title: Gene expression in Solenopsis invicta, Solenopsis richteri and hybrids

status: Public on Apr 01 2012

city: San Michele all'Adige

first: Lino

last: Ometto

state: Trento

address: Via Mach 1

department: Department of Biodiversity and Molecular Ecology

country: Italy

institute: Fondazione Edmund Mach

summary:
Ants provide remarkable examples of equivalent genotypes developing into divergent and discrete phenotypes. Diploid eggs can develop either into queens, which specialize in reproduction, or workers, which participate in cooperative tasks such as building the nest, collecting food, and rearing the young. In contrast, the differentiation between males and females generally depends upon whether eggs are fertilized, with fertilized (diploid) eggs giving rise to females and unfertilized (haploid) eggs giving rise to males. To obtain a comprehensive picture of the relative contributions of gender (sex), caste, developmental stage, and species divergence to gene expression evolution, we investigated gene expression patterns in pupal and adult queens, workers, and males of two species of fire ants, Solenopsis invicta and Solenopsis richteri. Microarray hybridizations revealed that variation in gene expression profiles is influenced more by developmental stage than by caste membership, sex, or species identity. The second major contributor to variation in gene expression was the combination of sex and caste. Although workers and queens share equivalent diploid nuclear genomes, they have highly distinctive patterns of gene expression in both the pupal and the adult stages, as might be expected given their extraordinary level of phenotypic differentiation. Overall, the difference in the proportion of differentially expressed genes was greater between workers and males than between workers and queens or queens and males, consistent with the fact that workers and males share neither gender nor reproductive capability. Moreover, between-species comparisons revealed that the greatest difference in gene expression patterns occurred in adult workers, a finding consistent with the fact that adult workers most directly experience the distinct external environments characterizing the different habitats occupied by the two species. Thus, much of the evolution of gene expression in ants may occur in the worker caste, despite the fact that these individuals are largely or completely sterile. Analyses of gene expression evolution revealed a combination of positive selection and relaxation of stabilizing selection as important factors driving the evolution of such genes.
Transcriptome analysis is a powerful tool for unveiling the distribution and magnitude of genetic incompatibilities between hybridizing taxa. The nature of such incompatibilities is closely associated with the evolutionary histories of the parental species and may differ across tissues and between the sexes. In eusocial insects, the presence of distinct castes that experience divergent selection regimes may result in additional distinct patterns of caste-specific hybrid incompatibilities. We analyzed levels of expression of >14,000 genes in two life stages of each caste and sex in the fire ants Solenopsis invicta and Solenopsis richteri and in their hybrids. We found strong contributions of both developmental stage and caste to gene expression patterns. In contrast, variability in expression was only weakly associated with species, with hybrid scores falling between those of the two parental species in both life stages and all castes. Hybrid incompatibilities were surprisingly modest, with only 16 genes in pupae and 18 genes in adults being mis-expressed, and indicating low levels of disruption in gene regulation in hybrids. The castes differed in numbers of mis-expressed genes, with males and workers each mis-expressing at least seven times as many genes as queens in both life stages. Interestingly, homologues of many of the mis-expressed genes have been implicated in behavioral variation in Drosophila melanogaster. General expression profiles of hybrids consistently were more similar to those of Solenopsis richteri than Solenopsis invicta, presumably because Solenopsis richteri trans-regulatory elements tend to be dominant to those of Solenopsis invicta and/or because there is an overall bias in the genetic composition of the hybrids towards Solenopsis richteri. Altogether, our results suggest that selection acting on each caste may contribute differently to interspecific divergence and speciation in this group of ants.

sample_organism: Solenopsis invicta x Solenopsis richteri

overall_design: We analyzed samples from two species, their hybrids: a total of 140 samples, consisting of either workers, queens or males (1-5 pooled individuals) and collected either as larvae, pupae or adults. Each sample was tested once (i.e. single biological replicate) against a common reference (dye-swap across experiments)


title: Integrative array-based approach identifies MZB1 as a frequently methylated putative tumor-suppressor in hepatocellular carcinoma  (MeDIP)

status: Public on Mar 31 2012

city: Tokyo

first: satoshi

last: matsumura

address: 1-5-45 Yushima, Bunkyo-ku

department: Dept. of Mol. Cytogenet.

country: Japan

institute: Inst. of Med. Sci., Tokyo Med. & Dent. Univ.

type: Methylation profiling by genome tiling array

summary: The analysis of DNA methylation profiles was performed by methylated DNA immunoprecipitation (MeDIP) using anti-5-methylcytidine antibody (Eurogentec, Seraing, Belgium) followed by the Human 244K Agilent CpG island microarray (Agilent, Santa Clara, CA)

overall_design: Genomic DNAs from Hep3B, HepG2 and HuH-7 cells were used for cancer samples and that from a normal liver tissue from surgical sample of colon cancer metastasis, as a control sample (C20)

first: Issei

last: Imoto

first: Ken-ichi

last: Kozaki

first: Takeshi

last: Matsui

first: Tomoki

last: Muramatsu

first: Mayuko

last: Furuta

first: Shinji

last: Tanaka

first: Michiie

last: Sakamoto

first: Shigeki

last: Arii

first: Johji

last: Inazawa


title: Abscission layer (AL) at the base of flower in rice using laser micro-dissection: NIL(qSH1) AL vs. Nipponbare AL, NIL(qSH1) AL vs. NIL(qSH1) upper region of AL, and NIL(qSH1) AL vs. NIL(qSH1) lower region of AL

city: Kita-gun

first: Saeko

last: Konishi-Sugita

state: Kagawa

address: 2393, Ikenobe, Miki-cho

department: Faculty of Agriculture

institute: Kagawa University

summary: Tissue-specific transcriptional profiling of the abscission layer (AL) at the base of young flower in rice using laser micro-dissection: NIL(qSH1) vs. Nipponbare.

overall_design: We used two rice varieties, NIL(qSH1) and Nipponbare. NIL(qSH1) is a nearly isogenic line containing the seed shattering gene qSH1. Seed shattering is easy in NIL(qSH1), but it is not in Nipponbare. So, we used some stages of young flower in NIL(qSH1) and some in Nipponbare. Four regions: 1. abscission layer region of NIL(qSH1), 2. upper abscission region of NIL(qSH1), 3. lower abscission layer region of NIL(qSH1), and 4. abscission layer region of Nipponbare. Sample experiments: NIL(qSH1) AL vs. Nipponbare AL, NIL(qSH1) AL vs. NIL(qSH1) upper region of AL, and NIL(qSH1) AL vs. NIL(qSH1) lower region of AL.

first: Hirokazu

last: Takahashi

first: Mikio

last: Nakazono

last: Izawa

first: Motohiro

last: Mihara

first: Ritsuko

last: Motoyama

first: Yoshiaki

last: Nagamura


title: Clonal competition with alternating dominance in multiple myeloma [44kCGH]

status: Public on Mar 28 2012

city: Phoenix

first: Jonathan

middle: J

last: Keats

state: Arizona

address: 445 N. Fifth Street

department: Integrated Cancer Genomics

country: USA

institute: Translational Genomics Research Institute (TGen)

summary:
Copy number and Gene expression profiling multiple myeloma patients at multiple stages of their individual clinical course
Identification of evolutionary paterns in multiple myeloma

overall_design: Copy number differences between individual CD138 purified tumor populations from multiple myeloma patients and control female using the Agilent 44B Human CGH microarray

first: P

middle: L

last: Bergsagel


title: C. elegans young adults cultured on Bacillus subtilis strain 67 vs cultured on E. coli OP50

status: Public on Mar 27 2012

city: Ipswich

first: Amit

last: Sinha

state: MA

address: 240 County Road

institute: New England Biolabs

summary: Transcriptional profiling of C. elegans young adult worms cultured on non-pathogenic Bacillus subtilis strain 67 versus age-matched worms cultured on the control lab food E. coli OP50. The goal was to identify genes regulated in response to differences in diet, which potentially confer immunity to later exposures to pathogenic Bacillus thuringiensis DB27.

overall_design:
One-condition experiment.
C. elegans young adults, cultured on : Bacillus subtilis strain 67 versus E. coli OP50. 4 biological replicates, including 2 dye-swaps.

first: Igor

last: Iatsenko

first: Ralf

last: Sommer


title: Array comparative genomic hybridization in oral cavity (head and neck) squamous cell carcinoma

city: New York

first: Luc

middle: GT

last: Morris

state: NY

address: 1275 York Avenue

institute: Memorial Sloan-Kettering Cancer Center

type: Genome variation profiling by genome tiling array

summary:
Genome wide high resolution assay of copy number in a series of frozen, microdissected head and neck cancers originating from the oral cavity.
The objective was to characterize areas of amplification and deletion in head and neck cancers arising from the oral cavity subsite.

overall_design: 31 tumors were snap frozen at the time of surgical resection, microdissected to >70% tumor content, and DNA extracted.

middle: G

first: Timothy

middle: A

last: Chan


title: Genomic profiling of renal cell carcinoma in patients with end-stage renal disease

status: Public on Mar 24 2012

city: Yufu-City, Oita

first: Toru

last: Inoue

address: Hasama-machi 1-1

department: Department of Molecular Pathology

institute: Faculty of medicineOita University

summary: In this study, eighty tumor samples from 63 patients with renal cell carcinoma (RCC)-end-stage renal disease (ESRD) were analyzed by array comparative genomic hybridization (array CGH) using the Agilent Whole Human Genome 4×44K Oligo Micro Array.

overall_design: 79 tumor samples from 63 patients with RCC-ESRD

first: Keiko

last: Matsuura

first: Taichiro

last: Yoshimoto

first: Lam

middle: T

last: Nguyen

first: Yoshiyuki

last: Tsukamoto

first: Chisato

last: Nakada

first: Naoki

last: Hijiya

first: Takahiro

last: Narimatsu

first: Takeo

last: Nomura

first: Fuminori

last: Sato

first: Yoji

last: Nagashima

first: Kenji

last: Kashima

first: Shingo

last: Hatakeyama

first: Chikara

last: Ohyama

first: Tomonori

last: Habuchi

first: Masayuki

last: Nakagawa

first: Masao

last: Seto

first: Hiromitsu

last: Mimata

first: Masatsugu

last: Moriyama


title: Differential microRNA Expression during Muscle Regeneration

status: Public on Apr 24 2012

city: San Antonio

first: Yongxin

last: Chen

state: TX

address: 7703 Floyd Curl Drive

department: Surgery

institute: University of Texas Health Science Center at San Antonio

summary: MicroRNAs (miRNAs) are important in the regulation of many biological processes including muscle development. However, little is known regarding miRNA regulation of muscle regeneration. In mature murine tibialis anterior muscle following injury, 298 miRNAs were significantly changed during the time course of muscle regeneration including 86 that were altered greater than 10-fold as compared to uninjured muscle. Temporal miRNA expression patterns were identified and included inflammation-related miRNAs (miR-223 and -147) that increased immediately after injury; this pattern contrasted to that of mature muscle-specific miRNAs (miR-1, -133a and -499) that were abruptly decreased following injury and then up-regulated in later regenerative events. Another cluster of miRNAs were transiently increased in the early days of muscle regeneration. This included miR-351, a miRNA that was also transiently expressed during myogenic progenitor cell (MPC) differentiation in vitro. Based on computational predictions, further studies demonstrated that E2f3 was a target of miR-351 in myoblasts. Moreover, knockdown of miR-351 expression inhibited MPC proliferation and promoted apoptosis during MPC differentiation, whereas miR-351 overexpression protected MPC from apoptosis during differentiation. Collectively, these observations suggest that miR-351 is involved in both the maintenance of MPC proliferation and the transition of MPC into differentiated myotubes. Thus, a novel, time-dependent sequence of molecular events during skeletal muscle regeneration has been identified, i.e., miR-351 inhibits E2f3 expression, a key regulator of cell cycle progression and proliferation, and promotes MPC proliferation and protects early differentiating MPC from apoptosis, important events in the hostile tissue environment after acute muscle injury.

overall_design: Skeletal muscles are damaged and repaired repeatedly throughout life. Muscle regeneration maintains locomotor function during aging and delays the appearance of clinical symptoms in neuromuscular diseases, such as Duchenne muscular dystrophy. The capacity for skeletal muscle growth and regeneration is conferred by satellite cells located between the basal lamina and the sarcolemma of mature myofibers. Upon injury, satellite cells reenter the cell cycle, proliferate, and then exit the cell cycle either to renew the quiescent satellite cell pool or to differentiate into mature myofibers. Despite recent advances, genes involved in these processes are still largely unknown. Understanding the molecular mechanisms that regulate satellite cell activities could promote development of novel countermeasures to enhance muscle regeneration that is compromised by diseases or aging. Using a muscle injury mouse model, we profiled miRNA expression during muscle regeneration.


status: Public on Mar 21 2012

first: Amit

last: Sinha

summary: Transcriptional profiling of P. pacificus young adult worms exposed to pathogen Xenorhabdus nematophila for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode C. elegans to the same pathogen. Other experiments which are a part of this study include expression profiling of C. elegans and P. pacificus on other pathogens including Staphylococcus aureus, Serratia marcescens and Xenorhabdus nematophila.

overall_design:
One-condition experiments.
P. pacificus young adults: Exposed to Bacillus thuringiensis DB27 versus exposed to E. coli OP50 : 4 hours. 4 biological replicates for each condition, including 2 dye-swaps.

first: Robbie

last: Rae

first: Igor

last: Iatsenko

first: Ralf

last: Sommer


summary: Transcriptional profiling of P. pacificus young adult worms exposed to pathogen Staphylococcus aureus for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode C. elegans to the same pathogen. Other experiments which are a part of this study include expression profiling of C. elegans and P. pacificus on other pathogens including , Bacillus thuringiensis DB27, Serratia marcescens and Xenorhabdus nematophila.

overall_design:
One-condition experiments.
P. pacificus young adults: Exposed to Staphylococcus aureus versus exposed to E. coli OP50 : 4 hours. 3 biological replicates for each condition, including 2 dye-swaps.


summary: Transcriptional profiling of P. pacificus young adult worms exposed to pathogen Serratia marcescens for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode C. elegans to the same pathogen. Other experiments which are a part of this study include expression profiling of C. elegans and P. pacificus on other pathogens including , Bacillus thuringiensis DB27, Serratia marcescens and Xenorhabdus nematophila.

overall_design:
One-condition experiments.
P. pacificus young adults: Exposed to Serratia marcescens versus exposed to E. coli OP50 : 4 hours. 4 biological replicates for each condition, including 2 dye-swaps.


summary: Transcriptional profiling of C. elegans young adult worms exposed to pathogen Xenorhabdus nematophila for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode Pristionchus pacificus to the same pathogen. Other experiments which are a part of this study include expression profiling of C. elegans and P. pacificus on other pathogens including Bacillus thuringiensis, Staphylococcus aureus, and Serratia marcescens.

overall_design:
One-condition experiments.
C. elegans young adults: Exposed to Xenorhabdus nematophila versus exposed to E. coli OP50 : 4 hours. 4 biological replicates for each condition, including 2 dye-swaps.


title: Pristionchus pacificus and Caenorhabditis elegans: Dauer and Dauer exit versus mix-stage comparisons

status: Public on Mar 22 2012

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

sample_organism:
Caenorhabditis elegans
Pristionchus pacificus

overall_design: Refer to individual Series

first: Christoph

last: Dieterich


title: C. elegans immune response to Staphylococcus aureus, 4 hour exposure

summary:
Transcriptional profiling of C. elegans young adult worms exposed to pathogen Staphylococcus aureus for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode Pristionchus pacificus to the same pathogen. Other experiments which are a part of this study include expression profiling of C. elegans and P. pacificus on other pathogens including Staphylococcus aureus, Serratia marcescens, Xenorhabdus nematophila.

Keywords: Expression profiling by array

overall_design:
One-condition experiments.
C. elegans young adults: Exposed to Staphylococcus aureus versus exposed to E. coli OP50 : 4 hours. 4 biological replicates for each condition, including 2 dye-swaps.


summary: Transcriptional profiling of P. pacificus young adult worms exposed to pathogen Xenorhabdus nematophila for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode C. elegans to the same pathogen. Other experiments which are a part of this study include expression profiling of C. elegans and P. pacificus on other pathogens including Bacillus thuringiensis DB27, Staphylococcus aureus, and Serratia marcescens.

overall_design:
One-condition experiments.
P. pacificus young adults: Exposed to Xenorhabdus nematophila versus exposed to E. coli OP50 : 4 hours. 4 biological replicates for each condition, including 2 dye-swaps.


status: Public on Mar 13 2012

summary:
Transcriptional profiling of C. elegans young adult worms exposed to pathogen Bacillus thuringiensis DB27 for 4 hours versus age-matched worms exposed to onctrol lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode Pristionchus pacificus to the same pathogen. Other experiments which are a part of this study include expression profiling of C. elegans and P. pacificus on other pathogens including Staphylococcus aureus, Serratia marcescens, Xenorhabdus nematophila.

Keywords: Expression profiling by array

overall_design:
One-condition experiments.
C. elegans young adults: Exposed to Bacillus thuringiensis DB27 versus exposed to E. coli OP50 : 4 hours. 3 biological replicates for each condition, including 1 dye-swap.


title: Pho85, Pcl1, and Hms1 Signaling Governs Candida albicans Morphogenesis Induced by Elevated Temperature or Hsp90 Compromise

status: Public on Mar 20 2012

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

country: Canada

institute: National Research Council of Canada

type: Genome binding/occupancy profiling by genome tiling array


summary: Transcriptional profiling of C. elegans young adult worms exposed to pathogen Serratia marcescens for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode Pristionchus pacificus to the same pathogen. Other experiments which are a part of this study include expression profiling of C. elegans and P. pacificus on other pathogens including Bacillus thuringiensis, Staphylococcus aureus, and Xenorhabdus nematophila.

overall_design:
One-condition experiments.
C. elegans young adults: Exposed to Serratia marcescens versus exposed to E. coli OP50 : 4 hours. 4 biological replicates for each condition, including 2 dye-swaps.


title: Allele-specific expression in familial pancreatic cancer

city: Baltimore

first: Aik Choon

last: Tan

state: MD

address: 1650 Orleans Street, RM 1M86

department: The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins

institute: Johns Hopkins University

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


title: P. pacificus and C. elegans exposed to various pathogens

platform_organism:
Caenorhabditis elegans
Pristionchus pacificus


title: mRNA degradation in Mycobacterium smegmatis under aerobic conditions

status: Public on Mar 08 2012

city: Seattle

first: Tige

last: Rustad

state: WA

address: 307 Westlake Avenue N, Suite 500

department: Pathobiology

institute: Seattle Biomedical Research Institute

summary:
Transcription was arrested using 50 ug/ul of rifampin leaving RNA degradation as the sole vector responsible for mRNA abundance.
mRNA half-lives were calculated from the decay of signal intensity from T0.

overall_design: Three replicates were sampled before transcription arrest, and after 5 and 10 minutes of mRNA decay for a total of 9 arrays.  Five minutes of RNA degradation occurred during the processing of these samples, therefore sample times, indicated in the sample name, represent 0, five, and ten minutes of RNA degradation.

first: William

last: Brabant


title: Gene expression profiling of C57BL/6 mouse lung tissue with various treatments

status: Public on Mar 14 2012

city: Philadelphia

first: Floyd

last: Dukes

state: PA

address: 3615 Civic Center Boulevard

institute: University of Pennsylvania


title: Global transcriptional profile at a higher fermentation temperature in jinggangmyicn-producing S.hygroscopicus 5008

status: Public on Feb 09 2012

city: shanghai

first: hang

last: wu

address: Huashan Road

country: China

institute: sjtu

summary: To explore the molecular mechanism of the positive thermoregulation on Jinggangmycin A biosynthesis, the transcriptomes of  S. hygroscopicus 5008 cultivated at 30℃ or 37℃ in liquid medium were compared by microarray analysis.

sample_organism: Streptomyces hygroscopicus subsp. jinggangensis 5008

overall_design: Global gene expression in the strain 5008 was measured at 30℃ or 37℃, respectively. Three independent experiments were performed at each condition.

first: Hang

last: Wu


title: Profiling of peripheral blood mononuclear cells from HIV-1-infected elite suppressors, viremic patients, and uninfected control donors

status: Public on Feb 22 2012

first: Kenneth

middle: W

last: Witwer

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

type:
Non-coding RNA profiling by array
Other


title: Tiled Microarray Identification of Novel Viral Transcript Structures and Distinct Transcriptional Profiles During Two Modes of Productive Murine Gammaherpesvirus 68 Infection.

status: Public on Feb 16 2012

city: Stony Brook

first: Laurie

last: Krug

address: 130 Life Sciences Bldg

department: Molecular Genetics and Microbiology

institute: Stony Brook University

type: Expression profiling by genome tiling array

summary:
We applied a custom tiled microarray to examine murine gammaherpesvirus 68 (MHV68) polyadenylated transcript expression in a timecourse of de novo infection of fibroblast cells and following phorbol ester-mediated reactivation from a latently-infected B cell line. During de novo infection, all ORFs were transcribed and clustered into four major temporal groups that were overlapping, yet distinct from clusters based on the phorbol ester-stimulated B cell reactivation timecourse. High-density transcript analysis at two-hour intervals during de novo infection mapped gene boundaries with a 20-nt resolution, including a previously undefined ORF73 transcript and the MHV68 ORF63 homolog of KSHV vNLRP1. ORF6 transcript initiation was mapped by tiled array and confirmed by 5' RACE. The ~1.3 kb region upstream of ORF6 was responsive to lytic infection and MHV68 RTA, identifying a novel RTA-responsive promoter. Transcription in intergenic regions consistent with the previously defined expressed genomic regions was detected during both types of productive infection. We conclude that the MHV68 transcriptome during de novo fibroblast infection and upon phorbol ester-stimulated B cell reactivation is dynamic and distinct, highlighting the need to evaluate further transcript structure and the context-dependent molecular events that govern viral gene expression during chronic infection.

This SuperSeries is composed of the SubSeries listed below.


title: The acute milk yield response to frequent milking in early lactation is mediated by genes transiently regulated by milk removal.

status: Public on Feb 27 2012

city: Burlington

first: Emma

middle: Hull

last: Wall

state: VT

address: 89 Beaumont Ave

department: Medicine

institute: University of Vermont

summary: Milking dairy cows four times daily (4X) instead of twice daily (2X) during early lactation stimulates an increase in milk yield that partly persists through late lactation; however, the mechanisms behind this response are unknown.  We hypothesized that the acute mammary response to regular milkings would be transient and would involve different genes from those that may be specifically regulated in response to 4X. Nine multiparous cows were assigned at parturition to unilateral frequent milking (UFM; 2X of the left udder half, 4X of the right udder half). Mammary biopsies were obtained from both rear quarters at 5 days in milk (DIM), immediately after 4X glands had been milked (Experiment 1; n = 4 cows), or 2.5 h after both udder halves had last been milked (Experiment 2; n = 5 cows).  Affymetrix GeneChip® Bovine Genome Arrays were used to measure gene expression.  Eight hundred and fifty five genes were differentially expressed in mammary tissue between 2X vs. 4X glands of cows in experiment 1 (FDR ≤ 0.05), whereas none were differentially expressed in experiment 2 using the same criterion.  We conclude that there is an acute transcriptional response to milk removal, but 4X milking did not elicit differential expression of unique genes.  Therefore, there does not appear to be a sustained transcriptional response to 4X milking on day 5 of lactation.  Using a differential expression plot of data from both experiments, as well as qRT-PCR, we identified at least two genes that may be responsive to both milk removal and to 4X milking.  Therefore, the milk yield response to 4X milking may be mediated by genes that are acutely regulated by removal of milk from the mammary gland.

overall_design: 8 samples from 4 cows in experiment 1; 6 samples from 3 cows in experiment 2

first: E

middle: H

first: J

middle: P

last: Bond

first: T

middle: B

last: McFadden


title: Genome-wide DNA methylation analyses in the brain reveal four differentially methylated regions between humans and non-human primates

status: Public on Mar 01 2012

city: Los Angeles

first: Jinkai

last: Wang

state: CA

address: 650 Charles E. Young Drive South, CHS 33-228

institute: University of California, Los Angeles

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

first: Xiangyu

last: Cao

first: Yanfeng

last: Zhang

first: Bing

last: Su


title: Resolution of ntla-dependent transcriptome using caged molecules

city: Stanford

first: James

last: Chen

address: 269 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University


title: Microarray analysis of gene expression in rams experimentally infected with a rough virulent strain of Brucella ovis (chronic 2 phase)

status: Public on Feb 08 2012

city: Botucatu

first: João Marcelo

middle: Azevedo de Paula

last: Antunes

state: São Paulo

address: FMVZ, Distrito de Rubião Júnior

department: Higiene Veterinária e Saúde Pública

country: Brazil

institute: UNESP

summary: The study demonstrated the gene expression through microarray analysis of total mRNA in rams experimentally infected with a rough (R) virulent strain of Brucella ovis in reproductive organs (epididymus, testicles, ampolae, vesicular glands, bulbourethral glands) and a pool of lymph nodes (inguinal and scrotal) at three different times: acute phase (60 days post challenge [dpc]), chronic phase 1 (120dpc), and chronic phase 2 (240dpc) of infection. To further define the gene expression changes associated with infected rams, the profiles of a control group (0 dpc) of rams was compared using the Affymetrix Bovine Genome Array. Of the 23,000 genes that were analyzed on the array, B. ovis infection in rams’ tissues revealed 139, 930 and 744 Differentially Expressed Genes (DEGs) in the acute, chronic 1, and chronic phase 2 of infection, respectively. Among the three phases of infection, 44 DEGs (30 known and 14 unknown genes) were expressed in common. The biological functions of immune cell trafficking, immunological disease, infectious disease, inflammatory disease, inflammatory response and cellular movement were significant at the three phases of infection. The results support the first microarray analysis of ram tissues infected with an R strain of B. ovis.

overall_design:
A total of twelve 12-month-old healthy Santa Inês rams, previously diagnosed as negative for brucellosis/visna maedi/toxoplasmosis/neosporosis, were selected for the study. The rams were kept in an isolated pen and experimentally challenged with a rough (R) virulent B. ovis PA strain (ATCC 25840). For the experiment, the rams were classified during the course of infection according to time: 0 dpc (control), 60 dpc (acute phase), 120 dpc (chronic phase 1) and 240 dpc (chronic phase 2). For each time, the tissues epididymus, testicles, ampolae, vesicular glands, bulbourethral glands, and a pool of lymph nodes (inguinal and scrotal) were collected. Three rams were euthanized and necropsied for tissues collection purposes for each time. To define the gene expression changes associated with infected rams, the profile of a control group (0 dpc) of rams was compared using microarray technology.
REPLACE
This dataset includes control samples and chronic 2 phase samples.

first: João

middle: M

last: de Paula Antunes

first: Susan

middle: D

last: Allendorf

first: Camila

last: Appolinário

first: Marina

last: Peres

first: Acácia

middle: F

last: Vicente

first: Clóvis

middle: R

last: Fonseca

first: Didier

middle: Q

last: Cagnini

first: Fernando

last: Listoni

first: Sony

last: Bicudo

first: Paula

last: Figueiredo

first: José

last: Buratini Júnior

first: Ruth

middle: C

last: Galindo

last: de La Fuente

first: Jane

last: Megid


title: Nitrogen-ion-beam implantation effect on rice dry seeds

city: Luoyang

first: Huiyuan

last: Ya

state: Henan

address: 71# Longmen Road

department: Life science Department

institute: Luoyang Nornal University

summary: Analysis of 96-hours-old-rice seedlings with promoted-growth induced by implantation with low-energy nitrogen ion beam. Ion-beam implantation can induce changes in 351 up-regulated transcripts and 470 down-regulated transcripts, including signaling proteins, kinases, plant hormones, transposable elements, transcription factors, non-coding protein RNAs, secondary metabolites, resistance proteins, peroxidase, chromatin modification and even miRNAs. Results provide insight into the molecular basis of biological effects of plants that implanted by ion beam.

overall_design: Three sample groups—the controls, the ion-beam implanted samples and vacuum-treated samples. Three replicates were included in each sample group. Radiation induced gene expression rice seedlings was measured at 96 hours after germination of the seeds.

first: Weidong

last: Wang


title: IGFBP2 driven glioma progression is prevented by blocking a clinically significant network of integrin, ILK, and NK-kB

status: Public on Feb 02 2012

city: Tampere

first: Matti

last: Annala

address: Korkeakoulunkatu 1

country: Finland

institute: Tampere University of Technology

summary: Insulin-like growth factor-binding protein 2 (IGFBP2) is increasingly recognized as a glioma oncogene, emerging as a target for therapeutic intervention. In this study, we used an integrative approach to characterizing the IGFBP2 network, combining transcriptional profiling of human glioma with validation in glial cells and the replication competent ASLV long terminal repeat with a splice acceptor/tv-a glioma mouse system. We demonstrated that IGFBP2 expression is closely linked to genes in the integrin and integrin-linked kinase (ILK) pathways and that these genes are associated with prognosis. We further showed that IGFBP2 activates integrin β1 and down- stream invasion pathways, requires ILK to induce cell motility, and activates NF-κB. Most significantly, the IGFBP2/integrin/ILK/NF-κB network functions as a physiologically active signaling pathway in vivo by driving glioma progression; interfering with any point in the pathway markedly inhibits progression. The results of this study reveal a signaling pathway that is both targetable and highly relevant to improving the survival of glioma patients.

overall_design: We performed cDNA microarray analysis to compare two stably expressing cell lines originating from SNB19; two clones expressing a mutant form of IGFBP2 that cannot bind integrin (RGD → RGE point mutation; referred to as RGE mutant); and two clones expressing wild-type IGFBP2. SNB19 clones transfected with empty vector were placed in the reference channel in each hybridization.

first: Kristen

last: Holmes

middle: J

first: Chua

last: Yingxuan

first: Sarah

last: Dunlap

first: Yuexin

last: Liu

first: Niek

last: Hugen

first: Lynette

last: Moore

first: David

last: Cogdell

first: Limei

last: Hu

last: Nykter

first: Kenneth

last: Hess

first: Gregory

middle: N

last: Fuller

first: Wei

last: Zhang


title: Slf1p and Sro9p affinity isolations; SLF1 overexpression

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

type:
Expression profiling by array
Other


title: Microarray analysis of gene expression in rams experimentally infected with a rough virulent strain of Brucella ovis (chronic 1 phase)

first: João Marcelo

last: Antunes

overall_design:
A total of twelve 12-month-old healthy Santa Inês rams, previously diagnosed as negative for brucellosis/visna maedi/toxoplasmosis/neosporosis, were selected for the study. The rams were kept in an isolated pen and experimentally challenged with a rough (R) virulent B. ovis PA strain (ATCC 25840). For the experiment, the rams were classified during the course of infection according to time: 0 dpc (control), 60 dpc (acute phase), 120 dpc (chronic phase 1) and 240 dpc (chronic phase 2). For each time, the tissues epididymus, testicles, ampolae, vesicular glands, bulbourethral glands, and a pool of lymph nodes (inguinal and scrotal) were collected. Three rams were euthanized and necropsied for tissues collection purposes for each time. To define the gene expression changes associated with infected rams, the profile of a control group (0 dpc) of rams was compared using microarray technology.
REPLACE
This dataset includes control samples and chronic 1 phase samples.

first: João

last: de Paula Antunes

first: Susan

last: Allendorf

first: Camila

last: Appolinário

first: Marina

middle: G

last: Peres

first: Acácia

last: Vicente

first: Clóvis

last: Fonseca

first: Didier

last: Cagnini

first: Fernando

last: Listoni

first: Sony

last: Bicudo

first: Paula

last: Figueiredo

first: José

last: Buratini Júnior

first: Ruth

last: Galindo

last: de La Fuente

last: Megid


title: Microarray analysis of gene expression in rams experimentally infected with a rough virulent strain of Brucella ovis (acute phase)

overall_design:
A total of twelve 12-month-old healthy Santa Inês rams, previously diagnosed as negative for brucellosis/visna maedi/toxoplasmosis/neosporosis, were selected for the study. The rams were kept in an isolated pen and experimentally challenged with a rough (R) virulent B. ovis PA strain (ATCC 25840). For the experiment, the rams were classified during the course of infection according to time: 0 dpc (control), 60 dpc (acute phase), 120 dpc (chronic phase 1) and 240 dpc (chronic phase 2). For each time, the tissues epididymus, testicles, ampolae, vesicular glands, bulbourethral glands, and a pool of lymph nodes (inguinal and scrotal) were collected. Three rams were euthanized and necropsied for tissues collection purposes for each time. To define the gene expression changes associated with infected rams, the profile of a control group (0 dpc) of rams was compared using microarray technology.
REPLACE
This dataset includes control samples and acute phase samples.

first: Jane


title: Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis

status: Public on Jan 20 2012

city: Lausanne

first: Ruben

last: Hartkoorn

state: Vaud

address: SV 3533 (Bâtiment SV) Station 19

department: GHI/SV

institute: EPFL


title: Mosaic Amplification of Multiple Receptor Tyrosine Kinase Genes in Glioblastoma

status: Public on Jan 01 2012

city: Boston

first: Matija

last: Snuderl

address: 55 Fruit St.

department: Pathology

institute: MAssachusetts General Hospital

summary:
Here we present a novel example of genetic heterogeneity in human malignant brain tumors, in which multiple closely-related driver genes are amplified and activated simultaneously in adjacent intermingled cells. We have observed up to 3 different receptor tyrosine kinases (EGFR, MET, PDGFRA) amplified in single tumors in different cells in a mutually exclusive fashion.
However, these subpopulations cannot be always observed with a genome wide studies such as aCGH. Here we include aCGH on three such mosaic cases.
Analyses were performed on 350 archival specimens of glioblastoma, WHO Grade IV, seen at the Department of Pathology, Massachusetts General Hospital from 2009 to 2011.

overall_design: CGH on three such mosaic cases.

first: A

last: Iafrate


title: Ralstonia solanacearum_GMI1000 and UW551_20 C and 28 C.

status: Public on Jan 15 2012

city: Madison

first: Lavanya

last: Babujee

address: Department of Plant Pathology

institute: UW-Madison

sample_organism:
Ralstonia pseudosolanacearum GMI1000
Ralstonia solanacearum UW551


title: Light effect on the hormonal and transcriptional status of winter and spring wheat plants during cold hardening

status: Public on Jan 31 2012

city: Budapest

first: Endre

last: Sebestyén

address: Üllői út 26.

department: 1st Department of Pathology and Experimental Cancer Research

country: Hungary

institute: Semmelweis University

summary: The effect of light during the development of freezing tolerance was studied in winter wheat (Triticum aestivum L. var. Mv Emese) and spring wheat variety Nadro. Ten-day-old plants were cold hardened at 5°C for 12 days either under normal (250 mmol m-2 s-1) or low light (20 mmol m-2 s-1) conditions.

overall_design: Samples of Emese (E) and Nadro (N) plants grown at 18°C under normal (NL) and low (LL) light fluences were compared to each other in a simple loop design and E-NL vs. E-LL; N-NL vs. N-LL; E-NL vs. NLL and E-LL vs. N-LL comparisons were made.

first: Vilmos

last: Soós


title: Pan-genomic analysis of bovine monocyte-derived macrophage gene expression in response to in vitro infection with Mycobacterium avium subspecies paratuberculosis

city: Dublin

first: David

middle: E

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

summary:
Background: Mycobacterium avium subspecies paratuberculosis (MPTb) is the causative agent of Johne’s disease, an intestinal disease of ruminants with major economic consequences. MPTb bacilli are phagocytosed by host macrophages upon exposure where they persist, resulting in lengthy subclinical phases of infection that can lead to immunopathology and disease dissemination. Consequently, analysis of the macrophage transcriptome in response to MPTb infection can provide valuable insights into the molecular mechanisms that underlie Johne’s disease. Here, we investigate pan-genomic gene expression in bovine monocyte-derived macrophages (MDM) purified from seven age-matched non-related females, in response to in vitro infection with MPTb (multiplicity of infection 2:1) at intervals of 2 hours, 6 hours and 24 hours post-infection.
Results: Differentially expressed genes were identified by comparing the transcriptomes of the infected MDM to the control MDM at each time point (adjusted P-value threshold ≤ 0.10). 1,050 differentially expressed unique genes were identified 2 hours post-infection, with 974 and 84 differentially expressed unique genes detected 6 hours and 24 hours post-infection, respectively. Furthermore, in the infected MDM the number of upregulated genes exceeded the number of downregulated genes at each time point, with the fold-change in expression for the upregulated genes markedly higher than that for the downregulated genes.
Conclusions: Inspection and systems analysis of the differentially expressed genes revealed changes in the expression profiles of genes involved in the inflammatory response, cell signalling pathways and apoptosis. The transcriptional changes associated with cellular signalling and the inflammatory response may reflect different immuno-modulatory mechanisms that underlie host-pathogen interactions during infection.

overall_design: Affymetrix GeneChip® Bovine Genome Arrays were used to examine gene expression of bovine monocyte-derived macrophages (MDM) after in vitro challenge with Mycobacterium avium subspecies paratuberculosis across a time series of 2 hr, 6 hr and 24 hr post-challenge. A 0 hr control treatment was also generated and seven different age-matched female Holstein-Friesian cattle were used for each time-point/treatment combination for a total of 49 microarrays, one of which was excluded from analysis since it did not pass quality control.

first: Maria

last: Taraktsoglou

first: Kate

last: Killick

first: Nicolas

last: Nalpas

first: John

middle: A

last: Browne

first: Stephen

last: Park

first: Karsten

last: Hokamp

first: Eamonn

last: Gormley

last: Magee


title: Transcriptional changes of phytoplasma under host switching between plant and insect

status: Public on Jan 16 2012

city: Bunkyo

first: Kenro

last: Oshima

state: Tokyo

institute: The University of Tokyo


title: Oryza sativa L. cv. Kita-ake: Wild type control vs. OsbZIP39deltaC overexpressed

city: Tsukuba

first: Hideyuki

last: Takahashi

address: Kannondai 2-1-2

institute: National Institute of Agrobiological Sciences

summary: Transcription factor encoded by OsbZIP39 gene is regulator of the Endoplasmic Reticulum Stress Response. The truncated form of OsbZIP39 without the transmembrane domain (OsbZIP39deltaC) is an active form. To identify the potential downstream genes regulated by OsbZIP39, we performed the rice 44k oligo microarray analysis.

overall_design: Total RNA was extracted from 7-day-old rice shoots of the wild type control and the OsbZIP39deltaC overexpression line grown on the MS medium, and subjected to 44k oligo-DNA microarray with 4 biological replicates.

first: Taiji

last: Kawakatsu

first: Yuhya

last: Wakasa

first: Shimpei

last: Hayashi

first: Fumio

last: Takaiwa


title: Specific post-translational histone mod. of neutrophil extracellular traps as immunogens & potential SLE Ab targets.

status: Public on Jan 26 2012

first: Chih Long

last: Liu

address: 269 Campus Drive

department: Medicine - Imm. & Rheum

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Escherichia coli
Gallus gallus
Homo sapiens
Bos taurus
Oryctolagus cuniculus
Mus musculus

overall_design: Refer to individual Series

first: ChihLong

first: Stephanie

last: Tangsombatvisit

first: Jacob

last: Rosenberg

first: Emily

last: Gillespie

first: Ash

last: Alizadeh

first: Or

last: Gozani

first: Paul

last: Utz


title: Microarray analysis of gene expression in rams experimentally infected with a rough virulent strain of Brucella ovis

first: João Marcelo

last: Antunes


title: Defl1 knockdown gene expression in Zebrafish 12.5 hpf embryos

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh, The Institute of Genetics and Cancer

summary: Microarray analysis was performed on tail bud stage morphants and stage-matched control injected embryos in order to determine any global gene expression changes occurring as a result of defbl1 knockdown.

overall_design: 2 biological replicates per treatment on single dye Agilent Array

first: Natalie

middle: L

last: Reynolds

first: Julia

last: Dorin


title: Effects of UV and temperature stress on snakelocks sea anemone: ectoderm and endoderm

city: NICE

first: Cecile

last: Sabourault

address: Faculte des Sciences, Parc Valrose, BP 71

department: Biology

country: France

institute: University of Nice

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


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

city: Duluth

first: Daniel

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

institute: US EPA

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

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

first: Natalia

last: Garcia-Reyero

first: B

last: Escalon

first: Kathleen

last: Jensen

first: Jenna

last: Cavallin

first: Elizabeth

last: Makynen

last: Durhan

first: Michael

last: Kahl

first: Linnea

last: Thomas

first: Edward

last: Perkins

first: Gerald

middle: T

last: Ankley


title: Impact of beta-arrestin-2 deficiency on intestinal tumorigenesis in Apc-mutated mice

city: Montpellier

first: Caroline

last: Bonnans

address: 141 rue de la Cardonille

department: Oncology

institute: Functional Genomic Institute


title: [URE3] Prion formation by the Candida albicans Ure2p (but not by C. glabrata Ure2p)-ScUre2

city: Bethesda

first: Huei-Fung

last: Tsai

address: 10 Center Dr. Bldg. 10 Rm. 11N228

department: LCID

institute: NIH/NIAID

summary: [URE3] is a prion (infectious protein) of the Saccharomyces cerevisiae Ure2p, a regulator of nitrogen catabolism. We find that the Ure2p of Candida albicans and C. glabrata also regulate nitrogen catabolism. Conservation of amino acid sequence within the prion domain of Ure2p has been proposed as evidence that the [URE3] prion helps its host. We show that the C. albicans Ure2p, which does not conserve this sequence, can nonetheless form a [URE3] prion, but the C. glabrata Ure2p, which does have the conserved sequence, cannot form [URE3]. These results suggest that the sequence is not conserved to preserve prion forming ability.

overall_design: Two groups (WT and ure2 mutant) consisted of 4 biological replicates in which a ure2 deleted strain sample was paired with the wild type strain sample. Each group included 1 reciprocally labeled sample.


title: Global gene expression analysis of heterotypic interactions between cancer cells and osteoblasts in vitro

status: Public on Jan 06 2012

city: Zurich

first: Michal

last: Rajski

address: Winterthurerstrasse 190

department: Institute of Physiology

institute: University of Zurich

summary:
Bone is the most common site of breast cancer metastasis, and this type of metastasis is a main cause of morbidity. Because breast cancer is a heterogeneous disease, the interactions between the cancer cells and the skeletal host cells, such as osteoblasts, might be diverse. Thus far, these tumor-osteoblast interactions have not yet been well characterized using a genomic approach. We hypothesized that gene expression signatures induced by tumor-osteoblast interactions might be of clinical relevance. To examine these gene expression signatures, we established an ex vivo co-culture model with benign human cells and a panel of 5 malignant breast epithelial cells in combination with primary human osteoblasts and determined associated gene expression changes using cDNA microarrays.

This SuperSeries is composed of the SubSeries listed below.


city: Newbury Park

first: Chetan

last: Deshpande

address: One Amgen Center Dr

department: Molecular Sciences

institute: Amgen Inc

summary: ChIP-on-chip experiment from Ramos cells to analyze genome-wide CRTC2 binding sites in germinal center B cells.  The goal was to combine information from our ChIP-on-chip and expression array analyses to compile a list of CRTC2 target genes.

overall_design: CRTC2 was immunoprecipitated from sheared chromatin isolated from untreated Ramos cells using 2 antibodies which recognize distinct epitopes on the CRTC2 protein.  Immunoprecipitates were compared to total input chromatin.  2 biological replicates were performed for each antibody.

first: Mara

middle: H

last: Sherman


title: Hsp90 Stress Potentiates Rapid Cellular Adaptation through Induction of Aneuploidy

status: Public on Dec 31 2011

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute


title: Gene transcription profiles showing early systemic response to E. coli (k2bh2) infection in bovine liver

city: Tjele

first: A.J. (Bart)

last: Buitenhuis

address: Blichers allé 20

department: Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology

country: Denmark

institute: Aarhus University

summary: We studied the response to infection and associated perturbations to the bovine liver’s normal function by examining gene transcription data from liver biopsies collected following an E. coli infection in the udder of primiparous dairy cows. This is the first study to examine gene transcription responses to systemic infection by the E. coli bacterium in dairy cows. First, we verified that the inoculation protocol resulted in systemic infection in the cows. This was done based on records on three clinical symptoms: body temperature and amount of E. coli bacteria and leukocytes in milk samples. Second, we examined gene transcription patterns underlying the clinical traits. Gene transcription levels at times of peak values for the clinical traits were estimated in the liver to study indications of an acute phase response to systemic E. coli infection in the cows. Finally, we compared gene transcription responses to E. coli infection and lipopolysaccaride (LPS) inoculation.

overall_design: Sixteen healthy, primiparous Danish Holstein-Friesian cows were challenged intramammarily with E. coli 4 to 6 weeks following parturition. Gene transcription levels for fifteen of the cows were used to study infection responses. We compared gene transcription levels before and after E. coli infection for all fourteen cows.

first: Peter

last: Sørensen

first: A

first: Hanne

middle: B

last: Jørgensen

first: Christine

middle: M

last: Røntved

first: Klaus

last: Ingvartsen


title: Global gene expression of bovine monocyte-derived macrophages in response to in vitro challenge with Mycobacterium bovis

first: David

last: MacHugh

summary:
Background: Mycobacterium bovis, the causative agent of bovine tuberculosis, is a major cause of mortality in global cattle populations. Macrophages are among the first cells types to encounter M. bovis following exposure and the response elicited by these cells is pivotal in determining the outcome of infection. Here, a functional genomics approach was undertaken to investigate global gene expression profiles in bovine monocyte-derived macrophages (MDM) purified from seven age-matched non-related females, in response to in vitro challenge with M. bovis (multiplicity of infection 2:1). Total cellular RNA was extracted from non-challenged control and M. bovis-challenged MDM for all animals at intervals of 2 hours, 6 hours and 24 hours post-challenge and prepared for global gene expression analysis using the Affymetrix® GeneChip® Bovine Genome Array.
Results: Comparison of M. bovis-challenged MDM gene expression profiles with the non-challenged MDM controls at each time point identified 3,529 differentially expressed genes after 2 hours post-challenge, with 5,211 and 6,150 differentially expressed genes detected at the 6 hour and 24 hour time points, respectively (adjusted P-value threshold ≤ 0.05). Notably, the number of downregulated genes exceeded the number of upregulated genes in the M. bovis-challenged MDM across all time points; however, the fold-change in expression for the upregulated genes was markedly larger than that for the downregulated genes. Systems analysis revealed enrichment for genes involved in: (1) the inflammatory response; (2) cell signalling pathways, including Toll-like receptors and intracellular pathogen recognition receptors (PRRs)-receptors; and (3) apoptosis.
Conclusions: The increased number of downregulated genes is consistent with previous studies showing that M. bovis infection is associated with the repression of host gene expression. The results also support important roles for MYD88-independent signalling and intracellular PRRs in mediating the host response to M. bovis, which to our knowledge have not been reported previously.

overall_design: Affymetrix GeneChip® Bovine Genome Arrays were used to examine gene expression of bovine monocyte-derived macrophages (MDM) after in vitro challenge with Mycobacterium bovis across a time series of 2 hr, 6 hr and 24 hr post-challenge. A 0 hr control treatment was also generated and seven different age-matched female Holstein-Friesian cattle were used for each time-point/treatment combination for a total of 49 microarrays.

last: Magee

first: Maria

last: Taraktsoglou

first: Kate

last: Killick

first: Nicolas

last: Nalpas

first: John

last: Browne

first: Stephen

middle: D

last: Park

first: Kevin

last: Conlon

last: Lynn

first: Karsten

last: Hokamp

middle: V

last: Gordon

first: Eamonn

last: Gormley


title: The PII protein GlnK is a pleiotropic regulator for morphological differentiation and secondary metabolism in Streptomyces coelicolor

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

country: Germany

institute: Institute for Bioinformatics and Medical Informatics

first: Alexander

last: Wentzel

first: Wolfgang

last: Wohlleben

first: Stream

last: Consortium


title: Gene expression profiles in skin biopsies of Red Deer Cervus elaphus experimentally infected with Bluetongue virus

city: Ciudad Real

first: Ruth

middle: Cecilia

last: Galindo

state: Ciudad Real

address: Ronda de Toledo s/n

department: Animal Health

country: Spain

institute: Instituto de Investigacion en Recursos Cinegéticos

summary: The aim of this study is to determine differential gene expression on skin biopsies of experimentally BTV-infected hinds (Cervus elaphus) using serotypes 1 and 8 to understand the possible role that these genes play during BTV infection.  Understanding the strategies used by this virus for their cellular uptake, and detection of differentially expressed transcripts in experimentally infected hosts, can provide identification of detailed information that might be used to prevent infection.

overall_design: Four seven-month-old red deer Cervus elaphus were kept in a P3 facility to be experimentally infected with Bluetongue virus, and 4 more red deer were kept as controls. Skin biopsies were taken at 14 days post-infection to determine gene expression in response to this virus.

first: Jorge

last: López-Olvera

first: Christian

last: Gortázar

first: José

last: de la Fuente


title: Identification and functional impact of genomic copy number variants in zebrafish, an important human disease model (Zebrafish Strain CNVs) (expression array)

status: Public on Dec 27 2011

city: Boston

first: Charles

last: Lee

state: MA

address: 221 Longwood Ave., EBRC-422

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

summary: Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates, but the zebrafish reference genome has no annotated CNV information.  We developed a zebrafish CNV map using 80 zebrafish genomes from laboratory strains (AB, Tubingen, and WIK) and one native population, identifying 6,080 CNV elements. Overlapping or adjacent CNVs account for 14.6% of the genome, representing four times the CNV levels from other vertebrates including humans. Highest intra-specific CNV levels were observed for Tubingen, a common laboratory strain due to high fecundity. Tubingen variation likely represents higher initial population size and composite population founders initiating the laboratory strain. Extensive zebrafish CNVs, along with associated phenotypic impacts, advocates for increased usage of isogenic strains for genetic studies intended for human disease translation.

overall_design: 7 full sib adult hybrid fish used for expression Quantatitive Trait Loci (eQLT) analysis to support CNV affects on gene expresion in zebrafish.

first: Kim

last: Brown

first: Kimberly

middle: P

last: Dobrinski

first: Arthur

middle: S

first: Omer

last: Gokcumen

first: Ryan

last: Mills

first: Xinghua

last: Shi

first: Wilson

last: Chong

first: Sthuthie

last: David

first: Paulo

last: Yoo

first: Samuel

last: Peterson

first: Towfique

last: Raj

first: Kwong

last: Choy

first: Barbara

last: Stranger

first: Jennifer

last: Freeman


title: TTF-1-induced ROR1 is required to sustain EGFR survival signaling in lung adenocarcinoma

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

summary: Adenocarcinoma is the most common histologic subtype of lung cancer, which is the leading cause of cancer death. We and others previously identified TTF-1, a lineage-specific transcription factor required for branching morphogenesis and physiological lung functions, as a lineage-survival oncogene in lung adenocarcinoma. However, how TTF-1 mediates survival signals remains elusive. Here we show that TTF-1 induces receptor tyrosine kinase-like orphan receptor 1 (ROR1), which in turn mediates TTF-1 survival signaling in lung adenocarcinoma. Inhibition of ROR1 impaired prosurvival signaling through the PI3K-AKT pathway and induced nuclear accumulation of FOXO1. These were found to be imposed, at least in part, through PTEN inactivation via c-Src, while ROR1 was shown to physically interact with and phosphorylate c-Src. ROR1 inhibition also elicited marked p38 activation, provoking ill-balance between prosurvival and proapoptotic signaling, and consequential “oncogenic shock.” In addition, we found that ROR1 is crucially involved in EGFR- and MET-mediated prosurvival signaling. ROR1 knockdown effectively induced apoptosis in lung adenocarcinoma cell lines with acquired EGFR TKI resistance conferred by a secondary T790M EGFR mutation, or HGF-elicited MET signaling and resultant switching of the addicted receptor tyrosine kinases (RTKs). Taken together, our findings indicate that ROR1 RTK is a very promising molecular target for development of a novel therapeutic means to treat this hard-to-cure cancer.

overall_design: Dye-swap experiment, vector control vs. stable TTF-1 transfectant of HPL1D, immortalized human peripheral lung epithelial cell line.

first: Tomoya

last: Yamaguchi

first: Ryoji

last: Sugiyama

first: Kiyoshi

last: Yanagisawa

first: Yasuyuki

last: Hosono

first: Yukako

last: Shimada

first: Chinatsu

last: Arima

first: Seiichi

last: Kato

first: Shuta

last: Tomida

first: Motoshi

last: Suzuki

first: Hirotaka

last: Osada


title: Identification of truncating mutations in HPCX1 families with NMD technology

city: Tampere

first: Henna

last: Mattila

address: Biokatu 8

department: Institute of Medical Technology

institute: University of Tampere

summary: In this study, nonsense-mediated mRNA decay (NMD) inhibition was used for the discovery of truncating mutations. Six prostate cancer (PRCA) patients and their healthy brothers were selected from a group of HPCX1-linked families. mRNA was isolated from their lymphoblastic cells after pharmacological treatment. Expression analyses were done using Agilent 44K oligoarrays, and selected genes were screened for mutations by sequencing.

overall_design: In order to identify genes containing inactivating mutations in the Xq27-q28 region, an NMD microarray analysis with Agilent 44K Whole Human Genome oligonucleotide microarrays was performed in the families showing the strongest linkage to HPCX1. Five families were chosen with 6 affected and 6 healthy controls. Lymphoblastoid cell lines were derived from whole blood and treated with emetine to block NMD pathway. Total RNA was extracted from harvested cells (treated and untreated) and labeled with Cy5 and Cy3. Labeled samples were hybridized to the Agilent 44K Whole Human Genome Oligonucleotide Microarrays. After hybridization microarrays were scanned and data was extracted using Feature Extraction software. The candidate genes (n=17) for subsequent sequence analysis were selected according to the microarray analysis.

first: Martin

last: Schindler

first: Jarkko

last: Isotalo

first: Tarja

last: Ikonen

first: Mauno

last: Vihinen

first: Hannu

last: Oja

first: Teuvo

middle: J

last: Tammela

first: Tiina

last: Wahlfors

first: Johanna

last: Schleutker


title: Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis

first: Charles

last: Lee

first: Kim

last: Brown

first: Kimberly

last: Dobrinski

first: Arthur

first: Omer

last: Gokcumen

first: Ryan

last: Mills

first: Xinghua

last: Shi

first: Wilson

last: Chong

first: Jin-Yun

last: Chen

first: Sthuthie

last: David

first: Paulo

last: Yoo

first: Samuel

last: Peterson

first: Towfique

last: Raj

first: Kwong

last: Choy

first: Barbara

last: Stranger

first: Robin

last: Williamson

first: Leonard

middle: I

last: Zon

first: Jennifer

last: Freeman


title: Identification of GABRA1 and LAMA2 as new DNA methylation markers in colorectal cancer

city: Daejeon

first: sunwoo

last: Lee

address: 829 tamnip-dong, yuseong-gu

country: South Korea

institute: Genomictree,Inc.


title: Identification of active microRNA/transcription factor feed-forward loops during human adipogenesis

status: Public on Dec 20 2011

city: Padova

first: Federica

last: Eduati

state: Italy

address: Via G. Gradenigo 6/B

institute: University of Padova

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


title: Array-Comparative Genomic Hybridization Reveals Loss of SOCS6 is Associated with Poor Prognosis in Primary Lung Squamous Cell Carcinoma

status: Public on Dec 25 2011

city: Brisbane

first: Krishna

middle: Bajee

last: Sriram

state: Queensland

address: Rode Road, Chermside

department: Department of Thoracic Medicine

country: Australia

institute: The Prince Charles Hospital

summary:
Primary tumor recurrence occurs commonly after surgical resection of lung squamous cell carcinoma (SCC). The aim of this study was to identify genes involved in recurrence in lung squamous cell carcinoma patients.
Array comparative genomic hybridization (aCGH) was performed on DNA extracted from tumour tissue from 62 patients with primary lung squamous cell carcinomas. aCGH data was analysed to identify genes affected by copy number alterations that may be involved in SCC recurrence. Candidate genes were then selected for technical validation based on differential copy number between recurrence and non-recurrence SCC tumour samples. Genes technically validated advanced to tests of biological replication by qPCR using an independent test set of 72 primary lung SCC tumour samples. 18q22.3 loss was identified by aCGH as significantly associated with recurrence (p=0.038). Although aCGH copy number loss associated with recurrence was found for seven genes within 18q22.3, only SOCS6 copy number loss was both technically replicated by qPCR and biologically validated in the test set.

overall_design: DNA copy number profiling using 44K element array comparative genomic hybridization microarrays of 62 primary lung squamous cell carcinomas.

first: Jill

middle: E

last: Larsen

first: Santiyagu

last: Savarimuthu Francis

first: Casey

last: Wright

first: Belinda

last: Clarke

first: Edwina

last: Duhig

first: Kevin

last: Brown

first: Nicholas

middle: K

last: Hayward

first: Ian

last: Yang

first: Rayleen

last: Bowman

first: Kwun

last: Fong


title: Identification by ChIP-on-Chip of ARX target genes, a transcription factor implicated in mental retardation and epilepsy

status: Public on Dec 22 2011

city: Brest

first: Gaelle

last: Friocourt

address: 46 rue Félix Le Dantec, CS51819

department: Molecular Genetics

institute: Inserm U613

summary: Genetic investigations of X-linked intellectual disabilities have implicated the ARX (Aristaless-related homeobox) gene in a wide spectrum of disorders extending from phenotypes characterised by severe neuronal migration defects such as lissencephaly, to mild or moderate forms of mental retardation without apparent brain abnormalities but with associated features of dystonia and epilepsy. Analysis of Arx spatio-temporal localisation profile in mouse revealed expression in telencephalic structures, mainly restricted to populations of GABAergic neurons at all stages of development. Furthermore, studies of the effects of ARX loss of function in humans and animal models revealed varying defects, suggesting multiple roles of this gene during brain development. However, to date, little is known about how ARX functions as a transcription factor and the nature of its targets. To better understand its role, we combined chromatin immunoprecipitation and mRNA expression with microarray analysis and identified a total of 1006 gene promoters bound by Arx in transfected neuroblastoma (N2a) cells and in mouse embryonic brain. Some of these promoters were enriched for a sequence very similar to a motif previously identified as Arx-binding motif and approximately 24% of Arx-bound genes were found to show expression changes following Arx overexpression or knock-down. Several of the Arx target genes we identified are known to be important for a variety of functions in brain development, including axonal guidance and synaptic plasticity and some of them suggest new functions for Arx. Overall, these results identified multiple new candidate targets for Arx and should help to better understand the pathophysiological mechanisms of intellectual disability and epilepsy associated with ARX mutations.

overall_design: ChIP-Chip experiments were performed with either Arx transfected N2a cells or mouse embryonic brains (E15.5). Three replicates were performed for each condition.

first: Marie-Lise

last: Quillé

first: Solenne

last: Carat

first: Edouard

last: Hirchaud

first: Daniel

last: Baron

first: Rémi

last: Houlgatte

first: Gaëlle


title: Global Identification of Potential Gene Biomarkers Associated with Ozone-induced Foliar Injury in Rice Seedling Leaves by Correlating their Symptom Severity with Transcriptome Profiling

status: Public on Dec 10 2011

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

summary: A combined approach of evaluating ozone (O3)-caused foliar injury symptom and global gene expression profiling was used to identify potential genes associated with severity of injury on leaves of O3 (200 ppb)-fumigated (1, 12, 24, 48, and 72 h) two-week-old rice (cv. Nipponbare) seedling along with appropriate control. Foliar injuries were evaluated up to 72 h using both qualitative visual scale and quantitative RGB (red-green-blue) image analysis methods. The (R-G)/(R+G) was found as the optimal quantitative RGB parameter to assess the foliar injury. Large-scale transcript profiling of leaves identified 270 genes linked with foliar injury. Of these genes, the expression levels of 139 genes showed significant differences (P < 0.05) between leaves without and with injury symptoms. When a rigorous correlation test was applied on these genes for their expression changes and relative (R-G)/(R+G) parameters, the expression of 93 genes were found to increase with increased foliar severity up to 72 h, showing a positive, tight correlation between a subset of gene expression and commonly observed O3-triggerred symptom of foliar injury with correlation coefficient below -0.80. Of 93 genes, genes involved in metabolism (29%) formed a major functional category. Reconstruction of the metabolic networks with identified metabolic genes provided insight into the cellular responses such as photorespiration, biosynthesis of secondary metabolites, and detoxification. The O3 effect on these cellular responses has been previously reported based on physiological and biochemical studies, validating our approach used in this study to globally identify O3-responsive biomarkers tightly linked with foliar injury symptom. This study provides evidence for the presence of large number of genes associated with the foliar injury symptom than thought before, and could serve as a resource of potential biomarkers to study mechanisms of visible injury development by O3.

overall_design: Comparison between healthy rice seedling leaves and ozone treated (for 48 h and 72 h) rice seedling leaves was performed. Three biological replicates (5 leaves in each replicate; pooled) were used, and dye-swaped.

first: Kyoungwon

last: Cho

first: Akihiro

last: Kubo

first: Junko

last: Shibato

first: Ganesh

last: Agrawal

first: Hikaru

last: Saji

first: Randeep

last: Rakwal


title: slc2a10/glut10 and TBFBR1

status: Public on Dec 17 2011

city: St. Louis

first: Seth

middle: Daniel

last: Crosby

address: 660 S. Euclid

department: Genetics

institute: Washington Univeristy School of Medicine


title: A genome-wide analysis reveals that the Drosophila transcription factor, Lola, promotes axon growth in part by suppressing expression of the actin nucleation factor, Spire

status: Public on Dec 03 2011

first: Edward

last: Giniger

state: MD

department: NINDS

institute: NIH


title: Gene expression study after 3 days of cold or salt exposure in a Solanum tuberosum cultivar called Desirée

city: Belvaux

first: Danièle

last: Evers

address: 41, rue du Brill

department: EVA

country: Luxembourg

institute: CRP-Gabriel Lippmann


title: aCGH profiling of prostate tumors

status: Public on Dec 19 2011

city: Stanford

first: Stephanie

last: Huang

address: 269 Campus Drive, CCSR 3240

department: Pathology

institute: Stanford University

summary: This experiment was an aCGH study on 86 prostate tumors samples. The samples were profiled on Agilent Human Genome 44karrays to identify recurrent regions of deletion and amplification, thus revealing potential new tumor suppressor genes and/or oncogenes involved in prostate cancer. The CGH profile on the 44k arrays revealed a deletion at 5q21 in 17% of samples.

overall_design: CGH analysis of 86 prostate tumor samples.

first: Jonathan

middle: R

last: Pollack


title: Gene expression profilling in bovine mammary gland pathophysiology

status: Public on Dec 02 2011

city: Berlin

first: Pawel

last: Lisowski

address: Hannoversche Str. 28

institute: Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association

summary: Transcriptional profiling in vivo in bovine secretory tissue from healthy (H) mammary gland and during infections with coagulase-negative Staphylococci (CoNS) and coagulase-positive Staphylococci (CoPS). The aim of this study was to examinate the global gene expression profiles of mammary gland tissues of infected and healthy (control) cows.

overall_design: Transcriptomes were compared of in the mammary glands of Holstein Friesian cows in two experiments, (H) vs (CoNS) cows and (H) vs (CoPS).

first: Ewa

last: Kosciuczuk

first: Joanna

last: Goscik

first: Justyna

last: Jarczak

first: Lech

last: Zwierzchowski

first: Emilia

last: Bagnicka


title: Transcriptional analysis of physiological pathways in a generalist herbivore: responses to different host plants and plant structures by the cotton bollworm (CBW) Helicoverpa armigera

status: Public on Dec 12 2011

city: Stockholm

first: Maria de la Paz

last: Celorio-Mancera

address: Svante Arrheniusväg 18 B

department: Zoology

country: Sweden

institute: Stockholm University


title: Ceratitis capitata gene expression

city: Pavia

first: Ludvik

middle: Marcus

last: Gomulski

state: PV

address: Piazza Botta 9

department: Biologia Animale

country: Italy

institute: University of Pavia


title: Transcriptional Response of Zebrafish Embryos Exposed to Neurotoxic Compounds Reveals a Muscle Activity Dependent hspb11 Expression

status: Public on Dec 01 2011

city: Leipzig

first: Wibke

last: Busch

address: Permoser Str. 15

department: Bioanalytical Ecotoxicology

institute: UFZ Helmholtz Centre for Environmental Research

summary: Acetylcholinesterase (AChE) inhibitors are widely used as pesticides and drugs. Their primary effect is the overstimulation of muscular activity. Whether AChE inhibitors and related neurotoxic compound also provoke specific changes in gene transcription patterns that allow to establish a mechanistic link useful for diagnostic purposes has, however, yet not been investigated. Therefore, as a proof of principle, we examined the transcriptomic response of a known AChE inhibitor, the organophosphate azinphos-methyl (APM), in zebrafish embryos and compared the response with two non-AChE inhibiting control compounds, 1,4-dimethoxybenzene (DMB) and  2,4-dinitrophenol (DNP). A highly specific cluster of APM induced gene transcripts was identified and a subset of strongly regulated genes was analyzed in more detail. The small heat shock protein hspb11 was found to be the most sensitive gene in response to AChE inhibitors. Comparison of expression in wild-type, ache and fixe mutant embryos revealed that hspb11 expression was dependent on the nicotinic acetylcholine receptor (nAChR) activity. Furthermore, modulators of intracellular calcium levels led to an hspb11 transcriptional up-regulation which suggest that elevated intracellular calcium levels and the resulting increase in muscular activity triggering hspb11 up-regulation. During early zebrafish development, hspb11 was specifically expressed in muscle pioneers and morpholino-knockdown resulted in defects in slow muscle myosin organization. These findings demonstrate that a combination of transcriptome and functional analyzes in the zebrafish embryo is able to correlate gene expression changes to the mechanism of action of neurotoxic compounds.

overall_design: Zebrafish embryos were exposed for 24 h and 48 h (26-50 and 2-50 hpf) to 5,83 µM of azinphos-methyl (APM), 509 µM of 1,4-dimethoxybenzene (DMB) and 14,2 µM 2,4-dinitrophenol (DNP), the respective LC10 of each compound, in order to determine mode of action specific responding genes, or not exposed and parallel treated as controls. 50 zebrafish embryos were used per treatment, and 4 biological independent replicates were analysed, respectively.

first: Nils

last: Klüver

first: Stefan

last: Scholz


title: Endothelial Cells Express a Unique Transcriptional Profile under Very High Wall Shear Stress Known to Induce Expansive Arterial Remodeling

city: Buffalo

first: Jennifer

last: Dolan

state: NY

address: 3435 Main Street

department: Neuroscience

country: USA

institute: University at Buffalo

summary: Chronic high flow can induce arterial remodeling, and this effect is mediated by endothelial cells (ECs) responding to wall shear stress (WSS). To assess how WSS above physiological normal levels affects ECs, we used DNA microarrays to profile EC gene expression under various flow conditions. Cultured bovine aortic ECs were exposed to no flow (0 Pa), normal WSS (2 Pa) and very high WSS (10 Pa) for 24 hrs. Very high WSS induced a distinct expression profile when compared to both no flow and normal WSS. Gene ontology and biological pathway analysis revealed that high WSS modulated gene expression in ways that promote an anti-coagulant, anti-inflammatory, proliferative and pro-matrix remodeling phenotype. A subset of characteristic genes was validated using quantitative polymerase chain reaction (qPCR): Very high WSS upregulated ADAMTS1, PLAU (uPA), PLAT (tPA) and TIMP3, all of which are involved in extracellular matrix processing, with PLAT and PLAU also contributing to fibrinolysis. Downregulated genes included chemokines CXCL5 and IL-8 and the adhesive glycoprotein THBS1 (TSP1). Expressions of ADAMTS1 and uPA proteins were assessed by immunhistochemistry in rabbit basilar arteries experiencing increased flow after bilaterial carotid artery ligation. Both proteins were significantly increased when WSS was elevated compared to sham control animals. Our results indicate that very high WSS elicits a unique transcriptional profile in ECs that favors particular cell functions and pathways that are important in vessel homeostasis under increased flow. In addition, we identify specific molecular targets that are likely to contribute to adaptive remodeling under elevated flow conditions.

overall_design: Time-matched Bovine Aortic Endothelial Cells were exposed to three flow conditions,  high WSS (10 Pa), normal WSS (2 Pa) and no flow (0 Pa) static controls for 24 hrs in an in vitro flow loop system. RNA was extracted and hybridized on Affymetrix microarrays. There were 9 samples in total, three flow conditions with three replicates each.

first: Fraser

last: Sim

first: Hui

last: Meng

first: John

last: Kolega


title: Human SW480 cells: Untreated vs H2O2 Treated

city: Baltimore

first: Wayne

last: Yu

address: 417 N. Caroline St.

department: Cancer Center

institute: Johns Hopkins University

summary: ChIP-on-chip tilling array comparing untreated human SW480 cells vs SW480 cells treated with 2mM H2O2 for 30min.  Exposing cells to the reactive oxygen species, hydrogen peroxide, recruits DNA methyltransferase 1 (DNMT1) to damaged chromatin. DNMT1 becomes part of a complex(es) containing DNMT3B and members of Polycomb Repressive Complex 4. The goal was to determine the effect of hydrogen peroxide treatment on chromatin, including changes in histone modifications and binding patterns of chromatin-associated proteins.

overall_design:
[Agilent-014706]: Two-condition: untreated SW480 cells (U) vs  H2O2 treated SW480 cells (T).  Five-mark: SIRT1, gamma-HA2X, DNMT1, DNMT3B, and EZH2.
[Agilent-014707]: Two-condition: untreated SW480 cells (U) vs  H2O2 treated SW480 cells (T).  Five-mark: SIRT1, gamma-HA2X, DNMT1, DNMT3B, and EZH2.
[Agilent-026595]: Two-condition: untreated SW480 cells (U) vs  H2O2 treated SW480 cells (T).  Five-mark: SIRT1, gamma-HA2X, DNMT1, DNMT3B, and H3.
[Agilent-027811]: Two-condition: untreated SW480 cells (U) vs  H2O2 treated SW480 cells (T).  Four-mark: H3, 3MeK4H3, AcK16H4, and 3MeK27H3.

first: Wei

last: Wang

first: Heather

last: O'Hagan

first: Stephen

last: Baylin


title: p27 binds to promoters of multiple genes leading to their repression

city: Barcelona

first: oriol

last: bachs

email: obachs@ub.edu, raffaellapippa@ub.edu

address: Casanova 143

department: Cell Biology, Immunology and Neurosciences

institute: University of Barcelona

summary: The role of the cyclin-cdk inhibitor p27 in tumorigenesis is still a controversial matter. We demonstrate here that p27 negatively regulates transcription of a number of genes (p27-target genes) involved in key cellular functions as RNA processing, translation, respiration and cell proliferation.

overall_design: Crosslinked chromatin from quiescent NIH3T3 cells was sonicated, incubated overnight with the rabbit anti-p27 and IgG antibodies as control

first: Raffaella

last: Pippa

first: Lluis

last: Espinosa

first: Gunes

last: Gundem

first: Ramón

last: García-Escudero

first: Ana

last: Domínguez

first: Cristina

last: Sainz

first: Arnaud

last: Besson

first: Maria

last: Pujol

first: Núria

last: López-Bigas

first: Jesus

last: Paramio

first: Oriol

last: Bachs


title: Comparison of SND2-overexpressing and wild type Arabidopsis thaliana Col-0 inflorescence stems

status: Public on Nov 30 2011

city: Pretoria

first: Steven

middle: Grant

last: Hussey

state: Gauteng

address: Lynnwood Road, Hatfield

country: South Africa

institute: University of Pretoria

summary: Homozygous T4 SND2-overexpressing Arabidopsis plants were grown alongside the wild type and the lower 100 mm of primary inflorescence stems sampled at 4 and 8 weeks of age

overall_design: A direct comparison was used (box plot). Three biological replicates and two technical replicates (dye swaps) were included for each experiment

first: Zander

last: Myburg


title: Lung biopsies from sensitized or control rhesus macaques

city: South San Francisco

first: Alex

last: Abbas

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary:
The aim of this study was to investigate differential expression in a house dust mite (HDM) exposure model of asthma in rhesus macaques.
HDM sensitization was performed by subcutaneous injection of HDM followed by intranasal HDM for 2-3 hours twice a week.

overall_design: Animals were mock-sensitized (PBS) or sensitized to HDM antigen.  Gene expression was measured in lung biopsies before and fifteen weeks after treatment.

first: Alexander

first: Janet

last: Jackman

first: Sherron

middle: L

last: Bullens

first: Grazyna

last: Fedorowicz

first: Bao

middle: T

last: Troung

first: Martha

last: Tan

first: Y

middle: G

last: Meng

first: Lauri

last: Diehl

first: Lisa

middle: A

last: Miller

first: Edward

last: Schelegle

first: Dallas

last: Hyde

first: Hilary

middle: F

last: Clark

first: Zora

last: Modrusan

first: Joseph

last: Arron

first: Lawren

middle: C

last: Wu


title: HoxD locus in the developing limb, digit, and brain

status: Public on Nov 28 2011

city: Lausanne

first: Thomas

last: Montavon

address: SV 2843, Station 19

institute: EPFL

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

overall_design: Refer to individual Series


title: The role of a novel CAR-induced gene TUBA8 in hepatocellular carcinoma cell lines

status: Public on Nov 29 2011

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: The Tuba8 gene was identified as a CAR-regulated gene that was induced during phenobarbital (PB) promotion of liver tumor. TUBA8 was then over-expressed in heaptocarcinoma cells to determine the function of TUBA8.

overall_design: First, identify genes that are regulated by CAR and are induced during liver tumor development. Second, overexpressiong of an identified gene in transformed cells to detemine the biolgical function of the gene product. In this manuscript, the TUBA8 gene was examined.

first: Hiroki

last: Kamino

first: Rick

last: Moore

first: Masahiko

last: Negishi


title: Ptch1+/- Nos2-/- medulloblastomas

first: Daniel

last: Haag

state: Santa Clara

address: 265 Campus Drive

department: ISCBRM

institute: Stanford School of Medicine


title: Genomic characterization of the MPNST

status: Public on Nov 26 2011

city: Tampere

first: Antti

last: Ylipää

address: Korkeakoulunkatu 1

institute: Tampere University of Technology

summary: Malignant peripheral nerve sheath tumor (MPNST) is a rare sarcoma that lacks effective therapeutic strategies. By characterizing recurrent gene copy number aberrations, we gain insight into the most altered pathways with the purpose of scanning possible therapeutic targets.

overall_design: We conducted a microarray-based comparative genomic hybridization profiling of two cohorts of primary MPNST tissue samples including 25 patients treated at The University of Texas MD Anderson Cancer Center and 26 patients from Tianjin Cancer Hospital. All samples had at least 90% tumor content. Commercially available normal genomic DNAs were used as control.

first: Jilong

last: Yang

first: Yan

last: Sun

first: Hong

last: Zheng

first: Kexin

last: Chen

first: Matti

last: Nykter

first: Jonathan

last: Trent

first: Nancy

last: Ratner

first: Dina

last: Lev

first: Wei

last: Zhang


title: Implication of Nos2 inactivation on genomic changes in Ptch1+/- medulloblastomas (array-CGH)

summary: The Ptch1+/-  strain constitues an established mouse model for the Shh-driven type of medulloblastoma. Combined Ptch1+/- Nos2-/- mice show a two-fold increased incidence for this tumor. Here, the impact of Nos2 inactivation on copy number alterations during medulloblastoma development was investigated by array-based comparative genomic hybridization (arrayCGH) of tumor samples from both genotypes.

overall_design: Medulloblastoma samples from five Ptch1+/- and seven compound Ptch1+/- Nos2-/- mice were analyzed. Cy5-labeled tumor DNA was combined with corresponding Cy3-labeled reference healthy wildtype genomic DNA to receive either sex-matched sample pairs or pairs of different gender for internal negative or positive control.

first: Petra

last: Zipper


title: Identification of potential biomarkers for patients with neurodegenerative parkinsonian syndromes using serum cytokine microarray analysis

status: Public on Nov 23 2011

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

institute: Eurac Researc


title: Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis

city: Dublin

first: David

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

institute: University College Dublin

summary:
Background: Mycobacterium bovis is the causative agent of bovine tuberculosis (BTB), a pathological infection with significant economic impact. Recent studies have highlighted the role of functional genomics to better understand the molecular mechanisms governing the host immune response to M. bovis infection. Furthermore, these studies may enable the identification of novel transcriptional markers of BTB that can augment current diagnostic tests and surveillance programmes. In the present study, we have analysed the transcriptome of peripheral blood leukocytes (PBL) from eight M. bovis-infected and eight control non-infected age-matched and sex-matched Holstein-Friesian cattle using the Affymetrix® GeneChip® Bovine Genome Array with features representing more than 23,000 gene transcripts and over 19,000 gene probe sets.
Results: Control and infected animals had similar mean white blood cell counts. However, the mean number of lymphocytes was significantly increased in the infected group relative to the control group (P = 0.001), while the mean number of monocytes was significantly decreased in the BTB group (P = 0.002). Hierarchical clustering analysis using gene expression data from all 5,388 detectable mRNA transcripts unambiguously partitioned the animals according to their disease status. In total, 2,960 gene transcripts were differentially expressed (DE) between the infected and control animal groups (adjusted P-value threshold ≤ 0.05); with the number of genes showing decreased relative expression (1,563) exceeding those displaying increased relative expression (1,397). Systems analysis using the Ingenuity Systems Pathway Analysis (IPA) Knowledge Base revealed an over-representation of DE genes involved in the immune response functional category. More specifically, 64.5% of genes in the affects immune response subcategory displayed decreased relative expression levels in the infected animals compared to the control group.
Conclusions: This study demonstrates that genome-wide transcriptional profiling of PBL can distinguish active M. bovis-infected animals from control non-infected animals. Furthermore, the results obtained support previous investigations demonstrating that mycobacterial infection is associated with host transcriptional suppression. These data support the use of transcriptomic technologies to enable the identification of robust, reliable transcriptional markers of active M. bovis infection

overall_design: Affymetrix GeneChip® Bovine Genome Arrays were used to examine gene expression of peripheral blood leukocytes from cattle infected with Mycobacterium bovis

first: Kate

last: Killick

first: John

last: Browne

first: Stephen

middle: D

last: Park

last: Magee

first: Irene

last: Martin

first: Kieran

last: Meade

middle: V

last: Gordon

first: Eamonn

last: Gormley

first: Cliona

last: O'Farrelly

first: Karsten

last: Hokamp


title: Human gastric cancer cell MKN45: MKN45-GFP control vs. highly metastatic sublines

status: Public on Nov 10 2011

city: Zhunan, Miaoli

first: Chiung-Tong

last: Chen

address: No. 35, Keyan Road

department: Institute of Biotechnology and Pharmaceutical Research

country: Taiwan

institute: National Health Research Institutes

summary: Gene expression profiles of in vitro selected highly metastatic MKN45-GFP sublines. The results were compared with MKN45-GFP control cell line to determine the metastasis associated genes.

overall_design: Four pairs compared experiment. Each pair was used MKN45-GFP cells as correlated control. Determining on the gene expression trends were by various metastatic ability of each subline.

first: Tsung-Fan

last: Tuan


title: Transcriptional glucocorticoid-response at the exon level and NR3C1 DNA-binding in childhood leukemia models: mRNA and ChIP-chip profiling

status: Public on Nov 15 2011


title: R. sphaeroides delta-cryB

status: Public on Nov 09 2011

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen


title: R. sphaeroides Δirr vs. R. sphaeroides 2.4.1 under microaerobic conditions

summary: Transcriptional profiling of R. sphaeroides Δirr compared to control R. sphaeroides 2.4.1 under microaerobic conditions.

overall_design: Two strain experiment under microarobic conditions (30 µM). 6 Biological replicas, independetly grown and harvested at OD660=0,4; 1-3 pooled in replicate 1, 4-6 pooled in replicate 2

first: Verena

last: Peuser

first: Sebastian

last: Metz


title: Transcriptional profiling of R. sphaeroides Δirr


title: Profiling of THP-1 cells infected with H37Rv (wild-type), ∆E (deletion mutant of PknE), C∆E (complemented ∆E)

city: chennai

first: Dinesh

last: Kumar

state: tamilnadu

address: mayor v.r ramanathan road

department: Immunology

country: India

institute: Tuberculosis research centre (ICMR)

summary: Goal was to determine cellular changes on global macrophage gene expression.

overall_design: Transcriptional profiling of  THP-1 differentiated macrophages infected with H37Rv, ∆E, C∆E comparing to control uninfected THP-1 macrophages.

first: Sujatha

last: Narayanan


title: Novel roles of C. elegans heterochromatin protein HP1 and linker histone HIS-24 in the regulation of innate immune gene expression and stress Response

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Linker histone H1 and heterochromatin protein 1 (HP1) are essential components ofheterochromatin which contribute to the transcriptional repression of genes. It has been shown that the methylation mark on the histone H1 serves as a specific recognition code for the chromodomain of HP1, however, the functional role of the HP1/H1 complex remains elusive. Using C. elegans, we elucidate the function of the linker histone variant HIS-24 and heterochromatin proteins HPL/HP1 in the cooperative transcriptional regulation of immunerelevant and stress resistance genes. We also show that HIS-24 and HPL act redundantly in vulval cell fate specification and gonad development. Finally, we provide the first evidence that HPL-1 interacts with HIS-24 at mono-methylated lysine 14 and associates in vivo with promoters of infection-inducible genes: the caenacin (cnc)- and the thaumatin (thn)- gene clusters. Our results highlight a functional link between epigenetic regulation by HP1/H1 the innate immune system and stress response.

overall_design: The experiment was performed using biological independent replicates of pooled worms. For the KO mutants we used duplicates and for WT condition quadruplicates.

first: Maja

last: Studencka

first: Anne

last: Konzer

first: Gael

last: Moneron

first: Dirk

last: Wenzel

first: Lennart

last: Opitz

last: Salinas-Riester

first: Cecile

last: Bedet

first: Francesca

last: Palladino

first: Marcus

last: Krüger

first: Stefan

middle: W

last: Hell

first: Jacek

last: Wisniewski

first: Ekkehard

last: Schulze

first: Monika

last: Jedrusik-Bode