title: Array CGH analysis of multiple myeloma (MM) and MGUS, Sapporo and Hiroshima samples

status: Public on Mar 01 2012

city: Tokyo

first: Masanori

last: Nojima

state: Tokyo

address: 4-6-1, Shirokanedai, Minato-ku

department: The Institution of Medical Science

institute: The University of Tokyo

summary: Multiple myeloma (MM) is a malignant plasma cell tumor characterized by various chromosomal aberrations. From the aspect of epigenetics, hypomethylation of DNA repetitive elements has been considered to induce chromosomal instability. We therefore have been interested in how it is related to chromosomal aberrations in MM. To address this, methylation levels of repetitive elements (including LINE-1, Alu and Satellite-alpha) and copy number alterations were measured in clinical samples (N=85). Bisulfite-pyrosequencing (N=85) and array-based comparative genomic hybridization (N=73) were used for these measurement, respectively. As results, methylation levels of repetitive elements were linearly associated with the degree of malignancy of plasma cells. Combined with hierarchical clustering of the result of aCGH, hypomethylation of repetitive elements was well associated with frequent chromosomal deletions. In particular, methylation levels of LINE-1 was significantly higher in samples with chromosome 13 deletion than the other (36.1% vs. 44.0%, P=0.010). The number of deleted probes was significantly correlated with LINE-1 methylation levels (R=-0.531). Finally, we observed significantly poorer prognosis in the lower LINE-1 methylation group (HR=2.8, P=0.015, compared to the higher methylation group). In conclusion, DNA methylation levels of repetitive elements, especially of LINE-1, are associated with the frequency of chromosomal deletions and prognosis in MM.

overall_design: 67 MM samples and 6 monoclonal gammopathy of undetermined significance (MGUS) samples were analyzed, all samples were selected by CD138 sorting

first: Yuka

last: Aoki


title: Affymetrix Cotton Genome  array expression data of root tissue of Gossypium herbaceum under drought stress and watered condition

status: Public on Mar 29 2012

city: Lucknow

first: Samir

middle: V

last: Sawant

state: UP

address: Rana Pratap Marg

department: Plant Molecular Biology

country: India

institute: CSIR-NBRI

summary:
Genome-wide Transcriptional Analysis of Genes Associated with Drought Stress in Gossypium herbaceum root
This experiment was designed to investigate the molecular mechanism associated with drought tolerance in root tissue of Gossypium herbaceum. The gene expression profiles of the root tissue using Affymetrix Cotton Genome Array were compared with drought tolerant and drought sensitive genotype of G.herbaceum under drought stress and watered condition. Many genes in various molecular function or biological processes were over- or under-represented between drought tolerant and sensitive genotype, suggesting various molecular mechanism and biochemical pathways are interlinked and tolerant genotype have developed multiple mechanisms as an adaptory behavior against drought stress.

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design: The transcriptional responses of root tissue in drought tolerant and sensitive genotype of Gossypium herbaceum under drought stress have been investigated. Physiological responses to drought stress, such as stomatal conductance, water use efficiency, root bending assay on different mannitiol concentration were also measured as indicators of imposed drought stress. Total RNA was isolated from root tissue from both genotype under drought stress and normal irrigated condition with three biological replicates

first: Alok

last: Ranjan

first: Neha

last: Pandey


title: Epigenome analysis of normal and cancer tissue from the uterine cervix

status: Public on Feb 23 2012

city: London

first: Andrew

middle: E

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

country: United Kingdom

institute: University College London

summary: The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in normal and cancer tissue from the uterine cervix. There are a total of 63 samples, 15 samples of normal histology and 48 cervical cancers. The normal cervical samples were from women who underwent a hysterectomy for uterine fibroids. The 48 cervical cancers were from women who were treated at the Innsbruck Medical University between 1990 and 2006.

overall_design: Bisulphite converted DNA from the 63 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Martin

last: Widschwendter

first: Heidi

last: Fiegl


title: Epigenome analysis of normal cells from the uterine cervix in a nested prospective case control study within the ARTISTIC trial

summary: The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in normal cells from the uterine cervix (liquid based cytology samples), obtained from 152 women in a nested prospective case-control study within the ARTISTIC trial. Out of the 152 women, 75 developed a cervical intraepitelial neoplasia of grade 2 or higher (CIN2+) after 3 years of sample collection. The rest of women (77) remained disease free (CIN2-).

overall_design: Bisulphite converted DNA from the 152 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Henry

last: Kitchener


title: Expression analysis of 52 glioma clinical samples (36 CIMP+ and 16 CIMP-) and 6 cell line samples

status: Public on Feb 16 2012

city: New York

first: FANG

last: FANG

state: NY

address: 1275 York Avenue

department: The Human Oncology and Pathogenesis Program

country: USA

institute: Memorial Sloan-Kettering Cancer Center

summary: Glioma CIMP (G-CIMP) is a powerful determinant of tumor pathogenicity but the molecular cause of G-CIMP is a fundamental question that is unresolved.  Here, we show that mutation of a single gene, isocitrate dehydrogenase 1 (IDH1), directly causes the G-CIMP in gliomas by remodeling the methylome.

overall_design: In this study 52 glioma clinic samples (36 CIMP+ and 16 CIMP-) were analyzed. Parental IDH1 wild-type and IDH1 mutant cells were passaged 40 and passage 40 were cell line was sent for expression array.

first: Fang

last: Fang

first: Timothy

last: Chan


title: Cervical cancer

status: Public on Feb 20 2012

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

overall_design: Refer to individual Series


title: IDH1 Mutation is a Master Regulator of Epigenomic Remodeling and is Sufficient to Establish the Glioma Hypermethylator Phenotype

type: Methylation profiling by genome tiling array


title: Preservation of bone mass and structure in hibernating black bears (Ursus  americanus) through elevated expression of anabolic genes

status: Public on Feb 15 2012

city: Shanghai

first: Haifang

last: Wang

address: 320 yueyang road

department: CAS-MPG Partner institute for Computational Biology

country: China

institute: Shanghai institute for biology science

summary: Physical inactivity reduces mechanical load on the skeleton, which leads to losses of bone mass and strength in non hibernating mammalian species. Although bears are largely inactive during hibernation, they show no loss in bone mass and strength. To obtain insight into molecular mechanisms preventing disuse bone loss, we conducted a large-scale screen of transcriptional changes in trabecular bone comparing winter hibernating and summer non hibernating black bears using a custom 12,800 probe cDNA microarray. A total of 241 genes were differentially expressed (P < 0.01 and fold change > 0.5) in the ilium bone of bears between winter and summer. The Gene Ontology and Gene Set Enrichment analysis showed an elevated proportion in hibernating bears of over-expressed genes in six functional sets of genes involved in anabolic processes of tissue morphogenesis and development including skeletal development, cartilage development and bone biosynthesis. Apoptosis genes demonstrated a tendency for down regulation during hibernation. No coordinated directional changes were detected for genes involved in bone resorption, although some genes responsible for osteoclast formation and differentiation (Ostf1, Rab9a, c- Fos) were significantly under expressed in bone of hibernating bears. Elevated expression of multiple anabolic genes without induction of bone resorption genes, and the down regulation of apoptosis related genes, likely contribute to the adaptive mechanism that preserves bone mass and structure through prolonged periods of immobility during hibernation.

overall_design: Black bears sampled during winter hibernation were compared with the animals sampled during summer. Bone RNA were hybridized on a custom 12,800 cDNA probe nylon membrane microarray platform . Six hibernating and six summer active bears were studied in this experiments.

first: Vadim

last: Fedorov

first: Anna

last: Goropashnaya

first: Oivind

last: Tøien

first: Nathan

middle: C

last: Stewart

first: Celia

last: Chang

first: Jun

last: Yan

first: Louise

last: Showe

first: Michael

middle: K

first: Seh

middle: W

last: Bonahue

first: Brian

middle: M

last: Barnes


title: Genome-Wide Mapping Of Time-Series ChIP-Seq Data For Human ERα Breast Cancer Cell Line (MCF-7)

status: Public on Jan 16 2012

city: Boston

first: Binhua

last: Tang

state: MA

address: 10 Shattuck Street

department: BMI

institute: Harvard Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
We report the genome-wide mapping of time-series ChIP-seq data sets of human breast cancer ERα cell line (MCF-7). The 4 time points cover the 0, 1, 4 and 24 hours, respectively.
MCF-7 cells were maintained in a hormone-free medium (phenol red–free MEM with 2 mmol/L L-glutamine, 0.1 mmol/L nonessential amino acids, 50 units/mL penicillin, 50 Ag/mL streptomycin, 6 ng/mL insulin, and 10% charcoal-stripped FBS) for three days. MCF-7 cells were treated with DMSO at the 0 hour time point, and E2 (108 mol/L) at the 1, 4 and 24 hours. 5 x 107 cells were cross-linked with 1% formaldehyde for 10 min, at which point 0.125 M glycine was used to stop the cross-linking.
In brief, after crosslinking, cells were treated by lysis buffers and sonicated to fragment the chromatin to a size range of 500-1000 bps. Chromatin fragments were then immunoprecipitated with 10ug of antibody/magnetic beads. The antibodies against ERα were purchased from Santa Cruz Biotechnology (Santa Cruz, sc-8005 X).
After immunoprecipitation, washing and elution, ChIP DNA was purified by phenol:chloroform:isoamyl alcohol and solubilized in 70 μl of water.
The ChIP DNA sample was run in 12% PAGE and the 100-300 bps DNA fraction was excised and eluted from the gel slice overnight at 4°C in 300 μl of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate) and was purified using a QIAquick purification kit (Qiagen, cat#:28104).
The library was constructed using Illumina genomic DNA prep kit by following its protocol (Illumina, cat#:FC-102-1002), clusters were generated on the Illumina cluster station (Illumina, cat#:FC-103-1002), DNA samples (20 nM per sample) quantified by an Agilent Bioanalyzer, were loaded onto Illumina Genome Analyzer IIx (GAIIx) for sequencing according to the manufacturer's protocol.
Reads generated from the Illumina GAIIx pipeline were aligned to the Human Genome Assembly (NCBI build 36.1/hg18) using the ELAND algorithm.

overall_design: E2-treated experiments on human breast cancer ERα cell line (MCF-7) across the 4 time points.

first: Victor

middle: X

last: Jin


title: Two Forkhead transcription factors regulate the division of cardiac progenitor cells by a Polo-dependent pathway - II

status: Public on Jan 30 2012

city: Bethesda

first: Shaad

middle: M.

last: Ahmad

state: MD

address: Building 10, Room 7N311, 10 Center Drive MSC 1654

department: Systems Biology Center

institute: National Heart Lung and Blood Institute

summary: The development of a complex organ requires the specification of appropriate numbers of each of its constituent cell types, as well as their proper differentiation and correct positioning relative to each other.  During Drosophila cardiogenesis, all three of these processes are controlled by jumeau (jumu) and Checkpoint suppressor homologue (CHES-1-like), two genes encoding forkhead transcription factors that we discovered utilizing an integrated genetic, genomic and computational strategy for identifying novel genes expressed in the developing Drosophila heart.  Both jumu and CHES-1-like are required during asymmetric cell division for the derivation of two distinct cardiac cell types from their mutual precursor, and in symmetric cell divisions that produce yet a third type of heart cell.  jumu and CHES-1-like control the division of cardiac progenitors by regulating the activity of Polo, a kinase involved in multiple steps of mitosis.  This pathway demonstrates how transcription factors integrate diverse developmental processes during organogenesis.

overall_design: GFP-positive cells were profiled from Stage 11-12 Drosophila embryos of the following two genotypes: twi-GAL4 UAS-2EGFP/UAS-jumu and twi-GAL4 UAS-2EGFP

first: Terese

middle: R

last: Tansey

last: Busser

middle: T

last: Nolte

first: Neal

last: Jeffries

first: Stephen

middle: S

last: Gisselbrecht

first: Nasser

last: Rusan

first: Alan

last: Michelson


title: Methylation analysis of 81 glioma clinical samples (49 CIMP+ and 32 CIMP-) and 53 cell line samples

first: FANG

last: FANG

overall_design: In this study 81 glioma clinic samples (49 CIMP+ and 32 CIMP-) were analyzed. Parental IDH1 wild-type and IDH1 mutant cells were passaged until passage 50.

first: Fang

last: Fang

first: Timothy

last: Chan


title: The CtsR and HrcA regulon of Lactobacillus plantarum WCFS1 at normal and elevated temperature  Nov 01, 2011   approved

status: Public on Jan 01 2012

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

summary: Transcriptome profiles of control Lactobacillus plantarum WCFS1 cells were compared with ctsR, hrcA, and ctsR-hrcA deletion mutants grown in MRS media at 28 and 40 degrees Celcius.

overall_design: Continuous cultures were performed in duplo on MRS media and whole genome transcriptome analysis was performed on the WCFS1 (WT), NZ3410CM (harboring a chlooramphenicol resistance marker (cat) replacement mutation in ctsR, dc), NZ3425CM (harboring a cat replacement mutation in hrcA, dh), and NZ3423 (harboring deletion mutation in ctsR and a cat replacement mutation inhrcA, dcdh) strains.

first: Hermien

middle: v

last: van de Veen

first: Roger

last: Bongers

first: Peter

last: Bron

last: Kleerebezem


title: Impact of nutrition on genome-wide gene expression during fruiting body development in Neurospora crassa

status: Public on Jun 01 2012

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: Fungal fruiting body size and form are influenced by the ecology of the species, including diverse environmental stimuli. Accordingly, nutritional resources available to the fungus during development can be vital to successful production of fruiting bodies. To investigate the effect of nutrition, perithecial development of N. crassa was induced on two different media, a sparsely nutritive Synthetic Crossing Medium (SCM) and a natural Carrot Agar (CA). Protoperithecia were collected before crossing, and perithecia were collected at 2, 24, 48, 72, 96, 120, and at full maturity 144 hours after crossing. No differences in fruiting body morphology were observed between the two media at any time point. A circuit of microarray hybridizations comparing cDNA from all neighboring stages was performed. For a majority of differentially expressed genes, expression was higher in SCM than in CA, and expression of core metabolic genes was particularly affected. Effects of nutrition were highest in magnitude before crossing, lowering in magnitude during early perithecial development. Interestingly, metabolic effects of the media were also large in magnitude during late perithecial development, at which stage the lower expression in CA presumably reflected the continued intake of diverse complex initial compounds, diminishing the need for expression of anabolic pathways. However, for genes with key regulatory roles in sexual development, including pheromone precursor ccg-4 and poi2, expression patterns were similar between treatments. When possible, a common nutritional environment is ideal for comparing transcriptional profiles between different fungi.  Nevertheless, the observed consistency of the developmental program across media, despite considerable metabolic differentiation is reassuring. This result facilitates comparative studies that will require different nutritional resources for sexual development in different fungi.

overall_design: Neurospora crassa mat A FGSC#2489 and mat-a FGSC 4200: Eight perithecial developmental stages, 0hr, 2 hr, 24 hr, 48 hr, 72 hr, 96 hr, 120 hr, and 144 hr were sampled and compared

first: Jeffrey

middle: P

last: Townsend


title: The chromatin protein Nupr1 regulates RelB-dependent NF-kB events necessary for pancreatic cancer development

status: Public on Feb 01 2012

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

summary: The objective of this study was to elucidate the role of Nupr1 in pancreatic tumorigenesis. Using the Pdx-1-cre;LSL-KrasG12D mouse as model we discovered that, in contrast to KrasG12D pancreas that develop multiple foci of pancreatic intraepithelial neoplasia (PanIN), KrasG12D;Nupr1KO pancreas were free from such lesions, indicating that Nupr1 is pivotal for PanIN formation. In vitro, MiaPaCa2 cells activated Nupr1 expression in response to nutrient deprivation and this expression was necessary for cell survival. Mechanistically, Nupr1 protected cells from stress-induced death by inhibiting apoptosis through an alternative RelBàIER3-dependent pathway and independent from activation of the classical RelA-based NF-kB pathway. In agreement with these findings, Nupr1, RelB and IER3 proteins were found co-expressed in PanINs from KrasG12D pancreas. Moreover, pancreas-specific KrasG12D;RelbDpanc mice displayed a delay in PanIN development associated with a lack of IER3 expression, further emphasizing the relevance of this pathway in vivo. Efficient PanIN formation was therefore dependent on the expression of Nupr1 and RelB, with the probable involvement of IER3. Finally, a significant correlation between expression of Nupr1, RelB and IER3 and a poor prognosis of patients with PDAC was found. Altogether, our results reveal a novel stress-related pathway that requires the functional interaction of Nupr1àRelBàIER3 in KrasG12D-dependent transformation of the pancreas and expand our understanding of the molecular machinery that mediates the early steps of pancreatic carcinogenesis.

overall_design: Since Nupr1 belongs to the HMG family of chromatin remodelers with transcriptional co-factor activity, Nupr1 could increase cell survival in a nutrient-deprived microenvironment by activating the expression of pro-survival genes. Moreover, considering that RelB, and not RelA/p65, is essential to the Nupr1-mediated survival mechanism that takes place upon nutrient deprivation-induced stress, we made the hypothesis that the two NF-kB transcription factors should activate different sets of genes among which a pivotal pro-survival gene would be exclusively dependent on RelB. In order to test this two hypothesis, an Affymetrix microarray analysis was performed using pancreatic cancer cells transfected with siCtrl or siNupr1 and cultured for 3, 6 or 9 hrs in EBSS; or transfected with siRelB, siRelA/p65 or siCtrl and cultured for 9 hrs in EBSS or Mock.

first: Tewfik

last: Hamidi

first: Hana

last: Algül

first: Carla

last: Cano

first: Maria

middle: J

last: Sandi

middle: I

last: Molejon

first: Marc

last: Riemann

first: Gwen

last: Lomberk

first: Jean-Charles

last: Dagorn

first: Falk

last: Weih

first: Raul

last: Urrutia

first: Roland

last: Schmid

first: Juan

last: Iovanna


status: Public on Dec 08 2011

city: Tianjin

first: Lei

last: Chen

address: 92 Weijin Rd

institute: Tianjin University

summary: Transcriptional profiling of the spxA1-null mutant of Streptococcus sanguinis SK36 compared with wild type. The spxA1 gene was inactivated in Streptococcus sanguinis SK36, and the mutant demonstrated opaque colony morphology, reduced hydrogen peroxide (H2O2) production, and reduced antagonistic activity against Streptococcus S. mutans UA159 both on plates and in liquid media. The mutant also showed decreased tolerance to high temperature, and acidic and oxidative stresses. Complementation of the ΔspxA1 mutant with spxA1 restored colony morphology, H2O2 production and stress tolerance to the ΔspxA1 mutant. The mutant also exhibited an ~5-fold reduction in competitiveness in an animal model of endocarditis, indicating the involvement of SpxA1 in endocarditis virulence. Microarray studies revealed that a number of SpxA1-upregulated genes are involved in oxidative stress. The expression of spxB and nox (which encode pyruvate oxidase and NADH oxidase, respectively, and are involved in H2O2 production and nox involved virulence) significantly decreased in ΔspxA1 compared with the wild type. This may be at least partly responsible for the decreased H2O2 production and reduced virulence in the ΔspxA1 mutant because spxB and nox were involved in H2O2 production and nox involved virulence.

overall_design: One-condition experiment: ΔspxA1 vs. S. sanguinis SK36 cells. Biological replicates: 3 wild type, 3 ΔspxA1, independently grown and harvested. One replicate (one wild type and one ΔspxA1 mixture) per array.

first: Xiuchun

last: Ge

first: Xiaojing

last: Wang

first: Jenishkumar

last: Patel

first: Ping

last: Xu


title: Expression data of tumor and non-tumor samples from patients with esophageal cancer

status: Public on Nov 19 2011

city: Hong Kong

first: Grace

last: Fu

address: 21 Sassoon Road

department: Clinical Oncology

country: Hong Kong

institute: The University of Hong Kong

summary: We used cDNA microarray to study the  gene expression profile between the tumor and non-tumor tissue samples from patients with esophageal cancer

overall_design: Pooled RNA from 10 pairs of primary ESCCs without family history and 5 pairs with family history, relative to their corresponding non-tumor tissues were compared by Affymetrix microarrays.

first: Ran-Ru

last: Qin


title: Zfp281 Functions as a Transcriptional Repressor for Pluripotency of Mouse Embryonic Stem Cells

status: Public on Dec 01 2011

city: NEW YORK

first: Jianlong

state: NEW YORK

address: 1428 MADISON AVE

department: Developmental and Regenerative Biology

institute: Mount Sinai School of Medicine

summary: Zfp281 is a partner protein of Nanog. To identify potential target genes of Zfp281, we generated Zfp281 null ESCs using gene targeting, and compared transcriptomic changes between multiple lines of wildtype, heterozygous and null ESCs.

overall_design: Total 8 ESC lines: 3 wildtype lines, 2 heterozygous lines, and 3 null lines.

first: Miguel

last: Fidalgo

first: P

last: Chandra Sheka

first: Yen-Sin

last: Ang

first: Yuko

last: Fujiwara

first: Stuart

middle: H

last: Orkin


title: DNA methylation epigenotype expanding to non-polycomb target genes, induced by Epstein-Barr virus infection in human gastric cancer

status: Public on Jan 04 2012

city: Meguro-ku

first: Atsushi

last: Kaneda

address: 4-6-1 Komaba

department: RCAST

country: Japan

type:
Expression profiling by array
Methylation profiling by array


title: Genetic variability of transcript abundance in pig peri-mortem skeletal muscle: eQTL localized genes involved in stress response, cell death, muscle disorders and metabolism.

status: Public on Nov 10 2011

city: Castanet tolosan

first: Laurence

last: Liaubet

address: chemin de borde rouge

department: Animal Genetic

country: France

institute: INRA

summary:
BACKGROUND: The genetics of transcript-level variation is an exciting field that has recently given rise to many studies. Genetical genomics studies have mainly focused on cell lines, blood cells or adipose tissues, from human clinical samples or mice inbred lines. Few eQTL studies have focused on animal tissues sampled from outbred populations to reflect natural genetic variation of gene expression levels in animals. In this work, we analyzed gene expression in a whole tissue, pig skeletal muscle sampled from individuals from a half sib F2 family shortly after slaughtering.

RESULTS: QTL detection on transcriptome measurements was performed on a family structured population. The analysis identified 335 eQTLs affecting the expression of 272 transcripts. The ontologic annotation of these eQTLs revealed an over-representation of genes encoding proteins involved in processes that are expected to be induced during muscle development and metabolism, cell morphology, assembly and organization and also in stress response and apoptosis. A gene functional network approach was used to evidence existing biological relationships between all the genes whose expression levels are influenced by eQTLs. eQTLs localization revealed a significant clustered organization of about half the genes located on segments of chromosome 1, 2, 10, 13, 16, and 18. Finally, the combined expression and genetic approaches pointed to putative cis-drivers of gene expression programs in skeletal muscle as COQ4 (SSC1), LOC100513192 (SSC18) where both the gene transcription unit and the eQTL affecting its expression level were shown to be localized in the same genomic region. This suggests cis-causing genetic polymorphims affecting gene expression levels, with (e.g. COQ4) or without (e.g. LOC100513192) potential pleiotropic effects that affect the expression of other genes (cluster of trans-eQTLs).

CONCLUSION: Genetic analysis of transcription levels revealed dependence among molecular phenotypes as being affected by variation at the same loci. We observed the genetic variation of molecular phenotypes in a specific situation of cellular stress thus contributing to a better description of muscle physiologic response. In turn, this suggests that large amounts of genetic variation, mediated through transcriptional networks, can drive transient cell response phenotypes and contribute to organismal adaptative potential.

overall_design: A wide genomic project was designed to combine genetic and transcriptome analysis. This project involved about 1,000 F2 pigs from 15 half-sib families to identify QTL for meat quality traits (Cherel et al., unpublished data). In this study, we focused on one family of 57 half sib F2 pigs. Total RNA was isolated from each of the 57 muscle samples using a commercial kit, and controlled for quality and concentration using an AGILENT 2100 bioanalyzer. cDNA was synthesized and labelled from 5 µg total RNA by simultaneous reverse transcription of mRNA using SuperScriptTM II RNase H- Reverse Transcriptase and 33P-deoxy-CTP. Each muscle sample mRNA was hybridized at 68°C during 24 h to one array. The arrays were then exposed to radioisotopic-sensitive imaging plates that were scanned thereafter with a phosphor imaging system at a 25 µm resolution. Hybridization images were quantified using a semi-automated software through a grid process with a fixed spot diameter. The output was then subjected to the data analysis process.

first: Valérie

last: Lobjois

first: Thomas

last: Faraut

first: Aurélie

last: Tircazes

first: Francis

last: Benne

first: Nathalie

last: Iannuccelli

first: Jérome

last: Glénisson

first: Annie

last: Robic

first: José

last: Pires

first: François

last: Hatey

first: Pascale

last: Le Roy

first: Magali

last: SanCristobal

first: Pierre

last: Cherel


title: Gene level expression profiling of colorectal cancer tissue samples

status: Public on Jan 06 2012

city: Oslo

first: Trude

middle: Holmeide

last: Ågesen

address: Ullernch. 70

department: Department of Cancer Prevention

country: Norway

institute: Oslo University Hospital

summary: By the use of whole genome transcription analysis, we aimed to develop a gene expression classifier to increase the likelihood of identifying stage II colorectal cancer (CRC) samples with a poor prognostic outcome. Gene expression measurement were measured by the GeneChip® Human Exon 1.0 ST Arrays from Affymetrix.

overall_design: We analyzed genome-wide expression at the gene-level for an independent series of colorectal cancer tissue biopsies using the Affymetrix Human Exon 1.0 ST platform.

last: Agesen

first: Anita

last: Sveen

first: Marianne

middle: A

last: Merok

first: Arild

last: Nesbakken

first: Rolf

last: Skotheim

first: Ragnhild

last: Lothe

first: Guro

last: Lind


title: Aberrant DNA methylation epigenotype expanding to non-polycomb target genes, induced by Epstein-Barr virus infection in human gastric cancer [Affymetrix Expression]

first: Atsushi

last: Kaneda

summary: Aberrant promoter methylation is known to be deeply involved in human gastric carcinogenesis, while association of Epstein-Barr virus (EBV) to the aberrant methylation has not been fully clarified. We analyzed promoter methylation in clinical gastric cancer cases using illumina's Infinium beadarray, and hierarchical clustering analysis classified gastric cancer into three subgroups: low and high methylation epigenotypes in EBV-negative cases, and markedly higher methylation epigenotype that was completely matched to EBV-positive cases. Three epigenotypes were characterized by three groups of genes: genes methylated specifically in the EBV-positive epigenotype (EBV(+)-markers, e.g. CXXC4, TIMP2, PLXND1), genes methylated both in EBV-positive and high epigenotypes (High-markers, e.g. COL9A2, EYA1, ZNF365), and genes methylated all in EBV-positive, high and low epigenotypes of gastric cancer (Common-markers, e.g. AMPH, SORCS3, AJAP1). Polycomb repressive complex (PRC)-target genes in ES cells were significantly enriched in High- and Common-markers (P=2x10-15 and 2x10-34, respectively), but not in EBV(+)-markers (P=0.2), suggesting a different cause for EBV(+)-marker methylation. Recombinant EBV was infected to low epigenotype gastric cancer cell, MKN7. In all the three independently established clones, DNA methylation was induced in High- and EBV(+)-markers after 18 weeks, demonstrating that EBV-positive epigenotype should involve methylation of Common-, High-, and EBV(+)-markers simultaneously. The de novo methylated genes were overlapped well among the three clones, and the methylation caused gene repression. In summary, gastric cancer was classified into three DNA methylation epigenotypes, EBV-positive gastric cancer showed markedly high methylation epigenotype expanding to non-PRC target genes, and EBV infection per se could induce the EBV-positive epigenotype.

overall_design: 3 EBV(+) clones and 1 mock clone of MKN7 were analyzed using Affymetrix U133p2 (4 samples)

first: Keisuke

last: Matsusaka

first: Genta

last: Nagae

first: Tetsuo

last: Ushiku

first: Yasuko

last: Kikuchi

first: Hiroshi

last: Uozaki

first: Yasuyuki

last: Seto

first: Kenzo

last: Takada

first: Hiroyuki

last: Aburatani

first: Masashi

last: Fukayama


title: Aberrant DNA methylation epigenotype expanding to non-polycomb target genes, induced by Epstein-Barr virus infection in human gastric cancer [Illumina Methylation]

overall_design: 51 clinical gastric cancer samples including 11 EBV(+) gastric cancer cases, 2 normal gastric mucosa samples and 2 peripheral blood cells were analyzed by Infinium to epigenotype gastric cancer (55 samples). In addition, 3 gastric cancer cell lines, 1 gastric cancer xenograft, and 5 methylation control samples were analyzed (9 samples). Moreover, two gastric cancer cell lines MKN7 and AGS were infected with recombinant EBV. 3 EBV(+) clones and 1 mock clone of MKN7, and 3 EBV(+) clones and 1 mock clone of AGS were analyzed (8 samples).


title: Deep sequencing of the degradome cDNA library in soybean

status: Public on Nov 02 2011

city: Beijing

first: Hu

last: Zheng

address: No.12 South Street, Zhongguancun, Haidian District

institute: Chinese Academy of Agricultural Sciences

type: Expression profiling by high throughput sequencing

summary: We deep sequenced a degradome library constructed from different soybean tissues. As a result, 19,830,257 represented 5,337,590 distinct signatures were obtained. 70.98% of the signatures were assigned to one soybean cDNA sequence and 24.05% matched with two cDNA sequences. 428 potential targets of small RNAs and 25 novel miRNA families were identified in soybean. A total of 211 potential miRNA targets including 150 conserved miRNA targets and 69 soybean-specific miRNA targets were identified. The signatures distribution on soybean primary miRNAs (pri-miRNAs) showed that most of the pri-miRNAs had the characteristic pattern of Dicer processing. The TAS3 small RNAs (siRNAs) biogenesis was conserved in soybean and nine Auxin Response Factors (ARFs) were identified as the TAS3 siRNA targets. The global identification of miRNAs targets would contribute to the functional research of the miRNA in soybean.

overall_design: one sample, We deep sequenced a degradome library constructed from different soybean tissues.

first: Zheng

last: Hu

first: Qiyan

last: Jiang

first: Rui

last: Chen

first: Shuo

last: Xu

first: Hui

last: Zhang


title: Brain expression data from adult mice prenatally exposed to ethanol

status: Public on Dec 16 2011

first: Katarzyna

last: Janus

state: ON

address: 1151 Richmond Street

institute: University of Western Ontario

summary:
Moderate alcohol exposure during pregnancy can result in a heterogeneous range of neurobehavioural and cognitive effects, termed fetal alcohol spectrum disorders (FASD).  We have developed a mouse model of FASD that involves moderate ethanol exposure throughout gestation achieved by voluntary maternal consumption.  This model results in phenotypes relevant to FASD.  Since ethanol is known to directly affect the expression of genes in the developing brain leading to abnormal cell death, changes to cell proliferation, migration, and differentiation, and potential changes to epigenetic patterning, we hypothesize that this leaves a long-term footprint on the adult brain.  However, the long-term effects of prenatal ethanol exposure on brain gene expression, when behavioural phenotypes are apparent, are unclear.
We used a microarray experiment and focused on the genes identified by both to evaluate the genome-wide alterations to the adult brain transcriptome caused by prenatal ethanol exposure.

overall_design: To generate samples, female C57BL/6J mice were given ethanol injections (2.5g/kg of ethanol in saline) twice on gestational days 8 and 11 to produce acute ethanol exposure effects. Control females were injected with the same volume of saline. Females were mated. Whole brain RNA from adult (postnatal day 70) male ethanol-exposed offspring was extracted. RNA samples from three mice were pooled to reduce litter effects and the pooled samples were hybridized on Affymetrix arrays (2 control and 2 ethanol chips, total n=12 mice). To generate samples, female C57BL/6J mice were given ethanol injections (2.5g/kg of ethanol in saline) twice on gestational days 14 and 16 to produce acute ethanol exposure effects.  Control females were injected with the same volume of saline.  Females were mated.  Whole brain RNA from adult (postnatal day 70) male ethanol-exposed offspring was extracted.  RNA samples from three mice were pooled to reduce litter effects and the pooled samples were hybridized on Affymetrix arrays (2 control and 2 ethanol chips, total n=12 mice).

first: Benjamin

last: Laufer

first: Shiva

last: Singh


title: mRNA profiling by androgen-induced tumor suppressor U19/EAF2 in the mouse prostate U19/EAF2 knockout

status: Public on Dec 17 2011

city: Houston

first: Fei

last: Su

state: TX

address: 3605 Cullen Blvd

institute: university of houston

summary: To elucidate potential mechanisms of U19/EAF2 action, we performed cDNA microarray analysis and identified 202 mRNA transcripts regulated by U19/EAF2 in the mouse ventral prostate. Of these transcripts, 167 are network eligible genes, with 63 associated with cancer and 24 with reproductive system diseases. Bioinformatics analysis indicated that U19/EAF2 knockout activates the RAS-BRAF-ERK signaling pathway, which is known to play important roles in carcinogenesis.

overall_design: prostate wild type and U19/EAF2 knockout

first: Jianhua

last: Luo

first: Zhou

last: Wang


title: brain expression data from adult mice exposed to ethanol at postnatal day 4 and 7

status: Public on Dec 20 2011

first: Morgan

last: Kleiber

state: Ontario

address: Biological and Geological Sciences Building

department: Biology

summary:
The developing brain is particularly sensitive to ethanol during the brain growth spurt or synaptogenesis (third human trimester equivalent).  This has been shown to lead to abnormal brain development and behavioural changes in the adult mouse that are relevant to those seen in humans with fetal alcohol spectrum disorders (FASD).  We evaluated the long-term (postnatal day 60 young adult) gene expression changes that occur in the brain due to ethanol exposure during synaptogenesis.
We used microarray analyses to evaluate the changes in brain gene expression at postnatal day 60 that occur due to ethanol treatment at postnatal days 4 and 7 (synaptogenesis).

overall_design: To generate samples, C57BL/6J pups were injected with ethanol (experimental) or saline (control) at postnatal days 4 and 7.   Pups were weaned at postnatal day 25 and sacrificed at postnatal day 60.  Total RNA was extracted from whole brain tissue and RNA from three male mice from three different litters were pooled as one biological replicate.  Each male ethanol-treated mouse represented in a sample was matched by a control littermate present in a control sample.  This study consists of two biological replicates for each experimental group (total mice used was n=12).


title: Deep sequencing of small RNAs from different tissues in soybean

type: Non-coding RNA profiling by high throughput sequencing

summary: Analysis of flanking genomic sequences of unique small RNAs enabled identification of 419 miRNAs. Expression analysis revealed that miRNAs were differentially expressed in different tissues and development stages. Prediction of the miRNA target genes suggested that they are involved in important processes in soybean growth and development. Most conserved soybean miRNAs guide the cleavage of conserved genes. Our study significantly increased the number of known conserved and non-conserved miRNAs in soybean. Our description of soybean miRNAs can be used for functional characterization.

overall_design: one sample, We sequenced 2,570,250 small RNAs representing 1,157,365 unique sequences from different soybean tissues using sequence-by-synthesis high-throughput sequencing


title: Deep sequencing of small RNAs and degradome cDNA library in soybean

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

overall_design: Refer to individual Series


title: Expression data from rice varieties IRAT109 and ZS97 for drought stress treatment in flag leaves

status: Public on Nov 05 2011

city: wuhan

first: ding

middle: xi

last: peng

address: No.1,Shizishan Street Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

summary: Comparative transcriptional profiling of two contrasting rice genotypes,IRAT109 (drought-resistant japonica cultivar) and ZS97 (drought-sensitive indica cultivar), under drought stress during the reproductive stage

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: Four samples with RWC in the range of 94–95% (no stress, D0), 83–88% (slight drought in which leaves were slightly rolled, D1), 74–78% (moderate drought in which about half of each leaf was rolled, D2), and 65–69% (severe drought in which all leaves were completely rolled, D3) were collected for expression profiling analysis using an Affymetrix GeneChip.

first: Ding

last: Peng

first: Xiong

last: Zhong


title: Analysis of a novel highly metastatic melanoma cell line identifies osteopontin as a new lymphangiogenic factor.

status: Public on Nov 16 2011

city: Muenster

first: Ruediger

last: Liersch

address: Albert-Schweitzer-Campus 1a

department: Department of Medicine - Hematology and Oncology

country: Germany

institute: University Hospital of Muenster,

summary: Tumor cell invasion and metastasis are hallmarks of malignancy. Despite recent advances in the understanding of lymphatic spread, the mechanisms by which tumors metastasize to sentinel/distant lymph nodes and beyond are poorly understood. To gain new insights into this complex process, we established a highly metastatic melanoma cell line (B16F1-variant) by in vivo passaging the B16 parental cell line through the lymphatic system. Here, we characterized morphology, rate of cell proliferation, colony formation, migration, tumorogenicity, lymph flow, and capacities to induce tumor- and sentinel lymph node- lymphangiogenesis. Furthermore, microarray-based comparative analysis bewteen parental and passaged cell lines was performed to identify specific gene expression profiles. The most differentially expressed gene was SPP (osteopontin), a secreted glycophosphoprotein which is known to be involved in cancer metastasis. Overexpression of osteopontin in B16 F1-variant was confirmed by Western blot and quantitative RT-PCR. Treatment of cultured lymphatic endothelial cells (LEC) with osteopontin promoted cell migration mediated by the integrin α9 pathway. Our results identify osteopontin as a novel lymphangiogenic factor.

overall_design: B16 and B16 variants were cultured in DMEM supplemented with 20% fetal bovine serum (FBS; Invitrogen, Grand Island, NY) supplemented with antibiotic-antimycotic solution. Every B16 variant was cultured in duplicates. Total cellular RNA was isolated using the Trizol reagent (Invitrogen, Carlsbad, CA) extracted with chloroform, precipitated with isopropanol, washed with 70% ethanol, and dissolved in DNase-free/RNase-free distilled water. The concentration of RNA was measured using NanoDrop ND-1000 spectrophotometer (Witec AG, Littau, Switzerland) and RNA quality was assessed using 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Digoxigenin-UTP–labeled cRNA was generated and amplified from 500ng of total RNA using the NanoAmp RT-IVT Labeling Kit (Applied Biosystems, Foster City, CA) following the manufacturer's protocol, and was hybridized to Applied Biosystems Mouse Genome Survey Microarrays V2.0. Chemiluminescence detection, image acquisition, and analysis were performed using the Chemiluminescence Detection Kit (Applied Biosystems) and the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following the manufacturer's protocol. A total of two biological replicates were generated for each B16 variant and each cell line data consisted of pooled RNA of two diffferent passage numbers.

first: Jay

last: Shin

first: Michael

last: Bayer

first: Christian

last: Schwoeppe

first: Christoph

last: Schliemann

first: Wolfgang

middle: E

last: Berdel

first: Rolf

last: Mesters

last: Detmar


title: Identification of SOX2-bound mRNA

status: Public on Oct 26 2011

city: ChiaYi

first: Chin

last: Li

address: 168 University Road, Minhsiung

department: Life Science

country: Taiwan

institute: National Chung Cheng University

summary:
In vitro pull down assay was performed using recombinant GST and GST fusion SOX2 protein to precipitate total RNA from urothelial carcinoma cell line BFTC905
Unbound RNA from both reactions and matrix-associated RNA from SOX2 pull down reaction was extracted using TRIZOL reagent

overall_design: This experiment is to identify mRNA bound by SOX2 under in vitro experimental condition


title: Gene expression profiling during Ara-C induced NB4 cell apoptosis

status: Public on Oct 15 2011

first: Lv

last: Yi

address: Haidian District,Tsinghua University

department: School Of Medicine

institute: Tsinghua University

summary: As the most important antimetabolite used to induce remission in children and adults with acute leukemia, cytosine arabinoside (Ara-C) is widely used in consolidation therapy of APL to reduce the relapse rate. In order to better understand the molecular mechanism underlying Ara-C induced cell early apoptosis, we examined the mRNA level changes of NB4 cells after Ara-C treatment over the 12 h time course using a human whole genome oligo-array.

overall_design: For each test and control sample at the 2, 4, 6, and 12 h time point, hybridization experiments were performed using a dye-swap strategy.

first: Yi

last: Lv


title: The role of photoreceptors in the light modulated cellulase gene expression in Neurospora crassa

status: Public on Oct 12 2011

city: Vienna

first: Doris

last: Tisch

state: Vienna

address: Gumpendorferstraße 1a

department: Chemical Engineering

country: Austria

institute: Technical University of Vienna

summary: Light represents an important environmental cue, which exerts considerable influence on the metabolism of fungi. Studies with the biotechnological fungal workhorse Trichoderma reesei (Hypocrea jecorina) have revealed an interconnection between transcriptional regulation of cellulolytic enyzmes and the light response. The filamentous fungus, Neurospora crassa, has been used as a model organism to study light and circadian rhythm biology. We therefore investigated whether light also regulates transcriptional regulation of cellulolytic enzymes in N. crassa. We show that the N. crassa photoreceptor genes wc-1, wc-2 and vvd are involved in regulation of cellulase gene expression, indicating that this phenomenon is conserved among filamentous fungi. Genome wide analysis of photoreceptor mutants and evaluation of results by analysis of mutant strains identified several candidate genes likely to play a role in light modulated cellulase gene expression.

overall_design: Three deletion strains (delta-wc-1 (FGSC 11712), delta-wc-2 (FGSC 11124) and delta-vvd (FGSC 11556)) and the wild type strain (FGSC 2489) at two different timepoints (28h or 40h) were analyzed. Cy3 and Cy5 dye swaps were performed.

first: Monika

last: Schmoll

first: Chaoguang

last: Tian

first: Jianping

last: Sun

first: N

last: Glass


title: The impact of chronic temperature elevation on the spleen anti-viral transcriptomic response in Atlantic cod (Gadus morhua)

status: Public on Oct 01 2011

city: St John's

first: Tiago

last: Hori

state: NL

address: 0 Marine Lab Rd

department: Ocean Sciences Centre

institute: Memorial University of Newfoundland

summary: This experiment was designed to investigate the impacts of non-lethal increases in temperature on the anti-viral transcriptomic response of Atlantic cod. Selected genes identified as differentially expressed between samples injected with pIC but held at different temperatures were validated using QPCR.

overall_design: This was a common reference design. For the common reference each individual sample analyzed in the microarray experiment contributed with equal amounts of RNA to a pool. Sixty individuals were analyzed representing 6 biological replicates from 10 different experimental groups. Two separate control groups were used. Non-injected groups at the final temperatures (i.e. 10°C and 16°C) were used as prior to injection controls. At each time-point and temperatures there was also a sham-injected time matched control (injected with phosphate buffered saline [PBS]). The time points were 6 and 24 hours post-injection. Immunostimulated fish were injected with a weight-based dose of poly (I:C)(2 µg per g of wet body mass).

first: Kurt

last: Gamperl

first: Marije

last: Booman

first: Gordon

middle: W

last: Nash

first: Matthew

last: Rise


title: Microarray Profile of Measles Virus Nucleocapsid Protein (MVNP) Regulated Gene Expression in RANKL and M-CSF stimulated normal human bone marrow derived non-adherent cells.

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary:
Paget’s disease of bone (PDB) is a chronic focal skeletal disorder that affects 2-3% of the population over the age of 60. PDB is inherited as an autosomal dominant trait with genetic heterogeneity.  SQSTM1/p62 UBA domain mutation (p62P392L) is widely identified in PDB and has been shown to increase osteoclastogenesis. Further, environmental factors such as paramyxovirus are implicated in PDB and MVNP has been shown to induce Pagetic phenotype in osteoclasts. However, the molecular mechanisms underlying p62P392L and MVNP stimulation of osteoclast differentiation in PDB are unclear. We therefore determined MVNP regulated gene expression profiling during osteoclast differentiation.
We identified 8.4% of genes were upregulated (> 4-fold) in MVNP transduced cells.  MVNP increased integrin β3 (63 fold), NFAT activating protein (6.5 fold), OSCAR (5.5 fold), TRAF5 (8.5 fold) mRNA expression compared to empty vector (EV) transduced cells. MVNP also elevated gene expression of cytokines/growth factors such as IL-17 (18 fold), IL-1F7 (10 fold), IL-17R (4.5 fold) and IL-11 (7 fold).   Interestingly, MVNP transduced cells demonstrated high level expression of signal regulatory protein beta 1 (SIRPβ1) (353 fold).  SIRPβ1 has been shown to interact with DAP 12, an ITAM containing adaptor protein which plays an important role in osteoclast differentiation.  Real-time PCR analysis of total RNA isolated from normal human peripheral blood monocytes transduced with MVNP confirmed upregulation of SIRPβ1 mRNA expression in the absence of RANKL stimulation. In contrast, RANKL stimulation did not alter SIRPβ1 expression in these cells. Furthermore, bone marrow mononuclear cells derived from patients with PDB showed high levels of SIRPβ1 mRNA expression compared to normal subjects.  Thus, MVNP regulated gene expression profiling during osteoclast differentiation provides new insights into molecular mechanisms and therapeutic targets to control elevated osteoclast activity in PDB.

overall_design: Total RNA isolated from normal human bone marrow mononuclear cells transduced with EV, MVNP retroviral expression vectors and stimulated with M-CSF and RANKL for 48 h were subjected to Agilent microarray (~26,000 genes) analysis. One replicate per treatment was hybridized.

first: Kumaran

last: Sundaram

first: Srinivasan

last: Shanmugarajan

first: Sakamuri

middle: V

last: Reddy


title: Regulation of gene expression by GLIPR1 in prostate cancer cells

status: Public on Sep 26 2011

first: Timothy

middle: C.

last: Thompson

state: Texas

address: 1515 Holcombe Blvd.

department: Genitourinary Medical Oncology

institute: MD Anderson Cancer Center

summary: Human glioma pathogenesis-related protein 1 (GLIPR1) and its mouse counterpart, Glipr1 are downregulated in prostate cancer (PCa) and other malignant cell lines, owing partly to methylation in the gene’s regulatory region. Loss of Glipr1 function predisposed mice to tumorigenesis. Restoration of GLIPR1 expression in prostate cancer cells and other malignant cells led to growth suppression and/or apoptosis. Here we show that restoring GLIPR1 expression in PCa cells leads to downregulated c-myc and cell cycle-related c-myc target genes, leading to the inhibition of cell cycle progression.

overall_design:
DNA microarray (Illumina HumanHT-12)
Prostate cancer cells were transduced with adenovirus-mediated GLIPR1 or control lacZ, grown in complete medium for 24 hours, synchronized by serum starvation for 24 hours, followed by serum restimulation for 30 min. RNA was prepared and subjected to DNA microarray analysis.

first: Likun

last: Li

first: Chengzhen

last: Ren

first: Guang

last: Yang

first: Elmoataz

last: Fattah

first: Alexei

last: Goltsov

first: SooMi

last: Kim

first: Ju-Seog

last: Lee

first: Sanghee

last: Park

first: Francesco

last: Demayo

middle: M

last: Ittmann

first: Patricia

last: Troncoso

middle: C


title: Comprehensive genomic profiling identified miRNA signatures associated with mammary tumor differentiation and development

status: Public on Jul 21 2011

city: Bethesda

first: Jeffrey

last: Green

address: Rm 4054, 37 Convent Drive

institute: NCI

summary:
We performed affymetrix gene expression profiling on mammary tumors from eight well-characterized genetically engineered Mouse (GEM) models of human breast cancer.
The gene expression data will be combined with the miRNA gene expression data from the corresponding mammary tumors and tissues for integrated miRNA and mRNA gene expression analysis, which are useful in improving the identification of miRNA targets from potential targets identified in silico.

overall_design: mRNA expression data for 41 mouse primary mammary tumors and 5 mouse normal mammary glands

first: Min

last: Zhu

first: Ming

last: Yi

first: Chang

first: Chuxia

last: Deng

first: Yi

first: Daniel

last: Medina

first: Robert

last: Stephen

first: Jeff


title: Affymetrix SNP array data for oral squamous cell carcinoma

status: Public on Sep 01 2011

city: Taoyuan

first: Chien-Hua

last: Peng

address: No. 5, Fu-Hsing ST.

institute: Chang Gung Memorial Hospital

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

summary: In order to identify biomarkers that contribute to genetic causes of OSCC, we attempt to identify copy number variation regions (CNV) in patients with OSCC. We identified and confirmed the clinical significance of amplification regions scattered from 8q22.2 to 8q24.3.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from normal oral tissues and OSCC specimens.
Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 112 OSCC specimens and 10 non-cancerous samples.

first: Chun-Ta

last: Liao

first: Yin-Ju

last: Chen

first: Ann-Joy

last: Cheng

first: Jyh-Lyh

last: Juang

first: Chi-Ying

last: Tsai

first: Wen-Ping

last: Hsieh

first: Tzu-Chen

last: Yen


title: Transcript and metabolite analysis in Trincadeira cultivar reveals novel information regarding the dynamics of grape ripening

status: Public on Sep 30 2011

city: Lisboa

first: Ana

middle: Margarida

last: Fortes

address: Campus da FCUL

department: Plant Biology

country: Portugal

summary: Background Grapes (Vitis vinifera L.) are economically the most important fruit crop worldwide. However, the complexity of molecular and biochemical events that lead to the onset of ripening of nonclimacteric fruits is not fully understood which is further complicated in grapes due to seasonal and cultivar specific variantion. The Portuguese wine variety Trincadeira gives rise to high quality wines but presents extremely irregular berry ripening among seasons probably due to high susceptibility to abiotic and biotic stresses.  Results Ripening of Trincadeira grapes was studied taking into account the transcriptional and metabolic profilings complemented with biochemical data. The mRNA expression profiles of four time points spanning developmental stages from pea size green berries, through veraison and mature berries (EL 32, EL 34, EL 35 and EL 36) and in two seasons (2007 and 2008) were compared using the Affymetrix GrapeGen® genome array containing 23096 probesets corresponding to 18726 unique sequences. Over 50% of these probesets were significantly differentially expressed (1.5 fold) between at least two developmental stages. A common set of modulated transcripts corresponding to 5862 unigenes indicates the activation of common pathways in between years despite the irregular development of Trincadeira grapes. These unigenes were assigned in the functional categories of “metabolism, development”, “cellular process”, “diverse functions”, “regulation overview”, “response to stimulus, stress”, “signaling”, “transport overview”, “xenoprotein, transposable element” and “unknown”. Metabolic profiling using 1H NMR spectroscopy associated to two-dimensional techniques showed the importance of metabolites related to oxidative stress response, amino acid and sugar metabolism as well as secondary metabolism in grape ripening. This information was integrated with transcriptional profiling obtained using genome array and qRT-PCR for five developmental stages (EL 32, EL 34, EL 35, EL 36 and EL 38).  Conclusions  Altogether the results provide new information regarding the network of events leading to grape ripening as well as highlight features that may be cultivar specific namely in what concerns the role of carbohydrates and growth regulators´ metabolism as well as epigenetic factors and signaling pathways.

overall_design: 4 time points in 2007 season. 3 time points in 2008 season. 3 biological replicates.

first: Maria

last: Pais


title: Peripheral blood mononuclear cells, control vs. Kashin-Beck Disease

status: Public on Sep 23 2011

city: Xi'an

first: xiaoming

last: wu

address: Xiangningxi Road No.28

institute: Xi'anjiaotongUniversity

summary: Objective: To investigate the differences between the gene expression profiles in peripheral blood mononuclear cells (PBMC) from normal controls and patients with Kashin-Beck disease (KBD).  Methods: Twenty KBD patients and 12 normal subjects were selected from a KBD-endemic area and divided into four pairs of KBD vs. control (KBD, n=5 per pair; control, n=3 per pair). RNAs were respectively isolated from KBD PBMCs and normal PBMCs. Gene expression profiles were analyzed by oligonucleotide microarray.

overall_design: Two-condition experiment, control vs. KBD PBM cells. Biological replicates: 4 control replicates, 4 KBD replicates.

first: Shuang

last: Wang

first: Xiong

last: Guo

first: Xiaoming

last: Wu

first: M

last: Lammi


title: Differential gene expression after gamma radiation in bis-benzimidazole-treated human glioblastoma using microarray analysis

status: Public on Aug 01 2011

city: Delhi

first: Vibha

last: Tandon

state: Delhi

address: Department of Chemistry

department: Department of Chemistry

institute: University of Delhi

summary: Radiation-induced DNA damage initiates a complex series of overlapping responses responsible for the maintenance of genome integrity. This study reports the expression analysis in response to DNA minor groove binding ligand (DMA-5-(4-methylpiperazin-1-yl)-2-[2’-(3,4-dimethoxyphenyl)-5`-benzimidazolyl] benzimidazole, an analogue of Hoechst 33342), with an emphasis on its ability to afford better protection in cells exposed to ionizing radiation.

overall_design: Four different types of samples were employed in the analysis: Control (untreated) cells, 50µM ligand-treated cells, 8.5Gy radiation-treated cells, and cells treated with 50µM ligand one hour prior to irradiation.

first: Navrinder

last: Kaur


title: affy_dormance_totalrna_sunflower-Molecular mechanisms of seed dormancy release: transcriptome evolution and ROS signalling during sunflower seed after-ripening.

status: Public on Jul 20 2011

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

summary: affy_dormance_sunflower - affy_dormance_totalrna_sunflower - We focus our research on the release of embryonic dormancy in sunflower seeds and more precisely on the molecular mechanisms controlling seed dormancy release during dry after-ripening. Our data show an increase of ROS during dormancy release associated with an increase of stored mRNA oxidation during after-ripening as shown with determination of the RNA oxidation marker : 8-hydroxyguanosine (8OHG) To assess to role of mRNA oxidation in this process, we isolated 8OHG-containing mRNA to identify oxidized transcript using microarray analysis.-The samples compared are the following:  1) Population of 50 embryonic axis from dry dormant seed (D) ie. Seed which have been frozen at -30°C after harvest to keep dormancy  2) Population of 50 embryonic axis from dry non dormant ie. Seeds which have been after-ripened (stored) at 70% RH during 2 month.  3) Embryonic axis from dry dormant seed but after ripened at very low relative humidity (2% RH) (control of storage: S). Replicates correspond to different batches of seeds from the same harvest which have been treated (after ripened) independently. - We want to compare D vs ND; D vs S and ND vs S.

overall_design: 6 arrays - SUNFLOWER; dormant vs non dormant seed embryo

first: Sandrine

last: Arribat

last: Balzergue

first: Hayat

last: Bouteau

first: Jérémie

last: Bazin

first: Marie-Laure

last: Martin-Magniette


title: Regulation of transcription by HIP1 protein interactor (HIPPI) in HeLa cells

status: Public on Sep 21 2011

city: Kolkata

first: Nitai

middle: Pada

last: Bhattacharyya

state: West Bengal

address: 1/AF Bidhannagar

department: Crystallography and Molecular Biology division

institute: Saha Institute of Nuclear Physics

summary: HIPPI is a novel transcription factor that regulates caspase1 gene expression. To find out new transcriptional targets of HIPPI and to investigate the effect of HIPPI on cellular transcriptome, microarray study is performed using HeLa cells exogenously transfected with Green Fluorescent Protein tagged HIPPI (GFP-Hippi) construct

overall_design: Total RNA extracted from HeLa cells transfected with empty GFP vector served as control and Total RNA extracted from HeLa cells transfected with GFP-Hippi construct served as test. Biological replicates: 4

first: Moumita

last: Datta


title: Role of HIP1 in HIPPI mediated transcription regulation in HeLa cells

summary: Nuclear entry of transcription factor HIPPI is mediated by its interacting partner Huntingtin Interacting Protein 1 (HIP1), a nuclear localization signal containing nucleo-cytoplasmic shuttling protein. In oredr to investigate the role of HIP1 in HIPPI mediated transcriptional regulation in cell, here we performed microarray experiments using stable HIP1 knocked down HeLa cells (Hip1Si) exogenously expressing Green fluorescent protein tagged HIPPI.

overall_design: Total RNA extracted from HIP1 knocked down HeLa cells (Hip1Si) transfected with empty GFP vector served as control and Total RNA extracted from Hip1Si cells transfected with GFP-Hippi construct served as test. Biological replicates: 4


title: Expression and SNP array data for oral squamous cell carcinoma

first: Chien-Hua

last: Peng

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

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

overall_design: Refer to individual Series


title: Regulation of transcription by HIPPI and its molecular partner HIP1


title: Dominant MLH1 epimutation linked to 5'UTR variant c.-27C>A

status: Public on Jul 01 2011

city: Sydney

first: Megan

last: Hitchins

state: NSW

address: Randwick High Street

department: Lowy Cancer Research Centre

country: Australia

institute: University of New South Wales

summary: Constitutional epimutations of tumor suppressor genes manifest as promoter methylation and transcriptional silencing of a single allele in normal somatic tissues, thereby predisposing to cancer. Constitutional MLH1 epimutations occur in individuals with young-onset cancer and demonstrate non-Mendelian inheritance through their reversal in the germline. We report a cancer-affected family showing dominant transmission of soma-wide highly mosaic MLH1 methylation and transcriptional repression linked to a particular genetic haplotype. The epimutation was erased in spermatozoa but reinstated in the somatic cells of the next generation. The affected haplotype harbored two single nucleotide substitutions in tandem: c.-27C>A located near the transcription initiation site and c.85G>T. The c.-27C>A variant significantly reduced transcriptional activity in reporter assays and is the probable cause of this epimutation.

overall_design:
Five members of a three-generation Caucasian Lynch syndrome family with an autosomal dominant MLH1 epimutation linked to a single nucleotide variant (c.-27C>A) within the MLH1 5'UTR were examined for copy number variations and retention of heterozygosity on chromosome 3. These five carriers of constitutional MLH1 methylation and the c.-27C>A variant were compared with 300 healthy Caucasian controls from the Wellcome Trust Case Control Consortium using three algorithms (QuantiSNP, PennCNV, COKGEN) to detect any copy number variants. The five family members studied were female (the proband II5, her affected mother I1, and three asymptomatic relatives II2, II4 and III2) are labeled according to the pedigree in Figure 3 of the associated publication (Hitchins et al., Cancer Cell, 2011).

The supplementary file 'GSE30348_gw6.lrr_baf.txt' contains log R ratio and B-allele frequency values in a tab-delimited format with one marker per row.

first: Robyn

last: Ward


title: Early effects of cdkf;1 RNAPII CTD Serine-7 kinase mutation on regulation of transcription in 7 days old Arabidopsis seedlings

city: Cologne

first: Csaba

last: Koncz

address: Carl-von-Linne-Weg 10

institute: Max-Planck Institute for Plant Breeding Research

summary:
Serine phosphorylation of conserved Y1S2P3T4S5P6S7 repeats of RNA polymerase II carboxy-terminal domain (RNAPII CTD) plays a central role in the regulation of transcription and co-transcriptional RNA processing. Maintenance of CTD phosphoserine-7 mark in Arabidopsis requires the CDKF;1 kinase, which mediates in vivo activation of downstream-acting CDKD CTD kinase family. Knockout mutations of CDKF;1 lead to over 50% reduction of RNAPII CTD Ser-7 phosphorylation as early as 7 days after germination in seedlings. The transcript profiling experiment aimed at determining how early changes in CTD Ser-7 phosphorylation affect global regulation of transcription.
We used Affymetrix ATH1-121501 Genome Array to compare global transcript levels in wild type and cdkf;1-2 mutant seedlings 7 days after germination.

overall_design: Wild type and cdkf;1-2 mutant Arabidopsis (Col-0) seedlings were grown in solid MSAR medium (Koncz, C., Martini, N., Szabados, L., Hrouda, M., Bachmair, A., and Schell, J. (1994). Specialized vectors for gene tagging and expression studies. In: Plant Molecular Biology Manual, Gelvin,S., and Schilperoort, B. (eds.), Kluwer Academic Publishers, Dordrecht-Boston-London, B2, 1-22.) containing ½ concentration of macro elements and 0.5% sucrose in Petri-dishes at 22°C, 120 mol/m2s light intensity and 8h light/16h dark period. Seedling were collected at 4h after the start of the light period in liquid nitrogen for RNA preparation.

first: Mohsen

last: Hajheidari

first: Bruno

last: Huettel


title: Mtb-mediated host transcriptional reponse is strain-specific

status: Public on Aug 30 2011

city: Newark

first: Mi-Sun

last: Koo

state: NJ

address: 225 Warren Street, W250Q

department: Public Health Research Institute

institute: University of Medicine and Dentistry of New Jersey

summary:
CDC1551 induced more vigorous immune response in murine bone marrow derived macrophage (BMM). In contrast, in HN878-infected cells, host transcriptional response was delayed but lasted longer.
HN878 induced more genes involved in host lipid metabolism than CDC1551 did.

overall_design: Murine bone marrow derived macrophages were infected with M. tuberculosis CDC1551 or HN878 up to 24 h.  Total RNA was processed for microarray and global gene expression was read.


title: Expression analysis in mouse female PGK12.1 ES cells by RNA-seq

status: Public on Jul 19 2011

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

institute: University of Washington

summary: Many animal species employ a chromosome-based mechanism of sex determination, which has led to coordinate evolution of dosage compensation systems. Dosage compensation not only corrects the imbalance in the number of X-chromosomes between the sexes, but is also hypothesized to correct dosage imbalance within cells due to mono-allelic X expression and bi-allelic autosomal expression, by upregulating X-linked genes (termed âOhnoâs hypothesisâ). Although this hypothesis is well supported by expression analyses of individual X-linked genes and by array-based transcriptome analyses, a recent study claimed that no such X upregulation exists in mammals and C. elegans based on RNA-sequencing and proteomics analyses. We provide RNA-seq RNA-seq analysis of mouse female PGK12.1 ES cells with two active X chromosomes and confirmed that the X chromosome is upregulated, consistent with the previous microarray study.

overall_design: Examination of expression of X-linked and autosomal genes in mouse female ES cells with two active X chromosomes.

first: Christine

last: Disteche


title: Mammalian X upregulation

type: Genome binding/occupancy profiling by genome tiling array

sample_organism:
Mus musculus
Mus musculus x Mus spretus

platform_organism:
Mus musculus
Mus musculus x Mus spretus


title: Trichoderma reesei transcript levels during mycoparasitism

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

institute: École normale supérieure

type: Expression profiling by genome tiling array

summary: To investigate the potential role in mycoparasitism, microarrays were used to examine T. reesei transcript levels when confronted with a potential prey (the plant pathogen Rhizoctonia solani) before contact, during first physical contact and during overgrowth of the host.

overall_design: Two biological pools by condition against a common reference control each sample hybridized in dye switch. On the two biological replicates we apply on the pretreated results the linear modeling approach implemented by lmFit and the empirical Bayes statistics implemented by eBayes from the limma R package (Smyth 2004).

first: Christian

last: Kubicek

first: Fanny

last: Coulpier

first: Stephane

last: Le Crom

first: Verena

last: Seidl

first: Susanne

last: Zeilinger


title: Enrichment profiles of Ser-5 phosphorylated RNA polymerase II (PolII S5p) in mouse female ES cells

summary:
Many animal species employ a chromosome-based mechanism of sex determination, which has led to coordinate evolution of dosage compensation systems. Dosage compensation not only corrects the imbalance in the number of X-chromosomes between the sexes, but is also hypothesized to correct dosage imbalance within cells due to mono-allelic X expression and bi-allelic autosomal expression, by upregulating X-linked genes (termed ‘Ohno’s hypothesis’). It is unknown whether any epigenetic mark or protein is involved in X upregulation in mammals.
Ser-5 phosphorylated RNA polymerase II (PolII S5p) is required for transcription initiation. Chromatin immunoprecipitation combined with DNA tiling array analysis (ChIP-chip) of PolII S5p in mouse female ES cells with two active X chromosomes demonstrated a greater enrichment of RNA polymerase II on X-linked genes relative to autosomal genes, suggesting that enhanced transcription initiation may play a role in X upregulation.

overall_design: Comparison of RNA PolII S5p enrichment on the X versus autosomes in mouse


title: Trichoderma sp. transcript levels during mycoparasitism

sample_organism:
Trichoderma virens
Trichoderma reesei
Trichoderma atroviride


title: Gene expression in mouse lung homogenates treated with synthetic TLR ligands to induce resistance

status: Public on May 01 2011

city: Houston

first: Scott

last: Evans

address: 1400 Holcombe Blvd

department: Pulmonary Medicine - Unit 1462

institute: University of Texas-M.D. Anderson Cancer Center

summary: Infectious pneumonias exact an unacceptable mortality burden worldwide.  Efforts to protect populations from pneumonia have historically focused on antibiotic development and vaccine-enhanced adaptive immunity.  However, we have recently reported that the lungs’ innate defenses can be therapeutically induced by inhalation of a combination of synthetic TLR ligands that synergize to protect mice against otherwise lethal pneumonia.  Simultaneous treatment with ligands for TLR2/6 and TLR9 conferred robust, synergistic protection against virulent Gram-positive and Gram-negative pathogens, as well as viruses.   Protection is associated with rapid pathogen killing in the lungs, and pathogen killing can be induced from lung epithelial cells in isolation.  Here we explore the mechanisms underlying this dramatic phenomenon by performing microarray gene expression analysis of mouse lungs treated by aerosol with PBS (sham treatment), Pam2CSK4 (TLR 2/6 ligand), ODN2395 (TLR9 ligand), or both TLR ligands.

overall_design: C57BL/6J mice were placed, unrestrained, in a aerosolization chamber and inhalationally exposed to 20 minute treatment with an 8 ml volume of PBS (sham), Pam2CSK4 10 ug/ml, ODN 2395 20 ug/ml, or the combination.  4 h after treatment, the mice were deeply anesthetized, their lungs were harvested, homogenized, and total RNA was extracted.  Amplified cRNA was hybridized to Illumina Sentrix MouseRef-8 v2 Beadhips, labeled with Cy3, and scanned on an Illumina iScan. At least 8 unique samples were obtained per condition.


title: Role of REG 1 in Entamoeba histolytica colitis

status: Public on May 24 2011

first: Christopher

last: Pan

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

summary:
Differential expression was used to access gene differences after Entamoeba histolytica infection.
Entamoeba histolytica is an important diarrheal pathogen worldwide, and induces apoptosis of the intestinal epithelium as part of its disease process.  Regenerating (REG) 1 protein is anti-apoptotic.  We investigated the involvement of REG 1 in E. histolytica colitis.  Colonic biopsy samples were obtained from 8 subjects with acute E. histolytica colitis, and again 60 day later during convalescence. Gene expression in the human colon during acute and convalescent E. histolytica disease was evaluated using microarray and confirmed by polymerase chain reaction (PCR).  REG 1 protein expression was evaluated with immunohistochemistry.  The mechanism of REG 1 involvement in E. histolytica disease was subsequently investigated with a mouse model.  REG 1A and REG 1B were the most upregulated genes in the human intestine in acute versus convalescent E. histolytica disease (p=0.003 and p=0.006 respectively).  PCR confirmed the microarray results (p=<0.001 and p=0.001 respectively).  Increased REG 1A and REG 1B protein expression was similarly observed by immunohistochemistry. REG 1 -/-mice were found to be significantly more susceptible to E. histolytica infection than wild type mice.

overall_design: Intestinal Biopsies were taken at day 1 and day 60 post infection.

first: Kristine

last: Peterson

first: William

last: Petri

first: Abdel

middle: G

last: Elkahloun


title: Trichoderma virens transcript levels during mycoparasitism

summary:
Combating the action of plant pathogenic microorganisms by antagonistic or mycoparasitic fungi has been announced as an attractive biological alternative to the use of chemical fungicides since more than 20 years, and gains additional importance in current trends to environmentally friendly agriculture. Taxa of the fungal genus Hypocrea/Trichoderma (Ascomycota, Hypocreales, Hypocreaceae) contain prominent examples of such biocontrol agents, because they not only antagonize plant-pathogenic fungi, but are also often rhizosphere competent and can enhance plant growth. Identification of the primary factors that regulate the mycoparasitic behaviour and metabolic activities related to it will therefore allow the full ecological significance of this trait to be explored. We performed the analysis of the genome sequence from two mycoparasitic and rhizosphere competent Trichoderma spp. – T. atroviride and T. virens – and compare it to that of the saprophyte T. reesei. The predicted gene inventory of the T. atroviride and T.virens genome, therefore, points to previously unknown mechanisms operating during biocontrol of plant pathogens. The availability of these genomes provides a unique opportunity to develop a deeper understanding of the processes fundamental to mycoparasitism and its application for the breeding of improved biocontrol strains for plant protection.

To investigate the potential role in mycoparasitism, microarrays were used to examine T. virens transcript levels when confronted with a potential prey (the plant pathogen Rhizoctonia solani) before contact, during first physical contact and during overgrowth of the host. The study presented here is the result of this analysis.

overall_design:
Two biological pools by condition against a common reference control each sample hybridized in dye switch. On the two biological replicates we apply on the pretreated results the linear modeling approach implemented by lmFit and the empirical Bayes statistics implemented by eBayes from the limma R package (Smyth 2004).

For mycoparasitism confrontation assays T. virens was grown on potato dextrose agar plates (BD Dicfo, Franklin Lakes, NJ, USA), covered with cellophane, in constant light at 25°C and harvested when the mycelia were ca. 5 mm apart (before contact), at contact of the mycelia and after T. virens had overgrown the host fungus Rhizoctonia solani by ca. 5 mm (after contact). As control T. virens was confronted with itself and harvested at contact. Peripheral hyphal zones from each confrontation stage were harvested and shock frozen in liquid nitrogen. Mycelia were ground to a fine powder under liquid nitrogen and total RNA was isolated using the guanidinium thiocyanate method (Sambrook, 2001).


title: Single tip transcriptomics of neighboring hyphae of Aspergillus niger

status: Public on May 17 2011

city: Amsterdam

first: Oskar

last: Bruning

address: Science Park 904

department: SILS

institute: University of Amsterdam

summary:
Mycelia of filamentous fungi explore new substrates by means of hyphae that extend from the periphery of the colony. Previously, it has been shown by immuno-labelling, reporter studies and in situ hybridization that these exploring hyphae are heterogenic with respect to protein secretion and transcription.
We performed single hyphal tip RNA profiling using microarrays to assess the differences in RNA accumulation in neighboring exploring hyphae

overall_design: Single tips from 5 neighboring exploring hyphae from a single colony were selected for RNA extraction, amplification and hybridization on Affymetrix microarrays

first: Charissa

last: de Bekker

first: Timo

last: Breit

first: Han

last: Wösten


title: Gene expression analysis of the colon with and without DNA methyltransferase 1 (Dnmt1) inhibition

status: Public on Apr 14 2011

city: Los Angeles

first: KwangHo

last: Lee

state: CA

address: 1441 Eastlake Ave NOR 6418

department: Biochemistry and Molecular Biology

institute: The University of Southern California

summary: We performed gene expression microarray to assess the effects of reduced DNA methylation on global gene expression. Gene expression profiles of colonic mucosa from mice with two different genotypes (Dnmt1LO/LO and Dnmt1LO/LO, TgVillacIGY) were compared. Dnmt1 expression is repressed only in the Dnmt1LO/LO, TgVillacIGY mice.

overall_design: Total RNA was isolated from the colonic mucosa of four mouse, two biological replicates of each genotype in two technical relicates.  Their gene expression profiles were obtained using the Illumina Ref-8 whole-genome expression BeadChip (MouseRef-8 v2.0). We processed our data using the Lumi Id and ReMOAT annotation data base (MouseWG-6 corresponding to GPL6887).

first: Shirley

last: Oghamian

first: Peter

last: Laird


title: miRNA expression profiles in Pancreatic Cystic tumours and Pancreatic Cancer

status: Public on May 18 2011

city: London

first: Adam

middle: Enver

last: Frampton

address: Hammersmith Hospital

institute: Imperial College

summary: MicroRNA (miRNA) expression profiles have been described in pancreatic ductal adenocarcinoma (PDAC), but these have not been compared with premalignant lesions. We wished to identify miRNA expression profiles in pancreatic cystic tumors with low malignant potential (serous microcystic adenomas) and high malignant potential (mucinous cystadenoma and intraductal papillary mucinous neoplasm (IPMN)) and compare these to PDAC and carcinoma-ex-IPMN (CEI).

overall_design: n= 20 samples Benign Pancreatic Cystic Tumour (n=7 Microcystic, n= 6 Mucinous, n= 7 IPMN) were compared with n= 9 samples of  carcinoma ex IPMN and n= 14 samples of pancreatic cancer (adenocarcinoma) for known homo sapiens miRNAs (mirbase 13).


title: Development of decidual cell polyploidy and bi-nucleation necessitates mitochondrial activity

status: Public on Apr 29 2011

city: Cincinnati

first: xinghong

last: ma

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary:
In the present study, to better define the aspects of decidual cell polyploidy, we isolated pure polyploid and non-polyploid decidual cell populations from the in vivo decidual bed. Three independent RNA pools prepared for each population were then subjected to the Affymetrix gene chip analysis for the whole mouse genome transcripts.
Our data revealed up-regulation of 1015 genes and down-regulation of 1207 genes in the polyploid populations, as compared to the non-polyploid group.

overall_design: We analyzed whole gnenome transcription from non-polyploid and polyploid cell populations using the Affymetrix GeneChip® Mouse Gene 1.0 ST Array . 3 replicates were performed.

first: Xinghong

last: Ma

first: Fei

last: Gao

first: Allison

last: Rusie

first: Jennifer

last: Hemingway

first: Alicia

last: Blackwell

first: Julie

last: Sroga

first: Anil

last: Jegga

first: Sanjoy

middle: K

last: Das


title: Identifying mRNA targets of microRNA in clear cell renal cell carcinoma

status: Public on Feb 28 2011

city: Nashville

first: Kimryn

last: Rathmell

state: TN

address: 2220 Pierce Ave

department: Medicine

institute: Vanderbilt

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

summary:
A bioinformatic approach to identify targets of microRNA in cancer.

Keywords: Patient sample study

overall_design:
Samples GSM413237-GSM413270: Total RNA from 17 RCC tumors and 17 corresponding non-tumor samples was hybridized against a common reference RNA (Perou CM, Sorlie T, Eisen MB, et al. Molecular portraits of human breast tumours. Nature 2000;406:747-752) for gene expression analysis.

Samples GSM413271-GSM413304: MicroRNA from 17 RCC tumors and 17 corresponding non-tumor samples were hybridized on a single channel platform for miRNA expression analysis.

first: Huiqing

last: Liu

first: A

middle: R

last: Brannon

first: Anupama

last: Reddy

first: Gabriela

last: Alexe

first: Michael

last: Seiler

first: Alexandra

last: Arreola

first: Jay

last: Oza

first: Ming

last: Yao

first: David

last: Juan

first: Louis

last: Liou

first: Shridar

last: Ganesan

first: W

first: Gyan

last: Bhanot


title: Exon level expression profiling of colorectal cancer tissue samples (validation sample series).

status: Public on May 19 2011

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

institute: Institute for Cancer Research, Oslo University Hospital

summary: Colorectal cancer is a heterogeneous disease molecularly characterized by inherent genomic instabilities, chromosome instability and microsatellite instability. In the present study we propose transcriptome instability as an analogue to genomic instability on the transcriptome level. Exon microarray data from two independent series of altoghether 160 colorectal cancer tissue samples was used for global alternative splicing detection using the FIRMA algorithm (aroma.affymetrix). The sample-wise amounts of these alternative splicing scores exceeding a defined threshold (deviating exon usage amounts) were summarized to provide the basis for description of transcriptome instability. This characteristic was shown to be associated with splicing factor expression levels and patient survival in both independent sample series.

overall_design: We analyzed genome-wide expression at the exon-level for two independent series of colorectal cancer tissue biopsies using the Affymetrix Human Exon 1.0 ST platform. This series of samples represents the validation series.

first: Trude

last: Ågesen

first: Arild

last: Nesbakken

first: Ragnhild

last: Lothe

first: Rolf

middle: I

last: Skotheim


title: Exon level expression profiling of colorectal cancer tissue samples


title: Differential Gene Expression in HDAC7-Deficient and Transgenic Thymocytes

status: Public on Apr 06 2011

city: Novato

first: Eric

last: Verdin

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary: Abstract of publicaton: CD4/CD8 double-positive (DP) thymocytes express the transcriptional repressor Histone Deacetylase 7 (HDAC7), a class IIa HDAC that is exported from the cell nucleus after T cell receptor (TCR) engagement. Through signal-dependent nuclear export, class IIa HDACs such as HDAC7 mediate signal-dependent changes in gene expression that are important to developmental fate decisions in multiple tissues. We report that HDAC7 is exported from the cell nucleus during positive selection in thymocytes, and regulates genes mediating the coupling between TCR engagement and downstream events that determine cell survival. Thymocytes lacking HDAC7 are inefficiently positively selected due to a severely shortened lifespan and exhibit a truncated repertoire of TCR Jalpha segments. The expression of multiple important mediators and modulators of the response to TCR engagement is altered in HDAC7-deficient thymocytes, resulting in increased tonic MAP kinase activity that contributes to the observed loss of viability. Remarkably, the activity of Protein Kinase D, the kinase that mediates nuclear export of HDAC7 in response to TCR signaling, is also increased in HDAC7-deficient thymocytes, suggesting that HDAC7 nuclear export governs a self-sustaining auto-excitatory loop. These experiments add to the understanding of the life/death decision in thymic T cell development, define a novel function for class IIa HDACs, and point to a novel feed-forward mechanism whereby these molecules regulate their own state and mediate stable developmental transitions. Title of manuscript: Nuclear Export of Histone Deacetylase 7 During Thymic Selection Mediates Immune Self-tolerance.  abstract of manuscript: Histone Deacetylase 7 (HDAC7) is a TCR signal-dependent regulator of differentiation that is highly expressed in CD4/CD8 double-positive (DP) thymocytes. Here we examine the effect of blocking TCR-dependent nuclear export of HDAC7 during thymic selection, through expression of a signal-resistant mutant of HDAC7 (HDAC7-?P) in thymocytes. We find that HDAC7-?P Transgenic thymocytes exhibit a profound block in negative thymic selection, but can still undergo positive selection, resulting in the escape of autoreactive T cells into the periphery. Gene expression profiling reveals a comprehensive suppression of the negative selection-associated gene expression program in DP thymocytes, associated with a defect in the activation of MAP kinase pathways by TCR signals. The consequence of this block in vivo is a lethal autoimmune syndrome involving the exocrine pancreas and other abdominal organs. These experiments establish a novel molecular model of autoimmunity and cast new light on the relationship between thymic selection and immune self-tolerance. Goal of Microarray experiment: We did these experiments to determine how alteration of the function of HDAC7, a site-specific and signal-dependent repressor of transcription, changes gene expression in CD4/CD8 DP thymocytes.

overall_design: Three biological replicate samples were prepared for each non-wild type mouse strain (Samples 7-18). Six biological replicates were prepared for the wild type strain (Samples 1-6). Total RNA was prepared from isolated CD4/CD8 Double-positive thymocytes and labeled with the Affymetrix Whole-Transcript labeling protocol. Labeled probes were hybridized to one Affymetrix Mouse Gene 1.0ST array each. Data from .cel files were normalized using RMA, in normalization groups representing each of the binary comparisons made. These binary comparisons between sample groups represent gene expression changes due to loss of HDAC7 (samples 1-3 vs. 7-9), transgenic expression of an HDAC7-VP16 fusion protein (samples 4-6 vs. 10-12), positive thymic selection (samples 1-6 vs. samples 11-15), and negative thymic selection (Samples 11-15 vs. samples 16-18).

first: Herbert

last: Kasler

first: Bryan

middle: D

last: Young

first: Denis

last: Mottet

first: Hyung

last: Lim

first: Amy

last: Collins

middle: N

last: Olson

first: Intelly

middle: S

last: Lee


title: Protein phosphorylations, mediated by pro-inflammatory cytokines IL-32g and IL-17A/F

status: Public on Apr 16 2011

city: Winnipeg

first: Neeloffer

last: Mookherjee

state: MB

address: 799-JBRC, 715 McDermot Ave

department: Internal Medicine

institute: University of Manitoba

summary:
Global kinase activity induced by cytokines IL-32g and IL-17A/F were determined using peptide arrays representing phophorylation targets
The objective of this study was to identify common and unique phosphorylation targets of pro-inflammatory cytokines IL-32 and IL-17. These cytokines are associated with the pathogenesis and severity of chronic inflammatory disorders, therefore signaling intermediates of these cytokines could be beneficial as alternate theraputic targets that may likely influence different inflammatory pathways.

platform_organism:
Bos taurus
Ovis aries

overall_design: Phosphorylation of proteins is a critical mechanism in the regulation of cellular processes. This process is meticulously regulated by enzymes known as kinases, which are increasingly being identified as drug targets for a variety of diseases. In this study we interrogated kinase activities (kinome) induced in the presence of the human recombinant cytokines IL-32g and IL-17A/F employing peptide arrays representing 300 peptides, printed in triplicate, representing select phosphorylation events. Human macrophage-like THP-1 cells were used for this comparative kinome analysis. Macrophage-like THP-1 cells were stimulated with either IL-32g  (20 ng/ml) or IL-17A/F (20 ng/ml) for 15 min, and the peptide arrays were used to comprehensively analyze protein phosphorylation profiles in the presence of these cytokines. Two independet biological experiments were performed and the kinoem analysis was done in triplicates for each. The phosphorylations of the peptides on the array were quantified in the cytokine-treated cells relative to the un-stimulated control cells. Differentially phosphorylated targets were defined as greater than 1.5 fold increase or decrease (p < 0.06) in phosphorylation compared to un-stimulated control cells.

first: Emily

last: Turner-Brannen

first: Ka-Yee

last: Choi

first: Ryan

last: Arsenault

first: Scott

last: Napper


title: Two Lysines in the Forkhead Domain of Foxp3 are Key to T Regulatory Cell Function

status: Public on Feb 05 2011

city: Philadelphia

first: Wayne

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

summary: The forkhead transcription factor, Foxp3, is pivotal to the development and function of CD4+CD25+ T regulatory (Treg) cells that limit autoimmunity and maintain immune homeostasis. Previous data indicated that many of the functions of Foxp3 are controlled by the acetylation of several lysines within the forkhead domain. We now show that mutation of each of two lysines within the forkhead domain of Foxp3, lysine at position 382 (K17) and lysine at position 393 (K18), impaired Treg suppressive function in vivo and in vitro. Lysine mutations also decreased Treg expression of multiple functionally important Foxp3-regulated genes, and inhibited the promoter remodeling of target genes (CTLA-4 and IL-2) without affecting Foxp3 expression level. These data point to the need for a further understanding of the effects of various post-translational modifications on Foxp3 function. Our studies also provide a rationale for developing small molecule inhibitors of such post-translational modifications so as to regulate Foxp3+ Treg function clinically.

overall_design: RNA from three independent samples from magnetically separated CD4+CD25- T-effector cells transduced with EV, WT-Fopx3, Foxp3-K17R or Foxp3-K18R

first: Yujie

last: Liu

first: Liqing

last: Wang

first: Rongxiang

last: Han

first: Ulf

middle: H

last: Beier


title: RNA sequencing reveals two major classes of gene expression levels in metazoan cells

city: Coventry

first: Daniel

last: Hebenstreit

address: Gibbet Hill Rd

institute: University of Warwick

summary: The expression level of a gene is often used as a proxy for determining whether the protein or RNA product is functional in a cell or tissue. Therefore, it is of fundamental importance to understand the global distribution of gene expression levels, and to be able to interpret it mechanistically and functionally. Here we use RNA sequencing of mouse Th2 cells, coupled with a range of other techniques, to show that all genes can be separated, based on their expression abundance, into two distinct groups: one group comprising of lowly expressed and putatively non-functional mRNAs, and the other of highly expressed mRNAs with active chromatin marks at their promoters. Similar observations are made in other data sets, including sources such as Drosophila.

overall_design: RNA-seq data of two biological replicates of murine Th2 cells.

first: Miaoqing

last: Fang

first: Muxin

last: Gu

first: Varodom

last: Charoensawan

first: Alexander

last: van Oudenaarden

first: Sarah

middle: A

last: Teichmann


title: Gene expression breast cancer

status: Public on Apr 27 2011

city: Edmonton

first: Kathryn

last: Graham

state: Alberta

address: 11560 University Ave

department: Oncology

institute: University of Alberta

summary:
Gene expression profiles were generated from 176 primary breast cancer patients and 10 normal breast samples.
This data is used to investigate the clinial relevance of genes of interest from in vitro studies, including FABP5 and DDX1.

overall_design: This Series represents RNA isolated from 176 primary breast cancer patients and 10 normal breast samples. Gene expression is compared between various subgroups depending on their clinical parameters.

first: John

last: Mackey


title: Role of retinoblastoma protein (Rb) in mouse Sertoli cells function

status: Public on Jan 01 2011

city: Turku

first: Sonia

last: Bourguiba-Hachemi

address: Kiinamyllynkatu 10

department: Dept Physiology

country: Finland

institute: University of Turku

summary: Gene expression profiling study of Sertoli cells (Sc)-specific Retinoblastoma (Rb) knockout (KO) mice. We generated a Sc-specific Rb knockout (Sc-RbKO) line and characterised its testicular phenotype. Sc-RbKO showed a progressive germ cell depletion leading to infertility and Sc dysfunction. We observed that up to 10 days old, Sc-RbKO mice present a phenotype similar to that of their WT siblings. This age was choosen to study the gene expression changes that would eventually lead to the described phenotypical changes. Sc-RbKO testis gene expression was compared to WT and to Sc-Rb+/- samples. Our Microarray results show changes of many genes involved in cell cycle control, DNA repair, apoptosis and misregulation of genes that may be important for proper Sertoli cell function such as tight junction formation, cell membrane and tissue remodeling.

overall_design: Total RNA extracted from 12 testicular samples, 5 controls, 3 hetorozygotes and 4 homozygotes.

first: Emmi

last: Rotgers

first: Adolfo

last: Rivero-Muller

first: Mirja

last: Nurmio

first: Martti

last: Parvinen

first: Lauri

last: Pelliniemi

first: Jorma

last: Toppari

first: Matteo

last: Da Ros