title: Gene expression in the colon of DSS-treated Pglyrp1-/-, Pglyrp2-/-, Pglyrp3-/-, and Pglyrp4-/- mice

city: Gary

first: Roman

last: Dziarski

state: IN

address: 3400 Broadway

institute: Indiana University School of Medicine-Northwest

summary: Pglyrp1-/-, Pglyrp2-/-, Pglyrp3-/-, and Pglyrp4-/- mice are all more sensitive than wild type (WT) mice to dextran sulfate sodium (DSS)-induced colitis. The purpose of this study was to determine which genes are differentially induced by DSS treatment in the colon of Pglyrp1-/-, Pglyrp2-/-, Pglyrp3-/-, and Pglyrp4-/- mice compared to WT mice. The results demonstrate higher induction of proinflammatory gene expression in Pglyrp1-/-, Pglyrp2-/-, Pglyrp3-/-, and Pglyrp4-/- mice than in WT mice after DSS treatment. The majority of genes whose expression is increased in Pglyrp1-/-, Pglyrp2-/-, Pglyrp3-/-, and Pglyrp4-/- mice but not in WT mice are interferon-inducible genes. Thus, Peptidoglycan Recognition Proteins Pglyrp1, Pglyrp2, Pglyrp3, and Pglyrp4 protect mice from excessive inflammatory response and damage to the colon by limiting expression of interferon-inducible genes in the colon.

overall_design: WT and Pglyrp1-/-, Pglyrp2-/-, Pglyrp3-/-, and Pglyrp4-/- mice (5/group) were either untreated or treated orally with 5% dextran sulfate sodium (DSS) in drinking water for 48 hrs. RNA was obtained from the colon from each mouse individually and assayed for gene expression using whole genome arrays (Affymetrix Mouse GeneChip® Gene 1.0 ST Array).

first: Sukumar

last: Saha

first: Dipika

last: Gupta

first: Jeanette

last: McClintick


title: IFN alpha-induced gene expression in human NK cells

status: Public on Aug 18 2010

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

summary:
NK cells are believed to contribute to the control of hepatitis C virus infection and pathogenesis of liver disease. Standard treatment of both acute and chronic hepatitis C is based on the administration of interferon alpha, however, the effects of type I interferons on human NK cells have not been studied in the context of hepatitis C. We therefore first performed a microarray screen for genes differentially regulated in human NK cells after stimulation of PBMC with recombinant interferon alpha-2b. One of the genes upregulated was TRAIL which was confirmed in vitro on the protein level.

Keywords: Interferon alpha; human NK cells; stimulation for 6 hours; cells sorted after stimulation of whole PBMC

overall_design: NK cells of PBMC of five healthy controls have been either isolated directly or after culturing for 6h in media containing 10% human AB serum supplemented with 1 and 100 ng/ml recombinant IFNa-2b. RNA of NK cells of the healthy controls was isolated and RNA was pooled for the hybridization.

first: K

middle: A

last: Stegman

first: R

first: H

last: Wedemeyer


title: Gene expression profiles of the diabetic glomerular endothelial cell

status: Public on Aug 16 2010

city: Cincinnati

first: Eric

middle: W

last: Brunskill

state: OH

address: 3333 Burnet Avenue

department: Developmental Biology

country: USA

institute: Cincinnati Children's Hospital

summary:
The objective of this study is to create an encyclopedia of all genes expressed in the glomerular endothelial cell under normal and diabetic conditions.  We utilized Tie2-GFP transgenic mice to mark cells of the glomerular endothelium.  To induce diabetic nephropathy (DB), a genetic model of DB, BKS.Cg-m +/+ Leprdb/J from Jax laboratories was used.  We utilized fluorescent activated cell sorting (FACS) to isolate glomerular endothelial cells from normal and diabetic mice.  The RNAs from these samples were isolated and utilized to hybridize to microarrays, which  offers a powerful, efficient and effective method for the creation of a  gene expression atlas.
Microarrays were used to identify the transciptional differences that occur in the glomular endothelium of a diabetic mouse.

overall_design: Diabetic and control mice carrying the Tie2-GFP transgenic were utilized to isolate the endothelial cells from the adult glomerulus.  The endothelial cells were isolated from the glomerulus using FACS.   RNA was isolated and the gene expression profiles were determined by microarrays.

first: S

middle: S

last: Potter


title: Expression data for wt/wt and KLF1 p.K288X/wt human erythroid progenitors

status: Public on Aug 31 2010

city: Rotterdam

first: Sjaak

last: Philipsen

address: Dr. Molewaterplein 50

department: Cell Biology

country: Netherlands

institute: Erasmus MC

summary: Hereditary Persistence of Fetal Hemoglobin (HPFH) is characterized by persistent high levels of fetal hemoglobin (HbF) in adults. Several contributory factors, both genetic and environmental, have been identified, but others remain elusive. Ten of twenty-seven members from a Maltese family presented with HPFH. A genome-wide SNP scan followed by linkage analysis revealed a candidate region on chromosome 19p13.12-13. Sequencing identified a nonsense mutation in the KLF1 gene, p.K288X, ablating the DNA binding domain of this key erythroid transcriptional regulator. Only HPFH family members were heterozygote carriers of this mutation. Expression profiling on primary erythroid progenitors revealed down-regulation of KLF1 target genes in HPFH samples. Functional assays demonstrated that, in addition to its established role in adult globin expression, KLF1 is a critical activator of the BCL11A gene, encoding a suppressor of HbF expression. These observations provide a rationale for the effects of KLF1 haploinsufficiency on HbF levels. To identify differentially expressed genes, RNA was isolated from erythroid progenitors (HEPs) cultured from peripheral blood of four HPFH (KLF1 p.K288X/wt) and four non-HPFH family members (wt/wt) and used for genome-wide expression analysis.

overall_design: A minimum of 1.5E6 HEPs were harvested at day12 of culture and RNA was extracted with Trizol reagent (Sigma) and purified using the RNeasy Mini Kit (Qiagen, Crawley, UK), including an on-column DNaseI digestion, according to the manufacturer’s instructions. RNA yield was determined using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). 8-10 micr-g of total RNA was analysed by microarrays using cells from day 12 of culture. Quality of the total RNA samples and the resulting cRNA was assessed on the Bioanalyzer. Fragmented biotinylated cRNA was prepared and 15μg hybridized to HG-U133 plus 2 GeneChips, according to the manufacturer’s protocols (Affymetrix). The data was normalized by Robust Multi-Array average (RMA) algorithm.

first: Jun

last: Hou


title: Gene expression signature and the prediction of recurrence in stage III colorectal cancer by DNA microarray

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

state: Tokyo

department: Department of Surgical Oncology

country: Japan

institute: University of Tokyo

summary:
Samples were taken from colorectal cancers in surgically resected specimens in 36 colorectal cancer patients. The expression profiles were determined using Affymetrix Human Genome U133 Plus 2.0 arrays. Comparison between the sample groups allow to identify a set of discriminating genes that can be used for molecular markers for predicting recurrence.
Keywords: repeat

overall_design: Thirty-six colorectal cancer patients who had undergone surgical resection of colorectal cancer were studied. In all patients, curative resection was performed and no patients had any distant metastasis at the time of operation (stage III patients). Among the 36 patients, 23 patients did not develop recurrence. On the other hand, 13 patients developed rucurrence such as liver metastases, lung metastases and distant lymph node metastases. The median follow up period was 4.5 years.

first: Takashi

last: Kobunai

first: Etsuko

last: Toda

first: Toshinori

last: Oka


title: Altered gene expressions of leukocyte transendothelial migration and cell communication pathways in periodontitis-affected gingival tissues

status: Public on Aug 13 2010

city: Niigata

first: Takehiko

last: Kubota

address: 2-5274, Gakkou-cho

department: Periodontology

institute: Niigata University Graduate School of Medical and Dental Sciences

summary:
Gene expressions relate to the pathogenesis of periodontitis and have a crucial role in local tissue destruction and susceptibility to the disease. The aims of the present study were to explore comprehensive gene expressions/transcriptomes in periodontitis-affected gingival tissues, and to identify specific biological processes.
The purpose of the present study was 1) to compare comprehensive gene expression/transcriptomes of periodontitis-affected gingival tissues with those of healthy tissues by using microarray and data mining technologies, and 2) to analyze significantly differentially expressed genes which belong to pathological pathways in periodontitis by qRT-PCR.

overall_design: Two distinct gingival samples including healthy and periodontal-affected gingiva were taken from 3 patients with severe chronic periodontitis. Total RNAs from 6 gingival tissue samples were used for microarray and data-mining analyses. Comparisons, gene ontology, and pathway frequency analyses were performed and identified significant biological pathways in periodontitis. Quantitative reverse transcription real-time polymerase chain reaction (qRT-PCR) analyse using 14 chronic periodontitis patients including 3 patients listed above and 14 healthy individuals showed 9 differentially expressed genes in leukocyte migration and cell communication pathways.

first: Daisuke

last: Abe

first: Taro

last: Shimizu

first: Toshiya

last: Morozumi

first: Naohiro

last: Nakasone

first: Manami

last: Itagaki

first: Hiromasa

last: Yoshie


title: Expression data from RCC cell lines to study metastasis progression

status: Public on Aug 15 2010

city: New York

first: Venkata

middle: J

last: Thodima

state: NY

institute: Memorial Sloan-Kettering Cancer Center

summary:
This study investigates the molecular signatures that drive Renal Cell Carcinoma (RCC) metastatic conversion using the metastatic (LM2) and non-metastatic (SN12C) RCC cell lines.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: To identify differences in gene expression associated with increasing metastatic activity, we subjected the three RCC cell types, SN12C, LM1, LM2 to gene expression profiling.

first: Miguel

last: Lopez-Lago


title: ECP mediated monocyte to DC differentiation

status: Public on Aug 14 2010

city: New Haven

first: Carole

middle: L.

last: Berger

state: CT

address: 333 Cedar Street

department: Dermatology

institute: Yale University

summary:
Extracorporeal photochemotherapy (ECP) is widely used to treat cutaneous T cell lymphoma, graft versus host disease and allografted organ rejection.  Its clinical and experimental efficacy in both cancer immunotherapy and autoreactive disorders suggests a novel mechanism.  This study reveals that ECP induces a high percentage of processed monocytes to enter the dendritic antigen presenting cell (DC) differentiation pathway, as determined by expression of relevant genes.  The resulting DC are capable of processing and presentation of exogenous antigen and are largely maturationally synchronized, as assessed by the level of expression of co-stimulatory surface molecules.  Principal component analysis of the ECP-induced monocyte transcriptome indicates that activation or suppression of more than 3500 genes produces a reproducible distinctive molecular signature.  Pathway analysis suggests that DC maturation may be triggered by transient adherence of passaged monocytes to plasma proteins coating the ECP plastic ultraviolet exposure plate.   Co-incubation with lymphocytes, simultaneously induced by ECP to undergo apoptosis, may accelerate conversion of monocytes to DC.  The efficiency with which ECP induces new functional DC supports the possibility that these cells participate prominently in the clinical successes of the treatment.  ECP may offer a practical source of DC for use in a spectrum of immunotherapeutic trials.
We have used microarrays to analyze the expression of genes modulated by ECP treatment.

overall_design: Samples were obtained pre-treatment, after ECP on day 0 and after overnight incubation of the ECP product on 3 cutaneous T cell lymphoma patients, 3 graft-versus host disease patients and 6 normals.

middle: L

first: Kristin

last: Hoffmann


title: Expression data from RCC paired tumors to study metastasis progression

summary:
This study investigates the molecular signatures that drive Renal Cell Carcinoma (RCC) metastatic conversion using the 16 paired Human tumor samples.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: To identify differences in gene expression associated with increasing metastatic activity, we subjected 16 paired human tumor samples to gene expression profiling.


title: Gene expression profilings of fetal human and mouse cerebral cortex exposed to alcohol

first: Kazue

last: Hashimoto-Torii

address: 333 Cedar St.

summary: A dataset for coordinated transcriptome analysis of the effect of ethanol on human embryonic cerebral slices in vitro and on the mouse embryonic cerebral cortex in a in vivo model.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
GW15 and 17 embryonic cortices that were obtained from the Human Fetal Tissue Repository at Albert Einstein College of Medicine. The research protocol was approved by Yale Human Investigation Committee. The medical histories of all samples did not present exposure to alcohol during pregnancy. The tissues were stored in L-15 Leibovitz medium on ice and were cut at 300 µm using a tissue chopper within 3 hours after the surgery. the slices were cultured on the membrane floating on the Neurobasal medium containing 50 mM ethanol or PBS with supplements for 24 hours in tissue culture plate with low evaporation lid (falcon, 353046).

Wild-type CD-1 pregnant mice were purchased from Charles River. For the mouse in vivo mFAE model, the pregnant dams of wild-type and transgenic mice were intraperitoneally injected with 25% ethanol/PBS (final 2.0g/kg weight) or PBS (as the control) once a day from E14 to E16.


title: RCC cell lines and paired tumors

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Factorial study for evaluating the effect of Affy platform and lab on gene expression measurements

city: Woburn

first: Christos

last: Hatzis

state: MA

address: 400 West Cummings Park, Suite 5350

institute: Nuvera Biosciences

summary:
Comparison of concordance in single and multi-gene genomic indices from data generated by two different laboratories (MD Anderson Cancer Center (MDA) and Jules Bordet Institute (JBI)) and on two different Affymetrix platforms (U113A and U133_Plus2).

We used a 2x2 factorial study in which 16 clinical breast cancer samples were profiled by both laboratories on both platforms (64 arrays total).

overall_design: Total RNA was extracted, cRNA was labeled and fragmented at MDA.  Fragmented cRNA was profiled on both platforms at MDA.  Fragmented cRNA was shipped to JBI where it was also profiled on both platforms.

first: W

middle: F

last: Symmans

last: Sotiriou


title: The human nose harbours a niche of olfactory ecto-mesenchymal stem cells displaying neurogenic and osteogenic properties

status: Public on Oct 08 2010

city: Berlin

first: Thomas

last: Häupl

address: Charitéplatz 1

department: Rheumatology

institute: Charité

summary:
We previously identified multipotent stem cells within the lamina propria of the human olfactory mucosa, located in the nasal cavity. We also demonstrated that this cell type differentiates into neural cells and improves locomotor behavior after transplantation in a rat model of Parkinson’s disease. Yet, next to nothing is known about their specific stemness characteristics. We therefore devised a study aiming to compare olfactory lamina propria stem cells from 4 individuals to bone marrow mesenchymal stem cells from 4 age- and gendermatched individuals. Using pangenomic microarrays and immunostaining with 34 cell surface marker antibodies, we show here that olfactory stem cells are closely related to bone marrow stem cells. However, olfactory stem cells exhibit also singular traits. By means of techniques such as proliferation assay, cDNA microarrays, RT-PCR, in vitro and in vivo differentiation, we report that, when compared to bone marrow stem cells, olfactory stem cells display i) a high proliferation rate; ii) a propensity to differentiate into osseous cells and iii) a disinclination to give rise to chondrocytes and adipocytes. Since peripheral olfactory stem cells originate from a neural crest-derived tissue and, as shown here, exhibit an increased expression of neural cellrelated genes, we propose to name them olfactory ecto-mesenchymal stem cells (OE-MSC). Further studies are now required to corroborate the therapeutic potential of OE-MSCs in animal models of bone and brain diseases.

Keywords: cell type comparison

overall_design: Expression profiles of olfactory ectomesenchymal stem cells, bone marrow MSC, periosteal cells, neural progenitors, and synovial fibroblasts were compared against each other and with different lineages of purified hematopoietic cells from bone marrow to characterise human olfactory ectomesenchymal stem cells molecularly

first: Bruno

last: Delorme

first: Emmanuel

last: Nivet

first: Julien

last: Gaillard

first: Jochen

last: Ringe

first: Arnaud

last: Devèze

first: Jacques

last: Magnan

first: Jérôme

last: Sohier

first: Michel

last: Khrestchatisky

first: François

last: Roman

first: Pierre

last: Charbord

first: Luc

last: Sensebé

last: Layrolle

last: Féron


title: Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells (Affymetrix)

status: Public on Aug 09 2010

city: Cambridge

first: Garrett

middle: M

last: Frampton

address: 9 Cambridge Center

department: Biology

institute: Whitehead Instute - MIT

summary: Knowledge of both the global chromatin structure and the gene expression programs of human embryonic stem (ES) cells and induced pluripotent stem (iPS) cells should provide a robust means to assess whether the genomes of these cells have similar pluripotent states.  Recent studies have suggested that ES and iPS cells represent different pluripotent states with substantially different gene expression profiles.  We describe here a comparison of global chromatin structure and gene expression data for a panel of human ES and iPS cells.  Genome-wide maps of nucleosomes with histone H3K4me3 and H3K27me3 modifications indicate that there is little difference between ES and iPS cells with respect to these marks.  Gene expression profiles confirm that the transcriptional programs of ES and iPS cells show very few consistent differences.  Although some variation in chromatin structure and gene expression was observed in these cell lines, these variations did not serve to distinguish ES from iPS cells.

overall_design: Examination of gene expression in 7 human ES cell lines, 8 human iPS cell lines, and 2 fibroblast cell line2.

first: Matthew

middle: G

last: Guenther

first: Frank

last: Soldner

first: Dirk

last: Hockemeyer

first: Maya

last: Militipova

first: Rudolf

last: Jaenisch

first: Richard

last: Young


title: Coupling p53 binding and nucleosome occupancy measurements at p53 binding sites

city: Rehovot

first: Efrat

last: Lidor Nili

address: Herzel

country: Israel

institute: Weizmann Institute of Science

type: Genome binding/occupancy profiling by genome tiling array

summary:
We were interested to explain why p53 binds some high affinity sites in contrast to other high affinity sites that are not bound by p53.
p53 binding was measured using p53 ChIP-CHIP and in parallel nucleosome occupancy was measured on these same sites
Comparison between p53 binding and nucleosome occupancy at p53 predicted binding sites

overall_design:
ChIP-CHIP of p53 from MCF7EcoR under Basal conditions and MCF7EcoR treated with NCS (Activated) and Mononucleosomal extraction from MCF7sip53, MCF7EcoR under Basal conditions and MCF7EcoR treated with NCS (Activated)
Expression analysis of MCF7sip53 and MCF7EcoR treated with NCS (Activated)

last: Nili

first: Moshe

last: Oren

first: Yair

last: Field

first: Eran

last: Segal


title: Gene profiling of apoptosis induced by heat stress in U937 human lymphoma cells

status: Public on Aug 11 2010

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

summary: Hyperthermia is widely used to treat patients with various cancers. 42.5˚C is well known as the inflection point of hyperthermia and generally up to 42˚C of hyperthermia is used in clinical cases combined with other therapies. Here, the effects of heat stress at 42 or 44˚C for 15 min on the gene expression in human lymphoma U937 cells were investigated using an Affymetrix GeneChip system. The cells were treated with heat stress (42 or 44°C for 15 min), followed by incubation for 0, 1, 3 or 6 h at 37°C. The percentage of DNA fragmentation was 8.4 ± 2.2 (mean ± SD) at 42°C for 6 h and 21.0 ± 2.0 at 44°C for 6 h. Of approximately 47,000 probe sets analyzed, many genes that were differentially expressed by a factor 2.0 or greater were identified in the cells treated with heat stress at 42 and 44°C.

overall_design: U937 cells, a human lymphoma cell line, were treated with heat stress (42 or 44°C for 15 min), followed by incubation for 0, 1, 3 or 6 h at 37°C. Non-treated cells served as the control. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChip® system with a Human Genome U133-plus 2.0 array for analysis of over 47,000 transcripts. Sample preparation for array hybridization was carried out as described in the manufacturer’s instruction

first: Yukihiro

last: Furusawa

first: Ichiro

last: Takasaki

first: Takashi

last: Kondo


title: Intratumor Heterogeneity and Precision of Microarray-Based Predictors of Breast Cancer Biology and Clinical Outcome

status: Public on Aug 12 2010

city: Durham

first: Dawn

last: Kernagis

state: NC

address: 2100 Erwin Rd

department: Pathology

institute: Duke University Medical Center

summary: Genome-wide expression profiling was performed on 50 core needle biopsies from 18 breast cancer patients using Affymetrix GeneChip Human Genome Plus 2.0 Arrays.

overall_design: Global profiles of expression were characterized using unsupervised clustering methods and variance components models. Precision of predictors of breast cancer biology and clinical outcome were evaluated by interclass correlation.

first: Michael

last: Datto

first: William

last: Barry


title: Gene-expression profile of breast cancer cell lines and sorted breast cancer epithelial cells

status: Public on Aug 17 2010

city: Boston

first: Qiyuan

last: Li

address: 44 Binney street

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: Most of the breast cancer samples used in clinical research contain multiple cell types other than epithelial cells alone. The non-epithelial cell types have have a substantial effect on the gene expression-profile, which is used to define molecular subtypes of the tumours. The purpose of this data set is to retrieve gene-expression profile within tumour epithelial cells. We collected 9 breast cancer epithelial cell lines and 5 tumour sampes from which epithelial cells were sorted and enriched using BerEp4 antibody coated beads. We profiled the mRNA expression level of these samples and classified probe sets into epithelial genes which were those genes with present calls in at least 50% of the samples. Then we derived an 23-gene signature based on only the epithelial genes to stratify breast cancer.

overall_design: Gene-expression profile analysis of 9 breast cancer epithelial cell lines and 5 tumour epithelium samples purified using BerEp4 antibody coated beads.

first: Andrea

last: Richardson


title: Analysis of the inflammatory transcription profiles of WT and Bid–/– microglia

status: Public on Sep 01 2010

city: Tel Aviv

first: Reuven

last: Stein

address: George S. Wise Faculty of Life Sciences,

institute: Tel - Aviv University

summary: Apoptosis is a controlled cell-death process mediated inter alia by proteins of the Bcl-2 family. Some proteins previously shown to promote the apoptotic process were found to have non-apoptotic functions as well. Microglia, the resident immune cells of the central nervous system, respond to brain derangements by becoming activated to contend with the brain damage. Activated microglia can also undergo activation-induced cell death. Previous studies have addressed the role of core apoptotic proteins in the death process, but whether or not these proteins also play a role in the activation process has not been reported. Here we explore the effect of the BH3-only protein Bid on the immunological features of microglia by subjecting both WT and Bid  deficient primary neonatal microglial cultures to LPS treatment (100 ng/ml, 3h) or left untreated  (control) and  analyzing their transcription profiles in order to study the role of Bid.

overall_design: 4 samples were analyzed. no replication.

first: Lior

last: Mayo

first: ayelet

last: Levy

first: Jasmine

last: Jacob-Hirsch

first: Ninette

last: Amariglio

first: Gideon

last: Rechavi


title: TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions

city: Piscataway

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

summary: Surprisingly few pathways signal between cells, raising questions about mechanisms for tissue-specific responses. In particular, Wnt ligands signal in many mammalian tissues, including the intestinal epithelium, where constitutive signaling causes cancer. Genome-wide analysis of DNA cis-regulatory regions bound by the intestine-restricted transcription factor CDX2 in colonic cells uncovered highly significant over-representation of sequences that bind TCF4, a transcriptional effector of intestinal Wnt signaling. Chromatin immunoprecipitation confirmed TCF4 occupancy at most such sites and co-occupancy of CDX2 and TCF4 across short distances. A region spanning the single nucleotide polymorphism rs6983267, which lies within a MYC enhancer and confers colorectal cancer risk in humans, represented one of many co-occupied sites. Co-occupancy correlated with intestine-specific gene expression and CDX2 loss reduced TCF4 binding.These results implicate CDX2 in directing TCF4 binding in intestinal cells. Co-occupancy of regulatory regions by signal-effector and tissue-restricted transcription factors may represent a general mechanism for ubiquitous signaling pathways to achieve tissue-specific outcomes.

overall_design:
A series of ChIP-chip experiments identified the CDX2 cistrome and discovered and validated extensive co-binding with TCF4 in colon cancer cell lines

Transcriptional profiling following shRNA-mediated CDX2 knockdown was employed to identify CDX2-dependent gene expression in the human colon cancer cell line Caco2

first: Verzi

last: Michael

first: Shivdasani

last: Ramesh


title: Gene expression profling of human breast carcinoma-associated fibroblasts treated with paclitaxol or doxorubicin at therapeutically relevant doses

status: Public on Aug 03 2010

city: Tainan city

first: Jimmy

middle: Jiun-Ming

last: Su

address: 1F,No 367,Sheng-Li Rd. North District

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes,Taiwan

summary:
Systemic chemotherapy inflicts cytotoxic injuries on breast carcinoma-associated fibroblasts.
We profiled the transcriptomes of human breast carcinoma-associated fibroblasts before and after clinically relevant cytotoxic stimuli induced by chemotheraputic agents.

overall_design: Breast cancer associated fibroblasts (BCAFs) were isolated from the tumor specimen by mechanical dissociation and differential centrifugation. The cells at early passages were treated with paclitaxol or doxorubicin at clinically revealent concentration. Total RNA was extracted from the cells at different time points post-treatment for gene expression profiling.

first: J

first: K

middle: K

last: Tsai


title: Genes regulated after transient knock-down of Pirin in WM-266 cells

status: Public on Aug 04 2010

city: Milan

first: Myriam

last: Alcalay

address: Via Adamello 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology

summary:
Pirin (PIR) is a putative transcriptional regulator abundantly expressed in melanocytes and in a subset of primary and metastatic melanomas. Ablation of PIR in the melanoma cell lines results in induction of a senescence-like phenotype.

Keywords: Transcriptional regulation, knock-down using siRNA

overall_design: We analyzed gene expression profiles of WM-266.4 metastatic melanoma cells after knock-down of PIR, which was achieved using a pool of four PIR-siRNA duplexes (siPIR). A pool of four non-targeting siRNA duplexes was used as control of off-target transcriptional effects (siCTR). Cells that underwent transfection with no oligonucleotides (oligofectamine only) were also included to measure all non-specific effects (NO cells). For each sample, an RNA pool was obtained by mixing equal quantities of total RNA from each of three independent RNA extractions. Each biotin-labeled target was hybridized to two GeneChip HG-U133 Plus v.2 arrays.


title: Cord blood multipotent stromal cells exploit a unique immune suppressive mechanism

city: Nijmegen

first: Ruurd

last: Torensma

address: GeertGrooteplein 28

department: Tumorimmunology

institute: Radboud University Nijmegen Medical Centre

summary:
Expression patterns of Dendritic cells co cultured with cord blood MSC were compared with cord blood MSC (USSC). Putative immune suppressive candidates were tested to explain this inhibition. We find that cord blood MSC themselves are hardly immunogenic as tested with allogeneic T-cells. Dendritic cells cocultured with second party T-cells evoked abundant proliferation that was inhibited by third party cord blood USSC. Optimal inhibition was seen with one cord blood USSC for every dendritic cell. Blocking HLA-G only saw partial recovery of proliferation. Several cytokines, prostaglandins, gangliosides, enzymes like arginase, NO synthase and indole amine 2,3-dioxygenase as well as the induction of Treg were not involved in the inhibition based on the microarrays and functional tests. Although the mechanism by which it does so remains partially undefined and subject to further study, cord blood multipotent stromal cells are strong inhibitors of the immune response and therefore allow their use in tissue regeneration settings in an allogeneic setting.

Keywords: Adult stem cells, developmental biology, gene expression, genomics, human cord blood, mesenchymal stem cells, cel type comparison

overall_design: Dendritic cells co cultured with cord blood MSC compared with cord blood MSC (USSC).

first: Lieke

last: van den Berk

first: Bastiaan

last: Jansen

first: Gosse

last: Adema

first: Gesine

last: Kögler

first: Carl

last: Figdor

first: Joris

last: Veltman

first: Christian

last: Gilissen


title: Expression data from hESCs, hiPSCs and human fibroblasts.

status: Public on Aug 06 2010

city: Los Angeles

first: Kathrin

last: Plath

state: CA

address: 615 Charles E. Young Drive South

department: Biological Chemistry

institute: UCLA

summary:
Detailed analysis comparing hiPSC lines that were newly generated and compared them to already established hiPSC lines
We used microarrays to detail various hiPSC lines to confirm faithful reprogramming.

overall_design: hESCs, hiPSCs and human fibroblasts for RNA extraction and hybridization on Affymetrix arrays.

first: Mark

middle: H

last: Chin

first: William

middle: E

last: Lowry


title: Transcriptional changes in IL-2, IL-12 and IL-18 stimulated human natural killer cells

status: Public on Aug 05 2010

city: Tampa

first: Matthew

middle: Adams

last: Smith

state: FL

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

summary: We used Affymetrix expression arrays to determine changes in gene expression associated with activation of human NK cells mediated through treatment with cytokines IL-2, IL-12 and IL-18 over a 24 hour period.

overall_design: Human natural killer cells were isolated via negative selection from PBMCs of healthy donors.  Cells were found to be > 95% CD3-CD56+.  RNA was harvested at time of isolation or after 24 hour stimulation from 8 x 10^6 cells per condition.  For stimulations, cells were incubated at 37C (5% CO2) in RPMI, suuplemented with 10% Fetal Bovine Serum at 1.5 x 10^6 cells/ml.  Cytokine stimualtions were conducted with IL-2 (100U/mL), IL-12 (10ng/mL) and IL-18 (100ng/mL) from 2 male donors (N = 4).  Expression analysis was carried out to determine transcriptional changes associated with 24 hr stimulation relative to freshly isolated cells.

first: Kenneth

last: Wright


title: Insulin-like growth factor-1 receptor inhibitor, AMG-479, in cetuximab-refractory head and neck squamous cell carcinoma

city: Nashville

first: Christine

middle: H.

last: Chung

state: TN

address: 777 PRB

department: Internal Medicine

institute: Vanderbilt University

summary:
Recurrent and/or metastatic head and neck squamous cell carcinoma (HNSCC) remains one of the most difficult cancers to treat with limited chemotherapeutic options. Here, we describe a patient with HNSCC who had complete response to methotrexate (MTX) after progressing on multiple cytotoxic agents; cetuximab, a monoclonal antibody (mAb) against Epidermal Growth Factor Receptor (EGFR), and AMG 479, a mAb against Insulin-like Growth Factor-1 Receptor (IGF-1R).
In tumor tissue of this patient we observed gene expression modulation by cetuximab and AMG 479 suggesting crosstalk between the EGFR and IGF-1R pathways that may have sensitized the tumor to MTX. This represents a promising novel approach to development of targeted agents in refractory cancer.
Keywords: tumor response

overall_design: 10 samples from different time points during course of treatment in a single individual.

first: Joel

last: Parker

first: Barbara

last: Murphy


title: Gene Expression Changes in Primary Human Nasal Epithelial Cells exposed to Formaldehyde in vitro

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

summary: Using various exposure conditions, we studied the induction of DNA-protein crosslinks (DPX) by formaldehyde (FA) and their removal in primary human nasal epithelial cells (HNEC). DPX were indirectly measured by the alkaline comet assay as the reduction of gamma ray – induced DNA migration. DPX are the most relevant primary DNA alterations induced by FA and the comet assay is a very sensitive method for the detection of FA-induced DPX. In parallel experiments, we investigated changes in gene expression by using a full genome human microarray. After a single treatment with FA (50 to 200 µM), concentration – and time-dependent changes in gene expression were seen under conditions that also induced genotoxicity. Repeated treatments with low FA concentrations (20 and 50 µM) did not lead to a significant induction of DPX but repeated treatments with 50 µM FA changed the expression of more than 100 genes. Interestingly, the expression of genes involved in the main pathway for FA detoxification and the repair of DPX were not specifically enhanced. A high degree of overlap was seen among the pattern of gene changes induced by FA in HNEC in comparison to recently published array studies for nasal epithelial cells from rats exposed to FA in vivo. Our results suggest that HNEC are a suited in vitro model for the characterization of FA-induced toxicity and the relationship between genotoxic and other cytotoxic effects.

overall_design: 39 arrays: several time points and doses of formaldehyde

first: Simone

last: Neuss

first: Günter

last: Speit


title: UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE) is an inducer of apoptotic processes in Capan-1 pancreatic carcinoma cells

status: Public on Aug 01 2010

first: Wolfgang

last: Kemmner

address: Lindenberger Weg 80

institute: ECRC Berlin

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

overall_design: Refer to individual Series


title: DNA methylation signatures define molecular subtypes of Diffuse Large B Cell Lymphoma

city: San Francisco

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

summary: We performed DNA methylation (HELP array) and gene expression profiling in 69 samples of diffuse large B cell lymphoma (DLBCL). First, by gene expression, two molecular subtypes of DLBCL termed as "germinal center B cell-like" (GCB) and "activated B cell-like" (ABC) DLBCL were assigned to the 69 DLBCL cases. Then, the supervised analysis using HELP data revealed strikingly different DNA promoter methylation patterns in the two molecular DLBCL subtypes. These data provide epigenetic evidence that the DLBCL subtypes are distinct diseases that utilize different oncogenic pathways.

overall_design:
The retrospective study included RNA and DNA extracted from 69 clinical samples.

This submission represents the gene expression component of the study.

first: Randy

middle: D

last: Gascoyne

first: Olivier

last: Element

first: Ari

last: Melnick


title: UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE) is an inducer of apoptotic processes in Capan-1 pancreatic carcinoma cells: GNE silencing

summary: Early invasive growth and metastasis are features of pancreatic cancer that rely on resistance to anoikis, an apoptosis program activated upon loss of adequate matrix anchorage. Re-expression of the tumor suppressor p16 reversed anoikis resistance of pancreatic cancer cells. This conversion to an anoikis-susceptible phenotype was found to be associated with a striking loss of GNE mRNA expression, prompting us to address the role of GNE in pancreatic cancer in more detail. GNE catalyzes a rate-limiting key step of the sialic acid biosynthesis and may have additional functions in the nucleus.

overall_design: Pancreatic cancer cells Capan-1. Three GNE-silencing samples and three control samples.

first: Pia

last: Kessel


title: Modeling oncogenic signaling in colon tumors by multidirectional analyses of microarray data

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: Background. Most colorectal cancers (CRC) arise in a progression through adenoma to carcinoma phenotypes as a consequence of altered genetic information. Clinical progression of CRC may occur in parallel with distinctive signaling alterations. We designed multidirectional analyses integrating microarray-based data with biostatistics and bioinformatics to elucidate the signaling and metabolic alterations underlying CRC development in the adenoma-carcinoma sequence.    Methodology/Principal Findings. Studies were performed on normal mucosa, adenoma, and CRC samples obtained during surgery or colonoscopy. Collections of cryostat sections prepared from the tissue samples were evaluated by a pathologist to control the relative cell type content. RNA was isolated from 105 macro- and 40 microdissected specimens. The measurements were done using Affymetrix GeneChip HG-U133plus2, and probe set data were generated using two normalization algorithms: MAS5 and GCRMA with LVS. The data were evaluated using pair-wise comparisons and data decomposition into SVD modes. The method selected for the functional analysis used the Kolmogorov-Smirnov test. Based on a consensus of the results obtained by two tissue handling procedures, two normalization algorithms, and two probe set sorting criteria, we identified six KEGG signaling and metabolic pathways (cell cycle, DNA replication, p53 signaling pathway, purine metabolism, pyrimidine metabolism, and RNA polymerase) that are significantly altered in both macro- and microdissected tumor samples compared to normal colon. On the other hand, pathways altered between benign and malignant tumors were identified only in the macrodissected tissues.  Conclusion/Significance. Multidirectional analyses of microarray data allow the identification of essential signaling alterations underlying CRC development. Although the proposed strategy is computationally complex and labor–intensive, it may reduce the number of false results.

overall_design: Gene expression profiles of 40 tissue samples representing distant full-thickness normal colon, normal colon mucosa dissected from tumor, adenoma, and carcinoma. Gene expression profiles of 105 tissue samples representing colon carcinomas, adenocarcinomas, and normal colon samples.

first: Magdalena

last: Skrzypczak

first: Tymon

last: Rubel

first: Agnieszka

last: Paziewska

first: Michal

last: Mikula

first: Dorota

last: Jarosz

first: Jacek

last: Pachlewski

first: Janusz

last: Oledzki

first: Jerzy

last: Ostrowski


title: Gene expression profiling of Down Syndrome (DS)-AMKL and non-DS AMKL samples

first: Zhe

last: Li

department: Division of Hematology/Oncology

institute: Children's Hospital Boston

summary:
The goal of this study is to define a gene expression signature unique to DS-AMKL (acute megakaryoblastic leukemia or FAB M7 leukemia).
A similar study was done previously, but using unfractionated patient leukemic samples. In this study, we sorted megakaryocytic leukemia blasts from patients and then compared their gene expression signatures to those from similarly sorted blasts from patients with non-DS AMKL. This allowed us to identify a gene expression signature more unique to DS-AMKL samples.

overall_design: The leukemic blasts were sorted based on CD41, CD7, CD117, CD33, and CD34 antibodies as previously described (Klin. Padiatr. 217, 126-134).

first: Jan-Henning

last: Klusmann

first: Dirk

last: Reinhardt

first: Stuart

last: Orkin


title: Induction of apoptotic processes in Capan-1 pancreatic carcinoma cells by restoration of p16INK4a expression

city: Berlin

first: Wolfgang

last: Kemmner

overall_design: Pancreatic cancer cells Capan-1. Three p16-transfectants and three mock-transfectants.


title: Genome-wide DNA Methylation Analysis Reveals Novel Targets for Drug Development in Mantle Cell Lymphoma

status: Public on Jul 31 2010

city: Bronx

first: Samir

last: Parekh

address: 1300 Morris Park Ave

department: Cancer center

institute: Albert Einstein College of Medicine

type: Methylation profiling by genome tiling array

summary: Mantle Cell Lymphoma (MCL) is a mostly incurable malignancy arising from naïve B cells (NBC) in the mantle zone of lymph node follicles. We analyzed genome-wide methylation in MCL patients using the HELP (Hpa II tiny fragment Enrichment by Ligation mediated PCR) assay and found significant aberrancy in promoter methylation patterns as compared to normal NBCs. Using biological and stringent statistical criteria, we further identified four hypermethylated genes CDKN2B, MLF-1, PCDH8, HOXD8 and four hypomethylated genes CD37, HDAC1, NOTCH1 and CDK5 where aberrant methylation was associated with inverse changes in mRNA levels. MassArray Epityper analysis confirmed the presence of differential methylation at the promoter region of these genes. Immunohistochemical analysis of an independent cohort of 14 MCL patient samples, confirmed CD37 surface expression in 93% of patients, validating its selection as a target for MCL therapy. Treatment of MCL cell lines with a novel small modular immunopharmaceutical(CD37-SMIP) resulted in significant loss of viability in cell lines with intense surface CD37 expression. Treatment of MCL cell lines with the DNA methyltransferase inhibitor decitabine resulted in reversal of aberrant hypermethylation and synergized with the HDAC inhibitor SAHA in induction of the four hypermethylated genes CDKN2B, MLF-1, PCDH8 and HOXD8. The combination of Decitabine and SAHA also resulted in potent and synergistic anti-MCL cytotoxicity as compared to either drug alone. In conclusion, our analysis shows prominent and aberrant methylation of the MCL genome and identifies novel differentially methylated and expressed genes in MCL cell lines and patient samples. Furthermore, our data suggest that differentially methylated genes can be targeted for therapeutic benefit in MCL.

overall_design: Gene expression profiling by array comprised of 8 mantle cell lymphoma (MCL) cell lines and 8 leukemic blast from blood from patients newly diagnosed with MCL. Unbiased genome-wide analysis of DNA methylation in leukemic blast from peripheral blood or pheresis products from 22 patients newly diagnosed with mantle cell lymphoma (MCL) prior to any treatment.  10 IgD+ Na ve B cells from specimens from healthy donors undergoing routine tonsillectomy were used as appropriate controls. Methylation patterns of 13 MCL cell lines were also compared.

first: Violetta

last: Leshchenko

first: Pei-Yu

last: Kuo

first: Rita

last: Shaknovich

first: David

middle: T

last: Yang

first: Tobias

last: Gellen

first: Yvonne

last: Remache

first: Marc

last: Weniger

first: Sarvish

last: Rafiq

first: Stephen

last: Suh

first: Andre

last: Goy

first: Wyndham

last: Wilson

first: Amit

last: Verma

first: Natarajan

last: Muthusamy

first: Brad

last: Kahl

first: John

last: Byrd

first: Adrian

last: Wiestner


title: Expression data from human liver with or without type 2 diabetes

city: Kanazawa

first: Hirofumi

last: Misu

address: 13-1 Takaramachi

institute: Kanazawa University

summary:
The liver may regulate glucose homeostasis by modulating the sensitivity/resistance of peripheral tissues to insulin, by way of the production of secreted proteins, termed hepatokines.
To identify hepatic secretory proteins involved in insulin resistance, we performed liver biopsies in humans with or without type 2 diabetes and conducted a comprehensive analysis of gene expression profiles.

overall_design: Samples for analysis were obtained from ten patients with type 2 diabetes and 7 subjects with normal glucose tolerance, who were admitted to Kanazawa University Hospital. Hepatic tissues were obtained with percutaneous needle liver biopsy, and immediately frozen in liquid nitrogen and stored at −80°C until use.

first: Toshinari

last: Takamura


title: Developmental stage-specific interplay between GATA1 and IGF signaling in fetal hematopoiesis and leukemogenesis

first: Zhe

last: Li


title: HeLa SCY1-like 1 esiRNA knockdown

status: Public on Jul 28 2010

city: Erlangen

first: Ingo

last: Hermann

address: Schwabachanlage 10

institute: Humangenetisches Institut

summary: Array-based characterisation of SCY1-like 1 (NM_020680.3) esiRNA knockdown

overall_design: 3 controls vs. 3 target knock downs

first: Cornelia

last: Kraus


title: HeLa cells treated with V-ATPase inhibitors or with desoxyferramine compared to HeLa in DMSO or medium with low LDL

status: Public on Jul 22 2010

city: Dallas

first: Michael

last: Roth

state: TX

address: 5323 Harry Hines Blvd

department: Biochemistry

institute: UT Southwestern

summary:
Expression data from HeLa cells treated with V-ATPase inhibitors or with desoxyferramine compared to HeLa treated with DMSO or medium with low LDL

To determine which genes respond first to low concentrations of V-ATPase inhibition, we treated HeLa cells with two different V-ATPase inhibitors, bafilomycin and phenylsalicylihalamide (LX1077) at concentrations that slow cell growth by only 20%.

To identify genes responding to expected effects of inhibiting the V-ATPase, expression data from inhibiting the V-ATPase was compared to that of chelating iron or incubating cells in medium with low LDL.

overall_design:
We used microarrays to detail the global programme of gene expression in HeLa cells at 6, 12 & 24 hours culture in the presence of V-ATPase inhibitors.  For each drug treatment, control cells were incubated at the same time with the same concentration of DMSO used as carrier for the drugs.

HeLa cells were also treated with the iron chelator, desoxiferamine for 6 or 12 hours or with medium with low LDL for 12 hours to identify genes that respond to low iron or low cholesterol. Each timepoint and each treatment has two independent replicates. Experimental samples were compared to control samples grown on the same day.

first: Sarah

last: Straud


title: Expression data from human liver cell line induced by PCB77

city: Washington DC

first: Sisir

middle: K.

last: Dutta

state: DC

address: 415 College Street, NW

institute: Howard University

summary:
Exposure to Polychlorobiphenyls (PCBs) is known to cause serious health effects in human but the gene expression profiles leading to development of different diseases is not fully understood. The knowledge of global gene expression will help us to develop early diagnostic biomarkers for PCB induced health effects.
We used microarrays to detail the global gene expression profile underlying the effects of PCB77 on human liver cells leading to identification of distinct classes of up-regulated and down-regulated genes and cellular processes.
Keywords: time course

overall_design: The HepG2 cells were grown for 48 hours in DMEM supplemented with 10% FBS and 1X Pennicillin-Streptromycin and treated with PCB77 for different times. Trizol extraction of total RNA was performed according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microgram of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HGU133 plus 2.0). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix GeneArray Scanner 3000. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

first: Supriyo

last: De

first: Somiranjan

last: Ghosh

first: Linda

last: Moses

first: Eric

last: Hoffman


title: Microarray expression analysis of PRF1 (perforin 1) haplotypes in patients with primary progressive multiple sclerosis

city: Barcelona

first: Unitat

middle: Estadistica

last: Bioinformatica

address: Passeig Vall d'Hebron, 119-129

department: Statistics and Bioinformatics Unit

country: Spain

institute: Vall d'Hebron Institut de Recerca

summary: A genetic study of the PRF1 gene has shown association of several polymorphisms with multiple sclerosis (MS). Haplotype analysis identified risk haplotypes strongly associated with male patients having the primary-progressive form of MS (PPMS). Gene expression microarrays were performed in 10 male PPMS patients carrying the risk (n=6) and protective haplotypes (n=4) in order to identify pathways associated with the risk haplotypes. Pathway analysis revealed overrepresentation of the cell killing gene ontology category among down-regulated genes in patients carrying risk haplotypes compared with patients carrying protective haplotypes.

overall_design:
Number of samples analyzed: 10
Protective haplotype samples: UOM982, EMA1473, MMC-998, CDP1842
Risk haplotype samples: UUS1554, RAU1550, RPS1011, AGS1013, PFB1530, MGA1014


title: Expression data from human liver cell line induced by PCB153

department: Biology

summary:
Exposure to Polychlorobiphenyls (PCBs) is known to cause serious health effects in human but the gene expression profiles leading to development of differnet diseases is not fully understood. The knowledge of global gene expression will help us to devlop early diagnostic biomarkers for PCB induced health effects.
We used microarrays to detail the global gene expression profile underlying the effects of PCB153 on human liver cells leading to identification of distinct classes of up-regulated and down-regulated genes and cellular processes.
Keywords: time course

overall_design: The HepG2 cells were grown for 48 hours in DMEM supplemented with 10% FBS and 1X Pennicillin-Streptromycin and treated with PCB153 for different times. Trizol extraction of total RNA was performed according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microgram of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HGU133 plus 2.0). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix GeneArray Scanner 3000. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.


title: Analysis of HeLa cells after transfection with miR-1 or miR-155, by microarray profiling

city: Singapore

first: Huili

last: Guo

address: 28 Medical Drive

country: Singapore

institute: National University of Singapore

summary: MicroRNAs (miRNAs) are endogenous ~22-nucleotide RNAs that mediate important gene-regulatory events by pairing to the mRNAs of protein-coding genes to direct their repression. Repression of these regulatory targets leads to decreased translational efficiency and/or decreased mRNA levels, but the relative contributions of these two outcomes have been largely unknown, particularly for endogenous targets expressed at low-to-moderate levels. Here, we use ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mRNA levels. For both ectopic and endogenous miRNA regulatory interactions, lowered mRNA levels account for most (≥84%) of the decreased protein production. These results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output.

overall_design: Examine mRNA expression levels in HeLa cells transfected with miR-1 or miR-155, versus mock-transfected cells, at two different time points post-transfection.

first: H

first: N

last: Ingolia

first: J

middle: S

last: Weissman

first: D

last: Bartel


title: Transcriptome analysis of human Wharton’s jelly stem cells

status: Public on Jul 26 2010

first: Woon-Khiong

last: Chan

email: dbscwk@nus.edu.sg, g0500139@nus.edu.sg

address: S2-05-19, 14 Science Drive 4

department: Biological Sciences

type:
Expression profiling by array
Third-party reanalysis

summary:
Human Wharton’s jelly stem cells (hWJSCs) are derived ethically in large amounts from the umbilical cord matrix. Besides their differentiation capabilities, WJSCs also display a notable lack of ability to form teratoma. hWJSCs have been shown to exert immunomodulatory effects and have recently been reported to kill or diminish cancer cell growth. These characteristics are important considerations for their use in cell therapy. In this transcriptome analysis, hWJSCs were profiled using Affymetrix DNA microarrays and compared to a panel of human stem cells and stromal cells. Although hWJSCs are multipotent, they expressed very low levels of the majority of stem cell markers, including POU5F1, NANOG, SOX2 and LIN28. BIRC5 has recently been shown to be required for teratoma formation in SCID mice. The lower levels of BIRC5 expression in hWJSCs compared to hESCs and the very low levels of stem cell markers might account for hWJSCs inability to form teratomas. IL12A which is known to be associated with the induction of apoptosis, was amongst the several cytokines identified to be significantly upregulated in hWJSCs. The ability of hWJSCs to compliment the host immune responses was further highlighted with the GO Biological Process analysis showing high association with immune system, chemotaxis and cell death. The ability to modulate immune responses confers hWJSCs an additional advantage in stem cell therapy and potentially allows hWJSCs as a form of treatment for cancer and immune disorders. In summary, the transcriptome profile of hWJSCs has provided indications on the genetic basis for their biological characteristics in immunomodulatory response, anti-cancer effects, and the lack of teratoma formation.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Refer to individual Series.
Two datasets analyses were performed. The first dataset contained duplicates of two hESCs, three hECCs, eight hWJSCs (passages 3, 4, 5, 8 and 20) and one hFC samples that were generated by our group. The second dataset contained a meta-analysis of the hWJSCs and hFC that were generated by our group and selected samples available from the public GEO database (human mesenchymal stem cells, umbilical vein endothelial cells, normal stroma, tumour stroma, fibroblast ).


title: Overview of gene expression alternatively modulated during the differentiation of human embryonic stem cells (hES)

status: Public on Jul 21 2010

city: EVRY

first: DENIS

middle: Alexandre

last: Jérôme

address: 5 rue Henri Desbruères

country: France

institute: INSERM/UEVE UMR 861, I-STEM, AFM

summary:
The transcriptome analysis was performed in triplicate using two human embryonic stem cells lines (hES_VUB01 and hES_SA01) by comparing the expression profiles of the undifferentiated hES cells and two types of progenitors derived from the hES cell lines: Neural progenitors (NPC) and Mesodermal progenitors (MSC).
Keywords: Cell type comparison

overall_design: hES (6 samples originated from the two cell line, in triplicate for each : hES_VUB01_1, hES_VUB01_2, hES_VUB01_3, hES_SA01_1, hES_SA01_2, hES_SA01_3) ; NPC (6 samples originated from the two cell line, in triplicate for each : NPC_VUB01_1, NPC_VUB01_2, NPC_VUB01_3, NPC_SA01_1, NPC_SA01_2, NPC_SA01_3) ; MSC (6 samples originated from the two cell line, in triplicate for each : MSC_VUB01_1, MSC_VUB01_2, MSC_VUB01_3, MSC_SA01_1, MSC_SA01_2, MSC_SA01_3).

first: Jérôme

last: Denis

first: Christelle

last: Rochon-Beaucourt

first: Lina

last: Kassar-Duchossoy

first: Cécile

last: Martinat

first: Benoite

last: Champon

first: Marc

last: Peschanski

first: Geneviève

last: Pietu


title: Expression data from human liver cells

first: Sisir

last: Dutta


title: Early passage mouse induced pluripotent stem (iPS) cells derivated from various somatic cell origins

status: Public on Jul 19 2010

city: Charlestown

first: Toshihiro

last: Shioda

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

summary:
Induced pluripotent stem (iPS) cells have been derived from various somatic cell populations through ectopic expression of defined factors. It remains unclear whether iPS cells generated from different cell types are molecularly and functionally similar. Here, we show that iPS cells obtained from fibroblasts, hematopoietic and myogenic cells exhibit distinct transcriptional and epigenetic patterns. Moreover, we demonstrate that cellular origin influences the in vitro differentiation potentials of iPS cells into embryoid bodies and different hematopoietic cells. Our results suggest that low-passage iPS cells retain a transient epigenetic memory of their somatic cells of origin, which manifests as differential gene expression and altered differentiation capacity. These observations might affect ongoing attempts to use iPS cells for disease modeling and also could be exploited for potential therapeutic applications to enhance differentiation into desired cell lineages.
This series consists of triplicated mRNA expression microarray data (Affymetrix mouse gene ST 1.0) for an early passage (passage 4) of mouse iPS cells derived from bone marrow granulocytes, splenic B cells, tail tip fibroblasts, and skeletel muscle precursor cells.

overall_design: iPS cells were generated by infecting somatic mouse cells with lentiviruses expressing Oct4, Sox2, Klf4, and cMyc. Total RNA was isolated from iPS cells at different passages.

first: Jose

last: Polo

first: Susanna

last: Liu

first: Maria

last: Figueroa

first: Warakorn

last: Kulalert

first: Sarah

last: Eminli

first: Kah

middle: Y

last: Tan

first: Effie

last: Apoltolou

first: Matthias

last: Stadtfeld

first: Yushan

last: Li

first: Toshi

first: Sridaran

last: Natesan

first: Amy

middle: J

last: Wagers

first: Ari

last: Melnick

first: Todd

last: Evans

first: Konrad

last: Hochedlinger


title: Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase

status: Public on Jul 20 2010

city: Beijing

first: Ming

last: Chen

address: Zhongguancun Nandajie 12th,Haidian Zone

country: China

institute: Biotechnology Research Institute, Chinese academy of Agricultural Sciences

summary:
RpoS, an alternative sigma factor, is critical for stress response in Escherichia coli.RpoS also acts as a global regulator for stress control of gene expression, and actually dose so in log stage and stationary stage.
To further understand the effect of environmental stresses on in ethanologenic strains, DNA microarrys was used to analyze the expression profiles of E. coli and its rpoS mutant strain.

overall_design: BW25113（rpoS-）and BW25113 were selected at log stages and stationary stage of early development for RNA extraction and hybridization on Affymetrix microarrays. To that end, we hand-selected BW25113 and BW25113（rpoS-） according at different treatments: BW25113（rpoS-）at log stage (BW25113(rpoS-) log), BW25113 at log stage (BW25113 log),BW25113（rpoS-）atstationary stage ( BW25113(rpoS-) stationary), BW25113 at stationary stage ( BW25113 stationary)

first: Min

last: Lin

first: Yongliang

last: Yan

first: Ying

last: Zhang


title: Transcriptome analysis of human Wharton’s jelly stem cells: in-house analysis

first: Woon-Khiong

last: Chan

summary: Human Wharton’s jelly stem cells (hWJSCs) are derived ethically in large amounts from the umbilical cord matrix. Besides their differentiation capabilities, WJSCs also display a notable lack of ability to form teratoma. hWJSCs have been shown to exert immunomodulatory effects and have recently been reported to kill or diminish cancer cell growth. These characteristics are important considerations for their use in cell therapy. In this transcriptome analysis, hWJSCs were profiled using Affymetrix DNA microarrays and compared to a panel of human stem cells and stromal cells. Although hWJSCs are multipotent, they expressed very low levels of the majority of stem cell markers, including POU5F1, NANOG, SOX2 and LIN28. BIRC5 has recently been shown to be required for teratoma formation in SCID mice. The lower levels of BIRC5 expression in hWJSCs compared to hESCs and the very low levels of stem cell markers might account for hWJSCs inability to form teratomas. IL12A which is known to be associated with the induction of apoptosis, was amongst the several cytokines identified to be significantly upregulated in hWJSCs. The ability of hWJSCs to compliment the host immune responses was further highlighted with the GO Biological Process analysis showing high association with immune system, chemotaxis and cell death. The ability to modulate immune responses confers hWJSCs an additional advantage in stem cell therapy and potentially allows hWJSCs as a form of treatment for cancer and immune disorders. In summary, the transcriptome profile of hWJSCs has provided indications on the genetic basis for their biological characteristics in immunomodulatory response, anti-cancer effects, and the lack of teratoma formation.

overall_design: This 'in-house' dataset contains duplicates of two hESCs, three hECCs, eight hWJSCs (passages 3, 4, 5, 8 and 20) and one hFC sample that were all generated by our group.

first: Chui-Yee

last: Fong

first: Li-Ling

last: Chak

first: Arijit

last: Biswas

first: Jee-Hian

first: Kalamegam

last: Gauthaman

first: Ariff

last: Bongso


title: Comparative genomics matches mutations and cells to generate faithful ependymoma models

city: Memphis

first: Richard

middle: James

last: Gilbertson

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St Jude Children's Research Hospital

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

summary: Genomic technologies have unmasked molecularly distinct subgroups among tumors of the same histological type; but understanding the biologic basis of these subgroups has proved difficult since their defining alterations are often numerous, and the cellular origins of most cancers remain unknown.  We sought to decipher complex genomic data sets by matching the genetic alterations contained within these, with candidate cells of origin, to generate accurate disease models.  Using an integrated genomic analysis we first identified subgroups of human ependymoma: a form of neural tumor that arises throughout the central nervous system (CNS).  Validated alterations included amplifications and homozygous deletions of genes not yet implicated in ependymoma.  Matching the transcriptomes of human ependymoma subgroups to those of distinct types of mouse radial glia (RG)—neural stem cells (NSCs) that we identified previously to be a candidate cell of origin of ependymoma - allowed us to select RG types most likely to represent cells of origin of disease subgroups.  The transcriptome of human cerebral ependymomas that amplify EPHB2 and delete INK4A/ARF matched most closely that of embryonic cerebral Ink4a/Arf-/- RG:  remarkably, activation of EphB2 signaling in this RG type, but not others, generated highly penetrant ependymomas that modeled accurately the histology and transcriptome of one human cerebral tumor subgroup (subgroup ‘D’).  Further comparative genomic analysis revealed selective alterations in the copy number and expression of genes that regulate neural differentiation, particularly synaptogenesis, in both mouse and human subgroup ‘D’ ependymomas; pinpointing this pathway as a previously unknown target of ependymoma tumorigenesis.  Our data demonstrate the power of comparative genomics to sift complex genetic data sets to identify key molecular alterations in cancer subgroups.

overall_design:
[human mRNA] samples: 83 human ependynoma primary tumors were collected and clustered into distinct classes by unsupervised methods and then compared to mouse model data.
[mouse mRNA] samples: 192 mouse tumors and cell lines were collected and clustered into distinct classes by unsupervised methods and then compared to human tumors.
[human miRNA] samples: 64 human ependynoma primary tumors were collected and miRNA expression was assesed and compared to genomic expression


title: Expression Data from BALB/c and Stat6-deficient bone marrow derived macrophages (BMDM)

city: München

first: Silke

last: Huber

address: Goethestrasse 31

department: Institute for Immunology

institute: LMU Munich

summary:
We used microarrays to find Stat6 dependent genes in control and IL-4 exposed bone marrow derived macrophages.

Alternatively activated macrophages (AAM) accumulate in tissues during Th2-associated immune responses like helminth infections and allergic disorders. These cells possess potent inhibitory activity against T cells. The differentiation of AAM depends on IL-4/IL-13-mediated activation of the transcription factor Stat6. Stat6 is also required in AAM to induce several genes, such as YM1, FIZZ1 and Arginase1.

overall_design: Macrophages were differentiated from bone marrow cells in supplemented RPMI 1640 for 7 days in the presence of 10% supernatant from the M-CSF producing fibroblast cell line L929. After removal of nonadherent cells, macrophages were detached using 5mM EDTA treatment, washed, counted, and replated at a density of 10x6 cells/mL. Macrophages were cultured for 24 hours in medium (control) or in the presence of IL-4 (10mg/mL). F4/80 positive macrophages were sorted with a purity of  99% and RNA was isolated (Trizol/Chloroform) according to the manufacturer's instructions. RNA was labeled (biotin), fragmented, and hybridized to the arrays according to the manufacturer's recommendations.

first: David

last: Voehringer

first: Reinhard

last: Hoffmann


title: Short-term (12h) ATRA treatment of embryoid bodies.

status: Public on Jul 16 2010

city: Debrecen

first: Zoltan

last: Simandi

address: Egyetem ter 1

department: BMBI

country: Hungary

institute: University of Debrecen

summary: We used microarrays to detail the global programme of gene expression in embryonic stem cells, early differentiated embrioid bodies and effect of short-term ATRA treatment.

overall_design: Expression data from undifferentiated mouse embryonic stem cells (D3), four-day old aggregated embrioid bodies and 12h atRA or DMSO treated embrioid bodies. Three replicates each.

first: Laszlo

last: Nagy


title: Integration of transcript expression, copy number and LOH analysis of infiltrating ductal carcinoma of the breast

status: Public on Jul 17 2010

city: Augusta

first: Lesleyann

last: Hawthorn

state: GA

department: Molecular Oncology

institute: Medical College of Georgia Cancer Center

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

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

overall_design: Refer to individual Series


title: Comparison of gene expression between CD133+ and CD133- SW620 human colon cancer cells

status: Public on Jul 29 2010

city: shanghai

first: Jian-Ming

last: Feng

address: zuzhongzhi Road

institute: Shanghai institute of Materia Medica

summary: CD133 has been widely used for identification and isolation of cancer stem cells in tumors although its role as a marker for cancer stem cell is still controversial . We isolated the CD133+ and CD133- cells from SW620 human colon cancer cell line and compared their biological characteristics, such as tumorigenicity,drug sensitivity, etc. Our study revealed that CD133+ SW620 cells were more tumorigenic and resistant to anti-cancer drugs. Correspondingly, they displayed different gene expression profile. However, it was observed that CD133- cells and CD133+ cells could mutually convert, indicating that CD133 expression was under dynamic and reversible regulations which might impose significant infulence on cells behaviors. Thus, our data challenge the role of CD133 as a marker for cancer stem cell.

overall_design:
There are two populations with distinct expression of CD133 in SW620 human colon cancer cell line. Microarray assays were employed to investigate the differentially expressed genes between the two populations, which may possess different tumorigenetic potential and sensitivity to anti-cancer drugs.
CD133+ and CD133- cells were isolated from  human colon cancer SW620 cell line  by magnetic cell sorting system. The clones from sorted CD133+ or CD133- populations were established. Clone cells were expanded and were further purified by using CD133 cell isolation kit before microarray assays.

first: Jian

middle: M

last: Ding

first: Ze

last: Miao


title: Gene expression profiles of E13.5 developing podocyte in the developing kidney isolated from MafB-GFP transgenic mice using FACS on 1.0 ST Array chip. (GUDMAP Series ID: 32)

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

summary: The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney. The central thesis is straightforward. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in FACS isolated components of the developing kidney. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone.

overall_design: MafB-GFP BAC transgenic mice were utilized to isolate the podocyte cells from the developing embryonic kidneys. Podocyte cells were isolated from the kidney using trypsinization and FACS. RNA was isolated and the gene expression profiles were determined by microarrays.

first: Steve

last: Potter

first: Eric

last: Brunskill


title: Encyclopedia of the expression levels of all genes in multiple components of the developing kidney


title: Compounds profiling on MCF7

status: Public on Jul 14 2010

city: Nerviano

first: Roberta

last: Bosotti

state: MI

address: viale Pasteur,10

department: Biotechnology

institute: Nerviano Medical Sciences srl

summary: The effects of several compounds on the MCF7 human adenocarcinoma mammary cell line were analysed by gene expression profiling.

overall_design:
Tested compounds: HSP90 inhibitors: 17AAG (Tanespimycin), NVP-AUY922,  NMS-E973 (cpd developed at NMS). CDK inhibitors: CDK-887 (cpd developed at NMS). Topoisomerase inhibitors: Doxorubicin, SN38 (active metabolite of Irinotecan).

The MCF7 cell line was treated with the different compounds for 6 hours at a dose equal to 5 times the IC50. Untreated MCF7 cells were used as a control. Two replicates per treatment.

first: Emanuela

last: Scacheri

first: Antonella

last: Isacchi

first: Laura

last: Raddrizzani


title: Gene expression profiles of renin producing cells in newborn and adult kidney isolated from Renin-YFP transgenic mice using FACS. (GUDMAP Series ID: 29)

summary: The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney.  The central thesis is straightforward. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in FACS isolated components of the developing kidney. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone

overall_design: Renin-YFP transgenic mice were utilized to isolate renin producing cells from the kidneys of either P0 neonatal pups or Adult mice. Renin producing cells were isolated from the kidney by fluorescent activated cell sorting (FACS). RNA was isolated from FACS sorted cells and the gene expression profiles were determined by microarrays.

first: A

last: Gomez


title: Flavopiridol profiling on A2780

summary: The effects of the CDK inhibitor Flavopiridol on the A2780 human adenocarcinoma ovary cell line were analysed by gene expression profiling.

overall_design: A2780 cells were treated with Flavopiridol for 6 hours at a dose equal to 5 times the IC50. Untreated A2780 cells were used as a control. Two replicates per treatment.

first: Giorgio

middle: G

last: Galli


title: Gene expression profiles of cap mesenchyme and renal vesicle isolated between P0-P4 from Crym-EGFP neonatal transgenic mice using FACS. (GUDMAP Series ID: 28)

summary: The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney.  The central thesis is straightforward. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in FACS isolated components of the developing kidney. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone.

overall_design: At E18.5, pups were isolated from CRYM-BAC transgenic mice and fostered to CD-1 mice.  Cap mesenchyme cells were isolated from the kidney by fluorescent activated cell sorting (FACS) on postnatal days 0, 1, 2, 3, and 4.  RNA was isolated from FACS sorted cells and  the gene expression profiles were determined by microarrays.


title: Gene expression profiles of E15.5 developing podocytes in the developing kidney isolated from MafB-GFP transgenic mice using FACS on 1.0 ST Array chip. (GUDMAP Series ID: 33)


title: CDK inhibitors and flavopiridol profiling on A2780 and MCF7 cells


title: CDK inhibitor PHA-848125 gene expression profiling on MCF7 cell line

summary: The effects of the CDK inhibitor PHA-848125  (referred to as CDK-125) on the MCF7 human adenocarcinoma mammary cell line were analysed by gene expression profiling.

overall_design: The MCF7 cell line was treated with PHA-848125 for 6 hours at a dose equal to 5 times the IC50. Untreated MCF7 cells were used as a control. Two replicates per treatment.


title: Pluripotent embryonic stem cells and multipotent adult germline stem cells reveal similar transcriptomes including pluripotency-related genes

status: Public on Jul 12 2010

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: DNA microarray analysis was performed with mouse multipotent adult germline stem cells (maGSCs) and embryonic stem cells (ESCs) from different genetic backgrounds cultured under standard ESC culture conditions and under differentiation-promoting conditions by the withdrawal of Leukemia Inhibitory Factor (LIF) and treatment with Retinoic Acid (RA). The analyzed undifferentiated cell lines are very similar based on their global gene expression pattern and show 97-99% identity dependent on the analyzed background. Only 621 genes are differentially expressed in cells derived from mouse 129SV-background, and 72 genes show differences in expression in cells generated from transgenic Stra8-EGFP/Rosa26-LacZ-background. Both maGSCs and ESCs express the same genes involved in the regulation of pluripotency, and even show no differences in the expression level of these genes. When comparing maGSCs with previously published signature genes of other pluripotent cell lines we could find that maGSCs share a very similar gene expression pattern with embryonic germ cells (EGCs). Also after differentiation of maGSCs and ESCs the transcriptomes of the cell lines are nearly identical which suggests that both cell types differentiate spontaneously in a very similar way. This is the first study comparing ESCs and a pluripotent cell line derived from an adult organism (maGSCs) on transcriptome level.

overall_design: For the comparison of different stem cell types (6 conditions) we hybridized 3 biological replicates per condition

first: Sandra

last: Meyer

first: Jessica

last: Nolte

first: Lennart

last: Opitz

last: Salinas-Riester

first: Wolfgang

last: Engel


title: A gene expression profile of BRCAness that is associated with outcome in ovarian cancer

status: Public on Jul 11 2010

city: boston

first: panagiotis

last: konstantinopoulos

address: 330 brookline av

department: hem/onc

institute: bidmc

summary:
A gene expression profile of BRCAness was defined in publicly available expression data of 61 patients with epithelial ovarian cancer (34 patients with BRCA-1 or BRCA-2 mutations and 27 patients with sporadic disease). This dataset is publicly available at http://jnci.oxfordjournals.org/cgi/content/full/94/13/990/DC1
The BRCAness profile was correlated with outcome in 70 patients with epithelial ovarian cancer and known outcome data.

overall_design: Correlation with outcome

first: Elena

last: Fountzilas


title: Gene expression profiling in Setx shRNA P19 cells, wild type human Setx P19 transfected cells with and without retionoic acid

status: Public on Jul 10 2010

city: brescia

first: andrea

last: bozzato

address: viale europa 11

institute: university of brescia

summary:
Analysis of senataxin effect on neuronal differentiation and neurite growth in RA-treated P19 cells by modulating senataxin expression levels.
Senataxin silencing does not grossly affect the gene expression profiles of P19 cells

overall_design: At day one total RNA from Setx shRNA P19 cells, wild type human Setx P19 transfected cells with and without retionoic acid were used to compare gene expression profiling versus P19 control cells

first: Andrea

last: Bozzato


title: Gene expression of Kit225 cells upon NC1153 treatment

status: Public on Jul 08 2010

first: Zsuzsanna

middle: S.

last: Nagy

address: Nagyerdei krt. 98

department: Biochemistry and Molecular Biology

summary:
NC1153 was shown to inhibit JAK3 tyrosine kinase. Lymphocytes survival depends on the integrity of STAT5, the primary downstream target of JAK3.
In this study microarrays were used to test the effect of a JAK3 inhibitor, NC1153, on the gene expression profile of a human leukemia cell line.

overall_design: Kit225 human leukemia cells were treated with NC1153 or DMSO (vehicle) for 12 h then harvested for RNA isolation.


title: Striatal microRNA controls cocaine intake through CREB signalling

city: Jupiter

first: Paul

middle: J.

last: Kenny

address: 130 Scripps Way

department: Molecular Therapeutics

institute: The Scripps Research Institute - Florida

summary:
MicroRNAs (miRNAs) regulate many basic aspects of cell biology including neuronal plasticity, but little is known of their roles in drug addiction. Extended access to cocaine can trigger the emergence of compulsive drug-seeking behaviors, but molecular mechanisms regulating this process remain unclear. Here we report that microRNA-212 (miR-212) is upregulated in the dorsal striatum of rats with extended access to cocaine. Striatal overexpression of miR-212 decreases, whereas its inhibition increases cocaine intake in rats with extended but not restricted drug access, suggesting that miR-212 serves as a protective factor against the development of compulsive drug seeking. The transcription factor CREB (cAMP response element-binding protein) is considered a core regulator of cocaine reward. We show that miR-212 controls responsiveness to cocaine by dramatically amplifying striatal CREB signaling. This action occurs through miR-212-enhanced Raf-1 activity, resulting in adenylyl cyclase sensitization and increased expression of the essential CREB co-activator TORC (Transducer of Regulated CREB; also known as CRTC). Our findings suggest that striatal miR-212 signaling plays a key role in vulnerability to addiction, and that noncoding RNAs such as the miRNAs may serve as novel targets for the development of anti-addiction therapeutics.
To identify potential targets for miR-212, we transfected cells with a vector to overexpress miR-212 or an empty vector. We then analyzed profiled gene expression using Affymetrix arrays.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design:
Human Affymetrix Study: Cells were transfected with a vector to overexpress miR-212 or an empty vector. We then analyzed profiled gene expression using Affymetrix arrays.

The complete, unfiltered set of signal intensity data for Samples miR-212 and pMIF, including miR-212/pMIF ratios, are in the supplementary file at the foot of the record. Probes excluded from analysis (pMIF intensity <100) are indicated in the supplementary file by a no in the far-right column, 'Passed data filtering and included in analysis: no/yes'. Probes that were included in the analyses (pMIF intensity >100) are indicated in the supplementary file by a yes in the 'Passed data filtering and included in analysis: no/yes' column.

Rat miRNA Study: Rats were permitted access to intravenous cocaine self-administration (0.5 mg/kg/infusion) for 7 consecutive days during restricted (1-h) or extended (6-h) daily sessions. Control rats remained coaine-naïve throughout. 24-h after the last session the dorsal striatum from each rats was removed, and RNA extracted for microarray profiling. There was a total of n=6 rats per access condition. RNA from 2 rats per access condition were pooled on to arrays, for a total of 3 arrays per access condition, and 9 arrays in total.


title: Expression data from MMP-8 wild type and KO mice with or without arthritis

city: Santiago de Compostela

first: Carmen

last: Conde

state: A Coruña

address: Choupana s/n

institute: Hospital Clinico Universitario

summary: Rheumatoid arthritis is an autoimmune disease in which joint inflammation lead to progressive cartilage and bone destruction. Matrix metalloproteinases (MMP) implicated in homeostasis of extracellular matrix (ECM) play a central role in cartilage degradation. The aim of this study was to investigate the role of MMP-8 (collagenase-2) suppression in the K/BxN serum-transfer arthritis model.

overall_design: Three male mice of each following groups: MMP-8 wild type and arthritic mice, MMP-8 wild type without arthritis (wild type control), MMP-8 KO and arthritic mice and MMP-8 KO without arthritis (KO control) were selected for RNA extraction, from ankle joints, and hybridation on Affymetrix microarrays. Male mice were used because they showed a trend to higher arthritis severity compared to female mice. In arthritic mice, ankle joints were taken 7 days after arthritis induction.

first: Samuel

last: García

first: Jerónimo

last: Forteza

first: Carlos

last: López-Otin

first: Juan

last: Gómez-Reino

first: Antonio

last: González


title: Gene expression profiles of adult visceral epithelium (syn: podocyte layer) isolated from MafB-GFP transgenic mice using FACS. (GUDMAP Series ID: 31)

first: GUDMAP

last: Developers

overall_design: Mafb-EGFP BAC transgenic mice were utilized to isolate the podocyte cells from the glomerlus from adult kidneys. The podocyte cells were isolated from the kidney using a combination of Collagenase A digestion, sieving and tyrpsinization. RNA was isolated and the gene expression profiles were determined by microarrays.

first: Steve

last: Potter

first: Eric

last: Brunskill


title: Gene expression profiles of adult renal corpusle isolated using sieving techniques. (GUDMAP Series ID: 30)

summary: The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney. The central thesis is straightforward. The use of microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in isolated components of the developing kidney. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone.

overall_design: CD-1 mice were utilized to isolate the renal corpusle from the kidneys of  adult mice. The  renal corpusle were isolated from the kidney using a sieving procedure.   RNA was isolated and the gene expression profiles were determined by microarrays.


title: Expression data from TKI258 treated 4T1 cells

status: Public on Jul 07 2010

city: Basel

first: Julien

middle: Herve

last: Dey

address: Maulbeerstrasse

department: growth control

country: Switzerland

institute: FMI

summary:
4T1 mouse mammary carcinoma cells have an autocrine FGFR active loop leading to constitutive activation of downstream signaling pathways. We found that FGFR inhibitors have a strong effect on the proliferation and survival of these cells.
We used microarray to understand the contribution of FGFR signaling to the tumorigenic phenotype of the 4T1 cells.

overall_design: 4T1 cells were grown in tissue culture and treated with TKI258 or DMSO as vehicle control for 16 hours. The RNA were extracted from three individual dishes per condition and hybridized on Affimetrix microarrays.

middle: H

first: Edward

last: Oakeley


title: Gene Expression Atlas for Human Embryogenesis

city: Wuhan

first: Wenxin

last: Li

email: liwxlab@whu.edu.cn, guomx@whu.edu.cn, jinyangc13@126.com, sparkler830305@hotmail.com

state: Hubei

address: Wuhan University, Luojia Hill,Wuhan 430072,China

department: College of Life Science

institute: Wuhan Univeristy

summary:
Gene expression profiling has provided critical insights into the molecular pathways underlying development of model organisms, however little information is available on regulated gene expression during human embryogenesis. We have now filled this important gap of knowledge by performing genome-wide microarray analysis of the Homo sapiens gene expression during the 4-9th week, a period when most organs develop.
We analyzed individually 3 embryos for each of the 4th, 5th, 6th, 7th, 8th, and 9th week of human embryonic development by using the Affymetrix U133 plus 2.0 human GeneChip array.About half of all human genes are expressed and 18.6% of the expressed genes were significantly regulated during this important period. We further identified over 5000 regulated genes, most of which were previously not known to be associated with animal development.  Our study also revealed that the genes involved here are distinct from those during early embryogenesis, which include three groups of maternal genes. Furthermore, we discovered that genes in a given developmental process are coordinately regulated. This led us to develop an easily searchable database of this entire collection of gene expression profiles, allowing for identification new genes important for a particular developmental process/pathway and deducing the potential function of a novel gene. The validity of the predictions from the database was demonstrated with two examples through spatiotemporal analyses of the two novel genes. Such a database should serve as a highly valuable resource for the molecular analysis of human development and pathogenesis.

overall_design: Human embryos were obtained from therapeutic termination of pregnancy induced by Mifepristone. Morphologically normal embryos were selected and staged according to the Carnegie classification and the Chinese embryonic developmental characteristics. Each whole embryo was micro-dissected from an intact trophoblast and stored directly in liquid nitrogen or homogenized using Trizol solution and then stored at -80oC. Total RNA was isolated from each whole embryo individually and each of the 3 RNA samples for each developmental time point was independently analyzed on a Human U133 plus 2.0 Genome Oligonucleotide Array.

first: Hong

last: Yi

first: Ming-Xiong

last: Guo

first: Lu

last: Xue

first: Jian

last: Ma

first: Yan

last: Zeng

first: Wei

last: Wang

first: Jin-Yang

last: Cai

first: Hai-Ming

last: Hu

first: Hong-Bing

last: Shu

first: Yun-Bo

last: Shi

first: Wen-Xin


title: Expression in Duodenum of Wild type and Onecut-2 knockout mice at postnatal days 15 and 30

city: Cincinnati

first: Bruce

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

summary: Ablation of the mouse gene for Onecut-2 was reported previously, but characterization of the resulting knockout mice was focused on in utero development, principally embryonic development of liver and pancreas.  Here, we examine postnatal development of these Onecut-2 knockout mice, especially the critical period prior to weaning. Microarray technology was used to determine the effect of Onecut-2 ablation on gene expression in duodenum, whose epithelium has among the highest levels of Onecut-2.  A subset of intestinally expressed genes showed dramatically altered patterns of expression.  Many of these genes encode proteins associated with the epithelial membrane, including many involved in transport and metabolism.  Previously, we reported that Onecut-2 was critical to temporal regulation of the adenosine deaminase gene in duodenum.  Many of the genes with altered patterns of expression in the Onecut-2 knockout mouse duodenum displayed changes in the timing of gene expression.

overall_design: Duodenal segments were isolated at postnatal days 15 and 30 from wild type 129 mice and 129 mice with the Onecut-2 gene ablated .  Total RNA was isolated in biological triplicate for each experimental time point.  Each triplicate contained RNA from 5-8 mice of the appropriate age and genotype.  Affymetrix microarray technology was used to compare gene expression in wild type duodenum at d15 to gene expression in wild type duodenum at d30 and to compare gene expression in duodenum from Onecut-2 knockout mice at d15 and d30 to each other and to the expression in wild type duodenum.

first: Dan

middle: A

last: Wiginton


title: Expression data from TKI258 treated 4T1 tumors

summary:
4T1 mouse mammary carcinoma cells have an autocrine FGFR active loop leading to constitutive activation of downstream signaling pathways. We found that FGFR inhibitors have a strong effect on 4T1 tumors in-vivo.
We used microarray to understand the contribution of FGFR signaling to the tumor formation upon TKI258 treatment.

overall_design: 4T1 cells were injected in the 4th mammary gland of Balb/C mice. After 7 days, daily treatment with TKI258 or water was performed for 14 days. At the end of the experiment, the RNA were extracted from three individual tumors per condition and hybridized on Affimetrix microarrays.


title: Differential Regulation of Mitogen-Activated Protein Kinases by Acetaminophen in TAMH cells

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Acetaminophen (APAP), a widely used analgesic and antipyretic that is considered to be relatively safe at recommended doses, is the leading cause of drug-induced liver failure in the United States.  3’-Hydroxyacetanilide (AMAP), a regioisomer of acetaminophen is useful as a comparative tool for studying APAP-induced toxicity since it is non-toxic relative to APAP.  TGF-alpha transgenic mouse hepatocytes were treated with both isomers to investigate mitogen-activated protein kinase cascades in order to differentiate their toxicological outcomes.  Mitogen-activated protein kinase (MAPK) cascade expression and activation were measured using microarray and Bioplex technologies, respectively.  APAP treatment led to c-Jun N-terminal kinase (JNK) activation, whereas AMAP treatment led to the activation of extracellular-signal-regulated protein kinase (ERK).  The microarray data suggested APAP treatment may upregulate gene expression at multiple levels of the JNK cascade including a JNK-related scaffold protein.  Expression data was related to phosphoprotein levels using the Bioplex system.  APAP treatment led to a significant activation of JNK compared to its regioisomer.  In contrast, microarray analysis of AMAP showed a slight upregulation of ERK gene activity.  Furthermore, Bioplex data showed AMAP treatment led to significant ERK phosphorylation compared to APAP.  Cell viability assays confirmed that  APAP-induced activation of JNK was related to higher rates of cell death, whereas activation of ERK by AMAP may be cytoprotective.

overall_design: 27 arrays, 9 experimental groups, 2hr AMAP, 2hr APAP, 2hr Control, 6hr AMAP, 6hr APAP, 6hr Control, 24hr AMAP, 24hr APAP, 24hr Control.

first: Richard

middle: P

last: Beyer

first: Brendan

last: Stamper

first: Fred

last: Farin

first: Theo

middle: K

last: Bammler

first: Sidney

last: Nelson


title: Identification of genes controlled by LMX1B in the developing limb, embryonic day (E) 13.5

status: Public on Jul 06 2010

city: Montreal

first: Xiao Wei Wendy

last: Gu

state: Quebec

address: 110, avenue des Pins Ouest

department: Neural Circuit Development Laboratory

country: Canada

institute: IRCM

summary: A control vs. genetic knockout experiment aimed at determining what RNAs are upregulated or downregulated in E13.5 mouse limb tissue lacking the Lmx1b gene. Because LMX1B is required for dorsal-ventral patterning of the limb, this screen gives insight into what putative downstream targets of Lmx1b contribute to dorsal-ventral patterning.

overall_design: The forelimb or hindlimb of wild-type controls or Lmx1b loss-of-function mutants was used for RNA extraction. Each array was hybridized with cDNAs of an individual limb.

first: Wendy

middle: X

first: Artur

last: Kania