title: Use of an immune-specific microarray for identifying transcriptome profiles associated to VHSV infection or vaccination with a G gene- DNA vaccine in turbot (Scophthalmus maximus)

status: Public on Apr 01 2015

city: Vigo

first: Patricia

last: Pereiro

state: Pontevedra

address: C/Eduardo Cabello, 6

department: Immunology and Genomics

institute: IIM-CSIC

summary: With the aim of shedding light on the protection conferred by the DNA vaccines based in the G glycoprotein of viral haemorrhagic septicaemia virus (VHSV) in turbot (Scophthalmus maximus) we have used a specific microarray highly enriched in antiviral sequences to carry out the transcriptomic study associated to VHSV DNA vaccination/infection. The differential gene expression pattern in response to empty plasmid (pMCV1.4) and DNA vaccine (pMCV1.4-G860) intramuscular administration with regard to non-stimulated turbot was analyzed in head kidney at 8, 24 and 72 hours post-vaccination. Moreover, the effect of VHSV infection one month after immunization was also analyzed in vaccinated and non-vaccinated fish at the same time points.

overall_design: A total number of 204 juvenile turbot were divided into 3 groups, two of them containing 72 fish and the last one 60 fish. Turbot were anaesthetized by immersion in 50 mg/ml buffered tricaine methanesulfonate (MS-222; Sigma) and then, fish from the first two groups were intramuscularly (i.m.) injected with 50 µl of PBS containing 2 µg of pMCV1.4 or pMCV1.4-G860. Turbot from the last batch were i.m. inoculated with 50 µl of PBS. At 8, 24 and 72 h after injection, 12 fish were removed from the first two tanks and, at 8 h after PBS inoculation, other 12 fish were taken from the last tank. These turbot were sacrificed by anaesthetic overdose and the head kidney was removed.  Equal amounts of tissue from three fish belonging to the same tank and sampling point were pooled, obtaining 4 biological replicates for each treatment and time point (3 turbot/replicate). The remaining fish (36 in the plasmid-injected groups and 48 in the PBS-inoculated tank) were maintained during one month and then, 12 fish from the PBS injected group were separated to another tank. This new group of fish was intraperitoneally (i.p.) injected with 50 µl of MEM + penicillin and streptomycin + 2% FBS (PBS - MEM group), whereas the other turbot were i.p. infected with a dose of VHSV860 of 5 x 105 TCID50/fish (pMCV1.4 - VHSV and pMCV1.4-G860 - VHSV groups). At 8, 24 and 72 hours after infection, 12 fish were removed from the VHSV-infected tanks, and at 8 h after MEM injection the 12 fish were taken from the non-infected tank. The fish were sacrificed by anaesthetic overdose and the head kidney was removed. Equal amounts of tissue from three fish belonging to the same tank and sampling point were pooled, obtaining 4 biological replicates for treatment and time point (3 turbot/replicate)

first: Sonia

last: Dios

first: Sebastián

last: Boltaña

first: Julio

last: Coll

first: Amparo

last: Estepa

first: Simon

last: Mackenzie

first: Beatriz

last: Novoa

first: Antonio

last: Figueras


title: Profiling of Salivary Exosomal microRNAs in Oral Lichen Planus Patients [set 1]

status: Public on Apr 30 2015

city: Daegu

first: Heon-Jin

last: Lee

address: 2177 Dalgubeol Daero

department: School of Dentistry, Microbiology and Immunology

country: South Korea

institute: Kyungpook National University

summary: In this study, we compared microRNA (miRNA) profiles of salivary exosomes of patients with oral lichen planus with those of healthy controls. Saliva samples from 16 patients with oral lichen planus and 8 healthy controls were divided into 2 sets and were examined by performing miRNA microarray analysis.

overall_design:
Examination of 8 oral lichen planus patients and 4 healthy controls. Each patient and control represent pooled RNAs from salivary exosomes of 8 patients and 4 healthy controls, respectively.
Please note that each set (i.e. set1 and set2) was analysed independently.


title: Transcriptome analysis of rice ABA deficient mutant Osaba1-1  and  wild-type before and 72h after Xanthomonas oryzae pv. oryzae (Xoo) infection

status: Public on May 15 2015

city: Beijing

first: Tian

last: Caijuan

address: NO.1 Beichen West Road, Chaoyang District

country: China

institute: Institute Of Microbiology Chinese Academy of Sciences

summary: ABA deficient mutant Osaba1-1 exhibits great resistance to Xanthomonas oryzae pv. oryzae (Xoo) infection. To investigate gene expression profile changes at whole genome level between Osaba1-1 and wild-type (Nipponbare) rice during Xoo infection, we employed microarray expression profiling as a discovery platform.

overall_design: Osaba1-1 and wild-type rice plants about 6.5 leaf stage were used in this experiment. For Xoo inoculation, tips (about 3cm) of the fifth and sixth fully expanded leaves were cut off, and then immersed into Xoo (PXO99 strain) inoculum (suspended in sterile distilled water containing 10mM MgCl2, OD≈0.5) immediately for about fifteen seconds. Inoculated rice leaves were collected (approximately 2 cm leaf fragment from the inoculation site) at 0h and 72h post inoculation. Three independent replicate samples were collected at each time point for microarray.

first: C

last: Tian

first: J

last: Qiu


title: miR-18b overexpression identifies mantle cell lymphoma patients with poor outcome and improves the MIPI-B prognosticator

city: Copenhagen

first: Ulrik

last: Ralfkiaer

address: Blegdamsvej 9

department: Hematology

country: Denmark

institute: Copenhagen University Hospital

summary:
Recent studies show that mantle cell lymphoma (MCL) express aberrant miRNA profiles, however, the clinical effect of miRNA expression has not previously been examined and validated in prospective, large, homogenously treated cohorts. We analyzed diagnostic MCL samples from the Nordic MCL2 and MCL3 clinical trials, in which all patients had received Rituximab-high-dose cytarabin alternating with Rituximab-maxiCHOP, followed by BEAM and autologous stem cell support. We performed genome-wide miRNA microarray profiling of 74 diagnostic MCL samples from the MCL2 trial (screening cohort). Differentially expressed miRNAs were re-analyzed by qRT-PCR. Prognostic miRNAs were validated by qRT-PCR in diagnostic MCL samples from 94 patients of the independent MCL3 trial (validation cohort).
Three miRNAs (miR-18b, miR-92a, miR-378d) were significantly differentially expressed in patients who died from MCL in both the screening- and the validation cohort. MiR-18b was superior to miR-92a and miR-378d in predicting high risk. Thus, we generated a new MIPI-B-miR prognosticator, combining expression-levels of miR-18b with MIPI-B data. This prognosticator improved identification of high risk patients compared to MIPI-B with regard to cause-specific survival (P=0.015), overall survival (P=0.006) and progression-free survival (P<0.001).  Transfection of two MCL cell lines with miR-18b decreased their proliferation rate without inducing apoptosis, suggesting miR-18b may render MCL cells resistant to chemotherapy by decelerating cell proliferation.   Thus, we conclude that overexpression of miR-18b identifies patients with poor prognosis in two large prospective MCL cohorts and adds prognostic information to MIPI-B. MiR-18b may reduce the proliferation rate of MCL cells as a mechanism of chemoresistance.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: For miRNA microarray profiling, 500 ng of total RNA from samples  (AM6000) was labeled with Hy3 fluorescent dyes, using the miRCURY LNA array power labeling kit (Exiqon A/S, Vedbæk, Denmark). Samples with RNA concentrations lower than 160 ng/µl were vacuum-centrifuged (speedvac) to obtain higher concentrations. All samples were labeled the same day with the same master mix to minimize technical variation.  The labeled samples were hybridized to miRCURY LNA 7th generation arrays (Manual version 2.2; Exiqon A/S, Vedbæk, Denmark), containing capture probes targeting all human miRNAs registered in  miRBASE release 18.0 (1896 human miRNAs). The hybridization was performed overnight at 56°C according to the manufacturer’s specifications using an HS4800 hybridization station (Tecan, Männendorf, Switzerland). Since it was not possible to hybridize all arrays at the same time point, samples were randomly split into six batches to minimize day-to-day variation in the hybridization process, and analyzed over six consecutive days. After hybridization, the microarray slides were scanned in an ozone free environment in order to prevent potential bleaching of the fluorescent Hy5 dye. Scanning was done using a G2565BA Microarray Scanner system (Agilent Technologies, Santa Clara, CA, USA) at 10-µm resolution, and the resulting TIFF images were analyzed using the GenePix 6.1 software on standard settings.

last: Husby

first: Christian

last: Garde

first: Roza

last: Zandi

first: Sara

last: Ek

first: Arne

last: Kolstad

first: Mats

last: Jerkeman

first: Anna

last: Laurell

first: Riikka

last: Räty

first: Lone

middle: B

last: Pedersen

first: Anja

last: Ehinger

first: Christer

last: Sundström

first: Marja-Liisa

last: Karjalainen-Lindsberg

first: Jan

last: Delabie

first: Erik

last: Clasen-Linde

first: Peter

last: Brown

first: Jack

last: Cowland

first: Christopher

middle: T

last: Workman

middle: H

last: Geisler

first: Kirsten

last: Grønbæk


title: Response of Candida glabrata to environmental iron availability

status: Public on Mar 21 2015

city: Hyderabad

first: Rupinder

last: Kaur

state: Telangana

address: Inner ring road, Uppal

country: India

institute: Centre for DNA Fingerprinting and Diagnostics

summary: To examine the response of Candida glabrata cells to iron-depleted and iron-repleted environmental conditions, transcriptional profiling analysis was carried out on wild-type and Cghog1∆ cells grown either in presence of BPS or ferric chloride. Genes involved in iron transport and homeostasis, oxidative phosphorylation, amino acid metabolic process and chromatin silencing were found to be differentially regulated.

overall_design: Agilent one-color experiment,Organism: Candida glabrata, Agilent Platform Custom Candida glabrata 8x15k designed by Genotypic Technology Private Limited.(AMADID: 49117), Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Vivek

middle: K

last: Srivastava

first: Korivi

middle: J

last: Suneetha


title: Expression analysis of the gene in microRNA-155 knockout mice and wildtype mice

status: Public on Mar 13 2015

city: Jinan

first: Qiji

last: Liu

address: 44# Wenhua Xi Rd

department: Department of Medical Genetics

institute: Shandong University School of Medicine

summary:
Investigation of whole genome gene expression level changes in four microRNA-155 knockout mice comparing with 4 wildtype mice
We found some gene expression level are different in two groups.

overall_design: A eight chip study using total RNA  from four separate wild-type mouse speens  and four separate microRNA-155 knockout mice speens

first: Qian

last: Xin


title: A high throughput protein microarray approach to classify HIV monoclonal antibodies and variant antigens

status: Public on Mar 10 2015

city: Irvine

first: Johannes

middle: S.

last: Gach

state: CA

address: 843 Health Sciences Rd

department: Medicine

country: USA

institute: University of California Irvine

summary: In recent years, high throughput discovery of human recombinant monoclonal antibodies (mAbs) has been applied, to greatly advance our understanding of the specificity, and functional activity of antibodies, against HIV. Thousands of antibodies have been generated and screened in functional neutralization assays, and antibodies, associated with cross-strain neutralization and passive protection in primates, have been identified. To facilitate this type of discovery, a high throughput-screening tool is needed, to accurately classify mAbs, and their antigen targets. In this study, we analyzed and evaluated a prototype microarray chip, comprised of HIV-1 recombinant proteins gp140, gp120, gp41, and several membrane proximal external region peptides. The protein microarray analysis of 11 HIV-1 envelope-specific mAbs revealed diverse binding affinities and specificities across clades. Half maximal effective concentrations, generated by our chip analysis, correlated significantly (P<0.0001) with concentrations from ELISA binding measurements. Polyclonal immune responses in plasma samples, from HIV-1 infected subjects, exhibited different binding patterns and reactivity against printed proteins. Examining the totality of the specificity of the humoral response in this way reveals the exquisite diversity, and specificity of the humoral response to HIV.

overall_design: HIV-1 specific monoclonal antibodies and serum samples of HIV-1 infected subjects were tested against a variety of different HIV-1 envelope proteins and derivatives.

first: Emmanuel

middle: Y

last: Dotsey

first: Andrea

last: Gorlani

first: Sampat

last: Ingale

first: Chad

last: Achenbach

first: Donald

middle: N

last: Forthal

first: Philip

middle: L

last: Felgner

middle: S


title: Profiling of Salivary Exosomal microRNAs in Oral Lichen Planus Patients

first: Heon-Jin

last: Lee

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

overall_design: Refer to individual Series


title: Cell cycle gene expression control

status: Public on May 01 2015

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

institute: UMass Medical School

summary: Gene expression data for cdc28-13 yeast released synchronously into the cell cycle.

overall_design: cdc28-13 yeast were arrested in G1 for 3 hours at 37 degrees.  Cells were rapidly cooled to 25 C by mixing with an equal volume of media at 13 C, and time points were taken every 10 minutes. Cells were rapidly pelleted, and mRNA was isolated and hybridized against midlog mRNA.

first: ChihLong


title: A genome-wide analysis of PhoP~P binding to chromosomal DNA reveals several novel features of the PhoPR-mediated phosphate limitation response in Bacillus subtilis

status: Public on Mar 05 2015

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

type: Genome binding/occupancy profiling by genome tiling array

summary: Identification of the specific PhoP binding regions on the B. subtilis chromosome during exponential and phosphate starvation growth phases. The data serves to extend the PhoPR regulon in Bacillus subtilis and its role in adaptation to phosphate-limiting conditions and cell wall metabolism, as well as implying a role in several other cellular processes.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: For each sample analyzed in this study three biological replicates were performed. Three different samples were taken from a strain expressing the PhoP-SPA protein as well as from wild-type (168) without a tagged PhoP. Samples were taken from exponentially growing cells in low phosphate medium (LPDM) as well as from phosphate-limited cells (T2). Each sample compares ChIP DNA vs. Total DNA from the same cells.

first: Letal

middle: I

last: Salzberg

first: Kevin

middle: M

last: Devine


title: Transcriptomic analysis of the early effects of sex steroid ablation on BM LT-HSCs 2 days post surgery.

status: Public on Mar 01 2015

city: Boston

first: Danika

middle: Mei Po

last: Khong

address: 51 Blossom Street

department: Massachusetts General Hospital

institute: Harvard Medical School

summary: Analysis of gene-expression alterations in primitive LT-HSCs as early as 2 days post sex steroid ablation. This study aimed to determine potential intrinsic changes occuring in the LT-HSC population associated with sex steroid ablation (SSA) at a timepoint that preceeded the earliest reported functional hematopoietic enhancements occuring at day 7 post SSA. These results are vital in providing insight into the role of LT-HSCs in initiating SSA-mediated immune regeneration.

overall_design: Total RNA obtained from BM-sorted LT-HSC 2 days after sex steroid ablation compared to sham sex steroid ablation controls.

first: Jarrod

last: Dudakov


title: Lin28b promotes fetal B lymphopoiesis through the transcription factor Arid3a [miRNA]

city: Philadelphia

first: Kyoko

last: Hayakawa

state: PA

address: 333 Cottman Avenue

institute: Fox Chase Cancer Center

summary:
Mouse B cell precursors from fetal liver and adult bone marrow generate distinctive B cell progeny when transplanted into immunodeficient recipients, supporting a two-pathway model for B lymphopoiesis, fetal “B-1” and adult “B-2”. Recently Lin28b was shown to be important for the switch between fetal and adult pathways; however, neither the mechanism of Lin28b action nor the importance of BCR signaling in this process was addressed. Here we report important advances in our understanding of the regulation of B 1/B-2 development.
First, modulation of Let-7 in fetal Pro-B cells is sufficient to alter fetal B-1 development to produce B cells resembling the progeny of adult B-2 development. Second, intact BCR signaling is required for generation of B1a B cells from Lin28b-transduced bone marrow progenitors, supporting a requirement for ligand-dependent selection, as is the case for normal B1a B cells. Third, the VH repertore of Lin28b-induced bone marrow B1a B cells differs from that of normal B1a. Finally we identify the Arid3a transcription factor as a key target of Let-7, whose ectopic expression is sufficient to induce B-1 development in adult Pro-B cells and whose knockdown blocks B-1 development in fetal Pro-B cells.

overall_design: 3 individual sorts of Fr.B/C fractions from bone marrow and fetal liver of BALB/c mice

first: Yan

last: Zhou

first: Yue-Sheng

last: Li

first: Srinivasa

last: Bandi

first: Lingjuan

last: Tang

first: Susan

middle: A

last: Shinton

first: Richard

middle: R

last: Hardy


title: Gene and microRNA expression profiling of breast tumors from Chinese and Italian women [gene]

status: Public on Mar 31 2015

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: Gene and miRNA profiles from a unique Chinese/Caucasian trans-ethnic collection of breast cancer from Shanghai (China) and Milan (Italy) were compared using an unsupervised approach that identified similar clusters of correlated features in Chinese and Caucasian datasets. Partition of gene expression data using previously published gene signatures, such as the PAM50 intrinsic gene list and the extracellular matrix (ECM) genes, revealed Chinese and Caucasian subgroups with equivalent gene and miRNA expression profiles. A significant reduction of Luminal-A tumors was observed in the Chinese series.

overall_design: Tissue samples from 78 Chinese (Han Chinese) and 97 Italian (South Europe Caucasian) consecutive primary breast tumors were subjected to gene and miRNA profiling. Tissue specimens, initially collected respectively in the Chinese and Italian hospitals, were all stored, randomly processed and analyzed in identical experimental conditions in the Italian center to minimize pre-analytical, instrumental and computational variability, enabling direct comparison of gene and miRNA profiles from the two groups.

first: Rosaria

last: Orlandi


title: Autoimmune peptide antigen reactivity in BXD2 mice with spontaneous systemic autoimmune disease Pepperchip 2.0

status: Public on Feb 28 2015

city: Birmingham

first: Jennie

last: Hamilton

state: AL

address: 1825 University Blvd.

department: Department of Medicine, Division of Clinical Immunology and Rheumatology

institute: University of Alabama Birmingham

summary: The aim of the array was to determine the BXD2 mouse sera IgG and IgM reactivity profile to linear peptide epitopes.  Pooled sera from three 6-9 month old BXD2 mice was diluted at 1:200 for IgG specific analysis or 1:1000 for IgM specific analysis and incubated on a PEPperPRINT peptide microarray platform printed with peptide autoantigens

platform_organism: Lactobacillus delbrueckii subsp. bulgaricus

platform_organism: Mycobacterium tuberculosis variant bovis

platform_organism: Human T-cell lymphotrophic virus type 1 (isolate MT-2)

platform_organism: Mycobacterium avium subsp. paratuberculosis K-10

overall_design: In this study, pooled sera from three 6-9 month old BXD2 mice was profiled for IgG and IgM specific autoantibody reactivity to peptide auto-epitopes printed in duplicate on a PepperPrint Chip.

first: John

middle: D

last: Mountz

first: Hui-Chen

last: Hsu


title: Autoimmune peptide antigen reactivity in BXD2 mice with spontaneous systemic autoimmune disease

summary: The aim of the study was to determine autoimmune BXD2 mouse sera reactivity to linear peptide epitopes from the Immune Epitope Database.  Pooled sera from six 8-10 month old BXD2 mice was diluted at 1:1000 and incubated on a PEPperPRINT peptide microarray platform printed with peptide autoantigens.

platform_organism:
Klebsiella pneumoniae
Proteus mirabilis
Mycobacterium tuberculosis
Homo sapiens
Human alphaherpesvirus 2
human gammaherpesvirus 4
Caprine arthritis encephalitis virus
Human endogenous retrovirus K
Torque teno virus

overall_design: In this study, pooled sera from six 8-10 month old BXD2 mice was profiled for anti-mouse IgG (H+L) analysis of autoantibody reactivity to peptide auto-epitopes printed in duplicate on a PepperPrint Chip.


title: Autoimmune peptide antigen reactivity in normal B6 mice Pepperchip 2.0

summary: The aim of the array was to determine the B6 mouse sera IgG and IgM reactivity profile to linear peptide epitopes.  Pooled sera from three 6-9 month old B6 mice was diluted at 1:200 for IgG specific analysis or 1:1000 for IgM specific analysis and incubated on a PEPperPRINT peptide microarray platform printed with peptide autoantigens

platform_organism: Mycobacterium avium subsp. paratuberculosis

overall_design: Pooled sera from three 6-9 month old B6 mice was profiled for IgG or IgM-specific analysis of autoantibody reactivity to peptide auto-epitopes printed in duplicate on a PepperPrint Chip.


title: The Assembly of miRNA-mRNA-protein Regulatory Networks Using High-throughput Expression Data (miRNA)

city: Pittsburgh

first: Jean-Francois

last: Mouillet

address: 204 Craft Ave

department: MWRI - OBGYN and Reproductive Sciences

institute: University of Pittsburgh

summary: Analyze miRNA expression levels in primary trophoblasts, derived from term human placenta and cultured under standard or hypoxic conditions

overall_design: Human placental trophoblasts were dispersed using a trypsin-deoxyribonuclease-dispase/Percoll method, plated in 6-well plates, and maintained in standard culture conditions (O2=20%). After 4 h (defined as time 0), the plates were divided to those in continued standard culture conditions, or to culture in hypoxia (O2=0%). Cells were then harvested at 6 h, 12 h, 24 h, 48 h and 72 h, and processed for miRNA arrays

first: Tianjiao

last: Chu

first: Thomas

middle: P

last: Conrads

first: Yoel

last: Sadovsky


title: General Approach for Tetramer Based Identification of Autoantigen Reactive B Cells: Characterization of La and snRNP Reactive B Cells in Autoimmune BXD2 Mice


title: Autoimmune peptide antigen IgG and IgM reactivity in B6 and BXD2 mice with spontaneous systemic autoimmune disease

summary: The aim of the study was to determine B6 and BXD2 mouse sera IgG and IgM reactivity to linear peptide epitopes at different ages.  Serum from B6 or BXD2 mice was diluted at 1:200 for IgG-specific analysis or 1:1000 for IgM specific analysis and incubated on a PEPperPRINT peptide microarray platform printed with peptide autoantigens.

overall_design: 80 pre-selected peptides based on a previous screen of pooled mouse serum BXD2 against the PEPperCHIP® Autoimmunity Microarray with 2,733 linear  B-cell epitopes were printed in duplicate in 16 copies on a custom PEPperCHIP® Peptide  Microarray.  Flag (DYKDDDDKGG) and  HA (YPYDVPDYAG) control peptides (10 spots each control) were randomly distributed in each array copy as controls.  Sera from 2, 5, or 9 month old B6 or BXD2 mice was profiled for anti-mouse IgG or IgM-specific analysis of autoantibody reactivity to the peptide auto-epitopes.


title: Lin28b promotes fetal B lymphopoiesis through the transcription factor Arid3a [wildtype tissue]

overall_design: 4 individual sorts of  Fr.A and Fr.B/C fractions in bone marrow and fetal liver of BALB/c mice


title: Taqman miRNA Array on Murine livers with varying amounts of carbon tetrachloride induced liver fibrosis

status: Public on Feb 25 2015

city: Baltimore

first: Tyler

last: Creamer

state: Maryland

address: 733 N Broadway

department: Genetic Medicine

institute: Johns Hopkins University

summary: Abstract from Knabel et al. PLoS One (2015): Fibrosis refers to the accumulation of excess extracellular matrix (ECM) components and represents a key feature of many chronic inflammatory diseases. Unfortunately, no currently available treatments specifically target this important pathogenic mechanism. MicroRNAs (miRNAs) are short, non-coding RNAs that post-transcriptionally repress target gene expression and the development of miRNA-based therapeutics is being actively pursued for a diverse array of diseases. Because a single miRNA can target multiple genes, often within the same pathway, variations in the level of individual miRNAs can potently influence disease phenotypes. Members of the miR-29 family, which include mir29a, miR-29b and miR-29c, are strong inhibitors of ECM synthesis and fibrosis-associated decreases in miR-29 have been reported in multiple organs. We observed downregulation of miR-29a/b/c in fibrotic livers of carbon tetrachloride (CCl4) treated mice as well as in isolated human hepatocytes exposed to the pro-fibrotic cytokine TGF-β. Importantly, we demonstrate that a single systemic injection of a miR-29a expressing adeno-associated virus (AAV) can prevent and even reverse histologic and biochemical evidence of fibrosis despite continued exposure to CCl4. The observed therapeutic benefits were associated with AAV transduction of hepatocytes but not hepatic stellate cells, which are the main ECM producing cells in fibroproliferative liver diseases. Our data therefore demonstrate that delivery of mir-29 to the hepatic parenchyma using a clinically relevant gene delivery platform protects injured livers against fibrosis and, given the consistent fibrosis-associated downregulation of miR-29, suggests AAV-miR-29 based therapies may be effective in treating a variety of fibroproliferative disorders.

overall_design:
The Taqman MicroRNA Array (Taqman Array Rodent MicroRNA A Cards v2.0, ABI) was run, using manufacturer's protocols, on 3 groups of mice with varying amounts fibrotic injury. The groups include carbon tetrachloride intraperitinially injected bi-weekly for 1, 4, and 8 weeks with n=4, 3, and 2 respectively for each group. The RNA was isolated from whole liver using the MiRvana miRNA Isolation Kit (Ambion) according to manufacturer's protocols.

The fold_change.txt contains the following data columns;
ID_Ref: mmu-miR being quantified
not-treated (FC): Fold Change compared to not-treated group using Geometric mean normalization
1 week (FC): Fold Change compared to not-treated group using Geometric mean normalization
4 weeks (FC): Fold Change compared to not-treated group using Geometric mean normalization
8 weeks (FC): Fold Change compared to not-treated group using Geometric mean normalization

first: Matthew

last: Knabel

first: Kalyani

last: Ramachandran

first: Sunil

last: Karhadkar

first: Hun-Way

last: Hwang

first: Raghu

last: Chivukula

first: Farooq

last: Sheikh

first: K

last: Clark

first: Michael

last: Torbenson

first: Robert

last: Montgomery

first: Andrew

last: Cameron

first: Joshua

last: Mendell

first: Daniel

last: Warren


title: Inhibition of Pseudomonas aeruginosa swarming motility by 1-naphthol and other bicyclic compounds bearing hydroxyl group.

status: Public on Feb 20 2015

city: Hamamatsu

first: Yosuke

last: Tashiro

state: Shizuoka

address: 3-5-1 Johoku Naka-ku

department: Graduate School of Engineering, Department of Applied Chemistry and Biochemical Engineering

country: Japan

institute: Shizuoka University

type: Expression profiling by genome tiling array

summary: Many bacteria convert bicyclic compounds, such as indole and naphthalene, to oxidized compounds, including hydroxyindoles and naphthols. Pseudomonas aeruginosa, a ubiquitous bacterium that inhabits diverse environments, shows pathogenicity against animals, plants and other microorganisms, and increasing evidence has shown that several bicyclic compounds alter the virulence-related phenotypes of P. aeruginosa. Here, we revealed that hydroxyindoles (4- and 5-hydroxyindoles) and naphthalene derivatives bearing hydroxyl groups specifically inhibit swarming motility but have minor effects on other motilities, including swimming and twitching, in P. aeruginosa. Further analyses using 1-naphthol showed that this effect is also associated with clinically isolated hyper swarming P. aeruginosa cells. Swarming motility is associated with the dispersion of cells from biofilms, and the addition of 1-naphthol maintained biofilm biomass without cell dispersion. Swarming inhibition did not mediate rhamnolipid production, which regulates swarming motility in P. aeruginosa. Transcriptome analyses revealed that 1-naphthol increases gene expression associated with multidrug efflux and represses gene expression associated with aerotaxis and pyochelin, flagellar, and pili synthesis. In the present study, we showed that several bicyclic compounds bearing hydroxyl groups inhibit the swarming motility of P. aeruginosa, and these results provide new insight into the chemical structures that inhibit the specific phenotypes of P. aeruginosa.

overall_design: In total 4 samples: gene expressions of P. aeruginosa with (2 samples) or without (2 samples) 1-naphthol

first: Hiromu

last: Oura

first: Masanori

last: Toyofuku

first: Kousetsu

last: Ueda

first: Tatsunori

last: Kiyokawa

first: Satoshi

last: Ito

first: Yurika

last: Takahashi

first: Seunguk

last: Lee

first: Hideaki

last: Nojiri

first: Toshiaki

last: Nakajima-Kambe

first: Hiroo

last: Uchiyama

first: Hiroyuki

last: Futamata

first: Nobuhiko

last: Nomura


title: Phenotype specific analyses of p53 reveal distinct regulatory mechanism for chronically activated p53

status: Public on Feb 27 2015

city: Cambridge

first: Suraj

last: Menon

address: Li Ka Shing Center, Robinson Way

country: United Kingdom

institute: Cambridge Research Institute, Cancer Research UK

summary: microarray analysis with and without sh-p53 in IMR90 (normal human diploid fiborblasts)

overall_design: Phenotypes were created by overexpression of RasG12V, E1A/RasG12V in IMR90 cells, in growing IMR90,  inr quiescent IMR90 cells (3 days confluence) and 24 or 48 hours Etoposide treated IMR90 cells were subjected to lentiviral knockdown of p53 or vector

first: Kristina

last: Kirschner


title: Elevated dairy fat intake in lactating women alters milk lipid and fatty acids without detectible changes in expression of genes related to lipid uptake or synthesis

status: Public on Feb 24 2015

city: Davis

first: Matt

last: Settles

address: 451 Health Sciences Sr

department: Genome Center

institute: University of California, Davis

summary: Previous work has demonstrated that elevated maternal lipid intake (particularly from dairy products) is associated with increased lipids and altered fatty acid profile in milk produced by healthy lactating women. We investigate our primary hypothesis that a maternal diet rich in full-fat dairy products would simultaneously increase milk lipid percent and expression of genes related to the uptake and/or de novo biosynthesis of milk lipids.

overall_design: Within a a randomized, crossover study we performed a microarray analysis comparing 6 lactating women with diets rich in full-fat or non-fat dairy products. Each woman consumed one of the two diets during timepoint one, and after a two week washout period, switched over to the other diet. The timepoint value indicates whether the particular dietary treatment was consumed first or second.

first: Sarah

last: Brooker

first: Janet

middle: E

last: Williams

first: Matthew

first: Mark

last: McGuire

first: Michelle


title: Gene expression profiling of FFPE breast cancer samples [Illumina DASL WG platform]

first: Maurizio

last: Callari

address: Via Amadeo, 42

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

summary:
The use of Affymetrix U133 2.0 Plus chips on FFPE samples when coupled with a qPCR-based sample pre-assessment step, yielded satisfactory results from the point of view of biological reliability. When compared with the Illumina DASL WG platform, specifically designed for degraded RNA, the data generated with the Affymetrix platform showed a wider interquartile range (1.32 vs 0.57, p<2.2x10-16) suggesting a superior discriminatory power within samples as indicated by the good agreement with the immunohistiochemically derived ER status.
FFPE primary breast cancer samples profiled using Illumina DASL WG platform after RNA amplification with the Nugen WT-Ovation FFPE System

overall_design: The following criteria were considered for a direct comparison of 12 GEPs obtained from Affymetrix and DASL platforms: gene variability as defined by IQR, ESR1 expression in ER status subgroups defined by IHC, distribution of fold changes for predefined ER related genes when comparing ER positive and negative samples.

first: Valeria

last: Musella

first: Vera

last: Cappelletti

first: Maria

middle: G

last: Daidone


title: Effects of fibroblast growth factors (FGF) on dissociated myelinating cultures

status: Public on Feb 18 2015

city: Glasgow

first: Chris

last: Linington

address: 120 University Avenue

department: Institute of Infection, Immunity and Inflammation

institute: University of Glasgow

summary: Analysis of the effects of three members of the FGF family (FGF1, FGF2 and FGF9) and bone morphogenic protein 4 (BMP4) on myelinating cultures generated from dissociated embryonic spinal cord. The results of both immediate (24 hours, T1 (24 hrs)) and long term treatments (10days, T2) give insights into the cumulative effects of sustained FGF and BMP mediated signal transduction in the pathogenesis of demyelinating diseases.

overall_design: Dissociated myelinating cultures were generated from neurosphere derived astrocytes (generated from striata of P1 Sprague-Dawley rats) and spinal cord cells from E15.5 Sprague-Dawley(SD) embryos. The effect of recombinant human FGF9 and other soluble factors on these in vitro myelinating cultures was investigated by adding them to the culture media after 18 days in vitro (DIV). The effects of each factor were analysed using three independent cultures at two time points (19DIV and 28 DIV).

first: Katja

last: Thuemmler

first: Maren

last: Lindner

first: Christopher


title: PLZF expression maps the early stages of ILC1 lineage development

status: Public on Feb 13 2015

city: Chicago

first: Albert

last: Bendelac

state: IL

address: 929 East 57th Street, GCIS W506

department: Pathology

institute: The University of Chicago

summary: Diverse populations of natural killer cells, which exert critical early cytolytic functions against virally infected cells, have recently been uncovered, raising issues of lineage relationships. We used expression of the transcription factor PLZF to identify the developmental intermediates of ILC1s, a subset of natural killer-like cells that are particularly abundant in the liver, and demonstrated a distinct precursor but parallel development and partial overlap with established classical NK stages. Using microarray analysis, we defined a set of PLZF-dependent genes that contributed to the lineage divergence between ILC1s and classical NK cells.

overall_design: Liver lymphocytes from pools of PLZF+/+ or PLZF-/- mice were sorted into ILC1s and cNKs for RNA isolation and Illumina expression profiling.

first: Michael

last: Constantinides

first: Herman

last: Gudjonson

first: Benjamin

last: McDonald

first: Isabel

last: Ishizuka

first: Philip

last: Verhoef

first: Aaron

last: Dinner


title: Pluripotent stem cells: Normal diploid line vs lines with deletions of Chr7

status: Public on Feb 16 2015

city: New York

first: Eirini

last: Papapetrou

state: NY

address: 1470 Madison Avenue

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

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

overall_design: Refer to individual Series


title: C. elegans (strain SS104, sterile mutant) Control vs. NAC RNAi

status: Public on Feb 12 2015

city: Konstanz

first: Tancred

last: Frickey

state: BW

address: Universitaetsstr. 10

department: Biology

country: Germany

institute: University of Konstanz

summary: Distribution of ribosome-associated mRNAs (RNCs) between the cytosol and the ER membrane in control and NAC depleted C. elegans

overall_design: Four-condition experiment, Control-Cytosol vs. Control-Membrane and NAC RNAi-Cytosol vs. NAC RNAi-Membrane. Biological replicates: 4 control replicates, 4 NAC-depleted replicates.

first: Martin

last: Gamerdinger


title: Gene expression profiling in thoracic aortas of 8 week and 16 week ApoE knockout mice on a western type diet

status: Public on Feb 03 2015

city: Oxford

first: Keith

last: Channon

address: Roosevelt Drive

department: Radcliffe Department of Medicine

institute: Oxford University

summary: Identification of novel pathways in the development of atherosclerosis. Here, we are looking at changes in gene expression that occur in the aorta with the development of atherosclerosis

overall_design: Analysis used RNA from thoracic aortas from chow fed ApoE knockout mice as control samples for comparison to the experimental samples from 8 week and 16 week ApoE knockout mice fed a western-type diet

first: Jyoti

last: Patel


title: The multikinase inhibitor Sorafenib targets mitochondria and synergizes with glycolysis blockade for cancer cell killing.

status: Public on Feb 04 2015

city: Rome

first: camilla

last: bernardini

address: L.go F.Vito 1

department: Human Anatomy

institute: UCSC

summary: Objective: identify novel and relevant aspects of Sorafenib action on liver cancer cells. We found that in rat hepatocholangiocarcinoma (LCSC-2) cells, exposure to the MEK/multikinase inhibitor sorafenib did not inhibit  ERK phosphorylation nor induced appreciable cell death in the low micromolar range; instead, the drug elicited a raise of intracellular reactive oxygen species (ROS) accompanied by a severe decrease of oxygen consumption and intracellular ATP levels, all changes consistent with  mitochondrial damage. Moreover, Sorafenib induced depolarization of isolated rat liver mitochondria, indicating a possible direct effect on the organelle. Microarray analysis of gene expression in sorafenib-trated cells revealed a metabolic reprogramming toward aerobic glycolysis, that likely accounts for resitance to drug toxicity in this cell line. Importantly, cytotoxicity was strongly potentiated by glucose withdrawal from the culture medium or by the glycolytic inhibitor 2-deoxy-glucose, a finding also confirmed in the highly malignant melanoma cell line B16F10. Mechanistic studies revealed that ROS are pivotal to cell killing by the Sorafenib + 2DG combination, and that a low content of intracellular oxidants is associated with resistance to the drug; instead, Thr172phosphorylation/activation of the AMP-activated protein kinase (AMPK), induced by Sorafenib, may exert protective effects, since cytotoxicity was enhanced by an  AMPK specific inhibitor and prevented by the AMPK activator Metformin. Overall, this study identifies novel and relevant aspects of Sorafenib action on liver cancer cells, including mitochondrial damage, induction of ROS and a metabolic cell reprogramming towards “glucose addiction”, potentially exploitable in therapy.

overall_design: Microarray analysis of gene expression in sorafenib-trated cells. LCSC-2 cells were incubated with sorafenib 2.5 mM under serum deprivation for 12 hours. The total RNA was isolated from LCSC2, 24h after treatment, using the RNeasy mini kit (Qiagen, Hilden, Germany),  RNA was quantified using a UV spectrophotometer and RNA quality and integrity were assessed Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). The resulting total RNA was then used to create the biotin-labeled library to be hybridized on GeneChip Rat Gene expression 1.0 st Array (Affymetrix, Santa Clara, CA, USA), according to the recommended experimental protocols provided by the suppliers. The CEL files resulting from the hybridization were analyzed using the Partek® Genomic Suite™ (Partek GS). Gene-level calculation was performed by Robust Multichip Average and normalization by quantile sketch.

first: Valentina

last: Tesori

first: Chiara

last: Piscaglia

first: Marta

last: Barba

first: Camill

last: Bernardini

first: Roberto

last: Scatena

first: Alessandro

last: Pontoglio

first: Laura

last: Castellini

first: Ausiliatrice

last: Puglisi

first: Giovanbattista

last: Pani

first: Antonio

last: Gasbarrini


title: Detection of copy number variation in patients with Pelizaeus-Merzbacher disease (PMD)

status: Public on Feb 09 2015

city: Wilmington

first: Grace

last: Hobson

state: Delaware

address: 1600 Rockland Road

department: Nemours Biomedical Research

institute: Nemours/AI duPont Hospital for Children

type: Genome variation profiling by genome tiling array


title: Detection of copy number variation in patients with Pelizaeus-Merzbacher disease (PMD) - Affymetrix

summary: The objective of the study was to investigate the extent of duplicated, triplicated, and quadruplicated regions in PMD patients so that junction analysis could be performed.

overall_design: 4 samples were analyzed. Replicates are not included.

first: Suzanne

last: McCahan


title: The genome-wide effects of ionising  on mutation induction in the mammalian germline

city: Leicester

first: Adeolu

last: Adewoye

address: University Road

department: Genetics

institute: University of Leicester

summary:
Investigation of genome-wide germline copy number mutations in mice after parental exposure to 3 Gy of acute X-rays
The level of copy number mutations in offspring of exposed paternal mice was substantially increased when compared to the control

overall_design: Overall 262 samples were used of which 93 were control samples and 169 treated samples. The control samples came from offspring of parents (C57BL6/J (male)  and  CBA/Ca (female)) with sham -ir while the treated samples were from offspring of 3 Gy whole-body acute irradiated paternal and non-exposed maternal. The treated samples classified into two groups: post-meiotic and pre-meiotic according to exposed status of the sperm that gave rise to the offspring. The reference sample for each offspring was equal mixture of paternal and maternal DNA.

middle: B

first: Yuri

last: Dubrova


title: Affymetrix OncoScan FFPE Array array data from Li-Fraumeni Syndrome tumors

city: Salt Lake City

first: Joshua

last: Schiffman

state: Utah

address: 2000 Circle of Hope Dr

department: Pediatric Oncology/Hematology

institute: Huntsman Cancer Institute

summary:
Loss of heterzygosity in TP53
Affymetrix OncoScan FFPE arrays were performed according to the manufacturer's directions on DNA extracted from tumors

overall_design: Copy number analysis of Affymetrix OncoScan FFPE array was performed for two osteosarcoma lung metastases, one lung adenocarcinoma, one meningioma, one pleomorphic sarcoma


title: Detection of copy number variation in patients with Pelizaeus-Merzbacher disease (PMD) - NimbleGen

overall_design: 10 samples were analyzed. Replicates are not included. The arrays were performed as a service by NimbleGen. Reference DNA was normal male NM002 from our lab.


title: Microarray analysis of Rhodobacter sphaeroides CceR and AkgR deletion strains

status: Public on Feb 02 2015

city: Madison

first: Timothy

last: Donohue

state: WI

address: 1552 University Avenue

department: Bacteriology

institute: University of Wisconsin - Madison

summary: To gain a better understanding of the transcription factors that regulate central carbon metabolism in Rhodobacter sphaeroides global gene expression analysis was used to determine genes under the regulatory influence of 2 transcription factors: CcmR (RSP_1663) and AkgR (RSP_0981) both predicted to be involved in the regulation of central carbon and energy metabolism.

overall_design: Microarray analysis conducted for deletion strains of 2 transcription factors known or predicted to be involved in the regulation of central carbon metabolism in Rhodobacter sphaeroides using the R. sphaeroides Affymetrix gene chip. These deletion mutant expression profiles were compared to that of wild type cells to determine differentially expressed genes regulated by these transcription factors.

first: Saheed

last: Imam


title: Gene expression analysis in cytoplasmic and nuclear fractions of P493-6 B cells with low c-myc expression to assess long noncoding RNA localization

status: Public on Feb 01 2015

city: Groningen

first: Melanie

last: Winkle

state: Groningen

address: Hanzeplein 1

department: Pathology & Medical Biology

country: Netherlands

institute: UMC Groningen

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

summary:
Myc is a well known transcription factor with important roles in cell cycle, apoptosis and cellular transformation. Long non-coding (lnc)RNAs have recently emerged as a important class of regulatory RNAs. Here, we show that lncRNAs are an extensive component of the Myc-regulated transcriptional program. Using the P493-6 inducible Myc model we demonstrate that both Myc-induced mRNAs and lncRNAs were significant enriched for Myc binding sites. In contrast to Myc-repressed mRNAs, Myc-repressed lncRNAs were significantly enriched for Myc binding sites. Subcellular localization analysis revealed that Myc-repressed lncRNAs and mRNAs are enriched in the nucleus while Myc-induced lncRNAs and mRNAs are enriched both in the cytoplasm and nucleus. Parallel analysis of differentially expressed lncRNAs and mRNAs identified 105 lncRNA-mRNA pairs that were in close vicinity, indicative for regulation in cis. To support the potential relevance of the Myc-regulated lncRNAs in cellular transformation, we analyzed their expression in primary Myc-high and Myc-low B-cell lymphomas. In total, 54% of the lncRNAs differentially expressed between the lymphoma subsets were identified as Myc-regulated in P493-6 cells. This study is the first to show that lncRNAs are an important factor within the Myc-regulated transcriptional program and indicates a marked difference between Myc-repressed lncRNAs and mRNAs.
Arrays: The total, cy3 labeled fraction and the cytoplasmic or nuclear, cy5 labeled fraction was hybridized on the same array. Data was imported and analyzed as a single color array.

overall_design: Expression of all known mRNAs and >10 000 lncRNAs was assessed in P493-6 B cells with low c-myc levels

first: Anke

last: van den Berg

first: Masoumeh

last: Tayari

first: Jantine

last: Sietzema

first: Martijn

last: Terpstra

first: Gertrud

last: Kortman

first: Debora

last: de Jong

first: Lydia

last: Visser

first: Arjan

last: Diepstra

first: Klaas

last: Kok

first: Joost

last: Kluiver


title: Gene expression analysis to identify long noncoding RNAs deregulated in Myc-driven B cell lymphoma

summary: Myc is a well known transcription factor with important roles in cell cycle, apoptosis and cellular transformation. Long non-coding (lnc)RNAs have recently emerged as a important class of regulatory RNAs. Here, we show that lncRNAs are an extensive component of the Myc-regulated transcriptional program. Using the P493-6 inducible Myc model we demonstrate that both Myc-induced mRNAs and lncRNAs were significant enriched for Myc binding sites. In contrast to Myc-repressed mRNAs, Myc-repressed lncRNAs were significantly enriched for Myc binding sites. Subcellular localization analysis revealed that Myc-repressed lncRNAs and mRNAs are enriched in the nucleus while Myc-induced lncRNAs and mRNAs are enriched both in the cytoplasm and nucleus. Parallel analysis of differentially expressed lncRNAs and mRNAs identified 105 lncRNA-mRNA pairs that were in close vicinity, indicative for regulation in cis. To support the potential relevance of the Myc-regulated lncRNAs in cellular transformation, we analyzed their expression in primary Myc-high and Myc-low B-cell lymphomas. In total, 54% of the lncRNAs differentially expressed between the lymphoma subsets were identified as Myc-regulated in P493-6 cells. This study is the first to show that lncRNAs are an important factor within the Myc-regulated transcriptional program and indicates a marked difference between Myc-repressed lncRNAs and mRNAs.

overall_design: Expression of all known mRNAs and >10 000 lncRNAs was assessed in primary lymphoma tissue with high c-myc levels (Burkitt lymphoma; BL) and low c-myc levels (chronic lymphocytic leukemia; CLL)


title: Long noncoding RNAs as a novel component of the Myc transcriptional network


title: Ozone-induced rice grain yield loss is controlled by ABERRANT PANICLE ORGANIZATION 1 gene

status: Public on Jan 31 2015

city: Tsukuba

first: Keita

last: Tsukahara

address: 2-1-12 Kannon-dai

institute: National Food Research Institute, NARO

summary: Rice grain yield is predicted to decrease in the future because of an increase in tropospheric ozone concentration. However, the underlying mechanisms are unclear. Here, we investigated the responses to ozone of two rice (Oryza Sativa L.) cultivars, Sasanishiki and Habataki. Sasanishiki showed ozone-induced leaf injury, but no grain yield loss. By contrast, Habataki showed grain yield loss with minimal leaf injury. A QTL associated with grain yield loss caused by ozone was identified in Sasanishiki/Habataki chromosome segment substitution lines and included the ABERRANT PANICLE ORGANIZATION 1 (APO1) gene. The Habataki allele of the APO1 locus in a near-isogenic line also resulted in grain yield loss upon ozone exposure, suggesting APO1 involvement in ozone-induced yield loss. Only a few differences in the APO1 amino acid sequences were detected between the cultivars, but the APO1 transcript level was oppositely regulated by ozone exposure: i.e., it increased in Sasanishiki and decreased in Habataki. Interestingly, the levels of some phytohormones (jasmonic acid, jasmonoyl-L-isoleucine, and abscisic acid) known to be involved in attenuation of ozone-induced leaf injury tended to decrease in Sasanishiki but to increase in Habataki upon ozone exposure. These data indicate that ozone-induced grain yield loss in Habataki is caused by a reduction in the APO1 transcript level through an increase in the levels of phytohormones that reduce leaf damage.

overall_design: Ozone induced gene expression in rice inflorescence meristem was measured at 6 month after exposure to dose of 43.7 nL L-1 (ambient air) and 85.7 nL L-1 (2-fold concentration compared to ambient air) (12 hours mean). The two culticars, Sasanishiki and Habataki, were used for each experiment.

first: Masanori

last: Tamaoki


title: Gene expression analysis to identify Myc-regulated long noncoding RNAs in B cells with variable Myc levels

summary:
Myc is a well known transcription factor with important roles in cell cycle, apoptosis and cellular transformation. Long non-coding (lnc)RNAs have recently emerged as a important class of regulatory RNAs. Here, we show that lncRNAs are an extensive component of the Myc-regulated transcriptional program. Using the P493-6 inducible Myc model we demonstrate that both Myc-induced mRNAs and lncRNAs were significant enriched for Myc binding sites. In contrast to Myc-repressed mRNAs, Myc-repressed lncRNAs were significantly enriched for Myc binding sites. Subcellular localization analysis revealed that Myc-repressed lncRNAs and mRNAs are enriched in the nucleus while Myc-induced lncRNAs and mRNAs are enriched both in the cytoplasm and nucleus. Parallel analysis of differentially expressed lncRNAs and mRNAs identified 105 lncRNA-mRNA pairs that were in close vicinity, indicative for regulation in cis. To support the potential relevance of the Myc-regulated lncRNAs in cellular transformation, we analyzed their expression in primary Myc-high and Myc-low B-cell lymphomas. In total, 54% of the lncRNAs differentially expressed between the lymphoma subsets were identified as Myc-regulated in P493-6 cells. This study is the first to show that lncRNAs are an important factor within the Myc-regulated transcriptional program and indicates a marked difference between Myc-repressed lncRNAs and mRNAs.
P493-6: 72h Tet treated (low c-myc levels), t=4h (intermediate c-myc levels), t=24h (high c-myc levels), untreated (steady state c-myc levels)

overall_design: Expression of all known mRNAs and >10 000 lncRNAs was assessed in P493-6 B cells with different c-myc levels


title: Expression data from Sus scrofa atria

city: Taipei

first: Tzu-Hao

last: Chang

address: 250 Wu-Xin Street

department: Graduate Institute of Biomedical Informatics

country: Taiwan

institute: Taipei Medical University

summary: Regulatory Mechanisms of Atrial Remodeling of Mitral Regurgitation Pigs

overall_design: This study enrolled 6 pigs (age: 18 months) and divided into three groups: mitral regurgitation pigs (MR) (n = 2;  2 males sacrificed 12 months after surgery), MR pigs treated with valsartan (MRV) (n = 2; 2 males age-matched to MR sacrificed 12 months after surgery), and normal control pigs (NC) (n = 2; 2 males age-matched to MR pigs). Valsartan (3.43 mg/kg/day), a type I angiotensin II receptor blocker, was administered from one week before surgery and then daily after surgery in the MRV group. We sought to systemically elucidate critical differences in the alteration of RNA expression pattern between the atrial myocardium of pigs with and without MR, and between the atrial myocardium of MR pigs with and without valsartan using high-density oligonucleotide microarrays and functional network enrichment analysis.

first: Mien-Cheng

last: Chen

first: Jen-Ping

first: Sheng-Da

last: Hsu

first: Hsien-Da

last: Huang

first: Wan-Chun

last: Ho

first: Feng-Sheng

last: Wang

first: Chang-Chun

last: Hsiao

first: Wen-Hao

last: Liu


title: Chromothripsis in healthy individuals affects multiple protein-coding genes and can result in severe congenital abnormalities in offspring [case 3]

city: Utrecht

first: Wigard

last: Kloosterman

address: Universiteitsweg 100

institute: University Medical Center Utrecht

summary:
Chromothripsis represents an extreme class of complex chromosome rearrangements (CCRs) with major effects on chromosomal architecture. Although recent studies have associated chromothripsis with congenital abnormalities, the incidence and pathogenic effects of this phenomenon require further investigation. Here, we analyzed the genomes of three families in which chromothripsis rearrangements were transmitted from a mother to her child. The chromothripsis in the mothers resulted in completely balanced rearrangements involving 8-23 breakpoint junctions across 3-5 chromosomes. Two mothers did not show any phenotypic malformations, although 3-13 protein coding genes were affected by breakpoints. Unbalanced but stable transmission of a subset of the derivative chromosomes caused apparently de novo complex copy number changes in two children. This resulted in gene dosage changes, which are likely responsible for their severe congenital phenotypes. In contrast, one child with severe congenital disease, carried all three chromothripsis chromosomes from his healthy mother, but one of the chromosomes acquired de novo rearrangements leading to copy number changes. These results show that the human genome can tolerate extreme reshuffling of chromosomal architecture, including breakage of multiple protein coding genes, without noticeable phenotypic effects. The presence of chromothripsis in healthy individuals strongly affects reproduction and is expected to substantially increase the risk of spontaneous abortions and severe congenital disease.
We analyzed one patient-parent-mother's parents quintet (case 1) and a patient-siblings-parent quintet (case 2) with Illumina beadchip arrays and one patient-parent trio (case 3)  to test for (de  novo) copy number variants and to analyze the parental origin of the complex rearrangements in these patients.

overall_design: This study represents one child-parent trio (case 3) test for (de novo) copy number variants in the child.

first: Mirjam

last: de Pagter

first: Markus

last: van Roosmalen

first: Annette

middle: F

last: Baas

first: Ivo

last: Renkens

first: Karen

last: Duran

first: Ellen

last: van Binsbergen

first: Masoumeh

last: Tavakoli-Yaraki

first: Ron

last: Hochstenbach

first: Lars

middle: T

last: van der Veken

first: Edwin

last: Cuppen


title: Chromothripsis in healthy individuals affects multiple protein-coding genes and can result in severe congenital abnormalities in offspring.


title: Gene expression profile for naïve CD4+ T cells after 60-hour-treatment by IL-27

city: Boston

first: Vijay

middle: K

last: Kuchroo

address: 77 Ave Louis Pasteur

department: Evergrande Center for Immunologic Diseases

institute: Brigham and Women's Hospital

summary:
The inhibitory receptor Tim-3 has emerged as a critical regulator of the T cell dysfunction that develops in chronic viral infections and cancers. However, little is known regarding the signaling pathways that drive Tim-3 expression. Here, we demonstrate that IL-27 induces NFIL3, which promotes permissive chromatin remodeling of the Tim-3 locus and induces Tim-3 expression together with the immunosuppressive cytokine IL-10. We further show that the IL-27/NFIL3 signaling axis is crucial for the induction of Tim-3 in vivo. IL-27-conditioned Th1 cells exhibit reduced effector function and are poor mediators of intestinal inflammation. This inhibitory effect is NFIL3 dependent. In contrast, tumor-infiltrating lymphocytes (TILs) from IL-27R-/- mice exhibit reduced NFIL3, less Tim-3 expression and failure to develop dysfunctional phenotype, resulting in better tumor growth control. Thus, our data identify an IL-27/NFIL3 signaling axis as a key regulator of effector T cell responses via induction of Tim-3, IL-10, and T cell dysfunction.
Through gene expression profile analysis, we identified a series of transcription factors that are induced by IL-27. Particularly, the induction of NFIL3 is highly relevant to Tim-3 expression.

overall_design: Naïve CD4+ T cells from C57BL/6 mice were stimulated with plate-bound anti-CD3 and anti-CD28 antibodies for 60 hours. The cells were subjected to gene profile analysis. A comparative transcriptome analysis between cells under neutral culture condition (Untreated) and cells treated with IL-27 (IL-27-treated) was peformed to screen transcription factors that are induced by IL-27 signaling.

first: Chen

last: Zhu


title: Chromothripsis in healthy individuals affects multiple protein-coding genes and can result in severe congenital abnormalities in offspring [case 1]

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

overall_design: Here, we analyzed one patient-parent-mother's parents quintet to test for (de novo) copy number variants and to analyze the parental origin of the complex rearrangements in these patients.

middle: J


title: Chromothripsis in healthy individuals affects multiple protein-coding genes and can result in severe congenital abnormalities in offspring [case 2]

summary: Chromothripsis represents an extreme class of complex chromosome rearrangements (CCRs) with major effects on chromosomal architecture. Although recent studies have associated chromothripsis with congenital abnormalities, the incidence and pathogenic effects of this phenomenon require further investigation. Here, we analyzed the genomes of three families in which chromothripsis rearrangements were transmitted from a female carrier to her child. The chromothripsis in the carriers resulted in completely balanced rearrangements involving 8-23 breakpoint junctions across 3-5 chromosomes. Two carriers did not show any phenotypic malformations, although 3-13 protein coding genes were affected by breakpoints. Unbalanced but stable transmission of a subset of the derivative chromosomes caused apparently de novo complex copy number changes in two children. This resulted in gene dosage changes, which are likely responsible for their severe congenital phenotypes. In contrast, one patient with severe congenital disease, carried all three chromothripsis chromosomes from his healthy mother, but one of the chromosomes acquired de novo rearrangements leading to copy number changes. These results show that the human genome can tolerate extreme reshuffling of chromosomal architecture, including breakage of multiple protein coding genes, without noticeable phenotypic effects. The presence of chromothripsis in healthy carriers strongly affects reproduction and is expected to substantially increase the risk of spontaneous abortions and severe congenital disease.

overall_design: We analyzed one patient-parent-mother's parents quintet (case 1) and a patient-siblings-parent quintet (case 2) with Illumina beadchip arrays and one patient-parent trio (case 3)  to test for (de  novo) copy number variants and to analyze the parental origin of the complex rearrangements in these patients. For case 2, the mother and patient's SNP array data was previously submitted [GSE37906]. aCGH data for case 3 is submitted seperately.


title: Genomic Screening of Testicular Germ Cell Tumors from Monozygotic Twins

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

type: Genome variation profiling by high throughput sequencing

summary: Genomic screening was performed for one family containing MZ twins with testicular germ cell tumors, in order to define alterations associated with risk of tumor development.

overall_design: Copy number alterations were evaluated using array-CGH (4x44K, Agilent Technologies) in one seminoma and one embryonal carcinoma (EC) from MZ twins. In addition, genomic alterations from the tumors and peripheral blood cells of the twins were compared to the parental genomes via their peripheral blood cells.

first: Sara

last: Silveira


title: Comparative microarray analysis of midgut tissues from feeding Rhipicephalus microplus and Rhipicephalus decoloratus adult females

city: Pretoria

first: Christian

last: Stutzer

state: Gauteng

address: Lynnwood road

department: Biochemistry

country: South Africa

institute: University of Pretoria

summary: Transcriptional profiling of midgut  tissues isolated from  Rhipicephalus microplus and Rhipicephalus decoloratus females at day 20 post infestation. This enabled the identification of transcripts that are species-specific or shared between the two tick species tested.

sample_organism:
Rhipicephalus microplus
Rhipicephalus decoloratus

overall_design: A direct comparison (Balanced block) was performed: Midgut tissues collected on  day 20 (post infestation) from R. microplus was compared to that of R. decoloratus. Biological replicates: 3 ; Technical replicates: 1.

first: Willem

last: van Zyl

first: Christine

last: Maritz-Olivier


title: Hemin and Iron transcriptome of Porphyromonas gingivalis (part 2)

status: Public on May 18 2015

city: Richmond

first: Janina

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

institute: Virginia Commonwealth University

summary: Transcriptional profiling of P. gingivalis cells comparing cells grown under iron replete conditions to that grown under iron depleted conditions

overall_design: Two-condition experiment, iron replete vs. iron deplete grown cells. Biological replicates: 4 independently grown and harvested bacterial cells. Two technical replicates (four replicates per array).


title: Chlamydophila psittaci negative ocular adnexal marginal zone lymphomas express self polyreactive B cell receptors

status: Public on Jan 30 2015

city: Stanford

first: Andrew

last: Gentles

address: 1201 Welch Road

institute: Stanford University

summary: The pathogenesis of Chlamydophila (C.) psittaci negative ocular adnexal extranodal marginal zone lymphomas (OAEMZLs) is poorly understood. OAEMZLs are monoclonal tumors expressing a biased repertoire of mutated surface immunoglobulins. Antigenic activation of the B cell receptor (BCR) may play a role in the pathogenesis of these lymphomas. We have analyzed the reactivity of recombinant OAEMZL immunoglobulins. OAEMZL antibodies reacted with self-human antigens, as demonstrated by enzyme-linked immunosorbent assays, HEp-2 immunofluorescence and human protein microarrays. All the analyzed recombinant antibodies (rAbs) exhibited polyreactivity by comprehensive protein array antibody reactivity and some rAbs also demonstrated rheumatoid factor activity. The identity of several reactive antigens was confirmed by microcapillary reverse-phase HPLC nano-electrospray tandem mass spectrometry. The tested rAbs frequently reacted with shared intracellular and extracellular self-antigens (e.g. galectin-3). Furthermore, these self-antigens induced BCR signaling in B cells expressing cognate surface immunoglobulins derived from OAEMZLs. These findings suggest that interactions between self-antigens and cognate OAEMZL tumor-derived BCRs are functional, inducing intracellular signaling. Overall our findings suggest that self-antigen-induced BCR stimulation may be implicated in the pathogenesis of C. psittaci negative OAEMZLs.

overall_design: Antibody Specificity Profiling with four OAEMZL rAbs (Ab4438, Ab4726, Ab5334, and Ab11274) performed on ProtoArray Human Protein Microarrays

first: Daxing

first: Shruti

last: Bhatt

first: Izidore

last: Lossos


title: ChIP-chip from human and mouse fetal brain

city: Oslo

first: Chandr

middle: Sekhar Reddy

last: Chilamakuri

address: Fådveien 15

department: Tumor Biology

country: Norway

institute: The Norwegian Radium Hospital

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: ChIP-chip from human fetal brain with H3K27Ac and H3K4Me1

summary: Enhancers can regulate the transcription of genes over long genomic distances. This is thought to lead to selection against genomic rearrangements within such regions that may disrupt this functional linkage. We tested this concept experimentally using the human X chromosome. We describe a scoring method to identify evolutionary maintenance of linkage between conserved non-coding elements and neighbouring genes. Chromatin marks associated with enhancer function are strongly correlated with the linkage score. We tested more than 1,000 putative enhancers by transgenesis assays in zebrafish to ascertain the identity of the target gene, with a focus on genes involved in X-linked intellectual disabilities (ID). The majority of active enhancers drive a transgenic expression in a pattern consistent with the known expression of a linked gene. These results show that evolutionary maintenance of linkage is a reliable predictor of an enhancer's function, and provide new information to discover the genetic basis of diseases caused by the mis-regulation of gene expression.

overall_design:
ChIP-chip from human fetal brain using H3K27Ac or H3K4Me1 antibodies.
Biological replicates: H3K27Ac_Rep1, H3K27Ac_Rep2
Biological replicates: H3K4Me1_Rep1, H3K4Me1_Rep2

first: Magali

last: Naville

first: Minaka

last: Ishibashi

first: Marco

last: Ferg

first: Hemant

last: Bengani

first: Silke

last: Rinkwitz

first: Monika

last: Krecsmarik

first: Thomas

last: Hawkins

first: Stephen

middle: W

last: Wilson

first: Elizabeth

last: Manning

first: Chandra

middle: S

first: David

first: Alexandra

last: Louis

first: F

middle: L

last: Raymond

first: Sepand

last: Rastegar

first: Uwe

last: Strähle

first: Boris

last: Lenhard

first: Laure

last: Bally-Cuif

first: Veronica

last: van Heyningen

last: FitzPatrick

last: Becker

first: Hugues

last: Crollius


title: Absence of heterozygosity due to template switching during replicative rearrangements

status: Public on Jan 29 2015

city: Houston

first: James

last: Lupski

address: One Baylor Plaza, 604B

institute: Baylor College of Medicine


title: ChIP-chip from mouse 14.5 days fetal brain with P300 and H3K4Me1

first: Chandr

last: Chilamakuri

overall_design:
ChIP-chip from mouse 14.5 days fetal brain using P300 or H3K4Me1 antibodies.
Biological replicates: P300_Rep1, P300_Rep2
Biological replicates: H3K4Me1_Rep1,H3K4Me1_Rep2

first: Magali

last: Naville

first: Minaka

last: Ishibashi

first: Marco

last: Ferg

first: Hemant

last: Bengani

middle: I


title: Absence of heterozygosity due to template switching during replicative rearrangements [Agilent-043871 9q_others]

summary: The goal of this experiment was to determine the size, genomic extent and gene content of complex rearrangements involving  chromosome 9q

overall_design: To determine size, genomic extent and gene content for each rearrangement, we used a customized tiling-path oligonucleotide microarray spanning the entire chromosomal region of chromosome 9 long arm. A 4X180K Agilent Technologies (Santa Clara, CA) microarray was designed using the Agilent e-array website.

first: Claudia

last: Carvalho


title: Transcriptome analysis of Wnt3a-treated triple-negative breast cancer cell lines.

status: Public on Jan 24 2015

city: PARIS

first: Thierry

last: Dubois

address: 26 rue d’Ulm

department: Recherche Center

country: France

institute: Institut Curie

summary: We analyzed the transcriptome of two different triple negative breast cancer (TNBC) cell lines to define a comprehensive list of Wnt target genes. Cells were treated with Wnt3a for 6h, 12h or 24h. We found up-regulated and down-regulated genes in response to Wnt3a treatment. They  are involved in the Wnt pathway itself, and also in TGFß, p53 and Hedgehog pathways. Thorough characterization of these novel potential Wnt target genes may reveal new regulators of the canonical Wnt pathway. The comparison of our list of Wnt target genes with those published in other cellular contexts confirms the notion that Wnt target genes are tissue-, cell line- and treatment-specific.

overall_design: Cells were seeded in six-well plates, serum starved overnight then treated with Wnt3a for the indicated times (6, 12 and 24 hours). Triplicates for each condition were included in the experiment.


title: Transcriptome analyses of pdr5Dyor1D mutant in yeasts

city: Paris

first: frederic

last: devaux

address: 15 rue de l'ecole de medecine

institute: Universite Pierre et Marie Curie

summary: ATP-binding cassette transporters Pdr5 and Yor1 from Saccharomyces cerevisiae control the asymmetric distribution of phospholipids across the plasma membrane as well as serving as ATP-dependent drug efflux pumps.  Mutant strains lacking these transporter proteins were found to exhibit very different resistant phenotypes to two inhibitors of sphingolipid biosynthesis that act either late (aureobasidin A:AbA) or early (myriocin: Myr) in the pathway leading to production of these important plasma membrane lipids.  These pdr5D yor1 strains were highly AbA resistant but extremely sensitive to Myr.  We provide evidence that these phenotypic changes are likely due to modulation of the plasma membrane flippase complexes: Dnf1/Lem3 and Dnf2/Lem3.  Flippases act to move phospholipids from the outer to the inner leaflet of the plasma membrane.  Genetic analyses indicate that lem3D mutant strains are highly AbA sensitive and Myr resistant.  These phenotypes are fully epistatic to those seen in pdr5D yor1 strains.  Direct analysis of AbA-induced signaling demonstrated that loss of Pdr5 and Yor1 inhibited the AbA-triggered phosphorylation of the AGC kinase Ypk1 and its substrate Orm1.  Microarray experiments found that a pdr5D yor1 strain induced a Pdr1-dependent induction of the entire Pdr regulon.  Our data support the view that Pdr5/Yor1 negatively regulate flippase function and activity of the nuclear Pdr1 transcription factor.  Together, these data argue that the interaction of the ABC transporters Pdr5 and Yor1 with the Lem3-dependent flippases regulate permeability of AbA via control of plasma membrane protein function as seen for the high-affinity tryptophan permease Tat2.

overall_design: the transcriptome of pdr5Dyor1D double mutants was compared either to wild type cells or to pdr5Dyor1Dpdr1D triple mutant.

first: Svetlana

last: Khakhina

first: Soraya

last: Johnson

first: Raman

last: Manoharlal

first: Sarah

last: Russo

first: Corinne

last: Blugeon

first: Sophie

last: Lemoine

first: Maitreya

last: Dunham

first: Ashley

last: Cowart

first: Frederic

last: Devaux

first: Scott

last: Moye-Rowley


title: CCm2-regulated cardiac genes in zebrafish

status: Public on Jan 26 2015

city: Potsdam

first: Salim

last: Abdelilah-Seyfried

address: Karl-Liebknecht Strasse 24-25, Bldg. 26

department: Animal Physiology

institute: University of Potsdam

summary: The aim of this study was to identify genes that are regulated by ccm2 signaling with the zebrafish heart at around 72 hours post fertilization.

overall_design: In total, 4 samples based on cDNA from extracted cardiac tissue were analyzed: 2 samples of ccm2 m201 mutant embryos and 2 WT control samples.


title: Transcriptome analysis of lungs from six different mouse strains after infection with highly pathogenic H5N1 influenza A virus [set 2]

status: Public on Jan 09 2015

city: St Louis

first: Adrianus

middle: Cornelis Maria

last: Boon

state: Missouri

address: 660 Euclid Avenue

department: Department of Medicine

institute: Washington University School of Medicine

summary:
Susceptible (DBA/2J, 129/SvImJ,  A/J) and Resistant (SM/J, C57BL/6J, Balb/cJ) mouse strain were inoculated with a highly pathogenic H5N1 influenza A virus (A/Hong Kong/213/2003) for 72 hours or not infected (control animals).
Differences in expression were analyzed and used to identify candidate genes and pathways that contributed to the difference in H5N1 pathogenesis in these two groups of mice.

overall_design: Female 6-8 weeks old animals were inoculated with H5N1 virus or not and 72 hours later the lungs were obtained and immediately homogenized in Trizol. The extracted RNA was submitted for Illumina Gene expression profiling.

middle: C

first: Richard

last: Webby


title: Expression Profiles of HepG2 cells treated with following compounds: Azathriopine, Furan, Tetradecanoyl phorbol acetate, Tetrachloroethylene, Diazinon and Dmannitol

status: Public on Jan 13 2015

city: Maastricht

first: Lize

last: Deferme

state: Limburg

address: Universiteitssingel 50

department: TGX

institute: Maastricht University

summary:
The transcriptomic changes induced in the human liver cell line HepG2 by  Azathriopine (250µM, Sigma-Aldrich), Furan (2mM, Sigma-Aldrich), Tetradecanoyl phorbol acetate  (500nM, Sigma-Aldrich), Tetrachloroethylene (2mM, Sigma-Aldrich), Diazinon (250µM, Sigma-Aldrich) and Dmannitol (250µM, Sigma-Aldrich) during 4, 8, 24, 48 and 72hrs
As a solvent control for Azathriopine, Furan, Diazinon and Tetradecanoyl phorbol acetate, DMSO was used (0.5%); As a solvent control for tetrachloroethylene, ethanol was used (0.5%); As a solvent control for D-mannitol, HBSS was used (0.5%)

overall_design: The study investigated differential gene expression in HepG2 cell line mRNA following 4, 8, 24, 48 and 72h hours of exposure to Azathriopine, Furan, Tetradecanoyl phorbol acetate, Tetrachloroethylene, Diazinon, D-mannitol, DMSO solvent control, ethanol solvent control and HBSS solvent control. Three biological replicates per compound/solvent. In total 135 arrays were analyzed in total.

first: Jarno

last: Wolters

first: Sandra

last: Claessen


title: Let-7, mir-98 and mir-181 as biomarkers for cancer and schizophrenia

status: Public on Jan 22 2015

city: HAIDARI

first: NIKOLAOS

last: SIAFAKAS

state: ATHENS

address: 1, RIMINI STR.

department: CLINICAL MICROBIOLOGY

country: Greece

institute: ATTIKON UNIVERSITY HOSPITAL

summary:
Recent evidence supports a role of microRNAs in cancer and psychiatric disorders such as schizophrenia and bipolar disorder, through their regulatory role on the expression of multiple genes. The rather rare co-morbidity of cancer and schizophrenia is an old hypothesis which needs further research on microRNAs as molecules that might exert their oncosuppressive or oncogenic activity in the context of their role in psychiatric disorders
The expression pattern of a variety of different microRNAs was investigated in patients (N=6) suffering from schizophrenia termed control, patients with a solid tumor (N=10) and patients with both schizophrenia and tumor (N=8). miRNA profiling was performed on whole blood samples using the miRCURY LNA™ microRNA Array technology (6th & 7th generation). Significant down-regulation of the let-7p-5p, miR-98-5p and of miR-183-5p in the study groups (tumor alone and tumor and schizophrenia) was observed (p<0.05). let-7, miR-98 and miR-183 may play an important oncosuppressive role through their regulatory impact in gene expression irrespective of the presence of schizophrenia

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
Lymphocryptovirus
human gammaherpesvirus 4
Rhadinovirus
Herpesvirus saimiri (strain 11)
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Investigation of the expression pattern of different microRNAs in patients with schizophrenia, patients with a solid tumor and patients with both schizophrenia and tumor, in an attempt to research on microRNAs as molecules that might exert  oncosuppressive or oncogenic activity in the context of their role in psychiatric disorders

first: Emmanouil

last: Rizos

first: Nikolaos

last: Siafakas

first: Eleni

last: Katsantoni

first: Vassilis

last: Zoumpourlis


title: Transcriptome analysis of lungs from six different mouse strains after infection with highly pathogenic H5N1 influenza A virus [set 1]

summary:
Susceptible (DBA/2J, 129/SvImJ,  A/J) and Resistant (SM/J, C57BL/6J, Balb/cJ) mouse strain were inoculated with a highly pathogenic H5N1 influenza A virus (A/Hong Kong/213/2003) for 24 and 168 hours. Uninfected control animals were included.
Differences in expression were analyzed and used to identify candidate genes and pathways that contributed to the difference in H5N1 pathogenesis in these two groups of mice.

overall_design: Female 6-8 weeks old animals were inoculated with H5N1 virus or not and 24 and 168 hours later the lungs were obtained and immediately homogenized in Trizol. The extracted RNA was submitted for Illumina Gene expression profiling.


title: Gene expression profiles of hexadecyl-4-124I-iodobenzoate(124I-HIB)-labeled adipose-derived stem cells (ADSCs) in vitro and in vivo

status: Public on Jan 06 2015

city: Seoul

first: Min Hwan

last: Kim

address: 75 Nowon-gil, Gongneung-Dong, Nowon-Gu

country: South Korea

institute: Korea Institute of Radiological and Medical Sciences

summary:
[1] Microarray analysis in the rat myocardial tissue: 124I-HIB transplanted MI model Vs. phosphate buffered saline (PBS) injected myocardial infarction (MI) model Vs. Sham operated model
[2] Microarray analysis in the rat adipose derived stem cells: 124I-HIB-labeled ADSCs Vs. Unlabeled ADSCs

overall_design:
[1] We investigated the change of gene expression profile in sham operated-, PBS injected- and 124I-HIB-labeled ADSCs transplanted myocardium in rat myocaridial infarction (MI) model.
[2] We compared gene expression profile with 124I-HIB labeled ADSCs and unlabeled ADSCs in vitro.

first: Yong

last: Lee

first: Min

middle: H


title: S100 calcium-binding proteins A8/A9 initiate the early inflammatory program in injured peripheral nerve

status: Public on Jan 01 2015

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

summary: To shed light on the early processes of immune response to peripheral nerve injury, we first used genome-wide transcriptional profiling and bioinformatics (Ingenuity, NextBio) pathway analyses of the proximal (P; regenerating) and distal (D; degenerating) nerve stumps at day 1 in the sciatic nerve axotomy model in rats. We identified a number of specific immunomodulatory genes and pathways that were regulated shortly post-injury in both the P and D segments, including all members of the interleukin (IL), chemokine, tumor necrosis factor (TNF), matrix metalloproteinase (MMP), toll-like receptor (TLR), tissue inhibitor of metalloproteinase (TIMP), ion channel and myosin families. Immunomodulatory calcium-binding S100A8 and S100A9 were the top up-regulated genes in both the D and P segments. In cultured Schwann cells stimulated with the purified S100A8/A9 heterodimer we recorded a high level of similarity of the activated genes and pathways with that of the injured nerve, especially in the activation of the chemokine and cytokine gene networks that support agranulocyte and granulocyte chemotaxis, adhesion, transmigration and rolling signaling pathways. We also confirmed activation of multiple cell death related gene networks supporting TNFR1, natural killer cell receptor and death receptor apoptosis signaling in the D stump, and the gluconeogenesis/glycolysis and cytoskeletal motility signaling in the P stump, corroborated by activation of ERK, PI3K and JNK kinase pathways. As compared to the D segment, multiple additional pathways were more efficiently upregulated in the P stump, including the IL-6 and -17, MMP-9, calcium, activated agranulocyte, leukocyte rolling and glutathione-mediated detoxification signaling pathways. These data suggest that shortly after nerve injury, upregulation of S100A8/A9 is responsible for the expression and release of chemokines and cytokines by Schwann cells, necessary to generate the initial chemotactic gradient and guide the hematogenous immune cells into the injury site.

overall_design: Gene expression profiling of total RNAs extracted from injured and non-injured rat sciatic nerves, and primary rat Schwann cells stimulated with S100A8/A9 proteins

middle: V

first: Alex

middle: Y

last: Strongin

first: Veronica

last: Shubayev


title: Mouse-human experimental epigenetic analysis unmasks dietary targets and genetic liability for diabetic phenotypes

city: Baltimore

first: Andrew

middle: P

last: Feinberg

address: 855 N Wolfe St

institute: Johns Hopkins School of Medicine

type: Methylation profiling by genome tiling array

summary: Using a functional approach to investigate the epigenetics of Type 2 Diabetes (T2D), we combine three lines of evidence – diet-induced epigenetic dysregulation in mouse, epigenetic conservation in humans, and T2D clinical risk evidence – to identify genes implicated in T2D pathogenesis through epigenetic mechanisms related to obesity. Beginning with dietary manipulation of genetically homogeneous mice, we identify differentially DNA-methylated genomic regions. We then replicate these results in adipose samples from lean and obese patients pre- and post-Roux-en-Y gastric bypass, identifying regions where both the location and direction of methylation change is conserved. These regions overlap with 27 genetic T2D risk loci, only one of which was deemed significant by GWAS alone. Functional analysis of genes associated with these regions revealed four genes with roles in insulin resistance, demonstrating the potential general utility of this approach for complementing conventional human genetic studies by integrating cross-species epigenomics and clinical genetic risk.

overall_design: Data for 57 mouse samples and 29 human samples are included. Mouse samples are split into groups high-fat and low-fat groups for each of five different tissues. Human samples are split into three groups - lean, obese pre-RYGB and post-RYGB.

first: Michael

last: Multhaup


title: Absence of heterozygosity due to template switching during replicative rearrangements [Agilent-041162 Chr6q_10q_14q]

first: James

last: Lupski

summary: The goal of this experiment was to determine the size, genomic extent and gene content of complex rearrangements involving multiple chromosomes

overall_design: To determine size, genomic extent and gene content for each rearrangement, we used a customized tiling-path oligonucleotide microarray spanning the entire chromosomal regions of chromosomes 6q, 10q, 14q. A 2X400K Agilent Technologies (Santa Clara, CA) microarray was designed using the Agilent e-array website.

first: Claudia

last: Carvalho

middle: R


title: JA-Ile coordinates anthesis and floral attractants in wild tobacco through COI1 dependent and independent mechanisms.

status: Public on Dec 31 2014

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

summary: Identification of coronatine/jasmonoyl-isoleucine-regulated transcripts and encoded metabolic processes in late stages of Nicotiana attenuata flower development.

overall_design: Floral buds at 4 DAP (4 days after corolla protruded and appeared outside sepals) of ir-aoc (silenced for ALLENE OXIDE CYCLASE)- treated with ctrl (control) or 1µM COR (coronatine) solution - were harvested on the morning before flowers would open. Flowers were dissected and 3 biological replicates of each tissue (complete corolla, style and gynoecium tissues) were collected. Individual replicates were obtained from 20+ flowers of each 2 plants. cDNA synthesized from extracted RNA pools were combined with an equal contribution of each tissue types. Microarray data (3 replicates obtained from 3 independently produced pools of cDNA) were 75-percentile normalized and analyzed using significance analysis of microarray (SAM, Benjamini-Hochberg FDR threshold of 5%) for differentially regulated genes between ctrl- and COR-treated flowers Significantly overrepresented GO categories were identified using the BINGO plugin for Cytoscape. A P-value significance for each differentially regulated gene was calculated using a hypergeometric test with a Benjamini and Hochberg false discovery rate correction. P < 0.05 was used as threshold for significantly enriched GO categories.

last: Stitz

first: Markus

last: Hartl

first: Ian

last: Baldwin

first: Emmanuel

last: Gaquerel


title: Microarray expression analysis of the main inflorescence in B. napus

city: Wuhan

first: Yi

last: Huang

state: Hubei

address: No. 2 Xudong Second Road, Wuchang District

department: Rapeseed Genetics and Breeding

country: China

institute: Oil Crops Research Institute, Chinese Academy of Agricultural Sciences

summary: The effect of the number of pods on the main inflorescence (NPMIs) on seed yield in Brassica napus plants grown at high density is a topic of great economic and scientific interest. We sought to identify patterns of gene expression that are associated with inflorescence and PMI differentiation and development in Brassica napus.

platform_organism:
Brassica napus
Brassica rapa
Brassica oleracea

overall_design: In this study, we monitored the gene expression profiles in the main inflorescence of two B. napus F6 RIL pools, each composed of nine extremely low- or high-PMI lines, and their elite parental lines Zhongshuang 11 (ZS11) and 73290, which exhibit striking differences in NPMIs at the pistil-stamen differentiation stage, using a Brassica 90K elements oligonucleotide array. We found that 4,805 of the 85,307 probes present in the array were differentially expressed, with a fold-change of at least 1.5, between the low- and high-NPMI samples. About 92.8% of the DEGs mapped to chromosomes that originated from B. rapa and B. oleracea, and 1.6% of the DEGs co-localized with two QTL intervals (PMI10 and PMI11) known to be associated with the NPMI.

first: Hanzhong

last: Wang


title: Brassica napus control vs. heat stress

status: Public on Jan 05 2015

first: yongming

last: zhou

address: No.1,Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: High temperature stress results in yield loss and alterations to seed composition during seed filling in oilseed rape (Brassica napus). However, the mechanism underlying this heat response is poorly understood. In this study, we employed a microarray analysis with silique walls and seeds from the developing siliques (20 days after flowering) of Brassica napus that had undergone heat stress.

overall_design: Two-condition experiment, control vs heat stress, 2 time points

first: Erru

last: Yu

first: Chuchuan

last: Fan

first: Qingyong

last: Yang

first: Xiaodong

last: Li

first: Bingxi

last: Wan

first: Yanni

last: Dong

first: Xuemin

first: Yongming

last: Zhou


title: Gene copy analysis of the F1 haploid progeny generated by Hypocrea jecorina CBS999.9 sexual development

status: Public on Jan 07 2015

city: Taipei

first: Ting-Fang

address: Academia Sinica. 128 Sec. 2, Academia Rd

department: Institute of Molecular Biology

institute: Academia Sinica

summary: H. jecorina undergoes a heterothallic reproductive cycle, and the mating yields asci with 16 linearly arranged ascospores. The sixteen ascospores are generated via two rounds of postmeiotic mitosis following the two meiotic divisions. We have discovered that viable aneuploid ascosporesare are frequently (~90%) generated due to a net gain of a conserved ~500 kbp genomic segment. Here we have compared whole genome gene copy number changes in the aneuploid F1 progeny, euploid F1 progeny, parental strains and the F1 progeny of RTU strain backcross with CBS999.97 .

overall_design: We determined genome-wide gene copy number in the genomes of ascospores generated from haploid wild-type strain. We also determined genome-wide gene copy number in the genomes of the F1 progeny of CBS999.97  wild type.

first: Chia-Ling

last: Chen

first: Yu-Chien

last: Chuang

first: Paul

last: Hsu

first: Shu-Yun

last: Tung


title: Streptococcus pneumoniae R6 genomic DNA

status: Public on Dec 29 2014

city: Majadahonda

first: Antonio

middle: J.

last: Martin-Galiano

state: Madrid

address: Ctra. Majadahonda-Pozuelo, km 2.2

department: Bacterial genetics

country: Spain

institute: Instituto de Salud Carlos III

summary: The most basic level of transcription regulation in Streptococcus pneumoniae is the organization of its chromosome in topological domains. In response to drugs that caused DNA-relaxation, a global transcriptional response was observed. Separate domains were identified depending of the transcription of their genes: up-regulated (U), down-regulated (D), non-regulated (N), and flanking (F). We show here that these distinct domains have different expression and conservation tendencies. Microarray fluorescence units under non-relaxation conditions, taken as a measure of gene transcription level, were significantly lower in F genes than in the other domains in the same range of AT content. Transcription level categorization of the domains was D>U>F. In addition, a comparison of 12 S. pneumoniae genome sequences evidenced conservation of gene composition in the U and D domains and extensive gene interchange in F domains. We tested domain organization by measuring the relaxation-mediated transcription of eight insertions of a heterologous Ptccat cassette, two in each type of domain, showing that transcription depended on their chromosomal location. Moreover, transcription from the four promoters directing the five genes involved in supercoiling homeostasis, located either in U (gyrB), D (topA), or N (gyrA and parEC) domains was analyzed both in their chromosomal locations and in a replicating plasmid. Although expression from the chromosomal PgyrB and PtopA showed the expected domain regulation, their expression was down-regulated in the plasmid, which behaved as a D domain. However, both PparE and PgyrA carried their own regulatory signals, their topology-dependent expression being equivalent in the plasmid or in the chromosome. In PgyrA a DNA bend acted as a DNA supercoiling sensor. These results revealed that DNA topology works as a general transcriptional regulator, superimposed to other kind of more specific regulatory mechanisms.

overall_design: Genomic DNA was extracted from S. pneumoniae R6 cultures during exponential growth, amplified and used for microarray hybridization. Two independent replicates were performed.

first: María

last: Ferrándiz

first: Adela

middle: G

last: de la Campa


title: Acute mammary and liver transcriptome response after an intra-mammary E. coli lipopolysaccharide challenge in postpartal dairy cows

status: Public on Dec 17 2014

city: Urbana

first: Juan

last: Loor

address: 1207 West Gregory Drive

department: Animal Sciences

institute: University of Illinois

summary: The study investigated the acute and simultaneous response of the mammary and liver transcriptome to an intra-mammary lipopolysaccharide (LPS) challenge in early-lactating cows, and its consequences on metabolic biomarkers and liver composition. At 7 days of lactation, 7 cows served as controls (CTR) and 7 cows (LPS) received an intra-mammary E. coli LPS challenge. The mammary and liver tissues were sampled at 2.5 h from challenge for transcriptomic profiling. Liver composition was evaluated at 2.5 h and 7 d after challenge and blood biomarkers were analized at -2, 3, 7 and 14 d from challenge. In mammary tissue, the LPS challenge resulted in 189 differentially expressed gene (DEG), with 20 downregulated and 169 upregulated, while in the liver were found 107 DEG with 42 downregulated and 65 upregulated in LPS vs CTR. In the udder, the Dynamic Impact Approach (DIA) highlighted the activation of NOD-like receptor signaling, Toll-like receptor signaling, RIG-I-like receptor signaling and Apoptosis pathways, while in the liver were inhibited the Fatty acid elongation in mitochondria and activated the p53 signaling pathway. The LPS induced the alteration of liver lipid metabolism (rise of total lipid and triglyceride concentration), a systemic inflammation (rise of blood ceruloplasmin and bilirubin) and an increase of body fat mobilization. In cows subjected to intra-mammary LPS, the mammary gland responds activating mechanisms of pathogen recognition. In the liver the response likely depends by mediators coming from udder and affects the liver functionality and mainly the fatty acid metabolism.

overall_design: Fourteen Holstein cows entering their second or greater lactation were used. Cows were housed in a ventilated tie-stall barn and were fed a common lactation diet (Net energy of lactation = 1.69 Mcal/kg DM) as a total mixed ration once daily (0600 h) and milked twice daily (0400 and 1600 h). A bovine oligonucleotide (70-mers) microarray with >13,000 annotated sequences developed at the University of Illinois, was used for transcript profiling.  Details on the development, annotation, and use of this microarray have been reported previously by Loor et al., 2007 (http://physiolgenomics.physiology.org/content/32/1/105.abstract).  Methods for microarray hybridization and scanning were as reported by Loor et al. (2007).  Briefly, slides were hydrated, dried, and placed in a UV Stratalinker 1800 (Stratagene, La Joya, CA) for ~5 min.  Slides were washed with 0.2% SDS solution, rinsed with MilliQ (Millipore) H2O, and placed in warm prehybridization soln for 45 min at 42 C. The same amount of Cy3- or Cy5-labelled cDNA from mammary or liver and a reference standard RNA pool (made of different bovine tissues) were co-hybridized using a dye-swap design (i.e., two microarrays per sample).  Slides were incubated for 48 h at 45 C prior to scanning. Criteria for evaluation of slide quality included: identification of number of spots with a minimum median signal intensity of 3 SD above background; keeping slides with a minimum of 20,000 spots with minimum median signal intensity of 3 SD above background in both Cy3 and Cy5 channels; and keeping slides with a minimum mean intensity of 400 relative fluorescent units in both Cy3 and Cy5 channels across the entire slide. Data from a total of 112 microarrays were normalized for dye and microarray effects (i.e., Lowess normalization and microarray centering) and used for statistical analysis. Data were analyzed using the Proc MIXED procedure of SAS (SAS, SAS Inst. Inc., Cary, NC).  Fixed effects were treatment (LPS challenge, control (no infsuion)) and dye.  Random effects included cow and microarray.  Raw P values were adjusted using Benjamini and Hochberg’s false discovery rate (FDR). Differences in relative expression due to treatment were considered significant at an FDR-adjusted P < 0.05. For a more stringent characterization between the two treatments, a 1.5-fold difference in mRNA expression was set as threshold among differentially expressed genes.

first: Andrea

last: Minuti

first: Zheng

first: Daniel

middle: E

last: Graugnard

first: Sandra

last: Rodriguez-Zas

first: Alejandro

last: Palladino

first: Felipe

last: Cardoso

first: Erminio

last: Trevisi