title: Gene expression profiles of Vcap xenograft tumors with chemical or physical denervation.

status: Public on Nov 30 2017

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

country: USA

institute: Baylor College of Medicine

summary: Carcinoma VCaP tumors that evolve in denervated rat prostate glands exhibited a significantly altered gene expression profile and phenotype as compared with VCaP tumors that evolve in the normal, innervated rat prostate gland. Interestingly, unilateral denervation resulted in a reduction in tumor size relative to control and the reduction was more pronounced with botox (chemical denervation) as compared with MPG excision (physical denervation). Chemical and Physical denervation yield similar gene expression profiles.

overall_design: VCaP human prostate cancer cells were grown as tumor xenografts. The effect of denervation on the tumors was assessed with botox (chemical denervation) and MPG excision (physical denervation).

first: Michael

last: Ittmann

first: Olga

last: Dakhova

first: Gustavo

last: Ayala


title: Genome-wide transcriptome analysis of the wild type compared to the deletion and overexpression mutants of the global regulator of secondary metabolism Lae1 in Fusarium fujikuroi

status: Public on Nov 05 2017

city: Freising

first: Ulrich

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

country: Germany

institute: Technische Universität München

summary:
We performed genome-wide transcriptome analyses of the Fusarium fujikuroi wild type compared to the ∆lae1 and OE:lae1 mutants under nitrogen limiting and nitrogen sufficient conditions
Lae1 was shown to be a master regulator of secondary metabolite gene clusters in F. fujikuroi. Deletion of the gene resulted in down-regulation, while overexpression resulted in up-regulation of several gene clusters, partially even under otherwise repressing conditions.

overall_design: 3 strains (WT; ∆lae1; OE:lae1) were analysed, each with 2 biological replicates

last: Güldener

first: Martin

last: Münsterkötter

first: Bettina

last: Tudzynski


title: Decoding the global transcriptomic profile under extreme manganese toxicity

status: Public on Nov 01 2017

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: To achieve extreme manganese stress, we used DmntP E. coli strain. We identified the pathways that are altered under manganese stress. Mainly, manganese altered the metabolism of iron in the cell. Therefore, we have shown that iron supplementation mitigates manganese toxicity. Overall, our data explains the basis of manganism in higher organisms.

overall_design: Escherichia coli were grown in LB, LB + manganese, or LB + manganese + iron.

first: Dipak

last: Dutta

first: Gursharan

last: Kaur

first: Vineet

last: Kumar

first: Amit

last: Arora


title: Gene expression profiles of normal and tumor tissues from denervated prostate and intact prostate .

summary: The phenotype and genotype of the tumors that arise in denervated prostates is not a measure of the effects of denervation on established tumors. Rather, it is a measure of their ability to escape the regulatory influence of the neural microenvironment and hence develop a resistance phenotype to denervation. This applies to human prostate cancer that arose in prostates with spinal cord injury. Our results indicate that tumors arising in denervated prostates have a significantly altered gene profile as compared to tumors arising in intact prostates.

overall_design: Gene expression profiles of normal and tumor tissues from denervated prostate and intact prostate (four groups, N=1 for each). All profiles were compare to the noncancer, intact prostate profile.


title: Mitochondrial DNA haplotypes induce differential patterns of DNA methylation that result in differential chromosomal gene expression patterns

city: Clayton

first: Justin

middle: C

last: St. John

state: Vic

address: 27-31 Wright St

department: Centre for Genetic Diseases

country: Australia

institute: Hudson Institute of Medical Research

summary: Mitochondrial DNA (mtDNA) haplotypes are associated with phenotypes and disease. To understand how mtDNA haplotypes induce these characteristics, we used four embryonic stem cell lines that have the same set of chromosomes but possess different mtDNA haplotypes. We show that mtDNA haplotypes influence changes in chromosomal gene expression and affinity for nuclear-encoded mtDNA replication factors to modulate mtDNA copy number, two events that act synchronously during differentiation. Global DNA methylation analysis showed that each haplotype induces distinct DNA methylation patterns, which, when modulated by DNA demethylation agents resulted in skewed gene expression patterns that highlight the effectiveness of the new DNA methylation patterns established by each haplotype. The haplotypes differentially regulate α-ketoglutarate, a metabolite from the TCA cycle that modulates the TET family of proteins, which catalyse the transition from 5-methylcytosine (DNA methylation) to 5-hydroxymethylcytosine (DNA demethylation). Our outcomes show a direct link between mtDNA haplotypes and DNA methylation profiles.

overall_design: 4 different mouse ES cell lines, distinguished by their mtDNA genome. 3 biological replicates of each cell line.

last: St John

first: William

last: Lee

first: Jodee

middle: A

last: Gould


title: miRNA expression data in unstimulated and TGF-β1-stimulated lung fibroblasts

city: Groningen

first: Jennie

last: Ong

address: Hanzeplein 1

country: Netherlands

institute: University Medical Center Groningen

summary: Lung fibroblasts play an important role in extracellular matrix homeostasis and this process is mainly regulated by transforming growth factor-beta (TGF-β). Hence, lung fibroblasts are postulated to play a crucial role in aberrant lung tissue repair and remodeling, which is a main factor in lung diseases like COPD. In this study, the effect of TGF-β1 on the miRNA expression in parenchymal lung fibroblasts is investigated.

overall_design: Primary parenchymal lung fibroblasts of 9 control subjects were cultured. After serum starving for 24 hrs, the fibroblasts were stimulated with and without TGF-β1 (100 U/ml TGF-β1, equivalent to 3.1 ng/ml) for 24 hours. The RNA was isolated using TRIzol according to the protocol of the manufacturer. The RNA samples were then hybridized with the Human GeneChip miRNA 1.0 array (Affymetrix).

first: Wim

last: Timens

first: Vijay

last: Rajendran

first: Arjan

last: Algra

first: Avrum

last: Spira

first: Marc

middle: E

last: Lenburg

first: Joshua

middle: D

last: Campbell

first: Maarten

last: van den Berge

first: Dirkje

middle: S

last: Postma

first: Anke

last: van den Berg

first: Joost

last: Kluiver

first: Corry-Anke

last: Brandsma


title: The mRNA and microRNA (miR) transcriptome of lung neutrophils during S. pneumoniae pneumonia in wild type (WT) mice

city: Chapel Hill

first: Claire

middle: M.

last: Doerschuk

state: NC

address: Marsico Hall 7205 CB#7248

department: Marsico Lung Institute

institute: University of North Carolina at Chapel Hill

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

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

overall_design: Refer to individual Series


title: The mRNA and microRNA (miR) transcriptome of lung neutrophils during S. pneumoniae pneumonia in wild type (WT) mice [mRNA]

summary:
These studies profiled the expression of mRNAs and microRNAs (miRs) in lung neutrophils in WT mice during S. pneumoniae pneumonia and performed in depth in silico analyses.
Lung neutrophils were isolated 24 hours after intratracheal instillation of PBS or S. pneumoniae, and mRNAs and miRs differentially expressed (DE) between S. pneumoniae- and PBS-treated samples were identified using microarrays.

overall_design: Lung neutrophils were isolated from WT mice 24 hours after intratracheal instillation of Streptococcus pneumoniae (SP) or an equivalent volume of phosphate-buffered saline (PBS).  mRNA expression was profiled using Mouse Gene 1.1 ST arrays (Affymetrix, Santa Clara, CA) which cover over 26,000 RefSeq transcripts.  microRNAs were profiled using SurePrint G3 Mouse miRNA 8X60K Microarray kits (Agilent, Santa Clara, CA) designed based on miRbase release 17.

first: John

last: Gomez

first: Hong

last: Dang

middle: M


title: DNA methylation profiling reveals common signatures of tumorigenesis and defines epigenetic prognostic subtypes of canine Diffuse Large B-cell Lymphoma

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

summary: In order to assess methylation profiles of dogs affected by DLBCL, a canine CpG microarray platform was developed. Probe design was carried out by the Agilent bioinformatic support team using proprietary prediction algorithms to locate CpG Islands on C. familiaris draft genome as deposited on Ensembl database (CanFam 3.1) and to design high quality oligo-probes. Microarray probes were selected in order to provide the highest possible coverage of dog genome. CDS regions and CpG islands were given top priority. A total of 170,000 probes (60mers, sense orientation) were designed on both CpG and CDS regions. In details, 102,000 probes were designed targeting a total of 36,807 CpG regions while 68,000 probes were directed against 672 CDS; average base pare tiling was 90 bp. Microarray probes were synthesized in situ using the Agilent non-contact ink-jet technology with a 4 x 180K format.

overall_design: Comparative analysis of methylation profiles of lymph nodes from n 37 canine DLBCLc and n 7 control dogs. Enriched-fraction and total gDNA (reference) obtained from 44 lymph node samples (37 cDLBCLs and 7 control dogs) were labelled independently with cyanine 5-deoxyuridine triphosphate (dUTP) and cyanine 3-dUTP, respectively. Sample labeling was performed by using SureTag Complete DNA Labeling Kit (Agilent Technologies) following the manufacturer’s recommendations.

first: Luca

last: Aresu


title: DNA methylation profiling of mouse tissues

status: Public on Nov 03 2017

city: Gdansk

first: Pawel

last: Sachadyn

address: Narutowicza 11/12

department: Molecular Biotechnology and Microbiology

country: Poland

institute: Gdansk University of Technology

type: Methylation profiling by genome tiling array

summary: The aim of the study was to find genomic regions that show differences in DNA methylation status between the MRL/MpJ mouse, which show enhanced regeneration response, and two control mouse strains C57BL/6J and BALB/c.

overall_design: genome-wide DNA methylation profiling in a collection of tissues (ears, heart, spleens, livers, bone marrows) of C57BL/6J, BALB/c and MRL/MpJ mouse

first: Paweł


title: Changes in the MicroRNA Expression Pattern Contribute to HIV-1 Tat-mediated Protection against Apoptosis and Impaired Cell Proliferation in CD4+ T Cells

status: Public on Nov 09 2017

city: Belfast

first: Guillermo

last: López-Campos

state: Northern Ireland

address: 97 Lisburn road

department: Centre for Experimental Medicine

country: United Kingdom

institute: Queen's University of Belfast

summary: HIV-1 infection changes the miRNA expression pattern in CD4+ T lymphocytes and its main regulator, Tat, has been appointed as an RNA silencing suppressor (RSS). Our group previously described that full-length Tat protects CD4+ T cells against FasL-mediated apoptosis and delays T-cell proliferation. Now we analyzed by microarrays and qRT-PCR the changes in the miRNA expression pattern of Jurkat cells induced by the intracellular expression of the two-exon Tat101 protein or the first-exon Tat72 in order to elucidate their role in the anti-apoptotic and anergic state exerted by Tat. It was determined that the expression of specific miRNAs such as hsa-miR-21, hsa-miR-222, hsa-miR-29a, and hsa-miR-1290 was up-regulated in Jurkat-Tat101. These miRNAs were related to the high activity of several transcription factors related to Tat such as NF-kB, SP1 and STAT3, and they repressed the expression of target mRNAs encoding proteins related to apoptosis and cell proliferation such as PTEN, PDCD4 and CDKN1B. In fact, mostly Jurkat-Tat101 showed an arrest at G2 phase and an impaired cytokinesis, resulting in giant, multilobulated nuclear cells. All these mechanisms would contribute to the role of Tat in HIV-1 immunosuppression and persistent infection, and the presence of Tat second exon would be essential.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: One microgram of total RNA extracted from triplicate independent samples of each Jurkat-Tat101, Jurkat-Tat72, and control cell lines was subjected to specific labeling of miRNAs using miRCURY LNA™ microRNA Hy3/Hy5 Power labeling kit (Exiqon, Vedbaek, Denmark), according to manufacturer’s instructions.

first: María

last: Sánchez-del Cojo

last: López-Huertas

first: Mercedes

last: Bermejo

first: Elena

last: Mateos

first: Sara

last: Rodríguez-Mora

first: José

last: Alcamí

first: Mayte

last: Coiras


status: Public on Nov 26 2017

city: Xiamen

first: Qi-Fan

last: Zheng

state: Fujian

address: South Xiang'an Road

department: Medical collage

country: China

institute: Xiamen University

type: Genome binding/occupancy profiling by genome tiling array

summary:
Subset heterogeneity of the mononuclear phagocyte system (MPS) is controlled by defined transcriptional networks and programs; however, the dynamic establishment of programs that control broad, orchestrated expression of transcription factors (TFs) during the progression of monocyte-into-phagocyte (MP) differentiation remains largely unexplored. By combining chromatin immunoprecipitation assays with gene expression profiling (ChIP-on-Chip), we show the extensive trimethylation of histone H3 lysine 4 (H3K4me3) as well as histone H3 lysine 27 (H3K27me3) occupancy with broad footprints at the promoters of MP differentiation-related TFs, such as HOXA and FOXO genes, KLF4, IRF8 and others. The rapid repression of HOXA genes was closely associated with the MP differentiation program. H3K4me3 participates in regulating HOXA genes at mild and terminal differentiation periods, while H3K27me3 maintains low-level expression of HOXA genes at phagocytic maintenance periods. Furthermore, the reprogramming of H3K27me3 plays a major role in the up-regulation of KLF4 and FOXO genes during MP differentiation. Importantly, the pharmacological inhibition of H3K4me3 and/or H3K27me3 strikingly promotes the differentiation programs of THP-1 and K562 cells as well as primary bone marrow-derived progenitors. Together, these findings elucidate mechanisms crucial to the dynamic establishment of epigenetic memory, which is central to the maintenance of the MP differentiation blockade.
THP-1 cells: control and 50 ng/ml PMA (Phorbol 12-myristate 13-acetate) treated for 72 h were collected for H3K4me3 and H3K27me3 ChIP-on-chip.

overall_design: H3K4me3 and H3K27me3 ChIP-on-chip detection in THP-1 cells: control vs. 50 ng/ml PMA treated for 72 h. Biological replicates: For H3K4me3, 3 control replicates, 3 PMA treatment replicates. For H3K27me3, no replicate.


title: Evaluation of CGH changes in different metastatic populations

status: Public on Nov 15 2017

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

type: Genome variation profiling by genome tiling array

summary: For many breast cancer (BCa) patients, symptomatic bone metastases appear after years or even decades of latency. How metastatic cells disseminate, and how micrometastatic lesions remain dormant and undetectable, are major questions in cancer research. Here we identify and functionally analyse a molecular mechanism involved in the bone metastatic latency of estrogen receptor (ER)+ BCa.

overall_design: Cells growing in the mouse for 170 days were compared with the initial population using Human CGH 3x720K Whole Genome Tiling 3.0 array

first: Sylwia

last: Gawrzak


title: Mapping alterations spatially and temporally during early stages of breast tumourigenesis [aCGH]

status: Public on Nov 02 2017

city: Toronto

first: Susan

last: Done

state: Ontario

address: 200 Elizabeth St. Rm 11E-228

department: Laboratory Medicine and Pathobiology

country: Canada

institute: University of Toronto

summary: Identifying genomic alterations that precede tumourigenesis of breast tumours will allow us to better understand tumour development and heterogeneity. In particular, by obtaining and profiling normal-epithelium samples at various distances from the tumour, we can draft both a spatial and temporal map of the genomic events and transcriptomic alterations that occur along the mammary duct (leading up to and including the tumour).

overall_design: Dataset consisting of 9 patients with breast cancer, from which multiple normal epithelium samples were obtained from along the duct leading to the tumour,  one sample from the contralateral duct, and a sample from the tumor itself

first: Moustafa

last: Abdalla


title: Gene expression analysis of kidney primary tubular epithelial cells (PTECs), SETD2-KD PTECs,  PBRM1-KD PTECs and ccRCC derived cell lines

city: GRONINGEN

first: Jun

last: Li

state: Netherlands

address: Esdoornlaan

department: Genetics

summary: Transcriptional profiling of human WT-PTECs, SETD2-KD PTECs, PBRM1-KD PTECs, and 10 different ccRCC derived cell lines. ccRCC derived cell lines showed distict expression signatures as compared to PTECs, some of them also present in SETD2-KD PTECs, and/or PBRM1-KD PTECs.

overall_design: Three PTECs of different origins were transduced with shRNA constructs against SETD2 (sh1 and sh2), or PBRM1 (sh-PB1 or sh-PB2), or with a non-targeting (NT) sequence. The PTECs were harvested when they were still proliferating, the immortalized ccRCC cell lines were mantained more than 10 passages after arrival.

first: Klaas

last: Kok

first: Anke

last: van den Berg

first: Rolf

middle: H

last: Sijmons

first: Helga

last: Westers

first: Joost

last: Kluiver

first: Jan

last: Osinga

first: Maaike

middle: B

last: van Werkhoven

first: Marc

last: Seelen

first: Debora

last: de Jong

first: Martijn

last: Terpstra


title: Expression profiling of SMMC-7721 cells: stably express lncRNA-PRAL vs control

status: Public on Nov 24 2017

city: shanghai

first: shu-han

last: sun

address: 800 Xiang-Yin Road

institute: Second Military Medical University

summary: lncRNA-PRAL induced transcriptional changes in SMMC-7721

overall_design: Two-condition experiment, control (AV-CON) vs lncRNA-PRAL expression (AV-PRAL). Each has 3 biological repeats.

first: Fu

last: Yang

first: Shu-han

last: Sun


title: Expression profiling of QSG-7701 and SMMC-7721 cells: stably express lncRNA-PRAL vs control


title: Low Serum Level of miR-485-3p Predicts Poor Survival in Patients with Glioblastoma Multiforme

city: Guangzhou

first: Nuoqing

last: Weng

state: Guangdong

address: 651，Dongfengdong road

institute: State Key Laboratory of Oncology in South China,Sun Yat-sen University

summary: We used microarrays to perform systematic profiling of human microRNAs in serum from glioblastoma multiforme (GBM)  patients to find potential biomarkers. By comparing the serum microRNA profiles of the GBM patients and healthy volunteers, potential biomarkers for GBM were investigated.  Using a custom microarray platforms containing 1843 species of miRNAs, we previously identified 19 serum miRNAs with differential expression in GBM patients.

overall_design: 30 microarrays containing 1843 human microRNAs were used to screen for potential biomarkers with significant differential expression levels between 22 GBM patients and 8 healthy volunteers.

first: Shao-Xiong

last: Wu

first: Hui-Yun

last: Wang

first: Zhi-Qiang

first: Mei-Yin

last: Zhang


title: Expression data in Human rectal mucosa before and after an dietary intervention with casein, soy protein or maltodextrin

status: Public on Nov 27 2017

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

summary:
The objective of the sudy is to evalute the effects of quantity and quality of protein intake on large intestine mucosa
We used microarrays to investigate gene expression in rectal biopsies before and after the diet

overall_design: Rectal biopsies were collected before and after a dietary intervention with casein, soy protein or maltodextrin (placebo),

first: Martin

last: Beaumont

first: François

last: Blachier


title: Expression profile of Arabidopsis pistil/silique upon induction of FRUITFULL

city: Wageningen

first: Marian

last: Bemer

address: Droevendaalsesteeg 1

department: Molecular Biology

institute: Wageningen University

summary: To determine the genes that are regulated by FRUITFULL (FUL) in the pistil/silique, we identied differentially expressed genes after induction of FRUITFULL in ful-1 FUL-GR lines using the AGRONOMICS1 tiling array. The inflorescences of flowering plants were dipped in 10 uM DEX solution or in Mock Solution, and the flowers/siliques from stages 12-16 were harvested after 8 hours. RNA was extracted and DNase treated, and subsequent steps and hybridization to the AGRONOMICS Tiling array were performed by the Functional Genomics Center Zurich.

overall_design: We generated several control samples to be able to identify genes that were differentially regulated by the DEX alone treatment instead of by the induction of FUL. A considerable number of genes was found to respond to DEX (samples ful-1 DEX vs ful-1 Mock). To identify the genes that were actually differentially upregulated because of FUL, we compared the samples ful-1_FUL-GR_DEX and ful-1_FUL_GR_Mock). All samples were performed in duplicate.

first: Jose

last: Muino

first: Gerco

last: Angenent


title: Effect of Paral1 deficiency on gene expression in 3T3-L1 cells

city: Lille

middle: Franck

last: FIRMIN

address: Boulevard du Professeur Jules Leclerc

department: Team 4

institute: Inserm U1011

summary: Paral1 is a novel adipocyte-specific lincRNA upregulated during adipogenesis of 3T3-L1 cells. Knockdown of Paral1 by siRNA transfection in 3T3-L1 cells followed by transcriptomic analyses was performed.

overall_design: 3T3-L1 adipogenesis was induced as in Dubois-Chevalier et al. NAR 2014. siRNA were transfected at the same time or after 7 days of differentiation. Transcriptome analyses of total RNA extracted from 3T3-L1 cells after two days of transfection with siRNA control (Ctrl-siRNA) or targeting Paral1 (Paral1-siRNA) were performed (D2 relates to cells transfected with siRNA upon indution of differentiation; D9 relates to cells transfected with siRNA after 7 days of differentiation). Three independent replicates were performed.

middle: F

last: Firmin


title: Expression data from 7-day-old dark-grown wild-type and dez mutant seedlings from control (1 µM) and high-Zn (100 µM) media

city: Bochum

first: Scott

last: Sinclair

address: Universitaetstrasse 150

institute: Ruhr Universitaet Bochum

summary:
The transition between growth in the dark (skotomorphogenesis) and growth in the light (photomorphogenesis) is one of the most critical in plant development. Here the newly identified mutant dez is photomorphogenic in the dark and is strongly enhanced in high Zn. dez displays a shortened hypocotyl, expanded cotyledons, an elongated root and differentiated plastids in the dark contrast to wild-type seedlings that are typically skotomorphogenic, with a long hypocotyl and unexpanded cotyledons protected by an apical hook, and undifferentiated etioplasts
We used microarrays to identify transcripts regulated in dez in high-Zn relative to wild-type in high-Zn, and dez in high-Zn relative to dez in control conditions.

overall_design: Two biological replicates of each genotype and condition (wild-type and dez, control and high-Zn) consisting of ~45 7-day-old seedlings each were harvested in dim green light and frozen in liquid nitrogen. RNA was extracted and hybridised to the Affymetrix ATH1 chip

first: Michael

middle: J

last: Haydon

first: Camille

last: Larue

first: Hiram

last: Castillo

first: Laura

last: Bonk

first: Ricardo

last: Stein

first: Daniel

last: Grollimund

first: Ulla

last: Neumann

first: Dominic

last: Begerow

first: Ute

last: Kraemer


title: Effect of Tunicamycin on Bovine Capillary Endothelial Cells

city: San Juan

first: Humberto

last: Ortiz-Zuazaga

state: PR

address: PO BOX 23334

department: High Performance Computing facility

institute: University of Puerto Rico

summary: GPT inhibitor Tunicamycin develops ER stress causing anti-angiogenic response in breast tumor microvasculature due to unfolded protein response-mediated apoptosis.  cDNA microarray identified 123 and 454 differentially regulated genes with 10 genes overlapping between 3h and 32 h of Tunicamycin treatment.  Alg-2 expression is inconsistent but not the Dpms. Evidences support that Tunicamycin completely destroys DPMS activity in capillary endothelial cells without affecting its protein or the mRNA levels but by knocking down the phosphorylation.  DPMS’ contribution to developing upr during ER stress has therefore been evaluated because of its inherent regulatory property of GPT.    FTIR spectroscopy confirmed protein denaturation.  Restablishing the phosphorylation status helps the DPMS regaining its activity.  As a result, ER stress is reduced reversing apoptosis and bringing more cells into cycling with normal cellular morphology.  Furthermore, differential expression of DPMS in breast tumor microvasculature during Tunicamycin therapy raises its potential as a tumor prognostic marker in the clinic.

overall_design:
The experimental design consisted of eight microarray experiments. Cy-3 labeled cRNA control targets were combined with Cy-5 labeled cRNA experimental targets obtained from 3 hrs and 32 hrs samples. The combined Cy-3 and Cy-5 cRNAs targets were used for probe hybridization onto the first, third, fifth, seventh microarray, respectively. Dye swapping was done using different biological replicates for both Cy-5 labeled control targets and the Cy-3 experimental targets (as above) and used for hybridization on the second, fourth, the sixth and the eight  microarray respectively. Dye swaps using different biological replicates were done to correct for any dye-bias.
Two arrays did not pass quality control and were removed from the experiment: Angiogenesis 3h Replicate 1, Angiogenesis 32h Replicate 2.

first: Aditi

last: Banerjee

first: Juan

last: Martinez

first: Maria

middle: O

last: Longas

first: Sandra

last: Peña de Ortiz

middle: G

first: Krishna

last: Baksi

first: Dipak

middle: K


title: Expression profiling of QSG-7701 cells: stably express lncRNA-PRAL vs control

first: shu-han

last: sun

summary: lncRNA-PRAL induced transcriptional changes in QSG-7701

first: Fu

last: Yang

first: Shu-han

last: Sun


title: The mRNA and microRNA (miR) transcriptome of lung neutrophils during S. pneumoniae (SP) pneumonia in wild type (WT) mice [miRNA]

first: Claire

last: Doerschuk

first: John

last: Gomez

first: Hong

last: Dang


title: High number of chromosomal copy number aberrations inversely relates to t(11;19)(q21;p13) translocation status in Mucoepidermoid Carcinoma of the Salivary Glands

city: Amsterdam

first: Johannes

middle: Hendrikus

last: Muatse

address: Gustav Mahlerlaan 81

department: Department of Oral and Maxillofacial Surgery and Oral Pathology

institute: VU University medical center

summary: genomic analysis using arrayCGH to gain insight into chromosomal copy number in mucoepidermoid carcinoma (MEC). Results suggest that two types of MECs can be distinguished: (i) a group of MECs without t(11;19)(q21;p13) translocation with many copy number aberrations (> 6), independent of histological grade, and (ii) a group of MECs with the t(11;19)(q21;p13) translocation with no or a few copy number aberrations (<6 ) with two exceptions classified as low and intermediate grade.

overall_design: Tumor DNA vs Normal DNA from surrounding tumor tissue. 27 parrafine embedded MEC samples of which 17 low grade, 6 intermediate grade and 4 high grade MEC samples were compared to normal surrounding tissue.

last: Matse

first: Enno

middle: I

last: Veerman

first: Jan

last: Bolscher

first: C

middle: R

last: Leemans

first: Bauke

last: Ylstra

first: Elisabeth

last: Bloemena


title: DNA Damage Induces a Secretory Program in the Quiescent Tumor Microenvironment that Promotes Adverse Prostate Cancer Phenotypes

status: Public on Nov 16 2017

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Benign quiescent cells in the tumor microenvironment respond to genotoxic stress by inducing a secretory program capable of promoting therapy resistance. Developing approaches to suppress the secretory program may improve treatment responses.

overall_design: Custom Agilent 44K whole human genome expression oligonucleotide microarrays were used to profile proliferating, quiescent, and ionizing-radiation treated PSC27 human primary prostate fibroblast cells.  RNA was amplified prior to hybridization against a common reference pool of prostate tumor cell lines.

first: Luis

last: Gomez-Serosi

first: Yu

first: Daniella

last: Bianchi-Frias

first: Peter

last: Nelson


title: Circulating microRNAs: a novel potential biomarker for diagnosing acute aortic dissection

city: Shanghai

first: Jian

last: Dong

address: 168 Changhai Rd

department: Department of Vascular Surgery

institute: Changhai Hospital

summary: Microarrays with 1,205 human microRNAs and 142 viral microRNAs were used for screening candidate diagnostic markers in the 3 categories of subjects from 24 plasma samples including acute aortic dissection, healthy and  aortic aneurysm subjects. There were two microRNAs overlapping in the 3 group comparisons. Finally, 16 candidate microRNAs discovered via microarrays were selected for the further validation.

overall_design: A microarray containing probes for 1,205 human microRNAs and 142 viral microRNAs was initially used to screen the significant differential expression levels of microRNAs between the acute aortic dissection (n=8) and control groups (n=16, 8 aortic aneurysm patients and 8 healthy volunteers).

last: Zhou

first: Zaiping

last: Jing


title: Liver kinase B1 deletion effect on brown adipose tissue

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

institute: Purdue University

summary: Analysis of brown adipose tissue (BAT) isolated from wildtype (WT) and liver kinase B1 (LKB1) deletion mice (Ad/LKB1). Results provide insight into molecular mechanisms underlying paralysis of Ad/LKB1 mice

overall_design: Two-condition experiment, WT BAT vs. Ad-LKB1 BAT. Biological replicates: 3 WT replicates, 3 Ad-LKB1 replicates. 3 x 2-color arrays.

first: Yan

last: Xiong

first: Tizhong

last: Shan

first: Chao

last: Wang


title: Aberrant striatal but not nigral gene expression profiles are specifically associated with dyskinesia behavior following levodopa treatment in the 6-hydroxydopamine lesioned rat

status: Public on Oct 31 2017

city: Grand Rapids

first: Jack

middle: W

last: Lipton

state: MI

address: 333 Bostwick Ave.

department: TSMM

institute: Michigan State University

summary: Levodopa-induced dyskinesia (LID) is a common consequence of prolonged pharmacotherapy for Parkinson's disease (PD). While LID becomes more common with long term exposure to levodopa, its development can be quite variable. We leveraged the variable expression of LID in a rat model to interrogate differential gene expression in the substantia nigra and striatum of animals that develop LID and those that do not. Differential expression of genes associated with LID was found only in striatum, not substantia nigra.

overall_design: All rats were unilaterally lesioned using identical parameters with either 6-hydroxydopamine or vehicle lesion. Success was determined by >90% reduction of DA in the striatum as measured by HPLC, and behaviorally using non-drugged motor behavior testing. Daily injections of levodopa or saline were commenced 3.5 weeks after 6-OHDA lesioning. LID behaviors were rated every other day for a total of seven sessions.

first: Kathy

last: Steece-Collier

first: Timothy

last: Collier

first: Fredric

last: Manfredsson

first: Mary

last: Winn

first: Allyson

last: Cole-Strauss

first: Jennifer

last: Stancati

first: Caryl

last: Sortwell


title: Histone H4K16 acetylation modulates the dynamics of linker H1 and heterochromatin protein HP1 in male X chromosome dosage compensation

city: Beijing

first: Tingting

last: Li

address: 38 Xueyuan Rd

department: Medical informatics

institute: Peking University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Drosophila dosage compensation is an epigenetic phenomenon in which the transcription of most genes on X-chromosome is enhanced by approximately two folds in males to equalize that in females. In this study, we provide evidence that transcriptional repressors, such as HP1 and linker histone H1, are globally reduced on male X chromosome. We further investigated the role of HP1 and linker H1 on X chromosome dosage compensation using flies with overexpression of HP1 and H1, we demonstrate that these repressors surpress H4K16 acetylation, presence of the elongating RNA Pol II and the transcription of the genes on male X chromosomes. To understand how H1 and HP1 are regulated on male X chromosome, we next explored the relationship between MOF and the two repressors of chromatin. We show that the hyperacetylation of H4K16 induced by MOF resulted in the loss of H1 and HP1 on chromatin and global chromatin decondensation. Our biochemical analysis further shows that the presence of acetylation on histone H4 at lysine 16 directly inhibits the interaction between histone H4 and linker H1. This study therefore provides novel clues on understanding the dynamic regulation of chromatin regulators on male X chromosome dosage compensation.

overall_design: In this study, we used ChIP-Seq to accurately map HP1 binding profiles on whole drosophila genome in drosophila S2 and Kc cells. Chromatin components do not work solely; they cooperate with each other to regulate the transcription activity. So besides HP1, we also generated ChIP maps of histone H1 and the histone marks H3K4me2, H3K9me2, H3K36me3 and H4K16Ac in drosophila S2 cells. Affinity-purified polyclonal antibody of HP1 was used in this experiment, 5ul for each ChIP. H4K16ac (07-329) and H3K4me2 (07-030) antibodies purchased from Upstate were also used in this experiment, 5ul for each ChIP. H3K36me3 (ab9050) and H3K9me2 (ab1220) antibodies were purchased from Abcam, 5ul for each ChIP. The polyclonal antibody for Sample H1_S2 was made by our lab (detailed information can be found in Ni et al.,2006 Genes Dev.).

first: Fanglin

last: Sun

first: Daoyong

last: Zhang


title: Early-onset sporadic rectal cancer : Wnt- vs. Wnt+ rectal tumor [CGH]

status: Public on Oct 30 2017

city: HYDERABAD

first: Murali

middle: Dharan

last: Bashyam

state: (Click to Select US State)

address: MJ MARKET

institute: CDFD

summary: Copy number profiling of early-onset sporadic rectal adenocarcinoma, comparing Wnt- and Wnt+ rectal tumor. Goal was to determine differentially altered genes between them based on global copy no.

overall_design: Two-condition experiment, Wnt- vs. Wnt+ rectal tumors. Wnt- tumors: 26, Wnt+ tumors: 16

first: Raju

last: Kumar


title: Circadian rythms of gene expression in a continuosly growing fish larva

city: Castellón

first: Josep

middle: A

last: Calduch-Giner

address: Ribera de Cabanes

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

summary: Gilthead sea bream larvae were sampled at  30 dph during a 24 h cycle taking 10 individuals every 3 hours (00:00, 03:00, 06:00, 09:00, 12:00, 15:00, 18:00, 21:00 and 24:00 h Zeitgeber time) and their expression profile was analyzed by means of a specific oligo-microarray. One-way ANOVA showed that 2,229 genes present in the microarray were differentially expressed among the nine temporal groups. Principal component analysis of these differentially expressed genes clearly showed a cyclic distribution of the groups along the two components that accounted for most of the total variation (48.3% and 32.8%, respectively). The k-means clustering of differentially expressed genes identified four major clusters with a sequential expression profile. Cluster 1 comprised the lowest number of genes (132), although their magnitude of response was higher than in the other clusters, with an early peak of expression at 0h zeitgeber time and the minimum after 12 h. Clusters termed as 2, 3 and 4 contained 675, 758 and 650 genes, respectively, and they also showed a circadian rhythmicity of expression with intensity peaks at 3h (cluster 2), 9-15h (cluster 3) and 18-21h zeitgeber time. For functional analysis of differentially expressed genes, the 92.6 % (2,052 genes) was eligible for pathway analysis in the IPA software. Regarding molecular and cellular functions, the most significant for cluster 1 were molecular transport, lipid metabolism, amino acid metabolism, nucleic acid metabolism, carbohydrate metabolism, and vitamin and mineral metabolism. Of note, the most significant canonical pathway in this cluster was thyroid hormone receptor and retinoid X receptor (TR/RXR) activation, represented by collagen alpha-3(VI) chain, cytochrome P450 7A1, phosphoenolpyruvate carboxykinase 1, and the three core mitochondrial isoforms of uncoupling proteins (UCP1, UCP2, and UCP3). Secondly, phototransduction was significantly over-represented by five genes: arrestin 3, cyclic nucleotide-gated channel alpha 1, cyclic nucleotide-gated channel alpha 1, phosducin, and guanylate cyclase activator 1B.   In cluster 2, the molecular functions “RNA post-transcriptional modification” and “DNA replication, recombination, and repair” were clearly the most significant. Overlapping analysis of associated canonical pathways identified for cluster 2 a group of 30 related genes, which were mainly involved with repair response to DNA damage and also cell cycle regulation. “Cell cycle” and “DNA replication, recombination, and repair” were also among the top molecular and cellular functions of cluster 3, together with “cellular assembly and organization”. Significant overlapping of canonical pathways from cluster 3 identified 72 genes mostly related to unfolded protein responses, oxidative stress, and regulation of cell cycle. By contrast, there were no clearly prominent molecular and cellular functions among the cluster 4 genes, and overlapping analysis only resulted in six related pathways (26 genes), including cell cycle and signaling processes related to embryogenesis (neuregulin signaling) and apoptosis (TWEAK -TNF-like weak inducer of apoptosis- signaling).   Seven genes in cluster 1-3 were unequivocally identified as classic activators of circadian rhythms (“clock genes”). These were the circadian protein homolog 3 (PER3) in cluster 1, PER1, PER2 and chryptophores 1 and 2 (CRYP1/CRYP2) in cluster 2, and aryl hydrocarbon receptor nuclear translocator-like (BMAL1) and circadian locomotor output cycles kaput (CLOCK) in cluster 3. Interestingly, correlation analysis showed that a number of genes in each of these three clusters shared the expression dynamics of the identified clock genes. Figure 7 shows the number of related genes for each one of the clock genes and their average expression profiles. The entire list of significantly correlated genes to these reference clock genes and their normalized intensity values is provided as supplemental material (Supplemental Table 2). Expression values of CRYP1, BMAL1 and CLOCK were also assessed by qPCR and results were quite consistent (r=0.93) with those of the microarray analysis.

overall_design: Larvae were sampled at  30 dph during a 24 h cycle taking 10 individuals every 3 hours (00:00, 03:00, 06:00, 09:00, 12:00, 15:00, 18:00, 21:00 and 24:00 h Zeitgeber time)

first: Jaume

last: Pérez-Sánchez

first: Manuel

last: Yúfera


title: Microarray analysis of gene expression patterns in wildtype and LIFR knockout and gp130 knockout ESCs

status: Public on Oct 19 2017

first: Naihe

last: Jing

state: Shanghai

address: 320 Yueyang road

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: Differentially expressed genes were screened by comparing with wildtype and LIFR knockout and gp130 knockout ESCs

overall_design: Comparasion of gene expression patterns in wildtype and LIFR knockout and gp130 knockout ESCs

first: Xiongjun

last: Wang

first: Yunbo

last: Qiao


title: Combined transcriptome and translatome analyses reveal a role for tryptophan dependent auxin biosynthesis in the control of DOG1 dependent seed dormancy

status: Public on Oct 23 2017

first: Leónie

last: Bentsink

summary: Transcriptome and translatome analyses of 6 and 24 hours imbibed seeds dormant and non-dormant seeds of NILDOG1-Cvi with and without addition of the transcription inhibitor Cordycepin. NILDOG1-Cvi is the Ler WT containing an introgression of the Cvi accession on chromosome 5, which includes the DOG1 gene (Bentsink et al., 2006).

overall_design: Gene expression of total and polysomal bound mRNA of 6 and 24 hours imbibed dormant and non-dormant NILDOG1-Cvi seeds in the presence of water or the tranacriptional inhibitor cordecypin. For each sample condition three replicates were used (two replicates were used for P_Cor_D24.CEL, P_Cor_ND24.CEL, P_Water_D24.CEL)

first: Bing

last: Bai

first: Ondrej

last: Novak

first: Karin

last: Ljung

first: Johannes

last: Hanson


title: Dormant origins and fork protection mechanisms rescue sister forks arrested by transcription

status: Public on Oct 11 2017

city: Pavia

first: Giordano

last: Liberi

address: Via Abbiategrasso 209

institute: Istituto di Genetica Molecolare IGM-CNR

summary: Yeast Sen1Senataxin is a RNA/DNA helicase that preserves replication forks across RNA Polymerase II-transcribed genes by counteracting RNA:DNA hybrids accumulation. We show that in Sen1-depleted cells early forks clashing head-on with transcription halt, and impair progression of sister forks within the same replicon. Unsolved replication-transcription collisions trigger the local firing of dormant origins that rescue arrested forks. In sen1 mutants the MRX and Mrc1/Ctf4-complexes protect those forks clashing with transcription by preventing genotoxic fork-resection events mediated by the Exo1 nuclease. Hence, sister forks within the same replicon remain coupled when one of the two forks halts. This is different when forks encounter double strand breaks. Moreover, the local firing of dormant origins is not prevented by checkpoint activation but depends on delayed adjacent forks. Furthermore, a productive head-on clash between replication and transcription requires the tuning of origin firing and coordination between Sen1, the MRX and Mrc1/Ctf4-complexes and Exo1.

overall_design: Genome-Wide Analysis of DNA Synthesis by BrdU Immunoprecipitation on Tiling Microarrays (BrdU-IP-chip) was carried out as described (Viggiani et al., 2010), employing anti-BrdU antibody (MBL M1-11-3). Labelled probes were hybridized to Affymetrix S.cerevisiae Tiling 1.0 (P/N 900645) arrays and processed with TAS software.

first: Alessandra

last: Brambati

first: Yathish

last: Achar


title: Analysis of Fusarium verticillioides gene expression in response to nitric oxide

city: Athens

first: Anthony

middle: E.

last: Glenn

state: GA

address: 950 College Station Rd

department: Toxicology & Mycotoxin Research Unit

institute: USDA, ARS, USNPRC, R.B. Russell Research Center

summary: Investigation of whole genome gene expression level changes in F. verticillioides M3125 when exposed to 1.5 mM DETA NONOate for 30 minutes.  Assessed in reference to unexposed M3125.  DETA NONOate is a nitric oxide (NO) donor with a half-life of approximately 56 hours at 27°C, pH 7.4, to liberate 2 moles of NO per mole of parent compound.

overall_design: A four chip study using total RNA recovered from two separate control cultures of F. verticillioides M3125 in PDB buffered with 0.1 M sodium phosphate and two separate experimental cultures of M3125 grown in the same buffered PDB plus the added treatment of 1.5 mM DETA NONOate.  The cultures were incubated for 30 minutes and then harvested by vacuum filtration and frozen in liquid nitrogen. The chips are a F. verticillioides custom 14K array based on platform GPL14669.

middle: E

first: Thomas

middle: T

last: Baldwin


title: Chromosomal microarray analysis for validation of the WGS-based CNV detection results in recurrent miscarriage couples

city: Hong Kong

first: Zirui

last: DONG

address: Shatin, N.T.

department: Dept. of Obstetrics and Gynaecology

institute: The Chinese University of Hong Kong

summary: In order to validate of CNV detection from low-coverage whole-genome sequencing in the blood samples from recurrent miscarriage couples, we employed a customized array Comparative Genomics Hybridization (aCGH, Agilent) approach as chromosomal microarray analysis (CMA) in present study for a cohort of 78 DNA samples from blood. CMA results were compared with low-coverage whole-genome sequencing detection results. 100% consistency was obtained in pathogenic or likely pathogenic CNVs detection.

overall_design: aCGH was perfomed in the samples with low-coverage whole-genome sequencing result and sufficient DNA amount (>500ng). Each clinical subject was referred for chomosomal analysis because of the clinical indication (recurrent miscarriage couples). Each case was detected by aCGH by using a healthy Chinese adult as control.

first: Kwong-Wai

last: CHOY

first: Huilin

last: WANG


title: Germ-free versus conventional mouse terminal ileum

status: Public on Sep 29 2017

city: Bethesda

first: Aleksandra

last: Nita-Lazar

state: MD

address: 9000 Rockville Pike BLDG 4 RM 109 MSC 0421

department: Laboratory of Immune System Biology, NIAID

institute: National Institutes of Health

summary: Transcriptomics (using DNA microarrays) was used to quantitatively compare the terminal ileum from conventional and germ-free mice (female and male; C57BL/10A and BALB/c strains).

overall_design: A reference-free experimental design was used. Each 2-color microarray was used to analyze one germ-free and one conventional sample (sex- and strain-matched). To mitigate label-effects, half of the samples of each experimental class were randomly selected to be labeled green, and the other half red. The experiment used 19 microarrays: four female C57BL/10A, five female BALB/c, five male C57BL/10A, and five male BALB/c. All of the microarrays were the same design (design number 017138, Agilent Technologies, Santa Clara, CA).

first: Nathan

middle: P

last: Manes


title: Screening for Protective Effect Target of Deproteinized Extract of Calf Blood and Its Mechanisms in Mice with CCl4-Induced Acute Liver Injury

status: Public on Sep 18 2017

city: jilin city

first: guangyu

last: xu

address: Binjiang Road 3999,jilin city,132013

institute: College of Pharmacy, Beihua University

summary: Liver injury is the common pathological basis of various liver diseases, and its existence for a long time is often a important initiation factor to lead to liver fibrosis, and even liver cirrhosis and hepatocellular carcinoma (HCC), so that the prevention and treatment of liver injury is one of the key links in the clinical therapy of liver diseases, and the timely control of the occurrence and development of liver injury will have an important clinical significance in the treatment of liver disorders. It has been reported that deproteinized extract of calf blood (DECB) can inhibit the replication of hepatitis B virus and has a protective effect on the liver function after a traumatic liver injury. However, there are few studies on the regulatory factors and mechanisms of DECB effects. In this study, an acute mouse liver injury model was established with carbon tetrachloride (CCl4), mRNA expression microarray was used to screen the differentially expressed genes and related pathways in mice in the DECB group and model group, and the target of protective effect of DECB and its related mechanism were found in mice with acute liver injury induced by carbon tetrachloride, which may provide an important theoretical basis for the further research and development of DECB.

overall_design: After they were acclimated to the laboratory environment for 3d, 20 male mice were randomly divided into 2 groups: model group (M), DECB group, 10 mice in each group.The DECB group was given DECB (1g/kg), and those in the M group (20 BW) were given normal saline (20mL/kg) intragastrically once daily continuously for 30d. At two hours after the last administration, mice in M and DECB groups were injected with 10% carbon tetrachloride blend oil (10mL/kg).

first: liping

last: an


title: A UBE2O-AMPKα2 axis that promotes tumor initiation and progression offers opportunities for therapy

status: Public on Sep 08 2017

city: Houston

first: Min Sup

last: Song

state: TX

address: 1515 Holcombe Blvd Unit 108

department: Molecular and Cellular Oncology

institute: MD Anderson Cancer Center

summary: UBE2O is localized in the 17q25 locus, which is known to be amplified in human cancers, but its role in tumorigenesis remains undefined. Here we show that Ube2o deletion in MMTV-PyVT or TRAMP mice profoundly impairs tumor initiation, growth and metastasis, while switching off the metabolic reprogramming of tumor cells. Mechanistically, UBE2O specifically targets AMPKα2 for ubiquitination and degradation, and thereby promotes activation of the mTOR-HIF1α pathway. Notably, inactivation of AMPKα2, but not AMPKα1, abrogates the tumor attenuation caused by UBE2O-loss, while treatment with rapamycin or inhibition of HIF1α ablates UBE2O-dependent tumor biology. Finally, pharmacological blockade of UBE2O inhibits tumorigenesis through the restoration of AMPKα2, suggesting the UBE2O-AMPKα2 axis as a potential cancer therapeutic target.

overall_design: In order to elucidate the pathophysiological impact of UBE2O loss, we generated mouse embryonic fibroblasts (MEFs), derived from day 13.5 embryos of C57BL6 mice, stably expressing control or Ube2o shRNA. We then performed microarray analysis in these cells. Three independent MEFs from each shRNA were analyzed. Gene expression profile analysis in these cells will reveal target genes and pathways differentially regulated upon UBE2O-loss.

first: Isabelle

last: Vila

first: Yixin

last: Yao

first: Goeun

last: Kim

first: Weiya

last: Xia

first: Hyejin

first: Sun-Joong

first: Mi

last: Park

first: James

last: Hwang

first: Enrique

last: Billalabeitia

first: Mien-Chie

last: Hung

first: Su

first: Min

middle: S


title: Discovery of transcription factor and regulatory network function through systematic deletion and quantitative phenotyping analysis in archaea

status: Public on Aug 31 2017

city: Durham

first: Amy

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University

summary: Halobacterium salinarum ∆cspD1 transcription factor deletion mutant and control strain NRC-1 of Halobacterium salinarum were grown to mid-logarithmic phase in batch mode in a New Brunswick BioFlo100 modular bench top fermentor (New Brunswick Scientific) in CM medium as described in (Schmid et al., 2007, Genome Res, 17(10):1399-413. At mid-log phase, oxygen sparging and agitation were stopped to induce anoxia. Cultures were incubated anaerobically overnight, then oxygen was sparged and RNA was collected at time points immediately prior to addition of oxygen and 5, 10, 20, 45, and 180 minutes afterwards. Although these data were published previously as part of a larger gene regulatory network study (Brooks et al., 2014, Mol Sys Biol, 10:740), the details of the experiment and specific analysis of the effect of ∆cspD1 deletion on gene expression were not reported.

overall_design: 6 samples from conditions of varying oxygen tension from strain delta-cspD1 were hybridized against RNA from wild type control NRC-1 strain (RNA batch d) on dye-swap arrays (replicates) for a total of 12 arrays.


title: Cardiac aldosterone and corticosterone regulated genes in mice with cardiomyocytes targeted mineralocorticoid receptor overexpression (MR-Cardio mice) and their controls (Ctrl mice)

status: Public on Sep 01 2017

city: Ottawa

first: Smail

last: Messaoudi

address: 451 smyth road

department: BMI

institute: University of Ottawa

summary: Inappropriate mineralocorticoid receptor (MR) activation is involved in cardiac diseases. MR binds aldosterone, but also glucocorticoids; the identity of the ligand responsible for the deleterious effects of cardiac MR activation is still unclear. Mice overexpressing MR in cardiomyocytes (MR-Cardio) and their controls (Ctrl) were treated for 7 days with aldosterone or corticosterone and a whole genome microarray analysis was performed.

overall_design: Six-group experiment: Control mice (Ctrl), transgenic mice (MR-Cardio), Ctrl mice + aldosterone treatment, MR-Cardio mice + aldosterone treatment, Ctrl mice + corticosterone treatment, MR-Cardio mice + corticosterone treatment. Five comparisons: Ctrl vs MR-Cardio, Ctrl vs Ctrl-Aldo, Ctrl vs Ctrl-Cortico, MR-Cardio vs MR-Cardio-Aldo, MR-Cardio vs MR-Cardio-Cortico

first: Veronique

last: Pelloux


title: Cardiac aldosterone regulated genes in mice with cardiomyocytes targeted mineralocorticoid receptor overexpression (MR-Cardio mice) and their controls (Ctrl mice)

summary: Inappropriate mineralocorticoid receptor (MR) activation is involved in cardiac diseases. The mechanisms are still unclears.  Mice overexpressing MR in cardiomyocytes (MR-Cardio) and their controls (Ctrl) were treated for 7 days with aldosterone and a whole genome microarray analysis was performed.

overall_design: Four-group experiment: Control mice (Ctrl), transgenic mice (MR-Cardio), Ctrl mice + aldosterone treatment, MR-Cardio mice + aldosterone treatment. Three comparisons: Ctrl vs MR-Cardio, Ctrl vs Ctrl-Aldo, MR-Cardio vs MR-Cardio-Aldo


title: DNA microarray analysis of colorectal tissue from Apc mutant mice

city: Tsuruoka

first: Kiyotoshi

last: Satoh

state: Yamagata

address: Mizukami 246-2, Kakuganji

department: Institute for Advanced Biosciences

country: Japan

institute: Keio University

summary: Cancer cells alter their metabolism for the production of precursors of macromolecules. However, the control mechanisms underlying this reprogramming are poorly understood. Here, we show that metabolic reprogramming of colorectal cancer is caused chiefly by aberrant MYC expression. Multi-omics-based analyses of paired normal and tumor tissues from 275 patients with colorectal cancer revealed that metabolic alterations occur at the adenoma stage of carcinogenesis, in a manner not associated with specific gene mutations involved in colorectal carcinogenesis. MYC expression induced at least 215 metabolic reactions by changing the expression levels of 121 metabolic genes and 39 transporter genes. Further, MYC negatively regulated the expression of genes involved in mitochondrial biogenesis and maintenance but positively regulated genes involved in DNA and histone methylation. Knockdown of MYC in colorectal cancer cells reset the altered metabolism and suppressed cell growth. Moreover, inhibition of MYC target pyrimidine synthesis genes such as CAD, UMPS and CTPS blocked cell growth, and thus they are potential targets for colorectal cancer therapy.

overall_design: Gene expression in normal and adenomatous tissue obtained from the large intestines of Apc+/Δ716 mice

first: Masahiro

last: Sugimoto

first: Rie

last: Kajino-Sakamoto

first: Yasushi

last: Kojima

first: Teruaki

last: Fujishita

first: M

middle: M

last: Taketo

first: Shinji

last: Fukuda

last: Aoki

first: Tomoyoshi

last: Soga


title: Insights on Osmotic Tolerance Mechanisms in Escherichia coli Gained from an rpoC Mutation

city: College Station

first: Katy

last: Kao

state: Texas

address: 3122 TAMU Room 200

department: Chemical Engineering

institute: Texas A&M University

summary: Transcriptional analysis of rpoC K370_A396dup mutants for tolerance to sodium chloride

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

overall_design: Mutant compared to wild-type reference during sustained exponential growth in 0.6 M NaCl, two biological replicates per sample

first: Yuqi

last: Guo

middle: D

last: Winkler

middle: C


title: Transcriptional signature of human pro-inflammatory TH17 cells

city: Boston

first: Dan

last: Hu

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

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

overall_design: Refer to individual Series


title: Gene expression profile of the RAG2 gene depletion on pig spleen

city: Seoul

first: Yun-Jung

last: Choi

address: 120 Neungdon-ro,Gwangjib-gu

department: Animal biotechnology

country: South Korea

institute: KONKUK University

summary: Pigs with severe combined immunodeficiency (SCID) may provide useful models for regenerative medicine, xenotransplantation, and tumor development and will aid in developing therapies for human SCID patients. Using a reporter-guided transcription activator-like effector nuclease (TALEN) system, we generated targeted modifications of recombination activating gene (RAG) 2 in somatic cells at high efficiency, including some that affected both alleles. Somatic-cell nuclear transfer performed with the mutated cells produced pigs with RAG2 mutations without integrated exogenous DNA. Biallelically modified pigs either lacked a thymus or had one that was underdeveloped. Their splenic white pulp lacked B and T cells. Under a conventional housing environment, the biallelic RAG2 mutants manifested a failure to thrive phenotype, with signs of inflammation and apoptosis in the spleen compared with age-matched wild-type animals by the time they were 4 wk of age. Pigs raised in a clean environment were healthier and, following injection of human induced pluripotent stem cells (iPSCs), quickly developed mature teratomas representing all three germ layers. The pigs also tolerated grafts of allogeneic porcine trophoblast stem cells. These SCID pigs should have a variety of uses in transplantation biology.

overall_design: We generated monoallelic RAG2 KO pigs using TALEN. We had collected spleen at postnatal day 17 and 29 from Wild type and RAG 2 KO pig.

first: Jin-Hoi

last: Kim


title: A member of the mycobiota modulates purine metabolism to increase intestinal permeability and colitis

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

summary: Transcriptome analysis of colons from germfree mice mono-associated with either S. cerevisae or R. aurantiaca

overall_design: Differential gene expression study comparing samples from germ-free control mice (4 replicates), mice infected with Saccharomyces cerevisiae (3 replicates) and mice infected with Rhodotorula aurantiaca. (4 replicates).

first: Tyson

last: Chiaro

first: Ray

last: Soto

first: W

middle: Z

last: Stephens

first: Jason

middle: L

last: Kubinak

first: Charisse

last: Petersen

first: Lasha

last: Gogokhia

first: Rickesha

last: Bell

first: Julio

last: Delgado

first: James

last: Cox

first: Warren

last: Voth

first: Jessica

last: Brown

first: David

middle: J

last: Stillman

first: Ryan

last: O’Connell

first: Anne

last: Tebo

first: June

last: Round


title: Gene expression profile of the RAG2 gene depletion on pig lymph node

first: Yun-Jung

last: Choi

overall_design: We generated monoallelic RAG2 KO pigs using TALEN. We had collected Lymph node at postnatal day 17 and 29 from Wild type and RAG2 KO pig.

first: Jin-Hoi

last: Kim


title: Gene expression profile of the RAG2 gene depletion on pig thymus

overall_design: We generated monoallelic RAG2 KO pigs using TALEN. We had collected thymus from Wild type and RAG2 KO pig.


title: Changes in Gene Expression in Space and Time Orchestrate Environmentally-Mediated Shaping of Root Architecture

status: Public on Aug 23 2017

city: Coventry

first: Miriam

last: Gifford

address: Gibbet Hill Road

department: School of Life Sciences

institute: University of Warwick

summary: Shaping of root architecture is a quintessential developmental response that involves the concerted action of many different cell types, is highly dynamic and underpins root plasticity. To determine to what extent the environmental regulation of lateral root development is a product of cell type preferential activities, we tracked transcriptomic responses to two different treatments that both change root development in Arabidopsis thaliana, at an unprecedented level of temporal detail. We found that individual transcripts are expressed with a very high degree of temporal and spatial specificity, yet biological processes are commonly regulated, in a mechanism we term response non-redundancy. Using causative gene network inference to compare the genes regulated in different cell types and during responses to nitrogen and a biotic interaction we found that common transcriptional modules often regulate the same gene families, but control different individual members of these families, specific to response and cell type. This reinforces that the activity of a gene cannot be defined simply as molecular function; rather, it is a consequence of spatial location, expression timing and environmental responsiveness.

overall_design: The response of cortical and pericycle cells, isolated using Fluorescence Activated Cell Sorting (FACS) was analysed 0 (before treatment) and 1, 2, 4, 6, 7, 10, 12, 14, 16, 20, 24 and 48 hours after treatment with 5mM KNO3 or S. meliloti in Arabidopsis thaliana Col0 roots; both genotypes carried GFP reporters marking either pericycle or cortical root cells.  Gene expression was analysed using NimbleGen 12 x 135K microarrays, designed for the TAIR10 genome. Seedlings were grown on low nitrogen (0.1mM KNO3) agar plates for 9 days, transferred to fresh plates containing either 0.1 mM KNO3 (untreated and S. meliloti).or 5 mM KNO3 plates.  At the end of the treatment, roots were harvested, protoplasts generated and GFP-marked epidermal and cortical cells isolated according to Gifford et al 2008 PNAS. All experiments were carried out in at least triplicate, with QC analysis used to select a complete array dataset.

first: Liam

last: Walker

first: Claire

last: Boddington

first: Jo

last: Hulsmans

first: Dafyd

last: Jenkins

first: Ying

last: Wang

first: Jesper

last: Grønlund

first: Dhaval

last: Patel

first: Jay

last: Moore

first: Sanjeev

last: Kumar

first: Anthony

last: Carter

first: Siva

last: Samavedam

first: Giovanni

last: Bonomo

last: Hersh

first: Gloria

last: Coruzzi

first: Nigel

last: Burroughs


title: Gene expression profile of the RAG2 gene depletion on pig spleen, thymus and lymph node

first: Yun-Jung

last: Choi


title: Engraftment and Repopulation Potential of Late Gestation Fetal Rat Hepatocytes

status: Public on Aug 22 2017

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

summary:
Liver transplantation is the only therapeutic option for patients with end-stage liver disease.  The shortage of donor organs has led to the search for alternative therapies to restore liver function and bridge patients to transplantation.  Our previous work has shown that the proliferation of late gestation E19 fetal hepatocytes is mitogen-independent.  This is manifested as differences in the control of ribosome biogenesis, global translation, cell cycle progression and gene expression.  In the present study, we investigated whether E19 fetal hepatocytes would engraft and repopulate an injured adult liver.
Methods: Fetal hepatocytes were isolated using a monoclonal antibody against a hepatic surface protein, leucine amino peptidase (LAP).  LAP+ and LAP- fractions were analyzed by immunofluorescence and microarray.  Immunopurified E19 liver cells from DPPIV+ F344 rats were transplanted via splenic injection into partial hepatectomized DPPIV- rats that had been pretreated with mitomycin C.
Results: Phenotypic characterization of the LAP+ fetal hepatocytes revealed that more than a third of the isolated cells expressed ductal markers.  Transcriptomic analysis revealed that these dual expressing cells represent a distinct subpopulation of less well differentiated hepatocytes.  Transplanted immunopurified LAP+ late gestation fetal hepatocytes formed small hepatic, endothelial and occasional ductal colonies within one month.  The average size of the colonies derived from the LAP+ cells increased so that by 10 months up to 35% of the liver was repopulated by donor-derived cells.
Conclusions: Our studies show that late gestation fetal hepatocytes, despite their being far along in the differentiation process, possess the capacity for extensive liver repopulation. This is likely related to the unexpected presence of a significant proportion of hepatocyte marker-positive cells maintaining a less well differentiated phenotype.

overall_design: Two subpopulations of E19 fetal rat hepatocytes were isolated using monoclonal antibodies against the hepatic cell surface marker leucine aminopeptidase and the ducal marker OC.2.  Adult hepatocytes were also isolated.  RNA was isolated from triplicate biological replicates of fetal LAP+/OC.2- and LAP+/OC.2+ cells as well as adult hepatocytes using the mirvana kit.  Affymetrix Rat ST 1.0 arrays were utilized.

first: Joan

last: Boylan

first: Heather

last: Francois-Vaughan

first: Philip

last: Gruppuso


title: The identification of novel genes involved in seed dormancy and after-ripening in Arabidopsis thaliana

status: Public on Aug 21 2017

city: Wageningen

first: Leónie

last: Bentsink

address: Droevendaalsesteeg 1

institute: Wageningen University

summary: We analysed the transcriptome of dormant and after-ripened imbibed seeds of different genotypes (Landsberg erecta and the different NILs) to identify dormancy and after-ripening genes that are absolutely required for these traits.

overall_design: Gene expression in imbibed dormant and after-ripened seeds was compared. For each sample, three replicates were used.

first: Farzaneh

last: Yazdanpanah

first: Johannes

last: Hanson

first: Henk

last: Hilhorst


title: Systematic investigation of multi-TLR sensing identifies novel regulators of sustained gene activation in macrophages.

status: Public on Aug 17 2017

first: Timothy

middle: G

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases


title: mouse BMDM poly(I:C), R848, or poly(I:C)+R848 stimulation

summary: Gene expression kinetics for BM-DM from C57BL/6 mice challenged by poly(I:C) , R848, poly(I:C)+R848 examined at 6 time points including 0.5, 1, 2, 4, 8, 12 h.

overall_design: BM-DM from C57BL/6 mice challenged by poly(I:C) , R848, poly(I:C)+R848  would be examined at 6 time points including 0.5, 1, 2, 4, 8, 12 h.

first: Bin

last: Lin

first: Iain

last: Fraser


title: Identification of ARR1 targets in the root of Arabidopsis thaliana

city: la jolla

first: Wolfgang

last: Busch

state: CALIFORNIA

address: Salk institute, 10010 n torrey pines rd

institute: Salk Institute for Biological Studies

summary: We performed a chromatin immunoprecipitation-based microarray experiment (ChIP chip) in order to identify ARR1 direct target genes

overall_design: ARR1 ChIP was performed with a GFP antibody for two independent biological replicates for each genotype (pARR1::ARR1:GFP (ARR1)  and Col-wt (control)). On each array ARR1 and control samples were hybridized in different colors. Moreover, a dye swap was perfomed. In total this resulted in 4 arrays (2 biological samples in 2 dye-swapped hybridizations).

first: Rossangela

last: Sozzani

first: Riccardi

last: Di Mambro


title: Gene expression profiles of rat tissues surrounding Vcap xenograft tumors with chemical or physical denervation.

status: Public on Nov 30 2017

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: We propose that nerves play a trophic function for epithelium, not only during development, but also in adult homeostasis. Hence, nerves are likely key in cancer progression. Furthermore nerves are a functional regulator of prostate cancer genesis and progression to malignancy.  A further understanding of the role of nerves in prostate cancer progression and a dissection of specific mechanisms would aid in identifying potential therapeutic targets that are centered on cancer-nerve interactions.  To address this in detail, we have examined the effects of nerve function in the VCaP prostate cancer xenograft model and have elucidated differential gene expression profiles in this model.

overall_design: Owing to the greater ease of surgical manipulation of the neural anatomy of rats, and the relative ease of maintenance of animals post-surgery, we choose a nude rat orthotopic VCaP model to test the functional significance of nerves in a human xenograft cancer model. For physical denervation we choose the major pelvic ganglia (MPG) excision, with particular care to avoid blood vessels since vessels and nerves are intimately connected and travel together in neurovascular bundles. For physical denervation we choose the major pelvic ganglia (MPG) excision, with particular care to avoid blood vessels. Sham surgery was used as control. In order to assess a comparative chemical denervation, we used Botulinum toxin (botox) and saline as a vehicle injection as control. To determine the effects of denervation on the non-neoplastic epithelium we laser captured the viable non neoplastic cancer epithelial cells, away from the tumors, in both the treated and control animals. We extracted RNA and performed gene array studies.

first: Michael

last: Ittmann

first: Olga

last: Dakhova

first: Gustavo

last: Ayala


title: Gene expression analysis of RNAs isolated from inguinal White Adipose Tissue (iWAT) of ZIP13-KO mice and their WT littermate mice

status: Public on Aug 15 2017

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

institute: POSTECH

summary: In order to assess overall gene expression change in objectively, we performed a microarray analysis of iWAT derived from ZIP13-KO mice and their WT littermate mice

overall_design: Triplicate experiments were performed for iWAT of Zip13-KO mice and their WT littermate mice. Total RNA was isolated from tissues using Qiazol (QIAGEN) following the manufacturers’ protocols.

first: Yoshio

last: Fujitani

first: Ayako

last: Fukunaka

first: Jinhyuk

last: Bhin


title: mouse BMDM dual PAMP stimulation with poly(I:C), R848, LPS, Pam3CSK3

summary: Gene expression kinetics for BM-DM from C57BL/6 mouse stimulated with four different TLR ligands poly(I:C), R848, LPS, Pam3CSK4 either singly or in paired combination, for 1 hour, 4 hour, or 8 hour.

overall_design: Mouse BM-DM cells were stimulated with four different reagents poly(I:C), R848, LPS, Pam3CSK4 either singly or in paired combination, for 1 hour, 4 hour, or 8 hour.


title: Transcriptome analysis of the endometrium, placenta, and liver in lactating and non-lactating dairy cows

status: Public on Aug 10 2017

city: Columbia

first: Matthew

last: Lucy

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: University of Missouri

summary: Infertility in lactating dairy cows is explained partially by the metabolic state associated with high milk production. The hypothesis was that lactating and non-lactating cows would differ in endometrial and placental transcriptomes during early pregnancy (day 28 to 42) and this difference would explain the predisposition for lactating cows to have embryonic loss at that time. Cows were either milked or not milked after calving. Reproductive [endometrium (caruncular and intercarunclar) and placenta] and liver tissues were collected on day 28, 35, and 42 of pregnancy. The primary hypothesis was rejected because no effect of lactation on mRNA abundance within reproductive tissues was found. Large differences within liver demonstrated the utility of the model to test an effect of lactation on tissue gene expression. Major changes in gene expression in reproductive tissues across time were found.  Greater activation of the transcriptome for the recruitment and activation of macrophages was found in the endometrium and placenta. Changes in glucose metabolism between day 28 and 42 included greater mRNA abundance of rate-limiting genes for gluconeogenesis in intercaruncular endometrium and evidence for the establishment of aerobic glycolysis (Warburg effect) in the placenta. Temporal changes were predicted to be controlled by CSF1, PDGFB, and JUN. Production of nitric oxide and reactive oxygen species by macrophages was a mechanism to promote angiogenesis in the endometrium. Reported differences in pregnancy development for lactating versus non-lactating cows could be explained by systemic glucose availability to the conceptus and appear to be independent of the endometrial and placental transcriptomes.

overall_design:
Liver, intercaruncular endometrium, caruncular endometrium, and placenta were sampled from Holstein dairy cows that were either lactating or non-lactating. RNA was extracted and hybridized on Affymetrix arrays. Samples were collected when the cows were pregnant on days 28, 35, or 42 of pregnancy

Please note that Group refers to the months of the year when the samples were collected. Group 1 samples were collected during March to July. Group 2 samples were collected during September to December.

first: Stephen

last: Moore


title: Single cell analysis of sister blastomeres of 2-cell mouse embryos respecting pair associations

status: Public on Aug 06 2017

city: Muenster

first: Michele

last: Boiani

address: Roentgenstrasse 20

institute: Max Planck Institute Muenster

summary:
Upon 2-cell embryo splitting, individual blastomeres were compared and contrasted with each other respecting pair associations (e.g. blastomere '1a' and '1b' of embryo 1, '2a' and '2b' of embryo 2, and so forth)
Transcriptome analysis followed by cluster analysis (Ward) was able to match a minority of the blastomeres with the correct sister blastomere

overall_design: Pair association (e.g. blastomere 'a' and 'b' from the same 2-cell embryo) was rigorously observed

first: Verena

last: Nordhoff


title: Massive reshaping of genome - nuclear lamina interactions during oncogene induced senescence (genome tiling)

city: Parkville

first: Carolyn

last: de Graaf

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute

summary: Background. Cellular senescence is a mechanism that virtually irreversibly suppresses the proliferative capacity of cells in response to various stress signals. This includes the expression of activated oncogenes, which cause Oncogene-Induced Senescence (OIS). A body of evidence points to the involvement of chromatin reorganization, including the formation of senescence-associated heterochromatic foci (SAHF). The nuclear lamina (NL) is an important contributor to genome organization and has been involved in cellular senescence and organismal aging. It interacts with multiple regions of the genome called lamina-associated domains (LADs). Some LADs are cell type-specific, while others are conserved between cell types and are referred to as constitutive LADs. Here, we used DamID to investigate the changes in genome-NL interactions in a model of OIS triggered by the expression of the BRAFV600E oncogene.  Results. We found that OIS cells lose most of their constitutive LADs (cLADS), suggesting the loss of a specific mechanism that targets cLADs to the NL. In addition, multiple genes relocated to the NL. Unexpectedly, they were not repressed, implying the abrogation of the repressive activity of the NL during OIS. Finally, OIS cells displayed an increased association of telomeres with the NL.  Conclusions. Our study reveals that senescent cells acquire a new type of LAD organization and suggest the existence of as yet unknown mechanisms that tether cLADs to the NL and repress gene expression at the NL.

overall_design: Examination of gene expression in cycling cells, after oncogene induced senescence, and after quiescence

first: Christelle

last: Lenain

first: Ludo

last: Pagie

first: Bas

last: van Steensel

first: Daniel

last: Peeper


title: Increased tumourigenesis in ApcMin/+ mice fed with a Western-type diet associates with changes in PDK4, Erk/Akt and mTor pathways, intestinal immunity and the expression of energy metabolism-related genes

status: Public on Aug 01 2017

city: Kuopio

first: Markus

last: Storvik

address: University of Eastern Finland

department: Pharmacology

country: Finland

institute: University of Eastern Finland

summary:
Western diet enhances intestinal tumorigenesis in Min/+ mice, associating with mucosal metabolic and inflammatory stress and loss of Apc heterozygosity
We investigated the interaction of WD and heterozygous mutation in the Apc gene in the histologically normal intestinal mucosa of ApcMin/+ (Min/+) mice. AIN-93G diet vs. a diet modified from AIN-93G, with high fat and low fiber, vitamin D, calcium and folate. (66.4% of total fat from milk, and 33.6% from rapeseed and sunflower oil)

overall_design: RNA from 1-3 mice small intestine per chip. Controls vs Western diet, males vs. females

first: Mikael

last: Niku

first: Anne-Maria

last: Pajari

first: Laura

last: Sarantaus

first: Essi

last: Päivärinta

first: Anu

last: Heiman-Lindh

first: Santeri

last: Suokas

first: Minna

last: Nyström

first: Marja

last: Mutanen


title: Expression data from Arabidopsis thaliana under mild oxidative stress elicited by methyl viologen and stress induced by the limited availability of phosphate

status: Public on Aug 07 2017

city: Yokohama

first: Atsushi

last: Fukushima

address: 1-7-22 Suehiro, Tsurumi

department: Center for Sustainable Resource Science

institute: RIKEN

summary: Plants possess highly sensitive mechanisms that monitor environmental stress levels for a dose-dependent fine-tuning of their growth and development. Differences in plant responses to severe and mild abiotic stresses have been recognized. Although many studies have revealed that glutathione can contribute to plant tolerance to various environmental stresses, little is known about the relationship between glutathione and mild abiotic stress, especially the effect of stress-induced altered glutathione levels on the metabolism. Here, we applied a systems biology approach to identify key pathways involved in the gene-to-metabolite networks perturbed by low glutathione content under mild abiotic stress in Arabidopsis thaliana. We used glutathione synthesis mutants (cad2-1 and pad2-1) and plants overexpressing the gene encoding gamma-glutamylcysteine synthetase, the first enzyme of the glutathione biosynthetic pathway. The plants were exposed to two mild stress conditions―oxidative stress elicited by methyl viologen (MV) and stress induced by the limited availability of phosphate. We observed that the mutants and transgenic plants showed similar shoot growth as that of the wild-type plants under mild abiotic stress. We then selected the synthesis mutants and performed multi-platform metabolomics and microarray experiments to evaluate the possible effects on the overall metabolome and the transcriptome. To understand the metabolic responses observed under mild abiotic stress, we conducted gene expression profiling by Affymetrix ATH1 GeneChip. pad2-1 and the wild type Col-0 samples were harvested at 18 day-old after germination under two different stresses, MV treatment and limited phosphorus conditions.

overall_design: According to Kusano, Tohge, Fukushima et al. (2011) The Plant Journal, we performed three independent hybridizations with the Affymetrix ATH1 GeneChip microarray according to the manufacturer's instructions (Affymetrix, http:// www.affymetrix.com). A single biological replicate was utilized in each hybridization. All raw data are available in the NCBI GEO (Barrett et al., 2013 NAR). The preprocessing and normalization/summarization of all CEL files were with the Bioconductor (Gentleman et al., 2004 Genome Biol) and a robust multi-chip average (RMA) (Bolstad et al., 2003 Bioinfo). The quality of GeneChip data was assessed by AFFYPLM package (Bolstad et al., 2005). We used the annotation of each gene in the CSV file ATH1-121501.na31.annot.csv (downloaded on April 2012) released by the Affymetrix ATH1 GeneChip microarray.　The differentially expressed genes were detected with the LIMMA package (Smyth, 2004), which provides FDR -adjusted p-values for multiple testing (Benjamini and Hochberg, 1995). The significance level was set at FDR < 0.05. We visualize the transcript profiles by MAPMAN 2.2.0 (Thimm et al., 2004). GO enrichment analysis was done with TAIR website (http://www.arabidopsis.org/) (Lamesch et al., 2012 NAR)

first: Miyako

last: Kusano


title: Single embryo analysis of monozygotic twin blastocysts of the mouse respecting pair associations

first: Michele

last: Boiani

summary:
Upon 2-cell embryo splitting, individual blastomeres were cultured in KSOM(aa) medium and developed into blastocysts, which were compared and contrasted with each other respecting pair associations (e.g. twin vs cotwin)
Transcriptome analysis revelaled minimal differences between twins and unmanipulated controls, in contrast to larger differences between twins and cotwins; these differences are mainly related to the epiblast lineage

overall_design: Pair association (e.g. twin and cotwin from the same 2-cell embryo) was rigorously observed

first: Verena

last: Nordhoff


title: Overexpression of MXRA7 in murine prostate cancer cell line RM1

status: Public on Jul 01 2017

city: Suzhou

first: Yiqiang

last: Wang

state: Jiangsu

address: 111 Renai Road

institute: Xi'an Jiaotong-Liverpool University

summary: Murine prostate cancer cells RM1 were transfected with a fakery murine MXRA7 cDNA in pcDNA3.1 vector. Controls were RM1 transfected with pcDNA3.1 vector. G418 resistant colonies were obtained, and gene expression profiling was performed using Agilent 4*44K array and dual labeling.

overall_design: Three triplicates were included for RM1-VE (vechile vector transfected RM1 cell line) and RM1-MXRA7 (MARA7 transfected RM1 cell line) respectively, thus producing three pairs of samples for array, namely MXRA7/VE rep1, rep2 rep3.

first: Yabin

last: Hu


title: MHC Class I antibody induced gene expression in mouse obliterative airway disease

status: Public on Jul 29 2017

city: Phoenix

first: Deepak

middle: K

last: Nayak

state: Arizona

address: 475 N. 5th Street

institute: University of Arizona College of Medicine

summary:
To further understand the early molecular events in antibody mediated chronic inflammation of the lungs, we utilized a murine Obliterative Airway Disease (OAD) model of native lungs where Abs to MHC class I induces bronchiolar obliteration and fibrosis. This study identified a unique transcriptional profile with a set of genes that were stimulated while another set of genes that were repressed in anti MHC I treated lungs compared to that of isotype treated lungs.
Lung transplantation (LTx) is an accepted clinical intervention for various intractable pulmonary dysfunctions. However, de novo Abs to mismatched donor HLA (DSA) predispose lung-grafts to chronic rejection, Bronchiolitis Obliterans Syndrome (BOS). The anti-MHC induced mouse OAD model, the only available preclinical model for study of early pathogenesis following MHC ligation, produces lesions analogous to BOS.

overall_design: Induction of gene expression was measured following intrabronchial administration of anti-MHC class I (H-2Kb) Ab at 200μg/mouse. Samples were collected on days 1, 2, 3 and 6 post-Ab administration. Isotype matched control Ab was administered at an equivalent dose and gene expression profile in isotype treated group served as the base line expression and was compared with that of anti-H-2Kb treated group. A total of 24 samples were processed with two treatment groups (anti-H-2Kb,  isotype), four time points (days 1, 2, 3 and 6) and three biological replicates.

first: Fangyu

last: Zhou

first: Jing

last: Huang

first: Moriya

last: Tsuji

first: Jinsheng

last: Yu

first: Ramsey

last: Hachem

first: Andrew

last: Gelman

first: Ross

last: Bremner

first: Min

last: Xu

first: Michael

last: Smith

first: Thalachallour

last: Mohanakumar


title: Estrogen receptor-dependent attenuation of hypoxia-induced changes in the lung genome of pulmonary hypertension rats

city: Indianapolis

first: Tim

last: Lahm

address: 980 W Walnut Street

institute: Indiana University

summary: 17β-estradiol (E2) exerts complex and context-dependent effects in pulmonary hypertension. In hypoxia-induced pulmonary hypertension (HPH), E2 attenuates lung vascular remodeling through estrogen receptor (ER)-dependent effects; however, ER target genes in the hypoxic lung remain unknown. In order to identify the genome regulated by the E2-ER axis in the hypoxic lung, we performed a microarray analysis in lungs from HPH rats treated with E2 (75 mcg/kg/d) ± ER-antagonist ICI182,780 (3 mg/kg/d). Untreated HPH rats and normoxic rats served as controls. Using a false discovery rate of 10%, we identified a significantly differentially regulated genome in E2-treated vs. untreated hypoxia rats. Genes most up-regulated by E2 encoded matrix metalloproteinase 8, S100 calcium binding protein A8, and IgA Fc receptor; genes most down-regulated by E2 encoded olfactory receptor 63, secreted frizzled-related protein 2, and thrombospondin 2. Several genes affected by E2 changed in the opposite direction after ICI182,780 co-treatment, indicating an ER-regulated genome in HPH lungs. The bone morphogenetic protein antagonist Grem1 (gremlin 1) was up-regulated by hypoxia, but found to be among the most down-regulated genes after E2 treatment. Gremlin 1 protein was reduced in E2-treated vs. untreated hypoxic animals, and ER-blockade abolished the inhibitory effect of E2 on Grem1 mRNA and protein. In conclusion, E2 ER-dependently regulates several genes involved in proliferative and inflammatory processes during hypoxia. Gremlin 1 is a novel target of the E2-ER axis in HPH. Understanding the mechanisms of E2 gene regulation in HPH may allow for selectively harnessing beneficial transcriptional activities of E2 for therapeutic purposes.

overall_design: Hypoxia untreated and treated with 17β-estradiol alone and 17β-estradiol + fulvestrant are compared to normoxia in rat lung tissue.

first: Jeanette

middle: N

last: McClintick

first: Andrea

last: Frump

first: Marjorie

last: Albrecht


title: Transcriptome and proteome analyses and the role of atypical calpain protein and autophagy in the spliced leader silencing pathway in Trypanosoma brucei

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

summary: Under persistent ER stress, Trypanosoma brucei parasites induce the spliced leader silencing (SLS) pathway. In SLS, transcription of the SL RNA gene, the SL donor to all mRNAs, is extinguished, arresting transsplicing and leading to programmed cell death(PCD). In this study, we investigated the transcriptome following silencing of SEC63, a factor essential for protein translocation across the ER membrane, and whose silencing induces SLS. The proteome of SEC63-silenced cells was analyzed with an emphasis on SLS-specific alterations in protein expression, and modifications that do not directly result from perturbations in trans-splicing. One such protein identified is an atypical calpain SKCRP7.1/7.2. Cosilencing of SKCRP7.1/7.2 and SEC63 eliminated SLS induction due its role in translocating the PK3 kinase. This kinase initiates SLS by migrating to the nucleus and phosphorylating TRF4 leading to shut-off of SL RNA transcription. Thus, SKCRP7.1 is involved in SLS signaling and the accompanying PCD. The role of autophagy in SLS was also investigated; eliminating autophagy through VPS34 or ATG7 silencing demonstrated that autophagy is not essential for SLS induction, but is associated with PCD. Thus, this study identified factors that are used by the parasite to cope with ER stress and to induce SLS and PCD.

overall_design: The transcriptome was analyzed by microarray for 3 days following induction of SEC63 silencing, and was compared to the transcriptome of uninduced cells (silenced cells from days 1, 2 and 3 days versus un-induced cells). Normalized data from two to four biological replicates were analyzed.

first: Ronen

last: Hope

first: Katarina

last: Egarmina

first: Konstantin

last: Voloshin

first: Shai

last: Carmi

first: Dror

last: Eliaz

first: Yaron

last: Drori

first: Shulamit

last: Michaeli


title: Adult Skin-derived Neural Precursors Engraft into the Hippocampus and Rescue Memory Dysfunction.

status: Public on Jul 14 2017

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

institute: The Westmead Institute for Medical Research

summary: Repopulation of brain circuits by neural precursors is a promising therapeutic strategy under investigation in animal models of neurodegeneration. Major limitations include a propensity for glial differentiation in vivo and the use of transgenic modifications that restrict rapid clinical translation. Here, we detail a two-step method for producing adult neural precursor cells from a small autologous skin sample. These cells express neural stem/progenitor cell markers, are highly homogenous, rate-limited by virtue of low number of maximal cell doublings, and differentiate almost exclusively into neurons without expression of glial molecular markers. These characteristics are recapitulated in vivo following transplantation in the aged rodent brain. Cell transplantation into the hippocampus is safe and leads to widespread neuronal engraftment and synaptogenesis. Donor cells display appropriate anatomical architecture, become electrophysiologically active and establish synaptic connections within the host brain. Moreover, selective hippocampally-dependent place recognition memory deficits are reversed. Adult skin-derived neural precursors overcome many of the limitations present in current stem cell therapies.   Accordingly, these cells have potential use as a cell therapy treatment for the regeneration of depleted or dysfunctional neuronal circuits in patients with neurodegenerative disorders.

overall_design: Primary cell culture was derived from canine fibroblast, brain and skin samples, RNA extract and put forward for Affymetrix array gene expression profiling

first: Aileen

last: Lowe

last: Valenzuela

first: Tomas

last: Duncan


title: Identification of differentially expressed miRNAs in drug resistant and drug sensitive breast cancer tissues

city: Jinan

first: Peng

last: Gao

address: Wen Hua Xi Road 44

institute: Shandong University

summary: To identify miRNAs involved in drug resistance of human breast cancer, a miRNA microarray was performed on 5 cases of drug resistant tissues and 5 cases of drug sensitive tissues.The expression levels of totally 2019 miRNAs in 5 pairs of matched, drug resistant and drug sensitive tissues were examined by microarray. There were 27 differentially expressed miRNAs between drug resistant and drug sensitive tissues were identified of which there were 11 significantly up-regulated while the other 16 were down-regulated in drug resistant tissues compared to drug sensitive tissues. It was found that miR-489 was one of the most downregulated miRNAs in drug resistant tissues.

overall_design: Group 1: Examination of miRNAs in drug resistant tissues (5 cases), including C100, C17, C28, C22 and C115. Group 2: Examination of miRNAs in drug sensitive tissues (5 cases), including H801, H31, H19, H20, and H32.

first: Xu

last: Chen


title: The putrescine production in Enterococcus faecalis is transcriptionally induced by tyrosine.

status: Public on Mar 31 2017

city: Villaviciosa

first: Victor

last: Ladero

state: Select if applicable

address: Paseo Rio Linares S/N

department: Technology and Biotechnology of dairy products

institute: IPLA-CSIC

summary: The aim was to study the transcriptional profiling of the E. faecalis V583 in presence and absence of tyrosine. We compared the expression profile of the strains grown in M17 medium with glucose as carbon source (GM17)  and suplemented with agmatine in presence and absence of tyrosine.

overall_design: E. faecalis V583 cells grown with 15 mM tyrosine (test) compared with E. faecalis V583 cells grown without tyrosine (reference). Both strains grown in GM17 medium suplemented with 5 mM agmatine.

first: Marta

last: Perez

first: Beatriz

last: del Rio

first: Begoña

last: Redruello

first: Anne

last: de Jong

first: Oscar

last: Kuipers

first: Jan

last: Kok

first: M

last: Martin

first: Maria

last: Fernandez

first: Miguel

middle: A

last: Alvarez


title: Proteome and secretome analysis reveals differential post-transcriptional regulation of Toll-like receptor responses

status: Public on Jun 12 2017

city: Bethesda

first: Timothy

last: Myers

summary: The innate immune system is the organism’s first line of defense against pathogens. Pattern recognition receptors (PRRs) are responsible for sensing the presence of pathogen-associated molecules. The prototypic PRRs, the membrane-bound receptors of the Toll-like receptor (TLR) family, recognize pathogen-associated molecular patterns (PAMPs) and initiate an innate immune response through signaling pathways that depend on the adaptor molecules MyD88 and TRIF. Deciphering the differences in the complex signaling events that lead to pathogen recognition and initiation of the correct response remains challenging. Here we report the discovery of temporal changes in the protein signaling components involved in innate immunity. Using an integrated strategy combining unbiased proteomics, transcriptomics and macrophage stimulations with three different PAMPs, we identified differences in signaling between individual TLRs and revealed specifics of pathway regulation at the protein level.

overall_design: RAW264.7 cells were treated with individual TLR ligands (100 ng/mL LPS, 1 μM P3C, and 1 μM R848 for stimulation of TLR4, TLR2, and TLR7, respectively) for either 1, 2 or 4 h. Two replicates for each condition.

first: Marijke

last: Koppenol-Raab

first: Virginie

middle: H

last: Sjoelund

first: Bhaskar

last: Dutta

first: Nathan

last: Manes

first: Zachary

last: Benet

first: Iain

last: Fraser

first: Aleksandra

last: Nita-Lazar


title: Population Prehistory in Island Southeast Asia

status: Public on Aug 02 2017

city: Tucson

first: Tatiana

middle: M.

last: Karafet

state: AZ

address: BSW #246, 1041 E Lowell Str.

department: ARL

institute: University of Arizona

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

summary: Affymetrix single nucleotide polymorphism (SNP) array data were collected to study genome-wide patterns of genomic variation across a broad geographical range of Island Southeast Asian populations. This region has experienced an extremely complex admixture history. Initially settled ~50,000 years ago, Island Southeast Asia has since been the recipient of multiple waves of population movements, most recently by Austronesian-speaking groups ultimately from Neolithic mainland Asia and later arrivals during the historic era from India and the Middle East. We have genotyped SNPs in ~500 individuals from 30 populations spanning this entire geographical region, from communities close to mainland Asia through to New Guinea. Particular attention has been paid to genomic data that are informative for population history, including the role of recent arrivals during the historic era and admixture with archaic hominins.

overall_design: 506 samples from 30 populations has been genotyped using the Affymetrix platform GPL18441

first: Michael

middle: F

last: Hammer

first: J

last: Lansing

first: Murray

last: Cox

first: Herawati

last: Sudoyo

first: Olga

middle: V

last: Savina


title: Genome-wide analysis of sphingosine-1-phosphate receptor-1 (S1PR1)-dependent gene expression in tumor-associated macrophages

status: Public on Jul 20 2017

city: Frankfurt

first: Andreas

last: Weigert

address: Theodor-Sern-Kai 7

department: Medicine

institute: Goethe-University

summary: The study was designed to identify a common set of genes under the control of S1PR1 in CD11b-high macrophages from both oncogene-induced breast tumors (PyMT) or carcinogen-induced fibrosarcomas (MCA). The goal was to identify common regulators of lymphangiogenesis in both models.

overall_design: Total RNA from FACS-sorted wildtype or S1PR1 knockout CD11b-high macrophages of PyMT and MCA tumors