title: Copy number profiling of PE ovarian cancer lines

status: Public on Jun 28 2010

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

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

summary: The PEO/PEA series of ovarian cancer cell lines was established in 1988 from progressive samples from three separate cases of ovarian cancer (Langdon et al., 1988).

overall_design: Copy number profiling of PE lines on Illumina Infinium Human1M-Duo v3 BeadChips

first: Susanna

last: Cooke

first: James

middle: D

last: Brenton


title: Genome-wide identification of Streptococcus pneumoniae genes essential for the development of experimental meningitis

status: Public on Nov 16 2010

city: Nijmegen

first: Peter

last: Burghout

address: Kapittelweg 29

department: Laboratory of Pediatric Infectious Diseases

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

summary: We applied genomic array footprinting (GAF) in the search for genes of S. pneumoniae essential during the establishment and progression of experimental meningitis. Four libraries with a total of 6,000 independent TIGR4 marinerT7 transposon mutants were injected intra-cisternally in rabbits, and cerebrospinal fluid (CSF) was collected after three, nine, and fifteen hours. Microarray analysis of mutant-specific probes from CSF samples and inocula identified 82 genes of which mutants had become attenuated and eleven genes of which mutants had become enriched during infection. Screening results particularly point to an essential role for capsular polysaccharides (cps), nutrient uptake, and metabolism in meningitis. Detailed study on directed mutants of a subset of sixteen GAF targets in an experimental model of rat meningitis revealed that ten were significantly attenuated or enriched during competitive infection. Furthermore, we showed that mutants of adenylosuccinate synthetase (purA), flavodoxin (fld), and the substrate binding protein (livJ) of a branched chain amino acid ABC-transporter were essential for full blown meningitis in a mono-infection setup of rat meningitis. Overall, the GAF screen revealed the general restraint on nutrients encountered by the pneumococcus in CSF, while, except for cps genes, no ‘classic’ virulence factors appeared to be required for infection. This knowledge will contribute to a better understanding of the molecular pathogenesis of pneumococcal meningitis.

overall_design:
The rabbit meningitis model was performed as previously described by Østergaard (PMID: 9661008 ). Briefly, 10E6 CFU of a S. pneumoniae mutant library was suspended in 20 µl beef-broth and injected into cisterna magna of four groups of four outbred New Zealand White rabbits of app. 2.5 kg (in one group one rabbit died). CSF (0.3 ml) samples were repeatedly obtained from the same rabbit by aspiration from indwelling spinal- and arterial cannules. Samples were collected before pleocytosis developed (three hrs), at the time of maximal pleocytosis (nine hrs), and at a time of slowing bacterial growth and abating pleocytosis (fifteen hrs ). Until further processing in the GAF protocol, CSF and inocula were stored with 15% glycerol at -80ºC.
The GAF technology was performed as described previously (PMID: 17261526 ). Briefly, stored inocula and CSF obtained during the experimental rabbit meningitis experiments were defrosted, diluted in GM17 medium supplemented with spectinomycin, and grown to mid-log phase. Chromosomal DNA was isolated, digested with AluI endonuclease, and used as a template for in vitro transcription initiated from the T7 promoters of the marinerT7 transposon that is present in each mutant. After removal of template DNA by DNAseI treatment, mutant-specific T7 RNA was reverse transcribed in the presence of fluorescent Cy3/Cy5-labeled dUTP nucleotides. Labeled Cy3/Cy5-cDNA from the CSF samples and oppositely labeled Cy5/Cy3 cDNA from the inocula were combined, purified, and washed by ultrafiltration. The cDNA was hybridized to pneumococcal microarrays containing, 2,087 ORFs of Streptococcus pneumoniae TIGR4 and 70-mer oligo's specific for the non-homologous ORFs in the R6, D39, 23F, INV104B, INV200, OXC141, and G54 strains, all spotted in duplicate (PMID: 18174343) . Dual channel array images were acquired on a GenePix 4200AL microarray scanner (Axon Instruments, Union City, CA). Microarray image files were analyzed with GenePix Pro software (Axon Instruments, Union City, CA). Spots were screened visually to identify those of low quality and removed from the data set prior to analysis. A net mean intensity filter based on hybridization signals obtained with R6-specific spots was applied in all experiments. Slide data were processed and normalized using MicroPreP (PMID: 15907200). Further analysis was performed using a CyberT implementation of the Student’s t test (cybert.microarray.ics.uci.edu). This web-based program lists the ratios of all intra-replicates (duplicate spots) and inter-replicates (different slides), the mean ratios per gene, and standard deviations and (Bayesian) p values assigned to the mean ratios. For identification of conditionally essential genes, only genes with a minimum of 6/8 (for groups of four rabbits) or 5/6  for the group of three rabbits) reliable measurements and a Bayesian p-value < 0.001 were included. Further selection criteria were applied, as only mutants displaying an average fold-change of >2.5 at a minimum of two time-points, or >4.0 at one time-point were accepted as significantly attenuated or enriched. The microarray data have been deposited in the NCBI Gene Expression Omnibus (GEO) database (www.ncbi.nlm.nih.gov/geo/) under GEO Series accession number ...

first: Tanja

middle: E

last: Molzen

first: Hester

middle: J

last: Bootsma

first: Christa

last: van der Gaast

first: Marc

last: Eleveld

first: Marcel

middle: M

last: Verbeek

first: Michael

last: Pedersen

first: Niels

last: Frimodt-Møller

first: Christian

last: Østergaard

middle: W


title: Genome wide DNA Methylation Study in Cornelia de Lange Syndrome

status: Public on Jul 07 2010

city: Philadelphia

first: IAN

middle: D.

last: KRANTZ

state: PA

address: 34th and Civic Blvd.

department: Division of Human and Molecular Genetics

country: USA

institute: The Children's Hospital of Philadelphia

summary: Differential DNA methylation was identified in CdLS, and correlates to cohesin binding as well. However, DNA methylation may only be one of several events that regulate gene expression in humans.

overall_design: 63 Lymphoblastoid cell lines (LCLs) from 39 CdLS probands, 2 RBS probands and 22 gender and racial matched healthy controls were tested on HumanMethylation27 DNA Analysis BeadChip (Illumina) which carries 27,578 highly informative CpG sites derived from the well-annotated NCBI CCDS database

first: Jinglan

last: Liu

first: Zhe

last: Zhang

first: Masashige

last: Bando

first: Takehiko

last: Itoh

first: Matthew

middle: A

last: Deardorff

first: Jennifer

middle: R

last: Li

first: Dinah

last: Clark

first: Maninder

last: Kaur

first: Kondo

last: Tatsuro

first: Antonie

last: Kline

first: Hugo

last: Vega

first: Celia

last: Chang

first: Laird

middle: G

last: Jackson

first: Nancy

middle: B

last: Spinner

first: Katsuhiko

last: Shirahige

first: Ian

last: Krantz


title: An 82-Year old woman with a palpable lymph node

status: Public on Jun 12 2010

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

summary: An 82-year-old woman with a history of LD stage SCLC of her left upper lobe nine years earlier, had been treated with five cycles chemotherapy cyclophosphamide, doxorubicin and etoposide (CDE)) resulting in a complete response. She received prophylactic cranial irradiation. Now she presented with a palpable mass in the right supra-clavicular fossa. Her further medical history revealed coronary vascular disease, for which she underwent PTCA; mild aortic valve stenosis and a pacemaker to treat a third degree AV block. She has NYHA class II. She had a history of cigarette smoking but she stopped when SCLC was diagnosed nine years ago. She had no dyspnea

overall_design:
Laboratory investigations were as follows: normal blood cell counts, renal and liver function.
An ultrasound of the neck revealed a mass in the right supraclavicular fossa extending behind the subclavicular vasculature into the mediastinum.  A computed tomography of the thorax showed an intrapulmonary leasion in the right upper lobe with extended lymph node masses until the supraclavicular fossa.  A FDG-PET combined with computed tomography revealed high uptake of FDG in the rightsided hilar mass with extension into the right upper lobe laterally and into the supraclavicular fossa. A biopsy was taken and revealed SCLC, staged as T2N3M1. M1 was based on a small mass adjacent to the right adrenal. The patient was treated with carboplatin-etoposide, resulting in a partial response. Shortly after finishing chemotherapy multiple brain metastases became symptomatic for which she refused further therapy. To answer the question is this a late relapse or a new primary, tissue was analysed with array CGH and compared to the array CGH profile of tissue from the tumour diagnosed nine years earlier


title: circad_pop1-circadian rhythm in the expression of genes involved in the formation of poplar wood

status: Public on Jun 05 2010

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

summary:
affy_orleans_circad - circad_pop1 -
Global  transcriptome analysis of tension wood  in poplar over a 24h period. Young differentiating xylem was harvested on the tension wood side of 6 month-old poplar trees grown in greenhouse conditions. The samples were harvested at 6 hour intervals throughout the day. The bioinformatic analysis will permit the identification of genes expressed in tension wood and  that cycle with a nycthemeral oscillation pattern.
Keywords: time course

overall_design: 10 arrays - poplar

first: Sandrine

last: Balzergue

first: Gilles

last: PILATE

first: Marie-Laure

middle: L

last: Martin-Magniette


title: Epigenetic and immune function profiles associated with post-traumatic stress disorder

status: Public on May 12 2010

city: Ann Arbor

first: Regina

last: de los Santos

address: 1415 Washington Heights

department: Epidemiology

institute: University of Michigan

summary: The biological underpinnings of post-traumatic stress disorder (PTSD) have not been fully elucidated. Previous work suggests that alterations in the immune system are characteristic of the disorder. Identifying the biological mechanisms by which such alterations occur could provide fundamental insights into the etiology and treatment of PTSD. Here we identify specific epigenetic profiles underlying immune system changes associated with PTSD. Using blood samples (n=100) obtained from an ongoing, prospective epidemiologic study in Detroit, the Detroit Neighborhood Health Study (DNHS), we applied methylation microarrays to assay CpG sites from over 14,000 genes among 23 PTSD-affected and 77 PTSD-unaffected individuals. We show that immune system functions are significantly overrepresented among the annotations associated with genes uniquely unmethylated among those with PTSD. We further demonstrate that genes whose methylation levels are significantly and negatively correlated with traumatic burden show a similar strong signal of immune function among the PTSD-affected. The observed epigenetic variability in immune function by PTSD is corroborated using an independent biological marker of immune response to infection, cytomegalovirus—a typically latent herpesvirus whose activity was significantly higher among those with PTSD. These results provide the first report of peripheral epigenomic and CMV profiles associated with mental illness and suggest a new biological model of PTSD etiology in which an externally experienced traumatic event induces downstream alterations in immune function by reducing methylation levels of immune-related genes.

overall_design: Bisulfite conversion of whole blood-derived DNA samples was performed using the EZ-96 DNA methylation kit from Zymo Research. One microgram (μg) of each sample (including controls) was subjected to bisulfite conversion following manufacturer’s recommended protocol. 100 samples were analyzed of which 23 are PTSD affected and 77 are PTSD-unaffected. There were four technical replicates comprised of duplicate samples of two randomly selected individuals from the n=100 and duplicate samples of the control human methylated and unmethylated DNA.

first: Monica

last: Uddin

first: Allison

last: Aiello

first: Derek

last: Wildman

first: Karestan

middle: C

last: Koenen

first: Graham

last: Pawelec

first: Emily

last: Goldmann

first: Sandro

last: Galea


title: Expression data from poplar apices

status: Public on May 28 2010

city: Houghton

first: Victor

last: Busov

address: 1400 Townsend Drive

department: Forest Resources and Environmental Science

institute: Michigan Technological University

summary:
We studied differences in gene expression between Populus P35S::EBB1  lines and control, affecting plant growth and differentiation, and dormancy. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes driven by overexpression of the EBB1 gene.
By screening activation tagging population, we identified the EARLY BUD-BREAK1 (EBB1) mutant. We positioned the tag, localized a putative candidate gene and verified transcription activation. The activated gene encodes an AP2/ERF  transcription factor similar to a small B1 gene-subfamily in Arabidopsis encoding strong regulators of meristem function and lateral organ outgrowth.  We fully recapitulated the phenotype by overexpression of the gene into the same genotype under a strong constitutive promoter (P35S::EBB1).  We also found that EBB1 transcript abundance in wild type plants increases during the period prior to bud-break, and in response to the hormone cytokinin.  Our data indicates that EBB1 plays an important role in the process of bud-break.

overall_design: Poplar apex was selected  for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous native expression of affected genes in P35S::EBB1  lines and control, in order to increase the resolution of expression profiles inducing the developmental changes in P35S::EBB1. To do that,  we selected apex tissue from greenhouse healthy plants.

first: Yordan

middle: S

last: Yordanov


title: Acquired chromosome abnormalities in the lungs of patients with Pulmonary Arterial Hypertension (Illumina)

status: Public on May 01 2010

city: Aurora

first: Christopher

last: Coldren

state: CO

address: 12700 East 17th Place

department: Medicine

institute: University of Colorado School of Medicine

summary: Vascular remodeling in pulmonary arterial hypertension (PAH) involves proliferation and migration of endothelial and smooth muscle cells, leading to obliterative vascular lesions. Previous studies have indicated that the endothelial cell proliferation is quasi-neoplastic, with evidence of monoclonality and instability of short DNA microsatellite sequences. To assess whether there is larger scale genomic instability, we performed genome-wide microarray copy number analysis on pulmonary artery endothelial (PAEC) and smooth muscle cells isolated from the lungs of PAH patients. Mosaic chromosomal abnormalities were detected in five of nine PAEC cultures from PAH lungs and zero of four controls. Fluorescent in situ hybridization analysis confirmed the presence of these abnormalities in vivo in two of three cases. One patient harbored a germline mutation of BMPR2, the primary genetic cause of PAH, and a somatic loss of chromosome-13, which constitutes a second hit in the same pathway by deleting Smad-8. In two female cases with mosaic loss of the X-chromosome, methylation analysis showed that the active X was deleted. Remarkably, one also showed completely skewed X-inactivation in the non-deleted cells, suggesting the PAEC population was clonal prior to the acquisition of the chromosome abnormality. Our data indicate a high frequency of genetically abnormal sub-clones within the lung vessels of patients with PAH and provide the first definitive evidence of a second genetic hit in a patient with a germline BMPR2 mutation. We propose that these chromosome abnormalities may confer a growth advantage and thus contribute to the progression of PAH.

overall_design: Cross-sectional study of genomic copy number in cells cultured from the lungs of PAH patients.

first: Micheala

last: Aldred

first: Suzy

last: Comhair

first: Marileila

last: Varella-Garcia

first: Kewal

last: Asosingh

first: Weiling

last: Xu

first: George

middle: P

last: Noon

first: Patricia

last: Thistlethwaite

first: Rubin

last: Tuder

first: Serpil

last: Erzurum

first: Mark

last: Geraci


title: DNA methylome of familial breast cancer identifies distinct profiles defined by mutation status

status: Public on Mar 12 2010

city: London

first: James

last: Flanagan

address: Du Cane Rd

department: Dept of Oncology

country: United Kingdom

institute: Imperial College London

type: Methylation profiling by genome tiling array

summary: It is now well understood that epigenetic alterations occur frequently in sporadic breast carcinogenesis, but little is known about the epigenetic alterations associated with familial breast tumors. We performed genome-wide DNA methylation profiling on familial breast cancers (n=33) to identify patterns of methylation specific to the different mutation groups (BRCA1, BRCA2 and BRCAx) or intrinsic subtypes of breast cancer (basal, luminal A, luminal B, HER2 and normal-like). We used methylated DNA immunoprecipitation (meDIP) on Affymetrix human promoter chips to interrogate methylation profiles across 25,500 distinct transcripts.

overall_design: MeDIP of familial breast tumor DNA ("b"=MeC antibody bound) compared to input DNA ("i" = input) for each sample


title: Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles (Illumina)

status: Public on May 17 2010

city: Fukuoka

first: Kenshi

last: Hayashi

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

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

summary: Copy number variations (CNVs) are abundant, possibly variable among populations, and can confer various phenotypic variations such as risk to complex disease. We determined a genome-wide high resolution SNP/CNV haplotype structure of Asians, by analyzing a collection of complete hydatidiform moles (CHMs) of Japanese, using high-density DNA arrays. CHMs are tissues carrying duplicated haploid genomes that originated from single sperm, and have advantages as materials over conventional diploid cells in detecting CNVs by hybridization, because greater S/N ratios are expected, and overlapping CNV segments are independently detected without being bothered by possible heterozygous situations. Overall occupancy of CNV segments per haploid found here was at a level similar to previous reports. Approximately a half of our polymorphic CNV regions have not been described in the previous report for Asians, but the frequencies of most of these new CNV regions were low. The limited number of examined samples is likely to be the reason that they have escaped detection in the previous report. Many common CNV regions are resolvable to clusters of CNV segmets (that is, CNV events) on the basis of mutual overlap of the segments. The similarity of haplotype backgrounds surrounding different CNV events within the same CNV regions suggests that ancestral recurrences of CNV events were predominantly haplotype preferential.

overall_design: Illumina Human1M-Duov3 BeadChip analyses were performed according to the manufacturer's directions on DNA extracted from 5 complete hydatidiform moles (CHMs) tissues collected throughout Japan.

first: Yoji

last: Kukita

first: Koji

last: Yahara

first: Koichiro

last: Higasa

first: Tomoko

last: Tahira

first: Kiyoko

last: Kato

first: Norio

last: Wake


title: Expression data from GA-modified polpar transgenic roots

status: Public on Apr 11 2010

first: Jiqing

last: Gou

email: jgou@mtu.edu, vbusov@mtu.edu

address: 1400 Townsend Dr.

institute: Michigan Tech University

summary: We studied expression in roots of transgenic poplar (7171B4 genotype) plants expressing PcGA2ox1 or rgl1 under 35S promoter. Dwarf, semidwarf, wt-like and wt plants were used.

overall_design: In vitro grown plants were sampled. Transgenic events with different levels of dwarfism were used. Two biological replications were used for each genotype.

first: Victor

last: Busov


title: Human Aging-associated DNA Hypermethylation Occurs Preferentially at Bivalent Chromatin Domains

status: Public on Feb 10 2010

city: Cambridge

first: Tsun-Po

last: Yang

address: Wellcome Trust Genome Campus

department: Human Genetics

institute: Wellcome Trust Sanger Institute

summary: There is a growing realization that some aging-associated phenotypes/diseases have an epigenetic basis. Here we report the first genome-scale study of epigenomic dynamics during normal human aging. We identify aging-associated differentially methylated regions (aDMRs) in whole blood in a discovery cohort, and then replicate these aDMRs in sorted CD4+ T-cells and CD14+ monocytes in an independent cohort, suggesting that aDMRs occur in precursor haematopoietic cells. Further replication of the aDMRs in buccal cells, representing a tissue that originates from a different germ-layer compared with blood, demonstrates that the aDMR signature is a multi-tissue phenomenon. Moreover, we demonstrate that aging-associated DNA hypermethylation occurs predominantly at bivalent chromatin domain promoters. This same category of promoters, associated with key developmental genes, is frequently hypermethylated in cancers and in vitro cell culture, pointing to a novel mechanistic link between aberrant hypermethylation in cancer, aging, and cell culture.

overall_design: We measured the methylation state of 27,578 CpG sites (Illumina HumanMethylation27 array) in whole blood samples from 93 heathy human females aged between 49 and 74, to discover sites which change methylation state with age.

first: Vardhman

middle: K

last: Rakyan

first: Thomas

last: Down

first: Siarhei

last: Maslau

first: Toby

last: Andrew

first: T

first: Huriya

last: Beyan

first: Pamela

last: Whittaker

first: Owen

middle: T

last: McCann

first: Sarah

last: Finer

first: Ana

last: Valdes

first: R

last: Leslie

first: Panos

last: Deloukas

first: Timothy

last: Spector


title: rewatering-Global gene expression in young differentiating xylem of poplar in response to a drought –rewatering cycle

status: Public on Jun 03 2010

first: sandrine

last: balzergue

summary:
affy_rewatering_poplar - rewatering - Biological question (15 lines max): Xylogenesis is a complex process and is highly influenced by environmental factors. Numerous studies have shown xylem structural acclimation to moderate and long-lasting water deficits. A decrease in cell lumen size and an increase in vessel density are generally observed. Other preliminary experiments in our laboratory focusing on a short and progressive drought-rewatering cycle in poplar show a gradual decrease in fibre size with decreasing water availability and an important rise in vessel number with irrigation recovery. This suggests a reorientation during the early stages of cambial derivatives differentiation towards vessel formation. The aim of this study is to characterize global gene expression in young differentiating xylem of poplar in response to a drought-rewatering cycle. Results should provide a comprehensive genomic basis for the xylem structural modifications observed.-The experimental design consisted in a differential water supply. Experiments were done on tilted trees to induce tension wood formation. Trees were regularly irrigated at full capacitance until July 18, 2007, the beginning of the experiment. Two sets of plants were designed. For each set, irrigation was withheld until July 25, 2007. At this time, one of the two sets (treated-sample) was re-irrigated at full capacitance during 14hrs (WDR) while the other one was maintained under water deficit (WD). Samples were collected after the 14hrs for all trees.

Keywords: treated vs untreated comparison

overall_design: 6 arrays - poplar

first: Sandrine

last: Balzergue

first: Jean-Charles

last: Leple

first: Marie-Laure

last: Martin-Magniette


title: Methylation Pattern of Human Mesenchymal Stromal Cells

status: Public on Feb 04 2010

city: Heidelberg

first: Simone

last: Bork

address: INF 410

department: Department of Medicine V

country: Germany

institute: University Hospital of Heidelberg

summary: In this study, we have analyzed DNA methylation changes upon long-term culture and aging of MSC by using the HumanMethylation27 BeadChip assessing 27,578 unique CpG sites. Cells were taken from bone marrow aspirates from iliac crest (BM) of healthy donors or from the caput femoris (HIP) of elderly patients that received femoral head prosthesis.Overall, the methylation pattern was maintained throughout both long-term culture and aging but highly significant differences were observed at specific CpG sites. Notably, methylation changes in MSC were related in long-term culture and aging in vivo.

overall_design:
Mesenchymal stromal cells (MSC) were isolated from human bone marrow as described before (Wagner et al., 2006, Exp Hematol, 34, 536-548; Wagner et al.,2008, PLoS One 21;3(5):e2213.; Wagner et al., PLoS One. 2009 Jun 9;4(6):e5846.)
Cells were always replated when grown to confluency. A sample for DNA isolation was taken at every passage until the cells finally became senescent. For methylation profiles upon long-term culture we used the samples of early passage (P2) and senescent passage (PX). For methylation profiles upon aging we have only used the samples of passage 2 of younger and elderly donors.

Gene expression data of these samples have been previously deposited unter GSE9593 and GSE12274.

first: S

last: Pfister

first: H

last: Witt

first: P

last: Horn

first: B

last: Korn

first: AD

last: Ho

first: W

last: Wagner


first: Thomas

last: Down

address: Tennis Court Road

department: WT/CRUK Gurdon Institute

institute: University of Cambridge

overall_design: We measured the methylation state of 27,578 CpG sites (Illumina HumanMethylation27 array) in sorted human blood cells to validate aging-associated DMRs.

first: Vardhman

last: Rakyan

first: Siarhei

last: Maslau

first: Toby

last: Andrew

first: Tsun-Po

last: Yang

first: Huriya

last: Beyan

first: Pamela

last: Whittaker

first: Owen

last: McCann


title: Genome wide DNA methylation profiling of United Kingdom Ovarian Cancer Population Study (UKOPS)

status: Public on Mar 01 2010

first: Andrew

last: Teschendorff

address: 72 Huntley Street

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

institute: University College London

summary:
The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in whole blood samples from 540 samples, of which 266 were samples taken from postmenopausal women with ovarian cancer and 274 were from age-matched healthy controls

Keywords: DNA methylation

overall_design: Bisulphite converted DNA from the 540 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Martin

last: Widschwendter


title: Comparative transcriptomics analysis of Populus leaves under nitrogen limitation: clone 1979

status: Public on Jan 04 2010

city: Athens

first: Chung-Jui

last: Tsai

state: GA

address: 120 Green Street

department: School of Forestry and Natural Resources

institute: University of Georgia

summary:
Gene expression response of Populus plants subjected to hydroponic nitrogen manipulation was analyzed using the Affymetrix poplar genome microarrays.

Keywords: stress response

sample_organism: Populus fremontii x Populus angustifolia

overall_design: Populus fremontii x angustifolia genotypes were grown hydroponically with either 5 mM (N+) or 0.125 mM (N-) nitrogen. Young leaves at Leaf Plastchron Index (LPI) 2 were sampled 4 weeks after the start of low N feeding. Mature leaves at Leaf Plastchron Index (LPI) 5 were sampled 4 or 8 weeks after the start of low N feeding. Two biological replicates were obtained for each condition.

first: Scott

last: Harding


title: MeDIP and ChIP-on-chip data from normal Prostate epithelial cells (PrEC) and the LNCaP cancer cell line

city: Darlinghurst

first: Aaron

last: Statham

state: NSW

address: 384 Victoria St

department: Cancer Department

country: Australia

institute: Garvan Institute of Medical Research

type: Genome binding/occupancy profiling by genome tiling array

summary:
To identify genomic regions which display concordant epigenetics alterations in prostate cancer, we performed MeDIP and ChIP-on-chip profiling of normal prostate epithelial cells (PrEC) and the prostate cancer cell line LNCaP.
These promoter arrays were integrated with expression arrays of the same cells to discover and characterise regions of Long Range Epigenetic Silencing (LRES) in prostate cancer.

overall_design: MeDIP and ChIP samples against active and repressive histone marks amplified and hybridised to Affymetrix Human Promoter 1.0R arrays, normalised to Input samples hybridised alongside

first: Marcel

last: Coolen

first: Clare

last: Stirzaker

first: Jenny

middle: Z

last: Song

first: Zena

last: Kassir

first: Carlos

last: Moreno

middle: N

last: Young

first: Vijay

last: Varma

first: Terence

last: Speed

first: Mark

last: Cowley

first: Paul

last: Lacaze

first: Warren

last: Kaplan

last: Robinson

first: Susan

last: Clark


title: Genomic architecture characterizes tumor progression paths and fate in breast cancer patients

status: Public on Dec 16 2009

city: Cold Spring Harbor

first: Jude

last: Kendall

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

type: Genome variation profiling by genome tiling array

summary: Distinct molecular subtypes of breast carcinomas have been identified, but translation into clinical use has been limited. We have developed two platform independent algorithms to explore genomic architectural distortion using array comparative genomic hybridization (aCGH) data to measure 1) whole arm gains and losses (WAAI) and 2) complex rearrangements (CAAI). By applying CAAI and WAAI to data from 595 breast cancer patients we were able to separate the cases into eight subgroups with different distribution of genomic distortion. Within each subgroup data from expression analyses, sequencing and ploidy indicated that progression occurs along separate paths into more complex genotypes. Histological grade had prognostic impact only in the Luminal related groups while the complexity identified by CAAI had an overall independent prognostic power. This study emphasizes the relationship between structural genomic alterations, molecular subtype and clinical behavior, and provides a score of genomic complexity as a new tool for prognostication in breast cancer.

overall_design: Array CGH of 266 breast tumor samples vs a male skin fibroblast reference sample, in color reversal.

first: Hege

last: Russnes

first: Hans

last: Moen Vollan

first: Ole

last: Lingjaerde

first: Alexander

last: Krasnitz

first: Pär

last: Lundin

first: Bjørn

last: Naume

first: Therese

last: Sørlie

first: Elin

last: Borgen

first: Inga

middle: H

last: Rye

first: Anita

last: Langerød

first: Suet-Feung

last: Chin

middle: E

last: Teschendorff

first: Philip

last: Stephens

first: Susanne

last: Månér

first: Ellen

last: Schlichting

first: Lars

middle: O

last: Baumbusch

first: Rolf

last: Kåresen

first: Michael

last: Stratton

last: Wigler

last: Caldas

first: Anders

last: Zetterberg

first: James

last: Hicks

first: Anne-Lise

last: Børresen-Dale


title: Expression profiling of hybrid necrosis in triploid hybrids crossed between tetraploid wheat and Aegilops tauschii

status: Public on Dec 23 2009

city: Kobe

first: Shigeo

last: Takumi

state: Hyogo

address: Rokkodai 1-1, Nada

department: Graduate School of Agricultural Science

institute: Kobe University

summary:
We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in hybrid necrosis-showing plants, which are triploid hybrids crossed between tetraploid wheat and diploid wheat progenitor Aegilops tauschii. Of the up-regulated genes, defense-related genes were most frequently found, whereas photosythesis-related genes down-regulated in the type I necrosis line. To validate the microarray data, RT-PCR and quantitative RT-PCR analyses for 22 selected genes were performed. Of the examined 15 up-regulated and 7 down-regulated genes, the expression pattern of only one down-regulated gene was inconsistent with the microarray data.
Together with cytological analysis of the necrotic tissues, the microarray analysis strongly suggests that an autoimmune response might be triggered by intergenomic incompatibility between the AB and D genomes in type I necrosis, and that genetically programmed cell death could be regarded as a hypersensitive response-like cell death similar to that observed in Arabidopsis intraspecific and Nicotiana interspecific hybrids.

overall_design: Expression patterns were compared between the two synthetic hexaploid lines showing the wild-type phenotype (as a reference) and hybrid necrosis. Total RNA samples were isolated from the 3-week-old seedling leaves. Two independent experiments were conducted.

first: Nobuyuki

last: Mizuno


title: Analysis of copy number profiles of several tumor samples of same patient reveals the successive steps in tumorigenesis

status: Public on Dec 01 2009

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

institute: Ligue Contre Le Cancer

summary:
We present the first computational approach to reconstruct the sequence of copy number alterations driving carcinogenesis from the analysis of several tumor samples of a same patient. Applied to BAC array-CGH and SNP array data from bladder and breast cancers, this method proved highly valuable to establish the clonal relationships between primary tumors and recurrences and to identify the chromosome aberrations at the initiation of tumorigenesis.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: SNP data from 20 bladder tumors

summary: We present the first computational approach to reconstruct the sequence of copy number alterations driving carcinogenesis from the analysis of several tumor samples of a same patient. Applied to BAC array-CGH and SNP array data from bladder and breast cancers, this method proved highly valuable to establish the clonal relationships between primary tumors and recurrences and to identify the chromosome aberrations at the initiation of tumorigenesis.

overall_design: An algorithm was developed to reconstruct tumors lineage and the sequence of copy number alterations along tumorigenesis from the analysis of several samples from a same patient. The data here consist in Illumina SNP data from 20 bladder tumors. 15 of these tumors (REF1 to REF15) come from independent samples and were used to compute the frequencies of breakpoints at each location. The 5 other samples (S4_A, S4_B, S5_A, S5_B, and S5_C) are multiple tumors from 2 patients. They were used to reconstruct the sequence of chromosome aberrations along cancer development in these 2 patients.

first: Yves

last: Allory

first: François

last: Radvanyi


title: Preclinical Validation of a Microarray Method for Full Molecular Karyotyping of Blastomeres in a 24-hour Protocol

status: Public on Dec 04 2009

city: Redwood City

first: David

middle: Scott

last: Johnson

state: CA

address: 2686 Middlefield Road, Suite C

institute: Gene Security Network

summary: BACKGROUND: Pre-implantation genetic screening (PGS) has been used in an attempt to determine embryonic aneuploidy. Techniques that use new molecular methods to determine the karyotype of an embryo are expanding the scope of PGS.  METHODS: We introduce a new method for PGS, termed “Parental Support” (PS), which leverages microarray measurements from parental DNA to “clean” single cell microarray measurements on embryonic cells and explicitly computes confidence in each copy number call. The method distinguishes mitotic and meiotic copy errors, and determines parental source of aneuploidy.  RESULTS: Validation with 459 single cells of known karyotype indicated that per-cell false positive and false negative rates are roughly equivalent to the “gold standard” metaphase karyotype. The majority of the cells were run in parallel with a clinical commercial PGS service. Computed confidences were conservative and roughly concordant with accuracy. To examine ploidy in human embryos, the method was then applied to 26 disaggregated cryopreserved cleavage stage embryos, for a total of 134 single blastomeres. Only 23.1% of the embryos were euploid, though 46.2% of embryos were mosaic euploid. Mosaicism affected 57.7% of the embryos. Counts of mitotic and meiotic errors were roughly equivalent. Maternal meiotic trisomy predominated over paternal trisomy, and maternal meiotic trisomies were negatively predictive of mosaic euploid embryos.  CONCLUSIONS: We have performed a major preclinical validation of a new method for PGS and found that the technology performs approximately as well as a metaphase karyotype. We also directly measured the mechanism of aneuploidy in cleavage stage human embryos and found high rates and distinct patterns of mitotic and meiotic aneuploidy.

overall_design: Single cells were isolated from buccal swabs, semen samples, adult blood, immortalized cell lines, and Day 3 cryopreserved embryos. Single tissue culture (lymphocytes) and buccal cells were isolated using a sterile stripper tip (Midatlantic Diagnostic, Mt. Laurel, NJ, USA) affixed to a pipette (Drummond Scientific, Broomall, PA, USA) and a stereoscope (Leica, Wetzlar, Germany). Embryos were thawed, and then individual blastomeres were separated using a micromanipulator (Transferman NK2-Eppendorf, Westbury, NY, USA) after zona pellucida drilling using acidified Tyrode’s solution. Sperm cells were manually isolated using a micromanipulator (Transferman NK2-Eppendorf). Aside from sperm, single cells were washed sequentially four times with wash buffer (5.6mg/ml KCl, 6mg/ml bovine serum albumin). Two different lysis/amplification protocols were used in the analysis: (i) Rubicon Whole Genome Amplification (Ann Arbor, MI, USA), and (ii) multiple displacement amplification (MDA) with Proteinase K Buffer (PKB). Protocol (i) was performed according to the manufacturer’s instructions. For protocol (ii), cells were placed in 5µl PKB (Arcturus PicoPure Lysis Buffer, 50mM DTT), incubated at 56°C for one hour, and then heat inactivated at 95°C for ten minutes. MDA reactions were incubated at 30°C for 2.5 hours and then 65°C for five minutes. Genomic DNA from bulk tissue (Epicentre MasterAmp Buccal Swabs, Madison, WI, USA) was isolated using the DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany). No template controls (buffer blanks) were performed for each amplification method. All buffer blanks produced intensities equivalent to the noise floor (an intensity of 1000 in the 95th percentile on the green detection channel).  Amplified single cells and bulk parental tissue were genotyped using the Illumina (San Diego, CA, USA) Infinium II genome-wide genotyping single nucleotide polymorphism (SNP) microarrays (HapMap CNV370Quad or CytoSNP-12 chips). For bulk tissue (i.e., parent samples), the standard Infinium II protocol (www.illumina.com) was used and required call rates of >99% using standard BeadStudio allele calling. All single cells were genotyped using a modified Infinium II genotyping protocol, such that the entire protocol, from single cell lysis through array scanning, was completed in fewer than 24 hours. The microarray protocol was performed as per the manufacturer’s instructions, except that the duration of the amplification and hybridization steps were reduced to 7 hours and 6 hours, respectively. Single cell array measurements that fell below the noise floor (an intensity of 1000 in the 95th percentile on the green detection channel) were removed from downstream analysis. For the MDA and Rubicon protocols, this represented approximately 1.6% and 1.3% of all amplifications, respectively.


title: Wound-induced gene expression changes in Populus: 90 hours; clone RM5

first: Chung-Jui

last: Tsai

summary:
Gene expression response of Populus plants subjected to leaf wounding was analyzed using the Affymetrix poplar genome microarrays.

Keywords: Stress response

overall_design: Populus fremontii x angustifolia genotypes were grown hydroponically.  Wounding treatment was applied by pinching leaves at Leaf Plastchron Index (LPI) 8-12 with pliers at a rate of 10 1-inch wounds per leaf.  Root tips (terminal 1 cm) and mature leaves (LPI 5) were sampled 90 hours after the treatment.  Two biological replicates were obtained for each condition.

first: Scott

last: Harding


title: Gene expression response of Populus tremuloides cell suspension cultures to methyl jasmonate feeding

summary:
Gene expression response of Populus cell cultures subjected to methyl jasmonate feeding was analyzed using the Affymetrix poplar genome microarrays.

Keywords: Stress response

overall_design: Populus tremuloides suspension cells were treated with methyl jasmonate (MJ) in DMSO or with DMSO alone (C).  Cells were harvested after 48 hours.  Two biological replicates were obtained for each condition.


title: Wound-induced gene expression changes in Populus: 1 week; clone RM5

summary:
Gene expression response of Populus plants subjected to leaf wounding was analyzed using the Affymetrix poplar genome microarrays.

Keywords: stress response

overall_design: Populus fremontii x angustifolia genotypes were grown hydroponically.  Wounding treatment was applied by pinching leaves at Leaf Plastchron Index (LPI) 8-12 with pliers at a rate of 10 1-inch wounds per leaf.  Young (LPI 0 and LPI 1) and mature leaves (LPI 5) were sampled 1 week after the treatment.  Two biological replicates were obtained for each condition.


title: Genome scale transcriptome analysis of shoot organogenesis in poplar

city: Corvallis

first: Yanghuan

last: Bao

state: OR

address: Department of Forest Science, Oregon State University, 321 Richardson Hall

department: Forest Science, and Genetics

institute: Oregon State University

summary:
Regeneration of transgenic cells remains a major obstacle to research and commercial deployment of transgenic plants for most species.
Our aims are to improve knowledge of gene regulatory circuits important to meristem organization, and to identify regulatory genes that might be useful for improving the efficiency of regeneration during transformation.
We analyzed gene expression during poplar regeneration using an Affymetrix GeneChip® array representing over 56,000 poplar transcripts.

Keywords: Time course

overall_design:
We focused on callus induction and shoot formation, thus sample RNAs were collected from tissues: prior to callus induction, 3 days and 15 days after callus induction, and 3 days and 8 days after the start of shoot induction.
Two biological replicates were used for each of the five time points.

first: Steven

last: Strauss

first: Palitha

last: Dharmawardhana

first: Todd

last: Mockler


title: Genome-wide recognition of PML/RARa binding sites

status: Public on Nov 26 2009

city: Shanghai

first: Jiantao

last: Shi

state: Shanghai

address: 197 Ruijin Rd II

country: China

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine (RJH-SJTU-SM)

summary:
PML/RARa is of crucial importance in acute promyelocytic leukemia (APL) both pathologically and therapeutically. Using a genome-wide approach, we identified in vivo PML/RARa binding sites in ZnSO4 treated PR9 cells. A total of 2,979 high quality binding sites were identified, representing 1,981 unique RefSeq genes.
The supplementary bed file contains all 2,979 high quality PML-RARa binding sites reported in the paper.

overall_design: RARa ChIP in ZnSO4 induced PR9 cells vs. Input in ZnSO4 induced PR9 cells.

first: Kankan

last: Wang

first: Ji

last: Zhang


title: Habituation to thaxtomin A provides enhanced and durable resistance to inhibitors of cellulose synthesis

status: Public on Oct 15 2009

city: Sherbrooke

first: Nathalie

last: Beaudoin

state: Quebec

address: 2500, Blvd Universite

department: Faculte des Sciences

country: Canada

institute: Universite de Sherbrooke

summary:
TA inhibits cellulose synthesis but its actual mode of action is unknown. Addition of TA to hybrid poplar (Populus trichocarpa x Populus deltoides) cell suspensions can activate a cellular program leading to cell death. In contrast, it is possible to habituate hybrid poplar cell cultures to grow in the presence of TA levels that would normally induce cell death. This habituation was performed by adding increasing levels of TA to cell cultures at the time of subculture over a period of 12 months. TA-habituated cells were then cultured in the absence of TA for more than 18 months.
These cells displayed a reduced size and growth compared to control cells and had fragmented vacuoles filled with electron-dense material. Habituation to TA was associated with changes in the cell wall composition, with a reduction in cellulose and an increase in pectin levels. Remarkably, high level of resistance to TA was maintained in TA-habituated cells even after being cultured in the absence of TA. Moreover, these cells exhibited enhanced resistance to two other inhibitors of cellulose biosynthesis, dichlobenil and isoxaben. Analysis of gene expression in TA-habituated cells using Affymetrix GeneChip Poplar Genome Array revealed that durable resistance to TA is associated with a major and complex reprogramming of gene expression implicating processes such as cell wall synthesis and modification, lignin and flavonoid synthesis, as well as DNA and chromatin modifications.

overall_design: Each sample was taken from an individual flask of control cells or TA-habituated resistant cells grown without the toxin for 18 months (TA(-)hab cells) that had grown for 5 d after subculture. Six arrays were hybridized, representing 3 arrays per cell type.

first: Viviane

last: Brochu

first: Marie

last: Girard-Martel

first: Isabelle

last: Duval

first: Sylvain

last: Lerat

first: Gilles

last: Grondin

first: Olivier

last: Domingue

first: Carole

last: Beaulieu


title: Genome-wide HIF-1, RNA polII, and H3K4me3 binding sites in U87 and HepG2 cells

status: Public on Oct 09 2009

city: Boston

first: Xiaobo

last: Xia

state: MA

address: 44 Binney St, Mayer 649

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: Hypoxia-Inducible Factor 1 (HIF-1) plays a key role in cellular adaptation to hypoxia. To better understand the determinants of HIF-1 binding and transactivation, we used ChIP-chip and gene expression profiling to define the relationship between the epigenetic landscape, sites of HIF-1 binding, and genes transactivated by hypoxia in two cell lines, HepG2 hepatoma cell line and U87 glioma cell line.

overall_design: U87 cells were cultured for 4 hours under normoxic or hypoxic (0.5%O2) conditions. Cells were fixed with 1% formaldehyde (37°C, 10 min) and lysed with 0.5% SDS lysis buffer. Chromatin was then sonicated to 500-1000bp fragments and immunoprecipitation carried out with HIF-1α pAb (Novus Biologicals, NB 100-134). RNA polymerase II and H3K4me3 ChIP were carried out using normoxic U87 or HepG2 cell samples with RNA polymerase II mAb (Abcam, ab5408) and H3K4me3 pAb (Abcam, ab8580). Triplicate ChIPed DNA and inputs were amplified and hybridized onto the Affymetrix Gene-Chip Human Tiling 2.0R Array Set. The MAT algorithm was used to identify peaks of probe intensity (‘‘hits’’).


title: Populus stress response: nitrogen limitation, leaf wounding, and methyl jasmonate feeding of cell culture

first: Chung-Jui

last: Tsai

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

first: Scott

last: Harding


title: The Populus Homeobox Gene ARBORKNOX2 Regulates Secondary Growth in trees

status: Public on Oct 01 2009

city: davis

first: Andrew

last: Groover

address: 1731 research park drive

department: Institute of Forest Genetics

institute: USDA FOREST SERVICE

summary:
Currently little is known about the genetic mechanisms regulating the vascular cambium or the secondary growth of stems.  We show here that the Populus Class I KNOX homeobox gene ARBORKNOX2 (ARK2) regulates both cell division in the cambium region and the differentiation of daughter cells in secondary xylem and phloem. ARK2 is expressed in the shoot apical meristem, and the vascular cambium region, reflecting some overlap in the regulation of these meristems.  ARK2 is expressed broadly in the cambium region and in differentiating lignified cells types before becoming progressively restricted to the cambium.
Populus overexpressing ARK2 present stem phenotypes with precocious cambium formation, delayed differentiation of cambium daughter cells, a wider cambium region, and ultimately less phloem fibers and secondary xylem. In contrast, Populus expressing RNAi or amicroRNA that target ARK2 transcripts present precocious differentiation of secondary phloem fibers and xylem, and ultimately more secondary xylem tissue and thicker secondary cell walls in phloem fibers and secondary xylem cells.
These phenotypes in turn correlate with changes in the expression of genes affecting cell division, auxin, and cell wall synthesis and lignification that indicate that ARK2 primarily affects woody tissue development by regulation of cell differentiation.  Notably, wood properties associated with secondary cell wall synthesis are negatively associated with ARK2 expression, including lignin and cellulose content.  Together, our results suggest that ARK2 functions primarily by negatively regulating cell differentiation during secondary growth.  We propose that ARK2 may identify a co-evolved regulatory module that influences complex wood properties relevant to ecological, industrial, and biofuels applications.

overall_design:
Gene expressions of three ARK2 overexpression transgenics plants and three ark2 artificial microRNA transgenics are detected with microarray.
Gene expressions of four wild type plants sample are used as control.

first: Juan

last: Du

first: Shawn

last: Mansfield


title: Role of the AMP deaminase Amd1p in purines interconversion in Saccharomyces cerevisiae

status: Public on Oct 30 2009

first: Laurent

last: Jourdren

address: 46 rue d'Ulm

department: Biologie

institute: École Normale Supérieure

summary:
In this work, we show that under specific conditions, defect in AMP deaminase activity strongly impairs yeast cell growth and we establish that AMP deaminase is required for correct balance between adenylic and guanylic nucleotides. Study of the Amd1p homologs, Yjl070p and Ybr284p, reveals that overexpression of these proteins cannot suppress phenotypes associated to /amd1/ deletion but instead mimic in a wild-type strain a loss of Amd1p function. Data presented combined  global transcription analyses to measurements of intracellular  nucleotides pools by HPLC.
Keywords: yeast strains implied in purines interconversion.

overall_design: 4 biological samples in dye-swap.

first: Christelle

last: Saint-Marc

first: Benoît

last: Pinson

first: Fanny

last: Coulpier

first: Olesia

last: Lisova

first: Bertrand

last: Daignan-Fornier


title: Me-DIP-chip data from osteosarcoma tumours

status: Public on Sep 08 2009

city: Toronto

first: Bekim

last: Sadikovic

state: Ontario

address: 555 University Avenue

institute: The SickKids Hospital and Princess Margaret Hospital

summary:
Malignant cells show major disruptions in DNA methylation profiles which manifest as aberrant hypermethylation and hypomethylation of gene promoters as well as global genomic hypomethylation. To date, many genes with aberrant promoter hypermethylation have been identified in essentially all forms of cancer including cell cycle regulators, DNA repair genes, genes associated with apoptosis, hormonal regulation, detoxification, metastasis, angiogenesis, and many others
We developed an effective high-resolution approach for mapping genome-wide, and cancer-specific DNA methylation profiles. We have used this approach to provide first genomic DNA methylation profiling in human paediatric osteosarcoma tumours

overall_design: We utilized this platform in combination with the methylated DNA immunoprecipitation (Me-DIP) to develop a comprehensive approach for detection of hypo- and hypermethylation changes at high resolution, and used it to detect such changes in human osteosarcoma tumours in relation to the normal human osteoblasts.


title: HepG2 hepatoma and U87 glioma cells: transcriptomic and genomic analyses


title: Genotype and time of day shape the Populus drought response

status: Public on Dec 31 2009

first: Malcolm

middle: M.

last: Campbell

state: ON

address: 25 Willcocks Street

department: Cell & Systems Biology

institute: University of Toronto

summary: As exposure to episodic drought can impinge significantly on forest health and the establishment of productive tree plantations, there is great interest in understanding the mechanisms of drought response in trees. The ecologically dominant and economically important genus Populus, with its sequenced genome, provides an ideal opportunity to examine transcriptome level changes in trees in response to a drought stimulus. The transcriptome level drought response of two commercially important hybrid Populus clones (P. deltoides · P. nigra, DN34, and P. nigra · P. maximowiczii, NM6) was characterized over a diurnal period using a 4 · 2 · 2 completely randomized factorial ANOVA experimental design (four time points, two genotypes, and two treatment conditions) using Affymetrix Poplar GeneChip microarrays. Notably, the specific genes that exhibited changes in transcript abundance in response to drought differed between the genotypes and/or the time of day that they exhibited their greatest differences. This study emphasizes the fact that it is not possible to draw simple, generalized conclusions about the drought response of the genus Populus on the basis of one species, nor on the basis of results collected at a single time point. The data derived from our studies provide insights into the variety of genetic mechanisms underpinning the Populus drought response, and provide candidates for future experiments aimed at understanding this response across this economically and ecologically important genus.

sample_organism:
Populus x canadensis
Populus maximowiczii x Populus nigra

overall_design: 48 arrays total. 2 genotypes (DN34, NM6), 4 time points (midnight, pre-dawn, mid-day, late day), 2 water regimes (well-watered, water-limited). 3 biological replicates per treatment.

first: Olivia

last: Wilkins

first: Levi

last: Waldron

first: Hardeep

last: Nahal

first: Nicholas

last: Provart

middle: M


title: Illumina HapMap CEU ( HumanCNV370-QuadV3 )

status: Public on Jul 27 2009

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

summary: HapMap samples

overall_design: 73 samples from HumanCNV370-Quadv3_CEU_Final_Call_Report.csv


title: Illumina HapMap YRI (1M-Duo)

summary: HapMap YRI samples

overall_design: 90  samples from 1M-Duo_YRI_Final_Call_Report.csv


title: Illumina HapMap CHB and JPT (HumanCNV370-QuadV3)

summary: HapMap samples

overall_design: 75 samples from HumanCNV370-Quadv3_CHB+JPT_Final_Call_Report.csv


title: Illumina HapMap YRI (HumanCNV370-QuadV3)

summary: HapMap samples

overall_design: 77 samples from HumanCNV370-Quadv3_YRI_Final_Call_Report.csv


title: Epigenomic Analysis of Aberrantly Methylated Genes in Colorectal Cancer

status: Public on Aug 18 2009

city: Seoul

first: Young-Ho

last: Kim

address: 50 Irwon-dong Gangnam-gu

department: Internal Medicine

country: South Korea

institute: Samsung Medical Center

summary: Determination of the profile of genes commonly aberrantly methylated in colorectal cancer (CRC) has substantial potential value for diagnostic and therapeutic application. However, our knowledge of the DNA methylation pattern in CRC is currently limited. Therefore, we analyzed the methylation profile of 27,578 CpG sites spanning more than 14,000 genes in CRC and in adjacent normal mucosa using beadchip array-based technology. We identified 621 CpG sites located in promoter region and CpG islands that were significantly hypermethylated in CRC compared to normal mucosa. Genes on chromosome 18 showed promoter hypermethylation most frequently. According to gene ontology analysis, the most common biologically relevant class of genes affected by methylation was the class associated with the cadherin signaling pathway.  In comparison with genome-wide expression array, mRNA expression was more like to be down-regulated in the genes demonstrating promoter hypermethylation, although this was not statistically significant. We validated 10 CpG sites that were shown to be hypermethylated in the array studies (ADHFE1, BOLL, SLC6A15, ADAMTS5, TFPI2, EYA4, NPY, TWIST1, LAMA1, GAS7) and 2 CpG sites showing hypomethylaion (MAEL, SFT2D3) in CRC compared to normal mucosa using pyrosequencing. The methylation status measured by pyrosequencing was consistent with the methylation array data. In conclusion, we have shown that methylation profiling based on beadchip arrays is an effective method for screening for aberrantly methylated genes in CRC. In addition, we identified novel methylated genes that are candidate diagnostic or prognostic markers for CRC.

overall_design: We measured the methylation status of the 27,578 CpG sites (Human Methylation27 DNA Analysis BeadChip) in 22 pairs of CRC tissue and adjacent normal mucosa to identify genes that are commonly aberrantly methylated in CRC.

first: Young

first: Yong


title: Illumina HapMap CHB and JPT (1M-Duo)

summary: HapMap CHB and JPT samples

overall_design: 90  samples from 1M-Duo_CHB+JPT_Final_Call_Report.csv


title: Expression profiling and functional analysis of poplar WRKY23 reveals a regulatory role in defense: WRKY23-RNAi

status: Public on Aug 01 2009

city: Sainte-Foy

first: Armand

last: Séguin

department: Laurentian Forestry Centre

institute: Natural Resources Canada

summary:
To investigate the function of poplar WRKY23, we generated PtWRKY23-overexpressing and -underexpressing (RNAi) plants. Transgenic plants were inoculated with Melampsora rust or mock-inoculated for assessment of rust-resistance and for gene expression profiling using the poplar Affymetrix GeneChip® to study the consequences of PtWRKY23 overexpression and underexpression. Transcriptome analysis of PtWRKY23 overexpressors revealed a significant overlap with the Melampsora-infection response. Transcriptome analysis also indicated that PtWRKY23 affects redox homeostasis and cell wall-related metabolism.

Keywords: genetic modification, stress response

overall_design:
Leaf discs from wildtype, WRKY23-overexpressor and WRKY23-RNAi plants were inoculated with Melampsora medusae f. sp. tremuloidae (Mmt) or were mock-inoculated (control). At five days post-inoculation, tissues were harvested for RNA extraction and hybridization on Affymetrix GeneChips®. Three biological replications were performed for each line and each inoculation or mock-inoculation. A total of 15 Affymetrix GeneChips® were used in this study. Data for the Mmt-inoculated WRKY23-RNAi plants were processed separately from the data for the WRKY23-overexpressor  plants.  The raw data for the Mmt-inoculated wildtype plants were the same in both cases.  Normalized data for the Mmt-inoculated wildtype plants that were processed with the Mmt-inoculated WRKY23-RNAi plants are denoted with an "a" suffix.

This part of the study includes 6 RNA samples consisting of three biological replicates for the Mmt-inoculated WT and WRKY23-RNAi (underexpressing) plants.

first: Valérie

last: Levée

first: Ian

last: Major

first: Caroline

last: Levasseur

first: Laurence

last: Tremblay

first: John

last: MacKay


title: Expression profiling and functional analysis of poplar WRKY23 reveals a regulatory role in defense: WRKY23-overexpressor

overall_design:
Leaf discs from wildtype, WRKY23-overexpressor and WRKY23-RNAi plants were inoculated with Melampsora medusae f. sp. tremuloidae (Mmt) or were mock-inoculated (control). At five days post-inoculation, tissues were harvested for RNA extraction and hybridization to Affymetrix GeneChips®. Three biological replications were performed for each line and each inoculation or mock-inoculation. A total of 15 Affymetrix GeneChips® were used in this study. Data for the WRKY23-overexpressor plants were processed separately from the data for the Mmt-inoculated WRKY23-RNAi plants. The raw data for the Mmt-inoculated wildtype plants were the same in both cases.

This part of the study includes 12 RNA samples consisting of three biological replicates for each of the mock-inoculated or Mmt-inoculated WT and WRKY23-overexpressing plants.


title: Expression profiling and functional analysis of poplar WRKY23 reveals a regulatory role in defense

overall_design: Refer to individual Series


title: Role of the Pho2p transcription factor in the transcriptional response associated to AICAR and SAICAR accumulation

status: Public on May 15 2009

city: PARIS

first: sophie

last: lemoine

institute: Ecole Normale Supérieure

summary:
We investigated the role of Pho2p in the transcriptional response associated to AICAR and SAICAR accumulation. In this work, global transcription analyses were combined to measurements of intracellular nucleotides pools by HPLC.

Keywords: Comparative genomic transcription analysis on total RNA from cells accumulating AICAR and SAICAR in a pho2 deletion context.

overall_design: One biological sample in dye swap

first: Benoît

last: Pinson

first: Fanny

last: Coulpier

first: Sophie

last: Lemoine


title: Role of the Snf1p protein kinase in the transcriptional response associated to AICAR and SAICAR accumulation

summary:
We investigated the role of Snf1p in the transcriptional response associated to AICAR and SAICAR accumulation. In this work, global transcription analyses were combined to measurements of intracellular nucleotides pools by HPLC.

Keywords: Comparative genomic transcription analysis on total RNA from cells accumulating or not AICAR and SAICAR nucleotide derivatives in a snf1 deletion context.

first: Bertrand

last: Daignan-Fornier


title: Role of the Pho4p transcription factor in the transcriptional response associated to AICAR and SAICAR accumulation

summary:
We investigated the role of Pho4p in the transcriptional response associated to AICAR and SAICAR accumulation. In this work, global transcription analyses were combined to measurements of intracellular nucleotides pools by HPLC.

Keywords: Comparative genomic transcription analysis on total RNA from cells accumulating AICAR and SAICAR in a pho4 deletion context.


title: Illumina HapMap CEU (1M-Duo)

summary: HapMap CEU samples

overall_design: 89  samples from 1M-Duo_CEU_Final_Call_Report.csv


title: Effect of  SAICAR accumulation on global transcription

summary:
We investigated the effects of SAICAR accumulation on transcriptional regulation of purine biosynthesis and other metabolic pathways. These data were compared to those obtained in the ade16ade17 vs WT comparison to determine the effects associated to accumulation of SAICAR alone. In this work, global transcription analyses were combined to measurements of intracellular nucleotides pools by HPLC.

Keywords: Comparative genomic transcription analysis on total RNA from cells accumulating or not SAICAR.


title: Effect of AICAR and SAICAR accumulation on global transcription (first part)

summary:
We investigated the effects of AICAR and SAICAR accumulation on transcriptional regulation of purine biosynthesis and other metabolic pathways. In this work, global transcription analyses were combined to measurements of intracellular nucleotides pools by HPLC.

Keywords: Comparative genomic transcription analysis on total RNA from cells accumulating or not AICAR and SAICAR nucleotide derivatives.


title: Effect of AICAR and SAICAR accumulation on global transcription (second part)

summary:
We investigated the effects of AICAR and SAICAR accumulation on transcriptional regulation of purine biosynthesis and other metabolic pathways. These data were compared to those obtained in the ade16ade17 vs WT data set to determine the transcriptional effects associated to AICAR/SAICAR accumulation and those due to ade16 and ade17 deletions. In this work, global transcription analyses were combined to measurements of intracellular nucleotides pools by HPLC

Keywords: Comparative genomic transcription analysis on total RNA from cells accumulating or lacking AICAR and SAICAR nucleotide derivatives.


title: Comparative transcriptomics analysis of Populus leaves under nitrogen limitation

status: Public on Feb 19 2009

first: Chung-Jui

last: Tsai

institute: University of Georgia


title: Me-DIP-chip data from osteosarcoma cell lines

status: Public on May 01 2009

first: Bekim

last: Sadikovic

summary:
Malignant cells show major disruptions in DNA methylation profiles which manifest as aberrant hypermethylation and hypomethylation of gene promoters as well as global genomic hypomethylation. To date, many genes with aberrant promoter hypermethylation have been identified in essentially all forms of cancer including cell cycle regulators, DNA repair genes, genes associated with apoptosis, hormonal regulation, detoxification, metastasis, angiogenesis, and many others
We developed an effective high-resolution approach for mapping genome-wide, and cancer-specific DNA methylation profiles. We have used this approach to provide first genomic DNA methylation profiling in osteosarcoma cells
Keywords: comparative profiling

overall_design: We utilized this platform in combination with the methylated DNA immunoprecipitation (Me-DIP) to develop a comprehensive approach for detection of hypo- and hypermethylation changes at high resolution, and used it to detect such changes in human osteosarcoma cells in relation to the normal human osteoblasts.


title: Promoter methylation profiles for ectopic vs. eutopic endometrium in SUP, VES and OME

status: Public on May 13 2009

first: Bruno

last: Borghese

address: 24, rue du Faubourg Saint-Jacques

department: Genetics and Development

institute: Institut Cochin

summary:
Several lines of evidence indicate that endometriosis could be partially due to epigenetic dysregulations. Hypermethylation of some key gene promoters, such as progesterone receptor or aromatase, has been reported to be associated with silencing of these genes. However, it is unknown whether global alterations in DNA methylation are a hallmark of endometriosis and to what extent they are involved in its pathogenesis. We conducted a whole-genome scanning of methylation status in more than 25,000 promoters using a combination of methylated DNA immunoprecipitation with hybridization to promoter microarray. We detailed a methylation profile for each subtype of the disease (superficial endometriosis, endometrioma and deep infiltrating endometriosis) and compared them to the profile obtained for the endometrium. Our results indicate that global methylation patterns are strongly correlated between the different disease subtypes, showing regions consistently hyper- or hypomethylated (more than 1.5-times) and others specific to one given subtype. However, there was no systematic correlation between promoter methylation and the expression of nearby genes, except for 35 that have never been previously associated to endometriosis and might be of outstanding importance in the disease development. Also, the distribution of hypermethylated regions appears located at the ends of the chromosomes whereas hypomethylation appears to be located randomly all over the chromosomes. This is a unique observation in a human disease, providing potential new insights into the understanding of endometriosis’ pathogenesis: we hypothesize that it might be a new mechanism that could confer protection against malignancy.

Keywords: Promoter microarrays

overall_design: We performed four hybridizations on Affymetrix GeneChip® Human Promoter 1.0R Arrays, with immunoprecipitated DNA, extracted from superficial endometriosis (SUP), endometrioma (OME), vesical endometriosis (VES) and eutopic endometrium (E), prepared from 5-patients pools, where the same patients providing the ectopic endometrium also provided the eutopic endometrium.

first: Sandrine

last: Barbaux

first: Françoise

last: Mondon

first: Guillaume

last: Pierre

first: Charles

last: Chapron

first: Daniel

last: Vaiman


title: Comparative transcriptomics analysis of Populus leaves under nitrogen limitation: clone 3200

address: 120 Green Street

summary:
Gene expression response of Populus plants subjected to hydroponic nitrogen manipulation was analyzed using the Affymetrix poplar genome microarrays.

Keywords: stress response

overall_design: Populus fremontii x angustifolia genotypes were grown hydroponically with either 5 mM (N+) or 0.125 mM (N-) nitrogen.  Young leaves at Leaf Plastchron Index (LPI) 2 were sampled 4 weeks after the start of low N feeding. Mature leaves at Leaf Plastchron Index (LPI) 5 were sampled 4 or 8 weeks after the start of low N feeding. Two biological replicates were obtained for each condition.

first: Scott

middle: A

last: Harding


title: Transcriptional profile of B. theta and E. rectale growing in the cecum of mice fed different diets

status: Public on Mar 01 2009

city: St Louis

first: Federico

last: Rey

state: MO

address: 4444 Forest Park Blvd

department: Pathology

institute: Washington University

summary: The adult human gut microbial community is typically dominated by two bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the interactions between their members. Here we examine the niches of representatives of both phyla in vivo.  Finished genome sequences were generated from E. rectale and E. eligens, which belong to Clostridium Cluster XIVa, one of the most common gut Firmicute clades. Comparison of these and 25 other gut Firmicutes and Bacteroidetes indicated that the former possess smaller genomes and a disproportionately smaller number of glycan-degrading enzymes. Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron, followed by whole genome transcriptional profiling of both organisms in their distal gut (cecal) habitat as well as host responses, high resolution proteomic analysis of cecal contents, and biochemical assays of carbohydrate metabolism. B. thetaiotaomicron adapts to E. rectale by upregulating expression of a variety of polysaccharide utilization loci (PULs) encoding numerous glycoside hydrolase gene families, and by signaling the host to produce mucosal glycans that it, but not E. rectale, can access. E. rectale adapts to B. thetaiotaomicron by decreasing production of its glycan-degrading enzymes, increasing expression of selected amino acid and sugar transporters, and facilitating glycolysis by reducing levels of NADH, in part via generation of butyrate from acetate, which in turn is utilized by the gut epithelium. This simplified model of the human gut microbiota illustrates niche specialization and functional redundancy within members of major gut bacterial phyla, and the importance of host glycans as a nutrient foundation that ensures ecosystem stability.

sample_organism:
Bacteroides thetaiotaomicron
Agathobacter rectalis

platform_organism:
Bacteroides thetaiotaomicron
Phocaeicola vulgatus
Parabacteroides distasonis
Methanobrevibacter smithii
Lachnospira eligens
Agathobacter rectalis

overall_design: We assessed how E. rectale and B. thetaiotaomicron were affected by changes in host diet. Groups of age- and gender-matched co-colonized mice were fed one of three diets that varied primarily in their carbohydrate and fat content: (i) the standard low-fat, plant polysaccharide-rich diet used for the experiments described above (abbreviated ‘LF/PP’ for low-fat/plant polysaccharide), (ii) a high-fat, ‘high-sugar’ Western-type diet (abbreviated HF/HS) that contained sucrose, maltodextrin, corn starch as well as complex polysaccharides (primarily cellulose) that were not digestible by B. thetaiotaomicron or E. rectale, and (iii) a control diet that was similar to (ii) except that the fat content was 4-fold lower (‘LF/HS’ for low-fat, high-sugar; n=5 mice per group).

first: Michael

last: Mahowald

first: Henning

last: Seedorf

first: Peter

middle: J

last: Turnbaugh

first: Jeffrey

middle: I

last: Gorodn


title: Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

overall_design: The interactions between E. rectale and B. thetaiotaomicron were characterized by performing whole genome transcriptional profiling of each species after colonization of gnotobiotic mice with each organism alone, or in combination. E. rectale was also profiled during in vitro growth.


title: Role of PsaR of Streptococcus pneumoniae D39 and TIGR4 in global gene expression and virulence

status: Public on Nov 19 2008

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

summary: Previous studies have indicated that PsaR of Streptococcus pneumoniae is a manganese-dependent regulator, negatively affecting the expression of at least seven genes. Here, we extended these observations by transcriptome and proteome analysis of psaR mutants in strains D39 and TIGR4. The microarray analysis identified three shared PsaR targets: the psa-operon, pcpA, and prtA. Additionally, we found 31 genes to be regulated by PsaR in D39 only, most strikingly a cellobiose-specific PTS and a putative bacteriocin operon (sp0141-sp0146). In TIGR4, 14 PsaR gene targets were detected, with the rlrA pathogenicity islet being the most pronounced. Proteomics confirmed most of the shared gene targets. To examine the contribution of PsaR to pneumococcal virulence, we compared D39 and TIGR4 wild-type (wt) and psaR-mutants in three murine infection models. During colonization, no clear effect was observed of the psaR mutation in either D39 or TIGR4. In the pneumonia model, small but significant differences were observed in the lungs of mice infected with either D39wt or ∆psaR: D39∆psaR had an initial advantage in survival in the lungs. Conversely, TIGR4∆psaR-infected mice had significantly lower bacterial loads at 24h only. Finally, during experimental bacteremia, D39∆psaR-infected mice had significantly lower bacterial loads in the blood stream than wt-infected mice for the first 24h of infection. TIGR4∆psaR showed attenuation at 36h only. In conclusion, our results show that PsaR of D39 and TIGR4 has a strain-specific role in global gene expression and in the development of bacteremia in mice.

overall_design: Microarray analysis was performed essentially as described (Hendriksen et al., 2007; Hendriksen et al., 2008a). In short, 500 ml of CDM was inoculated with 10-20 colonies from agar plates, and these cultures were statically grown at 37°C. Samples for RNA isolation were taken when the cultures reached an optical density (OD600) of 0.2 (mid-log growth). RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Hendriksen et al., 2007; Hendriksen et al., 2008a). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures. Synthesis, subsequent labeling of cDNA, and microarray hybridization was performed as described (Hendriksen et al., 2007; Kloosterman et al., 2006). In all cases, dye-swapping was performed with one of the three biological replicates. Microarrays used in this study were constructed as described (Hendriksen et al., 2007; Kloosterman et al., 2006) and contain amplicons representing 2,087 ORFs of S. pneumoniae TIGR4 and 184 ORFs unique for S. pneumoniae R6, all spotted in duplicate.

first: Wouter

last: Hendriksen


title: Comparative transcriptomic reveals signatures specific to various interactions with Melampsora rust fungi

status: Public on Nov 22 2008

city: Québec

first: Armand

last: Séguin

state: Québec

address: 1055 rue de PEPS

institute: Laurentian forestry Service

summary:
We aim to understand the global transcriptional response of hybrid poplar NM6 (Populus nigra x Populus maximoviczii) to infection by two biotrophic Melampsora fungi, M. larici-populina and M. medusae f. sp. deltoidae separately and simultanously. Transcript profilling revealed 699 differentially expressed genes whose expression level was equal or higher than 2-fold between infected and noninfected tissues. In the mixed infection, our results showed an additive response of the two pathogens.
Genes regulated as a result of Melampsora infection were generally induced and mainly involved in primary/secondary metabolism that include cell wall reinforcement and lignification, defense-related processes like pathogenesis-related and stress response, signal perception and transduction mechanisms and regulation of transcription.
Keywords: Stress response

overall_design: Poplar leaves were infected with Melampsora larici-populina and Melampsora medusae f. sp. deltoidae and the mixture of them (Mixed infection). At six day post-infection, tissues were harvested for RNA extraction and hybridization on Affymetrix microarrays. Three biological replications were obtained from infected and non infected leaves (control samples).

first: Aida

last: Azaiez

first: Valérie

last: Levée

first: Brian

last: Boyle


title: Genome-wide analysis of H3K79 methylation in  CD34+ CD19+ cells from normal marrow, MLL-rearranged or MLL-germline ALL

status: Public on Nov 04 2008

city: Plantagenet

first: Madeleine

middle: E.

last: Lemieux

address: 275 Main St., Suite 252

institute: Bioinfo

summary:
We created a mouse model where conditional expression of physiologic levels of an Mll-AF4 fusion oncogene induces development of acute lymphoblastic (ALL) or acute myeloid leukemias (AML). ChIP-chip analysis demonstrated increased histone H3 Lysine 79 (H3K79) dimethylation that correlated with Mll-AF4 associated gene expression profiles in murine ALLs, and in human MLL-rearranged leukemias. In addition, human MLL-rearranged ALLs can be distinguished from other ALLs by their genome-wide H3K79 methylation profiles.

Keywords: Cell type comparison

overall_design: DNA immunoprecipitated with anti-dimethyl-H3K79 antibodies from  normal CD34+CD19+ cells, leukemic bone marrow from MLL-rearranged ALL or MLL-germline ALL was hybridized to Affymetrix promoter tiling microarrays.


title: Glycan effect on Saccharolytic Human Distal Gut Symbiont, B. thetaiotaomicron

status: Public on Nov 21 2008

city: Ann Arbor

first: Eric

middle: Charles

last: Martens

address: 1150 West Medical Center Drive

department: Dept. of Microbiology and Immunology

institute: University of Michigan Medical School

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

platform_organism:
Bacteroides thetaiotaomicron
Phocaeicola vulgatus
Parabacteroides distasonis
Methanobrevibacter smithii
Lachnospira eligens
Agathobacter rectalis
Bifidobacterium longum


title: Looking for mitochondrial associated RNA

status: Public on Jun 01 2008

city: Paris

first: Stéphane

last: LE CROM

department: Biology Institute - IBENS

institute: École normale supérieure

summary:
We investigated the peripheral mitochondrial localization of nuclear-encoded mRNAs (MLR) in various conditions in which translation was inhibited or the mRNA binding protein context altered (Delta puf3). We used cell fractionation protocols together with microarray to assess the distribution of mRNAs between free and mitochondrion-bound polysomes.
Keywords: Mitochondrial-associated RNA localization in cells

overall_design:
GSM239122-GSM239127: mitochondrial associated RNA (three biological replicates each in dye swap)

GSM239128-GSM239131: mitochondrial associated RNA in presence of 200µg/ml cycloheximide (two biological replicates each in dye swap)

GSM239132-GSM239135: mitochondrial associated RNA in presence of 2.1mM puromycin (two biological replicates each in dye swap)

GSM239136-GSM239139: mitochondrial associated RNA in Delta Puf3 strain (two biological replicates each in dye swap)

first: Yann

last: Saint-George

first: Mathilde

last: Garcia

first: Thierry

last: Delaveau

first: Stephane

last: Le Crom

first: Sophie

last: Lemoine

first: Veronique

last: Tanty

first: Frederic

last: Devaux

first: Claude

last: Jacq


title: Effect of hypoxia on gene expression in Grey poplar

status: Public on Jan 31 2009

city: Freiburg

first: Juergen

last: Kreuzwieser

address: Georges-Koehler-Allee

department: Chair of Tree Physiology

institute: University of Freiburg

summary: The molecular responses of Grey poplar (Populus x canescens) following root hypoxia were studied in roots and leaves using transcript profiling. Grey poplar is a flooding tolerant tree species and analysis of the molecular response to hypoxia may indicate possible adaptation mechanisms to this stress.

overall_design: The root system of the poplar trees were flooded for up to 168 h. At three time-points (5 h, 24 h, 168 h) plants were collected and leaf and root tissue analysed separately. At each time-point non-flooded controls were collected and analysed as well.

first: Jost

last: Hauberg

first: Katherine

last: Howell

first: Adam

last: Carroll

first: Heinz

last: Rennenberg

first: A

last: Millar

first: James

last: Whelan


title: An experimental loop design improves the detection of congenital chromosomal aberrations by array CGH

status: Public on Dec 01 2007

city: Leuven

first: Joke

last: Allemeersch

address: Herestraat 49

country: Belgium

institute: VIB MicroArray Facility

summary:
Comparative genomic hybridization microarrays (array CGH or molecular
karyotyping) for the detection of congenital chromosomal aberrations is
the application of microarray technology that is coming fastest into routine clinical application. When using a two-channel microarray of genomic DNA probes for array CGH, the basic setup consists in hybridizing a patient sample against a normal reference sample and detecting copy number variations through the deviation of fluorescent signal intensity between patient and normal reference. Two major disadvantages of this setup are (1) the use of half of the resources to measure a (little informative) reference sample and (2) the possibility that deviating signals are caused by benign copy number variation
in the “normal” reference instead of a patient aberration. We therefore
propose a new experimental loop design that compares three patients in three hybridizations (Patient 1 vs. Patient 3, Patient 3 vs. Patient 2, and Patient 2 vs. Patient 1). We develop and compare two statistical methods (linear models of log ratios and mixed models of absolute measurements). In an analysis of data from 27 patients seen at our genetics center, this new setup together with the linear model analysis significantly overcomes the limitations of the classical setup. Furthermore, we observed that the linear models of the log-ratios had a higher signal-to-noise ratio than the mixed models of the absolute intensities. These improvements are important to guarantee a maximal efficiency of array CGH in a clinical setting and will therefore contribute to its quick adoption as a routine diagnostic tool. The method is implemented as a web application and is available at www.esat.kuleuven.be/loop.
Keywords: comparative genomic hybridization

overall_design: The data set consists out of nine loop designs or 27 patients with mental retardation (MR) and multiple congenital anomalies (MCA). The patients were seen at our genetics center (Center for Human Genetics, U.Z.Leuven).

first: Steven

last: Van Vooren

first: Femke

last: Hannes

first: Bart

last: De Moor

first: Joris

last: Vermeesch

first: Yves

last: Moreau


title: Wild type vs glnPA double mutant

status: Public on Feb 01 2008

first: Anne

last: Jong

summary:
This microarray experiment is part of a study addressing the importance of glutamine metabolism in Streptococcus pneumoniae for the virulence of this bacterium. To be able to gain more insight into the phenotype of a double mutant of glnA (TIGR 4 locus tag SP0502, encoding glutamine synthetase) and glnP (SP1241, encoding a permease component of a glutmine uptake ABC transporter), the transcriptome of this mutant, the glnPA double mutant, was determined in strain S. pneumoniae D39 grown in rich GM17 medium with 0.5 mg/ml glutamine. This revealed a big change in transcriptome in the mutant, especially a lot of amino acid and peptide metabolic genes.
Keywords: transcriptome analysis of D39 wild-type compared with its isogenic glnPA double mutant

overall_design: The wild-type strain D39 and its isogenic glnPA double mutant were grown in 4 biological replicates in GM17 with 0.5 mg/ml glutamine to an Optical Density at 600 nm of 0.3. From these cultures samples were prepared for transciptome determination with in-house printed microarrays covering the genomes of several S. pneumoniae species. The wild-type (control, Ch1) was labeled with Cy5 (3 samples) or Cy3 (1 sample) and vice versa for the samples of the glnPA mutant (target, Ch2). Samples were pair-wise compared on glass-microarray slides.

first: Tomas

middle: G

last: Kloosterman

first: Wouter

last: Hendriksen

first: Hester

last: Bootsma

first: Oscar

middle: P

last: Kuipers

first: Peter

middle: W

last: Hermans


title: Effect of adk1 knock-out mutation on global transcription

status: Public on Apr 17 2008

first: Laurent

last: Jourdren

institute: École Normale Supérieure

summary:
We investigated the effects of the variation in intracellular adenylic nucleotides pools due to the absence of the adenylate kinase Adk1p on the global yeast transcriptome. In this work, global transcription analyses were combined to measurements of intracellular nucleotides pools by HPLC.
Keywords: Comparative genomic transcription on total RNA from cells containing or not Adk1p.

first: Sébastien

last: Gauthier

first: Fanny

last: Coulpier

first: Manfred

last: Konrad

first: Bertrand

last: Daignan-Fornier

first: Benoît

last: Pinson


title: ChIP-chip analysis of human DREAM complex subunits in G0-arrested and S-phase synchronized cells

status: Public on Apr 17 2007

city: Beijing

first: Xiaopeng

last: Zhu

address: 15 Datun Street

institute: Institute of Biophysics, Chinese Academy of Sciences

summary:
This experiment is a part of global location analysis of the human DREAM complex including subunits: E2F4, RBL2/p130, LIN9 and LIN54.

Specifically, the regions in Human Promoter Array 1.0R (GPL5082) bound by:

E2F4 in G0-arrested T98G cells
E2F4 in S-phase synchronized T98G cells
LIN54 in G0-arrested T98G cells
LIN54 in S-phase synchronized T98G cells
LIN9 in G0-arrested T98G cells
LIN9 in S-phase synchronized T98G cells
p130 in G0-arrested T98G cells
p130 in S-phase synchronized T98G cells

were compared with input chromatin.

MAT (Model-based Analysis for Tiling Arrays) .bar and .bed output files provided as supplementary files.
Keywords: CHiP-chip genomic DNA

overall_design: This experiment is a part of global location analysis in G0 and S-phase synchronized cells of the human DREAM complex including E2F4, RBL2/p130, LIN9 and LIN54 subunits.

first: X

middle: S

last: Liu

first: Subhashini

last: Sadasivam

first: Larisa

last: Litovchick

first: James

last: DeCaprio


title: Epigenetic mapping and functional analysis in a breast cancer metastasis model using whole genome tiling arrays

status: Public on Jul 18 2008

city: London

first: Ann

last: Chambers

address: 790 Commissioner's Road E

department: Victoria research labs

institute: London Regional Cancer program

summary:
We have used a human gene promoter tiling microarray platform to analyze a cell line model of lymph node metastasis comprised of a poorly metastatic MDA-MB-468GFP human breast adenocarcinoma cell line and its highly metastatic variant (468LN). Gene networks and pathways associated with metastasis were identified and target genes associated with epithelial-mesenchymal transition (EMT) was validated with respect to DNA methylation effects on gene expression.
We integrated data from the tiling microarrays with targets identified by Ingenuity Pathway Analysis software and observed epigenetic variations in genes implicated in EMT and with tumor cell migration. We identified widespread genomic hyper- and hypo- methylation events in these cells and we confirmed functional associations between methylation status and expression of the CDH1, CST6, EGFR, SNAI2 and ZEB2 genes by quantitative RealTime PCR. Our data also suggest that the complex genomic reorganization present in cancer cells may be superimposed over promoter-specific methylation events that are responsible for gene-specific expression changes.

Keywords: Lymph node metastatic vs non metastatic

overall_design: DNA derived from three biological replicates of a highly metastatic (via Lymph Nodes) Breast cancer cell line (468GFP-LN) was compared to 3 biological replicates of DNA prepared from the parental cell line, 468GFP.

first: David

last: Rodenhiser

first: Joseph

last: Andrews

first: Wendy

last: Kennette

first: Bekim

last: Sadikovic

first: Ariel

last: Mendlowitz

first: Alan

middle: B

last: Tuck

middle: F


title: Growth of B. thetaiotaomicron on purified host mucosal glycans and glycan fragments

first: Eric

last: Martens

summary: Bacteroides thetaiotaomicron was grown and transcriptionally profiled on a number of different host mucosal glycans and their component mono- and disaccharides.

overall_design: Experiments are performed in biological duplicate (2 replicates per growth condition). All cultures were harvested at similar points in mid-log phase of growth in minimal medium plus 0.5% (total amount, w/v) of a defined carbon source. Cultures on individual carbon sources are designed to be referenced to a minimal medium glucose control (GSM302686 and 302791) grown in the same growth format. Note that the hybridization targets used for these two reference datasets are from the exact same prep used for similar targets on the GPL1821 platform (sets GSM301720 and 301721)

middle: C

first: Herbert

last: Chiang

first: Jeffrey

last: Gordon


title: Large-Scale Mapping and Validation of E. coli Transcriptional Regulation from a Compendium of Expression Profiles.

status: Public on Jan 22 2007

city: Boston

first: Timothy

last: Gardner

address: 44 Cummington St.

department: Biomedical Engineering

institute: Boston University

summary:
Machine learning approaches offer the potential to systematically identify transcriptional regulatory interactions from a compendium of microarray expression profiles. However, experimental validation of the performance of these methods at the genome scale has remained elusive. Here we assess the global performance of four existing classes of inference algorithms using 445 Escherichia coli Affymetrix arrays and 3,216 known E. coli regulatory interactions from RegulonDB. We also developed and applied the context likelihood of relatedness (CLR) algorithm, a novel extension of the relevance networks class of algorithms. CLR demonstrates an average precision gain of 36% relative to the next-best performing algorithm. At a 60% true positive rate, CLR identifies 1,079 regulatory interactions, of which 338 were in the previously known network and 741 were novel predictions. We tested the predicted interactions for three transcription factors with chromatin immunoprecipitation, confirming 21 novel interactions and verifying our RegulonDB-based performance estimates. CLR also identified a regulatory link providing central metabolic control of iron transport, which we confirmed with real-time quantitative PCR. The compendium of expression data compiled in this study, coupled with RegulonDB, provides a valuable model system for further improvement of network inference algorithms using experimental data.
Keywords: mapping transcriptional regulation

overall_design: To explore pathways of particular importance to antibiotic resistance, we assayed 121 conditions using 266 microarrays, including more than 50 genetic perturbations (overexpression or knockout) during norfloxacin-induced DNA damage response, overexpression of the ccdB toxin, and growth to stationary phase on low and high glucose

first: J

last: Faith

first: B

last: Hayete

middle: T

last: Thaden

first: I

last: Mogno

last: Wierzbowski

first: G

last: Cottarel

first: S

last: Kasif

last: Collins

first: T