title: Genome-wide alterations in yeast strains lacking RNase H1, RNase H2, or both RNase H1 and RNase H2

status: Public on Sep 23 2015

city: Durham

first: Karen

middle: Eileen

last: O'Connell

address: Box 3054 DUMC

department: Molecular Genetics and Microbiology

institute: Duke University

summary: Two types of RNA:DNA associations can lead to genome instability: the formation of R-loops during transcription and the incorporation of ribonucleotide monophosphates (rNMPs) into DNA during replication. Both ribonuclease (RNase) H1 and RNase H2 degrade the RNA component of R-loops, whereas only RNase H2 can remove one or a few rNMPs from DNA. We performed high-resolution mapping of mitotic recombination events throughout the yeast genome in diploid strains of Saccharomyces cerevisiae lacking RNase H1 (rnh1Δ), RNase H2 (rnh201Δ), or both RNase H1 and RNase H2 (rnh1Δ rnh201Δ). We found little effect on recombination in the rnh1Δ strain, but elevated recombination in both the rnh201Δ and the double-mutant strains; levels of recombination in the double mutant were about 50% higher than in the rnh201 single-mutant strain. An rnh201Δ mutant that additionally contained a mutation that reduces rNMP incorporation by DNA polymerase ε (pol2-M644L) had a level of instability similar to that observed in the presence of wild-type Polε. This result suggests that the elevated recombination observed in the absence of only RNase H2 is primarily a consequence of R loops rather than misincorporated rNMPs.

overall_design:
The details of these experiments are in press in Genetics
This diploid S.cerevisiae strain used here is a hybrid between W303-1A and YJM789. The backgrounds are diverged by about 50,000 polymorphisms that are surveyed by custom CGH microarrays containing SNP-specific probes (St. Charles et al., 2012; Genetics 190: 1267-1284; PMID 22267500). The whole genome array surveyed loss of heterozygosity (LOH) events throughout the genome of in wild type, pol2-M644L, rnh1Δ, rnh201Δ, rnh201Δ pol2-M644L, and rnh1Δ rnh201Δ mutant backgrounds in 10, 12, 10, 19, 17, and 22 samples, respectively. The names of these strains are KO_198,KO_234, KO_73, KO_75, KO_244, and KO_5, respectively. Another assay was performed mapping reciprocal crossover events on the right arm of chromosome IV in the rnh201Δ (strains KO_135 and KO188) and the rnh1Δrnh201Δ (strain KO_132) mutant backgrounds. A reporter system with a wild type ADE2 on the end of chromosome IV allowed us to detect crossovers by seeing a red-white sectored colony. Each reciprocal event was mapped by doing a microarray specific for the right arm of chromosome IV (St. Charles and Petes, 2013; PLoS Genet. 1267-1284 PMCID PMC3616911) on the red and white sides of sectors. 21 sectors were analyzed for the rnh201Δ mutant while 14 were analyzed for the rnh1Δ rnh201Δ mutant. We mapped crossovers on the right arm of chromosome IV in the rnh201Δ mutant in four different diploid isolates: KO135_5 (1R/1W, 2R/2W, 4R/4W, 5R/5W, 12R/12W, and 13R/13W), KO_135_6 (1R/1W, 4R/4W, 5R/5W, 7R/7W, 9R/9W, 11R/11W, 13R/13W, and 17R/17W), KO 188_1 (1R/1W, and 4R/4W), and KO188_2 (6R/6W, 7R/7W, 11R/11W, and 12R/12W). We mapped crossovers on the right arm of chromosome IV in the rnh1Δ rnh201Δ mutant in two different diploid isolates: KO_132_31 (2R/2W, 6R/6W, 8R/8W, 15R/15W, 17R/17W, 21R/21W, 22R/22W, and 24R/24W) and KO_132_29 (3R/3W, 7R/7W, 18R/18W, 24R/24W, and 34R/34W).

first: Sue

last: Jinks-Robertson

first: Tom

last: Petes


title: LncRNAs expression profiling in adipose tissues and during brown adipocyte differentiation

status: Public on Feb 28 2015

city: Ann Arbor

first: xuyun

last: zhao

state: Michigan

address: 210 washtenaw ave

country: USA

institute: Life Sciences Institute

summary: Brown and beige fats generate heat via uncoupled respiration to defend against cold, mechanistically, through the action of a network of transcription factors and cofactors. Here we globally profiled long noncoding RNAs (lncRNAs) gene expression during thermogenic adipocyte formation and identified Brown fat lncRNA 1 (Blnc1) as a novel nuclear lncRNA that promotes brown and beige adipocyte differentiation and function by forming a feedforward regulatory loop with EBF2 to drive adipogenesis toward thermogenic phenotype.

overall_design: LncRNAs expression were measured in BAT and WAT from mice injected saline/CL and during brown adipocyte differentiation with two replicates using Arraystar Mouse LncRNA microarray V2.0

first: Xu-Yun

last: Zhao

first: Siming

last: Li

first: Guo-Xiao

last: Wang

first: Qi

last: Yu

first: Jiandie

middle: D

last: Lin


title: Cardiac energy dependence on glucose activates metabolic genes controlled by mTOR

status: Public on Sep 29 2014

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

summary: Mice lacking the expression of Acsl1 in the heart (Acsl1H-/-) have impaired cardiac fatty acid oxidation and develop spontaneous cardiac hypertrophy due to increased mTOR activation. To explore how the loss of ACSL1 alters gene expression, we performed a global gene expression analysis on ventricular RNA isolated from Acsl1H-/- and Acsl1flox/flox mice ten weeks after tamoxifen treatment when ACSL1 protein is completely lost and the specific activity of ACSL1 in Acsl1H-/- hearts is reduced 90%

overall_design: Two-condition experiment, cadiac gene expression of Acsl1H-/- vs Acsl1flox/flox mice 10 weeks after tamoxifen treatment. Biological replicates: 3-4 per condition.

first: Cam

last: Patterson

first: Rosalind

middle: A

last: Coleman


title: Inositol requiring enzyme 1α augments angiogenesis for diabetic wound healing

status: Public on Sep 02 2015

city: DETROIT

first: JIEMEI

last: WANG

state: MI

address: 540 E CANFIELD STREET

department: CENTER FOR MOLECULAR MEDICINE AND GENETICS

institute: WAYNE STATE UNIVERSITY

summary: The microarray analysis is to investigate the different expression profile of microRNAs in bone marrow-derived progenitor cells from type 2 diabetic mice and healthy control mice.  microRNA expression profiles were compared between bone marrow-derived progenitor cells from either type 2 diabetic db/db mice or their in-colony control litter db/+ mice.

overall_design: Total RNA was extracted from bone marrow-derived progenitor cells from either type 2 diabetic db/db mice (Jackson lab, # 000642) or their in-colony control litter db/+ mice. N=3 per group.

first: Jie-Mei


title: Chip-chip and MIRA-chip from primary skin fibroblasts, derived of matched pairs of early and late donor age

status: Public on Oct 23 2014

city: Duarte

first: Marc

last: Jung

state: CA

address: 1500 East Duarte Street

department: Biology

institute: City Of Hope

type: Methylation profiling by genome tiling array

summary:
Aging signatures developed from a longitudinal study design are dominated by reduced transcription of genes involved in protein synthesis.
Aging is a multifactorial process where the impact of singular components still remains unclear. Furthermore, previous studies were focused on measuring specific traits such as DNA -methylation and used categorical group-wise designs, unable to capture intra-individual signature changes. Here we have developed a new method for a longitudinal, age-related analysis combining the merits of a pair-wise design with the statistical power of gene set enrichment analysis. We present an integrated analysis, including transcriptional changes and genome-wide epigenetic changes in DNA- methylation, H3K4- and H3K27- histone methylation in promoter regions. We tested our method on a rare collection of paired skin fibroblast samples from male middle age to old age transitions and obtained functional, age-related clusters. By using a set of only ten individuals, we could demonstrate a high overlap of functional terms to previously established tissue-independent age signatures including extracellular matrix, apoptosis and oxidative stress. Importantly, we identify protein translation-related processes as the main cluster of age-driven, specific down regulation.

overall_design: H3K4me3, H3K27me3 and DNA- methylation longitudinal aging profiles from primary skin fibroblasts from matched pairs of early (E) and late (L) stages in life.

first: Xiaoying

last: Zhang

first: Seung-Gi

last: Jun

first: Grigory

last: Gogoshin

first: Andrei

last: Rodin

first: Gerd

last: Pfeifer


title: Retinal Gene and Protein Expression Associated with CNTF-Induced Deconstruction of Photoreceptor Outer Segments in normal and CNGB3-achromatopsia dogs

status: Public on Dec 31 2014

city: Philadelphia

first: Sem

last: Genini

state: PA

address: 3900 Delancey Street

department: Clinical Studies

institute: University of Pennsylvania

summary:
Background: Intravitreal injection of CNTF leads to deconstruction and regeneration of photoreceptor outer segments in normal dogs, and improves the success rate of viral CNGB3 gene replacement therapy in dogs (> 1 year) with CNGB3-achromatopsia. Objectives: The goal of this study was to examine the changes caused by intravitreal CNTF injection to the retinal gene expression profiles and the retinal function of normal and CNGB3-achromatopsia affected dogs.
Retinal gene expression profiles were evaluated with canine specific Agilent Oligo Microarray containing 42,034 60-mer oligonucleotide probes.  Expression of eleven selected genes (BCL2, CCL2, STAT3, TNFRSF1A, ARR3, RHO, TYROBP, COL1A1, C3, CNGA1, and CNGB3) was quantified in the same RNA samples by quantitative real-time PCR. The results confirmed the differential expression levels observed with the microarray analysis.

overall_design: Five CNGB3-mutant dogs (age: ca. 11 months; carrying the D262N missense mutation CNGB3m/m) and 5 control dogs (age: ca. 11 months; homozygous CNGB3+/+; heterozygous CNGB3+/m) were injected with either 12 µg of intravitreal CNTF (right eye: OD) or PBS (left eye: OS, used as control).

first: Jessica

last: Rowlan

first: Meredith

last: Frie

first: Joshua

last: Laske

first: Simone

last: Iwabe

first: Shilpa

last: Rao

first: Alison

last: Duncan

first: Ingeborg

last: Langohr

first: Christine

last: Harman

first: Annie

last: Oh

first: Rong

last: Wen

first: Gustavo

last: Aguirre

first: András

middle: M

last: Komáromy


title: Transcriptome analysis of the ron3 mutant

status: Public on Oct 01 2014

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Determine the molecular processes affected by the ron3 mutation

overall_design: 4 hybridizations that each compare ron3- with the control Ler-genotypes; 2 dye swaps with biological replicates

first: Annemie

last: Van Minnebruggen

first: Pia

last: Neyt

first: Steven

last: De Groeve

first: Riet

last: De Rijcke

first: Maria

middle: R

last: Ponce

first: Jose

middle: L

last: Micol

first: Mieke

last: Van Lijsebettens


title: SIRT1 affects DNA methylation of polycomb group protein target genes (PCGTs), a hotspot of the epigenetic shift observed in ageing

status: Public on Mar 31 2014

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

summary: Beneficial effects of SIRT1 on healthspan are likely to be pleiotropic and may include effects on DNA methylation. We demonstrated recently that manipulating SIRT1 in human cells affected DNA methylation of a panel of test genes, and that genes with expression modified by dietary restriction corresponded with genes that underwent changes in DNA methylation during ageing. Here we tested the hypothesis that genes particularly susceptible to SIRT1-induced effects on DNA methylation across the genome map to genes for which DNA methylation changes during ageing. We increased or reduced SIRT1 expression in human intestinal (Caco-2) and vascular endothelial (HuVEC) cells by transient transfection with an expression construct or with siRNA, respectively. Effects on DNA methylation were measured by enriching for the methylated fraction then either sequencing (HuVEC) or hybridising to a human promoter microarray (Caco-2). Effects using these two different cell lines and techniques for analysis were remarkably consistent. Genes with a DNA methylation status affected by SIRT1 manipulation were enriched for those that undergo age-dependent changes in DNA methylation, thus supporting our hypothesis. Polycomb group protein target genes (PCGTs), which are suppressed by epigenetic mechanisms in stem cells and have been shown previously to correspond with loci particularly susceptible to age-related changes in DNA methylation, were over-represented within the set of genes showing altered DNA methylation in response to SIRT1 manipulation in both cell lines. We thus propose that effects of SIRT1 to extend healthspan include influences on the DNA methylation status of genes affected during ageing, in particular PCGTs.

overall_design: Analysis of methylation profiles of Caco-2 cells meeting the following conditions: SIRT1 overexpressed by transfection with pCMV6-ENTRY-SIRT1 (2 replicates), corresponding vector control (2 replicates), each of the siRNAs that target SIRT1 (1 & 2 replicates, respectively) and control siRNA (2 replicates).

first: Luisa

last: Wakeling

first: Laura

middle: J

last: Ions

first: Gail

last: Jenkins

first: Linda

last: Wainwright

first: Jill

last: McKay

first: Dianne

last: Ford


title: Human Pegivirus detected in a patient with severe encephalititis using a metagenomic pan-virus array

status: Public on Mar 19 2015

city: Livermore

first: Kevin

last: McLoughlin

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

summary: We used a metagenomic microarray to detect Human Pegivirus in serum and cerebrospinal fluid from a patient suffering from severe encephalitis.

overall_design: 2 clinical samples were analyzed for presence of virus using the MDA microarray.

first: Helena

last: Fridholm

first: Line

middle: O

last: Sørensen

first: Maiken

middle: W

last: Rosenstierne

first: Henrik

last: Nielsen

first: Finn

middle: T

last: Sellebjerg

first: Åse

middle: B

last: Andersen

middle: S

first: Anders

last: Fomsgaard


title: Expression profiling of long noncoding RNAs in mouse liver tissue

status: Public on May 01 2014

city: Beijing

first: Qinghua

last: Cui

address: 38 Xueyuan Road

country: China

institute: Peking University

summary: Long noncoding RNA profile in the liver after ischemia-reperfusion injury (IRI).

overall_design: In the study presented here, we mixed the three mouse livers after IRI and identified the genome-wide expression level of lncRNAs.

first: Cui

last: Qinghua

first: Yang

last: Jichun


title: Integrative epigenomic analysis of differential DNA methylation in bladder cancer

status: Public on May 28 2015

city: Lund

first: Mattias

last: Aine

address: Klinikgatan 28

department: Oncology

country: Sweden

institute: Lund University

summary:
Background
Urothelial carcinoma of the bladder (UC) is a common malignancy. Although extensive transcriptome analysis has provided insights into the gene expression patterns of this tumor type, the mechanistic underpinnings of differential methylation remain poorly understood. Multi-level genomic data may be used to profile the regulatory potential and landscape of differential methylation in cancer and gain understanding of the processes underlying epigenetic and phenotypic characteristics of tumors.

Methods
We perform genome-wide DNA methylation profiling of 98 gene-expression subtyped tumors to identify between-tumor differentially methylated regions (DMRs). We integrate multi-level publically available genomic data generated by the ENCODE consortium to characterize the regulatory potential of UC DMRs.

Results
We identify 5,453 between-tumor DMRs and derive four DNA methylation subgroups of UC with distinct associations to clinicopathological features and gene expression subtypes. We characterize three distinct patterns of differential methylation and use ENCODE data to show that tumor subgroup-defining DMRs display differential chromatin state, and regulatory factor binding preferences. Finally, we characterize an epigenetic switch involving the HOXA-genes with associations to tumor differentiation states and patient prognosis.

Conclusions
Genome-wide DMR methylation patterns are reflected in the gene expression subtypes of UC. UC DMRs display three distinct methylation patterns, each associated with intrinsic features of the genome and differential regulatory factor binding preferences. Epigenetic inactivation of HOX-genes correlates with tumor differentiation states and may present an actionable epigenetic alteration in UC.

overall_design: MeDIP hybridizations on 98 human urothelial carcinoma samples and 4 normal urothelium samples on Nimblegen 3x720K RefSeq Promoter and CGI aCGH arrays.

first: Pontus

last: Eriksson

first: Gottfrid

last: Sjödahl

last: Höglund


title: MeDIP-Chip of PrEC, LnCAP, and PC3 cells treated with vehicle control, sulforaphane, or 3,3’-diindolylmethane

status: Public on Jan 01 2014

city: Corvallis

first: Carmen

last: Wong

state: OR

address: 103 Milam Hall

department: Biological and Population Health Sciences

institute: Oregon State University

summary:
Effects of sulforaphane and 3,3’-diindolylmethane on genome-wide promoter methylation in normal prostate epithelial cells and prostate cancer cells
This study was undertaken to determine the genome-wide effects of sulforaphane (SFN) and 3,3’-diindolylmethane (DIM) on promoter methylation in normal prostate epithelial cells and prostate cancer cells.  Nimblegen Human DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Array was used in this study. We hypothesize that both SFN and DIM are effective dietary modulators of DNA methylation due to their inhibitory effects on DNMT expression, and that SFN and DIM can differentially affect the promoter methylation profiles in normal and cancerous prostate epithelial cells.

overall_design: Normal prostate epithelial cells (PrEC), androgen-dependent prostate cancer epithelial cells (LnCAP) and androgen-independent prostate cancer epithelial cells (PC3) were treated with vehicle control, 15uM SFN, or 15uM DIM for 48h in triplicates

first: Emily

last: Ho


title: Long non-coding RNAs and mRNAs profiles in mouse liver development

status: Public on May 20 2014

city: shanghai

first: shu-han

last: sun

address: 800 Xiang-Yin Road

institute: Second Military Medical University

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

summary: Many protein-coding oncofetal genes are highly expressed in murine and human fetal liver and silenced in adult liver. The protein products of these hepatic oncofetal genes have been used as clinical markers for the recurrence of hepatocellular carcinoma (HCC) and as therapeutic targets for HCC. Herein, we examined the expression profiles of long non-coding RNAs (lncRNAs) and mRNAs found in fetal and adult liver in mice.LncRNA-mPvt1 is an oncofetal RNA that was found to promote cell proliferation, cell cycling and the expression of stem cell-like properties of murine cells. Human lncRNA-hPVT1 promotes cell proliferation, cell cycling and the acquisition of stem cell-like properties in HCC cells by stabilizing NOP2 protein. Regulation of the lncRNA-hPVT1/NOP2 pathway may have beneficial effects in the treatment of HCC.

overall_design: We collected mouse fetal livers (E12.5, E14.5, E17.5 days), neonatal murine livers and adult murine livers (8 weeks). The total RNAs recovered from these developmental livers and were used to acquire different expression profiles of mRNAs and lncRNAs.

first: Fang

last: Wang

first: Shu-han

last: Sun


title: Schizosaccharomyces pombe splicing microarray

status: Public on Jul 13 2015

city: San Francisco

first: Jesse

last: Lipp

address: 600 16th Street

institute: UCSF

summary: Analysis of splicing defects in Schizosaccharomyces pombe upon chemical genetic inhibition of splicing kinases dsk1, lkh1, and prp4, as well as alanine-mutation of phosphorylated residues in the splicing factors bpb1, prp2, rsd1, srp1, srp2, usp101, usp103, sum3, prp22, cdc5, and cwf22. This study shows the splicing kinase dsk1 modulates splicing efficiency of introns with non-consensus splice sites, likely through phosphorylation of bpb1.  Modulation of splicing efficiency of transcripts through kinase signaling pathways may afford the necessary flexibility to tune the gene expression profile in response to environmental and developmental cues.

overall_design: Experiments were conducted as direct two-color designs with 2-3 biological replicates per genotype pairing. Raw microarray data was normalized with loess normalization using the R package limma. Log2-fold changes (perturbation over reference) are reported. Each splicing event on the custom-designed splicing microarray was monitored with an exon probe reading out mRNA changes, an intron probe for unspliced pre-mRNA, and a splice junction probe spanning the junction between two spliced exons. For the analysis of the splicing efficiency for a given intron, a score was calculated as exon*intron/junction.

first: Michael

last: Marvin

first: Kevan

last: Shokat

first: Christine

last: Guthrie


title: Gene expression in plep-1 mutant young adult hermaphrodites

status: Public on Apr 29 2015

city: New York

first: Luke

middle: Mackley

last: Noble

state: NY

address: 12 Waverly Place

institute: New York University

summary: a plep-1 mutant (MosI insertion line) was compared to the reference strain N2

overall_design: N2 and plep-1 samples were competitively hybridised against a pooled reference sample, with 3 biological and 4 technical replicates each

first: Matthew

middle: V

last: Rockman


title: Expression profiling of response to first-line aromatase inhibitor therapy

status: Public on Dec 05 2013

city: Amsterdam

first: Paul

last: Roepman

address: Science Park 406

country: Netherlands

institute: Agendia

summary: Fresh-frozen primary cancer specimens of 107 breast cancer patients whose metastases were treated with first-line aromatase inhibitors were evaluated for their whole genome mRNA expression profiles.

overall_design: Primary breast tumors (107) were analyzed against a common breast cancer reference pool (BRP).


title: Analysis of antibody production in a mouse model of Sjögren’s Syndrome

status: Public on Oct 17 2014

city: Dallas

first: yun

last: lian

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Auto-antigen array data show IgM from salivary B cells is enriched for anti-nuclear antigen specificity, including Ro (SSA) and La (SSB).

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: B cells were sort purified from spleen, cervical lymph nodes and submandibular salivary tissue (SMG) tissue of Id3-/- mice.  We also sort purified B cells from spleen and cervical lymph nodes of age and gender matched  C57BL/6 mice.  Cells (1x10^5 /well) were cultured in 5% RPMI 1640, stimulated with LPS (25 μg/mL) for 6 days, and supernatants harvested.  Sera from SS mice were harvested by cardiac puncture immediately following euthanasia.  Blood was allowed to clot for two hours and centrifuged at 2,000 g for twenty minutes.  Serum was removed and stored at -20°C until use. These undiluted supernatant samples and sera were used to perform the autoantigen array.

first: Jill

last: Kramer

first: Nichol

middle: E

last: Holodick

first: Teresa

last: Vizconde

first: Indu

last: Raman

first: Mei

last: Yan

first: Quan-Zhen

last: Li

first: Daniel

middle: P

last: Gaile

first: Thomas

last: Rothstein


title: Radiation Effects on a 3-Dimensional Model of Oral Mucositis

status: Public on Oct 16 2014

city: Pomona

first: Maria

last: Lambros

address: 309 E Second Street

department: Pharmaceutical Sciences

institute: Western Univ of Health Sci

summary: We studied the radiation effect on cell culture model of oral mucositis. The musositis model  (tissues) used is an organotypic model which consisted of 3 dimensional (3-D) cell cultures of primary human oral keratinocytes  grown on top of primary oral fibroblasts and resembles oral mucosal (tissues).  The tissues were purchased from MatTek corporation (Ashland, MA) and were grown on top of microporous membrane and supplemented with MatTek serum free media.  These tissues were irradiated with 12 and 2 Gy. Six hours after the irradiation the tissues were cut in half. Half of the tissue was used to extract total RNA (RNeasy Plus Mini kit, Qiagen, Germantown, MD) and the other half was used to evaluate the histology and the apoptosis. We had the following groups: Non-Irradiated Tissue, Irradiated Tissue with 12 Gy and Irradiated Tissues with 2 Gy.

overall_design: Human Prirmary 3-D Cultures of Human Keratinocytes grown on top of Human Fibroblasts were irradiated with 12 or 2 Gy and the effect of the radiation was studied 6 hours after the irradiation using histology, apoptosis assays and gene expression microarrays. There are 3 samples the control (non irradiated) is NTNI.  Each sample was done in triplicate.

first: Hari

last: Reddy

first: Lavanya

last: Kondapali

middle: K

last: DeSalvo


title: High resolution Hi-C analysis in S. pombe reveals fundamental elements of genome architecture [Expression Array]

status: Public on Oct 22 2014

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

type: Expression profiling by genome tiling array

summary: Eukaryotic genomes are folded into three-dimensional structures that govern diverse hromosomal procsses.  Studeis in Drosophila and mammals have revealed large self-associating tomological domains whose borders are enriched in cohesin/CTCF factors that are required for long-range intrations.  However, mechanisms governing higher-order folding of chromatin fivbers and the exact function of cohesin in this process remain poor understood.  Here we perform Hi-C to explore the organization of the Schizosaccharomyces pombe genome at high-resolution, which despite its small size comprises fundamental features found in higher eukaryotes.  Our analyses reveal that in addition to determinants of Rabl-like chromosome architecture, smaller locally interacting regions of chromatin, referred to as globules, are a distinctive features of S. pombe chromosome organization.  This feature of chromatin architecture requires a function of cohesin distinct from its role in sister chromatid cohesion.  Cohesin is enriched at globule boundaries and its loss causes disruption of local globule structure and global chromosome territories.   Heterochromatin, which selectively loads cohesin at specific loci including pericentromric and subtelomeric domains, is dispensable for globule formation but uniquely impacts genome organization through chromatin compaction by enforcing Rabl configuration.

overall_design: Agilent 60mer oligonucleotide custom array containing probes spanning large portion of chromosome 2 at 50bp resolution was used to profile expression levels in mutant cells and to compare them to levels in wild type cells.

first: Takeshi

last: Mizuguchi

first: Sameet

last: Mehta

first: Nitika

last: Taneja

first: Hernan

middle: D

last: Folco

first: Jemima

last: Barrowman

middle: I


title: miRNA expression atlas in male rat

status: Public on Nov 27 2013

city: TSUKUBA CITY

first: Keiichi

last: Minami

state: IBARAKI

address: 17-2 WADAI

department: Tsukuba Research Institute

country: Japan

institute: Ono pharmaceutical

summary: MicroRNAs (miRNAs) are small (~22 nucleotide) noncoding RNAs that play pivotal roles in regulation of gene expression. The value of miRNAs as circulating biomarkers is now broadly recognized; such tissue-specific biomarkers can be used to monitor tissue injury and several pathophysiological conditions in organs. In addition, miRNA profiles of normal organs and tissues are important for obtaining a better understanding of the source of modulated miRNAs in blood and how those modulations reflect various physiological and toxicological conditions. This work was aimed at creating an miRNA atlas in rats, as part of a collaborative effort with the Toxicogenomics Informatics Project in Japan (TGP2). We analyzed genome-wide miRNA profiles of 55 different organs and tissues obtained from normal male rats using miRNA arrays. The work presented herein represents a comprehensive dataset derived from normal samples profiled in a single study. Here we present the whole dataset with miRNA profiles of multiple organs, as well as precise information on experimental procedures and organ-specific miRNAs identified in this dataset.

overall_design: miRNA expression in rat various organs was measured with or without saline perfusion.  3 animals were used.

first: Takeki

last: Uehara


title: Expression profiling of long noncoding RNAs and mRNAs in mouse heart, whole blood (WB), and plasma.

status: Public on Nov 12 2013

first: Qinghua

last: Cui

summary: Long noncoding RNA profile in the heart, whole blood, and plasma before and heart failure (HF).

overall_design: In the study presented here, we mixed the five pairs of mouse hearts, whole blood, and plasma before and after HF and identified the genome-wide expression level of lncRNAs.

first: Cui

last: Qinghua

first: Geng

last: Bin


title: Cryptococcus neoformans gene expression in minimal media of wild type, ALL2 mutant, and ALL1ALL2 mutant cells

status: Public on Dec 09 2015

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

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

overall_design: Refer to individual Series


title: Effect of cardiomyocyte KLF5 deletion in cardiac gene expression profile

status: Public on Dec 05 2014

first: Konstantinos

last: Drosatos

address: 3500 N. Broad st

department: Pharmacology

institute: Temple University

summary: Kruppel-like factor 5 gene was deleted (Cre-lox) system specifically in cardiomyocytes (aMHC-promoter-driven expression of Cre) and RNA was purified from total hearts (TRIZOL method) following perfusion of the heart with PBS. Basal levels cardiac RNA was analyzed with whole genome microarray chips.

overall_design: There were two groups of mice: 4 mice that had KLF5 gene floxed without expressing Cre recombinase (control group) and 4 mice that were expressing Cre in cardiomyocytes and therefore KLF5 gene was deleted and thus not expressed in this particular cell type.


title: The Severe Pathogenicity of Infected Ferrets Depleted of Alveolar Macrophages with 2009 Pandemic H1N1 Influenza Virus

status: Public on Jan 29 2013

city: Deajeon

first: Heui Man

last: Kim

state: Deajeon

address: 99 Daehak ro

department: College of Veterinary Medicine

country: South Korea

institute: Chungnam national university

summary:
The infected ferrets depleted of alveolar macrophages showed up-regulation of inflammatory related genes compared to the infected ferrets which has alveolar macrophage.
There are three group of ferret. One is the infected ferrets depleted of alveolar macrophages. Another is the infected ferret non-depleted of alveolar macrophages. The other is mock

overall_design: This is the data of ferrets infected with influenza virus. After challenge influenza virus to animals, I collected total RNA from lung of ferret to compare their gene expression level which is related with inflammation. Control is the uninfected mock ferret. CL is the ferret which is treated with some medicine and challenged with influenza virus. PBS is the ferret untreated and challenged with influenza virus. In this study I just want to compare gene expression level of control, CL and PBS. These are all RNA of ferrets.

first: Sang

middle: H

last: Seo

first: Heui

first: Young

last: Kang


title: Long non-coding RNAs and microRNAs involved in integrated co-regulation of neuronal maturation [mRNA and lncRNA expression]

status: Public on Oct 24 2014

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

summary: Neurogenesis is a pro-survival process that comprises of dendritic and axonal growth, synaptogenesis, synaptic and neuronal pruning. These complex processes are determined by temporal gene expression during development, which is in turn tightly regulated by long non-coding RNAs and microRNAs. In this study, we investigated the processes implicated in the maturation of primary neuronal cultures based on RNA expression profiling. Correlation between neuron specific gene ontologies of mRNA and non-coding RNAs identified direct regulation of axonogenesis and dendritogenesis. Temporally regulated mRNA and their associated long non-coding RNAs were significantly overrepresented in proliferation and differentiation associated signalling, cell adhesion molecules and neurotrophin signalling pathways during neuronal maturation. Long non-coding RNAs associated with Axin2, Cntn1, Ncam1, Negr1, Ntrk2, Nrxn1 and Sh2b3 displayed an inverse expression profile to their mRNA whereas long non-coding RNA -mRNA pairs for Kit, Prkcb and Ralgds displayed similar expression profiles. These genes were also predicted targets of the altered miRNAs, miR-124, -128, -129-5p, -203, -218, -290-5p, -326, -329, -377 and -495. These microRNAs particularly regulate the cell adhesion molecules, Cntn1, Ncam1, Negr1 and Nrxn1 that determine axonogenesis and dendritogenesis, supporting the observed co-regulation of these biological processes by non-coding RNAs. Verification of expression of these long non-coding RNA-mRNA pairs in an in vitro model of ischemic-reperfusion injury showed an inverse expression profile, thus confirming their role(s) in maintenance of the neuronal structure and function. This neuronal transcriptome (mRNAs, lncRNAs, miRNAs) is in turn orchestrated by C/EBPα/β transcription factors and CTCF, thereby governing intricate control of neuronal development.

overall_design: mRNA and long non-coding RNA expression profiling of maturing primary cortical neurons from E15 mouse embryos and neurons subjected to oxygen-glucose deprivation. Maturing neurons were harvested on Days 2, 4, 6 and 8. Neurons on Day 6 were subjected to oxygen-glucose deprivation for different time periods and 24 hours reperfusion before being harvested.

first: K

first: A

last: Armugam

first: S

last: Sepramaniam

first: P

last: Kaur


title: Developmentally regulated lncRNAs expression in male germline

status: Public on Jun 30 2013

city: Reno

first: Nicole

last: Ortogero

state: Nevada

address: 1664 N. Virginia St

department: Physiology and Cell Biology

institute: University of Nevada, Reno

summary: To decipher the roles of non-coding RNAs during male germline development, we use the lncRNAs microarray to profile the genome-wide lncRNAs expression pattern in the male germline

overall_design: Testes samples from 6 time points were collected for lncRNAs and mRNAs microarray profiling

first: Jianqiang

last: Bao

first: Wei

last: Yan


title: The transcriptomic profile of peripheral blood nuclear cells in dogs with heart failure

status: Public on Jul 20 2013

city: Warsaw

first: Magdalena

last: Łój

address: Nowoursynowska 166

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

summary: The aim of the study was to identify genes which are differentially expressed in the blood of dogs suffering from heart failure (HF) in comparison to healthy control dogs. The dogs with HF were categorized according to the ISACHC classification system (International Small Animal Cardiac Health Council).

overall_design: RNA from healthy dogs and dogs with different stages of heart failure were hybridized to Agilent two color microarrays with a common reference.

last: Loj

last: Garncarz

first: Marta

last: Jaworska

first: Alicja

last: Majewska

first: Michał

last: Jank


title: Evaluation of quantitative miRNA gene expression platforms - custom microRNA GeneChip

status: Public on Aug 09 2013

city: Basel

first: Lukas

last: Baeriswyl

address: Fabrikstrasse 10

department: Human Genetics and Genomics

country: Switzerland

institute: Novartis Pharma AG

summary: MicroRNA microarray expression dataset used to develop novel and robust quality metrics to objectively assess platform performance of very different technologies.

overall_design: The HsMir v1s520779F custom array is primarly based on the commercially available Affymetrix microRNA microarray version 2.0 (Affymetrix GeneChip miRNA 2.0 Array datasheet P/N EXP00180 Rev 1) with i) microRNA probe sequences updated using miRBase version 17 ii) all human pre-microRNAs removed iii) all non-human sequences removed iv) all viral target sequences removed. In summary, the array contains 1738 mature microRNAs and 2333 other small RNAs (such as small nucleolar RNAs or small cajal body-specific RNAs) probe sequences plus the Affymetrix hybridization and normalization control probesets.

last: Hartmann


title: H3N2 canine influenza virus causes severe clinical signs in dogs with induction of genes related to inflammation and apoptosis

status: Public on Feb 22 2013

first: Heui Man

last: Kim

summary: We demonstrated canine influenza virus (H3N2) pathogenicity to dogs using microarray analysis. Many genes related to innate immunity, such as toll-like receptors, immune cells of natural killer cells, macrophages, neutrophils, nitric oxide and reactive oxygen species, and interferon, were induced.

overall_design: RNA was extracted from canine influenza virus H3N2-infected dogs. The lung RNA of uninfected dogs was used as a negative control. We compared gene expression levels between infected and uninfected dogs using microarray analysis.

last: Seo

middle: M


title: Acid Stress Increases Gene Expression of  Proinflammatory Cytokines in Madin Darby Canine Kidney Cells

status: Public on Mar 28 2012

city: Los Angeles

first: Thomas

middle: Thong

last: Nguyen

address: 11301 Wilshire Blvd

institute: Sachs Lab

summary: Metabolic acidosis exacerbates chronic kidney disease, in part, by stimulating renal endothelin production. To determine if acidosis alters expression of other genes, we examined the effect of exposure of MDCK cells to pH 7.4 and pH 7.0 for 24 hours on gene expression using a canine derived microarray.  Exposure to this pH stress for 24 hours led to increased expression of 278 genes (2.2% of the transcriptome) by at least two fold and 60 of these (21%) were upregulated by more than 3 fold. On the other hand, 186 genes (1.5% of the transcriptome) were down regulated by at least two fold and 16 of these (9%) were down regulated by 3 fold or more.  Ten percent of the genes upregulated by at least three fold encode proteins that are  pro-inflammatory cytokines, including colony stimulating factor 2, chemokine ligand 7, chemokine ligand 2 0, chemokine ligand 8, and interleukin 1α. Two others encode metallopeptidase . The most highly upregulated gene encodes a protein, lubricin, shown to be important in preventing cartilage damage and in tissue injury or repair.Upregulation of four genes were confirmed by qPCR. Housekeeping genes were not increased.

overall_design: There were a total of three biological replicates, each containing one control (incubated at pH 7.4) and one acidic (pH 7.0) sample, whose RNA were extracted on different dates. Microarray studies performed on these six samples were done in duplicate.

first: Suraja

last: Raj

first: David

last: Scott

first: George

last: Sachs

first: Jeffrey

middle: A

last: Kraut


title: A 13-gene signature predicting rapid development of brain metastases in breast cancer

status: Public on Jul 01 2012

city: Indianapolis

first: Sunil

last: Badve

state: IN

address: 350 West 11th street

department: Pathology

institute: Indiana University

summary:
Brain metastases from breast and other cancers constitute an important part of therapeutic failures and are associated with severe morbidity and mortality. Here, we have examined histopathological data and generated gene expression data in two independent cohorts of primary tumors from HER2-positive advanced breast cancer patients. We report that the combination of estrogen receptor (ER) negativity and expression of a novel 13-gene signature identify a subset of patients with rapid (median, 31 and 41 months in discovery and validation cohorts, respectively) versus slower (median, 66 months and 77 months in discovery and validation cohorts, respectively) development of brain metastases (P<0.0001). The 13-gene signature also predicted rapid brain metastasis formation within the ER-negative subset of patients (P=0.014). Interestingly, three of the genes in the signature (RAD51, BARD1, FANCG) function in DNA double strand break repair. Overexpression of RAD51 in immortal MCF-10A breast epithelial cells altered their three-dimensional acinar morphology to increase the percentage of invasive structures by 6.5 fold, in the presence or absence of HER2 overexpression. In summary, ER negativity and a novel 13-gene signature may have the potential to identify subpopulations at highest immediate risk for the development of brain metastases in HER2-positive advanced breast cancer. Our results also suggest that RAD51, found in the 13-gene signature, may promote aggressiveness in breast epithelial cells. These data may be useful in the design of brain metastasis preventive trials and may prompt new treatment strategies
Median normalized data provided

overall_design: Using Illumina DASL Cancer gene panel we analyzed gene expression of 502 oncogenes in 87 breast cancer patients. The data was divided into a training (n=62) and an internal validation set (n=25). Clincal parameters were noted for each patient. The data was analyzed in order to determine whether the 13-gene signature is associated with the brain metastasis-free survival (BMFS) when it was simply classified as being lower or higher than the median.

first: Renata

last: Duchnowska

first: Jacek

last: Jassem

first: Patricia

last: Steeg

first: Chirayu

last: Goswami


title: Transcript Profiling of Spinal Dorsal Horn in Response to Electroacupuncture on Rats at 24h

status: Public on May 31 2010

city: Shanghai

first: ke

last: wang

address: 151 Libing Road

institute: Shanghai Biochip Co., Ltd.

summary:
The electroacupuncture-induced analgesic effect has been used widely to alleviate diverse pains. However, significant individual variations in analgesic effect of EA for both experiments and clinics were reported. According to the sensitivity of the analgesic response to EA stimulation, the subjects could be categorized into high responders (HR) and low responders (LR). However, the molecular mechanism of individual variability in the analgesic response to acupuncture stimulation is still uncertain. This study aims to investigate the potential gene expression in spinal dorsal horn induced by 2Hz/100Hz electroacupuncture in HR and LR rats. Rats were given 2Hz or 100Hz electroacupuncture for 30 min and using cDNA microarrays to compare different gene expression in dorsal horn after 2Hz/100Hz electoacupunture stimulation. Transcriptome profiling analysis found that different regulation of gene expression after 2Hz/100Hz electroacupuncture in HR and LR rats at 24 hr time point.

Keywords: Transcriptome analysis

overall_design: Rats were exposed to different frequencies (2Hz or 100Hz) electroacupuncture stimlation for 30 min and nociceptive testing and returned to home cages for 24 hours before sacrificed. According to the sensitivity of the analgesic response to 2Hz or 100Hz EA stimulation, the rats divided into four groups: 2Hz-HR group, 2Hz-LR group, 100Hz-HR group and 100Hz-LR group. Subsequently analyzed their dorsal horn transcript profile using cDNA microarrays, the rats were without receiving electroacupuncture as control. The tissue of dorsal horn (DH) of the fifth and sixth lumbar (L5 and L6) of four or five rats were selected for transcript analysis in each group. The five control rats were mixed and labeled with cy5, each rat of experiment groups was labeled with cy3.

first: Ke

last: Wang

first: Fei

last: He

first: Libo

last: Lin

first: Qinghua

last: Zhang


title: Transcript Profiling of Spinal Dorsal Horn in Response to Electroacupuncture on Rats at two time points

status: Public on May 11 2010


title: Transcript Profiling of Spinal Dorsal Horn in Response to Electroacupuncture on Rats at 1h

status: Public on Apr 11 2010

summary:
The electroacupuncture-induced analgesic effect has been used widely to alleviate diverse pains. However, significant individual variations in analgesic effect of EA for both experiments and clinics were reported. According to the sensitivity of the analgesic response to EA stimulation, the subjects could be categorized into high responders (HR) and low responders (LR). However, the molecular mechanism of individual variability in the analgesic response to acupuncture stimulation is still uncertain. This study aims to investigate the potential gene expression in spinal dorsal horn induced by 2Hz/100Hz electroacupuncture in HR and LR rats. Rats were given 2Hz or 100Hz electroacupuncture for 30 min and using cDNA microarrays to compare different gene expression in dorsal horn. Transcriptome profiling analysis found that some co-regulated genes related with electroacupuncture or 2Hz or 100Hz freqencies. These co-regulated genes were plasticity-related by GO analysis. We also found some special regulated genes in HR vs. LR in 2Hz/100Hz electroacupuncture stimulation. These results suggested that neurotransmitter system and cytokine different between HR with LR in 2Hz electroacupuncture. But in 100Hz electroacupunture, there were many different regulated genes related with ribosome between HR with LR, which needs more studies to research the function and may play an important role in HR vs. LR by 100Hz electroacupuncture.

Keywords: Transcriptome analysis

overall_design: Rats were exposed to different frequencies (2Hz or 100Hz) electroacupuncture stimlation for 30 min and nociceptive testing and returned to home cages for 1 hours before sacrificed. According to the sensitivity of the analgesic response to 2Hz or 100Hz EA stimulation, the rats divided into four groups: 2Hz-HR group, 2Hz-LR group, 100Hz-HR group and 100Hz-LR group. Subsequently analyzed their dorsal horn transcript profile using cDNA microarrays, the rats were without receiving electroacupuncture as control. The tissue of dorsal horn (DH) of the fifth and sixth lumbar (L5 and L6) of four or five rats were selected for transcript analysis in each group. The five control rats were mixed and labeled with cy5, each rat of experiment groups was labeled with cy3.


title: Gene expression analysis of whole blood samples from patients with single and double primary tumors and healthy controls

status: Public on May 24 2008

city: Athens

middle: Panayiotis

last: Stathopoulos

state: Attiki

address: Souidias 55

department: Oncology Department

country: Greece

institute: Errikos Dunant hospital

summary:
RNA samples from the blood of patients with double tumors, single tumors and from healthy  control subjects are studied by gene expression analysis using the whole genome microarray  platform AB1700 from Applied Biosystems.  Gene expression profiles are derived from the microarray raw data by biostatistical analysis.  Differential gene expression between the study subgroups and categories is assessed:  On the one hand, all possible pairwise comparisons between the subgroups A, B, C, D, E  and N are made in order to elucidate characteristics of the individual subgroups. On the other hand, the higher-ranked categories “double cancer” (AB, consisting of subgroups A and B) and “single cancer” (category CDE, consisting of subgroups C, D and E) are compared to each other and to the normal controls (N). Finally, the category “double cancer” is compared to the different single cancer subgroups (C, D and E). Analysis on the level of the higher ranked categories “double cancer” and “single cancer” aims at identifying the common traits of patients who have developed two independent tumors, as opposed to patients with only one tumor entity and to healthy individuals.  Based on the functional annotation of the induced and repressed genes found in these comparisons, biological processes and pathways which are differentially activated in the subgroups or categories are identified, thus providing insights into their molecular characteristics.  Furthermore, gene expression data are used to derive classifier rules, which are aimed at discriminating subjects from the different subgroups and categories and may constitute the basis for a future diagnostic classification tool.

Keywords: microarray analysis, double-single primary malignancies

overall_design:
A total of 66 individuals were analyzed:The primary study group consisted of 24 patients with two primary malignancies (group AB)  (one of the primaries being of the breast, colon or ovary). The four control groups consisted of a total of 33 single cancer patiens: 10 with colon cancer (group C), 14 with breast cancer (group D), 9 with ovarian cancer (group E_) and 10 healthy individuals (group N).
4 samples (GECM-061_14, GECM-061_37, GECM-061_54 and GECM-061_72) were identifed as outliers by MA plots and therfore they were excluded from the study.

first: Athanasios

last: Armakolas


title: Real-time quantitative PCR analysis of BMI1-silenced human prostate cancer cells

status: Public on Feb 05 2013

city: AUSTIN

first: MOHAMMAD

middle: SALEEM

last: BHAT

state: MN

address: 801, 16th AVE NE

institute: UNIVERSITY OF MINNESOTA

summary:
BMI1-silenced Prostate cancer cells exhibited a significant change in the expression of several proliferation-associated genes. These included Cyclin-D1, BCL2, IL and NF-kappaB. An increased expression of p16, p15 and TIMP3 in BMI1-silenced tumor cells was observed
List of Selected Genes Modulated by BMI1-supression in Prostate cancer Cells

overall_design: qPCR gene expression profiling.  LNCaP and BMI1-silenced LNCaP cells were used as indicated in the summary. Equal amount of total RNA from each group was pooled prior to gene expression analysis.

first: Hifzur

middle: R

last: Siddique

first: Aijaz

last: Parray

first: Mohammad

last: Saleem


title: Expression data from human donor lung biopsies

status: Public on Jun 06 2007

first: Monika

last: Ray

address: 1 Brookings Deive P O Box 1045

institute: Washington University in St. Louis

summary:
Expression profile of human donor lungs that have developed primary graft dysfunction (PGD) after lung transplantation and those that have not.
In this study, we attempt to further our understanding of PGD by observing the changes in gene expression across donor lungs that developed PGD versus those that did not.
Keywords: stress response

overall_design: The 50 donor lung samples were divided into two groups - those that developed PGD after transplantation (PGD positive) and those that did not (PGD negative). PGD was defined as T0 Grade III dysfunction according to International Society for Heart and Lung Transplantation criteria, that is, a ratio (referred to as the P/F ratio) of partial pressure of arterial oxygen (PaO2) to fraction of inspired oxygen (FiO2) less than 200 in the first arterial blood gas in the intensive care unit after transplantation (generally 4-6 hours after actual reperfusion).

first: Sekhar

last: Dharmarajan


title: Radiation-specific DNA copy number aberration in rat mammary carcinoma.

status: Public on Aug 09 2010

city: Chiba

first: Daisuke

last: IIZUKA

address: 4-9-1, Anagawa, Inage-ku

institute: Research Institutes for Quantum Science and Technology

summary: Breast cancer ranks top in the incidence among the main sites of female cancer in Japan. The epidemiological study on atomic bomb survivors has suggested that the excess relative risk for breast cancer is higher than any other sites. Little is known, however, about the molecular mechanisms of breast cancer induction by radiation. Therefore, we analyzed here the genome-wide copy number aberration of radiation-induced rat mammary carcinomas using microarray-based comparative genomic hybridization (array-CGH).   Mammary carcinomas were induced by 2 Gy gamma irradiation of Sprague-Dawley (SD) rats at 3 or 7 weeks of age. We examined 14 mammary carcinomas induced by gamma-irradiation (2 Gy) and found 26 aberrations including trisomies of chromosomes 4 and 10 in 3 and 1 carcinomas, respectively, and deletion of chromosomes 3q35q36 and 5q32 (Cdkn2a and Cdkn2b region) in 2 and 2 carcinomas, respectively. On the other hand, only one aberration (amplification of chromosome 10q31) was observed in four spontaneous mammary carcinomas. These results suggest that the trisomy of chromosome 4 and deletion of chromosomes 3q35q36 and 5q32 were associated with radiation exposure.

overall_design: We performed aCGH on mammary carcinoma in Sprague-Dawley rat to identify radiation-specific DNA copy number aberration compared with spontaneous mammary carcinoma.

first: D

last: Iizuka

first: T

last: Imaoka

last: Takabatake

first: M

last: Nishimura

first: S

last: Kakinuma

first: Y

last: Shimada


title: FDB1_GM-CSFTyr577_Receptor_Mutant_Factorial_Time_Course_Study

status: Public on Dec 07 2010

city: Adelaide

first: Chung

last: Kok

state: South Australia

address: North Terrace

country: Australia

institute: South Australia Health and Medical Research Institute

summary: To understand better the mechanisms controlling the balance between proliferation and and differentiation during myelopoiesis we have utilized teh bi-potent FDB1 myeloid cell line which differentiates to granulocytes and macrophages in response to GM-CSF and thus provides a dissectable model to analyse the switch between growth and differentiation. This was further studied using this cell line in which a second site mutation Y577F had been generated. A factorial time-course design between the two cell lines and over time, combined with linear modelling and geneset enrichment analysis identified the expression changes associated with the switch between granulocyte differentiation and macrophage differentiation. We observed that a single intracellular tyrosine residue (Tyr577) mediates the granulocyte fate decision. The loss of granulocyte differentiation and enhanced macrophage differentiation observed in this second site mutant is associated with accumulation of Beta-Catenin and activation of Tcf4 and other Wnt Target genes.

overall_design: Factorial design. First Factor was cell type with levels FDB1 expressing FI-Delta receptor mutant and FDB1 expressing FI-Delta Y577F receptor mutant. Second factor is time with levels 0 and 72 hours. Two biological replicates wre prepared for each cell line and comparions were perfomed for each cell line and directly between cell lines at 0 and 72hs. Additional dye swaps were done with FI Delta and FIDelta Y577F at 0h and the FI Delta 0-72h comparison.

first: Christopher

last: Wilkinson

first: Anna

middle: L

last: Brown

first: Diana

middle: G

last: Salerno

first: Teresa

last: Sadras

first: Saumya

last: Samaraweera

first: Timothy

last: Sadlon

first: Michelle

last: Perugini

first: Ian

last: Lewis

first: Thomas

middle: J

last: Gonda

first: Richard

last: D'Andrea


title: Temporal expression profile of primary CD4+ T cell activation

status: Public on Dec 29 2007

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

summary:
Little is known about the global transcriptional program underlying CD4+ T-cell activation.  Using DNA microarrays and Q-RT-PCR, we examined the transcriptional profile of human CD4+ T-cell activation.  The goal of this study was to identify genes involved in the various facets of human CD4+ T-cell activation.
Keywords: time course

sample_organism:
Homo sapiens
Thymus

overall_design: CD4+ T cells isolated from peripheral blood were cultured with CD3, CD28, with or without IL-2 to induce T-cell activation. At each timepoint, cells were harvested and frozen for RNA isolation.  Three biological replicate experiments were analyzed and approximately one-half of the samples from each experiment were technically replicated.  Hybridizations were performed in a reference design with all samples labeled with Cy3 and a reference thymus total RNA  labeled with Cy5.

first: Min

last: Wang

first: Dirk

last: Windgassen

middle: T


title: TMPRSS2-ERG fusion prostate cancer is a molecularly distinct estrogen-sensitive subclass of aggressive prostate cancer

status: Public on May 28 2008

city: New York

first: Mark

middle: A.

last: Rubin

address: 1300 York Avenue Room C 410-A

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medical Center

summary:
Common epithelial cancers are believed to become more aggressive through the accumulation of multiple independent molecular events that lead to the deregulation of cell signaling. However, the discovery that the majority of prostate cancers harbor gene fusions of the 5'-untranslated region of androgen regulated TMPRSS2 promoter with ETS transcription factor family members has brought this paradigm into question1,2. TMPRSS2-ERG gene fusion is the most common molecular sub-type of prostate cancer. Recent work suggests that the TMPRSS2-ERG fusion is associated with a more aggressive clinical phenotype3. In the most advanced castration resistant prostate cancers where the androgen receptor has been inactivated, the TMPRSS2-ERG fusion remains functionally active. Here we show compelling clinical and gene expression data supporting the existence of a TMPRSS2-ERG fusion prostate cancer subclass. Using expression array profiling on 455 primary prostate tumors, we identified an 87 gene expression signature, distinguishing TMPRSS2-ERG fusion prostate cancer as a discrete molecular entity. Computational analysis suggested that this fusion signature was associated with estrogen receptor signaling. Functional studies demonstrated regulation of the TMPRSS2-ERG fusion transcript by estrogenic compounds. These data identify a previously unrecognized mechanism for regulation of the TMPRSS2-ERG, even in the absence of a functional androgen receptor, and thus may have broader implications in the treatment of prostate cancer.
Keywords: Prostate cancer, Expression array, Illumina, gene fusion, TMPRSS2, ERG, Signatures, Estrogen

overall_design:
Test Cohort: 388 cases from the population based Swedish-Watchful Waiting cohort. The cohort consists of men with localized prostate cancer (clinical stage T1-T2, Mx, N0); Validation cohort: The Physicians’ Health Study (PHS) cohort included 116 US men diagnosed with incidental prostate cancer between 1983 and 2003; 455 cases were annotated for TMPRSS2-ERG fusion.

Test Set: GSM208029 ... GSM208392
Validation Set: GSM208404 ... GSM208512

first: Sunita

last: Setlur


title: The Populus transcriptome in elevated CO2 reveals increased anthocyanin biosynthesis during delayed autumnal senescence

status: Public on Feb 01 2010

city: Southampton

first: Gail

last: Taylor

address: Bassett Crescent East

institute: University of Southampton

summary: Over recent decades the progression of natural autumnal senescence has been increasingly delayed across wide areas of the Northern Hemisphere and is thought to be caused by rising temperature.  Recently this delay has been shown to be partly attributable to rising atmospheric carbon dioxide concentrations [CO2].  Here, for the first time, we present a possible mechanistic explanation for this phenomenon. Using a plantation of Populus x euramericana grown at elevated [CO2] (e[CO2]) using Free-Air CO2 Enrichment (FACE) technology, we investigated the molecular and biochemical basis underlying this response. Using a poplar cDNA microarray where late growing season and senescing leaves from ambient [CO2] (a[CO2]) and e[CO2] were compared, revealed unique increases and decreases in transcript abundance in the e[CO2] treatment. Growth at e[CO2]caused the greatest increase in the abundance of transcripts catalysing steps in the anthocyanin biosynthetic pathway and an increase in leaf anthocyanin content. Leaf sucrose and starch content were also increased during senescence in e[CO2] and associated with a higher abundance of transcripts in the sucrose and starch biosynthetic pathways. We propose that in e[CO2], autumnal photosynthesis and sugar accumulation results in changes in genes expression that include further investment in secondary carbon metabolism leading to anthocyanin production. This enables prolonged leaf longevity during natural autumnal senescence through increased availability of carbon and improved stress tolerance while in contrast this may also have a negative effect on the control of dormancy.

platform_organism:
Populus trichocarpa x Populus deltoides
Populus euphratica
Populus tremula x Populus alba

overall_design:
Samples GSM398292..GSM398314 (late senescence samples only): Six replicate trees were labelled in the unfertilised sub-plots of plots 1-4 in the POP/EUROFACE site (http://www.unitus.it/euroface/) and the 10th leaf down from the closed apical bud of the dominant branch were labelled. Leaves were sampled to liquid nitrogen (18th October 2004) and stored at -80 oC. Extracted RNA was tested for quality and quantity and of that passing the test equal quantities of RNA from each replicate were taken and each sample from the control plots (plots 2 and 3) were randomly paired with a sample from and elevated CO2 plot (plots 1 and 4). From the resulting 9 dual channel hybridisations 6 had the control sample in the Cy3 channel and 3 had the elevated CO2 sample in the Cy3 channel.
The 6 samples with Cydye orientation as Cy3=control (ambient CO2) and Cy5 = treated (elevated CO2) are as follows:
GSM398296, GSM398301, GSM398303, GSM398304, GSM398305 and GSM398306.
The 3 samples with dye swap i.e Cy3 =  treated (elevated CO2) are as follows and Cy5 = control (ambient CO2) are as follows:
GSM398292, GSM398313 and GSM398314.

Samples GSM398426..GSM398474: Four replicate leaves per sub-plot were sampled and flash frozen into liquid nitrogen, on 31 August 2004, and prior to visible senescence but around the time of bud-set as given by Calfapietra et al., (2003) [1]. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were selected. On the 14th September twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. Four replicate leaves from within each sub-plot were sampled during each harvest (except on 18th October when six replicate leaves were sampled). Each sampling time was restricted to two hours within the same day and across sampling day’s uniform cloud free skies were chosen. September samplings took place between 15.00 and 17.00 when climatic variables were generally consistent; later in the season time of sampling was adjusted to an earlier two hour period after mid-day when climatic variables were generally consistent.  A chlorotic canopy was evident in plots five and six, as described by Liberloo et al. (2007) therefore any subsequent analysis was for plots one to four only. Six replicate labelled leaves were sampled (as above) from each sub-plot on 18th October 2004

first: Matthew

last: Tallis

first: Yunan

last: Lin

first: Alistair

last: Rogers

first: Jing

last: Zhang

first: Nathaniel

last: Street

first: Franco

last: Miglietta

first: David

middle: F

last: Karnosky

first: Paolo

last: DeAngelis


title: The landscape of gene expression in Arabidopsis

status: Public on Aug 01 2015

city: Manhattan

first: Eduard

last: Akhunov

state: Kansas

address: 2245 Buckingham St, Apt 10

department: Plant Pathology

institute: Kansas State University

type:
Expression profiling by array
Third-party reanalysis

summary: Transcriptome datasets from thousands of samples of the model plant Arabidopsis thaliana have been collectively generated by multiple individual labs. Although integration and meta-analysis of these samples has become routine in the plant research community, it is often hampered by the lack of metadata or differences in annotation styles by different labs. In this study, we carefully selected and integrated 6,057 Arabidopsis microarray expression samples from 304 experiments deposited to NCBI GEO. Metadata such as tissue type, growth condition, and developmental stage were manually curated for each sample. We then studied global expression landscape of the integrated dataset and found that samples of the same tissue tend to be more similar to each other than to samples of other tissues, even in different growth conditions or developmental stages. Root has the most distinct transcriptome compared to aerial tissues, but the transcriptome of cultured root is more similar to those of aerial tissues as the former samples lost their cellular identity. Using a simple computational classification method, we showed that the tissue type of a sample can be successfully predicted based on its expression profile, opening the door for automatic metadata extraction and facilitating re-use of plant transcriptome data. As a proof of principle we applied our automated annotation pipeline to 708 RNA-seq samples from public repositories and verified accuracy of our predictions with samples’ metadata provided by authors.

relation:
Affiliated with: GSE10016
Affiliated with: GSE10497
Affiliated with: GSE10501
Affiliated with: GSE10502
Affiliated with: GSE10646
Affiliated with: GSE10670
Affiliated with: GSE10749
Affiliated with: GSE11558
Affiliated with: GSE11708
Affiliated with: GSE11758
Affiliated with: GSE11807
Affiliated with: GSE11852
Affiliated with: GSE12404
Affiliated with: GSE12551
Affiliated with: GSE12715
Affiliated with: GSE12729
Affiliated with: GSE12856
Affiliated with: GSE12887
Affiliated with: GSE13596
Affiliated with: GSE13739
Affiliated with: GSE13783
Affiliated with: GSE13803
Affiliated with: GSE13833
Affiliated with: GSE14091
Affiliated with: GSE14106
Affiliated with: GSE14374
Affiliated with: GSE14420
Affiliated with: GSE14493
Affiliated with: GSE14496
Affiliated with: GSE14502
Affiliated with: GSE14646
Affiliated with: GSE14788
Affiliated with: GSE1491
Affiliated with: GSE15105
Affiliated with: GSE15189
Affiliated with: GSE15236
Affiliated with: GSE15577
Affiliated with: GSE15680
Affiliated with: GSE15689
Affiliated with: GSE15876
Affiliated with: GSE15939
Affiliated with: GSE16056
Affiliated with: GSE16333
Affiliated with: GSE16557
Affiliated with: GSE16722
Affiliated with: GSE16765
Affiliated with: GSE16964
Affiliated with: GSE17099
Affiliated with: GSE17159
Affiliated with: GSE17343
Affiliated with: GSE17464
Affiliated with: GSE17479
Affiliated with: GSE17499
Affiliated with: GSE17824
Affiliated with: GSE17845
Affiliated with: GSE18071
Affiliated with: GSE18112
Affiliated with: GSE18153
Affiliated with: GSE18329
Affiliated with: GSE18624
Affiliated with: GSE18818
Affiliated with: GSE18975
Affiliated with: GSE18978
Affiliated with: GSE18982
Affiliated with: GSE18985
Affiliated with: GSE19109
Affiliated with: GSE19241
Affiliated with: GSE19242
Affiliated with: GSE19245
Affiliated with: GSE19255
Affiliated with: GSE19258
Affiliated with: GSE19260
Affiliated with: GSE19261
Affiliated with: GSE19263
Affiliated with: GSE19264
Affiliated with: GSE19266
Affiliated with: GSE19267
Affiliated with: GSE19271
Affiliated with: GSE19273
Affiliated with: GSE19520
Affiliated with: GSE19603
Affiliated with: GSE19700
Affiliated with: GSE20005
Affiliated with: GSE20044
Affiliated with: GSE20231
Affiliated with: GSE20278
Affiliated with: GSE20493
Affiliated with: GSE20556
Affiliated with: GSE20586
Affiliated with: GSE20756
Affiliated with: GSE20897
Affiliated with: GSE21601
Affiliated with: GSE21611
Affiliated with: GSE21684
Affiliated with: GSE2169
Affiliated with: GSE21762
Affiliated with: GSE21786
Affiliated with: GSE21876
Affiliated with: GSE21920
Affiliated with: GSE21981
Affiliated with: GSE22942
Affiliated with: GSE22947
Affiliated with: GSE22951
Affiliated with: GSE22966
Affiliated with: GSE23210
Affiliated with: GSE23301
Affiliated with: GSE23331
Affiliated with: GSE23617
Affiliated with: GSE23846
Affiliated with: GSE24077
Affiliated with: GSE24169
Affiliated with: GSE24348
Affiliated with: GSE24517
Affiliated with: GSE2473
Affiliated with: GSE24738
Affiliated with: GSE24781
Affiliated with: GSE25067
Affiliated with: GSE25171
Affiliated with: GSE25489
Affiliated with: GSE26197
Affiliated with: GSE26266
Affiliated with: GSE26297
Affiliated with: GSE26679
Affiliated with: GSE26848
Affiliated with: GSE26983
Affiliated with: GSE27475
Affiliated with: GSE27508
Affiliated with: GSE27985
Affiliated with: GSE28224
Affiliated with: GSE28227
Affiliated with: GSE28297
Affiliated with: GSE28431
Affiliated with: GSE28446
Affiliated with: GSE2848
Affiliated with: GSE28600
Affiliated with: GSE28747
Affiliated with: GSE28800
Affiliated with: GSE29086
Affiliated with: GSE29187
Affiliated with: GSE29364
Affiliated with: GSE29543
Affiliated with: GSE29589
Affiliated with: GSE29657
Affiliated with: GSE29814
Affiliated with: GSE29941
Affiliated with: GSE30030
Affiliated with: GSE30095
Affiliated with: GSE30096
Affiliated with: GSE30097
Affiliated with: GSE30098
Affiliated with: GSE30099
Affiliated with: GSE30223
Affiliated with: GSE30492
Affiliated with: GSE30712
Affiliated with: GSE30910
Affiliated with: GSE31158
Affiliated with: GSE31587
Affiliated with: GSE31593
Affiliated with: GSE31778
Affiliated with: GSE31837
Affiliated with: GSE31977
Affiliated with: GSE32193
Affiliated with: GSE32566
Affiliated with: GSE3326
Affiliated with: GSE33344
Affiliated with: GSE33412
Affiliated with: GSE3350
Affiliated with: GSE33505
Affiliated with: GSE33790
Affiliated with: GSE34047
Affiliated with: GSE34130
Affiliated with: GSE34209
Affiliated with: GSE34231
Affiliated with: GSE34595
Affiliated with: GSE34667
Affiliated with: GSE34897
Affiliated with: GSE35057
Affiliated with: GSE35258
Affiliated with: GSE35325
Affiliated with: GSE35544
Affiliated with: GSE35580
Affiliated with: GSE35700
Affiliated with: GSE36011
Affiliated with: GSE36789
Affiliated with: GSE36797
Affiliated with: GSE36887
Affiliated with: GSE37014
Affiliated with: GSE37408
Affiliated with: GSE37484
Affiliated with: GSE38030
Affiliated with: GSE38878
Affiliated with: GSE38965
Affiliated with: GSE39090
Affiliated with: GSE39236
Affiliated with: GSE39268
Affiliated with: GSE39690
Affiliated with: GSE40061
Affiliated with: GSE40076
Affiliated with: GSE40245
Affiliated with: GSE40322
Affiliated with: GSE40998
Affiliated with: GSE41136
Affiliated with: GSE41779
Affiliated with: GSE41884
Affiliated with: GSE41958
Affiliated with: GSE41963
Affiliated with: GSE42007
Affiliated with: GSE42415
Affiliated with: GSE42896
Affiliated with: GSE43011
Affiliated with: GSE43818
Affiliated with: GSE43819
Affiliated with: GSE43947
Affiliated with: GSE44655
Affiliated with: GSE44793
Affiliated with: GSE45728
Affiliated with: GSE46107
Affiliated with: GSE46205
Affiliated with: GSE46621
Affiliated with: GSE4733
Affiliated with: GSE4847
Affiliated with: GSE48488
Affiliated with: GSE48915
Affiliated with: GSE50435
Affiliated with: GSE50526
Affiliated with: GSE50966
Affiliated with: GSE51215
Affiliated with: GSE52208
Affiliated with: GSE53071
Affiliated with: GSE5522
Affiliated with: GSE5530
Affiliated with: GSE5612
Affiliated with: GSE5615
Affiliated with: GSE5616
Affiliated with: GSE5617
Affiliated with: GSE5620
Affiliated with: GSE5621
Affiliated with: GSE5622
Affiliated with: GSE5623
Affiliated with: GSE5624
Affiliated with: GSE5625
Affiliated with: GSE5626
Affiliated with: GSE5627
Affiliated with: GSE5628
Affiliated with: GSE5629
Affiliated with: GSE5630
Affiliated with: GSE5631
Affiliated with: GSE5632
Affiliated with: GSE5633
Affiliated with: GSE5634
Affiliated with: GSE5636
Affiliated with: GSE5637
Affiliated with: GSE5638
Affiliated with: GSE5684
Affiliated with: GSE5685
Affiliated with: GSE5686
Affiliated with: GSE5688
Affiliated with: GSE5698
Affiliated with: GSE5730
Affiliated with: GSE5737
Affiliated with: GSE5738
Affiliated with: GSE5745
Affiliated with: GSE5751
Affiliated with: GSE5770
Affiliated with: GSE6151
Affiliated with: GSE6158
Affiliated with: GSE6160
Affiliated with: GSE6161
Affiliated with: GSE6174
Affiliated with: GSE6176
Affiliated with: GSE6177
Affiliated with: GSE6179
Affiliated with: GSE627
Affiliated with: GSE629
Affiliated with: GSE631
Affiliated with: GSE6556
Affiliated with: GSE6826
Affiliated with: GSE6832
Affiliated with: GSE6906
Affiliated with: GSE7353
Affiliated with: GSE7432
Affiliated with: GSE7631
Affiliated with: GSE7639
Affiliated with: GSE7641
Affiliated with: GSE7642
Affiliated with: GSE7743
Affiliated with: GSE7796
Affiliated with: GSE8319
Affiliated with: GSE8365
Affiliated with: GSE8785
Affiliated with: GSE8787
Affiliated with: GSE8951
Affiliated with: GSE911
Affiliated with: GSE9148
Affiliated with: GSE9605
Affiliated with: GSE9674
Affiliated with: GSE9719
Affiliated with: GSE9721
Affiliated with: GSE9728
Affiliated with: GSE9816
Affiliated with: GSE9955
Affiliated with: GSE9957
Affiliated with: GSE9996

overall_design: 6057 published Arabidopsis microarray samples from about 300 series assayed on the GPL198 were re-analyzed. Metadata were re-annotated and MAS5.0 was used to normalize the CEL files.

first: Fei

last: He

first: Shinjae

last: Yoo

first: Daifeng

last: Kumari

last: Gerstein

first: Doreen

last: Ware

first: Sergei

last: Maslov