title: Senseless-responsive genes in larval salivary glands of late Drosophila prepupae

first: Michael

last: Lehmann

summary:
When misexpressed in late Drosophila prepupae, the transcription factor Senseless (Sens) blocks death of the larval salivary glands that normally occurs in the early pupa. The aim of the experiment was to identify genes responding to Sens that might mediate the effect of the protein on cell death and other biological processes. The yeast transcription factor GAL4, expressed from a heat-inducible transgene (P{GAL4-Hsp70.PB}89-2-1), was used to drive expression of Sens from a UAS-sens transgene.  After crossing the GAL4 and UAS lines, expression of GAL4 was induced by a 30-min heat shock treatment (37 °C) of the progeny at 9 hours after puparium formation. Salivary glands were dissected at 14 hours after puparium formation and RNA isolated for microarray analysis with Affymetrix GeneChips. Control samples were obtained from animals treated the same way carrying one copy of the GAL4 transgene (progeny of a cross between flies of the P{GAL4-Hsp70.PB}89-2-1 and w1118 strains) and  w1118 animals. The microarray data identified several genes associated with programmed cell death, including caspase genes, which respond to Sens. In addition, the data show that many Drosophila genes respond to the yeast transcription factor GAL4 in a UAS-independent manner. To identify target genes of Sens that are of biological relevance, gene expression patterns in the presence of Sens were compared to gene expression patterns in both the presence and the absence of GAL4. This comparison revealed that Sens seems to preferentially downregulate targets that are upregulated by GAL4, suggesting that these genes may not necessarily constitute true transcriptional targets of Sens.
Keywords: ectopic expression experiment

overall_design: Experimental RNA samples were obtained in 3 biological replicates from sens-expressing salivary glands (SG_sens_14APF_rep1, SG_sens_14APF_rep2, SG_sens_14APF_rep3) and compared to control samples obtained from GAL4-expressing salivary glands (SG_1P{hsGAL4}89(S)_14APF_rep1) and non-GAL4-expressing salivary glands (SG_w1118_14APF_rep1, SG_w1118_14APF_rep2). All samples were compared using dChip and normalized to the same baseline array (median intensity 150).

first: Yanling

last: Liu


title: Comparison of gene expression in erythroblasts with the In(Lu) phenotype with normal erythroblasts.

status: Public on Aug 11 2008

city: Bristol

first: Belinda

last: Singleton

address: Southmead Road

country: United Kingdom

institute: Bristol Institute for Transfusion Sciences

summary:
In order to elucidate the molecular mechanism giving rise to the rare In(Lu) type of Lu(a-b-) blood group phenotype we compared the transcriptome of normal and In(Lu) erythroblasts at different stages of maturation. Many erythroid-specific genes had reduced transcript levels suggesting the phenotype resulted from a transcription factor abnormality. A search for mutations in erythroid transcription factors revealed mutations in the promoter or coding sequence of EKLF in 21 of 24 individuals with the In(Lu) phenotype. In all cases the mutant EKLF allele occurred in the presence of a normal EKLF allele. Individuals with the In(Lu) phenotype have no reported pathology indicating that one functional EKLF allele is sufficient to sustain human erythropoiesis. These data provide the first description of inactivating mutations in human EKLF and the first demonstration of a blood group phenotype resulting from mutations in a transcription factor.
Keywords: Time course and cell type comparison.

overall_design: Time course study looking at changes in gene expression during erythropoiesis in two cell types: cultured erythroblasts (days 4, 6 and 11) from normal blood donors and from those with the rare blood group In(Lu) phenotype. There are 20 samples in total (10 for each cell type). For each cell type there are 2 samples at day 4 (1 biological replicate, 2 technical replicates, and 4 samples at each of days 6 and 11 (2 biological replicates, 2 technical replicates).

first: Nicholas

last: Burton

first: Carole

last: Green

first: Leo

last: Brady

first: David

last: Anstee


title: Differential gene expression in peripheral blood CD14+ leukocytes from SRESS study particpants

status: Public on May 20 2008

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

country: USA

institute: UCLA School of Medicine

summary:
Gene expression profiling was carried out on peripheral blood CD14+ leukocytes from 21 stressed caregivers and controls (all adult).  The primary research question is whether gene expression differs in individuals from high stress vs low stress environments.
Keywords: Risk prediction


title: Nucleus- and cell-specific gene expression in monkey thalamus

status: Public on May 01 2008

city: Davis

first: Karl

middle: Daniel

last: Murray

address: 1544 Newton Court

institute: UC Davis

summary:
Nuclei of the mammalian thalamus are aggregations of neurons with unique architectures and input-output connections, yet the molecular determinants of their organizational specificity remain unknown. By comparing expression profiles of thalamus and cerebral cortex in adult rhesus monkeys we identified transcripts that are unique to dorsal thalamus or to individual nuclei within it. Real-time quantitative polymerase chain reaction and in situ hybridization analyses confirmed the findings. Expression profiling of individual nuclei microdissected from the dorsal thalamus revealed additional subsets of nucleus-specific genes. Functional annotation using Gene Ontology (GO) vocabulary and Ingenuity Pathway analysis revealed over-representation of GO categories related to development, morphogenesis, cell-cell interactions, and extracellular matrix within the thalamus- and nucleus-specific genes-many involved in the Wnt signaling pathway. Examples included the transcription factor TCF7L2, localized exclusively to excitatory neurons, a calmodulin-binding protein PCP4, the bone extracellular matrix molecules SPP1 and SPARC, and other genes involved in axon outgrowth and cell matrix interactions. Other nucleus-specific genes such as CBLN1 are involved in synaptogenesis. The genes identified likely underlie nuclear specification, cell phenotype and connectivity during development and their maintenance in the adult thalamus.
Keywords: brain region comparative analysis

overall_design: To determine the molecular underpinnings of nuclear specificity in the dorsal thalamus we isolated micro-punches of tissue from nucleus-specific regions and processed them for microarray analysis. Replicate samples from 5 separate dorsal thalamic nuclei were processed and compared to identify genes unique to each region. Affymetrix U133A Gene Chips were used. All of the samples were isolated from untreated adult monkey brain.

middle: D

first: Prabhakara

middle: V

last: Choudary

first: Edward

middle: G

last: Jones


title: Identification of RGA downstream genes by using steroid-inducible system

status: Public on May 28 2008

city: Singapore

first: Hao

last: Yu

address: Lower Kent Ridge Road

department: Biological Sciences

country: Singapore

institute: National University of Singapore

summary:
To understand the transcriptional program controlled by RGA, we took advantage of a functional steroid-inducible RGA proteins system in combination with microarray analysis to identify RGA target genes.
Keywords: steroid-inducible system

overall_design: We firstly compared the transcriptomes in ga1-3rgargl2RGA-GR inflorescence without flowers later than stage 12 induced by dexamesone- relative to mock-treatment, which revealed the differentially expressed genes corresponding to the RGA protein activity induced by dexamesone.As negative controls to exclude unexpected effects of transgenic T-DNA and Dex itself, RNAs derived from nontransgenic plants (ga1-3 rga rgl2) inflorescences treated with Dex were used. Three sets of biological independent replicates were collected.


title: Transcript profiling of oestrogen treatment of primary human neuronal and glial cell cultures

city: Stockholm

first: Linda

middle: Alexandra Csöregh

last: Nord

address: Karolinska University Hospital, Solna, C4:U1

department: Dept. of Women's and Children's Health

country: Sweden

institute: Karolinska Institute

summary:
The purpose of this experiment was to identify oestrogen regulated genes in human primary cell cultures of neuronal and glial cells modelling the developing human nervous system. We were especially interested in genes involved in proliferation, differentiation and migration of neuronal cells and genes involved in or linked to neurodegenerative diseases. We have therefore assessed gene expression changes, using Affymetrix GeneChips (HG-U133A), of oestrogen treated human neuronal/ glial cell cultures. We continued with 14 selected genes and confirmed the gene expression changes, by relative quantitative real time PCR, of 6 genes (p< 0.05) important in neuronal development, three of which also are suggested to have links to neurodegenerative diseases.
Keywords: Treatment vs Control

overall_design: Primary mixed neuronal/glial cell cultures were established from human brain tissue, which was obtained from 8-12 weeks old fetuses at legal abortion after informed consent from the patients. Procedures were approved by the local Ethics committee at the Karolinska University Hospital, Stockholm. A total of 23 tissue samples yielding 9 cell cultures were used in this experiment. Half of the cell cultures were treated with 2µM β-oestradiol the day after seeding. The duration of the oestrogen treatment was 7 days and the cells were harvested after 8 days of culturing for RNA extraction. Extracted RNA from untreated respectively oestrogen treated cell cultures were pooled yileding two samples, which were each hybridised to Affymetrix microarrys. In this study oestrogen treatment of human neuronal/glial cell cultures was found to regulate 6 genes important in the development of the nervous system.

middle: A

last: Csoregh

first: Eva

last: Andersson

first: Gabriel

last: Fried


title: Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster.

status: Public on May 14 2008

city: New York

first: Nicolas

last: Robine

state: NY

address: 430, East 67th Street, RRL 517

department: Developmental Biology

institute: Sloan-Kettering Institute

summary:
Cis-natural antisense transcripts (cis-NATs) have been speculated to be substrates for endogenous RNA interference (RNAi), but little experimental evidence for such a pathway in animals has been reported. Analysis of massive Drosophila melanogaster small RNA data sets now reveals that endogenous small interfering RNAs (siRNAs) are produced via bidirectional transcription. >100 cis-NATs with overlapping 3' exons generate 21-nt, Dicer-2 (Dcr-2)dependent, 3'-end modified siRNAs.

To determine whether any co-expressed cisNATs are denied entry into the RNAi pathway, we analyzed the gene expression profile of S2 cells. The analysis suggested that the processing of cis-NATs by RNAi are actively restricted, and the selected loci are enriched for nucleic acidbased functions and include Argonaute-2 (AGO2) itself.
Keywords: Gene expression

overall_design:
Drosophila Schneider cells (S2) were treated with dsRNA against GFP for 8 days. The treatment was done in duplicate. Total RNA was extracted from the dsRNA treated cells using trizol.

Gene expression analysis was conducted using Drosophila Genome 2.0 Genechip® arrays (Affymetrix, Santa Clara, CA). Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3¹ Amplification One-Cycle Target labeling kit according to manufacturer¹s protocol. For each array, 10ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450. Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the Genechip® Operating Software (Version 1.2.0.037).

first: Katsutomo

last: Okamura

first: Sudha

last: Balla

first: Raquel

last: Martin

first: Eric

middle: C

last: Lai


title: BTH treated mkk1, mkk2 and mkk1/2 knockout mutant

city: Kgs. Lyngby

first: Henrik

middle: Bjørn

last: Nielsen

address: Kemitorvet, Building 208,

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

summary:
Gene Expression profiling of the Arabidopsis thaliana MAP Kinase Kinases 1 (mkk1), MAP Kinase Kinases 2 (mkk2) knockout mutants and the double mutant mkk1/mkk2 before and 24 hours after treatment with the salicylic acid analog BTH, was measured by hybridisation to an Affymetrix ATH1 GeneChip.
Keywords: Gene expression. Combined mutant and treatment study

overall_design: Whole Arabidopsis thaliana mkk1, mkk2 and mkk1/mkk2 knockout mutants and wild type plants (Col-0) were sampled in triplicates before and 24 hours after BTH treatment.

middle: B

first: Berthe

middle: K

last: Fiil

first: Jin-long

last: Qiu

first: John

last: Mundy


title: Gene expression variation in Y-chromosome substitution lines of Drosophila melanogaster

status: Public on Apr 30 2008

city: Cambridge

first: Bernardo

last: Lemos

state: MA

address: 16 Divinity Avenue, Room 2105

institute: Harvard University

summary:
These arrays were done in the context of a study to probe gene expression variation across Y-chromosome substitution lines of Drosophila melanogaster
Keywords: polymorphism, evolution, chromosome substitution

overall_design: This series contains all the arrays and designs described in Lemos et al.

first: Luciana

middle: O

last: Araripe


title: Comparing gene expression between wild type and trichomeless mutants

city: Columbus

first: Manli

middle: Yang

last: Davis

state: OH

address: 318 W.12th Ave

department: Plant Cellular and Molecular Biology

institute: The Ohio State University

summary:
Trichomes are found on the leaf surface of many plant species. They can be classified into either glandular or non-glandular types. Glandular trichomes are usually multicelluar structures and have long been known to participate in defense against pathogens through the production of specialized chemical products. Non-glandular trichomes, such as those in Arabidopsis thaliana, have been hypothesized to have roles in physical defense against insects, UV protection, detoxification, and heat dispersal. However, it has been difficult to separate a physical role from other possible functions for non-glandular trichomes. We have taken advantage of several mutants in the trichome developmental pathway and gene expression analyses to identify a set of genes expressed predominantly in Arabidopsis trichomes.
Keywords: comparing gene expression between wild type and mutants

overall_design: We compared the gene expression between the wild type and three trichomeless mutants: gl1, ttg1 and gl3egl1 to see which genes' transcripts are enriched in trichomes.

last: Yang

first: Binh

last: Nguygen

first: Betsy

last: Read

first: Erich

last: Grotewold

first: Rebecca

middle: S

last: Lamb


title: Primary human epithelial cells exposed to coarse, fine and ultrafine particles

city: RTP

first: Edward

last: Karoly

state: NC

address: MD 58D

department: HSD

institute: U.S. EPA

summary:
The purpose of this study was to characterize global gene expression in human airway epithelial cells and identify cellular pathways associated with coarse, fine and ultrafine particulate matter (PM) exposures.  Ambient PM was collected in 3 different size fractions from Chapel Hill air, particles were extracted from foam or filter matrices and lyophilized.  Human primary airway epithelial cells were exposed to particles at 250μg/ml or vehicle control for 6h in culture.  Following exposure, RNA was isolated and hybridized to human HG U133A affymetrix chips.
Keywords: particle treatment

overall_design: Human primary epithelial cells were exposed to coarse, fine, ultrafine PM or vehicle control in culture for 6h.  Three biological replicates for each treatment (coarse, fine, ultrafine, control) were conducted at (250ug/ml).  12 Affymetrix chips (HG U133A) were used.

first: Michael

middle: T

last: Schmitt

first: Lisa

last: Dailey

first: Robert

last: Devlin


title: Camparision of gene expression among CL, INT, and CH flowers of C. kokaiensis in ATH1

status: Public on May 27 2008

city: Fukuoka

first: Shin-Ichi

last: Morinaga

state: Fukuoka

address: 6-10-1, Hakozaki

department: Department of Biology

country: Japan

institute: Kyushu University

summary:
The annual cleistogamous herb Cardamine kokaiensis is an endemic plant along the Kokai River in Japan. We examined the differences in gene expression patterns among cleistogamous (CL), intermediate (INT), and chasmogamous (CH) flower by cross-species microarray analysis using an Arabidopsis thaliana Affymetrix high-density oligonucleotide microarray (GeneChip ATH1). We then discuss the molecular basis of the evolution of cleistogamy. Our results help to clarify the molecular basis of the evolution of plant mating systems that depend on environmental conditions.
Keywords: flower type comparison

overall_design: gDNA hybridyzation data was used to calibration of cross-species microarray using Affymetrix ATH1. CH, INT, and CL flowers of C. kokaiensis were induced the chilling treatment before germination for 14 days or after germination for 14 or 28 days, respectively. We performed two biological replications per flower. Data analysis was conducted according to Hammond et al. (2005) that described the methods of calibration by gDNA hybridization.

first: Atsushi

middle: J

last: Nagano

first: Saori

last: Miyazaki

first: Minoru

last: Kubo

first: Taku

last: Demura

first: Hiroo

last: Fukuda

first: Satoki

last: Sakai

first: Mitsuyasu

last: Hasebe


title: Senseless-responsive and GAL4-responsive genes in larval salivary glands of late Drosophila prepupae

status: Public on May 29 2008

city: Fayetteville

last: Lehmann

state: AR

address: SCEN 601

institute: University of Arkansas

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

overall_design: Refer to individual Series


title: Expression analysis of the effect of protoplasting and FACS sorting in roots exposed to iron deficiency (-Fe)

status: Public on Apr 24 2008

city: Durham

first: Terri

middle: Anita

last: Long

department: Biology

institute: Duke University

summary:
In order to estimate the effects of protoplasting and FACS sorting procedures on -Fe regulated gene expression we generated expression profiles for whole roots that had been treated with -Fe for 24 hours and for roots that were protoplasted and FACS sorted after the initial 24 hour -Fe treatment.
Little is known about how developmental cues affect the way cells interpret their environment.  Here we characterize the transcriptional response of different cell layers and developmental stages of the Arabidopsis root to high salinity and find that transcriptional responses are highly constrained by developmental parameters.  These transcriptional changes lead to the differential regulation of specific biological functions in subsets of cell-layers, several of which correspond to observable physiological changes.  We show that known stress pathways primarily control semi-ubiquitous responses and use mutants that disrupt epidermal patterning to reveal cell-layer specific and inter-cell-layer effects.  By performing a similar analysis using iron-deprivation we identify common cell-type specific stress responses and environment-independent biological functions that define each cell type.
Keywords: effects of protoplasting and FACS sorting

overall_design: To estimate the effect that protoplasting and cell sorting has on the expression of -Fe regulated genes we prepared samples as in Birnbaum et al. (2005) Nat. Methods, except that all cells were collected after cell sorting.  Cells were collected from roots that had been exposed to iron deficient (-Fe) conditions (0.3mM Ferrozine in MS media containing no ferrous sulfate) for 24 hours prior to protoplasting.  Whole roots were also collected after a similar treatment regimen with -Fe.  Three replicates were performed per condition.

first: Jean

middle: Y

last: Wang

first: Philip

middle: N

last: Benfey


title: Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots

summary:
We performed a time course analysis (TC data set) of the response of whole seedling roots to -Fe at 6 time points after transfer (3, 6, 12, 24, 48, and 72 hours).
Little is known about how developmental cues affect the way cells interpret their environment.  Here we characterize the transcriptional response of different cell layers and developmental stages of the Arabidopsis root to high salinity and find that transcriptional responses are highly constrained by developmental parameters.  These transcriptional changes lead to the differential regulation of specific biological functions in subsets of cell-layers, several of which correspond to observable physiological changes.  We show that known stress pathways primarily control semi-ubiquitous responses and use mutants that disrupt epidermal patterning to reveal cell-layer specific and inter-cell-layer effects.  By performing a similar analysis using iron-deprivation we identify common cell-type specific stress responses and environment-independent biological functions that define each cell type.
Keywords: time course analysis

overall_design: Seedlings were grown for 5 days before transfer to iron deficient (-Fe) conditions (0.3mM Ferrozine in MS media containing no iron sulfate).  Whole roots were harvested at 6 time points after the transfer.


title: The Sf1-related nuclear hormone receptor Hr39 regulates Drosophila female reproductive tract development and function

status: Public on Apr 26 2008

city: Baltimore

first: Allan

last: Spradling

state: MD

address: 3520 San Martin Dr

department: Embryology

institute: Carnegie Institution/HHMI

summary:
The vertebrate nuclear hormone receptor steroidogenic factor 1 (SF1; NR5A1) controls reproductive development and regulates the transcription of steroid-modifying cytochrome P450 genes. We find that the SF1-related Drosophila nuclear hormone receptor HR39 is also essential for sexual development. In Hr39 mutant females, the sperm-storing spermathecae and glandular parovaria are absent or defective, causing sterility. Our results indicate that spermathecae and parovaria secrete reproductive tract proteins required for sperm maturation and function, like the mammalian epididymis and female reproductive tract. Hr39 controls the expression of specific cytochrome P450 genes and is required in females both to activate spermathecal secretion and repress male-specific courtship genes such as takeout. Thus, a pathway that, in vertebrates, controls sex-specific steroid hormone production, also mediates reproductive functions in an invertebrate. Our findings suggest that Drosophila can be used to model more aspects of mammalian reproductive biology than previously believed.
Keywords: mutant/wild-type comparison and tissue comparison

overall_design: Wild type and Hr39(04443) Spermathecae, Wild type and Hr39(04443) Reproductive Tract

first: Anna

last: Allen


title: Expression analysis of the salt stress response in Arabidopsis mutants with defects in hair patterning

city: Stanford

first: Jose

middle: Ramon

last: Dinneny

state: United States

address: 260 Panama St

department: Plant Biology

institute: Carnegie Institution for Science, Department of Plant Biology

summary:
We performed an expression analysis of the response of seedling root tips to 1 hour of treatment with 140mM NaCl using mutants defective in root hair patterning.
Cells are amazingly adept at integrating both external and internal cues to regulate transcriptional states.  While internal processes such as differentiation and cell-type specification are generally understood to have an important impact on gene expression, very little is known about how cells utilize these developmental cues to regulate responses to external stimuli.  Here we use the response to a well characterized environmental stress, high salinity, to obtain a global view of the role that cell identity plays in guiding transcriptional responses in the root of Arabidopsis.  Our analysis is based on three microarray data sets we have generated that explore transcriptional changes spatially among 6 cell layers and 4 longitudinal regions or temporally along 5 time points after salt treatment.  We show that the majority of the response to salt stress is cell-type specific resulting in the differential regulation of unique biological functions in subsets of cell layers.  To understand the regulatory mechanisms controlling these responses we have analyzed cis-element enrichment in the promoters of salt responsive genes and demonstrate that known stress regulatory elements likely control responses to salt occurring in multiple cell types.  Despite the extensive shift in transcriptional state that salt stress elicits, we are able to identify several biological processes that consistently define each cell layer and find that transcriptional regulators of cell-identity tend to exhibit robust cell-type specific expression.  Finally, using mutants that disrupt cell-type specification in the epidermis, we reveal cell autonomous and non-autonomous effects when cell identity is altered.  Together, these data elucidate a novel intersection between physiology and development and expand our understanding of how transcriptional states are regulated in a multi-cellular context.
Keywords: Response analysis of mutants

overall_design: Seedlings were grown for 5 days before being transferred to standard media or media supplemented with 140mM NaCl.  One hour after transfer, a razor blade was used to cut the root ~5 mm above the root tip.  Approximately 30 roots were pooled per replicate.  Two biological replicates were performed per genotype, per condition.

middle: R


title: Identification of AGL24 downstream genes by using XVE inducible system

first: Hao

last: Yu

summary:
To understand the transcriptional program controlled by AGL24, we took advantage of a functional estradiol-inducible AGL24 expression system in combination with microarray analysis to identify AGL24 target genes.
Keywords: inducible system

overall_design:
We firstly compared the transcriptomes in pER22-AGL24 seedlings induced by estradiol- relative to mock-treatment, which revealed the differentially expressed genes corresponding to the elevated AGL24 expression induced by estradiol. As a chemical, estradiol itself could trigger a series of elevated or repressed genes, which might represent a large portion of false positive targets of AGL24. To rule out the genes expressed exclusively in response to estradiol instead of induced AGL24 activity, we also compared the estradiol-induced transcriptomes in pER22-AGL24 relative to those in estradiol-induced wild-type seedlings because only the former contained the induced AGL24 expression. The genes showing different expression in these two comparisons only responded to induced AGL24 activity rather than estradiol- or mock-treatment.
Two replicates of microarray experiments were performed with biologically independent pools of samples. For pER22-AGL24 seedlings treated by estradiol- relative to mock-treatment, gene expression in mock-treated seedlings was used as the baseline, while for estradiol-treated pER22-AGL24 and wild-type seedlings, gene expression in estradiol-treated wild-type seedlings was used as the baseline.


title: Expression analysis of root cell-types after iron deficiency (-Fe) treatment

summary:
Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters.  Five different GFP-reporter lines were utilized allowing us to obtain transcriptional profiles for cells in all radial zones of the root.  FACS cell populations were isolated from roots grown under standard conditions or roots that had been transfered to -Fe media for 24 hours.
Little is known about how developmental cues affect the way cells interpret their environment.  Here we characterize the transcriptional response of different cell layers and developmental stages of the Arabidopsis root to high salinity and find that transcriptional responses are highly constrained by developmental parameters.  These transcriptional changes lead to the differential regulation of specific biological functions in subsets of cell-layers, several of which correspond to observable physiological changes.  We show that known stress pathways primarily control semi-ubiquitous responses and use mutants that disrupt epidermal patterning to reveal cell-layer specific and inter-cell-layer effects.  By performing a similar analysis using iron-deprivation we identify common cell-type specific stress responses and environment-independent biological functions that define each cell type.
Keywords: Cell-type specific analysis using FACS

overall_design: To gain a genome-scale understanding of the role that developmental processes play in regulating stimulus response, we examined the effect of -Fe stress on gene expression along the radial axis of the root. Cell identity is the main variable that changes along the radial axis with the epidermis representing the outermost tissue layer and the stele representing the inner most layer. 5 different GFP reporter lines were used to isolate specific populations of cells from the Arabidopsis root using FACS sorting of protoplasted cells. GFP-reporter lines were exposed to iron deficient (-Fe) conditions (0.3mM Ferrozine in MS media containing no ferrous sulfate) for 24 hours before hand.

first: Ji-young

last: Lee


title: COP9 signalosome (csn) mutant analysis

city: Freising

first: Claus

last: Schwechheimer

address: Emil-Ramann-Str. 4

department: Plant Systems Biology

country: Germany

institute: TUM

summary:
Transcript profiling analysis of csn3-1, csn4-1 and csn5 (csn5a-2 csn5b) light grown and dark grown mutant seedlings compared to light grown and dark grown wild type using Arabidopsis ATH1 GeneChip array
Keywords: mutant analysis, growth condition analysis

overall_design: We compare eight samples of 7 day-old light grown or dark grown csn3-1, csn4-1, and csn5 (csn5a-2 csn5b) mutant seedlings and light grown and dark grown wild type seedlings (3 independent biological replicates each).

first: E

middle: M

last: Dohmann

first: C

last: Nill


title: Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.

status: Public on Apr 25 2008

first: John

last: Harada

address: One Shields Avenue

institute: University of California, Davis

summary:
We collected globular stage seed compartments from 5 or 7-micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments of an Arabidopsis seed containing a globular stage embryo. For the purposes of this study we broke down the seed into 8 capturable compartments: embyro proper, suspensor, micropylar endosperm, peripheral endosperm, chalazal endosperm, chalazal seed coat, general seed coat, and whole seeds.
Keywords: cell type comparison

overall_design: Globular stage seed compartments were isolated using the LMD6000 system. Total RNA was amplified and hybridized with Affymetrix ATH1 Arabidopsis array for 17 samples (Embryo Proper, Micropylar Endosperm, Peripheral Endosperm, General Seed Coat, Chalazal Seed Coat, and Whole Seeds, 2 biological replicates each and Chalazal Endosperm with 3 biological replicates).

first: Sandra

middle: L

last: Stone

first: Julie

last: Pelletier

first: Ryan

last: Kirkbride

first: Xiao

middle: H

last: Lu

first: Mark

middle: F

last: Belmonte

first: Jiong

last: Fei

first: Anhthu

middle: Q

last: Bui

first: Robert

last: Goldberg


title: Time course expression analysis of the salt stress response in Arabidopsis roots

summary:
We performed a time course analysis (TC data set) of the response of whole seedling roots to 140mM NaCl at 5 time points after transfer (30 minutes, 1, 4, 16 and 32 hours).
Cells are amazingly adept at integrating both external and internal cues to regulate transcriptional states.  While internal processes such as differentiation and cell-type specification are generally understood to have an important impact on gene expression, very little is known about how cells utilize these developmental cues to regulate responses to external stimuli.  Here we use the response to a well characterized environmental stress, high salinity, to obtain a global view of the role that cell identity plays in guiding transcriptional responses in the root of Arabidopsis.  Our analysis is based on three microarray data sets we have generated that explore transcriptional changes spatially among 6 cell layers and 4 longitudinal regions or temporally along 5 time points after salt treatment.  We show that the majority of the response to salt stress is cell-type specific resulting in the differential regulation of unique biological functions in subsets of cell layers.  To understand the regulatory mechanisms controlling these responses we have analyzed cis-element enrichment in the promoters of salt responsive genes and demonstrate that known stress regulatory elements likely control responses to salt occurring in multiple cell types.  Despite the extensive shift in transcriptional state that salt stress elicits, we are able to identify several biological processes that consistently define each cell layer and find that transcriptional regulators of cell-identity tend to exhibit robust cell-type specific expression.  Finally, using mutants that disrupt cell-type specification in the epidermis, we reveal cell autonomous and non-autonomous effects when cell identity is altered.  Together, these data elucidate a novel intersection between physiology and development and expand our understanding of how transcriptional states are regulated in a multi-cellular context.
Keywords: Time course analysis

overall_design: Seedlings were grown for 4-5 days before transfer to standard media supplemented with 140 mM NaCl.  Whole roots were harvested at 5 time points after the transfer.

first: Jean

last: Wang

first: Philip

last: Benfey


title: Expression analysis of root cell-types after treatment with salt

first: Jose

last: Dinneny

summary:
Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters.  Six different GFP-reporter lines were utilized allowing us to obtain transcriptional profiles for cells in all radial zones of the root.  FACS cell populations were isolated from roots grown under standard conditions or roots that had been transfered to media supplemented with 140 mM NaCl for 1 hour.
Cells are amazingly adept at integrating both external and internal cues to regulate transcriptional states.  While internal processes such as differentiation and cell-type specification are generally understood to have an important impact on gene expression, very little is known about how cells utilize these developmental cues to regulate responses to external stimuli.  Here we use the response to a well characterized environmental stress, high salinity, to obtain a global view of the role that cell identity plays in guiding transcriptional responses in the root of Arabidopsis.  Our analysis is based on three microarray data sets we have generated that explore transcriptional changes spatially among 6 cell layers and 4 longitudinal regions or temporally along 5 time points after salt treatment.  We show that the majority of the response to salt stress is cell-type specific resulting in the differential regulation of unique biological functions in subsets of cell layers.  To understand the regulatory mechanisms controlling these responses we have analyzed cis-element enrichment in the promoters of salt responsive genes and demonstrate that known stress regulatory elements likely control responses to salt occurring in multiple cell types.  Despite the extensive shift in transcriptional state that salt stress elicits, we are able to identify several biological processes that consistently define each cell layer and find that transcriptional regulators of cell-identity tend to exhibit robust cell-type specific expression.  Finally, using mutants that disrupt cell-type specification in the epidermis, we reveal cell autonomous and non-autonomous effects when cell identity is altered.  Together, these data elucidate a novel intersection between physiology and development and expand our understanding of how transcriptional states are regulated in a multi-cellular context.
Keywords: Cell-type specific analysis using FACS

overall_design: To gain a genome-scale understanding of the role that developmental processes play in regulating stimulus response, we examined the effect of salt stress on gene expression along the radial axis of the root.  Cell identity is the main variable that changes along the radial axis with the epidermis representing the outermost tissue layer and the stele representing the inner most layer.  6 different GFP reporter lines were used to isolate specific populations of cells from the Arabidopsis root using FACS sorting of protoplasted cells.  GFP-reporter lines were grown under standard conditions before protoplasting and sorting or they were transfered to media supplemented with 140mM NaCl for 1 hour before hand.


title: Iron deficiency (-Fe) effect: Arabidopsis roots

first: Terri

last: Long


title: Expression analysis of the effect of protoplasting and FACS sorting in roots

summary:
In order to estimate the effects of protoplasting and FACS sorting procedures on salt regulated gene expression we generated expression profiles for whole roots that had been treated with salt for 1 hour and for roots that were protoplasted and FACS sorted after the initial 1 hour salt treatment.
Cells are amazingly adept at integrating both external and internal cues to regulate transcriptional states.  While internal processes such as differentiation and cell-type specification are generally understood to have an important impact on gene expression, very little is known about how cells utilize these developmental cues to regulate responses to external stimuli.  Here we use the response to a well characterized environmental stress, high salinity, to obtain a global view of the role that cell identity plays in guiding transcriptional responses in the root of Arabidopsis.  Our analysis is based on three microarray data sets we have generated that explore transcriptional changes spatially among 6 cell layers and 4 longitudinal regions or temporally along 5 time points after salt treatment.  We show that the majority of the response to salt stress is cell-type specific resulting in the differential regulation of unique biological functions in subsets of cell layers.  To understand the regulatory mechanisms controlling these responses we have analyzed cis-element enrichment in the promoters of salt responsive genes and demonstrate that known stress regulatory elements likely control responses to salt occurring in multiple cell types.  Despite the extensive shift in transcriptional state that salt stress elicits, we are able to identify several biological processes that consistently define each cell layer and find that transcriptional regulators of cell-identity tend to exhibit robust cell-type specific expression.  Finally, using mutants that disrupt cell-type specification in the epidermis, we reveal cell autonomous and non-autonomous effects when cell identity is altered.  Together, these data elucidate a novel intersection between physiology and development and expand our understanding of how transcriptional states are regulated in a multi-cellular context.
Keywords: Expression analysis

overall_design: To estimate the effect that protoplasting and cell sorting has on the expression of salt regulated genes we prepared samples as in Birnbaum et al. (2005) Nat. Methods, except that all cells were collected after cell sorting.  Cells were collected from roots that had been treated with 140mM NaCl for 1hr prior to protoplasting.  Whole roots were also collected after a similar treatment regimen with NaCl.  Two replicates were performed per condition.


title: Expression analysis of root developmental zones after treatment with salt

summary:
To gain a genome-scale understanding of the role that developmental processes play in regulating stimulus response, we examined the effect of salt stress on gene expression along the longitudinal axis of the root.  Since roots grow from stem cells located near the tip, the position of cells along the longitudinal axis can be used as a proxy for developmental time, with distance from the root tip correlating with increased differentiation.  To estimate the role developmental stage plays in regulating salt response, roots were dissected into four longitudinal zones (LZ data set) after transfer to standard or salt media and transcriptionally profiled.
Cells are amazingly adept at integrating both external and internal cues to regulate transcriptional states.  While internal processes such as differentiation and cell-type specification are generally understood to have an important impact on gene expression, very little is known about how cells utilize these developmental cues to regulate responses to external stimuli.  Here we use the response to a well characterized environmental stress, high salinity, to obtain a global view of the role that cell identity plays in guiding transcriptional responses in the root of Arabidopsis.  Our analysis is based on three microarray data sets we have generated that explore transcriptional changes spatially among 6 cell layers and 4 longitudinal regions or temporally along 5 time points after salt treatment.  We show that the majority of the response to salt stress is cell-type specific resulting in the differential regulation of unique biological functions in subsets of cell layers.  To understand the regulatory mechanisms controlling these responses we have analyzed cis-element enrichment in the promoters of salt responsive genes and demonstrate that known stress regulatory elements likely control responses to salt occurring in multiple cell types.  Despite the extensive shift in transcriptional state that salt stress elicits, we are able to identify several biological processes that consistently define each cell layer and find that transcriptional regulators of cell-identity tend to exhibit robust cell-type specific expression.  Finally, using mutants that disrupt cell-type specification in the epidermis, we reveal cell autonomous and non-autonomous effects when cell identity is altered.  Together, these data elucidate a novel intersection between physiology and development and expand our understanding of how transcriptional states are regulated in a multi-cellular context.
Keywords: Tissue specific analysis

overall_design: Roots were grown under standard conditions for 5 days then transfered to standard media or media supplemented with 140 mM NaCl.  One hour after transferring seedlings, roots were cut into 4 regions using a razor blade.  The first cut was made ~150 µm from the root tip at the point where the shape of the root transitions from conical to cylindrical (Zone 1).  The second cut was made ~200 µm above the first cut, at the point were the root becomes less optically dense, which marks the approximate end of the meristematic zone (Zone 2).  The third cut was made ~200-300 µm above the second cut, just below the region where root hairs begin to emerge (Zone 3).  The fourth cut was made ~1 mm above the third cut (Zone 4).


title: Expression analysis of root developmental zones after iron deficiency (-Fe) treatment

summary:
To gain a genome-scale understanding of the role that developmental processes play in regulating stimulus response, we examined the effect of -Fe stress on gene expression along the longitudinal axis of the root.  Since roots grow from stem cells located near the tip, the position of cells along the longitudinal axis can be used as a proxy for developmental time, with distance from the root tip correlating with increased differentiation.  To estimate the role developmental stage plays in regulating salt response, roots were dissected into four longitudinal zones (LZ data set) after transfer to standard or -Fe media and transcriptionally profiled.
Little is known about how developmental cues affect the way cells interpret their environment.  Here we characterize the transcriptional response of different cell layers and developmental stages of the Arabidopsis root to high salinity and find that transcriptional responses are highly constrained by developmental parameters.  These transcriptional changes lead to the differential regulation of specific biological functions in subsets of cell-layers, several of which correspond to observable physiological changes.  We show that known stress pathways primarily control semi-ubiquitous responses and use mutants that disrupt epidermal patterning to reveal cell-layer specific and inter-cell-layer effects.  By performing a similar analysis using iron-deprivation we identify common cell-type specific stress responses and environment-independent biological functions that define each cell type.
Keywords: root developmental zone analysis

overall_design: Roots were grown under standard conditions for 5 days then transfered to standard media or iron deficient (-Fe) conditions (0.3mM Ferrozine in MS media containing no ferrous sulfate).  24 hours after transferring seedlings, roots were cut into 4 regions using a razor blade.  The first cut was made ~150 µm from the root tip at the point where the shape of the root transitions from conical to cylindrical (Zone 1).  The second cut was made ~200 µm above the first cut, at the point were the root becomes less optically dense, which marks the approximate end of the meristematic zone (Zone 2).  The third cut was made ~200-300 µm above the second cut, just below the region where root hairs begin to emerge (Zone 3).  The fourth cut was made ~1 mm above the third cut (Zone 4).

last: A. Long


title: Effects of mitochondrial DNA on the gene expression profiles of human cells grown in culture and in tumor xenografts

status: Public on Apr 18 2008

first: Joseph

middle: Gerard

last: Hacia

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

summary:
Interactions between the gene products encoded by the mitochondrial and nuclear genomes play critical roles in normal eukaryotic cellular function. Here, we characterized the metabolic and transcriptional properties of A549 lung cancer cells and their isogenic mitochondrial DNA (mtDNA)-depleted rho zero counterparts grown in cell culture and as tumor xenografts in immune-deficient mice. A manuscript summarizing our conclusions is under review.
Keywords: genetic modification and culture conditions

overall_design: A549 rho zero and their parental A549 cells were grown in culture and as xenografts in nude mice.  All experiments conducted in culture were performed in triplicate (6 experiments total) and all experiments conducted in xenografts were performed in quadruplicate (8 experiments total).  A manuscript summarizing our experimental design is under review.

first: Darren

last: Magda

middle: G


title: Fork head-responsive genes in larval salivary glands of late Drosophila prepupae

status: Public on Mar 20 2008

first: Michael

last: Lehmann

summary:
When misexpressed in late Drosophila prepupae, the transcription factor Fork head (Fkh) blocks death of the larval salivary glands that normally occurs in the early pupa. The aim of the experiment was to identify genes responding to Fkh that might mediate the effect of the protein on cell death and other biological processes. Fkh was expressed in the line P[hs-Fkh111] from a heat-inducible transgene that encodes wild-type Fkh protein. Expression of Fkh was induced by incubating prepupae for 30 min in a 37 °C water bath, starting at 9.5 hours after puparium formation. Salivary glands were dissected at 14 hours after puparium formation and RNA isolated for microarray analysis with Affymetrix GeneChips. Control samples were obtained from w1118 animals treated the same way. The microarray analysis identified 55 genes annotated as functioning in apoptosis whose expression was at least 1.5-fold changed by Fkh. These genes include the death genes hid and reaper, which play a central role in the control of salivary gland death. Other groups of significantly enriched genes include genes functioning in autophagy, steroid-signaling pathways, salivary gland secretion, and phospholipid metabolism. In addition, the microarray data identify genes as responsive to Fkh that are known to be controlled by the FOXA counterparts of Fkh in vertebrates, indicating that target genes and biological processes controlled by Fkh are evolutionarily conserved.
Keywords: ectopic expression experiment

overall_design: Experimental RNA samples were obtained in 3 biological replicates from fkh-expressing salivary glands (SG_Fkh_14APF_rep1, SG_Fkh_14APF_rep2, SG_Fkh_14APF_rep3) and compared to control samples obtained in two biological replicates from the salivary glands of w1118 control animals (SG_w1118(3)_14APF_rep1, SG_w1118(3)_14APF_rep2). All samples were compared using dChip and normalized to the same baseline array (median intensity 134).

first: Yanling

last: Liu


title: Gene expression profiling of sav mutants

status: Public on Apr 01 2008

city: La Jolla

first: Joanne

last: Chory

address: 10010 N. Torrey Pines Road.

department: Plant Biology Laboratory

institute: The Salk Institute for Biological Studies

summary:
Plants grown at high densities perceive a decrease in the red to far-red (R:FR) ratio of incoming light, resulting from absorption of red light by canopy leaves and reflection of far-red light from neighboring plants. These changes in light quality trigger a series of responses known collectively as the shade avoidance syndrome. During shade avoidance, stems elongate at the expense of leaf and storage organ expansion, there is reduced branching, and flowering is accelerated. We identified several loci in Arabidopsis, mutations in which lead to plants defective in multiple shade avoidance outputs.  Here we describe SAV3, an aminotransferase, and show that SAV3 catalyzes the formation of indole-3-pyruvic acid (IPA) from L-tryptophan (L-Trp), the first step in a previously proposed, but uncharacterized, auxin biosynthetic pathway. This pathway can be rapidly deployed to biosynthesize auxin at the high levels required to initiate the multiple changes in body plan associated with shade avoidance.
Keywords: shade avoidance auxin brassinosteroid

overall_design: Wild type Col-0, sav3-2 and sav1-1 seedlings were used here. They were treated with or without 1hr of low R:FR light (R:FR ratio=0.7). Three independent biological replicates were used.

first: Yi

last: Tao

first: Fangxin

last: Hong


title: Expression data from Arabidopsis thaliana (Ler) rosette leaves after the release of singlet oxygen inside plastids

status: Public on Mar 18 2008

city: Zurich

first: Christophe

last: Laloi

address: Universitaetstrasse 2

department: Institute of Plant Science

country: Switzerland

institute: ETH Zurich

summary:
We used the flu mutant of Arabidopsis to detail gene expression in response to singlet oxygen. The conditional flu mutant of Arabidopsis accumulates excess protochlorophyllide in the dark within chloroplast membranes that upon illumination acts as a photosensitizer and generates singlet oxygen. Immediately after the release of singlet oxygen mature flu plants stop growing, whereas seedlings bleach and die. Within the first 30 min after the release of singlet oxygen rapid changes in nuclear gene expression occur. Distinct sets of genes were activated that were different from those induced by other reactive oxygen species, superoxide or hydrogen peroxide.
Keywords: Time course

overall_design: Arabidopsis thaliana rosette leaves were harvested after 30 min, 1h, and 2 h of reillumination following a 8h dark period for RNA extraction and hybridization on Affymetrix ATH1 microarrays.  Plants were grown on soil for 3 weeks under continuous light at 90 mmol. m-2 . s-1. For each sample, the rosette leaves of five to six 3-week-old plants (before they start bolting) were collected for RNA extraction. Total RNAs from two separate biological experiments were pooled for the preparation of cDNA and the subsequent synthesis of biotin-labeled complementary RNA as recommended by Affymetrix.

first: Dominika

last: Przybyla

first: Klaus

last: Apel


title: CSN4-1 mutant analysis

status: Public on Mar 25 2008

first: Claus

last: Schwechheimer

summary:
Transcript profiling analysis of csn4-1 light grown mutant seedlings compared to wild type using Arabidopsis ATH1 GeneChip array
Keywords: 7 day old light grown seedlings, wild type and mutant

overall_design: Three replicate samples were harvested and prepared from 7 day-old light grown wild type and csn4-1 mutant seedlings. RNA for microarray analysis was extracted using the RNeasyTM kit (Quiagen, Hilden, Germany). Complementary RNA was prepared from 6 µg of total RNA as described in Affimetrix _Expression Analysis Technical Manual using the One-Cycle Target Labeling and Control Reagents (Affimetrix, Santa Clara, CA). In brief, double-stranded cDNA was synthesized. Biotin-labeled target cRNA was prepared by cDNA in vitro transcription in the presence of biotinylated UTP and CTP. After purification, cRNA was fragmented and used to hybridize to the Arabidopsis ATH1 GeneChip array (Affimetrix, Santa Clara, CA). Hybridization, washing, staining, scanning and data collection were performed in an Affymetrix GeneChip® Fluidics Station 450 and GeneArray® Scanner. The microarray computaional analysis was performed on *.CEL and *.CHP data files.

first: Esther

last: Dohmann

first: Luz-Irina

last: Calderon-Villalobos


title: Expression data from human peripheral blood subsets

status: Public on Mar 01 2008

city: Dallas

first: Laurie

last: Davis

state: TX

address: 5323 Harry Hines Blvd

department: Internal Medicine

institute: UT Southwestern Medical Center

summary:
Gene expression profile studies have identified an interferon signature in whole blood or mononuclear cell samples from patients with systemic lupus erythematosus. This study was designed to determine whether specific lymphocyte and myeloid subsets freshly isolated from the blood of systemic lupus erythematosus patients demonstrated unique gene expression profiles compared to subsets isolated from healthy controls.
Keywords: patient compared to control

overall_design: The entire study included 67 samples. One CEL file was not available for SLE13_CD4


title: Gingival Epithelial Cell Transcriptional Responses to Pathogenic Oral Microbial Species.

city: Gainesville

first: Martin

last: Handfield

state: FL

address: 1600 SW Archer Road, BOX 100424

department: Oral Biology

institute: University of Florida

summary:
Transcriptional profiling was utilized to define the biological pathways of gingival epithelial cells modulated by co-culture with the oral pathogenic Porphyromonas gingivalis and Aggregatibacter (formerly actinobacillus) actinomycetemcomitans.
We used microarrays to detail the global programme of gene expression underlying infection and identified distinct classes of up- and down-regulated genes during this process.
Keywords: infection state

overall_design: Gingival epithelial HIGK cells were sham infected (CTRL) and infected with either the oral pathogenic P. gingivalis (Pg) or A. actinomycetemcomitans (Aa). These samples were hybridized to Affymetrix microarrays. Understanding how host cells have adapted to pathogens, and how barrier cells respond to limit their impact, provides a mechanistic biological basis of microbial disease in the mixed bacterial-human ecosystem of the oral cavity.

first: Richard

last: Lamont

first: Yoshiaki

last: Hasegawa

first: Jeffrey

last: Mans

first: Henry

middle: V

last: Baker


title: Gene Expression Profiles of Drosophila third instar larvae hemocytes to explain hemocyte development.

city: Seoul

first: Young-Joon

last: Kim

address: Yonsei Univ 134 Sinchon-dong Seodaemun-gu

country: South Korea

institute: Yonsei University

summary:
We measured gene expression profiles of third instar larvae hemocytes from selected strains related to hemocyte development. Every strain was purchased from commercial companies.
And we used microarray data to find what biological processes show abnormalities first, and which gene expressions show similarities and differences between selected strains.
Keywords: Strain comparison

overall_design: 200~300 Drosophila third instar larvae hemocytes from each of five lines were dissected to get at least 1 microgram of total RNA. Because all samples were hybridized to single-dye Affymetrix chip, control data were compared with data from each mutant.

first: Li-Hua

last: Jin


title: Expression data from Arabidopsis plants misexpressing AtMYB30 after Xanthomonas inoculation at early timepoints

status: Public on Feb 29 2008

city: Castanet-Tolosan

first: Dominique

last: ROBY

address: Chemin de Borde Rouge

country: France

institute: CNRS/INRA

summary:
Plant immune responses to pathogen attack involve various defense mechanisms and among them, the Hypersensitive Response (HR), a form of programmed cell death occurring at invasion sites.  AtMYB30, a transcription factor acts as a positive regulator of a cell death pathway conditioning the HR.
We show by microarray analyses of Arabidopsis plants misexpressing AtMYB30 that the genes encoding the four enzymes forming the acyl-coA elongase complex, responsible for very long chain fatty acids (VLCFA) biosynthesis, are putative targets.
Keywords: Time course after inoculation with a Xanthomonas strain, Xcc147, in Arabidopsis wild-type plants and transgenic plants (AtMYB30 overexpressor (ox) and antisense (as) lines

overall_design: 18 samples are analyzed : Leaves of 4 week-old plants syringe-infiltrated with the Xcc147 strain (or not) were harvested.  In experiment 1, we selected 4 timepoints : T0 (not inoculated), 90-105 min, 2-4 h and 6 h post inoculation in the wild-type line, and in a transgenic line overexpressing AtMYB30. Experiment 2 is a biological replicate of experiment 1 (except for 6 hpi). In experiment 3, we focused on the early timepoint 90-105 min to compare the wild-type line and an AtMYB30 antisense line. Experiment 4 is a biological replicate of experiment 3. Plant material was pooled when necessary, and frozen before RNA extraction and hybridization on Affymetrix ATH1 microarrays. As a screen for candidate target genes, we looked for genes, i) up-regulated in the wild-type line after inoculation with Xcc147 as compared to time T0 (not inoculated) , ii) over-expressed in the AtMYB30 overexpressor line compared to the wild-type, and iii) down-regulated in the AtMYB30 antisense line compared to the wild-type.

first: Sylvain

last: Raffaele

first: Fabienne

last: Vailleau

first: Amandine

last: Léger

first: Jérôme

last: Joubes

first: Otto

last: Miersch

first: Carine

last: Huard

first: Elisabeth

last: Blée

first: Sébastien

last: Mongrand

first: Frédéric

last: Domergue

last: Roby


title: Expression data from PDGF-treated SH-SY5Y cells

first: Alena

middle: A

last: Antipova

address: 7 Cambridge Center

institute: Broad Institute of Massachusetts Institute of Technology and Harvard University

summary:
We conducted a proof-of-concept experiment to explore the possibility of using gene expression-based high throughput screening (GE-HTS) to find inhibitors of a signaling cascade, using platelet derived growth factor receptor (PDGFR) signaling as the example.
To define ERK/PDGFR activation signature, we performed gene expression profiling using Affymetrix U133A arrays 0.5-4 hours following PDGF stimulation, thereby identifying those genes whose expression is correlated with PDGFR activity. In order to identify the component of the gene expression signature that was attributable to ERK activation by PDGFR (as opposed to other pathways downstream of PDGFR), we also pretreated the cells will the ERK inhibitors U0126 and PD98059, and repeated the gene expression profiling studies.
Keywords: time course, inhibitor treatment

overall_design: To define ERK/PDGFR activation signature, SH-SY5Y cells were grown to confluence and starved overnight in serum-free medium in order to silence any sustained effects from growth factor signaling. Prior to induction with 50ng/ml PDGF, cells were treated with pathway inhibitors 74 mM Apigenin or 50 mM U0126, or with DMSO (carrier) for 60 minutes. Total RNA was isolated 30 minutes after PDGF addition. Experiments were performed in duplicate. The RNA was processed and hybridized with Affymetrix U133A GeneChips.

first: Brent

last: Stockwell

first: Todd

last: Golub


status: Public on Mar 27 2008

city: Columbia

first: Gary

last: Stacey

state: MO

address: 1201 Rollins Road

department: Plant Sciences

institute: University of Missouri-Columbia

summary:
A LysM Receptor-like Kinase Mediates Chitin Perception and Fungal Resistance in Arabidopsis

Jinrong Wan,1 Xuecheng Zhang,1 David Neece,2 Katrina M. Ramonell,3 Steve Clough,2,4 Sung-yong Kim,1 Minviluz Stacey,1 and Gary Stacey1*

1Division of Plant Sciences, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO 65211, USA
2Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
3Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
4US Department of Agriculture, Soybean/Maize Germplasm, Pathology and Genetics Research, Urbana, IL 61801, USA

*To whom correspondence should be addressed. E-mail: staceyg@missouri.edu

Abstract:  Chitin, a polymer of N-acetyl-D-glucosamine, is found in fungal cell walls, but not in plants. Plant cells are capable of perceiving chitin fragments (chitooligosaccharides) to trigger various defense responses. We identified a LysM receptor-like protein (AtLysM RLK1) that is required for the perception of chitooligosaccharides in Arabidopsis. Mutation of this gene blocked the induction of almost all chitooligosaccharide-responsive genes (CRGs) and led to more susceptibility to fungal pathogens, but not to a bacterial pathogen. In addition, exogenously applied chitooligosaccharides enhanced resistance against both fungal and bacterial pathogens in the wild-type plants, but not in the mutant. Together, our data strongly suggest AtLysM RLK1 is the chitin receptor or a key part of the receptor complex and chitin is a PAMP (pathogen-associated molecular pattern) in fungi recognized by the receptor leading to the induction of plant innate immunity against fungal pathogens. Since LysM RLKs were also recently shown to be critical for the perception of the rhizobial lipo-chitin Nod signals, our data suggest that LysM RLKs not just recognize friendly symbiotic rhizobia (via their lipo-chitin Nod signals), but also hostile fungal pathogens (via their cell wall chitin). These data suggest a possible evolutionary relationship between the perception mechanisms of Nod signals and chitin by plants.
Keywords: chitooctaose, chitin receptor mutant

overall_design: wild type Col-0 and chitin receptor mutants treated with or without chitooctaose

first: Jinrong

last: Wan

first: Steve

last: Clough


title: camta3 mutant versus wild type microarray analysis

status: Public on Feb 20 2008

city: Tel Aviv

first: yael

last: Galon-Wolfenson

address: tel aviv university

country: Israel

institute: Tel Aviv University

summary:
camta3-1, camta3-2 and WT microarray experiments, statistical and bioinformatics analysis
Keywords: expression analysis; mutant versus wild type comparison

overall_design: Two biological replicates were taken for 3–week-old camta3-1 mutant (HF5 and HF9), camta3-2 mutant (HF6 and HF10) and wild type-WT (HF7 and HF8)


title: Transcript Profiling of TSC Tumor Fibroblasts in Human Patients

city: Bethesda

first: Eric

last: Billings

address: 10 Center Drive

institute: NHLBI

summary:
Patients with tuberous sclerosis complex (TSC) develop hamartomas containing biallelic inactivating mutations in either TSC1 or TSC2, resulting in mammalian target of rapamycin (mTOR) activation. Hamartomas overgrow epithelial and mesenchymal cells in TSC skin. The pathogenetic mechanisms for these changes had not been investigated, and the existence or location of cells with biallelic mutations (“two-hit” cells) that resulted in mTOR activation was unclear. We compared TSC skin hamartomas (facial angiofibromas and periungual fibromas) to normal-appearing skin of the same patient, and observed more proliferation and mTOR activation in hamartoma epidermis. “Two-hit” cells were not detected in the epidermis. Fibroblast-like cells in the dermis, however, exhibited allelic deletion of TSC2, in both touch preparations of fresh tumor samples and cells grown from TSC skin tumors, suggesting that increased epidermal proliferation and mTOR activation were not caused by second-hit mutations in the keratinocytes but by mesenchymal-epithelial interactions. Gene expression arrays, used to identify potential paracrine factors released by mesenchymal cells, revealed more epiregulin mRNA in fibroblast-like angiofibroma and periungual fibroma cells than in fibroblasts from normal-appearing skin of the same patient. Elevation of epiregulin mRNA was confirmed using real-time PCR, and increased amounts of epiregulin protein were demonstrated using immunoprecipitation and ELISA. Epiregulin stimulated keratinocyte proliferation and phosphorylation of ribosomal protein S6 in vitro. These results suggest that hamartomatous TSC skin tumors are induced by paracrine factors released by “two-hit” cells in the dermis, and that proliferation with mTOR activation of the overlying epidermis is an effect of epiregulin.
Keywords: Disease state analysis

overall_design: The study is of case/control design with biological replication.  Tumor (case) and normal (control) fibroblast cells were isolated from each of four patients (biological replicates).

first: Thomas

last: Darling


title: Identification of biological markers of sensitivity to high-clinical-risk-adapted therapy for DLBCL patients

city: Granada

first: Ana

middle: Isabel

last: Saez

state: Granada

address: Avda. Dr Oloriz, 16

country: Spain

institute: Red de Bancos de Tumores de Andalucía

summary:
Diffuse large B-cell lymphoma (DLBCL) has striking clinical and molecular variability.  Although a more precise identification of the multiple determinants of this variability is still under investigation, there is a consensus that high-clinical-risk DLBCL cases require a risk-adapted therapy, since intensification of chemotherapy with autologous stem-cell transplantation (ASCT) has been shown to improve the prognosis for high-risk patients in randomised clinical trials.

In spite of this, the protocols used for these patients have a high morbidity, associated with ASCT and the use of multiple drugs. This makes it important to identify patients that may take benefit from risk-adapted therapies, through the recognition of biological markers that provide information about both the tumoral cells and the microenvironment. Unfortunately, many of the studies so far performed have relied on heterogeneous series of patients, staged or treated with different protocols. For instance, some of the variability in DLBCL arises from the fact that this diagnosis is applied to de novo and secondary tumours, nodal and extranodal, irrespective of clinical stage, patient age and associated infections. Additionally, DLBCL includes some specific variants, such as mediastinal DLBCL and T/HRBCL, with specific prognostic parameters. This could prevent the identification of potential predictive biomarkers, because the results of many studies show that the search for predictive biomarkers should be promoted in the context of samples of clinically homogeneous patients enrolled in clinical trials. A further source of variability is the dependence of some predictive markers on specific therapeutic approaches, as is the case for the Bcl6 expression in DLBCL, since Bcl-6+ cases have been shown not to benefit from the addition of R to CHOP.
Here we have analysed a series of high-clinical-risk DLBCLs by a two-stage approach, first identifying functional signatures by expression analysis, then analysing surrogate biomarkers using tissue microarrays (TMAs). This eclectic approach could reveal new aspects of the relationship between the neoplastic cells and the microenvironment, leading to the identification of previously unknown prognostic markers. At the same time, the use of functional signatures to analyse expression-profiling data avoids the poor reproducibility of the data obtained from gene-by-gene analysis, and benefits from the existence of a growing body of data concerning the major pathways deregulated in DLBCL.
To avoid the bias of semiquantitative scoring, in this study we have quantified the markers included in the multivariate analysis.

Keywords: new biological variables, risk-adapted therapies

overall_design:
Patients
The study was performed in a series of 74 high-clinical-risk DLBCL patients included in a prospective trial from the GEL/TAMO Spanish Group (Grupo Español de Linfomas / Trasplante de Médula Ósea) between June 2001 and June 2005. High risk was defined as having either an age-adjusted IPI score >=2 or IPI <2 with a high β2 microglobulin level.
All patients received therapy with MegaCHOP, after which, patients were again evaluated for response by CT and Ga 67S. Patients with CT response and negative Ga 67S received another MegaCHOP cycle followed by BEAM and ASCT. Those patients with positive Ga 67S or without CT response underwent salvage treatment with Ifosfamide and Etoposide (IFE) for two courses, followed by BEAM and ASCT whenever a response had been achieved. From June 2003 Rituximab was added to the schema, before administering ASCT. Those patients with less than a Partial Response (PR) or progressive disease after IFE were removed from the study.
Diagnoses were revised by a panel of pathologists, following the World Health Organization (WHO)9 criteria. Only primary DLBCLs were included in this analysis. T-cell/histiocyte-rich large B-cell lymphomas (T/HRLBCLs) and mediastinal DLBCLs were excluded.
Patients included in this biological analysis were consecutive, selected only on the basis of the availability of formalin-fixed paraffin-embedded or frozen tissue representative of the tumour at diagnosis. The final number of cases analysed was 50. Frozen diagnostic tissue was available from a subset of ten of these patients.
Informed consent was obtained from the patients included in the trial under the supervision of the Local Ethical Committees.

Identifying biological function surrogate markers for clinical prediction
The expression profile was initially analysed in the ten samples from which frozen tissue was available. These included four patients who had died after treatment failure and six who were alive, with complete remission, and free of disease.
All frozen tissue corresponded to a representative area of the tumour with more than 60% of viable tumoral cells present.
We used a multistep gene-set-enrichment approach to identify functional pathways deregulated in DLBCLs resistant to the treatment strategy.
The design of the analysis was as follows (details on the procedure are included as Supplementary information on material and Methods) :
1.	Microarray analysis, using both cDNA and oligonucleotide microarrays in a set of 10 frozen diagnostic samples.
2.	Identification of biological function representative of differentially expressed genes, using the Gene Ontology database (http://bioinformatics.weizmann.ac.il/cards)
3.	Selection of surrogate immunohistochemical markers (representative of the biological function identified)
4.	Immunohistochemical study on Tissue Microarrays containing  diagnostic initial  biopsy tissue in a set of  50 patients
a.	Semiquantitative scoring
b.	Quantification of the most relevant markers

Identification of biological markers predicting treatment response
The relations between the semiquantitative measurement of the 60 proteins evaluated and the clinical outcome were analysed. The clinical end-points were: a) CR after 3 MegaCHOP, b) CR after IFE and, c) absence of progression after consolidation with HDT/ ASCT.
The chi-square statistic was used to assess associations between the protein-expression levels and the intermediate step of treatment. Significant relationships (p<0.05) and non-significant trends (p<0.1) were identified.
Failure was defined as progression or death attributable to the tumour. Failure-free survival (FFS) curves were plotted using the Kaplan-Meier method. Statistical significance of associations between individual variables and FFS was determined using the log-rank test. Significant relationships (p<0.05) and non-significant trends (p<0.1) were identified.
Genes were clustered on the basis of their biological similarities.
The accumulations or alternations of marker alterations were analysed by the chi-square and Spearman correlation tests. Only significant relationships (p<0.05) were considered further.
One surrogate marker for each altered main cellular function was selected. These markers were considered in order to develop a multivariate logistic regression model predicting failure of treatment. Proteins found to be potentially informative in this analysis were automatically scored.
Various multivariate models were fitted using step-up (forward) and step-down (backwards) variable selection and other heuristic procedures. By comparing the fits of these models, a final predictive logistic regression model was obtained. The final model estimates the odds ratio (OR), 95% confidence interval (CI) and significance (P) of each variable. General applicability of the model was tested by leave-one-out cross-validation. Different predictor models were found when using leave-one-out cross validation but these showed only small variations in the weight of each marker. Accuracy was also tested by the Receiver Operating Characteristic (ROC) curve, which estimates the discriminating ability of the model. The fit of the final model was assessed by the Hosmer-Lemeshow test.
To demonstrate the predictive capacity of the model, patients were ranked according to this score and then divided into quartiles.
Statistical analyses were performed using SPSS and R tools.

middle: I

first: Monica

last: Garcia-Cosio

first: Antonio

first: Jesus

last: Hernandez

first: Lidia

last: Sanchez-Verde

first: David

last: Alvarez

first: Paloma

last: De la Cueva

first: Raquel

last: Villuendas

first: Reyes

last: Arranz

first: Eulogio

last: Conde

first: Carlos

last: Grande

first: Jose

last: Rodriguez

first: Dolores

last: Caballeros

first: Miguel

last: Piris


title: Human Neuropheres

status: Public on Apr 02 2008

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary:
Three week old neurospheres cultured from 18, 20 and 22 week old human fetal brain tissue, generated from epidermal growth factor, platelet-derived growth factor, and platelet-derived growth factor and neurotrophin-3.
Keywords: neurosphere development

overall_design: this experiment include 9 samples and 18 replicates


title: Expression data of Arabidopsis thaliana rosettes during chilling

status: Public on Feb 15 2008

city: Potsdam

first: Björn

last: Usadel

address: Am Mühlenberg 1

institute: Max Planck Institute of Molecular Plant Physiology

summary:
To investigate the response of Arabidopsis thaliana plants to non-freezing, cool temperatures, we subjected four week old plants to various chilling temperatures at defined times during the diurnal cycle to control for diurnal effects on transcription. From the same plants, metabolites and enzyme activities were measured as well. Interestingly a gradual change could be observed over a wide range of temperatures. Some of which could be attributed to the CBF program.
Keywords: time course, different temperatures

overall_design:
Arabidopsis thaliana rosettes from 4 week old plants at a time point four hours into the light-period were transfered to various "chilling" temperatures (20 [control], 17, 14, 12, 10 and 8°C] and harvested after 6 or 78 hours (both 10 hours into the light period).

6 continuous treatments X 2 timepoints X 2 replicates

first: Oliver

middle: E

last: Bläsing

first: Yves

last: Gibon

first: Fabien

last: Poree

first: Melanie

last: Höhne

first: Manuela

last: Günther

first: Richard

last: Threthewey

first: Beate

last: Kamlage

first: Hendrik

last: Poorter

first: Mark

last: Stitt


title: Gene expression signature of cigarette smoking and its role in lung adenocarcinoma development and survival

first: Maxwell

last: Lee

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

summary:
Tobacco smoking is responsible for over 90% of lung cancer cases, and yet the precise molecular alterations induced by smoking in lung that develop into cancer and impact survival have remained obscure.   We performed gene expression analysis using HG-U133A Affymetrix chips on 135 fresh frozen tissue samples of adenocarcinoma and paired noninvolved lung tissue from current, former and never smokers, with biochemically validated smoking information.  ANOVA analysis adjusted for potential confounders, multiple testing procedure, Gene Set Enrichment Analysis, and GO-functional classification were conducted for gene selection. Results were confirmed in independent adenocarcinoma and non-tumor tissues from two studies.  We identified a gene expression signature characteristic of smoking that includes cell cycle genes, particularly those involved in the mitotic spindle formation (e.g., NEK2, TTK, PRC1). Expression of these genes strongly differentiated both smokers from non-smokers in lung tumors and early stage tumor tissue from non-tumor tissue (p<0.001 and fold-change>1.5, for each comparison), consistent with an important role for this pathway in lung carcinogenesis induced by smoking. These changes persisted many years after smoking cessation. NEK2 (p<0.001) and TTK (p=0.002) expression in the noninvolved lung tissue was also associated with a 3-fold increased risk of mortality from lung adenocarcinoma in smokers.   Our work provides insight into the smoking-related mechanisms of lung neoplasia, and shows that the very mitotic genes known to be involved in cancer development are induced by smoking and affect survival. These genes are candidate targets for chemoprevention and treatment of lung cancer in smokers.
Keywords: comparative genomics

overall_design: Overall, 180 adenocarcinoma and non-tumor tissue samples were selected for the analyses, including duplicate or triplicate samples from 14 subjects for quality control. From the original 180 samples, 148 provided sufficient quantity of high-quality RNA for microarray analyses; 13 additional samples were excluded because of problematic assays. Normalization was conducted on the remaining 135 microarrays. After normalization, 13 samples were excluded because of low percentage of tumor cells in the tumor tissues. This report is based on 122 samples, of which 15 duplicates were averaged, resulting in 107 final expression values from 58 tumor and 49 non-tumor tissues from 20 never smokers, 26 former smokers, and 28 current smokers.

first: MariaTeresa

last: Landi

first: Tatiana

last: Dracheva

first: Melissa

last: Rotunno

first: Jonine

middle: D

last: Figueroa

first: Huaitian

last: Liu

first: Abhijit

last: Dasgupta

first: Felecia

last: Mann

first: Junya

last: Fukuoka

first: Megan

last: Hames

first: Andrew

middle: W

last: Bergen

first: Sharon

last: Murphy

first: Ping

last: Yang

first: Angela

middle: C

last: Pesatori

first: Dario

last: Consonni

first: PierAlberto

last: Bertazzi

first: Sholom

last: Wacholder

first: Joanna

last: Shih

first: Neil

last: Caporaso

first: Jin

last: Jen


title: Expression data from thylakoidal ascorbate peroxidase overexpressor Arabidopsis thaliana (Col) rosette leaves

status: Public on Mar 13 2008

first: Christophe

last: Laloi

summary:
We used the flu mutant of Arabidopsis and a transgenic line that overexpresses the thylakoid-bound ascorbate peroxidase (tAPX) to address the interactions between different reactive oxygen species (ROS) signaling pathways. The conditional flu mutant of Arabidopsis accumulates excess protochlorophyllide in the dark within chloroplast membranes that upon illumination acts as a photosensitizer and generates singlet oxygen (1O2). Immediately after the release of singlet oxygen rapid changes in nuclear gene expression occur. Distinct sets of genes were activated that were different from those induced by other reactive oxygen species, superoxide or hydrogen peroxide (H2O2), suggesting that different types of active oxygen species activate distinct signaling pathways. It was not known whether the pathways operate separately or interact with each other. We have addressed this problem by modulating noninvasively the level of H2O2 in plastids by means of a transgenic line that overexpresses the thylakoid-bound ascorbate peroxidase (tAPX, line 14/2  PMID: 15165186). In the flu mutant overexpressing tAPX, the expression of most of the nuclear genes that were rapidly activated after the release of 1O2 was significantly higher in flu plants overexpressing tAPX, whereas in wild-type plants, overexpression of tAPX had only a very minor impact on nuclear gene expression. The results suggest that H2O2 antagonizes the 1O2-mediated signaling of stress responses as seen in the flu mutant. This cross-talk between H2O2- and 1O2-dependent signaling pathways might contribute to the overall stability and robustness of wild-type plants exposed to adverse environmental stress conditions.
Keywords: Single time point comparison

overall_design: Arabidopsis thaliana rosette leaves were harvested after 2 h of reillumination following a 8h dark period for RNA extraction and hybridization on Affymetrix ATH1 microarrays. The entire experiment was performed six times, providing independent biological replicates. For each of the six experiments, all four lines, wild-type, thylakoidal ascorbate peroxidase overexpressor (over tAPX, line 14/2), flu mutant and flu plants overexpressing thylakoidal ascorbate peroxidase were grown for 3 weeks under continuous light at 90 mmol. m-2 . s-1, transferred to the dark for 8 h, and reilluminated for 120 min before the rosette leaves of at least 10 plants per line were harvested. Total RNAs from three separate biological experiments were pooled (= 1 biological rep.) for the preparation of cDNA and the subsequent synthesis of biotin-labeled complementary RNA as recommended by Affymetrix.

first: Klaus

last: Apel


title: Expression data of Arabidopsis thaliana rosettes in an extended night

status: Public on Feb 14 2008

first: Björn

last: Usadel

summary:
Usually starch is nearly depleted at the end of the night. To induce a gradual depletion of carbon, we have analysed the global response of transcripts during an extension of the night, where carbon becomes severely limiting from about four hours onwards.
Keywords: time course

overall_design: Arabidopsis thaliana rosettes were harvested in successive timpoints in an extended night situation.

first: Oliver

last: Bläsing

first: Yves

last: Gibon

first: Kristin

last: Retzlaff

first: Melanie

last: Höhne

first: Manuela

last: Günther

first: Mark

last: Stitt


title: Gene Expression Study of Background, Progenitor and Stem Cell Populations from Human Umbilical Cord Blood

status: Public on Feb 13 2008

first: Theodore

last: Perkins

summary:
Gene expression study of populations of primary human hematopoietic cells from human cord blood including background, progenitor and stem cells.
Keywords: other

overall_design: This experiment include 4 samples each with 3 replicates on 2 platforms for a total of 24 GEO Samples


title: Naturally occurring copy-number polymorphism in Drosophila melanogaster

city: Cambridge

first: Erik

last: Dopman

address: 16 Divinity Ave, Bio. Labs

department: Organismic and Evolutionary Biology

institute: Harvard University

summary:
Thomas Hunt Morgan and colleagues identified variation in gene copy number in Drosophila in the 1920s and 1930s and linked such variation to phenotypic differences [Bridges, C. B. (1936) Science 83, 210]. Yet the extent of variation in the number of chromosomes, chromosomal regions, or gene copies, and the importance of this variation within species, remain poorly understood. Here, we focus on copy-number variation in Drosophila melanogaster. We characterize copy-number polymorphism (CNP) across genomic regions, and we contrast patterns to infer the evolutionary processes acting on this variation. Copy-number variation in D. melanogaster is non-randomly distributed, presumably due to a mutational bias produced by tandem repeats or other mechanisms. Comparisons of coding and noncoding CNPs, however, reveal a strong effect of purifying selection in the removal of structural variation from functionally constrained regions. Most patterns of CNP in D. melanogaster suggest that negative selection and mutational biases are the primary agents responsible for shaping structural variation.
Keywords: comparative genomic hybridization

overall_design: Genomic DNA from five natural isofemale lines were compared to the sequenced D. melanogaster strain with four replicates per comparison. Controls were self-self and male-female hybridization (three replicates per control).

middle: B

first: Daniel

last: Hartl


title: Transcriptome analysis of pho3

status: Public on Jan 31 2008

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

summary:
The aim of this proposal is to understand the impact of the pho3 mutation on the transcriptome.The mutant pho3 was isolated on the basis of a failure to induce acid phosphatase activity in roots in response to low Pi. The pho3 mutant had a P deficient phenotype in vitro and in the leaves of soil grown pho3 plants the total P content was again reduced. pho3 exhibited a number of characteristics normally associated with low-P stress, including severely reduced growth, increased anthocyanin content and starch accumulation. pho3 was shown to have an absolute requirement for exogenous sucrose as pho3 seedlings were arrested in early seedling development on sucrose-free medium and was unaffected by Pi-availability. pho3 was found to be insensitive to high concentrations of exogenous sucrose (10%) but was sensitive to glucose. pho3 also exhibited reduced sensitivity of seed germination to exogenous ABA (abi-phenotype), a response which has been linked to sucrose insensitivity in both sugar-sensing and ABA mutants. Two developmental stages have been selected on the basis of the physiological characterisation of pho3. Seedlings (1.02; 2 rosette leaves) grown in agar and compost-grown plants (3.90; rosette growth complete). Agar will be supplemented with 1% sucrose and 1/2 strength MS; plants will be grown under a 16 h light/8 h dark cycle. Comparisons will be made between pho3 and Wassilewskija (the genetic background of the mutant) at each stage.

Experimenter name: Julie Lloyd
Experimenter phone: 01206 873307
Experimenter institute: Department of Biological Sciences,
University of Essex
Experimenter address: Colchester!Series_summary = Experimenter zip/postal_code: CO4 3SQ
Experimenter country: UK
Keywords: genetic_modification_design

overall_design: 6 samples were used in this experiment

first: Julie

last: Lloyd

first: Zoe

last: Emmerson

first: Beatrice

last: Schildknecht


title: Identification of genes differentially expressed in dormant versus active axillary shoot apical mersitems

institute: Nottingham Arabidopsis Stock Centre (NASC)

summary:
The aim of this study is to identify genes differentially expressed during the transition between dormancy and activity in axillary shoot apical meristems. We have chosen to study this by comparing mRNA populations from the axillary buds of the auxin over-responding, apically dominant axr3-1 mutant of Arabidopsis,with those from the axillary buds of the auxin resistant axr1-12 bushy mutant. Preliminary investigation using cDNA AFLP has been successful in identifying differentially expressed transcripts in the buds of these two genotypes, thus demonstrating the importance of this study, however this is a time consuming procedure. Axillary buds from axr3-1 are seen to arrest at an early stage when the buds are approximately 2mm long and harvested at this point. Buds of a similar size were harvested from axr1-12 plants and the RNA extracted using Qiagen columns.These two mRNA samples will represent the dormant and active buds to be comparedin this experiment. The plants from which these buds were harvested were grown in adjacent p40 trays in a plant growth room. Between two and three buds were harvested from each plant.

Experimenter name: Sally Ward
Experimenter phone: 01904 328683
Experimenter fax: 01904 328682
Experimenter institute: University of York
Experimenter address: Dept of Biology (Area 11),
University of York,
Heslington,
York
Experimenter zip/postal_code: YO10 5DD
Experimenter country: UK
Keywords: genetic_modification_design

overall_design: 2 samples were used in this experiment

first: Sally

last: Ward

first: Ottoline

last: Leyser


title: FM95-14 expression verification

summary:
Undifferentiated FM95-14 human embryonic myoblasts contain myogenic stem/progenitor cells. Gene expression analysis and comparison to FM95-14 cells that have been allowed to differentiate will allow the ascertainment of genes that are implicated in myogenic lineage commitment.
Human myoblast were also differentiated for 4 days.
293FT-human embroynal kidney were used as a human control cell line for human myoblast study.
Keywords: other

overall_design: this experiment include 3 samples (293FT-human embroynal kidney, undifferentiated FM95-14 myoblast, and differentiated myoblast) with 3 replicates on 2 platforms for a total of 18 Samples.


title: Effect of Low RNA Sample Amount on Amplification Fidelity

summary:
The effect of low RNA sample amount on amplification fidelity was investigated.
Keywords: other

overall_design: This experiment include 3 samples on 2 platforms for a total of 6 GEO Samples.


title: Comparative gene expression profiling of group-housed, less aggressive vs. single-housed, more aggressive male flies

status: Public on Feb 08 2008

city: Pasadena

first: Liming

last: Wang

address: 1200 E. California Bl.

department: 216-76， Division of Biology

institute: California Institute of Technology

summary:
Social experience influences multiple behaviors of many animal species, including aggression. Social isolation often increases aggressiveness. To investigater the molecular basis of social influences on aggressiveness, we performed comparative gene expression profiling on heads from 6-day-old, single-housed, more aggressive and group-housed, less aggressive male flies.
Keywords: social experience

overall_design: 1 (single-housed) or 10 (group-housed) male flies were housed in plastic vials after eclosion for 6 days. Between 5-6pm on the 6th day, flies were frozen and their heads were harvested for Trizol RNA extraction and microarray experiment. Both single- and group-housing groups contained 3 biological replicates, which had a sampling pool of 20 heads.

first: David

middle: J

last: Anderson


title: Testing Arabidopsis for the presence of arbuscular mycorrhizal signalling pathways

summary:
Around two-thirds of all plant species form arbuscular mycorrhizasa symbiosis between plant roots and glomalean fungi that leads to the formation of intraradical organs of nutrient exchange and an extraradical network of fungal hyphae effectively extending the plant root system. The mycorrhiza plays a key role in plant nutrition and in enhancing plant resistance against pathogens and improving drought resistance. At present very little is known about the molecular basis of arbuscular mycorrhiza formation. Arabidopsis thaliana (as with all Brassicaceae) does not form arbuscular mycorrhizas (AM). Arabidopsis may either have lost essential gene functions or acquired new ones that prevent a successful symbiotic interaction. However given that mycorrhizal symbiosis developed very early during the evolution of land plants and that many ectomycorrhizal plant species can be colonised by AM fungi it is likely that important components of AM signalling pathways are conserved in all plants including Arabidopsis. Possibly the lack of AM development is a multigenic trait and this would make it difficult to isolate mutants that (re-)gain the ability to interact with AM fungi. What can be done however is firstly to test which parts of one or several putative AM signalling pathways are still functional and which ones are not. Secondly we can test whether negatively acting pathways such as those involved in defence against pathogenic microorganisms are induced upon inoculation with AM fungi. Together this work is likely to give important information of why Arabidopsis (and Brassicaceae) are behaving as non-hosts for AM fungi. In other words Arabidopsis will be an ideal system to study mechanisms of non-host "resistance" to AM colonisation. Elucidating these mechanisms will obviously make a great contribution to understanding the basis of the mycorrhizal interaction. Moreover using Arabidopsis as a tool it will be possible at the end to integrate the information obtained for AM signalling with that obtained for other developmental and environmentally triggered signalling pathways such as plant hormone signalling or plant defence responses. To produce an inventory of which Arabidopsis genes respond at all to inoculation with AM fungi a genome-wide screen for AM-controlled genes is proposed. RNA will be prepared from Arabidopsis roots treated with AM fungus and mock-inoculated control plants. Arabidopsis (Col-0) will be grown in pot culture (1:1 sand/Terra-Green) at low concentrations of phosphate. Three week-old plants will be inoculated with surface-sterilised spores of Gigaspora rosea. RNA will be isolated 3 days post inoculation.

Experimenter name: Hsiu-Ling Yap
Experimenter phone: 01904 434 302/304
Experimenter fax: 01904 434 312
Experimenter institute: University of York
Experimenter address: Department of Biology
University of York
P.O.Box 373
York!Series_summary = Experimenter zip/postal_code: YO10 5YW
Experimenter country: UK
Keywords: compound_treatment_design

overall_design: 4 samples were used in this experiment

first: Hsiu-Ling

last: Yap

first: Michael

last: Schultze


title: Effect of facioscapulohumeral dystrophy (FSHD) on skeletal muscle gene expression

status: Public on Mar 08 2008

city: Rochester

first: Stephen

last: Welle

address: 601 Elmwood Avenue

institute: University of Rochester

summary:
Muscle biopsies taken from vastus lateralis muscle of 30 normal subjects and 19 FSHD subjects (see PubMed ID 17151338)
Affymetrix U133A and U133B arrays were scanned both before (S1) and after (S2) antibody enhancement.
Effects of age and sex in normal subjects reported previously under GSE362, GSE674, and GSE9676.
Keywords: facioscapulohumeral dystrophy, skeletal muscle

overall_design: Gene expression profiles were generated for each individual for a total of 49 profiles (30 normal, 19 FSHD)