title: Coordination of engineered factors with TET1/2 promotes early stage epigenetic modification during somatic cell reprogramming

status: Public on Aug 08 2013

city: Atlanta

first: Tao

last: Wang

address: 615 Michael Street

department: Human Genetics

institute: Emory University

summary: Somatic cell reprogramming towards induced pluripotent stem cells (iPSCs) holds great promise in future regenerative medicine, however, the reprogramming process mediated by the traditional defined factors (OSNK) is slow and extremely inefficient. Here we show that a combination of modified reprogramming factors (OySyNyK), in which the transactivation domain of the Yes-associated protein is fused to OCT4, SOX2 and NANOG respectively, could be used to establish a highly efficient and rapid reprogramming system for iPSC generation. We show that the efficiency of OySyNyK-induced iPSCs was up to 100-fold higher than that of induction by traditional OSNK. Moreover we show that the reprogramming by OySyNyK is very rapid (initiated at 24 h versus 5 d by OSNK). Compared with OSNK, we found that OySyNyK factors significantly increased the expression of Tet1/2 at the early stage, which will interact with OSNK factors, and co-occupy pluripotency loci in the genome for somatic cell reprogramming. Our studies not only establish a rapid and highly efficient iPSC reprogramming system, but also uncover a novel mechanism by which OSNK factors coordinate with TET proteins to regulate 5hmC-mediated epigenetic control, thereby promoting somatic cell reprogramming.

overall_design: We examined DNA hydroxymethylation progression of reprogramming intermediates. To this end, we profiled the genome-wide 5hmC distribution in MEFs, the reprogramming intermediates at different stages induced by either the OSNK or OySyNyK methods, and iPSCs using the chemical capture approach

first: Yujing

last: Li


title: Large scale variation in copy number in chicken breeds

status: Public on Aug 21 2013

city: Wageningen

first: richard

last: crooijmans

address: de Elst 1

department: Animal Breeding and Genomics Centre

country: Netherlands

institute: Wageningen University

type: Genome variation profiling by genome tiling array

summary:
Background: Detecting genetic variation is a critical step in elucidating the molecular mechanisms underlying phenotypic diversity. Until recently, such detection has mostly focused on single nucleotide polymorphisms (SNPs) because of the ease in screening complete genomes. Another type of variant, copy number variation (CNV), is emerging as a significant contributor to phenotypic variation in many species.

Here we describe a genome-wide CNV study using array comparative genomic hybridization (aCGH) in a wide variety of chicken breeds.

Results: We identified 3,154 CNVs, grouped into 1,556 CNV regions (CNVRs). Thirty percent of the CNVs were detected in at least 2 individuals. The average size of the CNVs detected was 46.3 kb with the largest CNV, located on GGAZ, being 4.3 Mb. Approximately 75% of the CNVs are copy number losses relatively to the Red Jungle Fowl reference genome. The genome coverage of CNVRs in this study is 60 Mb, which represents almost 5.4% of the chicken genome. In particular large gene families such as the keratin gene family and the MHC show extensive CNV.

Conclusions: A relative large group of the CNVs are line-specific, several of which were previously shown to be related to the causative mutation for a number of phenotypic variants. The chance that inter-specific CNVs fall into CNVRs detected in chicken is related to the evolutionary distance between the species.

Our results provide a valuable resource for the study of genetic and phenotypic variation in this phenotypically diverse species.

overall_design: In total 62 chicken  DNA samples (derived from 15 lines) were analyzed against the chicken reference animal UCD001 (the same induvidual that was used to generate the chicken genome reference sequence (ICGSC, 2004)

first: Richard

middle: P

last: Crooijmans

first: Mark

middle: S

last: Fife

first: Tomas

last: Fitzgerald

first: Shurnevia

last: Strickland

first: Hans

middle: H

last: Cheng

first: Pete

last: Kaiser

last: Redon

first: Martien

middle: A

last: Groenen


title: Integrative transcriptomic and proteomic analysis of osteocytic cells exposed to fluid flow reveals novel mechano-sensitive signaling pathways

status: Public on Jul 01 2013

city: Richland

first: Katrina

middle: M

last: Waters

state: WA

address: 902 Battelle Blvd; MSIN J4-18

department: Biological Sciences Division

country: USA

institute: Pacific Northwest National Laboratory

summary:
Osteocytes, positioned within bone’s interstitial space, are subject to fluid flow upon whole bone loading.  Such fluid flow is widely theorized to be a mechanical signal transduced by osteocytes, initiating a poorly understood cascade of signaling events mediating bone metabolism.  The objective of this study was to utilize high-throughput approaches to examine the time course of flow-induced changes in osteocyte gene transcript and protein levels.
Microarray analysis demonstrated fluid flow regulation of genes consistent with known anabolic loading responses, including Ptgs2, NF-κB inhibitors, MAP3 kinases, and Wnt/β-catenin pathway signaling molecules.  However, two of the most highly up-regulated gene products—Cxcl1 and Cxcl2, confirmed by qPCR—have not previously been reported to be responsive to fluid flow.  Gene ontology analysis suggested a highly significant inflammatory and immune response, with cellular functions including trafficking, cell-to-cell signaling, and tissue development.  Proteomic analysis of the same samples demonstrated greatest up-regulation of the ATP-producing enzyme NDK, calcium-binding Calcyclin, and G protein-coupled receptor kinase 6.  An integrative pathway analysis merging fold changes in transcript and protein levels predicted signaling nodes not directly detected at the sampled time points, including STAT3 and c-Myc.  These results extend our knowledge of the osteocytic response to fluid flow, most notably up-regulation of Cxcl1 and Cxcl2 as a possible paracrine agent for osteoblastic and osteoclastic recruitment.

overall_design: Osteocyte-like MLO-Y4 cells were subjected to 2 hours of 10 dyn/cm2 oscillating fluid flow in parallel-plate fluid flow chambers and harvested for analysis at 0, 2, 8, and 24 hours post-flow incubation.  Parallel control samples from sham treated cells were also collected at each time point.

first: Norman

middle: J

last: Karin

first: Henry

last: Donahue


title: HuMiChip analysis of Saliva microbiota

status: Public on Aug 15 2013

city: Norman

first: Qichao

last: Tu

state: OK

address: 101 David L Boren Blvd

institute: University of Oklahoma

summary:
Human saliva microbiota is phylogenetically divergent among host individuals yet their roles in health and disease are poorly appreciated. We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults. Saliva microbiota in the pilot population featured a vast diversity of functional genes. No significant distinction in gene number or diversity indices was observed between healthy and caries-active microbiota. However, co-presence network analysis of functional genes revealed that caries-active microbiota was more divergent in non-core genes than healthy microbiota, despite both groups exhibited a similar degree of conservation at their respective core genes. Furthermore, functional gene structure of saliva microbiota could potentially distinguish caries-active patients from healthy hosts. Microbial functions such as Diaminopimelate epimerase, Prephenate dehydrogenase, Pyruvate-formate lyase and N-acetylmuramoyl-L-alanine amidase were significantly linked to caries. Therefore, saliva microbiota carried disease-associated functional signatures, which could be potentially exploited for caries diagnosis.

The DMFT INDEX (Decayed, Missing, Filled [DMF] teeth index used in dental epidemiology) values are provided for each sample


title: LncRNA expression profiles for 6 human samples derived from patients with gastric cancer

status: Public on Jun 12 2013

city: Ningbo

first: Junming

last: Guo

address: 818 Fenghua Road

department: Department of Biochemistry and Molecular Biology, and Zhejiang Provincial Key Laboratory of Pathophysiology

country: China

institute: Ningbo University

summary: Investigation of lncRNA expression profile of gastric cancer

overall_design: A six chip study using total RNA extracted from three gastric cancer tissues and three paracancerous tissues


title: Paired subcloned human large cell lung carcinoma cell lines: low-metastatic 95C vs high-metastatic 95D

status: Public on Jun 11 2013

city: Shanghai

first: Gentao

last: Liu

address: 507 Zhengmin Rd

institute: Tongji University School of Medicine

summary: The paired low-metastatic 95C and high-metastatic 95D cell lines were subcloned from a low differentiated human large cell lung carcinomacell line PLA-801. The cells were well authenticated and published by several research groups. The cells were kindly provided by Professor Ying-Lin Lu, Department of Pathobiology, Institute of Basic Medical Sciences, Academy of Military Medical Sciences, Beijing, China on Dec. 5，2009. As described The 95C and 95D cells were cultured in RPMI 1640 (Invitrogen, USA) with 100 units/mL penicillin, 100 μg/mL streptomycin and 10% calf bovine serum, and grown at 37° C in atmosphere with 5% CO2. miRNAs differential expression between 95C and 95D was measured using a miR human_01_H10.1_080277 miRNA array (LC Sciences Houston, USA).

overall_design: Paired subcloned human large cell lung carcinomacell line PLA-801 of low-metastatic 95C and high-metastatic 95D cell lines.  Biological replicates:1. Five replicate per array.

first: Heyong


title: Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones

status: Public on Jun 20 2013

city: Princeton

first: Xuefeng

last: Peng

state: NJ

address: Guyot Hall

department: Geosciences

institute: Princeton University

summary: Ammonia-oxidizing archaea (AOA) have been reported at high abundance in much of the global ocean, even in environments such as pelagic oxygen minimum zones (OMZs), where conditions seem unlikely to support aerobic ammonium oxidation. Due to the lack of information on any potential alternative metabolism of AOA, the AOA community composition might be expected to differ between oxic and anoxic environments, indicating some difference in ecology and/or physiology of the AOA assemblage. This hypothesis was tested by evaluating AOA community composition using a functional gene microarray that targets the ammonia monooxygenase gene subunit A (amoA). The relationship between environmental parameters and the biogeography of the Arabian Sea and the Eastern Tropical South Pacific (ETSP) AOA assemblages was investigated using principal component analysis (PCA) and redundancy analysis (RDA). In both the Arabian Sea and the ETSP, AOA communities within the core of the OMZ were not significantly different from those inhabiting the oxygenated surface waters above the OMZ. The AOA communities in the Arabian Sea were significantly different from those in the ETSP. In both oceans, the abundance of archaeal amoA gene in the core of the OMZ was higher than that in the surface waters. Our results indicate that AOA communities are distinguished by their geographic origin. RDA suggested that temperature was the main factor that correlated with the differences between the AOA communities from the Arabian Sea and those from the ETSP. Physicochemical properties that characterized the different environments of the OMZ and surface waters played a less important role than did geography in shaping the AOA community composition.

sample_organism:
synthetic construct
marine metagenome

overall_design: Two-color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.

first: Amal

last: Jayakumar

first: Bess

last: Ward


title: Transcriptional Corepressors HIPK1 and HIPK2 Control Angiogenesis via TGF-b-TAK1-depdendent Mechanism

status: Public on Jun 01 2013

city: San Francisco

first: Yulei

last: Shang

state: CA

address: 513 Parnassus street

department: Pathology

institute: UCSF

summary: Transforming growth factor-b (TGF-b) regulates various aspects of vascular development, yet the signaling mechanisms of TGF-b in the control of angiogenesis remain poorly characterized. Here we show that homeodomain interacting protein kinases, HIPK1 and HIPK2, are transcriptional corepressors that regulate TGF-b-depednent angiogenesis during embryonic development. Loss of HIPK1 and HIPK2 leads to marked up-regulations of several potent angiogenic genes, including Vegf and Mmp10, which result in excessive endothelial proliferation and poor adherens junction formation. This robust phenotype can be recapitulated by siRNA knock down of Hipk1 and Hipk2 in human umbilical vein endothelial cells, as well as in endothelial cell-specific TGF-b type II receptor (TbRII) conditional mutants. The effects of HIPK proteins are mediated through its interaction with MEF2C and HDAC7, and this interaction can be further enhanced by TGF-b and TAK1. Remarkably, TGF-b-TAK1 signaling activates HIPK2 by phosphorylating a highly conserved tyrosine residue Y-361 within the kinase domain. Point mutation in this tyrosine completely eliminates the effect of HIPK2 in the transcriptional suppression of target genes. Together, these results reveal a previously unrecognized role of HIPK proteins in connecting TGF-b signaling pathway with the transcriptional programs for angiogenesis in early embryonic development.

overall_design: In this study, a total of 36,000 transcripts and ESTs (a total of 30,000 unique genes) was used to acquire expression profiles among the control, Hipk1-/-, Hipk2-/-, and Hipk1-/-;Hipk2-/- E9.5 embryos. This will allow us unsupervised and successfully to analyze the transcriptomes and finally to reveal the role of HIPK1 and HIPK2 in the signal transduction mechanism downstream of TGF-b and the transcriptional control of angiogenic gene expression during the critical stages of vascular morphogenesis.

first: Christina

middle: N

last: Doan

first: Thomas

middle: D

last: Arnold

first: Sebum

last: Lee

first: Louis

middle: F

last: Reichardt

first: Eric

last: Huang


title: Nasopharyngeal carcinoma patient samples: radio-sensitive samples vs. radio-resistant samples

status: Public on Sep 21 2013

city: shanghai

first: shu

last: yang

address: State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science

institute: Fudan University

summary: Expression profiling of nasopharyngeal carcinoma patients comparing radio-sensitive samples with radio-resistant samples.

overall_design: Two condition-experiments, radio-sensitive and radio-resistant nasopharyngeal carcinoma patients. Biological replicates: 8 radio-sensitive, 12 radio-resistant, different donors in the same hospital. One patient per array.

first: Shu

last: Yang

first: Jiaxin

last: Chen

first: Yi

first: Zheng

last: Zhang

first: Kehe

first: Hai

last: Wu

first: Yao

last: Li


title: Mechanism of protective immunity against Vibrio anguillarum infection in zebrafish bath-vaccinated with MVAV6203

status: Public on Jun 06 2013

first: zhang

last: hua

address: meilong road No.130

institute: ECUST Ehua institution

summary: MVAV6203, an live attenuated vaccine showed a strong protection against V. anguillarum for Paralichthys olivaceus, Epinephelus coioides and zebrafish. However the mechanism of its protection, especially the mucosal-related response induced by immersion vaccination, is not fully understood. This study was conducted to reveal the changes of genes involved in both innative and adaptive immunity. For gene expression analysis, spleen of zebrafish from 3 vaccinated groups and 3 control groups  were hybridized on a 4×44K aglient whole zebrafsih genome oligo microarray. Functional analysis of the microarray data was performed using KEGG and Gene Ontology (GO) analysis. Microarray gene expression analysis showed that the Th17-like immune response may  play vital role in orchestrating the mucosal barrier against pathogen.

overall_design: Zebrafish were randomly divided into three vaccinated groups and three control groups. V.anguillarum MVAV6203 was cultured in high-salt Luria (LB) medium at 30 for 16h. The cells were harvested by centrifugation and rinsed twice in 2% saline. The desired number of cells was adjusted to 1.0E+08 CFU/mL with 2% saline. Six groups of 70 zebrafish were immersed in the aerated cell-resuspended saline or 2% saline for 10min at 24℃. At 28 days post-vaccination pool of spleen tissue of 10 zebrafish from each group was harvested for microarray hybridization.

first: Hua

first: Chao

last: Fei

first: Haizhen

first: Minjun

first: Qin

first: Yuanxing


title: Somatic copy number alterations associating with alcohol drinking and smoking in head and neck squamous cell carcinoma

city: Tokyo

first: Mitsuyoshi

last: Urashima

address: Nishishimbashi 3-25-8, Minato-ku

country: Japan

institute: Jikei University School of Medicine

summary:
Background: The most important risk factors for head and neck squamous carcinoma (HNSCC) are tobacco smoking and alcohol consumption, while subgroups are caused by infection with human papillomaviruses (HPV) or Epstein-Barr virus (EBV). Here, we studied alterations of somatic copy-number in whole genome, p16 protein and TP53 mutations by alcohol drinking, smoking and viral infections.

Methods: We conducted a prospective cohort study. DNA obtained from tumors and margin samples as well as peripheral blood was assayed by array comparative genomic hybridization using Agilent Whole Human Genome 180K. Mutations of p53 gene by direct sequencing, detection of HPV by polymerase-chain-reaction (PCR), quantification of EBV by reverse transcription-PCR and p16 immunohistochemical (IHC) staining were also performed.

overall_design:
prospective cohort study: 225 tumor samples were analyzed by Agilent-022060 SurePrint G3 Human CGH miroarray 4x180K. Log2 Ratio (tumor sample DNA/normal DNA) were compared among none alcohol drinkers, moderate alcohol drinkers, heavy alcohol drinkers, none smokers, moderate smokers, heavy smokers and both.

Sample characteristics weres scored as following;

Human Papilloma Virus Infection (gene detected by PCR in tumor sample): positive=1; negative=0

p16 protein immunohistochemistry: positive=1; negative=0

tumor grade: matured=0; moderate=1; immature=2

Radiotherapy with or without chemotherapy after operation: performed =1; not performed =0

Recurrence/relapse: rec =1; not rec =0

suvival status:death=1; survive=0

smoking status (Pack year of smoking): none smoker=0; pack-year <20 = 1 (moderate smoker); pack-year <=20 = 2 (heavy smoker)

alcohol drinking: Alcohol drinkers were divided into non-drinker or less than one drink per day =0: one and more but less than two drinks per day = moderate drinker 1:  two and more drinks per day=heavy drinker 2:  during the 20 years preceding their treatment for HNSCC. One drink was defined as containing approximately 10g of alcohol, which is considered equal to 30 ml of hard liquor, 100 ml of wine containing 12% alcohol, or 360 ml of beer.

first: Takanori

last: Hama


title: Osteotropism in breast cancer metastasis

status: Public on Jun 07 2013

city: Baltimore

first: Scott

last: Kominsky

state: MD

address: 720 Rutland Ave, Ross 209

institute: Johns Hopkins University School of Medicine

summary: Breast cancer metastases develop in the bone more frequently than any other site, and are a common cause of morbidity in the form of bone pain, pathological fractures, nerve compression, and life-threatening hypercalcemia.  Despite ongoing research efforts, the molecular and cellular mechanisms that regulate breast cancer cell homing to and colonization of the bone as well as resultant pathological bone alteration remain poorly understood. To identify key mediators promoting breast cancer metastasis to bone, we utilized an immunocompetent, syngeneic murine model of breast cancer metastasis employing the mammary tumor cell line NT2.5.  Following intracardiac injection of NT2.5 cells in neu-N mice, metastases developed in the bone, liver, and lung, closely mimicking the anatomical distribution of metastases in breast cancer patients.  Using an in vivo selection process, we established NT2.5 sub-lines demonstrating an enhanced ability to colonize the bone and liver.  Genome-wide cDNA microarray analysis comparing gene expression between parental NT2.5 cells and established sub-lines was performed.

overall_design: Individual samples of RNA from parental NT2.5 cells, early passage (BO3 and LI1) sub-lines, and final passage (BO6 and LI3) sub-lines were compared using GeneChip® Mouse Genome 430 2.0 Arrays

middle: L


title: Increased endoplasmic reticulum stress response is involved in clopidogrel-induced apoptosis of gastric epithelial cells

status: Public on Jun 04 2013

city: Nanjing

first: wu

middle: hai

last: lu

address: 68 Changle Road

institute: nanjing first hospital

summary:
Clopidogrel is associated with a series of gastrointestinal side effects, such as bleeding complications and recurrent gastric ulcer; however, their mechanisms are largely unclear.  In this study, human gene expression microarray and gene ontology analysis were utilized to evaluate the effects of clopidogrel on gene expression in human gastric epithelial cells (GES-1)
Keywords: Clopidogrel; Gastric injury; GES-1 cell line

overall_design: The Agilent Whole Human Genome Oligo Microarray was measured at 24 hours after GES-1 cells were exposure to clopidogrel ( 1.5mmol/l). The experimental set up the control group and the clopidogrel group. Three chips were performed on each group.

first: Hai-Lu

first: Zhen-Yu


title: Toxicogenomics and phenotypic characterization of adult female zebrafish liver treated with arsenic [As(V)]

city: Singapore

first: Choong Yong

last: UNG

address: 14 Science Drive 4

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

summary: We performed microarray-based expression profiling on liver of male zebrafish exposed to 15ppm (~ 192 µM) of arsenic [As(V)] for 8-96 h, to identify global transcriptional programs and biological pathways involved in chloroaniline-induced adaptive responses under in vivo environment.

overall_design: We analyzed 12 arrays of chloroaniline-treated adult female zebrafish liver and 12 arrays of control fish.

first: Choong-Yong

last: Ung

first: Sie-Hong

last: Lam

first: Hlaing

last: Myintzu

first: Sinnakarupan

last: Mathavan

first: Zhiyuan

last: Gong


title: Toxicogenomics and phenotypic characterization of adult male zebrafish liver treated with nitrophenol

summary: We performed microarray-based expression profiling on liver of male zebrafish exposed to 7 mg/L of nitrophenol for 8-96 h, to identify global transcriptional programs and biological pathways involved in chloroaniline-induced adaptive responses under in vivo environment.

overall_design: We analyzed 12 arrays of nitrophenol-treated adult male zebrafish liver and 12 arrays of control fish.


title: Cold induced RNA-binding proteins influence alternative polyadenylation

status: Public on May 01 2013

first: Yuting

last: Liu

department: Functional Genomics

institute: PICB

type: Expression profiling by high throughput sequencing

summary: We employed PAR-CLIP, a recently developed method based on   RNA-protein crosslinking, to identify Cirbp and Rbm3 binding sites at transcriptome-level. Genome-wide RNA-seq analysis indicated that cold temperature leads to extensive 3’UTR lengthening whereas the loss of Cirbp or Rbm3 resulted in 3’UTR shortening. Combining with   PAR-CLIP results, we found that these two RBPs repress the polyadenylation adjacent to their   binding sites.

overall_design: Examination of the binding sites of Cirbp and Rbm3 by PAR-CLIP and their influence on the transcriptome by RNA-seq. PARCLIP was performed as in Hafner et al. 2010 Cell 141, 129–141, with MEFs cell lines stably expressing FLAG-tagged Cirbp and Rbm3. We used 4-thiouridine (4SU) to enhance the crosslink. For RNA-seq, polyadenylated RNA from the mock-transfected cells at 37°C or 32°C with two replicates, siCirbp-1, siCirbp-2, siRbm3-1 and siRbm3-2 MEFs at 37°C were sequenced on Solexa GAII using 76bp single-end kits according to the manufacturer’s instructions.

first: Jun

last: Yan


title: Ontogeny, distribution and potential roles of hydroxymethylcytosine in human liver function

status: Public on Jul 29 2013

city: Tartu

first: Mart

last: Kals

address: Riia 23b

country: Estonia

institute: Estonian Genome Center

type: Methylation profiling by high throughput sequencing

summary:
Background: Interindividual differences in liver functions such as protein synthesis, lipid and carbohydrate metabolism and drug metabolism are influenced by epigenetic factors. The role of the epigenetic machinery in such processes has, however, been barely investigated. 5-hydroxymethylcytosine (5hmC) is a recently re-discovered epigenetic DNA modification that plays an important role in the control of gene expression.
Results: In this study, we investigate 5hmC occurrence and genomic distribution in 8 fetal and 7 adult human liver samples in relation to ontogeny and function. LC-MS analysis shows that in the adult liver samples 5hmc comprises up to 1% of the total cytosine content, whereas in all fetal livers it is below 0.125%. Immunohistostaining of liver sections with a polyclonal anti-5hmC antibody shows that 5hmC is detected in most of the hepatocytes. Genome-wide mapping of the distribution of 5hmC in human liver samples by next-generation sequencing shows significant differences between fetal and adult livers. In adult livers, 5hmC occupancy is overrepresented in genes involved in active catabolic and metabolic processes, whereas 5hmC elements which are found in genes exclusively in fetal livers and disappear in the adult state, are more specific to pathways for differentiation and development.
Conclusions: Our findings suggest that 5-hydroxymethylcytosine plays an important role in the development and function of the human liver and might be an important determinant for development of liver diseases as well as of the interindividual differences in drug metabolism and toxicity.

overall_design: 8 fetal and 7 adult human liver samples

first: Maxim

last: Ivanov

first: Marina

last: Kacevska

first: Isabel

last: Barragan

first: Kie

last: Kasuga

first: Anders

last: Rane

first: Andres

last: Metspalu

first: Lili

last: Milani

first: Magnus

last: Ingelman-Sundberg


title: Differential gene expression in cartilage from the mouse DMM osteoarthritis model

status: Public on Apr 11 2013

city: Parkville

first: Lynn

last: Rowley

state: Vic

address: Flemington Road

country: Australia

institute: Murdoch Childrens Research Institute

summary: Transcriptional profiling of mouse cartilage comparing destabilised medial meniscal operated knee joints to sham operated knee joints in both wild type C57Bl/6 and C57Bl/6 ADAMTS5Dcat mice at 1, 2 and 6 weeks post DMM surgery. The goal was to determine the differential gene expression with the onset of arthritis, both early, mid and late timepoints and to assess the gene expression differences when aggrecan loss is prevented in the ADAMTS5Dcat mouse.

overall_design: The overall design of the experiment is to compare DMM (right leg) to sham operated (left leg) cartilage from the same mouse. In order to identify genes involved in early and late arthritis, RNA was collected from cartilage samples from mice at 1, 2 and 6 weeks post surgery. In addition, to isolate genes differentially expressed downstream of aggrecan loss, the RNA as described was collected from C57Bl/6 wild type mice and ADAMTS5Dcat mice. Four mice were used at each timepoint with their left leg being the control Sham and their right leg the experimental DMM. One sample from the wild type 1wk post operation and one ADAMTS5Dcat dye swap were removed from the analysis for technical reasons.

first: John

last: Bateman

first: Daniele

last: Belluoccio

first: Ben

last: Chan

first: Katrina

last: Bell

first: Amanda

last: Fosang

first: Chris

last: Little


title: Progressive epigenetic changes in milk protein gene loci during functional differentiation of the mammary gland: ChIP-Seq part I

status: Public on Mar 02 2013

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The role of chromatin in mammary gland development and differentiation has not been defined. Here we have studied the changes in chromatin conformation in the mammary gland during the lactation cycle at milk protein gene loci, whose gene expression marks functional differentiation of the mammary gland

overall_design: histone modification patterns were studied using ChIP-seq in Lactating (day 8) mammary gland tissue, Mammary epithelial cells Isolated from 12 week virgin (diestrus) mammary gland tissue, and liver from 8 day lactating female.

first: Monique

last: Rijnkels

first: Courtneay

last: Zadrowski

first: Joseph

last: Hernandez

first: Vani

last: Potluri

first: Austine

last: Lin

first: Danielle

last: Lemay

first: Liguo

last: Wang

first: Wei

last: Li


title: Exon Level Expression Profiling: Induced adult neurogenesis  in the olfactory epithelium

city: Lexington

first: Paula

last: Heron

address: 800 Rose St.

institute: University of Kentucky

summary:
Transcriptome analysis of RNA samples from mice olfactory epithelium
Gene expression profiling in the olfactory epithelium was performed to obtain a better understanding of the processes mediating cell replacement.

overall_design: We analyzed epitheliual tissue from 3 adult male mice  at 5 days following ipsilateral olfactory bulbectomy (OBX). Total RNA was isolated and anlayzed  using the Affymetrix  Mouse Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool.

first: Neeraja

last: Sammeta

first: Melissa

last: Nickell

first: Arnold

last: Stromberg

first: Patrick

last: Breheny

first: Timothy

last: McClintock


title: Gene expression pattern of synovial cells from inflammatory and normal areas of osteoarthritis synovial membrane

status: Public on May 20 2013

city: Liege

first: Cecile

last: LAMBERT

address: avenue de l Hopital, 3

country: Belgium

institute: University of Liege

summary: The aim of this study was to compare the gene expression pattern of synovial cells from inflammatory (I) or normal/reactive (N/R) areas of a synovial membrane harvested from the same osteoarthritis (OA) patient. This study is the first to identify different expression pattern between two areas of the synovial membrane in the same patient. These differences concern several key pathways involved in OA pathogenesis (inflammation, cartilage metabolism, Wnt signaling and angiogenesis). This analysis also provides interesting information regarding new potent intermediates as potentiel targets for the future therapeutic.

overall_design: Synovial tissues were obtained from 12 knee OA patients at the time of total knee replacement. The inflammatory status of the synovial membrane was characterized according to macroscopic criteria and sorted as N/R and I. Biopsies were cultured separately for 7 days. Microarray gene expression profiling between N/R and I areas was performed.

first: Yves

last: Henrotin

first: Cécile

last: Lambert


title: Age-Related Changes Following in vitro Stimulation with Rhodococcus equi of Peripheral Blood Leukocytes from Neonatal Foals

status: Public on May 31 2013

city: College Station

first: Priyanka

last: Kachroo

address: University Drive

institute: Texas A&M University

summary: The objectives of this study were 2-fold: 1) to compare the expression profiles at specific ages of blood leukocytes from foals stimulated with virulent R. equi with those of unstimulated leukocytes; and, 2) to characterize the age-related changes in the gene expression profile associated with blood leukocytes in response to stimulation with virulent R. equi.

overall_design: Peripheral blood leukocytes were obtained from 6 foals within 24 hours (h) of birth (day 1) and 2, 4, and 8 weeks after birth. The samples were split, such that half were stimulated with live virulent R. equi, and the other half served as unstimulated control. For one hyb design: we hybridized 6 samples stimulated and 6 unstimulated at each time point (30 mL of blood was treated with live virulent R. equi (Strain ATCC 33701) and the remaining 30 mL of blood with PBS ). For time course: 6 samples from day1 stimulated hybridized to week2 stimulated; day1 stimulated hyb to week 4 stimulated and day1 stimulated hyb to week8 stimulated. RNA was extracted and the generated cDNA was labeled with fluorescent dyes for microarray hybridizations using an equine microarray.

first: Ivan

last: Ivanov

first: Ashley

middle: G

last: Seabury

first: Mei

last: Liu

first: Bhanu

last: Chowdhary

first: Noah

last: Cohen


title: Expression data from E14.5 mouse agonadal urogential ridges

city: Boston

first: Jose

last: Teixeira

state: MA

address: 55 Fruit St.

department: VCRB

institute: Massachusetts General Hospital

summary: We analyzed global mRNA expression in urogenital ridges of embryos that were either heterozygous for the Müllerian Inhibiting Substance type II receptor or homozygously deleted to study the genes regulated by MIS during Müllerian duct regression.

overall_design: Approximately 200 mosue embryos were sorted for heterozygous or homozygous deletion of the MISR2, urogenital ridges were collected and the gonads were discarded.  mRNA was prepared from pooled ridges and sent for Affymetrix analysis.


title: Toxicogenomics and phenotypic characterization of adult female zebrafish liver treated with nitrophenol

first: Choong Yong

last: UNG

overall_design: We analyzed 12 arrays of nitrophenol-treated adult female zebrafish liver and 12 arrays of control fish.

first: Choong-Yong

last: Ung

first: Sie-Hong

last: Lam

first: Hlaing

last: Myintzu

first: Sinnakarupan

last: Mathavan

first: Zhiyuan

last: Gong


title: Estradiol modulates gene expression in the monkey iliac artery

status: Public on Apr 05 2013

city: Vermillion

first: Kathleen

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

institute: University of South Dakota

summary:
Objective:  To examine the effect of estradiol on gene expression in the monkey iliac arteries.
Design:  Eight ovariectomized cynomolgus monkeys were on a high fat diet for 6.5 years.  The left iliac artery was biopsied before randomization to estradiol (1 mg Estrace® per day, n=4) or vehicle (n=4) for 8 months.  The right iliac artery was obtained at necropsy.  Gene expression in the iliac arteries in response to estradiol was determined by DNA microarray and confirmed by real time RT-PCR.
Results:  Atherosclerotic lesions in the iliac arteries ranged in size from 0-0.61 mm2 in estrogen-treated animals and from of 0-0.873 mm2 in controls.  106 genes were shown to be down-regulated and 26 genes were up-regulated in the monkey iliac arteries in response to estradiol.  Among the genes shown to be up-regulated by DNA microarray and confirmed by real time RT-PCR were components of the insulin-like growth factor (IGF) pathway, IGF-1, IGF binding protein 4 (IGFBP4) and IGFBP5.  Components of the Wnt signaling pathway were also up-regulated, including secreted frizzled-related protein 2 (SFRP2), SFRP4, low density lipoprotein receptor-related protein 6 (LRP6), and Wnt 1 inducible signaling pathway protein 2 (WISP2).
Conclusions:   The modest effect of estradiol on gene expression in monkey iliac arteries reported herein may reflect a reduction in response to estradiol as a result of the effect of the altered environment of the artery containing atherosclerotic plaque.

overall_design:
Experiment Design:
Goal of the experiment:  To examine differential gene expression in the iliac arteries of ovariectomized cynomolgous monkeys on a high fat diet in response to treatment with estradiol.

Brief description of the experiment:
Objective:  To examine the effect of estradiol on gene expression in the monkey iliac arteries.
Design:  Four ovariectomized cynomolgous monkeys were on a high fat diet for 6.5 years.  The left iliac artery was biopsied before randomization to estradiol (1 mg Estrace® per day, n=4) for 8 months.  The right iliac artery was obtained at necropsy after treatment.  Gene expression in response to estradiol was determined by CodeLink Whole Human (Applied Microarrays, Tempe, AZ) DNA microarray and confirmed by real time RT-PCR.
Results:  Atherosclerotic lesions in the iliac arteries ranged in size from 0-0.61 mm2 (mean 0.34 ± 0.13 mm2) in pretreatment arteries and 0-1.411 (mean 0.789 ± 0.31mm2) in post-estrogen treated arteries.  106 genes were shown to be down-regulated and 26 genes were up-regulated in the monkey iliac arteries in response to estradiol.  Among the genes shown to be up-regulated by DNA microarray and confirmed by real time RT-PCR were components of the insulin-like growth factor (IGF) pathway, IGF-1, IGF binding protein 4 (IGFBP4) and IGFBP5.  Components of the Wnt signaling pathway were also up-regulated, including secreted frizzled-related protein 2 (SFRP2), SFRP4, low density lipoprotein receptor-related protein 6 (LRP6), and Wnt 1 inducible signaling pathway protein 2 (WISP2).
Conclusions:   The modest effect of estradiol on gene expression in monkey iliac arteries reported herein may reflect a reduction in response to estradiol as a result of the effect of the altered environment of the artery containing atherosclerotic plaque.

Keywords:  nonhuman primate, hormone replacement

Experimental factors:  hormone treatment

Experimental design:  Female cynomolgous monkeys (n=4) had been ovariectomized for 4 years and on a high fat diet for 6.5 years. The left iliac artery was removed at surgical biopsy.  Animals were treated with estradiol for 8 months, then necropsied.  The right iliac artery was obtained at necropsy.  The presence and size of atherosclerotic plaque was quantified in the iliac arteries.  Arterial tissue from the iliac arteries was used for DNA microarray analysis of gene expression.

Quality control steps:  The cRNA that was synthesized from each iliac artery was used for hybridization to a single CodeLink (Applied Microarrays, Tempe, AZ) whole human microarray.  Only one sample was hybridized with each slide and only one dye (Alexa 647) was used so no dye swaps were necessary.  Bacterial control spikes were used as per manufacturer's instructions.

Samples used, extract preparation and labeling:
The origin of each biological sample:  The samples were iliac arterial tissue from cynomolgous monkeys.

Manipulations of biological samples and protocols used:  Cynomolgous monkeys were placed on a high fat diet 6.5 years before the experiment and ovariectomized 4 years prior to the experiment to induce a surgical menopause.  The left iliac artery was surgically removed from each animal in the study before treatment with estradiol, the the right iliac artery was removed after the treatment period at necropsy.  The presence and size of atherosclerotic plaque was quantified in the iliac arteries

Experimental factor:  hormone treatment

Technical protocols:  The iliac arteries were homogenized in TRI reagent, bromochloropropane and sodium acetate were added, and the samples were centrifuged to separate the phases.  The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity of RNA were evaluated by an Agilent Bioanalyzer using the RNA 6000 Nanoassay LabChip.

Labeled cRNA was prepared using the MessageAmp II-Biotin enhanced kit (Ambion).  0.275 microgram of total iliac artery RNA was mixed with bacterial control RNA spikes and primed with T7 oligo(dT) primer for 10 min at 70C.  (The bacterial control spikes included araB, entF, fixB, gnd, hisB, and leuB.)  The first strand of cDNA was synthesized with first strand buffer, dNTP mix, RNase inhibitor, and reverse transcriptase for 2 h at 42C.  The second strand cDNA synthesis reaction was prepared using second strand buffer, dNTP mix, DNA polymerase mix, and RNase H; the reaction was carried out for 2h at 16C.  The double-stranded cDNA was purified on QIAquick columns (Qiagen) and the eluent was dried down in a SpeedVac concentrator.  The double-stranded cDNA was resuspended in a mixture containing T7 reaction buffer, T7 ATP, T7 GTP, T7 UTP, T7 CTP, biotin-11-UTP, and T7 enzyme mix for the synthesis of cRNA.  The cRNA synthesis reaction was terminated after 14h at 37C by purifying the cRNA on RNeasy columns (Qiagen).  The concentration of cRNA was determined by spectrophotometry.

Hybridization procedures and parameters:  10 micrograms of cRNA was mixed with fragmentation buffer and heated to 94C for 20 min.  The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides, and hybridized for 18 hours at 37C.
The slides were washed in 0.75x TNT (Tris-HCl, NaCl, Tween-20) at 46C for 1h then incubated with streptavidin-Alexa 647 fluorescent dye for 30 min at room temperature.  The Alexa fluor was prepared in TNB blocking buffer (0.1M Tris-HCl, 0.15M NaCL, 0.5% NEN Blocking Reagent-PerkinElmer)  The slides were then washed 4 times for 5 min each in 1x TNT and twice in 0.05% Tween 20 for 5 sec each.  The slides were dried by centrifugation and scanned in an Axon GenePix 4000B scanner.

first: Susan

last: Appt

first: Abha

last: Chalpe

first: Connie

last: Mark-Kappeler

first: Thomas

middle: C

last: Register

middle: B

last: Clarkson


title: Toxicogenomics and phenotypic characterization of adult male zebrafish liver treated with chloroaniline

summary: We performed microarray-based expression profiling on liver of male zebrafish exposed to 30 µg/L of chloroaniline for 8-96 h, to identify global transcriptional programs and biological pathways involved in chloroaniline-induced adaptive responses under in vivo environment.

overall_design: We analyzed 12 arrays of chloroaniline-treated adult male zebrafish liver and 12 arrays of control fish.


title: Transcriptome profiling of maize anthers infected by Ustilago maydis

status: Public on Mar 21 2013

city: Stanford

first: John

last: Fernandes

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

summary:
Two-organism transcriptome profiling of infected maize anthers demonstrated that there are anther-specific gene expression programs for both the pathogen and the host.
Two-dye, competitive microarray hybridizations were performed on Agilent oligo arrays.  Confocal microscopy on other anthers demonstrated that U. maydis was in contact with all anther
lobe cell types by 3 days post-infection and that the pathogen disrupted both host cell division and cell expansion patterns.

sample_organism:
Zea mays
Mycosarcoma maydis

platform_organism:
Zea mays
Mycosarcoma maydis

overall_design:
Four replicates comparing mock and infected samples at 3dpi for anthers of 0.3 - 0.6 mm.
maize, pathogen, fungus, Ustilago

first: Linda

last: Nguyen

first: Virginia

last: Walbot


title: Hippo Signaling Regulates Differentiation and Maintenance in the Exocrine Pancreas

status: Public on Feb 14 2013

city: Philadelphia

first: Tao

last: Gao

state: PA

address: 421 Curie Blvd, BRB II/III, Room 527

institute: University of Pennsylvania

summary: The Hippo signaling pathway has become recognized as a context-dependent regulator of cell proliferation, differentiation, and apoptosis in species ranging from Drosophila to human. In this study, we sought to understand whether Hippo signaling plays a role in pancreatic development and organ homeostasis.

overall_design: We analyzed mRNA from 5 samples each from control and DKO mouse pancreas using Affymetrix MouseGene 1.0 ST Array platfrom. Array data was processed by Affymetrix array computational tools.

first: Dawang

last: Zhou

first: Chenghua

last: Yang

first: Targinder

last: Singh

first: Alfredo

last: Penzo-Mendez

first: Ravikanth

last: Maddipati

first: Alexandros

last: Tzatsos

first: Nabeel

last: Bardeesy

first: Joseph

last: Avruch

first: Ben

middle: Z

last: Stanger


title: Gene expression in Longissimus lumborum and Semimembranosus skeletal muscles in pig using the GenmascqChip (custom 15K Agilent microarray)

status: Public on Jan 10 2013

city: saint-gilles

first: marie

last: damon

address: domaine de la prise

country: France

institute: INRA

summary: Transcriptional profiling between two different skeletal muscles (Longissimus and Semimembranosus) in pig

overall_design: The 90 pigs (females and barrows) used in gene expression analyses are part of a larger F2 population of 1,000 animals, setup within the framework of a QTL detection program. These animals were produced as a second generation intercross between two commercial sire lines (F016, Pietrain type line, and FH019, synthetic line from Hampshire, Duroc and Large-White founders, FRANCE-HYBRIDES, St Jean de Braye, France).

first: Marie

last: Damon

first: Annie

last: Vincent

first: Frédéric

last: Hérault


title: Toxicogenomics and phenotypic characterization of adult female zebrafish liver treated with chloroaniline

first: Choong Yong

last: UNG

first: Choong-Yong

last: Ung

first: Sie-Hong

last: Lam

first: Hlaing

last: Myintzu

first: Sinnakarupan

last: Mathavan

first: Zhiyuan

last: Gong


title: Gene expression changes in liver tissues from alcohol treated mice

status: Public on Feb 12 2013

city: Washington

first: Henghong

last: Li

state: DC

address: 3970 Reservoir Rd., NW

department: Biochemistry

institute: Georgetown University

summary: transcriptomic changes in the early stages of ALD in mice fed the Lieber-Decarli liquid diet with or without alcohol for four months to identify biomarkers for the early stage of alcohol induced liver damage. Mice were sampled after 1, 2 and 4 months treatment.

overall_design: Two-condition experiment, control vs. alcohol treated at specified time point. Sample pooled from six biological replicates in each group. Reverse-fluorescence replicates.


title: Microarray analysis of transcriptional responses to abscisic acid and salt stress in Arabidopsis thaliana

status: Public on Mar 28 2013

city: Harbin

first: Yujia

last: Liu

address: 26 Hexing Road

institute: Northeast Forestry University

summary: To investigate differences in plant responses to salt and ABA stimulus, differences in gene expression in Arabidopsis in response to salt and ABA were compared using an Agilent oligo microarray. Four-week-old Arabidopsis thaliana ecotype Columbia (Col-0) seedlings were treated with either 150 mM NaCl or 10 μM ABA for 6 hours; unstressed seedlings (control sample) were collected in parallel to avoid the possible effects of circadian rhythms. The results revealed that 31 genes were up regulated by both NaCl and ABA stress, and 23 genes were down-regulated by these stressors. To provide further validation of our microarray experiment data, ten genes from this signature were quantified in the same RNA samples by quantitative real-time PCR.

overall_design: Differentially expression genes of Arabidopsis thaliana were measured under salt stressed, ABA stressed and normal condition for 6 hours, respectively. Three independent experiments were performed at each treatment using different plants for each experiment.

first: Yucheng

last: Wang


title: Molecular and functional features demarcate embryonic and induced pluripotent stem cells in rabbits

status: Public on Jan 11 2013

city: jouy en josas

first: barbara

last: schmaltz-barbara

address: domaine de vilvert

summary: Little is known about the molecular and functional features of pluripotent stem cells (PSCs) in rabbits. To address this, we derived and characterized two types of rabbit PSCs from the same breed of New Zealand White rabbits: four lines of embryonic stem cells (rbESCs), and three lines of induced PSCs (rbiPSCs) that resulted from reprogramming adult skin fibroblasts. All lines were dependent on fibroblast growth factor 2. All rbESC lines exhibited molecular and functional properties typically associated with primed pluripotency. The rbESC lines also exhibited a cell cycle with a prolonged G1 phase and a DNA damage checkpoint prior to entry into the S phase, which are two features typically associated with the somatic cell cycle. In contrast, the rbiPSC lines exhibited some characteristics of naïve pluripotency as defined in rodents, including resistance to single cell dissociation by trypsin, robust activity of the distal enhancer of the mouse Oct4 gene, and expression of naïve-specific genes. According to gene expression profiles, rbiPSCs were closer to the rabbit inner cell mass than rbESCs. We propose that rbiPSCs self-renew in an intermediate state between naïve and primed pluripotency, which represents a key step toward the generation of bona fide naïve PSC lines in rabbits

overall_design: The patterns of stage specific embryonic antigen (SSEA) expression were also assessed between cell lines. All two rbiPSC lines exhibited heterogeneous expression of SSEA1 and SSEA4 that leads to obtain 3 different cell sub-populations (SSEA1+, SSEA1+/4+, SSEA1-/4-). All four rbESC lines expressed only SSEA1 and not SSEA4. Then, for this category of cell lines, we used 3 different cell sub-populations (SSEA1+, SSEA1-, and total which contained all cell types). Three independent experiments were performed for each line and for each cell sub-population.

first: Barbara

last: Schmaltz-Panneau

first: Luc

last: Jouneau

first: Cédric

last: Cabau

first: Véronique

last: Duranthon


title: rRNA cleavage ensures translational cessation in the mature sperm

status: Public on Mar 11 2013

city: Detroit

first: Stephen

last: Krawetz

state: MI

address: 275 E. Hancock

department: Center for Molecular Medicine and Genetics

institute: Wayne State University School of Medicine

summary: We report how unique RNA seq profiles of ribosomal RNA (18S, 28S) present in sperm indicate specific cleavage sites.  Additionally, these sequencing results reveal how overall character of RNA (GC content) can significantly affect overall distribution of mapped reads.

overall_design: Examination of rRNA population and distribution in spermatozoa

first: Graham

last: Johnson

first: Edward

last: Sendler


title: 450k Analysis of 42 FFPE HPV+ and HPV- HNSCC samples

status: Public on Nov 30 2012

city: London

first: Matthias

last: Lechner

address: Gower Street

department: UCL Cancer Institute

country: United Kingdom

institute: University College London

summary: The methylation analysis of 21 FFPE HPV+ HNSCC samples and 21 FPPE HPV- HNSCC samples by Infinium HumanMethylation450 BeadChip

overall_design: Analysis of 42 450k methylation profiles, comprising 21 HPV+ HNSCC samples and 21 HPV- HNSCC samples

first: Tim

last: Fenton

first: James

last: West

first: Gareth

last: Wilson

first: Andrew

last: Feber

first: Christina

last: Thirlwell

first: Harpreet

middle: K

last: Dibra

first: Amrita

last: Jay

first: Lee

last: Butcher

first: Fiona

last: Gratrix

first: Nirali

last: Patel

first: Francis

last: Vaz

first: Paul

last: O'Flynn

first: Nicholas

last: Kalavrezos

middle: E

last: Teschendorff

first: Chris

last: Boshoff

first: Stephan

last: Beck


title: Gene expression profiling of breast carcinomas using leftovers from diagnostic Fine Needle Aspiration Cytology

status: Public on Dec 20 2012

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

summary:
INTRODUCTION. Gene expression profiling has emerged as a potentially useful tool for personalized management of breast cancer. Adequate RNA can be obtained for this scope from dedicated fine-needle aspiration cytology (FNAC), with the limitation that separate sampling prohibits direct comparison with the material used for cytology. The aim of this study was to investigate whether syringe leftovers of cytological smears obtained in diagnostic FNACs can be successfully used to extract RNA for reliable PCR- and microarray-based gene expression analysis.

METHODS. Twenty-eight FNACs were performed under ultrasound guide. After preparing two smears for cytological diagnosis, the syringes were immediately rinsed with Trizol® to extract RNA from residual material. The abundance and type of cells obtained from the smears was recorded and compared to RNA amounts and quality as determined by spectrophotometry and RT-PCR. FNAC leftovers of eleven breast cancers of different size, histological type, grade and immunoprofile were then selected for gene expression profiling using oligonucleotide microarrays.

RESULTS. FNAC leftovers yielded an average of over 10 micrograms of RNA, more proportional to the amount of cells on the smear than to the lesion size, and adequate for expression analysis in 26/28 cases. The samples chosen for microarray analysis were clustered according to four criteria: (i) gene expression profiles of all detected genes; (ii) gene expression profiles of a previously defined stromal gene signature; (iii) “biological scores”, related to diagnostic cytological variables; (iv) “technical scores”, related to RNA/cRNA/microarray quality controls. Clusters generated by both expression profiles partitioned the samples in well-distinguished subgroups that were highly overlapping with clusters obtained using biological scores. Conversely, poor overlap was observed with clusters based on technical scores, demonstrating that sample divergences in RNA quality and amounts due to acquisition, handling and processing did not severely influence gene expression profiling.

CONCLUSIONS. The syringe leftover after the smearing procedures of FNAC samples is suitable for RNA banking even when taken from small, non-palpable breast lesions, which guarantees congruity between morphological and molecular analysis. RNA yield mostly correlates with cellularity of the smears, and gene expression profiles are consistent with the cytologic features, and therefore with tumour biology.

overall_design: Eleven fine needle aspirates, each from a different breast cancer.

first: Anna

last: Sapino


title: ChIP-seq analysis of SRT1 and H3K9ac in MH63 and srt1 RNAi.

status: Public on Feb 10 2013

city: Wuhan

first: zhong

last: xiaochao

address: 狮子山街1号

institute: National center of plant gene research（Wu han）

summary: We report the high-throughput profiling of H3K9ac and SRT1 in MH63 and SRT1 RNAi. By obtaining about 8 million pair-end reads from H3K9ac and 6 million pair-end reads from SRT1, we find that about 45% of rice genes are marked by H3K9ac in 11 day-old seedlings. There are 1824 genes may be bound directly by OsSRT1. OsSRT1 is a site-specific deacetylase involved in deacetylation of H3K9 over specific genes. Overlapping between increased H3K9ac peaks in the RNAi plants and that of OsSRT1-binding was found over 37 genes, suggesting that OsSRT1 directly targeted to these genes for H3K9 deacetylation. The observations that H3K9ac was enriched at the 5’ end of genes larger than 1.5 kb and OsSRT1 RNAi enhanced the enrichment at that position. However, the OsSRT1-binding was found to be enriched over gene bodies. While the meaning of this binding profile is not yet clear, it is speculated that OsSRT1 may contribute to maintain the low level of H3K9ac in the gene body.  In addition, this work revealed that OsSRT1 is enriched over retrotransposons.

overall_design: Examination of H3K9ac in MH63(WT) and SRT1-RNAi, OsSRT1 in MH63.

first: Xiaochao

last: Zhong

first: Daoxiu

last: Zhou


title: Gene expression in chow or HFD-fed OGG1-/- livers

status: Public on Dec 16 2012

city: Portland

first: Harini

last: Sampath

state: OR

address: 3181 SW Sam Jackson Park Rd

department: CROET

institute: OHSU

summary: Gene expression in livers of male wild-type (WT) and OGG1-deficient (Ogg1-/-) mice fed either a chow diet or a high-fat diet (HFD) were examined. Mice were fed the diet for 10 weeks prior to tissue collection and were 22 weeks of age at the time of tissue collection.

overall_design: 24 Total samples were analyzed. We generated the following pairwise comparisons using GeneSifter: WT Chow vs Ogg1-/- Chow; WT HFD vs. Ogg1-/- HFD using t-test followed by Benjamini and Hochberg correction.  An adjusted p-value less than 0.05 was considered to be statistically significant.

first: Vladimir

last: Vartanian

first: M

middle: R

last: Rollins

first: R

last: Lloyd


title: Gene expression profiling of ampullary carcinomas classifies ampullary carcinomas into biliary-like and intestinal-like subtypes that are prognostic of outcome

status: Public on Jan 01 2013

city: Houston

first: Jiexin

last: Zhang

state: TX

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

summary:
Adenocarcinomas of the ampulla of Vater are classified as biliary cancers, though the exact epithelium of origin for these cancers is not known.
We sought to molecularly classify ampullary adenocarcinomas in comparison to known adenocarcinomas of the pancreas, extrahepatic bile duct, and duodenum by gene expression analysis.

overall_design: We analyzed 32 fresh-frozen resected, untreated periampullary adenocarcinomas (8 pancreatic, 2 extrahepatic biliary, 8 duodenal, and 14 ampullary) using the Affymetrix U133 Plus 2.0 genome array.

first: Michael

last: Overman


title: Bartonella quintana: growth phase and temperature response

status: Public on Dec 05 2012

city: San Francisco

first: Christopher

middle: S

last: Nelson

institute: UCSF

summary: Transcriptional profiling of Bartonella quintana grown on a plate at 28C and 37C for various time points.

overall_design: Comparing each individual sample in cy5 to a pooled mix of all samples in cy3 to preserve a common denominator.


title: The SCFFBXO28 ubiquitin ligase coordinates CDK activity with MYC-mediated transcription in the cell cycle and predicts poor survival in breast cancer

status: Public on Feb 28 2013

city: Stockholm

first: Daniel

last: Klevebring

address: Nobels väg 12A

department: Medical Epidemiology and Biostatistics

country: Sweden

institute: Karolinska Institutet

summary: Investigation of differentially expressed genes in human HCT116 cells after knockdown of FBXO28 for 16h and 36h.

overall_design: FBXO28 knockdown and control HCT116 cells. 4 replicates per time point (16h, 36h), including dye swaps.


title: An Organ Culture System to Model Early Degenerative Changes of the Intervertebral Disc: II Profiling Global Gene Expression Changes

status: Public on Nov 29 2012

first: Dessislava

last: Markova

address: 1015 Walnut

department: Orthopaedic Surgery

institute: Thomas Jefferson University

summary:
To mimic a degenerative insult, rat intervertebral discs were cultured in the presence of TNF-alpha, IL-1beta and serum limiting conditions.
Gene expression analysis was performed using a microarray to identify differential gene expression between experimental and control groups.

overall_design: The discs were collected and the annulus fibrosus (AF) was separated from the nucleus pulposus (NP). Total RNA from NP was used for RNA extraction and hybridization on Affymetrix microarrays: Control group - Ctr-1, Ctr-2, Ctr-3, Ctr-4 and Experimental group-Exp-1, Exp-2, Exp-3, Exp-4.

last: Kepler

first: Sankar

last: Addya

first: Hallie

last: Murray

first: Alexander

last: Vaccaro

first: Irving

last: Shapiro

first: David

last: Anderson

first: Todd

last: Albert

first: Makarand

middle: V

last: Risbud


title: Transcriptome analysis of multiple pre-meiotic anther stages and laser microdissected cell types in maize

status: Public on May 01 2013

first: John

last: Fernandes

summary:
Transcriptomes from multiple pre-meiotic stages of wild type, mac1, and msca1 maize anthers were characterized by microarray hybridization. The goal was to characterize the developmental progression as the anther specifies five cell types and grows rapidly precedeing meiotic entry. The stages characterized were immature anther primordia (0.15 mm long in maize) containing just stem cells, through somatic and germinal cell fate specification (0.20 and 0.25 mm), mitotic proliferation (0.4 mm), and finally the birth of the middle layer and tapetum (0.7 mm). To obtain cell-type specific markers, at 0.7 mm we also compared whole anthers to collections of laser-microdissected anther cell types including the archesporial cells (pre-meiotic germinal cells), nutritive layers (middle layer and tapetum) and structural layers (endothecium and epidemis) of the anther lobe.
keyword: anther development, maize, male-sterile

overall_design:
Three loop designs covered the early stages (up to 0.7 mm) with two replicates for each comparison.
The first loop had 0.2 mm long anthers and compared wild type versus mac1 mutant versus msca1 mutant in a three vertex loop design.
The second loop had four vertices and compared 0.15 mm WT anther primordia, 0.25 mm WT anthers, 0.4 mm WT anthers and finally 0.4 mm mac1 mutant anthers.
The third had 0.7 mm anthers in a three vertex loop with the nutritive layers (middle layer and tapetum) at one vertex, the germinal pre-meiotic cells at another vertex, and whole anthers at a third vertex.  The whole anther samples were also, separately and outside of the loop, compared in four replicates to the structural layers (endothecium and epidermis).

first: Kelliher

last: Timothy

first: Virginia

last: Walbot


title: Global gene expression in response to West Nile virus in mouse spleen and liver

status: Public on Dec 19 2012

city: Seattle

last: Katze

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: Purpose of this experiment was to further understand how innate immune defenses impact host response and West Nile virus tissue tropism. This study examined host-transcriptional response to West Nile virus in permissive and nonpermissive tissues using wildtype mice and mice with genetically altered interferon signaling pathways.

overall_design: Age-matched six to twelve week old mice were inoculated subcutaneously in the left rear footpad with 100 PFU of West Nile virus isolate TX 2002-HC (WNV-TX) in a 10 microL inoculum diluted in Hanks balanced salt solution (HBSS) supplemented with 1% heat-inactivated FBS. Mice were monitored daily for morbidity and mortality. Expression oligonucleotide arrays were performed on RNA isolated from spleen and liver tissues from strain and time-matched mock infected mice (n=2) and WNV-TX infected wild type (WT; n=3; day 4 post-infection), Ips-1-/-(n=3; day 4 post-infection), Ifnar-/- (n=3; day 2 post-infection), and Ips-1-/-xIfnar-/- (DKO; n=3; day 4 post-infection) mice.

first: Mehul

last: Suthar

first: Margaret

last: Brassil

first: Gabriele

last: Blanik

first: Aimee

last: McMillan

first: Sean

last: Proll

first: Sarah

last: Belisle

last: Gale


title: Expression analysis of uncultured and culture-derived colony forming unit-monocytes and megakaryocytes

status: Public on Sep 13 2012

city: Toronto

first: Wenlian

last: Qiao

state: Ontario

address: Room 1110, 160 College Street

country: Canada

institute: University of Toronto

summary:
The cellular composition of heterogeneous samples can be predicted from reference gene expression profiles that represent the homogeneous, constituent populations of the heterogeneous samples. However, existing methods fail when the reference profiles are not representative of the constituent populations. We developed PERT, a new probabilistic expression deconvolution method, to address this limitation. PERT was used to deconvolve cellular composition of variably sourced and treated heterogeneous human blood samples. Our results indicate that even after correcting batch effects, cells presenting the same cell surface antigens display different transcriptional programs when they are uncultured versus culture-derived. Given gene expression profiles of culture-derived heterogeneous samples and profiles of uncultured reference populations, PERT was able to accurately recover proportions of pure populations composing the heterogeneous samples. We anticipate that PERT will be widely applicable to expression deconvolution problems using profiles from reference populations that vary from the corresponding constituent populations in cellular state but not cellular identity.
Gene expression microarray to examine transcriptome variations between uncultured and culture-deried blood cells of the same phenotype as defined by the on and off expression of antigens.

overall_design: Fresh human umbilical cord blood-derived and serum free culture-derived colony-forming unit-monocytes (CFU-M) and megakaryocytes (MEGA) were compared respectively

first: Wendy

first: Gerald

last: Quon

first: Elizathbeth

last: Csaszar

first: Mei

last: Yu

first: Quaid

last: Morris

first: Peter

middle: W

last: Zandstra


title: Lineage-depleted (Lin-) cell and mono-nucleated cell (MNC), and uncultured and culture-derived colony forming unit-monocytes and megakaryocytes

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

overall_design: Refer to individual Series


title: Expression profiles of lineage-depleted (Lin-) cell and mono-nucleated cell (MNC) samples derived from human umbilical cord blood

summary:
The cellular composition of heterogeneous samples can be predicted from reference gene expression profiles that represent the homogeneous, constituent populations of the heterogeneous samples. However, existing methods fail when the reference profiles are not representative of the constituent populations. We developed PERT, a new probabilistic expression deconvolution method, to address this limitation. PERT was used to deconvolve cellular composition of variably sourced and treated heterogeneous human blood samples. Our results indicate that even after correcting batch effects, cells presenting the same cell surface antigens display different transcriptional programs when they are uncultured versus culture-derived. Given gene expression profiles of culture-derived heterogeneous samples and profiles of uncultured reference populations, PERT was able to accurately recover proportions of pure populations composing the heterogeneous samples. We anticipate that PERT will be widely applicable to expression deconvolution problems using profiles from reference populations that vary from the corresponding constituent populations in cellular state but not cellular identity.
Human umbilical cord blood-derived lineage negative cells and mononucleated cells

overall_design: Cellular compositions of mononucleated cell and lineage negative cell compartments were deconvolved based on the gene expression profiles


title: Characterization of gene expression profiles induced by HIC-1 reactivation on breast cancer

status: Public on Nov 06 2012

city: Shanghai

first: Yingyan

address: Shanghai Ruijin 2nd Road No.197

department: Department of Surgery

institute: Shanghai Ruijin Hospital

summary: To explore the molecular mechanisms and signal pathways induced by restoring tumor suppressor gene HIC-1 on breast cancer cells.  We have employed whole genome microarray expression profiling as a discovery platform to identify the differential genes induced by HIC-1 gene activation. Small activating RNA (saRNA) that targeted promoter region was used, and MCF-7 breast cancer cell line was selected as cell model. After 96h for saRNA transfection, the cells were collected and the whole genome expression profiles were analyzed. Three independent experiments were repeated for different groups. With the treshold of  p<0.01 and fold change >=2 or <-2, there were 1375 differential expression genes, which are related to cell cycle, apoptosis, cell migration, cell invasion and cell proliferation.

overall_design: SaRNA induced gene expression in human breast cancer cell MCF-7 was measured at 96 hours after transfection by 50 nM saRNA. Three independent experiments were performed for experimental group and control group.

first: Wei

last: Zhang


title: Expression values from wild-type retinas and retinas with a mutant Rhodopsin transgene (Tg(RHO P347S)) with and without Endothelin-2 (EDN2)

status: Public on Jul 16 2012

first: Alexa

middle: Natalie

last: Bramall

address: 101 College St.

institute: Hospital for Sick Children

summary: Expression of the Endothelin-2 (Edn2) mRNA is greatly increased in the photoreceptors (PRs) of mouse models of inherited PR degeneration. To identify retinasl gene whose expression is directly or indirectly regulated by EDN2 in the presence of the Tg(RHO P347S) mutant allele, we defined mRNAs that were differentially expressed in Edn2+/+, Edn2-/-, Tg(RHO P347S) Edn2+/+, and Tg(RHO P347S) Edn2-/- retinas.

overall_design: RNA was extracted from Edn2+/+, Edn2-/-, Tg(RHO P347S) Edn2+/+, and Tg(RHO P347S) Edn2-/- retinas at postnatal day 21 (PN21) and hybridized to Affymetrix arrays

first: Roderick

last: McInnes


title: STATs Shape the Active Enhancer Landscape of T Cell Populations

status: Public on Nov 24 2012

city: Bethesda

first: Golnaz

last: Vahedi

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

institute: National Institutes of Health

summary: Signaling pathways are intimately involved in cellular differentiation, allowing cells to respond to their environment by regulating gene expression. While enhancers are recognized as key elements that regulate selective gene expression, the interplay between signaling pathways and actively used enhancer elements is not clear. Here, we use CD4+ T cells as a model of differentiation, mapping the acquisition of cell-type-specific enhancer elements in T-helper 1 (Th1) and Th2 cells. Our data establish that STAT proteins have a major impact on the acquisition of lineage-specific enhancers and the suppression of enhancers associated with alternative cell fates. Transcriptome analysis further supports a functional role for enhancers regulated by STATs. Importantly, expression of lineage-defining master regulators in STAT-deficient cells fails to fully recover the chromatin signature of STAT-dependent enhancers. Thus, these findings point to a critical role of STATs as environmental sensors in dynamically molding the specialized enhancer architecture of differentiating cells.

overall_design: Active enhancer elements were defined as p300-high/H3K4me1-high. Using ChIP-seq, we mapped active enhancer landscapes of two CD4+ T helper cells, Th1 and Th2. To investigate the effect of STAT proteins on this landscape, we profiled active enhancers in the absence of STATs. Overall, STATs deficiency had a major impact on recruitment of p300. In addition, ectopic expression of master regulators T-bet and GATA3 in STAT-deficient cells failed to recover most active enhancers.

first: Hayato

last: Takahashi

first: Shingo

last: Nakayamada

first: Hong-wei

last: Sun

first: Vittorio

last: Sartorelli

first: Yuka

last: Kanno

first: John

middle: J

last: O’Shea


title: Microarray analysis of At-med16-1 and wild type (Col-0) infected with the avirulent bacterial pathogen  Pst DC3000/avrRpt2

status: Public on Jun 30 2012

city: Gainesville

first: Zhonglin

last: Mou

state: FL

address: 981 Museum Road

department: Microbiology and Cell Science & Plant Molecular and Cellular  Biology

institute: University of Florida

summary: The goal of the microarray experiment was to identify defense genes that were differentially expressed in the Arabidopsis mutant At-med16-1 and wild type in response to infection of the avirulent bacterial pathogen Pst DC3000/avrRpt2.  Results indicated that, compared with the wild type, several positive regulators of SAR (systemic acquired resistance) were downregulated and a group of SAR negative regulators were upregulated in At-med16-1.

overall_design: Three biological replicates with leaves from 8 plants per sample were collected at 0, 4, 8, and 24 hours after inoculation with the avirulent bacterial pathogen Pst DC3000/avrRpt2.  After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Equal amount of RNA from the 3 biological replicates were pooled as one sample for microarray analysis.

first: Xudong

first: Yanping

first: Jin

last: Yao

first: Yijun


title: TFH cell dynamics in Rhesus Monkeys during SIV infection

status: Public on Jun 19 2012

city: Port St. Lucie

first: Xiaoyong

address: 9801 SW Discovery Way

institute: VGTI, FL

summary: Cells from SIV-negative (SIVnegative_p17, n=5; SIVnegative_p18, n=5) and SIV-chronic (ChronicSIVinfection_p18, n=6) SP tissues were sorted for microarray studies. RNA samples were prepared using the Illumina beads station assay and hybridized to the Illumina HumanHT-12 version 4 Expression BeadChip according to the Illumina’s instruction. The data were normalized with the quantile normalization method of Bioconductor package limma . Missing values were imputed with R package impute (http://cran.rproject.org/web/packages/impute/index.html). Genes with significant differential expression levels were identified using Bioconductor limma package with >= 1.5 fold change (up or down), the false discovery rate (FDR) adjusted P value < 0.05.

overall_design: Cells from SIV-negative (SIV and SIV-chronic SP) tissues were sorted for micorarray studies

first: Constantinos

last: Petrovas

first: Elias

last: Haddad


title: Transcriptome responses to combined biotic and abiotic stresses in Arabidopsis thaliana

status: Public on Jan 31 2013

city: Kongens Lyngby

first: Simon

last: Rasmussen

address: Kemitorvet, Building 208

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

summary:
Biotic and abiotic stresses limit agricultural yields, and plants are often simultaneously exposed to multiple stresses. Combinations of stresses such as heat and drought or cold and high light intensity, have profound effects on crop performance and yeilds
To analyze such responses, we initially compared transcriptome changes in ten Arabidopsis thaliana ecotypes using cold, heat, high light, salt and flagellin treatments as single stress factors or their double combinations.

overall_design: Arabidopsis thaliana plants of ecotypes (Col, Ler, C24, Cvi, Kas1, An1, Sha, Kyo2, Eri and Kond) were subjected to the following stress treatments: Salt, Cold, Heat, High Light (HL), Salt+Heat, Salt+HL, Cold+HL, Heat+HL, as well as FLG (Flagellin, flg22 peptide), Cold+FLG, Heat+FLG

first: Pankaj

last: Barah

first: Maria

last: Suarez-Rodriguez

first: Pia

last: Friis

first: Atle

middle: M

last: Bones

first: Henrik

last: Nielsen

last: Mundy


title: A Random-Forest Based Algorithm for Prediction of Enhancers From Histone Modifications

status: Public on May 10 2012

city: LA JOLLA

first: Nisha

last: Rajagopal

address: 9106 REGENTS RD APT F

institute: UCSD

summary: Transcriptional enhancers play critical roles in regulation of gene expression, but their identification has remained a challenge.  Recently, it was shown that enhancers in the mammalian genome are associated with characteristic histone modification patterns, which have been increasingly exploited for enhancer identification.  However, only a limited number of histone modifications have previously been investigated for this purpose, leaving the questions answered whether there exist an optimal set of histone modifications that could improve the enhancer prediction.  Here, we address this issue by exploring a rich dataset produced by the human Epigenome Roadmap Project. Specifically, we examined genome-wide profiles of 24 histone modifications in human embryonic stem cells and fibroblasts, and developed a Random-Forest based algorithm to integrate histone modification profiles for identification of enhancers.As a training set, we used histone modification profiles at genome-wide binding sites of p300 in the two cell types identified using ChIP-seq.  We show that this algorithm not only leads to more accurate and precise prediction of enhancers than previous methods, but also helps identify an optimal set of three chromatin marks for enhancer prediction.

overall_design: ChIP-Seq Analysis of  p300 in hESC H1 and IMR90 cells. Sequencing was done on the Illumina Genome Analyzer II platform for the H1 data and Illumina HiSeq for IMR90.Data was mapped to hg18 using Bowtie.

first: Wei

last: Xie

first: Sarit

last: Klugman

first: Audrey

last: Kim

first: Yan

last: Li

first: Fulai

last: Jin

first: Samantha

last: Kuan

first: Lee

last: Edsall

first: David

last: Hawkins

first: Jason

last: Ernst

first: Manolis

last: Kellis

last: Stamatoyannopoulos

first: Bing

last: Ren


title: The retinoblastoma orthologue, rblA, is a major regulator of S-phase, mitotic, and developmental gene expression in Dictyostelium

status: Public on May 18 2012

city: Montreal

first: Kimchi

middle: Audrey

last: Strasser

state: Quebec

address: 7141 Sherbrooke Street West

department: Biology

institute: Concordia University

summary: The retinoblastoma tumour suppressor, Rb, has two major functions. First, it represses genes whose products are required for S-phase entry and progression, thus stabilizing cells in G1. Second, Rb synergizes with factors that induce cell cycle exit and terminal differentiation. Dictyostelium lacks a G1 phase in its cell cycle but it has a retinoblastoma orthologue, rblA. Using mRNA-Seq transcriptional profiling, we show that rblA strongly represses hundreds of genes whose products are involved in S-phase and mitosis. Both S-phase and mitotic genes are expressed at a single point in late G2 and again in mid-development, near the time when cell cycling is reactivated. RblA also activates a set of genes unique to slime moulds that function in terminal differentiation. Like its mammalian counterpart, Dictyostelium RblA plays a dual role, regulating cell cycle progression and transcriptional events leading to terminal differentiation. In the absence of a G1 phase, however, RblA functions in late G2 controlling the expression of both S-phase and mitotic genes.

overall_design: RNA was isolated from an rblA-disruptant and the parental strain when the cells were vegetatively growing or while the cells were developing (at the early culminant stage). Total RNA was also isolated from wild type cells synchronized using the cold-shock protocol (Maeda, J Gen Microbiol 132:1189-1196 (1986)). T0 to T13 represent the hours after the shift up from 9.5C to 22C, a regime that synchronizes the cells in the cell cycle.

first: Gareth

last: Bloomfield

first: Asa

last: MacWilliams

first: Adriano

last: Ceccarelli

first: Harry

first: Adrian

last: Tsang

first: Ian

last: Reid


title: Expression profiling of anthracyline-induced cardiotoxicity

status: Public on Aug 30 2012

city: Washington

first: Timothy

last: McCaffrey

address: 2300 I Street NW

department: Department of Biochemisty & Molecular Biology

institute: The George Washington University

summary: Whole blood RNA from women with, and without, chemotherapy-induced cardiotoxicity were profiled to identify possible biomarkers of sensitivity to heart failure. RNA was analyzed by PaxGene stabilization and purification, DNAse treatment, NuGen labeling, Affymetrix U133 plus 2 microarray analysis.

overall_design: Four groups of women were identified. The main effect was for women with chemo-induced heart failure (Group A) compared to women with a history of chemo, but no heart failure (Group B).  To identify transcripts that might be generally associated with heart failure, women with breast cancer, but prior to chem (Group C) with normal ejection fractions, were compared to women who did not have breast cancer, but had heart failure for unrelated reasons (Group D).

middle: A

first: Jannet

last: Lewis


title: Expression data from cAMP-treated WT or IFN-gR1-deficient T cells

status: Public on Jul 24 2012

city: Kyoto

first: Chengcan

last: Yao

address: Yoshida, Sakyo-ku

department: Pharmacology

institute: Kyoto University

summary:
cAMP inhibits TCR signaling, T cell proliferation, cytokine production and T cell function.
We used microarrays to detail the global programme of gene expression in TCR-activated WT or IFN-gR1-deficient CD4+ T cells by db-cAMP.

overall_design: CD4+ T cells were purified from spleens of WT or IFN-gR1-deficient mice by autoMACS, and activated with anti-CD3 plus anti-CD28 for 15 h. db-cAMP or vehicle control (med) was added into cultures for the last 3 h.

first: Shuh

last: Narumiya


title: Transcriptomic analysis of folic acid effects in doxorubicin-induced cardiotoxicity

status: Public on Nov 12 2015

city: Berlin

first: Georgios

last: Kararigas

address: Hessische Str. 3-4

country: Germany

institute: Charite University Hospital

summary:
Doxorubicin (DOXO), a chemotherapeutic drug, is cardiotoxic.
We hypothesized that folic acid is an effective therapeutic agent in a mouse model of DOXO-induced cardiotoxicity.  We performed genome-wide expression profiling to identify the underlying mechanisms.

overall_design: Male C57Bl6 2-mo old mice received DOXO (1x20 mg/kg, ip) or saline (sham). FA (10 mg/d) or placebo (plac) was administered 7d before DOXO administration until the end of the experiment (10d).


title: Transcriptome analysis of EYA2 non-expressing pancreatic cancer cell lines with stable transfectant overexpressing EYA2

city: Baltimore

first: AUDREY

last: VINCENT

address: 1550 Orleans Street, CRBII

department: Pathology

institute: Johns Hopkins University

overall_design: We analyzed Panc2.5 and Panc3.014 stable transfectant (overexpressing EYA2) and control (empty pcDNA6.2/cLumio-DEST vector) cell transcriptomes using the Affymetrix Exon Array ST1.0 platform. Statistical analysis of gene expression array data was completed with Partek Genomic Suite 6.4 software.

first: Audrey

last: Vincent

first: Seung-Mo

last: Hong

first: Chaoxin

last: Hu

first: Noriyuki

last: Omura

first: Angela

last: Young

first: Margaret

last: Griffith

first: Anirban

last: Maitra

first: Michael

last: Goggins


title: Haloperidol response across genetic backgrounds

status: Public on May 06 2012

city: Portland

first: Ovidiu

middle: Dan

last: Iancu

address: 3181 SW Sam Jackson Road

institute: OHSU

summary: We performed short-term bi-directional selective breeding for haloperidol-induced catalepsy, starting from three mouse populations of increasingly complex genetic structure: an F2 intercross, a heterogeneous stock (HS) formed by crossing four inbred strains (HS4) and a heterogeneous stock (HS-CC) formed from the inbred strain founders of the Collaborative Cross (CC). All three selections were successful, with large differences in haloperidol response emerging within three generations. Genome-wide analysis between the selected lines revealed post-selection loss of allelic diversity concurrent with significant genetic differences. In spite of large phenotypic differences, absolute gene-expression changes were modest and not concordant across selections. However, gene coexpression patterns changed significantly, as revealed by the weighted gene co-expression network analysis. In particular, we detected three modules (de novo subnetworks) that (a) were functionally enriched for neurobehavioral traits and (b) showed independently detectable changes in network connectivity across selections. By inferring strain contributions from the parental lines, we are able to identify significant differences in allelic content between the selected lines concurrent with large changes in transcript connectivity. Importantly, this observation implies that genetic polymorphisms can affect transcript and module connectivity without large changes in absolute expression levels. We conclude that, in this case, selective breeding acts at the subnetwork level, with the same modules but not the same transcripts affected across the three selections.

overall_design: Equal numbers of males and females (~200 total) from the founder populations (F2, HS4 and HS-CC) were phenotyped for haloperidol response using a two-step process that resulted in assigning animals to one of four groups; “1” was the least responsive, and “4” was the most responsive. Breeding pairs were selected from the most extreme response groups. The selection and breeding were continued for two additional generations; in the third generation, parents were bred for three rounds to produce progeny for gene expression. For each genetic background the submitted samples are labeled as either High or Low based on their response to haloperidol.

middle: D

first: Denesa

last: Oberbeck

first: Priscila

last: Darakjian

first: Sunita

last: Kawane

first: Jason

last: Erk

first: Shannon

last: McWeeney

first: Robert

last: Hitzemann


title: Early-stage breast cancer

status: Public on May 09 2012

city: seoul

first: SeungHyun

last: Jung

state: seoul

address: catholic university, medical college, banpo-dong

department: Department of Biochemistry

country: South Korea

institute: Catholic University of Korea

summary:
Copy number alteration profiling of human early-stage (stage I and II) breast cancers.
We aimed to describe the commonly occurred chromosome alterations in early-stage breast cancer (stage I and II) and to explore the implications of the recurrently altered regions (RAR) on the patient prognosis. For this purpose, we analyzed the DNA copy number alterations (CNAs) across the whole genome using oligoarray-comparative genomic hybridization (CGH) in the discovery set of EBC patients.

overall_design: 48 cases of early-stage breast cancer were used in this study.

first: Seung-Hyun

first: Yeun-Jun

last: Chung


title: Gene Expression Changes in Non-Dysplastic Mucosa from Patients with Ulcerative Colitis Harboring Remote Neoplastic Lesions

status: Public on Apr 20 2012

city: Chicago

first: Yong

last: Huang

state: IL

address: 900 East 57th Street

department: Medicine

institute: University of Chicago

summary:
Background and Aims: Individuals with ulcerative colitis (UC) are at increased risk for colorectal cancer, although underlying mechanisms are incompletely understood. We sought to identify a potential gene expression signature in non-dysplastic distal mucosa that as a “genetic field effect” could be a marker for remote neoplastic lesions.

Results: 468 genes were significantly up-regulated and 541 genes were significantly down-regulated >2-fold in UC patients with neoplasia compared to UC patients without neoplasia. Nine genes (ACSL1, BIRC3, CLC, CREM, ELTD1, FGG, S100A9, THBD, and TPD52L1) were progressively and significantly up-regulated from controls to quiescent non-dysplastic UC to UC with neoplasia. Immunostaining of proteins revealed increases in tissue expression of S100A9 and REG1 in UC-associated cancer and in non-dysplastic tissue from UC patients harboring remote neoplasia, compared to UC patients without dysplasia and normal controls.

Conclusions: Gene expression changes occur as a field effect in UC patients without active inflammation who harbor a remote dysplastic lesion. Further characterization of these genes and proteins might elucidate pathways of carcinogenesis in IBD and lead to the development of more accurate, less invasive markers of dysplasia in those at increased risk.

overall_design: Microarray assay were conducted on 20 RNA samples isolated from colon mucosa of 20 patients. Of these patients, 5 were normal controls, 4 had quiescent UC, and 11 had UC with neoplasia. Patients were included if they had a previous clinical diagnosis of UC confirmed by an expert GI pathologist, a disease duration > 7 years, and an extent of disease >20 cm proximal to the anal verge.

first: Joel

last: Pekow

first: Urszula

last: Dougherty

first: Edward

last: Gometz

first: Jeff

last: Nathanson

first: Greg

last: Cohen

first: Shawn

last: Levy

first: Masha

last: Kocherginsky

first: Nanda

last: Venu

first: Maria

last: Westerhoff

first: John

last: Hart

first: Amy

last: Noffsinger

first: Stephen

last: Hanauer

first: Roger

last: Hurst

first: Alessandro

last: Fichera

first: Loren

last: Joseph

first: Qiang

last: Liu

first: Marc

last: Bissonnette


title: Fetal programming of hepatic transcriptome in response to gestational low dietary protein levels in the pig

status: Public on Jul 21 2012

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

summary: German landrace gilts were fed a low protein diet (LP, 6% CP) throughout their whole pregnancy. Subsequently hepatic transcriptome profiles of the offspring were analysed at prenatal (94 dpc) and postnatal stages (1, 28, 188 dpn)

overall_design: per stage offspring of 8 gilts were collected for expression profiling

first: Siriluck

last: Ponsuksili

first: Michael

last: Oster


title: PGE2 promotes recovery from established Nephrotoxic Serum Nephritis in mice.

status: Public on Apr 23 2012

city: Augusta

first: Nino

last: Kvirkvelia

state: GA

institute: Georgia Health Sciences University

summary:
We induced acute nephritis by single injection of sheep nephrotoxic serum in mice and then treated the mice with prostaglandin E2.
We used microarrays to examine the global  gene expressions during recovery from nephrotoxic nephritis by prostaglandin E2.

overall_design: Acute nephristis was induced in female mice by single injection of sheep Nephortoxc Serum (NTS), followed by prostaglandin E2 administration daily starting from day 2 after NTS administration.  Mice were sacrificed on day 7 and RNAs were isolated from kidney.  The RNA samples were subjected to mouse gene 1.0 ST array analysis.

first: Malgorzata

last: McMenamin

middle: P

last: Madaio


title: Aberrant expressed genes in AML

status: Public on Apr 17 2012

first: Sebastian

last: Ochsenreither

state: Berlin

address: Hindenburgdamm 30

department: Hematology/Oncology

institute: Charite Berlin

type:
Expression profiling by array
Third-party reanalysis

summary: Acute myeloid leukemia (AML) is one of the most common and deadly forms of hematopoietic malignancies. We hypothesized that microarray studies could identify aberrantly expressed genes selectively expressed in AML blasts, believing that these genes may be potential therapeutic targets for adoptive T-cell strategies

overall_design: We compared gene expression profiles between leukemic blasts from 30 AML patients (this series and GSE9476) and prepublished samples of normal hematopoietic cells from healthy donors (N=17, GSE9476) and testis samples (N=2, GSE1133).

first: D

middle: L

last: Stirewalt

first: E

last: Pogosova-Agadjanyan


title: Gene expression data from muscle sample of pig commercial herd Pix(DLxDE).

status: Public on Dec 04 2012

summary:
In this study, we used correlation analysis of the expression profiles and carcass traits to produce a list of functional candidate genes under the assumption that genes with strong correlation between their expression values and drip belong to pathways or networks relevant for the control of the trait.
Expression QTL analyses for transcripts showing trait dependent expression were done in order to identify genes which show trait associated expression.

overall_design: 207 crosbred pig were hybridized to Affymetrix Porcine Genome Arrays.


title: Global transcriptional profiling of oleaginous yeast Rhodosporidium toruloides under nitrogen limitation.

city: Dalian

first: Zhiwei

last: Zhu

state: Liaoning

address: 457 Zhongshan Rd.

department: Division of Biotechnology

institute: Dalian Institute of Chemical Physics, Chinese Academy of Science

summary: Nitrogen limitation is a major regulator to initiate lipid overproduction in oleaginous fungi. To examine the influence of nitrogen starvation, chemiostat cultures of R. toruloides in defined media with abundant ammonium (MM) or minute ammonium (MM-N) were performed to obtain steady-state samples. Then Illumina's digital gene expression (DGE) technology was used for high-throughput transcriptome profiling of these samples.

overall_design: Two samples cultured in minimum media with abundant ammonium (MM) or minute ammonium (MM-N)

first: Sufang

last: Zhang

first: Zhongbao

last: Zhao


title: DNA Methylation Profiles of Airway Epithelial Cells and PBMCs from Healthy, Atopic and Asthmatic Children.

city: Vancouver

first: Dorota

last: Stefanowicz

address: Rm 166 - 1081 Burrard St.

department: James Hogg Research Centre

institute: UBC

summary:
DNA methylation profiling of airway epithelial cells (AECs) and peripheral blood mononuclear cells (PBMCs) from normal, atopic and asthmatic subjects. The Illumina GoldenGate Methylation Cancer Panel I was used to obtain DNA methylation profiles across approximately 1505 CpGs in AECs and PBMCs.
Samples included 7 healthy, 9 atopic, 4 atopic asthmatic and 5 non-atopic asthmatic subjects. Please note that only some of the samples are matched (i.e. AECs and PBMCs from the same individual) due to DNA quality or sample collection (i.e. only one sample (AEC or PBMC) was collected from the patient).

overall_design: Bisulphite converted DNA from the 41 samples were hybridised to the Illumina GoldenGate Methylation Beadchip

first: Darryl

last: Knight


title: mRNA expession profiles in prostate carcinoma cells

status: Public on Mar 23 2012

city: Northbrook

last: Falduto

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary:
Malignant cells that survive repeated radiation fractions undergo molecular changes and may differ in treatment response to subsequent molecular-targeted therapy.  We assess changes in cell lines of varying p53 status after various fractionation regimens to determine if p53 influences gene expression and if multi-fractionated radiation can induce molecular pathways changes.
Differences in gene expression exist between cell lines and after varying radiation regimens that are p53 dependent.  As the duration of changes is at least 24 hours, it may be possible to use radiation-inducible targets for molecular-targeted therapy rather than depend on the presence of mutations, thus enhancing efficacy of targeted agents.

overall_design: Whole genome gene expression of 78 samples from three human prostate carcinomal cell lines exposed to various radiation protocols.  Three biological replicates were run for each treatment.

first: C

middle: N

last: Coleman

first: Sanjeewani

last: Palayoor

first: Molykutty

last: John-Aryankalayil

first: Charles

middle: B

last: Simone


title: The application of nonsense-mediated mRNA decay inhibition to the identification of breast cancer susceptibility genes

status: Public on Apr 12 2012

city: Brisbane

first: Julie

middle: Kim

last: Johnson

state: Queensland

address: 300 Herston Road

department: Genetics and Population Health

institute: Queensland Institute of Medical Research

summary:
Identification of novel, highly penetrant, breast cancer susceptibility genes will require the application of additional strategies beyond that of traditional linkage and candidate gene approaches. Approximately one-third of inherited genetic diseases, including breast cancer susceptibility, are caused by frameshift or nonsense mutations that truncate the protein product [1]. Transcripts harbouring premature termination codons are selectively and rapidly degraded by the nonsense-mediated mRNA decay (NMD) pathway. Blocking the NMD pathway in any given cell will stabilise these mutant transcripts, which can then be detected using gene expression microarrays. This technique, known as gene identification by nonsense-mediated mRNA decay inhibition (GINI), has proved successful in identifying sporadic nonsense mutations involved in many different cancer types. However, the approach has not yet been applied to identify germline mutations involved in breast cancer. We therefore attempted to use GINI on lymphoblastoid cell lines (LCLs) from multiple-case, non-BRCA1/2 breast cancer families in order to identify additional high-risk breast cancer susceptibility genes.
We applied GINI to a total of 24 LCLs,established from breast-cancer affected and unaffected women from three multiple-case non-BRCA1/2 breast cancer families. We then used Illumina gene expression microarrays to identify transcripts stabilised by the NMD inhibition.

overall_design: Total RNA obtained from the lymphoblastoid cell lines derived from 24 individuals.

middle: K

first: Nic

last: Waddell

first: Georgia

last: Chenevix-Trench