title: mRNA expression in blood of 18 schizophrenia patients and 12 healthy controls

status: Public on Dec 05 2014

city: Wuxi

first: Fuquan

last: Zhang

address: 156 Qianrong Rd

institute: Wuxi mental health center

summary: The study profiles genome-wide mRNA expression in blood from 18 early-onset SZ (EOS) cases and 12 healthy controls. A total of 1070 mRNAs were detected by the microarrays in our samples.

overall_design: 18 schizophrenia samples and 12 healthy controls were used to acquire blood expression profiles

first: Xu

last: Yong

first: Zhang

last: Fuquan


title: Gene expression analyses of GSC11 cell in stem cell culture conditions or in differentiation conditions for 1, 3, or 7 days

status: Public on Feb 27 2015

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

country: USA

institute: Baylor Colleage of Medicine

summary: Although fetal bovine serum (FBS) induces the differentiation of cancer stem cells, the underlying mechanism by which this is accomplished has not been clarified. Whether reactive oxygen species affect the differentiation of cancer stem cells in solid tumors as they do in normal stem cells is not known. This study aimed to determine the role of reactive oxygen species in the FBS-induced differentiation of glioblastoma stem cells. We found that FBS activated the oxidative stress response system in glioblastoma stem cells (GSCs). The resulting differentiated cells showed tremendous increases in mitochondrial superoxide and oxygen consumption, accompanied by a loss in stem cell markers and a gain in differentiation markers. The antioxidant N-Acetyl-Cysteine (NAC) inhibited the mitochondrial superoxide increase and prevented the glioblastoma stem cells from differentiating. It appears that FBS-induced cancer stem cell differentiation is caused by mitochondrial activation, which depends on increases in levels of mitochondrial superoxide.

overall_design: GSC11 cells were cultured in stem cell medium or differentiated medium for 1, 3, or 7 days in triplicate. Total RNA was extracted from 12 samples. Microarray experiment and data analysis were done at Dept. of Systems Biology, MDACC (Houston, USA)

first: Feng

last: Wang

first: Ju-Seog

last: Lee

first: Peng

last: Huang


title: Esophageal cancer intratumor heterogeneity revealed by multi-region whole exome sequencing and aCGH

status: Public on Dec 31 2014

city: Calgary

first: Wei

last: Wu

address: 3330 Hospital Dr. NW

country: Canada

institute: 1.Zhengzhou Central Hospital, Affiliated to Zhengzhou University, China; 2. University of Calgary

type: Genome variation profiling by genome tiling array

summary: Cancer is a disease of the genome. Many genomic abnormalities have been found in a variety of cancer types, which are believed to be attributable to tumorigenesis as well as resistance to treatment and recurrence. Genomic heterogeneity in the same type of cancer or within a tumor reveals the complexity of cancer biology so that intratumor heterogeneity has become an inherent feature of cancer. In this study, we use whole-exome sequencing and array comparative genomic hybridization technology to examine the mutational profiling and copy number changes from multi-region samples within an esophageal cancer in order to understand the genomic phylogeny in the evolution of intratumor heterogeneity in esophageal cancer.

overall_design: Four spatially separated tumor samples and a fifth adjacent non-tumor sample were harvested from two patients with esophageal squamous cell carcinomas. An additional, local metastatic sample was obtained from one of the patients. DNAs from these samples were subjected to whole-exome sequencing and array comparative genomic hybridization. Comprehensive bioinformatic analyses were performed.

last: Cao


title: Expression data from wild-type (WT) and lrrc19 gene knockout (KO) mice intestines

status: Public on Oct 21 2014

city: Tianjin

first: Rongcun

last: Yang

state: Tianjin

address: 94 Weijin Road

department: Immunology

country: China

institute: School of Medicine, Nankai University

summary: LRRC19 (Leucine repeat receptor containing 19) is a newfound Toll-like receptor without definite function reported. We have detected that the lrrc19 gene had a high expression level in both human and mouse intestines and concentrated on the effect of this immune receptor in mediating the process of enteritis and intestinal cancer. To have a systematic understanding on the influence of this gene on the intracelluar environment of intestinal cell, we have conducted a microarray experiment to compare the transcriptomes of the WT and KO mice intestines under the same experimental condition.

overall_design: Gut epithelial cells of WT and KO mice of the same physiological and maintaining condition were isolated and then total RNAs were extracted from them, which could reflect the respective transcription profile of WT and KO mice. These RNAs were detected by microarray and the influence of lrrc19 gene on intestine could be revealed to some extent.


title: Epigenetic reprogramming and small RNA silencing of transposable elements in pollen.

status: Public on Sep 04 2014

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

type: Non-coding RNA profiling by high throughput sequencing

summary: The mutagenic activity of transposable elements (TEs) is suppressed by epigenetic silencing and small interfering RNAs (siRNAs), especially in gametes that would transmit transposed elements to the next generation. In pollen from the model plant Arabidopsis, we show that TEs are unexpectedly reactivated and transpose, but only in the pollen vegetative nucleus, which accompanies the sperm cells but does not provide DNA to the fertilized zygote. TE expression coincides with down-regulation of the heterochromatin remodeler DECREASE IN DNA METHYLATION 1 and of most TE siRNAs. However, 21 nucleotide siRNA from Athila retrotransposons is generated in pollen and accumulates in sperm, indicating that siRNA from TEs activated in the vegetative nucleus can target silencing in gametes. We propose a conserved role for reprogramming in germline companion cells, such as nurse cells in insects and vegetative nuclei in plants, to reveal intact TEs in the genome and regulate their activity in gametes.

overall_design: Mature pollen was collected from Columbia reference strain plants by vacuum filtration (Johnson-Brousseau and McCormick, 2004). DNA and RNA were isolated from a ddm1-2 plant in the Columbia reference background. Small RNAs of 19–28 nt were size selected by denaturing 15% PAGE, and cloned as in Brennecke et al. (2007). Additional details regarding the cloning of small RNAs are found in the Supplemental Data. The small RNA libraries were sequenced on Illumina 1G sequencer. The total number of sequences perfectly matching the Arabidopsis genome were as follows: WT inflorescence, 4,158,848 (2,286,133 unique); WT pollen, 1,034,665 (437,984 unique); ddm1 inflorescence, 4,098,772 (1,637,771 unique); and WT sperm, 760,651 (429,972 unique).

first: Keith

middle: R

last: Slotkin

first: Matthew

last: Vaughn

first: Filipe

last: Borges

first: Miloš

last: Tanurdžić

first: Jörg

middle: D

last: Becker

first: José

last: Feijó


title: Noncoding RNAs in human intervertebral disc degeneration: an integrated microarray study

status: Public on Apr 03 2015

city: Xi'an

first: Hai-Qiang

email: hqwang@sntcm.edu.cn, drwanghq@163.com

address: Xixian Avenue, Xixian District

department: Insititute of Integrative Medicine

institute: Shaanxi University of Chinese Medicine

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

Each of the SubSeries contained in this SuperSeries represents identical RNA samples used for hybridization to different array platforms.

overall_design:
Refer to individual Series

Previous affiliation: Department of Orthopaedics, Xijing Hospital, Fourth Military Medical University)


title: The long noncoding RNA expression profile of human intervertebral disc degeneration identified by microarray analysis

status: Public on Nov 17 2014

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

summary: In addition to the well-known short noncoding RNAs as miRNAs, increasing evidence suggests that long noncoding RNAs (lncRNAs) act as key regulators in a wide aspect of biologic processes. Dysregulated expression of lncRNAs has been demonstrated being implicated in a variety of human diseases. However, there is relative paucity of information regarding the role of lncRNAs in intervertebral disc degeneration (IDD) hitherto. We have addressed the expression profiles of miRNAs in IDD previously. To determine whether lncRNAs is differentially expressed in IDD, we employed a lncRNA-mRNA microarray analysis of human nucleus pulposus (five degenerative as IDD and five normal specimens as control). With abundant probes accounting for 33,045 lncRNAs and 30,215 coding transcripts in our microarray, microarray data profiling indicated that 18995 lncRNAs and 14635 mRNAs were detected in all samples with 2309 lncRNAs and 3017 mRNAs differentially expressed in degenerated samples. Amongst them, 164 lncRNAs (97 up and 67 down) and 265 mRNAs were highly differentially expressed with an absolute fold change greater than ten. The upregulated mRNAs included the extracellular matrix components as COL1A2, LUM, FN1ACAN, DCN and ITFG2. 1100 lncRNAs and 1379 mRNAs were altered in the same direction in at least 4 of the 5 degenerative samples with fold change greater than 2 respectively. Three lncRNAs were chosen for the real-time quantitative PCR (qRT-PCR) analysis. qRT-PCR results showed a high consistency with the microarray data.

overall_design:
In this study, to explore the potential involvement of lncRNAs in IDD, we conducted lncRNA and mRNA profiling in 5 human control nucleus pulposus tissue and 5 degenerative nucleus pulposus tissue by microarray.Biological replicates: 5 control, 5 degenerated, independently harvested.

Previous affiliation: Department of Orthopaedics, Xijing Hospital, Fourth Military Medical University)

first: Zhong-Yuan

last: Wan

first: Zhuo-Jing

last: Luo


title: Next Generation Sequencing Identification of HBV-MLL4 integration and its molecular basis in Chinese hepatocellular carcinoma

status: Public on Mar 31 2015

city: Shanghai

first: Hua

last: Dong

address: 199 Liangjing Rd.

institute: astrazeneca

type: Expression profiling by high throughput sequencing

summary:
Purpose: To gain molecular insights of HBV integration that may contribute to HCC tumorigenesis, we performed whole transcriptome sequencing and whole genome copy number profiling of hepatocellular carcinoma (HCC) samples from 50 Chinese patients.
Results: We identified a total of 33 HBV-human integration sites in 16 of 44 HBV-positive HCC tissues, which were enriched in HBV genotype C-infected patients. In addition, significantly recurrent HBV-MLL4 integration (18%; 8/44) was found in this cohort of patients.
Conclusions: This is the first report on the molecular basis of the MLL4 integration driving MLL4 over-expression. HBV-MLL4 integration occurred frequently in Chinese HCC patients, representing a unique molecular segment for HCC with HBV infection.

overall_design: mRNA profiles of 50 Chinese Hepatocellular Carcinoma patients and 5 adjacent tissues by Illumina Hiseq 2000.

first: Lan

last: Zhang

first: Ziliang

last: Qian

first: Zhenggang

last: Ren

first: Qunsheng

last: Ji


title: Identification of RNAs associated with S. cerevisiae or N. crassa Puf3

status: Public on Mar 16 2015

city: Stanford

first: Greg

last: Hogan

state: CA

address: 259 Campus Drive

institute: Stanford University / HHMI

summary: Affinity purification of S. cerevisiae or N. crassa Puf3 from S. cerevisiae cells and identification of associated RNAs by microarray

overall_design: Two-condition experiment, RNAs associated with purified Puf3 vs depleted supernant. Biological replicates: 3 x N. crassa Puf3, 3 x S. cerevisiae Puf3, and 3 x mock. One replicate per array.

first: Hogan

last: Greg


title: Exposure of radiation on mouse lung

status: Public on Aug 21 2014

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

summary: This study was designed to identify molecular changes induced by radiation in mouse lung.

overall_design: Mouse left lung was irradiated with a single dose of radiation. Total RNA from the irradiated lung tissue was subject to single channnel microarray.

first: Yoon-Jin

last: Lee

first: Hee

last: Jin

first: Ga-Young

last: Kang

first: Jaeho

last: Cho

first: Yun-Sil


title: Global transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism

status: Public on Jul 17 2014

city: Malmö

first: Joao

last: Fadista

address: Jan Waldenströms gata 35

country: Sweden

institute: Lund University Diabetes Centre

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

overall_design: Refer to individual Series

first: João

first: Leif

last: Groop


title: Blood gene expression profiles associated with symptoms of generalized anxiety disorder

status: Public on Dec 01 2014

city: Decatur

first: Aliza

middle: P.

last: Wingo

state: GA

address: 1670 Clairmont Rd

department: Psychiatry

institute: Atlanta VAMC/Emory University

summary: Prospective epidemiological studies found that generalized anxiety disorder (GAD) can impair immune function and increase risk for cardiovascular disease or events. Mechanisms underlying the physiological reververations of anxiety, however, are still elusive. Hence, we aimed to investigate molecular processes mediating effects of anxiety on physical health using blood gene expression profiles of 546 community participants. Of these, 179 met the status of controls and 157 cases of anxiety.

overall_design: We examined genome-wide differential gene expression in anxiety, as well as associations between nine major modules of co-regulated transcripts in blood gene expression and anxiety. There were a total of 546 subjects.

middle: P

last: Gibson


title: Genome Wide Identification of SARS-CoV Susceptibility Loci Using the Collaborative Cross

status: Public on Jan 06 2015

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: RNA was isolated from the lungs of mock and infected control and Trim55-/- mice at 2 and 4 DPI.

overall_design: Groups of age matched Trim55-/- and C57BL/6J control mice were infected with 10^5 PFU of MA15 for four days and monitored daily for weight loss and signs of disease.

first: Lisa

middle: E

last: Gralinski

first: Martin

middle: T

last: Ferris

first: Richard

last: Green

first: David

middle: L

last: Aylor

first: Mark

last: Heise

first: Fernando

last: Pardo-Manuel de Villena

first: Ralph

middle: S

last: Baric

middle: G


title: Global transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism [expression array]

summary: Here we harnessed the potential of expression arrays in 89 human pancreatic islet donors (different levels of blood glucose (HbA1c)) to identify genes regulated in this relevant tissue for type 2 diabetes (T2D).

overall_design: Islets from cadaver donors were provided by the Nordic Islet Transplantation Programme (www.nordicislets.org), Uppsala University. The microarrays were performed using GeneChip® Human Gene 1.0 ST whole transcript according to Affymetrix standard protocol.


title: Molecular and Structural Bases of Hypothalamic Development

status: Public on Dec 19 2014

city: Beaverton

first: Alejandro

last: Lomniczi

state: OR

address: 505 NW 185th Ave

department: Neuroscience

institute: Oregon National Primate Research Center - OHSU

summary: To compare the global profile of hypothalamic gene expression in agonadal male infants before and after activation of the neurobiologic brake that arrests pulsatile GnRH release during the juvenile phase of development.

overall_design: Affymetrix arrays were used to detect global changes in gene expression in the hypothalamus of of the agonadal rhesus monkey during development.

first: Sergio

last: Ojeda

first: Tony

middle: M

last: Plant

first: R

last: Ramaswamy

first: Valerie

last: Matagne


title: Genome-wide map of long non-coding RNA steroid receptor RNA activator (SRA) and its associated RNA heliase p68 in human pluripotent stem cells NTERA2

status: Public on Jun 18 2014

city: BETHESDA

first: Gary

last: Felsenfeld

state: MD

address: 9000 Rockville Pike

institute: NIDDK, NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed Chromatin Isolation by RNA Purification (ChIRP) of SRA and ChIP of p68 following by high-throughput sequencing in NTERA2 cell line. We find that SRA localizes with p68 genome-wide at genes whose function is involved in embryonic development.

overall_design: SRA ChIRP and p68 ChIP of triplicate samples.

first: Patompon

last: Wongtrakoongate

first: Gregory

last: Riddick


title: HPV E6 Impairs Translesion Synthesis by Blocking POLη Induction

status: Public on May 01 2020

city: Manhattan

first: Nicholas

last: Wallace

state: KS

address: 266 Chalmers Hall

institute: Kansas State University

type:
Third-party reanalysis
Expression profiling by array

summary: Many DNA tumor viruses inhibit or repurpose host DNA repair pathways to evade viral defense mechanisms or promote their own replication. High risk genus α human papillomaviruses (α-HPVs) express two versatile oncogenes (α-HPV E6 and E7) that use both approaches simultaneously. To identify new interactions with DNA repair pathways, we conducted a computational analysis of gene expression in cervical cancer (CaCx) transcriptomic datasets and identified a frequent upregulation of translesion synthesis (TLS) genes. TLS polymerase genes, particularly the gene for POLη (POLH), did not follow this pattern. Characterization of α-HPV oncogene expressing cell lines and premalignant cervical tissue confirm these data. They also show that the increased TLS protein abundance come in response to nucleoside depletion. Primary and transformed cell lines to demonstrate that α-HPV E6 blocks POLη induction by degrading p53. Lack of POLη dooms the pathway, preventing it from facilitating tolerance of replication stress. Failed TLS results in replication fork stalling and collapse into deleterious double strand breaks in the DNA (DSBs). Consequently, cellular genome fidelity decreases in a manner consistent with the mutations that accumulate during CaCx progression. Alterations in TLS are determinants for the efficacy of the chemotherapeutics most often used to treat CaCx (cisplatin and carboplatin). Exogenous expression of POLη protected CaCx cells from cisplatin-associated toxicity/damage, effectively stabilizing their genome. TLS polymerase expression is also a prognostic factor in CaCx. Analysis of the cancer genome atlas database (TCGA) shows increased expression of these genes correlated with over a decade shorter median survival.

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overall_design:
Total Samples: 313 from 5 data sets (GSE9750, GSE7803, GSE6791, GSE63514, GSE29570). Data was included based on availability on disease stage information. Data was normalized and merged into a single matrix to allow analysis and comparison of all 5 datasets.

data processing/re-analysis step:
gene expression data was downladed from GEO2R and normalized via feature scaling
normalized datasets were merged into a matrix containing 313 samples and 25203 gene IDs
gene IDs were matched with corresponding gene names
First column contains row-names (disease stage and gene names) Columns 2-314 contain normalized gene expression data

first: Sebastian

middle: O

last: Wendel

first: Jazmine

last: Snow

first: Tyler

last: Bastian

first: Laura

last: Brown

first: Candy

last: Hernandez

first: Emily

last: Burghardt

first: Andrew

last: Khan

first: Vaibhav

last: Murthy

first: Daniel

last: Neill

first: Zachary

middle: C

last: Smith

first: Kevin

last: Ault

first: Ossama

last: Tawfik

first: Cen

last: Wu


title: Long RNA Seq on Sham vs MI Adult Mouse Heart

status: Public on May 06 2014

city: Lausanne

first: Frederic

last: Burdet

address: Quartier Sorge - Batiment Amphipole

country: Switzerland

institute: Swiss Institute of Bioinformatics

summary: We systematically identified, annotated and characterised the mouse long non-coding transcriptome during myocardial infarction, revealing hundreds of novel heart specific lncRNAs with unique functional and regulatory characteristics.

overall_design: 2 conditions, 4 biological replicates per condition

first: Samir

last: Ounzain

first: Rudi

last: Micheletti

first: Tal

last: Beckmann

first: Blanche

last: Schroen

first: Michael

last: Alexanian

first: Iole

last: Pezzuto

first: Stefania

last: Crippa

first: Mohamed

last: Nemir

first: Alexandre

last: Sarre

first: Rory

last: Johnson

first: Jerome

last: Dauvillier

first: Mark

last: Ibberson

first: Roderic

last: Guigo

first: Ioannis

last: Xenarios

first: Stephane

last: Heymans

first: Thierry

last: Pedrazzini


title: RNA-mediated paternal heredity of diet induced type II diabetes and obesity.

status: Public on Jan 16 2014

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Epidemiological surveys first indicated that obesity and type II diabetes generated by lipid rich diets may be efficiently inherited, both paternally and maternally. This apparent exception to the fundamental law of non heritability of acquired characters was more recently documented in laboratory organisms but the transgenerational signal remained a matter of speculation. Here we show that experimental transfer to healthy one-cell embryos of testis RNA prepared from males raised on high-fat-diet (HFD) results in the development of obesity and diabetes in the adult. Body weight, fasting glucose levels, response to insulin, glucose tolerance, RNA levels of leptin and stearoyl-CoA desaturase were all affected in mice born after RNA microinjection to the same extent as in the progenitors and in their sexual offspring. Surprisingly, neither microarray hybridization nor deep sequencing of the inducer and control RNAs showed a differential expression of known regulators of adipogenesis, but only modest variations in a series of transcripts. Transgenerational maintenance appears as one instance of the RNA-mediated heredity of epigenetic traits previously demonstrated in experimental systems ranging from the worm to the mouse. The relationship between lipid-rich diet and changes in testicular RNAs on one side and the nature of the mark imprinted on the one-cell embryo by RNA transfer and responsible for pathological developments at later stages are questions of interest for future studies.

overall_design: Two experimental groups composed of four individuals. Controls = M1N,M2N,TN1,TN2 and Experimentals= M1W,M2W,M3W,M5W.

first: M

last: Rassoulzadegan

first: P

last: Barbry

first: S

last: Fourre

first: K


title: Minimal metabolic pathway structure is consistent with associated macromolecular interactions.

status: Public on Jun 30 2014

city: La Jolla

first: Bernhard

last: Palsson

address: 9500 Gilman Dr

department: Bioengineering

institute: UC San Diego

summary: We sequenced mRNA of three dual perturbation experiments of E. coli K12 MG1655 changing both genetic and environmental conditions. Each dual perturbation experiment consists of four RNA-seq samples (WT, WT+nutrient supplementation, transcription factor KO, transcription factor KO+nutrient supplementation). The three conditions are: 1) adenine supplementation/nac KO, 2) L-tryptophan supplementation/cra KO, 3) anaerobic/mntR KO.

overall_design: Determination of whether a transcription factor plays a regulatory role in a particular environmental shift by examining differential expression of mRNA levels.

first: Aarash

last: Bordbar

first: Harish

last: Nagarajan

first: Nathen

last: Lewis

first: Haythem

last: Latif

first: Ali

last: Ebrahim

first: Stephen

last: Federowicz

first: Jan

last: Schellenberger


title: Global gene expression analysis of anthracycline-resistant breast cancer cell lines

status: Public on Jan 24 2014

city: Toronto

first: Marsela

last: Braunstein

address: 661 University Avenue, Suite 510

institute: Ontario Institute for Cancer Research

summary: Drug resistance in breast cancer is the major obstacle to a successful outcome following chemotherapy treatment. While upregulation of multidrug resistance (MDR) genes is a key component of drug resistance in multiple cancers, the complexity and hierarchy of non-MDR driven drug resistance pathways are still largely unknown. The aim of this study was to identify pathways contributing to anthracycline resistance using isogenic drug resistant breast cancer cell lines. We generated isogenic MDA-MB-231, MCF7, SKBR3 and ZR-75-1 epirubicin-resistant breast cancer cell lines, which were cross-resistant to doxorubicin and SN-38; the SKBR3 cell line was also resistant to taxanes. Epirubicin-resistant cells were morphologically different from native cells, and had alterations in apoptosis and cell cycle profile. Using gene expression and small-molecule inhibitor analyses we identified deregulation of histone H2A and H2B genes in all four cell lines. These genes contribute to several biological pathways, which include cell cycle, chromosomal maintenance, epigenetics, RNA and mitochondrial transcription. Histone deacetylase and cell cycle/DNA damage small molecule inhibitors reversed resistance and were cytotoxic for all four epirubicin-resistant cell lines confirming that histone and cell cycle pathways are associated with epirubicin resistance. This study has established model systems for investigating drug resistance in all four breast cancer subtypes and revealed key pathways that contribute to anthracycline resistance.

overall_design: The global gene expression analysis included 4 parental (anthracycline sensitive) and 4 resistant breast cancer cell lines, in biological triplicates.

first: Linda

last: Liao

first: Nicola

last: Lyttle

first: Karen

middle: J

last: Taylor

first: Paul

last: Krzyzanowski

first: Irina

last: Kalatskaya

first: Lincoln

last: Stein

first: Richard

last: Marcellus

first: Johh

last: Bartlett

first: Melanie

last: Spears


title: Expression in blood of schizophrenia patients and healthy controls

status: Public on Dec 05 2014

city: Wuxi

first: Fuquan

last: Zhang

address: 156 Qianrong Rd

institute: Wuxi mental health center

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

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


title: Gene expression study in CLL of B-cell receptor triggering (miRNA study)

status: Public on Jan 01 2014

city: Aviano

first: daniela

last: marconi

address: Via franco Gallini 2

country: Italy

institute: CRO AVIANO

summary: The B-cell receptor (BCR) plays an important role in pathogenesis and progression of chronic lymphocytic leukemia (CLL). We investigated the BCR triggering-dependent microRNA modulation by stimulating CLL cells with immobilized anti-IgM. miRome of immobilized anti-IgM stimulated CLL cells (n=16) identified a substantial upregulation of miR-132 in both unmutated (UM) and mutated (M) IGHV subgroups. A parallel gene expression profile and an in-silico analysis to identify miR-132 target genes¸ allowed us to focus on SIRT1, that encodes for a histone deacetylase targeting several proteins including TP53. We defined a reduction of SIRT1 protein levels upon immobilized anti-IgM stimulation (P=0.001), and a concomitant increase in TP53 acetylation (P=0.0072). The TP53 target gene CDKN1A was consistently up-regulated in immobilized anti-IgM stimulated CLL cells. Of note, the miR-132 constitutive expression levels in CLL cases (n=134) were of similar magnitude of those obtained in in vitro immobilized anti-IgM stimulated CLL cells.  Additionally, high miR-132 expression levels retained a favorable prognostic impact in M (P=0.005), but not in UM CLL patients (P=0.968). The described miR-132/SIRT1/TP53 axis, sequentially characterized by BCR triggering, miR-132 up-regulation, SIRT1 down-regulation and TP53 acetylation, should be considered in the light of emerging drugs targeting the BCR pathway in CLL.

overall_design: investigated the BCR triggering-dependent gene expression modulation by stimulating CLL cells with immobilized anti-IgM.

first: Riccardo

last: Bomben

first: Valter

last: Gattei


title: Gene expression study in CLL of B-cell receptor triggering


title: Gene expression in Bacillus subtilis treated with human PGRP, gentamicin, and CCCP

status: Public on Jul 25 2014

city: Gary

first: Roman

last: Dziarski

state: IN

address: 3400 Broadway

institute: Indiana University School of Medicine-Northwest

summary:
Human Peptidoglycan Recognition Proteins (PGRPs) kill bacteria, likely by over-activating stress responses in bacteria. To gain insight into the mechanism of PGRP killing of Bacillus subtilis and bacterial defense against PGRP killing, gene expression in B. subtilis treated with a control protein (bovine serum albumin, BSA), human recombinant PGRP (PGLYRP4), gentamicin (aminoglycoside antibiotic), and CCCP (membrane potential decoupler) were compared. Each treatment induced unique and somewhat overlapping pattern of gene expression. PGRP highly increased expression of genes for oxidative and disulfide stress, detoxification and efflux of Cu, As, and Zn, several transporters, repair of damaged proteins and DNA, energy generation, histidine and cysteine synthesis, envelope lysis and remodeling, and other stress responses. PGRP also caused marked decrease in the expression of genes for phosphate uptake and utilization, Fe uptake, and motility.
Gene expression microarray in B. subtilis exposed to a human bactericidal innate immunity protein, PGRP, showed induction of oxidative stress response and defense genes, with different expression pattern than B. subtilis exposed to an aminoglycoside antibiotic and a membrane potential decoupler.

overall_design: B. subtilis was treated with PGRP (human recombinant PGLYRP4), gentamicin, or CCCP (carbonyl cyanide 3-chlorophenylhydrazone). RNA was obtained from each culture and assayed for gene expression using custom whole genome Affymetrix 900513 GeneChip B. subtilis Genome Array. Each experiment was repeated 3 times.

first: Des

last: Kashyap

first: Dipika

last: Gupta


title: Gene expression study in CLL of B-cell receptor triggering (mRNA Study)

summary: The B-cell receptor (BCR) plays an important role in pathogenesis and progression of chronic lymphocytic leukemia (CLL). We investigated the BCR triggering-dependent mRNA modulation by stimulating CLL cells with immobilized anti-IgM. miRome of immobilized anti-IgM stimulated CLL cells (n=16) identified a substantial upregulation of miR-132 in both unmutated (UM) and mutated (M) IGHV subgroups. A parallel gene expression profile and an in-silico analysis to identify miR-132 target genes¸ allowed us to focus on SIRT1, that encodes for a histone deacetylase targeting several proteins including TP53. We defined a reduction of SIRT1 protein levels upon immobilized anti-IgM stimulation (P=0.001), and a concomitant increase in TP53 acetylation (P=0.0072). The TP53 target gene CDKN1A was consistently up-regulated in immobilized anti-IgM stimulated CLL cells. Of note, the miR-132 constitutive expression levels in CLL cases (n=134) were of similar magnitude of those obtained in in vitro immobilized anti-IgM stimulated CLL cells.  Additionally, high miR-132 expression levels retained a favorable prognostic impact in M (P=0.005), but not in UM CLL patients (P=0.968). The described miR-132/SIRT1/TP53 axis, sequentially characterized by BCR triggering, miR-132 up-regulation, SIRT1 down-regulation and TP53 acetylation, should be considered in the light of emerging drugs targeting the BCR pathway in CLL.

overall_design: Investigated the BCR triggering-dependent gene expression modulation by stimulating CLL cells with immobilized anti-IgM.


title: Transcriptional response of mouse thyroids following in vivo 211At exposure reveals distinct gene expression profiles

status: Public on Feb 13 2013

city: Göteborg

first: Nils

last: Rudqvist

state: VG

address: Gula stråket 2b

institute: Gothenburg university

summary:
Transcriptomic profiling of normal mouse thyroid tissue following 211At irradiation
Astatine-211 (211At) is an alpha particle emitting halogen with almost optimal linear energy transfer (LET) for creating DNA double strand breaks, and is thus proposed for radionuclide therapy when bound to tumor-seeking agents. Un-bound 211At accumulates in the thyroid gland. The concept of basal radiation-induced biological effects in thyroid tissue is to a high degree unknown and is most valuable.
Female BALB/c nude mice were i.v. injected with 0.064-42 kBq of 211At resulting in absorbed doses to the thyroid gland of 0.05-32 Gy. Thyroids were removed at 24 h after injection and total RNA was extracted from pooled thyroids and processed in triplicate using Illumina MouseRef-8 Whole-Genome Expression Beadchips. Nexus Expression 2.0 was used for data analysis.
Thyroids exposed to 211At revealed distinctive gene expression profiles compared to non-irradiated controls. More genes were affected at low absorbed doses (0.05 and 0.5 Gy) compared to intermediate (1.4 Gy) and high absorbed doses (11 and 32 Gy) and the proportion of dose-specific genes increased with decreased absorbed dose. This result might be the manifestation of increased heterogeneous irradiation with decreasing absorbed dose, indicating a bystander effect. Also, 1.4 Gy often had an opposite regulation compared to the other absorbed doses. No inflammatory effects were seen while 0.05 and 11 Gy affected the immune system. Effects on the cellular response to outer stress and cell cycle regulation and proliferation were seen at 1.4 and 11 Gy.
These results indicate that the cellular response to ionizing radiation is complex and differs with absorbed doses.

overall_design: Total RNA was isolated from fresh-frozen tissue samples (Normal balb/c mouse thyroids)

first: Toshima

middle: Z

last: Parris

first: Emil

last: Schüler

first: Khalil

last: Helou

first: Eva

last: Forssell-Aronsson


title: Gene expression data following Neurogenin 1 expression in mouse embryonic stem cells

status: Public on Jan 15 2013

city: Ann Arbor

first: K Sue

last: OShea

state: MI

address: 3051 BSRB, 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

summary:
To study the early gene expression events involved in neurogenesis, we expressed the bHLH neural determination factor neurogenin 1 in mouse embryonic stem cells.
We used microarray to examine the program of gene expression at 24, 48, 72 hours of transgene expression.

overall_design:
Mouse embryonic stem cells were engineered to express neurogenin 1 using a tet-sensitive expression system.
RNAs from uninduced and induced cells were isolated at 24, 48, and 72 hours of differentiation and subjected to microarray analysis.

first: K

last: O'Shea

first: J

last: Velkey


title: Genome wide mapping of PSF binding sites in prostate cancer cells

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

summary: Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. We identified androgen-regulated long non-coding RNA, CTBP1-AS, located in the antisese region of CTBP1 gene. CTBP1-AS activate AR signaling by epigenetically repress AR-associated cofactors such as CTBP1 by interactign with RNA-binding protein PSF and recruiting HDAC complex to the target promoters. In order investigated the PSF target genes, we performed ChIP-seq analysis of PSF binding sites in prostate cancer cell line, LNCaP cells. We identified androgen dependent PSF binding regions in prostate cancer cell genome. We observed PSF bindings around the promoters of androgen repressed genes such as CTBP1, p53 and SMAD3.

overall_design: ChIP-sequence analysis of PSF binding sites in prostate cancer cells

first: Shuichi

last: Tsutsumi

first: Satoshi

last: Inoue

first: Hiroyuki

last: Aburatani


title: Global gene expression profiles of MT knockout and wild-type mice in the condition of doxorubicin-induced cardiomyopathy

status: Public on Aug 10 2013

city: Shanghai

first: Yi

last: Shuai

address: 1380, Zhongshan (W.)

department: Department of Toxicology

institute: Shanghai Municipal Center for Disease Control & Prevention

summary: The present study was designed using MT knockout mice in concert with genomic approaches to explore the possible molecular and cellular mechanisms involved in the protective effects of MT against DOX cardiotoxicity. MT-Ⅰ/Ⅱ null (MT-/-) mice and corresponding wild-type mice (MT+/+) were administrated with a single dose of DOX (15 mg/kg, i.p.) or an equal volume of saline. Animals were sacrificed on the 4th day after DOX administration and samples were collected for further analyses. Global gene expression profiles of cardiac mRNA from two genotype mice revealed that 381 characteristically MT-responsive genes were identified between MT+/+ mice and MT-/- mice in response to DOX, including fos, ucp3, car3, atf3, map3k6, etc.. Functional analysis implied MAPK signaling pathway, p53 signaling pathway, Jak-STAT signaling pathway, PPAR signaling pathway, Wnt signaling pathway, etc. might be involved to mediate the protection of DOX cardiomyopathy by MT. Results from the present study not only validated the previously reported possible mechanisms of MT protection against DOX toxicity, but also provided new clues into the molecular mechanisms involved in this process.

overall_design: Male MT+/+ & MT-/- mice (6-8 weeks old) were randomly assigned to treatment or control groups and administrated with a single dose of DOX (15 mg/kg, i.p.) or an equal volume of normal saline solution (NS) respectively. Animals were sacrificed on the 4th day after DOX injection, and samples were collected for further microarray analyses.


title: RNA-mediated paternal heredity of diet-induced obesity and type II diabetes

status: Public on Feb 14 2013

city: Nice

first: Valerie

last: Grandjean

address: Parc Valrose

department: University of Nice

institute: INSERM

summary: Gene expression analysis of testis RNA obtained from mice fed on High Fat and Standard diets. The aim of the study is to identify differentially expressed transcript in testis of the obese males which might be involved in the RNA-mediated paternal heredity of diet-induced obesity and typeII diabete

overall_design: Total RNA obtained from testis of mice fed on High Fat and standard diets

first: Minoo

last: Rassoulzadegan

first: Valérie


title: Giardia lamblia WB: 5'5npac control vs. pPPax2

status: Public on Dec 01 2012

city: Taipei

first: Chin-Hung

last: Sun

address: Department of Parasitology, College of Medicine, National Taiwan University

department: Department of Parasitology

country: Taiwan

summary: Transcriptional profiling of Giardia lamblia WB comparing control 5'5npac cells with pPPax2 cells.

overall_design: Two-condition experiment 5'5npac cells with pPPax2 cells.


title: Examination of the MAPK pathway gene expression in patient samples

status: Public on Jun 03 2013

city: Philadelphia

first: Louise

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

summary: Microarray analysis of total RNA isolated from samples of circulating tumor cells from 7 patients before romidepsin infusion (0 hours), at 4 h after initiation of the infusion (4 hours) and 24 h after initiation of the infusion (24 hours).

overall_design: MAPK pathway related genes were selected to see differences between patient blood samples after roomidepsin treatment at 0 hour, 4 hour and 24 hour.

first: RW

last: Robey

first: AR

last: Chakraborty

first: VL

last: Luchenko

first: Z

last: Zhan

first: RL

last: Piekarz

last: Gillet

first: AV

last: Kossenkov

last: Wilkerson

first: LC

first: NL

last: Collie

first: MM

last: Gottesman

first: SE

last: Bates


title: The genetic basis for differential macrophage activation

status: Public on May 18 2013

city: Edinburgh

first: Musa

last: Hassan

state: Scotland

address: Easter Bush

department: Roslin

country: United Kingdom

institute: University of Edinburgh

summary: Differential macrophage activation mediate genetic differences to a variety of inflammatory pathologies. We wanted to elucidate the transcriptional and regulatory programs regulating differential macrophage activation in genetically diverse mouse strains.

overall_design: Bone marrow-derived macrophages (BMDMs) from AJ and C57BL/6j mice were left unstimulated, stimulated with IFN/TNF, or IL-4, or CpG, or LPS or  IFN/TNF and infected with a type II (Pru A7) strain of Toxoplasma gondii, or infected with Pru A7 and gene expression analyzed 18 hrs later.

first: Kirk

last: Jensen

first: Jeroen

last: Saeij


title: Transcriptional perturbations caused by tumor virus proteins

status: Public on Jul 20 2012

city: Tucson

first: Megha

last: Padi

state: AZ

address: 1071 East Lowell St.

department: Molecular and Cellular Biology

institute: University of Arizona

summary:
Genotypic differences greatly influence susceptibility and resistance to disease. Understanding genotype-phenotype relationships requires that phenotypes be viewed as manifestations of network properties, rather than simply as the result of individual genomic variations. Genome sequencing efforts have identified numerous germline mutations associated with cancer predisposition and large numbers of somatic genomic alterations. However, it remains challenging to distinguish between background, or “passenger” and causal, or “driver” cancer mutations in these datasets. Human viruses intrinsically depend on their host cell during the course of infection and can elicit pathological phenotypes similar to those arising from mutations. To test the hypothesis that genomic variations and tumour viruses may cause cancer via related mechanisms, we systematically examined host interactome and transcriptome network perturbations caused by DNA tumour virus proteins. The resulting integrated viral perturbation data reflects rewiring of the host cell networks, and highlights pathways that go awry in cancer, such as Notch signalling and apoptosis. We show that systematic analyses of host targets of viral proteins can identify cancer genes with a success rate on par with their identification through functional genomics and large-scale cataloguing of tumour mutations. These complementary approaches together result in increased specificity for cancer gene identification. Combining systems-level studies of pathogen-encoded gene products with genomic approaches will facilitate prioritization of cancer-causing driver genes so as to advance understanding of the genetic basis of human cancer.
We profiled the transcriptome of human cells expressing tumor virus proteins, in order to trace pathways through which viral proteins could alter cellular states.

overall_design: To examine transcriptome network perturbations directly in human cells, we generated expression constructs fusing each viral ORF (open reading frame) to a tandem epitope tag and introduced each construct into IMR-90 normal human diploid fibroblasts. Total RNA was isolated from IMR-90 cells expressing viORFs and gene expression was assayed on Human Gene 1.0 ST arrays.

first: Orit

last: Rozenblatt-Rosen

first: Rahul

last: Deo

first: Guillaume

last: Adelmant

first: David

last: Hill

first: Karl

last: Münger

first: Jarrod

last: Marto

first: John

last: Quackenbush

first: Frederick

last: Roth

first: James

last: DeCaprio

first: Marc

last: Vidal


title: Gene expression profiling of esophageal adenocarcinoma

status: Public on Apr 11 2012

last: Beer

state: Michigan

address: 1500 E Medical Center Dr. CCGC 6431

department: Surgery

institute: University of Michigan Medical School

summary:
Specimens were collected from esophageal adenocarcinoma patients undergoing esophagectomy for adenocarcinoma at the University of Michigan Health System between 1991 and 2004. Written consent was obtained from each patient according to the approval and guidelines of the University of Michigan institutional review board. Patients receiving treatment with chemotherapy and/or radiotherapy prior to surgery were excluded.
Tissue samples were fresh-frozen in liquid nitrogen and stored at −80 °C until use.

overall_design: Cellularity of tumor samples were assured to be greater than 70% before sample RNA was isolated. RNA from 22 adenocarcinoma samples was extracted and processed for hybridization on Affymetrix Human Genome U133A 2.0 Array.

first: Andrew

last: Chang

first: Amy

last: Silvers

first: Lin

last: Lin


title: Distinctive microRNA profiles and target genes of aberrant microRNAs in leukemia chicken infected by subgroup J avian leukosis virus

status: Public on Mar 10 2014

city: guang-zhou

first: HongMei

last: Li

state: Guang -dong

address: wu shan

institute: South China Agricultural University

summary: Subgroup J avian leukemia is a type of oncology infectious disease caused by Subtype J of avian leukosis virus (ALV-J). It mainly encroaches on bone marrow cells, and metastasizes to liver, kidney, splenic ellipsoids and other organs, leading to myeloid leukosis (ML) and other malignancies, resulting in significant economic losses. microRNA play important roles in oncology infectious diseases. We used miRNA microarray analysis to detail the relationship of aberrant microRNAs and chicken ALV-J leukemia, and to try to find the potential diagnostic and therapeutic target for infections of subtype J of leukemia.

overall_design: ALV-J-infected and non-infected ten-week-old chicken liver tissues were sampled for the array assay. A1, A2, and A3 are the ALV-J infection group samples, and DA1, DA2, and DA3 are the control samples. 623 mature miRNA sequences were assembled and integrated into the LC miRNA microarray design, and different miRNA expressions were measured on the 7000HT Fast Real-Time PCR system.

first: Hongmei

first: Qingmei

last: Xie

first: Yingzuo

last: Bi


title: Global transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism [RNA-seq]

status: Public on Jul 17 2014

city: Malmö

first: Joao

last: Fadista

address: Jan Waldenströms gata 35

institute: Lund University Diabetes Centre

summary: Here we harnessed the potential of RNA sequencing in 89 human pancreatic islet donors to identify genes and exons regulated in this relevant tissue for T2D.

overall_design: mRNA profiles of 89 human pancreatic islet donors having different levels of blood glucose (HbA1c) with and without T2D. The data was generated by deep sequencing using Illumina HiSeq 2000.

first: João

first: Leif

last: Groop


title: Barrett's esophageal tissues and esophageal adenocarcinoma specimens

first: David

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

overall_design: Refer to individual Series


title: MicroRNAs expression profiling of human nucleus pulposus cells: control vs. degeneration

status: Public on Jan 01 2012

city: Xi'an

first: Hai-Qiang

last: Wang

address: Xixian Avenue, Xixian District

institute: Shaanxi University of Chinese Medicine

summary: MicroRNAs expression profiling of human nucleus pulposus cells derived from patients with disc degeneration in comparison with those derived from patients with scoliosis as control.

overall_design:
Two-condition experiment: control nucleus pulposus cells vs. degenerative nucleus pulposus cells. Biological replicates: 3 control, 3 degenerated, independently harvested. Four replicates per array.

The supplementary file 'GSE19943_fold_pvalue.txt' contains fold-changes and p-values.

Previous affiliation: Department of Orthopaedics, Xijing Hospital, Fourth Military Medical University)

first: H

middle: Q

first: X

last: Yu

first: Z

middle: H

last: Liu

last: Cheng

last: Luo


title: Gene expression profiling of Barrett’s esophageal tissues and esophageal adenocarcinoma specimens

overall_design: Cellularity of metaplastic, dysplastic, and tumor samples were assured to be greater than 70% before sample RNA was isolated. RNA from 31 Barrett’s and 15 adenocarcinoma samples was extracted and processed for hybridization on Affymetrix HG-U133A microarrays.

first: Jules


title: Transfection of rat Sertoli cells with human androgen receptor leads to alternated gene expression without androgen incubation

status: Public on May 15 2014

city: Giessen

first: Melanie

last: Markmann

state: Hessen

address: Rudolf-Buchheim-Str. 7

department: Anaesthesiology

country: Germany

institute: University of Giessen

summary: We introduced a full-length human AR into the expression vector pcDNA 6.2 C-EmGFP and transfected AR-deficient rat Sertoli cells (93RS2) by electroporation. We compared gene expression levels of AR-deficient Sertoli cell line (93RS2_noAR) and a full-length-human-AR transfected Sertoli cell line (93RS2_AR17) using microarray analysis.

overall_design: We analyzed 3 arrays for the noAR cell line and 3 arrays for the AR17 cell line.

first: Daniela

last: Fietz

first: Dennis

last: Lang

first: Lutz

last: Konrad

first: Hamid

last: Hossain

first: Martin

last: Bergmann


title: Genome-wide analysis of gene expression in LIF and LIF plus CHIR99021 in C57BL/6 mouse embryonic stem cells(B6 mESCs)

status: Public on Aug 29 2013

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

summary:
Analysis of genes induced by CHIR99021
CHIR99021 is a inhibitor of glycogen synthase kinase 3 (GSK3) and can promote B6 mESC sef-renewal when combined with LIF in serum condition.

overall_design: Total RNA obtained from B6 mESCs treated with LIF or LIF/CHIR99021 for 12 hours.

first: Ye

last: Shoudong

first: Ying

last: Qilong


title: Expression data from Neural Progenitor cells cultured on 2D flat surfaces and in 3D scaffolds

status: Public on Dec 23 2009

city: Athens

first: William

last: Kisaalita

address: Dritmier Engineering Center

institute: University of Georgia

summary: A genomic expression comparison was done among neural progenitor cells cultured on 2D substrates, 3D porous polystyrene scaffolds, and as 3D neural spheres (in vivo surrogate), with the goal of assessing the feasibility of establishing the meaning of 3D and associated physiological relevance at the molecular level

overall_design: Neural progenitor cells were cultured on 2D surfaces, in 3D scaffolds and as 3D neural spheres. Chemical cues are controlled by coating. Only spacial properties of the culture systems were compared.

first: Yinzhi

last: Lai


title: Comparison of human and mouse dendritic cell subsets by genome-wide expression profiling

status: Public on Jan 24 2008

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

institute: IGBMC

summary:
Dendritic cells (DCs) are a complex group of cells which play a critical role in vertebrate immunity. Spleen or lymph node resident DCs are subdivided into conventional DC (cDC) subsets (CD11b and CD8alpha in mouse; BDCA1 and BDCA3 in man) and plasmacytoid DCs (pDCs). It is currently unclear if these various DC populations belong to a unique hematopoietic lineage and if the subsets identified in the mouse and human systems are evolutionary homologs. To bring novel insights into these questions, we sought conserved genetic signatures for these DCs through the analysis of a compendium of genome-wide expression profiles of mouse or human leukocytes.
We show through clustering analysis that all spleen resident DC subsets form a distinct branch within the leukocyte family tree, and reveal a transcriptomal signature evolutionary conserved in all these DC subsets. Moreover we identify a large gene expression program shared between mouse and human plasmacytoid DCs, and smaller conserved profiles shared between mouse and human cDC subsets. Finally, we use compendium analysis to re-evaluate the classification of interferon-producing killer DCs (IKDCs) and lin-CD16+HLA-DR+ cells, which have both been claimed to be DCs, and show that these cells are more closely linked to NK or myeloid cells, respectively. Our study thus provides a unique resource for future investigation of the evolutionarily conserved molecular pathways governing the ontogeny and functions of leukocyte subsets, especially DCs.
Keywords: cell type comparison of wild-type spleen leukocyte subsets, including palsmacytoid dendritic cells, CD8alpha conventional dendritic cells, and CD11b conventional dendritic cells

overall_design: This study includes data from cell sort purified dendritic cells, B cells, NK cells, and CD8 T cells. 2 or 3 independent replicates were made for each cell type. The genearray was performed in an attempt to investigate the relationships between DCs subsets and with other leukocytes, in mouse, in human, and between these 2 species. To this end, public data for mouse CD4 T cells and macrophages, as well as public data for human leukocyte subsets were also used in the analysis. The results have led to the identification of specific transcriptional programs conserved between human and mouse dendritic cell subsets.

first: M

last: DALOD

first: S

last: ROBBINS

first: P

last: KASTNER

last: CHAN

first: ML

last: SELLARS


title: Expression data from MMP3 and control transgenic mice

status: Public on Nov 18 2010

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

summary:
Effect of induction of MMP3 expression in CCSP-rtTA/tet-MMP3 transgenic mice, fed doxycycline for 14 weeks
We used microarrays to detail the global programme of gene expression following MMP3 expression

overall_design: Transgenic mice (CCSPrt-TA/tet-MMP3 or CCSPrtTA control mice) were fed doxycycline from week 6 to week 20, then lungs were removed, formalin fixed, and embedded in paraffin.  Sections were sliced from the paraffin blocks for RNA extraction.


title: Gene expression profiling in Wistar male rat left ventricle with chronic and severe aortic valve regurgitation

status: Public on Mar 31 2010

city: Quebec

first: Jacques

last: Couet

address: 2725 chemin Sainte-Foy

institute: Centre de Recherche de l'Hopital Laval

summary: Aortic valve regurgitation (AR) imposes a severe volume overload to the left ventricle (LV) which results in dilation, eccentric hypertrophy and eventually loss of function. Little is known about the impact of AR on LV gene expression. We therefore conducted a gene expression profiling study in the LV of male Wistar rats with chronic (9 months) and severe AR.

overall_design: Five male Wistar rats had one or two aortic valve leaflets punctured with a catheter under echocardiographic guidance in order to induce severe regurgitation (>65% of blood regurgitating during diastole from the aorta to the left ventricle). Five additional rats were sham-operated. The animals were sacrificed 9 months after the procedure and their left ventricle collected for RNA extraction and microarray analysis.

first: J

first: D

last: Lachance

last: Champetier

last: Arsenault


title: CENTDIST: Discovery of Co-associated Factors by Motif Distribution

status: Public on Apr 25 2012

city: Singapore

first: Cheng Wei

last: Chang

address: Genome Institute of Singapore Genome #02-01 60 Biopolis Street

department: Computational and Mathematical Biology 1

country: Singapore

institute: GIS

summary: Transcription factors (TFs) do not function alone but work together with other TFs (called co-TFs) in a combinatorial fashion to precisely control the transcription of target genes. Mining co-TFs is thus important to understand the mechanism of transcriptional regulation. Although existing methods can identify co-TFs, their accuracy depends heavily on the chosen background model and other parameters such as the enrichment window size and the PWM score cut-off. In this study, we have developed a novel web-based co-motif scanning program called CENTDIST (http://compbio.ddns.comp.nus.edu.sg/~chipseq/centdist/). In comparison to current co-motif scanning programs, CENTDIST does not require the input of any user-specific parameters and background information. Instead, CENTDIST automatically determines the best set of parameters and ranks co-TF motifs based on their distribution around ChIP-seq peaks. We tested CENTDIST on 14 ChIP-seq datasets and found CENTDIST is more accurate than existing methods. In particular, we applied CENTDIST on an Androgen Receptor (AR) ChIP-seq dataset from a prostate cancer cell line and correctly predicted all known co-TFs (8 TFs) of AR in the top 20 hits as well as discovering AP4 as a novel co-TF of AR (which was missed by existing methods). Taken together, CENTDIST, which exploits the imbalanced nature of co-TF binding, is a user-friendly, parameter-less, and powerful predictive web-based program for understanding the mechanism of transcriptional co-regulation.

overall_design: Genome-wide binding analyses of AP4 in LNCaP with DHT (5alpha-dihydrotestosterone) stimulation using ChIP-Seq.

first: Zhizhuo

last: Zhang

first: Cheng

middle: W

first: Wan

last: Goh

first: Wing-Kin

last: Sung

first: Edwin

last: Cheung


title: Using individual coping styles to explain within-population variation in adaptive gene expression

status: Public on Sep 08 2012

city: Chile

first: Sebastian

last: Boltana

state: Bio BIO

address: Edmundo Larenas s/n, Barrio Universitario. Biotechnology Center

department: Oceanografia

country: Chile

institute: Universidad de Concepcion

summary: Individual stress coping style has profound effects on how animals respond to environmental change, and individuals within a population strikingly differ in how gene expression shifts in response to challenge. This study used a wild type Zebrafish (Danio rerio) population to: 1) identify and screen for individual coping style using a screening protocol for risk taking in groups and 2) do global transcriptomics of brains from proactive, reactive or randomly chosen individuals (n=10/group) under control conditions. Results show that within our population proactive and reactive individual coping styles can be accurately identified and may represent 10-30% of individuals within the population. Microarray data analyses identify fundamental differences between the three different groups where variance in gene expression values are reduced by using coping style as an explanatory variable.  Furthermore, significant differences in mRNAs and related biological processes suggest that even under identical environmental conditions the molecular mechanisms that underpin physiological processes are very different between proactive and reactive individuals within a population.

overall_design: Experimental tank was an 18 litre glass aquarium (dimensions (LxWxH): 40 X 25 X 20cm) lined on three sides with white paper; the front wall was not covered to allow the observer to record the behaviour and divided at 1/3 of his length with a black PVC screen with a 3cm diameter hole in the middle. All the tank surfaces around this third area of the tank were covered with dark paper and closed on the upper part with a removable lid to provide a shelter for the animals. The hole was covered with the same PVC plastic material and removed once the screening started to allow the fish enter the novel environment. Food was not supplied the day before to ensure that during the test the fish were hungry and they had to make the decision to leave a safe area in order to forage. Boldness was measured as the time taken by individual fish to leave a group from a safe, darkened area. It hence represents the willingness of a fish to explore a new, potentially dangerous environment, or boldness. Tests were conducted with groups of 9 randomly-selected fish from stocking tanks. Fish were familiar to each other in the sense that they were previously held in the same stocking tank. Test started with a 10 min. habituation period in the sheltered area with the hole closed with a PVC screen and the top of the sheltered area of the tank also covered to provide a complete quiet place. Then the lid covering the hole was gently removed. Either the first 3 fish to exit the shelter or fish with latency times inferior to 10 minutes were considered bold fish and were removed gently with a fish net from the test tank and placed apart in another tank. Latency times of emergency from the sheltered area were recorded individually.  Next 3 animals to emerge before 15 minutes were considered intermediate and also removed gently. At the end of this last 15 minutes, animals that still remained inside the sheltered area were considered shy. Intermediates were discarded and fish selected for different coping strategies where placed in different tanks for posterior molecular analysis. Selected animals were killed by an overdose of MS-22 and the brains were sampled. Individual tissue samples were homogenized into 0.3 ml of Tri-Reagent and stored at -80C for further molecular analysis.

first: Simon

last: MacKenzie


title: Prognostic gene signature for AML

status: Public on Feb 07 2013

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

summary: Acute myeloid leukemia (AML) is a heterogeneous disease in respect of molecular aberrations and prognosis. We used gene expression profiling of 562 patients treated in the German AMLCG 1999 trial to develop a gene signature that predicts survival in AML.

overall_design: Analysis of 562 samples (140 HGU-133plus2; 422 HGU-133A; 422 HGU-133B) from adult patients with acute myeloid leukemia (AML).

first: Vindi

last: Jurinovic

first: Klaus

last: Metzeler

first: Maria

last: Sauerland

first: Zlatana

last: Pasalic

first: Annika

last: Dufour

first: Stephanie

last: Schneider

first: Purvi

last: Kakadia

first: Karsten

last: Spiekermann

first: Ulrich

last: Mansmann

first: Thomas

last: Büchner

first: Wolfgang

last: Hiddemann

first: Stefan

last: Bohlander


title: Abundant Quantitative Trait Loci for CpG Methylation and Expression Across Human Brain Tissues

status: Public on Apr 20 2010

city: Bethesda

first: J Raphael

last: Gibbs

address: 35 Convent Drive, Bldg 35/1A1015, MSC3707

department: Computational Biology Core

institute: National Institutue on Aging, NIH

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

summary:
A fundamental challenge in the post-genome era is to understand and annotate the consequences of genetic variation, particularly within the context of human tissues. We describe a set of integrated experiments designed to investigate the effects of common genetic variability on DNA methylation, mRNA expression and microRNA (miRNA) expression in four distinct human brain regions. We show that brain tissues may be readily distinguished based on methylation status or expression profile. We find an abundance of genetic cis regulation mRNA expression and show for the first time abundant quantitative trait loci for DNA CpG methylation. We observe that the largest magnitude effects occur across distinct brain regions. We believe these data, which we have made publicly available, will be useful in understanding the biological effects of genetic variation.

Authorized Access data:
Mapping of GEO sample accessions to dbGaP subject/sample IDs is available through dbGaP Authorized Access, see http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000249.v1.p1

overall_design: Because of our interest in genomic regulation of expression and neurological disorders we embarked upon a series of experiments to provide a brain region-specific contextual framework for genetic and epigenetic regulation of gene expression. We obtained frozen brain tissue from the cerebellum, frontal cortex, pons and temporal cortex from 150 subjects (total 600 tissue samples). We undertook four separate assays across this series; first, genome-wide SNP genotyping; second, assay of >27,000 CpG methylation sites in each of the four brain regions; third, mRNA expression profiling of >22,000 transcripts in all four brain regions; and, fourth, miRNA expression profiling of 735 miRNA transcripts. Here we discuss the results of these experiments, particularly in the context of integrated datasets to define expression and CpG methylation quantitative trait loci (eQTL and methQTL) and detailing differences and similarities across brain regions.

first: Jesse

middle: R

first: Marc

last: van der Brug

first: Dena

last: Hernandez

first: Bryan

last: Traynor

first: Michael

middle: A

last: Nalls

first: Shiao-Lin

last: Lai

first: Sampath

last: Arepalli

first: Allisa

last: Dillman

first: Ian

last: Rafferty

first: Juan

last: Troncoso

first: Robert

last: Johnson

first: H

last: Zielke

first: Luigi

last: Ferrucci

first: Dan

last: Longo

first: Mark

last: Cookson

first: Andrew

middle: B

last: Singleton