title: Validation study: Response-predictive gene expression profiling of glioma progenitor cells in vitro

status: Public on Feb 21 2016

city: Regensburg

first: Sylvia

last: Moeckel

address: Franz-Josef-Strauss-Allee 11

department: Neurology

institute: University Clinic Regensburg

summary: Background. In a previous publication we introduced a novel approach to identify genes that hold predictive information about treatment outcome. A linear regression model was fitted by using the least angle regression algorithm (LARS) with the expression profiles of a construction set of 18 glioma progenitor cells enhanced for brain tumor initiating cells (BTIC) before and after in vitro treatment with the tyrosine kinase inhibitor Sunitinib. Profiles from treated progenitor cells allowed predicting therapy-induced impairment of proliferation in vitro. Prediction performance was validated in leave one out cross validation. Methods. In this study, we used an additional validation set of 18 serum-free short-term treated in vitro cell cultures to test the predictive properties of the signature in an independent cohort. We assessed proliferation rates together with transcriptome-wide expression profiles after Sunitinib treatment of each individual cell culture, following the methods of the previous publication. Results. We confirmed treatment-induced expression changes in our validation set, but our signature failed to predict proliferation inhibition. Conclusion. Although the gene signature published from our construction set exhibited good prediction accuracy in cross validation, we were not able to validate the signature in an independent validation data set. Reasons could be regression to the mean, the moderate numbers of samples, or too low differences in the response to proliferation inhibition. At this stage and based on the presented results, we conclude that the signature does not warrant further developmental steps towards clinical application.

overall_design: 40 samples; 18 brain tumor initiating cells (BTICs); 2 treatment conditions: 1 µM Sunitinib or 0.00025% DMSO with supplementation of VEGF and PDGF-AB for 6 hours

first: Anja-Katrin

last: Bosserhoff

first: Rainer

last: Spang

first: Peter

last: Hau


title: RNA sequencing of patient derived cell lines in pancreatic cancer

status: Public on Aug 01 2016

city: Dallas

first: Erik

last: Knudsen

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: University of Texas Southwestern Medical Center

type: Expression profiling by high throughput sequencing

summary: Gene expression levels of pancreatic cell lines

overall_design: RNA was extracted from cell lines and subjected to 50bp paired-end RNA sequencing

middle: S


title: Stimulation of isolated plasmacytoid dendritic cells (pDCs) with TLR9 agonist CpG C (CpG) and TLR7 agonist imiquimod (IMQ)

status: Public on Mar 17 2016

city: Parkville

first: CSL

last: Research

state: VIC

address: 30 Flemington Rd

country: Australia

institute: CSL Limited / bio21 Institute

summary: The purpose of this experiment was to assess the genes upregulated when pDCs were stimulated with TLR7 agonist imiquimod and TLR9 agonist CpG C.

overall_design: pDCs were isolated from six healthy donors by FACS sorting, and were stimulated with CpG and imiquimod for 18 hours, after which RNA was extracted for next generation sequencing on the Illumina HiSeq platform. Unstimulated samples were included as controls.

first: Shereen

last: Oon

first: Huy

last: Huynh

first: Tsin-Yee

last: Tai

first: Milica

last: Ng

first: Katherine

last: Monaghan

first: Mark

last: Biondo

first: Gino

last: Vairo

first: Eugene

last: Maraskovsky

first: Andrew

middle: D

last: Nash

first: Ian

middle: P

last: Wicks

first: Nicholas

middle: J

last: Wilson


title: Genome-wide analysis of ex vivo gene expression of 4T1 series mouse mammary tumors

status: Public on Jan 18 2016

city: Barcelona

first: Alexandra

last: Avgustinova

address: C/ Baldiri Reixac 10

country: Spain

institute: IRB Barcelona

summary: Analysis of factors upregulated in highly aggressive 410.4 and 4T1 tumour cells compared to the less aggressive 4T07 tumour cells at gene expression level. The question addressed in the present study was which secreted factors are differentially expressed by these cells and therefore could account for the observed difference in fibroblast activation in these tumours. Results provide important characterisation of the ex vivo expression profiles of highly aggressive vs. non-aggressive tumour cells.

overall_design: 4T07, 410.4 or 4T1 cells were inoculated into the mammary fat pad of Ub-GFP mice and total RNA from FACSorted GFP-negative; CD45-negative tumour cells was isolated.

first: Clare

middle: M

last: Isacke


title: Neuron-specific changes in gene expression caused by NPC1 deficiency

status: Public on Jul 27 2016

city: Strasbourg

first: Frank

middle: W.

last: Pfrieger

address: 8 allée du Général Rouvillois

country: France

institute: Centre National de la Recherche Scientifique, University of Strasbourg

summary:
Background: Niemann-Pick type C is a rare autosomal recessive lysosomal storage disorder presenting aggravating neurologic symptoms due degeneration of specific types of CNS neurons. At present, it is not well understood how neurons react to NPC1 deficiency and why some neuronal cell types are more vulnerable than others.
Purpose: We took aimed to uncover how a specific type of CNS neuron that can be highly purified reacts to NPC1 deficiency based on changes in gene expression.
Methods: Retinal ganglion cells were purified from individual one-week old Balb/c mice homozygous for a mutant NPC1 allele (NPC1m1N) and wildtype littermates (n = 4 mice each genotype) using immunopanning. Total RNA was isolated from acutely isolated neurons and subjected to RNAseq using 4 biological replicates for each genotype.
Results: Our analysis revealed a strong downregulation of transcripts known to be decreased in mutant mice including Npc1 and Calb1 thus validating our approach. We observed a strong upregulation of genes for cellular cholesterol accretion and the downregulation of those for cholesterol release. Other changes including downregulation genes involved in the immune response and synaptic components.
Conclusions: The observed changes suggest that neurons already at one week of age sense a cholesterol deficit because lipids accumulate in the endosomal-lysosomal system and cannot be redistributed intracellularly.

overall_design: Gene expression analysis by RNAseq in retinal ganglion cells acutely purified from eight-days-old NPC1-deficient mice and wildtype littermates

middle: W


title: Hyperexpression of transcribed noncoding RNA containing ultraconserved genomic regions 8 promotes bladder tumorigenesis

status: Public on Mar 23 2016

city: Naples

first: Amelia

last: Cimmino

address: via pietro Castellino 111

department: IGB

country: Italy

institute: CNR

summary: Ultraconserved regions (UCRs) are segments of the human genome located in both intragenic and intergenic regions that are highly conserved in orthologous regions of the human, rat, and mouse genomes. Their transcriptional products, called T-UCRs, compose a new category of long noncoding RNA (lncRNAs). Most importantly, recent data suggests that T-UCRs are altered at the transcriptional level in human tumorigenesis and the aberrant T-UCRs expression profiles can be used to differentiate human cancer types.  MicroRNAs and  other types of non-codingRNAs have been shown to greatly contribute at biological function of cancer and are increasingly being used to help prognosticate patients with bladder cancer, this is not yet the case for T-UCRs. The presence and the roles for T-UCRs across different species is largely unknown rendering their investigation particularly important in our understanding the biology of cancer.  Using genome-wide profiling, we identified 293 T-UCRs that were dysregulated in bladder tumor (n = 24) but not normal bladder tissues (n = 17) samples. The greatest change in expression was for the ultraconserved element 8 (uc.8+), whose expression significantly increased (6.7 fold; P = 0.001) in bladder cancer tissues. Dysregulated expression was validated for several T-UCRs in 60 patients and 16 healthy donors. We found that T-UCR 8+ acts as a natural decoy RNA for miR-596 in patients and bladder cancer cells. As a result, expression of matrix metallopeptidase 9, a direct target of this microRNA, was upregulated, thereby promoting cancer cell growth, migration, and invasion. We also observed that mir-596 mediated a network of interactions among uc.8+, uc.339+, uc.195+, and uc.388+, which appeared to be dysregulated in bladder tumors. Transcribed ultraconserved ncRNAs provide an evolutionarily-conserved regulatory layer that modulates miRNA levels, and opens up the possibility for the development of useful markers for diagnosis and prognosis, as well as for the development of new RNA-based cancer therapies.

platform_organism:
Homo sapiens
Mus musculus

overall_design: In this study the genome-wide expression of T-UCRs in 17 normal bladder tissue samples obtained from healthy donors and 24 bladder tumor samples was analysed To identify variation in the expression of T-UCRs among cancerous, pericancerous, and normal bladder tissue samples, the UCG profiles of bladder tumor and matched pericancerous tissue (urothelium surrounding tumors) samples collected from three BlCa patients was analysed.

first: Michele

last: Olivieri

first: Montano

last: Durso

first: Ferdinando

last: Febbraio


title: Genome-wide identification of BRAT- and PUM-associated mRNAs reveals PUM-independent functions for BRAT in translational repression and mRNA degradation during the Drosophila maternal-to-zygotic transition

status: Public on Mar 30 2015

city: Toronto

first: Timothy

last: Hughes

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

summary: Here, we analyze the RNA-binding preferences of the Drosophila melanogaster BRAT protein using RNAcompete.

overall_design: In the RNAcompete assay, purified GST-tagged BRAT is incubated with an excess of RNA pool and bound RNA from individual pulldown experiments are directly labeled and hybridized to a custom Agilent 244K microarray.

first: John

last: Laver

first: Xiao

last: Li

first: Debashish

last: Ray

first: Kate

middle: B

last: Cook

first: Hua

last: Luo

first: Karen

last: Fung

middle: R

first: J

middle: T

last: Westwood

first: Sachdev

last: Sidhu

first: Quaid

last: Morris

first: Howard

last: Lipshitz

first: Craig

middle: A

last: Smibert


title: The crystal structure of the NHL domain in complex with RNA reveals the molecular basis of Drosophila Brain tumor-mediated gene regulation

status: Public on Sep 14 2015

summary: Here, we analyze the RNA-binding preferences of several NHL containing RNA-binding proteins (BRAT, NCL-1, TRIM71, WECH, LIN-41, TRIM56, and MEI-P26) using RNAcompete.

overall_design: In the RNAcompete assay, purified GST-tagged RNA-binding protein is incubated with an excess of RNA pool and bound RNA from individual pulldown experiments are directly labeled and hybridized to a custom Agilent 244K microarray.

first: Inga

last: Loedige

first: Leonhard

last: Jakob

first: Thomas

last: Treiber

first: Mathias

last: Stotz

first: Nora

first: Janosch

last: Hennig

first: Julia

middle: C

last: Engelmann

first: Michael

last: Krahn

first: Gunter

last: Meister


title: Salmonella enterica subsp. Enteric sv. Typhimurium in vivo induced enterocyte transcriptional response

status: Public on Sep 01 2014

city: Aachen

last: Hornef

address: Steppenbergallee 203

department: Medical Microbiology

country: Germany

institute: RWTH Áachen University

summary: 1-day-old C57BL/6 mice were left untreated (co) or orally infected with 10E2 CFU wildtype (wt) or delta invC SPI1 mutant Salmonella Typhimurium (ATCC14028). Four biological replicates obtained from individual animals were exmained; each group contained animals from at least 2 different litters. On day 4 p.i., animals were sacrificed and intestinal epithelial cells were isolated from total small intestine  (protocol according to: Lotz et al., J. Exp. Med. 2006). Total RNA was isolated by TriZol and its purity was examined using a Bioanalyzer. We used microarrays to detail the global gene expression in primary total isolated intestinal epithelial cells.

overall_design: Four biological replicates of isolated intestinal epithelial cells obtained 4 daysp.i. from neonate mice infected at the age of 1 day (each group with animals from at least two litteres). Single color array.

first: Marcus

last: Fulde

first: Kaiyi

last: Zhang


title: Transcriptome of mouse mature B cell lines A20 transfected with membrane IgE

status: Public on Feb 17 2015

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: We report the effect on genes expression of membrane IgE expression in the mouse mature B cell line A20

overall_design: Examination of 2 stable transfectants IgE+ compared to untranfected or membrane IgM+ control transfectants

first: Brice

last: Laffleur

first: Michel

last: Cogné


title: A compendium of RNA-binding motifs for analysis of gene regulation

status: Public on May 10 2013

first: Timothy

last: Hughes

summary: RNA binding proteins are key regulators of gene expression, yet only a small fraction of these proteins has been functionally characterized.  Here, we report the first large-scale analysis of the RNA motifs recognised by RNA binding proteins, encompassing 205 distinct proteins from 24 diverse eukaryotes.  The sequence specificities of RBPs display deep evolutionary conservation, such that the recognition preferences for a large fraction of metazoan RNA binding proteins can be inferred from the sequences of their binding domains.  The motifs we identify in vitro correlate well with in vivo RNA-binding data.  Moreover, we can associate them with distinct functional roles in diverse types of post-transcriptional regulation, enabling new insights into the functions of RNA binding proteins in both normal physiology and in human disease. These data provide an unprecedented global view of RBPs and their targets and constitute an invaluable resource for defining post-transcriptional regulatory mechanisms in eukaryotes.

overall_design: Here, we analyze the RNA-binding preferences of 205 distinct RNA-binding proteins from 24 different eukaryotes, using RNAcompete. In this assay, purified GST-tagged RBPs are incubated with an excess of RNA pool and bound RNA from individual pulldowns are directly labeled, hybridized to a custom Agilent 244K microarray, and analyzed computationally to identify RNA-binding motifs.

first: Debashish

last: Ray

first: Hilal

last: Kazan

first: Kate

last: Cook

first: Matthew

last: Weirauch

first: Hamed

last: Najafabadi

first: Xiao

last: Li

first: Mihai

last: Albu

first: Hong

last: Zheng

first: Ally

last: Yang

first: Serge

last: Gueroussov

first: Manuel

last: Irimia

first: Leah

middle: H

last: Matzat

first: Ryan

middle: K

last: Dale

first: Sarah

last: Smith

first: Christopher

last: Yarosh

first: Seth

last: Kelly

first: Behnam

last: Nabet

first: Desirea

last: Mecenas

first: Weimin

first: Rakesh

last: Laishram

first: Mei

last: Qiao

first: Fabio

last: Piano

first: Anita

last: Corbett

first: Russ

last: Carsten

first: Brendan

last: Frey

first: Richard

last: Anderson

first: Kristen

last: Lynch

first: Luiz

middle: O

last: Penalva

first: Elissa

last: Lei

first: Benjamin

last: Blencowe

first: Andrew

middle: G

last: Fraser

first: Quaid

last: Morris


title: Transciptome profile of neonatal small intestinal CD4 T cells

status: Public on May 22 2015

first: Mathias

last: Hornef

summary: The intestine harbors more immune cells then the rest of the body together in order to maintain a state of tolerance towards the microbiota as well as food antigen on one side and recognition and immune response to invading pathogens on the other side. At birth the intestine transitions from a sterile organ to a highly exposed environment. At the same time the murine adaptive immune system starts to form and newly generated T and B cells home to the intestine. The present study aims to understand the function of CD4 T cells in the neonatal small intestine (SI). For that the transcriptional profiles of CD4 T cells isolated from the SI of 6- and 11-days-old neonates were compared to their counterparts in mLN and thymus as well as to adult CD4 T cells from the lamina propria (LP) and Peyers patches (PP).

overall_design: 4 true biological replicates in single color mode were analyzed in each group.

first: Natalia

last: Torow


title: Comparison of transcriptional profiles of PBMCs from HIV-infected rapid progressors and chronic progressors

status: Public on May 01 2013

city: Shenyang

first: zining

last: zhang

state: Liaoning

address: No 155, Nanjingbei street, Heping District

department: 1st affiliated hospital

country: China

institute: China Medical University

summary: A significant percentage of HIV-infected individuals experience a sharp decline in CD4+ T cell counts and progress to AIDS quickly after primary infection. Identification of biomarkers distinguishing rapid progressors (RPs) versus chronic progressors (CPs) is critical for early clinical intervention and could provide novel strategies to facilitate vaccine design and immune therapy. mRNA and miRNA expression profiles in the peripheral blood mononuclear cells (PBMCs) of RPs and CPs were investigated at 111±22 days (Mean±SD) of HIV infection. The association of mRNA and miRNA expression with disease progression was examined by receiver operating characteristic analysis and Kaplan-Meier survival analysis. Pathway enrichment analysis showed that genes with deregulated expression in RPs are primarily involved in apoptosis pathways. Furthermore, we found that 5 miRNAs (miR-31, -200c, -526a, -99a and -503) in RPs were significantly decreased compared to those in CPs (P<0.05). The decreased expression of these miRNAs was associated with rapid disease progression of HIV infection with a 94% predictive value as measured by the area under the curve. The upregulated predicted targets from the 5 signature miRNAs and all upregulated genes identified from mRNA microarray converged to the apoptosis pathway. Moreover, overexpression of miR-31 in primary human T cells promoted their survival. Our results have identified a distinct transcriptomic signature in PBMCs of RPs and provided novel insights to the pathogenesis of HIV infection.

overall_design: A cohort of primary HIV infected individuals with different disease outcome were enrolled in this study. We included 6 individuals with rapid disease progression (RP), seven with chronic disease progression (CP). The HIV infected individuals were never on therapy before the time of sample taken.

first: Zi-Ning

last: Zhang

first: Jun-Jie

last: Xu

first: Ya-Jing

last: Fu

first: You-Wen

last: He

first: Qi-Jing

last: Li

first: Hong

last: Shang


title: Homeostatic intestinal epithelial gene expression

status: Public on Aug 23 2014

summary: Intestinal epithelial cells of 28-day-old female mice were isolated according to a recently published protocol (Lotz et al., J Exp. Med. 2006).

overall_design: Isolated intestinal epithelial cells of four individual animals (four biological replicates) were examined. Single color array.


title: Gene expression profiles of Sunitinib-treated but not untreated short-term serum-free cultures predict treatment response of human high-grade gliomas in vitro

status: Public on Oct 07 2014

first: Christian

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

institute: University of Regensburg

summary: High-grade gliomas are amongst the most deadly human tumors. Treatment results are overall disappointing. Nevertheless, in several trials around 20% of patients respond to therapy. Diagnostic strategies to identify those patients that will ultimately profit from a specific targeted therapy are urgently needed. Gene expression profiling of untreated tumors is a well established approach for identifying biomarkers or diagnostic signatures. However, reliable signatures predicting treatment response in gliomas do not exist. Here we suggest a novel strategy for developing diagnostic signatures. We postulate that predictive gene expression patterns emerge only after tumor cells have been treated with the agent in vitro. Moreover, we postulate that enriching specimens for tumor initiating cells sharpens predictive expression patterns. Here, we report on the prediction of treatment response of cancer cells in vitro. As a proof of principle we analyzed gene expression in 18 short-term serum-free cultures of high-grade gliomas enhanced for brain tumor initiating cells (BTIC) before and after in vitro treatment with the tyrosine kinase inhibitor Sunitinib. Profiles from treated but not from untreated glioma cells allowed to predict therapy-induced impairment of proliferation of glioma cells in vitro. Prediction can be achieved with as little as 6 genes allowing for a straightforward translation into the clinic once the predictive power of the signature is shown also in vivo. Our strategy of using expression profiles from in vitro treated BTIC-enriched cultures opens new ways for trial design for patients with malignant gliomas.

overall_design: 72 samples; 18 brain tumor initiating cells (BTICs); 4 treatment conditions: 1 µM Sunitinib or 0.00025% DMSO with and without the combination of  recombinant growth factors VEGF and PDGF-AB for 6 hours

first: Sylvia

last: Moeckel

first: Katharina

last: Meyer

first: Anja-Katrin

last: Bosserhoff

first: Rainer

last: Spang

first: Peter

last: Hau


title: lncRNA expression profiles for preterm premature rupture of membrane (PPROM)

status: Public on Dec 18 2013

city: Staten Island

first: Nanbert

last: Zhong

state: NY

address: 1050 Forest Hill Road

department: Human Genetics

institute: New York State Institute fro Basic Research in Developmental Disabilities

summary: Investigation of lncRNA expression profile of PPROM

overall_design: Arraystar Human LncRNA Array v2.0 was applied to study 40 placentas.

first: Xiucui

last: Luo

first: Jing

last: Pan

first: Yang

last: Gu

first: Qingxi

last: Shi

first: Meijiao

first: Julia


title: Effects of eye opening on gene expression in the superficial layers of the rat superior colliculus

status: Public on Sep 09 2015

city: Boston

first: Rory

last: Kirchner

state: MA

address: 677 Huntington Ave

department: Department of Biostatistics

institute: Harvard T.H. Chan School of Public Health

summary: We performed RNA-seq on six samples of P20 Sprague Dawley rat superior colliculus, three control rats that underwent eye opening at P14 until P20 and three deprived rats which had their eyes glued closed from P14 until P20. Each sample was created from two pooled colliculi.

overall_design: RNA-seq of the superior colliculus with and without long term light deprivation.

first: Andrew

last: Bolton

first: Yasunobu

last: Murata

first: Sung-Yon

last: Kim

last: Young

first: Tru

last: Dang

first: Yuchio

last: Yanagawa

first: Martha

last: Constantine-Paton


title: Lack of effect in desensitization with intravenous immunoglobulin and rituximab in highly-sensitized patients

status: Public on Aug 30 2011

city: New York

first: Bin

last: Ye

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

summary: Background: We aimed to investigate the effects of intravenous immune globulin (IVIG) and rituximab desensitization treatment on kidney transplant rate and blood gene expression profiles by microrarrays.   Methods: We enrolled patients with PRA levels >50% and on the deceased-donor waiting list for >5 years. Patients received IVIG (2.0 g/kg) on day 0 and 30; and rituximab (375 mg/m2) on day 15. The antibodies with mean fluorescence intensity (MFI) values > 5,000 were reported to UNET as unacceptable antigens. The gene expression profiles of blood samples collected in PAXGene tube were studied by Affymetrix HuGene 1.0 ST expression arrays.   Results: 40 of the 415 patients (10%) on the waiting list were eligible for desensitization treatment and 11 completed the treatment. While 15 of the remaining 29 patients (52%) received a transplant without therapy, only 2 of the 11 desensitized patients (18%) received transplant during a median follow-up of 217 days. While there were no statistically significant difference in demographics, desensitized patients had higher cPRA values (97% vs. 77%, p=0.0005) and more number of unacceptable antigens (39 vs. 10, p=0.0001). There was no significant change in the mean number of unacceptable antigens (39 ± 22 versus 39 ± 23) or reduction in the mean MFI values (11,333 ± 3,133 vs 11,289 ± 3,386). Analysis of genes chosen as significantly differentially expressed revealed downregulation of genes involved in B cells and immune system (CD79a, B and T lymphocyte associated transcript, B cell scaffold protein, CD22, CXCR5, fas apoptotic inhibitory protein). Gene set enrichment analysis using Pathogenesis Based Transcripts created by Edmonton Group demonstrated significant downregulation  of B cell associated (p=0.04) and immunoglobulin transcripts (p=0.03).  Conclusion: Although, desensitization with IVIG and rituximab decreases the expression of B cell and immunoglobulin associated transcripts, it was not successful in increasing kidney transplant rate or in decreasing the number of unacceptable antigens.

overall_design:
Total of 28 arrays included in this study, which corresponding to 9 individuals with paired pre/post treatment samples and an additional 10 untreated control individuals.
pair_analysis_normData.txt for paired analysis of pre/post treatment;
ordinary_analysis_normData.txt for non-paired analysis include all samples, except for 38 Pax V0 and 56 Pax V1, which shows technicial bias and lowest array quality, hence removed from analysis.

first: Enver

last: Akalin

first: Yi

last: Bao

first: R

last: Calder

first: K

last: Marfo

first: M

last: Ling

first: S

last: Greenstein

first: J

last: Chapochnick-Friedman

first: D

last: Glicklich

first: G

last: de Boccardo

last: Kinkhabwala


title: Modelling schizophrenia using human induced pluripotent stem cells

status: Public on Aug 13 2011

city: la jolla

first: jonathan

last: sebat

state: CALIFORNIA

address: 9500 gilman drive

department: Psychiatry

institute: University of California San Diego

type: Genome variation profiling by genome tiling array

summary: Schizophrenia (SCZD) is a debilitating neurological disorder with a world-wide prevalence of 1%; there is a strong genetic component, with an estimated heritability of 80–85%1. Although post-mortem studies have revealed reduced brain volume, cell size, spine density and abnormal neural distribution in the prefrontal cortex and hippocampus of SCZD brain tissue2 and neuropharmacological studies have implicated dopaminergic, glutamatergic and GABAergic activity in SCZD3, the cell types affected in SCZD and the molecular mechanisms underlying the disease state remain unclear. To elucidate the cellular and molecular defects of SCZD, we directly reprogrammed fibroblasts from SCZD patients into human induced pluripotent stem cells (hiPSCs) and subsequently differentiated these disorder-specific hiPSCs into neurons (Supplementary Fig. 1). SCZD hiPSC neurons showed diminished neuronal connectivity in conjunction with decreased neurite number, PSD95-protein levels and glutamate receptor expression. Gene expression profiles of SCZD hiPSC neurons identified altered expression of many components of the cyclic AMP and WNT signalling pathways. Key cellular and molecular elements of the SCZD phenotype were ameliorated following treatment of SCZD hiPSC neurons with the antipsychotic loxapine. To date, hiPSC neuronal pathology has only been demonstrated in diseases characterized by both the loss of function of a single gene product and rapid disease progression in early childhood. We now report hiPSC neuronal phenotypes and gene expression changes associated with SCZD, a complex genetic psychiatric disorder.

overall_design: 4 samples/no replicates/genotyped for copy number variation, using the same refrence sample on nimblegen's 080131_HG18_WG_CGH_v2DCR_HX1 design, a dual color microarry, 2.1 million probes platform.

first: Kristen

last: Brennand

first: Jonathan

last: Sebat

first: Fred

last: Gage


title: Whole genome scanning of lung tumors and mucosal biopsies on Affymetrix NspI-250K platform

status: Public on Jan 11 2013

city: Richmond

first: Santanu

last: Dasgupta

state: VA

address: 1220 E Broad Street

institute: Virginia Commonwealth University

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

summary:
Matched normal lymph node, tumors and corresponding mucosal biopsies from 4 lung cancer patients were scrutinized on Affymetrix 250K-NspI array platform. Frequently deleted regions genes were identified based on the LOH call as per manufacturer's guidelines and normalization.
Frequently deleted genes in the tumors and mucosa were identified though this approach

overall_design: Affymetrix 250K-NspI- SNP arrays were performed according to the manufacturer's directions on DNA extracted from lung cancer and corresponding mucosal biopsy specimens. LOH analysis was done to identify genes that are frequently deleted.

first: David

last: Sidransky


title: RETIRED

status: Public on Oct 14 2004

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary: This Series has been retired because it described mouse data, but the underlying data were from rat.

first: Ray

last: Dingledine


title: Assessing the importance of target type for oligonucleotide microarray experiments

status: Public on Jul 27 2010

city: AUBIERE

first: Peyret

last: Pierre

address: 24, avenue des landais

institute: CNRS - Blaise Pascal University

summary: In order to assess the effect on signal variability of the type of target used for oligonucleotide microarray experiments, we hybridized double and single stranded DNA of three genes on a Nimblegen High Density microarray. This slide carries specific probes (two lengths: 30 and 50 nucleotides, for a total of 7456 probes) targeting every region of selected genes.

sample_organism:
Sphingomonas paucimobilis
Dehalococcoides mccartyi VS
Methylosinus trichosporium OB3b

platform_organism:
Methylosinus trichosporium
Sphingomonas paucimobilis
Dehalococcoides mccartyi VS

overall_design: Probes of 30 nucleotides and 50 nucleotides, covering the full length of three genes (ahdA1C, mmoC and vcrA) by a one nucleotide step, were designed and in situ synthesized in six replicates on a 4*72K Nimblegen Custom Microarray. Double and single stranded DNA of the three genes were hybridized as target.

first: Mathieu

last: Roudel

first: Eric

last: Dugat-Bony

first: Olivier

last: Goncalves

last: Peyretaillade

first: Pierre

last: Peyret


title: Exploring Molecular Determinants of Disease Progression in Psoriasis by Comparing Different Clinical Subtypes Having Similar Core Transcriptomes

status: Public on Jan 10 2016

city: Sacramento

first: JAEHWAN

last: KIM

state: CA

address: 10535 Hospital Way

department: Dermatology

institute: University of California, Davis

type:
Expression profiling by array
Third-party reanalysis

summary: To understand the mechanism of disease progression in psoriasis, we defined Asian small plaque psoriasis (small psoriasis) and Asian intermediate plaque psoriasis (intermediate psoriasis) as psoriasis subtypes with limited disease progression, and compared their cellular and molecular signatures with the classic subtype of Western large plaque psoriasis (large psoriasis; GSE30999).

overall_design:
Transcriptome analyses in pre-treatment skin biopsies from patients with Asian small and intermediate plaque psoriasis.
12 Asian small plaque psoriasis skin biopsy tissues (7 lesional and 5 non-lesional skin) and 15 Asian intermediate plaque psoriasis skin biopsy tissues (7 lesional and 8 non-lesional skin).

GCRMA (using gcrma package from R/Bioconductor) and adjusted for batch effect. The expression data was combined with Western large psoriasis (GSE30999). Using a normalization based upon quantiles, the expression data was normalized based upon a specified normalization distribution of GSE30999 (see publication for GSE67853).

The complete dataset representing: (1) 12 Asian small plaque psoriasis Samples, (2) 15 Asian intermediate plaque psoriasis Samples, and (3) 130 Western large plaque psoriasis Samples from GSE30999 (re-processed), is linked below as a supplementary file.

first: James

last: Krueger

first: Mayte

last: Suárez-Fariñas

first: Jaehwan

last: Kim