title: Sexually dimorphic transcriptomic responses in the largemouth bass to the neuroactive pesticide dieldrin

status: Public on Apr 17 2011

city: Gainesville

first: Christopher

last: Martyniuk

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

summary: In this study, both male and female sexually regressed largemouth bass (Micropterus salmoides) (LMB) were fed a nominal concentration of 3.0 mg dieldrin/kg in feed for 60 days.  A third group of male LMB was fed both 3.0 mg dieldrin/kg dieldrin and 0.7 mg E2/kg  in feed.  E2 was used as a model compound to elicit estrogenic effects via ER signaling.

overall_design: There were four samples analyzed for 1) control males 2) control females 3) males fed 3 mg/kg dieldrin 4) females fed 3.0 mg/kg dieldrin, and 5) males fed 3.0 mg/kg dieldrin +  0.7 mg/kg E2. There was a total of 20 microarrays and sample processed.

first: Chris

first: Nicholas

last: Doperalski

first: Kevin

last: Kroll

middle: S

last: Barber

first: Nancy

last: Denslow


title: Gene expression screening during early granulation tissue formation (I)

status: Public on Dec 07 2010

city: Turku

first: Miretta

last: Tommila

address: Kiinamyllynkatu 10

department: Lääketieteellisen biokemian ja genetiikan laitos

country: Finland

institute: Turun yliopisto

summary: Hydroxyapatite-coated cellulose induces a quicker and stronger inflammatory response compared to uncoated cellulose. Furthermore, the coated cellulose increases the homing at circulating bone-marrow derived progenitor cells. For this reason, Illumina microarray was used to study the early gene expression of  the forming granulation tissue in the hydroxyapatite-coated sponges.

overall_design: A total of six samples from six different rats was analyzed.  Three samples were collected after 24 hours of implantation and three after 72 hours of implantation.

first: Christoffer

last: Stark

first: Anne

last: Jokilammi

first: Ville

last: Peltonen

first: Risto

last: Penttinen

first: Erika

last: Ekholm


title: Exon array analysis reveals neuroblastoma tumors have distinct alternative splicing patterns according to stage and MYCN amplification status

status: Public on Mar 01 2011

city: Gaithersburg

first: Javed

last: Khan

state: MD

address: 8717 Grovemont Circle

country: USA

institute: National Cancer Institute

summary: This dataset contains Human Exon 1.0 ST Array data from 47 neuroblastoma samples

overall_design: In this study, we used exon array profiling to investigate global alternative splicing pattern of 47 neuroblastoma samples in stage 1 and stage 4 with normal or amplified MYCN copy number (stage 1-, 4- and 4+).

first: Xiang

last: Guo

first: Qing-Rong

last: Chen

first: Yong

last: Song

first: Jun

last: Wei


title: Small Molecule Amiloride Modulates Oncogenic RNA Alternative Splicing to Devitalize Human Hepatocellular Carcinoma Huh-7 Cells

status: Public on Mar 31 2011

city: Hsin-Chu

first: Sophia

last: Chan

address: 75 Bo-Ai Street

department: Institute of Bioniformatics and Systems Biology

country: Taiwan

institute: National Chiao Tung University

summary: Screening small molecules and drugs for activity to modulate alternative splicing, we found that amiloride, distinct from four other intracellular pH-affecting analogues, could “normalize” the splicing of BCL-X, HIPK3 and RON/MISTR1 transcripts in human hepatocellular carcinoma Huh-7 cells. To elucidate the underlying mechanisms, our proteomic analyses of amiloride-treated cells detected hypo-phosphorylation of splicing factor SF2/ASF and also decreased levels of SRp20 and two un-identified SR proteins. We further observed decreased phosphorylation of AKT, ERK1/2 and PP1, while increased phosphorylation of p38 and JNK, suggesting that amiloride treatment down-regulated kinases and up-regulated phosphatases in the signal pathways known to affect the splicing factor protein phosphorylation. The amiloride effects of splicing factor protein hypo-phosphorylation and“normalized”oncogenic RNA splicing were both abrogated by pre-treatment with a PP1 inhibitor. We then performed global exon array analysis of Huh-7 cells treated with amiloride for 24 hours. Using gene array chips (Affymetrix GeneChip® Human Exon 1.0 ST Array of >518000 exons of 42974 genes) for exon array analysis (set parameters of correlation coefficient ≥ 0.7, splicing index ≤ -1.585 , and log2 ratio ≤ -1.585), we found that amiloride influenced the splicing patterns of 551 genes involving at least 584 exons, which included 495 known protein-coding genes involving 526 exons, many of which play key roles in functional networks of ion transport, extracellular matrix, cytoskeletons  and genome maintenance. Cellular functional analyses revealed subsequent invasion and migration defects, cell cycle disruption, cytokinesis impairment, and lethal DNA degradation in amiloride-treated Huh-7 cells. This study thus provides mechanistic underpinnings for exploiting small molecule modulation of abnormal RNA splicing for cancer therapeutics.

overall_design: Target was prepared from 3 biological replicates of 0.5mM amiloride-treatment for 24hr and 3 control untreatment from Huh7 cell line and hybridized to the Affymetrix Human Exon 1.0 ST Array. The values of the hybridized probesets were normalized and analyzed for gene expression using dChip2010 software.

first: Jan-Gowth

last: Chang

first: Lu-Ping

last: Chow

first: Den-Mei

last: Yang

first: Hui-Hua

last: Lin

first: Wen-Ling

first: Hsien-Da

last: Huang

first: Wen-Hsin

first: Ya-Sian

first: Cheng-Hao

last: Hung

first: Wen-Kuang


title: Exon-array profiling of squamous cell carcinoma and adenocarcinoma in human cervical FFPE samples

status: Public on Feb 17 2011

city: Manchester

first: Hui Sun

last: Leong

address: Wilmslow Road

department: The University of Manchester

country: United Kingdom

institute: Cancer Research UK Manchester Institute

summary: Degradation and chemical modification of RNA in formalin-fixed paraffin-embedded (FFPE) samples hamper their use in expression profiling studies. In this study, we investigated the feasibility of gene expression signature generation from archival FFPE materials. Nineteen cervical squamous cell carcinoma (SCC) and nine adenocarcinoma (AC) 10~16-year-old FFPE samples were profiled using Affymetrix Exon 1.0 ST arrays. A comparison of the global gene expression changes between SCC and AC revealed 1217 differentially expressed genes. Of these, 1062 showed significantly higher expression levels in SCC relative to AC, and 155 genes were found to be specifically upregulated in AC.  When the 1217-gene signature was tested on a fresh-frozen human non-small cell lung cancer (NSCLC) series, it correctly separated the 58 NSCLC samples into SCC and AC. In conclusion, our results showed that clinically and biologically relevant gene expression profiles can be derived from FFPE samples with Exon array profiling.

overall_design: The study population contains 28 FFPE human cervix samples (19 SCC and 9 AC). Histopathology assessment and p63 IHC were performed on all samples to confirm their histological subtypes. Total RNA was extracted and hybridised to Affymetrix Human Exon 1.0 ST arrays. Expression values were normalised using RMA. Only exonic probesets that were flagged as present (DABG< 0.01) in at least three samples were retained for further analysis. LIMMA was used to identify probesets that were differentially expressed between SCC and AC subtypes, using FDR ≤ 0.01 and absolute fold-change ≥ 2 as cutoff.

first: John

last: Hall

first: Hui

first: Lucile

last: Armenoult

first: Gillian

middle: E

last: Newton

first: Helen

middle: R

last: Valentine

first: Joely

middle: J

last: Irlam

first: Carla

last: Möller-Levet

first: Kanwal

middle: A

last: Sikand

first: Stuart

middle: D

last: Pepper

first: Crispin

last: Miller

first: Catharine

middle: M

last: West


title: Transcript and differential exon level changes in T-REx-293 cells after Tat-SF1 depletion

status: Public on Feb 16 2011

city: Durham

first: Heather

email: hnb3@duke.edu, hbmiller@ncsu.edu

state: NC

address: Research Drive

department: Molecular Genetics and Microbiology

institute: Duke University

summary: In order to identify genes with different overall transcript levels or differential exon levels (alternative processing) between the groups Control and Tat-SF1KD, we studied 11 hybridizations on the HumanExon10ST array using mixed model analysis of variance. 526 genes with significant transcript level differences between the groups and 1397 genes with significant differential exon levels were found, including 99 genes with both transcript and exon level differences (p<0.01).

overall_design: Total RNA from cells under 2 different conditions were collected: control cells and Tat-SF1 KD cells. Cells stably expressing an empty vector or a GFP-specific shRNA composed the control group. Two different shRNAs specific to Tat-SF1 composed the Tat-SF1 KD group. Biological triplicates were isolated from each of the above samples, resulting in a total of 12 samples. One sample (Empty Vector, biological replicate 3) did not pass quality control metrics, and was excluded from the analysis, leaving 11 final samples.

middle: B

first: Mariano

last: Garcia-Blanco

first: Timothy

middle: L

last: Robinson


title: Rapamycin effect on gene expression: dependence on c-Myc

status: Public on Oct 25 2010

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

summary: This experiment utilized rat fibroblasts that are wild-type for c-Myc (TGR-1 cells) and null for c-Myc (HO15.19 cells).  Both were treated treated with rapamycin for 24 hr (comparison group, vehicle control).

overall_design: Cells were studied under conditions that supported proliferation.  Rapamycin (50nM or DMSO vehicle control) was added for 24 hr after which RNA was prepared and analyzed.

first: Rosa

middle: H

last: Jimenez

first: Joan

last: Boylan

last: Sedivy

first: Philip

last: Gruppuso


title: Epigenetic Regulation of IL17RC in Age-related Macular Degeneration (MeDIP-chip)

status: Public on Mar 21 2011

city: Bethesda

first: Lai

last: Wei

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

type: Methylation profiling by genome tiling array

summary:
Age-related macular degeneration (AMD) is the leading cause of irreversible blindness in the elderly population worldwide. Recent studies have demonstrated strong genetic associations between AMD and single nucleotide polymorphisms (SNPs) within genes such as CFH and HTRA1. However, we found monozygotic twins had discordant AMD phenotypes (one with disease, the other without disease), suggesting that an epigenetic mechanism may control the pathogenesis of AMD.

We obtained genomic DNA from the twins' peripheral blood mononuclear cells (PBMCs) and subjected it to DNA methylation-chip analysis (MeDIP-chip) that profiled genome-wide DNA methylation patterns on promoters of all genes and microRNAs. Our MeDIP-chip analysis identified 256 genes with hypo-methylated promoters only in the twins with AMD and 744 genes with hyper-methylated promoters only in the twins with AMD. Importantly, the promoter region of IL17RC was associated with hypo-methylated CpG sites only in the twins with AMD but not in the twins without AMD.

overall_design: Three pairs of twins with discordant AMD phenotypes. MeDIP-chip analysis of DNA methylation patterns in PBMCs.

first: Robert

last: Nussenblatt

first: Robyn

last: Guymer

first: Paul

last: Baird


title: Retinoid X receptor gamma signaling accelerates CNS remyelination

status: Public on Oct 22 2010

city: Cambridge

first: Julien

last: Bauer

state: Cambridgeshire

address: Tennis court road

institute: Cambridge University

summary: The molecular basis of CNS myelin regeneration (remyelination) is poorly understood.  Here we generate a comprehensive transcriptional profile of the separate stages of spontaneous remyelination following focal demyelination in the rat CNS.  White matter tracts in the rat caudal cerebellar peduncles were focally demyelinated using 0.1% ethidium bromide, the lesions were isolated using laser capture microdissection at 5, 14 and 28 days postlesion, followed by RNA extraction and Illumina beadarray analysis of differentially expressed transcripts.  We found transcripts encoding retinoid acid receptor RXR-gamma is highly differentially expressed during remyelination, and that oligodendrocyte lineage cells express RXR-gamma in rat tissues undergoing remyelination and in active and remyelinated MS lesions. RXR-gamma knockdown by RNA interference or RXR-specific antagonists severely inhibit oligodendrocyte differentiation in culture.  In RXR-gamma deficient mice, adult oligodendrocyte precursor cells efficiently repopulate lesions following demyelination, but display delayed differentiation into mature oligodendrocytes.  Administration of the RXR agonist 9-cis-retinoic acid to demyelinated cerebellar slice cultures and to aged rats following demyelination results in more remyelinated axons. RXR-gamma is therefore a positive regulator of endogenous oligodendrocyte precursor cell differentiation and remyelination, and may be a pharmacological target for CNS regenerative therapy.

overall_design: 9 Samples analysed, 3 different time points each with 3 biological replicates.

first: Jeffrey

middle: K

last: Huang

first: Andrew

last: Jarjour

first: Brahim

last: Nait-Oumesmar

first: Christophe

last: Kerninon

first: Anna

last: Williams

first: Wojciech

last: Krezel

first: Hiroyuki

last: Kagechika

first: Chao

last: Zhao

first: Anne

last: Evercooren

first: Pierre

last: Chambon

first: Charles

last: Ffrench-Constant

first: Robin

last: Franklin


title: EMT is the dominant program in human colon cancer

status: Public on Apr 25 2011

city: West Point

first: Michael

last: Nebozhyn

state: PA

address: Mail Stop WP53B-120, 770 Sumneytown Pike, Building 53, P.O. Box 4

department: GpGx/Computational System biology

institute: Merck, Inc

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

overall_design: Refer to individual Series


title: Alternative splicing in HeLa cells after sodium butyrate treatment

status: Public on Feb 03 2011

city: Prague

first: David

last: Stanek

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics

summary: We analyzed a role of histone deacetylases in alternative splicing regulation. Using human exon arrays we identified a list of 683 genes whose splicing changes after HDAC inhibition with sodium butyrate.

overall_design: 6 samples (3 nontreated controls and 3 sodium butyrate treated cells)

first: J

last: Hnilicova

last: Jarrells

first: D


title: Significant Downregulation of Platelet Gene Expression in Metastatic Lung Cancer

status: Public on Oct 15 2010

city: Aurora

first: Tzu Lip

last: Phang

state: CO

address: 12700 East 19th Avenue

department: Medicine

institute: University of Colorado, Denver

summary: Platelets have multiple roles in cancer cell metastasis.  In this work we employed exon microarray technology to address platelet gene expression in metastatic non small cell lung cancer versus controls without cancer.  We found that 197 of the 200 genes with the most significantly altered expression levels had their expression levels downregulated.

overall_design: Retrospective observational study. Total of 12 samples: 6 controls and 6 lung cancer samples.

first: Tzu

last: Calverley


title: Expresssion data in K562 cells, before and after TPA induction and including a RUNX1 knockout construct or a control structure

status: Public on Jan 10 2011

city: Rechovot

first: Ram

last: Jaschek

address: P.O Box 26

country: Israel

institute: Weizmann Institute of Science

overall_design: Examination of gene expression in K562 cells, before and following TPA induction and with or without a RUNX1 KO construct or control

first: Niv

last: Pencovich


title: Gene expression screening during early granulation tissue formation (II)

first: Miretta

last: Tommila

summary: Subcutaneous implantation of cellulose sponges has been used for decades to induce vital granulation tissue formation. Illumina microarray was done in order to study the early gene expression in the granulation tissue formation.

first: Christoffer

last: Stark

last: Jokilammi

first: Ville

last: Peltonen

first: Risto

last: Penttinen

first: Erika

last: Ekholm


title: Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription (expression)

city: Singapore

first: Sachel

last: Mok

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

summary: Artemisinin resistance in Plasmodium falciparum malaria has emerged in western Cambodia.  This is a major threat to global plans to control and eliminate malaria as the artemisinins are a key component of antimalarial treatment throughout the world.  Using DNA microarrays we identify key features of a transcriptional profile that are associated with the delayed parasite clearance phenotype.  These include reduced expression of several basic metabolic and cellular pathways in the early stages, and increased expression of essentially all functionalities associated with protein metabolism in the later stages of P. falciparum intraerythrocytic development.  This is consistent with the reduced ring stage susceptibility that characterizes artemisinin resistant P. falciparum.  This modulation of the P. falciparum intraerythrocytic transcriptome may result from differential expression of several regulatory proteins such as transcription factors of chromatin remodeling associated factors.  In addition, the artemisinin resistant phenotype is strongly associated with a specific pattern of copy number variations, some of which are linked with differential expression of several regulatory proteins such as histone 4 and zinc permease.  This study reports the first global transcriptional survey of artemisinin resistant parasites and provides a set of candidate genes for further investigation.

overall_design: 11 P. falciparum parasites (field isolates) which are either Artemsinin resistant or sensitive from 3 study sites (Pailin in Cambodia, Xepon in Laos, Mae Sot in Thailand) were sampled, grown ex-vivo over 48 hours and harvested at regular intervals. RNA from a total of 91 samples were extracted. Synthesis of target DNA was carried out as previously described: Mackinnon, M.J. et al. Comparative transcriptional and genomic analysis of Plasmodium falciparum field isolates. PLoS Pathog 5, e1000644 (2009), and used in microarray hybridizations.

first: Joan

last: Sim

first: Zbynek

last: Bozdech


title: Critical role of the hydrogen peroxide-responsive nuclear kinase CK1-alpha-LS in vascular cell activation

status: Public on Dec 11 2010

city: Boston

first: James

middle: R.

last: Stone

state: MA

address: Simches 8236, 185 Cambridge Street

institute: Massachusetts General Hospital

summary: CK1-alpha-LS was knocked down in human coronary artery smooth muscle cells.  Gene level and exon level changes in expression were assessed.

overall_design: CK1-alpha-LS was knocked down in human coronary artery smooth muscle cells using retrovirus containing shRNA targeting the alternatively spliced L-insert.

first: Mikhail

middle: P

last: Panchenko

first: Zakir

last: Siddiquee

last: Dombkowski

first: Yuriy

middle: O

last: Alekseyev

first: Marc

last: Lenburg

first: Thomas

last: MacGillivray

first: Frederic

middle: I

last: Preffer


title: Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription

type:
Expression profiling by array
Genome variation profiling by array


title: Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB (Exon array)

status: Public on Sep 01 2010

city: Santa Clara

first: Jason

middle: Wray

last: Hubbard

state: CA

address: 3380 Central Expressway

institute: Affymetrix Inc

summary: To gain global insights into the role of the well-known repressive splicing regulator PTB we analyzed the consequences of PTB knockdown in HeLa cells using high-density oliogonucleotide splice-sensitive microarrays. The major class of identified PTB-regulated splicing event was PTB-repressed cassette exons, but there was also a substantial number of PTB-activated splicing events. PTB repressed and activated exons showed a distinct arrangement of motifs with pyrimidine-rich motif enrichment within and upstream of repressed exons, but downstream of activated exons. The N-terminal half of PTB was sufficient to activate splicing when recruited downstream of a PTB-activated exon. Moreover, insertion of an upstream pyrimidine tract was sufficient to convert a PTBactivated to a PTB-repressed exon. Our results demonstrate that PTB, an archetypal splicing repressor, has variable splicing activity that predictably depends upon its binding location with respect to target exons.

overall_design: Target was prepared from 6 biological replicates of PTB/nPTB knockdown and 6 control mock knockdowns from HeLa S3 cell line and hybridized to the Affymetrix Human Exon 1.0 ST Array.  Two groups of three replicates each were collected at two different times.

first: Miriam

last: Llorian

first: Schraga

last: Schwartz

first: Tyson

last: Clark

first: Dror

last: Hollander

first: Lit-Yeen

last: Tan

first: Rachel

last: Spellman

first: Adele

last: Gordon

first: Anthony

middle: C

last: Schweitzer

first: Pierre

last: de la Grange

first: Gil

last: Ast

first: Christopher

middle: W

last: Smith


title: Expression data from human stomach cell lines (MKN45 and MKN45P)

status: Public on Jun 01 2010

city: Nagaizumi-cho

first: Keiichi

last: HATAKEYAMA

state: Sunto-gun, Shizuoka

address: 1007 Shimonagakubo

country: Japan

institute: Shizuoka Cancer Center Research Institute

summary: Analysis to find splicing variants that are differentially expressed in a highly metastatic stomach cancer cell line, MKN45P, versus its parental cell line, MKN45

overall_design: Comparison between highly metastatic gastric cancer cell line MKN45P and its parental cell line MKN45

last: Hatakeyama

first: Yorikane

last: Fukuda


title: Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB


title: Time course study of experimental cardiac hypertrophy in rat

status: Public on May 01 2010

city: Umea

first: Urban

last: Hellman

address: Nus 6M

department: Public health and clinical medicine

country: Sweden

institute: Umea University

summary:
To further investigate the role of hyaluronan and the regulation of its synthesis in cardiac hypertrophy, quantitative measurements of myocardial hyaluronan was correlated to gene transcription in hypertrophic cardiac tissue.
Factor analysis was used to study correlation over time.

overall_design: Abdominal aorta was ligated in Wistar rats. Heart was excised 1 day, 6 days and 42 days after operation. Aorta ligated animals was compared to sham operated animals. N=6 in each time group, except aorta ligated after six days where n=5.

first: Stellan

last: Mörner

first: Anna

last: Engström-Laurent

first: Jane-Lise

last: Samuel

first: Anders

last: Waldenström


title: Exon-Level Expression Data from Primary B Cells, Early Proliferating EBV-infected B Cells and Lymphoblastoid Cell Lines

status: Public on Nov 15 2010

first: Luftig

last: Laboratory

address: 220 CARL Bldg Duke U Med Center

department: MGM

summary: Eptstein-Barr Virus, an oncogenic herpesvirus, infects and immortalizes human B cells in culture into indefinitely-proliferating LCLs. We examined the gene expression of primary B cells during the process of infection and growth transformation at the exon level to analyze early and late virus-induced changes in expression and exon usage.

overall_design: 4 samples each of total RNA were extracted from purified resting B Cells, sorted early-proliferating EBV infected cells, and monoclonal LCLs, for a total of 12. Human Exon Array 1.0 data was then RMA normalized and analyzed in XRay and GenePattern.

first: Eleonora

last: Forte

first: Jason

last: Tourigny

first: Micah

last: Luftig


title: Persistence of seed-based activity following microRNA segmentation

status: Public on Nov 12 2010

city: Seattle

first: Lee

last: Lim

state: WA

institute: Rosetta Inpharmatics

summary: microRNAs are ∼22 nucleotide regulatory RNAs that are processed into duplexes from hairpin structures and incorporated into Argonaute proteins. We find that a nick in the middle of the guide strand of an miRNA sequence allows for seed-based targeting characteristic of miRNA activity. Insertion of an inverted abasic, a dye, or a small gap between the two segments still permits target knockdown. While activity from the seed region of the segmented miRNA is apparent, activity from the 3' half of the guide strand is impaired, suggesting that an intact guide backbone is required for contribution from the 3' half. miRNA activity was also observed following nicking of a miRNA precursor. These results illustrate a structural flexibility in miRNA duplexes and may have applications in the design of miRNA mimetics.

overall_design: For the microarray portion of the paper, a miR-124 duplex containing a segmented guide strand (G10.12/P) or an intact guide strand (G/P) was transfected into HCT-116 dicer- cells. Profiles were compared with mock transfections.

first: Guillaume

last: Chorn

first: Lihong

last: Zhao

first: Alan

last: Sachs

first: Mike

last: Flanagan


title: Whole-transcript and exon-level expression data for human primary and metastatic prostate cancer samples and control normal adjacent benign prostate

status: Public on Jun 24 2010

city: New York

first: Barry

middle: Stephen

last: Taylor

state: NY

address: 1275 York Avenue, Box #460

institute: Memorial Sloan-Kettering Cancer Center

summary: Current knowledge of prostate cancer genomes is largely based on relatively small patient cohorts using single modality analysis platforms. Here we report concordant assessment of DNA copy number, mRNA and microRNA expression and focused exon resequencing in prostate tumors from 218 patients with primary or metastatic prostate cancer with a median of 5 years clinical follow-up, now made available as a public resource. Mutations in known, commonly mutated oncogenes and tumor suppressor genes such as PIK3CA, KRAS, BRAF and TP53 are present but generally rare. However, integrative analysis of mutations with copy number alterations (CNAs) and expression changes reveal alterations in the PI3K, RAS/RAF and androgen receptor (AR) pathways in nearly all metastatic samples and in a higher frequency of primary samples than previously suspected based on single-gene studies. Other new findings include evidence that the nuclear receptor coactivator NCOA2 functions as a driver oncogene in ~20 percent of primaries. Tumors with the androgen-driven TMPRSS2-ERG fusion were significantly associated with a small, previously unrecognized, prostate-specific 3p14 deletion that, through mRNA expression and resequencing analysis, implicates FOXP1, RYBP and SHQ1 as candidate cooperative tumor suppressors. Comparison of transcriptome and DNA copy number data from primary tumors for prognostic impact revealed that CNAs robustly define clusters of low- and high-risk disease beyond that achieved by Gleason score. In sum, this integrative genomic analysis of a substantial cohort of tumors clarifies the role of several known cancer pathways in prostate cancer, implicates several new ones, reveals a previously unappreciated role for CNAs in prognosis and provides a blueprint for clinical development of pathway inhibitors.

overall_design: Human prostate samples were profiled on Affymetrix Human Exon 1.0 ST arrays per manufacturer's instructions.

middle: S

first: Nikolaus

last: Schultz

first: Haley

last: Hieronymus

first: Charles

last: Sawyers


title: Molecular and Functional Characterization of the role of RNA silencing components in Cryptococcus neoformans

city: Seoul

first: Yong-Sun

last: Bahn

address: 134 Shinchon-dong Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

summary:
The RNA interference (RNAi) mediated by homology-dependent degradation of the target mRNA with small RNA molecules plays a key role in controlling transcription and translation processes in a number of eukaryotic organisms. The RNAi machinery is also evolutionarily conserved in a wide variety of fungal species, including pathogenic fungi. To elucidate the physiological functions of the RNAi pathway in Cryptococcus neoformans that causes fungal meningitis, here we performed genetic analyses for genes encoding Argonaute (AGO1 and AGO2), RdRP (RDP1), and Dicers (DCR1 and DCR2) in both serotype A and D C. neoformans. The present study shows that Ago1, Rdp1, and Dcr2 are the major components of the RNAi process occurring in C. neoformans. However, the RNAi machinery is not involved in regulation of production of two virulence factors (capsule and melanin), sexual differentiation, and diverse stress response. To further gain insights into the global regulatory circuit governed by the RNAi pathway, comparative transcriptome analysis using the serotype A and D RNAi mutants was performed. Notably, an increase in transcript abundance of active transposons, such as T2 and T3, was observed in the rdp1Δ mutant.   Therefore, this study can improve our understanding of the role of the RNAi genes in human fungal pathogens including C. neoformans.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Cryptococcus deneoformans JEC21
Cryptococcus neoformans H99


status: Public on Apr 02 2010

city: Baltimore

first: Kim

last: Walter

address: 1550 Orleans St.

institute: Johns Hopkins University

summary:
Expression data from pancreatic cancer cell lines and non-neoplastic pancreatic cell line HPDE
To identify genes epigenetically silenced and regulated in pancreatic cancer

overall_design: We compared the gene expression profiles of 6 pancreatic cancer cell lines (panc215, A32-1, A38-5, panc2.5, panc2.8, and panc3.014), to the non-neoplastic pancreas cell line, HPDE. We also compared the baseline gene expression of the pancreatic cancer cell lines to expression patterns after treatment with 5-aza-dC alone, TSA alone, and to a combination of 5-aza-dC/TSA.

first: Noriyuki

last: Omura

first: Margaret

last: Griffith

first: Audrey

last: Vincent

first: Ang

last: Li

first: Seung-Mo

last: Hong

first: Kimberly

first: Michael

last: Borges

last: Goggins


title: Trichoderma reesei QM6a CGH self hybridization

status: Public on Mar 16 2010

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

country: France

institute: École normale supérieure

summary: We perform a self hybridisation comprative genomic hybridization (CGH) in order to validate the probe tiling design we done on Trichoderma reesei. This hybridization was done using QM6a wild type strain.

overall_design: One biological replicate

last: Le Crom

first: Brion

last: Christian

first: Antoine

last: Margeot

first: Hugues

last: Mathis


status: Public on Apr 22 2010

summary:
Gene expression analysis of pancreatic cancer associated fibroblasts and control fibroblasts
To identify signaling pathways important in tumor-stromal cell interactions, we performed gene expression profiling on pancreatic cancer associated fibroblast cultures and control fibroblast cultures using Affymetrix Exon arrays.

overall_design: We analyzed 3 control fibroblast cultures and 9 pancreatic cancer associated fibroblast cultures using the Affymetrix Human Exon 1.0 ST platform.  Gene expression levels were compared using Partek (version 6.3beta).

last: Omuri


title: Molecular and Functional Characterization of the role of RNA silencing components in Cryptococcus neoformans [RNAi_Serotype D]

summary: The RNA interference (RNAi) mediated by homology-dependent degradation of the target mRNA with small RNA molecules plays a key role in controlling transcription and translation processes in a number of eukaryotic organisms. The RNAi machinery is also evolutionarily conserved in a wide variety of fungal species, including pathogenic fungi. To elucidate the physiological functions of the RNAi pathway in Cryptococcus neoformans that causes fungal meningitis, here we performed genetic analyses for genes encoding Argonaute (AGO1 and AGO2), RdRP (RDP1), and Dicers (DCR1 and DCR2) in both serotype A and D C. neoformans. The present study shows that Ago1, Rdp1, and Dcr2 are the major components of the RNAi process occurring in C. neoformans. However, the RNAi machinery is not involved in regulation of production of two virulence factors (capsule and melanin), sexual differentiation, and diverse stress response. To further gain insights into the global regulatory circuit governed by the RNAi pathway, comparative transcriptome analysis using the serotype A and D RNAi mutants was performed. Notably, an increase in transcript abundance of active transposons, such as T2 and T3, was observed in the rdp1Δ mutant.   Therefore, this study can improve our understanding of the role of the RNAi genes in human fungal pathogens including C. neoformans.

overall_design: RNAi_D: 6 slides are used in this analysis, 3 biological replicate experiments are performed, total RNAs are extracted from 4 strains (NE519 MAT alpha, NE520 MAT a backcrossed Wild type strain, NE517 rdp1 mutant MAT alpha, NE518 rdp1 mutant MAT a). We use Cy5 as rdp1 mutant dye and Cy3 as a WT dye

first: Guilhem

last: Janbon

first: Shinae

last: Maeng

first: Dong-Hoon

last: Yang

first: Young-Joon

last: Ko

first: Kwang-Woo

last: Jung

first: Frédérique

last: Moyrand

first: Anna

last: Floyd

first: Joseph

last: Heitman


title: Transcriptome profiling in 6-hydroxydopamine hemiparkinsonian rats reveals methamphetamine-mediated dopamine-independent changes in striatal gene expression.

status: Public on Sep 21 2010

first: Jean Lud

last: Cadet

address: 251 Bayview Blvd, Suite 200

department: Molecular Neuropsychiatry Research Branch

institute: NIDA, IRP

summary: Unilateral injections of 6-hydroxydopamine into the medial forebrain bundle (MFB) is used extensively as a model of Parkinson’s disease. The present experiments examined whether a single injection of methamphetamine (METH) (2.5 mg/kg) could still influence striatal gene expression after 6-hydroxydopamine (DA)-induced destruction of the nigrostriatal dopaminergic pathway in the rat. Unilateral injections of 6-hydroxydopamine into the MFB resulted in total striatal dopamine depletion on the lesioned side. This injection also caused decreased striatal serotonin (5-HT) and 5-hydroxyindoleacetic acid (5-HIAA) levels. DA depletion was associated with increases in 5-HIAA/5-HT ratios which were potentiated by the METH injection.  Microarray analyses revealed changes (+ 1.7-fold, p < 0.025) in the expression of 67 genes on the lesioned side in comparison to the intact side of the saline-treated hemiparkinsonian animals. These include follistatin, neuromedin U, and tachykinin 2 which were up-regulated.  METH administration caused increases in the expression of several genes including c-fos, Egr1, and NOR-1 on the intact side. On the DA-depleted side, METH administration also increased the expression of 61 genes including Pdgfd and COX-2. There were METH-induced changes in 16 genes that were common in the DA-innervated and DA-depleted sides.  These include c-fos and NOR-1 which show greater changes on the normal DA side.  The present study documents METH-mediated DA-independent transcriptional alterations of several genes in the DA-denervated striatum. Our results also implicate serotonin as an important player in METH-induced gene expression because the METH injection also caused significant increases in 5-HIAA/5-HT ratios on the DA-depleted side.

first: Jean

first: Christie

last: Brannock

first: Irina

last: Krasnova

first: Bruce

last: Ladenheim

middle: T

last: McCoy

first: Jenny

last: Chou

first: Elin

last: Lerhmann

first: William

last: Wood

first: Kevin

middle: G

last: Becker

first: Yun

last: Wang


title: Molecular and Functional Characterization of the role of RNA silencing components in Cryptococcus neoformans [RNAi_Serotype A]

first: Yong-Sun

last: Bahn

overall_design: RNAi_A: 16 slides are used in this analysis, 3 or 2 biological replicate experiments are performed, total RNAs are extracted from 3 strains (H99 Wild type strain, ago1Δ , rdp1Δ), We use the mixed all of total RNAs from this experiment as a control RNA. We use Cy5 as Sample dye and Cy3 as a control dye. 2nd experiment sample are dye swaped.

first: Guilhem

last: Janbon

first: Shinae

last: Maeng


title: Genome wide mapping of the haematopoietic system transcriptome

status: Public on Feb 03 2010

city: montpellier

first: tondeur

last: sylvie

address: 80 avenue augustin fliche

department: hopital saint eloi

institute: IRB

summary: Recent advances in high density oligonucleotides microarray technology have brought solutions for molecular profiling of human samples at an unprecedented resolution. We mapped whole blood RNA from healthy volunteers and CD34+ from cytapheresis to Human Exon ST 1.0 microarrays. We compared mature blood cells samples with immature CD34+ samples and each of these compartiement with a broad panel of solid tissues. By scanning the expression of over one million known or predicted exons, transcripts such as INPP4B, NEDD9 CD74 and VAV3 were identified as alternatively transcribed between haematopoietic system and solid tissues. The very large combinatorial complexity conveyed by alternative splicing contributes to the specific functional properties of blood cells and haematopoietic stem cells. The gene expression profiles are freely accessible through a dynamic web atlas, providing to the medical and scientific community a simple mean to interrogate and visualize this reference dataset. Finally, the relevance and the precision provided by this exon expression map suggest that exon arrays may be a powerful tool to link specific peripheral whole blood exon signatures modifications to many diseases such as cancer or auto-immune disorders.

overall_design: We analyzed 4 whole blood samples from healthy subjects and 3 CD34+ cells samples from cytapheresis using the Affymetrix Human Exon 1.0 ST microarray

first: Sylvie

last: Tondeur

first: John

last: De Vos


title: Whole brains and frontal lobes of rat offsprings exposed perinatally to low doses of 2,2',4,4'-tetrabromodiphenyl ether

status: Public on Jan 13 2010

city: Sherbrooke

first: Alexander

last: Suvorov

state: Quebec

address: 3001, 12e avenue Nord

country: Canada

institute: Université de Sherbrooke

summary: Analysis of developmental toxicity of environmental toxin 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) at the level of gene expression. Dams of Wistar rats were exposed to environmentaly relevant doses of BDE-47 at gestation and lactation. Gene expression in total brains and frontal lobes was analysed in offspring on postnatal day 10.

overall_design: Dams were randomly distributed among three groups (3 dams per group) and exposed by caudal injection (0.3 ml/kg body weight) on GD 15, PND 1 and PND 5. Dams of the control group received vehicle: ethanol 95%, Cremophor EL, and sterile water (1:1:8, v/v); dams of exposed group 1 received 0.002 mg/kg body weight (BW) of BDE-47 in vehicle, and dams of exposed group 2 received 0.2 mg/kg body weight (BW) of BDE-47 in vehicle. One female pup per litter was selected randomly and sacrificed by decapitation on PND 10. Total RNA was extracted from total brain and frontal lobe samples of these pups and used for microarray analysis.

first: Larissa

last: Takser


title: Liver of rat offsprings exposed perinatally to low doses of 2,2',4,4'-tetrabromodiphenyl ether

summary: Background: Polybrominated diphenyl ethers are a group of flame-retardant chemicals appearing increasingly in the environment. Their health effects and mechanisms of toxicity are poorly understood.Objectives: We screened for the sensitive effects and mechanisms of toxicity of 2,2 ,4,4 -tetra-bromodiphenyl ether (BDE-47) by analyzing the gene expression profile in rats exposed to doses comparable to human exposure.Methods: Wistar dams were exposed to vehicle or BDE-47 (0.002 and 0.2 mg/kg body weight) every fifth day from gestation day 15 to postnatal day 20 by injections to caudal vein. Total RNA was extracted from the livers of pups and hybridized to the whole-genome RNA expression micro-arrays. The list of genes 2-fold differentially expressed was exported to PANTHER and Ingenuity Systems for analysis of enriched ontology groups and molecular pathways.Results: Oxidoreductase and transferase protein families were enriched in exposed rats as were these biological process categories: carbohydrate metabolism; electron transport; and lipid, fatty acid, and steroid metabolism. Four signaling pathways (cascades of activation of drug-metabolizing enzymes) and 10 metabolic pathways were significantly enriched. Drug-metabolizing enzymes appear to be regulated by BDE-47 through an aryl hydrocarbon receptorindependent mechanism. Direct interaction with retinoid X receptor or its upstream cascade may be involved. The main metabolic effects consisted of activation of metabolic pathways: alpha- and omega-oxidation of fatty acids, glycolysis, and starch hydrolysis.Conclusions: Altered expression of genes involved in metabolic and signaling pathways and functions of the organism occurs after perinatal exposure of rat offspring to BDE-47 at doses relevant for the general population.

overall_design: Dams were randomly distributed among two groups (3 dams per group) and exposed by caudal injection (0.3 ml/kg body weight) from GD 15 to PND 20 every 5 days (a total of 6 injections/dam). Dams of the control group received vehicle: ethanol 95%, Cremophor EL, and sterile water (1:1:8, v/v); dams of exposed group 1 received 0.002 mg/kg body weight (BW) of BDE-47 in vehicle, and dams of exposed group 2 received 0.2 mg/kg body weight (BW) of BDE-47 in vehicle. Dams and pups were kept together until weaning on PND 21. After weaning, dams, male and female pups were separated. One male and one female pup per litter were selected randomly and sacrificed by decapitation on PND 27. Total RNA was extracted from liver samples of these pups and used for microarray analysis.


title: Genome Wide Analysis of Immune Activation in Human T and B Cells Reveals Distinct Classes of Alternatively Spliced Genes

status: Public on Jan 08 2010

city: La Jolla

first: Sunil

last: Kurian

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

summary:
Alternative splicing of pre-mRNA is a mechanism that increases the protein diversity of a single gene by differential exon inclusion during post-transcriptional processing. While alternative splicing is established to occur during lymphocyte activation, little is known about the role it plays during the immune response. Our study is among the first reports of a systematic genome-wide analysis using whole exon DNA microarrays integrating alternative splicing and differential gene expression. Purified human CD2+ T or CD19+ B cells were activated using protocols to model the early events in post-transplant allograft immunity and sampled as a function of time during the process of immune activation. Here we show that 3 distinct classes of alternatively spliced and/or differentially expressed genes change in an ordered manner as a function of immune activation. We mapped our results to function-based canonical pathways and demonstrated that some are populated by only one class of genes, like integrin signaling, while other pathways, such as purine metabolism and T cell receptor signaling, are populated by all three classes of genes. Our studies augment the current view of T and B cell activation in immunity that has been based exclusively upon differential gene expression by providing evidence for a large number of molecular networks populated as a function of time and activation by alternatively spliced genes, many of which are constitutively expressed.

Keywords: T cells, B cells, alternative splicing, exon

overall_design: CD2+ T-lymphocytes and CD19+ B-lymphocytes were purified from peripheral blood mononuclear cells (PBMC) of 10 normal human donors. Freshly isolated, resting CD2+ T-cells were resuspended in RPMI-1640 complete media and activated with CD3/CD28 Dynal beads. Cultures were sampled at 24, 48 and 72hrs. A subset of isolated, resting cells immediately stabilized by RNALater solution were used as the baseline comparison (Time 0). Freshly isolated CD19+ magnetic-bead purified resting B cells were resuspended in RPMI-1640 complete media to which anti-CD40 antibody was added, followed by cross-linking with goat-anti-mouse anti-IgG1. The cells were then cultured with rIL2 and rIL10 (100 ng/ml each) to simulate the T-cell dependent B cell activation of an alloimmune response. RNA was extracted at time 0, 24, 48 and 72 hours post activation using the mirVana miRNA Isolation Kit.  The GeneChip®   The RNA was converted into labeled cDNA using the GeneChip® WT Sense Target Labeling kit (Affymetrix). Labeled cDNA was hybridized to Affymetrix Human Exon 1.0 ST arrays. Data for mRNA transcript profiles were generated in the form of CEL files using standard protocols (http://www.affymetrix.com/).

middle: M


title: The responses of astrocytes stimulated by extracellular a-synuclein

status: Public on Jan 12 2010

first: Seung-Jae

last: Lee

address: 1 Hwayang-dong, Gwangjin-Gu

institute: Konkuk university

summary: Abnormal neuronal aggregation of a-synuclein is implicated in the development of Parkinson’s disease. Glial cells also show extensive a-synuclein pathology and are thought to contribute to disease progression. However, the mechanism that produces the glial a-synuclein pathology and the interaction between neurons and glia in the disease-inflicted microenvironment remain unknown. Here, we show that in neuronal cells misfolded a-synuclein proteins are selectively translocated into vesicles, leading to exocytosis of the aggregated forms. More importantly, our data demonstrate that astrocytes take up the neuron-derived a-synuclein aggregates and produce a-synuclein inclusions similar to the ones found in human brains. This uptake is paralleled by changes in the gene expression profile reflecting an inflammatory response. These results suggest that astroglial a-synuclein pathology is produced by cell-to-cell transmission of neuronal a-synuclein aggregates. This transmission step is thus an important mediator of pathogenic glial responses and could qualify as a new therapeutic target.

overall_design: To determine how astrocytes respond to extracellular a-synuclein, gene expression profiles were established and analyzed for nearly 22,000 rat genes using the Illumina RatRef-12 Expression BeadChip. Total RNA was isolated from astrocytes exposed for 6h or 24h to conditioned medium from cultures of a-synuclein or lacZ expressing cells.

first: He-Jin

first: Ji-Hoon

last: Cho

first: Sangchul

last: Rho

first: Daehee

last: Hwang


title: Hematopietic system high resolution transcriptome

status: Public on Oct 01 2009

summary: Recent advances in high density oligonucleotides microarray technology have generated solutions for molecular profiling of human samples at an unprecedented resolution. We mapped whole blood RNA from healthy volunteers and CD34+ collected by cytapheresis from patients to Exon ST 1.0 microarray probing for most known and predicted human exons. Comparison with a broad panel of solid tissues showed that blood displayed the largest tissue specific signature. This unique expression profile comprised transcripts from every blood cell compartment. Moreover, by scanning the expression of over one million different exons, several transcripts were identified as alternatively transcribed between whole blood and solid tissues, or CD34+ and other tissues. The precision of this expression map, at the exon resolution, and the coverage of every blood cell type and hematopoietic stem cells suggest that it will be possible to link specific whole blood exon signatures to many diseases such as cancer or auto-immune disorders and to discover alternative splicing events specific of mature blood cells or stem cells compartment.

overall_design: 4 samples of whole blood from adult healthy donors and 3 samples of CD34+ cells obtained by selection after cytapheresis.

first: Céline

last: Pangault

first: Rima

last: Benmahdi

first: Mohammed

last: Daoudi

first: Aurélie

last: Cubizolle

first: Said

last: Assou

first: Tanguy

last: Lecarrour

first: Laure

last: Nadal

first: Véronique

last: Pantesco

first: Samir

last: Hamamah

first: Jean-Francois

last: Schved

first: Bernard

last: Klein

first: Thierry

last: Fest


title: Comparative genome analysis of exosomal mRNA derived from Tspan8-overexpressing and Tspan8-negative rat pancreas tumors

status: Public on Oct 30 2009

city: Eggenstein-Leopoldshafen

first: Irina

last: Nazarenko

address: Hermann-von-Helmholtz-Platz 1

department: Institute of Toxicology and Genetics

country: Germany

institute: Karlsruhe Insitute of Technology (KIT)

summary: We recently described that tumor-derived exosomes containing the tetraspanin Tspan8 induce angiogenesis. However, not much is known about exosome-endothelial cell interactions and there are no clues on the role of tetraspanins, which are a constitutive component of exosomes. We used the stably Tspan8 expressing rat adenocarcinoma cell line AS-Tspan8, to explore how exosomal Tspan8 supports angiogenesis. Tspan8 contributed to a selective recruitment of proteins and mRNA into exosomes. A genome-wide microarray analysis revealed that both, AS- and AS-Tspan8-exosomes contain about 1500 transcripts, from which 285 are over 3 fold enriched in AS-Tspan8-exosomes. We confirmed high levels mRNA of transcription factors MycN and Spi-C, elongation factor B(SIII), TCEB-1, fibroblast growth factor binding protein 1 (FGFBP1) and growth and differentiation factor-3 (GDF3) in AS-Tspan8-exosomes compared to AS-exosomes and to the parental cells by RT-PCR. VEGF mRNA was not enriched in AS-Tspan8 cells or exosomes. Expression of CCL20, prothrombin, bone morphogenetic protein-2, several Ras and MAPK family members and a phosphatase2A subunit was below the detection level in exosomes.

overall_design: The array consists of 12 samples. Samples 1-6 represent total RNA from non-treated endothelial cells (1,2) cells co-cultured with Tspan8-negative exosomes (3,4) and cells co-cultured with Tspan8-positive exosomes (5,6).  Samples 7 and 8 contain total RNA isolated from cells, from which exosomes are derived. Total RNA from Tspan8-negative exosomes represets samples 9,10; and total RNA from Tspan8-positive exosomes represents samples 11,12.

first: Alexandra

last: Baumann

first: Andrea

last: Hellwig

first: Margot

last: Zöller


title: Regulation of Splicing by Clinical Drugs

status: Public on Feb 28 2010

city: philadelphia

first: Ihab

last: Younis

address: 415 Curie Blvd

department: Biochemistry and Biophysics

institute: University of Pennsylvania

summary:
Alternative splicing analysis after treatment with three clinically aproved drugs
Bioactive compounds have been invaluable for dissecting the mechanisms, regulation and functions of cellular processes. However, very few such reagents have been described for pre-mRNA splicing. To facilitate their systematic discovery, we developed a high throughput cell-based assay that measures pre-mRNA splicing utilizing a quantitative reporter system with advantageous features. The reporter, consisting of a destabilized, intron-containing luciferase expressed from a short-lived mRNA, allows rapid screens (<4 hr) thereby obviating potential toxicity of splicing inhibitors. We describe three inhibitors (out of >23,000 screened), all pharmacologically active: clotrimazole, flunarizine and chlorhexidine. Interestingly, none was a general splicing inhibitor. Rather, each caused distinct splicing changes of numerous genes.

overall_design: Treated HeLa cells with clotrimazole, flunarizine, chlorhexidine or DMSO for 6 hours followed by analysis of total RNA on human exon 1.0 ST platform. Three biological replicates were used for each treatment.

first: Gideon

last: Dreyfuss

first: Kimberly

last: Dittmar


title: Sporadic ALS has compartment-specific aberrant exon splicing and altered cell-matrix adhesion biology

status: Public on Nov 07 2009

first: John

last: Ravits

address: 1201 Ninth Avenue

department: Translational Research

institute: Benaroya Research Institute

summary: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive weakness from loss of motor neurons. The fundamental pathogenic mechanisms are unknown and recent evidence is implicating a significant role for abnormal exon splicing and RNA processing. Using new comprehensive genomic technologies, we studied exon splicing directly in 12 sporadic ALS and 10 control lumbar spinal cords acquired by a rapid autopsy system that processed nervous systems specifically for genomic studies. ALS patients had rostral onset and caudally advancing disease and abundant residual motor neurons in this region. We created two RNA pools, one from motor neurons collected by laser capture microdissection and one from the surrounding anterior horns. From each, we isolated RNA, amplified mRNA, profiled whole-genome exon splicing, and applied advanced bioinformatics. We employed rigorous quality control measures at all steps and validated findings by qPCR. In the motor neuron enriched mRNA pool, we found two distinct cohorts of mRNA signals, most of which were up-regulated: 148 differentially expressed genes (p≤10−3) and 411 aberrantly spliced genes (p≤10−5). The aberrantly spliced genes were highly enriched in cell adhesion (p≤10−57), especially cell-matrix as opposed to cell-cell adhesion. Most of the enriching genes encode transmembrane or secreted as opposed to nuclear or cytoplasmic proteins. The differentially expressed genes were not biologically enriched. In the anterior horn enriched mRNA pool, we could not clearly identify mRNA signals or biological enrichment. These findings, perturbed and up-regulated cell-matrix adhesion, suggest possible mechanisms for the contiguously progressive nature of motor neuron degeneration.

overall_design: 22 total samples were analyzed.  We used a proprietary Exon Splice ANOVA algorithm in Partek Genomics Suite Version 6.4 to calculate both each gene’s differential expression, which is determined by a composite expression of all its exons comparing between disease and control, and each gene’s exon splice index, which is determined by exon-to-exon comparison between disease and control after correcting for other variables, including overall differential gene expression.  The analysis was repeated using the anterior horns from the same samples.

first: Stuart

last: Rabin


title: Modulation of gene expression by rapamycin in hepatic cell lines, H5D and GN5

status: Public on Sep 20 2009

city: Providence

first: Jennifer

last: Sanders

address: 593 Eddy Street

institute: Rhode Island Hospital

summary: Two rat hepatic cell lines, GN5 and H5D, were characterized for the effect of rapamycin on gene expression.  These cells lines are tumorigenic and display intermediate sensitivity to the growth inhibitory effects of rapamycin.  The goal of this experiment was to assess the effect of rapamycin on gene expression independent of effects on cell proliferation.

overall_design: Total RNA for each of four experimental groups was prepared and analyzed in triplicate:  GN5, Vehicle Control; GN5, Rapamycin; H5D, Vehicle Control; H5D, Rapamycin

first: Rosa

last: Jimenez

first: Joan

last: Boylan

middle: A

first: Philip

last: Gruppuso


title: Transcript profiling in Arabidopsis gdh mutants

status: Public on Jan 01 2010

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

summary:
Trancript profiling in arabidopsis gdh mutant.  Identification of the function and regulation of the GDH enzyme in plants. Comparison of transcriptome in leaves, stems and roots in wild type versus triple GDH (1, 2, 3)-defficient mutant and in wild type versus GDH3- defficient mutant.

Keywords: wt vs mutant comparison

overall_design: 12 dye-swap - CATMA arrays

first: Jean-Pierre

last: Renou

first: Frédéric

last: Dubois

first: Bertrand

last: Hirel

first: Marie-Laure

middle: L

last: Martin-Magniette


title: Exon array profiling detects EML4-ALK fusion in breast, colorectal and non-small cell lung cancers.

status: Public on Sep 18 2009

city: South San Francisco

first: Li

last: Li

address: 1 DNA Way

institute: Genentech, Inc

summary:
Exon array profiling of human primary tumor tissue samples including breast, colon and NSCLC.
This dataset includes expression profiles of 153 human primary tumors that were acquired from different commerical vendors and characterized as having >60% tumor content.

overall_design: 153 samples including 84 breast, 26 colorectal and 43 NSCLC were profiled on Affymterix human Exon 1.0 array.

first: Zora

last: Modrusan


title: Methamphetamine preconditioning responses to methamphetamine-induced injury in the rat ventral midbrain

status: Public on Mar 04 2010

first: Jean

middle: Lud

last: Cadet

address: 251 Bayview Blvd.

institute: DHHS/NIH/NIDA  Intramural Research Program

summary: Methamphetamine (METH) is an illicit drug which is neurotoxic to the mammalian brain. Numerous studies have revealed significant decreases in dopamine and serotonin levels in the brains of animals exposed to moderate-to-large METH doses given within short intervals of time. In contrast, repeated injections of small nontoxic doses of the drug followed by a challenge with toxic METH doses afford significant protection against monoamine depletion. The present study was undertaken to test the possibility that repeated injections of the drug might be accompanied by transcriptional changes involved in rendering the nigrostriatal dopaminergic system refractory to METH toxicity. Our results confirm that METH preconditioning can provide significant protection against METH-induced striatal dopamine depletion.  In addition, the presence and absence of METH preconditioning were associated with substantial differences in the identity of the genes whose expression was affected by a toxic METH challenge.

overall_design: Following habituation, rats were injected intraperitoneally with either (+-)-METH-hydrochloride (NIDA, Baltimore, MD) or an equivalent volume of 0.9% saline for a period of three weeks as described in Table S1 in supplemental data. The saline- or METH-pretreated animals received either saline or METH (5 mg/kg x 8 at 1 h intervals) challenges 72 hours after the preconditioning period. Similar doses of METH are known to cause significant decreases in the levels of monoamines in the rat striatum (Graham et al., J. Neurochem. 2008; 105:1873-1885, Cadet et al, Neurotox. Res. 2009; 15:252-259) which received dopaminergic terminals from midbrain dopaminergic cell bodies located in the substantia nigra (SN) and ventral tegmental area (VTA) (Lindvall and Björklund, Biochem Psychopharmacol 1978; 19:1-23, Domesick, Ann N Y Acad Sci. 1988; 537:10-26). Thus, the four groups of animals were: saline/saline (SS), saline/METH (SM), METH/saline (MS), and METH/METH (MM). The various groups were compared to the saline control group (SS group).

first: Michael

last: McCoy


title: Skeletal muscle characteristics of inherited low and high aerobic exercise capacity

status: Public on Apr 01 2010

city: Jyväskylä

first: Heikki

last: Kainulainen

address: Seminaarinmäki

department: Department of Biology of Physical Activity

institute: University of Jyväskylä

summary: Epidemiological studies reveal a strong link between low aerobic capacity and metabolic and cardiovascular diseases. Two-way artificial selection of rats based on low and high intrinsic exercise capacity has produced two strains that also differ in risk for metabolic syndrome (Koch LG, Britton SL. Artificial selection for intrinsic aerobic endurance running capacity in rats. Physiol Genomics 5:45-52, 2001). Here we investigated skeletal muscle characteristics and genotype-phenotype relationships behind high and low inherited aerobic exercise capacity and the link between oxygen metabolism and metabolic disease risk factors in rats derived from generation 18. This population (n=24) of high capacity runners (HCR) and low capacity runners (LCR) differed by 615% in maximal treadmill running capacity. LCR were significantly significantly heavier and had increased blood glucose, serum insulin and triglyceride concentration. HCR had higher resting metabolic rate than LCR. Capillaries/mm2 and capillary-to-fiber ratio were significantly greater in HCR rats in soleus and gastrocnemius and capillary-to-fiber ratio in extensor digitorum longus (EDL) muscle. Subsarcolemmal mitochondrial area was 96% (p<0.01) and intermyofibrillar area was 32% (p<0.05) larger in HCR soleus. Microarray results showed that 126 genes were significantly up-regulated and 113 genes were down-regulated in HCR (p<0.05). Functional clustering and unbiased correlation analysis of muscle microarray data revealed that genes up-regulated in HCR were related to mitochondria,  carboxylic acid and lipid metabolism, and oxidoreductase activity. In conclusion, our data show that aerobic capacity is strongly linked to the architecture of energy transfer and corroborate the importance of oxygen metabolism as the determinant of metabolic health and complex metabolic diseases such as metabolic syndrome and type 2 diabetes.

overall_design: Total RNA obtained from gastrocnemius muscle was compared between rat strains of low and high inherited aerobic exercise capacity.


title: Gene expression in adipose tissue and liver from a spontaneous rat model of Type 2 diabetes

status: Public on Jul 14 2009

city: Oxford

first: Cecilia

last: Lindgren

address: Roosevelt Drive

institute: Wellcome Trust Centre for Human Genetics, University of Oxford

summary: Type 2 diabetes (T2D) is characterized by hyperglycaemia and defects in insulin secretion and action at target tissues. Using the Illumina RatRef-12 v1.0 array, gene expression was assessed in two insulin-target tissues (liver and adipose tissue) from seven-month-old spontaneously diabetic (Goto-Kakizaki [GK]) and non-diabetic (Brown-Norway [BN]) rats. This study was performed in parallel with miRNA expression profiling of the same rats.

overall_design: Experiment comparing GK and BN rat strains for two different tissues. Biological replicates: 4 GK and 5 BN for adipose tissue and 3 GK and 5 BN for liver (RNA extracted from both tissues per rat). One sample hybridised to each array.

first: Helen

middle: E

last: Lockstone

first: Blanca

last: Herrera

last: Taylor

first: Quin

middle: F

last: Wills

first: Amy

last: Barrett

first: Pamela

last: Kaisaki

first: Carme

last: Camps

first: Cristina

last: Fernandez

first: Jiannis

last: Ragoussis

first: Dominique

last: Gauguier

first: Mark

last: McCarthy


title: Alternative Splicing in Erythropoiesis

status: Public on Jul 01 2009

city: Santa Clara

first: Jason

last: Hubbard

address: 3380 Central Expressway

institute: Affymetrix Inc

summary:
Differentiating erythroid cells execute a unique gene expression program that insures synthesis of the appropriate proteome at each stage of maturation. Standard expression microarrays provide important insight into erythroid gene expression, but cannot detect qualitative changes in transcript structure, mediated by RNA processing, that alter structure and function of encoded proteins. We analyzed stage-specific changes in the late erythroid transcriptome via use of high resolution microarrays that detect altered expression of individual exons. Ten differentiation-associated changes in erythroblast splicing patterns were identified, including the previously known activation of protein 4.1R exon 16 splicing. Six new alternative splicing switches involving enhanced inclusion of internal cassette exons were discovered, as well as three changes in use of alternative first exons. All of these erythroid stage-specific splicing events represent activated inclusion of authentic annotated exons, suggesting they represent an active regulatory process rather than a general loss of splicing fidelity. The observation that three of the regulated transcripts encode RNA binding proteins (SNRP70, HNRPLL, MBNL2) may indicate significant changes in the RNA processing machinery of late erythroblasts.  Together these results support the existence of a regulated alternative pre-mRNA splicing program that is critical for late erythroid differentiation.

Keywords: Time course; Splicing-sensitive microarray

overall_design: For Exon array hybridizations:  3 biological replicates of day 7, 2 biological replicates of day 10, 3 biological replicates of day 14; For HJAY array hybridizations:  5 biological replicates each were analyzed from day 7 and day 14.  One day 14 replicate was deemed an outlier and removed from subsequent analyses.

first: Miki

last: Yamamoto

first: Tyson

last: Clark

first: Sherry

last: Gee

first: Jeong-Ah

last: Kang

first: Anthony

last: Schweitzer

first: Amittha

last: Wickrema

first: John

last: Conboy


title: Affymetrix Gene Chip Human Exon 1.0 ST Array expression profiling of 41 human breast cancer cell lines

status: Public on Jun 23 2009

city: Rotterdam

first: Muhammad

last: Riaz

state: Rotterdam

address: Dr. Molewaterplein 50

department: Medical Oncology

country: Netherlands

institute: Erasmuc Medical Centre

summary: Gene expression analysis under normal culture conditions (RPMI-10%FBS) and at optimal cell densities.

overall_design: We have analysed 41 samples, of which OCUB-F and OCUB-M are from same tumor. Tha data were processed by analysing the expression of core level exons and transcript assignments are based upon hg18 genome build up.

first: Mieke

last: Schutte

first: Pim

middle: J

last: French


title: Expression in adipose tissue and liver from a spontaneous rat model of Type 2 diabetes

first: Cecilia

last: Lindgren

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

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

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Catma1-bou-bou mutant characterisation: Autotrophic growth acquisition in the ABOUTDESOUFFLE (bou) mutant

status: Public on Feb 05 2009

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

summary:
rs07-09_bou - catma1-bou - Autotrophic growth acquisition is abolished in the bou mutant in Arabidopsis thaliana. BOU encodes a putative mitochondrial acyl carnitine carrier. bou mutant is blocked at the cotyledon stage. Autotrophic growth of the bou mutant can be achieved with addition of sugar in the medium or in darkness. Moreover, BOU gene expression is activated by light and depends on plant developmental stage. We wish to determine what are the consequences of bou gene mutation at the transcriptome level. We wish to understand whether bou growth arrest is due to the modification of specific genes expression or to a general effect on metabolism at the transition from heterotrophic to autotrophic growth.  - Seeds from a heterozygous plants were grown for either 5 or 8 days after germination on synthetic medium (MS/2) without sugar under continuous light. We harvested cotyledon-stage blocked plants (bou phenotype) from three independent Petri dishes and also green seedlings with true leaves and fully developed root (heterozygotes with a wild-type phenotype) . We also grew independently Col-O plants for 5 and 8 days to compare them with the bou mutants.
Keywords: gene knock in (transgenic),normal vs disease comparison,time course

overall_design: 5 dye-swap - CATMA arrays

first: Ludivine

last: Taconnat

first: Jean-Pierre

middle: P

last: Renou

first: Pierre

last: Carol

first: Marie-Laure

last: Martin-Magniette


title: Cardiac precursor differentiation from hESCs by lentiviral promoter drug selection

status: Public on Oct 24 2008

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary:
Several of the essential core transcriptional control elements in human embryonic stem cells (ESCs) have been identified, but the production and function of alternative isoforms in self-renewal, pluripotency and tissue lineage specification remain largely unknown.
We have modified the H9 ESC line to allow for drug selection of human pluripotent ESCs and cardiac progenitors. Exon-level microarray expression data from undifferentiated ESCs and day 40 cardiac precursors were used to identify differentially expressed and alternative splice isoforms during differentiation.

Keywords: comparison

overall_design: RNA from a homogenous population of undifferentiated hESCs (REX1-neo promoter drug selection) and differentiated day 40 cardiomyocytes (alpha MHC-puro promoter drug selection) was isolated and profiled with exon-tiling arrays.

first: Bruce

last: Conklin


title: Basal gene expression of primary osteoblasts

status: Public on Nov 15 2008

city: London

first: Simon

middle: Charles

last: Rawlinson

address: 4 Newark Street

institute: Bart's and The London School of Medicine and Dentistry

summary:
Osteoblasts derived from different functional skeletal sites were analysed for gene expression profiles

Keywords: Cell type comparison

overall_design: Collagenase digested osteoblasts were derived from two bone sites (calvaria and ulna) of an adult rat, maintained in culture for 3 passages then prepared for RNA analysis


title: Whole Genome Exon Arrays Identify Differential Expression of Alternatively Spliced, Cancer-related Genes in Lung Cancer

status: Public on Oct 17 2008

city: Bethesda

first: Liqiang

last: Xi

address: 10 Center Dr. Bldg 10 Rm 2N110

department: Lab of Pathology

institute: NIH/NCI

summary:
Alternative processing of pre-mRNA transcripts is a major source of protein diversity in eukaryotes and has been implicated in several disease processes including cancer. In this study we have performed a genome wide analysis of alternative splicing events with the GeneChip Human Exon 1.0 ST Array from Affymetrix in lung adenocarcinoma. We found that ~13.3% of the 17800 core Refseq genes appear to have alternative transcripts that are differentially expressed in lung adenocarcinoma versus normal. According to their known functions the largest subset of these genes (30.8%) is believed to be cancer related. Detailed analysis was performed for several genes using PCR, quantitative RT-PCR and DNA sequencing. We found overexpression of ERG variant 2 but not variant 1 in lung tumors and overexpression of CEACAM1 variant 1 but not variant 2 in lung tumors but not in breast or colon tumors. We also identified a novel, overexpressed variant of CDH3 and verified the overexpression of a novel variant of P16. These findings demonstrate how analysis of alternative pre-mRNA processing can shed additional light on differences between tumors and normal tissues as well as between different tumor types. Such studies may lead to the development of additional tools for tumor diagnosis, prognosis and therapy.

Keywords: Alternative splice analysis of exon data with ANOVA compared tumor and matched normal

overall_design: 20 tumor/normal paired specimens (n=40). Tumor samples are from lung adeno carcinoma whereas normals are from adjacent normal lung tissue.

first: Andrew

last: Feber

first: Vanita

last: Gupta

first: Maoxin

last: Wu

middle: D

last: Bergemann

first: Rodney

last: Landreneau

first: Virginia

middle: R

last: Litle

first: Arjun

last: Pennathur

first: James

last: Luketich

first: Tony

last: Godfrey


title: Transcriptome responses of duodenal epithelial cells to endurance swimming in female rats.

status: Public on Nov 07 2008

city: Bangkok

first: Narattaphol

last: Charoenphandhu

address: Rama 6 Rd, Rachthevee

department: Department of Physiology

country: Thailand

institute: Faculty of Science, Mahidol University

summary:
Intestinal calcium absorption is the sole pathway to supply calcium to the body and duodenum is the most efficient site of calcium absorption. Endurance exercise with moderate intensity significantly increased the intestinal calcium absorption. The unloaded non-impact excercise, such as swimming may enhance calcium absorption. However, the cellular and molecular mechanisms of this change have not been investigated. Thus, a genome-wide study by using microarray should reveal changes in the expression of several transporter genes in the intestinal absorptive cells of swimming excercised rats.

Keywords: Gene expression; Comparative genomic hybridization

overall_design: Twelve rats were randomly divided into control and swimming groups. Swimming rats were initially trained for a week until they could swim non stop 1 hour/day.  Swimming frequency was 5 days/week for 2 weeks. The age-matched control  remained sedentary for 2 weeks in a swimming pool. At the end of the swimming protocol, the intestinal segments of rats were removed for total RNA extraction and microarray study.

first: Kannikar

last: Wongdee

first: Jarinthorn

last: Teerapornpuntakit


title: Gene Expression Analysis in an Animal Model of Cortical Dysplasia-CONTROL GROUP

status: Public on Dec 10 2008

city: Cleveland

first: Girish

last: Hiremath

address: 9500 Euclid Avenue

department: Neurosurgery

institute: Cleveland Clinic

summary: Cortical Dysplasia (CD) is the histopathological substrate in almost half of all drug-resistant epilepsy. Little is known about the gene expression profile of CD. As such information may help target therapeutics more effectively, our aim was to perform a gene expression analysis of an animal model of cortical dysplasia induced by in utero irradiation. THIS SERIES (GSE13676) INCLUDES ALL (AND ONLY) CONTROL SAMPLES (9).

overall_design: Nine offspring from irradiated animals, and nine age-matched controls were sacrificed at post-natal day 60. Cortex and hippocampal regions were separated, and total ribonucleic acid (RNA) was extracted using a commercially available kit (Qiagen®). RNA was then subjected to a gene expression analysis using an oligonucleotide microarray platform (Illumina®). After statistical analysis, genes were considered differentially expressed when a p value less than .001 was observed. Real-time, quantitative polymerase chain reaction (RT-qPCR) was used to confirm microarray results for three genes via the Livak method.

middle: K

first: Cristiane

middle: Q

last: Tilelli

first: Banu

last: Gopalan

first: Yaomin

last: Xu

first: Imad

last: Najm


title: Mechanism and transcriptional program of YB-1 in breast cancer cell lines.

status: Public on Oct 31 2008

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

institute: Veracyte, Inc

summary:
YB-1 controls epithelial-mesenchymal transitions by restricting translation of growth-related mRNAs and enabling expression of EMT-inducing transcription factors. We used microarrays to characterize the direct transcriptional and indirect translational regulation of mRNAs by exogenous YB-1 in breast cancer cell lines.

Keywords: gene expression profiling

overall_design: To evaluate this in a genome-wide manner we compared microarray expression profiles of total mRNA and mRNAs isolated from Ps (translationally active) or post-Ps (translationally inactive) fractions of MCF10AT-MSCV vs. MCF10AT-YB-1 cells

first: Poul

last: Sorensen

first: Valentina

last: Evdokimova


title: Genome-wide analysis of mechano-responsive gene expression by tenocytes in fascicles subjected to cyclic tensile strain

status: Public on Jul 23 2008

first: Eijiro

last: Maeda

address: Mile End Road

department: Engineering

institute: Queen Mary, University of London

summary:
Analysis of mechano-regulation of tenocyte metabolism at gene expression level. The hypothesis tested in the present study was that cyclic tensile strain influence the balance of anabolism/catabolism of tenocytes. Results provide important information of the response of tenocyte to cyclic tensile strain, such as specific mechano-responsive genes, up- or down-regulated specific anabolic/catabolic cellular functions.

Keywords: gene expression array-based, stress response, functional analysis

overall_design: Total RNA obtained from isolated tendon fascicles subjected to 1 or 24 hours in vitro cyclic tensile strain was analysed in triplicate by comparison with unstrained control fascicles. A total of 12 RNA samples were analysed (3 samples each from strained and unstrained group at each time point).

first: Christina

last: Fleischmann

first: Charles

last: Mein

first: David

last: Lee


title: Gene Expression Analysis in an Animal Model of Cortical Dysplasia-IRRADIATED GROUP

summary: Cortical Dysplasia (CD) is the histopathological substrate in almost half of all drug-resistant epilepsy. Little is known about the gene expression profile of CD. As such information may help target therapeutics more effectively, our aim was to perform a gene expression analysis of an animal model of cortical dysplasia induced by in utero irradiation. THIS SERIES (GSE13697) INCLUDES ALL (AND ONLY) EXPERIMENTAL SAMPLES--I.E. IRRADIATED/CORTICAL DYSPLASIA (9).


title: Exon-level summary data from Affymetrix Human Exon 1.0 ST array

status: Public on Sep 15 2008

city: Pittsburgh

first: Rakesh

last: Sindhi

address: 3705 Fifth Avenue

department: Hillman Center for Pediatric Transplantation

institute: Children’s Hospital of Pittsburgh

summary:
The Affymetrix Human Exon 1.0 ST array was used to measure differential splicing patterns in archived RNA isolated from 26 of 80 children (11 Rejectors and 15 Non-Rejectors). The exon-level probe summaries reported in this series were computed using the Affymetrix Power Tools (APT) software and 'rma-sketch' normalization method.
Keywords: Affymetrix 1.0 ST exon array; exon-level analysis

overall_design: Exon-level probes were filtered based on APT's detection above background (DABG) p-value greater than 0.05 in n-1 samples leaving 218,402 of the original 287,329 exon-level probes.

first: Brandon

middle: W

last: Higgs


title: HnRNPLL is a global regulator of alternative splicing in activated T cells

status: Public on Jun 20 2008

city: Frederick

first: Shalini

last: Oberdoerffer

address: 1050 Boyles Street

institute: National Cancer Institute

summary:
HnRNPLL was identified as a critical regulator of CD45 alternative splicing in a lentiviral shRNA screen. RNAi-mediated depletion of hnRNPLL eliminated the activation-induced induced transition from the CD45RA to the CD45RO isoform. HnRNPLL is induced during the process of T cell activation, raising the possibility that it regulates a broad program of alternative splicing in activated T cells. To test this possibility and to identify additional potential targets of hnRNPLL, we performed exon array analysis on RNA isolated from five cellular conditions: 1) activated peripheral CD4+ T cells, 2) peripheral CD4+ T cells infected with a control shRNA directed against GFP, 3) peripheral CD4+ T infected with an shRNA directed against hnRNPLL, 4) naïve cord blood CD4+ T cells, and 5) cord blood CD4+ T cells that had been activated with anti-CD3 and anti-CD28 for 24 hours. The RNA was hybridized to Affymetrix human exon arrays and the hybridization signals were analyzed with XRAYTM software (Biotique). Using stringent filters for non-expressed probesets, we identified 132 genes that showed significant alternative exon usage (p<0.01) in response to hnRNPLL knockdown, but not in response to shGFP infection. Of these 132 genes, 36 also showed significant alternative exon usage in response to activation of cord blood cells, which results in an approximate 5-fold increase in hnRNPLL expression. We thus conclude that induction of hnRNPLL represents a mechanism by which cells can rapidly shift their transcriptomes during the process of T cell activation.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: naive/activated ANOVA group

summary:
In order to identify genes with differential gene expression or alternative splicing between the groups naive and activated we study 4 hybridizations on the Human Exon 1.0 ST array using mixed model analysis of variance.  1904 genes with significant gene expression differences between the groups and 1603 genes with significant exon-group interaction (a symptom of alternative splicing) were found, including 427 genes with both gene and possible splicing differences (p<0.01).  Contingency table analysis of the set of studied genes and a dataset of known pathways and gene classifications revealed that the set of alternatively spliced and expressed genes were found to be significantly over-represented in groups of the GOMolFn, GOProcess, GOCellLoc, and Pathway classes  (p<0.01).
Algorithm ANOVA study of 4 Human Exon 1.0 ST files.

overall_design: Factorial arrangment

first: Anjana

last: Rao


title: Expression data from RNAi knockdown HeLa cells

status: Public on Dec 01 2007

city: Giessen

first: Lee-Hsueh

last: Hung

state: Hessen

address: Heinrich-Buff-Ring 58

department: Biochemistry

institute: University of Giessen

summary:
One day before transfection, HeLa cells were seeded in 6-well culture plates (1.5 x 10e5 cells per well) or 10-cm culture dishes (4.3 x 10e5 cells per dish). siRNA duplex (at a final concentration in culture medium of 30 nM) was transfected with Lipofectamine 2000 (Invitrogen) according to the manufacturer's instructions. siRNA duplices specific for human hnRNP L, human hnRNP LL, and luciferase GL2 were from MWG Biotech (Ebersberg, Germany).
Keywords: control / knockdown comparison

overall_design: 12 chips

first: Lee

middle: H

first: Albrecht

last: Bindereif


title: LL-sh4/uninfected/shGFP ANOVA group

summary:
In order to identify genes with differential gene expression or alternative splicing between the groups LL-sh4, uninfected, and shGFP we study 6 hybridizations on the Human Exon 1.0 ST array using mixed model analysis of variance.  842 genes with significant gene expression differences between the groups and 1118 genes with significant exon-group interaction (a symptom of alternative splicing) were found, including 192 genes with both gene and possible splicing differences (p<0.01).  Contingency table analysis of the set of studied genes and a dataset of known pathways and gene classifications revealed that the set of alternatively spliced and expressed genes were found to be significantly over-represented in groups of the GOMolFn, GOProcess, GOCellLoc, and Pathway classes  (p<0.01).
Algorithm ANOVA study of 6 Human Exon 1.0 ST files.


title: The orthologue of the RNA chaperone Hfq is essential for cell motility of the cyanobacterium Synechocystis PCC 6803

status: Public on Mar 15 2008

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary:
The gene ssr3341 was previously suggested to encode an orthologue of the RNA chaperone Hfq in Synechocystis sp. strain PCC 6803. When a phototactic strain of this cyanobacterium was insertionally inactivated at ssr3341, the mutants were not transformable, and were rendered non-phototactic compared to the wild type. The loss of motility was complemented by re-introduction of the wild-type gene, correlated with the re-establishment of type IV pili on the cell surface. Microarray analyses revealed a small set of genes with drastically reduced transcript levels in the knock-out mutant over wild-type cells. Among the most strongly affected genes are with slr1667, slr1668, slr2015, slr2016 and slr2018 five genes which belong to two operons that previously were shown to be involved in motility and controlled by the SYCRP1-cAMP receptor protein. This fact constitutes a link between cAMP signalling, motility, and the involvement of RNA-based regulation. This is the first report demonstrating a functional role of Hfq in cyanobacteria.
Keywords: comparative expression profiling

overall_design: Microarray experiments were carried out as two-color hybridizations on custom designed 8-pack 15K Synechocystis sp. microarrays (AMADID 016989) from Agilent Technologies (Santa Clara, USA).

first: Dennis

last: Dienst

first: Thomas

last: Wallner

first: Wolfgang

last: Hess

first: Annegret

last: Wilde


title: Identification of differentially regulated splice variants and novel exons in glial brain tumors using exon arrays

status: Public on Jan 29 2008

first: Pim

last: French

address: Dr Molewaterplein 50

department: Neurology

institute: Erasmus MC

summary:
Aberrant splice variants are involved in the initiation and/or progression of glial brain tumors. We therefore set out to identify splice variants that are differentially expressed between histological subgroups of gliomas. Splice variants were identified using a novel platform that profiles the expression of virtually all known and predicted exons present in the human genome. Exon-level expression profiling was performed on 26 glioblastomas, 22 oligodendrogliomas and 6 control brain samples. Our results demonstrate that Human Exon arrays can identify subgroups of gliomas based on their histological appearance and genetic aberrations. We next used our expression data to identify differentially expressed splice variants. In two independent approaches, we identified 49 and up to 459 exons that are differentially spliced between glioblastomas and oligodendrogliomas a subset of which (47% and 33%) were confirmed by RT-PCR. In addition, exon-level expression profiling also identified >700 novel exons. Expression of ~67% of these candidate novel exons was confirmed by RT-PCR. Our results indicate that exon-level expression profiling can be used to molecularly classify brain tumor subgroups, can identify differentially regulated splice variants and can identify novel exons. The splice variants identified by exon-level expression profiling may help to detect the genetic changes that cause or maintain gliomas and may serve as novel treatment targets.
Keywords: cell type comparison

overall_design: 6 adult non diseased brain, 26 glioblastomas, 21 oligodendrogliomas

first: Justine

last: Peeters

first: Sebastiaan

last: Horsman

first: Elza

last: Duijm

first: Ivar

last: Siccama

first: Martin

last: van den Bent

first: Theo

last: Luider

first: Johan

last: Kros

first: Peter

last: van der Spek

last: Sillevis Smitt


title: Expression Analysis of 17 human T-ALL cell lines

status: Public on Oct 20 2007

city: Houston

first: Wei

last: Li

state: TX

address: one baylor plaza, MS BCM305

institute: Baylor College of Medicine

summary:
Using array CGH and fiber-FISH, we found that several human T-ALL have tandem duplication of the MYB gene on one allele, we used microarray gene expression analysis to determine if increased MYB expression correlates with gene duplication
Keywords: cell type comparison

overall_design: RNA from 17 T-ALL cell lines

first: Jennifer

last: O’Neil

first: Joelle

last: Tchinda

first: Alejandro

last: Gutierrez

first: Lisa

last: Moreau

first: Richard

middle: S

last: Maser

first: Kwok-Kin

last: Wong

first: Keith

last: McKenna

first: X

last: Shirley Liu

first: Bin

last: Feng

first: Donna

last: Neuberg

first: Lewis

last: Silverman

first: Daniel

last: DeAngelo

first: Jeffery

last: Kutok

first: Rodney

last: Rothstein

first: Ronald

last: DePinho

first: Lynda

last: Chin

first: Charles

last: Lee

first: A

last: Thomas Look


title: Nrf2-related oxidative stress response and impaired dopamine biosynthesis in a PC12 cell model of Huntington’s disease

status: Public on Sep 29 2008

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

institute: Leiden University Medical Center

summary:
Huntington’s disease (HD) is a devastating disease for which currently no therapy is available. It is a progressive autosomal dominant neurodegenerative disorder that is caused by a CAG repeat expansion in the HD gene, resulting in an expansion of polyglutamines at the N-terminal end of the encoded protein, designated huntingtin, and the accumulation of cytoplasmic and nuclear aggregates. Not only is there a loss of normal huntingtin function, upon expansion of the CAG repeat there is also a gain of toxic function of the huntingtin protein and this affects a wide range of cellular processes. To identify groups of genes that could play a role in the pathology of Huntington’s disease, we studied mRNA changes in an inducible PC12 model of Huntington’s disease before and after aggregates became visible. This is the first study to show the involvement Nrf2-responsive genes in the oxidative stress response in HD. Oxidative stress related transcripts were altered in expression suggesting a protective response in cells expressing mutant huntingtin at an early stage of cellular pathology. Furthermore, there was a down-regulation of catecholamine biosynthesis resulting in lower dopamine levels in culture. Our results further demonstrate an early impairment of transcription, the cytoskeleton, ion channels and receptors. Given the pathogenic impact of oxidative stress and neuroinflammation, the Nrf2-ARE signaling pathway is an attractive therapeutic target for neurodegenerative diseases.
Keywords: Gene expression analysis, Huntington's disease, oxidative stress, PC12 cell model

overall_design: For each construct, we performed duplicate experiments with 2 independent cell lines for each construct yielding 2 biological replicates. Furthermore, from each cell line, two separate RNA isolations were performed serving as technical replicates. For PC12 cells with no construct, only a technical replicate was used. RNA was harvested prior to induction (day 0), after 24 hours of induction (day 1) and after 5 days of induction of exon 1 huntingtin fragments with normal (Q23) and extended (Q74) glutamine repeat length.

first: Willeke

last: van Roon-Mom

first: Barry

last: Pepers

first: Carola

last: Verwijmeren

first: Johan

middle: T

last: den Dunnen

first: Josephine

middle: C

last: Dorsman

first: Gert-Jan

middle: B

last: van Ommen


title: Temperature acclimation

status: Public on Jan 06 2006

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
Adult male fish were exposed to the various temperature acclimation conditions as outlined in the published manuscript and RNA was extracted from fish at each time point as listed in the experiment set description.
Abstract: Eurythermal ectotherms commonly thrive in environments that expose them to large variations in temperature on daily and seasonal bases. The roles played by alterations in gene expression in enabling eurytherms to adjust to these two temporally distinct patterns of thermal stress are poorly understood. We used cDNA microarray analysis to examine changes in gene expression in a eurythermal fish, Austrofundulus limnaeus, subjected to long-term acclimation to constant temperatures of 20, 26 and 37 degrees C and to environmentally realistic daily fluctuations in temperature between 20 degrees C and 37 degrees C. Our data reveal major differences between the transcriptional responses in the liver made during acclimation to constant temperatures and in response to daily temperature fluctuations. Control of cell growth and proliferation appears to be an important part of the response to change in temperature, based on large-scale changes in mRNA transcript levels for several key regulators of these pathways. However, cell growth and proliferation appear to be regulated by different genes in constant versus fluctuating temperature regimes. The gene expression response of molecular chaperones is also different between constant and fluctuating temperatures. Small heat shock proteins appear to play an important role in response to fluctuating temperatures whereas larger molecular mass chaperones such as Hsp70 and Hsp90 respond more strongly to chronic high temperatures. A number of transcripts that encode for enzymes involved in the biosynthesis of nitrogen-containing organic osmolytes have gene expression patterns that indicate a possible role for these 'chemical chaperones' during acclimation to chronic high temperatures and daily temperature cycling. Genes important for the maintenance of membrane integrity are highly responsive to temperature change. Changes in fatty acid saturation may be important in long-term acclimation and in response to fluctuating temperatures; however cholesterol metabolism may be most critical for short-term acclimation to fluctuating temperatures. The variable effect of temperature on the expression of genes with daily rhythms of expression indicates that there is a complex interaction between the temperature cycle and daily rhythmicity in gene expression. A number of new hypotheses concerning temperature acclimation in fish have been generated as a result of this study. The most notable of these hypotheses is the possibility that the high mobility group b1 (HMGB1) protein, which plays key roles in the assembly of transcription initiation and enhanceosome complexes, may act as a compensatory modulator of transcription in response to temperature, and thus as a global gene expression temperature sensor. This study illustrates the utility of cDNA microarray approaches in both hypothesis-driven and 'discovery-based' investigations of environmental effects on organisms.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

overall_design: Computed

first: Jason

last: Podrabsky


title: Hypoxia related splice variants in HNSCC

status: Public on Oct 07 2009

city: Manchester

first: Carla

middle: Sofia

last: Moller-Levet

address: Wilmslow Road

department: Paterson Insitute for Cancer Research

institute: The University of Manchester

summary: The identifcation of alternatively spliced transcript variants specific to particular biological processes in  tumours should increase our understanding of cancer. Hypoxia is an important factor in cancer biology  and associated splice variants may present new markers to help with planning treatment. A method was  developed to analyse alternative splicing in exon array data, using probeset multiplicity to identify genes  with changes in expression across their loci, and a combination of the splicing index and a new metric  based on the variation of reliability weighted fold changes to detect changes in the splicing patterns. The  approach was validated on a cancer/normal sample dataset in which alternative splicing events had been  confirmed using RT-PCR. We then analysed ten head and neck squamous cell carcinomas using exon  arrays and identified differentially expressed splice variants in five samples with high versus five with  low levels of hypoxia-associated genes (Winter et al, 2007; Cancer Res 67:3441-9). The analysis identified a splice variant of LAMA3 (Laminin    3), LAMA3-A, known to be involved in tumour cell invasion and progression. The full-length transcript  of the gene (LAMA3-B) did not appear to be hypoxia-associated. The results were confirmed using  qualitative real time PCR. In a series of 59 prospectively-collected head and neck tumours (Winter et al, 2007; Cancer Res 67:3441-9), expression  of LAMA3-A had prognostic significance whereas LAMA3-B did not. This work illustrates the potential  for alternatively spliced transcripts to act as biomarkers of disease prognosis with improved specificity  for particular tissues or conditions over assays which do not discriminate between splice variants.

overall_design: In (Winter et al, 2007; Cancer Res 67:3441-9) 59 Head and Neck Squamous Cell Carcinoma (HNSCCs) samples were processed onto Affiymetrix HG-U133 Plus2 3'IVT arrays, prior to any treatment at the time of primary surgery and a set of 99 genes up-regulated in hypoxia was obtained by analysis of genes whose in vivo expression clustered with the expression of 10 well-known hypoxia-regulated genes (e.g. CA9, GLUT1, and VEGF). A Hypoxia Score (HS) was defined as the median value of expression for these 99 genes. High HS values indicate higher hypoxia relative to lower values and were an adverse prognostic factor in an independent  microarray dataset. Here, we first eliminated samples from the study with a high percentage of absent calls by removing the top 10-th quantile of the samples ordered by number of absent calls, and then selected the 5 least and 5 most hypoxic samples as defined by the HS values. Confirmation of hypoxia status was carried out by investigating CAIX protein expression in histological sections. There was a statistically significant increased CAIX expression in the samples with high HS values (p=0.024). These 10 samples were then processed onto Affiymetrix Human Exon 1.0ST arrays using manufacturers' standard protocols. Following hybridization, we investigated the similarity in expression profiles among the 10 exon arrays. Multidimensional scaling and hierarchical clustering of the samples based on a reduced set of probesets (exonic probesets flagged present; DABG p-value< 0:01 in at least half of all the samples; N=172,204) confirmed that the samples are partitioned by high and low HS values, as expected.

first: Guy

middle: N

last: Betts

first: Adrian

middle: L

last: Harris

first: Jarrod

last: Homer

first: Catharine

middle: M

last: West

first: Crispin

last: Miller