title: Physiological, biochemical and genome-wide transcriptional analysis reveals that elevated CO2 mitigates the impact of combined heat wave and drought stress in Arabidopsis thaliana at multiple organizational levels

status: Public on Apr 24 2014

city: Antwerp

last: Asard

state: Antwerpen

address: Groenenborgerlaan 171

department: Department of Biology

country: Belgium

institute: University of Antwerp

summary:
Genome-wide transcriptional profiling of Arabidopsis thaliana to a combination of heatwave and drought under ambient and elevated CO2. Goal of this study was elucidate the transcriptional responses to a combination of heat wave and drought, and to see  how these responses are modifed under future climate (high) CO2.
Climate changes increasingly threaten plant growth and productivity. Such changes are complex and involve multiple environmental factors, including rising CO2 levels and climate extreme events. As the molecular and physiological mechanisms underlying plant responses to realistic future climate extreme conditions are still poorly understood, a multiple organizational level-analysis (i.e. eco-physiological, biochemical and transcriptional) was performed, using Arabidopsis exposed to incremental heat wave and water deficit under elevated CO2.The climate extreme resulted in biomass reduction, photosynthesis inhibition, and considerable increases in stress parameters. Photosynthesis was a major target as demonstrated at the physiological and transcriptional levels. In contrast, the climate extreme treatment induced a protective effect on oxidative membrane damage, most likely as a result of strongly increased lipophilic antioxidants and membrane-protecting enzymes. Elevated CO2 significantly mitigated the negative impact of a combined heat and drought, as apparent in biomass reduction, photosynthesis inhibition, chlorophyll fluorescence decline, H2O2 production and protein oxidation. Analysis of enzymatic and molecular antioxidants revealed that the stress-mitigating CO2 effect operates through up-regulation of antioxidant defense metabolism, as well as by reduced photorespiration resulting in lowered oxidative pressure. Therefore, exposure to future climate extreme episodes will negatively impact plant growth and production, but elevated CO2 is likely to mitigate this effect.

overall_design: Transcriptome analysis was performed by Agilent Arabidopsis (V4) 4x44K platform which represented all known genes in the Arabidopsisgenome. Experiments were performed using a modified loop design (Knapen et al., 2009). This design consisted of total 8 arrays; sample from each treatment was labelled once and has 4 biological replicates, two of which were labelled in red and two in green

first: Gaurav

last: Zinta

first: Hamada

last: AbdElgawad

first: Malgorzata

last: Domagalska

first: Lucia

last: Vergauwen

first: Dries

last: Knapen

first: Ivan

last: Nijs

last: Janssens

first: Gerrit

middle: T

last: Beemster


title: Notch signaling-dependent gene expression in the developing mouse lung

status: Public on Mar 13 2014

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

country: USA

institute: Boston University

summary:
Transcriptional profiling of Control and RbpjkCNULL lungs from  E18.5. For microarray profiling, total RNA from E18.5 lungs was submitted for labeling and hybridization (Mouse Gene 1.0 ST Whole Genome Array, Affymetrix) to the Boston University Microarray Core facility.
Clara cells (CCs) are a morphologically and operationally heterogeneous population of secretoglobin Scgb1a1-expressing secretory cells crucial for airway homeostasis and post-injury repair. Insights into the extent and origin of CC diversity have been hindered by the limited knowledge of markers of these cells and their precursors. To identify novel putative markers of CCs we characterized global changes in gene expression in embryonic lungs in which CCs were suppressed by conditional disruption of Notch signaling (Rbpjkcnull). Microarray profiling and Real Time PCR (qRT-PCR) identified eleven genes differentially downregulated in the E18.5 airways of Rbpjkcnull compared to controls, nearly half not previously known to mark CCs. Remarkably, in situ hybridization (ISH) revealed overlapping but also distinct domains of expression of these genes in E18.5 controls. Notably, Reg3g, Chad, Gabrp and Lrrc26 were selectively expressed in CCs of proximal airways and Upk3a expression was highly enriched in a CC subpopulation surrounding Neuroepithelial Bodies (NEBs). All genes expressed in the adult airways were found to be expressed in adult CCs and downregulated by selective CC ablation in a Naphthalene model of injury. Flow cytometry-based isolation of CCs from different airway regions of adult B1-EGFP reporter mice and qRT-PCR corroborated the spatial enrichment in gene expression observed by ISH. Remarkably, although, Scgb3a2, Upk3a, Cyp2f2, Cbr2, Krt15 could be detected unambiguously in airway progenitors as early as E14.5, only Scgb3a2 and Upk3a had their expression suppressed by disruption of Notch signaling, implicating both genes as the earliest markers for CC differentiation. Our study supports the idea that the diversification of the CC phenotype already arises during embryonic development and identifies candidate markers that can be used to investigate this process.

overall_design: Control (n=3) versus RbpjkCNULL(n=3)

first: Arjun

last: Guha


title: A new approach for the study of lung smooth muscle phenotypes and its application in asthma

summary:
We developed a new method for the isolation of bronchial smooth muscle cells. This method is built upon a double fluorescent mouse SMA-GFP;NG2-DsRed and cell sorting.
Using this method, we isolated bronchial smooth muscle cells from control and asthmatic C57BL/6J mice for gene profiling.

overall_design: Double fluorescent mice were induced to develop asthma using OVA.  Bronchial smooth muscle cells were purified from asthmatic and control mice for mRNA array.

first: Xingbin

last: Ai

first: Alan

last: Fine


title: Molecular characterization of tumor cells from the cerebrospinal fluid and matched primary tumors from metastatic breast cancer patients with leptomeningeal disease

status: Public on Jan 09 2014

city: San Francisco

first: Mark

last: Magbanua

state: CA

address: 1450 3rd Street, PO Box 589001

department: HemOnc

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

type: Genome variation profiling by genome tiling array

summary:
We purified tumor cells in the CSF (“CSFTC”) from 15 metastatic breast cancer patients diagnosed with leptomeningeal disease using a two-step method involving immunomagnetic enrichment and fluorescence-activated cell sorting (IE/FACS). Magnetic beads coated with mAb to the epithelial cell adhesion marker (EPCAM) were used to enrich for tumor cells and were further purified by FACS analysis.
For DNA profiling, isolated CSFTC were subjected to molecular characterization through genome-wide copy number analyses. Genomic analyses were then compared with those performed on the corresponding archival primary tumors.
For RNA profiling, isolated CSFTC were then subjected to molecular characterization through gene expression profiling via QPCR analysis of 64 cancer-related genes

overall_design:
CGH: 17 CSFTC samples from 13 patients were successfully profiled ,1 patient had 5 timepoints, 6 of 13 patients had matched to copy number data archival tumors
RNA: 18 samples from 5 patients had successful gene expression data of the 64 genes measured in triplicates. For non-tumor controls, 9 of the samples had matching gene expression data from sorted leuckocytes (+CD45 cells) obtained from the same draw.

middle: J

first: Janet

middle: H

last: Scott

first: Louai

last: Hauranieh

first: Michelle

last: Melisko

first: Eduardo

middle: V

last: Sosa

first: Andrea

last: Kablanian

first: Ritu

last: Roy

first: John

middle: W

last: Park


title: Assessment of hematopoietic failure due to RPL11 deficiency in a zebrafish model of Diamond–Blackfan anemia by deep sequencing

status: Public on Jan 21 2014

city: Beijing

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

country: China

institute: Beijing Institute of Genomics

type: Expression profiling by high throughput sequencing

summary: To comprehensively reflect the impact of RPL11 deficiency on the transcriptome of zebrafish embryos, we collected 40–50 RPL11-deficient and MO control zebrafish embryos at 48 hpf from separate experiments and constructed two mRNA-seq sequencing libraries in parallel. High-throughput sequencing was performed on the Hi-Seq2000 sequencing platform in parallel. The number of sequenced gene transcript reads was 35–40 million. We found that hemoglobin biosynthetic and hematological defects in RPL11-deficient zebrafish were related to dysregulation of iron metabolism-related genes, including tfa, tfr1b, alas2 and slc25a37, which are involved in heme and hemoglobin biosynthesis. In addition, we found reduced expression of the hematopoietic stem cells (HSC) marker c-myb and HSC transcription factor tal1 and hoxb4a in RPL11-deficient zebrafish embryos, indicating that the hematopoietic defects may be related to impaired HSC differentiation and proliferation. However, RPL11 deficiency did not affect the development of other blood cell lineages such as granulocytes and myelocytes.

overall_design: Compare 2 different transcriptomes of RPL11-deficient and MO control zebrafish embryos

first: Xiangdong

last: Fang


title: Effects of high-fat induced obesity on gene expression in mouse kidney

status: Public on Jan 11 2014

city: Zurich

first: Zhibo

last: Gai

state: Schweiz

address: Wagistrasse 14

department: Department of Clinical Pharmacology and Toxicology

country: Switzerland

institute: University Hospital Zurich

summary: Global gene expression in the 20-week remnant kidneys of uninephrectomized mice fed either a chow or a high fat diet was compared with kidney tissue from the corresponding sham groups. Results provide insight into mechanisms underlying effects of high-fat induced obesity on gene expression in mouse kidney.

overall_design: Male C57/BJ mice aged 6 weeks were randomly assigned to uninephrectomy (UNX) or sham procedures and fed with a high fat diet or control chow diet. All mice were sacrificed under anesthesia 20 weeks after surgery and kidneys were harvested. 3-4 total RNA samples per group were analyzed and gene expression was compared between groups.


title: microRNAs profiling in hippocampal cells of Self-Sustaining Status Epilepticus (SSSE) mouse model

status: Public on Jan 01 2014

city: Bonn

first: Khalid

middle: A.

last: Abnaof

state: North Rhine-Westfalina

address: Dahlmann Straße 2

department: Algorithmic Bioinformatics

country: Germany

institute: Bonn-Aachen International Centre for Information Technology (B-IT)

summary: Status Epilepticus (SE) is induced in mice (C57Bl/6J) through electrical stimulation (90min, 100 ms trains of 1 ms, 2 trains per 1 s, 250 μA peak current intensity). RNA was extracted from the hippocampi at 24 h and 28 d after induction. In wild-type RNA was extracted on the 22nd day. microRNA expressions were measured via microarray technology using Exiqon's miCURY™ LNA Arrays.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: 3 conditions, SSSE mouse model at 24 h and 28 d, and a control group, each of 8 replicates.

first: Anita

last: Kretschmann

first: Benedicte

last: Danis

first: Lidija

last: Andonovic

first: Marijke

last: van Rikxoort

first: Franziska

last: Siegel

first: Manuela

last: Mazzuferi

first: Patrice

last: Godard

first: Etienne

last: Hanon

first: Holger

last: Fröhlich

first: Rafal

middle: M

last: Kaminski

first: Patrik

last: Foerch

first: Alexander

last: Pfeifer


title: microRNAs profiling in hippocampal cells of mouse with Pilocarpine-induced Status Epilepticus (SE)

summary: SE was induced in mice (NMRI) chemically by a single dose of Pilocarpine (300mg/kg;i.p.). RNA was extracted from the hippocampi of treated and wild-type mice at 24 h and 28 d after induction. microRNA expressions were measured via microarray technology using Exiqon's miCURY™ LNA Arrays.

overall_design: 4 conditions, Pilocarpine treated mice at 24 h and 28 d, and the control wild-type at the same types, each of 8 replicates.


title: microRNAs profiling in hippocampal cells of mouse with Sound-induced Seizure

summary: After an electrically induced seizure, mice (NMRI) received electrical stimulation (current intensity 44 mA, 0.2 ms monopolar pulses at 6 Hz frequency for 3 s). RNA was extracted from the hippocampi at 0, 3, 6, 24 and 72 h after the seizure. microRNA expressions were measured via microarray technology using Exiqon's miCURY™ LNA Arrays.

overall_design: Time-course design, treated cells at 0, 3, 6, 24, and 72 h, with 7 replicate each


title: Comparative miRNA expression of normal skin from control and lesional skin from mice

status: Public on Dec 31 2013

city: Shanghai

first: Yan

last: Sha

state: Shanghai

address: South Rd chongqing 280

department: Shanghai Institute of Immunology

institute: Shanghai jiao tong university

summary: The efficacy of monoclonal antibodies against either interleukin (IL)-17 or the IL-17 receptor in psoriasis therapy provides strong evidence that IL-17 is the major inflammatory mediation in this disease. However, how IL-17 induces epidermal hyperplasia in psoriasis remains largely unknown. Here, we show that IL-17 actives NF-kB in keratinocytes and initiates the NF-kB-dependent transcription of microRNA-31 (miR-31), one of the most abundant microRNAs in the epidermis of lesional skin of psoriasis and two related mouse models. Similar to IL-17 deficiency (IL-17-/-), knocking out miR-31 (miR-31-/-) or targeting it by antagomir-31 prevents keratinocytes Ki67 expression and inhibits acanthosis and dermal inflammation in psoriasis mouse model. Moreover, PPP6c, a negative regulator restricting G0/G1 to G2/M phase progression in the cell cycle, is diminished in human psoriatic epidermis and is directly targeted by miR-31. Inhibition of ppp6c is functionally important for the biological effects of miR-31 in the development of epidermal hyperplasia. Thus, our data define IL-17-inducede miR-31 and its target ppp6c as critical factors for hyperproliferative epidermis in psoriasis.

overall_design: Epidermis samples from affected ears derived from 3 CD18hypo PL/J mice (DIS) or normal ears derived from 3 CD18hypo C57BL/6J mice(2128) were used for RNA extraction and hybridization on Affymetrix microarrays. We sought to compare miRNA expression of normal skin from control and lesional skin.

first: Honglin

last: Wang

first: Sha

last: Yan

first: Lingyun

last: Zhang

first: Zhaoyuan

last: Liu


title: Targeting Myc signaling pathway by inhibition of histone demethylase JMJD2B (ciclopirox)

city: Memphis

first: JUN

last: YANG

state: TN

address: 262 Danny Thomas Place

department: Surgery

institute: St Jude Children's Research Hospital

summary: Epigenetic alterations appear to modulate Myc signaling. We investigated the role of the histone demethylase JMJD2B in Myc-mediated neuroblastoma pathogenesis. We demonstrate that Myc physically interacts with and recruits this epigenetic modifier, which removes repressive H3K9 methyl marks from Myc-target genes. JMJD2B regulates neuroblastoma proliferation and, together with MYCN amplification, identifies a subgroup of poor prognosis patients. We identify a novel histone demethylase inhibitor, ciclopirox, which targets JMJD2B and, consequently, Myc signaling, thereby inhibiting neuroblastoma proliferation and inducing differentiation. In xenograft studies, genetic and pharmacologic inhibition of JMJD2B resulted in significant tumor growth restriction. Our findings provide insight into epigenetic regulation of Myc via histone methylation and proof-of-concept for pharmacologic inhibition of histone demethylases to target Myc signaling in cancer.

overall_design: 8 samples were treated with vehicle or ciclopirox.

first: Jun

last: Yang

first: Andew

last: Davidoff


title: Microarray profiling of PFC, HPC and STR from subjects with schizophrenia, bipolar, MDD or control

city: Groton

first: Thomas

middle: A

last: Lanz

state: CT

address: Eastern Point Rd

department: Multi-Omics & Biomarkers

institute: Pfizer

summary: Schizophrenia is a complex psychiatric disorder encompassing a range of symptoms and  etiology dependent upon the interaction of genetic and environmental factors.  Several risk genes, such as DISC1, have been associated with schizophrenia as well as bipolar disorder (BPD) and major depressive disorder (MDD), consistent with the hypothesis that a shared genetic architecture could contribute to divergent clinical syndromes.  The present study compared gene expression profiles across three brain regions in post-mortem tissue from matched subjects with schizophrenia, BPD or MDD and unaffected controls.  Post-mortem brain tissue was collected from control subjects and well-matched subjects with schizophrenia, BPD, and MDD (n=19 from each group).  RNA was isolated from hippocampus, Brodmann Area 46, and associative striatum and hybridized to U133_Plus2 Affymetrix chips.  Data were normalized by RMA, subjected to pairwise comparison followed by Benjamini and Hochberg False Discovery Rate correction (FDR).  Samples derived from patients with schizophrenia exhibited  many more changes in gene expression across all brain regions than observed in BPD or MDD.  Several genes showed changes in both schizophrenia and BPD, though the magnitude of change was usually larger in schizophrenia.  Several genes that have variants associated with schizophrenia were found to have altered expression in multiple regions of brains from subjects with schizophrenia.  Continued evaluation of circuit-level alterations in gene expression and gene-network relationships may further our understanding of how genetic variants may be influencing biological processes to contribute to psychiatric disease.

overall_design: Pre-frontal cortex, striatum and hippocampus were obtained from subjects with schizophrenia, bipolar disorder, major depressive disorder and matched controls.


title: Targeting Myc signaling pathway by inhibition of histone demethylase JMJD2B (siRNA)

overall_design: 8 samples were transfected with two different siRNAs for control, JMJD2B, MYCN and JARID1A.


title: Comparative high density microarray analysis of global 5hmC patterns in mouse brain and liver following independent affinity based enrichment protocols.

status: Public on Dec 01 2013

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

type: Methylation profiling by genome tiling array

summary:
On mouse tiled microarrays (GPL17802), we profile 5hmC in WT mouse livers and brains following fragment enrichment by one of three affinity based techniques: i- antibody (HmeDIP), ii- Chemical capture (hMeSeal) and iii-JBP-1 protein affinity (JBP). HmeDIP and hMeSeal both return similar patterns of 5hmC whilst JBP enriched patterns (carriedo out on brain only) resemble background noise.  5hmC is largely found to reside in the bodies of active genes as well as being enriched over enhancer and promoter proximal regions.
WT C57BL/6 mice aged 30-32 days old at time of organ removal. Tissues taken and frozen in liquid nitrogen prior to DNA extraction.

overall_design: Genomic DNA was sonicated (Bioruptor, Diagenode) to produce DNA fragments ranging in size from 200 to 1,000 bp, with a mean fragment size of around 300 bp.  i- HmeDIP:  antibody enrichment carried out as previously reported by Thomson et al 2013 (doi:10.1093/nar/gkt232).   ii- HmeSeal: Enrichment based on the hMe-Seal based techniques described by Song et al 2010 (doi: 10.1038/nbt.1732) and marketed by Active motif under the name hydroxymethyl-collector kit. iii- JBP-1 affinity purification: Enrichment carried out using the Quest 5hmC DNA enrichment kit marketed by Zymo research.

middle: P

first: Jennifer

last: Hunter

first: Richard

middle: R

last: Meehan


title: Expression Data from E16.5 hearts from WT and FOG-2R3K5A siblings

city: Cambridge

first: Eric

last: Svensson

address: 220 Massachusetts Avenue

institute: Novartis

summary:
Heart development is modulated by FOG-2/NuRD interactions. FOG-2R3K5A is unable to recuit the NuRD complex and this results in cardiac defects such as ASD, VSD, and thin ventricular walls
We used microarrays to detail the changes in gene expression in FOG-2R3K5A hearts to determine misexpression of genes that may be causing the observed phenotypes.

overall_design: Whole hearts from E16.5 Wild-type and FOG-2R3K5A siblings were processed for RNA extraction and hybridization on Affymetrix microarrays. We used three biological replicates of each genotype.

middle: C

first: Zhiguang

last: Gao

first: Audrey

middle: S

last: Garnatz


title: Expression data from citrus fruit (Citrus sinensis L. Osbeck)

city: WUHAN

first: Kady

last: Chan

address: xueyuan street

institute: Huazhong agricultural university

summary:
An antifungal aroma substance, 2-phenylethanol (PEA), was isolated from antagonistic yeast strain Kloeckera apiculata extract. Microarry were used to analyse its role citrus.
We used microarrays to detail the global programme of gene expression underlying Citrus were treated with 1.0x108 cells/ml K. apiculata (KA), PEA (0.15%), the extract (1000xdilute) and control (CK) for 24 h,

overall_design: An antifungal aroma substance, 2-phenylethanol, was isolated from antagonistic yeast strain Kloeckera apiculata. To analyse its role in Citrus response,Citrus were treated with  K. apiculata , 2-phenylethano (0.15%), the extract (1000xdilute) and control (CK) for 24 h, respectively. The fresh epicarp of citrus was separated by knife and directly frozen in liquid nitrogen for RNA extraction and hybridization on Affymetrix microarrays.

first: Pu

first: Chen

last: Kai


title: Genome wide analysis of human iPS cell lines generated with non-integrative plasmids and knock-down of P53 gene

city: Horsholm

first: Christian

last: Clausen

address: Kogle Alle 2

department: Mammalian Cell Technology

country: Denmark

institute: Bioneer

summary: The primary aim of this study is to evaluate the effect of transient knock down of P53 as a tool to increase the efficiency of a non-integrative methodology for reprogramming adult human normal dermal fibroblasts. This study demonstrate that transient knockdown of P53 is an efficient way to produce iPSC containing minimal genomic alterations, which meets the increased demand for iPSC in personalized drug screening campaigns.

overall_design: Total RNA was isolated from 3 iPS cell lines generated without P53 knockdown and 3 generated with P53 knockdown. In addition total RNA was isolated from the parental normal human dermal fibroblasts and from a reference human iPS cell line from Systembio (SBI).

first: Mikkel

last: Rasmussen

first: Bjoern

last: Holst

first: Joergen

last: Nielsen

first: Lis

last: Hasholt

first: Poul

last: Hyttel


title: MeDIP-chip from head and neck squamous cell carcinoma tissues and normal subjects

status: Public on Jun 19 2014

first: yun

middle: xiao

last: zhang

address: Room 305, Building #1,639 Zhi Zao Ju Road

department: Oral Mucosal Diseases

institute: Shanghai Ninth People's Hospital Affiliated Shanghai JiaoTong University School of Medicine

summary: Profiling the genome-wide methylation status of head and neck squamous cell carcinoma and normal subjects

overall_design: Screening HNSCC-related candidate methylation gene by comparison of HNSCC tissues vs normal subjects.

first: Wei

last: Jiang

first: Xiao

middle: Y

last: Zhang


title: Deletion of HCMV US17 alters host immune genes at 12 hpi and ER stress genes at 96 hpi.

status: Public on Nov 30 2013

city: Ann Arbor

first: Stephen

middle: J.

last: Gurczynski

state: MI

address: 109 Zina Pitcher Pl, Room 4062

department: Internal Medicine

institute: University Of Michigan

summary:
Infection of human fibroblasts with either human cytomegalovirus strain AD169 or a recombinant virus deleted for HCMV US17
Illumina HT-12 beadarrays were used to quantitate levels of host transcripts at either 12 or 96 hpi.

overall_design: Cells were infected in biological triplicates at both 12 and 96 hours post infetion

first: Philip

middle: E

last: Pellett


title: RNA expression data from Halobacterium NRC-1 in varied extracellular salinity conditions

status: Public on Dec 21 2013

city: Seattle

first: Nicolas

last: Pinel

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

type: Expression profiling by genome tiling array

summary: Halobacterium salinarum is an extreme halophilic archaeon adapted to total salinities upwards of 4 M. Here we studied gene expression in H. salinarum grown in ten ion composition media that vary in two major aspects of ion composition: [NaCl] and Mg:K ratio.

overall_design: Samples were taken from the Δura3 parental strain cells at mid-log phase (OD600 = 0.4-0.5) during growth in ten different media. RNA from growth in each media was compared with a standard RNA reference, extracted from H. salinarum NRC-1 grown in batch culture in the standard growth media to OD = 0.471. Two biological replicates were performed for each media, with the exception of one replicate only for M12.

first: Karlyn

middle: D

last: Beer

first: Elisabeth

last: Wurtmann

first: Nitin

last: Baliga


title: Targeting Myc signaling pathway by inhibition of histone demethylase JMJD2B

first: JUN

last: YANG

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

overall_design: Refer to individual Series


title: Transcriptional profiles of non-transgenic and OsEREBP1 over-expressed transgenic plants

status: Public on Nov 15 2013

city: Hyderabad

first: Rajeshwari

last: Ramanan

state: Andhra Pradesh

address: Uppal Road

department: Plant Science

country: India

institute: Centre for Cellular and molecular biology

summary:
Overexpression of a transcription factor OsEREBP1 results in attenuation of disease symptoms upon infection with bacterial pathogen Xanthomonas oryzae pv. oryzae and tolerance to drought stress in transgenic rice plants.
Microarray analysis was performed to identify genes regulated by the rice transcription factor OsERBP1.

overall_design: Three independent replicates of the experimental OsEREBP1-ox transgenic plants and the control non-transgenic Kitaake plants were grown under normal conditions.

first: Madhavi

middle: B

last: Mylavarapu

first: V

last: Jisha

first: Ramesh

last: Palaparthi


title: Diagnostic utility of high quality RNA in diverse clinical semen and sperm samples

status: Public on Nov 23 2013

city: Pittsburgh

first: Andrew

last: Georgiadis

address: 203 Craft Ave.

institute: UPMC

summary: We report quantitation of specific mRNAs in two RNA samples isolated from normozoospermic whole semen

overall_design:
Examination of 2 different normozoospermic semen samples by RNA-seq

Please note that raw data for 'GSM1273824: AY4' is incomplete.

first: Alexander

last: Yatsenko


title: TEL-AML1 (ETV6-RUNX1) in B-cells and leukemia (part 6)

status: Public on Nov 04 2013

city: Düsseldorf

first: Pablo

last: Landgraf

address: Moorenstraße 5

department: Clinic of Pediatric Oncology, Hematology and Clinical Immunology

institute: Heinrich-Heine University Düsseldorf

summary: We identified directly and indirectly regulated target genes utilizing an inducible TEL-AML1 system derived from the murine pro B-cell line BA/F3 and a monoclonal antibody directed against TEL-AML1. By integration of promoter binding identified with ChIP-on-chip, gene expression and protein output through microarray technology and stable labelling of amino acids in cell culture (SILAC), we identified directly and indirectly regulated targets of the TEL-AML1 fusion protein.

overall_design: Bound promoter regions of immunoprecipitated TEL-AML1 associated genes were first compared to input material and enrichment was calculated. The same was performed for empty vector control cell lines, also treated with the induction reagent mifepriston. Enriched promoter regions were then compared of the both sets. 2 independent replicates each (4 arrays) were performed.

first: Yvonne

last: Linka

first: Sebastian

last: Ginzel

first: Marcus

last: Krüger

first: Astrid

last: Novosel

first: Michael

last: Gombert

last: Kremmer

first: Jochen

last: Harbott

first: Ralf

last: Thiele

first: Arndt

last: Borkhardt


title: TEL-AML1 (ETV6-RUNX1) in B-cells and leukemia (part 5)

first: Elisabeth


title: TEL-AML1 (ETV6-RUNX1) in B-cells and leukemia (part 4)

type: Genome binding/occupancy profiling by genome tiling array

overall_design: Bound promoter regions of immunoprecipitated TEL-AML1 associated genes were first compared to input material and enrichment was calculated. 3 independent replicates were performed.


title: myb118 mutation; Identification of genes misregulated in developing seeds of Arabidopsis in response to the myb118 mutation.

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary:
ra12-06_myb118; myb118 mutation
What are the genes over expressed or down regulated in seeds in response to a myb118 mutation?

Plants of the different genotypes (wild-type, myb118 mutant, myb118 antisense lines named 0E3 and T16) were grown in a green house, their flower were tagged and seeds were harvested 10 days after anthesis. Seeds were extracted from the siliques, stored at -80°C prior to RNA extraction.

overall_design: 6 dye-swap - normal vs transgenic comparaison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Sébastien

last: Baud

first: Marie-Laure

last: Martin-Magniette


title: TEL-AML1 (ETV6-RUNX1) in B-cells and leukemia (part 2)

overall_design: Bound promoter regions of immunoprecipitated TEL associated genes were first compared to input material and enrichment was calculated. The same was performed for empty vector control cell lines, also treated with the induction reagent mifepriston. Enriched promoter regions were then compared of the both sets. 3 independent replicates each (6 arrays) were performed.


title: Racial Difference in Human Platelet PAR4 Reactivity Reflects Expression of PCTP and miR-376c

city: Houston

first: Chad

last: Shaw

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

summary:
Racial differences in the pathophysiology of atherothrombosis are poorly understood.  We explored the function and transcriptome of platelets in healthy black (n=70) and white (n=84) subjects.
Numerous differentially expressed (DE) RNAs were associated with both race and PAR4 reactivity, including phosphatidylcholine transfer protein (PCTP), and platelets from blacks expressed higher levels of PC-TP protein.

overall_design: Purified platellets were obtained from 154 healthy volunteers not taking blood thinning medication, suffering from blood diseases or otherwise excluded for health reasons. RNA was extracted and profiled on these subjects.  Simultaneously, purified platelets were phenotyped using aggregation in response to stimulation with agonist.  The agonist response scores and races as ewll as gene expression values on these individuals are provided.

first: Paul

middle: F

last: Bray


title: TEL-AML1 (ETV6-RUNX1) in B-cells and leukemia

first: Pablo

last: Landgraf

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: TEL-AML1 (ETV6-RUNX1) in B-cells and leukemia (part 3)

overall_design: Bound promoter regions of immunoprecipitated AML1 associated genes were first compared to input material and enrichment was calculated. The same was performed for empty vector control cell lines, also treated with the induction reagent mifepriston. Enriched promoter regions were then compared of the both sets. 3 independent replicates each (6 arrays) were performed.

first: Yvonne

last: Linka


title: TEL-AML1 (ETV6-RUNX1) in B-cells and leukemia (part 1)

first: Sebastian

last: Ginzel


title: Transcript atlases reveal that artery tertiary lymphoid organs but not secondary lymphoid organs control key steps of atherosclerosis T cell immunity in aged apoe-/- mice.

status: Public on Oct 30 2013

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

department: Medicine

institute: Ludwig Maximilians Universität München

summary:
Tertiary lymphoid organs (TLOs) emerge in response to nonresolving inflammation but their roles in adaptive immunity remain unknown. Here, we explored artery TLOs (ATLOs) to delineate atherosclerosis T cell responses in apoe-/- mice during aging. Though the T cell repertoire showed systemic age-associated contractions in size and modifications in subtype composition and activation, wt and apoe-/- mice were equally affected. In contrast, ATLOs - but not wt aortae, apoe-/- aorta segments without ATLOs or atherosclerotic plaques - promoted T cell recruitment, altered characteristics of T cell motility, primed and imprinted T cells in situ, generated CD4+/FoxP3-, CD4+/FoxP3+, CD8+/FoxP3- effector and central memory cells, and converted naïve CD4+/FoxP3- T cells into induced Treg cells. ATLOs also showed substantially increased antigen presentation capability by conventional dendritic cells (DCs) and monocyte-derived DCs but not by plasmacytoid DCs. Thus, the senescent immune system specifically employs ATLOs to control dichotomic atherosclerosis T cell immune responses. We assembled transcriptome maps of wt and apoe-/- aortae and aorta-draining RLNs and identified ATLOs as major sites of atherosclerosis-specific T cell responses during aging: Transcriptome atlases of wt and apoe-/- abdominal aortae and associated draining RLNs were constructed from laser capture microdissection (LCM)-based whole genome mRNA expression microarrays yielding 6 maps: wt adventitia (tissue-1); wt RLN (tissue-2); apoe-/- ATLOs (tissue-3); apoe-/- RLN (tissue-4); apoe-/- adventitia without adjacent plaques (tissue-5), and plaques (tissue-6). Several two-tissue comparisons within the transcriptome atlases are noteworthy: Unexpectedly, transcriptomes of wt and apoe-/- RLNs were virtually identical; additonal data revealed that transcriptomes of RLNs were strikingly similar to those of inguinal LNs which do not drain the aorta adventitia (as shown of India ink injection experiments of surgically exposed aortae); in sharp contrast, wt adventitia versus ATLOs revealed 1405 differentially expressed transcripts many of which encoded members of GO terms immune response and inflammatory response; the ATLO-plaque comparison also showed > 1000 differentially expressed transcripts; however, wt adventitia versus apoe-/- adventitia without plaque showed few genes (< 5 % of differentially expressed transcripts of the wt adventitia-ATLO comparison). Thus, the aorta transcriptome atlases support the conclusion that neither aorta-draining apoe-/- RLNs nor ILNs participate in atherosclerosis-specific T cell responses. In addition, they demonstrate that T cell responses in the diseased aorta are highly territorialized. Finally, these data show that the immune responses carried out in ATLOs differ significantly from those carried out in plaques. We next identified three major clusters within the transcriptome atlases through ANOVA analyses and application of strict filters: An adventitia cluster, a plaque/ATLO cluster, and a LN/plaque cluster. The total number of differentially expressed genes in each cluster were examined for GO terms immune response, inflammatory response, T cell activation, positive regulation of T cell response, and T cell proliferation. Within the adventitia cluster, similarities of transcriptomes of wt adventitia and apoe-/- adventitia without associated plaque versus ATLOs indicate that a robust number of immune response-regulating genes are selectively expressed in ATLOs which are located within a distance of few µm of the adventitia without associated plaques indicating a very high degree of territoriality of the atherosclerosis T cell response. Furthermore, unlike the total number of differentially regulated transcripts, the majority of transcripts among GO terms immune response and inflammatory response, was up-regulated. Inspection of the plaque/ATLO cluster provided further information: The majority of immune response regulating genes where expressed at a higher level in ATLOs when compared to plaques though plaques also contained a significant number of immune response regulating genes; the reverse is true for genes regulating inflammation. Finally, the lymph node cluster revealed that though the majority of immune response regulating genes resides in both wt and apoe-/- RLNs (with little differences between them) ATLOs express a selected set of immune response regulating genes at a higher level when compared to LNs. In addition, the inflammatory component of ATLOs when compared to LNs is documented by the finding that many more genes regulating inflammation reside in ATLOs even when compared to those of plaques.
Key words:
T cell response in atherosclerosis; Laser capture microdissection; transcriptome atlas of atherosclerosis.
Citations:
Gräbner R. et al. Lymphotoxin beta receptor signaling promotes tertiary lymphoid organogenesis in the aorta adventitia of aged ApoE-/- mice. J Exp Med 2009 Jan 16;206(1):233-48. PMID: 19139167;
Moos M. et al. The lamina adventitia is the major site of immune cell accumulation in standard chow-fed apolipoprotein E-deficient mice. Arterioscler Thromb Vasc Biol. 2005 Nov;25(11):2386-91. Epub 2005 Sep 22. PMID: 16179593;
Beer M. et al. Laser-capture microdissection of hyperlipidemic/ApoE-/- mouse aorta atherosclerosis. Methods Mol Biol. 2011;755:417-28. PMID: 21761324;
Weih F. et al. Control of Dichotomic Innate and Adaptive Immune Responses by Artery Tertiary Lymphoid Organs in Atherosclerosis. Front Physiol. 2012;3:226. Epub 2012 Jul 6. PMID: 22783198.

overall_design: Wild-type and apoE-deficient mice on the C57BL/6J genetic background were maintained on a standard mouse chow. Total aortae were removed at the age of 6 (n=3), 32 (n=3), or 78 (n=3) w and microarrays were prepared from total RNA extracts or extracts of atherosclerotic lesions and adventitiae obtained by the use of a laser dissection microscope. In addition, aorta associated LNs or distant LNs were prepared from both mouse genotypes.


title: Expression data from neonatal human foreskin keratinocytes (NHKs) with NFX1-123 endogenous expression, overexpression, or knocked down expression, with or without HPV16E6 co-expression

status: Public on Oct 15 2013

first: Rachel

last: Katzenellenbogen

address: 1900 Ninth Ave

department: Adolescent Medicine

institute: Seattle Children's Research Institute

summary:
GSM1056261-GSM1056272: NFX1-123 has been shown to associate with a number of RNA processing proteins, such as cytoplasmic poly(A) binding proteins (PABPC), to affect mRNA stability and translational efficiency of target genes.  The high-risk human papillomavirus type 16E6 (HPV 16E6) induces telomerase activity by activation of hTERT, the catalytic subunit of telomerase.  NFX1-123 can bind to hTERT mRNA and increase its stability in HPV 16E6 expressing keratinocytes (16E6 NHKs).  Little is known regarding what other transcripts, and downstream signaling pathways,  may be dependent on NFX1-123.  In order to determine additional cellular transcripts affected by HPV 16E6 and NFX1-123, we assessed global gene expression changes in cells in which NFX1-123 was overexpressed or knocked down by short hairpin RNAs (shRNA) when compared to an isogenic scramble control, in three independently derived 16E6 NHKs
GSM1212499-GSM1212510: NFX1-123 has been shown to associate with a number of RNA processing proteins, such as cytoplasmic poly(A) binding proteins (PABPC), to affect mRNA stability and translational efficiency of target genes.  The high-risk human papillomavirus type 16E6 (HPV 16E6) induces telomerase activity by activation of hTERT, the catalytic subunit of telomerase.  NFX1-123 can bind to hTERT mRNA and increase its stability in HPV 16E6 expressing keratinocytes (16E6 NHKs).  Little is known regarding what other transcripts, and downstream signaling pathways,  may be dependent on NFX1-123.  In order to determine additional cellular transcripts affected solely by  NFX1-123, we assessed global gene expression changes in cells in which NFX1-123 was overexpressed or knocked down by short hairpin RNAs (shRNA) when compared to an isogenic scramble control, in three independently derived NHKs.

overall_design:
GSM1056261-GSM1056272: Three independent 16E6 expressing NHK cell lines were expanded and transduced with: short hairpin RNA (sh1) that knocked down NFX1-123 by 20%, short hairpin RNA (sh3) that knocked down NFX1-123 by 80%; a non-targeting isogenic shRNA scramble control; or a NFX1-123 overexpression construct with a FLAG-tag (FNFX1-123WT) that increased its RNA expression on average 3.5-fold.  In total, twelve samples were used for the microarray, derived from the three initial NHK cell lines.
GSM1212499-GSM1212510: Three independent  NHK cell lines were expanded and transduced with: short hairpin RNA (sh1) that knocked down NFX1-123 by 40%, short hairpin RNA (sh3) that knocked down NFX1-123 by 83%; a non-targeting isogenic shRNA scramble control; or a NFX1-123 overexpression construct with a FLAG-tag (FNFX1-123WT) that increased its RNA expression on average 14.0-fold.  In total, twelve samples were used for the microarray, derived from the three initial NHK cell lines.

first: Portia

last: Vliet-Gregg

first: Jennifer

last: Hamiliton


title: Differentially expressed genes by anti tumor treatment in human cancer cell lines

status: Public on Sep 25 2013

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

country: Japan

institute: Chiba University

summary: To identify differentially expressed genes by anti cancer treatments (microRNAs, siRNAs and chemical compounds) in human cancer, several cell lines (prostate cancer, renal cell carcinoma and head and neck squamous cell carcinoma) were subjected to Agilent whole genome microarrays.

overall_design: Human cancer cell lines (PC3, DU145, LNCap, A498, 786-O, FaDu and SAS) were treated with miRNAs (miR-145, miR-375, miR-23b, miR-24, miR-27b and miR-29a), siRNAs (si-CAV2, si-LAMB3 and si-GOLM1) and chemical compunds (genistein, wogonin and CXCL10).


title: Global analysis of DNA methylation changes during progression of oral tumorigenesis

status: Public on Sep 18 2013

city: Vancouver

first: Rebecca

last: Towle

state: BC

department: Integrative Oncology

country: Canada

institute: British Columbia Cancer Research Centre

type:
Methylation profiling by array
Expression profiling by array

summary: Objectives: Earlier studies involving a priori gene selection have identified promoter regions deregulated by DNA methylation changes in oral squamous cell cancers (OSCCs) and precancers. Interrogation of global DNA methylation patterns for such specimens has not been reported, though such analyses are needed to uncover novel molecular factors driving disease. Materials and Methods: We evaluated global DNA methylation patterns for 30 biopsies obtained from 10 patients undergoing surgical removal of an OSCC or carcinoma in situ (CIS). From a disease field in each patient, we collected i) dysplastic, ii) CIS or OSCC, and iii) adjacent normal biopsies. DNA isolated from each biopsy was profiled for methylation status using the Illumina HumanMethylation27K platform. Results: Our data demonstrate that aberrant methylation of promoter CpG islands exists across oral precancer and OSCC genomes. Non-hierarchical clustering of all methylation data revealed distinct methylation patterns between the normal and the CIS/OSCC tissues (with results for dysplastic biopsies split between groups).  Multiple genes exhibiting recurrent aberrant DNA methylation were found for both dysplastic and CIS/OSCC groups, and included enrichment for genes found in the WNT and MAPK signaling pathways. Conclusion: In identifying aberrant DNA methylation at the earliest stages of oral precancer and finding recurring epigenetic disruption of specific genes/pathways across our analyzed cohort, we conclude that CpG methylation changes are a hallmark of oral cancer progression and that global DNA methylation analyses are an essential component for wider studies seeking to derive biomarkers or potentially druggable targets for improving oral cancer outcomes.

overall_design: Bisulphite converted DNA from the 30 samples were hybridised to the Illumina Infinium 27k Human Methylation BeadChip v1.2. Total RNA from 30 oral cancer samples were hybridized to Agilent 4x44k gene expression microarray.

first: R

first: D

last: Truong

first: K

last: Hogg

first: W

last: Robinson

first: C

last: Poh

last: Garnis


title: Expression data from EGR1-transfected H1299 cells vs normal H1299 cells

status: Public on Sep 17 2013

city: Guangzhou

first: Huihua

last: Zhang

address: 601, west Huangpu avenue, Tianhe district

department: Biomedicine Institute & Cell Biology Department

institute: Jinan University

summary:
The functions of EGR1, a multifunctional transcription factor, in prostate cancer are well documented. However, little is known about the functions of EGR1 in lung cancer. we observed the function of EGR1 in non-small cell lung carcinoma (NSCLC) and identified the genes that influence cell fate and tumor development.
We used microarrays to detail the global programme of gene expression and identified genes differentially expressed when EGR1-overexpressed.

overall_design: We have demonstrated that EGR1 is able to increase cell apoptosis, and inhibit metastasis. And we sought to find genes distributed to  decrease the malignancy of human non-small cell lung cancer regulated by EGR1. To that end, H1299 cells were transfected either EGR1 or pcDNA3.1. After 48h, cells were collected for RNA extraction and hybridization on Affymetrix microarrays (PEGR1 VS PCDNA3.1).

first: Xiaojia

last: Chen


title: Profiling the transcriptome: synaptoneurosomes capture the molecular effects of alcohol consumption

status: Public on Oct 28 2013

city: Austin

first: Dana

last: Moat

state: Texas

address: 2500 Speedway, MBB 1.138

department: Waggoner center for alcohol and addiction research

institute: University of Texas at Austin

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

summary:
Action of alcohol on synaptic mRNA in the amygdala of mice
Chronic alcohol consumption induces changes in gene expression, causing persistent long-term neuro-adaptations and the remodeling of synaptic structures. These alcohol-induced synaptic changes may rely specifically on the local translation of mRNAs in the synaptic compartments of the cell. We profiled the transcriptome from synaptoneurosomes (SN) and paired total homogenates (TH) of amygdala to analyze the synaptic adaptations induced by chronic voluntary alcohol consumption in mice.
In the SN both the number of alcohol-responsive mRNAs and the magnitude of fold-change were greater than in the TH. Accordingly, the SN detected many genes with coordinated patterns of expression producing a highly connected mRNA network in gene co-expression analysis. The greater sensitivity of the SN preparation allowed for improved cell-type specificity analysis, revealing an up-regulation of alcohol-responsive astrocytic and microglial modules that correlated with alcohol consumption. Alcohol was found to induce changes in the SN functionally important biological pathways, including long-term potentiation, long-term potentiation depression, glutamate pathway, neuro-immune, RNA-processing and translational machineries and provided overlap with changes seen in human alcoholic brain. Transposable elements were responsive to alcohol and found in the down-regulated neuronal mRNA module, which may underlie some of the coordinated gene expression changes associated with alcohol.
We provide evidence that enrichment of synaptic components reveals a more intricate network of coordinated gene expression. Increased resolution captures the molecular effects of synaptic manipulations and provides an improved technique for identifying therapeutic targets for alcohol abuse.

Local translation of mRNAs in the synapse plays a major role in synaptic structure and function. Chronic alcohol use causes persistent changes in synaptic mRNA expression, possibly mediated by microRNAs localized in the synapse. We profiled the transcriptome of synaptoneurosomes (SN) from the amygdala of mice chronically consuming 20% ethanol in a continuous two-bottle choice test to identify the microRNAs that target alcohol-induced mRNAs. SN are membrane vesicles containing pre- and post-synaptic compartments of neurons and astroglia and are a unique model for studying the synaptic transcriptome. We previously showed that chronic alcohol regulates mRNA expression in a coordinated manner. Here, we examine microRNAs and mRNAs from the same samples to define alcohol-responsive synaptic microRNAs and their predicted interactions with targeted mRNAs. We used a combination of unbiased bioinformatic methods (differential expression, correlation, co-expression, microRNA-mRNA target prediction, co-targeting and cell type specific analyses) to identify key alcohol-sensitive microRNAs. Bidirectional mRNA-microRNA prediction analysis showed that a subset of alcohol-responsive microRNAs were predicted to target many alcohol-responsive mRNAs. We found microRNAs-mRNAs with overlapping patterns of expression that correlated with the amount of alcohol consumed. Cell-type specific analysis revealed a significant number of the alcohol-responsive mRNAs and microRNAs that were unique to glutamate neurons and were highly predicted to target each other. Chronic alcohol appears to perturb the coordinated microRNA regulation of mRNAs in SN, a mechanism that may explain the aberrations in synaptic plasticity affecting the alcoholic brain.

platform_organism:
Mus musculus
synthetic construct

overall_design: Synaptoneurosomes (SN) and Paired total homogenates (TH) were prepared from the same homogenate. 42 microarrays were used in total for the alcohol-control mRNA analysis (8 alcohol treated mice and 13 controls), 21 SN and 21 paired TH. 2 TH (control) samples were found outliers and were removed from the analysis. For the SN vs. TH analysis, the 2 TH samples found outliers were removed with the 2 paired SN samples. 40 microarrays were used in total for the alcohol-control miRNA analysis (8 alcohol treated mice and 12 controls), 20 SN and 20 paired TH.

last: Most

first: Laura

last: Ferguson

first: Yuri

last: Blednov

last: Mayfield

last: Harris


title: Role and function of Pten in BCR-ABL1 driven pre-B cells

status: Public on Jun 03 2013

city: Los Angeles

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

summary: In order to investigate the function of Pten in ALL, we isolated bone marrow cells from Pten fl/fl mice and transformed them with BCR-ABL1. In a second transduction the BCR-ABL1 driven pre-B cells were transformed either with CRE-ERT2 or ERT2 (PMIP) and after 2 days of treatment with 4OH-Tamoxifen (0.5 micromolar) subjected to gene expression analysis.

overall_design: Two days after treatment with 4OH-Tamoxifen (0.5 micromolar) total RNA of Puromycin resistant cells was extracted and subjected to gene expression analysis.

first: seyedmehdi

last: shojaee


title: Defining an invasion signature at the leading edge of cutaneous squamous cell carcinoma (SCC): IL-24 driven MMP-7 and MMP-13 expression.

status: Public on Apr 30 2013

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary:
Purpose: Primary cutaneous squamous cell carcinoma (SCC) can be an invasive cancer in skin and has the potential to metastasize. We aimed to define the cancer related molecular changes that distinguish non-invasive from invasive SCC.

Experimental design: We used laser capture microdissection technique in combination with cDNA microarray analysis in order to determine molecular changes that associate with SCC progression.

Results: We defined invasion-associated genes as those udifferentially regulated only in SCC invasive nests, but not in actinic keratosis-like dysplasia or SCC in situ regions, compared to normal epidermis. We designated these genes as “invasion signature gene set of cutaneous SCC”. Overall we found 383 up- and 354 down-regulated probe-sets that constitute the invasion signature gene set. As part of this profile, SCC invasion is associated with aberrant gene expression changes of numerous MMPs including MMP7 (FCH=5.43, FDR<0.01) and MMP13 (FCH=12.53, FDR<0.01). IL-24 is also up-regulated in the leading invasive edge of SCC (FCH=6.74, FDR<0.01). IL-24 enhanced mRNA expression of both MMP7 and MMP13 in a human SCC cell line. Laminin332, which is one of the target molecules of MMP7, had altered expression at the leading edge of SCC invasion nests at both the genomic and protein level.

Conclusions: We defined the distribution of MMPs within human cutaneous SCC tissue showing distinct expression with progression from normal skin to actinic keratosis to SCC in situ to invasive carcinoma. We further suggest a potential role for IL-24 in progression to invasion via MMP7 and MMP13.

overall_design: Laser capture microdissection was performed on 5 cases of actinic keratosis, 5 cases of in situ SCC, and 5 cases of invasive SCC.

first: Hiroshi

last: Mitsui

last: Suárez-Fariñas

first: James

middle: G

last: Krueger


title: Cavin1 Deficiency Alters Lung macrophage homeostasis in Mouse

status: Public on Jun 07 2013

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
Caveolae are cell membrane invaginations that are highly abundant in adipose tissue, endothelial cells and lung and are present at lower levels in other tissues. The formation of caveolae is dependent of the expression of various structural proteins that serve as scaffolding for these membrane invaginations. Cavin1 is a newly identified structural protein whose deficiency leads to absence of caveolae formation and to the development of a lipodystrophic phenotype. In this study we show Cavin1 expression is critical for regulating macrophage number and gene-expression (phenotype) in the lung.
We used microarrays to detail the global programme of gene expression in alveolar macrophage in a Cavin1 knock-out mouse and identified distinct classes of dysregulated genes during this process.

overall_design: Bronchoalveolar Lavage performed though a 22-gauge needle tied in place to trachea with PBS containing 0.5 mM ethylenediaminetetraacetic acid (EDTA). Aliquots of 0.5 to 1 ml were instilled into the lungs under direct observation to ensure that all segments of lung were inflated, and aspirated back into the syringe. This was repeated five times per mouse. RNA was extracted from extracted alveolar macrophages and hybridized to Affymetrix microarrays for gene expression analysis.

first: Praveen

last: Govender

first: Ross

last: Summer


title: Gene expression profiles of Hodgkin’s lymphoma cells

status: Public on Jul 16 2013

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

summary: By using high-density DNA microarrays, we analyzed the gene-expression profile of Hodgkin's lymphoma cell lines.

overall_design: RNA was extracted from established Hodgkin's lymphoma cell lines and analyzed with Affymetrix Human Exon 1.0ST microarrays.

first: Stefanie

last: Kewitz

first: Julia

last: Müller


title: Comparison of nucleotide-resolution, genome-wide transcriptome maps of Escherichia coli K12 strain BW25113 and Streptomyces coelicolor A3(2) strain M145.

status: Public on Apr 20 2013

city: Leeds

first: David

last: Romero A.

state: West Yorkshire

address: Woodhouse lane

institute: University of Leeds

summary: This data contained within this entry was produced as part of a study that included differential RNA-sequencing.

sample_organism:
Escherichia coli K-12
Streptomyces coelicolor A3(2)

overall_design: S. coelicolor and E. coli reference strains were grown in batch culture with shaking. The E. coli sample was extracted during mid-exponential growth, while the S. coelicolor sample was extracted at the start of pigmented antibiotic production.

last: Romero

first: Yu-fei

last: Lin

first: Lira

last: Mamanova

first: Kenneth

middle: J

last: McDowall


title: Development of gene expression signatures for miR-218 overexpression

status: Public on Apr 19 2013

city: Newhaven

first: Jiangbing

last: zhou

address: 310 Cedar Street, Ste LH 412A

institute: Yale university

summary: To investigate differences in gene expression after overexpression miR-218 in U251MG

overall_design: 2 Samples, one transduced with miR-control and one with miR-218.

first: Yanyang

last: Tu

first: Yongsheng

last: zhang


title: Expression data during plantaris muscle hypertrophy induced by synergist ablation in young adult mice

status: Public on May 21 2013

city: Lexington

first: Thomas

last: Chaillou

state: KY

address: University of Kentucky, Department of Physiology, 800 Rose Street

institute: Department of Physiology

summary: Global gene expression patterns were determined from microarray results on day 1, 3, 5, 7, 10 and 14 during plantaris muscle hypertrophy induced by synergist ablation in young adult mice (5 months).

overall_design: For each time point, two Affymetrix chips (Mouse Gene 1.0 ST) were used with 100 ng of total RNA derived from a pooled sample of either the right or left plantaris muscles from six animals.

first: Jonah

last: Lee

first: Jonathan

middle: H

last: England

first: Karyn

middle: A

last: Esser

first: John

last: McCarthy


title: Expression data from mammary tumors from a MOLF/Ei x PyMT mouse cross

status: Public on Jul 06 2013

city: Bethesda

first: Kent

last: Hunter

state: MD

address: 37/4048 37 Convent Drive

department: Center for Cancer Research

institute: National Cancer Institute

summary: Mouse genetic crosses were established between the PyMT model of metastatic breast cancer and MOLF/Ei strain. Tumors were harvested from the animals for gene expression analysis to identify genes associated with progression to distant metastatic disease.

overall_design: Gene expression of 134 samples from the MOLF cross were assayed on Affymetrix chips.


title: Crizotinib inhibits metabolic inactivation of gemcitabine in ortothopic pancreatic tumors derived from primary cells with c-Met overexpression

status: Public on Aug 30 2013

city: Amsterdam

first: Amir

last: Avan

address: DE BOELELAAN 1118

country: Netherlands

institute: VU University Medical Center

summary: Pancreatic ductal adenocarcinoma (PDAC) remains a major unsolved health problem. Most drugs that pass preclinical tests fail in these patients, emphasizing the need of appropriate preclinical models to test novel anticancer strategies. We developed four orthotopic mouse models employing primary human PDAC cells expressing Firefly and Gaussia luciferases, enabling bioluminescence monitoring of tumor growth and metastasis formation. Additional tumor characterization was performed using MR and high frequency ultrasound imaging. Genomic and immunohistochemical analysis revealed c-Met amplification and overexpression in one of four models. Analysis of c-Met inhibitors in vitro showed that crizotinib had the most potent effect. Moreover, we demonstrated synergistic effects between crizotinib and gemcitabine – the standard of care therapeutic in PDAC patients - in vitro and in vivo. Importantly, crizotinib reduced the cytidine deaminase activity in PDAC cells causing prolonged activity of gemcitabine due to diminished metabolic inactivation, as measured by LC-MS/MS. This might at least in part explain the observed prolonged survival of concomitantly treated mice with PDAC tumors and metastases. In conclusion, our orthotopic PDAC models enabled PDAC tumor imaging, and showed genetic, histopathological and metastatic features similar to their originator tumors. This allowed the identification of c-Met as a potential therapeutic target in PDAC, and revealed a cytidine deaminase-mediated synergistic mechanism between crizotinib and gemcitabine, a combination of drugs that warrants further investigation for the potential treatment of PDAC patients.

overall_design:
12 test samples in total [4 PDAC models (PDAC-1, PDAC-2, PDAC-3, PDAC-4; in three panel: primary human PDAC, primary tumor culture and mouse sample)] and reference sample (healthy control (mix/pool of healthy volunteers DNA) were analyzed as following (8 hybridizations);

PDAC-1 primary human-Cy3 vs PDAC-4 cultured cells -Cy5
PDAC-1 cultured cells-Cy3 vs PDAC-4 mouse-Cy5
PDAC-1 mouse-Cy3 vs reference-Cy5
PDAC-2 primary human-Cy3 vs reference-Cy5
PDAC-2_cultured cells-Cy3 vs PDAC-2 mouse-Cy5
PDAC-3_primary human-Cy3 vs reference-Cy5
PDAC-3_cultured cells-Cy3 vs PDAC-3 mouse-Cy5
PDAC-4 primary human-Cy5 vs reference-Cy3

Normalized log2 ratio of (sample/references) data were calculated for 12 samples [*txt files on Series records].

Description of experimental/analysis design in r-program to generate 12 samples from 8 raw data files is provided in README.txt [Series supplementary file]

first: Viola

last: Caretti

first: Niccola

last: Funel

first: Elena

last: Galvani

first: Mina

last: Maftouh

first: Richard

last: Honeywell

first: Tonny

last: Lagerweij

first: Olaf

last: Van Tellingen

first: Daniela

last: Campani

first: Dieter

last: Fuchs

first: Gerrit

last: Schuurhuis

first: Ugo

last: Boggi

first: Godefridus

last: Peters

last: Würdinger

first: Elisa

last: Giovannetti


title: Transcriptome dynamics of the dormancy - growth transition in Douglas-fir needles

status: Public on Jun 05 2013

city: Corvallis

last: Cronn

state: OR

address: 3200 SW Jefferson Way

department: PNW Research Station

institute: USDA Forest Service

summary: We report sequencing the transcriptome of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) during spring bud burst.

overall_design: Samples from needle tissue of two half-sibs from two families each, nested within three seed sources, were sequenced (total of six families and 12 individuals).  Samples were taken at seven time points with the failure of one library, resulting in 83 total sequenced samples.  Three time points were used for transcriptome assembly and 4 time point were analyzed for differential expression across time and within seed sources.

first: Brian

last: Knaus

first: Peter

last: Dolan

first: Dee

last: Denver

first: Jil

middle: L

last: Wegrzyn

first: Tara

middle: N

last: Jennings

first: J

last: St Clair


title: Dynamic changes in liver 5-hydroxymethylcytosine profiles upon non-genotoxic carcinogen exposure [Replicated control vs. pb treated study]

status: Public on Mar 25 2013

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

institute: University of Edinburgh

summary: Dynamic changes in the mouse liver DNA methylome associated with short (1 day) and prolonged (7, 28 and 91 days) exposure to the rodent liver non-genotoxic carcinogen (NGC), phenobarbital (PB).

overall_design:
Full expression dataset (all time points: 1, 7, 28, 91 days)
Replicated control vs. pb treated study

middle: P

first: Jennifer

middle: M

last: Hunter

first: Harri

last: Lempiainen

first: Arne

last: Mueller

first: Remi

last: Terranova

first: Jonathan

last: Moggs

middle: R

last: Meehan


title: Whole Genome Expression Array in Human T-cell Acute Lymphoblastic Leukemia

city: Istanbul

first: ozden

last: hatirnazng

address: IU DETAE Vakıf Gureba C

country: Turkey

institute: Istanbul University

summary:
Childhood T-ALL samples were compared with thymocyte subsets
we compared key molecules of wnt signaling pathway in our cohort

overall_design: RNA was isolated from the bone marrow samples of childhood T-ALL patients at the time of diagnosis with a blast count over 90% and hybridized to Affymetrix GeneChip HU-133 Plus.2 .Thymic subsets were sorted by FACS and labeled as DN(CD3,CD4,CD8 neg), DP3poz tot(CD3,CD4,CD8poz), DP3neg(CD3neg,CD4,CD8poz), ISP(Immature single positive), SP4(Single positive CD4), SP8 (Single positive CD8).

first: Ozden

last: Hatirnaz Ng

first: Ugur

last: Ozbek


title: Analysis of Unique and Overlapping Patterns of Gene Expression After Treatment of Zebrafish Embryos with Estradiol and/or Dioxin

status: Public on Dec 05 2012

first: Boston University

last: Microarray and Sequencing Resource

state: MA

summary: To increase the utility of the zebrafish gene expression bioassay for assessing EDC effects on multiple gene targets and tissue types, and to expand our understanding of genetic overlap between estrogen receptor (ER) and arylhydrocarbon receptor (AhR) mediated signaling pathways, we conducted microarray analysis of zebrafish embryos exposed to estradiol and dioxin alone or in combination. Of >16,000 probe sets on the array, 34 were regulated by estradiol (E2), 86 by dioxin (TCDD) and 109 by E2+TCDD (as chosen by >2-fold change and p<0.1). Of 62 genes selected for verification by QPCR, 14 genes, or 22% were reproducibly up- or down-regulated, offering potential additional target genes for screening of estrogen- and dioxin-like EDC. The majority of these successful hits, 11, were TCDD-responsive. In addition, all of the target genes routinely evaluated in this laboratory (AroB, Vtg1, and Esr1: E2-responsive; Cyp1a: TCDD- responsive; Vtg1: E2+TCDD-responsive) were verified with these arrays, testifying to the power of microarray analysis in finding reliable responsive genes.  However, over two-thirds of the novel up- or down- regulated probes were not annotated as zebrafish genes, and many of the identified genes were changed only 2- to 3-fold, an effect often not reproduced by QPCR.  Additional responsive genes were identified for each treatment condition, and while low levels of expression and low magnitude fold changes make those for E2 responsiveness or interaction between E2 and TCDD response unlikely to serve as robust biomarkers, their response to EDCs may assist in understanding the regulation of existing biomarkers and zebrafish endocrine systems as a whole.  In addition to a source for potential EDC screening biomarkers, these studies provide an entry point to further study physiological effects of ER and AHR ligands and cross-talk between these signaling pathways, in a physiologically relevant in vivo model.

overall_design: Hybridizations of three biological replicates (n=30 zebrafish embryos/larvae pooled per treatment group) were performed, in two independent batches, for each of four treatment groups: 0.1% DMSO (control), 0.1µM E2, 1nM TCDD, and 0.1µM E2 + 1nM TCDD

first: Lucinda

last: Griffin

first: Gloria

middle: V

last: Callard


title: Transcriptome profiling of potato hypersensistive response to PVY infection

status: Public on Oct 01 2013

city: Ljubljana

first: Spela

last: Baebler

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

summary: Our aim was to investigate involvement of  salicylic acid signalling in Ny-mediated hypersensistive response by comparison of transcriptomic response to the Potato Virus Y in potato plants of genotypes Rywal, bearing Ny-1 allele and NahG-Rywal, unable to accumulate salicylic acid in three time points (1, 3 and 6 days post inoculation) after viral inoculation.

overall_design: Inoculated leaves of  mock- and virus- inoculated plants (four each) were sampled 1, 3 and 6 days after inoculation (dpi). POCI microarrays were used (one-color design)

first: Marko

last: Petek

first: Kamil

last: Witek


title: SRp20 regulates Genome-wide Alternative RNA splicing events in U2OS cells

status: Public on Dec 30 2012

city: Frederick

first: Zhi-Ming

last: Zheng

department: HIV DRP Program

summary: To examine the effects of SRp20 on genome-wide RNA splicing in tumor cells, we utilized Exonhit SpliceArray to compare genome-wide changes of RNA splicing and transcription in U2OS cells with or without knockdown of SRp20 by RNAi.

overall_design: U2OS cells were treated by SRp20 siRNA or non-specific siRNA, each performed in triplicate. A human genome-wide splice-array assay was performed by using a service provider ExonHit Therapeutics, Inc (Gaithersburg, MD). Fifty ng of total RNA isolated from U2OS cells with or without knockdown of SRp20 was quality controlled and analyzed by using Affymetrix GeneChip platform to profile the expression of 20,649 genes and splicing events of 19,066 genes.

first: Masahiko

last: Ajiro

first: Rong

last: Jia

first: Yanqin

last: Yang

first: Jun

last: Zhu

first: Zhi


title: Expression profiles of cell populations purified from human CRC (4 ways)

status: Public on Jan 17 2013

city: Barcelona

first: Alexandre

last: CALON

address: Dr. Aiguader, 88

country: Spain

institute: Hospital del Mar Medical Research Institute (IMIM)

summary:
The survival of isolated metastatic cells and expansion into macroscopic tumour has been recognized as a limiting step for metastasis formation in several cancer types yet the determinants of this process remain largely uncharacterized. In colorectal cancer (CRC), we identify a transcriptional programme in tumour-associated stromal cells, which is intimately linked to a high risk of developing recurrent disease after therapy. A large proportion of CRCs display mutational inactivation of the TGF-beta pathway but paradoxically they are characterized by high TGF-beta production. In these tumours, TGF-beta instructs a transcriptional programme in stromal cells, which confers a high risk of developing metastatic disease.
We purified by FACS CD31(+), CD45(+), FAP(+) and Epcam(+) populations from fresh CRC samples and assessed their gene expression profiles

overall_design: Freshly obtained tumours from 6 CRC patients treated at Hospital del Mar or Hospital Clinic (Barcelona, Spain) were minced and incubated with Collagenase IV (100 U mL-1). Enzymatic reaction was stopped by adding 10% FBS, single cells were collected by sequential filtering and resuspended in ammonium chloride (0.15M) to lyse erythrocytes. Cells were stained with FAP unconjugated rabbit antibody. After two washes with HBSS, cells were stained with an APC conjugated anti-rabbit antibody; anti-hEPCAM/TROP1-FITC, anti-CD31-PE and anti-CD45-PE-Cy7 conjugated antibody. Dead cells were labelled with Propidium Iodide. Fluorescence Activated Cell Sorting (FACS) was used to separate 2000 cells from each population; [CD45(+), EPCAM(-), CD31(-), FAP(-)], [CD45(-) EPCAM(+), CD31(-), FAP(-)], [CD45(-), EPCAM(-), CD31(+),FAP(-)] and [CD45(-), EPCAM(-), CD31(-), FAP(+)].

last: Calon

first: Elisa

last: Espinet

first: Eduard

last: Batlle


title: Human CRC cell populations

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

overall_design: Refer to individual Series


title: IP of 5-methylcytosine (5-mC) enriched DNA fragments from control and PB treated mouse livers (91 day)

status: Public on Nov 10 2012

first: John

last: Thomson

summary:
5-mC is an epigenetic modification of the DNA base cytosine with roles in gene silencing events, imprinting and X inactivation. Phenobarbital (PB) is a well studied non-genotoxic carcinogen with roles in epigenetic perturbation.  We profile 5mC in both control mouse livers as well as in the livers of 91 day PB treated mice. 5mC is largely found to reside in the bodies of active genes and promoter levels are perturbed upon PB induced gene activation events.
5-mC is assocated with promoters fo silent genes. Upon PB exposire a handfull of genes are induced which reveal decreases in promoter 5mC levels

overall_design: comparison of 5-mC profiles in 5 control and 5 PB exposed mouse livers (dose: 91day PB)

first: Harri

last: Lempiäinen


title: IP of 5-methylcytosine (5-hmC) enriched DNA fragments from control and PB treated mouse livers (91 day)

summary:
5-hmC is an epigenetic modification of the DNA base cytosine with roles in gene silencing events, imprinting and X inactivation. Phenobarbital (PB) is a well studied non-genotoxic carcinogen with roles in epigenetic perturbation.  We profile 5hmC in both control mouse livers as well as in the livers of 91 day PB treated mice. 5hmC is largely found to reside in the bodies of active genes and promoter levels are perturbed upon PB induced gene activation events.
5-hmC is assocated with promoters fo silent genes. Upon PB exposire a handfull of genes are induced which reveal decreases in promoter 5hmC levels

overall_design: comparison of 5-hmC profiles in 5 control and 5 PB exposed mouse livers (dose: 91day PB)


title: IP of 5-methylcytosine (5-hmC) enriched DNA fragments from control and PB treated mouse livers (1 day)

summary:
5-hmC is an epigenetic modification of the DNA base cytosine with roles in gene silencing events, imprinting and X inactivation. Phenobarbital (PB) is a well studied non-genotoxic carcinogen with roles in epigenetic perturbation.  We profile 5hmC in both control mouse livers as well as in the livers of 1 day PB treated mice. 5hmC is largely found to reside in the bodies of active genes and promoter levels are perturbed upon PB induced gene activation events.
5-hmC is assocated with promoters fo silent genes. Upon PB exposire a handfull of genes are induced which reveal decreases in promoter 5hmC levels

overall_design: comparison of 5-hmC profiles in 5 control and 5 PB exposed mouse livers (dose: 1day PB)


title: IP of 5-methylcytosine (5-mC) enriched DNA fragments from control and PB treated mouse livers (1 day)

summary:
5-mC is an epigenetic modification of the DNA base cytosine with roles in gene silencing events, imprinting and X inactivation. Phenobarbital (PB) is a well studied non-genotoxic carcinogen with roles in epigenetic perturbation.  We profile 5mC in both control mouse livers as well as in the livers of 1 day PB treated mice. 5mC is largely found to reside in the bodies of active genes and promoter levels are perturbed upon PB induced gene activation events.
5-mC is assocated with promoters fo silent genes. Upon PB exposire a handfull of genes are induced which reveal decreases in promoter 5mC levels

overall_design: comparison of 5-mC profiles in 5 control and 5 PB exposed mouse livers (dose: 1day PB)


title: Genome-Wide Methylation Analysis of Breast Cancer Cell Lines

status: Public on Mar 01 2013

city: Baltimore

first: leslie

last: cope

address: 550 N. Broadway

institute: leslie cope

summary: To evaluate the methylation profiles of breast cell lines, we performed methylation profiling of 55 well-characterized breast cancer cell lines on the Illumina HumanMethylation27 (HM27) platform and made use of publicly available methylation profiles of primary breast tumors for comparison. The available annotation for each cell line includes estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) status, as well as the tumor type, and the age of each patient. Additionally, recent publications have described genome-wide mRNA expression profiles for most of these lines, and samples were classified on the basis of the expression profile into Basal A (BaA), Basal B/Claudin Low (BaB/CLDNlow) and Luminal (Lu) subtypes. Finally, GI50 has been calculated for these cell lines for 77 approved therapeutic agents. We find that the DNA methylation profiles of breast cancer cell lines largely retain the features that characterize primary tumors, although there are crucial differences as well.

overall_design: We assayed DNA methylation in 55 breast cancer cell lines. DNA extracted from breast cell lines was bisulfite treated and hybridized to Illumina HM27 arrays.

first: Leslie

last: Cope

first: Mary

last: Fackler

first: Kala

last: Visvananthan

first: Antonio

middle: C

last: Wolff

first: Saraswati

last: Sukumar


title: IP of 5-methylcytosine (5-mC) enriched DNA fragments from control and PB treated mouse livers (7 day)

summary:
5-mC is an epigenetic modification of the DNA base cytosine with roles in gene silencing events, imprinting and X inactivation. Phenobarbital (PB) is a well studied non-genotoxic carcinogen with roles in epigenetic perturbation.  We profile 5mC in both control mouse livers as well as in the livers of 7 day PB treated mice. 5mC is largely found to reside in the bodies of active genes and promoter levels are perturbed upon PB induced gene activation events.
5-mC is assocated with promoters fo silent genes. Upon PB exposire a handfull of genes are induced which reveal decreases in promoter 5mC levels

overall_design: comparison of 5-mC profiles in 5 control and 5 PB exposed mouse livers (dose: 7day PB)


title: Dynamic changes in liver 5-hydroxymethylcytosine profiles upon non-genotoxic carcinogen exposure

status: Public on Sep 12 2012

summary: 29-32 days old male mice where either treated with Phenobarbital or untreated

overall_design: Replicated control vs. pb treated study

last: Lempiäinen

first: Jamie

last: Hackett

first: Colm

middle: E

last: Nestor

first: Arne

last: Müller

first: Federico

last: Bolognani

first: Edward

last: Oakeley

first: Dirk

last: Schübeler

first: Rémi

last: Terranova

first: Diana

last: Rheinhardt

first: Jonathan

last: Moggs

first: Richard

last: Meehan


title: RNA-seq of Pacific oyster Crassostrea gigas under different developmental stages and stress treatments

status: Public on Sep 13 2012

city: Qingdao

first: Fei

last: Xu

address: 7 Nanhai Road

institute: Institute of Oceanology, Chinese Academy of Sciences

summary: Deep sequencing of samples from different development stages, different adult organs and different stress treatments of Pacific oyster Crassostrea gigas

overall_design: Samples of 38 developmental stages from egg to juvenile were analyzed using single-end 49 bp RNA-seq. Two libraries mixed by RNAs from different developmental stages were analyzed using paired-end 90 bp RNA-seq. A total of 11 samples mainly from 8 organs (mantle, gill,adductor muscle, digestive gland, hemocyte, labial palp, female gonad and male gonad) were analyzed using paired-end 90 bp RNA-seq. At the same time, single-end 49 bp RNA-seq was conducted on 61 samples collected from adult oysters subjected to 9 types of environmental stressors (exposure to air, salinity, temperature, and exposure to metals).

first: Guofan

last: Zhang

first: Xiaodong

last: Fang

first: L

last: Li

first: F

first: X

last: Wang


title: Persistent androgen receptor-mediated transcription in castration-resistant prostate cancer under androgen-deprived conditions

status: Public on Oct 02 2012

city: St. Louis

first: Keith

last: Decker

state: MO

address: 660 S. Euclid Ave, Campus Box 8220

department: Internal Medicine

institute: Washington University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: The androgen receptor (AR) is a ligand-inducible transcription factor that mediates androgen action in target tissues. Upon ligand binding, the AR binds to thousands of genomic loci and activates a cell-type specific gene program. Prostate cancer growth and progression depend on androgen-induced AR signalling. Treatment of advanced prostate cancer through medical or surgical castration leads to initial response and durable remission, but resistance inevitably develops. In castration-resistant prostate cancer (CRPC), AR activity remains critical for tumor growth despite androgen deprivation. While previous studies have focused on ligand-dependent AR signalling, in this study we explore AR function under the androgen-deprived conditions characteristic of CRPC. Our data demonstrate that the AR persistently occupies a distinct set of genomic loci after androgen deprivation in CRPC. These androgen-independent AR occupied regions have constitutively open chromatin structures that lack the canonical androgen response element and are independent of FoxA1, a transcription factor involved in ligand-dependent AR targeting. Many AR binding events occur at proximal promoters, which can act as enhancers to augment transcriptional activities of other promoters through DNA looping. We further show that androgen-independent AR binding directs a distinct gene expression program in CRPC, which is necessary for the growth of CRPC after androgen withdrawal.

overall_design: LNCaP, C4-2B, or 22RV1 cells were cultured in hormone-free media for 3 days and then treated with ethanol vehicle or DHT (10nM) for 4h or 16h prior to ChIP-seq or RNA-seq assays. For siRNA transfection, cells were transfected with AR siRNA or control siRNA for 3 days prior to RNA-seq assays.

first: Dali

last: Zheng

first: Yuhong

last: He

first: Tamara

last: Bowman

first: John

last: Edwards

first: Li

last: Jia


title: IP of 5-methylcytosine (5-mC) enriched DNA fragments from control and PB treated mouse livers (28 day)

last: Thomson

summary:
5-mC is an epigenetic modification of the DNA base cytosine with roles in gene silencing events, imprinting and X inactivation. Phenobarbital (PB) is a well studied non-genotoxic carcinogen with roles in epigenetic perturbation.  We profile 5mC in both control mouse livers as well as in the livers of 28 day PB treated mice. 5mC is largely found to reside in the bodies of active genes and promoter levels are perturbed upon PB induced gene activation events.
5-mC is assocated with promoters fo silent genes. Upon PB exposire a handfull of genes are induced which reveal decreases in promoter 5mC levels

overall_design: comparison of 5-mC profiles in 5 control and 5 PB exposed mouse livers

first: Jamie

last: Hackett


title: IP of 5-methylcytosine (5-hmC) enriched DNA fragments from control and PB treated mouse livers (7 day)

summary:
5-hmC is an epigenetic modification of the DNA base cytosine with roles in gene silencing events, imprinting and X inactivation. Phenobarbital (PB) is a well studied non-genotoxic carcinogen with roles in epigenetic perturbation.  We profile 5hmC in both control mouse livers as well as in the livers of 7 day PB treated mice. 5hmC is largely found to reside in the bodies of active genes and promoter levels are perturbed upon PB induced gene activation events.
5-hmC is assocated with promoters fo silent genes. Upon PB exposire a handfull of genes are induced which reveal decreases in promoter 5hmC levels

overall_design: comparison of 5-hmC profiles in 5 control and 5 PB exposed mouse livers (dose: 7day PB)

first: Harri

last: Lempiäinen


title: IP of 5-hydroxymethylcytosine (5-hmC) enriched DNA fragments from control and PB treated mouse livers (28 day)

summary:
5-hmC is a novel epigenetic mark derived from oxidation of methylcytosine. Phenobarbital (PB) is a well studied non-genotoxic carcinogen with roles in epigenetic perturbation.  We profile 5hmC in both control mouse livers as well as in the livers of 28 day PB treated mice. 5hmC is largely found to reside in the bodies of active genes and promoter levels are perturbed upon PB induced gene activation events.
5-hmC is enriched in the bodies of active genes as well as a subset of TSS regions associated with transcriptional silencing. Upon PB exposire a handfull of genes are induced which reveal increases in promoter 5hmC levels

overall_design: comparison of 5hmC profiles in 5 control and 5 PB exposed mouse livers


title: Changes in histone modifications H3K4me2, H3k27me3 and H3K36me3 due to phenobarbital in mice

overall_design: Replicated control/treated study with IP and Input per group and antibody

last: Lempiäinen

first: Colm

last: Nestor

first: Arne

last: Müller

first: Federico

last: Bolognani

first: Edward

last: Oakeley

first: Dirk

last: Schübeler

first: Rémi

last: Terranova

first: Diana

last: Rheinhardt


title: A gene co-expression network in whole blood of schizophrenia patients is independent of antipsychotic-use and enriched for brain-expressed genes

status: Public on Jul 09 2012

city: Los Angeles

first: Simone

last: de Jong

state: California

address: 695 Charles E. Young Drive south

institute: UCLA

first: Marco

last: Boks

first: Tova

last: Fuller

first: Eric

last: Strengman

first: Esther

last: Janson

first: Carolien

last: de Kovel

first: Anil

last: Ori

first: Nancy

last: Vi

first: Flip

last: Mulder

first: Jan

middle: D

last: Blom

first: Birte

last: Glenthoj

first: Chris

last: Schubart

first: Wiepke

last: Cahn

first: Rene

last: Kahn

first: Steve

last: Horvath

first: Roel

last: Ophoff


title: Peripheral blood gene expression as a novel genomic biomarker in complicated sarcoidosis

status: Public on Jul 01 2012

city: Reno

first: Tong

last: Zhou

state: NV

address: 1664 N Virginia St

institute: University of Nevada School of Medicine

summary:
Sarcoidosis, a systemic granulomatous syndrome invariably affecting the lung, typically spontaneously remits but in ~20% of cases progresses with severe lung dysfunction or cardiac and neurologic involvement (complicated sarcoidosis). Unfortunately, current biomarkers fail to distinguish patients with remitting (uncomplicated) sarcoidosis from other fibrotic lung disorders, and fail to identify individuals at risk for complicated sarcoidosis.
We utilized genome-wide peripheral blood gene expression analysis to identify a gene signature distinguishing sarcoidosis from healthy controls, which also served as a molecular signature for complicated sarcoidosis.

overall_design: Total RNA was isolated from PBMCs using standard molecular biology protocols without DNA contamination or RNA degradation. Sample processing (e.g., cDNA generation, fragmentation, end labeling, hybridization to Affymetrix GeneChip Human Exon 1.0 ST arrays) was performed per manufacturer’s instructions. A total of 29 African descent American (AA) and 10 European descent American (EA) patients with sarcoidosis were included in the overall sarcoidosis cohort with 18 AA and 4 EA patients diagnosed with complicated sarcoidosis.

first: Wei

last: Zhang

first: Nadera

last: Sweiss

first: Edward

middle: S

last: Chen

first: David

last: Moller

first: Kenneth

last: Knox

first: Shwu-Fan

last: Ma

first: Michael

last: Wade

first: Imre

last: Noth

first: Roberto

middle: F

last: Machado

first: Joe

last: Garcia


title: IP of 5-hydroxymethylcytosine (5-hmC) and 5-methylcytosine (5-mC) enriched DNA fragments from control and PB treated mouse livers

first: John

last: Thomson

first: Richard

last: Meehan

first: Harri

last: Lempiäinen

first: Jamie

last: Hackett

first: Jonathan

middle: G

last: Moggs

first: Arne

last: Müller


title: RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance

status: Public on Apr 25 2012

city: Dunsany

first: Chris

last: Creevey

state: Co. Meath

address: Grange

department: Animal & Bioscience Research Department

country: Ireland

institute: Teagasc

summary: Background: The liver is central to most economically important metabolic processes in cattle. However, the changes in expression of genes that drive these processes remain incompletely characterised. RNA-seq is the new gold standard for whole transcriptome analysis but so far there are no reports of its application to analysis of differential gene expression in cattle liver. We used RNA-seq to study differences in expression profiles of hepatic genes and their associated pathways in individual cattle in either mild negative energy balance (MNEB) or severe negative energy balance (SNEB). NEB is an imbalance between energy intake and energy requirements for lactation and body maintenance. This aberrant metabolic state affects high-yielding dairy cows after calving and is of considerable economic importance because of its negative impact on fertility and health in dairy herds. Analysis of changes in hepatic gene expression in SNEB animals will increase our understanding of NEB and contribute to the development of strategies to circumvent it.     Results: RNA-seq analysis was carried out on total RNA from liver from early post partum Holstein Friesian cows in MNEB (n=5) and SNEB (n=6). 12,833 genes were deemed to be expressed (>4 reads per gene per animal), 413 of which were shown to be statistically significantly differentially expressed (SDE) at a false discovery rate (FDR) of 0.1% and 200 of which were SDE (FDR of 0.1%) with a ≥2-fold change between MNEB and SNEB animals. GOseq/KEGG pathway analysis showed that SDE genes with ≥2- fold change were associated (P <0.05) with 9 KEGG pathways. Seven of these pathways were related to fatty acid metabolism and unexpectedly included ‘Steroid hormone biosynthesis’, a process which mainly occurs in the reproductive organs rather than the liver.    Conclusions: RNA-seq analysis showed that the major changes at the level of transcription in the liver of SNEB cows were related to fat metabolism. 'Steroid hormone biosynthesis', a process that normally occurs in reproductive tissue, was significantly associated with changes in gene expression in the liver of SNEB cows. Changes in gene expression were found in this pathway that have not been previously been identified in SNEB cows.

overall_design: 11 liver RNA samples were analysed in total, 6 samples were from SNEB animals and 5 samples from MNEB animals

first: Matthew

last: McCabe

first: Sinead

last: Waters

first: Dermot

last: Morris

last: Kenny

last: Lynn

first: Christopher


title: SERPINA6, BEX1, AGTR1, SLC26A3, and LAPTM4B are markers of resistance to neoadjuvant chemotherapy in HER2-negative breast cancer

status: Public on Dec 01 2012

first: Jelle

middle: Johannes

last: ten Hoeve

address: Plesmanlaan 121

department: Molecular Biology

institute: Netherlands Cancer Institute

summary:
Abstract

Introduction
Response rates to chemotherapy remain highly variable in breast cancer patients. We set out to identify genes associated with chemotherapy resistance. We analyzed what is currently the largest single-institute set of gene expression profiles derived from breast cancers prior to a single neoadjuvant chemotherapy regimen (dose-dense doxorubicine and cyclophophamide).
Methods
We collected, gene expression-profiled and analyzed 178 HER2-negative breast tumor biopsies (‘NKI dataset’). We employed a recently developed approach for detecting imbalanced differential signal (DIDS) in order to identify markers of resistance to treatment. In contrast to traditional methods, DIDS is able to identify markers that show aberrant expression in only a small subgroup of the non-responder samples.
Results
We found a number of markers of resistance to anthracycline-based chemotherapy. We validated our findings by the analysis of three external datasets, which contained 456 HER2-negative samples in total. Since these external sets included patients who received differing treatment regimens we could only validate markers of general chemotherapy resistance. There was a highly significant overlap in the markers identified in the NKI dataset and the other three datasets. Five resistance markers, SERPINA6, BEX1, AGTR1, SLC26A3, and LAPTM4B, were identified in three of the four datasets (p-value overlap <1e-6). These five genes identified resistant tumors that could not have been identified by merely taking ER-status or proliferation into account.
Conclusion
The identification of these genes might lead to a better understanding of the mechanisms involved in (clinically) observed chemotherapy resistance and could possibly assist in the recognition of breast cancers in which chemotherapy does not contribute to response or survival.

overall_design: We collected, gene expression profiled and analyzed 178 HER2-negative breast tumor biopsies, obtained from patients scheduled to undergo neoadjuvant therapy.

first: Jorma

last: de Ronde

first: Esther

last: Lips

first: Lennart

last: Mulder

first: Andrew

last: Vincent

last: Wesseling

first: Marja

last: Nieuwland

first: Ron

last: Kerkhoven

first: Marie-Jeanne

middle: T

last: Vrancken Peeters

first: Gabe

last: Sonke

first: Sjoerd

last: Rodenhuis

first: Lodewyk

last: Wessels


title: Noncoding RNA expression in myocardium from infants with tetralogy of Fallot [miRNA profiling]

status: Public on Jul 12 2012

city: Kansas City

first: Douglas

last: Bittel

address: 2401 Gillham Rd

department: Genetics research

institute: Childrens Mercy Hospital

summary: This is the first report characterizing noncoding RNA expression in a congenital heart defect. The striking shift in expression of noncoding RNAs reflects a fundamental change in cell biology, likely impacting expression, transcript splicing and translation of developmentally important genes and possibly contributing to the cardiac defect. The importance of noncoding RNAs (ncRNA), especially microRNAs, for maintaining stability in the developing vertebrate heart has recently become apparent. However, there is little known about the expression pattern of ncRNA in the human heart with developmental anomalies. We examined the expression of microRNAs and small nucleolar RNAs (snoRNAs) in right ventricular myocardium from 16 infants with nonsyndromic tetralogy of Fallot (TOF) without a 22q11.2 deletion, three fetal heart samples and eight normally developing infants. We found 61 microRNAs and 135 snoRNAs to be significantly changed in expression in myocardium from children with TOF compared to normally developing comparison subjects. The pattern of ncRNA expression in TOF myocardium had a remarkable resemblance to expression patterns in fetal myocardium, especially for the snoRNAs. Potential targets of microRNAs with altered expression were enriched for gene networks of importance to cardiac development. We derived a list of 229 genes known to be critical to heart development and found 44 had significantly changed expression in TOF myocardium relative to normally developing myocardium. These 44 genes had significant negative correlation with 33 microRNAs, each of which also had significantly changed expression. The primary function of snoRNAs is targeting specific nucleotides of ribosomal RNAs and spliceosomal RNAs for biochemical modification. The targeted nucleotides of the differentially expressed snoRNAs were concentrated in the 28S and 18S ribosomal RNAs and two spliceosomal RNAs, U2 and U6. In addition, in myocardium from children with TOF, we observed splicing variants in 51% of the critical cardiac developmental genes. Taken together, these observations suggest a link between snoRNA level in the myocardium, spliceosomal function and heart development.

first: James

last: O’Brien Jr

first: Nataliya

last: Kibiryeva

first: Xin-Gang

last: Zhou

first: Jennifer

last: Marshall

first: Gary

middle: K

last: Lofland

first: Michael

last: Artman

first: Jie

last: Chen


title: A Validated Gene Signature from Peripheral Blood Mononuclear Cells in Pulmonary Hypertension Associated with Sickle Cell Disease

status: Public on Jun 07 2012

first: Tong

summary: Pulmonary hypertension (PH) is a serious complication of sickle cell disease (SCD) associated with increased mortality. Gene expression profiles of peripheral blood mononuclear cells (PBMC) have been studied in pulmonary arterial hypertension and in SCD. We hypothesized that a PBMC-derived gene signature in SCD patients may be utilized as a PH biomarker. Twenty-seven patients with homozygous SCD underwent transthoracic echocardiography and PBMC isolation. PH was defined as estimated right ventricular systolic pressure (RVSP)>30 mmHg with a peak tricuspid regurgitation velocity (TRV)>2.5m/s. Genome-wide gene expression profiles were correlated against PH severity using RVSP and TRV as surrogates, which yielded 631 potentially dysregulated transcripts.

overall_design: Total RNA was isolated from PBMCs using standard molecular biology protocols without DNA contamination or RNA degradation. Sample processing (e.g., cDNA generation, fragmentation, end labeling, hybridization to Affymetrix GeneChip Human Exon 1.0 ST arrays) was performed per manufacturer’s instructions. A total of 27 African descent American patients with sickle cell disease were included in the microarray analysis.

first: A

middle: A

last: Desai

first: H

last: Ahmad

first: T

first: S

last: Trevino

first: M

last: Wade

first: N

last: Raghavachari

last: Peters-Lawrence

first: G

middle: J

last: Kato

last: Thiruvoipati

first: K

last: Turner

last: Artz

first: Y

last: Huang

last: Patel

middle: X

last: Jason

first: R

last: Lang

first: J

last: Garcia

last: Machado