirmed by real-time PCR.

overall_design: RNA was extracted from 3 pairs of HCC and normal liver tissue harvested from patients to undergo microarray study.

first: Haoran

last: Peng

first: Masaharu

last: Ishida

first: Atsushi

last: Saito

last: Kamiya

first: James

middle: P

last: Hamilton

first: Rongdang

last: Fu

first: Alexandru

last: Olaru

first: Fangmei

last: An

first: Irinel

last: Popescu

first: Razvan

last: Iacob

first: Simona

last: Dima

first: Sorin

last: Alexandrescu

last: Grigorie

first: Anca

last: Nastase

first: Ioana

last: Berindan-Neagoe

first: Ciprian

last: Tomuleasa

last: Graur

last: Zaharia

first: Michael

middle: S

last: Torbenson

first: Esteban

last: Mezey

first: Minqiang

last: Lu


title: Effect of Glucocorticoids on microRNA, lncRNA and mRNA Expression Profiles of the Human Bone Microcirculatory Endothelial Cells from Femoral Head

status: Public on Jan 05 2015

city: Beijing

first: Qingsheng

last: Yu

address: No 2, East Yinghua Rd, Chaoying District

institute: China-Japan Friendship Institute of Clinical Medical Sciences

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


title: Gene expression following treatment with HDAC6 inhibitor C1A

status: Public on Jan 06 2015

city: London

first: Maciej

last: kaliszczak

address: Du Cane road

department: Surgery and Cancer

country: United Kingdom

institute: Imperial College London

summary:
RNA Extraction from a human colon tumor developed in a xenograft mouse (Extraction from fresh frozen tumor tissue material).
The affymetrix Human genome U219 array plate was used. Sequences used in the design of the array were selected from the Uingene database 219, RefSeq version 36, and full length human mRNAs from GenBank. Measure gene expression of more than 36 000 transcipts and variants per sample, which represent more than 20 000 genes.

overall_design: Study performed under contract by Alpha Metrix Biotech, Rodermark, Germany. Full details are available upon request. Processed data are available on the series record and consists of the differentially expressed genes identified in the comparison of the 14d_treated vs 24h_treated samples.

last: Kaliszczak


title: Effect of Glucocorticoids on lncRNA and mRNA Expression Profiles of the Human Bone Microcirculatory Endothelial Cells from Femoral Head

status: Public on Jan 01 2015

summary: Appropriate gene expression patterns form the basis for bone microcirculatory endothelial cells’ function and bone morphology. Although previous studies have elucidated the impact of hydrocortisone on bone microcirculatory endothelial cells’ specific gene expression, the exact differential transcriptomes and comprehensive gene expression profiles remain unknown. We have investigated the mRNA and lncRNA expression patterns before and after hydrocortisone administration of bone microcirculatory endothelial cells. At mRNAs level totally 518 differentially expressed genes were identified. Furthermore, we identified 73 upregulated and 166 downregulated long non-coding RNAs after administration of hydrocortisone. These RNAs appeared to be highly important to gene co-expression network. Transcriptomic analysis of bone microcirculatory endothelial cells from human samples is highly informative due to their relevance to the large number of expressed genes. Our study provides a very valuable basis for investigation of genes, regulation and their co-expression network contributing to hydrocortisone induced disorders.

overall_design: Two-condition experiment, hydrocortisone treated vs. untreated bone microcirculatory endothelial cells. Biological replicates: 8 control replicates, 8 treated replicates.

first: Wanshou

last: Guo


title: Pseudogene INTS6P1 regulates its cognate gene INTS6 through competitive binding of miR-17-5p in hepatocellular carcinoma [miRNA]

first: Florin

last: Selaru

first: Haoran

last: Peng

first: Masaharu

last: Ishida

first: Atsushi

last: Saito

last: Kamiya

first: James

last: Hamilton

last: Fu

last: Olaru

last: An

last: Popescu

middle: T


title: Gene expression profiles of adult murine osteoblasts and cementoblasts

status: Public on Dec 31 2014

city: Grafton

first: Brya

last: Matthews

state: Auckland

address: 85 Park Rd

department: Molecular Medicine and Pathology

country: New Zealand

institute: University of Auckland

summary: Cementoblasts are cells that line the surface of the tooth root and produce a mineralized tissue known as cementum. Cementum is critical for attachment of the tooth to the adjacent periodontal ligament and has a similar biochemical composition to bone, however it differs in that it lacks vasculature and innervation, and does not undergo remodelling. It has been difficult to define markers that specifically identify cementoblasts. In order to compare the transcriptome of fully developed cementoblasts with neural crest derived (calvarial) osteoblasts in vivo, we used osteocalcin-GFP (OC-GFP) mice. Cells were isolated by digestion of calvaria (osteoblasts) or extracted molars (cementoblasts) and purified by FACS sorting for GFP positive cells before RNA extraction and microarray analysis.

overall_design: OC-GFP positive cells were isolated by FACS from enzymatically digested calvaria, or extracted molars from 5-7 week old OC-GFP mice. Total RNA was extracted and amplified for microarray analysis. Samples were pooled from 6-10 mice. 3 replicates are included for each sample.

first: Ivo

last: Kalajzic


title: Transcriptome analysis of Mycobacterium tuberculosis clinical isolates.

city: Boston

first: Kim

last: Lewis

state: MA

address: 360 Huntington Ave

institute: Northeastern University

summary: Bacterial persister cells are phenotypic variants of regular cells that are tolerant to antibiotics. Analysis of clinical isolates of M. tuberculosis showed that strains vary substantially in their tolerance to antibiotics. The level of persisters was very high is some isolates, suggesting that these are hip mutants. We investigated gene expression differences in eight clinical isolates, four of which we characterized as high-persister strains and four as low-persister, or regular, strains. Comparison of gene expression patterns may provide clues as to the genetic mechanisms underlying persister formation.

overall_design: Exponential phase cultures of eight clinical isolates were challenged in biological triplicate with the antibiotic D-cycloserine and cells were colllected at Day 0 and Day 7 for transcriptome analysis.

first: Heather

middle: L

last: Torrey


title: IMI MARCAR Project: towards novel biomarkers for cancer risk assessment

status: Public on Apr 29 2015

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
synthetic construct


title: Effect of Glucocorticoids on microRNA Expression Profile of the Human Bone Microcirculatory Endothelial Cells from Femoral Head

last: Yu

summary: Appropriate gene expression patterns form the basis for bone microcirculatory endothelial cells’ function and bone morphology. Although previous studies have elucidated the impact of hydrocortisone on bone microcirculatory endothelial cells’ specific gene expression, the exact differential transcriptomes and comprehensive gene expression profiles remain unknown. We have investigated the microRNA expression patterns before and after hydrocortisone administration of bone microcirculatory endothelial cells. Only 5 microRNAs were Benjamini-Hochberg characterized over 368 microRNAs candidates. Transcriptomic analysis of bone microcirculatory endothelial cells from human samples is highly informative due to their relevance to the large number of expressed genes. Our study provides a very valuable basis for investigation of genes, regulation and their co-expression network contributing to hydrocortisone induced disorders.


city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

summary: Gene expression data of micro RNA from mouse muscle cell line C2C12 at day 0, day4 and day8

overall_design: miRNAs of cell line C2C12 at day 0 day 4 and day 8  were hybridized to Affymetrix miRNA-3 Array.

first: Siriluck

last: Ponsuksili


title: Comparison of gene expression profiles of Sca-1+ and Sca-1- cells post alveolar injury induced by P. aeruginosa

city: Chicago

first: Yuru

last: Liu

state: Illinois

address: 835 S. Wolcott Ave.

department: Pharmacology

institute: University of Illinois

summary: Alveolar type II cells were isolated from mice before P. aeruginosa injection (basal state) and at 72 h post-PA, and were separated into Sca-1+ and Sca-1- populations.   Gene expression profile in the following four groups of cells were compared: non-PA Sca-1-, non-PA Sca-1+, 72 h post-PA Sca-1- and 72 h post-PA Sca-1+.

overall_design: To determine whether the Sca-1+ type II cells appear post alveolar injury displayed generalized expression of progenitor-cell-specific genes, we compared gene expression profile of the isolated Sca-1+ and Sca-1- type II cells before and post p. aeruginosa indeced injury.


title: An In Vivo Screen Uncovers Repression of Lipoprotein Lipase by MiR-29a as a Mechanism for Lipid Flux Away From the Liver

city: San Francisco

first: Aras

middle: N

last: Mattis

state: California

address: 35 Medical Center Way

institute: UCSF

summary:
We screened for miRNA-regulated genes in adult mouse hepatocytes by a novel AAV8-Ttr-Cre delivery system deleting a floxed Dicer1 and blocking the processing of mature miRNAs.
We then used a microarray to analyze the genes at T0 (just before injection), T1 (2 weeks after injection), T2 (4 weeks after injection)

overall_design: Dicer1 fl/fl male mice on a mixed 129S4 and C57BL/6 background were injected at 8-10 weeks of age with AAV8-Ttr-Cre to delete hepatocyte-specific Dicer1. Liver RNA analyzed at 0, 2 and 4 weeks.

first: Holger

last: Willenbring


title: Amniocytes (AM) vs. Immortalized AM

city: naples

first: marco

last: miceli

address: De crecchio,7

country: Italy

institute: Second University of Naples

summary: Transcriptional profiling of AM (amniocytes) vs. three different immortalized AM-derived cell lines. Immortalization of AM-derived cell lines by lentiviral vector with hTERT and E6-E7.

overall_design: Different experimental conditions: AM (amniocytes) vs. MePR-0A (immortalized AM-derived epitheloid cell line), MePR-2B (immortalized AM-derived fibroblastoid cell line) and MePR-3A (immortalized AM-derived fibroblastoid cell line). Biological replicates: 2 for each sample, independently grown and harvested.

first: Marco

last: Miceli

first: Carmela

last: Dell'Aversana


title: Exploring the gene expression associated with Pten deficiency in the developing inner ear

first: Hyung Jin

last: Kim

address: 187 Osongsaengmyeong 2-ro

department: Division of Intractable Diseases, Center for Biomedical Sciences

institute: Korea National Institute of Health

summary: In our recent study, we reported the function of phosphatase and tensin homolog (PTEN) during inner ear development. PTEN is necessary for neuronal maintenance, such as neuronal survival and accurate nerve innervations of hair cells. To better understand the genes and signaling networks related to auditory neuron maintenance, we examined the profiles of differentially expressed genes (DEGs) using microarray analysis in Pten-deficient mice at E14.5. We identified 46 statistically significant DEGs using Significant Analysis of Microarrays (SAM) analysis with a false discovery rate (FDR) equal to zero. Among the DEGs, expression levels of candidate genes and expression domains were validated by quantitative real-time polymerase chain reaction (RT-PCR) and in situ hybridization, respectively.    Ingenuity pathway analysis (IPA) with DEGs identified significant signaling networks associated with cellular movement and axon guidance. Significant networks revealed that Spp1-mediated cellular movement and G-protein signaling 4 (RGS4)-Akt are related with axon guidance. This result was consistent with the phenotypic defects of spiral ganglion in Pten conditional knockout (cKO) mice (e.g., abnormal migration of spiral ganglion and irregular formation of neuritis). From this study, we suggest two key regulatory signaling networks mediated by Spp1 and RGS4, which may play potential roles in neuronal differentiation of developing auditory neurons.

overall_design: Embryonic day 14.5 inner ear tissues from Pten conditional knockout (cKO: Pax2Cre/+;PtenloxP/loxP) and littermate wild type (PtenloxP/+ and PtenloxP/loxP) were used (60 embryos of each group). Total RNA from three independent pools of inner ears from each group was extracted with TRIZOL, amplified using Ambion amplification kit, and cRNA (750 ng) was hybridized to Illumina MouseRef-8 v 2.0 Expression Bead Chips. Three biological replicates (three chips for wild-type samples and three chips for Pten cKO samples) were performed for microarray hybridization experiments.

first: Hyung-Jin

first: Jihee

last: Ryu

first: Hae-Mi

last: Woo

first: Samuel

last: Cho

first: Min-Kyung

last: Sung

first: Sang-Cheol

first: Mi-Hyun

last: Park

first: Taesung

first: Soo-Kyung

last: Koo


title: Drug treatment of colorectal and endometrial cancer cell lines

city: Helsinki

first: Johanna

last: Lotsari-Salomaa

address: Haartmaninkatu 8

department: Department of Medical Genetics

institute: University of Helsinki

summary:
We used expression profiling of colorectal cancer and endometrial cancer cell lines treated with demethylating agents to search for epigenetically regulated miRNAs.
The study included three MMR-deficient colorectal cancer cell lines (HCT116, HCT15, and RKO), two MMR-proficient colorectal cancer cell lines (SW480, and T84) and two MMR-deficient endometrial cancer cell lines (AN3CA and HEC59).

overall_design:
Cancer cell lines were cultured and divided to two parts. One part of cell culture was treated with demethylating agents (5 uM 5-aza-2' deoxycytidine, Sigma A3656, for 96 hours and with 300 nM trichostatin, Sigma T1952, for 18 hours).
The other part of cancer cell line was cultured without treatments. All treatments were performed in duplicates.

first: Sippy

last: Kaur

last: Lotsari


title: Homeobox transcription factors involved in fruiting body development of Volvariella volvacea

status: Public on Dec 19 2014

city: Fuzhou

first: Baogui

last: Xie

state: Fujian

address: Shangdian Road

department: Mycological Research Center

institute: mrcfafu

summary: The genome of V. volvacea revealed 47 genes encoding homeobox transcription factors. Of them, 8 differentially expressed homeobox transcription factors were obtained by comparing the gene expression during primordia and elongation formation. Furthermore, quantitative real-time PCR was performed on selected genes with different expression levels to demonstrate the utility of digital gene expression for gene expression profiles during fruiting body formation. The results showed that five homeobox transcription factors were up-regulated during primordia formation, and three homeobox transcription factors were down-regulated from the egg stage to elongation stage. Overall, a critical role for homeobox transcription factor was believed to contribute to the fruiting body formation.

overall_design: Using the 3'-tag digital gene expression (DGE), we compared the gene expression profiles in fruiting body development of V. volvacea.

first: Youjin

last: Deng

first: Li

last: Meng

first: Yongxin

last: Tao

first: Bingzhi

last: Chen


title: To detect change of gene expression after knock-down of hormone receptor in hepatocellular carcinoma cell line [miRNA]

city: Shanghai

first: Hui

last: Nie

address: 800 Dongchuan Road

institute: Shanghai Cancer Institute

overall_design: Specific hormone receptor was knocked down by sh-RNA in hepatocellular carcinoma

first: Huizhen

first: Jun

last: Li


title: Gene expression analysis of EBV-encoded dUTPase in hDCs

city: Columbus

first: Maria-Eugenia

last: ariza

state: OH

address: 460 Medical Center Drive, Room 365

department: Department of Molecular Virology, Immunology and Medical Genetics

institute: Institute for Behavioral Medicine Research

summary:
Gene expression patterns provide insight into complex biological networks in which viruses and host cells interact. Dendritic cells are the most potent antigen presenting cells of the immune system and are crucial for the initiation of T-cell responses to viral pathogens. To better understand the biological effects of the EBV-encoded dUTPase on gene modulation in cells that play a central role in innate and adaptive immune responses, microarray gene expression profiling studies were performed in untreated or EBV-encoded dUTPase treated hDCs using the human genome U133 Plus 2.0 GeneChip.
The results of this study identified over 800 differentially expressed genes between control and EBV-encoded dUTPase treated samples for each normalized data set using the criteria fold change >2 and p<0.05.

overall_design: The effect of the EBV-encoded dUTPase on gene expression in human dendritic Langerhan cells (hDCs), derived from human umbilical cord blood (HUCB) cells, was determined by treating hDCs with purified EBV-encoded dUTPase (10 µg/ml), for 4 h and then compared the gene expression in these cells to untreated controls. A total of 5 samples (2 controls and 3 treated) were analyzed.

first: Maria

last: Ariza

first: Marshall

last: Williams

first: Pierre

last: Rivailler


title: Expression data from Hematopoietic stem cells

status: Public on Dec 17 2014

city: Cincinnati

first: Xiaoli

address: 3333 Burnet Ave

institute: CCHMC

summary:
Objective: Microarray analysis was used to determine the molecular mechanism underlying Fancd2 and Foxo3a double knockout mice HSCs exhaustion.
Methods: SLAM cells were obtained from WT, Fancd2KO, Foxo3aKO and DKO bone marrow cells. Total RNA from SLAM cells was purified by RNeasy kit (Qiagen) following the manufacturer’s procedure. And then the RNA was fluorescently labeled and hybridized to Affmetrix Mogene 2.0 ST array. Data was analyzed by Genespring GX11 software.
Results: a large proportion of differentially expressed genes in dKO HSCs belonged to cell cycle control. Another group of up-regulated genes were those involved in the differentiation of HSCs. Other differentially regulated transcripts included genes known to be involved in oxidative stress response, or to have roles in DNA repair.
Conclusion: Cell cycle, DNA repair, DNA binding and hematopoietic lineage differentiation pathways might have been perturbed in HSC exhaustion.

overall_design: Mouse Femurs and tibias from WT, Fancd2KO, Foxo3aKO and DKO mice were flushed to dissociate the BM fraction.  The mononuclear cells were isolated by Ficoll (GE Healthcare) gradient centrifugation. Single SLAM (Lin-ckit+Sca-1+CD34-) cells were sorted. RNA was extracted, labelled, and quantified using the Mouse ST-2 microarray.

first: Qishen

last: Pang


title: Expression data from MOLT-4 and CCRF-CEM cells grown in serum free medium, untreated, treated with direct (A-769662) and indirect (AICAR) AMPK activators.

city: Esch-sur-Alzette

first: Ines

last: Thiele

address: 7, avenue des Hauts-Fourneaux

department: Luxembourg Centre for Systems Biomedicine

country: Luxembourg

institute: University of Luxembourg

summary: Two human acute lymphoblastic leukemia cell lines (Molt-4 and CCRF-CEM) were treated with direct (A-769662) and indirect (AICAR) AMPK activators. Molt-4 and CCRF-CEM cells were obtained from ATCC (CRL-1582 and CCL-119). Control samples were used for the analysis of metabolic differences between cell lines. Therefore the data was analyzed in combination with, metabolomic data, and the genome-scale reconstruction of human metabolism. For experiments cells were grown in serum-free medium containing DMSO (0.67%) at a cell concentration of 5 x 105 cells/mL.

overall_design: We analyzed acute lymphoblastic leukemia cell lines (Molt-4 and CCRF-CEM) treated with direct (A-769662) and indirect (AICAR) AMPK activators, along with controls. We used the Affymetrix GeneChip Human Exon 1.0 ST Array to measure whole genome exon expression.

first: Maike

last: Aurich

first: Sigrun

last: Hrafnsdottir


title: Analysis of copy number variations among Chinese cattle breeds

status: Public on Dec 30 2014

city: Yangling

first: Liangzhi

last: Zhang

state: Shaanxi

address: No.22 Xinong Road

department: College of Animal Science and Technology

institute: Northwest A&F University

summary:
Here we describe a genome-wide analysis of copy number variations (CNVs) in Chinese domestic cattle by using array comparative genomic hybridization (array CGH) and quantitative PCR (qPCR). We conducted array CGH analysis on 30 male cattle individuals, animals from consisting of 12 breeds of Bos taurus/Bos indicus, 1 Bos grunniens and and two ones of Bubalus bubalis breeds for with beef, and/or dairy or dual purpose.
We identified over 470 candidate CNV regions (CNVRs) in Bos B. taurus/B. indicus; 118 candidate CNV regions (CNVRs) in B. grunniens, 139 CNVRs in B. bubalis. Furthermore, based on the Y haplotypes of B. taurus/ B. indicus, Wwe also identified 69, 337, and 251 candidate CNV regions (CNVRs) in the sub-groups of Y1, Y2 and Y3 haplotypes.

sample_organism:
Bos taurus
Bos grunniens
Bubalus bubalis

overall_design: The custom aCGH chips that interrogated the whole genome CNVs were build for 30 cattles from diverse Chinese cattle breeds with Angus as reference sample.

first: Hong


title: Molecular dissection of drought tolerance mechanisms in rice by comparative deep transcriptome sequencing

first: Fan

state: Beijing

address: 12 South Zhong-Guan-Cun St.

institute: CAAS

summary:
To dissect the molecular mechanisms underlying drought tolerance (DT) in rice, transcriptome differences of a DT introgression line H471, the DT donor P28 and the drought sensitive recurrent parent HHZ under drought stress were investigated using deep transcriptome sequencing.
Results revealed a differential constitutive gene expression prior to stress and distinct global transcriptome reprogramming among three genotypes under time-series drought stress, consistent with their differential genotypes and DT phenotypes.

overall_design: DT introgression line H471, the DT donor P28 and the drought sensitive recurrent parent HHZ under drought stress were investigated using deep transcriptome sequencing.The drought stress treatment was started by withholding water at the tillering stage. The days were counted after the AWC in the soil reached 20% to allow drought measurements at precisely determined intervals, and the soil water content reached 15%, 10% and 7.5% after 1d, 3d and 4d drought treatment, respectively.Three top leaves for each sample were harvested for each genotype under 1d and 3d drought stress and control conditions. All samples were immediately frozen in liquid nitrogen and stored at -80°C and then for transcriptome sequencing.

first: Liyu

last: Huang

first: Binying

last: Fu

first: Yongli

last: Zhou


title: The cockroach Blattella germanica obtains nitrogen from uric acid through a metabolic pathway shared with its bacterial endosymbiont

status: Public on Dec 08 2014

city: Barcelona

first: Guillem

last: Ylla

state: Catalonia

address: Passeig Marítim de la Barceloneta, 37

country: Spain

institute: Institute of Evolutionary Biology

summary: Uric acid stored in the fat body of cockroaches is a nitrogen reservoir mobilized in times of scarcity. The discovery of urease in Blattabacterium cuenoti, the primary endosymbiont of cockroaches, suggests that the endosymbiont may participate in cockroach nitrogen economy. However, bacterial urease may only be one piece in the entire nitrogen recycling process from insect uric acid. Thus, in addition to the uricolytic pathway to urea, there must be glutamine synthetase assimilating the released ammonia by the urease reaction to enable the stored nitrogen to be metabolically usable.

overall_design: None of the Blattabacterium genomes sequenced to date possess genes encoding for those enzymes. To test the host's contribution to the process, we have sequenced and analysed Blattella germanica transcriptomes from the fat body. We identified transcripts corresponding to all genes necessary for the synthesis of uric acid and its catabolism to urea, as well as for the synthesis of glutamine, asparagine, proline and glycine, i.e. the amino acids required by the endosymbiont. We also explored the changes in gene expression with different dietary protein levels. It appears that the ability to use uric acid as a nitrogen reservoir emerged in cockroaches after its age-old symbiotic association with bacteri

first: Rafael

last: Patiño-Navarrete

first: Maria-Dolors

last: Piulachs

first: Xavier

last: Belles

first: Andrés

last: Moya

first: Amparo

last: Latorre

first: Juli

last: Peretó


title: Protein Microarrays Identify Disease Specific Anti-Cytokine Autoantibody Profiles in Immunodeficiency

status: Public on Dec 25 2014

city: stanford

first: Jacob

last: Rosenberg

state: Ca

address: 269 Campus Drive, CCSR 2240

country: USA

institute: Stanford University

summary: 57 serum samples from immunodeficiency patients were screened on custom designed protein microarrays for the presence of autoantibodies against cytokines, chemokines, growth factors, and other candidate autoantigens.

overall_design: One hundred four purified biomolecules including known autoantigens, as well as cytokines, chemokines, growth factors and receptors were printed on the arrays. All targets were printed in triplicate. Arrays were probed with diluted serum and autoantibodies were detected with a Cy5 conjugated anti-human IgG secondary.

first: Paul

middle: J

last: Utz


title: Methanol and Methylamine Utilization Pathways in Methyloversatilis universalis FAM5: Genome Wide Gene Expression and Mutagenesis Studies

status: Public on Dec 04 2014

city: Seattle

first: David

middle: A. C.

last: Beck

state: WA

address: Benjamin Hall IRB, Rm 440, UW Box 355014

department: ChemE & eScience Institute

institute: University of Washington

summary: Methyloversatilis universalis FAM5 utilizes single carbon compounds such as methanol or methylated amines as a sole source of carbon and energy. Expression profiling reveals distinct sets of genes altered during growth on methanol vs methylamine. Growth on methanol results in activation of mdh2 and a number of known accessory proteins. As expected, all genes for N-methylglutamate pathway were induced during growth on methylated amine. Among other functions, responding to a switch from methanol to methylated amines, are a heme-containing amine dehydrogenase (QHNDH), a PQQ-dependent methanol dehydrogenase homologue, a distant homologue of formaldehyde activating enzyme (fae3), molybdenum containing formate dehydrogenase, a set of transporters homologues to urea/ammonium transporters and amino-acid permeases. Genes encoding the PQQ-dependent methanol dehydrogenase and associated cytochrome, the enzymes from the assimilatory H4F-dependent pathway, and the tungsten-containing aldehyde oxidoreductase were down-regulated during growth on methylamine. Genes essential for carbon assimilation (serine cycle) and H4MTP-pathway for formaldehyde oxidation show similar level of expression on both C1-carbon sources. Phenotypic analysis of mutants lacking functional QHNDH had no growth defect on C1-compounds. M. universalis FAM5 strain with the methylene-tetrahydrofolate dehydrogenase lesion, a key enzyme of the H4-folate pathway, were not able to use any C1-compound, methanol or methylated amines. Methyloversatilis universalis FAM5 possesses three homologs of the formaldehyde activating enzymes. The relative expression of two of the formaldehyde activating enzyme (fae1) and fae2 did not change after the shift from methanol to methylamine growth. The relative expression of the third homologs, fae3, was significantly upregulated by methylamine. Single and double fae 2 and fae 3 mutants display similar to wild type growth  on methanol or methylamine. Strains lacking fae1 lost the ability to grow on both C1-compounds. However upon incubation on methylated amines the fae1-mutant produce revertants (fae1R ). The revertant strains displayed an impaired growth on methylamine but were not able to use methanol. Double mutations in fae1R / fae3 or fae1R/fae2 and triple mutant fae1R/fae2/fae3 showed similar to fae1R phenotype. The metabolic pathways for utilization methanol and methylamine in Methyloversatilis universalis FAM5 are reconstructed.

overall_design: Methyloversatilis universalis FAM5 grown on methanol and methylamine with two biologial replicates for each condition. RNA-Seq was used for transcriptomics.

first: Nathan

last: Good

first: Andrew

last: Lamb

middle: A

first: N

last: Martinez-Gomez

first: Amanda

last: Smith

first: Marina

last: Kalyuzhnaya


title: Tetraspanin family member, CD82, regulates expression of EZH2 via inactivation of p38 MAPK signaling in leukemia cells. The novel function of CD82 and its impact on BCL2L12 via AKT/STAT5 signal pathway in acute myelogenous leukemia cells.

city: Nankoku

first: Chie

last: Nishioka

address: Oko-cho, Nankoku, Kochi

country: Japan

institute: Kochi University

summary:
We recently found that the tetraspanin family member, CD82, which is aberrantly expressed in chemotherapy-resistant CD34+/CD38− acute myelogenous leukemia (AML) cells, negatively regulates matrix metalloproteinase 9, and plays an important role in enabling CD34+/CD38− AML cells to adhere to the bone marrow microenvironment. This study explored novel functions of CD82 that contribute to AML progression.    We employed microarray analysis comparing the gene expression profiles between CD34+/CD38− AML cells transduced with CD82 shRNA and CD34+/CD38− AML cells transduced with control shRNA. Real-time RT-PCR and western blot analysis were performed to examine the effect of CD82 knockdown on the expression of the polycomb group member, enhancer of zeste homolog 2 (EZH2), in leukemia cells. A chromatin immunoprecipitation assay was performed to examine the effect of CD82 expression on the amount of EZH2 bound to the promoter regions of tumor suppressor genes in leukemia cells. We also utilized methylation-specific PCR to examine whether CD82 expression influences the methylation status of the tumor suppressor gene promoter regions in leukemia cells.    Microarray analysis revealed that levels of EZH2 decreased after shRNA-mediated depletion of CD82 in CD34+/CD38− AML cells. Moreover, the antibody-mediated blockade of CD82 in leukemia cells lowered EZH2 expression via activation of p38 MAPK signaling, decreased the amount of EZH2 bound to the promoter regions of the tumor suppressor genes, and inhibited histone H3 lysine 27 trimethylation in these promoter regions, resulting in upregulation of the tumor suppressors at both the mRNA and protein levels.
The aim of this study was to explore the biological functions of a tetraspanin family protein––CD82–– expressed aberrantly in chemotherapy-resistant CD34+/CD38- acute myelogenous leukemia (AML) cells. Microarray analysis of patient-isolated CD34+/CD38- AML cells revealed that the levels of anti-apoptotic protein BCL2L12 were downregulated after CD82 depletion by specific shRNA. Western blot analysis indicated that BCL2L12 was aberrantly expressed in patient-isolated AML cells and AML cell lines. Furthermore, CD82 blockade by a specific antibody downregulated BCL2L12 in parallel with de-phosphorylation of STAT5 and AKT, while pharmacological inhibition of STAT5 and AKT activation decreased BCL2L12 expression in leukemia cells. In addition, shRNA-mediated downregulation of BCL2L12 increased the levels of cleaved caspase 3and suppressed proliferation of leukemia cells, impairing their engraftment in immunodeficient mice. Taken together, our results indicate that CD82 regulated BCL2L12 expression via STAT5A and AKT signaling and stimulated proliferation and engrafting of leukemia cells, suggesting that CD82 and BCL2L12 may be promising therapeutic targets in AML.

overall_design: Two-condition experiment, 3 control shRNA-transduced CD34+CD38- AML cells (CS2) vs 3 CD82 shRNA-transduced CD34+CD38- AML cells (CD82). 3 control shRNA-transduced CD34+CD38- AML cells (CS2) vs 3 STAT5A shRNA-transduced CD34+CD38- AML cells (00-2).

first: Takayuki

last: Ikezoe

first: Asako

last: Takeuchi

first: Atsuya

last: Nobumoto

first: Masato

last: Tsuda

first: Akihito

last: Yokoyama


title: Stress response of Cupriavidus metallidurans strains

status: Public on Dec 16 2014

city: Halle/Saale

first: Cornelia

last: Große

department: Faculty of Biology/Microbiology

summary: Response of Cupriavidus metallidurans CH34, AE104 and delta zupT mutant to Zn/EDTA stress

overall_design: In this study 3 different treatments were performed to acquire expression profiles of the total genome of Cupriavidus metallidurans

last: Grosse

first: Dietrich

middle: H

last: Nies


title: Expression analysis in roots and leaves of asparagus bean accesions B47 and B128 under well-watered and soil drought conditions

status: Public on Nov 26 2014

city: Hangzhou

first: Pei

last: Xu

address: 198 Shiqiao Rd

department: Vegetable Institute

institute: Zhejiang Academy of Agricultural Sciences

summary:
Investigation of whole genome gene expression level changes in two asparagus bean accesions B47 and B128 under drought stress, compared to well-watered conditions.
Two organs, leaf and root, were sampled for each accesion under both well-watered and drought conditions.

overall_design: A 24-chip study using total RNA. A total of 29,471 unigenes, 26,156 functionally annotated, were represented on the microarray, and a total of 24 microarrays (2 genotypes × 2 tissues × 2 treatments × 3 replicates) were produced for hybridization.


title: Transcriptional profiling of E. coli cultures exposed to green or red CdTe Quantum Dots 50 µg/ml

status: Public on Dec 01 2014

city: Santiago

middle: Enrique

last: Loyola

state: Santiago

address: Avenida Libertador Bernardo O'Higgins 340

country: Chile

institute: OMICS Solutions, Centro Nacional de Genómica y Bioinformática

summary: E. coli cultures were exposed to green or red CdTe Quantum Dots 50 µg/ml during 15 min. Total RNA was extracted and cDNA labeled probes were generated by reverse transcription using Alexa 555 and Alexa 647 fluorophores. These probes were used to hybridize genomic slides containing genomic arrays to determine global transcriptional changes.

overall_design: Two-conditions experiment, Quantum Dots treated cells vs. Untreated control cells. Biological replicates: 3 control, 3 toxicants exposed cells, independently grown and harvested. One replicate per array


title: Levator Ani Satellite Cells (LASCs) treated with Nonsteroidal Androgen Receptor Agonist (NARA)

status: Public on Nov 20 2014

city: Indianapolis

first: James

last: MacKrell

state: IN

address: 355 East Merrill St

department: Musculoskeletal

institute: Eli Lilly & Company

summary:
High regenerative capacity of adult skeletal muscle relies on a self-renewing depot of adult stem cells, termed muscle satellite cells (MSCs).  A novel MSC line was isolated from the rat levator ani muscle and termed Levator Ani Satellite Cells (LASCs).
Androgen, a known mediator of overall body composition and specifically skeletal muscle mass, has been shown to regulate MSCs.  The use of non-steroidal androgen receptor agonists (NARA) aims to retain the beneficial influence of androgen on skeletal muscle, while circumventing undesirable cardiovascular and prostate-related side-effects.
Primary objectives: 1) Identify biomarkers of satellite cell growth and differentiation, 2) Characterize a novel muscle satellite cell line, 3) Understand the effects of androgen (NARA) on rat satellite cell activation and recruitment.

overall_design:
LASCs will be treated with one of the following conditions (N=4 for all groups):  1) 0.2% DMSO, 4 hours; 2)  10 nM NARA, 4 hours;  3) 0.2% DMSO, 48 hours; 4) 10nM NARA, 48 hours
RNA was extracted using the PerfectPure RNA isolation kit (5 Prime, Gaithersburg, MD).  Five micrograms of total RNA from each sample was labeled and hybridized to Affymetrix Rat Genome 230_2.0 microarrays according to Affymetrix protocols. Each microarray was washed and stained using an Affymetrix Fluidics Station 400 and scanned in an Affymetrix confocal GeneArray scanner. Affymetrix MAS5.0 software was used to scale data to a target intensity of 1500 and calculate transcript abundance (signal). Microarray signal intensities were generated by Affymetrix Expression Console using the MAS5 algorithm with targeted trimmed mean signal set to 1500. The gene chips were checked for quality control by their detection calls, chip pairwise correlation, and principal components analysis (PCA). Three chips (GSM1550754, GSM1550757, and GSM1550758) were identified as outliers and excluded from analysis for obvious low correlation with and deviating on PCA plots from the rest of the chips.

first: Venkatesh

last: Krishnan

first: Benjamin

last: Yaden

first: Keyue

last: Chen

first: Heather

last: Bullock

first: Henry

middle: U

last: Bryant