title: Cardiac Purkinje cell versus ventricular myocyte gene profile

status: Public on Nov 30 2014

city: New York

first: Eugene

middle: E

last: Kim

state: NY

address: 522 First Ave. Smilow 807

department: Medicine

institute: New York University School of Medicine

summary:
Affymetrix array gene expression analysis using RNA isolated from Purkinje cells and ventricular myocytes from the Cntn2-EGFP/ a-MHC-Cre/ floxed-tdTomato compound transgenic dual fluorescence reporter mouse
Cardiac Purkinje cells are important triggers of ventricular arrhythmias associated with heritable and acquired syndromes. The mechanisms responsible for this pro-arrhythmic behavior are incompletely understood. Here, through transcriptional profiling of genetically labeled cardiomyocytes, we identified expression of Purkinje cell protein-4 (Pcp4), a putative regulator of calmodulin and Ca2+/calmodulin-dependent kinase II (CaMKII) signaling, exclusively within the His-Purkinje network. Using Pcp4-null mice and acquired cardiomyopathy models, we demonstrate that reduced expression of PCP4 is associated with CaMKII activation, abnormal electrophysiology, dysregulated intracellular calcium handling and pro-arrhythmic behavior in isolated Purkinje cells. We also show that Pcp4-null mice display profound autonomic dysregulation and arrhythmic behavior in vivo. Together, these results demonstrate that PCP4 regulates cardiac excitability through both Purkinje cell autonomous and central mechanisms and identify this modulator of CaMKII signaling as a potential arrhythmia-susceptibility candidate.

overall_design: Purkinje cells and ventiruclar myocytes were isolated from 4 separate hearts, yielding 4 replicates of each group.

first: Akshay

last: Shekhar

first: Jia

last: Lu

first: Xianming

last: Lin

first: Fang-Yu

last: Liu

first: Jie

last: Zhang

first: Mario

last: Delmar

first: Glenn

last: Fishman


title: Global Reorganization of Chromatin Architecture during Embronic Stem Cell Differentiation

status: Public on Feb 18 2015

city: La Jolla

first: Jesse

middle: R

last: Dixon

state: CA

address: 10010 N. Torrey Pines Rd.

country: USA

institute: Salk Institute for Biological Studies

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The 3D organization of the genome is important for regulation of diverse nuclear processes ranging from transcription to DNA replication. Knowledge of the higher order chromatin structure is critical for understanding mechanisms of gene regulation by long-range control elements such as enhancers and insulators. We describe high resolution, genome-wide dynamic chromatin interaction maps in human embryonic stem cells (hESC) as they differentiate into four distinct embryonic cell lineages. Extensive reorganization of higher-order chromatin structure occurs during hESC differentiation. In this process, topological domains remain largely intact but inter-domain association patterns change dramatically, coincident with widespread changes in chromatin state and gene expression. Moreover, using proximity ligation sequencing to generate chromosome span haplotypes, widespread allele biased gene activities are detected. The allelic gene expression patterns can be correlated to epigenetic state at distal enhancers, supporting the role of these elements in regulating gene expression over a distance.

overall_design:
Two biological replicates of Hi-C experiment and one replicate of CTCF ChIP-Seq experiment in embryonic stem cells and 4 other differentiated cell-types from H1 cell line. Re-analysis of data from GSE16256 in an allele specific manner is linked as supplementary data.

Hi-C data generated in this study can be visualized at www.3dgenome.org.

first: Inkyung

last: Jung

first: Siddarth

last: Selvaraj

first: Bing

last: Ren


title: SEQC Toxicogenomics Study: microarray data set

status: Public on Aug 08 2014

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

summary:
The comparative advantages of RNA-Seq and microarrays in transcriptome profiling were evaluated in the context of a comprehensive study design. Gene expression data from Illumina RNA-Seq and Affymetrix microarrays were obtained from livers of rats exposed to 27 agents that comprised of seven modes of action (MOAs); they were split into training and test sets and verified with real time PCR.

contributor: DrugMatrix, National Toxicology program (NTP)

overall_design: 105 samples were selected from the DrugMatirx tissue/RNA bank that is now owned by the National Toxicology Program (NTP). The samples were split into 2 sets, training and test, to allow for the evaluation of classifiers derived from the data. There were 63 samples in the training set and 42 in the test set. Of the 63 samples in the training set 45 were derived from rats treated with test agent and 18 were control samples (3 sets of 6). 39 of the test set samples were derived from test agent treated animals and 6 were from vehicle and route matched controls.   Five MOAs were represented in the training set and 4 MOAs were in the test set.  Two of the MOAs were duplicated from the test set and two were without representation in the training set. For each test agent there were three rats treated, in accordance with the common practice in the field of toxicology. For each MOA there were three representative test agents to ensure adequate power for detecting the MOA signatures.

first: Scott

middle: S

last: Auerbach

first: Weida

last: Tong


title: Inhalation exposure of hexanal in rats (mRNA)

status: Public on Aug 06 2014

city: Seoul

first: Yoon

last: Cho

address: hwarang-ro 14

country: South Korea

institute: KIST

summary: To further development of insight into the mechanism of toxicity, it is important to employ whole genome microarray expression profiling as a discovery platform to ientify genes with the potential to distinguish hexanal exposure across an exposure range relevant for toxicologic mechanisms. However, few reports have described the effect of hexanal on gene expression profiles using animal model. In this respect, we studied the expression profiles of mRNAs in hexanal-exposed in rats by microarray analysis.

overall_design: To evaluate the gene expression in lung tissue of rats after exposure of hexanal, Fischer-344 rats were inhaled to three concentrations (600, 1000, 1500 mg/m3) for 5 weeks. mRNA expression analysis was conducted using Rat GE(v3) 4X44K microarray (Agilent Technologies, USA).

first: Jae-Chun

last: Ryu


title: Transcriptomic analysis of wild-type (WT) and curled-cotyledon(cco) mutant in soybean

status: Public on Jun 11 2014

city: Nanjing

first: Shi

last: Guixia

state: Jiangsu

address: Weigang num.1

institute: Nanjing Agricultural University

type: Expression profiling by high throughput sequencing

summary: Soybean is one of the most economically important crops in the world. The cotyledon is the nutrient storage area in seeds, and it is critical for seed quality and yield. Cotyledon mutants are important for the genetic dissection of embryo patterning and seed development.Here, we characterised a soybean curled-cotyledon (cco) mutant. Compared with wild-type (WT), the entire embryos of cco mutant resembled the “tail of swallow”. To explore the molecular mechanisms underlying soybean cotyledon development, we executed RNA-Seq using the Illumina HiSeq2000 system.

overall_design: Pods at 7DAF collected from WT and cco were analyzed by RNA-seq.

first: Deyue

last: Yu

first: Guixia


title: Pathological activation of canonical nuclear-factor kB by synergy of tumor necrosis factor alpha and TNF-like weak inducer of apoptosis in mouse acute colitis

status: Public on May 30 2014

city: Cambridge

first: Suzanne

last: Szak

state: MA

address: 14 Cambridge Ctr

department: Drug Discovery

institute: BiogenIdec, Inc.

summary:
To test the efficacy of TNFR-Fc and anti-TWEAK mAb treatment alone and in combination
Tumor necrosis factor (TNF)-alpha is a major effector in various inflammatory conditions. TNF-like weak inducer of apoptosis (TWEAK) is a member of the TNF superfamily that promotes inflammatory tissue damage through its receptor, FGF-inducible molecule 14 (Fn14). Since both TWEAK and TNF-alpha have been shown to mediate pathological responses through inter-dependent or independent pathways by in vitro, the potential interplay of these pathways was investigated in a mouse colitis model. Acute colitis was induced by rectal injection of trinitrobenzene sulfonic acid (TNBS), with administration of control IgG, TNF receptor (TNFR)-Ig chimeric protein, anti-TWEAK monoclonal antibody, or the combination of TNFR-Ig and anti-TWEAK antibody. On day 4, disease severity was evaluated and gene expression profiling was analyzed using whole colon tissue. Levels of transcript of TWEAK, Fn14 and NF-kB-related molecules were measured in purified colon epithelial cells (ECs). NF-kB activation was investigated with Western blot and immunohistochemical analysis. As a result, activation of the canonical, but not noncanonical NF-kB pathway was the hallmark of inflammatory responses in this model. Inflammation induced upregulation of Fn14 only in ECs but not in other cell types. Combination treatment of TNFR-Ig and anti-TWEAK antibody synergistically reduced disease severity in comparison with the control antibody or single agent treatment. Gene expression profile of the colon indicated downregulation of canonical NF-kB pathway with combination treatment. In conclusion, synergistic activation of canonical NF-kB by TWEAK and TNF-alpha is critical for the induction of inflammatory tissue damage in acute inflammation.

overall_design: TNBS colitis was induced by intrarectal administration of a 2 % solution of TNBS in phosphate-buffered saline (PBS): ethanol (1:1).  For acute inflammatory responses, 70 μg/g body weight of TNBS was given on day 0 and animals sacrificed on day 4. One hour prior to administration of TNBS, groups of mice were injected i.p. with the control IgG2a mAb (anti-human CD20) (10 mg/kg), TNFR-Ig (0.3 mg/kg), anti-TWEAK (mP2D10, 10 mg/kg), the combination of TNFR-Fc (0.3 mg/kg) and anti-TWEAK mP2D10 (10 mg/kg), or were untreated. For single agent and combination treatments groups, 0.3 mg/kg TNFR-Ig was employed, since 1 mg/kg of TNFR-Ig markedly ameliorated TNBS colitis but 0.3 mg/kg was much less effective as monitored by the effect on colon length and body weight.  Colon tissue was rolled and snap-frozen in liquid nitrogen. Specimens for RNA extraction were cut from the frozen rolled colon.  A set of experiments using 5-8 mice for each experimental group was performed twice, labelled 7 and 10 in the CEL files. Total number of mice for each experimental condition was as follows; untreated TNBS colitis group, 8; control antibody, 15; TNFR-Ig, 12; anti-TWEAK mAb, 14; combination of TNFR-Ig and anti-TWEAK mAb, 15.

first: Linda

middle: C

last: Burkly

first: Taeko

last: Dohi


title: Inhalation exposure of hexanal in rats

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

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

overall_design: Refer to individual Series


title: Genome-wide methylation maps for untreated and Aza treated AML3 cells

status: Public on Jul 01 2014

city: Glasgow

first: Peter

last: Adams

address: Switchback Rd, Bearsden

country: United Kingdom

institute: University of Glasgow, Beatson Institute for Cancer Research

type: Methylation profiling by high throughput sequencing

summary: AML3 cells were treated with Azacytidine and compared against untreated cells

overall_design: Examination of methylation status in human untreated and Azacytidine treated AML3 cells

first: Kirstin

last: Lund

first: Tony

last: McBryan

first: John

middle: J

last: Cole

middle: D


title: Whole-genome Haplotype Reconstruction using Proximity-ligation and Shotgun Sequencing

status: Public on Nov 03 2013

first: Jesse

last: Dixon

summary: Rapid advances in high-throughput DNA sequencing technologies are accelerating the pace of research into personalized medicine. While methods for variant discovery and genotyping from whole genome sequencing (WGS) datasets have been well established, linking variants together into a single haplotype remains a challenge. An understanding of complete haplotypes of an individual will help clarify the consequences of inheriting multiple alleles in combination, identify novel disease associations, and augment studies of gene regulation. Although numerous methods have been developed to reconstruct haplotypes from WGS data, chromosome-span haplotypes at high resolution have been difficult to obtain. Here we present a novel method to accurately reconstruct chromosome-span haplotypes from proximity-ligation and DNA shotgun sequencing. We demonstrate the utility of this approach in producing high-resolution chromosome-span haplotype phasing in mouse and human. While proximity-ligation based methods were originally designed to investigate spatial organization of the genome, our results lend support for their use as a general tool for haplotyping in the future.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Hi-C experiments in two replicates of Human GM12878 Lymphoblastoid cells and two replicates of F123 mouse ES cells (4 total samples)

first: Siddarth


title: Aiolos promotes anchorage independence by silencing p66Shc transcription in lung carcinoma A549 cells

status: Public on Sep 13 2013

city: Tianjin

first: Zhenyi

last: Ma

address: 22 Qixiangtai Road

department: Biochemistry and Molecular Biology

institute: Tianjin Medical University

summary: Anchorage of tissue cells to their physical environment is an obligate requirement for survival that is lost in mature hematopoietic and in transformed epithelial cells. Here we find that a lymphocyte lineage-restricted transcription factor, Aiolos, is frequently expressed in lung cancers and predicts markedly reduced patient survival. Aiolos decreases expression of a large set of adhesion-related genes, disrupting cell-cell and cell-matrix interactions. Aiolos also reconfigures chromatin structure within the SHC1 gene, causing isoform-specific silencing of the anchorage reporter p66Shc and blocking anoikis in vitro and in vivo. In lung cancer tissues and single cells, p66Shc expression inversely correlates with that of Aiolos. Together, these findings suggest that Aiolos functions as an epigenetic driver of lymphocyte mimicry in metastatic epithelial cancers.

overall_design: Two-condition experiment, A549-empty vs. A549-Aiolos cells. Biological replicates: 3 control, 3 transfected, independently grown and harvested. One replicate per array.

first: Zhe

last: Liu

first: Lance

last: Terada

first: Xichuan

last: Li

first: Zhao

last: Xu

first: Wei

last: Du

first: Zhi

last: Yao

first: Yiliang

last: Wei

first: Zhenfa

last: Zhang

first: Hao

last: Wang

first: Baocun

last: Sun

first: Xiulan

last: Zhao

first: Lin

last: Minna

first: Zhiyan

last: Zhu

first: Yimei

last: Gong

first: Qing

last: Niu

first: Litao

last: Qin

first: Luc

last: Girard


title: Integrative genome-wide gene expression profiling of clear cell renal cell carcinoma in Czech Republic

status: Public on Jun 03 2013

city: Lyon

first: Magdalena

middle: Barbara

last: Wozniak

address: 150 cours Albert Thomas

department: Genetics

country: France

institute: International Agency for Research on Cancer

summary: We conducted whole-genome expression profiling on 101 pairs of ccRCC tumours and adjacent non-tumour renal tissue from Czech patients using the Illumina HumanHT-12 v4 Expression BeadChips to explore the molecular variations underlying the biological and clinical heterogeneity of ccRCC.

overall_design: Total RNA obtained from frozen ccRCC tumour and adjacent non-tumour renal tissue.

first: Ghislaine

last: Scelo


title: Conserved Topological Domains in Mammalian Genomes Identified by High-resolution Analysis of Chromatin Interactions

status: Public on Apr 10 2012

first: Feng

last: Yue

address: 9500 Gilman Dr.

institute: Ludwig Institue for Cancer Research

summary: The spatial organization of the genome is intimately linked to its biological function, yet our understanding of higher order genomic structure is limited.  Here we present high-resolution analyses of chromosomal organization in pluripotent and differentiated human and murine cell types determined using the Hi-C technique. We find that the mammalian genome is composed of over 1000 topological domains, which are stable among different cell types and highly conserved across species.  These megabase-long genomic structures, defined by prominent local chromatin interactions and separated by narrow boundary regions, likely function to restrict regulatory interactions between cis-acting elements and limit the spreading of heterochromatin during cellular differentiation. Interestingly, the boundaries are enriched not only for binding sites of the insulator protein CTCF, but also for promoters of house keeping genes, supporting a role for both CTCF and housekeeping genes in the establishment or maintenance of the topological domains.

overall_design: Hi-C experiment were conducted in mESC, hESC and IMR90 cells

first: Jesse

last: Dixon

first: Bing

last: Ren


title: Genome-wide Analysis of Chromatin Interactions in Human Cells

status: Public on Oct 20 2013

city: Cleveland

first: Fulai

last: Jin

state: OH - OHIO

address: 10900 Euclid Avenue

institute: Case Western Reserve University

summary: Millions of cis-regulatory sequences have recently been found in the human genome, but the function of most cis-elements are not yet clear, in part due to the difficulty in determining their regulatory targets, which are often located millions of base pairs away and separated by one or more unrelated genes. To address this problem, the Hi-C method has been developed to identify long-range looping interactions in a genome-wide, unbiased fashion.  However, current data analysis of Hi-C datasets cannot fully resolve regulatory interactions between enhancers and promoters due to the low resolution.  Here, we generated a high-depth Hi-C dataset and applied a new analysis method that offers improved resolution permitting genome-wide identification of nearly one million chromatin interactions.  We demonstrated the use of Hi-C to identify target promoters of enhancers regulated by NF-κB signaling and signal-dependent dynamic chromatin interaction at these enhancers in human cells. Surprisingly, our results showed that most NF-κB binding sites are looped to their regulatory targets prior to activation of the signaling pathway, and appear to undergo little change during signaling. This observation suggests that the chromatin organization landscape, once established in a cell type, is rather stable and may influence the selection and activation of target genes by a transcription factor.

overall_design: We performed Hi-C analysis using a human fibroblast cell line IMR90 before and after NF-κB activation. In the meantime, we also performed ChIP-seq experiments to map the location of NF-κB p65 subunit, RNA polymerase II, p300, and several histone modifications (including H3K4me1, H3K4me3, H3K27ac and H3K36me3) in IMR90 cells before and after transient TNF-α stimulation. Additionally, to monitor the dynamic transcription profiles, we also performed Global Run-On sequencing (GRO-seq).

first: Yan

last: Li


title: CPDR tumor-benign 80 genechip dataset

status: Public on Sep 29 2011

city: Rockville

first: Albert

last: Dobi

state: MD

address: 1530 E. Jefferson St

institute: CPDR USU

summary: From over 300 patients two groups were selected which had prostate tumors with either well differentiated (WD) or poorly differentiated (PD) after radical Prostatectomy. The PD group had Gleason score 8-9, seminal vesicle invasion, and poorly differentiated tumor cells; the WD group had Gleason score 6-7, no seminal vesicle invasion, and well to moderately differentiated tumor cells. LCM compatible specimens were selected from age and race (Caucasians) matched PD or WD patients with no family history of CaP. Matching normal epithelal cells were also selected for the analysis.

overall_design: From 40 patients specimens were obtained under an IRB-approved protocol from patients treated with radical prostatectomy (RP) at Walter Reed Army Medical Center (WRAMC).


title: Absence of significant overlap in transcriptional patterns between operationally  tolerant liver and kidney recipients

status: Public on Jan 01 2012

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Transplant recipients spontaneously accepting their grafts in the absence of immunosuppression demonstrate the feasibility of attaining allograft tolerance in humans. Previous studies have identified blood transcriptional and cell phenotypic markers specific for either liver or kidney tolerant recipients, but the two settings have not been directly compared yet employing the same platforms. To identify potential similarities in immune parameters between recipients tolerant to different organs, we analyzed blood samples from tolerant and non-tolerant liver and kidney recipients employing whole genome expression microarrays. Tolerant and non-tolerant liver and kidney recipients differed in their peripheral blood expression patterns, but no significant overlap was observed between the two datasets. This was confirmed at the functional level by employing gene set enrichment analysis.The lack of obvious similarities in immune parameters associated with liver and kidney tolerant recipients implies the involvement of different mechanisms in the two settings and argues against the existence of a common immunological constant of spontaneous operational tolerance in clinical transplantation.

overall_design: The complete database comprised the expression measurements of 54,675 genes for liver and kidney trasplant inmunotolerance groups (n=12 for each group).A group of 12 samples from Healthy volunteer are included.

first: J

first: A

last: Pallier

first: R

last: Danger

first: M

last: Martinez-Llordella

last: Lopez

last: Londoño

last: Rimola

middle: P

last: Soulillou

first: S

last: Brouard

last: Sanchez-Fueyo


title: Cell-Type-Specific TGF-beta Signaling is Targeted to Genes that Control Cell Identity: ChIP-Seq

status: Public on Aug 24 2011

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Smad3 co-occupies DNA binding sites with master transcription factors.

overall_design: Pu.1, MyoD, Oct4, IgG, Smad3, and Smad2/3 ChIP-Seq.

first: Alan

last: Mullen

first: David

last: Orlando

first: Jamie

last: Newman

first: Roshan

last: Kumar


title: Cell-Type-Specific TGF-beta Signaling is Targeted to Genes that Control Cell Identity


title: FACS-sorted cells from Young Adults Vaccinated with Influenza TIV or LAIV Vaccines during 2008/09 Flu Season

status: Public on Jul 10 2011

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

summary:
Systems vaccinology has emerged as an interdisciplinary field that combines systems wide measurements and network and predictive modeling applied to vaccinology.
Here we used the systems vaccinology approach to study the molecular mechanisms underlying the innate responses to the trivalent inactivated influenza (TIV) and live attenuated influenza (LAIV) vaccination in humans, and to identify early gene signatures that predict the magnitude of the antibody responses to influenza vaccination.

overall_design: During the 2008 influenza season, healthy adults were vaccinated with TIV (6 vaccinees) or LAIV (6 vaccinees), and blood samples isolated at day 0 and at day 7  post-vaccination. Cell subsets (B cells, Monocytes, mDCs and pDCs) were FACS-sorted from frozen PBMCs. Microarrays were performed using amplified total RNA.

middle: I

first: Bali

last: Pulendran


title: Transcript profile changes associated with lateral root fasciation in temperature-sensitive mutants

status: Public on Feb 10 2012

city: Tokyo

first: Munetaka

last: Sugiyama

address: Hakusan 3-7-1, Bunkyo-ku

department: Botanical Gardens, Graduate School of Science

country: Japan

institute: The University of Tokyo

summary: Control of the dimensions of organ primordia is crucial for proper organogenesis in the development of multicellular organisms. Lateral root formation is a major type of plant organogenesis important for postembryonic development of the root system. Lateral root formation begins with a few rounds of asymmetric, anticlinal cell division (formative cell division) in the pericycle, which determines the basal dimensions of root primordia. Here we show, based on molecular genetic analysis of temperature-dependent fasciation (TDF) mutants of Arabidopsis thaliana, that mitochondria play an unexpected role in the restriction of formative cell division and thus in the control of the basal dimensions of lateral root primordia. Three TDF mutants, root redifferentiation defective 1 (rrd1), rrd2, and root initiation defective 4 (rid4), exhibit lateral root fasciation from excess formative cell division under high-temperature conditions. We identify RRD1 as encoding a poly(A)-specific ribonuclease (PARN)-like protein and RRD2 and RID4 as encoding pentatricopeptide repeat (PPR) proteins. Subcellular localization and predicted functions of these proteins implicate them in poly(A)-dependent RNA degradation in mitochondria. This characterization is supported by the finding that mitochondrial RNAs with poly(A) tails, most of which are mRNAs of respiratory chain components, accumulate at an unusually high level in these TDF mutants.

overall_design: Explants of three mutants (rrd1, rrd2, rid4) and wild type were cultured on B5 medium supplemented with 0.5 mg/L IBA for the induction of lateral root formation. After 12 hours of culture at 28C, explants were collected and used for microarray analysis. Analysis was performed in three biological replicates.

first: Kurataka

last: Otsuka


title: Time Course of Young Adults Vaccinated with Influenza TIV Vaccine during 2008/09 Flu Season

overall_design: During the 2008 influenza season, healthy adults were vaccinated with TIV (28 vaccinees), and blood samples isolated at days 0, 3, 7  post-vaccination. Microarrays were performed using total RNA extracted from the peripheral blood mononuclear cells of vaccinees.


title: Time Course of Young Adults Vaccinated with Influenza LAIV Vaccine during 2008/09 Flu Season

overall_design: During the 2008 influenza season, healthy adults were vaccinated with LAIV (28 vaccinees), and blood samples isolated at days 0, 3, 7  post-vaccination. Microarrays were performed using total RNA extracted from the peripheral blood mononuclear cells of vaccinees.


title: Sequential Binary Gene-Ratio Tests Define a Novel Molecular Diagnostic Strategy for Malignant Pleural Mesothelioma

status: Public on May 01 2013

city: Boston

first: Assunta

last: De Rienzo

state: Massachusetts

address: 75 Francis Street

department: Surgery

institute: Brigham and Women's Hospi

summary: The gene-expression ratio  technique was used to design a molecular signature to diagnose MPM from among other potentially confounding diagnoses and differentiate the epithelioid from the sarcomatoid histological subtype of MPM.

overall_design: Microarray analysis was performed on 113 specimens including MPMs and a spectrum of tumors and benign tissues comprising the differential diagnosis of MPM.  A sequential combination of binary gene-expression ratio tests was developed to discriminate MPM from other thoracic malignancies .  This method was compared to other bioinformatic tools and this signature was validated  in an independent set of 170 samples.  Functional enrichment analysis was performed to identify differentially expressed probes.

first: William

middle: G

last: Richards

first: Beow

middle: Y

last: Yeap

first: Melissa

middle: H

last: Coleman

first: Peter

last: Sugarbake

first: Lucian

last: Chirieac

first: Yaoyu

last: Wang

first: John

last: Quackenbush

first: Roderick

middle: V

last: Jensen

first: Raphael

last: Bueno


title: Systems biology of vaccination for seasonal influenza in humans


title: Comparison of lymphoblastoid cell gene expression with immunofluorescent chromosome banding

status: Public on Oct 26 2010

city: Birmingham

last: Halsall

address: Medical School, Vincent Drive

department: Cancer and Genomic Sciences

institute: University of Birmingham

summary:
Metaphase chromosome staining was used to provide a high level overview of the pattern of histone modifications (H3K27ac, H3K27me3 and H3K4me3) at a single cell level in human lymphoblastois cells.
These epigenomic banding patterns were related to various genomic features including gene and CpG island density as well as gene expression.

overall_design: A 3 array study using RNA extracted from 3 separate cultures of human lymphoblastoid cells as biological replicates

first: Bryan

middle: M

last: Turner


title: Time Course of Young Adults Vaccinated with Influenza TIV Vaccine during 2007/08 Flu Season

overall_design: During the 2007 Influenza season, healthy adults were vaccinated with TIV (9 vaccinees), and blood samples isolated at days 0, 3, 7  post-vaccination. Microarrays were performed using total RNA extracted from the peripheral blood mononuclear cells of vaccinees.


title: Gene Expression of Bone Marrow Plasma Cells from Healthy Donors (N=22), MGUS (N=44), and Smoldering Myeloma (N=12)

status: Public on Oct 06 2006

city: Little Rock

first: Shaughnessy

middle: Jr.

last: John

state: AR

address: 4301 West Markham St., Slot 776

institute: Myeloma Institute for Research and Therapy

summary:
This series represents bone marrow aspirates from smoldering multiple myeloma patients
Keywords: other

overall_design: We analyzed arrays for plasma cells from 22 cases of healthy donors, 44 cases of MGUS, and 12 cases of smoldering myeloma

last: Shaughnessy


title: Prognostic gene signature for normal karyotype AML

status: Public on Aug 22 2008

city: Munich

first: Klaus

last: Metzeler

address: Marchioninistr. 15

department: Department of Internal Medicine III

country: Germany

institute: University of Munich

summary:
Patients with cytogenetically normal acute myeloid leukemia (CN-AML) show heterogeneous treatment outcomes. We used gene expression profiling to develop a gene signature that predicts overall survival (OS) in CN-AML. Based on data from 163 patients treated in the German AMLCG 1999 trial and analyzed on oligonucleotide microarrays, we used supervised principal component analysis to identify 86 probe sets (representing 66 different genes) which correlated with OS, and defined a prognostic score based on this signature. When applied to an independent cohort of 79 CN-AML patients, this continuous score remained a significant predictor for OS (hazard ratio [HR], 1.85; P=0.002), EFS (HR, 1.73; P=0.001), and RFS (HR, 1.76; P=0.025). It kept its prognostic value in multivariate analyses adjusting for age, FLT3 ITD and NPM1 status. In a validation cohort of 64 CN-AML patients treated on CALGB study 9621, the score also predicted OS (HR, 4.11; P<0.001), EFS (HR, 2.90; P<0.001), and RFS (HR, 3.14, P<0.001) and retained its significance in a multivariate model for OS. In summary, we present a novel gene expression signature that offers additional prognostic information for patients with CN-AML.

Keywords: clinical outcome

overall_design:
Training set: Samples GSM311598-GSM311923. Analysis of 163 samples of bone marrow or peripheral blood mononuclear cells from adult patients with untreated acute myeloid leukemia.
Test set: Samples GSM316652-GSM316730. Analysis of 79 samples of bone marrow or peripheral blood mononuclear cells from adult patients with untreated acute myeloid leukemia.

first: Manuela

last: Hummel

first: Ulrich

last: Mansmann

first: Wolfgang

last: Hiddemann

first: Stefan

middle: K

last: Bohlander

first: Christian

last: Buske


title: Transcriptome uterus

status: Public on Sep 01 2009

city: Nouzilly

first: Joel

last: Gautron

address: UR83 Recherches avicoles

institute: INRA

summary:
cDNA microarrays were used to identify the expression of the genes in uterus by comparison with two others regions of the oviduct not involved in the shell deposition. A total of 605 sequences specifically over-expressed were revealed. The expression of 15 of them was also confirmed using qRT-PCR, and confirmed the microarray expression. The 605 uterine transcripts corresponded to 469 and 437 different genes and proteins respectively. A global interpretation of their functions was assessed using the Gene Ontology terms and the most over-represented terms are relative to the mineral transport and transfer necessary to the calcification process. The study has revealed 53 proteins which could be secreted to be deposited in the shell to be biologically actives. The study of their functions reveals proteins known for their involvement in the biomineralization or with calcium binding properties to interact with the mineral phase during the eggshell fabric. A large group of proteins could be involved in the folding of the matrix, and a notable group of uterine secreted proteins was also identified as antibacterial to contribute to the antimicrobial protection of the egg. Finally the study revealed proteases and protease inhibitors which could play an active role in the regulation of the protein activities in the acellular uterine fluid where the eggshell is formed.

Keywords: Laying hen, eggshell, oviduct, uterine expression, cDNA microarray, indirect cDNA labelling, Alexa Fluor dyes

overall_design: A balanced block hybridization design (Dye switch) was used where half of the samples were labelled with Alexa® 555 fluorescent dye and the other half with Alexa® 647. A total of 16 microarray slides were used for hybridization to 32 samples that correspond to four tissue contrast (uterus versus magnum and uterus versus white isthmus).

first: J

first: V

last: Jonchere

first: L

last: Cogburn

first: C

last: Hennequet-Antier

first: Y

last: Nys


title: Gene Expression Profiles of Multiple Myeloma

status: Public on Jun 01 2006

summary:
Samples in this series are pre-treatment bone marrow aspirates from multiple myeloma patients.

Keywords = Multiple Myeloma, Bone Marrow, Pre-Treatment
Keywords: other

overall_design:
Samples in this series are:

1. CD-138-selected plasma cells from bone marrow of patients with newly diagnosed multiple myeloma subsequently treated with high dose therapy and stem cell transplants termed Total Therapy 2 (pre-treatment TT2)

2. CD-138-selected plasma cells from bone marrow of patients with newly diagnosed multiple myeloma subsequently treated with Total Therapy 3 (pre treatment TT3).

Overall Design:

Gene expression signatures were used to: 1) develop unsupervised hierarchical cluster classes; 2) establish links with outcome following stem cell transplantation

CEL files are available upon request via a Materials Transfer Agreement. Please contact Dr. John Shaughnessy  for details.

first: John


title: Identification of a B cell signature associated with renal transplant Tolerance in humans

status: Public on Jun 09 2010

city: Bethesda

first: Sai

last: Kanaparthi

address: 7500 Old Georgetown Rd

department: BiG

institute: Immune Tolerance Network

summary:
In this study, investigators recruited the largest reported cohort of tolerant kidney transplant recipients who maintained their graft after ceasing to take their immunosuppression drug, and compared this cohort to subjects with stable  allograft function while on immunosuppression and healthy non transplated, controls.  Using gene expression studies, they identified genetic markers that are strong candidates for predicting kidney transplant candidates who may benefit from minimization or withdrawl of immunosuppression.
Microarrays were used to detect expressed gene profiles of whole-blood total RNA from subjects in the tolerant, standard immunotherapy and healthy control participants

overall_design: Total of 19 Tolerant (TOL) participants, 27 Standard Immunotherapy (SI) participants, and 12 Healthy Controls (HC)

first: Kenneth

last: Newell

first: Adam

last: Asare

first: Vicki

last: Seyfert-Margolis

first: Larry

last: Turka


title: SEQC Project

status: Public on Jun 17 2014

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

institute: Fudan University

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

sample_organism:
Homo sapiens
Rattus norvegicus
synthetic construct

overall_design: Refer to individual Series

first: Charles

last: Wang

first: Christopher

middle: E

last: Mason

first: Matthias

last: Fischer

first: Zhiyu

last: Peng

first: Scott

last: Auerbach

first: James

last: Fuscoe

first: Weida

last: Tong

first: Zhenqiang

last: Su


title: RNA profiling in lungs of WT and HGF transgenic mice with or without exposure to carcinogen

status: Public on Dec 31 2010

city: Pittsburgh

first: Jill

last: Siegfried

state: PA

address: The Hillman Cancer Center, UPCI Research Pavilion Suite 2.18, 5117 Centre Avenue

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

summary: The hepatocyte growth factor (HGF)/c-Met signaling pathway is known to mediate vascularization. We have previously demonstrated that expression of a human HGF transgene in the small airways produced mice (HGF TG) that were more susceptible to the tobacco carcinogen, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). We also have observed that HGF TG mice display significantly enhanced vascularization in the lungs that increases over time compared to wild-type (WT) littermates. To analyze which genes might contribute to increased vascularization from HGF overexpression in the airways, RNA and protein were isolated from whole lungs of individual HGF TG and WT adult mice. We profiled the mRNA expression of several hundred genes representative of six biological pathways involved in transformation, angiogenesis, and tumorigenesis using two commercial microarrays. Significant changes in expression over a 1.5-fold boundary were also observed in lung tumors derived from NNK-treated HGF TG mice.

overall_design:
Lung tumors were induced by exposing mice to four weekly i.p. injections of 3mg NNK (15μg/μl) over 2 weeks. Whole lungs from control untreated animals were dissected after sacrifice at 10, 20, or 40 wks of age, and NNK induced lung tumors were dissected from the animals at 20 or 40 weeks of age.

Total RNA was extracted from whole lung or isolated tumors from HGF TG or WT mice using TRIzol reagent and the Array Grade Total RNA Isolation Kit. The cDNA  was generated and labeled using the TrueLabeling-AMP Linear RNA Amplication Kit.

RNA was analyzed from 28 mice in total. The angiogenesis array was used to analyze 10 samples taken from 40 week old mice (HGF TG untreated [n=4], WT untreated [n=4], HGF TG NNK treated [n=1], WT NNK treated [n=1]) and 6 samples from 20 week old mice (HGF TG untreated [n=2], WT untreated [n=2], HGF TG NNK treated [n=1], WT NNK treated [n=1]).

The cancer gene array was used to analyze 8 samples taken from 40 week old mice (HGF TG untreated [n=2], WT untreated [n=2], HGF TG NNK treated [n=2], WT NNK treated [n=2]) and 4 samples from 20 week old mice (HGF TG untreated [n=2], WT untreated [n=2]).

first: Cassandra

last: Henry

first: Ariel

last: Lopez-Chavez

first: Kate

last: Brizzi

first: Laura

last: Stabile


title: A Compendium of Chromatin Contact Maps Reveal Spatially Active Regions in the Human Genome

status: Public on Nov 15 2016

city: La Jolla

first: Anthony

last: Schmitt

state: California

address: 9500 GILMAN DR., BLDG. CMME RM 2071

department: Cellular and Molecular Medicine

institute: UC San Diego

summary: The three-dimensional configuration of DNA is integral to all nuclear processes in eukaryotes, yet our knowledge of the chromosome architecture is still limited. Genome-wide chromosome conformation capture studies have uncovered features of chromatin organization in cultured cells, however, genome architecture in human tissues has yet to be explored.  Here, we report the most comprehensive survey to date of chromatin organization in human tissues. Through integrative analysis of chromatin contact maps in 21 primary human tissues and cell types, we discover genomic regions that exhibit unusually high levels of local chromatin interactions. These frequently interacting regions (FIREs) are enriched for active enhancers and are located near tissue-specifically expressed genes. Unlike previously identified chromatin loops, FIREs tend to engage in promiscuous local chromatin interactions in a tissue-specific manner. FIRE formation is dependent on the Cohesin complex. Additionally, we show that FIREs can help annotate function of non-coding sequence variants.

overall_design:
The study contains new Hi-C datasets in 11 primary adult tissues. 4 of the 11 tissues have biological replicates, which is defined as two datasets from the same tissue type but from different donor individuals.The study also contains analysis of 3 previously published tissue Hi-C datasets (Leung et al., 2015), as well as several other cell lines from other studies as noted throughout our study. The study also contains the re-analysis and integration of previously published RNA-seq by the Roadmap Epigenomics Consortium (GEO database under accession number GSE16256 and from SRA database under accession umber SRP000941).
all the Hi-C data generated in this study can be visualized in 3dgenome.org


title: DNA methylation analysis of astroblastomas

status: Public on Mar 20 2019

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

type:
Methylation profiling by array
Third-party reanalysis

summary: Astroblastomas represent rare cerebral tumors of the central nervous system (CNS).  The status of astroblastoma as a distinct molecular entity is controversial, largely because the molecular features of astroblastomas have not been comprehensively evaluated.  Herein, we used methylation profiling to compare the signatures of astroblastoma to a reference cohort of brain tumor entities.  We found that astroblastomas are molecularly heterogenous and share molecular features with known brain tumor entities including plexomorphic xanthoastrocytoma, high-grade neuroepithelial tumor with MN1 abnormalities, as supratentorial ependymomas with RELA fusions.

overall_design: 23 unique astroblastomas were profiled using Illumina Infinium Human MethylationEpic Bead Array (n=23 total samples). The series includes re-analyzed data of 195 samples from GSE90496. The entire data matrix with the average beta values for all 218 analyzed samples is available at the foot of this page.

first: B

last: Orr

first: T

last: Lin