title: A novel non-coding RNA within WHSC1 is over-expressed in t(4;14)-positive multiple myeloma and other cancers

city: St. Louis

first: Mack

last: Su

state: Missouri

address: 660 South Euclid Avenue

institute: Washington University in St. Louis School of Medicine

type: Non-coding RNA profiling by genome tiling array

summary: We designed oligonucleotide tiling arrays spanning the t(4;14) breakpoint region on chromosome 4 to identify additional oncogenic RNAs in an unbiased fashion.

overall_design: Four (4) multiple myeloma bone marrow samples with t(4;14) and twelve (12) MM BM samples without t(4;14) were analyzed. Furthermore, seven (7) bladder (1 normal, 6 malignant), eight (8) colon (1 normal, 7 malignant) and eight (8) esophagus (2 normal, 6 maligant) tissue samples were analyzed. Finally, five (5) multiple myeloma cell line samples with t(4;14) - three (3) of LP-1 and two (2) of H929 - and three (3) MM cell line samples and three (3) non-MM cell line samples without t(4;14) - three (3) of U266 and three (3) of Hela - were analyzed.

first: Liang

last: Chu

middle: Y

first: Leonard

middle: B

last: Maggi Jr.

first: Lan

last: Lu

first: Chelsea

last: Mullins

first: Seth

last: Crosby

first: Gaofeng

last: Huang

first: Wee-Joo

last: Chng

first: Ravi

last: Vij

middle: H

last: Tomasson


title: Non-small-cell lung tumor and normal lung tissue methylation

status: Public on Jul 03 2012

city: Hanover

first: Brock

middle: Clarke

last: Christensen

state: NH

address: 7650 Remsen

country: USA

institute: Dartmouth Medical School

summary: Using paired tumor and non-tumor lung tissues from 47 individuals we identified common changes in DNA methylation associated with the development of non-small cell lung cancer. Pathologically normal lung tissue taken at the time of cancer resection was matched to tumorous lung tissue and together were probed for methylation status using Illumina GoldenGate arrays. For each matched pair the change in methylation at each CpG was calculated (the odds ratio), and these ratios were averaged across individuals and ranked by magnitude to identify the CpG’s with the greatest change in methylation associated with tumor development.

first: Heather

last: Nelson

middle: C

first: Karl

middle: T

last: Kelsey


title: Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation

status: Public on Jul 01 2012

city: Tallahassee

first: Benjamin

last: Pope

state: FL

address: 319 Stadium Dr

department: Biological Science

institute: Florida State University

type: Genome variation profiling by genome tiling array

summary: The expansion of repressive epigenetic marks has been implicated in heterochromatin formation during embryonic development, but the general applicability of this mechanism is unclear. Here we show that nuclear rearrangement of repressive histone marks H3K9me3 and H3K27me3 into non-overlapping structural layers characterizes senescence-associated heterochromatic foci (SAHF) formation in human fibroblasts. However, the global landscape of these repressive marks remains unchanged upon SAHF formation, suggesting that in somatic cells heterochromatin can be formed through the spatial repositioning of pre-existing repressively marked histones. This model is reinforced by the correlation of pre-senescent replication timing with both the subsequent layered structure of SAHFs and the global landscape of the repressive marks, allowing us to integrate microscopic and genomic information. Furthermore, modulation of SAHF structure does not affect the occupancy of these repressive marks nor vice versa. These experiments reveal that high-order heterochromatin formation and epigenetic remodeling of the genome can be discrete events.

overall_design: Profile comparison of normal growing (control) and Ras-induced senescent IMR90 cells.

middle: D

first: Tamir

last: Chandra

first: M

last: Nakao

last: Narita


title: Affymetrix SNP-array data for 2 ETV6/RUNX1-positive Acute Lymphoblastic Leukemia samples and corresponding normal samples

city: Lund

first: Henrik

last: Lilljebjörn

address: Lund University Hospital

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

summary: Acute lymphoblastic leukemia (ALL), the most common malignant disorder in childhood, is typically associated with numerical chromosomal aberrations, fusion genes or small focal deletions, thought to represent important pathogenetic events in the development of the leukemia. Mutations, such as single nucleotide changes, have also been reported in childhood ALL, but these have only been studied by sequencing a small number of candidate genes. Herein, we report the first unbiased sequencing of the whole exome of two cases of pediatric ALL carrying the ETV6/RUNX1 (TEL/AML1) fusion gene (the most common genetic subtype) and corresponding normal samples. A total of 14 somatic mutations were identified, including four and seven protein-altering nucleotide substitutions in each ALL. Twelve mutations (86%) occurred in genes previously described to be mutated in other types of cancer, but none was found to be recurrent in an extended series of 29 ETV6/RUNX1-positive ALLs. The number of single nucleotide mutations was similar to the number of copy number alterations as detected by single nucleotide polymorphism arrays. Although the true pathogenetic significance of the mutations must await future functional evaluations, this study provides a first estimate of the mutational burden at the genetic level of t(12;21)-positive childhood ALL.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from 2 leukemic bone marrow samples and two corresponding normal blood samples.

first: Thoas

last: Fioretos


title: Transcriptome Microarray Gene Expression Analysis of Heliconius butterfly forewing and hindwing tissues across pupal development reveals genes underlying wing pattern variation

city: Raleigh

last: Hines

state: NC

address: Campus Box 7614

department: Genetics

institute: North Carolina State University

type: Expression profiling by genome tiling array

summary: Heliconius butterfly wing pattern diversity offers a unique opportunity to investigate how natural genetic variation can drive the evolution of complex adaptive phenotypes. Here we took a large-scale transcriptomic approach to identify the network of genes involved in Heliconius wing pattern development and variation. This included applying 147 microarrays representing the Heliconius transcriptome to assay shifts in gene expression across pupal development among several wing pattern morphs of Heliconius erato. We focused in particular on genes differentially expressed relative to the gene optix, which controls red pattern elements in wings. We combined expression results from three hindwing morphs from Peru and from dissected basal to apical wing elements in two forewing morphs to uncover two main classes of genes. First we looked for candidate upstream regulators of optix by determining transcripts expressed differently across basal to apical sections of the forewing prior to optix expression. Second, we assessed how optix regulates downstream gene expression by targeting transcripts with differential expression similar to optix, where expression differs among red wing pattern elements of both the forewing and hindwing.

sample_organism: Heliconius erato etylus x Heliconius himera

overall_design: This study is an analysis of two distinct datasets generated using the same microarray platform. One dataset involved comparative analysis of forewing sections of different color morphs, while the other compared whole hindwings with different color patterns. For the forewing analysis we compared proximal, medial, and distal wing sections of two color pattern morphs: H. erato petiverana and a hybrid H. himera x H. erato etylus. The proximal section in H. erato petiverana is black and the hybrid form orange/red, the medial section is red in H. erato petiverana and pale yellow in the hybrid form, and the distal section is black in both races. For the hindwing analysis, we compared hindwing color pattern gene expression in three races that meet in a hybrid zone in Peru. H. erato emma has a rayed hindwing, H. erato favorinus has a yellow-barred hindwing, and H. erato amphritrite has a black hindwing. Wings were dissected at five time intervals: 1, 3, and 5 days after pupation, when orange/red ommochrome pigments were beginning to be expressed (~7 days after pupation), and when black melanin pigments were starting to pepper the center of the wings (~8 days after pupation). In the forewings, Days 1, 3, and 5 were at 12, 36, and 60 hours post-pupation. In the hindwings these stages were sampled at 24, 48, and 72 hours. Samples hybridized to microarrays included three replicates each of each race, stage, and wing section for forewings (3 replicates x 2 morphs x 3 wing sections x 5 stages, with one replicate wing missing for Day 1 H. e. petiverana = 87 samples) and four replicates of each stage and race for hindwings (4 replicates x 3 races x 5 stages = 60 samples). Total RNA was extracted and converted to cDNA. Cy3-labeling of samples, hybridization, and array scanning was performed according to NimbleGen protocols (2008): for the forewings this was performed at the City of Hope Functional Genomics Core, while the hindwings were run separately at NCSU.Samples were hybridized to NimbleGen HD2 12-plex arrays. These arrays include 12 identical subarrays with 135,000 60 bp probes each, each hybridizing a separate sample. Samples were distributed across arrays to prevent repeat conditions as much as possible and to space similar conditions in different regions of the slide. The array design involved two classes of probes. First there was a tiling component involving 89,310 probes tiled across three genomic intervals. Results from the tiling data were used for the initial discovery of the optix gene and are not the focus of the present study. The second component involved a representation of a set of 12,450 transcript contigs at 1-6X coverage for a total of 40,046 probes, with a mean coverage of 3-4 probes per contig. The number of probes for each contig depended on the ability to create suitable probes according to NimbleGen probe selection criteria and was limited by the small size of some transcripts and the minimum spacing criterion of 15 bp apart. Sequences of low complexity and high repeats with the rest of the genome (>5X representation), determined by comparison against 1.6 MB of genomic sequence available at the time, were avoided for designing probes. An additional 3,248 random probes were placed on the array for quality control.

middle: M

first: Riccardo

last: Papa

first: Robert

last: Reed

first: W

middle: O

last: McMillan


title: The gene responses of the rice plant treated with both continuous simulated acid fog (pH3.0) and natural fog (pH5.6) treatments

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

country: Japan

institute: NARO/HARC

summary: Rice plants cultivated on mountain areas are frequently exposed to acid fog and natural fog events. In this report, we analyzed the expression profiles of the rice plant with acid fog (SiAF) or neutral fog (SiNF) treatment for 1 and 7 days. Microarray results suggested that ROS generation was induced by not only SiAF, but also SiNF treatment, and it occurred in apoplast, not in organelles. Genes for defense- and stress-responses was also induced by both SiAF and SiNF treatments. The induction occurred in plants treated with SiAF for both 1 day and 7 days, and it was also detected in plants treated with SiAF for 7 days. These results suggest that both SiAF and SiNF treatments are abiotic stresses accompanying ROS generation in apoplast.

overall_design:
Comparison between continuous fog treated shoots and control shoots.
Biological replicates: 3 simulated acid fog (pH 3.0) treated (SiAF) for 1 day; 3 simulated acid fog (pH 3.0) treated (SiAF) for 7 days; 3 simulated neutral fog (SiNF) treated for 1 day; 3 simulated neutral fog (SiNF) treated for 7 days; 3 controls for 1 day; 3 controls for 7 days.
Independently grown and harvested.
Cultivar: Hinohikari
1 sample derived from 5 plants grown under the same conditons.
Total: 18 samples, 12 comparisons.

first: Shoko

last: Saji

last: Ito

first: Hideyuki

last: Shimizu

first: Shoshi

last: Kikuchi

first: Hikaru


title: Detection of copy number variations in rice using array-based comparative genomic hybridization

city: Hangzhou

first: Ping

last: Yu

state: Zhejiang Province

address: 359 Tiyuchang Road

department: Rice Germplasm Evaluation

country: China

institute: China National Rice Research Institute

summary:
Copy number variations (CNVs) can create new genes, change gene dosage, reshape gene structures, and modify elements regulating gene expression. As with all types of genetic variation, CNVs may influence phenotypic variation and gene expression. CNVs are thus considered major sources of genetic variation. Little is known, however, about their contribution to genetic variation in rice.
To detect CNVs, we used a set of NimbleGen whole-genome comparative genomic hybridization arrays containing 715,851 oligonucleotide probes with a median probe spacing of 500 bp. We compiled a high-resolution map of CNVs in the rice genome, showing 641 CNVs between the genomes of the rice cultivars ‘Nipponbare’ (from O. sativa ssp. japonica) and ‘Guang-lu-ai 4’ (from O. sativa ssp. indica).  These CNVs contain some known genes. They are linked to variation among rice varieties, and are likely to contribute to subspecific characteristics.

overall_design: Genomic DNA isolated from Nipponbare and Guang-lu-ai 4. Cy5 labeled DNA from Nipponbare used as reference and Cy3 labeled DNA from Guang-lu-ai 4 was hybridized to the 720K rice tiling array including three replicates. Fluorescence intensity data were normalized with qspline algorithm and ratio data were analyzed with the circular binary segmentation algorithm. Copy number variation calls were made if the averaged Log2 ratio of a segment was shifted by 1.0 from the baseline.

first: Xing-Hua

last: Wei


title: ETS2 and Mesp1 trans-differentiate human dermal fibroblasts into cardiac progenitors

city: Houston Road

middle: Joel

last: Schwartz

state: Texas

address: 4800 Calhoun

department: Biology and Biochemistry

institute: University of Houston

summary:
We explored the role of mammalian ETS1/2 and Mesp homologues of cardiogenic transcription factors of Ciona intestinalis, to convert primary human dermal fibroblasts into cardiac progenitors. ETS1/2 and Mesp homologues of cardiogenic transcription factors of Ciona intestinalis, to convert primary human dermal fibroblasts into cardiac progenitors. Here we show murine Ets2 has an obligatory role for directing cardiac progenitors during cardiopoesis in embryonic stem cells. ETS2 converted fibroblasts into KDR/Flk1+ replicative cells but, like the purported cardiac master regulatory gene Mesp1, could not by itself generate cardiac progenitors de novo from fibroblasts. Co-expression of both Ets2 and Mesp1, however, successfully reprogrammed differentiated fibroblasts into cardiac progenitors, as shown by the de novo appearance of core cardiac transcription factors, gap junction proteins, sarcomeric proteins, electrical activity and contractility. ETS2 and Mesp1 sit at the pinnacle of the cardiopoesis regulatory hierarchy and are well suited for treating human heart disease.
Co-expression of both Ets2 and Mesp1, reprogrammed differentiated fibroblasts into cardiac progenitors

overall_design: All sample were done in triplicates, controls were NHDF and ETS2 only infected cells. NHDF were first infected with Doxycyline redulated (Doxy-) ETS2 lentivirus and supplemented with doxycycline for 1 week, sequentially cells were infected with Doxy-Mesp1 and treated for 1 more week. Cells were then aggegated to form EB and hangdrop for 1 week, at the end of that period cells were plated and samples were taken every 24 hrs

first: Jose

middle: F

last: Islas

first: Yu

last: Liu

first: Kuo-Chan

last: Weng

first: Shuxing

last: Zhang

first: Allan

last: Prejusa

first: John

last: Harger

first: Ashley

last: Benham

first: Tsuey-Ming

last: Chen

first: Dinakar

last: Iyer

first: Yutao

last: Xi

first: Mark

last: Mercola

last: Oshima

first: Preethi

last: Gunaratne

first: James

last: Willerson

first: Vladimir

last: Potaman

middle: J


title: Gene expression based analysis of Streptococcus uberis 0140J and vru (sub0144) mutant

city: Sutton Bonington

first: Sharon

last: Egan

state: Leicestershire

address: Sutton Bonington Campus

department: School of Veterinary Medicine and Sciences

country: United Kingdom

institute: University of Nottingham

summary:
Comparison of bacterial strains S. uberis 0140J with isogenic mutant (same strain) with lesion 5 basepairs upstream of ATG start codon of the vru or sub0144 gene. Bacteria were grown in stationary culture in THB media at 37C with triplicate samples extracted at early exponential (OD550 =0.42) at late exponential (OD550 =0.75) phases of growth
Microarray analysis performed on custom made S. uberis 0140J array containing 3780 features of 60mer oligonucleotides in triplicate with two probes for each individual gene

overall_design: We investigated the role of Vru in vivo and the effect of its absence on transcriptional control of gene expression using a custom designed genome-wide microarray performed on custom made S. uberis 0140J array containing 3780 features  in triplicate with two probes for each individual gene. Triplicate samples analysed in loop design with Cy5 and Cy3 dye swap performed and gene expression compared at two difference phases of bacterial growth

middle: A

last: Leigh


title: Study of Cj1501 function in Campylobacter jejuni

status: Public on Jul 02 2012

city: Norwich

first: Bruce

middle: MacKenzie

last: Pearson

state: Norfolk

address: Colney Lane

department: Food Safety

institute: Institute of Food Research

summary: In order to study the function of the Campylobacter jejuni Cj1501 gene, a series of experiments were carried out. Three strains were constructed: a Cj1501 knockout strain, a strain where the Cj1501 knockout was complemented in trans, and a strain with a second copy over-expressing Cj1501 from an fdxA promoter. The transcriptomes of these were all compared to the wild-type strain. The arrays are all from RNA isolated in mid-exponential growth from independent biological replicates.

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

overall_design:
Batch cultures of Campylobacter jejuni NCTC 11168 were grown in 50 ml volumes of Brucella broth in 70cm tissue culture flasks. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (5% Oxygen, 10% Carbon dioxide, 85% Nitrogen) from Don Whitley Scientific, Ltd which also maintained the growth temperature at 37 ºC. RNA was extracted from C. jejuni cultures grown to an OD600 of approximately 0.4. Briefly, 0.1 volume of 5% phenol in ethanol was mixed with the broth culture, and after centrifugation RNA was isolated with Tri Reagent (Sigma) and chloroform. RNA was further purified using the RNeasy kit (Qiagen) according to the manufacturer’s instructions. The RNA was treated with Turbo DNA-free (Ambion) to remove any residual DNA according to the manufacturer’s instructions. RNA concentration was determined using the Nanodrop Spectrophotometer NS-1000 (Thermo Scientific).

Two or three independent RNA preparations (biological replicates) of each sample type were labelled and hybridized to custom-designed Agilent microarrays. Equal quantities of RNA from test and control cultures were labelled by using nucleotide homologues of dUTP containing either Cy3 or Cy5 fluorescent dye (Perkin Elmer). For each microarray slide, the test strain was labelled with Cy3-dUTP, while the wild-type sample was labelled with Cy5-dUTP. RNA (15 µg) was primed with 5 µg pd(N)6 random hexamers (Amersham Biosciences). The Affinity Script kit (GE Healthcare) was used to produce cDNA, and hybridized (Agilent Hi-RPM Gene Expression Hybridization Kit) to the microarray slide according to the manufacturer’s instructions. Microarrays were scanned at 5 µm using an Axon 4000A scanner, and images were acquired using GenePix Pro 3.0 software (Axon).

Related analysis reference: Holmes K., Mulholland F., Pearson B. M., Pin C., McNicholl-Kennedy J., Ketley J. M., Wells J. M. (2005) Campylobacter jejuni gene expression in response to iron limitation and the role of Fur Microbiology-SGM 151 243-257 (PMID 15632442).

first: Francis

middle: L

last: Shaw

first: Frances

last: Mulholland

first: Gwenaelle

last: Le Gall

first: Ida

last: Porcelli

first: Arnoud

last: van Vliet


title: Changes in rice NILs panicle expression profile in response to drought stress at reproductive stage

first: Kouji

last: Satoh

summary: The current knowledge of drought stress transcriptomes in rice are mostly relying on comparative studies of diverse genetic background under drought. A more reliable approach is to use near-isogenic lines (NILs) with a common genetic background (Donar parent: Aday Sel, Recurrent parent: IR64),  but contrasting levels of resistance to drought stress under initial exposure to water deficit. Here, we examined two pairs of NILs in IR64 background with contrasting drought tolerance. We obtained gene expression profile in panicles of rice NILs under different levels of drought stress help to identify genes and mechanisms involved in drought stress.

overall_design: Comparison between drought and well-watered panicle.   Biological replicates: 3 (0.2FTSW (Fraction of transpirable soil water)-treated: 3, 0.5FTSW-treated: 3, 1.0FTSW-treated (control): 3).  Independently grown and harvested.  Genotypes: 5 (Drought resistant: IR77298-14-1-2-B-10, IR77298-5-6-B-18, Drought susceptive: IR77298-14-1-2-B-13, IR77298-5-6-B-11, IR64)  1 samples derived from 5 plants grown under same conditons.  Total 45 samples, 30 data

first: Ali

last: Moumeni

first: Ramaiah

last: Venuprasad

first: Somayanda

last: Impa

first: Rachid

last: Serraj

first: Arvind

last: Kumar

first: Hei

last: Leung

first: Shoshi

last: Kikuchi


title: Changes in rice NILs root expression profile in response to drought stress at reproductive stage

summary: The current knowledge of drought stress transcriptomes in rice are mostly relying on comparative studies of diverse genetic background under drought. A more reliable approach is to use near-isogenic lines (NILs) with a common genetic background (Donar parent: Aday Sel, Recurrent parent: IR64),  but contrasting levels of resistance to drought stress under initial exposure to water deficit. Here, we examined two pairs of NILs in IR64 background with contrasting drought tolerance. We obtained gene expression profile in roots of rice NILs under different levels of drought stress help to identify genes and mechanisms involved in drought stress.

overall_design: Comparison between drought and well-watered roots.   Biological replicates: 3 (0.2FTSW (Fraction of transpirable soil water)-treated: 3, 0.5FTSW-treated: 3, 1.0FTSW-treated (control): 3).  Independently grown and harvested.  Genotypes: 5 (Drought resistant: IR77298-14-1-2-B-10, IR77298-5-6-B-18, Drought susceptive: IR77298-14-1-2-B-13, IR77298-5-6-B-11, IR64)  1 samples derived from 5 plants grown under same conditons.  Total 45 samples, 30 data


title: Transcript Profiling of the Common Bean - Rhizobium Symbiosis under Oxidative Stress

city: Cuernavaca

first: Mario

last: Ramírez

state: Morelos

address: Avenida Universidad S/N

department: Functional Genomics of Eukaryotes

country: Mexico

institute: Centro de Ciencias Genomicas-UNAM

summary: A wide range of environmental stresses lead to an elevated production of reactive oxygen species (ROS) in plant cells thus resulting in oxidative stress. The biological nitrogen fixation in the legume - Rhizobium symbiosis is at high risk of damage from oxidative stress. Common bean (Phaseolus vulgaris) active nodules exposed to the herbicide Paraquat (1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate) that generates ROS accumulation, showed a reduced nitrogenase activity and ureide content. We analyzed the global gene response of stressed nodules using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST). A total of 4,280 ESTs were differentially expressed in oxidative stressed bean nodules; of these 2,218 were repressed. These genes were grouped in 44 different biological processes as defined by Gene Onthology. Analysis with the PathExpress bioinformatic tool, adapted for bean, identified five significantly repressed metabolic path

platform_organism:
Glycine max
Phaseolus vulgaris

overall_design: This work presents the transcriptional profile of bean nodules, induced by strain Rhizobium tropici CIAT 899, under oxidative stress, generated experimentally by adding the herbicide Paraquat (1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate) for 48 hours. We analyzed the transcript profile, via microarray hybridization, using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST). A total of 4,280 ESTs were differentially expressed in oxidative stressed bean nodules; of these 2,218 were repressed.

first: Roberto

last: Ferrarini

first: Francesca

last: Sparvoli

first: Bianca

last: Castiglioni

first: Paola

last: Cremonesi

first: Dario

last: Panzeri

first: Alessandra

last: Stella

first: Francesco

last: Strozzi

first: Georgina

last: Hernández


title: High-throughput RT-PCR analysis of Colon Adenocarcinoma Stem Cell Lines

city: New York

first: Zeynep

middle: H.

last: Gumus

state: NY

address: 1300 York Ave

department: Physiology and Biophysics

institute: Cornell University

summary: Human early stage colon adenocarcinoma stem cell line was FACS-sorted for CCR9- and CCR9+ cell groups and differential expression was identified via Wafergen SmartChip

overall_design: RT-PCR gene expression profiling. CCR9- and CCR+ cells were FACS-sorted. 24 hours afterwards, cells were treated with 100ng/ml human CCL25 for 30 min. RNA was extracted from both populations using PureLink RNA Mini kit (Invitrogen) and analyzed using the SmartChip Real-Time PCR System

first: Joyce

last: Chen

first: Robert

last: Edwards

first: Serena

last: Tucci

first: Pengcheng

last: Bu

first: Jeff

last: Milsom

first: Sang

last: Lee

first: Winfried

last: Edelmann

last: Gümüş

first: Xiling

last: Shen

first: Steven

last: Lipkin


title: Gene expression dynamics in yeast BY4741 and a strain lacking MSN2 and MSN4 responding to 0.4mM H2O2 over time (0-60min)

status: Public on Jun 18 2012

city: Madison

first: Dana

last: Huebert

state: WI

address: 425G Henry Mall

institute: University of Wisconsin-Madison

summary: Numerous factors have been implicated in regulating gene expression changes, including changes to nucleosome occupancy.  Here we followed dynamic changes to nucleosome occupancy, gene expression and DNA binding of the transcription factor Msn2p genome-wide in yeast cells responding to hydrogen peroxide and reveal new relationships between regulators of stress-dependent gene expression in yeast.

overall_design: Gene expression was measured in response to 0.4mM H2O2 in the S288c derivative BY4741 in wild-type cells and cells lacking MSN2 and MSN4. A single replicate of a time course spanning from 4 to 60 minutes after treatment in each cell type.  An additional 3 repliactes were collected from cells 30 minutes after treatment.

first: Audrey

middle: P

last: Gasch


title: Nucleosome occupancy in yeast BY4741and a strain lacking MSN2 and MSN4 responding to 20 min treatment with 0.4mM H2O2

type: Genome binding/occupancy profiling by genome tiling array

overall_design: Nucleosome occupancy was measured in the S288c derivative BY4741 and a strain lacking MSN2 and MSN4. Nucleosomes were isolated from unstressed yeast and yeast treated for 20 min with 0.4mM H2O2.  Nucleosomal samples were compared in a 2-color, competitive hybridization to sheared genomic DNA.


title: Msn2p occupancy dynamics in yeast BY4741 responding to 0.4mM H2O2 over time (0-60 min)

summary: Numerous factors have been implicated in regulating gene expression changes, including changes to nucleosome occupancy.  Here we followed dynamic changes to nucleosome occupancy, gene expression and DNA binding of the transcription factor Msn2p genome-wide in yeast cells responding to hydrogen peroxide. and reveal new relationships between regulators of stress-dependent gene expression in yeast.

overall_design: Msn2p occupancy was measured in response to 0.4mM H2O2 in the S288c derivative BY4741 with an integrated myc-tagged Msn2p.  A single replicate of the time course was performed with time points at 0, 4, 12, 20, 40 and 60 minutes after treatment.


title: Whole-genome gene expression level changes in P19.6 mouse embryonal carcinoma cells compared to P19.6 cells treated for 48 hours with all-trans retinoic acid

status: Public on Jun 04 2012

city: Rennes

first: Aurelien

last: Serandour

address: Bâtiment 13, Campus de Beaulieu

department: UMR CNRS 6290

country: France

institute: Université de Rennes 1

summary: Enhancers are developmentally-controlled transcriptional regulatory regions whose activities are modulated through histone modifications or histone variant deposition. Here, we show by genome-wide mapping that the newly discovered DNA modification 5-hydroxymethylcytosine (5hmC) is dynamically associated with transcription factor binding to distal regulatory sites during neural differentiation of mouse P19 cells as well as during adipocyte differentiation of mouse 3T3-L1 cells. Functional annotation reveals that regions gaining 5hmC are associated with genes expressed either in neural tissues when P19 cells undergo neural differentiation or in adipose tissue when 3T3-L1 cells undergo adipocyte differentiation. Furthermore, distal regions gaining 5hmC together with H3K4me2 and H3K27ac in P19 cells behave as differentiation-dependent transcriptional enhancers. Identified regions are enriched in motifs for transcription factors regulating specific cell fates like Meis1 in P19 cells and PPARgamma in 3T3-L1 cells. Accordingly, a fraction of hydroxymethylated Meis1 sites were associated with a dynamic engagement of the 5mC hydroxylase Tet1. In addition, kinetic studies of cytosine hydroxymethylation of selected enhancers indicated that DNA hydroxymethylation is an early event of enhancer activation. Hence, acquisition of 5hmC in cell-specific distal regulatory regions may represent a major event of enhancer progression toward an active state and participate in selective activation of tissue-specific genes

overall_design: A 6-chip study aiming to characterize regulated genes in P19.6 mouse embryonal carcinoma cells following 48 hours treatment with 1µM all-trans retinoic acid. RNAs were prepared from three independent triplicate experiments.

first: Aurélien

last: Sérandour


title: Comparative transcriptional analysis of bacillus subtilis cells overproducing either secreted proteins, lipoproteins or membrane proteins

status: Public on May 25 2012

city: Groningen

first: Bogumila

last: Marciniak

address: Nijenborgh 7

department: Department of Genetics

country: Netherlands

institute: Rijksuniversiteit Groningen

summary:
Background. Bacillus subtilis is a favorable host for the production of industrially relevant proteins because of its capacity of secreting proteins into the medium to high levels, its GRAS (Generally Recognized As Safe) status, its genetic accessibility and its capacity to grow in large fermentations. However, production of heterologous proteins still faces limitations.
Results. This study aimed at the identification of bottlenecks in secretory protein production by analyzing the response of B. subtilis at the transcriptome level to overproduction of eight secretory proteins of endogenous and heterologous origin and with different subcellular or extracellular destination: secreted proteins (NprE and XynA of B. subtilis, Usp45 of Lactococcus lactis, TEM-1beta -lactamase of Escherichia coli), membrane proteins (LmrA of L. lactis and XylP of Lactobacillus pentosus) and lipoproteins (MntA and YcdH of B. subtilis). Responses specific for proteins with a common localization as well as more general stress responses were observed. The latter include upregulation of genes encoding intracellular stress proteins (groES/EL, CtsR regulated genes). Specific responses include upregulation of the liaIHGFSR operon under Usp45 and TEM-1 beta-lactamase overproduction; cssRS, htrA and htrB under all secreted proteins overproduction; sigW and SigW-regulated genes mainly under membrane proteins overproduction; and ykrL (encoding an HtpX homologue) specifically under membrane proteins overproduction.
Conclusions. The results give better insights into B. subtilis responses to protein overproduction stress and provide potential targets for genetic engineering in order to further improve B. subtilis as a protein production host.

overall_design: Samples for transcriptome analyses were induced at the exponential-growth phase (OD600 = 0.7) with 0.1% subtilin (subtilin containing supernatant of subtilin producing B. subtilis strain ATCC 6633). Cells were harvested 30 min after induction. Three or four independent cultures of each strain (target strains and controls) were used, and cells were sampled for microarray experiment.

first: Bogumiła

first: Hein

last: Trip

first: Patricia

last: van der Veek

first: Oscar

last: Kuipers


title: H. salinarum transcriptome dynamics in response to 0.85mM extracellular copper

status: Public on Jun 30 2012

city: Seattle

first: Wyming

middle: Lee

last: Pang

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Halobacterium salinarum is a halophillic archea that is capable of sustaining growth despite dramatic changes to the concentration of ions in its extracellular environment.  Here we studied H. salinarum's specific adaptation response to the transition metal copper.

overall_design: Analysis utilized pre-treatment (time < 0min) samples as controls for all subsequent timepoints.  Time course samples were taken at +0, 5, 10, 20, 40, 80, 160, and 320min post treatment.  Interarray comparisons were normalized relative to a reference RNA sample generated from unperturbed H. salinarum batch culture in rich medium at OD600 0.6-0.8.

first: Amardeep

last: Kaur

first: Alexander

middle: V

last: Ratushny

first: Aleksandar

last: Cvetkovic

first: Sunil

last: Kumar

first: Min

last: Pan

first: Adam

last: Arkin

first: John

last: Aitchison

first: Michael

middle: W

last: Adams

first: Nitin

middle: S

last: Baliga


title: Identification of target genes of ABI3 [Agilent 2x244k]

status: Public on Jun 01 2012

city: Gatersleben

first: Gudrun

last: Moenke

address: Corrensstr. 3

country: Germany

institute: IPK

summary: ABI3 is a key regulator of seed development in Arabidopsis and other plants.To identify DNA fragments(promoters) bound by ABI3 we performed array based ChIP analysis.

overall_design: Two ChIP experiments were performed with chromatin of seeds of Arabidopsis and an anti-ABI3 antibody directed against a N-terminal fragment of ABI3, raised in rabbits. Non precipitated chromatin (input) served as control.

first: Urs

last: Haehnel

last: Seifert

first: Lothar

last: Altschmied


title: Functional inactivation of Thyroid Transcription Factor-1 in PCCl3 thyroid cells

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

summary:
Thyroid Transcription Factor-1 (TTF-1) is a key regulator of thyroid development and function. In order to identify the genes whose expression depends on TTF-1 transcriptional activity within the thyrocyte we analyzed the consequence of the functional inactivation of this factor in PCCl3 cells.
The expression of a fusion protein composed of the DNA binding domain of TTF-1 and of the strong repressive domain of the Engrailed protein (Engr HD) resulted in a dramatic loss of epithelial cell morphology and in proliferation arrest. These changes were reversed when the inhibition of endogenous TTF-1 was relieved. No change was observed when a similar fusion protein containing point mutations abolishing DNA binding activity (Engr HDm) was produced in the cells.

overall_design:
Microarrays hybridizations were performed on PCCl3 cells expressing a TTF1 antagonist (Engr HD –Dox) versus non-expressing cells (Engr HD +Dox), and on cells expressing the control protein (Engr HDm – Dox) versus non-expressing cells (Engr HDm + Dox).
After amplification and labelling, sample pairs were hybridized onto Rat MI ReadyArray (Microarrays Inc., Alabama USA). The oligonucleotides set consists of 34,717 70-mer transcript probes representing genes and alternative splice products from the Operon Biotechnologies' Array Ready Oligo Set version 3.0 for Rattus norvegicus. Hybridizations were replicated with dye swap.

first: Christiane

last: Christophe-Hobertus

first: Anne

last: Lefort

first: Frédérick

first: Daniel

last: Christophe


title: Abnormal Wnt and PI3Kinase signaling in the malformed intestine of lama5 deficient mice

city: Illkirch

first: Bernard

last: Jost

address: 1, rue  Laurent Fries

institute: IGBMC

summary: Laminins are major constituents of basement membranes and are essential for tissue homeostasis. Laminin-511 is highly expressed in the intestine and its absence causes severe malformation of the intestine and embryonic lethality. To understand the mechanistic role of laminin-511 in tissue homeostasis, we used RNA profiling of embryonic intestinal tissue of lama5 knock out mice combined with cell culture experiments and siRNA mediated knock down and identified a lama5 specific gene expression signature. Our data provide a mechanistic link between laminin alpha5 gene deficiency and the physiological phenotype. We show that laminin alpha5 plays a crucial role in both epithelial and mesenchymal cell behavior by regulating Wnt and PI3K signaling. We provide evidence that a laminin-511 substratum prevents chemical-induced apoptosis in a PI3K-dependent manner and that laminin-511 represses Wnt signaling. We conclude that conflicting signals are elicited in the absence of lama5, which alter cell adhesion, migration as well as epithelial and muscle differentiation. Conversely, adhesion to laminin-511 may serve as a potent regulator of the PI3K/Akt and Wnt signaling pathways that are interconnected. Thus deregulated adhesion to laminin-511 may be instrumental in diseases such as human pathologies of the gut where laminin-511 is abnormally expressed.

overall_design:
The microarray experiments were performed in quadruple with independently prepared RNA from mutant (Laminin alpha5-deficient mouse) and wild-type embryonic intestines derived from 4 different litters.
For each RNA sample, a dye-swap labeling and hybridization was performed using a common reference RNA sample corresponding to 15.5-day embryonic intestines of C57B1/6J mice.

first: Léa

last: Ritié

first: Caroline

last: Spenlé

first: Joël

last: Lacroute

first: Anne-Laure

last: Bolcato-Bellemin

first: Olivier

last: Lefebvre

first: Christine

last: Bole-Feysot

first: Annick

last: Klein

first: Michèle

last: Kedinger

first: Dominique

last: Bagnard

first: Gertraud

last: Orend

first: Patricia

last: Simon-Assmann


title: Human cerebrospinal fluid autoantibody lipid microarray profiling (Fig. 2C)

status: Public on May 09 2012

city: Stanford

first: William

last: Robinson

state: CA

address: 269 Campus Drive

institute: Stanford University

summary: Lipids comprise 70% of the myelin sheath, and autoantibodies against lipids may contribute to the demyelination that characterizes multiple sclerosis (MS). We used lipid antigen microarrays and lipid mass spectrometry to identify bona fide lipid targets of the autoimmune response in MS brain and an animal model of MS to explore the role of the identified lipids in autoimmune demyelination. We found that autoantibodies in MS target a phosphate group in phosphatidylserine and oxidized phosphatidylcholine derivatives. Administration of these lipids ameliorated experimental autoimmune encephalomyelitis by suppressing activation and inducing apoptosis of autoreactive T cells, effects mediated by the lipids' saturated fatty-acid side chains.  Thus, phospholipids represent a natural anti-inflammatory class of compounds that have potential as novel therapeutics for MS.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design:
Fig. 2C. Mini-Array II: IgG antibody reactivity to lipids constituting polar head-group and side-chain modifications of PGPC in CSF samples from relapsing remitting MS patients and other neurological disease controls. Lipid hits with the lowest FDR (q=0.016) were clustered according to their reactivity profiles.

19 different lipids were custom-spotted in duplicate using the CAMAG Automatic TLC Sampler (ATS4) robot to spray 200 nl of 10 to 100 pmol of lipids onto PVDF membranes affixed to the surface of microscope slides. The slides were probed with cerebrospinal fluid (CSF) from 26 human patient samples. 27 slides total: 12 relapsing-remitting MS, 13 other neurological disease, 1 healthy control (not included in this submission), and 1 secondary Ab alone (not included in this submission). CSF diluted 1/20. HRP-conjugated secondary Ab (donkey anti-human IgG) diluted 1/8000. ECL for 3 minutes.

first: Peggy

last: Ho

first: Jennifer

last: Kanter

first: Amanda

last: Johnson

first: Sirisha

last: Narayana

first: Mohsen

last: Khademi

first: Tomas

last: Olsson

first: Lawrence

last: Steinman

middle: H


title: Identification of target genes of ABI3 [SAP]

first: Gudrun

last: Moenke

type: Genome binding/occupancy profiling by array

summary: ABI3 is a key regulator of seed development in Arabidopsis and other plants.To identify DNA fragments (promoters) bound by ABI3 we performed array based ChIP analysis.

overall_design: Five ChIP-chip experiments were performed with chromatin of seeds of Arabidopsis and an anti-ABI3 antibody directed against a N-terminal fragment of ABI3, raised in rabbits. Non precipitated chromatin (input) served as control.

first: Urs

last: Haehnel

first: Michael

last: Seifert

first: Lothar

last: Altschmied


title: Human cerebrospinal fluid autoantibody lipid microarray profiling (Fig. 2A)

overall_design:
Fig. 2A. Mini-Array I: IgG antibody reactivity to various glycero-3-phosphocholine lipids in CSF samples from patients with relapsing remitting MS and from control patients with other neurological disease. Lipid hits with the lowest FDR (q=0.029) were clustered according to their reactivity profiles.

47 different lipids were custom-spotted in duplicate using the CAMAG Automatic TLC Sampler (ATS4) robot to spray 200 nl of 10 to 100 pmol of lipids onto PVDF membranes affixed to the surface of microscope slides. The slides were probed with cerebrospinal fluid (CSF) from 24 human patient samples. 25 slides total: 13 relapsing-remitting MS, 11 other neurological disease, and 1 secondary Ab alone (not included in this submission). CSF diluted 1/20. HRP-conjugated secondary Ab (goat anti-human IgM/IgG) diluted 1/175. ECL for 3 minutes.


title: Characterization of the Bradyrhizobium japonicum NtrC regulon by DNA Microarray analysis.

city: Columbia

last: Franck

state: MO

address: 1201 East Rollins St.,        201 Lifes Science Center

department: Division of Plant Sciences

institute: University of Missouri-Columbia

summary: The Bradyrhizobium japonicum NtrC regulatory protein influences gene expression in response to changes in intracellular nitrogen status.  Under conditions of low nitrogen, phosphorylation of NtrC results in up-regulation of a number of genes involved in nitrogen metabolism and nitrogen acquisition.  To better define the exact nature of NtrC’s influence on gene expression, a ntrC mutation was created in B. japonicum and transcriptional profiling was performed by DNA microarray analysis of both the mutant and wild type strains.

overall_design: Bradyrhizobium japonicum USDA 110 and a ntrC mutant in the USDA 110 background were cultured in minimal medium supplemented with 10mM ammonium and 10mM glutamate as nitrogen sources.  Three biological replicates were prepared for each strain and dye swap replications were performed for each hybridization producing a total of six slides.

first: Jing

last: Qiu

first: Gary

last: Stacey


title: Time-course microarray study of Cryptococcus neoformans var. neoformans (JEC20xJEC21) sexual development

status: Public on May 01 2012

first: Christina

last: Hull

address: 1300 University Ave, 687 Medical Sciences Center

department: Biomolecular Chemistry

summary: To identify the genome-wide transcriptional changes that occur throughout sexual developmen of C. neoformans, we conducted a time-course microarray experiment spanning six developmental stages to generate a temporal expression pattern for each known gene. C. neoformans a x α co-cultures were grown under sexual development conditions (V8 agar), and RNA was harvested at 0.5, 6, 12, 24, 48, and 72 hours post-mixing. Time points were chosen based on microscopic identification of cell types of interest: fusants, filaments (early and late), basidia, and spores (Figure 1B). Microarray hybridizations were conducted in a loop design, with each sample serving as a reference for the following time point in the experiment (e.g. 0.5 hours vs. 6 hours, 6 hours vs. 12 hours, etc).

overall_design: The experiment spanned six time points of development: 0.5 hours, 6 hours, 12 hours, 24 hours, 48 hours and 72 hours. Hybridizations were conducted in a loop design, with each sample serving as the reference for the consecutive time point - resulting in 5 experimental comparisons: .5hr vs 6 hr, 6 hrs vs 12 hrs, 12 hrs vs 24 hrs, 24 hrs vs 48 hrs, and 48 hrs vs 72 hrs. Each comparison consistent of duplicate hybridizations with dye swaps. Arrays contain duplicate genomes, resulting in eight-fold coverage within each comparison. (total of 20 hybridizations)

first: Steven

last: Giles

first: Emilia

last: Kruzel


title: Gene expression in the blood of SIV infected Rhesus macaques following in vivo PD-1 blockade

status: Public on Apr 27 2012

city: Atlanta

first: RAVI

last: DYAVAR SHETTY

state: Georgia

address: 954 Gatewood RD NE

department: Microbiology and Immunology

institute: emory university

summary: Hyperimmune activation is one of the strong predictors of disease progression during pathogenic immunodeficiency virus infections and is mediated in part by sustained type I interferon (IFN) signaling. Combination antiretroviral therapy suppresses hyperimmune activation only partially in HIV-infected individuals. Here, we show that blockade of Programmed Death-1 (PD-1) during chonic SIV infection significantly reduces the expression of transcripts associated with type I IFN signaling in the blood and colorectal tissue of rhesus macaques (RM). The effect of PD-1 blockade on type I IFN signaling was durable and persisted under high viremia, a condition that is seen in nonprogressive SIV infection in their natural hosts. The reduced type I IFN signaling was associated with enhanced expression of some of the junction-associated genes in the colorectal tissue and a profound decrease in LPS levels in plasma suggesting a possible repair of gut associated junctions and decreased microbial translocation. The reduced type I IFN signaling was also associated with enhanced immunity against gut resident pathogenic bacteria, control of gut associated opportunistic infections and survival of SIV-infected RMs. These results reveal novel mechanisms by which PD-1 blockade enhances survival of SIV-infected RMs and have implications for development of novel therapeutic approaches to control HIV/AIDS.

overall_design: SIV negative controls (n=4); SIV infected and control antibody (SYNAGIS) treated (n=3); and SIV infected Programmed Death 1 antibody (PD-1 Ab) treated (n=3) groups of  Rhesus macaques PBMCs were isolated by Ficoll-paque plus medium (Amersham) and were lysed in to RNA later reagent (Qiagen) and samples were homogenized with Qiagen Shredder (Qiagen). RNA was extracted with Rneasy mini kit (Qiagen) and was used for microarray experiments. Rhesus GeneChip assays were performed in the Yerkes Microarray Core Facility (www.microarray.emory.edu), one of the Affymetrix Microarray Core Labs.The 0.5µg of total RNA sample was analyzed on Rhesus Macaque Genome GeneChip that consists of over 52,000 probe sets (Affymetrix, Santa Clara, CA). Target RNA labeling, hybridization and post-hybridization processing were performed following the Affymetrix GeneChip Expression Analysis standard protocols. In brief, RNA sample was first reverse-transcribed using T7-Oligo(dT) Promoter Primer and SuperScript II in the first-strand cDNAs synthesis reaction. Following RNase H-mediated second-stranded cDNA synthesis, the double-stranded cDNAs were purified by use of a GeneChip sample clean-up module and served as templates in the generation of biotinylated complementary RNAs (cRNAs) in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix by in vitro transcription (IVT) reaction. The biotinylated cRNAs were cleaned up, fragmented, and hybridized to the rhesus macaque expression arrays at 45°C for 16 h with constant rotation at 60 rpm. The gene chips were then washed and stained with Affymetrix fluidics stations 450 and scanned on Affymetrix scanner 3000. The images are processed to collect raw data with GeneChip Operating Software (GCOS) 1.4.

first: Ravi

last: Shetty

first: Rama

middle: R

last: Amara


title: Human cerebrospinal fluid autoantibody lipid microarray profiling (Fig. 1A)

first: William

last: Robinson

overall_design:
Fig. 1A. Lipid-array profiling of IgG+IgM antibody reactivity in cerebrospinal fluid (CSF) samples from MS patients (relapsing remitting MS; secondary progressive MS; primary progressive MS), healthy controls, and other neurological disease controls. Lipid hits with the lowest FDR (q=0.048) were clustered according to their reactivity profiles.

48 different lipids were custom-spotted in duplicate using the CAMAG Automatic TLC Sampler (ATS4) robot to spray 200 nl of 10 to 100 pmol of lipids onto PVDF membranes affixed to the surface of microscope slides. The slides were probed with cerebrospinal fluid (CSF) from 59 human patient samples. 60 slides total: 18 relapsing-remitting MS, 14 secondary-progressive MS, 1 primary-progressive MS, 21 other neurological disease, 5 healthy control, 1 secondary Ab alone (not included in this submission). CSF diluted 1/10. HRP-conjugated secondary Ab (goat anti-human IgM/IgG) diluted 1/8000. ECL for 3 minutes.

first: Peggy

last: Ho

first: Jennifer

last: Kanter

first: Amanda

last: Johnson

last: Narayana


title: Further Insights into the Mode of Action of the Lipoglycopeptide Telavancin through Global Gene Expression Studies

status: Public on Apr 14 2012

city: Normal

first: Arunachalam Muthaiyan

email: amuthai@gmail.com, bjwilkin@ilstu.edu

state: IL

address: Julian Hall

department: Biological Sciences

institute: Illinois State University

summary: Background: Telavancin is a novel semi-synthetic lipoglycopeptide derivative of vancomycin with a decylaminoethyl side chain that is active against Gram-positive bacteria including Staphylococcus aureus strains resistant to methicillin or vancomycin.  This study describes transcriptome alterations in S. aureus strain ATCC29213 treated with telavancin for 15 min and 60 min   in comparing with other agents treatment, including  vancomycin, enduracidin, m-chlorophenylhydrazone.

overall_design: MHB cultures (biological replicates: N=3) were then grown to exponential phase (OD580=0.35) before the addition of telavancin(8 µg/ml final concentration), or vancomycin (10 /µg ml) or  CCCP (2 µg/ ml );  or enduracidin (1 µg ml) and incubated for an additional 15 min , and 60 min before sampling.  Dye-swapping was performed between samples.

first: Yang

last: Song


title: Comparative analyses of resistance pathways of Arabidopsis thaliana and soybean (Glycine max) to Fusarium virguliforme and to deoxynivalenol of Gibberella zeae

status: Public on Apr 12 2012

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
Microarray experiments allow the dissection genome wide patterns of mRNA abundances and improve understanding of the molecular basis of the plant defense responses. These global and simultaneous analyses of TA profiles enable variations in mRNA abundances under specific treatments to be compared. In order to compare the plant resistance mechanism to DON toxicity and infection of Fusarial pathogens, microarray data from Arabidopsis thaliana cells challenged with the mycotoxin DON was compared to the data from the plants responding to F. virguliforme infestations. The microarray chip contained over 10,000 different ESTs (AFGC) was employed in both analyses. The first objective of this approach was to identify genes that were transcriptionally regulated when plants were treated with the toxin. The second objective using the microarray data was to identify resistance pathways where these co-regulated genes were positioned. The parallel comparison on transcriptional activities among soybean and Arabidopsis after fungal pathogen Fsg pathogenesis and Arabidopsis with DON treatment was also performed.
Infection: Using F. virguliforme spores
Compound Based Treatment: Time seedlings were exposed to Deoxynivalenol

first: David

last: Lightfoot

first: Patrick

last: Hart


title: Functional environmental genomics of a municipal landfill soil

status: Public on Apr 16 2012

city: Amsterdam

first: Dick

last: Roelofs

state: Noord-Holland

address: De Boelelaan 1085

department: Animal Ecology

institute: VU University

summary: We investigated the toxicity of soil samples derived from a former municipal landfill site in the South of the Netherlands, where a bioremediation project is running aiming at reusing the site for recreation. Both an organic soil extract and the original soil sample was investigated using the ISO standardised Folsomia soil ecotoxicological testing and gene expression analysis. The 28 day survival/reproduction test revealed that the ecologically more relevant original soil sample was more toxic than the organic soil extract. Microarray analysis showed that the more toxic soil samples induced gene regulatory changes in twice as less genes compared to the soil extract. Consequently gene regulatory changes were highly dependent on sample type, and were to a lesser extent caused by exposure level. An important biological process shared among the two sample types was the detoxification pathway for xenobiotics (biotransformation I, II and III) suggesting a link between compound type and observed adverse effects. Finally, we were able to retrieve a selected group of genes that show highly significant dose-dependent gene expression and thus were tightly linked with adverse effects on reproduction. Expression of four cytochrome P450 genes showed highest correlation values with reproduction, and maybe promising genetic markers for soil quality. However, a more elaborate set of environmental soil samples is needed to validate the correlation between gene expression induction and adverse phenotypic effects.

overall_design: paired reference design was used testing animals exposed to two concentrations of an environemntal soil sample  and two concentrations of the subsequent soil extract. 4 biological replicates per condition containing 25 grams of soil and 10 23day-old animals per replicate.

first: D

first: M

last: de Boer

first: V

last: Agamennone

first: P

last: Bouchier

first: J

last: Legler

first: N

last: van Straalen


title: Stress response study in Arabidopsis thaliana using DNA millichips

first: Jamison

last: Wolfer

address: 425 Henry Mall

department: Biotechnology Center

institute: University of Wisconsin

summary: Our goal was to create a DNA chip that is as easy, convenient and inexpensive as an agarose gel.  For a first generation solution, we describe a low cost, easy to use de novo synthesis oligonucleotide microarray technology that draws on the inherent flexibility of the maskless array synthesizer for in situ synthesis of thousands of photolithographically produced oligonucleotides covalently attached to a microscope slide. The method involves physically subdividing the slide into 1 x 1 mm 'millichips' that are hybridized to fluorescent RNA or DNA of biological origin, in a microfuge tube at an ordinary laboratory benchtop, rather than in dedicated hybridization chambers.  Fluorescence intensity is then measured with a standard microxcope rather than sophisticated DNA chip scanners.  For proof of principle, we measured changes in the transcriptome of Arabidopsis plants induced by growth in the presence of three major environmental abiotic stresses (temperature, light and water status), in all possible combinations. Validation by comparison with qRT-PCR showed a high correlation coefficient and analysis of variance indicated a high technical reproducibility. These experiments demonstrate that low cost DNA 'millichips' can be made and reliably used at the benchtop in a normal laboratory setting, without assistance of core facilities containing costly specialized instrumentation.

overall_design: An average of three to four technical replicates and six biological replicates for each treatment and control group were performed resulting in a total of 457 individual millichip experiments for this study.

first: Kurt

last: Heinrich

first: DongGee

last: Hong

first: Melissa

last: LeBlanc

first: Michael

last: Sussman


title: Comparison of transcription profiles of C. neoformans during rabbit or human infection

status: Public on Apr 11 2012

city: Lynchburg

last: Price

state: VA

address: 1971 University Blvd.

department: Biology & Chemistry

institute: Liberty University

summary: Ubiquitination is a reversible protein modification involved in various cellular processes in eukaryotic cells.   Deubiquitinating enzymes, the proteins responsible for the removal of ubiquitin, act as essential regulators to maintain ubiquitin homeostasis and to exquisitely regulate protein degradation via the ubiquitination pathway.  Cryptococcus neoformans is an important basidiomycete pathogen that causes life-threatening meningoencephalitis primarily within the immunocompromised population.  In order to understand the possible influence deubiquitinating enzymes have on growth and virulence of the model pathogenic yeast Cryptococcus neoformans, we generated deletion mutants of 7 putative deubiquitinase genes.  Compared to other deubiquitinating enzyme mutants, a ubp5∆ mutant exhibited severely attenuated virulence and many distinct phenotypes, including decreased capsule formation, hypomelanization, defective sporulation, and elevated sensitivity to several external stressors (such as high temperature, oxidative and nitrosative stresses, high salts, and antifungal agents).  Ubp5 appears to be the major deubiquitinating enzyme in C. neoformans for maintaining a pool of free ubiquitin for stress responses, supports the evolutionary divergence of Cryptococcus sp. from the model yeast S. cerevisiae, and provides an important paradigm for understanding the potential role of deubiquitination in virulence by other pathogenic fungi.  In addition, other putative deubiquitinase mutants (doa4∆ and ubp13∆) exhibit similar phenotypes to the ubp5∆ mutant, illustrating possible functional overlap among deubiquitinating enzymes in C. neoformans.  Certain functioning deubiquitinating enzymes are essential for the virulence composite of C. neoformans and provide an additional yeast survival and propagation advantage in the host.

overall_design: New Zealand White rabbits were inoculated with WT strain H99 and harvested by intracisternal spinal tap on days 1, 3, 4, and 7.  For the human sample, RNA was extracted from CSF obtained from a de-identified patient with cryptococcal meningitis.

first: Wei

last: Fang

first: Dena

last: Toffaletti

first: Jennifer

last: Tenor

first: Marisol

last: Betancourt-Quiroz

first: Wei-hua

last: Pan

first: Wan-qing

last: Liao

first: John

last: Perfect


title: DNA hypermethylation in placental tissues: placental tissues vs. maternal peripheral bloods

status: Public on Feb 22 2012

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

institute: BioChainBJ

summary: Noninvasive prenatal diagnosis currently used does not achieve desirable levels of sensitivity and specificity. Recently, fetal methylated DNA biomarkers in maternal whole blood have been explored for noninvasive prenatal detection. However, such efforts cover only chromosomal aneuploidy; fetal methylated DNA biomarkers for detecting single-gene disease remain to be discovered. To address this issue, we systematically screened significantly hypermethylated genes in fetal tissues compared with maternal blood for noninvasive prenatal diagnosis of various inherited diseases. First, Methylated-CpG island recovery assay combined with CpG island array was performed in four maternal peripheral bloods and their corresponding placental tissues. Subsequently, direct bisulfite sequencing and combined bisulfite restriction analysis (COBRA) were carried out to validate the reliability of methylation microarray analysis. As results, 310 significantly hypermethylated genes in fetal tissues were detected by microarray. Two of five randomly selected hypermethylated genes detected by microarray were confirmed to be hypermethylated in fetal tissue samples by direct bisulfite sequencing. All four randomly selected hypermethylated genes detected by microarray were confirmed to be hypermethylated in five independent amniotic fluid samples and five independent chorionic villus samples from 10 pregnant women by CORBA. In conclusions, We found a lot of hypermethylated genes and methylation sites in fetal tissues, some of which have great potential to be developed into molecular markers for noninvasive prenatal diagnosis of monogenic disorders. Further clinical study is warranted to confirm these findings.

overall_design: Paired experiments,  placental tissues vs. maternal peripheral bloods. Biological replicates: 4 placental tissues and 4 correspoding maternal peripheral bloods.

first: Aihua

last: Yin

first: Xiangzhong

last: Zhang

first: Jing

last: Wu

first: Li

last: Du

first: Tianwen

last: He

first: Xiaozhuang


title: The influence of long-term copper contaminated agricultural soil at different pH levels on microbial communities and springtail transcriptional regulation

status: Public on Apr 04 2012

first: Tjalf

last: de Boer

address: Science Park 406

institute: MicroLife Solutions

summary: Copper has long been applied for agricultural practices. Like other metals, copper is highly persistent in the environment and biologically active long after its use has ceased. Here we present a unique study on the long-term effects (27 years) of copper and pH on soil microbial communities and on Folsomia candida, an important representative of the soil macrofauna, in an experiment with a full factorial, random block design. Bacterial communities were mostly affected by pH. These effects were prominent in Acidobacteria, while Actinobacteria and Gammaroteobacteria communities were affected by original and bioavailable copper. Reproduction and survival of the collembolan F. candida was not affected by the studied copper concentrations. However, the transcriptomic responses to copper reflected a mechanism of copper transport and detoxification, while pH exerted effects on nucleotide and protein metabolism and (acute) inflammatory response. We conclude that microbial community structure explained the history of copper contamination, while gene expression analysis of F. candida is associated with the current level of bioavailable copper. Combined analysis at various trophic levels is highly relevant in the context of assessing long-term soil pollution.

overall_design: A single channel, interwoven loop design was used to test animals exposed to the copper-spiked field soil samples. The field soil was spiked with 4 copper and 4 pH treatments yielding 16 combinations. Combinations are displayed in the Sample descriptions, with 1 – 4 representing the copper concentrations from low to high, and A-D representing the soil pH from low to high. 4 biological replicates per copper/pH combination were used. Each replicate contained 25 grams of soil and thirty 23-day-old animals.

middle: E

first: Neslihan

last: Tas

first: Martin

last: Braster

first: Erwin

last: Temminghoff

first: Wilfred

last: Röling

first: Dick

last: Roelofs


title: Transcriptional changes due to UBP5 mutation under temperature stress

first: Michael

last: Price

overall_design: In this study, transcription profiles of ubp5 mutant and WT Cryptococcus neoformans strains were compared in a dye-swap experiment following 1hr exposure to either 30C or 37C.

first: Wei

last: Fang

first: Dena

last: Toffaletti

first: Jennifer

last: Tenor

first: Marisol


title: Combinatorial effects of microRNA to suppress the myc oncogenic pathway (miRNA data)

status: Public on Apr 09 2012

city: Madrid

first: Lorena

last: Di Lisio

address: C/ Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

summary: microRNA importance in the myc pathway in Burkitt lymphoma.

overall_design: MicroRNA data from the Agilent human miRNA platform. 12 Burkitt lymphomas were compared with 14 non-tumoral controls (lymph nodes, tonsils and CD19+CD10+ sorted cells). Significantly deregulated miRNAs were computed using the Significant Analysis of Microarray (SAM) analysis from the TM4 pathway and the limma package.

first: María

last: Bueno

first: Gonzalo

last: Gómez-López

first: Nerea

last: Martínez

first: Miguel

last: Piris

first: Marcos

last: Malumbres


title: Colorectal tissue gene expression in SIV negative and SIV positive Rhesus macaques and sooty mangabeys

status: Public on Sep 06 2011

first: RAVI

last: DYAVAR SHETTY

summary: In SIV/HIV infection, the gastrointestinal tissue dominates as an important site due to the impact of massive mucosal CD4 depletion and immune activation-induced tissue pathology. Unlike AIDS-susceptible rhesus macaques, natural hosts do not progress to AIDS and resolve immune activation earlier. Here, we examine the role of dendritic cells in mediating immune activation and disease progression. We demonstrate that plasmacytoid dendritic cells (pDC) in the blood upregulate β7-integrin and are rapidly recruited to the colorectum following a pathogenic SIV infection in rhesus macaques. These pDC were capable of producing proinflammatory cytokines and primed a Tc1 response in vitro. Consistent with the upregulation of β7-integrin on pDC, in vivo blockade of α4β7-integrin dampened pDC recruitment to the colorectum and resulted in reduced immune activation. The upregulation of β7-integrin expression on pDC in the blood was also observed in HIV-infected humans but not in chronically SIV-infected sooty mangabeys that show low levels of immune activation. Our results uncover a new mechanism by which pDC influence immune activation in colorectal tissue following pathogenic immunodeficiency virus infections.

sample_organism:
Cercocebus atys
Macaca mulatta

overall_design:
SIV negative controls (n=4) and week 12 post SIV infected (n=4) groups of Rhesus macaques and SIV negative controls (n=4) and week 55 post SIV infected (n=4) groups of Sooty mangabeys colorectal tissue biopsies were collected in to RNA later reagent (Qiagen) and were homogenized with syringe and needle method. RNA was extracted with Rneasy mini kit (Qiagen) and was used for microarray experiments. Rhesus GeneChip assays were performed in the Yerkes Microarray Core Facility (www.microarray.emory.edu) , one of the Affymetrix Microarray Core Labs.The 0.5µg of total RNA sample was analyzed on Rhesus Macaque Genome GeneChip that consists of over 52,000 probe sets (Affymetrix, Santa Clara, CA). Target RNA labeling, hybridization and post-hybridization processing were performed following the Affymetrix GeneChip Expression Analysis standard protocols. In brief, The 5 μg of RNA sample was first reverse-transcribed using T7-Oligo(dT) Promoter Primer and SuperScript II in the first-strand cDNAs synthesis reaction. Following RNase H-mediated second-stranded cDNA synthesis, the double-stranded cDNAs were purified by use of a GeneChip sample clean-up module and served as templates in the generation of biotinylated complementary RNAs (cRNAs) in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix by in vitro transcription (IVT) reaction. The biotinylated cRNAs were cleaned up, fragmented, and hybridized to the rhesus macaque expression arrays at 45°C for 16 h with constant rotation at 60 rpm. The gene chips were then washed and stained with Affymetrix fluidics stations 450 and scanned on Affymetrix scanner 3000. The images are processed to collect raw data with GeneChip Operating Software (GCOS) 1.4.
Tissue: Colorectal tissue
Time after SIV infection: 12 weeks for SIV infected Rhesus macaques, 55 weeks for Sooty mangabeys
Infection: SIVmac251 infection for Rhesus macaques, SIVsm infection for Sooty mangabeys

first: Ravi

last: Dyavar-Shetty

first: RamaRao

last: Amara


title: ChIP-chip from pregnant female mouse pituitary with POU1F1 (PIT-1)

status: Public on Oct 29 2011

city: Marseille Cedex 15

first: Jean-Paul

last: Herman

address: Bld Pierre Dramard

department: CRN2M - UMR6231

institute: CNRS

summary:
POU1F1 regulates, in the pituitary, the development of the prolactin-, growth hormone- and thyrotropin ß-expressing lineages and the expression of these hormone in the mature pituitary through the direct regulation of their promoters. Besides these functions, POU1F1 is also involved in other cellular processes in the pituitary, such as cell division and survival, but the genomic targets involved in these actions are not known.
The present ChIP-chip study identified a large number of hitherto unknown potential direct targets that might be involved in these actions, such as Tcf4, Lmo4, Pax6, Trp53 etc.

overall_design: ChIP-chip was done from pregnant female mouse (C57Bl/6J) pituitary (3 pools of 12 pituitary anterior lobes, corresponding to three biological replicates) with POU1F1 (PIT-1)

first: Jean-Louis

last: Franc


title: MRLxSM eQTL in Liver by RMA on Ensembl transcripts

status: Public on Nov 28 2011

city: Bar Harbor

first: Ricardo

middle: Alejandro

last: Verdugo

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

summary: A QTL analysis between inbred mouse strains MRL/MpJ and SM/J was performed to identify genetic loci influencing high-density lipoprotein (HDL) cholesterol and triglycerides (TG) at eight weeks of age in F2 mice fed a chow diet. In order to narrow down lists of candidate genes, expression levels from liver tissue were used to test for differential expression among parental and F1 strains and to scan for eQTL in F2 animals. We provide evidence for Mppe1 (Chr 18) as an HDL QTL candidate gene and Cyp2d26 (Chr 15) as a TG QTL candidate gene.

overall_design: MRL/MpJ (MRL) mice were crossed with male SM/J (SM) mice; their progeny were intercrossed to produce 371 F2 animals. Of these, 282 F2 males and females were profiled with Affy Mouse Gene 1.0 ST arrays for an eQTL study. Three animals from each parental and the F1 strains from each sex, i.e. 18 in total, were also profiled for testing differential expression. A total of 300 samples are included in the dataset. The mice were weaned at 3 weeks on a chow diet. At 13 weeks of age, mice were single housed for 3 days and fasted for 4 hours prior to being sacrificed. Tissue collection was performed between noon and 1pm to avoid variations due to circadian rhythm.

first: Magalie

last: Leduc

first: Rachael

last: Hageman

first: Shirng-Wern

last: Tsaih

first: Kenneth

last: Walsh

first: Gary

last: Churchill

first: Beverly

last: Paigen


title: Retinal whole genome microarray analysis after irradiated injury of intraorbital nerve in the monkey

status: Public on Sep 30 2011

city: Chengdu

first: Chen

last: Jing

address: West China Hospital

department: Department of Neurosurgery

institute: West China Hospital, Sichuan University

summary: To obtain and analyze early retinal changes at molecular level at 24h after ipsilateral intraorbital nerve radiation injury by gamma knife surgery

overall_design: Unilateral intraorbital optic nerves of three Rhesus Macaques were treated by gamma knife surgery (GKS) with irradiated doses of 15Gy, while the contralateral optic nerves and retinas served as the control. Gene expression profiles of control and affected retinas were analyzed with Affymetrix Rhesus Macaque Genome arrays at 24h after treatment

first: Yong

last: Xia

first: Jun

last: Chen

first: Li

last: Xiong

first: Jiagang

last: Liu

first: Xuesong

first: Lu

last: Ma

first: Qiao

last: Zhang

first: Chao

last: You

first: Jing

first: Xuyang

first: Xiaoyu

last: Wang

first: Yan

last: Ju


title: Transcript response of CSF survival mutants in CSF or serum

first: Michael

last: Price

overall_design: WT strain H99, mutant strains 1A10 (ena1∆, CNAG_00531), and 14A4 (pik1∆, CNAG_07744) were incubated in filter-sterilized human CSF or serum from anonymous human donors at 37°C with shaking, and harvested at either 1 or 24 hours post-resuspension in each biological fluid for RNA extraction.

first: Wei

last: Fang

first: Dena

last: Toffaletti

first: Jennifer

last: Tenor

first: Marisol

last: Betancourt-Quiroz

first: Wei-hua

last: Pan

first: Wan-qing

last: Liao

first: John

last: Perfect


title: Comparison of transcription profiles for C. neoformans during rabbit infection

overall_design: WT Cryptococcus neoformans strain H99 was incubated in pooled ex vivo human CSF obtained from de-identified patients and harvested after 24hr for RNA extraction. New Zealand White rabbits were inoculated with WT strain H99 and harvested by intracisternal spinal tap on days 1 and 7 for RNA extraction.


title: Comparative Pathogenesis of Three Human and Zoonotic SARS-CoV Strains in Cynomolgus Macaques

status: Public on Sep 01 2011

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: The severe acute respiratory syndrome (SARS) epidemic was characterized by increased pathogenicity in the elderly due to an early exacerbated innate host response. SARS-CoV is a zoonotic pathogen that entered the human population through an intermediate host like the palm civet. To prevent future introductions of zoonotic SARS-CoV strains and subsequent transmission into the human population, heterologous disease models are needed to test the efficacy of vaccines and therapeutics against both late human and zoonotic isolates.  Here we show that both human and zoonotic SARS-CoV strains can infect cynomolgus macaques and resulted in radiological as well as histopathological changes similar to those seen in mild human cases. Viral replication was higher in animals infected with a late human phase isolate compared to a zoonotic isolate. Host responses to the three SARS-CoV strains were similar and only apparent early during infection with the majority of genes associated with interferon signalling pathways.This study characterizes critical disease models in the evaluation and licensure of therapeutic strategies against SARS-CoV for human use

overall_design: 4 strains, time course, lungs

first: Barry

last: Rockx

first: Friederike

last: Feldmann

first: Douglas

last: Brining

first: Don

last: Gardner

first: Rachel

last: LaCasse

first: Lisa

last: Kercher

last: Long

first: Rebecca

last: Rosenke

first: Kimmo

last: Virtaneva

first: Daniel

first: Stephen

last: Porcella

last: Mattoon

last: Parnell

first: Ralph

last: Baric

first: Heinz


title: Transcriptional architecture of the primate neocortex

status: Public on Mar 21 2012

first: Susan

last: Sunkin

address: 551 N. 34th Street

institute: Allen Institute for Brain Science

summary: Genome-wide transcriptional profiling allows characterization of the molecular underpinnings of neocortical organization, including cortical areal specialization, laminar cell type diversity and functional anatomy.  Microarray analysis of individual cortical layers across sensorimotor and association cortices in rhesus macaque demonstrated robust and specific laminar and areal molecular signatures driven by differential expression of genes associated with specialized neuronal function.  Gene expression corresponding with laminar architecture was generally similar across cortical areas, although genes with robust areal patterning were often highly laminar as well, and these patterns were more highly conserved between macaque and human as compared to mouse.  Layer 4 of primate primary visual cortex displayed a distinct molecular signature compared to other cortical regions, a specialization not observed in mouse.  Overall, transcriptome-based relationships were strongest between proximal layers in a cortical area, and between neighboring areas along the rostrocaudal axis, reflecting in vivo cortical spatial topography and therefore a developmental imprint.

overall_design: Tissue from male and female monkeys (n = 2-3 animals/gender) was collected from anterior cingulate gyrus (ACG), layers 2, 3, 5, 6; orbitofrontal cortex (OFC), layers 2, 3, 5, 6; dorsolateral prefrontal cortex (DLPFC), layers 2-6; primary motor cortex (M1), layers 2, 3, 5, 6; primary somatosensory cortex (S1), layers 2-6; primary auditory cortex (A1), layers 2-6; primary visual cortex (V1), layers 2-6 including 4A, 4B, 4Calpha (4Ca), 4Cbeta (4Cb); secondary visual cortex (V2), layers 2-6; middle temporal area (MT), layers 2-6; temporal area (TE), layers 2-6; hippocampus, CA1, CA2, CA3, dentate gyrus (DG); and dorsal lateral geniculate nucleus (LGN), magnocellular, parvocellular and koniocellular divisions. Due to the limited number of samples that could be amplified concurrently, amplifications were performed in 3 batches (batches A-C, containing 102, 119 and 10 experimental samples, respectively).  To control for batch effects, common RNA pool control samples were amplified and hybridized in each batch.  These included LCM extracted hippocampus CA3 samples from the current study and a whole rhesus brain RNA pool (Biochain).  These control samples were hybridized in 6 replicates in batch A and B and in 3 replicates in batch C (3 replicates per 96 well plate).


title: Inter-strain Heterogeneity in Responses to TCDD

status: Public on Aug 17 2011

city: Toronto

first: Cindy

middle: Q.

last: Yao

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

summary: We profiled hepatic transcriptional responses of 6 strains of rats with varying sensitivity to a dioxin, TCDD, at 19 hours following exposure. The resistant rats exhibited significantly reduced transcriptional responses in comparison to the sensitive strains. We hypothesize that genes which show differential changes between the resistant and sensitive rats may potentially explain sensitivity.

overall_design: Rats with varying sensitivities (Long-Evans, L-E; Han/Wistar, H/W; Fischer 344, F344; Wistar, Wis; Line-A, Ln-A; and Line-C, Ln-C) were treated with 100 ug/kg TCDD or corn oil vehicle and euthanized 19 hours post-treatment. Each treatment group contains four or six animals (biological replicates), each of which was assayed on an individual microarray.

first: Paul

middle: C

last: Boutros

first: Raimo

last: Pohjanvirta

first: Allan

middle: B

last: Okey

middle: Q


title: Whole transcriptome analysis of rosetting Plasmodium falciparum parasites

status: Public on Jul 01 2011

city: Edinburgh

first: Antoine

last: Claessens

address: West Mains Road

department: Institute of Immunology and Infection Research

institute: Edinburgh university

summary: Background:  The cytoadherence of Plasmodium falciparum is thought to be mediated by variant surface antigens (VSA), encoded by var, rif, stevor and pfmc-2tm genes. The last three families have rarely been studied in the context of cytoadherence. As most VSA genes are unique, the variability among sequences has impeded the functional study of VSA across different P. falciparum strains. However, many P. falciparum genomes have recently been sequenced, allowing the development of specific microarray probes to each VSA gene.  Methods:  All VSA sequences from the HB3, Dd2 and IT/FCR3 genomes were extracted using HMMer. Oligonucleotide probes were designed with OligoRankPick and added to the 3D7-based microarray chip. As a proof of concept, IT/R29 parasites were selected for and against rosette formation and the transcriptomes of isogenic rosetting and non-rosetting parasites were compared by microarray.   Results:  From each parasite strain 50-56 var genes, 125-132 rif genes, 26-33 stevor genes and 3-8 pfmc-2tm genes were identified. The ability of the VSA-supplemented microarray chip to detect cytoadherence-related genes was assessed using P. falciparum clone IT/R29, in which rosetting is known to be mediated by PfEMP1 encoded by ITvar9. Whole transcriptome analysis showed that the most highly upregulated gene in rosetting parasites was ITvar9 (19 to 429-fold upregulated over six time points). Only one rif gene (IT4rifA_042) was upregulated by more than 4-fold (5-fold at 12 hours post-invasion), and no stevor or pfmc-2tm genes were upregulated by more than 2-fold.  49 non-VSA genes were upregulated in rosetting parasites by more than 3-fold in at least two time-points, although none as markedly as ITvar9.   Conclusions:  We demonstrate that the VSA of newly sequenced P. falciparum strains can be added to the 3D7-based microarray chip, allowing the analysis of the entire transcriptome of multiple strains. For the rosetting clone IT/R29, the striking transcriptional upregulation of ITvar9 was confirmed, and the data did not support the involvement of other VSA families in rosette formation.

overall_design: Plasmodium falciparum parasites, strain IT/R29, were selected for (R29R+) or against (R29R-) rosetting. Both cultures (R29R+ and R29R-) were tightly synchronised before a timecourse experiment was performed. 6 samples, named time points 1 to 6, were taken every 8 hours. 12μg of RNA from the R29 non-rosetting parasites at each of the 6 time points was combined together to form the reference pool. The pool and 12μg of each individual time point sample from both rosetting and non-rosetting parasites were then used for cDNA synthesis. For microarray hybridizations,each cDNA sample was coupled to Cy5 (red dye) while Cy3 (green dye) was added to the pool. Cy5-labelled time point samples were mixed with the same amount of Cy3-labelled pool sample. The solution was loaded on a microarray slide and hybridized for 14–16 h.

first: Ashfaq

last: Ghumra

first: Archana

last: Patkar

first: Sachel

last: Mok

first: Zbynek

last: Bozdech

first: J

middle: A

last: Rowe


title: An integrated model of stress-dependent gene expression in yeast

status: Public on Aug 18 2011

city: Madison

first: Audrey

middle: P.

last: Gasch

address: 425-g Henry Mall

department: Laboratory of Genetics

institute: University of Wisconsin Madison

summary: Microarray timecourses followed the gene expression response of Saccharomyces cereviciae to osmotic shock, over 4 hours. Data was compared to timecourses of quantitative proteomic data to understand the dynamic relationship between RNA and protein

overall_design: The dynamic genomic expression response to osmotic shock (0.7M NaCl) was measured in Saccharomyces cereviciae, over the course of 4 hours in biological triplicate. Six timepoints were taken for each time course, for a total of 18 tiled-genomic Nimblegen arrays against the S288c yeast genome.

first: Scott

last: Topper

first: Violet

middle: M

last: Lee

first: Josh

middle: J

last: Coon


title: Affymetrix Cytogenetics array data for a study of D45-deficiency resulting from uniparental disomy: a novel cause of SCID

status: Public on Feb 10 2012

city: Philadelphia

first: JIANMING

last: PEI

state: PA

address: 333 Cottman Ave.

department: Population Science

institute: Fox Chase Cancer Center

summary: Analysis of the molecular etiologies of severe combined immunodeficiency (SCID) has led to important insights into the control of immune cell development. Most cases of SCID result from either X-linked or autosomal recessive inheritance of mutations in a known causative gene. However, in some cases, the molecular etiology remains unclear.  To identify the cause of SCID in a patient known to lack the protein tyrosine phosphatase CD45, we utilized single nucleotide polymorphisms (SNP) Cytogenetics arrays; The patient’s mother was heterozygous for an inactivating mutation in CD45, while the paternal alleles exhibited no detectable mutations. The patient exhibited a single CD45 mutation identical to the maternal allele.  Patient SNP array analysis revealed no change in copy number but loss of heterozygosity for the entire length of chromosome 1 (Chr1), indicating that disease was caused by uniparental disomy (UPD) with isodisomy of the entire maternal Chr1 bearing the mutant CD45 allele.  Non-lymphoid blood cells and other mesoderm and ectoderm-derived tissues retained UPD of the entire maternal Chr1 in this patient who had undergone successful bone marrow transplantation. These findings represent the first reported case of SCID caused by UPD and suggest UPD should be considered in SCID and other recessive disorders, especially when the patient appears homozygous for an abnormal gene found in only one parent.  Evaluation for alterations in other genes affected by UPD should also be considered in such cases.

overall_design:
Affymetrix SNP Cytogenetics arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved sorted PMBC and buccal samples.
Copy number and allele analysis of Affymetrix Cytogenetics arrays was performed for the patient's and his parent's samples.

first: Joseph

middle: L

last: Roberts

first: Rebecca

last: Buckley

first: Biao

last: Luo

first: Jianming

last: Pei

first: Alla

last: Lapidus

first: Suraj

last: Peri

first: Qiong

last: Wei

first: Jinwook

last: Shin

first: Roberta

last: Parrott

first: Roland

last: Dunbrack

last: Testa

first: Xiao-Ping

last: Zhong

first: David

last: Wiest


title: Xanthomonas oryzae pv. oryzae (Indian Isolate): Wild type vs. rpfF mutant

status: Public on Apr 02 2011

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: Transcription profiling of the DSF regulon in Xanthomonas oryzae pv. oryzae (Xoo) using wild type and the rpfF mutant. Cell-cell signaling mediated by the quorum sensing molecule known as Diffusible Signaling factor (DSF) is required for virulence of Xanthomonas group of plant pathogens. DSF in different Xanthomonas and the closely related plant pathogen Xylella fastidiosa regulates diverse traits in a strain specific manner. The transcriptional profiling performed in this study is to elucidate the traits regulated by DSF from the Indian isolate of Xanthomonas oryzae pv. oryzae, which exhibits traits very different from other Xanthomonas group of plant pathogen. In this study, transcription analysis was done between a wild type Xanthomonas oryzae pv. oryzae strain and an isogenic strain that has a mutation in the DSF biosynthetic gene rpfF.

overall_design: Agilent one-color experiment, Organism: Xanthomonas oryzae, Agilent-025096  Genotypic Technology Pvt. Ltd. designed Custom Xanthomonas oryzae  8x15k, Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442).

first: Chatterjee

last: Subhadeep


title: Intra- and Inter-Individual Variance of Gene Expression in Human Placenta

status: Public on Mar 02 2011

city: hsinchu

first: wei-chung

last: cheng

address: adqwerqr ew

country: Taiwan

institute: NTHU

summary: Variance in microarray studies has been widely discussed as a critical topic of the identification of differentially expressed gene; however, few studies have addressed the influence of estimating variance.  To break intra- and inter-individual variance in clinical studies down to three levels: technical, anatomic, and individual, we designed experiments and algorithms to investigate three forms of variances. As a case study, a group of “inter-individual variable genes” were identified to exemplify the influence of underestimated variance on the statistical and biological aspects in identification of differentially expressed genes. Our results showed that inadequate estimation of variance inevitably led to the inclusion of non-statistically significant genes into those listed as significant, thereby interfering with the correct prediction of biological functions. Applying a higher cutoff value of fold changes in the selection of significant genes reduce/eliminate the effects of underestimated variance. Our data demonstrates that an appropriate evaluation of variance is critical in selecting significant genes of differential expression. If the estimation of precise variance has not been adequately considered in the experimental design, using a higher fold change criteria is one possible solution to overcome the difficulties associated with the identification of significant genes, but it paid by losing the number of selected genes.

overall_design: A total of 11 normal placenta tissues obtained from 9 healthy individuals with term pregnancies, whom underwent cesarean section without labor pain. The first sample group (G1) was composed of samples 1 to 9 of nine individuals. The second sample group (G2) contained 8-1, 8-2 and 8-3, which were three different placental tissues taken from the same individual. The third sample group (G3) consisted of two technical replicates, 8-3_1 and 8-3_2, using the identical RNA pool. Sample 8-3 is estimated by sample 8-3_1 and 8-3_2.  Sample 8 is estimated by sample 8-1, 8-2 and 8-3.

first: Wei-Chung

last: Cheng

first: Wun-Yi

last: Shu

first: Chia-Yang

last: Li

first: Min-Lung

last: Tsai

first: Cheng-Wei

last: Chang

first: Chaang-Ray

last: Chen

first: Hon-Zu

first: Tzu-Hao

last: Wang

first: Ian

last: Hsu


title: WFUBMC Primate Center  X-96-23: Cynomolgus macaque response to hormone replacement therapy

status: Public on Feb 12 2011

city: Winston-Salem

first: Charles

last: Wood

state: NC

address: Medical Center Blvd

department: Pathology

institute: Wake Forest University School of Medicine

summary: X-96-23 had 5 groups. Each of 4 groups had a different treatment type and there was also a control group. A total of 16 samples was sent for micro array analysis. Three treatment groups and the control group were used for analysis. The treatments were CEE; CEE+MPA; and OD14-HIGH. There are four samples from each of these three treatment groups and four control samples. The OD14-HIGH and the treatment not analyzed-OD14-LOW--were independent treatments for another study. The groups of interest here are the Control; CEE; and CEE+MPA.

overall_design: WFUBMC Primate Center  X-96-23: 4 treatment groups


title: Extensive effects of in vitro oocyte maturation on rhesus monkey cumulus cell transcriptome

status: Public on May 22 2011

first: Young

middle: Shin

last: Lee

address: 3307 N. Broad Street AHB 557

department: Fels Institute for Cancer Research and Molecular Biology

institute: Temple University

summary: The elaboration of a quality oocyte is integrally linked to the correct developmental progression of cumulus cell phenotype. In humans and non-human primates, oocyte quality is diminished with in vitro maturation. To determine the changes in gene expression in rhesus monkey cumulus cells (CC) that occur during the final day prior to oocyte maturation and how these changes differ between in vitro and in vivo maturation (IVM and VVM), we completed a detailed comparison of transcriptomes using the Affymetrix gene array. We observe a large number of genes differing in expression when comparing IVM-CC and VVM-CC directly, but a much larger number of differences comparing the transitions from the pre-oocyte maturation to post- IVM and post-VVM state. We observe a truncation or delay in the normal pattern of gene regulation, but also remarkable compensatory changes in gene expression during IVM. Among the genes affected in cumulus cells by IVM are those that contribute to productive cell-cell interactions between cumulus cell and oocyte and between cumulus cells. Numerous genes involved in lipid metabolism are incorrectly regulated during IVM, and the synthesis of sex hormones appears not suppressed during IVM. We identify a panel of 24 marker genes, the expression of which should provide the foundation for understanding how IVM can be improved, for monitoring IVM conditions, and for diagnosing oocyte quality.

overall_design: We compared transcriptomes of cumulus cells isolated from in vitro matured cumulus-oocyte complexes COCs (IVM-CC) and from in vivo matured COCs (VVM-CC) to identify potential cumulus cell markers of oocyte quality. The global gene expression profile of pre-maturation cumulus cells (PM-CC) was used to developmental transitions between IVM and VVM.

first: Catherine

last: VandeVoort

first: John

middle: P

last: Gaughan

first: Uros

last: Midic

first: Zoran

last: Obradovic

first: Keith

last: Latham


title: Listeria monocytogenes Grown at Refrigeration Temperature Shows Reduced Acid Survival and an Altered Transcriptional Response to Acid Shock

city: Ithaca

first: Reid

last: Ivy

address: 412 Stocking Hall

department: Food Science

institute: Cornell University

summary: Survival of the foodborne pathogen Listeria monocytogenes in acidic environments (e.g., stomach and low pH foods) is vital to its transmission. L. monocytogenes grows at temperatures as low as 2°C, and refrigerated, ready-to-eat foods have been sources of L. monocytogenes outbreaks. The purpose of this study was to determine whether growth at a low temperature (i.e., 7°C) affects the response of L. monocytogenes to sudden acid shock.

platform_organism:
Listeria monocytogenes
Listeria innocua

overall_design: A full genome microarray was used to determine changes in L. monocytogenes 10403S gene expression after exposure to acidified brain-heart infusion (BHI; pH 3.5) for 5 or 15 min.  To determine changes in gene transcription after acid treatment, separate competitive hybridizations were performed between cDNA from untreated cells (grown at 7°C or 37°C to log or stationary phase) and (i) cells acid treated for 5 min or (ii) cells acid treated for 15 min.  For L. monocytogenes grown to log or stationary phase, competitive hybridizations were performed between total cDNA from non-acid-treated cells grown to 7°C and non-acid-treated cells grown to 37°C to determine baseline differences in gene transcription between growth temperatures prior to acid treatment.  For each experiment, four biological replications were completed. Hybridizations were carried out with dye swapping (i.e., for each comparison, each cDNA from each condition was labeled with each dye exactly twice) to help minimize dye incorporation bias.

first: Kathryn

last: Boor

first: Martin

last: Wiedmann


title: Dynamics of the Transcriptome in the Primate Ovulatory Follicle

status: Public on Feb 15 2011

city: Beaverton

first: fuhua

last: xu

state: OR

address: 505 NW 185th Ave

institute: Oregon National Primate Research Center

summary:
Experiments were designed to evaluate changes in the transcriptome (mRNA levels) in the ovulatory, luteinizing follicle of rhesus monkeys, using a controlled ovulation (COv) model that permits analysis of the naturally selected, dominant follicle at specific intervals (0, 12, 24, 36 hours) after exposure to an ovulatory (exogenous hCG) stimulus during the menstrual cycle. Total RNA was prepared from individual follicles (n=4-8/timepoint), with an aliquot used for microarray analysis (AffymetrixTM Rhesus Macaque Genome Array) and the remainder applied to quantitative real-time PCR (q-PCR) assays. The microarray data from individual samples distinctly clustered according to timepoints, and ovulated follicles displayed markedly different expression patterns from unruptured follicles at 36 h. Between timepoint comparisons revealed profound changes in mRNA expression profiles. The dynamic pattern of mRNA expression for steroidogenic enzymes (CYP17A, CYP19A, HSD3B2, HSD11B1, HSD11B2), StAR, and gonadotropin receptors (LHCGR, FSHR) as determined by microarray analysis correlated precisely with those from blinded q-PCR assays. Patterns of mRNA expression for EGF-like factors (AREG, EREG) and processes (HAS2, TNFAIP6) implicated in cumulus-oocyte maturation/expansion were also comparable between assays. Thus, several mRNAs displayed the expected expression pattern for purported theca (e.g., CYP17A, AREG), granulosa (CYP19A, FSHR), cumulus (HAS2, TNFAIP6) cell, and surface epithelium (HSD11B) related genes in the rodent/primate preovulatory follicle. This database will be of great value in analyzing molecular and cellular pathways associated with periovulatory events in the primate follicle (e.g. follicle rupture, luteinization, inflammatory response, and angiogenesis), and for identifying novel gene products controlling mammalian fertility.

Keywords: time course

overall_design: Total RNA was prepared from individual follicles (n=4-8/timepoint). Dominant follicles were selected specific intervals (0, 12, 24, 36 hours) after exposure to an ovulatory (exogenous hCG) stimulus during the menstrual cycle.

first: Fuhua

last: Xu

first: Richard

last: Stouffer

first: Jorg

last: Miller

first: Jon

middle: D

last: Hennebold

first: Jay

middle: W

last: Wright

first: Gabriele

last: Leder

first: Michaele

last: Peters

first: Tim

last: Wintermantel

first: Bernhard

last: Lindenthal