title: Determination of the nascent transcriptional rates in a TEToff::ARB1 conditional mutant.

status: Public on Jun 05 2017

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

type: Genome binding/occupancy profiling by array

summary: Transcription of eukaryotic genes involves dynamic interactions between RNA polymerases and chromatin that are facilitated by auxiliary factors. One of these chromatin factors is Spt6, encoded by an essential gene that plays regulatory functions throughout all eukaryotes, from yeast to human. We have performed a genetic analysis of Spt6 function by isolating yeast mutations that confer synthetic-lethality to a conditional spt6 allele under permissive conditions. In addition to genes encoding other general transcription factors, such mutations also include genes involved in pre-rRNA processing and ribosomal subunit assembly, among them DBP6 and ARB1. Using an in vivo depletion system for Arb1, the transcriptional response upon the impairment of ribosome assembly, and the potential involvement of Spt6 as a regulator was investigated. Subsequent analyses included the transcriptomic profiles of a set of viable null mutants, lacking genes functionally involved in different steps of ribosome biogenesis. We found that the genes encoding factors directly involved in ribosome assembly change their expression level in response to the impairment of the ribosome biogenesis pathway, and Spt6 plays a role in this regulation by tuning RNA polymerase II transcription during the elongation phase. This regulation does not uniformly affect all ribosome-related genes, since different subsets of genes were induced or repressed in response to different specific malfunctions in ribosome biogenesis. Together, these data extend our understanding of the regulation of ribosome related genes and provide insight into the mechanisms by which defects in ribosome biogenesis lead to a specific regulation of their expression at the level of transcription elongation.

overall_design: Cells: SPT6 arb1∆ pCEN-TEToff::ARB1 (wt) or spt6-140 rb1∆ pCEN-TEToff::ARB1 (mutant), were grown in YPD at 26ºC to 0.25 OD600. At that time 5 µg/mL Doxicycline was added and let to stand for 4 or 8 h in the same conditions. Then each sample (wt or mutant) was separated in two aliquots. One of them was used for Genomic Run-On (GRO) and the other for RNA pol II Immunoprecipitation with 8WG16 antibody (RPCC) using published protocols. Filters were also hybridized with random-primed genomic DNA and the GRO signals were corrected by dividing them for the gDNA signals from the same filter. Immunoprecipitated (IP) signals were divide by whole cell extract signals from the same filters for the RPCC samples. More details as described in Pelechano et al (2009) PLos Genet. Two replicates of the whole experiment were done.

first: José

middle: E

last: Pérez-Ortín

first: Fernando

last: Gómez-Herreros

first: Vicent

last: Pelechano

first: Sebastián

last: Chávez


title: Sorafenib induces variations of the DNA methylome in human hepatocellular carcinoma cells.

status: Public on Jun 30 2017

city: Brescia

first: Alessandro

last: Salvi

address: viale Europa 11

country: Italy

institute: University of Brescia

type: Methylation profiling by genome tiling array

summary: Sorafenib is currently the standard treatment for advanced hepatocellular carcinoma (HCC). Epigenetic alterations such as DNA methylation, play a decisive role in the development and progression of HCC. To our knowledge, there are no studies that have analyzed the global DNA methylation changes in HCC cells treated with sorafenib. Using MeDip-chip technologies we analyzed sorafenib effects on the methylome of human HCC cells. We found 1230 differentially methylated genes in HA22T/VGH cells treated with sorafenib compared to untreated cells. Gene ontology and pathway analysis found enriched several GO terms related to transcription factors and different pathways involved in tumorigenesis and cancer progression. Among the genes differentially methylated we found genes related to apoptosis (FOXO3, SMAD2, p21), angiogenesis (EPAS1) and invasion (MMP3, MMP7, RAC1, RHOC), genes belonged to pathways deregulated in HCC such as RAF/MEK/ERK (MAPK3, MAP2K2), JNK (MAPK8, MAP2K7), JAK-STAT (JAK1, STAT3, STAT5, CCND3), PI3K/AKT/mTOR (TSC2, PRKCZ) and NF-κB (IKBKG, MALT1, MAP3K14) and cancer-associated non-coding genes such as MALAT1, miR-149 and miR-675. We found a general trend where oncogenes were hypermethylated and tumor suppressor genes were hypomethylated after sorafenib treatment. Finally, we validated MeDip-chip results on several differentially methylated genes using COBRA and direct bisulfite sequencing and for these genes we evaluated the relationship between methylation level and mRNA expression.Our results suggest that in HCC cells sorafenib could affect the methylation level of genes associated to cancer-related processes and pathways related to sorafenib mechanism of action. These results identified novel sorafenib targets genes which could be targets in a new design of multi-target and combined therapies, and to better understand the emergence of resistance in HCC.

overall_design: In this work, HA22T⁄VGH HCC cells were maintained in RPMI-1640 (Life Technologies) supplemented with 10% fetal bovine serum at 37°C in a 5% CO2 incubator. Sorafenib (Nexavar®, Bayer Corporation) was dissolved in 100% DMSO (Sigma-Aldrich) and diluted in DMEM (Life Technologies) to the required concentration with a final DMSO concentration of 0.1%. Cells were cultured in 10 cm Ø plates up to almost confluence and were treated with sorafenib (5 µM) or solvent (0.1% DMSO) for 24 hours. Genomic DNA was extracted from treated and untreated cells using Wizard Genomic DNA Purification Kit (Promega) according to the manufacturer’s instructions and quantified using NanoDrop (Thermo Fisher Scientific). Global DNA methylation profiles of sorafenib treated and untreated cells were obtained by methylated DNA immunoprecipitation coupled with Affymetrix Human Promoter 1.0R Tiling Arrays (MeDip-chip) using a modification of the Affymetrix chromatin immunoprecipitation assay protocol. Genomic DNA from sorafenib treated and untreated cells was fragmented using micrococcal nuclease (New England Biolabs) to obtain DNA fragments ranging from 200 to 500 nucleotides and used them as input (IN) DNA. Agilent Bioanalyzer with the RNA 6000 Nano LabChip Kit was used to check the size of fragmented DNA. Part of IN DNA (4 µg) was immunoprecipitated (IP) with 10 µl of anti-5-MethylCytosine Antibody (Eurogentec, BI-MECY-0100) using Dynabeads® Protein G immunoprecipitation kit (Life Technologies). The methylated enriched DNA was purified by standard phenol/chloroform procedure and isopropanol precipitated. The MeDip was performed in duplicate for each DNA sample starting with initial fragmentation step. A total of 200 ng of IN and IP DNA was amplified with the Affymetrix Chromatin Immunoprecipitation Assay Protocol and hybridized on Human Promoter 1.0R arrays. Totaling 3 arrays per each cellular condition (2 IP DNA and 1 IN DNA) were performed. The CEL files were imported into Partek® Genomics Suite® (PGS). The differences between sorafenib treated and untreated cells were analyzed using ANOVA. Significantly differentially methylated regions (DMR) were obtained using the MAT algorithm (model-based analysis of tiling arrays algorithm). Using PGS function, each DMR was associated to its nearest gene of human genome. The genomic coordinates of each DMR were calculated based on UCSC human genomic assembly version 18.

first: Edoardo

last: Abeni

first: Michele

last: Traversa

first: Bruna

last: Arici

first: Giuseppina

middle: D

last: Petro


title: Autoanitbody Biomarkers for the Early Detection of Serous Ovarian Cancer [Validation Screen]

status: Public on Jun 01 2017

city: Tempe

first: Benjamin

middle: A

last: Katchman

state: AZ

address: 727 E. Tyler St.

country: USA

institute: Arizona State University

summary:
Introduction: Serous ovarian cancer is the leading cause of gynecological cancers, with a 5-year survival rate below 45% due in part to the nonspecific symptoms and lack of accurate screening for early detection. In comparison, patients diagnosed at an early stage have a five-year survival rate of 92%, demonstrating the urgent need for biomarkers for the early detection of disease. Serum from patients with serous ovarian cancer contain antibodies to tumor antigens that are potential biomarkers for early detection. The purpose of this study is to identify a panel of novel serum autoantibody (AAb) biomarkers for the early diagnosis of serous ovarian cancer.

Methods: To detect AAb we probed high-density programmable protein microarrays (NAPPA) containing 10,247 antigens with sera from patients with serous ovarian cancer (n = 30 cases/ 30 healthy controls) and measured bound IgG. We identified 735 promising tumor antigens using cutoff values of 10% sensitivity at 95% specificity and K-value>0.8, as well as visual analysis and evaluated these with an independent set of serous ovarian cancer sera (n = 30 cases/ 30 benign disease controls/ 30 heathy controls). Thirty-nine potential tumor autoantigens were identified with sensitivities ranging from 3 to 39.7% sensitivity at 95% specificity and were retested using an orthogonal programmable ELISA assay. A total of 13 potential tumor antigens were identified for further validation using an independent ovarian cancer sera set (n = 44 cases/ 34 healthy controls). Sensitivities at 95% specificity were calculated and a serous ovarian cancer classifier was constructed. In addition, we evaluated a longitudinal study using blinded serous pre-diagnostic ovarian cancer sera (n = 9 cases/ 90 controls) to examine the value of three (CTAG1, CTAG2, and p53) of these AAb in comparison to CA 125.

Results: We identified 11-AAbs (ICAM3, CTAG2, p53, STYXL1, PVR, POMC, NUDT11, TRIM39, UHMK1, KSR1, and NXF3) that distinguished serous ovarian cancer cases from healthy controls with a combined 45% sensitivity at 100% specificity. In our longitudinal analysis, p53- and CTAG-AAb were detected up to 9 months prior to ovarian cancer diagnosis and increased with CA 125 levels.

Conclusion: These are potential circulating biomarkers for the early detection of serous ovarian cancer, and warrant confirmation in larger clinical cohorts. In addition, p53- and CTAG1/2-AAb are detected in a subset of women with ovarian cancer up to 9 months prior to clinical diagnosis. Their utility as a biomarker for early detection, beyond CA 125, warrant further investigation.

overall_design:
Subsequent immunoreactivity conformation was compared between 29 serous ovarian cases, 28 benign ovarian disease controls, and 29 healthy controls against 735 human proteins that were printed on microscope slides.

Contrubuted by: Arizona State University


title: Mapping of nucleolus-associated chromosomal domains during replicative senescence.

status: Public on Jun 18 2017

city: Regensburg

first: Stefan

last: Dillinger

address: Universitätsstr. 31

country: Germany

institute: University Regensburg

type: Genome binding/occupancy profiling by genome tiling array

summary: Nucleolus-associated DNA was isolated from cross-linked proliferating and senescent IMR90 human fibroblasts and hybridized against genomic (1) or non-nucleolar (2) DNA to map nucleolus-associated chromosomal domains.

overall_design: Comparison of nucleolus-associated DNA from proliferating IMR90 cells to senescent IMR90 cells.

first: A

last: Németh

first: S


title: Effect of AK144841 SiRNAs on the whole transcriptome of a mouse cell line (mSCC-38 cells) isolated from chemically-induced skin carcinoma (SCC )  (DMBA/TPA model)

status: Public on Jun 07 2017

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: This study aims at demonstrating that a newly identified LncRNA AK144841, strongly up-regulated in mouse  skin carninoma , is effectivelly endowed of a biological activity and  could play a role in the tumor development. Here we used siRNA to invalidate AK144841 and  analyse the consequences of this manipulation on the  transcriptome of mouse SCC cell line  This approach will also permit to  to identify potential target of this LncRNA.

overall_design: Cultured mSCC-38 cells were transfected with 2 distinct siRNA (Si1AK and Si2AK) or a control siRNA (SiC) using RNAimax. After 72hrs in culture cells were harvested , RNA were extracted and purified. 600ng of Cy3 labelled ARN were hybridized with a 8x60k Agilent array. Non tranfected cells were also included in the experiment.

first: G

last: Ponzio

first: N

last: Nottet

first: B

last: Mari

first: K

first: P

last: Barbry

first: R

last: Rezzonico


title: Vaccine-induced modulation of gene expression in turbot peritoneal cells: A microarray approach

status: Public on May 01 2017

city: LUGO

first: Belen

middle: G

last: Pardo

state: LUGO

address: Avda. Carballo Calero s/n

department: Zoology, Genetics and Physical Anthropology

country: Spain

institute: University of Santiago de Compostela

summary: We used a microarray approach to examine changes in gene expression in turbot peritoneal cells after injection of the fish with vaccines containing the ciliate parasite Philasterides dicentrarchi as antigen and one of the following adjuvants: chitosan-PVMMA microspheres, Freund´s complete adjuvant, aluminium hydroxide gel, and Matrix-Q (Isconova, Sweden). We identified 374 genes that were differentially expressed in all groups of fish. Forty-two genes related to tight junctions and focal adhesions and/or actin cytoskeleton were differentially expressed in free peritoneal cells. The profound changes in gene expression related to cell adherence and cytoskeleton may be associated with cell migration and also with the formation of cell-vaccine masses and their attachment to the peritoneal wall. Thirty-five genes related to apoptosis were differentially expressed. Although most of the proteins coded for by these genes have a proapoptotic effect, others are antiapoptotic, indicating that both types of signal occur in peritoneal leukocytes of vaccinated fish. Interestingly, many of the genes related to lymphocytes and lymphocyte activity were downregulated in the groups injected with vaccine. We also observed decreased expression of genes related to antigen presentation, suggesting that  macrophages (which were abundant in the peritoneal cavity after vaccination) did not express these genes during the early inflammatory response in the peritoneal cavity. Finally, several genes that participate in the inflammatory response were differentially expressed, and most participated in resolution of inflammation, indicating that an M2 macrophage response is generated in the peritoneal cavity of fish one day post vaccination.

overall_design: The early cell response in the peritoneal cavity after vaccination was measured at 1, 3 and 5 days after injection with antigen in PBS, with microespheres containing  covalently linked antigen to their surface in PBS  or with a mixture of antigen and the following adjuvants: Montanide Isa 763 A, aluminium  hydroxide gel or Matrix-Q. The control group was injected intraperitoneally with  phosphate-buffered saline.

first: Francisco

last: Fontenla

first: Verónica

last: Blanco-Abad

first: Belén

first: Iria

last: Folgueira

first: Manuel

last: Noia

first: Antonio

last: Gómez-Tato

first: Paulino

last: Martínez

first: José

middle: M

last: Leiro

first: Jesús

last: Lamas


title: Autoanitbody Biomarkers for the Early Detection of Serous Ovarian Cancer

first: Benjamin

last: Katchman

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


title: Ethanol enhances high-salinity stress tolerance by detoxification of reactive oxygen species in Arabidopsis and rice

status: Public on May 31 2017

city: Yokohama

first: Akihiro

last: Matsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

summary: To analyze the molecular function of ethanol in salt stress responses in Arabidopsis, we conducted microarray analysis using 4-day-old plants, which were treated with 0.3 % ethanol or water for 24 h, and then treated with or without 100 mM NaCl for 2 h

overall_design: Microarray analysis was conducted using ethanol-treated and non-treated plants subjected to non-stress and salt-stress condition for 2 h.

first: Huong

last: Mai Nguyen

first: Kaori

last: Sako

first: Yuya

last: Suzuki

first: Mohamad

last: Golam Mostofa

first: Chien

last: Van Ha

first: Maho

last: Tanaka

first: Lam-Son

last: Phan Tran

first: Yoshiki

last: Habu

first: Motoaki

last: Seki


title: Analysis of microRNA expression profiles in Xp11 renal cell carcinoma compared to normal adjacent tissue.

status: Public on Apr 27 2017

city: Baltimore

first: Luigi

last: Marchionni

state: MD

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

summary: Renal cell carcinomas (RCCs) with Xp11 translocation (Xp11 RCC) constitute a distinctive molecular subtype characterized by chromosomal translocations involving the Xp11.2 locus, resulting in gene fusions between the TFE3 transcription factor with a second gene (usually ASPSCR1, PRCC, NONO, or SFPQ). RCCs with Xp11 translocations comprise up to 1-4% of adult cases, frequently displaying papillary architecture with epithelioid clear cells.

overall_design: We analyze the miRNA expression profiles of Xp11 RCC compared to matched normal renal parenchyma using microarray. We further compare Xp11 RCC with other RCC histologic subtypes using publically available datasets, identifying common and distinctive microRNA signatures along with the associated signaling pathways and biological processes. Overall, Xp11 RCC more closely resemble clear cell rather than papillary RCC. Furthermore, among the most differentially expressed miRNAs specific for Xp11 RCC, we identify miR-148a-3p, miR-221-3p, miR-185-5p, miR-196b-5p, and miR-642a-5p to be up-regulated, while miR-133b and miR-658 were down-regulated. Finally, Xp11 RCC is most strongly associated with microRNA expression profiles modulating DNA damage responses, cell cycle progression and apoptosis, and the Hedgehog signaling pathway

first: Masamichi

last: Hayashi

first: Elisa

last: Guida

first: Akira

last: Ooki

first: Enrico

last: Munari

first: Fayez

middle: J

last: Jabboure

first: Wikum

last: Dinalankara

first: Al

last: Raza

first: George

last: Netto

first: Mohammad

middle: O

last: Hoque

first: Pedram

last: Argani


title: Array comparative genomic hybridization of tumor tissue developed in TH-MYCN (hemizygote) mice [Agilent-015028]

status: Public on Apr 01 2017

city: Nagoya

first: Shoma

last: Tsubota

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Molecular Biology

institute: Nagoya University Graduate School of Medicine

type: Genome variation profiling by high throughput sequencing

summary: In order to investigate the chromosomal alterations (gains or losses) of tumor tissuees developed in TH-MYCN mice, a neuroblastoma model, we carried out array comparative genomic hybridization. We investigated whether chromosomal alterations occured in the tumor tissues developed in the abdomen of TH-MYCN hemizygote mice.

overall_design: Eleven biological replicates of tumor tissues developed in abdomen of TH-MYCN mice were subjected to array CGH.

first: Satoshi

last: Kishida

first: Yasuko

last: Yoshida

first: Kenji

last: Kadomatsu


title: Molecular Characteristics of High-Dose Melphalan Associated Oral Mucositis in Patients with Multiple Myeloma: A Gene Expression Study on Human Mucosa

status: Public on Dec 19 2016

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

summary:
Background

Toxicity of the oral and gastrointestinal mucosa induced by high-dose melphalan is a clinical challenge with no documented prophylactic interventions or predictive tests. The aim of this study was to describe molecular changes in human oral mucosa and to identify biomarkers correlated with the grade of clinical mucositis.

Methods and Findings

Ten patients with multiple myeloma (MM) were included. For each patient, we acquired three buccal biopsies, one before, one at 2 days, and one at 20 days after high-dose melphalan administration. We also acquired buccal biopsies from 10 healthy individuals that served as controls. We analyzed the biopsies for global gene expression and performed an immunohistochemical analysis to determine HLA-DRB5 expression. We evaluated associations between clinical mucositis and gene expression profiles. Compared to gene expression levels before and 20 days after therapy, at two days after melphalan treatment, we found gene regulation in the p53 and TNF pathways (MDM2, INPPD5, TIGAR), which favored anti-apoptotic defense, and upregulation of immunoregulatory genes (TREM2, LAMP3) in mucosal dendritic cells. This upregulation was independent of clinical mucositis. HLA-DRB1 and HLA-DRB5 (surface receptors on dendritic cells) were expressed at low levels in all patients with MM, in the subgroup of patients with ulcerative mucositis (UM), and in controls; in contrast, the subgroup with low-grade mucositis (NM) displayed 5–6 fold increases in HLA-DRB1 and HLA-DRB5 expression in the first two biopsies, independent of melphalan treatment. Moreover, different splice variants of HLA-DRB1 were expressed in the UM and NM subgroups.

Conclusions

Our results revealed that, among patients with MM, immunoregulatory genes and genes involved in defense against apoptosis were affected immediately after melphalan administration, independent of the presence of clinical mucositis. Furthermore, our results suggested that the expression levels of HLA-DRB1 and HLA-DRB5 may serve as potential predictive biomarkers for mucositis severity

overall_design: Conseccutive mucosa biopsies from 10 multiple myeloma patients: one biopsi and blood test before melphalan; one biopsi and blood test 2 days after melphalan; one biopsi and blood test 21 days after melphalan. 10 biopsies and blood tests from healthy controls

first: Mette

last: Marcussen

middle: S

first: Heidi

last: Christensen

first: Preben

last: Johansen

first: Søren

last: Nielsen

first: Ilse

last: Christiansen

first: Olav

last: Bergmann

first: Martin

last: Bøgsted

first: Karen

last: Dybkær

first: Mogens

last: Vyberg

first: Hans

last: Johnsen


title: Autoanitbody Biomarkers for the Early Detection of Serous Ovarian Cancer [Discovery Screen]

first: Benjamin

last: Katchman

overall_design:
The immunoreactivity was compared between 30 serous ovarian cancer cases and 30 healthy controls against 10,247 human proteins that were printed on microscope slides.

Contrubuted by: Arizona State University


title: Array comparative genomic hybridization of tissue developed in TH-MYCN (hemizygote) mice

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

overall_design: Refer to individual Series


title: Array comparative genomic hybridization of spheres derived from TH-MYCN (hemizygote) mice [Agilent-027441]

summary: It has been already reported that there are undifferentiated/proliferating neuroblasts in the postnatal sympathetic ganglia in TH-MYCN mice, a neuroblastoma model. We established suitable spheroid culture condition that selectively isolates undifferentiated neuroblasts from superior mesenteric ganligon (SMG) of TH-MYCN mice. In order to investigate the chromosomal alterations (gains or losses) of spheres derived from TH-MYCN mice, we carried out array comparative genomic hybridization. We investigated whether chromosomal alterations occured during early neuroblastoma tumorigenesis in TH-MYCN mice.

overall_design: Primary spheres were cultured from SMG of E13.5 and 3-week-old TH-MYCN mice, and from tumor tissues of TH-MYCN mice. Eight biological replicates of primary spheres from tumor tissues of TH-MCYN mice were subjected to the array CGH. Passageable spheres were obtained by subculturing primary spheres derived from E13.5 and 3-week-old TH-MYCN SMG. Six biological replicates of E13.5 TH-MYCN spheres and eight biological replicates of 3-week-old TH-MYCN spheres were subjected to array CGH.

first: Miki

last: Ohira


title: Tumor microenvironment derived exosomes pleiotropically modulate cancer cell metabolism

status: Public on Apr 23 2016

city: Houston

first: Prahlad

middle: T.

last: Ram

state: TX

address: 7435 Fannin St.

department: Systems Biology

institute: University of Texas MD Anderson Cancer Center

summary: Cancer-associated fibroblasts (CAFs) are a major cellular component of tumor microenvironment in most solid cancers. Altered cellular metabolism is a hallmark of cancer, and much of the published literature has focused on neoplastic cell-autonomous processes for these adaptations. We demonstrate that exosomes secreted by patient-derived CAFs can strikingly reprogram the metabolic machinery following their uptake by cancer cells.

overall_design: Total RNA obtained from purified exosomes from patient derived CAFs

first: Hongyun

last: Zhao

first: Lifeng

last: Yang

first: Joelle

last: Baddour

first: Abhinav

last: Achreja

first: Vincent

last: Bernard

first: Tyler

last: Moss

first: Juan

middle: C

last: Marini

first: Thavisha

last: Tudawe

first: Elena

last: Seviour

first: F

last: San Lucas

first: Hector

last: Alvarez

first: Sonal

last: Gupta

first: Sourindra

middle: N

last: Maiti

first: Laurence

last: Cooper

first: Donna

last: Peehl

middle: T

first: Anirban

last: Maitra

first: Deepak

last: Nagrath


title: Expression data from CD8 memory T cells after IN immunization compared to IM immunization

status: Public on Jan 28 2017

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

summary: Intranasal (IN) immunization induces different genotype expression in CD8 memory T cells compared to the CD8 memory T cells induced by intramuscular (IM) immunization. We used microarrays to detail the global program of gene expression underlying the differential induction after IN or IM immunization.

overall_design: CD8-specific memory T cells were sorted after IN or IM immunization with STxB-E7 vaccine with the following immunization protocol: Prime with STxB-E7 + aGalCer at D0, and boost with STxB-E7 at D21. The cells were collected and sorted 7 days after the boost.

first: Mevyn

last: Nizard


title: miRNA expression profiling of snap-frozen primary papillary thyroid carcinomas (PTC) and normal thyroids

status: Public on Nov 01 2016

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

summary: The purpose of this study was to identify de-regulated miRNAs in human papillary thyroid carcinoma (PTC). To this aim miRNA expression profiles of PTCs and normal thyroid samples were compared. Tissue specimens were selected  by an expert pathologist. Details about the histological type of tumor samples are provided.

overall_design: miRNA expression profiles for 19 primary papillary thyroid carcinomas and 5 normal thyroids were generated using Agilent microarray platform.

first: Maria

last: Grazia Borrello

first: Paola

last: Romeo

first: Emanuela

last: Minna

first: Loris

last: De Cecco

first: Silvana

last: Pilotti


title: Genome-wide methylation profiles in primary intracranial germ cell tumors indicate primordial germ cell origin of germinoma [Agilent]

status: Public on Apr 01 2016

city: Chuo-ku

first: Shintaro

last: Fukushima

address: 5-1-1 Tsukiji

institute: National Cancer Center Research Institute

summary: The pathogenesis of intracranial germ cell tumors (iGCTs) is not yet fully uncovered despite exhaustive genomic analyses. By means of a genome-wide methylation analysis, we show that pure germinoma is characterized by global DNA low methylation, a unique epigenetic feature distinct from all other subtypes of iGCTs. The patterns of methylation strongly resemble that of primordial germ cells (PGC) at the migration phase, indicating the cells of origin. Unlike PGC, however, hypomethylation extends to LINE1 retrotransposon. Microdissected histologically and epigenetically distinct components of mixed-GCTs shared identical mutations in the MAPK or PI3K pathways, suggesting that the genetic alterations were likely to have occurred at the pre-implantation phase in early embryogenesis. Thus, we propose iGCTs are “Zygotoma”.

overall_design: Genomic DNA from the 81 GCTs were hybridized to the SurePrint G3 Human CGH 8 × 60 K Oligo Microarrays G4450A (Agilent Technologies, Santa Clara, CA).


title: Gene expression profile in the pectoralis muscle of penguin juveniles artificially acclimated to marine life

status: Public on Aug 31 2016

city: Bremerhaven

first: Cyril

last: Degletagne

address: Am Handelshafen

department: Functional Ecology

institute: Alfred Wegener Institute

summary:
In the present study, we were interested in gene expression changes in the pectoralis muscle of juvenile king penguins during the transition from terrestrial to marine life. Strictly terrestrial during their first year after hatching, king penguin chicks must then depart to sea to reach nutritional emancipation and pectoralis muscle is largely involved in penguin adaptation to the marine environment.
To compare these transcriptomic profiles, we realized heterologous hybridization on Affymetrix GeneChip Chicken Genome Arrays, as the chicken is the closest model species for which microarrays are available. The development of a new algorithm, MaxRS, allow us to determine differentially expressed genes implicated in energetic metabolism or involved in cellular defense against reactive oxygen species and associated injuries.
Data from NI and SA penguin juveniles are already on GEO n°GSE17725

overall_design: We compared muscle sample biopsy from 4 penguin juveniles captured just before they undergone their first immersion to cold water (named NI for Never Immersed), 3 penguin juveniles that had completly accomplished their acclimation to marine life (named SA for Sea Acclimated) and 3 penguin juveniles experimentally immersed in cold water (named AA for Artificially Acclimated). AA penguins are NI penguins that moulted in captivity and then are subjected to experimental immersions in cold water (8°C) to simulate acclimatization to marine life. The protocol consisted in a ten successive immersions (5 hours every 2 days) in a water tank (1.2m width, 2.0m long, 1.0m deep).

first: Benjamin

last: Rey

last: Dégletagne

first: Céline

last: Keime

first: Claude

last: Duchamp


title: Differential Gene Expression in Liver, Gill and Olfactory Tissues of Coho Salmon (Oncorhynchus kisutch) after Acclimation to Salinity.

status: Public on Mar 22 2016

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Most Pacific salmonids undergo smoltification and transition from freshwater to saltwater. Saltwater acclimation requires salmonids to make various adjustments in color, shape, size, metabolism, catabolism, and osmotic and ion regulation. The molecular mechanisms underlying this transition are largely unknown. The present study acclimated coho salmon (Oncorhynchus kisutch) to four different salinities (<0.5, 8, 16, and 32 ppth) and assessed gene expression through microarray analysis of gill, liver and olfactory tissues. Gills are involved in osmotic regulation, liver plays a role in energetics, and olfactory tissues are involved in behavior. Between all salinity treatments, liver had the highest number of differentially expressed genes at 1,616. Gills had 1,074 differentially expressed genes and olfactory tissue had 924. The difference in the number of differentially expressed genes may be due to the higher responsiveness of liver to metabolic changes after salinity acclimation to provide energy to fuel other metabolic and osmoregulatory tissues like gills. Differentially expressed genes were tissue and salinity treatment dependent. There were no genes differentially expressed in all salinity treatments and all three tissues. Five genes were targeted for microarray confirmation by qPCR and included CCAAT/enhancer binding protein ? (CEBPB), calpain 1 (CAPN1), proto-oncogene, serine/threonine kinase (Pim1), aldolase B, fructose-bisphosphate (aldob), and complement component 3 (c3).   qPCR expression profiles of these genes matched array outputs. Gene ontology term analysis revealed biological processes, molecular functions, and cellular components that were significant. Most terms were tissue dependent. For liver, oxygen binding and transport terms were highlighted, suggesting possible impacts on metabolism. For gills, muscle and cytoskeleton related terms were emphasized and for olfactory tissues, immune response related genes were accentuated. Interaction networks were examined in combination with GO terms and determined similarities between tissues for potential osmosenors and signal transduction cascades. Overall this study suggests that Pacific salmonids share many salinity acclimation molecular mechanisms with other species, with a few new genes identified, and that although the three tissues shared certain underlying mechanism, many of the differentially expressed genes were tissue-specific.

overall_design: To assess how salinity acclimation in coho salmon (Oncorhynchus kisutch) impacted gene expression in gills, liver, and olfactory tissues.

first: Richard

middle: P

last: Beyer

first: Lindley

last: Maryoung

first: Ramon

last: Lavado

first: Theo

middle: K

last: Bammler

first: Evan

last: Gallagher

first: Patricia

middle: L

last: Stapleton

first: Federico

last: Farin

first: Roman

last: Sasik


title: Let-7 coordinately suppresses components of the amino acid sensing pathway to induce autophagy

status: Public on Aug 03 2015

summary: Macroautophagy (hereafter autophagy) is the major pathway by which macromolecules and organelles are degraded. Autophagy is regulated by the mTOR signaling pathway, which is the focal point for integration of metabolic information, with mTORC1 playing a central role in balancing biosynthesis and catabolism. Of the various inputs to mTORC1, the amino acid sensing pathway is among the most potent. Based upon transcriptome analysis of neurons subjected to nutrient deprivation, we identified let-7 as a microRNA capable of promoting neuronal autophagy. We found that let-7 activates autophagy by coordinately down-regulating the amino acid sensing pathway to prevent mTORC1 activation. Let-7 induced autophagy in the brain and greatly reduced protein aggregates in a lentivirus model of polyglutamine disease, establishing the physiological relevance of let-7 for in vivo autophagy modulation. Moreover, peripheral delivery of let-7 anti-miR repressed autophagy in muscle and white fat, suggesting that let-7 autophagy regulation extends beyond the CNS. Hence, let-7 plays a central role in nutrient homeostasis and proteostasis regulation in higher organisms.

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

overall_design: Using sets of wild-type C57BL/6J mice, we established primary cortical neuron cultures from P0 littermates, and cultured these neurons (n = 3 / set) in CM or NLM for 4 hrs.

first: Amy

last: Dubinsky


title: New molecular insights into modulation of platelet reactivity in aspirin-treated patients using a network-based approach [NanoString]

status: Public on Feb 18 2016

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary: Platelet reactivity (PR) in cardiovascular (CV) patients is variable between individuals and modulates clinical outcome. However, the determinants of platelet reactivity are largely unknown. Integration of data derived from high-throughput omics technologies may yield novel insights into the molecular mechanisms that govern platelet reactivity. The aim of this study was to identify candidate genes modulating platelet reactivity in aspirin-treated cardiovascular patients PR was assessed in 110 CV patients treated with aspirin 100mg/d by aggregometry using several agonists. 12 CV patients with extreme high or low PR were selected for transcriptomics, proteomics and miRNA analysis.

overall_design: 2 extreme patient groups, 6 samples per group

first: A

last: Zufferey

first: M

first: J

last: Reny

first: S

last: Nolli

first: D

last: Schvartz

last: Docquier

first: I

last: Xenarios

last: Sanchez

first: P

last: Fontana


title: Transcriptional profiling of Aspergillus fumigatus H515 strain in response to alkaline or calcium shift

status: Public on Sep 30 2015

city: Manchester

first: Margherita

last: Bertuzzi

address: Core Technology Facility, 46 Grafton Street

department: Institute for Inflammation and Repair

country: United Kingdom

institute: University of Manchester

summary: The functional coupling of calcium-mediated signalling and alkaline tolerance has been demonstrated in multiple fungi. The applied relevance of such interplay extends most notably to fungal pathogens of man where the physiological pH of serum and tissues exerts considerable alkaline stress. Drugs targeting the calcium-dependent phosphatase, calcineurin, are potent antifungal agents but also perturb human calcineurin signalling, it has therefore been postulated that abrogation of fungal alkaline tolerance could offer a valuable therapeutic adjunct. To study the interdependency of pH- and calcium-mediated intracellular signalling in the major human fungal pathogen A. fumigatus, we examined the transcriptional response following exposure to 200 mM calcium chloride or alkaline pH (pH 8.0).

overall_design: To study the interdependency of pH- and calcium-mediated intracellular signalling in the major human fungal pathogen A. fumigatus we examined the transcriptional response following exposure to 200 mM calcium chloride or alkaline pH (pH 8.0).

first: O

last: Loss

first: W

last: Nierman

first: E

last: Bignell


title: Characterization of deletions of the HBB locus by array comparative genomic hybridization

status: Public on May 06 2015

first: Daniel

middle: E

last: Sabath

department: Laboratory Medicine

type: Genome variation profiling by genome tiling array

summary: Array-CGH used to characterize HBB deletions causing beta thalassemia and HPFH

overall_design: Two-color experiment comparing thalssemia/HPFH subjects with normal DNA

last: Bender

first: Vijay

last: Sankaran

first: Esther

last: Vamos

first: Alex

last: Kentsis

first: Hye-Son

last: Yi

first: Harvey

last: Greisman


title: Genes enabling phenotypic plasticity evolve canalized gene expression by their limited associations with transcriptional regulators

status: Public on Oct 02 2014

city: Bloomington

first: Richard

middle: Nathan

last: Keith

state: IN

department: School of Public and Environmental Affairs

institute: Indiana University

summary:
Global climate change increasingly polarizes environments, presenting unprecedented challenges to many organisms (Smol, 2012). Polarization occurs not only in the spatial dimension, producing greater desert drought and tropical rainfall, for example, but also in the temporal dimension by making a local environment more variable over time. Many organisms survive these fluctuating environmental conditions by manifesting multiple distinct phenotypes through developmental processes that enable phenotypic plasticity (Pigliucci et al., 2006; Parsons et al., 2011). As with early development, these processes are expected to strictly regulate gene expression to canalize phenotype, despite the genetic diversity within populations (Alberch, 1982; Riska, 1986, Pigliucci et al., 1996).  For plasticity to evolve, natural selection must act on genes that regulate trait variation, e.g, those conferring norms of reaction to a specific set of conditions. Despite the importance of these reaction norms for coping with environmental challenges, the genetic framework underlying phenotypic plasticity remains poorly defined, making it impossible to study how they function, differ among natural populations, and evolve. Here we used arsenic, a chemical inhibitor of salinity acclimation, to identify genes involved in transforming the gill from its freshwater to its seawater architecture in the euryhaline teleost Fundulus heteroclitus. Linear model interaction terms associated with the combined effect of arsenic and salinity challenge revealed an antagonistic relationship between arsenic exposure and salinity acclimation
Exposure to arsenic during salinity acclimation yielded gene expression values similar to those observed in unexposed fish that remained in a stable environment, demonstrating that arsenic prevents changes in gene expression that normally enable osmotic plasticity. The gene sets defined by the interaction terms showed reduced inter-individual variation, suggesting unusually tight control, consistent with the hypothesis that they participate in a canalized developmental response.  Evidence that natural selection acts to preserve their canalized gene expression was obtained by referencing three populations that differ in their adaptive tolerance to salinity changes (Whitehead et al., 2011). Specifically, populations adapted to withstand the widest salinity range showed both reduced transcriptional variation in genes enabling gill plasticity and an increased osmoregulatory capacity, highlighted by more stable plasma chloride concentrations in response to an osmotic challenge. Finally, we observed significantly fewer associations between genes underlying trait variation and their transcriptional regulators compared to genes that responded to only arsenic or salinity. Collectively, our results demonstrate that phenotypic plasticity converges on a molecular solution that parallels early development, in which the expression of phenotypic plasticity genes and phenotypes are canalized in part by reducing trans-regulatory complexity.

overall_design: 36 Sample comparisons with fish gills exposed to freshwater, freshwater to seawater for 1 hour, freshwater to seawater for 1 hour with arsenic, freshwater to seawater for 24 hours, freshwater to seawater for 24 hours with arsenic, and freshwater with arsenic for 48 hours

first: Joseph

middle: R

last: Shaw

first: Thomas

middle: H

last: Hampton

first: Benjamin

last: King

first: Andrew

last: Whitehead

first: Fernando

last: Galvez

first: Robert

last: Gross

first: R

first: Emily

last: Notch

first: Dawoon

last: Jung

first: Stephen

last: Glaholt

first: John

last: Colbourne

first: Celia

middle: Y

last: Chen

first: Bruce

last: Stanton


title: miR-155-5p regulates immune cell recruitment to the fetal lung after choriodecidual Group B Streptococcal infection

status: Public on Aug 05 2015

first: James

last: MacDonald

summary: Mechanisms underlying in utero fetal lung injury remain poorly defined, and a greater understanding of pathways regulating these processes may lead to novel therapies that prevent lung injury before birth. MicroRNAs (miRNAs) are small non-coding, endogenous RNAs that regulate gene expression and have been implicated in the pathogenesis of lung disease. We sought to determine whether differentially expressed miRNAs in the fetal lung following choriodecidual infection are associated with elevation of amniotic fluid (AF) cytokine levels and acute lung injury in a nonhuman primate model. After inoculating ten chronically catheterized pregnant monkeys (Macaca nemestrina) at 118-125 days gestation (term=172 days) with either Group B Streptococcus (GBS) 1 x 106 colony forming units (n=5) or saline (n=5) in the choriodecidual space, we extracted fetal lung mRNA and miRNA and profiled changes in expression. We identified 9 differentially expressed miRNAs (p<0.05, >1.5 fold change) in the GBS-exposed fetal lungs by microarray, but of these only miR-155-5p was significantly elevated by qRT-PCR (p=0.016). The microarray log2 intensity of miR-155-5p positively correlated with fetal lung injury scores and AF IL-1? and TNF-??levels (R2=0.54, p=0.016). In situ hybridization revealed that miR-155-5p is expressed throughout the fetal lung, which led us to investigate mechanisms that regulate miR-155-5p expression. Significantly elevated miR-155-5p expression was observed when immortalized human fetal airway epithelial (FeAE) cells were exposed to IL-6 and TNF-??. Overexpression of miR-155-5p in FeAE cells increased production of IL-6, CCL5/RANTES and CXCL10/IP-10. Using a luciferase reporter assay, we validated FGF9 as an authentic target of miR-155-5p, which is essential to development of the lung mesenchyme and distal epithelial branching. Collectively, these results suggest that a choriodecidual inflammatory response leads to increased AF cytokine levels, which induce miR-155-5p expression.  In turn, miR-155-5p activates and recruits leukocytes (IL-6, CCL5/RANTES) and inhibits fetal lung angiogenesis (CXCL10/IP-10), meschenchymal development and epithelial branching (targets FGF9 mRNA). A therapy to antagonize miR-155-5p may ameliorate perinatal lung injury.

overall_design: Ten chronically catheterized pregnant monkeys (Macaca nemestrina) at 118-125 days gestation (term=172 days) received choriodecidual inoculation of either: 1) Group B Streptococcus (n=5) or 2) saline (n=5).  Cesarean section and fetal necropsy was performed in the first week after GBS or saline inoculation regardless of labor.  RNA was extracted from fetal lungs and profiled by microarray.  Results were analyzed using single gene, Gene Set, and Ingenuity Pathway Analysis.  Validation was by RT-PCR and immunohistochemistry.

first: Theodor

last: Bammler

last: Beyer

first: Ryan

middle: M

last: McAdams

first: Jeroen

last: Vanderhoeven

first: Federico

last: Farin

first: Michael

middle: G

last: Gravett

first: Craig

last: Rubens

first: Kristina

last: Adams-Waldorf

first: Lakshmi

last: Rajagopa

first: Xinna

last: Zhang

middle: W

last: Bierle

first: Samantha

last: Weed

first: Erica

last: Boldenow

first: Jesse

last: Tsai


title: Hypoxia promotes stem cell phenotypes and poor prognosis through epigenetic regulation of DICER [MCF7]

status: Public on Sep 30 2014

city: Toronto

first: Cindy

last: Yao

address: 661 University Avenue, Suite 510

country: Canada

institute: OICR

summary: MicroRNAs are small regulatory RNAs that post-transcriptionally control gene expression. Reduced expression of DICER, the enzyme involved in microRNA processing, is frequently observed in cancer and is associated with poor clinical outcome in various malignancies. Yet the underlying mechanisms are not well understood. Here, we identify tumor hypoxia as a regulator of DICER expression in large cohorts of breast cancer patients. We show that DICER expression is suppressed by hypoxia through an epigenetic mechanism that involves inhibition of oxygen-dependent H3K27me3 demethylases KDM6A/B and results in silencing of the DICER promoter. Subsequently, reduced miRNA processing leads to derepression of the miR-200 target ZEB1, stimulates the epithelial to mesenchymal transition and ultimately results in the acquisition of stem cell phenotypes in human mammary epithelial cells. Our study uncovers a previously unknown relationship between oxygen-sensitive epigenetic regulators, miRNA biogenesis and tumor stem cell phenotypes that may underlie poor outcome in breast cancer.

overall_design: miRNA profiling of MCF7 cells in normal or hypoxic conditions or after DICER knockdown in MCF7 cells.

first: Twan

last: van den Beucken

first: Elizabeth

last: Koch

first: Kenneth

last: Chu

first: Rajesha

last: Rupaimoole

first: Peggy

last: Prickaerts

first: Michiel

last: Adriaens

first: Jan

last: Voncken

first: Adrian

last: Harris

first: Francesca

last: Buffa

first: Syed

last: Haider

first: Maud

last: Starmans

first: Mircea

last: Ivan

first: Cristina

first: Chad

last: Pecot

first: Paul

last: Boutros

first: Anil

last: Sood

first: Marianne

last: Koritzinsky

first: Bradly

last: Wouters


title: Hypoxia promotes stem cell phenotypes and poor prognosis through epigenetic regulation of DICER [HMLER]

first: Cindy

last: Yao

overall_design: A total of 12 samples were analyzed.  For each condition tested, 3 independent experiments were carried out (biological repicates).

first: Twan

last: van den Beucken

first: Elizabeth


title: Phenotypic Convergence  in Bacterial Adaptive Evolution to Ethanol Stress

status: Public on Jul 21 2014

city: Suita

first: Takaaki

last: Horinouchi

address: 6-2-3, Furuedai

institute: Quantitative biology center, RIKEN

type: Expression profiling by genome tiling array

summary: Although the relationship between phenotypic plasticity and evolutionary dynamics has attracted large interest, very little is known about the contribution of phenotypic plasticity to adaptive evolution. In this study, we analyzed phenotypic and genotypic changes in E. coli cells during adaptive evolution to ethanol stress. To quantify the phenotypic changes, transcriptome analyses were performed.

overall_design: We previously obtained 6 independently evolved ethanol tolerant E. coli strains, strains A through F, by culturing cells under 5% ethanol stress for about 1000 generations and found a significantly larger growth rate than the parent strains  (Horinouchi et al, 2010, PMID: 20955615). To elucidate the phenotypic changes that occurred during adaptive evolution, we quantified the time-series of the expression changes by microarray analysis. Starting from frozen stocks obtained at 6 time points (0, 384, 744, 1224, 1824 and 2496 hours) in laboratory evolution, cells were cultured under 5% ethanol stress, and mRNA samples were obtained in the exponential growth phase for microarray analysis.

first: Shingo

last: Suzuki

first: Chikara

last: Furusawa


title: Large-scale downregulation of cytokeratins in amniotic epithelium after Group B Streptococcus choriodecidual infection in Macaca nemestrina: a pathway to PPROM

status: Public on Nov 18 2014

first: James

last: MacDonald

summary: Early events leading to intrauterine infection remain poorly defined, but may hold the key to a therapeutic intervention for preterm delivery.  To determine early molecular pathways associated with membrane weakening that may progress to preterm premature rupture of membranes (PPROM), we examined the effects of Group B Streptococcus (GBS) on fetal membranes after a choriodecidual infection.

overall_design: Ten chronically catheterized pregnant monkeys (Macaca nemestrina) at 118-125 days gestation (term=172 days) received choriodecidual inoculation of either: 1) Group B Streptococcus (n=5) or 2) saline (n=5).  Cesarean section and fetal necropsy was performed in the first week after GBS or saline inoculation regardless of labor.  Macaca nemestrina chorioamnion samples were obtained at the site of inocculation immediately after cesarean delivery 4 days after GBS inoculation and 7 days after saline inoculation.  RNA was extracted and profiled by microarray.  Results were analyzed using single gene, Gene Set, and Ingenuity Pathway Analysis.  Validation was by RT-PCR and immunohistochemistry.

first: Theodor

last: Bammler

first: Richard

last: Beyer

first: Ryan

last: McAdams

first: Jeroen

last: Vanderhoeven

first: Federico

last: Farin

first: Michael

last: Gravett

first: Craig

last: Rubens

first: Kristina

last: Adams-Waldorf

first: Lakshmi

last: Rajagopal

first: Raj

last: Kapu

first: Aasthaa

last: Bansa

first: Min

last: Spencer

first: Mei

last: Deng


title: Over-expression of miR-146a in basal-like breast cancer cells confers enhanced tumorigenic potential in association with altered p53 status

status: Public on Jun 30 2014

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

summary: The tumor suppressor p53 is the most frequently mutated gene in human cancers, mutated in 25-30% of breast cancers. However, mutation rates differ according to breast cancer subtype, being more prevalent in aggressive estrogen receptor (ER) negative tumors, basal-like and HER2 amplified subtypes. This heterogeneity suggests that p53 may function differently across breast cancer subtypes. We used RNAi-mediated p53 knockdown (KD) and antagomir-mediated KD of microRNAs to study how gene expression and cellular response to p53 loss differ in luminal vs. basal-like breast cancer. As expected, p53 loss caused down regulation of established p53 targets (e.g. p21 and miR-34 family) and increased proliferation in both luminal and basal-like cell lines. However, some p53-dependent changes were subtype-specific, including expression of miR-134, miR-146a, and miR-181b. To study the cellular response to miR-146a upregulation in p53-impaired basal-like lines, antagomir knockdown of miR-146a was performed. KD of miR-146a caused decreased proliferation and increased apoptosis, effectively ablating the effects of p53 loss. Furthermore, we found that miR-146a upregulation decreased NF-kB expression and downregulated the NF-kB-dependent extrinsic apoptotic pathway (including TNF, FADD, and TRADD) and antagomir-mediated miR-146a KD restored expression of these components, suggesting a plausible mechanism for miR-146a-dependent cellular responses. These findings are relevant to human basal-like tumor progression in vivo, since miR-146a is highly expressed in p53-mutant basal-like breast cancers.  These findings suggest that targeting miR-146a expression may have value for altering the aggressiveness of p53 mutant basal-like tumors.

overall_design: reference x sample

first: Rupninder

last: Sandhu

first: Monica

last: D’Arcy

first: Jason

middle: I

last: Herschkowitz

first: Katherine

middle: A

last: Hoadley


title: A cross-comparison of technologies for the detection of microRNAs from FFPE samples of hepatoblastoma patients [NanoString]

status: Public on May 03 2015

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

summary: This work highlights similarities and differences between three platforms (next-generation sequencing, microarray and NanoString) for detecting miRNAs and compares their strengths and weaknesses.

overall_design: miRNA expression profiles were determined in Hepatoblastoma FFPE samples using a NanoString platform.

first: Anna

last: Leichter

first: Vicky

last: Fan

first: Peter

last: Tsai

first: Rachel

middle: V

last: Purcell

middle: J

last: Sullivan

last: Eccles


title: A comparision of the transcriptional profiles of the Muscle from cattle raised outdoors on pasture versus indoors on high dietary supplement

status: Public on Jan 01 2014

city: Dublin 4

first: Marion

middle: Teresa

last: Ryan

address: Belfield

department: Veterinary Sciences

country: Ireland

institute: University College Dublin

summary: The objective of this study was to characterise a small panel of differentially expressed genes in the muscle that could be utilised to authenticate animals raised on pasture versus animals raised indoors on a concentrate based diet.

overall_design: Seven replicates per sample group, fourteen in total

first: Torres

last: Sweeney

first: Alex

last: Lejeune

first: A

last: Moloney

first: Stephen

last: Park

first: G

last: Downey

first: Ruth

last: Hamill

first: Paul

last: McGettigan

first: Frank

last: Monahan


title: Hypoxia promotes stem cell phenotypes and poor prognosis through epigenetic regulation of DICER

first: Cindy

last: Yao

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

overall_design: Refer to individual Series


title: MicroRNA Expression of Mouse Cochleae during Aging

status: Public on Mar 12 2013

city: Omaha

first: David

last: He

state: Nebraska

address: 2500 California Plaza

department: Department of Biomedical Sciences

institute: Creighton University

summary:
To identify which miRNAs are involved in the onset and progression of age-related hearing loss in the mammalian cochlea
We used miRNA microarrays to screen miRNAs which exhibit the differential expression in the expressing levels during aging of the cochlea

overall_design: The organ of Corti (OC), one of the major pathological sites of presbycusis in cochlea, was collected separately at 3 timepoints during the life span. Two strains were selected: C57BL/6J and CBA/J. The selected time points were: Postnatal 21 days (P21), 3 month (3m) and 9 month (9m) for C57 mice, and P21, 9m, 16m for CBA mice.

first: Qian

last: Zhang

first: Huizhan

middle: Z

last: Liu

first: Edward

last: Walsh

first: JoAnn

last: McGee

first: Garrett

last: Soukup


title: Copper-induced deregulation of microRNA expression in the zebrafish olfactory system

status: Public on Apr 30 2014

first: James

middle: William

last: MacDonald

summary: Although environmental trace metals, such as copper (Cu), can disrupt normal olfactory function in fish, the underlying molecular mechanisms of metal-induced olfactory injury have not been elucidated. Current research has suggested the involvement of epigenetic modifications. To address this hypothesis, we analyzed microRNA (miRNA) profiles in the olfactory tissues of Cu-exposed zebrafish. Our data revealed 2, 10, and 28 differentially expressed miRNAs in a dose response pattern to three increasing Cu concentrations. Numerous deregulated miRNAs were involved in neurogenesis (let-7, miR-7a, miR-128 and miR-138), indicating a role for Cu-mediated toxicity via interference with olfactory neurogenesis.  Putative gene targets of deregulated miRNAs were identified when interrogating our previously published microarray database, including those involved in olfactory cell growth and proliferation, cell death, and cell morphology. Moreover, several miRNAs (miR-203a, miR-199*, miR-16a, miR-16c, and miR-25) were inversely correlated with the depression of key genes within olfactory signal transduction pathways, which likely contributed to the inhibition of olfactory function. Our findings provide novel insight into the epigenetic regulatory mechanisms of metal-induced neurotoxicity of fish olfactory system, and identify novel miRNA biomarkers of metal exposures.

overall_design: 12 one-year-old adult AB strain zebrafish were exposed to Cu concentrations of 0, 6.3, 16 and 40 ppb Cu.

first: Theodor

last: Bammler

first: Richard

middle: P

last: Beyer

first: Lu

last: Wang

first: Evan

last: Gallagher


title: Global Gene Expression Profiles of Cecropin B Induces Resistance in Haemophilus parasuis

status: Public on Dec 11 2012

city: Wuhan

first: chunmei

last: wang

address: Hongshan district, No.1

country: China

institute: huazhong agriculture university

summary: To understand the mechanism of the adaptations, global gene expression profiles of the cecropin B--resistant strains of Haemophilus parasuis, The development of cecropin B (CB) resistance in H. parasuis SH0165 by exposing SH0165 using various concentrations of CB was investigated. One colony of bacterial cultures grown on TSA containing 30μg/mL CB was named CBR30, CBR30 cultured in TSA without CB for 50 passages was named CBR30-50. we used microarray technology to analyze the variation of the H. parasuis SH0165 transcriptional profile in CBR30 and CBR30-50. Our analysis to identify several genes whose system could be involved in inorganic ion transport, amino acid transport, and metabolism. Quantitative PCR was used to validate the differential expression of selected genes.

overall_design: The H. parasuis SH0165 control group was normal culture with no tilmicosin at OD600 >0.3 (12 h). The H. parasuis CBR30 was normal culture with 30μg/mL cecropin B at OD600 >0.3 (20 h). The H. parasuis CBR30-50 was normal culture with no cecropin B at OD600 >0.3 (12 h). Three independent experiments were performed on each group using a different sample for each experiment.

first: C


title: Genomic hybridizations for the parents and progeny of the Toxoplasma gondii I X III genetic cross

status: Public on Jan 11 2012

city: St Louis

first: Michael

middle: Sean

last: Behnke

state: MO

address: 660 S. Euclid Ave

department: Molecular Microbiology

institute: Washington University School of Medicine

summary: The parents and progeny of the I X III genetic cross were genotyped using the ToxoGeneChip in order to generate a more detailed genetic map.  We also used the genomic hybridization data to look for copy number variations (CNV) and segmental duplications.

overall_design:
The ToxoGeneChip microarray (http://ancillary.toxodb.org/docs/Array-Tutorial.html) was used to hybridize genomic DNA for the parents and progeny of the I X III cross.
The parents of the cross are CTGara and GT1-Fudr.  The rest comprise the 34 informative progeny.

first: M

middle: S

first: J

middle: C

last: Wootton

last: White


title: miRNA Profiles in patients and controls

status: Public on Dec 31 2014

city: Homburg

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

summary: This project analyzes peripheral blood profiles of patients of various diseases and controls.

overall_design: n = 94 normal controls, n = 15 long lived individuals and n = 940 patients have been screened for the complete miRNA repertoire according to miRNAse V12-14. Please note that each miRNA has been measured in at least seven replicates and the median of the replica has been computed.


title: Expression and genomic hybridization data for the Toxoplasma gondii I X III cross

type:
Expression profiling by array
Genome variation profiling by array


title: Choriodecidual Infection Downregulates Angiogenesis and Morphogenesis Pathways in Fetal Lungs from Macaca Nemestrina

status: Public on Apr 23 2013

summary: Intrauterine exposure to amniotic fluid (AF) cytokines is thought to predispose to bronchopulmonary dysplasia (BPD).  We evaluated the effects of GBS exposure on RNA expression in fetal lung tissue to determine early molecular pathways associated with fetal lung injury that may progress to BPD.

middle: K

first: Ryan

last: McAdams

first: Jeroen

last: Vanderhoeven

first: Federico

last: Farin

last: Gravett

first: Craig

middle: E

last: Rubens

first: Kristina

last: Adams-Waldorf


title: Pancreatic cancer and pancreatitis miRNA profiles

status: Public on Jan 01 2012

summary: This project analyzes pancreatic tissue profiles of pancreatic cancer patients, pancreatitis patients, and controls. Since miRNAs are known to be valuable diagnostic markers, we asked whether respective patterns of pancreatic cancer patients can be detected in biopsies. The project aimed at an impoved understanding of complex profiles rather than single markers. Thus, a high-throughput technique was necessary, profiling all known miRNAs integratively. Three markers have been validated by using qPCR.

overall_design: n = 22 normal controls, n = 27 pancreatitis samples, and n = 136 pancreatic cancer samples have been screened for the complete miRNA repertoire. Please note that each miRNA has been measured in seven replicates and the median of the replica has been computed.

first: Andrea

last: Bauer


title: Correlation between DNA methylation and gene expression in the brains of patients with bipolar disorder and schizophrenia

status: Public on Jun 30 2013

city: Changsha

first: Chao

last: Chen

state: Hunan

address: 110 Xiangya Road

department: State Key Lab of Medical Genetics

institute: Central South University

summary:
Aberrant DNA methylation and gene expression have been reported in postmortem brain tissues of psychotic patients, but until now there has been no systematic evaluation of synergistic changes in methylation and expression on a genome-wide scale in brain tissue. In this study, genome-wide methylation and expression analyses were performed on cerebellum samples from 39 patients with schizophrenia, 36 patients with bipolar disorder, and 43 unaffected controls, to screen for a correlation between gene expression and CpG methylation. Out of 71,753 CpG gene pairs (CGPs) tested across the genome, 204 were found to signiﬁcantly correlate with gene expression after correction for multiple testing [p < 0.05, false discovery rate (FDR) q < 0.05]. The correlated CGPs were tested for disease-associated expression and methylation by comparing psychotic patients with bipolar disorder and schizophrenia to healthy controls. Four of the identiﬁed CGPs were found to signiﬁcantly correlate with the differential expression and methylation of genes encoding phosphoinositide-3-kinase, regulatory subunit 1 (PIK3R1), butyrophilin, subfamily 3, member A3 (BTN3A3), nescient helix-loop-helix 1 (NHLH1), and solute carrier family 16, member 7 (SLC16A7) in psychotic patients (p < 0.05, FDR q < 0.2). Additional expression and methylation datasets were
used to validate the relationship between DNA methylation, gene expression, and neuropsychiatric diseases. These results suggest that the identiﬁed differentially expressed genes with an aberrant methylation pattern may represent novel candidate factors in the etiology and pathology of neuropsychiatric disorders.

overall_design: A total of 155 postmortem cerebellum brains were used in this study,  including 47 bipolar disorder, 46 schizophrenia, 15 depression patients and 47 normal controls. All were of European Ancestry. We also designed 13 random replicates in our experiment. Illumina Infinium HumanMethylation27 BeadChip was used for DNA methylation profiling. The assay was performed at the Genomics Core Facility at Northwestern University.

first: Chunyu

last: Liu


title: Expression Quantitative Trait Locus (eQTL) Mapping of Stage-specific Gene Expression in Progeny from a type I X III Genetic Cross of Toxoplasma gondii

summary: The control of gene expression in Toxoplasma is not well understood.  As we and others have shown, this organism does contain bipartite promoters that are sufficient to induce gene expression.  This information can be used in downstream experiments to identify proteins that bind to experimentally confirmed cis elements.  One of these methods, yeast one-hybrid is currently being employed to identify proteins which bind to the BAG1 and B-NTPase promoter elements.  Another powerful method that can be used to identify genomic regions containing controllers of gene expression takes advantage of genetic linkage mapping provided by genetic crosses, called expression quantitative trait locus (eQTL) mapping.  In the eQTL approach, one uses gene expression as quantitative traits, or phenotypes, in QTL mapping.  QTL mapping is a proven method in Toxoplasma  that has recently identified apicomplexan-specific virulence factors in both the Type II X III and Type I X III crosses (Saeij et al., 2006, Taylor et al., 2006, Su et al., 2002).  With the recent design of the Affymetrix Toxoplasma GeneChip one can gather gene expression profiles for all predicted genes in the Toxoplasma genome in a rapid and reproducible way.  Combining the power of Affymetrix gene expression technology and QTL mapping can lead to the identification of genes with differential expression in the parents and progeny of a genetic cross and then to the identification of the genomic regions that contain mechanisms that have an effect on expression.  The first description of combining global gene expression profiles with QTL mapping was published by Brem et al. using the model organism Saccharomyces cerevisiae (Brem et al., 2002).   Since that time, eQTL projects have been described for several other organisms including human, mouse, rat, maize, Arabidopsis, barley, eucalyptus, and wheat (Gibson & Weir, 2005).  There are two mapping location types expected when using gene expression profiles as phenotypes.  Mapping of gene expression profiles can lead to linkage of a locus (region) containing the gene being mapped, thus cis to the gene.  Although the boundaries of the locus will contain many genes, it is presumed that for most cis QTLs sequence polymorphisms in the regulatory region(s) of the gene being mapped are the cause of the observed expression differences.  The other mapping location type expected is one where the expression profile maps to a locus not containing the gene being mapped, or trans to the gene (Ronald et al., 2005).  The most interesting trans loci are those that have multiple genes mapping to the same locus in trans, or to a trans hotspot.  These hotspots likely contain factor(s) that regulate many genes, such as transcription factors or factors involved in upstream signal transduction pathways that can eventually lead to a number of transcriptional changes (Yvert et al., 2003).  Here we describe the results of an eQTL project using the gene expression profiles for the parents and 34 informative progeny of the type I-GT1-Fudr X type III-CTGara cross for both the tachyzoite and bradyzoite stages.  This is the first time global gene expression profiles have been used to determine linkage to regions presumed to be controllers of transcription using the Affymetrix Toxoplasma GeneChip.  The dominant genomic associations found were those mapping cis and there were several regions, or hotspots, where multiple genes map in trans.  In addition, we observed an unexpected finding suggesting there are several duplication events in the parasites of the Type I X III cross which may also have consequences on gene expression levels.

overall_design:
The ToxoGeneChip microarray (http://ancillary.toxodb.org/docs/Array-Tutorial.html) was used to measure both tachyzoite and bradyzoite mRNA expression in the parents and progeny of the I X III cross.  For each of the two developmental expression sets, genome-wide  eQTL scans were run for each gene specific probeset on the microarray.
The parents of the cross are CTGara and GT1-Fudr.  The rest comprise the informative progeny.

last: Lehmann


title: Transcriptional profile of Candida albicans bcr1 knockout.

status: Public on Nov 04 2011

city: Dublin

first: Geraldine

last: Butler

department: School of Biomolecular and Biomedical Science

institute: University Colege Dublin Conway Institute

summary: Whole genome microarrays were used to compare the transcriptional profile of Candida albicans bcr1 knockout to wild type cells.

overall_design: RNA was isolated from DAY286 (wild type) or bcr1 delete (CJN702) grown in SD medium supplemented with 50 mM glucose and 10% feotal calf serum and labeled with Cy3 or Cy5. Four independent biological replicates were compared. Two dye swaps were perfomed so that two of the four DAY286 cultures were labeled with Cy3, and two were labeled with Cy5.

first: Genevieve

last: Vidanes

first: Sarah

middle: L

last: Maguire


title: Conserved and divergent roles of Bcr1 and CFEM proteins in Candida parapsilosis and Candida albicans

status: Public on Nov 05 2011

sample_organism:
Candida albicans
Candida parapsilosis

platform_organism:
Candida albicans
Candida parapsilosis


title: lncRNAs and mRNAs expression profile in liver diseases including HCC

status: Public on Jan 22 2014

city: Baltimore

first: Jie

last: Wang

state: Maryland

address: 400 N Broadway

institute: Johns Hopkins University

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

summary: Sustained hepatic inflammation can contribute to cancer initiation and progression via tumor-initiating cell expansion, but underlying mechanisms remains unknown. Expression profiles of lncRNAs/mRNAs were measured in normal, chronic hepatitis, cirrhotic and cancerous livers. We found abundant disease-related lncRNAs/mRNAs deregulated across different stages of inflammation-triggered liver disease and refined a transformation gene signature to distinguish pathological liver tissues. Amongst this signature, a conserved lncRNA DANCR was silenced in normal adult liver, but overexpressed in fetal and cancerous livers. Remarkably, increased DANCR significantly correlates with poor prognosis in multiple-center cohorts and is directly induced by inflammatory pathways including NF-κB and STAT3. DANCR could suppress cell differentiation and drive expansion of tumor-initiating cells, leading to chemoresistance. Moreover, in vitro and in vivo inhibition confirms the significance of DANCR as a therapeutic target when combined with other chemotherapy. We illustrate the role of DANCR relies on the regulation of CTNNB1 in a novel miRNA-blocking manner. Our studies reveal the expression of lncRNAs/mRNAs in normal and pathological livers and suggest the importance of oncofetal lncRNA DANCR in inflammation-induced malignant transformation, offering a potential prognostic marker and a therapeutic target for HCC.

overall_design: In the study, we profiled lncRNA/mRNA expression in 10 normal livers (NL), 10 chronic inflammatory livers (IL), 10 cirrhotic livers (CL), 13 early HCC (eHCC) and 13 advanced HCC (aHCC) samples.

first: Sheng-xian

last: Yuan

first: Fu

last: Yang

first: Qi-fei

last: Tao

first: Li-li

first: Yuan

first: Hao

last: Zheng

first: Zhen-guang

first: Qing-guo

last: Xu

first: Ling

last: Zhang

first: Fang

first: Lei

last: Sun

first: Wei-ping

last: Zhou


title: Transcriptional profile of Candida albicans DAY286 culture without ketoconazole versus DAY286 culture with 0.04 μg/ml ketoconazole, both at 20% oxygen (normoxia).

status: Public on Nov 15 2010

first: Alessandro

last: Guida

address: belfield

summary: Whole genome microarray were used to generate the transcriptional profile of C.albicans in the presence of ketoconazole.

overall_design: RNA was isolated from DAY286 grown with or without ketoconazole in YPD medium in normoxia at 30 degree Celsius for 3.5 h, and labeled with Cy3 or Cy5. Four independent biological replicates were compared. 2 dye swaps were perfomed so that 2 out of 4 samples isolated from DAY286 in normoxic culture without ketoconazole were labeled with Cy3, and 2 were labeled with Cy5.

first: John

middle: M

last: Synnott


title: Transcriptional profile of Candida albicans DAY286 versus UPC2 delete, both at 1% oxygen (hypoxia).

summary: Whole genome microarray were used to generate the transcriptional profile of C.albicans UPC2 delete in hypoxia.

overall_design: RNA was isolated from DAY286 or UPC2 delete grown in YPD medium in hypoxia at 30 degree Celsius for 3.5 h, and labeled with Cy3 or Cy5. Nine independent biological replicates were compared. 3 dye swaps were perfomed so that 6 out of 9 samples isolated from DAY286 in hypoxic culture were labeled with Cy3, and 3 were labeled with Cy5.

first: Geraldine


title: Hypoxia, ketoconazole, and the UPC2 gene in Candida albicans


title: Transcriptional profile of Candida albicans during Hypoxic conditions.

summary: Whole genome microarray were used to generate the transcriptional profile of C.albicans in hypoxic condition.

overall_design: RNA was isolated from DAY286 grown in YPD medium in normoxia or hypoxia at 30 degree Celsius for 3.5 h, and labeled with Cy3 or Cy5. Eight independent biological replicates were compared. 2 dye swaps were perfomed so that 6 out of 8 samples isolated from normoxic culture were labeled with Cy3, and 2 were labeled with Cy5.


title: global gene expression profiles in primary human hepatocytes exposed to phytochemicals

status: Public on Jul 19 2010

first: James

last: MacDonald

summary: Primary human hepatocytes were treated with 2 non-cytotoxic concentrations of sulforaphane (SFN; 10 and 50 uM) phenethyl isothiocyante (PEITC; 10 and 25 uM), 3,3'-diindolylmethane (DIM; 10 and 50 uM), or one concentration of oltipraz (OPZ; 30 uM) for 48 hours.  Given the considerable heterogeneity of the human population, it was essential that each experiment was performed with hepatocytes from the same liver, i.e. each liver served as its own control.   Each treatment was performed on three batches of human hepatocytes, each derived from a separate liver.

overall_design: 32 arrays, 8 experimental groups.

first: Richard

last: Beyer

first: Theodor

last: Bammler


title: Gene expression profile in the pectoralis muscle of penguin before and after acclimatisation to marine life

status: Public on May 25 2010

city: Bremerhaven

first: Cyril

last: Degletagne

institute: Alfred Wegener Institute

summary:
In the present study, we were interested in gene expression changes in the pectoralis muscle of juvenile king penguins during the transition from terrestrial to marine life. Strictly terrestrial during their first year after hatching, king penguin chicks must then depart to sea to reach nutritional emancipation and pectoralis muscle is largely involved in penguin adaptation to the marine environment.
To compare these transcriptomic profiles, we realized heterologous hybridization on Affymetrix GeneChip Chicken Genome Arrays, as the chicken is the closest model species for which microarrays are available. The development of a new algorithm, MaxRS, allow us to determine differentially expressed genes implicated in energetic metabolism or involved in cellular defense against reactive oxygen species and associated injuries.

overall_design: We compared muscle sample biopsy from 4 penguin juveniles captured just before they undergone their first immersion to cold water (named NI for Never Immersed) and 3 penguin juveniles that had completly accomplished their acclimation to marine life (named SA for Sea Acclimated).

last: Dégletagne

first: Céline

last: Keime

first: Benjamin

last: Rey

first: Marc

last: de Dinechin

first: Fabien

last: Forcheron

first: Paul

last: Chuchana

first: Pierre

last: Jouventin

first: Christian

last: Gautier

first: Claude

last: Duchamp


title: CP 5hr

status: Public on Feb 24 2004

city: Seattle

institute: University of Washington

summary:
embryos exposed to 40 uM 4-hydroperoxycyclophosphamide (4CP) for 5 hours at 37°C
Keywords: other


title: HS 1hr

summary:
embryos exposed to 43°C for 15 minutes (HS) followed by 1 hour at 37°C
Keywords: other


title: HS 5hr

summary:
embryos exposed to 43°C for 15 minutes (HS) followed by 5 hours at 37°C
Keywords: other


title: Transcriptional Response to Aging and Caloric Restriction in Heart and Adipose Tissue

status: Public on Oct 23 2007

summary:
Sustained caloric restriction (CR) extends lifespan in animal models but the mechanism and primary tissue target(s) have not been identified. Gene expression changes with aging and CR were examined in both heart and subcutaneous white adipose tissue (WAT) of F344 male rats using Affymetrix® RAE 230 arrays and validated by qRT-PCR on 18 genes. In heart, age- associated changes but not CR-associated changes in old. In WAT, genes were identified where the aging change is suppressed by CR (candidate markers of healthy aging) and those affected by CR but not normal aging (candidate longevity assurance genes). 10-21% of age-associated genes were regulated in common between tissues. Gene set enrichment analysis (GSEA) revealed coordinate small magnitude changes in ribosomal, proteasomal, and mitochondrial genes with similarities between heart and WAT. Further analysis revealed PPARgamma as a potential upstream regulator of altered gene expression in old CR WAT. These results demonstrate a reduced mRNA response to CR with age in heart relative to WAT. In WAT, we identified candidate CR mimetic targets and candidate markers of healthy aging. These data suggest a role for subcutaneous WAT in the effects of CR and strengthen the role for PPAR signaling in aging and CR while indicating that the effects of CR in heart can occur independent of global changes in mRNA level.
Keywords: Aging Caloric Restriction

overall_design: Tissues (n=5-7 animals per group) were obtained from the NIH-NIA aging rodent tissue bank. According to supplier records, animals were housed in a specific pathogen free barrier facility under contract with BioReliance. AL animals were housed 3 per cage and CR animals were housed singly. CR (60% of AL) was initiated at 4 months of age with a switch from the NIH 31 to NIH fortified diet. F344 male rats were sacrificed at 4 months (4AL) or 28 months of age (28AL, 28CR). Animals with gross tumor pathologies were excluded from the study. All animals were euthanized by CO2 asphixiation and tissues were frozen in liquid nitrogen then stored at –80°C. Subcutaneous WAT was collected from the abdominal region. Recorded body weights differed dramatically between the 3 groups (4AL = 253±8 g, 28AL = 382±20 g, 28CR = 288±7 g) and heart weight as a fraction of body weight was not significantly different between the groups (data not shown). The apical ~1/3 of the heart was homogenized for the expression studies. Sections from the cut face were stained with haematoxylin and eosin to confirm expected aging-associated pathology changes.

first: Nancy

last: Linford

first: Pater

last: Rabinovitch


title: Embryo exposure to heat shock and teratogen

summary:
Analysis of embryos exposed to either:
[1] 40 uM 4-hydroperoxycyclophosphamide for 1 or 5 hours at 37°C
[2]   43°C heat shock for 15 minutes  followed by 1 or 5 hours at 37°C

This SuperSeries is composed of the SubSeries listed below.

first: R


title: CP 1hr

summary:
embryos exposed to 40 uM 4-hydroperoxycyclophosphamide (4CP) for 1 hour at 37°C
Keywords: other


title: Transcriptome analysis of Escherichia coli C strains (wt and PKH5000, a butanol-tolerant mutant) after 1-butanol treatment

status: Public on Jul 01 2013

city: Daejeon

first: Haeyoung

last: Jeong

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: KRIBB

summary:
The goal of this study is to explore genes that are differentially expressed in E. coli C strains (wt and a butanol-tolerant mutant) after 1-butanol treatment. The butanol-tolerant mutant strain PKH5000 (denoted by 'E' for 'evolved') were derived from KCTC 2571 (wt) (denoted by 'A' for 'ancestral') by proton beam irradiation.
0 and 1 in sample title mean before and after butanol treatment, respectively.

overall_design: All microarray experiments were carried out in triplicate (rep1-3). Probes were spotted in duplicate on separate area of each microarray slide, which produces two GPR files (a and b suffixes).

first: Sun

middle: H

last: Kim


title: Autoantibody Epitope Spreading in the Pre-Clinical Phase Predicts Progression to Rheumatoid Arthritis

status: Public on Sep 10 2011

city: Stanford

first: William

last: Robinson

state: CA

address: 269 Campus Dr

institute: Stanford University

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

overall_design: Refer to individual Series