title: Comprehensive Investigation of Archival and Prospectively Collected Samples Reveals No Association of the XMRV Gammaretrovirus with Prostate Cancer

city: San Francisco

first: Charles

last: Chiu

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

summary: XMRV, or xenotropic murine leukemia virus (MLV)-related virus, is a novel gammaretrovirus originally identified in studies that analyzed tissue from prostate cancer patients in 2006 and blood from patients with chronic fatigue syndrome (CFS) in 2009. However, a large number of subsequent studies failed to confirm a link between XMRV infection and CFS or prostate cancer. On the contrary, recent evidence indicates that XMRV is a contaminant originating from the recombination of two mouse endogenous retroviruses during passaging of a prostate tumor xenograft (CWR22) in mice, generating laboratory-derived cell lines that are XMRV-infected. To confirm or refute an association between XMRV and prostate cancer, we analyzed prostate cancer tissues and plasma from a prospectively collected cohort of 39 patients as well as archival RNA and prostate tissue from the original 2006 study. Despite comprehensive microarray, PCR, FISH, and serological testing, XMRV was not detected in any of the newly collected samples or in archival tissue, although archival RNA remained XMRV-positive. Notably, archival VP62 prostate tissue, from which the prototype XMRV strain is derived, tested negative for XMRV on re-analysis. Analysis of viral genomic and human mitochondrial sequences revealed that all previously characterized XMRV strains are identical and that the archival RNA had been contaminated by an XMRV-infected laboratory cell line. These findings reveal no association between XMRV and prostate cancer, and underscore the conclusion that XMRV is not a naturally acquired human infection.

overall_design:
The Virochip microarray (version 5.0, Viro5AGL-60K platform) was used to screen RNA extracts from prostate tissue for XMRV to determine whether there is an association between the virus and prostate cancer.

We used the ViroChip microarray to screen 22 archived prostate biopsies extracted in 2006 and 39 prospectively collected prostate biopsies for the virus, Xenotropic Murine Leukemia Virus-Related Virus (XMRV). We used custom-commercial microarrays from Agilent Technologies. The microarray platform GPL11662 consists of 62,976 probes [PMID 21779173], including all of the viral probes from the previous v2.0 (MV), v3.0 (V3) and v4.0 (V4) designs [PMIDs 18768820, 16983602, 16609730, 12429852, 9843981].

For this study, 61 experimental ViroChip microarrays derived from prospectively collected RNA extracted prostate tissue and frozen RNA from archived prostate from a 2006 study were analyzed. Additionally, two XMRV-positive control microarrays from the cell line, 22Rv1, were hybridized, for a total of 63 ViroChip microarrays. Some RNA extracts were enriched for polyadenylated (polyA) transcripts prior to hybridization.

middle: Y

first: Deanna

last: Lee


title: Deregulated sex chromosome gene expression with male germ cell-specific loss of Dicer1 (miRNA array data)

status: Public on Sep 10 2012

city: Bar Harbor

first: Timothy

middle: Michael

last: Stearns

state: ME

address: 600 Main Street

department: Computational Sciences

country: USA

institute: The Jackson Laboratory

summary: MicroRNAs (miRNAs) are a class of endogenous, non-coding RNAs that mediate post-transcriptional gene silencing by inhibiting mRNA translation and promoting mRNA decay. DICER1, an RNAse III endonuclease encoded by Dicer1, is required for processing short 21-22 nucleotide miRNAs from longer double-stranded RNA precursors. Here, we investigate the loss of Dicer1 in mouse postnatal male germ cells to determine how disruptions in the miRNA biogenesis pathway may contribute to infertility. Reduced levels of Dicer1 transcripts and DICER1 were confirmed in germ cell knock-out (GCKO) testes by postnatal day 18 (P18). Compared to wild-type (WT) at 8 weeks, GCKO males had no change in body weight, yet showed significant reductions in testis mass and sperm number. Histology and fertility tests confirmed spermatogenic failure in GCKO males. Array analyses at P18 showed 96% of miRNA genes were down-regulated and 37% of protein-coding genes were differentially expressed in GCKO testes. Interestingly, we observed preferential overexpression of genes on the sex chromosomes in GCKO testes, with more than 80% of the genes overlapping those proposed to undergo meiotic sex chromosome inactivation (MSCI) in the germ cells. Compared to WT, GCKO mice showed higher percentages of cells at early meiotic stages (leptotene and zygotene) but lower percentages at later stages (pachytene, diplotene and metaphase I), providing evidence that deletion of Dicer1 leads to disruptions in meiotic progression. Furthermore, we observed fewer elongating spermatids with proper translational activation of transition protein 2 (Tnp2), protamine 1 and 2 (Prm1 and Prm2) in GCKO testes after step 12-14. Therefore, deleting Dicer1 in early postnatal germ cells causes misregulation of transcripts encoded by genes on the sex chromosomes, impairs meiotic progression and post-meiotic translational control and results in spermatogenic failure and infertility.

overall_design: Total RNA, including miRNAs, were purified from a total of six individual mouse samples. The tissue collected was obtained from wild-type (control; n=3) and Dicer1 germ cell knockout (mutant; n=3) testes on P18. One miRNA GCKO sample, M36, was determined to be of poor quality and was excluded from the study; thus, a total of five miRNA samples were analyzed.

first: Anne

middle: R

last: Greenlee

first: Meng

middle: S

last: Shiao

first: Elizabeth

last: Snyder

first: F

middle: W

last: Buass

first: Tongjun

last: Gu

middle: M

first: Manju

last: Sharma

middle: P

last: Murchison

first: Gabriella

middle: C

last: Puenta

first: Robert

middle: E

last: Braun


title: Genomic and transcriptomic analyses of Lactococcus lactis strains

status: Public on Sep 07 2012

city: Toulouse

first: Muriel

last: Cocaign-Bousquet

address: 135 avenue de Rangueil

department: UMR5504 INSA/CNRS - UMR792 INSA/INRA

country: France

institute: Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés

type:
Expression profiling by array
Genome variation profiling by array

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

overall_design: Refer to individual Series


title: Goldengate Methylation analysis: Ewing Sarcoma

status: Public on Sep 01 2012

city: Nashville

first: Scott

last: Borinstein

address: 2200 Pierce Ave

institute: Vanderbilt University

summary: Methylation array analysis of Ewing sarcoma primary tumors and cell lines compared to mesechymal stem cells

overall_design: Bisulfite converted DNA analyzed by bead array


title: Analysis of gene expression of Peripheral Blood Mononuclear Cells (PBMC) in Systemic Juvenile Idiopathic Arthrits (sJIA)

status: Public on Sep 06 2012

city: Stanford

first: Claudia

last: Macaubas

state: CA

address: 300 Pasteur Drive

department: Pediatrics

institute: SUMC

summary: sJIA patients were recruited through the Stanford Pediatric Rheumatology Clinic. All sJIA study subjects met amended ILAR criteria for the diagnosis of SJIA. The study was approved by the Stanford Institutional Review Board.

first: Chetan

last: Deshpande


title: Engineering endochondral ossification using Sonic Hedgehog for bone regeneration

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: Endochondral ossification (EO) is the natural route for the regeneration of large and mechanically challenged bone defects. Regeneration occurs via a fibrocartilagenous phase which turns into bone upon vascularization and the formation of a transient collagen type X extra cellular matrix. These two critical initiator of EO are mediated by Hedgehog proteins. We investigated a tissue engineering approach using Sonic Hedgehog (Shh) as a pleiotropic factor regulating the in vitro formation of a vascularized bone tissue precursor for in vivo endochondral bone formation. The tissue engineered graft was formed using human mesenchymal stem cells and prevascularized using human umbilical vein endothelial cells. We show that Shh induced, in vitro, the maturation of the engineered vascular network along with the expression of collagen type X which resulted, in vivo, in an improved vascularization and the rapid formation of large amounts of osteoids through EO. Osteoids further matured into, currently unmatched, clinically relevant amount of lamellar bone including osteoclasts, bone lining cells and bone marrow-like cavities. This result suggests that Hh is a master regulator of EO allowing for the formation of complex tissues with considerable therapeutic potential for bone regeneration.

overall_design: The effect of Cyclopamine on expression of Hedgehog, angiogenesis and axon guidance marker genes was analyzed by seeding a coculture of 92% hMSCs and 8% huvEC supplemented or not in cyclopamine, for 12 days

first: N

last: Rivron

first: C

last: Raiss

first: J

last: Rouwkema

last: Liu

first: A

last: Nandakumar

first: R

last: Truckenmuller

last: Gretz

middle: A

last: vanBlitterswijk


title: Slr0643, a S2P Homolog, Is Essential for Acid Acclimation in Cyanobacterium Synechocystis sp. PCC 6803

status: Public on Sep 18 2012

city: Guangzhou

first: Gu

last: CHEN

address: 381 Wushan Road

country: China

institute: South China University of Technology

summary: Every cyanobacterial species contains gene encoding site-2-protease (S2P) homolog. The studied prokaryotic S2P homologs play essential roles in regulating stress response through intramembrane proteolysis of membrane-bound anti-sigma factors. Here, gene of Slr0643, one of four S2P homologs in Synechocystis sp. PCC 6803, was insertionally disrupted to explore its physiological role. Only a partially segregated mutant was obtained, indicating its indispensability for growth. The partially disrupted mutant could not grow at pH 6.5, while wild type acclimated to pH 6.5 quickly. The slr0643 gene expression was transiently induced after pH transfer from 7.5 to 6.5. Both evidences demonstrated the pivotal role of fully functional Slr0643 in acid acclimation. DNA microarray and quantitative RT-PCR analyses decoded genes involved in early acid acclimation and revealed differentially expressed genes due to slr0643 disruption at both pH conditions. Early acid acclimation to pH 6.5 included upregulation of sigH, hik16 and hik35, and downregulation of pcrR and sigG; as well as downregulation of porins and upregulation of inorganic carbon and nitrogen transporters. Defective photosynthesis and excess expression of NADH dehydrogenase, together with over upregulation of carbon transporter and repression of nitrogen transporter and metabolism gene contributed to the acid lethality of mutant at pH 6.5. Most interestingly, analysis of microarray data revealed the close relationship between slr0643 disruption and expression of sigH operon. Therefore it was implied that Slr0643/Sll0857/SigH might acts through S2P/anti-Sigma factor/Sigma factor mechanism to play a role in acid acclimation.

overall_design: Loop design was used to compare differential expression of wild type and mutant at pH 7.5 and pH 6.5 respectively, including dye-swape. Biological variation was sampled by extracting RNA from three independent experiments and pooling them together before hybridizations. Two or four replicate chips for each comparison and two replicate printings per chip represent technical repeats.

first: Xu

last: ZHANG

first: Chunyan

last: Qin

first: Yuling

last: Wang


title: microRNA profiling in duodenal ulcer disease caused by Helicobacter pylori infection in a Western population.

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: The aim of this study was to identify and assess the utility of miRNAs as diagnostic surrogate markers for H.pylori infection. For this purpose, we analyzed the miRNA expression profile by microarrays in the antral mucosa of well characterized dyspeptic patients and then applied the most significant set of miRNAs to an independent validation group. Our results shows that a set of miRNAs are deregulated during chronic gastric inflammation and that this set may be may be useful as a surrogate marker for determining the presence of H.pylori.

overall_design: Total RNA from antral biopsies from patients with Helicobacter pylory (Hp) infection (with or without virulence factor caG) and healthy volunteers were isolated. MiRNA expression profiles were analyzed using miRNA microarray platform.

first: S

last: Lario

first: M

middle: J

last: Ramírez-Lázaro

last: Aransay

last: Montserrat

last: Casalots

first: F

last: Junquera

last: Alvarez

last: Segura

last: Campo

first: X

last: Calvet


title: RcsB  contributes to the distinct stress fitness between Escherichia coli O157:H7 curli variants of 1993 Hamburger-associated outbreak strains

status: Public on Aug 31 2012

city: Albany

first: Craig

middle: T

last: Parker

address: 800 Buchanan St

department: PSM

institute: USDA ARS

summary: Curli are adhesive fimbriae of Enterobactericaeae and are involved in surface attachment, cell aggregation and biofilm formation. We previously reported that natural curli variants of E. coli O157:H7 (EcO157) displayed distinct acid resistance; however, this difference was not linked to the curli fimbriae per se. Here, we investigated the underlying molecular basis of this phenotypic divergence between the curli variants. Among curli-producing (C+) variants isolated from the 1993 U.S. hamburger-associated outbreaks strains, we identified large deletions in the rcsB gene that encodes the response regulator of RcsCDB two-component signal transduction system of rcsB ,. Further comparison of stress fitness revealed that C+ variants were also significantly more sensitive to heat shock, but remained similar resistance to osmotic stress and oxidative damage as curli-deficient (C-) variants. Transcriptomics analysis uncovered a large number of differentially expressed genes between the curli variants, characterized by the enhanced expression of genes related to biofilm formation, virulence, catabolic activity and nutrients uptake, but marked decrease in transcription of genes related to various stress resistance in C+ variants. Supplying C+ variants with a functional rcsB restored cells resistance to heat shock and acid challenge, but blocked the curli production, confirming that inactivation of RcsB in C+ variants was the basis of fitness segregation within the EcO157population. This study provides an example of how genome instability of EcO157promotes the intra-population diversification, generating sub-populations carrying an array of distinct phenotypes that may confer the pathogen survival advantages in host and nonhost environments.

overall_design: Three replicates for isolates RM6607R, RM6607W, RM6608R, RM6608W independently grown from single colonies in LB broth and incubated at 28°C overnight on a shaker (150 rpm).  The cells were collected by centrifugation, washed once in LBNS broth, and inoculated in 25ml of LBNS broth with a concentration equivalent to 0.001OD600 ml-1. The cultures were incubated at 28°C for 24 h with aeration (150 rpm). At the end of incubation, ice-cold phenol-ethanol (5%:95%) solution was immediately added to culture at a final concentration of 20% (volume), and the mixture was incubated on ice for 30 min.  The cells were collected by centrifugation at 4°C and the pellets were stored at -80°C until RNA extraction. The cells were collected by centrifugation, washed once in LBNS broth, and inoculated in 25ml of LBNS broth with a concentration equivalent to 0.001OD600 ml-1. The cultures were incubated at 28°C for 24 h with aeration (150 rpm). At the end of incubation, ice-cold phenol-ethanol (5%:95%) solution was immediately added to culture at a final concentration of 20% (volume), and the mixture was incubated on ice for 30 min.  The cells were collected by centrifugation at 4°C and the pellets were stored at -80°C until RNA extraction. RNA was isolated using Promega SV Total RNA kit.  A type 2 gene expression experimental design was used, with fluorescently labeled genomic DNA as a reference channel in each experiment as described by Lucchini, S., et al. 2005. Infect Immun 73:88-102.

first: Michelle

middle: Q

last: Carter

first: Jacqueline

last: Louie

first: Steven

last: Huynh

first: Clifton

middle: K

last: Fagerquist

first: Maria

last: Brandl

first: Robert

last: Mandrell


title: Characterizing gene regulatory networks in the brain of largemouth bass inhabiting rivers containing high levels of methyl-mercury

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF


title: Array CGH analysis of human colorectal tumors

city: Sapporo

first: Eiichiro

last: Yamamoto

address: South-1, West-16, Chuo-ku

country: Japan

institute: Sapporo medical university

type: Genome variation profiling by genome tiling array

summary: The concept of the CpG island methylator phenotype (CIMP) in colorectal cancers (CRCs) is widely accepted, though the timing of its occurrence and its interaction with other genetic defects early during carcinogenesis remains largely unknown. Our aim was to uncover the molecular evolution of CIMP CRCs through integrative analysis of endoscopic, histological and molecular signatures in precancerous and malignant colorectal lesions.

overall_design: A total of 84 endoscopically obtained human colorectal tumor was analyzed using Agilent CGH microarray. Copy number aberration was compared with clinicopathological features and DNA methylation status.

first: Hiromu

last: Suzuki


title: Methylated CpG island amplification (MCA) microarray analysis of human colorectal tumors

type: Methylation profiling by genome tiling array

summary: The concept of the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC) is widely accepted, though the timing of its occurrence and its interaction with other genetic defects are not fully understood. Our aim in this study was to unravel the molecular development of CIMP cancers by dissecting their genetic and epigenetic signatures in precancerous and malignant colorectal lesions.

overall_design: A total of 88 samples (16 normal colon tissues taken from adjacent tumor tissue, 70 colorectal tumor tissues and 2 cell lines) was analyzed using MCA microarray. Aberrant DNA methylation was compared with clinicopathological features and copy number.


title: Gene-expression profiling of prostate tumors

status: Public on Aug 23 2012

last: Stanford Microarray Database

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary: Increasing evidence suggests that prostate cancer is overdiagnosed and overtreated, and prognostic biomarkers would aid in treatment selection. To define prognostic biomarkers for aggressive prostate cancer, we carried out gene-expression profiling of 98 prostate tumors and 52 benign adjacent prostate tissue samples with detailed clinical annotation. We identified 28 transcripts significantly associated with recurrence after radical prostatectomy including NuSAP, a protein that binds DNA to the mitotic spindle. Elevated NuSAP transcript levels were associated with poor outcome in two independent prostate cancer gene-expression datasets. To characterize the role and regulation of NuSAP in prostate cancer, we studied the expression of NuSAP in the LNCaP and PC3 human prostate cancer cell lines. Posttranscriptional silencing of the NuSAP gene severely hampered the ability of PC3 to invade and proliferate in vitro. The promoter region of the NuSAP gene contains two CCAAT boxes and binding sites for E2F. Transient transfection of an E2F1 cDNA and 431bp of the NuSAP promoter demonstrated E2F1 as an important regulator of expression. Deletion of the E2F-binding site at nucleotide 246 negated the effects of E2F1 on NuSAP expression. Electrophoretic mobility shift assays demonstrated that nuclear extracts of cells overexpressing E2F1 bound directly to the E2F-binding site in the NuSAP promoter region. Finally, immunohistochemistry showed a strong correlation between E2F1 and NuSAP expression in human prostate cancer samples. NuSAP is a novel biomarker for prostate cancer recurrence after surgery and its overexpression appears to be driven in part by E2F1 activation.

first: Zulfiqar

last: Gulzar


title: Microarray analysis of up-regulated genes accompanying filial imprinting in domestic chicks (Gallus gallus domesticus)

status: Public on Aug 20 2012

city: Sagamihara-shi

first: Shinji

last: Yamaguchi

state: Kanagawa

address: Midori-ku, Suwarashi,

department: Pharmaceutical Sciences

institute: Teikyo University

summary: Newly-hatched domestic chick serves as an important model for studies of neural and behavioral plasticity, particularly with respect to learning and memory such as filial imprinting. Imprinting is assumed to be a unique case of recognition learning with some characteristic features, such as sensitive period and irreversibility. However, the molecules involved in the memory process are yet to be fully identified. To address this issue, we attempted to identify the genes differentially expressed at an earlier phase of filial imprinting than described in our previous report (Brain Res. Bull.76, 275-281 (2008)). One-day-old chicks were trained for imprinting for 1 h and whole brains were collected and used for cDNA microarray analysis and quantitative RT-PCR. We identified 18 genes upregulated accompanying filial imprinting. These results suggested that the increase of these 18 genes associated with filial imprinting might play an important role in the acquisition of memory in the filial imprinting.

overall_design: Total RNA was extracted from whole brains of trained chicks (n=16) and control dark-reared chicks (n=16). Using these total RNAs, we performed RT-PCR to distinguish male chicks from females. Then total RNAs were separated and mixed in four groups (1, male trained (n=8); 2, female trained (n=8); 3, male dark-reared (n=8); and 4, female dark-reared chicks (n=8)), and we performed cDNA microarray expression analysis to identify the upregulated genes following imprinting (1 versus 3 and 2 versus 4).

first: Koichi

last: Homma


title: microRNAs expression profile in Myotonic Dystrophy type-2 (DM2) patients

status: Public on Aug 27 2012

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

summary:
Myotonic Dystrophy Type-2 (DM2) is an autosomal dominant disease caused by the expansion of a CCTG tetraplet repeat. It is a multisystemic disorder, affecting skeletal muscles, the heart, the eye, the central nervous system and the endocrine system
The expression of 365 miRNAs was measured in the muscle of DM2 patients and compared it to controls and were identified distinct miRNAs modulated in DM2 patients compared to controls.

overall_design: Our study included 10 DM2 and 9 control (CTR) muscle biopsies from biceps brachii. DM2 and CTR were age- and sex- matched. Most DM2 patients had myotonia and cataract, two disease hallmarks, while differences in other clinical parameters (muscle strenght, diabetes, CPK, FT3, FT4, TSH, ejection fraction) were not significant. miRNAs expression was assessed by Applied Biosystems Human TaqMan Low Density Array (TLDA, v1.0).

first: Simona

last: Greco

first: Pasquale

last: Fasanaro

first: Alessandra

last: Perfetti

first: Giovanni

last: Meola


title: Bi-phenotypic B-lymphoid/myeloid cells expressing low levels of Pax5 - potential targets of BAL development

status: Public on Aug 14 2012

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Retroviral transduction of Pax5-deficient pro/preB cell lines with a doxycycline-inducible (TetON) form of the human Pax5 (huPax5) gene yielded cell clones which could be induced to different levels of huPax5 expression. Clones inducible to high levels developed B220+/CD19/+IgM+ B cells, while clones with low levels differentiated to B220+/CD19- /CD11b+/Gr-1- B-lymphoid/myeloid “bi-phenotypic” cells in vitro and in vivo. “Bi-phenotypic” cells could also be developed from high level-inducible cells by lower concentrations of doxycycline, inducing lower levels of huPax5 in vitro. Microarray analyses of genes expressed at these lower levels of huPax5 identified C/ebpα, C/ebpδ, Pu.1, Csf1r, Csf2r and Gata-3 as myeloid-related genes selectively expressed in the pro/preB cells which can develop under myeloid/lymphoid conditions to “bi-phenotypic” cells. Therefore, reduced expression of huPax5 during the induction of early lymphoid progenitors to B-lineage-committed cells can fix this cellular development at a stage that has previously been seen during embryonic development and in ALL-like “bi-phenotypic” acute leukemias (BAL).

overall_design: Microarray experiments were performed as dual-color hybridizations. In order to compensate specific effects of the dyes and to ensure statistically relevant data analysis, a color-swap dye-reversal was performed.

first: Szandor

last: Simmons

first: Ingrid

last: Wolf

last: Drewell

first: Corinne

last: Bouquet

first: Fritz

last: Melchers


title: miRNA profiling of Jurkat with stably integrated HTLV1-LTR in the presence of HTLV-1 Tax

status: Public on Aug 09 2012

city: Doylestown

first: Rasha

last: Elbaz

address: 3805 Old Easton Road

institute: Drexel University College Of Medicine

summary: RNA interference (RNAi) is a natural cellular mechanism to silence gene expression and is predominantly mediated by microRNAs (miRNAs) that target messenger RNA. Viruses can manipulate the cellular processes necessary for their replication by targeting the host RNAi machinery. This study explores the effect of human T-cell leukemia virus type 1 (HTLV-1) transactivating protein Tax on the RNAi pathway in the context of a chromosomally integrated viral long terminal repeat (LTR) using a CD4(+) T-cell line, Jurkat.

overall_design: Jurkat cells with stably integrated HTLV1-LTR were transfected with either pCMV-Tax or pCMV. Total miRNA was isolated, labeled and hybridized to the miRNA microarray as described by the manufacturer (Invitrogen). The hybridized slides were then analyzed on a GenePix scanner.

first: Saifur

last: Rahman

first: Kevin

last: Quann

first: Devanshi

last: Pandya

first: Shruti

last: Singh

first: Zafar

last: Khan

first: Pooja

last: Jain


title: Genome-wide copy number aberrations and methylation profiles in human colorectal lesions

first: Eiichiro

last: Yamamoto


title: Transcriptional repression of Hox genes by binding of HP1 and methylated H1 to H3K27me3 in C. elegans

status: Public on Aug 13 2012

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Elucidation of the biological role of H1 and HP1 in mammals has been difficult owing to the existence of a least 11 distinct H1 and three HP1 subtypes in mice. Therefore we decided to study the function of HP1 (HPL-1 and HPL-2) and H1 (HIS-24) related proteins in C. elegans, since hpls and his-24 deficient nematodes are viable. Global transcriptional analysis of the mutant animals revealed that expression of only a small number of genes was affected and HPLs, and HIS-24 appear to influence the expression of genes through either activation or repression. Interestingly, knockout of HPL-2 and HIS-24 caused chromatin structure changes in the germline without altering core histone modifications. Furthermore, the mutant animals showed abnormal development of the male tail and the ectopic expression of C. elegans HOM-C genes (egl-5 and mab-5) involved in the developmental patterning of the mating structures. Surprisingly, H3K27me3 chromatin mark presented at the C. elegans HOM-C gene promoters was recognized by HPL-2 and methylated form of HIS-24. We propose that methylated HIS-24 and HPL-2 bind independently to PcG target loci that have been trimethylated at H3K27 by C. elegans MES-2 [E(Z)] to transcriptionally repress  the Hox genes. Our results establish interplay of the H3K27me3 binding proteins, HP1/HPLs and H1/HIS-24 in the regulation of positional identity in the C. elegans males.

overall_design: The experiment was performed using biological independent replicates of pooled worms. For all KO mutants we used duplicates.

first: Maja

last: Studencka

first: Radosław

last: Wesołowski

first: Lennart

last: Opitz

last: Salinas-Riester

first: Monika

last: Jedrusik-Bode


title: Gene expression analysis of bovine day 16 embryos obtained from SCNT and IVP pregnancies

status: Public on Aug 15 2012

city: Bonn

first: Simret

middle: Betsha

last: Weldenegodguad

address: Endenicher Allee 15

department: ITW

institute: University of Bonn

summary: In vitro production systems, as well as cloning technology, may lead to persistent aberrations of gene expression patterns during embryonic and fetal development. In order to get a global overview of gene expression alteration induced by in vitro environment and somatic cell nuclear transfer, we performed microarray analysis of day 16 conceptuses obtained from SCNT, IVP and AI pregnancies.

overall_design: Day 7 blastocysts generated from AI, IVP and SCNT were transferred to synchronized cows. Comparable length of day 16 embryos were recovered and used for transcriptome analysis using GeneChip bovine genome array

last: Betsha

first: Michael

last: Hoelker

first: Dessie

last: Salilew-Wondim

first: Eva

last: Held

first: Franca

last: Rings

first: Christine

last: Grose-Brinkhause

first: Mehmet

last: Ulas Cinar

first: Vitea

last: Havlicek

first: Urban

last: Besenfelder

first: Ernst

last: Tholen

first: Christian

last: Looft

first: Karl

last: Schellander

first: Dawit

last: Tesfaye


title: Methylation profiling in gastric cancer

status: Public on Aug 17 2012

city: Daejeon

first: Myung Soon

last: Kim

address: Yeusung-gu

department: R&D

country: South Korea

institute: Genomictree

summary: Methylation profiling in gastric cancer : normal serum vs Early and Advanced cancer serum

overall_design: Direct comparison experiment : Normal vs EGC, Normal vs AGC

first: Nayoung

first: Taejeong

last: Oh


title: Chitin oligosaccharide-responsive genes in suspension-cultured rice cells

status: Public on Jul 25 2012

city: Tokyo

first: Kazunori

last: Okada

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

department: Biotechnology Research Center

institute: The University of Tokyo

summary: Chitin is a major component of fungal cell walls and serves as a molecular pattern for the recognition of potential pathogens in the innate immune systems of both plants and animals. In plants, chitin oligosaccharides have been known to induce various defense responses in a wide range of plant cells including both monocots and dicots. We identified chitine oligosaccharide-responsive genes in suspension-cultured rice cells 1-12 h after treatment using rice 44k microarray.

overall_design: Expression profiling in rice cells treated with chitin oligosaccharide for 1, 2, 4, 6, 8 and 12 h was compared with that in untreated control using two-color method with two biological replicates.

first: Koji

last: Miyamoto

first: Tetsuya

last: Chujo

first: Naoto

last: Shibuya

first: Hisakazu

last: Yamane

first: Hideaki

last: Nojiri


title: Ribosomal biogenesis genes play an essential and p53-independent role in pancreas development

status: Public on Jul 17 2012

city: Baltimore

first: Steven

last: Leach

state: MD

address: 733 N. Broadway, BRB 471

department: The Department of Surgery and Institute for Genetic Medicine

institute: Johns Hopkin University

summary: Analysis of transcriptional profiles in Sbds(ATG) MO-injected embryos with and without coinjection of p53(ATG) MO. We identified a large number of changes in transcript abundance associated with loss of Sbds.  Among the 24,278 annotated zebrafish genes in the platform, 4,892 significantly differentially expressed genes were identified.

overall_design: Embryos were carefully staged at 24 hpf and RNA was extracted from approximately 50 embryos per condition in Trizol, followed by purification using RNA miniprep columns (Qiagen).  Four independent experiments were extracted.  cDNA microarrays were performed at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Microarray Core Facility using 4x44K Zebrafish gene expression microarray slides (Agilent, Santa Clara, CA).

first: E

last: Provost

first: X

last: Zhone

first: S

middle: D


title: Microbe-induced inflammatory cytokines in Il10-/- colon tissue

status: Public on Jul 04 2012

city: Chapel Hill

first: Janelle

last: Arthur

state: NC

address: 111 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

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

overall_design: Refer to individual Series


title: Amyotrophic lateral sclerosis

status: Public on Jul 26 2012

city: Boston

first: Oleg

last: Butovsky

state: MA

address: 77 Avenue Louis Pasteur, Office 614

department: Center of Neurologic Diseases

institute: Brigham and Women's Hospital, Harvard Medical School

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


title: Transcriptomic analysis of porcine skeletal muscles exposed to a single bout of endurance exercise

status: Public on Jul 13 2012

city: Aarhus

first: Lene

middle: Nagstrup

last: Conley

state: Denmark

address: Langelandsgade 140

department: Department of Chemistry

country: Denmark

institute: University of Aarhus


title: P. falciparum (lab strain 3d7) schizonts vs. P. falciparum (lab strain 3d7) reference RNA pool

status: Public on Jul 15 2012

city: Singapore

first: Ramya

last: Ramadoss

address: 60 Nanyang Drive, 04n-18, School of Biological Sciences

country: Singapore

institute: Nanyang Technological University, School of Biological Sciences


title: High-resolution genome-wide transcriptomics analysis of O. dioica development

status: Public on Jul 24 2012

city: Bergen

first: Eric

last: Thompson

address: Thormøhlensgt. 55

country: Norway

institute: Sars International Centre for Marine Molecular Biology

type: Expression profiling by genome tiling array

summary: The developmental transcriptomics of every significant developmental stage of O. dioica at ultra-high resolution.

overall_design: 18 samples were included, each in technical triplicate (and one with 4 replicates). These samples included 12 developmental time-point providing high-resolution interrogation of the complete animal life cycle. A further 3 samples specifically interrogated adult ovary, testis and somatic tissues. Finally, 3 samples were included that covered animal transcriptomics response under restrictive conditions that induce developmental growth arrest.

first: Gemma

last: Danks

first: Coen

last: Campsteijn

first: Stephen

last: Butcher

first: Harsha

last: Doddapaneni

first: Bolei

last: Fu

first: Raul

last: Petrin

first: Mrutyunjaya

last: Parida

first: Raghu

last: Metpall

first: Boris

last: Lenhard

first: Patrick

last: Wincker

first: Daniel

last: Chourrout

first: J

last: Manak


title: Modulation of glutamine metabolism by the PI3K-PKB/c-akt-FOXO network regulates autophagy

status: Public on Jul 22 2012

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology


title: Bovine cartilage zone arrays

status: Public on Aug 01 2012

city: La Jolla

first: Shawn

middle: Patrick

last: Grogan

address: 10550 N. Torrey Pines Road, MEM161

department: MEM

institute: TSRI

summary:
Objective. Identify novel genes and pathways specific to superficial (SZ), middle (MZ) and deep zones (DZ) of normal articular cartilage.
Methods.  Articular cartilage was obtained from knees of 4 normal human donors. The cartilage zones were dissected on a microtome. RNA was analyzed on human genome arrays. Data obtained with human tissue were compared to bovine cartilage zone specific DNA arrays. Genes differentially expressed between zones were evaluated using direct annotation for structural or functional features, and by enrichment analysis for integrated pathways or functions.
Results. The greatest differences were observed between SZ and DZ in both human and bovine cartilage. The MZ was transitional between the SZ and DZ and thereby shared some of the same pathways as well as structural/functional features of the adjacent zones. Cellular functions and biological processes enriched in the SZ relative to the DZ, include most prominently ECM receptor interactions, cell adhesion molecules, regulation of actin cytoskeleton, ribosome-related functions and signaling aspects such as Interferon gamma, IL4, CDC42Rac and Jak-Stat. Two pathways were enriched in the DZ relative to the SZ, including PPARG and EGFR_SMRTE.
Conclusion. These differences in cartilage zonal gene expression identify new markers and pathways that govern the unique differentiation status of chondrocyte subpopulations.

overall_design: 6 samples, 2 bovine  donors, 3 conditions each donor (SZ, MZ and DZ), 0 donor replicates, comparisons made between SZ, MZ and DZ to identify differentially expressed genes.

first: Stuart

middle: F

last: Duffy

first: Chantal

last: Pauli

first: James

last: Koziol

first: Andrew

last: Su

first: Darryl

last: D'Lima

first: Martin

last: Lotz


title: Evidence of an Increased Pathogenic Footprint in the Lingual Microbiome of Untreated HIV Infected Patients

status: Public on Jun 26 2012

first: Bruce

last: Paster

address: 140 Fenway

institute: The Forsyth Institute

summary: Opportunistic oral infections are ultimately presented in a vast majority of HIV-infected patients, often causing debilitating lesions that also contribute to deterioration in nutritional health.  Although appreciation for the role that the microbiota is likely to play in the initiation and/or enhancement of oral infections has grown considerably in recent years, little is known about the impact of HIV infection on host-microbe interactions within the oral cavity.  In the current study, we characterize modulations in the bacterial composition of the lingual microbiome in patients with treated and untreated HIV infection.  Bacterial species profiles were elucidated by microarray assay and compared between untreated HIV infected patients, HIV infected patients receiving antiretroviral therapy, and healthy HIV negative controls.  The relationship between clinical parameters (viral burden and CD4+ T cell depletion) and the loss or gain of bacterial species was evaluated in each HIV patient group.

overall_design: Characterization of modulations in the dorsal tongue (lingual) microbiota that are associated with chronic HIV infection.

first: Paster

last: Bruce

first: George

last: Michael


title: Zebrafish macrophage stimulating protein (Msp) mutants compared to wild types at 3 and 6 dpf

first: Leonie

last: Huitema

address: Uppsalalaan 8

department: Schulte-Merker group

institute: Hubrecht Institute

summary: This microarray was performed in attempt to find (novel) related genes in the msp/ron signaling pathway during embryonic development

overall_design: Embryos from mutant versus wild type crosses were raised in standard E3 medium at 28 degrees Celcius. At 3 dpf and 6 dpf total RNA from (n=30) msp mutant versus wild type embryos was isolated using the Rnaesy mini kit (Qiagen) according to the manufactures protocol.

first: Stefan

last: Schulte-Merker

first: Ive

last: Logister


title: K. lactis mating type regulator ChIP-chip

city: San Francisco

first: Trevor

last: Sorrells

department: Biochemistry and Biophysics

institute: University of California, San Francisco

type: Genome binding/occupancy profiling by genome tiling array

summary: We examine how different transcriptional network structures can evolve from an ancestral network. We show that regulatory protein modularity, conversion of one cis-regulatory sequence to another, distribution of binding energy among protein-protein and protein-DNA interactions, and exploitation of ancestral network features all contribute to the evolution of a novel mode of regulation at a conserved gene set. The formation of this derived mode of regulation did not disrupt the ancestral mode and thereby created a hybrid regulatory state where both means of transcription regulation (ancestral and derived) contribute to the conserved expression pattern of the network. Finally, we show how this hybrid regulatory state has resolved in different ways in different lineages to generate the diversity of regulatory network structures observed in modern species.

overall_design: Six samples were analyzed, three of which were controls and three of which were experimental


title: Gene expression arrays comparing Kluyveromyces lactis wild-type a cells to MATa2 knock-out a cells and wild-type alpha cells to MATalpha2 knock-out alpha cells

status: Public on Jun 30 2012

first: Lauren

middle: N

last: Booth

address: 600 16th Street, N374

department: Micobiology and Immunology

summary: We examine how different transcriptional network structures can evolve from a common, ancestral network. We show that regulatory protein modularity, conversion of one cis-regulatory sequence to another, distribution of binding energy among protein-protein and protein-DNA interactions, and exploitation of ancestral network features all contribute to the evolution of a novel mode of regulation at a conserved gene set. The formation of this derived mode of regulation did not disrupt the ancestral mode and thereby created a hybrid regulatory state where both means of transcription regulation (ancestral and derived) contribute to the conserved expression pattern of the network. Finally, we show how this hybrid regulatory state has resolved in different ways in different lineages to generate the diversity of regulatory network structures observed in modern species.

overall_design: a2 KO and alpha2 KO mRNA abundance was measured relative to a WT cell of the same mating type. 2 replicates each. Dye-swaps were performed.

first: Christopher

middle: R

last: Baker

first: Alexander

last: Johnson


title: Effect of carbon monoxide and the CO sensor CooA on gene expression in Desulfovibrio vulgaris Hildenborough

status: Public on Jul 31 2012

city: Berkeley

first: Lara

last: Rajeev

address: 1 Cyclotron Road

institute: Lawrence Berkeley Lab

summary: Investigating the role of carbon monoxide and a CO sensor protein CooA in the physiology of Desulfovibrio vulgaris Hildenborough using whole genome expression analysis

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Comparison of whole genome expression changes in the wild type and a strain deleted for CooA (DVU2097) in the presence and absence of carbon monoxide

first: Aifen

last: Zhou

first: Marcin

last: Joachimiak

first: David

last: Stahl


title: Chemosensitization of DLBCL cells in vitro and in vivo by demethylating nucleoside analogues

status: Public on Jul 30 2012

city: New-York

first: thomas

last: clozel

state: NY

address: 1300 York Avenue

department: Hematology-Oncology

institute: Weill Cornell Medical College

overall_design:
Refer to individual Series.

Supplementary file [gene expression]: To better approach the delta analysis and find differences between sensitive cell lines and resistant cell lines to doxorubicin, we filtered the gene expression matrix for probes with a greater standard deviation among all samples greater than 0.5. We therefore kept 11842 probesets that we used for the analysis.


title: Hierarchical regulation in a KRAS pathway-dependent transcriptional network revealed by a reverse-engineering approach

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

institute: Charite Universitätsmedizin Berlin


title: Mouse primary astrocytes: LCN2 protein treated vs. control

city: Daegu

first: Kyoungho

last: Suk

address: 101 Dong-In, Joong-gu

department: Department of Pharmacology

institute: Kyungpook National University School of Medicine

summary: Transcriptional profiling of mouse primary astrocytes comparing control untreated astrocytes with astrocytes treated with recombinant LCN2 protein (10 micro gram/ml). Goal was to determine the effects of LCN2 treatment on global gene expression in astrocytes. A secreted protein lipocalin-2 (LCN2) has been implicated in diverse cellular processes including cell morphology and migration. We have previously demonstrated that lcn2 mediates reactive astrocytosis. In order to further understand the role of lcn2 in the CNS, astrocyte transcriptome was analyzed following LCN2 treatment. Chemokines were the major group of genes upregulated by LCN2.

overall_design: Two-condition experiment, control untreated astrocytes vs. LCN2 protein treated astrocytes. Biological replicates: 1 control replicates, 1 treated replicates.

first: Shinrye

last: Lee


title: Profiling proteome-scale antibody responses to M. tuberculosis

status: Public on Jul 06 2012

city: Bronx

first: Shajo

last: Kunnath-Velayudhan

address: 1300 Morris Park Ave

department: Microbiology and Immunology

institute: Albert Einstein College of Medicine

sample_organism:
Macaca fascicularis
Homo sapiens


title: extracellular calcium chelation experiment_P. falciparum (lab strain 3d7) schizonts vs P. falciparum (lab strain 3d7) reference RNA pool

first: Ramya

last: Ramadoss


title: Gene expression after single and dual insulator protein knock-downs in Drosophila Kc cells.

status: Public on Jun 18 2012

city: Atlanta

first: Edward

last: Ramos

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

summary:
Transcriptional changes assayed with two bilogical replicates in wild type and RNAi mediated insulator knock-downs
RNAi mediated insulator knock-downs cause changes in the H3K27me3 levels and spread of Topoisomerase II
In order to understand the role of insulators in gene expression and regulation we used Drosophila Kc cells to knock-down single and multiple insulators in combination to assay for transcriptional changes.

overall_design: Two biologial replicates were prepared in independent experiments. Each cDNA samples were labeled with Cy3 dye and hybridized and scaned as per manufactures instructions at Florida State University Nimblegen facility.

first: Kevin

last: Van Bortle

first: Eduardo

last: Torre


title: Expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with human adipocytes, adipose tissue explants or control M199 medium

city: Dublin

first: Graham

last: Pidgeon

address: St. James' Hospital

country: Ireland

institute: Trinity College Dublin

first: Emma

middle: H

last: Allott

first: Melissa

last: Morine


title: Genes induced in Xenopus foregut endoderm by mesoderm

status: Public on Jun 12 2012

city: Cincinnati

first: Alan

last: Kenny

state: OH

address: 3333 Burnet Avenue

department: Neonatology

institute: Cincinnati Children's Hospital Medical Center

summary:
Foregut organogenesis is regulated by inductive interactions between the endoderm and the adjacent mesoderm.  We identified  genes induced in the foregut progenitors by the adjacent mesoderm.
We used microarrays to detail the global programme of early foregut endoderm gene expression resulting from mesoderm induction and identified distinct classes of up-regulated genes during this process.

overall_design: Xenopus foregut endoderm explants cultured from Stages 15 to 23 either intact with mesoderm or as endoderm alone.  Total RNA was isolated from the endoderm of these two culture conditions in quadruplicate and were subjected to Affymetrix microarray analysis.

first: Aaron

middle: M

last: Zorn

middle: P


title: Synthetic lethality between Rb, p53 and miR-17~92 in retinal progenitors suppresses retinoblastoma formation

status: Public on Jul 05 2012

city: Gent

first: Pieter

last: mestdagh

address: De Pintelaan 185

country: Belgium

institute: Center for Medical Genetics

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Murine livers post DEN treatment: c-Jun f/f vs. c-Jun Dli

status: Public on Aug 08 2012

city: Vienna

first: Harald

last: Scheuch

state: Vienna

address: Dr. Bohrgasse 7

department: Core Facilities

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

overall_design:
Refer to individual Series

** Six samples in each Series represent the same set of biological source material hybridized to 4 different arrays (named IMP internal: 35MM, 40MM, 41MM, and 43MM).

first: Lijian

last: Hui

first: Erwin

last: Wagner


title: Transcriptional response of adipose tissue depots to a high energy feeding regimen in Japanese Black and Holstein steers

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

summary: Three Japanese Black (JB) and 3 Holstein (HS) steers were fed a high energy diet and were slaughtered with 26 months of age. Intramuscular (IMF) and subcutaneous fat (SCF) was sampled to reveal differences in the expression profiles between the breeds and adipose depots.

overall_design: Pair wise comparison of JB and HS within IMF and SCF; pairwise comparision of IMF and SCF over both breeds.

first: Siriluck

last: Ponsuksili

first: Steffen

last: Maak


title: ChIP-chip to determine the regulation of the binding targets of a2 and alpha2 in Lachancea kluyveri

status: Public on Jun 29 2012

first: Lauren

last: Booth

overall_design: Epitope-tagged strains were compared to untagged control strains. The a2 ChIP (C-terminally myc tagged) and its corresponding untagged control were performed in a cells. The alpha2 ChIP (C-terminally myc tagged) and its corresponding untagged control were performed in alpha cells. Two biological replicates were performed for the tagged ChIPs and one replicate was performed for the untagged ChIPs.

first: Christopher

last: Baker

first: Trevor

last: Sorrells

first: Alexander

last: Johnson


title: A TARBP2-dependent miRNA expression profile determines cancer stem cell properties and provides new candidate therapeutic reagents in Ewing's sarcoma

status: Public on Jun 20 2012

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

institute: University of Turin

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


title: Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress in leaf tissue and during fibre development stages.

status: Public on Jun 04 2012

city: New delhi

first: Padmalatha

state: Delhi

address: Pusa campus

department: Plant Biotechnology

country: India

institute: NRCPB

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii


title: A light-regulated genetic module was recruited to carpel development in flowering plants following a structural change to SPATULA

city: Lyon

first: Charles

last: Scutt

address: 46 allee d'Italie

department: RDP

institute: ENS de Lyon

summary: One of the key innovations of the flowering plants is their female reproductive organ, the carpel. Here we show that a mechanism controlling carpel margin development in the model flowering plant Arabidopsis thaliana was recruited from light-regulated processes. This recruitment followed the loss from the basic Helix-Loop-Helix transcription factor SPATULA (SPT) of a domain previously responsible for its negative regulation by phytochrome. We propose that the loss of this domain was a prerequisite for the light-independent expression in female reproductive tissues of a genetic module that also promotes shade avoidance responses in vegetative organs. Striking evidence for this proposition is provided by the restoration of wild type carpel development to spt mutants by low red/far-red light ratios, simulating vegetation shade, which we show to occur via PHYB, PIF4 and PIF5. Our data illustrate the potential of modular evolutionary events to generate rapid morphological change, and thereby provide a molecular basis for neo-Darwinian theories that describe this non-gradualist phenomenon. Furthermore, the effects shown here of light quality perception on carpel development lead us to speculate on the potential role of light-regulated mechanisms in plant organs that, like the carpel, form within the shade of surrounding tissues.

overall_design:
The SPATULA (SPT) coding sequence was fused to the 5’-extremity of a sequence encoding the 75 C-terminal residues of the viral VP16 transcriptional activator and inserted into the pG0229-35S:GR plant transformation vector  between the CaMV-35S promoter and sequences encoding the rat glucocorticoid receptor (GR), so as to conserve the entire reading frame. The resulting plasmid was transferred to Agrobacterium tumefaciens C58/pMP90 cells and used to transform A. thaliana Col-0 plants by standard methods. A homozygous, single-copy transformant was identified, from which two populations of ten T3 descendents were grown and treated by dipping of inflorescences for 2 min in cycloheximide (CHX; 10 µg/ml) containing Silwet L-77 surfactant (0.01% v/v). This treatment reduced translation to approximately 5% of its native level in inflorescence tissues, as measured by the in vivo incorporation of [35S]-methionine into proteins. One hour later, inflorescence tissues of the two plant populations were dipped for 2 min in CHX solution, as described above, with and without dexamethasone (DEX; 10 µM). After a further 2h, treated inflorescences, excluding open flowers, were harvested and pooled prior to RNA extraction for global gene expression analyses.

Microarray analyses were performed using CATMA microarrays each containing 31776 gene-specific tags corresponding to 22089 A. thaliana genes. Three biological replicates were performed, based on three entirely separate induction experiments involving T3 plants from the same T2 parent. A transformed line containing a construction in which SPT had been replaced by an initiation codon and nuclear localization signal (NLS) was used to verify that the targets identified did not respond to the nuclear translocation of VP16-GR protein alone (35S:NLS-VP16-GR plants). In this NLS control experiment, two biological replicates were performed. One technical replicate with fluorochrome reversal was performed for each biological replicate. The labeling of cRNAs with Cy3-dUTP or Cy5-dUTP (Perkin-Elmer-NEN Life Science Products), the hybridization of these cRNAs to microarrays, and the subsequent scanning of microarrays, was performed as described by Lurin et al. (2004) Plant Cell 16, 2089-2103.

first: Mathieu

middle: C

last: Reymond

first: Geraldine

last: Brunoud

first: Aurelie

last: Chauvet

first: Jaime

last: Martínez-Garcia

first: Marie-Laure

last: Martin-Magniette

first: Francoise

last: Moneger


title: SuperSeries for the study of expression analysis of the PfmR (TTHB023) in T. thermophilus HB8

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

institute: RIKEN Harima Institute

first: Yoshihiro

last: Agari

first: Keiko

last: Sakamoto


title: Gene expression Difference in oocytes derived from adult and prepubertal Cattle

status: Public on Jun 01 2012

city: Kagoshima

first: Dorji

last: Dorji

address: Korimoto

department: Faculty of Agriculture

institute: Kagoshima University

summary:
Developmental competences of oocytes derived from prepubertal heifers are lower than those derived from adult counterparts. The objective of this study was to identify a range of genes associated with reduced oocyte competence that are differentially expressed between adult versus prepubertal donors. Microarray experiments were conducted using total RNA isolated from GV and MII stages oocytes collected from adult and prepubertal animals using Affymetrix GeneChip Bovine Genome Array containing 24,072 probe sets representing over 23,000 transcripts.  A total of 549 and 333 genes were differentially expressed between prepubertal versus adult bovine MII and GV stages oocytes respectively. Out of these, 312 and 176 genes were up-regulated, while 237 and 157 were down-regulated in prepubertal when compared with adult MII and GV oocytes respectively. Ontological classification of the differentially expressed genes revealed that up-regulated genes in adult oocytes were involved in signal transduction, regulation of transcription DNA-dependent, and transport. Results from the present study indicated that significant number of genes were differentially expressed (>2-fold, p<0.01) between the two groups. Thus the decreased developmental competence of oocytes from prepubertal heifers may be induced due to difference in gene expression abundance as observed in our study. In conclusion, transcript abundance analyses of oocytes using microarray approach have been carried out in bovine and several other species. However, to our knowledge, this is the first study carried out to examine genes expression differential abundance in oocytes derived from perpubertal versus adult Japanese Black Cattle.
Bovine 4b PP biological rep1, Bovine 78b PP biological rep2, Bovine 79 PP biological rep3 represents GV stage oocytes derived from Prepubertal (PP) heifer group, while Bovine 74b A  biological rep1, Bovine 80b A biological rep2, Bovine 81 A biological rep3 represents GV stage oocytes derived from Adult (A) cow group. Bovine 7 PP biological rep1, Bovine 53 PP biological rep2, Bovine 57 PP biological rep3 represents MII stage oocytes derived from Prepubertal heifer group, while Bovine 59 A biological rep1, Bovine 70 A biological rep2, Bovine 71 A biological rep3 represents MII stage oocytes from Adult cow group.

overall_design: The ovaries of adult cows (Japanese black cattle) were collected from local abattoir while ovaries of prepubertal Japanese black heifers (9 to 12 months old) were collected by spay device at several commercial farms. The collected ovaries of both the adult cows and prepubertal heifers groups were transported to the research laboratory in 0.67% (w/v) NaCl solution containing 100 mg/L kanamycin sulfate (Meiji Seika, Tokyo, Japan). For both groups, cumulus oocyte complexes (COCs) from ovarian follicles 2 to 8 mm in diameter were aspirated by using an 18 gauge needle (Terumo co, Tokyo, Japan) attached to a 5 ml disposable syringe (Nipro, Osaka, Japan). After collection, the COCs were washed twice with Tyrode-lactate-pyruvate-polyvinylalcohol (Hepes-TLP-PVA) and TCM 199 (Invitrogen, Gibco, NY, USA) supplemented with 10% heat-inactivated fetal bovine serum (maturation medium). Only COCs with evenly granulated cytoplasm surrounded by multiple layers of compact cumulus cells were used in all the experiments. The COCs (70 to 80) were placed in 200 µL drop of the maturation medium  in petri dish (35x10mm, Becton Dickinson Labware, Oxnard, CA, USA) covered with paraffin liquid (Nacalai Tesque Inc, Kyoto, Japan) and cultured at 38.5°C in a humidified atmosphere of 5% CO2 in air for 20 to 22 h for maturation.

first: Kazuchika

last: Miyoshi

first: Mitsutoshi

last: Yoshida


title: Mycobacterium avium subsp. paratuberculosis gene transcription in simulated phagosomal environment and in human macrophage infection

city: Amherst

first: Andrea

last: Cossu

address: 102 Holdsworth way

department: Department of Food Science

institute: University of Massachusetts, Amherst

platform_organism: Mycobacterium avium subsp. paratuberculosis K-10

overall_design: Refer to individual Series

first: Valentina

last: Rosu


title: Gene Expression profile in preimplantation in vitro embryos derived from Prepubertal heifers and Adult Cattle

summary:
Age of the donor animal has a significant influence on the oocyte’s ability to complete maturation and acquire the mRNA and proteins required for normal embryonic development. It is well known that developmental competence is reduced in oocytes derived from juvenile animals when compared to that derived from adults. However, the molecular mechanisms associated with these differences are not well elucidated. The aim of this study was to analyze the transcriptome differences between adult versus prepubertal derived preimplantation embryos and to identify genes associated with oocyte developmental potential. We performed cDNA microarray analysis on populations of preimplantation embryos (8- to 16-cell and Day 7 blastocysts) derived from adult versus prepubertal Japanese Black cattle. Total RNA was extracted and amplified in a linear fashion and then subjected to the microarray hybridization using the Affymetrix GeneChip Bovine Genome Array. The Bovine Array contains 24 072 probe sets representing over 23000 transcripts and 19000 UniGene clusters.
Following normalization of the microarray data, analysis revealed differences in gene expression abundance in 8- to 16-cell and blastocysts harvested from adult versus prepubertal heifers. Results indicated that a total of 591 and 490 genes were differentially expressed (≥2-fold) in 8- to 16-cell and blastocyst respectively between the two groups (p<0.01). In 8- to 16-cell stage, 373 genes were up-regulated and 218 gens down-regulated in adult when compared to the prepubertal heifer group. In case of blastocyst stage embryos, 242 genes were up-regulated and 248 genes were down-regulated in adult when compared to prepubertal group.

overall_design: The ovaries of adult cows (Japanese black cattle) were collected from local abattoir while ovaries of prepubertal Japanese black heifers (9 to 12 months old) were collected by spay device at several commercial farms. The ovaries were transported to the research laboratory in 0.67% (w/v) NaCl solution containing 100 mg/L kanamycin sulfate. COC were placed in 200 µL drop of the maturation medium (TCM 199 + 10% FBS) and cultured at 38.5°C in a humidified atmosphere of 5% CO2 in air for 20 to 22 h for in vitro maturation (IVM). After 20 to 22 h IVM, the COC were fertilized in vitro with frozen–thawed semen of Japanese Black bull in BO medium. Six hours after IVF, oocytes were denuded of surrounding cumulus cells by gentle pipetting in a solution of 0.1% (w/v) hyaluronidase. The presumptive zygotes were cultured in CR1aa medium supplemented with fatty acid-free BSA (Sigma) for 2 days and cultured in CR1aa medium supplemented with 10% (v/v) fetal bovine serum (FBS) for next 5 days at 38.5 °C in 5% CO2, 5% O2 and 90% N2  with high humidity (15 to 20 zygotes per 50 µl microdrop). 8- to 16-cell refers to day 3, 70 to 72 hours post insemination( hpi) preimplantation embryo stage containing 8 to 16 cells, while blastocyst refer to pre-hatching day 7 expanded blastocysts. Pools of 8- to 16- cell embryos (50 in each sample) and blastocysts (10 in each sample) from prepubertal and adult groups were used for cDNA microarray.

last: MIYOSHI

last: YOSHIDA


title: The profiling of gene expression in pupa stage of Drosophila melanogaster: Wildtype vs. dicer-2 mutant

status: Public on May 21 2012

city: Seoul

first: Do-hwan

last: Lim

address: Anam-dong 5-ga, seongbuk-gu

department: college of life sciences and biotechnology

institute: Korea Univ.

summary: To investigate transcriptional effects caused by a severe defect in endo-siRNA production, a gene expression profiling was performed on Drosophila dicer-2 pupae compared to wild-type.

overall_design: Two-condition experiment, Wildtype pupa vs. dicer-2 mutant pupa. Biological replicates: each 3 replicates.

first: Young

middle: S

last: Lee


title: Targets of the transcription factor Brachyury in differentiating mouse ES cells

status: Public on May 29 2012

city: Cambridge

first: Amanda

middle: Lisabeth

last: Evans

state: Cambridgeshire

address: Tennis Court Road

department: Cancer Research UK Gurdon Institute

country: United Kingdom

institute: Wellcome Trust

summary:
Brachyury (or T) is expressed in the primitive streak, tailbud and notochord of the early mouse embryo (Herrmann et al., 1990; Wilkinson et al., 1990). It plays a key role in early development: mouse embryos lacking functional Brachyury protein fail to gastrulate properly, do not form a differentiated notochord, and lack structures posterior to somite seven (Chesley, 1935; Dobrovolskaïa-Zavadskaïa, 1927; Naiche et al., 2005; Wilson et al., 1995; Wilson et al., 1993; Yanagisawa et al., 1981)
We apply a ChIP-on-chip approach to identify targets of Brachyury during mouse ES cell differentiation. ES cells provide an abundant source of differentiating cells and the identification of Brachyury targets in such cells will shed light on the mechanisms of ES cell differentiation and, by analyzing the targets in the developing embryo, will reveal to what extent they provide a bone fide model of early mouse development.

overall_design:
The brachyury IP expts used 3 independent biological replicates hybridised to design 1 and 2 chips per replicate
Design 1 raw file AE_251471610189 + Design 2 raw file AE_251471710182 = replicate 1
Design 1 raw file AE_251471610716 + Design 2 raw file AE_251471710724 = replicate 2
Design 1 raw file AE_251471610717 + Design 2 raw file AE_251471710725 = replicate 3
in all cases IP DNA label was Cy5 and whole chromatin Cy3
Design 1 files  GSM417692
Design 2 files  GSM417704
Isotype control experiment performed 1 x ie design 1  raw file AE_251471610714
design 2 raw file AE_251471710722 in GSM417714 and GSM417756
 IP DNA label was Cy5 and whole chromatin Cy3 as for brachyury data

middle: L

first: Roger

last: Pederson

first: Ludovic

last: Vallier

first: Micheal

middle: J

last: Gilchrist

first: Thomas

last: Down

first: Fiona

last: Wardle

first: Smith

last: James


title: omparison of gene expression during meiosis between wild-type and deficient strains of Coprinopsis cinerea

status: Public on May 15 2012

city: Bloomington

first: Claire

last: Burns

state: IN

address: 1001 E 3rd St

country: USA

institute: Indiana University

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


title: Promoters Recognized by Forkhead Proteins Exist for Individual 21U-RNAs

city: Stanford

first: Grace

last: Zheng

address: CCSR 2140, 269 Campus Dr

institute: Stanford University

summary: C. Elegans 21U-RNAs are equivalent to the piRNAs discovered in other metazoans and have important roles in gametogenesis and transposon control. The biogenesis and molecular function of 21U-RNAs and piRNAs are poorly understood. Here, we demonstrate that transcription of each 21U-RNA is regulated separately through a conserved upstream DNA motif. We use genomic analysis to show that this motif is associated with low nucleosome occupancy, a characteristic of many promoters that drive expression of protein-coding genes, and that RNA polymerase II is localized to this nucleosome-depleted region. We establish that the most conserved 8-mer sequence in the upstream region of 21U-RNAs, CTGTTTCA, is absolutely required for their individual expression. Furthermore, we demonstrate that the 8-mer is specifically recognized by Fordhead family (FKH) transcription factors and that 21U-RNA expression is diminished in several FKH mutants. Our results demonstrate a novel paradigm for simultaneous regulation of thousands of small non-coding transcription units.

overall_design: Comparisons of H3 and H2B positions on Chromosome 4 relative to the positions of 21U-RNAs.

first: Germano

last: Cecere

middle: Y

first: Andres

last: Mansisidor

first: Katherine

middle: E

last: Klymko

first: Alla

last: Grishok


title: Methylation profiling of neuro-ectodermal cell line with and without demethylating treatment.

status: Public on May 01 2012

city: Rotterdam

first: Floor

last: Duijkers

address: Dr. Molewaterplein 50-60 Ee15-02

department: Pediatric Oncology-Hematology

institute: Erasmus MC

summary: 6 neuro-ectodermal cell lines were treated with 30 nM Decitabine (72 hour) and 25 nM trichostatin A (48 hour) and 6 were untreated

overall_design: 6 untreated and 6 treated, each sample labeled with Cy5 and normal blood pool with Cy3


title: Identification of XMRV Infection-Associated microRNAs in Four Cell Types in Culture

status: Public on May 06 2012

city: Bethesda

first: Krishna

last: Ketha

address: 8800 Rockville Pike

department: Division of Hematology

institute: CBER/FDA


title: Human cerebrospinal fluid autoantibody lipid microarray profiling

status: Public on May 09 2012

first: William

last: Robinson

address: 269 Campus Drive

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium


title: Aspergillus niger mutants: induction by various carbon sources

status: Public on May 07 2012

city: Ribeirao Preto

first: Wagner

middle: Rodrigo

last: de Souza

state: Sao Paulo

address: Av do Cafe

department: Pharmaceutical Sciences

country: Brazil

institute: University of Sao Paulo


title: Clostridium difficile strain 630 heat stress experiment

status: Public on Apr 20 2012

city: Coleraine

first: Nigel

middle: G

last: Ternan

state: Co. Londonderry

address: Cromore Road

department: School of Biomedical Sciences

institute: University of Ulster

summary: Transcriptomic analysis of C. difficile strain 630 subjected to a clinically relevant heat stress (41°C ) and compared to unstressed cells (37°C ).  Heat stress was induced in biological triplicate broth cultures in the early exponential phase (D650nm=0.3) of growth and cells were harvested at late log phase (D650 = 1.1).  Goal was to determine effects of mild heat stress on gene expression.

overall_design: Two condition experiment, heat stressed vs. control. Biological replicates: 3 control replicates, 3 heat stressed replicates, with dye flip

first: Shailesh

last: Jain

first: Malay

last: Sirivastava

first: Geoff

last: McMullan


title: Do globins in the microaerophile Campylobacter jejuni function in nitrosative stress tolerance under oxygen limitation?

status: Public on May 23 2012

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

institute: University of Sheffield

sample_organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

first: Carlos

last: Avila-Ramirez

middle: K


title: Transcript profiling of drought responsiveness in two contrasting rice genotypes during vegetative stage stress

city: makati

first: Raveendran

last: Muthurajan

state: manila

address: Metro Manila

department: Entomology and Plant Pathology

country: Philippines

institute: International Rice Research Institute

summary:
Rice (Oryza sativa), the major staple food crop is being cultivated under varying ecosystems ranging from irrigated lowland to rainfed upland environments.  Improvement in the rice production under drought prone unfavourable environment depends on the development of drought tolerant genotypes which needs thorough understanding of physiological and molecular events behind the tolerance mechanism. There is considerable genetic variation for drought tolerance mechanism within the cultivated gene pool. To understand the diversity of drought response, two indica rice genotypes namely, i) Apo,  an up-land drought tolerant indica veriety from Philippines and ii) IR64, a popular high yielding drought susceptible genotype were selected for this study. We used the 22K rice Oligoarray from Agilent technologies to study the transcript profile in the leaves of the two contrasting rice genotypes under control and drought stressed conditions during vegetative phase.
Keywords: Drought response

overall_design: We used Agilent rice gene chips (G4138A) to investigate the transcript level changes in rice leaf tissues during drought stress. We used two contrasting rice genotypes (IR64 drought susceptible and Apo drought tolerant) differing in their degree of drought tolerance. Plants were grown under green house conditions and drought stress was imposed on 33rd DAS. Leaf sampling was done in both control and drought stressed plants after 6 days of drought stress. Three replications of microarray experiments were carried out by hybridizing the control samples against the drought stressed samples.

first: Kouji

last: Satoh

first: Ramil

last: Mauleon

first: LaxmiPraba

last: Manavalan

first: Qiang

last: Gan

first: Guozhen

last: Liu

first: Tiegang

last: Lu

first: Ulat

last: Jun

first: Richard

last: Bruskiewich

first: Renee

last: Lafitte

first: Shoshi

last: Kikuchi

first: Hei

last: Leung


title: Chip-chip from WT and Polycomb Component Knock Out Mouse ES cells for H2AZ, H3K27me3, EZH2 and Ring1B.

status: Public on Apr 16 2012

city: Edinburgh

first: Rob

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

institute: The University of Edinburgh

summary: The essential histone variant H2A.Z localises to both active and silent chromatin sites. In embryonic stem cells (ESCs), H2A.Z is also reported to co-localise with polycomb repressive complex 2 (PRC2) at developmentally silenced genes. The mechanism of H2A.Z targeting is not clear, but a role for the PRC2 component Suz12 has been suggested. Given this association, we wished to determine if polycomb functionally directs H2A.Z incorporation in ESCs. We demonstrate that the PRC1 component Ring1B interacts with multiple complexes in ESCs. Moreover, we show that although the genomic distribution of H2A.Z co-localises with PRC2, Ring1B and with the presence of CpG islands, H2A.Z still blankets polycomb target loci in the absence of Suz12, Eed (PRC2) or Ring1B (PRC1). Therefore we conclude that H2A.Z accumulates at developmentally silenced genes in ESCs in a polycomb independent manner.

overall_design: Array design includes 2 biological replicates for all samples and technical replication (dye swaps for H3K27me3_WT_ES, EZH2_WT_ES, EZH2_RING1b_KO_ES, H2AZ_WT_ES(2), H2AZ_Eed_KO_ES and H2AZ_Suz12_KO_ES). Ring1B_WT_ES is represented by a single replicate.

first: Catherine

last: Botting

first: Graeme

last: Grimes

first: Wendy

middle: A

last: Bickmore

first: Ragnhild

last: Eskeland


title: Transcriptional responses to NNK and selenocystine in mouse lungs.

city: Salt Lake City

first: Philip

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

summary:
This study evaluated transcriptional effects of the lung carcinogen NNK ( 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone) injection and selenocystine consumption on the murine lung. Female A/J mice at 5 weeks of age were obtained from The Jackson Laboratory. Animals were stabilized on an unsupplemented AIN-76 diet for one week prior to being given the selenium supplemented diet. The basal level of selenium in the diet is 0.35 ppm Se, the selenocytine supplemention was at 15 ppm. NNK was administered i.p. as a single 10 uM injection in 0.2 mL saline.
With this protocol, 100% of animals reproducibly develop lung tumors after 3 months. Three days after NNK administration, animals were provided AIN-76A diets supplemented with selenocystine at 15 ppm selenium ad libitum for 10 days. Animals were sacrificed thirteen days after NNK administration. Lung tissue was harvested, immediately homogenized in Trizol and frozen. The organic extracted RNAs were run over Qiagen RNeasy columes before quantifying and qualifying them. All samples had RNA quality index's greater than 9.

overall_design:
Four groups of A/J mice were utilized with 4 biological replicates per group. 1) Untreated - controls on the AIN-76 diet (0.35 ppm Se). 2) NNK treated - single injection of NNK, maintained on norma AIN-76 diet, sacraficed after 13 days. 3) SECY - selenocystine supplemented (15 ppm) for 10 days on a AIN-76 diet then sacraficed. 4) NNK plus SECY - single injection of NNK, after 3 days, selenocystine supplemented (15 ppm) diet for 10 days then sacraficed. RNAs from the the four untreated mice were combined to phenotypically anchor the dual color expression profile.
mouse lung responses to NNK injection and/or selenocystine dietary supplementation

first: Micheal

last: Franklin


title: The impact of experience-dependent and independent factors on gene expression in songbird brain

status: Public on May 31 2012

city: Urbana

first: Kirstin

last: Replogle

state: IL

address: 1206 W Gregory Drive

institute: University of Illinois

summary:
Songbirds provide rich natural models for studying the relationships of brain anatomy, behavioral function, environmental signals and gene expression.  Under the Songbird Neurogenomics Initiative, investigators from more than a dozen laboratories collected brain samples from six species of songbird under a range of experimental conditions, and 488 of these samples were analyzed systematically for gene expression by microarray.  ANOVA was used to test 32 planned contrasts in the data, revealing the relative impact of different factors.  The brain region from which tissue was taken had the greatest influence on gene expression profile, affecting the majority of signals measured by the 18,848 non-redundant cDNAs spotted on the microarray. Social and environmental manipulations had highly variable impact, ranging from nil in some cases to robust in others.  Several specific genes were identified as points of interest in the evolution of mechanisms by which environmental signals influence behavior. The data were also analyzed using Weighted Gene Co-expression Network Analysis (WGCNA) followed by Gene Ontology (GO) analysis. This revealed modules of co-regulated genes that are also enriched for specific functional annotations such as  “ribosome” (expressed more highly in juvenile brain) and “dopamine metabolic process” (expressed more highly in striatal song control nucleus Area X).  These results underscore the complexity of influences on neural gene expression and provide a resource for studying how these influences are integrated during natural experience.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Sturnus vulgaris
Haemorhous mexicanus
Melospiza melodia
Taeniopygia guttata
Loxia curvirostra
Zonotrichia leucophrys gambelii

first: Jenny

last: Drnevich

first: Arthur

last: Arnold

first: Gregory

middle: F

last: Ball

first: Eliot

last: Brenowitz

first: Thomas

last: Hahn

first: Frank

last: Johnson

first: Sarah

last: London

first: Peter

last: Lovell

last: Mast

first: Claudio

last: Mello

first: Motoko

last: Mukai

first: Christy

last: Strand

first: Juli

last: Wade

first: John

last: Wingfield

first: David

last: Clayton


title: Male-dominant activation of rat renal organic anion transporter 1 (Oat1) and 3 (Oat3) expression by transcription factor BCL6

status: Public on Apr 18 2012

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: Organic anion transporters 1 (Oat1) and 3 (Oat3) play a critical role in transport of organic anions, including frequently prescribed drugs, across cell membranes in proximal tubules of kidneys. In rats, these transporters are known to be male-predominant and testosterone dependently expressed. The molecular mechanisms that are involved in the sex-dependent expression are unknown. Our aim was to identify genes that show a sex-dependent expression and could be involved in sex-dependent regulation of Oat1 and Oat3.

overall_design: Comparison of gene expression in cortical kidney slices between 4 male and 4 female RCCHanTMWIST rats. Each animal were analyzed as a separate sample.

first: Waja

last: Wegner

first: Brigitta

last: Burckhardt

first: Gerhard

first: Maja

last: Henjakovic


title: Expression profile analysis of Drosophila melanogaster embryonic and larval MANF mutants together with paternal rescue and overexpression conditions

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: To find out possible pathways and processes influenced by DmMANF we  compared the changes in MANF null and overexpressing animals. We used two developmental stages of Drosophila, st 17 embryos and 29-50 hrs after egg laying (AEL) larvae. The timing were decided according to the lethality of MANF mutants with or without maternal contribution of MANF. Maternal and zygotic MANF mutants (MANFmzD96) were compared to paternal rescue and wild type embryos of the same age. Zygotic MANF mutants (MANFD96) with maternal contribution were compared to wild type and MANF ectopic overexpression larvae harvested well before the average lethality occured (75 hrs AEL). The changes in expression profiles were more drastic in MANFmzD96 embryos than in MANFD96 larvae. Gene ontology annotations were analyzed and clustered by DAVID. The major result was alterations in  membranes, changes in membrane transporter expressions and disturbed intracellular membrane traffic. The results were verified by qPCR and transmission electron microscopy.

overall_design: Two developmental stages - 21-24 hrs and 29-50 hrs AEL of MANFD96 mutants without and with maternal contribution were compared to wild type (Wmix means crossed w1118 x w- ) and with paternal rescue or ectopic overexpression of MANF respectively by Drosophila Agilent microarray expression platform.

first: Mari

last: Palgi

first: Riitta

last: Lindström

first: Petri

last: Auvinen

first: Tapio

middle: I

last: Heino


title: Monitoring of functional gene responses to biostimulation from TCE-contaminated sites using a functional microarray

status: Public on Apr 03 2012

city: AUBIERE

first: Peyret

last: Pierre

address: 24, avenue des landais

country: France

institute: CNRS - Blaise Pascal University

type:
Genome variation profiling by array
Expression profiling by array

platform_organism: Shewanella Pseudomonas Methylosinus Nitrosomonas Mycobacterium Geobacter Thauera Desulfitobacterium Dehalobacter Sulfurospirillum Dehalococcoides


title: Pleiotropic Effects of Deubiquitinating Enzymes on Growth and Pathogenesis of Cryptococcus neoformans

status: Public on Apr 11 2012

city: Lynchburg

first: Michael

last: Price

state: VA

address: 1971 University Blvd.

department: Biology & Chemistry

institute: Liberty University

sample_organism:
Cryptococcus neoformans
Cryptococcus neoformans H99

platform_organism:
Cryptococcus neoformans
Cryptococcus deneoformans


title: Global gene expression analysis of normal and ripening inhibitor (rin) mutant tomatoes during ripening

status: Public on Apr 02 2012

city: Tsukuba

first: Yasuhiro

last: Ito

state: Ibaraki

address: 2-1-12 Kannondai

department: Food Biotechnology Division

country: Japan

institute: National Food Research Institute

summary: Ripening is an important stage of fruit development to determine its quality as a diet. A tomato (Solanum lycopersicum) MADS-box transcription factor, RIPENING INHIBITOR (RIN), has been believed to serve as a regulator of ripening lying upstream of ethylene-dependent and ethylene-independent pathways. Here, we have conducted global gene expression analysis to comprehensively identify tomato genes whose expressions are affected by the rin mutation using microarray with RNA samples from the normal and rin mutant tomato fruits at the pre-ripening (mature green) and ripening (pink coloring) stages. By analysing this microarray data, we identified 342 of positively regulated and 473 negatively regulated genes by RIN, which showed >5 and <0.2 of the fold change ratio (FC) of normal fruits at the ripening stage relative to those at the pre-ripening stage, respectively, in a RIN-dependent manner.  A chromatin immunoprecipitation (ChIP) analysis of the normal ripening tomatoes with the anti-RIN antibody revealed that the positively regulated gene set contained at least 13 direct RIN targets.

overall_design: We monitored global gene expression in normal (PK331 cultivar) and rin mutant (PK353 cultivar) tomatoes at the pre-ripening (mature green, G) and ripening (pink coloring, P) stages using microarray with three biological replicates for each sample.

first: Fujisawa

last: Masaki

first: Toshitsugu

last: Nakano


title: Gene expression analysis of host spleen responses to Marek's disease virus infection in susceptible and resistant chickens

city: Beijing

first: Ning

last: Yang

address: 2nd Yuanmingyuan West Road

department: Animal Science

country: China

institute: China Agricultural University

summary: To investigate gene expression profiles in susceptible spleens (SS) and resistant spleens (RS) from MDV-infected chickens and non-infected spleens (NS) from controls. Twelve spleens were chosen from three groups (four samples per group) to be used in chicken genome microarray to examine differential gene expression. In total, there were 4317 and 2593 differentially expressed (DE) genes in SS vs. NS and in SS vs. RS, respectively. However, no DE genes were found in RS vs. NS. The expression of twenty-four genes was verified by qPCR. In this study, we found weak, but detectable host immune response still existed in the late neoplastic transformation phase of MDV infection. Toll-like receptor pathway was affected in susceptible spleens compared to non-infected and resistant spleens. IL10 seemed to be exploited by virus to facilitate tumorigenesis. The expression of many members in insulin growth factor system was altered. IGFBP4 and IGFBP7 might be associated with MD lymphoma transformation. The expression profiles in resistant spleens were similar to those in non-infected spleens, which indicated most genes returned to baseline expression levels. Although latent MDV infection persists in resistant chicken for the whole life, it won’t interfere with normal function of genes.

overall_design: Four susceptible spleens with tumors were obtained at 46-55 d.p.i., four resistant spleens were removed from survivors at 55-56 d.p.i. from MDV infected chickens, and four non-infected spleens were from controls at 40-56 d.p.i. Twelve one-color microarrays were utilized to detect differential gene expression among three groups.

first: Ling

last: Lian

first: Lujiang

last: Qu

first: Hongyan

last: Sun

first: Yanmei

last: Chen

first: Susan

last: Lamont

first: Changjun

last: Liu


title: Genetic toxicology and toxicogenomic analysis of 3 cigarette smoke condensates in vitro reveals few differences between high and low tar brands

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

summary: This experiment investigated the response of mouse pulmonary epithelial cells in culture (FE1 cell line) to 3 different brands of cigarette smoke condensate. The three brands represent a full flavour, regular and king-size light cigarettes. These vary in some key chemical consistuents. Brand #1 has the highest tar content. The cells were exposed to two doses: one at approximately 50% cytotoxicity, and the other at approximately 20%. Both doses were clastogenic. The major pathways affected included xenobiotic metabolism, cell cycle, apoptosis, oxidative stress and inflammation. Although brand #1 exhibited the most numbers of genes that were differentially expressed, there did not appear to be any major differences in the expression profiles between the brands. Although some genes did not reach statistical significance, in general there was consistency in the direction of fold changes for genes across all brands.

overall_design: MutaMouse FE1 cells in culture (derived from lung epithelial cells) were exposed to cigarette smoke condensate (CSC) collected from 3 brands: Brand #1 – Full Flavor; Brand #3 – Regular; Brand #5 – Light King Size. Experiments were performed on 5 replicates per condition (i.e., n=5 per group); one replicate was removed from 4 groups later in the study. Cells were exposed at 70% confluence in 150 mm plates to either 45 µg/ml or 90 µg/ml CSC alongside cells exposed to 1% DMSO (Sigma-Alderich, Canada) in 1:1 DMEM:F12 (without FBS). Cells were exposed to CSC for 6 hours and then either: (a) immediately harvested, or (b) washed in PBS and cultured for another 4 hours in fresh media. The two time points were called 6 hours or 10 hours (6 hours exposure, 4 hours recovery for the latter). Cells were harvested with TRIzol (Invitrogen) and stored at -80oC. RNA was extracted and labelled, and hybridized to Agilent 22K mouse development microarrays following the manufacturer's protocol (Agilent Technologies Inc., USA). Arrays were washed and scanned on a ScanArray Express (Perkin-Elmer Life Sciences), and data were acquired with ImaGene 5.5 (BioDiscovery Inc.). Biological samples were hybridized in Cy5, and Stratagene Universal Reference RNA was hybridized in Cy3.

first: Carole

last: Yauk

first: Sabina

last: Halappanavar

first: Paul

last: White

first: Rebecca

last: Maertens

first: Julie

last: Buick


title: Sex-biased gene expression in Drosophila melanogaster larvae

status: Public on Apr 08 2012

city: Houston

first: Richard

last: Meisel

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

summary: Genes with sex-biased expression in adults experience unique evolutionary dynamics. It is unclear, however, whether the selection pressures responsible for these well documented patterns also act upon genes with sex-biased expression in other developmental stages. To examine this, we measured expression in male and female Drosophila melanogaster larvae.

overall_design: Drosophila melanogaster wandering third instar larvae were sexed using the visible gonad. RNA was isolated from three replicate samples of male and female larvae and one sample each of adult males and females. RNA was prepared following the manufacturer's instructions, using single color labelling. Each sample/replicate was hybridized to one sector of the Agilent 4 sector array (a total of two arrays were used), with the following design: Array 1 had one larval male sample, one larval female sample, one adult male sample, and one adult female sample; Array 2 had two larval male samples and two larval female samples.

last: Clark


title: Temporal dynamics of human cells co-cultivated with Aspergillus fumigatus

status: Public on Apr 17 2012

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

institute: University of Wuerzburg


title: Global Methylation Patterns in Idiopathic Pulmonary Fibrosis

status: Public on Apr 19 2012

city: Pittsburgh

first: Einat

middle: Inna

last: Rabinovich

state: PA

address: 3500 Terrace St

department: Medicine

institute: University of Pittsburgh

summary:
Idiopathic Pulmonary Fibrosis (IPF) is a chronic progressive lung disease that affects more than 5 million people worldwide with a steady increase in both incidence and mortality. There is currently no effective therapy and the median survival without transplant is 2-5 years. The etiological factor is unknown, but several observational and pathogenesis studies suggest that environmental agents may cause IPF.
DNA methylation is a type of chemical modification of DNA such environmental and occupational factors, that can induced a changes in the regulation of biological processes and link to diseases such as a cancer.
We hypothesize that the global changes in methylation patterns of IPF lungs caused by environmental factors. In this study we will identify the global methylation signatures of the IPF lung and to compare to methylation signature of lung cancer. The DNA methylation profiles of IPF lung tissue differs from control lung but it shares great similarity with that of lung cancer.

overall_design: Immunoprecipitated methylated DNA from 12 IPF lungs, 10 lung adenocarcinomas and 10 normal histology lungs obtained from the same group of adenocarcinoma patients was hybridized to Agilent human CpG Islands Microarrays. Only probes with a hybridization Tm value between 79 C and 93C were included in the analysis because these show higher quality signal. All probes were divided according to their Tm into 14 groups/bins differing by 1C. Probe signals in each bin were standardized to have an average of 0 and a standard deviation of 1. To work in a CpG island oriented manner, we scored each island for its likelihood to be methylated. For that purpose, each probe was mapped to the genome and the signals of the probes that were mapped to a single CpG island were averaged to obtain the island’s methylation score. Data analysis was performed using BRB-Array Tools and DAVID Bioinformatics Resources software packages.

first: Naftali

last: Kaminski

first: Zohar

last: Yakhini


title: A High-dose of genistein down-regulates TGF-beta pathway genes in human uterine leiomyoma cells

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: High doses of genistein show an inhibitory effect on uterine leiomyoma (UtLM) cell proliferation. Using microarray analysis and Ingenuity Pathways AnalysisTM, we identified genes (up- or down-regulated, ≥1.5 fold, P ≤ 0.001), functions and signaling pathways that were altered following treatment with an inhibitory concentration of genistein (50 ìg/ml) in UtLM cells. Downregulation of TGF-â signaling pathway genes, activin A, activin B, Smad3, TGF-â2 and genes related to cell cycle regulation, with the exception of the upregulation of the CDK inhibitor P15, were identified and validated by real-time reverse transcriptase-polymerase chain reaction studies. Western blot analysis further demonstrated decreased protein expression of activin A and Smad3 in genistein-treated UtLM cells. Moreover, we found that activin A stimulated the growth of UtLM cells, and the inhibitory effect of genistein was partially abrogated in the presence of activin A. Overexpression of activin A and Smad3 were found in tissue samples of leiomyoma compared to matched myometrium, supporting the contribution of activin A and Smad3 in promoting the growth of UtLM cells. Taken together, these results suggest that downregulation of activin A and Smad3, both members of the TGF-â pathway, may offer a mechanistic explanation for the inhibitory effect of a high-dose of genistein on UtLM cells, and might be potential therapeutic targets for treatment of clinical cases of uterine leiomyomas.

overall_design: Cells were treated with either genistein (50 μg/ml) (4’, 5, 7-Trihydroxyisoflavone; Sigma Chemical Company, St. Louis, MO, USA) or the vehicle control [0.3% dimethylsulfoxide (DMSO), Sigma] for 24 h. the samples from the flasks that received the same treatment were pooled, then concentrated to > 9 ìg/ìl by Microcon 30 columns (Amicon:Millipore, Bedford, MA, USA).  Three replicates for the treatment, and one pooled control, were submitted for microarray analysis. Gene expression analysis was conducted using Agilent Whole Human Genome arrays (Agilent Technologies, Palo Alto, CA, USA).

first: X

last: Di

first: D

last: Andrews

first: C

last: Tucker

first: L

last: Yu

first: A

middle: B

last: Moore

last: Zheng

last: Castro

first: T

last: Hermon

last: Dixon