title: Spreading of heterochromatin is limited to specific families of maize retrotransposons

status: Public on Nov 26 2012

first: Steve

last: Eichten

country: USA

type: Methylation profiling by genome tiling array

summary:
Transposable elements have the potential to act as controlling elements to influence the expression of genes.  The current paradigm suggests that heterochromatic silencing can spread beyond the borders of the transposable element and influence the chromatin state of neighboring low-copy sequences.   This would allow transposable elements to condition obligatory or facilitated epialleles and act as controlling elements.  The maize genome contains numerous families of class I transposable elements (retrotransposons) that are present in moderate to high copy numbers and many are found in regions near genes which provides an opportunity to test whether the spreading of heterochromatin from retrotransposons is prevalent.  We have investigated the extent of heterochromatin spreading into flanking DNA around each family of retrotransposons through profiling of DNA methylation and di-methylation of lysine 9 of histone 3 (H3K9me2) in low-copy regions of the maize genome.  The effects of different retrotransposon families on local chromatin are highly variable.  Some LTR families exhibit enrichment of heterochromatic marks within 800-1200 base pairs of the insertion site while other families have very little evidence for spreading of heterochromatic marks. The analysis of chromatin state in genotypes that lack specific insertions suggests that the adjacent heterochromatin results from spreading of silencing rather than insertion-site preferences.  Genes that are located near elements that exhibit spreading of heterochromatin tend to be expressed at lower levels than other genes.  Our findings suggest that a subset of LTR retrotransposon families may act as controlling elements influencing neighboring sequences while the majority of elements have little effect on flanking sequences
Transposable elements comprise a substantial portion of many eukaryotic genomes.  These mobile fragments of DNA can result in mutations through insertions into genes but may also affect the regulation of genes they insert near.  There is evidence that the majority of transposable elements are epigenetically silenced and in some cases this silencing may affect neighboring sequences.  However, evolutionary theory would predict that there would be selective pressures for transposable elements to limit their effects on neighboring genes.  The maize genome has a complex organization with many genes flanked by retrotransposons.  We profiled the spread of heterochromatin from the retrotransposons into nearby low copy sequences for 150 high copy retrotransposon families.  While the manymajority of retrotransposons exhibit little to no spreading of heterochromatin there are a small number ofsome retrotransposon families that influence the chromatin state of surrounding regions.  The families may represent bad “neighbors” that spread heterochromatin and influence nearby genes.

overall_design:
6 total samples: 3 replicates of B73 H3k9 and 3 replicates of Mo17 H3k9
3 total samples: mop1 mutant, b73.zmet2 (zmet2.m1 mutant in B73 background) and mo17.zmet2 (zmet2.m1 mutant in Mo17 background)

first: Irina

last: Makarevitch

first: Amanda

last: Waters

first: Steven

first: Matthew

last: Vaughn

first: Nathan

last: Springer


title: Immunomagnetic enrichment and flow cytometric isolation of breast cancer circulating tumor cells (CTCs) for genomic characterization

status: Public on Dec 31 2012

city: San Francisco

first: Mark

last: Magbanua

state: CA

address: 1450 3rd Street, PO Box 589001

department: HemOnc

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

type: Genome variation profiling by genome tiling array

summary:
We developed a novel approach to isolate tumor cells with high purity from blood via immunomagnetic enrichment followed by fluorescence activated cell sorting (IE/FACS) and examined copy number alterations in these cells.
Magnetic beads coated with EpCAM mAb were added to blood to enrich for tumor cells. Enriched samples were then subjected to FACS analysis using differentially labeled mAbs to distinguish tumor cells (EpCAM+) from leukocytes (CD45+) during sorting. DNA from isolated tumor cells was subjected to whole genome amplification (WGA) and copy number analysis via array comparative genomic hybridization (CGH). The assay was evaluated using BT474 and MCF7 breast cancer cell lines and in CTCs from 5 metastatic breast cancer (MBC) patients with matched archival primary tumors and later extended to an additional 97 MBC patients.

overall_design: Evaluation of the assay on isolated breast cancer cell lines spiked into blood correctly identified the known genomic alterations with high reproducibility. In clinical studies, comparison of CTCs with matched archival primary tumors confirmed shared lineage with notable divergence. In addition, serial testing of CTCs confirmed reproducibility, and indicated genomic change over time. Analysis of genomic profiles of CTCs from 102 MBC patients revealed common copy number alterations including gains in 1q and 8q and losses in 8p and 11q. Comparison with a published CGH dataset of primary breast tumors revealed similar frequencies of recurrent genomic copy number aberrations.

first: Mark-Jesus

middle: M

first: Eduardo

middle: V

last: Sosa

first: Ritu

last: Roy

first: Lauren

middle: E

last: Eisenbud

first: Janet

middle: H

last: Scott

first: Adam

last: Olshen

first: Dan

last: Pinkel

first: Hope

middle: S

last: Rugo

first: John

middle: W

last: Park


title: Expression analysis of human pancreatic cancer cell lines (Capan-1, Panc-1, Panc-1+ve and Panc-1-ve) and pancreatic ductal cell line (HPDE)

status: Public on Nov 21 2012

city: Suwon

first: pooja

last: Dua

address: Chun-chun Dong, Jang-an Gu

department: Chemistry

country: South Korea

institute: Sungkyunkwan University

summary:
Analysis of differentially expressing genes in whole genome wide analysis of aptamer SQ2 positive cells (Capan-1, Panc-1, Panc-1+ve) and SQ2 negative cells (Panc-1-ve and HPDE)
Panc-1 +ve and Panc-1-ve cell lines were generated from  Panc-1 cell line based upon its hetergenous binding to aptamer SQ2. Detailed procedure of generation of these cell lines are described in Pooja Dua, Hye Suk Kang, Seung-Mo Hong, Ming-Sound Tsao, Soyoun Kim, and Dong-ki Lee. 2012 Alkaline Phosphatase ALPPL2 is a novel pancreatic carcinoma-associated protein. Cancer Research

overall_design: A five chip study using total RNA recovered from Capan-1, Panc-1, Panc-1+ve, Panc-1-ve and HPDE cells. Each chip measures 45,033 genes with three  60 mer probe pairs per target.

first: Pooja

first: Dong-ki

last: Lee


title: Alkaline Phosphatase ALPPL2 is a novel pancreatic carcinoma-associated protein

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

overall_design: Refer to individual Series


title: Expression analysis of RNAi mediated ALPPL2 knockdown in ALPPL2 expressing Panc-1 cells (Panc-1+ve)

summary:
Analysis of differentially expressing genes in whole genome wide analysis of ALPPL2 expressing Panc-1 cells (Panc-1+ve) via siRNA mediated knockdown of ALPPL2
Panc-1 +ve and Panc-1-ve cell lines were generated from  Panc-1 cell line based upon its hetergenous binding to aptamer SQ2. Detailed procedure of generation of these cell lines are described in Pooja Dua, Hye Suk Kang, Seung-Mo Hong, Ming-Sound Tsao, Soyoun Kim, and Dong-ki Lee. 2012 Alkaline Phosphatase ALPPL2 is a novel pancreatic carcinoma-associated protein. Cancer Research

overall_design: A four chip study using total RNA recovered from Panc-1+ve cells transfected with siALPPL2-2, siALPPL2-3, siGFP control  and Lipofectamine 2000 treatament . Each chip measures 45,033 genes with three  60 mer probe pairs per target.


title: Restoration and reinforcement of acclimatizing responses during the adaptation of an unfit, metabolically engineered strain

status: Public on Nov 08 2012

city: Cambridge

first: Sean

middle: Michael

last: Carroll

state: MA

address: Biological Laboratories, Room 3084, 16 Divinity Ave

department: Organismic and Evolutionary Biology

institute: Harvard University

summary: Organisms cope with physiological stressors through acclimatizing mechanisms in the short-term, and through adaptive mechanisms over evolutionary timescales. Whereas the former offer a consistent and largely predictable buffer against stressors, myriad paths of adaptation are often possible. Our work examined whether knowledge of acclimatizing responses could be informative of  aspects of future adaptation, using as a model system a strain of Methylobacterium extorquens AM1 that was experimentally engineered and then evolved with a novel central metabolism. The engineered strain is markedly slower and less fit than wild-type, which is reflected in microarray analyses by hundreds of genes with differential expression, and also altered levels NAD(P)(H) metabolites. Yet after 600 generations of evolution in the lab, eight replicate populations founded from an engineered ancestor showed substantial but variable improvements in growth using the engineered metabolic pathway. Using information from wild-type, engineered, and adapted physiological states, we determined the extent to which physiological processes were restored, unrestored, reinforced, or novel after experimental evolution. Overall, we found that the vast majority of gene expression perturbations from the engineered strain are restored to wild-type like conditions after experimental evolution but were accompanied by a modest number of unrestored processes, varying instances of novel expression, and a few rare instances where expression changes from acclimation were reinforced through adaptive evolution. One such example was in the reinforced up-regulation of pntAB transhydrogenase, whose increased expression and activity correlated with the restoration of NAD(P)(H) metabolism towards wild-type levels and with increased growth rate in the evolved lineages. Thus, while trajectories of physiological adaptation may still be difficult to predict a priori, our results demonstrate that information from acclimatizing responses can provide a “direction” to hypothesize which changes in physiology arose as a consequence of adaptation versus those that may have caused it .

overall_design: Single-color microarray hydridization of total RNA isolated from mid-exponentially grown cultures of wildtype, engineered, and eight experimentally evolved populations of Methylobacterium extorquens AM1, each represented by three biological replicates

first: Christopher

middle: J

last: Marx


title: Identification of genes regulated by XOct-25 overexpression in Xenopus ectoderm

status: Public on Oct 05 2012

city: Higashi-hiroshima

first: Atsushi

last: Suzuki

state: Hiroshima

address: Kagamiyama 1-3-1

department: Graduate School of Science

country: Japan

institute: Hiroshima University

summary: The Xenopus POU class V transcription factor XOct-25 has been shown to inhibit BMP-dependent epidermal differentiation and promote neural induction in the ectoderm during early embryogenesis.  In order to identify genes that act downstream of XOct-25, transcriptional profile of Xenopus ectodermal cells overexpressing XOct-25 was compared with control cells by using a DNA microarray method.

overall_design:
Two independent experiments.  Each experiment contains ectodermal cells overexpressing XOct-25 and corresponding control cells.  Xenopus embryos were injected at the 8-cell stage with mRNA encoding GR-XOct-25, a hormone-inducible version of XOct-25.  Explants from stage 9 embryos were treated with or without dexamethazone (DEX) until the sibling embryos reached stage 10.5, when they were used for RNA extraction.  The explants cultured without DEX was used as a control sample.
biological replicates: Sample name XOct-exp 1, Sample name XOct-exp 2

first: Kimiko

last: Takebayashi-Suzuki

last: Kitayama

first: Chie

last: Terasaka-Iioka

first: Naoto

last: Ueno


title: Effect of virX regulator on the expression of chromosomal genes of Clostridium perfringens

status: Public on Oct 01 2012

city: Kanazawa

first: Tohru

last: Shimizu

state: Ishikawa

address: 13-1, Takara-machi

department: Department of Bacteriology

institute: Kanazawa University

summary: The microarrays were subjected to two-color hybridization using Cy5 and Cy3 dyes incorporated in the cDNAs synthesized from total RNA samples of strains. We compared each gene’s transcription level between the wild-type (WT) strain 13 (labeled by Cy5) and the virX-mutant strain (TS186) (labeled by Cy3) on a single DNA microarray.

overall_design: Total RNA was isolated from exponentially growing cells from thevirX mutant and the wild-type. Gene expression levels were compared between thevirX mutant and wild-type strain 13

first: T

first: K

last: Ohtani

first: S

last: Kuhara

last: Tashiro

last: Yamamoto

first: A

last: Enomoto


title: Copper-regulated genes of Bradyrhizobium japonicum

city: Zürich

first: Hans-Martin

last: Fischer

address: Vladimir-Prelog-Weg 4

department: Microbiology

country: Switzerland

institute: ETH Zürich

summary: Copper-limiting growth conditions were thought to cause an induction of genes possibly involved in copper uptake and sorting. This rationale in mind, we performed microarray analyses on B. japonicum cells grown in three variations of the BVM minimal medium. Variant 1 contained 2 μM CuSO4 (copper excess). Variant 2 was prepared in HCl-treated glassware without any copper added (copper starvation). The residual copper concentration in this copper-starvation medium was analyzed by GF-AAS and determined to be 5 nM. Variant 3 (extreme copper limitation) was prepared like variant 2 but with the addition of 10 μM BCS and 1 mM ascorbic acid where BCS chelates Cu(I) selectively, and ascorbic acid reduces any Cu(II) to Cu(I). Changes in the transcription profiles were recorded by the pairwise comparison of cells grown in variant 2 vs. 1, and variant 3 vs. 2. Only a small set of genes were differentially up- or down-regulated when copper-starved cells were compared with cells grown in copper excess. Most notably, five genes located adjacent to each other on the B. japonicum genome displayed an increased expression: bll4882 to bll4878. The five genes were named pcuA, pcuB, pcuC, pcuD, and pcuE (mnemonic of proteins for Cu trafficking). The genes with decreased expression are either of unknown function or – not surprisingly – play a role in copper resistance. Extreme copper limitation (variant 3 vs. 2) did not further enhance the expression of the five pcu genes. Instead, another cluster of adjacent genes was strongly up-regulated: bll0889 to bll0883, which code for unidentified transport functions. Incidentally, the list also includes the copper chaperone ScoI. Taken together, copper-limiting growth conditions have led to the de-repression of genes potentially involved in copper acquisition.

overall_design: Microarray-based transcriptome analysis of B. japonicum 110spc4 wild-type cells  grown under normal, copper-limiting and copper excess conditions

first: Fabio

last: Serventi

first: Zeb

middle: A

last: Youard

first: Valérie

last: Murset

first: Simona

last: Huwiler

first: Doris

last: Bühler

first: Miriam

last: Richter

first: Ronny

last: Luchsinger

first: Robert

last: Brogioli

first: Martina

last: Niederer

first: Hauke

last: Hennecke


title: Gene expression analysis distinguishes tissue specific and gender related functions among adult Ascaris suum tissues.

status: Public on Sep 30 2012

city: St. Louis

first: Makedonka

last: Mitreva

state: Missouri

address: 4444 Forest Park Ave

institute: The Genome Institute

summary:
Over a billion people are infected by Ascaris spp. intestinal parasites. We investigated gene expression by various tissues of adult A. suum, and used that information to help resolve basic functions of these tissues, basic biology of parasitism and functional aspects of nematode genomes.

The A. suum genome was sequenced and assembled to allow generation of microarray elements. Expression of over 40,000 60-mer elements was investigated in a variety of tissues from both male and female adult worms. Nearly 50 percent of the elements for which signal was detected exhibited differential expression among different tissues. The unique profile of transcripts identified for each tissue clarified functional distinctions among tissues, such as chitin binding in the ovary and peptidase activity in the intestines. Interestingly, hundreds of gender specific elements characterized female or male intestinal tissues, respectively. A. suum genes from the same family were frequently expressed differently among tissues. Transcript abundance for genes specific to A. suum, by comparison to Caenorhabditis elegans, varied to a greater extent among tissues than for genes conserved between A. suum and C. elegans. Analysis using C. elegans protein interaction data identified functional modules conserved between these two nematodes, resulting in identification of functional predictions of essential subnetworks of protein interactions and how these networks may vary among nematode tissues. A notable finding was very high module similarity between adult reproductive tissues and intestine.

Our data identified gene and predicted protein determinants that distinguish functions of individual adult A. suum tissues as well those that likely serve all the tissues investigated in our study. The size of A. suum adults (30-40 cm compared to less than 1 cm for many nematodes) enabled this resolution and will facilitate experimental dissection of individual and interactive functions of these tissues in this and other parasitic nematodes.

overall_design:
10 samples were prepared from the tissues of adult worms of both genders to be analyzed.  Two to three replicates were done for each sample, swapping dyes and channel for the test and the control for each sample.  The control consisted of pooled worm tissues from both genders with an equal amount being included from each sample.

These samples and the control were hybridized against an Agilent 4x44k format custom chip spotted with 42,212 probes.   This probeset was created from 38,768 predicted protein coding sequences from an Ascaris suum genome survey sequence (GSS) project, and also from 5,176 EST contigs that were not covered by this predicted GSS gene-set.   These 43,944 putative gene sequences from Ascaris suum  were filtered for cross-reaction to non-coding sequences using Agilent eArray, and our final set of 42,212 probes was determined.

first: Xin

last: Gao

first: Zhengyuan

last: Wang


title: Gene expression from the rice leaf elongation zone of 7th leaf under various soil moisture treatments

status: Public on Sep 26 2012

city: Metro Manila

first: Andrew

last: Cal

address: DAPO BOX 7777

country: Philippines

institute: International Rice Research Institute

summary:
Leaf rate elongation is extremely sensitive to soil water status.
Global gene expression of the leaf elongation zone was profiled at three different levels of soil moisture in two genotypes. Leaf elongation in IR64 is more sensitive to decreased soil moisture than in moroberekan.

overall_design: 2 genotypes: IR64, Moroberekan; 3 treatments: FTSW 1, FTSW 0.5, FTSW 0.2


title: Role of a GntR-family response regulator LbrA in Listeria monocytogenes biofilm formation

status: Public on Sep 06 2012

city: Columbus

first: Hua

state: OH

address: 2015 Fyffe CT

department: Food Science and Technology

institute: The Ohio State University

summary: The formation of Listeria monocytogenes biofilms contributes to persistent contamination in food processing facilities. A microarray comparison of L. monocytogenes between the transcriptome of the strong biofilm forming strain (Bfms) Scott A and the weak biofilm forming (Bfmw) strain F2365 was conducted to identify genes potentially involved in biofilm formation.  Among 951 genes with significant difference in expression between the two strains, a GntR-family response regulator encoding gene (LMOf2365_0414), designated lbrA, was found to be highly expressed in Scott A relative to F2365. A Scott A lbrA-deletion mutant, designated AW3, formed biofilm to a much lesser extent as compared to the parent strain by a rapid attachment assay and scanning electron microscopy. Complementation with lbrA from Scott A restored the Bfms phenotype in the AW3 derivative.  A second microarray assessment using the lbrA deletion mutant AW3 and the wild type Scott A revealed a total of 304 genes with expression significantly different between the two strains, indicating the potential regulatory role of LbrA in L. monocytogenes. A cloned copy of Scott A lbrA was unable to confer enhanced biofilm forming potential in F2365, suggesting that additional factors contributed to weak biofilm formation by F2365. Findings from the study may lead to new strategies to modulate biofilm formation.

overall_design: Two comparisons were performed between 1) strong biofilm former Listeria monocytogenes strain ScottA versus weak biofilm former Listeria monocytogenes strain F2365; 2) Listeria monocytogenes ScottA LbrA deletion mutant strain versus Listeria monocytogenes ScottA. Four replicates were loaded for the first comparison and two replicates were loaded for the second comparison.

last: Wassinger

first: Lu

last: Zhang

first: Erin

last: Tracy

last: Munson

first: Sophia

last: Kathariou


title: Human breast cancer invasion signature

status: Public on Sep 05 2012

city: Bronx

first: Antonia

last: Patsialou

state: NY

address: 1301 Morris Park Ave

department: Anatomy and Structural Biology

institute: Albert Einstein College of Medicine

summary:
Introduction:  Metastasis of breast cancer is the main cause of death in patients. Previous genome-wide studies have identified gene expression patterns correlated with cancer patient outcome, however these were mostly derived from whole tissue without respect to cell heterogeneity. In reality, only a small subpopulation of migratory and invasive cells inside the primary tumor is responsible for escaping and initiating dissemination and metastasis. When whole tissue is used for molecular profiling, the expression pattern of these cells is masked by the majority of the non-invasive tumor cells. Therefore, little information is available about the crucial early steps of the metastatic cascade: migration, invasion and entry of tumor cells into the systemic circulation.
Method: In the past, we have developed an in vivo invasion assay which can capture specifically the highly motile tumor cells in the act of migrating inside living tumors (Wyckoff et al., 2004, Cancer Research). Here, we used this assay in orthotopic xenografts of human MDA-MB-231 breast cancer cells to selectively isolate the invasive cell subpopulation of the primary tumor. We then performed microarray analysis to compare the gene expression profile of these invading tumor cells to the average primary tumor cells. In this way, we derived a gene signature specific to breast cancer migration and invasion in vivo.

overall_design: Each sample of invasive (INV) and average primary tumor cells (APTC) was pooled from two tumor-bearing mice.  RNA was extracted, made into cDNA, then amplified with the Clontech SMART amplification kit.  Human reference RNA (Clontech) was amplified with identifical protocol.  Each sample was then hybridized in a 28K Human cDNA microarray chip, custom printed from Albert Einstein College of Medicine (http://microarray1k.aecom.yu.edu/).  Four replicates were used per group (Invasive vs. Average Primary Tumor).

first: Yarong

first: Juan

last: Lin

first: Kathleen

last: Whitney

first: Sumanta

last: Goswami

first: Paraic

last: Kenny

first: John

last: Condeelis


title: Transcriptome of sevenless (sev) in the eye imaginal disc.

status: Public on Jan 10 2013

city: barcelona

first: Natalia

last: Mora

state: barcelona

address: avd. Diagonal 643

department: Genetics

country: Spain

institute: University of Barcelona

summary:
The Sevenless receptor (Sev) is a key component of the complex regulatory network involved in R7 photoreceptor determination. However the genetic program that responds to Sev is still unknown. Here, we explore the transcriptional profile downstream of Sev, using eye imaginal discs from third instar larvae of the sev mutants sevS11 and sevd2 compared with wild-type controls.
Keywords: loss and gain of function analysis

overall_design: Eye imaginal discs from alleles sevd2 and sevS11 were dissected. Four microarrays were hybridized for sevd2 and three for sevS11 (total of 7 experiments) in biological replicate pairs, such that the total RNA from the sample used as a starting material came from different extractions. Both arrays from each pair were hybridized with the same amplified RNA from sample and common reference (obtained using the Amino-Allyl Messageamp II aRNA Amplification Kit from Ambion, Inc) but with dyes (Cy3 and Cy5 from Amersham, Inc) swapped to take dye-bias into account.

first: Isabel

last: Almudí

first: Berta

last: Alsina

first: Montserrat

last: Corominas

first: Florenci

last: Serras


title: Affymetrix SNP array data for breast cancer formation in mouse

status: Public on Sep 04 2012

city: Wildau

first: Christoph

last: Standfuß

address: Bahnhofstraße

department: Bioinformatics

country: Germany

institute: Technical University of Applied Sciences

type: Genome binding/occupancy profiling by SNP array

summary:
We investigated the CNAs in a four stage tumorigenesis model. This model included copy number analyses in non-transgenic NMRI mice (normal) and in transgenic SVT/t mice: non-malignant hyperplastic mammary glands and breast cancers, as well as breast cancer derived cell lines.
We focused our research on copy number analyses to compare the genomic alterations that occur during tumorigenesis. We addressed the question, whether common predisposed chromosomal breakpoints could be seen to promote malignant transformation. We can report a characteristic increase of copy number alterations from normal to tumor stage in our model. Furthermore, we have identified chromosomal segments and found characteristic fragmentations.

overall_design: Affymetrix SNP array analysis was performed with Mouse Diversity Genotyping Arrays (Affymetrix). DNA was extracted from frozen biopsies of mammary tumor samples of six mice and two cell lines. Normalization and allele summarization were performed with the BRLMM-P algorithm provided  and copy number analysis was performed for the each sample using the average signal intensity of both normal samples as the reference for copy number inference.

first: Heike

last: Pospisil

first: Andreas

last: Klein

last: Standfuss


title: Expression data from control and heat shocked mouse spermatocytes and hepatocytes

status: Public on Aug 22 2012

city: Gliwice

first: Joanna

last: Polanska

address: Akademicka 16

department: Automatic Control

country: Poland

institute: Silesian University of Technology

summary:
In somatic cells elevated temperature induces activation of the heat shock transcription factor 1 (HSF1) what leads to heat shock proteins synthesis and cytoprotection. However, in the male germ cells (spermatocytes) upon HSF1 activation, caspase-3 dependent apoptosis is induced and spermatogenic cells are actively eliminated.
To elucidate a mechanism of such diverse HSF1 activity we carried out genome-wide transcriptional analysis in control and heat-shocked cells, either spermatogenic or somatic. As model somatic cells we used hepatocytes that respond to hyperthermia in a classical way by induction of heat shock genes transcription. As spermatogenic cells we used a fraction of cells enriched with spermatocytes, which are the most sensitive to damage in elevated temperatures. Using isolated spermatocytes we avoided the influence of the somatic testicular component on the our final results. Genes that are differently regulated during hyperthermia in both types of cells have been identified.

overall_design: On Affymetrix gene chip arrays we analyzed RNA isolated from spermatocytes or hepatocytes, either untreated (control) or after heat shock and 2h of recovery at physiological temperature. Analyses were done in triplicate.

first: Wieslawa

last: Widlak

first: Malgorzata

last: Kus-Liskiewicz

first: Magdalena

last: Olbryt


title: Variation in DNA methylation patterns more common among maize inbreds than among tissues

status: Public on Aug 27 2012

city: St. Paul

first: Steve

middle: R

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

summary:
Epigenetic marks such as DNA methylation can act as heritable marks on a genome leading to unique regulation of genomic sequences. As a transient mark, DNA methylation has been identified as a possible mechanism for reversible genetic regulation of cells derived through either mitotic or meiotic cellular division. Although variation between epigenetic states is known to exist between individuals, there is little known about the variability of DNA methylation patterns between different developmental stages of an individual. We have assessed genome-wide DNA methylation patterns in four tissues of two inbred maize lines: B73 and Mo17. Although hundreds of regions of differential methylation are present between the two genotypes, few examples of tissue-specific DNA methylation variation were observed. The lack of clear epigenetic variation between tissues indicates the limited impact of DNA methylation on developmental processes within maize.
meDIP-chip analysis of four maize tissues identifed few tissue-specific DNA methylation variable regions (tDMRs), whereas hundreds of genotype-specific DMRs were identified that were conserved across tissues.

overall_design: Methylation profiles for tassel, embryo, endosperm, and leaf of the maize inbred lines B73 and Mo17. Three biological replications for each tissue of each genotype were performed. A custom 2.1M NimbleGen array (GPL13499) was used for embryo, endosperm, and leaf, and a custom 3x1.4M NimbleGen array containing a subset of probes from the 2.1M NimbleGen array (GPL15621) was used for tassel. All of the processed data is based on the largest number of comparable probes (~1.4M) between the two arrays.

first: Steven

first: Mattew

last: Vaughn

first: Ruth

last: Swanson-Wagner

first: Nathan

last: Springer


title: Reactive oxygen species-inducible ECF σ factor involved in singlet-oxygen responsiveness of Bradyrhizobium japonicum

status: Public on Aug 24 2012

first: Hans-Martin

last: Fischer

summary: Expression data from B. japonicum strains 110spc4 (wild type), 0202 (Dbll1028), 9688 (Dblr3038-39)  grown micro-oxically unstressed or stressed with 2 mM H2O2 for 10 min and strain 9692 (Dblr3039)  grown micro-oxically

overall_design: Comparative transcriptome analysis of  B. japonicum strains 110spc4, 0202, 9688, and 9692 grown micro-oxically with or without exposure to 2 mM H2O2 for 10 min

first: Nadezda

last: Masloboeva

first: Luzia

last: Reutimann

first: Philipp

last: Stiefel

first: Rainer

last: Follador

first: Nadja

last: Leimer

first: Hauke

last: Hennecke

first: Socorro

last: Mesa


title: The effects of progesterone on the fathead minnow testis

status: Public on Jul 02 2012

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

summary: The objectives of the study were to determine the effects of progesterone in the male testis. Reproductive fathead minnows were used in the study. Testis at stage 2 and 3 were dissected and testis explants were treated progesterone or no progesterone (10^-6M and 10^-8M) for 12 hours. Androgens were measured and there was a significant increase in testosterone, but not 11-tetotetosterone. Gene expression analysis was performed in the testis which genes were differentially regulated by progesterone.

overall_design: testis explants were treated with 10^-6M progesterone for 12 hours; 6 control and 4 treatment samples

first: Yasmin

last: Chishti


title: Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells [mRNA]

status: Public on Jul 16 2012

city: Boston

first: Peter

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

summary: Variation in chromatin composition and organization often reflects differences in genome function. Histone variants, for example, replace canonical histones to contribute to regulation of numerous nuclear processes including transcription, DNA repair and chromosome segregation. Here we focus on H2A.Bbd, a rapidly evolving variant found in mammals but not in invertebrates. We report that in human cells, nucleosomes bearing H2A.Bbd form unconventional chromatin structures enriched within actively transcribed genes and characterized by shorter DNA protection and nucleosome spacing. Analysis of transcriptional profiles from cells depleted for H2A.Bbd demonstrated widespread changes in gene expression with a net down-regulation of transcription and disruption of normal mRNA splicing patterns. In particular, we observed changes in exon inclusion rates and increased presence of intronic sequences in mRNA products upon H2A.Bbd depletion. Taken together, our results indicate that H2A.Bbd is involved in formation of a specific chromatin structure that facilitates both transcription and initial mRNA processing.

overall_design: Gene expression was measured in two replicates of the HeLa cells expressing H2A.Bbd-FLAG histone, which were treated with shRNA with no homology to the human genome.

first: Michael

middle: Y

last: Tolstorukov

first: Joseph

last: Goldman

first: Cristele

last: Gilbert

first: Vasily

last: Ogryzko

first: Robert

last: Kingston


title: Comparison of gene expression and mutant fitness in Shewanella oneidensis MR-1

status: Public on Jul 19 2012

city: Berkeley

first: Morgan

middle: N

last: Price

address: 1 Cyclotron Road Mailstop 977-152

department: Physical Biosciences Division

institute: Lawrence Berkeley Lab

overall_design: Expression data for 15 growth conditions in mid-exponential phase and expression data across growth phases for 3 of those conditions

first: Kelly

last: Wetmore

first: Adam

last: Deutschbauer

middle: P

last: Arkin


title: The MTAP-CDKN2A Locus Confers Susceptibility to a Naturally Occurring Canine Cancer

status: Public on Jul 03 2012

city: Bethesda

first: Heidi

middle: G

last: Parker

state: MD

address: 50 South Dr. Rm 5347

department: CGB

institute: NHGRI

summary: Well-defined, closed breeding populations coupled with excessive disease predispositions among purebred domestic dog breeds offer unique advantages to genetic studies of disease susceptibility. Advantages offered by canine population substructure, combined with similarity to human disease in terms of clinical presentation and response to treatment, make the dog a particularly attractive system for finding genes associated with cancer. Cancers that have been difficult to study in human families or populations are of particular interest, especially those associated with one or a small number of breeds and a high level of occurrence. Histiocytic sarcoma (HS) is a rare and poorly understood neoplasm in humans, however it occurs in 15-25% of Bernese Mountain Dogs (BMD). By combining genome-wide association studies from two geographic populations of BMD followed by fine mapping and sequencing, we have identified a cancer-associated haplotype within the MTAP/CDKN2A locus that is present in 95% of all affected BMD. The haplotype is within the region homologous to human chromosome 9p21, which has been implicated in numerous complex genetic diseases including several cancers. These results demonstrate the power of studying distinctive malignancies in highly predisposed dog breeds. Here, we establish a naturally occurring model of cancer susceptibility due to CDKN2 dysregulation, thus providing insight regarding this cancer-associated, complex, and yet poorly understood genomic region.

overall_design: Genomic DNA was collected from affected and unaffected BMD in North America (NA) and Europe. Both independent and combined genome-wide association studies (GWAS) were used to identify cancer-associated loci.

first: Elaine

last: Ostrander


title: Effects of DHT on the ovary of fathead minnow

status: Public on Jul 31 2012

summary: Fathead minnow ovary explants were incubated with DHT at 10^-6M for 6, 9, and 12 hours. Estrogen production was significantly increased in these ovaries at all three time points.

overall_design: control 6 hours (n=4), DHT 6 hours (n=5), control 9 hours (n=5), DHT 9 hours (n=5), control 12 hours (n=4), DHT 12 hours (n=4),

first: Anna

last: Ornostay


title: Exposure of microaerobic Campylobacter jejuni to diffusible molecules from chicken caecal contents

status: Public on Aug 07 2012

city: Sheffield

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

country: United Kingdom

institute: University of Sheffield

summary:
Campylobacter jejuni is the major cause of acute gastroenteritis in the developed world. It is usually acquired through contaminated poultry as C. jejuni causes a silent asymptomatic infection of the chicken. Pathogens face different sources of stress during its transit through the gut.
In this study, we describe the ability of C. jejuni to survive nitrosative stress at very low oxygen levels that reflect those in hypoxic gut environments. Specifically, we here explore an innovative model of signal recognition during colonization. We use a diffusion capsule to feed small, diffusible molecules from chicken caecal matter into a microaerobic C. jejuni culture to study the transcriptomic changes mounted as response to chemical signals present in the chicken gut. We find that in early stages of exposure to the caecal contents (10 min) the dual component colonization regulator, dccR, plays an important yet not fully understood role.  Although the caecal material contains cyanide derived from plant sources, we find no role for a truncated globin (encoded by ctb), which has previously been implicated in resistance to this haem ligand.

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

overall_design:
Batch cultures of wild-type C. jejuni NCTC 11168 were grown in 200 ml volumes of Mueller-Hinton broth in 500 ml baffled flasks. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (10% Oxygen, 10% Carbon dioxide, 80% Nitrogen) from Don Whitley Scientific, Ltd, which also maintained the growth temperature at 42 ºC. When mid-exponential phase was reached, a custom-made diffusion capsule (as described in Pirt, 1971) containing chicken caecal contents was placed for 10, 30, or 60 minutes. After the exposure, 30 ml samples of both treated and untreated cells were mixed immediately on ice with 3.56 ml 100% ethanol and 185 µl phenol to stabilize the RNA. The cells were subsequently harvested by centrifugation. Total RNA was purified by using a Qiagen RNeasy Mini kit as recommended by the supplier.

Equivalent amounts of RNA (15 μg) from control and test cultures were used as template for synthesis of labelled cDNA. Labelling was done by using dCTP nucleotide analogues containing either Cy3 or Cy5 fluorescent dyes. RNA was primed with 9 μg pd(N)6 random hexamers (Amersham Biosciences). For annealing, the mixture was incubated for 10 min at 65oC and then 10 min at room temperature. Each reaction mixture (0.5 mM dATP, dTTP and dGTP, 0.2 mM dCTP, 0.1 mM DTT (Invitrogen) and 1 mM Cy3-dCTP or Cy5-dCTP, total volume 25ul) was incubated for 3 h at 42 oC with 200 U of Superscript III RNase-H Reverse Transcriptase (Invitrogen). The reaction was terminated by the addition of 5ul 1 mM NaOH and heating the tube to 65 oC for 10 min to hydrolyse the RNA. Then it was neutralised with 5ul 1 M HCl and 1 M TE (pH 8). Purification of cDNA was done with a PCR purification kit (Qiagen). The cDNA was eluted and resuspended in 30 μl elution buffer (Qiagen, supplied in kit).

Each slide set (control slide and dye-swap) was prepared as follows: For the control slide, Cy3-dCTP labelled control cDNA was mixed with Cy5-dCTP labelled test cDNA. For the dye-swap slide, Cy5-dCTP labelled control cDNA was mixed with Cy3-dCTP labelled test cDNA. This is made to compensate for possible differences in the labelled nucleotides incorporation. The slides used were C. jejuni OciChip® arrays from Ocimum Biosolutions. The cDNA mixture for each slide was dried by evaporation for approximately 35 min in a SPD 121P SpeedVac® (Thermo Savant, Waltham, MA, USA).

The dry cDNA was resuspended in pre-warmed (42ºC) salt-based hybridisation buffer (Ocimum Biosolutions) and was heated to 95 °C for 3 min and then placed on ice for 3 min. The spotted area of the slide (located with an array finder) was enclosed within a gene frame (MWG/Ocimum). The cDNA suspension was distributed through the inner space of the gene frame and enclosed with an air-tight coverslip. The slides were incubated for 16-24 hours at 42º C in sealed MWG hybridisation chambers shaken in a water bath. After incubation, gene frames and coverslips were removed and slides washed sequentially in 2x, 1x, 0.2x y 0.1x SSC buffer, by shaking for 5 minutes at 80 rpm at 37º C pre-warmed buffer. (2x buffer was supplemented with 1% SDS). Then the slides were dried by centrifugation at 250 x g for 5 min.

Slides were scanned using an Affymetrix 428 scanner. The processing of images and quantification of the microarrays signal was done using software from Biodiscovery Inc. (ImaGene, version 4.0 and GeneSight, version 4.0). Spots with signal intensity lower than background or other significant blemishes were eliminated from subsequent processing. Mean values from each channel were then log2 transformed and normalised using the LOWESS to remove intensity-dependent effects in the log2 (ratios) values. The Cy3/Cy5 fluorescent ratios were calculated from the normalised values. Significance analysis of the data used the Student's t test to determine the probability that the average of the experimental replicates was significantly different from the average of the control replicates. p-values for the data were calculated by treating each slide as a repeat using Genesight 4. Genes differentially regulated ≥ 2-fold and displaying a p-value of ≤ 0.05 were defined as being statistically significant and differentially transcribed.

first: Carlos

last: Avila-Ramirez

middle: K


title: miRNA expression during liver regeneration in the chronic ethanol-fed rat

status: Public on Jul 23 2012

city: Philadelphia

first: Rachael

last: Dippold

state: PA

address: 1020 Locust St., JAH 222

department: Pathology, Anatomy, and Cell Biology

institute: Thomas Jefferson University

summary: miRNA expression was profiled before and during liver regeneration following 2/3 partial hepatectomy (PHx) in chronic ethanol-fed (EtOH) and pair-fed carbohydrate control (CHO) rats.  Prior to PHx, EtOH animals were fed a liquid diet containing 36% of the calories from ethanol for 5 weeks.  Left lateral and medial (LLM) lobes were removed at time of PHx and used as t = 0 biological controls.  Remnant liver tissue (PHx) was harvested 1 h, 6 h, 12 h, and 24 h after PHx.  RNA from 4 biological replicates was pooled for profiling miRNA expression on Agilent Rat miRNA Microarrays v1.0.

overall_design: miRNA expression was profiled in the chronic ethanol-fed (EtOH) and carbohydrate control pair-fed (CHO) liver prior to (LLM) and 1 h, 6 h, 12 h, and 24 h after partial hepatectomy (PHx).

first: Jan

middle: B

last: Hoek


title: Chemical perturbation of Trypanosoma brucei procyclic form cells

status: Public on May 30 2012

city: Montreal

first: Hamed

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

country: Canada

institute: McGill University

summary: T. brucei PF cells were treated with several chemical reagents and anti-trypanosomatid drugs. The effect of each chemical perturbation on the transcriptome of T. brucei was examined by transcript profiling of treated vs. control cells. The results indicated widespread changes, suggesting that the transcriptome of T. brucei is highly responsive to environmental factors that perturb its metabolic and biological pathways.

overall_design: 11 chemical perturbations, each co-hybridized with a common reference RNA from control non-treated cells. One array per treatment.

first: Chad

last: MacPherson

first: Reza

last: Salavati


title: The ureic-based herbicide linuron and the model anti-androgen flutamide regulate common gene networks in the fathead minnow (Pimephales promelas) ovary

first: Christopher

last: Martyniuk

summary: The herbicide linuron is an endocrine disruptor with a suspected anti-androgenic mode of action (MOA) but the complete MOA for LIN is not fully characterized.  The objectives of this study were to better characterize the MOA of LIN in the fathead minnow (FHMs) ovary by comparing expression profiles of LIN to dihydrotestosterone (DHT) and flutamide (FLUT), both model compounds with well defined androgenic and anti-androgenic MOAs respectively. Ovarian explants from vitellogenic FHMs were exposed to 10-6 M, 10-7 M, and 10-8 M of DHT, FLUT, and LIN in vitro in a12 hour incubation experiment.  Ovary explants exposed to DHT showed a significant increase in E2 production compared to controls but FLUT and LIN did not affect E2 production.  Microarray analysis and support vector machine classification revealed that expression patterns of FLUT and LIN in the ovary were more similar to each other compared to DHT and other androgens.  Gene set enrichment analysis identified the notch signaling cascade was affected by all three chemicals.  DHT down-regulated the WNT-Frizzled pathway while LIN down-regulated angiopoietin receptor signaling and increased biosynthesis of cholesterol.  LIN shared 27 expression sub-networks (e.g. beta-3 adrenergic receptor, MAP3K1, interleukin, signlaing) in common with FLUT, and only 4 sub-networks with DHT.  A reciprocal gene expression network was constructed using DHT and FLUT data, and the network revealed that steroid metabolism, translation, and DNA replication are potentially regulated through AR signaling.  This study characterizes cell pathways associated with E2 production and identifies cell signaling cascades that may be disrupted by ureic-based herbicides in the ovary.

overall_design: 16 samples total; 4 control, 4 DHT, 4 Flutamide, 4 LIN


title: JIL kinase - marker of active chromatin and sensor of dosage compensation (ePol)

status: Public on May 08 2012

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

type: Genome binding/occupancy profiling by genome tiling array

summary: ChIP-chip profiles of RNA Polymerase II phosphorylated on serine 2 in Drosophila S2 cells.

overall_design: RNA Polymerase II phosphorylated on serine 2 ChIP in Drosophila S2 cells. 3 biological replicates with dye-swaps.

first: C

last: Regnard

first: T

first: A

last: Mitterweger

first: I

last: Dahlsveen

first: P

last: Becker


title: MNNG/HOS cells and sarcospheres

status: Public on May 23 2012

city: GUANGZHOU

first: haotong

last: wu

address: CHINA GUANGZHOU

country: China

institute: SUN YAT-SEN UNIVERSITY

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

overall_design: Refer to individual Series


title: Tumorgenic properties of high-dose ionizing radiation of primary cancer-associated fibroblasts

status: Public on Apr 16 2012

city: Tromsø

first: Chris

last: Fenton

address: Thor Knutsen vg 6

department: Microarray

country: Norway

institute: UITO

summary: In the context of radiotherapy, the effects elicited by ionizing radiation on the supportive stroma of tumors remains understudied. Tumor infiltrating fibroblasts are abundantly found in the stromal tissue of most tumor types and are key determinants of tumor progression and metastasis. Given the clinical attention that ablative radiotherapy is gaining nowadays, and the paramount role played by CAFs in cancer sustainability, in this study the effect of high-dose ionizing radiation on primary CAF?S have been investigated. We have used high-throughput transcriptome analysis to ascertain in which degree tumor stromal fibroblast become pro-tumorigenic or anti-tumorigenic after ablative irradiation. Hence, genome-wide transcriptome analysis has been carried out on CAFs isolated from NSCLC tumors after receiving a single dose of 18 Gray. The expressions of relevant genes have been validated by real-time PCR, and transformed cellular pathways have been checked by functional assays. Overall, our data reveals profound changes in biological pathways including cellular stress, DNA damage, cell cycle, aging, apoptosis, oxidative stress, and matrix remodeling. Ablative radiation doses may exert both pro-and anti-tumorigenic effects on CAFs. The ultimate effect of such disturbances merits further investigation in more complex in vivo settings.

overall_design: Established primary cancer-associated fibroblasts (CAFs) obtained from non-small-cell lung cancer (NSCLC) patient material were irradiated with a single dose of 18 Gy and total RNA was isolated 24 hrs after treatment.

first: Ruth

last: Paulssen

first: Inigo

last: Martinez-Zubiaurre

first: Hagar

middle: M

last: Taman

first: Turid

last: Hellevik

first: Ingvild

last: Pettersen


title: Expression analysis of human osteosarcoma cell line MNNG/HOS sarcospheres, hypoxia-induced sarcospheres and TGF-beta1-induced sarcospheres

summary: Invastigation of whole genome gene expression level changes in human osteosarcoma cell line MNNG/HOS sarcospheres,hypoxia-induced sarcospheres and TGF-beta1 induced sarcospheres.

overall_design: A three chip study using total RNA cover from three cultures of  human osteosarcoma cell line MNNG/HOS sarcospheres, hypoxia-induced sarcospheres and TGF-beta1-induced sarcospheres. Each chip measures the expression level of 45033 genes from osteosarcoma cell line MNNG/HOS.

first: Yan

last: Zhang

first: Haixia


title: TGF-beta1 effect on human osteosarcoma cell line MNNG/HOS

summary: Investigation of whole genome gene expression level changes in human osteosarcoma cell line MNNG/HOS treated by TGF-beta1 for three days (mesophase) and five days (sarcospheres iOSCs), compared to non-treatment cells (residual adherent cells).

overall_design: A three chip study using total RNA cover from three cultures of non-treatment human osteosarcoma cell line MNNG/HOS (residual adherent cells),  TGF-beta1 treated three days osteosarcoma cell line MNNG/HOS (mesophase) and TGF-beta1 treated five days osteosarcoma cell line MNNG/HOS ( only collected the suspending sarcospheres iOSCs). Each chip measures the expression level of 45033 genes from osteosarcoma cell line MNNG/HOS.


title: Heritable epigenetic variation among maize inbreds

status: Public on Nov 21 2011

first: Steve

last: Eichten

summary: Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence.  Methylation of cytosine residues provides a mechanism for the inheritance of epigenetic information.  We have profiled the distribution of DNA methylation in the large, complex genome of Zea mays (ssp. mays).  DNA methylation levels are higher near the centromeres and are generally inversely correlated with recombination and gene expression levels.  However, genes that are located in non-syntenic genomic positions relative to species related closely to maize exhibit higher levels of DNA methylation independent of expression state.  A comparison of the DNA methylation levels in two different inbred genotypes, B73 and Mo17, allowed for the identification of approximately 700 differentially methylated regions.  The regions of differential methylation in B73 and Mo17 often occur in intergenic regions but some of these regions are located within or near genes.  There is evidence that variation in DNA methylation levels can occur in genomic regions that are identical-by-descent, illustrating the potential for epigenetic variation that is not tightly linked to genetic changes.  A comparison of the genotype and epigenotype in a panel of near-isogenic lines reveals evidence for epigenetic variation that is conditioned by linked regions as well as examples of epigenetic variation that is conditioned by unlinked genomic regions.  Our many examples of epigenetic variation, including some without tightly linked genetic variation, have implications for plant breeding and for natural selection.

overall_design: Methylation profiles in seedling tissue of the maize inbred lines B73 and Mo17. Each genotype was compared for three biological replications using a gene-focused custom 2.1M NimbleGen array.

last: Swanson-Wagner

first: Steven

first: Mattew

last: Vaughn

first: Nathan

last: Springer


title: Metabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch culture

status: Public on Dec 31 2011

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

summary: Bacteria in the genus Streptomyces are soil dwelling oligotrophs and important producers of secondary metabolites. Previously we showed that global mRNA expression was subject to a series of metabolic and regulatory switches during the life time of a fermentor batch culture of S. coelicolor M145. Here we analyse the proteome from eight time points from the same fermentor culture and, as phosphate availability is an important regulator of secondary metabolite production,  compare this to the proteome of a similar time course from an S. coelicolor mutant, INB201 (ΔphoP), defective in the control of phosphate utilisation. The proteomes provide a detailed view of enzymes involved in central carbon and nitrogen metabolism. Trends in protein expression over the time courses were deduced from a protein abundance index which also revealed the importance of stress pathway proteins in both cultures. As expected the ΔphoP mutant was deficient in expression of PhoP-dependent genes and several putatively compensatory metabolic and regulatory pathways for phosphate scavenging were detected. Notably there is a succession of switches that co-ordinately induce the production of enzymes for five different secondary metabolite biosynthesis pathways over the course of the batch cultures and these were not confined to the stationary phase.

overall_design: 36 samples, no replicates; one hour resolution from 23-36h and 41-48h; half hour resolution from 36-41h; two hour resolution 48-60h; sample missing for 34 h

first: Alexander

last: Wentzel

first: Margaret

middle: C

last: Smith

first: Stream

last: Consortium


status: Public on Feb 21 2012

first: Ariel

last: Grostern

address: 209 O'Brien Hall

department: Civil & Environmental Engineering

institute: UC Berkeley

summary: Analysis of gene expression in Pseudonocardia dioxanivorans strain CB1190 during growth with dioxane, glycolate or pyruvate.

overall_design: Three treatments, based on carbon source used for growth: pyruvate, dioxane and glycolate. Triplicate microarrays (biological replicates) were prepared for each treatment. Pyruvate was used as the reference treatment for subsequent analysis. Gene expression changes were compared pair-wise: dioxane vs. pyruvate, and glycolate vs. pyruvate

last: Sales

first: Lisa

last: Alvarez-Cohen


title: Effects of bisphenol A on ovarian gene expression in fathead minnows and zebrafish [FHM data set]

status: Public on Jan 01 2012

city: Duluth

first: Daniel

middle: L.

last: Villeneuve

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

institute: US EPA

summary: Effects of bisphenol A (BPA) on ovarian transcript profiles as well as targeted endpoints with endocrine/reproductive relevance were examined in two fish species, fathead minnow (Pimephales promelas) and zebrafish (Danio rerio), exposed in parallel using matched experimental designs. Four days of waterborne exposure to 10 µg BPA caused significant vitellogenin induction in both species. However, zebrafish were less sensitive to effects on hepatic gene expression and steroid production than fathead minnow and the magnitude of vitellogenin induction was more modest. The concentration-response at the ovarian transcriptome level was non-monotonic and violated assumptions that underlie proposed methods for estimating hazard thresholds from transcriptomic results. However, the non-monotonic profile was consistent among species and there were nominal similarities in the functions associated with the differentially expressed genes, suggesting potential activation of common pathway perturbation motifs in both species. Overall, the results provide an effective case study for considering the potential application of ecotoxicogenomics to ecological risk assessments and provide novel comparative data regarding effects of BPA in fish.

overall_design: Fish were exposed to 0, 0.01, 0.1, 1.0, 10, or 100 µg BPA/L delivered in a continuous flow (45 ml/min) of sand filtered, UV treated, Lake Superior Water, without the use of carrier solvents. The design employed six replicate tanks per treatment. Three of the replicates were loaded with three male and three female zebrafish per tank, while the remaining three replicates were loaded with three male and three female fathead minnows. Addition of fish to the exposure tanks was staggered by replicate such that all sampling could be completed within 60 min of the desired 96 h exposure duration. After 96 h of exposure, fish were anesthetized in a buffered solution of tricaine methanesulfonate (MS-222; Finquel; Argent, Redmond, WA, USA) and weighed. Blood was collected from the caudal vasculature using microhematocrit tubes, centrifuged to separate the plasma, and plasma was stored at -80oC until analyzed. Liver, gonad, and brain tissues (including pituitary gland) were snap frozen in liquid nitrogen and stored at -80oC until extracted. Total RNA was isolated from ovary tissue of both fathead minnow and zebrafish using RNeasy kits (Qiagen, Valencia, CA, USA). RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and RNA was quantified spectrophotometrically (Nanodrop). Total RNA samples were stored at -80oC until used for microarray analyses. Ovarian transcripts from 32 fathead minnows (n=5 per treatment, except for control and 1.0 µg BPA/L, n=6) were analyzed using a custom, 15,000 gene microarray (GEO Platform Accession GPL9248) purchased from Agilent Technologies (Palo Alto, CA, USA). Ovarian transcripts from 34 zebrafish (n=6 per treatment, except 0.01 and 0.1 µg BPA/L, n=5) were analyzed using a commercial 44,000 feature microarray (Agilent design 019161; GEO Platform Accession GPL6457). The same hybridization and scanning procedures were used for both platforms. Briefly, microarrays were hybridized following the manufacturer’s guidelines for One-Color Microarray-Based Gene Expression Analysis (version 5.7; Agilent). Hybridizations were conducted with 1 µg of total RNA. Complementary DNA synthesis, cRNA labeling, amplification, and hybridizations were performed following the manufacturer’s kits and protocols (Quick Amp labeling kit; Agilent). Scanning was conducted at 5 µm resolution using an Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc., Concord, Ontario, Canada). Data were extracted from microarray array images using Agilent Feature Extraction Software (Agilent; Palo Alto, CA, USA).

middle: L

first: Natalia

last: Garcia-Reyero

first: B

last: Escalon

first: Kathleen

last: Jensen

first: Jenna

middle: E

last: Cavallin

first: Elizabeth

last: Makynen

last: Durhan

first: Michael

middle: D

last: Kahl

first: Linnea

last: Thomas

first: Edward

last: Perkins

first: Gerald

middle: T

last: Ankley


title: Song stimulation: Conspecific song vs Control and Heterospecific song

status: Public on Nov 22 2011

city: Uppsala

first: Göran

last: Arnqvist

address: Norbyvägen 18D

department: Ecology and Genetics

country: Sweden

institute: Uppsala University

summary: Transcriptional profiling of courtship song stimulated females in Drosophila melanogaster comparing females exposed to conspecific song to those exposed to either white-noise (control) or heterospecific song (D. simulans)

overall_design: Three condition experiment, D. melanogaster (mel_song) song stimulated vs. Control (no_song) and vs. D. simulans (sim_song) stimulated females. Biological replicates: 7 for D_mel_song, 4 for no_song, 3 for D_sim_song. One replicate per array. Each sample contains 120 pooled female heads, collected from three independent experiments. Technical replication: two arrays with reverse labeling for each contrast.

first: Elina

last: Immonen

last: Ritchie


title: The role of the Tra1p transcription factor of Magnaporthe oryzae in spore adhesion and pathogenic development

status: Public on Mar 03 2012

city: Kaiserslautern

first: Karsten

last: Andresen

address: Erwin-Schroedinger-Str. 56

institute: IBWF

last: Breth

first: D

last: Odenbach

first: M

last: Schroeder

last: Bode

first: E

last: Thines

first: L

last: Antelo

first: K

first: A

last: Yemelin

first: N

last: Schlink

middle: J

last: Foster


title: Effects of bisphenol A on ovarian gene expression in fathead minnows and zebrafish

first: Daniel

last: Villeneuve

sample_organism:
Danio rerio
Pimephales promelas

platform_organism:
Danio rerio
Pimephales promelas


title: Human testis-derived embryonic stem cell-like cells are not pluripotent, but possess potential of mesenchymal progenitors.

status: Public on Nov 02 2011

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

summary: Comparison of whole genome gene expression profiles of human testis derived ES-like cells with pluripotent stem cells (human embryonic stem cell lines), adult human bone marrow derived mesenchymal stem cells and human dermal fibroblasts.

overall_design: Microarray study with total RNA of three testis derived ES-like cells clusters of one indivual (1) cultured in three different culture conditions A, B,C and embryoid bodies (EB) derived from them at 4, 7, 10, 14 and 18 days of suspension culture. Biological duplicates of  human ES cell lines (HUES-1, GFP-hES-3),human bone marrow derived MSC (BMMSC1 and 2) and human dermal fibroblasts (DFB1 and 2) (LONZA CC-2511) at different passages were used as comparison groups.

last: Van Pelt

first: S

last: Repping

first: T

last: Breit

first: J

middle: V

last: Chikhovskaya


title: DNA methylation data from human keratinocyte-derived iPS cells (N9) and ES cells

status: Public on Nov 29 2011

city: Baltimore

first: Akiko

last: Doi

address: 855 N Wolfe St, Rangos 580

department: Medicine

institute: Johns Hopkins University School of Medicine

summary:
Genome-wide DNA methylation of early and late passaged keratinocyte-derived iPS cells were compared to ES cells.
We used custom Nimblegen microarrays to determine the genome-wide DNA methylation in human keratinocyte-derived iPS cells and ES cells

overall_design: We isolated genomic DNA from human stem cells  and somatic cells and hybridized to custom-designed Nimblegen microarrays (CHARM arrays).

first: Kitai

last: Kim

first: George

middle: Q

last: Daley

first: Andrew

last: Feinberg


title: Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context (ChIP-chip)

status: Public on Mar 19 2012

first: Joshua

middle: WK

last: Ho

address: 41 Avenue Louis Pasteur

department: Department of Medicine

institute: Brigham and Women's Hospital

summary: The Drosophila MSL complex mediates dosage compensation by increasing transcription of the single X chromosome in males approximately two-fold. This is accomplished through recognition of the X chromosome and subsequent acetylation of histone H4K16 on X-linked genes. Initial binding to the X is thought to occur at a subset of sites. However, the consensus sequence motif of entry sites (“MSL recognition element” or MRE) is only slightly enriched on the X (~2 fold), and only a fraction of them is utilized by the MSL complex. Here we ask whether chromatin context could distinguish between utilized and non-utilized copies of the motif, by comparing their relative enrichment for histone modifications and chromosomal proteins mapped in the NHGRI modENCODE project. Through a comparative analysis of the chromatin features in male S2 cells, which contain MSL complex, and female Kc cells, which lack the complex, we find that the presence of active chromatin modifications, together with an elevated local GC content in surrounding sequence, has strong predictive value for functional MSL entry sites, independent of MSL binding. We tested these sites for function in Kc cells by RNAi knockdown of Sxl, resulting in induction of MSL complex. We show that ectopic MSL expression in Kc cells leads to H4K16 acetylation around these sites, and a relative increase in X chromosome transcription. Collectively, our results support a model in which a pre-existing active chromatin environment, coincident with H3K36me3, contributes to MSL entry site selection. The consequences of MSL targeting of the male X chromosome include increase in nucleosome lability, enrichment for H4K16 acetylation and JIL-1 kinase, and depletion of linker histone H1 on active X-linked genes. Our finding serves as a model to understand how chromatin and local sequence features are involved in the selection of functional protein binding sites in the genome.

overall_design: The key Drosophila female sex determinant protein, SXL, represses dosage compensation by inhibiting MSL2 translation.  Loss of SXL results in the expression, stabilization, and targetting of the MSL complex in female cells.  Therefore, depletion of SXL by RNA interference (RNAi) in female Kc cells will lead to a MSL2-dependent increase in transcription from the female X chromosomes, consistent with the induction of dosage compensation. In this experiment, we generated ChIP-chip profiles of H4K16 acetylation (H4K16ac) in Kc cells of control (GFP) and Sxl RNAi. For ChIP, we used Upstate (now Millipore) anti-H4K16ac antibody, catalog # 07-329, lot #JBC1355376.

first: Marnie

last: Gelbart

first: Artyom

middle: A

last: Alekseyenko

first: Erica

last: Larschan

middle: W

first: Shouyong

last: Peng

first: Peter

last: Park

first: Mitzi

middle: I

last: Kuroda


title: Microarray analysis of the transcriptome in the primate corpus luteum during chorionic gonadotropin administration simulating early pregnancy.

city: Beaverton

first: Cecily

middle: Vauna

last: Bishop

state: OR

address: 505 NW 185th Ave

department: Division of Reproductive & Developmental Sciences

institute: Oregon National Primate Research Center

summary: To explore chorionic gonadotropin (CG)-regulated gene expression in the primate corpus luteum (CL), adult female rhesus macaques were treated with a model of simulated early pregnancy (SEP). Total RNA was isolated from individual CL and hybridized to Affymetrix™ GeneChip Rhesus Macaque Genome Arrays The level of 1192 transcripts changed expression > 2-fold (one-way ANOVA, FDR correction; P<0.05) during SEP when compared to Day 10 untreated controls, and the majority of changes occurred between Days 10 and 12 of SEP. To compare transcript levels between SEP rescued and regressing CL, previously banked rhesus GeneChip array data from the mid- to late and very late luteal phase were analyzed with time-matched intervals in SEP. Comparing RMA-normalized transcripts from the natural cycle with those from luteal rescue revealed 7677 transcripts changing in expression pattern >2 fold (one-way ANOVA, FDR correction; P<0.05) between the two groups.  Clustering of samples revealed that the SEP samples possessed the most related transcript expression profiles. Regressed CL (days 18-19, around menses) were the most unlike all other CL. The most affected KEGG pathway was Steroid Biosynthesis, and most significantly absent pathways following SEP treatment includes groups of genes whose products promote cell-death. By further comparing the genome-wide changes in luteal gene expression during rescue in SEP, with those in CL during luteolysis in the natural menstrual cycle, it is possible to identify key regulatory pathways promoting fertility.

overall_design: Simulated early pregnancy (SEP) treatment was begun on day 9 as Duffy and Stouffer (1997) by treatment of females with recombinant human chorionic gonadotropin (hCG; Novarel™, Ferring Pharmaceuticals Inc. Parsippany, NJ, USA) in increasing dosages (15, 30,45,90,180,360,720,1440, and 2880 IU) twice daily by intramuscular injection. CL were collected by laparotomy on days 10, 12, 15, and 18, representing 1, 3, 6 and 9 days of hCG treatment (n=4 CL/day). Additionally, luteal day 10 untreated CL were collected to serve as baseline controls for SEP CL. All CL were dissected away from luteal tissue, sectioned, and snap-frozen in liquid nitrogen and stored at -80°C until RNA and protein isolation by TRIzol® extraction (Invitrogen, Carlsbad, CA, USA) according to manufacturer’s protocols.

first: C

last: Satterwhite

first: L

last: Xu

last: Hennebold

first: R

last: Stouffer


title: Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm

status: Public on Dec 16 2011

city: St. Paul

first: Steve

middle: R

last: Eichten

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

summary: Imprinting describes the differential expression of alleles based upon their parent of origin.  Deep sequencing of RNAs from maize endosperm and embryo tissue 14 days after pollination was used to identify imprinted genes among a set of ~12,000 genes that were expressed and contained sequence polymorphisms between the B73 and Mo17 genotypes.  The analysis of parent-of-origin patterns of expression resulted in the identification of 100 putative imprinted genes in maize endosperm including 54 maternally expressed genes (MEGs) and 46 paternally expressed genes (PEGs).  Three of these genes have been previously identified as imprinted while the remaining 97 genes represent novel imprinted maize genes.  A genome-wide analysis of DNA methylation identified regions with reduced endosperm DNA methylation in, or near, 19 of the 100 imprinted genes.  The reduced levels of DNA methylation in endosperm are caused by hypomethylation of the maternal allele for both MEGs and PEGs in all cases tested.  Many of the imprinted genes with reduced DNA methylation levels also show endosperm-specific expression patterns.  The imprinted maize genes were compared with imprinted genes identified in genome-wide screens of rice and Arabidopsis and at least 10 examples of conserved imprinting between maize and each of the other species were identified.

overall_design: Methylation profiles across endosperm tissue in B73 and Mo17 were assayed for three biological replications using a custom 2.1M gene-focused NimbleGen array.

first: Amanda

last: Waters

first: Ruth

last: Swanson-Wagner

first: Steven

first: Mattew

last: Vaughn

first: Nathan

last: Springer


title: DNA copy number variation from human Wilms' Tumor samples

status: Public on Aug 29 2011

city: Shanghai

first: Yun

last: Liu

address: 130 Dong An Road

institute: Fudan University

summary:
Genome-wide DNA copy number was studied to determine whether the Wilms' tumor samples generally show normal copy number variation comparing to the colon tumor samples
We used custom Nimblegen microarrays to determine the genome-wide DNA copy number in human Wilms' Tumor samples

overall_design: We isolated genomic DNA from human Wilms' tumor tissues and hybridized to custom-designed Nimblegen microarrays (CHARM arrays).

first: Andrew

middle: P

last: Feinberg


title: Microarray analysis highlights immune response of Pacific oysters as a determinant of resistance to summer mortality

status: Public on Apr 22 2011

city: Plouzane

first: Arnaud

last: Huvet

address: Ifremer centre de Brest BP 70

department: Physiologie Fonctionnelle des Organismes Marins

country: France

institute: IFREMER

summary: Summer mortality of Crassostrea gigas is the result of a complex interaction between oysters, their environment and pathogens. A large genetic basis and a high heritability were demonstrated for the observed variation in resistance to summer mortality, which offered the possibility to develop lines of oysters that were resistant (R) or susceptible (S) to summer mortality. Previously, genome-wide expression profiling of R and S oyster gonads highlighted reproduction and antioxidant defense as constitutive pathways that operate differentially between these two lines. Here, we show that signaling in innate immunity also operates differentially between these lines and we postulated that it is at the main origin of their difference of survival in the field. From the already published microarray data, we employed an ANOVA analysis that reveals a specific “immune” profile at the date preceding the mortality. In addition, we conducted a microarray profiling of two other tissues, gills and muscle, that also showed an over-representation of the immune genes (46%) among the selected genes. Eleven genes were pinpointed to be simultaneously differentially expressed between R and S lines in the three tissues. Among them, ten are related to “Immune Response”. The kinetics of their mRNA levels appeared clearly different between lines and suggests that in environment, R oysters had the capacity to modulate signaling in innate immunity whereas S oysters did not. This study enhances our understanding of the complex summer mortality syndrome and provides candidates of interest for further functional and genetics studies.

overall_design:
For microarray analysis, R and S oysters were sampled three times (dates 1 to 3: May 25, June 6, and June 20, respectively). On each date, 3 replicates of 8 oysters were sampled from each line (R and S) for three tissues (gonad, muscle and fills) and all the samples prepared for total RNA extraction. Furthermore, the entire tissues of 10 wild oysters were collected, pooled and homogenized to constitute a single total RNA sample for use as a reference in all slide hybridizations and RT-PCR analysis.

For microarray hybridizations, 5µg of total RNA were directly labeled by reverse transcription and then purified using the Direct ShipShot Labeling kit (Promega). This reaction was performed for each of the 18 samples, with Cy5 (red) incorporation. The reference sample was Cy3-labeled (green) in 18 separate tubes following the same protocol. The 18 Cy3-labeled cDNAs were next pooled, and then divided once more into 18 samples to obtain a homogeneous reference.

Equimolar amounts of cDNA samples and cDNA reference labeled with Cy5 and Cy3, respectively, were SpeedVac evaporated and mixed into a single pool with the hybridization buffer (ChipHyb™ hybridization buffer, Ventana Discovery, Tucson, AZ, USA). They were then co-hybridized on the same microarray slide, in a Ventana hybridization station (Ventana Discovery, Tucson, AZ, USA).

The data submitted here correspond to the mean of the three replicates for each line and each date, representing 18 samples.

first: Elodie

last: Fleury


title: Gene expression in human endothelial cell with innate immunity stimulation

status: Public on Mar 01 2011

city: Fukuoka

first: Hisanori

last: Nishio

address: Maidashi 3-1-1, Higashi-ku

department: Pediatrics

institute: Kyushu University

summary: This is an investigation of whole genome gene expression level in human coronary endothelial cells (HCAEC) and human pulmonary endothelial cells (HPAEC) stimulated by FK565 or LipidA. We show that parenteral administration of a pure synthetic Nod1 ligand, FK565, induces site-specific vascular inflammation in mice, which is prominent in and aortic root including aortic valves, slight in aorta and absent in other arteries. The in vitro production of proinflammatory chemokine/cytokine by FK565 is higher in HCAEC than in HPAEC, suggesting that site-specific vascular inflammation is at least in part ascribed to an intrinsic nature of the vascular cell itself.

overall_design: A six chip study using total RNA recovered from HCAEC and HPAEC which were stimulated by LipidA or FK565 in vitro. HCAEC and HPAEC were stimulated with FK565 (10µg/mL) or LipidA (100ng/mL) for 24 hours in 12-well plates (10,000 cells/cm2). Total RNA was extracted and subjected to RNA microarray analysis.

first: Kazuyuki

last: Ikeda

first: Shunsuke

last: Kanno

first: Sagano

last: Onoyama

first: Tamami

last: Tanaka

first: Koichi

last: Kusuhara

first: Yukari

last: Fujimoto

last: Fukase

first: Katsuo

last: Sueishi

first: Toshiro

last: Hara


title: Histone 4 Lys-20 Mono-Methylation by SET8 Mediates Wnt Target Gene Activation

status: Public on Dec 29 2010

first: Zhenfei

last: li

address: No.320 Yueyang Road

institute: Institute of Biochemistry and Cell Biology

summary:
Histone methylation has an important role in transcriptional regulation. However, unlike H3K4 and H3K9 methylation, the role of H4K20 mono-methylation (H4K20me-1) in transcriptional regulation remains unclear. Here we show that Wnt3a specifically stimulates H4K20 mono-methylation at TBE (TCF-binding element) via the histone methylase SET8. Additionally, SET8 is crucial for activation of the Wnt reporter gene and target genes in both mammalian cells and zebrafish. Furthermore, SET8 interacts with TCF4/LEF1 directly, and this interaction is regulated by Wnt3a. Therefore, we conclude that SET8 is a Wnt signaling mediator and is recruited by LEF1/TCF4 to regulate the transcription of Wnt-activated genes, possibly via H4K20 mono-methylation at the target gene promoters. Our findings also indicate that H4K20me-1 is a marker for gene transcription activation, at least in canonical Wnt signaling.
This chip experiment was carried out to find out how many genes would be regulated by SET8 after Wnt3a CM stimulated HEK293 cells.

overall_design: Total RNA was extracted from HEK293 cells after siRNA transfection (control or SET8 shRNA) for about 40 hours and then induced with Control or Wnt3a CM for 7 hours using TRIzol (Invitrogen) and the RNeasy kit (Qiagen). Three pairs of samples: si-control + control CM / si-control + Wnt3a CM 7 h / si-SET8 + Wnt3a CM. Samples were amplified and labeled using a NimbleGen One-Color DNA Labeling Kit.

last: Li

first: Fen

last: Nie

first: Lin


title: Identification of the receptor tyrosine kinase AXL in triple negative breast cancer as a novel target for the human miR-34a microRNA (miRNA study)

status: Public on Dec 31 2010

city: Bethesda

first: Mark

last: Mackiewicz

address: 37 Convent Drive

department: National Cancer Institute

institute: National Institutes of Health

summary: Triple negative breast cancer (TNBC) is histologically characterized by the absence of the hormone receptors estrogen and progesterone, in addition to having a negative immunostain for HER-2.  The aggressiveness of this disease and lack of targeted therapeutic options for treatment is of high clinical importance.  MicroRNAs are short 21- to 23 nucleotide endogenous non-coding RNAs that regulate gene expression by binding to mRNA transcripts, resulting in either decreased protein translation or mRNA degradation.  Dysregulated expression of miRNAs is now a hallmark of many human cancers.  In order to identify a miRNA/mRNA interaction that is biologically relevant to the triple negative breast cancer genotype/phenotype, we initially conducted a miRNA profiling experiment to detect differentially expressed miRNAs in cell line models representing the triple negative (MDA-MB-231), ER+ (MCF7), and HER-2 overexpressed (SK-BR-3) histotypes.  We identified human miR-34a expression as being  >3-fold down (from its median expression value across all cell lines) in MDA-MB-231 cells, and identified AXL as a putative mRNA target using multiple miRNA/target prediction algorithms.  The miR-34a/AXL interaction was functionally characterized through ectopic overexpression experiments with a miR-34a mimic.  In reporter assays, miR-34a binds to the putative target site within the AXL 3’UTR to affect luciferase expression.  We also observed degradation of AXL mRNA and decreased AXL protein levels, as well as cell signaling effects on AKT phosphorylation and phenotypic effects on cell migration.  Finally, we present an inverse correlative trend in miR-34a and AXL expression for both cell line and patient tumor samples.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: The small RNA (sRNA) fraction from four separate passages (biological replicates) of MCF7, SK-BR-3, MDA-MB-231, and MCF10A cells were extracted using Qiagen’s miRNeasy kit following the manufacturer’s instructions (Qiagen; Germantown, MD).  Five micrograms of sRNA was labeled with either Cy3 (MCF10A) or Cy5 (breast cancer cell) fluorescent label (GE Healthcare; Piscataway, NJ) using the mirVana miRNA labeling kit (Ambion; Austin, TX).  The labeled products were hybridized to miRVana miRNA Bioarrays V2 (Ambion, Austin, TX) and washed following the manufacturer’s protocol.  Each array was comprised of 328 human miRNA probes in addition to 114 mouse and 46 rat miRNAs.  The comparative hybridization for each breast cancer cell line to the reference MCF10A cell line control was conducted in quadruplicate (n=12 total arrays).  Processed arrays were scanned for dual channel hybridization using a GenePix 4000B scanner (Molecular Devices; Sunnyvale, CA).  Analyses were performed using BRB-Array Tools Version 3.8.1 (http://linus.nci.nih.gov/BRB-ArrayTools.html).  Replicate spots for each miRNA were averaged within the array, background adjusted, and log2 normalized.  Normalization was performed using a per chip median normalization method.  Only those miRNAs with at least a 3-fold change in expression from its median value across all arrays, in at least 33% of all arrays tested, were retained.  Samples and genes were hierarchical clustered with average linkage under the Euclidian distance similarity metric using the Cluster 3.0 (http://rana.stanford.edu/software) and Java TreeView 1.1.4r3 applications.  MiRNA probes of mouse, rat, and manufacturer’s (Ambion) origins that passed the gene filter were excluded from future analyses.

first: Konrad

last: Huppi

first: Jason

last: Pitt

first: Robert

last: Cornelison

first: Tiffany

last: Dorsey

first: Stefan

last: Ambs

first: Natasha

last: Caplen


title: Transcriptome analysis in Human leprosy patients

status: Public on Mar 17 2011

city: Seoul

first: Tae Hoon

last: Kim

state: Socho-gu

address: 505 Bonpo-dong

department: Pathology

institute: Medical College of the Catholic University

summary: Leprosy is classified from paucibacillary leprosy (TT and BT) to multibacillary leprosy (BB, BL, and LL). In our study, we focus on selecting or classfying the significant genes to discriminate between paucibacillary and multibacillary group  and the important genes to distinguish between blood and the corresponding tissue in patients.

overall_design:
· Human Adult Normal Skin Sample (Commercial;Cat#1234218); 6 patients of leprosy (Blood and Tissue sample (Pathologic classification: BT); 6 patients of leprosy (Blood and Tissue sample (Pathologic classification: MB))
· In blood sample, BT sample vs MB sample
· In tissue sample, Normal Skin sample vs tissue BT sample or tissue MB sample
· Single Color Microarray
· All experiments are performed one replicate

first: Tae-Hoon

first: Tae-Jin

last: Kang

first: Armi

last: Maghanoy

first: Irene

middle: B

last: Mallari

first: Marivic

middle: F

last: Balagon

first: Hye-Won

last: Park

first: Seung-Jun

first: Gue-Tae

last: Chae


title: Genome-Wide Profiling of Astrocytic Gliomas

status: Public on Sep 14 2010

city: Heidelberg

first: Grischa

last: Toedt

address: Im Neuenheimer Feld 280

department: Molecular Genetics (B060)

institute: German Cancer Research Center (DKFZ)

type:
Expression profiling by array
Genome variation profiling by array

summary: Genomic aberrations were determined by array-based comparative genomic hybridization in 131 diffuse astrocytic gliomas, including 87 primary glioblastomas (pGBIV), 13 secondary glioblastomas (sGBIV), 19 anaplastic astrocytomas (AAIII), and 12 diffuse astrocytomas (AII). Expression profiling was performed for 74 tumors (42 pGBIV, 11 sGBIV, 13 AAIII, 8 AII).

overall_design: 131 aCGH experiments. 87 EP experiments (x2 dye swap). DNA and RNA extracted from the same patients.

first: Sebastian

last: Barbus

first: Marietta

last: Wolter

first: Joerg

last: Felsberg

first: Bjoern

last: Tews

first: Frederic

last: Blond

first: Michael

last: Sabel

first: Stefanie

last: Hofmann

first: Christian

last: Hartmann

first: Hiroko

last: Ohgaki

first: Andreas

last: von Deimling

first: Wiestler

last: Otmar

first: Meinhard

last: Hahn

first: Peter

last: Lichter

first: Guido

last: Reifenberger

first: Bernhard

last: Radelwimmer


title: microRNA epxression patterns can discriminate between patients with oligometastatic and polymetastatic progression: cell lines

status: Public on Dec 09 2010

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

institute: University of Viginia

summary:
Cancer staging and treatment frequently assume a binary division of tumors into localized or metastatic cancers. We proposed a state of metastatic disease defined by the number of metastases termed oligometastases.  Patients with oligometastatic disease may be cured with localized methods of cancer treatment. We analyzed miRNA expression from paraffin blocks of primary or metastatic tumor samples derived from oligometastatic (? 5 metastases) patients treated with high dose localized radiotherapy.  We report patterns of miRNA expression in the metastatic and primary tumor samples that identify patients who failed to progress to widespread polymetastases. We created a model of oligometastases of human tumors in immune compromised mice.  The miRNA patterns of gene expression derived from patients accurately identified oligometastatic patterns in the mouse model as compared to animals that developed widespread metastases.  MiRNA signatures may identify patients most likely to benefit from aggressive curative treatment of limited metastatic disease.

Injection of MDA-MB-435-GFP cancer cells into the mammary fat pad of female athymic mice to develop spontaneous macroscopic lung metastasis. Tail vein experimental lung colonization assay was performed to model the development of MDA-MB-435-GFP Oligo- or Poly-metastases in the lung in vivo.

overall_design: Cell lines: Total RNA were derived from MDA-MB-435-L1-GFP (Ol-like) or MDA-MB-435-L1Mic (Poly-like) cell lines.

first: Rosie

middle: H

last: Xing

first: Yves

last: Lussier

first: Ralph

last: Weichselbaum


title: Effects of a short-term exposure to the fungicide prochloraz on endocrine function and gene expression in female fathead minnows (Pimephales promelas)

status: Public on Feb 03 2011

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

summary: Prochloraz is a fungicide known to cause endocrine disruption through effects on the hypothalamic-pituitary-gonadal (HPG) axis. To determine the short-term impacts of prochloraz on gene expression and steroid production, adult female fathead minnows (Pimephales promelas) were exposed to the chemical (0 or 300 μg/L) for a time-course of 6, 12 and 24 h. Consistent with inhibition of cytochrome P450 17α-hydroxylase/17,20-lyase (CYP17) and aromatase (CYP19), known molecular targets of prochloraz, plasma 17β-estradiol (E2) was reduced within 6 hours. Ex vivo E2 production was significantly reduced at all time-points, while ex vivo testosterone (T) production remained unchanged. Consistent with the decrease in E2 levels, plasma concentrations of the estrogen-responsive protein vitellogenin were significantly reduced at 24 h. Genes coding for CYP19, CYP17, and steroidogenic acute regulatory protein were up-regulated in a compensatory manner in ovaries of the prochloraz-treated fish. In addition to targeted quantitative real-time polymerase chain reaction analyses, a 15k feature fathead minnow microarray was used to determine gene expression profiles in ovaries. From time-point to time-point, the microarray results showed a relatively rapid change in the differentially expressed gene (DEG) profiles associated with the chemical exposure. Functional analysis of the DEGs indicated changes in expression of genes associated with cofactor and coenzyme binding (GO: 0048037 and 0050662), fatty acid binding (GO:0005504) and organelle organization and biogenesis (GO: 0006996). Overall, the results from this study are consistent with compensation of the fish HPG axis to inhibition of steroidogenesis by prochloraz, and provide further insights into relatively rapid, system-wide, effects of a model chemical stressor on fish.

overall_design:
RNA samples for each treatment/time point combination were used for microarray analysis (total of 23 arrays).  For the microarray work, total RNA was isolated from ovary samples using RNeasy kits (Qiagen, Valencia, CA, USA).  The RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and quantity was determined using a Nanodrop® ND-1000 spectrophotometer.  Total RNA was stored at -80oC until analyzed with oligonucleotide microarrays. Microarray analysis was conducted at the US Army Engineer Research and Development Center (Vicksburg, MS, USA) using a 15k feature fathead minnow microarray (GEO: http://www.ncbi.nlm.nih.gov/geo/; Accession platform number GPL9248) designed by Dr. Nancy Denslow (University of Florida, Gainesville, FL, USA) and manufactured by Agilent Technologies (Palo Alto, CA, USA). The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies) was used for microarray hybridizations. One µg of total RNA was used for all hybridizations. The cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer’s kits and protocols (Quick Amp Labeling kit; Agilent Technologies). An Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc., Sunnyvale, CA, USA) was used to scan microarray images at 5 μm resolution.  Data were resolved from microarray images using Agilent Feature Extraction software (Agilent Technologies).
Statistical analyses were conducted using Statistica 8 (StatSoft Inc., Tulsa, OK, USA) and GraphPad Instat v. 3.01 (GraphPad Software, San Diego, CA, USA). Data were tested for normality and homogeneity of variance. When data conformed to parametric assumptions, data were analyzed using a parametric one-way ANOVA with chemical treatment as the independent variable. When data did not conform to parametric assumptions, they were either transformed (log 10) or analyzed using a non-parametric Kruskall–Wallis test (p≤ 0.05). The data are presented as means with standard errors of the mean. Differences were considered significant at p ≤ 0.05.
Microarray data were imported into the Rosetta Resolver 7.2 system for gene expression analysis (Rosetta Biosoftware, Kirkland, WA, USA). Data were normalized using the default, text loader, intensity profile builder settings in the Rosetta Resolver system. Significantly DEGs were identified using one-way ANOVA (p < 0.01) with no multiple testing correction

first: Sarah

middle: Y

last: Skolness

first: Elizabeth

last: Durhan

last: Garcia-Reyero

first: Kathleen

middle: M

last: Jensen

last: Kahl

last: Makynen

first: Dalma

last: Martinovic-Weigel

first: Edward

last: Perkins

first: Daniel

middle: L

last: Villeneuve

first: Gerald

last: Ankley


title: Dual-species microarray for assessing gene expression in stromal microenvironment, cancer cells and their interactions

status: Public on Aug 04 2010

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Clock genes in human oral mucosa

status: Public on May 17 2010

first: Kay

last: Nieselt

address: Sand 14

institute: Institute for Bioinformatics and Medical Informatics

summary:
Circadian rhythms are daily oscillations of multiple biological processes driven by endogenous clocks. Imbalance of these rhythms has been associated with cancerogenesis in humans. To further elucidate the role of the circadian clock in cellular growth control, tumor suppression and cancer treatment, a standard of circadian gene regulations in healthy men is essential.
Comparative microarray analyses were conducted investigating the relative mRNA expression of clock genes throughout a 24-hour period in biopsies obtained from oral mucosa of eight healthy diurnally active male study participants.
A custom-designed oligo-based microarray which in addition to oncogenes and inflammatory genes contains probes for 20 clock genes and 70 clock-associated genes in human was used.
Keywords: Human gene expression study

overall_design: Reference design with Cy3 labeled uniRNA and Cy5 labeled sample RNA.

first: Derek

last: Zieker

first: Katharina

last: Buck

first: Isabel

last: Jenne


title: Autoregulation of fixK2 gene expression in Bradyrhizobium japonicum

status: Public on Jun 11 2010

city: Zürich

first: Hans-Martin

last: Fischer

address: Vladimir-Prelog-Weg 4

department: Microbiology

institute: ETH Zürich

summary: Expression data from B. japonicum bll2758::aphII strain (7414) grown micro-oxically. This study includes also the expression data of a fixK2 and a fixJ mutant grown in free-living micro-oxic condition (samples GSM313721 to GSM313734 in GEO record number GSE12491) and the wild type strain grown micro-oxically (samples GSM210246 to GSM210268 in GEO record number GSE8478).

overall_design: B. japonicum bll2758::aphII strain (7414) transcriptome was determined. This study includes also the expression data of a fixK2 and a fixJ mutant grown in free-living micro-oxic condition (samples GSM313721 to GSM313734 in GEO record number GSE12491) and the wild type strain grown micro-oxically (samples GSM210246 to GSM210268 in GEO record number GSE8478).

first: Luzia

last: Reutimann

first: Socorro

last: Mesa

first: Hauke

last: Hennecke


title: Dual-species microarray for assessing gene expression in stromal microenvironment, cancer cells and their interactions (v1 array)

status: Public on Jul 22 2010

first: Yong

last: Huang

summary: Design a human-mouse dual-species microarray to provide a technology for investigation of cancer-stromal interaction in xenograft model.

overall_design: Reference RNA from human and mouse were labeled using Cy5, while the mixture of human and mouse RNA were labeled using Cy3. Samples were hybridized on customized-commercial array with Agilent probes and user-designed species-specific probes (Human-mouse dual-species array HomoMusArray v1).

first: Xinan

last: Yang

first: Younghee

last: Lee

first: Rosie

last: Xing

first: Yves

last: Lussier


title: Expression differences between inversions and their progenitors in Drosophila melanogaster embryos

status: Public on May 05 2010

city: Cambridge

first: Lisa

last: Meadows

address: Downing Street

department: Department of Genetics

institute: University of Cambridge

summary: Inversions have a breakpoint within a "neighbourhood" of embryonically expressed genes and the other breakpoint megabases away. The gene expression neighbourhood is therefore intact in the progenitor but disrupted in the inversion.

overall_design: 1 progenitor stock and 1 inversion stock, 4 biological replicates for each, including 2 dye swaps.

first: Steve

last: Russell


title: Identifying genetic determinants needed to establish a human gut symbiont in its habitat

status: Public on Sep 16 2009

city: St. Louis

first: Andrew

last: Goodman

state: MO

address: Campus Box 8510, 4444 Forest Park Ave

department: Center for Genome Sciences

institute: Washington University School of Medicine

summary:
The human gut microbiota is a metabolic organ whose cellular composition is determined by a dynamic process of selection and competition. To identify microbial genes required for establishment of human symbionts in the gut, we developed an approach (insertion-sequencing, or INSeq) based on a mutagenic transposon that allows capture of adjacent chromosomal DNA to define its genomic location. We used massively parallel sequencing to monitor the relative abundance of tens of thousands of transposon mutants of a saccharolytic human gut bacterium, Bacteroides thetaiotaomicron, as they established themselves in wild-type and immunodeficient gnotobiotic mice, in the presence or absence of other human gut commensals.  In vivo selection transforms this population, revealing functions necessary for survival in the gut: we show how this selection is influenced by community composition and competition for nutrients (vitamin B12). INSeq provides a broadly applicable platform to explore microbial adaptation to the gut and other ecosystems.

Keywords: Other

overall_design: 57 samples analyzed, 1 of these is the reference (input) sample

first: Jeffrey

last: Gordon