title: Post-zygotic structural variants in histologically normal breast tissue may predispose to sporadic breast cancer [SET 2]

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


title: Post-zygotic structural variants in histologically normal breast tissue may predispose to sporadic breast cancer [SET 1]

status: Public on Oct 01 2015

city: Uppsala

first: Chiara

last: Rasi

state: Sweden

address: Husargatan 3

department: Department of Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

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

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

overall_design:
We studied 282 female breast cancer patients that were assessed as affected by sporadic disease at the time of diagnosis and all underwent mastectomy. In total, 1162 UMs (uninvolved margin tissues), ranging from 1 to 14 UMs per patient, taken outside the location of clinically characterized index primary tumor, were analyzed on Illumina arrays. For each subject, DNA from at least one control tissue was also analyzed, which was predominantly blood DNA, alternatively skin-derived DNA. We also studied primary tumor (PT), or up to 3 primary tumor foci from patients with diagnosis of multifocal disease. This GEO project contains the genotyping profiles (processed and normalized data including Log R Ratio and B allele frequency) for these 1162 UMs used in the study. Information on phenotypes (age at diagnosis, tumor focality, tumor grade, tumor molecular phenotype) is also provided, whenever available.
SET1: 21 experiments runned on the platform GPL18636 (Illumina Human660W-Quad v1.0). Please note that GPL18636 on GEO has chromosome coordinates in the genome buid 36. Although, the identifiers in the matrix table 21_experiments_GPL18636_Human660w_hg19.txt), match the  GPL18636 IDs,  the chromosomal positions (column 3, “Position”) is reported in chromosomal build 37 (to allow directly comparisonwith all the other samples, which are runned on platforms that already support chromosome build 37).


title: Study of microRNA associated with gemcitabine’s anti-tumor effect

status: Public on Sep 15 2015

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: The miRNAs expression was markedly altered with the treatment of gemcitabine on human CCC cells in vitro.  And various miRNAs induced by gemcitabine may contribute to tumor regression in vitro .

overall_design: Using a custom microarray platform, we analyzed the expression levels of 1042 human miRNA probes in the cell lines in vitro that were treated with and without gemcitabine.

first: Yuka

last: Toyota

first: Tsutomu

last: Masaki


title: MicroRNA profiling of the developing mammary gland identifies miR-184 as a candidate breast tumour suppressor gene  (miRNA)

city: Sydney

first: Daniel

last: Roden

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute

summary: The study of mammalian development has offered many insights into the molecular aetiology of cancer. We previously used analysis of mammary morphogenesis to discover a critical role for GATA-3 in mammary developmental and carcinogenesis. In recent years an important role for MicroRNAs (miRNAs) in a myriad of cellular processes in development and in oncogenesis has emerged. In this study, microRNA profiling of stromal and epithelial cellular subsets microdissected from the developing mouse mammary gland revealed many microRNAs with expression restricted to various cellular subsets. MicroRNA-184 (miR-184) was exclusively expressed in epithelial cells and markedly upregulated during differentiation of the proliferative, invasive cells of the pubertal terminal end bud (TEB) into ductal epithelial cells in vivo and in FACS-sorted mammary stem cells (MaSCs) versus luminal epithelial cells. miR-184 expression was silenced in mouse tumour models compared to non-transformed epithelium and in a majority of breast cancer cell line models. Ectopic reactivation of miR-184 inhibited the proliferation and self-renewal of metastatic triple negative breast cancer (TNBC) cell lines in vitro and delayed tumour formation and reduced metastasis in vivo. Gene expression studies uncovered multi-factorial direct regulation of genes in the AKT/mTORC1 pathway by miR-184. In clinical breast cancer tissues, expression of miR-184 is lost in primary TNBCs while the miR-184 promoter is methylated in a subset of lymph node metastases from TNBC patients. These studies elucidated a new layer of regulation in the PI3K/AKT/mTOR pathway with relevance to mammary development and tumour proliferation and metastasis.

overall_design: micro-RNA expression analysis of TEBs, DUCTs and stroma from mouse mammary glands

first: Yuwei

last: Phua

first: Akira

last: Nguyen

middle: L

first: Ben

last: Elsworth

first: Iva

last: Nikolic

first: Jessica

last: Yang

first: Andrea

last: Mcfarland

first: Roslin

last: Russell

first: Warren

last: Kaplan

first: Mark

last: Cowley

first: Radhika

last: Nair

first: Elena

last: Zotenko

first: Shixiong

last: Tan

first: Carlos

last: Caldas

first: Susan

last: Clark

first: Hossein

last: Kouros-Mehr

first: Alexander

last: Swarbrick


title: Gene expression changes with viral infection in Agaricus bisporus

status: Public on Sep 14 2015

city: MAIDSTONE

first: KERRY

middle: STEVEN

last: BURTON

address: NEW ROAD, EAST MALLING

country: United Kingdom

institute: EAST MALLING RESEARCH

summary: Agaricus bisporus is a soil-inhabiting fungus which is cultivated for production of white button mushrooms. A disease of A. bisporus has been previously described with a range of disease symptoms (yield loss, pinning delay, cap distortions and cap browning) which has been given collective name of “Mushroom Virus X” (MVX). The causes of this disease are not clear however prior to this research an association was found between the disease and double-stranded RNA molecules in the mushroom fruitbodies. The experiment was designed to examine causes and host responses of the disease causing the Brown Cap symptom in the cultivated mushroom A. bisporus. This microarray experiment was performed before the Agaricus bisporus genome was sequenced. The gene sequences used to design probes were from known and novel A. bisporus sequences and sequences of transcript fragments identified by Suppression Subtractive Hybridization of non-symptomatic and virus-diseased A. bisporus mushroom fruitbodies. The A. bisporus mushroom fruitbodies were grown on composted wheat straw using commercial cultivation procedures. The gene expression comparison was made of RNA isolated from 32 mushroom fruitbodies (Agaricus bisporus) samples: 20 samples from 5 separate virus-infected commercial mushroom farms with crops displaying the brown symptom (4 replicate samples per farm) and 12 samples from a non-infected crop grown at the University of Warwick. The precise composition of the viral load was the subject of this and future research/papers. Abstract of Manuscript submitted to Applied and Environmental Microbiology: Characterizing the viral agents causing brown cap mushroom disease of Agaricus bisporus by Daniel Eastwood, Julian Green, Helen Grogan, and Kerry Burton (Paper #AEM01093-15). The symptoms of viral infections of fungi range from cryptic to severe but there is little knowledge of the factors involved in this transition of fungal/viral interactions. Brown Cap Mushroom Disease of the cultivated Agaricus bisporus is economically important and represents a model system to describe this transition. Differentially expressed transcript fragments between mushrooms showing the symptoms of Brown Cap Mushroom Disease and control white non-infected mushrooms have been identified and sequenced. Ten of these RNA fragments have been found to be up-regulated over a thousand-fold between diseased and non-diseased tissue but are absent from the Agaricus bisporus genome sequence and hybridise to double-stranded RNA’s extracted from diseased tissue. We hypothesize these transcript fragments are viral and represent components of the disease-causing agent, a bipartite virus with similarities to the family Partitiviridae. The virus fragments were found at two distinct levels within infected mushrooms, at raised levels in infected, non-symptomatic, white coloured mushrooms and much greater levels (3,500-87,000 times greater) in infected mushrooms exhibiting brown colouration. In addition, differential screening revealed 9 up-regulated and 32 down-regulated host Agaricus bisporus transcripts. Chromametric analysis was able to distinguish colour differences between non-infected white mushrooms and white infected mushrooms at an early stage of mushroom growth. This method may be the basis for an ‘on-farm’ disease detection assay.

overall_design: A gene expression comparison was made between diseased mushroom displaying the brown cap symptom with characteristic double-strand RNA profiles (banding pattern on gels) and non-symptomatic virus-free mushrooms. In total RNA was isolated from 32 mushroom fruitbody (Agaricus bisporus) samples: 20 samples from 5 separate virus-infected commercial mushroom farms with crops displaying the brown symptom (4 replicate samples per farm) and 12 samples from a non-infected crop grown at the University of Warwick. Commercially-grown mushrooms are produced in “flushes” at approximately weekly intervals. The samples were collected from commercial farms when symptoms were reported to us but these were from different flushes: Farm1 from the 2nd flush; Farm 2 from the 1st flush; Farm 3 from the 3rd flush; Farm 4 from the 1st flush; and Farm 9 from the 1st flush. To allow for comparisons on the basis of Flush Number, the non-infected mushrooms grown at the University of Warwick were sampled from the first, second and third flushes, 4 mushrooms sampled from each flush.

first: Daniel

middle: C

last: Eastwood

first: Julian

middle: M

last: Green

first: Helen

last: Grogan

first: Kerry

middle: S

last: Burton


title: Vibrio cholerae O395 toxSL33S vs toxSL33S delta rpoE

status: Public on Aug 26 2015

city: Hanover

first: Salvador

last: Almagro-Moreno

state: NH

address: 112 Vail Building

department: Microbiology and Immunology

country: USA

institute: Geisel School of Medicine at Dartmouth

summary: Transcriptional profiling of Vibrio Cholerae RpoE deletion mutant in toxSL33S mutation background

overall_design: Synchronized samples grown in virulence inducing conditions, strains independently grown and harvested

first: Michael

middle: Z

last: Root

first: Ronald

middle: K

last: Taylor

first: Carol

last: Ringelberg

first: Gabriela

last: Kovacikova


title: Post-zygotic structural variants in histologically normal breast tissue may predispose to sporadic breast cancer [SET 4]

first: Chiara

last: Rasi

overall_design:
We studied 282 female breast cancer patients that were assessed as affected by sporadic disease at the time of diagnosis and all underwent mastectomy. In total, 1162 UMs (uninvolved margin tissues), ranging from 1 to 14 UMs per patient, taken outside the location of clinically characterized index primary tumor, were analyzed on Illumina arrays. For each subject, DNA from at least one control tissue was also analyzed, which was predominantly blood DNA, alternatively skin-derived DNA. We also studied primary tumor (PT), or up to 3 primary tumor foci from patients with diagnosis of multifocal disease. This GEO project contains the genotyping profiles (processed and normalized data including Log R Ratio and B allele frequency) for these 1162 UMs used in the study. Information on phenotypes (age at diagnosis, tumor focality, tumor grade, tumor molecular phenotype) is also provided, whenever available.
The 201-300 samples out of 811 experiments runned on platform GPL18224 (Infinium HumanOmniExpressExome)


title: Linking transcriptional responses to organismal tolerance reveals mechanisms of thermal sensitivity in a mesothermal endangered fish

status: Public on Aug 25 2015

city: Davis

first: Lisa

last: Komoroske

state: CA

address: One Shields Ave

department: Wildlife, fish and conservation biology

institute: University of California, Davis

summary: We exposed adult delta smelt to varying levels of sublethal thermal stress to quantify the genes involved in their cellular stress response and identify sublethal stress thresholds

overall_design: Fourty-nine samples were run on fourty-nine arrays, with 3-6 replicates for each treatment or control

first: Richard

middle: E

last: Connon

first: Ken

last: Jeffries

first: Nann

middle: A

last: Fangue


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

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

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

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

last: Ross-Adams

first: Alastair

last: Lamb

first: Silvia

last: Halim

first: Mark

last: Dunning


title: Real-time quantitative PCR analysis of tomato bZIP genes under biotic stress and plant hormone treatments

status: Public on Aug 20 2015

city: Hangzhou

first: Dayong

last: Li

state: Zhejiang

address: 866 Yuhangtang Rd

department: Institute of Biotechnology

country: China

institute: Zhejiang University

summary: We used Bio-Rad laboratories, lnc. PCR assay panel to analyze expression levels of bZIP genes in various biotci stress and plant hormone treatments. Tomato (Solanum lycopersicum) cv. Suhong 2003 were reared in growth chambers at 24 ± 1 °C with a photoperiod of 14 h light/10 h dark and light intensity of 200 μE m2 s-1. For analysis of gene expression, 4-week-old tomato plants were treated by foliar spraying with 100 μM methyl jasmonate (MeJA), 100 μM 1-amino cyclopropane-1-carboxylic acid (ACC), 100 μM SA or 0.1% ethanol as a control and samples were collected at indicated time points after treatment. For analysis of gene expression in response to pathogen infection, whole plant inoculation assays for B. cinerea (spore density of 1×10 5 spores/mL) and vacuum infiltrated inoculation assays for Pst DC3000 along with corresponding mock inoculation controls were performed.

overall_design: The experiment was designed to gain insight into the temporal and spatial transcription patterns of 59 bZIP genes in tomato.The experiment was designed to examine the transcription patterns of 59 bZIP genes in tomato in response to two different biotic stresses (Botrytis cinerea, Pst DC3000) and three (SA, MeJA and ACC) plant hormone treatments.

first: D

middle: Y

first: F

last: Fu

first: H

middle: J

last: Zhang

last: Song


title: Longissimus cervicis muscle of beef steers with divergent Warner Bratzler Shear Force (WBSF) residuals following different post-mortem treatments (electrically stimulated v. non-stimulated)

status: Public on Aug 28 2015

city: College Station

first: Robert

middle: Neil

last: Vaughn

state: TX

address: 0965 Agronomy

department: Soil and Crop Sciences

institute: Texas A&M University

summary: Transcriptional profiling of bovine skeletal muscle comparing expression differences of a population of beef cattle selected for divergent response (shear force residuals) to post-mortem treatment (electrical stimulation)

overall_design: 4 condition experiment utilizing 47 total samples (originally 48, one sample could not be used). Samples were broken in to high/low groups based on residual WBSF following electrical stimulation (ES) and without electrical stimulation (NES). There are 4 groups based on residual WBSF: High-ES (12), Low-ES (11), High-NES (12), and Low-NES (12)

middle: N

first: Kelli

last: Kochan

first: Penny

last: Riggs


title: Differentially Expressed microRNAs in Bone Marrow Mesenchymal Stem Cell-derived Microvesicles in Young and Older Rats and Their Effect on Tumor Growth Factor-β1-mediated Epithelial-Mesenchymal Transition in HK2 cells

city: Nanjing

first: Yan

last: Wang

address: 300 Guangzhou Road

institute: the First Affiliated Hospital of Nanjing Medical University

summary: miRNA profiles of the Young-MSC-MVs and Old-MSC-MVs were analyzed with a quantitative PCR (qPCR)-based array of the whole rat genome. Further analysis revealed the expression of miR-344a, miR-133b-3p, miR-294, miR-423-3p, and miR-872-3p was significantly downregulated in Old-MSC-MVs than in Young-MSC-MVs (p<0.05).

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: miRCURY LNA Array (v.18.0) was used to identify differentially expressed miRNAs in BM-MSC-MVs of 3-month-old and 24-month-old Fisher344 rats.

first: Xuefeng

last: Sun

first: Weihong

last: Zhao


title: Transcriptome analysis of thermal adaptive E. coli (part 2)

status: Public on Aug 14 2015

city: Tsukuba

first: Bei-Wen

last: Ying

state: Ibaraki

address: 1-1-1 Tennoudai

institute: University of Tsukuba

type: Expression profiling by genome tiling array

summary: Two E. coli genotypes (type_II and type_III) that showing a mutation either within rpoH or upstream of groESL were isolated in the thermal adaptative evolution. Transcriptome analyses of the two genotypes exponentially growing at both regular and high temperatures were performed.

overall_design: Cells exponentially growing at 37ºC or 45ºC were collected for the transcriptome analysis. Every 3 biological replications were performed.

first: Kazuma

last: Yama

first: Tetsuya

last: Yomo


title: Mesenchymal stem cells use extracellular vesicles to outsource mitophagy and shuttle micro RNAs

status: Public on Aug 17 2015

city: Pittsburgh

first: Luis

last: Ortiz

state: PA

address: 100 Technology Drive Room 557

department: Environmental and Occupational Health

institute: University of Pittsburgh

summary: Background:  Mesenchymal stem cells (MSCs) and macrophages are fundamental components of the stem cell niche and function coordinately to regulate hematopoietic stem cell self-renewal and mobilization.  Recent studies indicate that mitophagy and healthy mitochondrial function are critical to the survival of stem cells but how these processes are regulated in MSCs is unknown.  Here we show that MSCs manage intracellular oxidative stress by targeting depolarized mitochondria to the plasma membrane via arrestin domain-containing protein 1-mediated microvesicles , which are then engulfed and re-utilized via a process involving fusion by macrophages resulting in enhanced bio-energetics.  Furthermore, we show that MSCs simultaneously shed miRNA-containing exosomes that inhibit macrophage activation by suppressing Toll-like receptor (TLR) signaling, thereby de-sensitizing macrophages to the ingested mitochondria.  Collectively, these studies mechanistically link mitophagy and MSC survival with macrophage function, thereby providing a physiologically relevant context for the innate immuno-modulatory activity of MSCs.

overall_design: Total RNA was isolated from 5 different human MSC donor populations or their exosomes using the Qiagen miRNeasy Mini Kit (PN 217004) according to the manufacturer’s instructions.  Samples were then analyzed using human microRNA microarrays from Agilent   (Version 3, PN: G4470C) and data analyzed using Agilent GeneSpring GX 11 software.

first: Giuseppe

last: DeIuliis


title: Post-zygotic structural variants in histologically normal breast tissue may predispose to sporadic breast cancer.

first: Chiara

last: Rasi

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

overall_design: Refer to individual Series


title: Virtual Microdissection of Pancreatic Ductal Adenocarcinoma Reveals Tumor and Stroma Subtypes.

status: Public on Sep 07 2015

city: Chapel Hill

first: Richard

last: Moffitt

state: NC

address: 450 West Drive

institute: University of North Carolina

summary: Pancreatic ductal adenocarcinoma (PDAC) remains a lethal disease with a 5-year survival of 4%. A key hallmark of PDAC is extensive stromal involvement, which makes capturing precise tumor-specific molecular information difficult. Here, we have overcome this problem by applying blind source separation to a diverse collection of PDAC gene expression microarray data, which includes primary, metastatic, and normal samples. By digitally separating tumor, stroma, and normal gene expression, we have identified and validated two tumor-specific subtypes including a â€œbasal-likeâ€ subtype which has worse outcome, and is molecularly similar to basal tumors in bladder and breast cancer. Furthermore, we define 'normal' and 'activated' stromal subtypes which are independently prognostic. Our results provide new insight into the molecular composition of PDAC which may be used to tailor therapies or provide decision support in a clinical setting where the choice and timing of therapies is critical.

overall_design:
Analysis of the landscape of gene expression in pancreatic adenocarcinoma. Data include 145 primary and 61 metastatic PDAC tumors, 17 cell lines, 46 pancreas and 88 distant site adjacent normal samples. Arrays represent distinct samples.

The SPOT column in the raw data file (linked to each sample record) contains Agilent feature extraction numbers (included in the 'GPL4133-20424.txt' linked to the platform records).

first: Yeh

last: Jen Jen


title: Comparative gene expression analyses identify luminal and basal subtypes of canine invasive urothelial carcinoma that mimic patterns in human invasive bladder cancer

city: West Lafayette

first: Deborah

last: Knapp

address: 625 Harrison Street

institute: Purdue University

summary: Microarrays were used to assay the gene expression profile of canine normal bladder from non-tumor bearing dogs and compared to that of bladder tumor in dogs.

overall_design: Work was conducted to compare gene expression array results between tissue samples from iUC and normal bladder in dogs. Affymetrix canine 2.0 chips were used to conduct the experiment.

first: Deepika

last: Dhawan

first: Melissa

last: Paoloni

first: Shweta

last: Shukradas

first: Dipanwita

last: Roy Choudhury

first: Bruce

last: Craig

first: José

last: Ramos-Vara

first: Noah

last: Hahn

first: Patty

last: Bonney

first: Chand

last: Khanna

middle: W


title: EAG2 potassium channel with evolutionarily conserved function as a brain tumor target

status: Public on Aug 09 2015

city: San Francisco

first: Charlie

last: Kim

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

summary: Microarray profiling of amplified total RNA isolated from FACS-sorted Drosophila neuroblasts

overall_design: 2 samples per group, RNA isolated and amplified. Hybridized as a one color experiment.

first: Juri

last: Reimand

first: Charles

first: Xi

last: Huang

first: Ye

last: He

first: Yuh

last: Jan

first: Lily


title: TDP-43 can directly affect splicing profiles and isoform production of genes involved in the apoptotic and mitotic cellular pathways

status: Public on Aug 11 2015

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary:
In recent times, high throughput screening analyses have broadly defined the RNA cellular targets of TDP-43, a nuclear factor involved in neurodegeneration. A common outcome of all these studies is that changing the expression levels of this protein can alter the expression of several hundred RNAs within cells. What still remains to be clarified is which changes represent direct cellular targets of TDP-43 or just secondary variations due to the general role played by this protein in RNA metabolism. Using a HTS-based splicing junction analysis we have now identified 162 splicing events that are consistent with being directly controlled by TDP-43. Validation of the data, both in neuronal and non-neuronal cell lines demonstrated that TDP-43 substantially alters the levels of isoform expression in four genes potentially important for neuropathology: MADD/IG20, STAG2, FNIP1, and BRD8. Most importantly, for MADD/IG20 and STAG2 these changes could also be confirmed at the protein level. These alterations were also observed in a cellular model that successfully mimics TDP-43 loss of function effects following its aggregation. These novel splicing events may represent potential biomarkers to predict disease onset, progression, and to test the efficacy of novel therapeutic agents to recover TDP-43 functional properties.
We have performed an HTS-based splicing junction analysis of a series of stable cell lines that lack TDP-43, overexpress this factor, or express an RNA-binding mutant, in order to find splicing events, potentially associated with neurodegenerativce diseases, regulated by this splicing factor.

overall_design:
Samples were analyzed in triplicate from:
The following samples were analyzed in triplicate: wild-type HEK-293 cells, siTDP43-treated HEK-293 cells, siTDP43-treated HEK-293 cells overexpressing a flagged-wildtype TDP-43, siTDP43-treated HEK-293 cells overexpressing a RNA-binding deficient mutant.

first: Emanuele

last: Buratti


title: Yeast mutants that allow long-distance transcriptional activation

status: Public on Aug 15 2015

city: Boston

first: Fred

last: Winston

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: In this study we isolated polygenic mutants that allow activation of a reporter in which the GAL1 UAS is 799 bp from the HIS3 TATA and open reading frame. Several different mutants were isolated, each with multiple mutations. The mutants were tested after growth on glucose, galactose, and raffinose.

overall_design: Two experimental replicates grown as described above except for samples 1.2 and 2.3b, which contain only one each: 1.2-sample 2 and 2.3a-sample 1.


title: Transgenic overexpression of Pla2g10 display alopecia and epidermal hyperplasia

status: Public on Aug 08 2015

city: Setagaya

first: Kei

last: Yamamoto

state: Tokyo

address: 2-1-6 kamikitazawa

department: Lipid Metabolism Project

institute: Tokyo Metropolitan Institute of Medical Science

summary: Microarray gene profiling of skin from PLA2G10-Tg mice in comparison with that from control mice yielded data for explaining the overall tendency of Tg skin to show hair follicle distortion and epidermal hyperplasia associated with hyperkeratosis in the absence of inflammation

overall_design: Pla2g10-Tg/+ mice and littermate controls (C57BL/6 background); 25-day old; skin; pooled from 4 mice for each genotype.

first: Yasumasa

last: Nishito

first: Makoto

last: Murakami


title: Influence of bovine virus diarrhoea virus on the transcriptome profile of bovine endometrium in response to bacterial lipopolysaccharide.

status: Public on Aug 05 2015

city: Hatfield

first: Zhangrui

last: Cheng

state: Hertfordshire

address: Hawkshead Lane

department: Production and Population Health

institute: Royal Veterinary College

summary: Infection with non-cytopathic bovine viral diarrhea virus (ncpBVDV) is associated with uterine disease and infertility. This study investigated the influence of ncpBVDV on immune functions of the bovine endometrium by testing the response to bacterial lipopolysaccharide (LPS) at the level of whole-transcriptomic gene expression. Analysis showed that approximately 30% of the 1,006 genes altered by LPS are involved in immune response.  Many innate immune genes that typically respond to LPS were inhibited by ncpBVDV including those involved in pathogen recognition, inflammation, interferon response, chemokines, tissue remodeling, cell migration and cell death/survival. Infection with ncpBVDV can thus compromise immune function and pregnancy recognition thereby potentially predisposing infected cows to postpartum bacterial endometritis and reduced fertility.

overall_design: Primary cultures of mixed epithelial and stromal cells derived from bovine endometrium were divided into 4 treatment groups (CONT; CONT+LPS; ncpBVDV; ncpBVDV+LPS) with n=6 separate batches of cells used for each treatment. After the cells were cultured for 4 days, they were infected with ncpBVDV for 4 days followed by the LPS treatments for 6 h. Total RNA in the cells were extracted using a Qiagen RNeasy Mini kit and analyzed using 24 Affymetrix Bovine Gene 1.1 ST Arrays. Processing, normalization and further analysis of the microarray data were performed using  RMA16 built in Genespring GX software version 12.5 (Agilent Technologies) with the annotation files provided by the company which had annotation of over 95% of the probes.

first: Chike

middle: F

last: Oguejiofor

first: D

last: Wathes

first: Ayimuguli

last: Abudureyimu

first: Olivia

last: Anstaett

first: Joe

last: Brownlie

first: Ali

last: Fouladi-Nashta


title: Analysis of gene expression and splicing after doxycycline-induced knockdown of SRSF3

status: Public on Aug 06 2015

city: Rockford

first: Xiaolong

state: IL

address: 1601 Parkview Ave.

department: Biopharmaceutical Sciences

institute: University of Illinois at Chicago

summary: SRSF3 is overexpressed in human invasive ovarian cancer and its overexpression is required for cancer cell growth and survival. To decipher the mechnisms behind the role of SRSF3 in ovarian cancer, we examined the gene expression and splicing in the ovarian cancer cell line that was engineered to express a doxycycline-induced SRSF3 siRNA, which was able to knockdown SRSF3 expression by 90% and induce apoptosis.

overall_design: Total RNAs extracted from A2780/SRSF3si2, a subline of ovarian cancer cell line A2780, treated with or without doxycycline at 0.1ug/ml for three days were analyzed using Affymetrix GeneChip® Human Exon 1.0 ST Array

first: Pei

last: Zhang


title: Real-time quantitative PCR analysis of tomato bZIP genes in various tissues

first: Dayong

last: Li

summary: We used Bio-Rad laboratories, lnc. PCR assay panel to analyze expression levels of bZIP genes in various tissues or organs. Tomato (Solanum lycopersicum) cv. Suhong 2003 were reared in growth chambers at 24 ± 1 °C with a photoperiod of 14 h light/10 h dark and light intensity of 200 μE m2 s-1. The roots, stem,leaves,  flower, and fruits were collected from flowering plants for tissue expression analysis.

overall_design: The experiment was designed to gain insight into the temporal and spatial transcription patterns of 59 bZIP genes in tomato.

first: F

last: Fu

first: H

last: Song


title: Analysis of the molecular dialogue between Botrytis cinerea and Vitis vinifera reveals a clear shift in defence mechanisms during berry ripening.

status: Public on Aug 10 2015

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

institute: INRAE

summary: Full transcriptomes of the Botrytis cinerea wild-type strain B0510 inoculated on mature grapevine berries (Marselan cultivar) at 16h, 24h, 48h, and in vitro were compared to identify B. cinerea genes diffentially expressed during the infection stages.

overall_design: Grapevine berries were inoculated with Botrytis cinerea conidia and samples were taken at 16h, 24h and 48 hours post-inoculation. An additional control sample corresponding to mycelium growing on static liquid minimal medium was included in the experimental design in order to identify genes that would be differentially expressed between in vitro and in planta growth conditions. 3-4 replicates were performed. The 13 total-RNA samples were used for hybridization on NimbleGen 4plex gene expression arrays (20,885 gene models from Botrytis cinerea with three 60-mer probes per gene).

first: Jani

last: Kellioniemi

first: Sophie

last: Trouvelot

first: Marie

last: Heloir

last: Simon

first: Berengere

last: Dalmais

first: Patrick

last: Frettinger

first: Agnes

last: Cimerman

first: Marc

last: Fermaud

first: Jean

last: Roudet

first: Sylvain

last: Baulande

first: Christophe

last: Bruel

first: Mathias

last: Choquer

first: Linhdavanha

last: Couvelard

first: Mathilde

last: Duthieuw

first: Alberto

last: Ferrarini

first: Victor

last: Flors

first: Pascal

last: Le Pecheur

first: Elise

last: Loisel

first: Guillaume

last: Morgant

first: Nathalie

last: Poussereau

last: Pradier

first: Christine

last: Rascle

first: Lucie

last: Trda

first: Benoit

last: Poinssot

first: Muriel

last: Viaud


title: RNA expression in fly thoraxes of 4 WT, 4 dCanA1 and 4 dCanA-14F calcineurin mutant fly lines

status: Public on Aug 04 2015

city: Cincinnati

first: Bruce

last: Aronow

state: OH

address: 240 Albert Sabin Way

department: Biomedical Informatics, Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary:
Canonical protein phosphatase 3 (Ppp3) / calcineurin signaling is central to numerous physiological processes. Here we provide evidence that calcineurin plays a pivotal role in controlling systemic energy and body weight homeostasis. Knockdown of calcineurin in Drosophila melanogaster led to a decrease in body weight, and energy stores, and increased energy expenditure.
D. melanogaster piggyBac transposon insertion mutants (Thibault et al., 2004) (PBac{WH}CanA1[f01787] (Calcineurin A1) and  PBac{WH}CanA-14F[f02374] (CanA at 14-F)) and the isogenic wildtype w1118 strain (BL-6326) were ordered from Exelixis Drosophila Stock Collection at Harvard Medical School.

overall_design: RNA was isolated from the thorax of 50 flies per sample. Whole genome tiling gene arrays were utilized to reveal distinctly deregulated gene patterns that appeared in both mutants (n=4, respectively) as compared to the WT controls (n=4).

first: Matthias

middle: H

last: Tschöp

first: Paul

middle: T

last: Pfluger


title: Transgenic overexpression of Pla2g2f at a level relevant to skin pathology display alopecia and psoriasis-like epidermal hyperplasia

first: Kei

last: Yamamoto

summary: Pla2g2f is dominantly expressed in the suprabasal layer of mouse epidermis. Microarray gene profiling supported the overall tendency of epidermal and sebaceous gland hyperplasia as well as alopecia in Pla2g2f-transgenic skin.

overall_design: Pla2g2f-Tg/+ mice and littermate controls (C57BL/6 background); 25-day old; skin; pooled from 4 mice for each genotype.

first: Yasumasa

last: Nishito

first: Makoto

last: Murakami


title: Formaldehyde exposure alters miRNAs expression profiles in olfactory bulb

city: hang zhou

first: guifa

last: li

address: Zhejiang University School of Medicine Department of Neurobiology

department: Department of Neurobiology

institute: Zhejiang University School of Medicine

summary: Neurotoxicity of formaldehyde (FA) in the human health attracted intensive studies Long-term exposure to FA leads to learning and memory decline and is responsible for the multiple chemical sensitivity (MCS) or sick building syndrome (SBS). It was cleared that Formaldehyde impairs Learning and Memory in Hippocampal. however ,it is unclear if FA can disturb the olfactory bulb function miRNAs alterations were related to environmental chemical exposure. It was reported that  FA inhale altered  miRNAs  expression in the nasal Epithelium and lung cells. In the present study, FA inhalation significatly alters miRNA expression profiles within olfactory bulb

overall_design: Eight week ICR male mouse. Mice were randomly assigned to three groups. The FA group exposed to 3ppm FA for six hours for consecutive 1 and 7days in a chamber which was described previously. The standard group was kept in same condition except the FA. After expose, both group mice were deeply anesthetized with isoflurane and decapitated. The OB was rapidly dissected

first: jing

last: yang


title: Aspergillus nidulans strains R21 and ∆gprH during growth in minimal media (MM) and carbon starvation

status: Public on Aug 01 2015

city: Ribeirao Preto

first: Neil

last: Brown

address: Av. do Cafe

country: Brazil

institute: USP

summary: Transcriptome of A. nidulans R21 and ∆gprH strains when grown on MM+1% glucose for 24 hours and transferred to MM with no carbon for 4 and 8 hours

overall_design: Three conditions: MM with glucose for 24 hours and MM without glucose for 4 and 8 hours. Two strains R21 and ∆gprH. Three biological repetitions of each point.

first: Gustavo

last: Goldman


title: A Global Transcriptome Analysis of BMSC from different confluences, But Gene Expression Profiling Suggested Comprised Pro-angiogenesis Effects

city: Bethesda

first: Jiaqiang

last: Ren

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

summary: Ex vivo expansion of Bone Marrow Stromal Cells (BMSC) is required to obtain clinical dose for cellular therapy, and different labs use different confluence in their practice, however, the impacts of 100% confluence on the biological properties of BMSC remain controversial. In this study, we detected the changes occurred to BMSCs when they reached 100% confluence, including viability, population doubling time (PDT), apoptosis, colony formation, immunosuppression, proteins in the culture supernatant, and surface markers; we also performed gene expression profiling and microRNA profiling on 50%, 80% and 100% confluent BMSCs. Our results showed that 100% confluent BMSCs had similar level of immunosuppression to 80% confluent BMSCs; they increased the expression of CD10, CD54, CD106, CD200, TLR4, but decreased CD49f and PODXL; we detected of 39 proteins in the culture supernatant, which displayed different patterns and an increase on the PEDF/VEGF ratio was observed with higher confluence. We identified 26 differentially expressed microRNAs, which were reported to be involved in the proliferation and differentiation of BMSC; and 2708 genes that were involved in extracellular matrix, cell adhesion, immune response and inflammatory response; particularly, angiogenesis inhibitor PEDF, and Wnt Singling inhibitors DKK1, DKK2, and DKK3 were up-regulated by 100% confluent BMSCs. These data suggest that 100% confluent BMSC may retain immunosuppressive activities but have comprised pro-angiogenesis effects.

sample_organism:
Homo sapiens
human gammaherpesvirus 4

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
human gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus macacae

overall_design: Design GEO: Gene expression profiling on BMSCs of 3 confluences (50%, 80% and 100%) from 5 healthy donors: 09FC37 (n=3), 09FC43 (n=3), 09FC44 (n=3), 09FC45 (n=3), 09FC49 (n=3) as biological repeats.


title: Expression of miRNA induced by SDF-1/CXCR4 system on oral cancer

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

institute: Toray Industries,Inc.

summary: We examined the metastasis-related miRNAs induced by SDF-1/CXCR4 system, using oral cancer cells.  Consequently, we identified 4 kinds of upregulated-miRNAs in B88-SDF-1.

overall_design: The metastasis-related miRNAs induced by SDF-1/CXCR4 system in oral cancer are largely unknown.  Thus, we examined the metastasis-related miRNAs induced by SDF-1/CXCR4 system, using four types of oral cancer cells; mock cells vs forced-expression of SDF-1cells and parental cells vs parental cells treated by SDF-1.

last: Kinouchi

first: Daisuke

last: Uchida


title: The effect of vitamin D supplementation on tumorigenesis in a thioacetamide (TAA)-induced rat intrahepatic cholangiocarcinoma model

city: Gueishan Township

first: Chun-Nan

last: Yeh

state: Taoyuan County

address: No.5, Fusing St.

department: General Surgery

country: Taiwan

institute: Chang Gung Medical Foundation

summary: In this study, we investigated the effect of vitamin D supplementation on tumorigenesis in a thioacetamide (TAA)-induced rat intrahepatic cholangiocarcinoma model as vitamin D is known to have a spectrum of anticancer activities. Using PET, we found that tumor formation and progression were suppressed in rats fed a diet supplemented with 6 IU/g vitamin D3(+6D) as compared to the group fed a 2 IU/g vitamin D3 diet (+2D) or controls. Microarray analysis of the tumors that arose revealed that vitamin D supplementation caused significant up- and down regulation in 21 and 16 genes, respectively.

overall_design: There are 9 tissue samples (3 rats in each group labeled as (+6), (+2) and control). Duplicate analysis were used for each sample.

first: Kun-Chun

last: Chiang

first: Kun-Ju

last: Lin

first: Li-Jen

last: Su

first: Tzu-Chen

last: Yen

first: Jong-Hwei

last: Pang

first: Atsushi

last: Kittaka

first: Chi-Chin

last: Sun

first: Miin-Fu

last: Chen

first: Yi-Yin

last: Jan

first: Horng-Heng

last: Juang

first: Ta-Sen

first: Tai


title: Bovine granulosa cells of dominant follicles at 60 days postpartum; effect of negative energy balance on transcriptome

status: Public on Jul 31 2015

city: Quebec

first: Annie

last: Girard

state: Quebec

address: 2440, boul. Hochelaga

department: Sciences animales

country: Canada

institute: Université Laval

summary: Granulosa cells of dominant follicles originating from dairy cows with severe negative energy balance (BHBH) or mild negative energy balance (BHBL) were compared. Mild negative energy balance (BHBL) is the reference.

overall_design: Two conditions experiment (BHBH and BHBL); Four pools of 3 biological replicates for each group (total = 12 cows for each group); Two technical replicates per pool (dye-swap).

first: Isabelle

last: Dufort

first: Marc-André

last: Sirard


title: Transcriptomic profiling of male European eel (Anguilla anguilla) livers at sexual maturity

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

summary: Gene expression analyses have been performed on liver tissue of sexually mature and immature males using microarrays. 60 eels were transferred to two independent temperature controlled recirculation water units connected to two 500 L cylindro-conical tanks (30 fish per tank) where the fish were acclimated to seawater (35 PSU salinity) over a 2 week period.Eel males in one of the seawater units were injected intramuscularly every week over a 140 day period with 2000 IU hCG/kg (human chorionic gonadotropin, Sigma–Aldrich Chemical) dissolved in 0.9% saline to induce sexual maturation. Eel males in the other recirculation unit were injected weekly over the same period with 0.9% NaCl (vehicle).At the end of the experiment, eels were anesthetized in a solution of 0.1mg/L tricaine methanesulfonate (MS-222, Sigma Aldrich) and blood samples collected into heparinized syringes. Tissues (brain, liver and gonads) were collected from sexually immature (n=12)  and sexually mature males (n=12).RNeasy Mini Kit (Qiagen) was used to extract RNA from the livers. Tissue samples were pooled and, therefore, each of the biological replicates (n= 4 sexually immature, n=4 sexually mature) contains tissue from three fish. Total RNA concentration was determined using the Nanodrop ND-100 spectrophotometer (NanoDrop Technologies) and sample integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Microarray analysis was conducted using an European eel-specific array consisting of a total of 14,913 probes based on a large collection of high-throughput transcriptomic sequences (Pujolar et al. 2012). Probe sequences and further details on the microarray platform can be found on the GEO database under accession number GPL15124. Data was normalized using a quantile normalization procedure using R (http://www.r-project.org)

overall_design: A comparative analysis of gene expression was conducted between sexually mature and immature males. Sample labelling and hybridization were conducted following the details in Pujolar et al. (2012). Hybridized slides were scanned at 5 µm resolution using an Agilent DNA microarray scanner. Slides were scanned at two different sensitivity levels (XDR Hi 100% and XDR Lo 10%) and the two linked images generated were analysed together. Data were extracted and background subtracted using the standard procedure in Agilent Feature Extraction (FE) software v. 9.5.1. Hybridization success was evaluated using flag values, excluding those intensities not equal to 1.

first: Milan

last: Massimo

first: Pujolar

last: Marti

first: Canário

last: Adelino

first: Churcher

last: M Allison


title: RNA Profiles Reveals Familial Aggregation of Molecular Subtypes in non-BRCA1/2 Breast Cancer Families

city: Odense C

first: Martin

middle: Jakob

last: Larsen

address: Sdr. Boulevard 29

department: Dept. of Clinical Genetics

country: Denmark

institute: Odense University Hospital

summary: In more than 70% of families with a strong history of breast and ovarian cancers, pathogenic mutation in BRCA1 or BRCA2 cannot be identified, even though hereditary factors are expected to be involved. It has been proposed that tumors with similar molecular phenotypes also share similar pathophysiological mechanisms. Grouping into molecularly homogeneous subsets may therefore be of potential value for further genetic analysis in order to identify new high penetrance breast cancer genes. In the current study, the aim was to investigate if global RNA profiling can be used to identify functional subgroups within breast tumors from families tested negative for BRCA1/2 germline mutations and how these subgroupings relate to different breast cancer patients within the same family. By analyzing a collection of 70 breast tumor biopsies from 58 families, we show that distinct functional subgroupings, similar to the intrinsic molecular breast cancer subtypes, exist. The distribution of subtypes was markedly different from the distribution found among BRCA1/2 mutation carriers. From 11 breast cancer families, breast tumor biopsies from more than one affected family member were included in the study. Notably, in 8 of these families we found that patients from the same family shared the same tumor subtype, showing a tendency of familial aggregation of tumor subtypes (p-value = 1.7e-3). Our finding indicates involvement of hereditary factors in these families in which family members may carry genetic susceptibility not just to breast cancer but to a particular subtype of breast cancer. Using our previously developed BRCA1/2-signatures, we identified 7 non-BRCA1/2 tumors with a BRCA1-like molecular phenotype and provide evidence for epigenetic inactivation of BRCA1 in three of the tumors. In addition, 7 BRCA2-like tumors were found. This is the first study to provide a biological link between breast cancers from family members of high risk non-BRCA1/2 families in a systematic manner, suggesting that future genetic analysis may benefit from subgrouping families into molecularly homogeneous subtypes in order to identify new high penetrance susceptibility genes.

overall_design: Gene expression profiling of 253 breast tumor samples. Breast tumor tissue from 125 patients with germline mutations in BRCA1 (n = 33) or BRCA2 (n = 22) or with no detectable germline mutation in BRCA1 or BRCA2 (n = 70) were included in the study. Serving as a representative control group, primary breast tumor samples (n = 128) were randomly selected among available samples originating from the same department and time period as for the hereditary samples. The study was conducted using Agilent-029949 Custom SurePrint G3 Human GE 8x60K Microarray platform.

first: Mads

last: Thomassen

first: Qihua

last: Tan

first: Anne-Vibeke

last: Lænkholm

last: Bak

first: Kristina

middle: P

last: Sørensen

first: Mette

last: Andersen

first: Torben

last: Kruse

first: Anne-Marie

last: Gerdes


title: Increased virulence mediated by subinhibitory concentrations of Cefotaxime (CTX)

status: Public on Jul 23 2015

city: valdivia

first: Cristia

middle: Felipe

last: Molina

state: --- Select a state ---

address: Universidad Austral, Isla teja

department: Bioinformatics

country: Chile

institute: AUSTRAL-omics

summary: Identification of mutants under negative selection mediated by a non-lethal concentration of CTX

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Two condition experiment, transposon library exposed during 3 h to CTX  vs. Non-exposed control transposon library (paralelly growing). Biological replicates: 3 control, 3 antibiotic exposed cells, independently grown and harvested. One replicate per array.

first: R

middle: C

last: Molina-Quiroz

first: C

last: Silva


title: Ogataea angusta DL1 strain: Control vs. hac1 deletion mutant in exponential growth

status: Public on Jul 22 2015

city: Seoul

first: Hye Yun

last: Moon

state: Seoul

address: , 221 Heukseok-dong, Dongjak-gu

department: Department of Life Science

country: South Korea

institute: Chung-Ang university

summary: Transcriptional profiling of hac1 deletion mutant compared to wild type (control).

overall_design: Wild type vs. hac1 deletion mutant of Ogataea angusta DL1 strain in exponential growth. Two biological replicates, with dye-swaps.

first: Hy

first: Hyu

last: Kang


title: Pichia angusta DL1 strain: Control vs. ER stress

summary: Transcriptional profiling of ER stress condition comparing control (untreated), dithiothreitol (DTT) treated, or tunicamycin (TM) treated conditions on P. angusta DL1 strain.

overall_design: Six-condition experiment: normal condition vs. ER stress condition (TM 30, 60, 120min; DTT 30, 60, 120min) in P. angusta DL1 strain. Independently grown and harvested. Two replicates per array.

first: Hye

first: Hyun


title: An antifungal benzimidazol reveals novel sterols after inhibition of Erg11.

status: Public on Jun 30 2015

city: Stuttgart

first: Steffen

last: Rupp

address: Nobelstr. 12

department: MBT

country: Germany

institute: Fraunhofer IGB

summary: Fungal infections are a serious health problem in clinics especially in the immune-compromised patient. Disease ranges from widespread superficial infections like vulvovaginal infections to life-threatening systemic candidiasis. Especially for systemic mycoses only a limited arsenal of antifungals is available. The most commonly used classes of antifungal compounds used include azoles, polyenes and echinocandines. Due to emerging resistance to standard therapy and significant side effects and high costs for several antifungals.,there is a medical need for new antifungals in the clinic and general practice. In order to expand the arsenal of compounds with antifungal activities we previously screened a compound library, using a new type of activity-selectivity (AS) assay analysing both the antifungal activity and the compatibility with human cells at the same time. One compound, ((S)-2-(1-aminoisobutyl)-1-(3-chlorobenzyl) benzimidazole (EMC120B12)), showed high antifungal activity against several species of pathogenic yeasts including C. glabrata and C. krusei, species which are highly refractory to antifungals, especially to the commonly used azoles. Here we could show by transcriptional profiling and sterol analysis that the target of this new antifungal compound is the ergosterol pathway. The effects of EMC120B12 on sterol biosynthesis mimic those of fluconazole, strongly indicating that EMC120B12 also targets ERG11 like the azols. But not only the marker sterol 14 methylergosta 8,24(28) dien 3β,6α diol accumulated in C. krusei under EMC120B12 treatment, but also hitherto unknown related sterols. The novel sterols have a 3β,6α diol structure. Furthermore, this is the first time that a benzimidazole structure has been shown to result in a block of the sterol pathway by accumulating marker sterols connected to ERG11 inactivation.

overall_design: In total, three biological replicates were performed. All experiments were performed as dye swaps. Thus, in total 18 arrays have been hybridzed. Hybridization experiments included an untreated reference sample and a sample of cells treated with either ((1S)-1-[1-(3-chlorobenzyl)-1H-benzimidazol-2-yl]-2-methylpropyl-amine) (EMC120B12), Fluconazole or Nocodazole. The array included one technical replicate of each probe.

first: Petra

last: Keller

first: Christoph

last: Müller

first: Isabel

last: Engelhardt

first: Ekkehard

last: Hiller

first: Karin

last: Lemuth

first: Karl-Heinz

last: Wiesmüller

first: Franz

last: Bracher


title: Gene Expression in Taxol Resistance SKOV3 Cells (I)

status: Public on Jul 16 2015

city: Kwei-San

first: Ching-Kuey

middle: Chuck

last: Chao

state: Tao-Yuan

address: 259, Wen-Hwa 1 Rd

department: Biochemistry and Molecular Biology

institute: Chang-Gung University

summary: To investigate the differences in gene expression between parental SKOV3 cells and the two taxol-resistant cell lines SKOV3/Tx50 and SKOV3/Tx600.

overall_design: Two Taxol resistant cell lines were established by stepwise increasing Taxol concentration. RNA from these resistant lines and its parental SKOV3 cells were labeled with Cy5 and were hybridized to oligo DNA array. Signals were scanned and analyzed to find out the candidate genes involved in Taxol resistant mechanism.

first: S

middle: L

last: Huang

first: N

last: Sun

first: H

last: Lu


title: A Pitx2-miRNA pathway modulates cell proliferation in myoblasts and skeletal-muscle satellite cells and promotes their commitment to a myogenic cell fate

status: Public on Jun 10 2015

city: Jaen

first: Francisco

middle: J.

last: Esteban

state: Jaen

address: Campus Las Lagunillas s/n

department: Experimental Biology

country: Spain

institute: University of Jaen

summary: The acquisition of a proliferating cell status from a quiescent state as well as the shift between proliferation and differentiation are key developmental steps in skeletal-muscle stem cells (satellite cells) to provide proper muscle regeneration. However, how satellite-cell proliferation is regulated, though, is not fully understood. Here, we report that the c-isoform of the transcription factor Pitx2 increases cell proliferation in myoblasts by down-regulating the miRNAs miR-15b, miR-23b, miR-106b, and miR-503. This Pitx2c-miRNA pathway also regulates cell proliferation in early-activated satellite cells, enhancing the Myf5+ satellite cells and thereby promoting their commitment to a myogenic cell fate. This study reveals unknown functions of several miRNAs in myoblast and satellite-cell behaviour and thus may have future applications in regenerative medicine.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: mirVana microarrays (Ambion) were used to profile microRNA signature at different Pitx2 overexpression conditions, namely two different doses (4 and 8 µg CMV-Pitx2c plasmid, respectively) after 24 hours of  transfection in SOL8 skeletal myogenic cells. 20 µg of total RNA was used to hybridize two distinct microRNA microarrays on each condition analyzed.

first: Estefanía

last: Lozano-Velasco

first: Daniel

last: Vallejo

first: Chris

last: Doherty

last: Hernández-Torres

first: Diego

last: Franco

first: Amelia

last: Aránega


title: Effect of pH on gene expression in two glucosyl ceramide (GlcCer) mutant strains of Cryptococcus neoformans H99

status: Public on May 30 2015

city: Stony Brook

first: Maurizio

last: Del Poeta

state: NY

address: 150 Life Science Building

department: Molecular Genetics and Microbiology

institute: Stony Brook University

summary: Background  The sphingolipid Glucosylceramide (GlcCer) and factors involved in the fungal GlcCer pathways were shown earlier to be an integral part of fungal virulence, especially in fungal replication at 37°C, in neutral/alkaline pH and 5% CO2 environments (e.g. alveolar spaces). Two mutants (null mutants’ delta-gcs1 and delta-smt1 lacking glucosylceramide synthase 1 gene and C9 sphingolipid methyltransferase 1 gene respectively) of this pathway were attenuated in virulence and have a growth defect at the above-mentioned conditions. These mutants with either no or structurally modified GlcCer located on the cell-membrane have reduced membrane rigidity, which may have altered not only the physical location of membrane proteins but also their expression, as the pathogen’s mode of adaptation to changing need. Importantly, pathogens are known to adapt themselves to the changing host environments by altering their patterns of gene expression.   Results   By transcriptional analysis of gene expression, we identified six genes whose expression was changed from their wild-type counterpart grown in the same conditions, i.e they became either down regulated or up regulated in these two mutants. The microarray data was validated by real-time PCR, which confirmed their fold change in gene expression. The 6 genes we identified, viz siderochrome-iron transporter (CNAG_02083), monosaccharide transporter (CNAG_05340), glucose transporter (CNAG_03772), membrane protein (CNAG_03912), membrane transport protein (CNAG_00539), and sugar transporter (CNAG_06963), all of which are membrane-localized and have significantly altered gene expression levels. Therefore, we speculate that these genes function either independently or in tandem with a structurally modified cell wall/plasma membrane resulting from the modifications of the GlcCer pathway and thus possibly disrupt trans membrane signaling complex, which in turn contributes to Cryptococcal osmotic, pH, ion homeostasis and its pathobiology.  Conclusion   Gene expression microarrays identified 6 genes by gene set enrichment analysis and validated by qRT-PCR, which are involved in the trans membrane signaling network in Cryptococcus neoformans, controlling the rigidity of the membrane in neutral-alkaline pH and therefore the pathobiology of the fungus in these conditions.

overall_design: WT vs ∆smt1 at pH 4, WT vs ∆smt1 at pH 7.2±0.2, WT vs ∆gcs1 at pH 4, WT vs ∆gcs1 at pH 7.2±0.2

first: Arpita

last: Singh

first: Antonella

last: Rella

first: John

last: Schwacke

first: Caterina

last: Vacchi-Suzzi

first: Chiara

last: Luberto


title: Pichia angusta DL1 strain: Control+ER stress vs. hac1+ER stress

first: Hye Yun

last: Moon

summary: Transcriptional profiling of Control and hac1 deletion mutant in ER stress condition on P. angusta DL1 strain.

overall_design:
WT+ER stress vs. hac1 deletion mutant+ER stress.
Six-condition experiment: Control+ER stress (TM 30, 60, 120min; DTT 30, 60, 120min) vs. hac1 deletion mutant+ER stress condition (TM 30, 60, 120min; DTT 30, 60, 120min) in P. angusta DL1 strain. Independently grown and harvested. Dye-swapping.

first: Hy

first: Hyun

last: Kang


title: The expression profiles of extracellular matrix-related genes in the presence or absence of EBI3 in the PCR array

status: Public on May 08 2015

city: Kumamoto

first: Hideo

last: Kudo

address: Chuo-ku, Honjo, 1-1-1

department: Dermatology

institute: Kumamoto University

summary:
We performed a PCR array of 84 ECM-related genes using RNA obtained from dermal fibroblasts stimulated with or without EBI3.
18 of the 84 genes were upregulated and 22 genes were downregulated in EBI3-treated fibroblasts in comparison with untreated cells.

overall_design: In the present study, we examined the involvement of the IL-12 family cytokines in the expression of the extracellular matrix.


title: Differential microRNA expression profiling between human induced pluripotent stem cells (iPSCs) and human neonatal dermal fibroblasts (NDFs).

status: Public on May 09 2015

city: Brno

first: Tomas

last: Barta

address: Pekarska 53

department: International Clinical Research Center (FNUSA-ICRC)

country: Czech Republic

institute: St. Anne's University Hospital Brno

summary: We have employed microRNA expression profiling of iPSCs and NDFs as a discovery platform to identify microRNAs involved in reprogramming of NDFs to iPSCs.

overall_design: Using Agilent human miRNA (V3) 8X15K microarray, we performed microRNA profiling of iPSCs at passage 20 and NDFs at passage 5

first: Majlinda

last: Lako

first: David

last: Montaner


title: Copy number variation of human intestinal stem cells with different passage in culture (two pedigrees, passage 5, 10, 15 and 20)

status: Public on May 29 2015

city: Houston

first: Frank

last: McKeon

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

summary: Stem cells of the gastrointestinal tract, pancreas, liver, and other columnar epithelia collectively resist cloning in their elemental states. Here we demonstrate the cloning and propagation of highly clonogenic, “ground state” stem cells of the human intestinal and colon. To assess the genomic stability of our intestinal stem cells, we serially passaged two independent intestinal stem cell pedigrees derived from the ileum of one late fetal demise case and tested them after 50 (passage 5; P5), 100 (P10), 150 (P15) and 200 days (P20) of continuous proliferation. DNA from cells at these passages cells was analyzed by SNP array based copy number variation analysis (CNV).  Although at P15 and P20,  partial aneuploidy in some of pedigrees was observed, there are almost no CNVs at P5 and P10 in both pedigrees.

overall_design: SNP array based copy number variation study was performed for 2 pedigrees from human fetal ileal stem cells (passage 5, 10, 15 and 20) to assess genomic stability at chromosomal level.

first: Xia

last: Wang

first: Yusuke

last: Yamamoto

first: Ting

last: Zhang

first: Wa

last: Xian


title: Activation of defense pathways in Scots pine bark after feeding by Pine Weevil (Hylobius abietis)

status: Public on Apr 01 2015

city: Helsinki

first: Tommaso

last: Raffaello

address: Latokartanonkaari 7 PO Box 27

department: Forest Sciences

country: Finland

institute: University of Helsinki

summary: Coniferous trees  use the oleoresin, a mixture of non-volatile non-volatile diterpene acids and a large (20-50%) volatile fraction of mono- and sesquiterpenes, as a defence tool against damaging herbivores and pathogens. Volatilization of monoterpenes increases  viscosity of oleoresin and finally leading to polymerization of resin and a formation of protective solid plug. Resin storing conifers form an important source of volatile organic compounds (VOCs) mainly dominated by volatile monoterpenes. In the atmosphere, conifer VOCs react with ozone and OH and nitrous oxide radicals forming secondary organic compounds. This project seeks a better understanding of the genetic control of conifer defences and the role of monoterpenoid compounds under biotic stresses.

overall_design: Two separate samples were analysed (control-unchallenged and treatment-infected with the insect). There were a total of 3 biological replicates for the control samples and another set of three  biological replicates for the treatment samples.

first: Andriy

last: Kovalchuk

first: Emad

last: Jaber

first: Susanna

last: Keriö

first: Rajendra

last: Ghimire

first: Walt

last: Lorenz

first: Jeffrey

last: Dean

first: Jarmo

middle: K

last: Holopainen

first: Fred

middle: O

last: Asiegbu


title: Gene Expression Profiling of Hormonal Regulation Related to the Residual Feed Intake of Holstein Cattle

status: Public on Mar 24 2015

city: nanjing

first: yumeng

last: xi

state: jingsu

address: tongwei street 6

institute: nanjing agriculture university

summary: An accumulation of over a decade of research in cattle has shown that genetic selection for decreased residual feed intake (RFI), defined as the difference between an animal’s actual feed intake and its expected feed intake, is a viable option for improving feed efficiency and reducing the feed requirements of herds, thereby improving the profitability of cattle producers. Hormonal regulation is one of the most important factors in feed intake. To determine the relationship between hormones and feed efficiency, we performed gene expression profiling of hormonal regulation in whole blood of Chinese Holstein cattle with low and high RFI coefficients. 857 differential expression genes (from 24683 genes) were found. Among these, 415 genes were up-regulated and 442 genes were down-regulated in the low RFI group. The gene ontology (GO) search revealed 6 significant terms and 64 genes associated with hormonal regulation, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) selected the adipocytokine signaling pathway, insulin signaling pathway. In conclusion, the study indicated that the molecular expression of genes associated with hormonal regulation differs in dairy cows, depending on their RFI coefficients, and that these differences may be related to the molecular regulation of the leptin-NPY and insulin signaling pathways.

overall_design: Gene chip analysis of the Bovine Genome Array was performed by an outside service provider (LC-Bio.CO., LTD, Houston, U.S.). Total RNA from the two blood specimens was individually hybridized with two gene chips.

first: Xi

last: Yumeng


title: Gene Expression Profile of H1299 Cells from Tissue of 4D Model

status: Public on Mar 12 2015

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: We have developed a 4D lung cancer model that forms perfusable tumor nodules. We determined if the model could be modified to mimic metastasis. We modified the 4D lung cancer model by seeding H1299 cells via the trachea only to the left lobes of the acellular lung matrix. The model was modified so that the tumor cells can reach the right lobes of the acellular lung matrix only through the pulmonary artery as circulating tumor cells (CTC). We determined the gene expressions of the primary tumor, CTCs, and metastatic lesions using the Human OneArray chip. All cell lines formed a primary tumor in the left lobe of the ex vivo 4D lung cancer model. The CTCs were identified in the media and increased over time. The CTC gene signature predicted poor survival in lung cancer patients. A unique set of genes were significantly expressed in CTC compared to the primary tumor and metastatic lesion.  The 4D lung cancer model can isolate tumor cells in three phases of tumor progression. This 4D lung cancer model may mimic the biology of lung cancer metastasis and may be used to determine its mechanism and potential therapy in the future.

overall_design: We compared the gene expression profile (Human OneArray v6 chip) of primary tumor, CTCs, and metastatic tumors from the ex vivo (4D) model seeded with H1299 for different days.

first: Min

last: Kim

first: Dhruva

last: Mishra


title: Gene Expression in Taxol Resistance SKOV3 Cells

first: Ching-Kuey

last: Chao

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

overall_design: Refer to individual Series


title: Modulation of the immune system during postpartum uterine inflammation [expression]

status: Public on May 07 2015

city: Auckland

first: Caroline

middle: Gwendolyn

last: Walker

state: Outside the US or Canada

address: 3A symonds st

department: University of Auckland

country: New Zealand

institute: DairyNZ Ltd

summary: Post-partum uterine inflammation (endometritis) is associated with lower fertility at both the time of infection and after the inflammation has resolved. It was hypothesized that aberrant DNA methylation may be involved in the sub-fertility associated with post-partum uterine inflammation. The objective of this study was to characterize genome-wide DNA methylation and gene expression in the endometrium of dairy cows with sub-clinical endometritis. Endometrial tissues were obtained at 29 days post-partum (n=12) and Agilent two-colour microarrays were used to characterize transcription and DNA methylation profiles. Analyses revealed 1,856 probes to be differentially expressed in animals with subclinical endometritis (SUI, n=6) compared with control cows (NUI, n=6, P<0.05, Storey Multiple testing correction). No significant associations among DNA methylation and gene expression were detected. Further analysis of gene expression data using GeneGo Metacore and Gene Set Enrichment Analysis identified several pathways and processes enriched in the comparison. Several pathways that are involved in the innate immune response were enriched in SUI cows. Consistent with the presence of microorganisms in the uterus, there was enrichment for the Toll-like receptor (TLR) signaling pathway, including increased expression of the transcription factor NFKB1, the pro-inflammatory cytokines IL1A and IL1B, downstream chemokines, cytokines, and acute phase and antimicrobial proteins in the endometrium of SUI cows. Furthermore, the chemokine signaling pathway was enriched in SUI cows, with increased expression of genes that attract cells of the innate immune system. Increased expression of IL-8 and CXCL6, chemotactic factors for recruitment of neutrophils along with the immune cell surface marker PTPRC in SUI cows is consistent with the greater number of polymorphonuclear cells present in the uterus of these cows. Several antimicrobial peptides (LAP, TAP, DEFB1, DEFB10, DEFB103B, DEFB7) and acute phase proteins, including SAA3, LBP, and the complement gene CFB, had greater expression in SUI cows. Gene expression profiles in cows with subclinical endometritis in this study indicate that the immune response is activated, potentially resulting in a local pro-inflammatory environment in the uterus. If this period of inflammation is prolonged, it could result in tissue damage or failure to complete involution of the uterus, which may create a sub-optimal environment for future pregnancy.

overall_design: 12 animals were enrolled in this study, 2 samples from each animal were used for microarray analysis consisting of caruncular and intercaruncular endometrium. A reference design was used for hybridisation, whereby each of the 24 samples were hybridised to individual microarrays along with a pooled reference sample. The reference sample was generated by taking equal concentrations of each of the experimental samples.

middle: G


title: Modulation of the immune system during postpartum uterine inflammation

type: Methylation profiling by genome tiling array


title: Expression profiles of microRNA in bovine raw milk exosome and supernatant without exosome

status: Public on Mar 09 2015

city: Zama-City

first: Hirohisa

last: Izumi

state: Kanagawa-Pref.

address: 1-83, 5-Chome, Higashihara

department: Nutrition Research Department

country: Japan

institute: Morinaga Milk Industry Co., Ltd.

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


title: An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network.

status: Public on Mar 20 2015

city: New York

first: Patrick

last: Eichenberger

email: pe19@nyu.edu, arb401@nyu.edu

state: New York

address: 12 Waverly Place

department: Center for Genomics and Systems Biology

institute: New York University

summary: Organisms from all domains of life use gene regulation networks to control cell growth, identity, function, and responses to environmental challenges. Although accurate global regulatory models would provide critical evolutionary and functional insights, they remain incomplete, even for the best studied organisms. Efforts to build comprehensive networks are confounded by challenges including network scale, degree of connectivity, complexity of organism-environment interactions, and difficulty of estimating the activity of regulatory factors. Taking advantage of the large number of known regulatory interactions in Bacillus subtilis, we use new methods to integrate transcriptomics data with computational tools to simultaneously estimate transcription factor activities and learn a substantially expanded transcriptional regulatory network for this bacterium. To assess the accuracy of our model we tested 2030 predictions and confirmed 1485 regulatory interactions (36% of the full model), thus significantly increasing our understanding of various cell processes, such as spore formation.

overall_design: 260 samples including biological replicates. See sample description for more detailed experiment design.


title: Medicago truncatula roots treated with symbiotic lipochitooligosaccharides

status: Public on Mar 23 2015

city: Hannover

first: Helge

last: Küster

address: Herrenhäuser Str. 2

department: Institut für Pflanzengenetik

institute: Leibniz Universität Hannover

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula


title: Expression profiles of microRNA in bovine raw milk exosome and supernatant without exosome [mRNA array]

summary: We have reported that microRNAs are present in human, bovine, and rat milk whey. Milk whey miRNAs were resistant to acidic condition and to RNase. Thus, milk miRNAs were thought to be present packaged into membrane vesicles like exosome. However, body fluid miRNAs have been reported that there are in different forms. To clarify which miRNAs species are exist in exosome and which species are exist in another form, we used bovine raw milk and purified total RNA from exosome fraction and ultracentrifugated supernatant fraction, and analyzed by miRNA microarray.

overall_design: Three bovine raw milk samples were prepared and mixed equally. These raw milks are usually used for R&D in our laboratory. For example, trial manufacturing.


title: Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas

status: Public on Feb 20 2015

city: Nantes

first: Rossana

last: Sussarellu

address: Rue de l'Ile d'Yeu

department: Ressources Biologiques et Environnement

institute: Ifremer

summary: Originating from Northeast Asia, the Pacific oyster Crassostrea gigas has been introduced into a large number of countries for aquaculture purpose. Following introduction, the Pacific oyster has turned into an invasive species in an increasing number of coastal areas, notably in Northern Europe. To explore adaptation on reproductive traits of population considered as invasive, we set up a common garden experiment based on the comparison of progenies from two populations of Pacific oyster sampled in France and Denmark. A female-biased sex-ratio and a higher condition index were observed in the Danish progeny, possibly reflecting an evolutionary reproductive strategy to increase the potential success of natural recruitment in recently settled population. Using multifarious statistical approaches and accounting for sex differences we identified several genes differentially expressed between the Danish and French progenies, and with an intermediate expression level in hybrids (additive behavior). Candidate transcripts included mRNA coding for sperm quality and insulin metabolism known to be implicated in coordinated control of reproduction. Our results suggest adaptation of invasive populations during expansion acting on reproductive traits, and in particular on a female-biased sex-ratio, fertility and gamete quality.

overall_design: A common garden experiment was performed in order to compare progenies from two populations of Pacific oyster sampled in France and Denmark and their hybrids. Progenies were reared under standard hatchery and nursery conditions until gonadal maturation. The employed arrays were Agilent 60-mer 4x44K custom microarrays, containing 31,918 C. gigas ESTs, designed by Dheilly et al. (2011).

first: R

first: A

last: Huvet

first: L

last: Fast Jensen

first: S

last: Lapègue

first: V

last: Quillien

first: C

last: Lelong

first: F

last: Cornette

first: N

last: Bierne

first: P

last: Boudry


title: Identification of Replication Timing Domains Using DNN-HMM

status: Public on May 25 2015

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

type:
Third-party reanalysis
Other

summary:
Purpose: Sixteen GSM Samples from GSE34399 was used to identify four different types of replication timing domains.

Methods: 1. Chromosome 1 of Bj_Rep1 was manually annotated. 2. We developed a new supervised method called DNN-HMM (Deep Neural Network-Hidden Markov Model), and used the manual annotation as the training set to learn a model. 3. The model learnt in Step 2 was used to divide the un-annotated Repli-seq datas into four different replication domains (early replication domain, down transition zone, late replication domain, up transition zone).

Result: We used DNN-HMM to identify four different replication timing domains respectively in fifteen cell lines. The accuracy of identification was about 87%, and the overlapping percentage of two independent replicates of Bj cell line was about 83%.

Data File Formats :(bed)
chrom - The name of the chromosome
chromStart - The starting position of the feature in the chromosome
chromEnd - The ending position of the feature in the chromosome
category - The domain identified (denoted by: ERD, short for early replication domain; DTZ, short for down transition zone; LRD, short for late replication domain; UTZ, short for up transition zone)

overall_design: Repli-seq datas from GSE34399 were used as the raw datas. After mapping and normalization, the signals from six cell cycle fractions: G1/G1b, S1, S2, S3, S4, G2 (six fraction profile) were merged into a matrix. The six-dimensional matrix then was used as input of DNN-HMM to identify replication timing domains.

first: Feng

last: Liu


title: Characterization of Gene Expression in hepatic stellate cell (HSC)

status: Public on Dec 31 2014

city: ShangHai

first: Yang

last: Bu

address: 180 Fenglin Road

institute: Liver Cancer Institute, Zhongshan Hospital, Fudan University

summary: The HOA OneArray® 60-mer, oligonucleotide microarray consists of a total of  probes covering 31,747genes of human. Through a validation study, total RNA isolated from HSC were used for comparison of gene expression profiles via microarray examination. A list of significantly differentially expressed genes was generated; 1,205  genes were  up-regulated genes, and1,323 genes were  down-regulated genes.

overall_design:
The Phalanx microarray platform is based upon the hybridization of a single labeled sample (derived from RNA), followed by one-channel detection. The intensity of the hybridization signal is used to determine target concentration. In order to validate the technical quality of each probe in our arrays, we carried out 6 independent hybridizations on samples representing two different treatments.
HSC cells treated with Syy (a small compound that can inhibit exocrine of hepatic stellate cells) or control.

first: Qing

middle: A

last: Jia


title: Identification of the gene(s) responsible for ocular abnormalities of Hirosaki Small Eye Rat (HiSER)

status: Public on Dec 13 2014

city: Aomori

first: Naoki

last: Nanashima

state: Aomori

address: 58-1 Mase, Hamadate

department: Department of Nutrition

institute: Aomori University of Health and Welfare

summary: HiSER, established in our laboratory, exhibits ocular abnormalities including opacity, lens involution, and retinal detachment. To identify a causative gene(s) of the HiSER phenotype, microarray analysis was performed between HiSER and normal (SDR) eyes.

overall_design: Total RNA was extracted from HiSER and normal (SDR) eyes, and subjected to microarray analysis.


title: Maternal Plane Of Nutrition During Late Gestation And Weaning Age Alter Offspring Transcriptome Profiles Of Longissimus Muscle In Angus × Simmental

status: Public on Feb 03 2015

city: Urbana

first: Sonia

middle: Josefina

last: Moisá

state: IL

address: 1207 W. Gregory Dr.

department: Animal Sciences

institute: University of Illinois

summary: We evaluated if a higher plane of maternal nutrition during late gestation and weaning age alters the offspring’s Longissimus muscle (LM) transcriptome. A microarray analysis was performed in LM samples of early (EW) and normal weaned (NW) Angus × Simmental calves born from cows that were grazing endophyte-infected tall fescue/red clover pastures with no supplement (low plane of nutrition (LPN)), or supplemented with 2.3 kg of dried distiller’s grains with solubles and soyhulls (70% DDGS/30% soyhulls) (medium plane of nutrition (MPN)) during the last 90 days of gestation. Biopsies were harvested at 78, 187 and 354 days of age. Bioinformatics analysis highlighted that offspring transcriptome did not respond markedly to cow plane of nutrition, resulting in only 13 differentially expressed genes. However, weaning age and a high-starch diet strongly impacted the transcriptome, especially the immediate activation of the lipogenic program in EW steers. In addition, between 78 and 187 days of age, these animals had an activation of the innate immune system due presumably to macrophage infiltration in intramuscular fat. Between 187 and 354 days of age (i.e. the fattening phase), NW steers had an activation of the lipogenic transcriptome machinery, while EW steers had a clear gene transcription inhibition. The latter appears to have occurred through the epigenetic control of histone acetylases, which were down-regulated. Higher cow plane of nutrition alone affected 35 genes in the LM of steers that underscore the presence of a mechanism of macrophage infiltration likely originating from localized oxidative stress as a result of increased levels of hypoplasia and hypertrophy in LM.

overall_design: A subset of 20 Angus x Simmental beef cows from the University of Illinois Dixon Springs Agriculture Center (DSAC) in Simpson, IL, were selected from a group of animals utilized in a parallel study75. Main effects evaluated were maternal plane of nutrition during late gestation and postnatal management of the offspring. Three months prior to the projected parturition date cows were assigned to treatments (low or medium plane of nutrition) in a split-plot design. Low plane of nutrition (LPN) was achieved by grazing endophyte-infected tall fescue/red clover pastures during July, August, and September with no supplement. Medium plane of nutrition cow diet (MPN) was achieved by grazing endophyte-infected tall fescue/red clover pastures supplemented with 2.3 kg of dried distiller’s grains with solubles and soyhulls (70% DDGS/30% soyhulls). Angus x Simmental steer calves were randomly assigned to early or normal weaning treatments within each gestational treatment. This allowed for 10 animals for each postnatal treatment and 5 animals of each of the interactions of gestational × postnatal treatments. At 78 ± 2 days postpartum, early-wean offspring were weaned, transported to Urbana Beef Unit, and adapted to a high-starch diet until they had ad libitum consumption. At 187 ± 2 days postpartum, normal-wean offspring were weaned and transported to Urbana Beef Unit. All offspring were co-mingled among treatments. LM biopsies were sampled from a subset of 5 animals per gestational × postnatal treatment at time of early weaning (~78 days) and at time of normal weaning (~187 days), and during the last week prior to harvest (~ 354 days). After normal weaning, all offspring were placed on a common, corn grain-based high-starch finishing diet that is typical of industry management (CP% = 18.1, NDF% = 25.3, ADF% = 14.3, crude fat % = 5.1). All the offspring in the study were harvested at a commercial packing plant when they reached the selected end point target back fat thickness of 1.1 cm. Reported final body weight (BW) was calculated from hot carcass weight using a 62% dressing percentage. In the present study, we used a transcriptome-wide bovine microarray (Agilent-015354 Bovine Oligo Microarray-4x44K) that contains 21,475 unique genes and transcripts of Bos Taurus, with two probes per gene. The methods used for hybridization and scanning were according to manufacturer’s protocols and Loor et al45. The microarray data were deposited in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/gds) with accession number GSE-XXXX. GeneSpring GX (Agilent Technologies) was used for data visualization and preliminary data mining. Subsequently, the entire microarray data set with associated statistical P-values were imported into Ingenuity Pathways Analysis ® (IPA, www.ingenuity.com) in order to examine the number of activated and inhibited differentially expressed genes (DEG). Entrez Gene IDs were used to identify individual sequences. Data from the microarray analysis were normalized for dye and microarray effects (i.e., Lowess normalization and array centering) and used for statistical analysis. The MIXED procedure of SAS (SAS Institute, Inc., Cary, NC, USA) was used for statistical analysis. Fixed effects were treatment (early weaning, normal weaning), diet (low and medium cow plane of nutrition), time (78, 187, and 354 days of age), first, second and third order interactions between diet, time and treatment, and dye (Cy3, Cy5) and random effects included steer and microarray. Raw P values were adjusted using Benjamini and Hochberg’s false discovery rate (FDR). Bioinformatics analysis of microarray data was performed using DIA 10 and information from the freely-available online databases Kyoto Encyclopedia of Genes and Genomes (KEGG) and Database for Annotation, Visualization, and Integrated Discovery (DAVID) v6.7 databases. A list of gene identifiers (Entrez Gene IDs) was uploaded all at once to extract and summarize functional annotations associated with groups of genes or with each individual gene. The significance value associated with biological processes and pathways is a measure of the likelihood that the distribution of DEG in these pathways and biological processes is due to chance. The significance is expressed as a P-value, which is calculated using the right-tailed Fisher's Exact Test and adjusted using FDR. Details of the DIA approach and its validation have been reported previously. The interpretation of the bioinformatics analysis was performed following the same approach as our previous study.

middle: J

first: Daniel

last: Shike

first: Lindsay

last: Shoup

first: Sandra

last: Rodriguez Zas

first: Juan

last: Loor


title: Microarray analysis of gene expression profiles in PBHA-treated THP-1 cells after LPS stimulation

status: Public on Nov 17 2014

city: Taipei

first: George

last: Hsiao

address: No. 250, Wu-Hsing Str

department: Pharmacology

institute: Taipei Medical University

summary:
Using microarray analysis, 219 differentially expressed genes were isolated between the LPS group and LPS/PBHA treatment-group (fold change > or < 1.5). These genes were analyzed by KEGG system to reveal the important issues.
The analyses of gene ontology were shown that the genes of the specific classes “Chemokine signaling pathway”, ”Cytokine-cytokine receptor interaction”, ”RIG-I-like receptor signaling pathway”, ”Leukocyte transendothelial migration”, and “MAPK signaling pathway” showed markedly different patterns between both groups by KEGG analysis system.

overall_design: In this study presented here, human THP-1 cells were pretreated with only vehicle (resting group), vehicle and LPS  (50 ng/ml), or PBHA (10 μM) and LPS (50 ng/ml). After stimulation, the total cellular RNAs were manipulated for analyses of gene expression.

first: Wan-Ru

last: Chang


title: AMPK activation exerts anti-senescence effect in human follicle dermal papilla cells

status: Public on Nov 01 2014

first: Guang-Huar

last: Young

state: Taiwan (TWN)

address: 6F.-3, No.21, Ln. 583, Ruiguang Rd., Neihu Dist., Taipei City 114, Taiwan (R.O.C.)

department: Scientific Research

summary: We investigated the role of AMPK activation in the progression of senescence in HFDPCs. The anti-senescence effects of adenine, a recently identified AMPK activator, were determined in a comparison with AICAR, a pharmacological AMPK activator, in HFDPCs. The results showed that either adenine or AICAR induced phosphorylation of Thr172 of AMPK in HFDPCs. As revealed by microarray analysis, significant changes of gene expression pattern were observed in the high-passage HFDPCs compared with that at lower passage level.

overall_design: A chip study using total RNA recovered from three separate wild-type cultures of Human follicle dermal papilla cells (HFDPCs) and three separate cultures of a triple adenine-treated cells.

first: Han-Min

last: Chen


status: Public on Sep 11 2014

city: Guangzhou

first: Xiaochun

last: Bai

state: Guangdong

address: No.1838, North Guangzhou Avenue

department: Department of Cell Biology

institute: Southern Medical University

summary: To screen miRNAs specifically regulated by mTORC1 or mTORC2, a global miRNA expression profile in MCF-7 cells treated with rapamycin or PP242 (mTORC1/2 kinase inhibitor) was developed using microarray.

overall_design: control,  rapamycin or PP242 treated human MCF-7 cells were harvested 48h post-treatment and subjected to total RNA extraction.


title: Influence of Sex on Basal and Dickkopf-1 Regulated Gene Expression in the Bovine Morula

status: Public on Aug 06 2014

city: Gainesville

first: Anna

middle: Carolina

last: Denicol

state: FLORIDA

address: 28 NW 35th Terrace

institute: University of Florida

summary: Sex affects function of the developing mammalian embryo as early as the preimplantation period. There were two goals of the current objective. The first was to determine the degree and nature of differences in gene expression between female and male embryos in the cow at the morula stage of development. The second objective was to determine whether DKK1, a molecule known to alter differentiation of the blastocyst, would affect gene expression differently for female and male morulae. In Experiment 1, female and male embryos were treated with DKK1 at Day 5 after insemination. Morulae were harvested 24 h after treatment, pooled in groups of 20 for microarray analysis and RNA subjected to analysis of gene expression by microarray hybridization. There were 662 differentially expressed genes between females and males and 128 of these genes had a fold change ≥ 1.5 between the two sexes. Of the genes upregulated in females, 49.5% were located in the X chromosome. Functional analysis predicted that cell survival was greater in female embryos. Experiment 2 involved a similar design except that transcripts for 12 genes previously reported to be affected by sex, DKK1 or the interaction were quantified by quantitative polymerase chain reaction. Expression of all genes tested that were affected by sex in experiment 1 was affected in a similar manner in Experiment 2. In contrast, effects of DKK1 on gene expression were largely not repeatable in Experiment 2. The exception was for the Hippo signaling gene AMOT, which was inhibited by DKK1. In Experiment 3, embryos produced by fertilization with unsorted sperm were treated with DKK1 at Day 5 and abundance of transcripts for CDX2, GATA6, and NANOG determined at Days 5, 6 and 7 after insemination.  There was no effect of DKK1 on expression of any of the three genes.  In conclusion, female and male bovine embryos have a different pattern of gene expression as early as the morula stage, and this is due to a large extent to expression of genes in the X chromosomes in females. Differential gene expression between female and male embryos is likely the basis for increased resistance to cell death signals in female embryos and disparity in responses of female and male embryos to changes in the maternal environment.

overall_design: Bovine embryos produced with X- or Y-sorted sperm were cultured in vitro and treated with vehicle or DKK1 at day 5 of development and harvested at day 6 for RNA isolation, amplification and hibridization to Affymetrix Bovine Gene 1.0 ST arrays. The study was done in 5 replicates using pools of 20 morulae for each treatment.

first: Beatriz

middle: S

last: Leão

first: Kyle

middle: B

last: Dobbs

first: Gisele

middle: Z

last: Mingoti

first: Peter

last: Hansen