title: Expression data from Integrin-linked kinase (ILK)-deficient epidermis

city: London

first: David

last: Carter

state: ON

address: 1151 Richmond Street North

department: London Regional Genomics Centre

institute: Robarts Research Institute

summary: ILK is essential for proper development of hair follicles, and for epidermal integrity and repair after injury. To better understand the pathways modulated by ILK in the epidermis, we compared the transcriptomes of ILK-deficient and -expressing epidermis using microarray analyses.

overall_design: Ilktm1Star (with floxed Ilk alleles) and Tg(KRT14-cre)1Amc/J mice were bred, and the resulting mice were bred again with Ilktm1Star mice, to generate animals heterozygos for the  KRT14-cre transgene and either heterozygous (ILK-expressing) or homozygous (ILK-deficient) for the floxed Ilk alleles. The epidermis of 3 day-old animals was harvested and used to prepare RNA for the microarrays. The animals used were littermates. RNA from the epidermis of five ILK-deficient and five ILK-expressing mice were used.

first: Lina

last: Dagnino

last: Judah

first: Alena

last: Rudkouskaya


title: Pfizer Molecular Profile Data for Cell Lines

status: Public on Jan 19 2012

city: San Diego

first: Keith

middle: A

last: Ching

state: CA

address: 10777 Science Center Dr.

department: Computational Sciences

country: USA

institute: Pfizer, Inc.

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

summary: Baseline gene expression for cell lines growing in culture were measured by Affymetrix U133Plus2 arrays.  Copy Number Variation for selected cell lines was also measured.

overall_design: Baseline gene expression for cell lines growing in culture were measured by Affymetrix U133Plus2 arrays.  Three different sources of arrays were combined. Arrays were from Pfizer, Wyeth Breast Panel, and Wyeth NCI50 subset of NCI60 cell lines.  CNV was determined by Affymetrix SNP6.0 arrays.

first: Maruja

middle: E

last: Lira

first: Maryann

last: Whitley

first: Dan

last: Johnston

first: Chris

last: Coughlin

first: Kim

last: Arndt

first: Paul

last: Rejto

first: Christine

last: Huard

first: Adam

last: Pavlicek

first: James

middle: G

last: Christensen

first: Nathan

middle: V

last: Lee


title: Expression data from human HEK293 cells

status: Public on Jan 14 2012

city: New Haven

last: Wu

address: 10 Amistad Street

institute: Yale University

summary:
LPA, which can signal through the Ga12/13 family of G proteins, is a potent stimulator of fibroblast migration.  LPA downregulate mTOR activity dependent on protein synthesis in cell migration and bleomycin-induced lung fibrosis.
We used microarray to identify LPA-regualted gene expression and find potent regulators in this process.

overall_design: HEK293 cells were treated with or without LPA. Then RNA was extracted and Hybridization was done on Affymetrix microarrays.

first: Xiaoqing

last: Gan


title: Genome-scale reconstruction of the PurR regulon reveals its role in the adenine stimulon of Escherichia coli K-12 MG1655

status: Public on Jan 12 2012

city: La Jolla

first: Bernhard

last: Palsson

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

type: Genome binding/occupancy profiling by genome tiling array

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

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Refer to individual Series


title: Gene expression analysis between the pancreatic tissues of Pdx1-cre;Kras LSL-G12D and Pdx-cre;KrasLSL-G12D;IKK2/beta F/F mice

status: Public on Jan 24 2012

city: Houston

middle: J

last: Chiao

state: Texas

address: 1515 Holcombe Blvd

department: Department of Molecular and Cellular Oncology

institute: The University of Texas M. D. Anderson Cancer Center

summary: Constitutive Kras and NF-kB activation is identified as signature alterations in human pancreatic ductal adenocarcinoma (PDAC). Here, we report that pancreas-targeted IKK2/beta inactivation inhibited NF-kB activation and completely suppressed PDAC development. Our findings demonstrated that NF-kB is required for development of pancreatic ductal adenocarcinoma that was initiated by Kras activation.

overall_design: Pancreatic tissue from 4 groups of mice were used in this project: (1) the pancreas normal appearance of Pdx1-cre;KrasLSL-G12D;IKK2/beta mice, (2) the normal pancreas of Pdx1-cre;KrasLSL-G12D mice, (3) the pancreatic lesion of pancreatic intraepithelial neoplasia (PanIN) of Pdx1-cre;KrasLSL-G12D mice, and (4) the pancreatic lesion of PDAC of Pdx1-cre;KrasLSL-G12D mice. Each group included three mice. RNA samples from mouse pancreas were hybridized on GeneChip Mouse Gene 1.0 ST arrays (Affymetrix). Group (1) and group (2) were compared, and group (2), group (3) and group (4) were compared.

first: Jianhua

last: Ling


title: The expression profiles of AML cell lines

status: Public on Jan 18 2012

city: Miyazaki

first: Yusuke

last: Saito

address: 5200 Kihara, Kiyotake

country: Japan

institute: Miyazaki University

summary: EVI1 is one of the famous poor prognostic markers for a chemotherapy-resistant acute myeloid leukemia (AML). To identify molecular targets on the surface of leukemia cells with EVI1high expression, we compared the gene expression profiles of several AML cell lines by DNA microarray

overall_design: To search for novel molecular targets in refractory myeloid leukemia with high EVI1 expression, we initially analyzed the gene expression profiles of 12 human myeloid cell lines. Four cell lines with chromosome 3q26 abnormalities (UCSD/AML1, HNT-34, Kasumi-3 and MOLM-1) expressed EVI1High, and eight myeloid cell lines without chromosome 3q26 abnormalities (HEL, HL-60, K052, THP-1, FKH-1, K051, NH and OIH-1) expressed low levels of EVI1 (EVI1Low)

first: Kazuhiro

last: Morishita


title: Novel Properties of Side Population cells in Soft-tissue Sarcoma, and How They May Be Targeted to Develop Potential Therapies

status: Public on Jan 17 2012

city: Toronto

first: Qingxia

last: Wei

address: 101 College Street

department: Development Biology

country: Canada

institute: Hospital for Sick Children

summary:
Tumours contain heterogeneous cell populations. A population enriched in tumour-initiating potential has been identified in soft-tissue sarcoma (STS) by the isolation of side population (SP) cells. In this study, we compared the gene expression profiles of SP and non-SP cells in STS and identified Hedgehog (Hh) and Notch pathways as potential candidates for the targeting of SP cells. Upon verification of the activation of these pathways in SP cells, using primary tumor xenografts in NOD-SCID mice as our experimental model, we used the Hh blocker Triparanol and the Notch blocker DAPT to demonstrate that the suppression of these pathways effectively depleted the abundance of SP cells, reduced tumour growth, and inhibited the tumour-initiating potential of the treated sarcoma cells upon secondary transplantation. The data provide additional evidence that SP cells act as tumour initiating cells and points to Hh and Notch pathways as enticing targets for developing potential cancer therapies.
We used microarrays to detail the difference in gene expressions between the side population cells in soft-tissue sarcoma in comparison to the bulk non-side-population cells.

overall_design: To examine whether certain pathways may be differentially regulated in SP cells versus non-SP cells, which represent the bulk of tumour cells, we compared the gene expression profiles of SP and non-SP cells in four primary STS tumours each from different patient. Upon surgical excision, these tumours were dissociated mechanically and enzymatically into individual cells. Via Hoechst dye staining and flow-cytometry, these primary tumour cells were sorted into distinct side population and non-side population fractions. Total RNA is extracted from an equal number of SP and NSP cell from each primary tumour. cDNA from each sample was generated from the isolated total RNA and hybridized onto Affymetrix Human Genome EukGE-WS2v4 gene chips against the same reference cDNA library. After initial processing of the raw data, using the Genespring® GX software, the expression of SP cells from each tumour was normalized against the expression of the corresponding non-SP cells. A gene list was constructed by selecting genes that were regulated in the same direction (SP vs. NSP) in all sample pairs with a fold change greater than 1.25. This list was examined using Genespring® GX significant pathway function to identify differentially regulated pathways.

first: Chang

middle: Y

last: Wang

first: Ben

last: Alman


title: Expression data from BDC2.5 TCR Tg thymocytes on B6g7 and NOD background

status: Public on Jan 10 2012

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: The aim of this study was to quantify the impact of NOD genetic vatiation on the transcriptional programs induced by the alpha beta-TCR at the DN to DP transition in the BDC2.5 TCR Tg model

overall_design:
CD4 and CD8-complement mediated depletion followed by FACS
Experiment type: BDC2.5 TCR Tg or polyclonal B6g7 versus NOD

first: Michael

last: Mingueneau

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: Expression data from BDC2.5 TCR Tg, preselected Rag-/-.B6 and Rag-/-.NOD.H2b thymocytes upon antigenic stimulation

summary: The aim of this study was to quantify the impact of NOD genetic vatiation on thymic negative selection transcriptional programs.

overall_design:
Pre-selected BDC2.5 TCR Tg DP thymocytes from non-selecting B6 and NOD.H2b backgrounds were purified (Dynal CD8 FlowComp), mixed in a 1:1 ratio and stimulated with BDC mimotope-loaded TCRa-/-/NOD splenocytes for indicated periods of time and double sorted by FACS as Thy1.2+Dump-CD4+CD8+; Dump includes CD19, Gr1, CD11b, CD11c, CD49b. Following cell sorting into trizol, RNA was purified, labeled and hybridized to Affymetrix arrays.
experiment type: unstimulated versus stimulated BDC/B6.Rag-/- and BDC/NOD.H2b.Rag-/- DP thymocytes


title: Profiling Side Population Cells in Malignant Fibrous Histiocytoma

summary:
We are currently studying the mechanisms that confer tumour initiating potential upon SP, and as part of this work, we undertook gene profiling studies comparing expression between SP and non-SP cells, initially focusing on the most common soft tissue sarcoma, malignant fibrous histiocytoma (or MFH)
Sarcomas contain a subpopulation of cells which exclude Hoechst dye (SP cells) and are enriched for tumor initiating potential.  The persistence of SP cells could be responsible for relapse or a failed response to therapy. Expression profiles were compared between the SP and non-SP cells from malignant fibrous histiocytoma (MFH) tumors using microarray. The Hedgehog and Notch pathways were activated in SP cells.  Blocking these pathways in MFH xenografts established in NOD-SCID mice depleted the abundance of SP cells and reduced tumor growth. Intriguingly, treatment also substantially inhibited the potential for successful secondary transplantation. The data provides support that SP cells act as tumor initiating cells in sarcomas and suggests targeting the SP as an enticing approach for sarcoma therapy.

overall_design: In this study, we studied six MFH tumours, and identified a number of signaling pathways that were consistently activated in the SP population compared to the non-SP population.


title: Expression data from pancreatic CD45+ immune cells

summary: The aim of this study was to explore what molecular and cellular processes predicate the conversion from insulitis to diabetes. The transcriptional profiles of CD45+ immune cells collected from pancreas of a cohort of age-matched female mice, which were scanned by MRI to determine the risk of diabetes development.

overall_design:
A cohort of five females was MRI-scanned at 10 weeks of age, their pancreas was removed immediately after final imaging, and CD45+ cells were sorted from the dispersed tissue for microarray analysis of gene expression. Genes whose transcript levels were positively or negatively correlated with these  MRI signals were selected for further study.
correlation between pancreatic gene expression and autoimmune diabetes development

first: Wenxian

last: Fu


title: Withdrawal of immunosuppressive therapy in stable liver transplant recipients

status: Public on Jan 09 2012

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Complications due to long-term administration of immunosuppressive therapy increase the morbidity and mortality of liver transplant recipients. Discontinuation of immunosuppressive drugs in recipients spontaneously developing operational tolerance could substantially lessen this burden. However, this strategy results in the development of rejection in a high proportion of recipients who require lifelong immunosuppression. Thus, there is a need to identify predictive factors of successful drug withdrawal and to define the clinical and histological outcomes of operationally tolerant liver recipients.  Methods.  We enrolled 102 stable liver transplant recipients in an immunosuppression withdrawal trial in which drugs were gradually discontinued over a 6-9 month period.  Patients with stable graft function and no signs of rejection in a liver biopsy conducted 12 months after cessation of immunosuppressive therapy were considered operationally tolerant. Results. Out of the 98 recipients who completed the study, immunosuppression discontinuation was successful in 41 recipients and rejection occurred in 57. Rejection episodes were mild and were resolved in all cases. Development of tolerance was independently associated with time elapsed since transplantation, recipient age, and male gender. No histological damage was apparent in protocol biopsies performed after successful drug withdrawal.

overall_design: PBMC gene expression profiling was assessed by DNA microarray in liver trasplanted patients groups: A group of inmunetolerant patients (TOL ;n=20), a group of non inmunotolerant (NonTOL; n=25). Finally from these two groups (Tolerant pTOL=12 and Non Tolerant pNonTOL=14 ) a sample is obtained a year after weaning.

first: C

last: Benitez

first: M

middle: C

last: Londoño

last: Martinez-LLordella

last: Lopez

first: R

last: Miquel

first: J

first: F

last: Bohne

first: T

last: Manzia

last: Angelica

last: Daoud

first: P

last: Larcier

last: Pirenne

first: A

last: Rimola

first: G

last: Tissone

last: Sanchez-Fueyo


title: Gene expression study reveals compromised Pattern Recognition Receptors and Interferon Signaling in fullterm Low birth Weight newborns

status: Public on Jan 15 2012

city: Bangalore

first: Bionivid

last: Technology

address: Bangalore

country: India

institute: Bionivid Technology

summary: Low Birth Weight (LBW) newborns (with weight less than 2500g) suffer a higher frequency and severity of microbial infection than normal birth weight (NBW) newborns. Morbidity and mortality of LBW infants due to infectious diseases are known to be high and it has been associated with compromised immune functions, however, the complete understanding of the cause is lacking. We, therefore, conducted a gene expression study to identify all the defective pathways and functions in the LBW newborns using DNA microarray. RNA were isolated from the umbilical cord blood of the NBW and LBW newborns and processed for chip hybridisation. Our results suggest down-regulation of genes participating in several canonical pathways vital in the defense response against microbes and perpetuation of immune responses. Pattern recognition receptors (PRRs) and Interferon signaling appear to be most significantly impacted pathways. The information generated from this study may help in depth understanding of the cause of higher frequency of infections in LBW and thus, in turn help devise better therapeutic interventions.

overall_design: Total 12 subjects were included in the study. 4 NBW newborns umblical cord blood samples served as control and 8 LBW newborns umblical cord blood samples were treated as the experimental samples for the study.

first: Vikas

last: Singh

first: Ashok

last: Kumar

first: Shiva

middle: M

first: Geeta

last: Rai


title: Expression data from three endothelial cell lines derived from murine embryonic stem cells expressing VE-cadherin, N-cadherin or both

city: Milano

first: Costanza

last: Giampietro

address: Via Adamello 16

country: Italy

institute: Campus IFOM-IEO

summary:
Endothelial cells (ECs) express two members of the cadherin family, VE- and N-cadherin. While VE-cadherin induces EC homotypic adhesion, N-cadherin function in ECs remains largely unknown. EC-specific inactivation of either VE- or N-cadherin leads to early foetal lethality suggesting that these cadherins play a non-redundant role in vascular development.
Goal of this study was to further investigate this hypothesis analyzing both additive and divergent functions of the two cadherins in ECs.

overall_design: The three endothelial cell lines were cultured. Total RNA was extracted using commercial homogenization (QIAshredder) and purification (RNeasy Mini Kit) reagents (Qiagen). Quality control (QC) of the RNA samples was performed using an Agilent Bioanalyzer 2100 (Agilent Technologies). Two different RNA extractions were processed for each of the cell lines under analysis, and each sample was labelled and hybridized to a Mouse Gene 1.0 ST Genechip array according to the manufacturer’s specifications (Affymetrix Inc). Data were analysed using Partek Genomics Suite v6.3 software (RMA algorithm). Differentially expressed genes were identified through ANOVA, using a fold change cutoff >2 and a p-value of 0.05.

first: Andrea

last: Taddei

first: Monica

last: Corada

first: GianMaria

last: Sarra-Ferraris

first: Myriam

last: Alcalay

first: Ugo

last: Cavallaro

first: Fabrizio

last: Orsenigo

first: Maria

last: Lampugnani

first: Elisabetta

last: Dejana


title: Transcriptional profiling of liver samples from Lmna Gly609Gly knock-in mice

status: Public on Jan 13 2012

city: Oviedo

first: Jose

last: Freije

state: Asturias

address: C/ Fernando Bongera s/n

department: Bioquimica y Biologia Molecular

institute: Universidad de Oviedo

summary: Hutchinson-Gilford Progeria Syndrome (HGPS) is caused by a point mutation in the LMNA gene that activates a cryptic donor splice site and yields a truncated form of prelamin A called progerin. Small amounts of progerin are also produced during normal aging. Studies with mouse models of HGPS have allowed the recent development of the first therapeutic approaches for this disease. However, none of these earlier works have addressed the aberrant and pathogenic LMNA splicing observed in HGPS patients because of the lack of an appropriate mouse model. We report herein a genetically modified mouse strain that carries the HGPS mutation. These mice accumulate progerin, present histological and transcriptional alterations characteristic of progeroid models, and phenocopy the main clinical manifestations of human HGPS, including shortened life span and bone and cardiovascular aberrations. By using this animal model, we have developed an antisense morpholino–based therapy that prevents the pathogenic Lmna splicing, dramatically reducing the accumulation of progerin and its associated nuclear defects. Treatment of mutant mice with these morpholinos led to a marked amelioration of their progeroid phenotype and substantially extended their life span, supporting the effectiveness of antisense oligonucleotide–based therapies for treating human diseases of accelerated aging.

overall_design: 6 samples, three from LmnaG609G/G609G mice and three from control Lmna+/+ mice

first: Fernando

last: Osorio

first: José

first: Carlos

last: Lopez-Otin


title: MOLECULAR CHARACTERIZATION OF LIVER ALLOGRAFTS FROM OPERATIONALLY TOLERANT TRANSPLANT RECIPIENTS (Affymetrix)

first: Juanjo

last: Lozano

summary: In clinical organ transplantation complete cessation of immunosuppressive therapy can be successfully accomplished in selected recipients providing a proof-of-principle that allograft tolerance is attainable in humans. The intra-graft molecular pathways associated with human allograft tolerance, however, have not been comprehensively studied before. In this study we analyzed sequential liver tissue samples collected from liver recipients enrolled in a prospective multicenter immunosuppressive withdrawal clinical trial. Tolerant and non-tolerant recipients differed in the intra-graft expression of genes involved in the regulation of iron homeostasis.These results point to a critical role of iron homeostasis in the regulation of intra-graft alloimmune responses in humans and provide a set of novel biomarkers to conduct drug-weaning trials in liver transplantation.

overall_design: The complete database comprised the expression measurements of 54,675 genes for liver inmunotolerance groups: 9 Tolerant (TOL) 10 Non Tolerant (Non TOL).A subset of 5 tolerant samples  (TOL POST) were taken 1 year after inmunosuppresive therapy.

first: F

middle: F

last: Bohne

first: M

last: Martínez-Llordella

first: J

first: R

last: Miquel

first: C

last: Benítez

last: Londoño

first: T

last: Manzia

first: D

last: Swinkels

first: H

last: Tjalsma

last: López

last: Abraldes

first: E

last: Riani

last: Pirenne

first: A

last: Rimola

first: G

last: Tisone

last: Sánchez-Fueyo


title: Genome wide expression data from discordant twins (ulcerative colitis, primary mucosal tissue)

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

summary:
Background and aims. The etiopathology of inflammatory bowel diseases is still poorly understood. To date, only few little data are available on the microbiota composition in ulcerative colitis (UC), representing a major subform of inflammatory bowel diseases. Currently, one of the main challenges is to unravel the interactions between genetics and environmental factors in the onset or during the progression and maintenance of the disease. The aim of the present study was to analyse twin pairs discordant for UC for both gut microbiota dysbiosis and host expression profiles at a mucosal level and to get insight into the functional genomic crosstalk between microbiota and mucosal epithelium in vivo.   Methods. Biopsies were sampled from the sigmoid colon of both healthy and diseased siblings from UC discordant twin pairs but also from healthy twins. Microbiota profiles were assessed by 16S rDNA libraries while mRNA expression profiles were analysed from the same volunteers using Affymetrix microarrays.
Results. UC patients showed a dysbiotic microbiota with lower diversity and more species belonging to Actinobacteria and Proteobacteria phyla. On the contrary, their healthy siblings’ microbiota contained more bacteria from the Lachnospiracea and Ruminococcaceae family than did healthy individuals . Sixty-three host transcripts significantly correlated with bacterial genera in healthy individuals whereas only 43 and 32 correlated with bacteria in healthy and UC siblings from discordant pairs, respectively. Several transcripts related to oxidative and immune responses were differentially expressed between unaffected and UC siblings.  Conclusion. A loss of crosstalk between gut microbiota and host was highlighted in UC patients. This defect was also striking in healthy siblings from discordant pairs, as was the lower biodiversity within the microbiota. Our results suggest disease-relevant interactions between host transcriptome and microbiota. Moreover, unusual aerobic bacteria were noticed in UC mucosal microbiota, whereas healthy siblings from discordant pairs had higher percentages of potentially beneficialusual commensal  bacterial species.

overall_design:
Paired samples (twins) were analyzed to obtain data independent of genetic variation
Samples GSM560961-GSM560976 correspond to publication with PMID: 21621540.
Samples GSM560961-GSM560976, GSM1012177-GSM1012180 correspond to publication with PMID: 22826509.

last: Häsler


title: The amniotic fluid transcriptome: a source of novel information about human fetal development

status: Public on Jan 11 2012

city: Medford

first: Donna

middle: K

last: Slonim

address: 161 College Ave.

department: Computer Science

institute: Tufts University

summary:
Amniotic fluid (AF) is a complex biological material that provides a unique window into the developing human. Residual AF supernatant contains cell-free fetal RNA. The objective of this study was to develop an understanding of the AF core transcriptome by identifying the transcripts ubiquitously present in the AF supernatant of euploid midtrimester fetuses.
We detected 476 well-annotated genes present in all twelve AF samples. Functional analysis identified 6 physiological systems represented in the AF core transcriptome, including musculoskeletal and nervous system development and function and embryonic/ organismal development. mTOR signaling was identified as a key canonical pathway. Twenty-three highly organ-specific transcripts were identified; six of these are known to be highly expressed by fetal brain.  This study demonstrates that AF cell-free fetal RNA can provide biological information about multiple fetal organ systems.

overall_design: This was an in silico investigation of gene expression in 12 euploid midtrimester AF samples acquired primarily for advanced maternal age.  We focused on the transcripts called “present” in all of the samples.  Functional analyses were performed using Ingenuity software. Fetal-organ specificity was examined for each transcript using the GNF Gene Expression Atlas. For fetal organs not represented in the atlas, manual literature searching and Ingenuity analysis were used.

first: Lisa

last: Hui

first: Heather

last: Wick

first: Kirby

middle: L

last: Johnson

first: Diana

middle: W

last: Bianchi


title: NOD genetic variation influences ab/gd lineage decisions when TCRa is prematurely expressed, but not the process of negative selection.

first: CBDM

last: Lab

first: Michael

last: Mingueneau

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: SRC1 gene regulation in endocrine resistant breast cancer cells

city: Dublin

first: Yuan

last: Hao

state: Ireland

address: Bioinformatics,Conway Institute, UCD

country: Ireland

institute: UCD

summary: The development of breast cancer resistance to endocrine therapy results from an increase in cellular plasticity leading to the development of a steroid independent tumour.  The p160 steroid coactivator protein SRC-1, through interactions with developmental proteins and other non-steroidal transcription factors drives this tumour adaptability.  Here, using discovery studies we identify ADAM22, a non-protease member of the ADAMs family, as a direct target of SRC-1, independent of estrogen receptor(ER). Molecular, cellular, in vivo and clinical studies confirmed SRC-1 as a regulator of ADAM22 and established a role for ADAM22 in endocrine resistant tumour progression.  ADAM22 has the potential to act as a therapeutic drug target and a companion predictive biomarker in the treatment of endocrine resistant breast cancer.

overall_design: 14 samples representing 4 conditions were analysed. Samples were transfected with either a siRNA targetting SRC1 or a control scrambled siRNA. Samples were subject to tamoxifen treatment or untreated.

first: Damian

last: McCartan

first: Jarlath

last: Bolger

first: Aílis

last: Fagan

first: Christopher

last: Byrne

first: Li

last: Qin

first: Marie

last: McIlroy

first: Jianming

last: Xu

first: Arnold

last: Hill

first: Peadar

last: Ó Gaora

first: Leonie

last: Young


title: Lineage-committed osteoclast precursors circulate in blood and settle down into bone

status: Public on Jan 07 2012

city: Nagano

first: Toshihide

last: Mizoguchi

address: 1780 Gobara, Hiro-oka, Shiojiri

institute: Matsumoto Dental Univ.

summary: Osteoclasts are derived from the monocyte/macrophage lineage, but little is known about osteoclast precursors in circulation. Bone marrow cells were subdivided into three populations; RANKhighFmslow, RANKhighFmshigh and RANKlowFmshigh. GeneChip analysis confirmed that the expression levels of monocyte-macrophage markers such as Emr1 (F4/80), Itgam (CD11b) and Csf1 (c-Fms) were lower in the RANKhighFmslow than RANKlowFmshigh population. In contrast, cells in the RANKhighFmslow population expressed higher levels of osteoclast markers such as Car ll (carbonic anhydrase ll), Mmp9 (matrix metalloproteinase 9), Acp5 (acid phosphatase 5) and Tfrc (transferrin receptor). These results suggest that RANKhighFmslow cells express few of the phenotypes of monocytes, and their differentiation into osteoclasts occurs at a slightly more advanced stage than that of the RANKlowFmshigh population.

overall_design: RANKhighFmslow cells and RANKlowFmshigh cells were isolated from bone marrow in ddY mice by FACS (Fluorescent activated cell sorting). Differential expression levels of mRNA were determined by GeneChip analysis.

first: Akinori

last: Muto

first: Nobuyuki

last: Udagawa

first: Susumu

last: Ito

first: Ichiro

last: Kawahara

first: Yoshimitsu

last: Abiko

first: Atsushi

last: Arai

first: Suguru

last: Harada

first: Yasuhiro

last: Kobayashi

first: Yuko

last: Nakamichi

first: Josef

last: Penninger

last: Noguchi

first: Naoyuki

last: Takahashi


title: Hfq virulence regulation in enterohemorhagic Escherichia coli O157:H7 strain 86-24

status: Public on Jan 06 2012

city: Baltimore

first: David

last: Rasko

state: MD

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

summary: Escherichia coli O157:H7 is a food-borne pathogen that causes bloody diarrhea and hemolytic uremic syndrome. Hfq is an sRNA chaperone protein that is involved in post-transcriptional regulation of virulence genes in pathogenic bacteria. In EHEC strain EDL933, Hfq acts a negative regulator of the locus of enterocyte effacement (LEE) that encodes most of the proteins involved in type three secretion and attaching and effacing lesions. We deleted hfq in E. coli O157:H7 strain 86-24 and compared global transcription profiles of the hfq mutant to the wild type strain in exponential growth phase. Deletion of hfq affected transcription of genes common to nonpathogenic and pathogenic strains of E. coli as well as pathogen-specific genes. Downregulated genes in the hfq mutant included ler as well as genes encoded in LEE2-5 that encode for type three secretion and AE lesion formation. Decreased expression of the LEE genes in the hfq mutant occurred at mid-, late, and stationary growth phases in both LB and DMEM media as detected by qRT-PCR. We also confirmed decreased regulation of the LEE genes by examining secreted proteins and AE lesion formation by the hfq mutant and WT strains. Deletion of hfq also caused decreased expression of the two-component system qseBC involved in inter-kingdom signaling and virulence gene regulation in EHEC as well as an increase in stx2AB expression that encodes for the deadly Shiga toxin. Altogether, these data indicate that Hfq plays a different regulatory role in EHEC 86-24 from what has been reported for EHEC strain EDL933 and that the role of Hfq in EHEC virulence regulation extends beyond the LEE.

overall_design: Comparison of transcriptional regulation of the WT 86-24 isolate and the hfq mutant for the identification of regulated targets that were followed up by functional analysis.

first: M

last: Kendall

first: D

first: V

last: Sperandio


title: MOLECULAR CHARACTERIZATION OF LIVER ALLOGRAFTS FROM OPERATIONALLY TOLERANT TRANSPLANT RECIPIENTS

first: Juanjo

last: Lozano

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

overall_design: Refer to individual Series


title: RET fusion genes, BCR-RET and FGFR1OP-RET, are associated with chronic myelomonocytic leukemia, display sensitivity to Sorafenib, an inhibitor of tyrosine-kinase activity and enhance monocytic differentiation

city: TOULOUSE

first: Naïs

last: PRADE

address: Place du Dr. Baylac

country: France

institute: CHU Purpan

summary: Myeloproliferative neoplasms are frequently associated with aberrant constitutive tyrosine kinase (TK) activity resulting from point mutations or chimaeric fusion genes, such as BCR ABL1 or JAK2 V617F. We report here for the first time in hematological malignancies, two novel fusion genes involving the TK RET, BCR-RET and FGFR1OP-RET, in chronic myelo monocytic leukemia (CMML) cases. The two RET fusion genes lead to the aberrant activation of RET, are able to transform hematopoietic cells and skew the hematopoietic differentiation program towards the monocytic/macrophage lineage. We also report that the BCR-RET fusion protein is insensitive to Imatinib but sensitive to Sorafenib in vivo. CMML is an hematopoietic malignancy associated with the frequent activation of the RAS pathway. The RET fusion genes seems to constitutively mimic the same signaling pathway than RAS mutations. Overall, the RET fusion genes behaviors in the monocytic lineage underlie the role of the normal RET TK activity during the physiological monocytic differentiation.

overall_design: We analysed BAF/3 cells infected by BCR-RET, FGFR1OP-RET or BCR-ABL1P210 fusion genes retroviruses and sorted out using EGFP fluorescence, with Affymetrix GeneChip MouseGene 1.0 ST platform.

first: Eric

last: Delabesse

last: Prade


title: Microarray Expression Data from Haematopoietic Differentiated Human Embryonic Stem Cells

city: Newcastle upon Tyne

first: Sun

last: Yung

address: Central Parkway

department: Institute of Genetic Medicine

country: United Kingdom

institute: Newcastle University

summary:
The underlying mechanisms which are responsible and govern early haematopoietic differentiation during development  are poorly understood. Gene expression comparison between pluripotent human embryonic stem cells and earliest haematopoietic progenitors may reveal novel transcripts and pathways and provide crucial insight into early haematopoietic lineage specification and development.
Understanding of transcriptional cues that direct differentiation of human embryonic stem cells (hESC) to defined and functional cell types is essential for their future clinical applications. In this study we have undertaken a comparative transcriptional approach of haematopoietic progenitors derived from hESC at various stages of a feeder and serum free differentiation method and have shown that the largest transcriptional changes occur during the first four days of differentiation. Data mining based on molecular function pointed to RhoGTPase signalling as key regulator of this differentiation. Inhibition of this pathway using a chemical inhibitor (Y26732) resulted in a significant downregulation of haematopoietic progenitors throughout the differentiation window, thus uncovering a previously unappreciated role for RhoGTPase signalling in differentiation of hESC to haematopoietic lineages.

overall_design: There are a total of 4 samples within this microarray experiment with 2 biological replicates for each sample.  Pluripotent human embryonic stem cells (day 0) underwent  haematopoietic differentiation and  at various stages of development (day 4, day 6, day8) differentiated  cells were FACS sorted for two key haemangioblast markers, CD31 and KDR.

first: Maria

last: Ledran

first: Inmaculada

last: Moreno-Gimeno

first: Ana

last: Conesa

last: Montenero

first: Joaquin

last: Dopazo

first: Nicholas

last: Slater

first: Iliana

last: Paraskevopoulou

first: Viviana

last: Bisbal

first: Deborah

last: Burks

first: Mauro

last: Santibanez-Coref

first: Ruben

last: Moreno

first: Joanne

last: Mountford

first: Lyle

last: Armstrong

first: Majlinda

last: Lako


title: Targeted ErbB3 loss in mammary organoids harvested from ErbB3 DOX-KO mice +/- DOX treatment

status: Public on Jan 04 2012

city: Nashville

first: Justin

last: Balko

state: TN

address: 777 Preston Research Building

department: Medicine

institute: Vanderbilt University

summary: Mammary organoids harvested from ErbB3 DOX-KO mice, which utilize MMTV-Cre transgene expression in the LE to cause genomic recombination at floxed ErbB3 alleles in ErbB3FL/FL were cultured in the presence or absence of doxycycline to induce ErbB3 loss.  The gene expression shift following DOX-induced ErbB3 loss in the 3D organoids was examined by microarray.

overall_design: Gene expression patterns were interrogated in mammary organoids from ErbB3 inducible-knockout mice cultured in the presence of absence of doxycycline.  Three biological replicates of the experiment were performed, resulting in a total of 6 samples (3 treatment, 3 control).

first: Rebecca

middle: S

last: Cook


title: Simple and efficient transcriptome profiling from a single embryo

city: Philadelphia

first: Don

last: Baldwin

state: PA

address: 277 John Morgan, 3620 Hamilton Walk

department: Pathology and Lab Medicine

institute: University of Pennsylvania

summary: Measuring the global gene expression pattern in a single cell has been technically challenging, but is potentially very useful for understanding variation in biological processes between cells and for studying gene regulation during early embryo development with single cell resolution. To advance these applications, multiple systems for single-cell RNA extraction in addition to crude cell lysis followed by RNA profiling were examined and used for genomic data analysis. Our results indicate that some of these methods are suitable for analyzing even a portion of the total RNA from a single oocyte or embryo, with low variance among technical replicates across a wide dynamic range of expression. These methods will not only be helpful for genomic and epigenetic research to identify regulatory mechanisms of early development and molecular signatures of embryo classes, but can also provide great potential for clinical analysis of small biopsy samples or pre-implantation genetic disease screening.

overall_design: RNA from single mouse oocytes was purified using Qiagen Rneasy Mini or Arcturus PicoPure kits. Crude lysates of single oocytes were also prepared in NuGEN direct lysis buffer.  Three replicate oocytes for each of the three sample preparation methods were used.  Total RNA was amplified by NuGEN Ovation One-Direct ribo-SPIA, cDNA products were biotinylated, and labeled targets were hybridized to Affymetrix Mouse Gene 1.0ST Arrays.

first: Fanyi

last: Zeng

first: Jun

last: Ma

first: Xiaoshuang

last: Yan


title: Expression changes in Yy1 knock down mouse embryonic stem cells

first: Diego

last: Pasini

address: Via Adamello, 16

department: Experimental Oncology

institute: European Institute of Oncology

summary: We have determined the global gene expression upon loss of function of the Yy1 transcription factor in mouse embryonic stem cells

overall_design: Total RNA was extracted from ES cells transiently transfected with yy1-specific or scrampled-control siRNA oligos 48 hr post-transfection.

first: Pietro

last: Vella


title: mRNA decay analysis in the mouse myoblast cell line, C2C12 cells treated with conrtol-, Cugbp1- or Mbnl1-siRNA

status: Public on Jan 03 2012

city: Nagoya

first: Akio

last: Masuda

state: Aichi

address: 65 tsurumai-cho, Showa-ku

institute: Nagoya University Graduate School of Medicine

summary:
CUGBP1 and MBNL1 are developmentally regulated RNA-binding proteins that are causally associated with myotonic dystrophy type 1. Using HITS-CLIP anlysis, we found CUGBP1 and MBNL1 preferentially bind to alternatively spliced introns and exons, as well as to the 3' UTRs.
To analyze more directly the role of CUGBP1/MBNL1 binding to the 3’ UTR, we performed global analysis of mRNA stability in C2C12 cells using expression arrays, and found that CUGBP1 and MBNL1 regulate decay of endogenous mRNAs.

overall_design: We analyzed total RNA of C2C12 cells treated with control-, Cugbp1- or Mbnl1-siRNA. We analyzed 3 time points after addition of actionmycin D (0, 2.5, 5 hours).

first: Kinji

last: Ohno


title: Expression array of peripheral neuro-ectodermal cell lines

status: Public on Jan 01 2012

city: Rotterdam

first: Floor

last: Duijkers

address: Dr. Molewaterplein 50-60 Ee15-02

department: Pediatric Oncology-Hematology

country: Netherlands

institute: Erasmus MC

summary:
To study differentially expressed genes in neuro-ectodermal cell lines
MYCN amplification (NMA) is the most important prognostic factor in neuroblastoma (NBL) patients, however 70% of advanced stage NBL are non-NMA and lack known driving oncogenic events. Gene expression profiles (HU133plus2.0 arrays, Affymetrix) of 17 NBL and 5 peripheral neuro-ectodermal cell lines were used to identify potential subgroups of NBL cell lines with a distinct gene signature. One group of non-NMA NBL cell lines was identified with a distinct gene expression profile and characterized by high expression of AXL. AXL is a tyrosine kinase receptor which plays a role in the metastatic process of cancer. We hypothesized that AXL contributes to the metastasizing potential of non-NMA NBL and tested if AXL silencing diminishes malignant properties of high AXL expressing cell lines. AXL was silenced in two non-NMA NBL cell lines by using a lentiviral shRNA construct that was able to transduce these cell lines with >90% infection efficiency. AXL mRNA expression level was efficiently knocked-down resulting in a severe decrease of migration of AXL positive cell lines GI-M-EN and SH-EP-2, and decreased invasion of GI-M-EN. Morphologically, AXL knockdown induced more rounded cells with a loss of contact. Intracellularly, we observed induction of stress fibers (immunofluorescence F-actin) in GI-M-EN. These changes in cytoskelet were associated with decreased migration.  No effects were observed for cell proliferation, apoptosis or downstream pathways. In conclusion, AXL is identified as a possible mediator of NBL metastasis.

overall_design: Arrays were performed with 5 different PNET cell lines, which were used as controls for 17 NBL cell lines (GSE22771)


title: Gene expression changes in the human diaphragm following cardiothoracic surgery

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

summary: It is unknown how soon the diaphragm begins to start the process of atrophy following the start of MV. We hypothesized that genes responsible for maintaining diaphragmatic contractile function, stress response, energy transduction would be altered over the course of a 5 hour cardiothoracic surgery.

overall_design: Two diaphragm biopsies were obtained from 5 male patients (~67 +/- 11 years) undergoing cardiothoracic surgery. The first biopsy was obtained as soon as the diaphragm was exposed; the second biopsy was obtained as late in the surgery as possible (4.9 +/- 1.8 hours). We profiled mRNA from the 5 pairs of muscle biopsies with a microarray (Affymetrix Human Genome U133 Plus 2.0).

first: Tseng-Tien

last: Huang

first: Harshavardhan

last: Deoghare

first: Barbara

last: Smith

first: Thomas

last: Beaver

first: Henry

last: Baker

first: A

middle: D

last: Martin


title: Gene expression profiling after induction of WTX in HEK293 cells

city: Charlestown

first: Woo

middle: Jae

last: Kim

state: Ma

department: Cancer Center

institute: Massachusetts General Hospital

summary: WTX encodes a tumor suppressor, frequently inactivated in Wilms tumor, with both plasma membrane and nuclear localization. WTX has been implicated in beta-catenin turnover, but its effect on nuclear proteins is unknown. We report an interaction between WTX and p53, derived from the unexpected observation of WTX, p53 and E1B 55K colocalization within the characteristic cytoplasmic body of adenovirus-transformed kidney cells. In other cells without adenovirus expression, the C-terminal domain of WTX binds to the DNA binding domain of p53, enhances its binding to CBP, and increases CBP/p300-mediated acetylation of p53 at Lys 382. WTX knockdown accelerates CBP/p300 protein turnover and attenuates this modification of p53. In p53-reconstitution experiments, cell cycle arrest, apoptosis, and p53-target gene expression are suppressed by depletion of WTX. Together, these results suggest that WTX modulates p53 function, in part through regulation of its activator CBP/p300.

overall_design: Affymetrix microarray gene expression profiling was performed to identify differentially expressed genes following overexpression of WTX in HEK293 clones after 12 hour induction of WTX

first: Miguel

middle: N

last: Rivera

first: Erik

last: Coffman

first: Daniel

last: Haber


title: Modeling lethal prostate cancer variant with small cell carcinoma features [expression profile]

city: Houston

first: Jiexin

last: Zhang

state: TX

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

summary:
Purpose: Small-cell prostate carcinoma (SCPC) morphology predicts for a distinct clinical behavior, resistance to androgen ablation, and frequent but short responses to chemotherapy. The model systems we report reflect the biology of the human disease and can be used to improve our understanding of SCPC and to develop new therapeutic strategies for it.
Experimental Design: We developed a set of CRPC xenografts and examined their fidelity to their human tumors of origin. We compared the expression and genomic profiles of SCPC and large cell neuroendocrine carcinoma (LCNEC) xenografts to those of typical prostate adenocarcinoma xenografts and used a panel of 60 human tumors to validate our findings using immunohistochemistry.
Results: We show that SCPC and LCNEC xenograft models retain high fidelity to their human tumors of origin and are characterized by a marked upregulation of UBE2C and other M-phase cell cycle genes in the absence of AR, retinoblastoma (RB1) and cyclin D1 (CCND1) expression and confirm these findings in a panel of CRPC patients’ samples. In addition, array comparative genomic hybridization of the xenografts showed that the SCPC/LCNEC tumors display more copy number variations than the adenocarcinoma counterparts and that there is amplification of the UBE2C locus and microdeletions of RB1 in a subset of these, but no AR nor CCND1 deletions. Moreover, the AR, RB1, and CCND1 promoters showed no CpG methylation in the SCPC xenografts.
Conclusion: Modeling human prostate cancer with xenografts allows in-depth and detailed studies of its underlying biology. The detailed clinical annotation of the donor tumors enables associations of anticipated relevance to be made. Futures studies in the xenografts will address the functional significance of the findings.

overall_design: 22 samples were analysed, that included MDA PCa 79 (n = 3), 117-9 (n = 3), 130 (n = 2), 144-4 (n = 4), 144-13 (n = 5), 146-10 (n = 3), 155-2 (n = 1), and 155-12 (n = 1). MDA PCA 79, 117-9 and 130 samples had the pathologic characteristics of prostate adenocarcinoma and were compared against MDA PCA 144-4, 144-13, 146-10 and 155-12 that have the pathologic features of prostate small cell/ large cell neuroendocrine carcinoma

first: Ana

last: Aparicio

first: Sankar

last: Maity

first: Vassiliki

last: Tzelepi

first: Lu

last: Jing-Fang

first: Brittany

last: Kleb

first: Nora

last: Navone

first: Shoudan

last: Liang


title: Modeling lethal prostate cancer variant with small cell carcinoma features

type: Genome variation profiling by genome tiling array


title: Time-course effect of estradiol and estradiol-BSA on early gene expression in T47D cells

city: Heraklion

first: George

last: Notas

address: PO BOX 2208

country: Greece

institute: University of Crete

summary: Estrogens have been reported to activate several processes via membrane binding to either classic estrogen receptors (ERs) or GPR30. We have used either estradiol or BSA-conjugated estradiol in order to initiate membrane-initiated actions and ICI 172,780 (ICI) or G15 to explore ER- and GPR30-related transcription. Our results show that the majority of G15-inhibited transcription is depending on ERs, as it is also inhibited by ICI. However, a small number of transcripts, related to specific actions/pathways is either exclusively inhibited by G15, providing evidence about a specific GPR30 signature, or not inhibited by ICI or G15 suggesting the existence of another, yet unidentified estrogen receptor.

overall_design: Cells after a 4h incubation with medium containing 10% charcoal stripped FBS were incubated with or without E2-BSA (10-6M) in the presence or absence of specific antagonists, in RPMI 1640 supplemented with 10% charcoal stripped FBS, for 3 hours. Total RNA was isolated using Nucleospin II columns (Macheray-Nagel, Dttren, Germany), according to the manufacturer’s instructions. RNA was labeled and hybridized according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual), using the HGU133A plus 2 chip, analyzing a total of 54675 transcripts. Signals were detected by an Affymetrix microarray chip reader.

first: Marilena

last: Kampa

first: Elias

last: Castanas


title: Expression data from human HT-29 immortalized colorectal adenocarcinoma cell line

city: Budapest

first: Wichmann

last: Barna

address: Szentkirály

country: Hungary

institute: SOTE

summary: Gene expression profiling for identification of genes regulated by DNA methylation

overall_design: Total RNA was extracted from HT-29 cell line was hybridized on Affymetrix HGU133 Plus 2.0 microarrays

first: Sandor

last: Spisak

first: Orsolya

last: Galamb

first: Barna

last: Wichmann

first: Bela

last: Molnar


title: Time-course effect of estradiol and estradiol-BSA on early gene expression in SKBR3 cells

overall_design: Cells after a 4h incubation with medium containing 10% charcoal stripped FBS were incubated with or without E2-BSA (10-6M) in the presence or absence of specific antagonists, in McCoys's 5A medium supplemented with 10% charcoal stripped FBS, for 3 hours. Total RNA was isolated using Nucleospin II columns (Macheray-Nagel, Dttren, Germany), according to the manufacturer’s instructions. RNA was labeled and hybridized according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual), using the HGU133A plus 2 chip, analyzing a total of 54675 transcripts. Signals were detected by an Affymetrix microarray chip reader.


title: Expression data comparing Huh7 cells transduced with shRNA CD24 (knockdown) or non-target control

city: Hong Kong

first: Kin Wah

last: Lee

address: 21 Sassoon Road

country: China

institute: The University of Hong Kong

summary:
To identify CD24 signaling pathway
Affymetrix Human Genome U133 Plus GeneChip 2.0

overall_design: shRNA CD24 (knockdown) or non-target control (NTC) was stably transduced into Huh7 HCC cells by lentiviral approach

first: Terence


title: Time-course effect of estradiol and estradiol-BSA on early gene expression in MDA-MB-231 cells


title: Expression data from diet-induced obesity Oma1-deficient mice.

city: Oviedo

first: Jose

last: Freije

address: C/ Fernando Bongera s/n

institute: Universidad de Oviedo

summary: Transriptional profiling of white adipose tissue extracted from obese mice.

overall_design: White adipose tissues were extrated from Oma1-deficient mouse and control after 20 weeks of diet-induced obesity. RNA were extracted and hybridated with Mouse Gene 1.0 ST from Affymetrix microarrays.

first: Pedro

last: Quirós

first: Carlos

last: López-Otín


title: Time-course effect of estradiol and estradiol-BSA on early gene expression


title: Subcutaneous and omental white adipose tissue biopsies analysed from three obese patients

city: Aberdeen

first: Claus

last: Mayer

address: Greenburn Road

institute: Biomathematics & Statistics Scotland

summary: The objective was to characterize differences in the secretome of human omental compared with subcutaneous adipose tissue using global gene expression profiling. Gene expression was measured using Affymetrix microarrays in subcutaneous and omental adipose tissue (n=3 independent subjects; 6 arrays). Predictive bioinformatic algorithms were employed to identify those differentially expressed genes that code for secreted proteins and to identify common pathways between these proteins.  All patients provided informed written consent before inclusion in the study which was approved by the North of Scotland Research Ethics Committee (NOSREC).

overall_design:
The subcutaneous and omental white adipose tissue biopsies were analysed from three obese patients (BMI 39.1+/-1.9 kg/m2; age 36 +/- 8 years) who had fasted overnight.
Subcutaneous and omental white adipose tissue biopsies were taken at the time of surgery for vertical banded gastroplasty from n=3 independent subjects who had fasted overnight. (6 arrays).

Adipose tissue samples were obtained within 5 minutes of the tissue being extracted from the patients and frozen immediately in liquid nitrogen. Subjects had fasted overnight prior to surgery. Total RNA was extracted using the RNeasy Lipid tissue mini kit followed by incubation with RNase free DNase (Qiagen, Crawley, West Sussex) for DNA-free RNA, following the manufacturer's instructions (Qiagen, Crawley, West Sussex). RNA was quantified on the Agilent 2100 Bioanalyser (Agilent Technologies, South Queensferry, West Lothian). This also shows the quality of the RNA extracted from the tissues. Only RNA showing no degradation (RIN greater than 9.0) was processed further.

The DNA-free RNA from the subcutaneous and omental adipose tissue samples from the patients was then sent to a commercial company for analyses. The RNA from three volunteers (6 arrays ) was fragmented and hybridised to Human Affymetrix U133 plus 2 (Santa Clara, CA) gene chips  following the Affymetrix protocol by the MRC Geneservice (MRC HGMP Resource centre, Babraham, Cambridge). Briefly, the Affymetrix one-cycle target labelling and control reagents were used to synthesize Biotin-labelled cRNA. The concentration of the cRNA was measured using a Nanodrop (Thermoscientific) and Agilent bioanalyser to rule out the possibility that only very short cRNA products were formed. This could have caused a 3’-5’ bias and influenced the data analysis. Approximately 20µg cRNA was used for further fragmentation and finally 10µg was used for the hybridisations. The Affymetrix protocols were followed for the hybridisations, washing, staining and scanning of the chips

first: Nigel

last: Hoggard

first: Morevn

last: Cruickshank

first: Kim

last: Moar

first: Shabina

last: Bashir

first: Claus-Dieter


title: Expression data from human omental and subcutaneous adipose tissue taken from volunteers undergoing bariatric surgery

overall_design: Refer to individual Series


title: Expression data from normal human and unstable angina patient.

status: Public on Dec 31 2011

city: Beijing

first: Xiaojuan

last: Ma

address: 1 Xiyuan Caochang, Haidian District

department: Department of Cardiovascular Disease

institute: Xiyuan Hospital, China Academy of Chinese Medicine Sciences

summary: 20 patients with unstable angina were divided into patient group by using coronary angiography. The sex- and age-matched healthy individuals were enrolled as control group. Venous bloods were collected for extracting RNA.

overall_design: We used the Human Genome U133 plus 2.0 genechip produced by Affymetrix to detail the global gene expression in blood sample from normal human and unstable angina patient.  1 control and 2 test samples.

first: Ma

last: Xiao-juan

first: Yin

last: Hui-jun


title: Human colon epithelial cells treated with Clostridium difficile Toxins A and B

city: Charlottesville

first: Kevin

middle: Michael

last: D'Auria

state: VA

address: 415 Lane Road, Room 2041

department: Biomedical Engineering

institute: University of Virginia

summary: Toxin A and B from Clostridium difficile are the primary virulence factors in Clostridium difficile disease. The changes in gene transcription of human colon epithelial cells were investigated in vitro in order to better understand the many effects of both toxins.

overall_design: HCT-8 cells were treated with 100 ng/ml of either Toxin A or B (TcdA or TcdB). RNA was isolated 2, 6, and 24 hours after addition of toxin from untreated and toxin-treated cells.

first: Gina

last: Donato

first: Mary

last: Gray

first: Glynis

last: Kolling

first: Cirle

last: Warren

first: Jason

last: Papin

first: Erik

last: Hewlett


title: Gene expression analysis of FHL2-knockout mouse liver

first: Chor Fung

last: NG

address: Shatin, New Territories

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary:
FHL2 is known to be deregulated in liver cancer. In the present study, microarray gene expression profiling was performed to identify the genes regulated downstream of FHL2
In this dataset, we compared the RNA samples from livers of FHL2 knockout mice and those of wild-type (WT) mice.

overall_design: FHL2 knockout mice was initially generated by Chu et al. 2000. RNA from three mice per group (male, age: 10-11 weeks) were pooled and the two groups were subjected to analysis .

first: Chor-Fung

last: Ng

first: Stephen

last: Tsui


title: Epigenetic repression of cardiac progenitor gene expression by Ezh2 is required for postnatal cardiac homeostasis

city: San Francisco

first: Alisha

last: Holloway

address: 1650 Owens Street

institute: Gladstone Institutes

summary: Adult-onset diseases can be associated with in utero events, but mechanisms for such temporally distant dysregulation of organ function remain unknown.  The polycomb histone methyltransferase, Ezh2, stabilizes transcription by depositing repressive histone marks during development that persist into adulthood, but the function of Ezh2-mediated transcriptional stability in postnatal organ homeostasis is not understood. Here, we show that Ezh2 stabilizes the postnatal cardiac gene expression program and prevents cardiac pathology, primarily by repressing the homeodomain transcription factor Six1 in differentiating cardiac progenitors. Loss of Ezh2 in embryonic cardiac progenitors, but not in differentiated cardiomyocytes, resulted in postnatal cardiac pathology, including cardiomyocyte hypertrophy and fibrosis. Loss of Ezh2 caused broad derepression of skeletal muscle genes, including the homeodomain transcription factor Six1, which is expressed in cardiac progenitors but is normally silenced upon cardiac differentiation. Many of the deregulated genes are direct Six1 targets, implying a critical requirement for stable repression of Six1 in cardiac myocytes. Indeed, upon de-repression, Six1 promotes cardiac pathology, as it was sufficient to induce cardiac hypertrophy. Furthermore, genetic reduction of Six1 levels almost completely rescued the pathology of Ezh2-deficient hearts. Thus, repression of a single transcription factor in cardiac progenitors by Ezh2 is essential for stability of the adult heart gene expression program and homeostasis. Our results suggest that epigenetic dysregulation during discrete developmental windows can predispose to adult disease and dysregulated stress responses.

overall_design: Global gene expression profiles of Ezh2-deficient hearts. The right ventricle and the interventricular septum of five wild type (Ezh2f/f) and four Ezh2-deficient (Ezh2f/f;Mef2cAHF::Cre) mice were analyzed.

first: Benoit

last: Bruneau

first: Paul

last: Delgado


title: Ribavirin Treated Huh7.5.1 Cells

city: Bethesda

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: The combination of peginterferon and ribavirin is the standard treatment for chronic hepatitis C.  Our recent clinical study suggests that ribavirin augments the induction of interferon stimulated genes (ISGs) in patients treated for HCV infection [1].  In order to further characterize the mechanisms of action of ribavirin, we examined the effect of ribavirin treatment on ISG induction in cell culture. In addition, the effect of ribavirin on infectious HCV cell culture systems was also studied. Similar to interferon-alpha, ribavirin potently inhibits JFH-1 infection of Huh7.5.1 cells in a dose-dependent manner, which spans the physiological concentration of ribavirin in vivo. Microarray analysis and subsequent quantitative PCR assays demonstrated that ribavirin treatment resulted in the induction of a distinct set of ISGs. These ISGs, including IRF7 and IRF9 are known to play an important role in anti-HCV responses. When ribavirin is used in conjunction with interferon, induction of specific ISGs is synergistic when compared to either drug applied separately. Direct up-regulation of these antiviral genes by ribavirin is mediated by a novel mechanism different from those associated with interferon signaling and intracellular double stranded RNA sensing pathways such as RIG-I and MDA5. RNA interference studies excluded the activation of the Toll-like receptor and NF-KappaB pathways in the action of ribavirin. In conclusion, our study suggests that ribavirin, acting via a novel innate mechanism, potentiates the anti-HCV effect of interferon. Understanding the mechanism of action of ribavirin would be valuable in identifying novel antivirals.

overall_design: RNA from three samples were treated with Ribavirin and compared to three PBS treated samples

first: Emmanuel

last: Thomas

first: Jordan

last: Feld

first: Qisheng

last: Li

first: Zongyi

last: Hu

first: Michael

last: Fried

first: Jake

last: Liang


title: Time-course effect of estradiol and estradiol-BSA on early gene expression in MCF-7 cells

first: George

last: Notas

overall_design: Cells after a 4h incubation with medium containing 10% charcoal stripped FBS were incubated with or without E2-BSA (10-6M) in the presence or absence of specific antagonists, in DMEM/F12 (1:1) supplemented with 10% charcoal stripped FBS, for 3 hours. Total RNA was isolated using Nucleospin II columns (Macheray-Nagel, Dttren, Germany), according to the manufacturer’s instructions. RNA was labeled and hybridized according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual), using the HGU133A plus 2 chip, analyzing a total of 54675 transcripts. Signals were detected by an Affymetrix microarray chip reader.

first: Marilena

last: Kampa

first: Elias

last: Castanas


title: EARLY DETECTION OF LUNG CANCER BY MOLECULAR MARKERS IN ENDOBRONCHIAL LINING FLUID

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

institute: German Cancer Research Center and National Center of Tumor Diseases

type:
Expression profiling by array
Expression profiling by RT-PCR

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


title: Expression gene (angiocrine) profile of various activated endothelial cells

city: New York

first: Bisen

last: Ding

state: NY

address: 1300 York Avenue

institute: Cornell Medical College

summary: Endothelial cells were transduced with different genes modulating signaling pathways and compared to GFP transduced control group to identify changes in the expression of the angiocrine factors.

overall_design: The experiment compared endothelial genetic changes upon Akt, MAP kinase and PymT activation.

first: Hideki

last: Kobayashi

first: Jason

last: Butler

first: Rebekah

last: O’Donnell

first: Mariko

first: Bi-Sen

first: Bryant

last: Bonner

first: Koji

last: Shido

first: Daniel

last: Nolan

first: Laura

last: Benjamin

first: Vi

last: Chiu

first: Shahin

last: Rafii


title: Comparison of post-mortem tissue from Brodman Brain BA22 region between schizophrenic and control patients

city: Stevenage

first: Julie

last: Huxley-Jones

state: Hertfordshire

address: Gunnels Wood Road

department: Computational Biology

institute: GlaxoSmithKline Pharmaceuticals

summary:
Transcriptional analysis of the superior temporal cortex (BA22) in schizophrenia: Pathway insight into disease pathology and drug development
Schizophrenia is a highly debilitating psychiatric disorder which is known to have heritable genetic and environmental components. To gain some insight into the mechanisms underpinning both positive and negative symptoms of the disease, we determined the genome wide expression of mRNA transcripts in post-mortem tissue from the superior temporal cortex (Brodmann Area 22, BA22) in schizophrenic and control patients. The BA22 region is known to mediate the positive pathophysiology of schizophrenia; we compared this to the anterior prefrontal cortex (BA10) from the same subjects, which is known to mediate negative symptoms. Following adjustments for confounding clinical, sample and experimental sources of variation, we carried out gene set enrichment analysis in each region using pathway data. We identified an over-representation of genes involved in cytoskeletal remodelling, neurodevelopment, cell adhesion, cellular signalling, neurotransmission and autophagy. Collectively our analysis indicates a disruption of processes underpinning synaptic plasticity in both regions. Region-specific changes support the dysregulation of distinct pathways in the BA10 and BA22 regions. This may highlight new therapeutic opportunities to treat both negative and positive symptoms of the disease.

overall_design: Post-mortem derived BA22 tissue from schizophrenic and control patients were compared. Age, gender, post-mortem delay and pH of brain lysates data were also captured.

first: Michael

middle: R

last: Barnes

first: Peter

last: Maycox

first: Mark

last: Lennon

first: Amy

last: Molesworth

first: Fiona

last: Kelly

first: Stewart

last: Bates

first: Adam

last: Taylor

first: Juliet

last: Reid

first: Neil

last: Jones

first: Jorn

last: Schroeder

first: Carol

last: Scorer

first: Ceri

last: Davies

first: Jim

last: Hagan

first: James

last: Kew

first: Claire

last: Angelinetta

first: Tariq

last: Akbar

first: Steven

last: Hirsch

first: Ann

last: Mortimer

first: Thomas

first: Jackie

last: deBelleroche


title: Expression data from G9a overexpression and knockdown lung cancer cell lines

city: Taipei

first: Min-Liang

last: Kuo

address: No. 1,Section 1, Jen-Ai Road

country: Taiwan

institute: National Taiwan University

summary:
G9a is the major mammalian H3-K9 methyltransferase that targets euchromatic regionsand is essential for murine embryogenesis . We demonstrate that G9a is endowed with methyltransferase activity to concomitantly repress the downstream effector Ep-CAM, thereby promoting the invasion step of the invasion-metastasis cascade.
We used microarrays to detail the G9a regulated gene expression underlying invasion-metastasis cascade and identified distinct classes of up-regulated genes during this process.

overall_design: Lung adenocarcinoma cells with G9a knockdown or overexpression were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Michael

last: Hsiao


title: Transcriptomes From the Deep Cones During FIbroproliferative Cutaneous Healing in the Duroc/Yorkshire Porcine Model

city: Ames

first: Oliver

last: Couture

state: IA

address: 2255 Kildee

institute: Iowa State University

summary: The goal was to obtain the differential transcriptome in the deep cones between shallow and deep wounds and between the Yorkshire and Duroc breeds over time.

sample_organism:
Homo sapiens
Sus scrofa

platform_organism:
Homo sapiens
Sus scrofa

overall_design: We made shallow and deep wounds on the backs of 3 Yorkshire and 3 Duroc pigs, biopsied the wounds at 1 2 3 12 and 20 weeks, extracted and amplified the RNA from the deep cones, and hybridized the Affymetrix GeneChip®. We compared wound depth by breed over time; the system included 3 factors (depth, breed and time). The system also included repeated measures since the same pigs were used at each time. It also included paired data since the shallow and deep wounds compared were located on the same pig.

first: Loren

last: Engrav


title: Gene expression analysis of TGF-beta signaling-disrupting gastric cancer cell line 2MLN

status: Public on Dec 30 2011

city: Bunkyo-ku

first: Mitsunobu

last: Kano

state: Tokyo

address: Hongo 7-3-1

department: Graduate School of Medicine

institute: The University of Tokyo

summary: Diffuse-type gastric carcinoma is a poor-prognostic cancer with high expression of transforming growth factor (TGF)-β and thick stromal fibrosis. However, detailed investigations on the roles of TGF-β signaling in diffuse-type gastric carcinoma have not been performed. We generated two diffuse-type gastric carcinoma cell lines, dominant-negative TGF-β type II receptor expressing cells (2MLN-dnTβRII) and GFP-expressing cells (2MLN-GFP). Cells were subcutaneously or orthotopically injected into nude mice. Although dnTβRII did not affect the growth of OCUM-2MLN in vitro, it accelerated the growth of subcutaneously or orthotopically transplanted tumors in vivo. By microarray analysis, we found gene expression of TSP-1, an angiogenic inhibitor, was down-regulated in dnTβRII tumors. This results suggested disruption of TGF-β signaling in diffuse-type gastric carcinoma cells leads to alteration of tumor microenvironment and acceleration of tumor growth.

overall_design: We generated two OCUM-2MLN-derived gastric carcinoma cell lines; 2MLN-dnTβRII, which expresses dominant negative form of TβRII, and control 2MLN-GFP, which expresses GFP. The transplanted tumors of these cell lines were subjected to gene expression analysis with Affymetrix U133 plus2 arrays.

first: Akiyoshi

last: Komuro

first: Masakazu

last: Yashiro

first: Caname

last: Iwata

first: Yasuyuki

last: Morishita

first: Erik

last: Johansson

first: Yoshiko

last: Matsumoto

first: Akira

last: Watanabe

first: Hiroyuki

last: Aburatani

first: Kunihiko

last: Kiyono

first: Yo-taro

last: Shirai

first: Hiroshi

middle: I

last: Suzuki

first: Kosei

last: Hirakawa

first: Kohei

last: Miyazono


title: p38alfa and ATF2 act differentially depending on DUSP1 expression in NCSCL in response to cisplatin

city: Pamplona

first: Eva

last: Bandres

address: Avda Pio XII, 55

department: Cancer Research Program

institute: Center for Applied Medical Research (CIMA), University of Navarra

summary:
DUSP1 is involved in different cellular pathways including cancer cell proliferation, angiogenesis, invasion and resistance to chemotherapy. To gain insight into the cellular signaling pathways involving DUSP1 actions and the response to Cisplatin (CDDP) in non small cell lung cancer (NSCLC), we have used a double strategy that combines microarray and SiRNA technology. This strategy provided a differential expression profile of genes involved in CDDP response in NSCLC cell line regulated by DUSP1 using H460 and H460cri and a time course to CDDP.

KEYWORDS: Expression profiling by array in cells with genetic modification in response to CCDP treatment

overall_design: The human non small lung cancer cell line H460 used in this study was from ATCC (American Type Culture Collection). The cell line was maintained in RPMI (Gibco, Invitrogen) supplemented with 10% bovine serum and transfected by Lipofectamine Plus Reagent from Life Technologies as directed by the manufacturer. The DUSP1 pSuperRetro-derived vectors were constructed as described (Chattoppadhyay et al., 2006). Clones expressing siRNA for DUSP1 were selected for their ability to grow in the presence of puromycin  and kept for selection. Stable transfection was confirmed by Western blotting. We analyzed the differences in expression of 47000 genes in H460 cells expressing DUSP1SiRNA (H460cri) compared with the parental cell line H460pSuperRetro vector (H460v) after 0, 1, 3 and 6 hours of CDDP exposure, in order to know the different pathways that were activated by CDDP treatment dependent on expression of DUSP1. RNA was extracted and quality control was checked before hybridization on Affymetrix microarrays.

first: Veronica

last: Moncho-Amor

first: Inmaculada

last: deCaceres

first: Cristobal

last: Belda-Iniesta

first: Jesús

last: Garcia-Foncillas

first: Rosario

last: Perona


title: Expression data from murine vaginal samples following adjuvant treatment

city: Gothenburg

first: Ali

middle: Mohaghegh

last: Harandi

address: Medicinaregatan 7A

department: Microbiology and Immunology

country: Sweden

institute: University of Gothenburg

summary:
Vaccine research today is focused on using safer, highly purified or recombinant antigens with poor immunogenicity, which has created a need for potent adjuvants. Rational design of effective and safe mucosal adjuvants for human use necessitates a thorough understanding of the mode of action of successful candidate adjuvants.
We used microarray to comprehend the molecular signatures of mucosal adjuvants in the mouse vagina. The adjuvants studied, CpG-ODN and α-GalCer have previously been shown to be potent mucosal adjuvants in mice when administrered together with a glycoprotein from HSV-2.

overall_design: Two individual experiments were performed, called ES1 and ES2, each experiment contained 4 groups of mice. All mice were pre-treated with progesteron (DP) before intravaginally recieveing either CpG ODN, α-GalCer or their respective buffers, PBS and PBS/Tween. Vaginas were excised at 3 different time-points; 4h, 24h and 48h following adjuvant delivery.

first: Madelene

last: Lindqvist

first: Srinivas

last: Veerla

first: Intawat

last: Nookaew


title: Expression data in UPEC cystitis in female C57BL/6 mice

status: Public on Dec 28 2011

city: Gold Coast

first: Glen

last: Ulett

state: QLD

address: Parklands Drive

department: School of Medical Science

country: Australia

institute: Griffith University

summary:
Data defines for the first time a whole bladder transcriptome of UPEC cystitis in female C57BL/6 mice using genome-wide expression profiling to map early host response pathways stemming from UPEC colonization
We used microarrays to detail the global programme of gene expression in UPEC UTI in mice

overall_design: Whole mouse bladder collected at 2h following transurethral infection for RNA extraction and hybridization on Affymetrix microarrays. Non-pooled samples were used, with one array per mouse to expand power of expression profiles. Control mice received only PBS as a mock infection. Group sizes were five mice per group, and therefore five arrays were used per group.

first: Benjamin

last: Duell

first: Alison

last: Carey


title: Expression data in UPEC cystitis in female CBA mice

summary:
Data defines for the first time a whole bladder transcriptome of UPEC cystitis in female CBA mice using genome-wide expression profiling to map early host response pathways stemming from UPEC colonization
We used microarrays to detail the global programme of gene expression in UPEC UTI in mice


title: Blood genomic expression profile for ischemic stroke (IS)

city: Lisbon

first: Sofia

middle: A

last: Oliveira

state: Portugal

address: Av. Prof Egas Moniz

department: Edificio Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

summary:
Stroke is a “brain attack” cutting off vital blood, and consequently the nutrients and oxygen vital to the brain cells that control everything we do. Stroke is a complex disease with unclear pathogenesis resulting from environmental and genetic factors.
To better understand IS´s etiology, we performed genomic expression profiling of patients and controls.

overall_design: Gene expression profiling was performed in peripheral blood mononuclear cells (PBMCs) of 20 IS patients and 20 sex- and age-matched controls using Affymetrix microarrays.

first: Tiago

last: Krug

first: José

last: Ferro

first: Mário

last: Silva

first: Ilda

last: Matos

first: Gabriela

last: Lopes


title: Gene expression in iPrEC cell line transfected with wild-type USP2A, mutant USP2A, or empty vector.

status: Public on Dec 27 2011

city: Baltimore

first: Luigi

last: Marchionni

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

country: USA

institute: Johns Hopkins University

summary: Gene expression was measured on the Affymetrix platform in  iPrEC cell line transfected with wild-type USP2A, mutant USP2A, or empty vector.

overall_design: Gene expression was measured in 3 distinct groups (cell transfected with wild-type USP2A, mutant USP2A, or the empty vector). For each group 5 biological replicates were obtained and gene expression was measured on the Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. Differential gene expression was obtained for all the 3 possible pair-wise comparisons (WT versus MUT, WT versus EV, and MUT versus EV).

first: Barbara

last: Benassi

first: Richard

last: Flavin

first: Massimo

last: Loda

first: Giovanni

last: Blandino

first: Marina

last: Marani

first: Sabrina

last: Strano

first: Paola

last: Muti

first: Yunfeng

last: Pan

first: Dipanjan

last: Chowdry

first: Silvio

last: Zanata


title: SCREENING STUDY TO IDENTIFY DIAGNOSTIC MARKERS FOR LUNG CANCER IN ENDOBRONCHIAL LINING FLUID

first: Ruprecht

last: Kuner

summary: We investigated whether biomarker analysis in endobronchial epithelial lining fluid (ELF) collected by bronchoscopic microsampling may be useful for a definitive preoperative diagnosis. Therefore we compared ELF samples close to nodule and from the contralateral site from patients with malignant or benign diagnosis.

overall_design:
ELF samples have been derived from early stage NSCLC patients and controls. LIMMA analysis was performed to identify differentially expressed genes associated to a malignant diagnosis.
keywords: disease subtype analysis

first: Holger

last: Sueltmann

first: Christian

last: Bender

first: Michael

last: Meister

first: Nicolas

last: Kahn

first: Thomas

last: Muley


title: Programming human pluripotent stem cells into adipocytes

status: Public on Dec 25 2011

city: NYC

first: Tim

last: Ahfeldt

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

overall_design: Refer to individual Series


title: Programming human pluripotent stem cells into adipocytes [Affymetrix]

summary: The utility of human pluripotent stem cells as a tool for understanding disease and as a renewable source of cells for transplantation therapies is dependent on efficient differentiation protocols that convert these cells into relevant adult cell types. Here we report the robust and efficient differentiation of human pluripotent stem cells into adipocytes. We found that inducible expression of PPARG2 in pluripotent stem cell-derived mesenchymal progenitor cells programmed their development towards an adipocyte cell fate. Using this approach, multiple human pluripotent cell lines were differentiated into adipocytes with efficiencies of 85% to 90%. These pluripotent stem cell-derived adipocytes retained their identity independent of transgene expression, could be maintained in culture for several weeks, expressed mature markers, and exhibited mature functional properties such as lipid catabolism in response to a beta-adrenergic stimulus. Global transcriptional and lipid metabolomic analyses further confirmed the identity and maturity of these pluripotent stem cell-derived adipocytes.

overall_design:
Mesenchymal progenitor cells (MPCs) derived from human embryonic stem cells hESCs and induced pluripotent stem cells (iPSCs) along with adipose-derived stromal vascular cells (ADSVCs) were subjected to induction of PPAR2 and compared to primary fat samples. Overall 2 ADSVC (ADSVC 24 nd 49) lines, 1 hESC (HUES9) line and 1 iPSC (BJRiPS) line were differentiated into MPCs, PPAR2 programmed, and compared to untreated MPCs and primary fat samples from 2 individuals. Each condition is either represented in duplicate or triplicate on affymetrix HuGene-1_0-st arrays. MPCs derived from the hESC lines HUES2 and HUES8, ADSVCs, and BJRiPS were also run on a separate platform (HG-U133_Plus_2) with more GEO presence to facilitate analysis (34 samples, two platforms total).

Supplementary file(s):
GeneSymbol-collapsed data represent the final normalized data used for analyses in the manuscript.


title: Expression data from 3 gamma-secretase or mock-treated mantle cell lymphoma (MCL) cell lines

status: Public on Dec 22 2011

city: Toronto

first: Robert

last: Kridel

state: ON

address: 101 College Street, Rm 12-311

country: Canada

institute: Princess Margaret Cancer Centre

summary:
We identified recurrent NOTCH1 mutations in 12% of MCLs. 2 out of 10 tested MCL cell lines (Rec-1 and SP-49) were sensitive to inhibition of the NOTCH pathway by gamma-secretase inhibition.
The aim of this study was to identify transcriptional targets of NOTCH signaling in MCL.

overall_design: 3 MCL cell lines (Mino, Rec-1, SP-49 treated with Mock or 1 micromolar compound E for 24 hours, in duplicate.

first: Randy

last: Gascoyne


title: Comparison of the transcriptome of K-LEC spheroids to control LEC spheroids

status: Public on Dec 21 2011

city: Helsinki

first: Paive

last: Ojala

state: (Haartmaninkatu 8)

department: Biomedicum Helsinki

country: Finland

institute: University of Helsinki

summary: Kaposi sarcoma is the most common cancer in AIDS patients and is typified by red skin lesions.The disease is caused by the KSHV virus (HHV8) and is recognisable by its distinctive red skin lesions. The lesions are KSHV infected spindle cells expressing markers of the lymphatic endothelial and blood vessel endothelial cells as well as other cell types. The effects of KSHV infection of lymphatic endothelial cells (LEC) cultured in 3D matrix for three days were assayed using Affymetrix hgu133plus2 chips.

overall_design: There are n=3 of  1.  control LEC spheroids (LEC), 2. KSHV infected LEC spheroids (K-LEC)

first: Simonas

last: Laurinavicius

first: Fang

last: Cheng

first: Stephen

last: Henderson

first: Päivi


title: Inflammation switches the differentiation program of Ly6Chi monocytes from anti-inflammatory macrophages to inflammatory dendritic cells in the colon

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Dendritic cells (DCs) and macrophages (MPs) are important for immunological homeostasis in the colon. We found that F4/80hi CX3CR1hi (CD11b+CD103-) cells account for 80% of mouse colonic lamina propria (cLP) MHC-IIhi cells. Both CD11c+ and CD11c- cells within this population were identified as MPs based on multiple criteria, including a MP transcriptome revealed by microarray analysis. These MPs constitutively released high levels of IL-10 at least partially in response to the microbiota via an MyD88-independent mechanism. In contrast, cells expressing low to intermediate levels of F4/80 and CX3CR1 were identified as DCs, based on phenotypic and functional analysis and comprise three separate CD11chi cell populations: CD103+CX3CR1-CD11b- DCs, CD103+CX3CR1-CD11b+ DCs and CD103-CX3CR1intCD11b+ DCs. In non-inflammatory conditions, Ly6Chi monocytes differentiated primarily into CD11c+, but not CD11c- MPs. In contrast, during colitis, Ly6Chi monocytes massively invaded the colon and differentiated into pro-inflammatory CD103-CX3CR1intCD11b+ DCs, which produced high levels of IL-12, IL-23, iNOS and TNF. These findings demonstrate the dual capacity of Ly6Chi blood monocytes to differentiate into either regulatory MPs or inflammatory DCs in the colon, and that the balance of these immunologically antagonistic cell types is dictated by microenvironmental conditions.

overall_design: FACS sorted expression from normal controls

first: Aymeric

last: Rivollier

first: Jianping

last: He

first: Abhisake

last: Kole

first: Vassilis

last: Valatas

first: Brian

last: Kelsall


title: Iron Chelators Treatment on DMS-53 Human Lung Cancer Cell

city: Sydney

first: Des

middle: Raymond

last: Richardson

state: New South Wales

address: 92-94 Parramatta Rd, Sydney

department: Bosch Institute

institute: University of Sydney

summary: The molecular role of iron in gene expression remains poorly characterized. Moreover, the alterations in global gene expression after iron chelation remains unclear and are important to assess for understanding the molecular pathology of iron-depletion and the biological effects of iron chelators. We assessed the effect on whole genome gene expression of two iron chelators (desferrioxamine and Dp44mT). These studies are important for understanding the molecular and cellular effects of iron-depletion.

overall_design:
The DMS-53 cells were incubated with either control medium or this medium containing DFO (250 µM) or Dp44mT (25 µM) for 24 h at 37oC. These concentrations were used since our previous studies demonstrated that under these conditions these chelators lead to up-regulation of iron-responsive genes such as the TfR1 after this incubation time. Moreover, the higher concentration of DFO was implemented due to its limited ability to permeate cell membranes.
Total RNA was isolated from cells in 1 mL of TRIzol® reagent (Invitrogen). Samples were then prepared and hybridized to the Human Genome U133 Plus 2.0 430 2.0. The human GeneChip® U133 Plus 2.0 consists of greater than 47,000 transcripts and variants from over 38,500 well characterized human genes. On completion of hybridization and washing, microarray chips were scanned with the Affymetrix GeneChip® Scanner 3000 (Affymetrix).

first: Yu

last: Yu

first: Yohan

last: Suryo Rahmanto


title: Defining a No Observable Transcriptional Effect Level (NOTEL) for low dose N-OH-PhIP exposures in human BEAS-2B bronchioepithelial cells

city: piscataway

first: Qi

last: Wang

state: NJ

address: 170 Frelinghuysen Road

department: EOHSI

institute: Rutgers University

summary: The estimation of acceptable exposure levels for genotoxicants is accomplished by defining thresholds from apical endpoints, or by modeling points of departure from data that are acquired from high dose experiments, followed by linear extrapolation of the response through zero. We recently proposed that low dose exposure-induced transcriptional changes that can be linked to mechanisms of pathogenesis could provide a more sensitive alternative for defining thresholds for biological responses. In the present study, we used gene expression profiling data to determine an empirical transcriptional dose response threshold for the food and tobacco smoke borne carcinogen, 2-amino-1-methyl-6-phenylimidazo[4,5]pyridine (PhIP) in human BEAS-2B bronchial epithelial cells exposed to concentrations of N-hydroxylated PhIP ranging from 1 x 10-6 to 5 x 10-10 M.

overall_design: The goal was to determine transcriptional dose response threshold (NOTEL) of human BEAS-2B bronchial epithelial cells exposed to the food and tobacco smoke borne carcinogen, 2-hydroxy-mino-1-methyl-6-phenylimidazo[4,5]pyridine (N-OH-PhIP). BEAS-2B cells  at ~ 70% confluence were treated with  doses of N-OH-PhIP  that varied over five orders or magnitude. Triplicate cell cultures were  exposed to either DMS (control) or nine different doses of N-OH-PhIP at concentrations ranging from 1 x 10-6 to 5 x 10-10 M.

first: Helmut

last: Zarbl


title: Expression data from mouse lung epithelium after allergen challenge

city: La Jolla

first: Taylor

last: Doherty

state: CA

address: 9500 Gilman Dr 0635

institute: UC San Diego

summary:
Changes occur in the lung epithelium after allergen challenge that may give insight into asthma pathogenesis and we sought to identify novelepithelial genes induced by allergen exposure.
We used microarrays to identify up-regulated genes induced by allergen challenge in lung epithelium.

overall_design: Epithelal brushing of the large airways in mouse lungs was performed 24 hours after  Alternaria allergen or PBS control challenge 24.  Collected epithelial cells underwent RNA extraction and hybridization on Affymetrix microarrays. There are a total of 6 samples, 3 allergen and 3 control samples.

first: Naseem

last: Khorram

first: David

middle: H

last: Broide


title: In-transit extremity melanoma III

city: Durham

first: Christina

last: Augustine

state: NC

address: VAMC RmE4001 508 Fulton St.

department: Surgery

institute: Duke University Medical Center

summary: An evaluation of biopsies from patients with in-transit extremity melanoma who have been treated with melphalan in the setting of isolated limb infusion or isolated limb perfusion. Gene expression profiles were obtained from 21 lesions across 19 patients and evaluated for expression that correlated with response to melphalan isolated limb infusion.

overall_design: Chemotherapy response analysis:  complete response - CR; partial response - PR; stable disease - SD; progressive disease - PD; not evaluable - n.e.

first: Douglas

last: Tyler


title: Identifying breast cancer biomarkers

city: Barcelona

first: Francisco

middle: Javier

last: Lopez

address: Rossello, 153

department: Centre Esther Koplowitz

country: Spain

institute: Center for International Health Research at Barcelona (CRESIB)

summary: Background: Breast cancer is a heterogeneous neoplasm. Distinct subtypes of breast cancer have been defined, suggesting the existence of molecular differences contributing to their clinical outcomes. However, the molecular differences between HER2 positive and negative breast cancer tumors remain unclear. Objective: The aim of this study was to identify a gene expression profile for breast tumors based on HER2 status. Material and methods: The HER2 status was determined by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) in 54 breast tumor samples. Using Affymetrix microarray data from these breast tumors, we established the expression profiling of breast cancer based on HER2 IHC and FISH results. To validate microarray experiment data, real-time quantitative reverse transcription-PCR was performed. Results: We found significant differences between the HER2-positive and HER2-negative breast tumor samples, which included overexpression of HER2, as well as other genes located on 17q12, and genes functionally related to migration. Conclusion: Our study shows the potential of integrated genomics profiling to shed light on the molecular knowledge of HER2-positive breast tumors.

overall_design: The tumor samples under study correspond to 54 primary breast carcinomas. They included 15 cases with a HER2 IHC3+ score with HER2 gene amplification, 13 cases with IHC2+ score with amplification and 13 without HER2 gene amplification, and 13 cases IHC0/1+ score without HER2 gene amplification. 12 samples of breast normal tissues from breast cancer patients were also included as a reference. Neither overexpression nor amplification of HER2 was observed.

first: Marta

last: Cuadros

first: Carlos

last: Cano

middle: J

first: Armando

last: Blanco

first: Angel

last: Concha


title: Gene expression profiling in A2780, CP70 and CP70 following Decitabine and/or PXD101 treatment

status: Public on Dec 20 2011

city: London

first: Wei

last: Dai

address: Du Cane Road

department: Sugery and Cancer

institute: Imperial College London

summary: Multiple DNA methylation changes have been associated with the acquisition of drug resistance; however it remains uncertain how many of these changes may represent critical DNA methylation drivers of chemoresistance. Using gene expression profiling method on HGU133plus2 array, we identified a total of 1370 genes showing significant gene expression changes with 687 genes going up and 683 genes going down in the resistant (cp70) versus sensitive cell lines (A2780) by Rank Product (FDR<5%). Combining expression profiling with methylation profiling data we found out of 245 hypermethylated and down-regulated genes in the resistant cell line, 41 genes were up-regulated following Decitabine treatment alone, 45 genes up-regulated following combined treatment of Decitabine and PXD101, and only 10 genes up-regulated following PXD101 treatment alone. Altogether we found a small set of genes as being potential key drivers of chemoresistance and should be further evaluated as predictive biomarkers, both to existing chemotherapies, but also to epigenetic therapies used to modulate drug resistance.

overall_design: Gene expression profiling was obtained from A2780, and CP70 before and after Decitabine and/or PXD101 treatment. Each sample have biological triplicates. Using Rank Product package in R (version 2.10.1), differentially expressed genes with FDR<5% were identified.

first: Constanze

last: Zeller

first: Nicola

last: Steele

first: Afshan

last: Siddiq

first: Andrew

last: Walley

first: Sian

last: Rizzo

first: Ate

last: ven der Zee

first: Jane

last: Plumb

first: Robert

last: Brown


title: Genome-wide methylation and expression profiling study identifies candidate DNA methylation drivers of acquired cisplatin resistance in ovarian cancer.

type:
Expression profiling by array
Methylation profiling by array

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


title: Gene expression profiling of primary acute lymphoblastic leukemia (ALL) cells

city: Uppsala

first: Jessica

last: Nordlund

address: Academic Hospital, Entrance 70, 3rd floor

department: Medical Sciences

institute: Uppsala University

summary: The aim of this study was to benchmark digital gene expression (DGE) profiling by massively parallel sequencing against the most commonly used method for gene expression analysis. We compared the DGE levels to expression levels from Affymetrix arrays. Data from Affymetrix Human Genome U133 plus 2.0 GeneChips was available for 12 of the 21 RNA samples from ALL patient cells analyzed by DGE.

overall_design: Genome-wide expression analysis of 12 primary ALL samples by Affymetrix Human Genome U133 Plus 2.0 GeneChips.

first: Ann-Christine

last: Syvänen


title: A phase II neoadjuvant trial of anastrozole (A), fulvestrant (F) and gefitinib (I - iressa) in patients with newly diagnosed estrogen receptor positive breast cancer

city: Houston

first: Suzanne

last: Fuqua

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Endocrine therapy in patients with breast cancer can be limited by the problem of resistance. Preclinical studies suggest that complete blockade of the estrogen receptor (ER) combined with inhibition of the epidermal growth factor receptor (EGFR) can overcome endocrine resistance. We tested this hypothesis in a phase II neoadjuvant trial of anastrozole and fulvestrant combined with gefitinib in postmenopausal women with newly diagnosed ER-positive breast cancer. After a baseline tumor core biopsy, patients were randomized to receive anastrozole and fulvestrant (AF) or anastrozole, fulvestrant, and gefitinib (AFG) for 3 weeks.  After a second biopsy at 3 weeks, all patients received AFG for 4 months and surgery was done if the tumor was operable. The primary endpoint was best clinical response by RECIST criteria and secondary endpoints were toxicity and change in biomarkers. The study closed after 15 patients were enrolled because of slow accrual. Median patient age was 67 years and median clinical tumor size was 7 cm. Four patients had metastatic disease present. Three patients withdrew before response was assessed. In the remaining twelve patients, there were two complete clinical responses (17%), three partial responses (25%), five had stable disease (41%), and two (17%) had progressive disease. Most common adverse events were rash in four patients, diarrhea in four, joint symptoms in three, and abnormal liver function tests in three. There were no grade 4 toxicities and all toxicities were reversible. At 3 weeks, cell proliferation as measured by Ki-67 was significantly reduced in the AFG group (p value= 0.01) with a parallel reduction in the expression of the Cyclin D1 (p value=0.02). RNA microarray data showed a corresponding decrease in the expression of cell cycle genes. These results suggest that AFG was an effective neoadjuvant therapy and consistently reduced proliferation in ER-positive tumors.

overall_design: We tested this hypothesis in a phase II neoadjuvant trial of anastrozole and fulvestrant combined with gefitinib in postmenopausal women with newly diagnosed ER-positive breast cancer. After a baseline tumor core biopsy, patients were randomized to receive anastrozole and fulvestrant (AF) or anastrozole, fulvestrant, and gefitinib (AFG, also known as AFI) for 3 weeks.  After a second biopsy at 3 weeks, all patients received AFG for 4 months and surgery was done if the tumor was operable. The primary endpoint was best clinical response by RECIST criteria and secondary endpoints were toxicity and change in biomarkers. The study closed after 15 patients were enrolled because of slow accrual. Median patient age was 67 years and median clinical tumor size was 7 cm. Four patients had metastatic disease present. Three patients withdrew before response was assessed. In the remaining twelve patients, there were two complete clinical responses (17%), three partial responses (25%), five had stable disease (41%), and two (17%) had progressive disease. Most common adverse events were rash in four patients, diarrhea in four, joint symptoms in three, and abnormal liver function tests in three. There were no grade 4 toxicities and all toxicities were reversible. At 3 weeks, cell proliferation as measured by Ki-67 was significantly reduced in the AFG group (p value= 0.01) with a parallel reduction in the expression of the Cyclin D1 (p value=0.02). RNA microarray data showed a corresponding decrease in the expression of cell cycle genes. These results suggest that AFG was an effective neoadjuvant therapy and consistently reduced proliferation in ER-positive tumors.

first: Suleiman

last: Massarweh

first: Yee

last: Tham

first: Jian

last: Huang

first: Krystal

last: Sexton

first: Heidi

last: Weiss

first: Anna

last: Tsimelzon

first: Amanda

last: Bayer

first: Mothaffar

last: Rimawi

middle: Y

last: Cai

first: Susan

last: Hilsenbeck

first: Richard

last: Elledge