title: Transcriptome outcome of oligodendrocyte precursor cells following VCAM1 knockdown

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Transcriptome outcome of rat oligodendrocyte precursor cells, which were knocked down with short-hairpin RNA (shRNA) for vascular cell adhesion molecule 1 (VCAM1)

overall_design: Toray 3D-Gene microarray technique was used for transcriptome analysis of VCAM1- or control luciferase shRNA-knocked down, rat oligodendrocyte precursor cells

first: Junji

last: Yamauchi

first: Yuki

last: Miyamoto


title: Differential gene expression underlying ovarian phenotype determination in honey bee, Apis mellifera, caste development

status: Public on Oct 06 2016

city: Alfenas

first: Angel

middle: Roberto

last: Barchuk

state: Minas Gerais

address: Rua Gabriel Monteiro Silva 700, Campus Unifal

department: Cell and Developmental Biology

country: Brazil

institute: Federal University of Alfenas

summary: Adult honey bee queens and workers drastically differ in ovary size. This adult ovary phenotype difference becomes established during the last two larval instars, when massive programmed cell death in the ovaries of worker larvae leads to the degeneration and removal of 95-99% of the ovariole anlagen. The higher juvenile hormone (JH) levels in queen larvae protect their ovaries against such degeneration. To gain insights into the molecular architecture underlying this divergence critical for adult caste fate we performed a microarray analysis contrasting RNA extracts from fourth and early fifth instar queen and worker ovaries. While for the fourth instar we found differential expression (log2FC > 1.0) for only nine genes, the number of differentially represented transcripts (DRTs) increased to 56 in early fifth instar ovaries. From these, 18 had their expression levels further analyzed by real-time PCR (RT-qPCR). For 13 of these the expression differed significantly between queen and worker ovaries at least one time point in development, and interestingly, genes with enzyme functions were overexpressed in workers, while genes related to transcription and signaling were so in queens. For the RT-qPCR confirmed genes we further analyzed their response to JH, revealing a significant up-regulation for two genes, one encoding a short chain dehydrogenase (SDR) and the other heat shock protein 90 (Hsp90). Five other genes, including Hsp60 and hexamerin 70b, were significantly down-regulated by JH. As SDR genes have previously come up as differentially expressed in different transcriptome assays in honey bee larvae, and heat shock proteins are involved in hormone responses, these are interesting candidates for further functional assays.

overall_design: RNA samples (from pools of ovaries) from L4 and L5F queens and workers were hybridized in pairs (queen/worker) and in dye-swaps (Cy3/Cy5).

first: Denyse

middle: C

last: Lago

first: Fernanda

last: Humann

middle: R

first: Joseph

middle: A

last: Kuruvilla

first: Klaus

middle: H

last: Hartfelder


title: Zfy genes are required for efficient meiotic sex chromosome inactivation (MSCI) in spermatocytes

status: Public on Oct 05 2016

city: Canterbury

first: Peter

middle: James

last: Ellis

state: Kent

address: Stacey Building

department: School of Biosciences

country: United Kingdom

institute: University of Kent

summary:
During spermatogenesis, germ cells that fail to synapse their chromosomes or fail to undergo meiotic sex chromosome inactivation (MSCI) are eliminated via apoptosis during mid-pachytene. Previous work showed that Y-linked genes Zfy1 and Zfy2 act as “executioners” for this checkpoint, and that wrongful expression of either gene during pachytene triggers germ cell death. Here, we show that in mice, Zfy genes are also necessary for efficient MSCI and the sex chromosomes are not correctly silenced in Zfy-deficient spermatocytes.
In addition to this microarray data set, qPCR and RNA FISH data were used to confirm that MSCI is leaky in males lacking Zfy genes. The array data demonstrates that transgenic restoration of Zfy2 corrects the MSCI leakage phenotype. The associated RNA FISH data demonstrates that Zfy1 and Zfy2 are both able to correct the leakage phenotype.

overall_design: This experiment compares testis gene expression at 17.5 days post partum from XEO,Sry males (lacking all Y genes except Sry and Eif2s3y) with XE,Z2O,Sry males in which Zfy2 has been transgenically restored (n = 4 per genotype).

first: Nadege

last: Vernet

first: Shantha

last: Mahadevaiah

first: Dirk

last: de Rooij

first: Paul

last: Burgoyne


title: Acclimation of oxygenic photosynthesis to iron starvation is controlled by the sRNA IsaR1 in cyanobacteria

status: Public on Oct 01 2016

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

country: Germany

institute: University of Freiburg

summary: Oxygenic photosynthesis contains multiple proteins that possess Fe2+ or Fe/S complexes as co-factors or prosthetic groups. Accordingly, its composition is heavily re-organized when iron becomes limiting as a nutrient factor, a situation that is frequently encountered in nature. However, the molecular mechanisms controlling the reorganization of the photosynthetic system upon iron deprivation have remained enigmatic. Here we show that the small regulatory RNA IsaR1 (Iron-stress activated RNA 1) plays a pivotal role in acclimation to low iron conditions. The transcription factor Fur cannot facilitate iron starvation dependent repression of it’s targets because it requires iron for DNA binding. We show that the Fur repressed sRNA IsaR1 fulfills this repressor function in iron homeostasis. The IsaR1 regulon consists of at least 15 direct targets, including Fe2+-containing proteins involved in photosynthetic electron transfer, the detoxification of anion radicals, citrate cycle, and in tetrapyrrole biogenesis. We demonstrate that IsaR1 is absolutely necessary to maintain physiological levels of Fe/S cluster biogenesis proteins during iron deprivation. Consequently, IsaR1 affects the acclimation of the photosynthetic apparatus to iron starvation at three levels: (i) directly, via posttranscriptional repression of gene expression and indirectly, (ii) via the suppression of Fe/S cluster co-factor and (iii) pigment biosynthesis. Homologs of IsaR1 are widely conserved throughout the cyanobacterial phylum. We conclude that IsaR1 is a riboregulator of central importance. These findings provide a new perspective for studies of the regulation of iron homeostasis in photosynthetic organisms.

overall_design: We monitored gene expression of a Synechocystis PCC6083 IsaR1 deletion strain (ΔIsaR1) prior to iron depletion (0h) and 3h, 12h, 24h, 48h and 72h after iron depletion by DFB addition. The gene expression was compared to that of Synechocystis PCC6803 WT cultures which were grown and treated in parallel. The data for the WT iron depletion stress response are already published (PMID: 23275872) and stored in the Geo database (GSE39804). Furthermore, we used a strain expressing IsaR1 (IsaR1OE) under control of the copper inducible petE promoter on the pVZ plasmid. The respective control strain (WT_pVZ) carries a pVZ plasmid with the petE promoter followed by the rho terminator. Both strains were sampled prior to copper addition (0h) and 6h after strong ectopic induction of IsaR1 by copper addition. Each sample was done in two independent biological replicates.

first: Gergana

last: Kostova

first: Linda

last: Vuorijoki

first: Verena

last: Schön

first: Taro

last: Kadowaki

first: Tuomas

last: Huokko

first: Yagut

last: Allahverdiyeva-Rinne

first: Yukako

last: Hihara

first: Matthis

last: Futschik

first: Eva-Mari

last: Aro

first: Wolfgang

last: Hess


title: Distinct transcriptome responses to water limitation in isohydric and anisohydric grapevine cultivars

status: Public on Sep 30 2016

city: San Pietro in Cariano

first: Marianna

last: Fasoli

state: Verona

address: Via della Pieve 70

department: Biotechnology

country: Italy

institute: University of Verona

summary:
Grapevine (Vitis vinifera L.) is an economically important crop with a wide geographical distribution, reflecting its ability to grow successfully in a range of climates. However, many vineyards are located in regions with seasonal drought, and these are often predicted to be global climate change hotspots. Climate change affects the entire physiology of grapevine, with strong effects on yield, wine quality and typicity, making it difficult to produce berries of optimal enological quality and consistent stability over the forthcoming decades.
Here we investigated the reactions of two grapevine cultivars to water stress, the isohydric variety Montepulciano and the anisohydric variety Sangiovese, by examining physiological and molecular perturbations in the leaf and berry. A multidisciplinary approach was used to characterize the distinct stomatal behavior of the two cultivars and its impact on leaf and berry gene expression. Positive associations were found among the photosynthetic, physiological and transcriptional modifications, and candidate genes encoding master regulators of the water stress response were identified using an integrated approach based on the analysis of topological co-expression network properties. In particular, the genome-wide transcriptional study indicated that the isohydric behavior relies upon the following responses: i) faster transcriptome response after stress imposition; ii) faster abscisic acid-related gene modulation; iii) more rapid expression of heat shock protein (HSP) genes and iv) reversion of gene-expression profile at rewatering. Conversely, that reactive oxygen species (ROS)-scavenging enzymes, molecular chaperones and abiotic stress-related genes were induced earlier and more strongly in the anisohydric cultivar.
Overall, the present work found original evidence of a molecular basis for the proposed classification between isohydric and anisohydric grapevine genotypes.

overall_design: Two, six and 27 days after water deprivation (three time points), three pools of leaves and three pools of berries were sampled per every date at midday (11.0-12.00 hours) from control and treated vines of both Sangiovese and Montepulciano cultivars, entailing 36 leaf and 36 berry samples. Moreover, biological triplicates of leaves were collected after re-watering (46 days after stress imposition) from control and recovered vines of both Sangiovese and Montepulciano cultivars, entailing 12 samples. The entire microarray experiment comprises a total of 84 samples.

first: Silvia

last: Dal Santo

first: Alberto

last: Paliotti

first: Sara

last: Zenoni

first: Giovanni Battista

last: Tornielli

first: Paola

last: Paci

first: Sergio

last: Tombesi

first: Tommaso

last: Frioni

first: Oriana

last: Silvestroni

first: Andrea

last: Bellincontro

first: Claudio

last: D'Onofrio

first: Fabiola

last: Matarese

first: Matteo

last: Gatti

first: Stefano

last: Poni

first: Mario

last: Pezzotti


title: Expression data from chick embryo olfactory placodes during initial period of GnRH neuronal production

city: London

first: Anthony

last: Graham

address: Guys Campus

department: Developmental Neurobiology

institute: Kings College London

summary: We used microarrays to detail the global program of gene expression underlying gonadotropin-releasing hormone (GnRH) generation and delamination from the olfactory placode.

overall_design: Olfactory placodes were dissected from chick embryos at HH stages 16, 18 and 20.

first: Subathra

last: Poopalasundaram


title: Copy number alterations in primary tumors and metastases from a BALB-NeuT murine breast cancer transplantation model

city: Regensburg

first: Michael

last: Grauvogl

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

institute: University of Regensburg

summary: Genome profiling of primary tumors and matched metastases from a BALB-NeuT murine breast cancer transplantation model. The first goal of this study was to investigate the differences of primary tumors and metastases with regard to copy number alterations. The second goal was to infer phylogenetic trees reflecting the evolutionary paths of primary tumors and their derived metastases (only mice with at least one metastasis were used for phylogenetic analyses).

overall_design: Small pieces (2 mm in diameter) of mammary glands obtained from transgenic BALB-NeuT mice were transplanted into the cleared fat pads of wild type BALB/c mice. Primary tumors were removed when they reached a size of 5-10 mm in diameter. Thereafter, mice were sacrificed 17 weeks after curative surgery and metastases were extracted. 54 primary tumors and 44 matched metastases were profiled by aCGH. For each sample the spleen DNA of a wild type BALB/c mouse was used as reference.

first: Christian

last: Reimelt

first: Hedayatollah

last: Hosseini

first: Christoph

last: Klein

first: Rainer

last: Spang


title: Transcriptome of Medicago truncatula abi5 mutants during seed development

status: Public on Sep 24 2016

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

country: France

institute: INRAE

summary: A transcriptome analysis of developing abi5 and wild type (R108) seeds from Medicago truncatula was performed to decipher the role of ABI54 in the regulation of late seed maturation and seed longevity.

overall_design: Transcriptome of Medicago WT (R108 background)  lines (3 replicates) compared with two Medicago Tnt1 insertion lines in Medtr7g104480, named abi5-1 (NF4383) and abi5-2 (NF3376) using the Medicago_v1 NimbleGen chip

first: Emmanuel

last: Terrasson

first: Olivier

last: Leprince

first: Sandra

last: Pelletier


title: Human macrophages response depends on the infectious agent: is this null hypothesis (H0) an unquestionable dogma?

city: MONTPELLIER

first: Paul

last: CHUCHANA

address: 80 rue Augustin Fliche

institute: CNRS

summary: The macrophage is a pluripotent activity in response to infections. We used the central position of this cell type, in an ex vivo system for studying its responses to various infectious agents. Our model is based on cellular macrophages derived from human monocytes purified from healthy individuals. We have stimulated or not the macrophages to obtain paired samples, in a naive environment. Transcriptomic analyzes of match paired and standardized data generated results showing (i) the existence of specific signatures of the infectious agent and its strategy, and (ii) the preponderant existence of macrophage responses specifically related to individuals. The null hypothesis H0, according to which the response of the macrophage is exclusively specific for the pathogen, is refuted. Our results open new perspectives in which the macrophage innate response may be intrinsically associated with the individual.

overall_design:
Two paired experimental conditions, NT vs. Treated cells. 5 experimental treatments: TbgB2/7/1; LdLDD8; LiITMAP263; LiLEM75, E0111:B4. Biological replicates: 6

Trypanosoma brucei gambiense bloodstream forms (TbgB2/7/1)
Leishmania donovani LdLDD8 = MHOM/IN/80/Ldd 8, clone 2
Leishmania infantum LiITMAP263 = MHOM/MA/67/ITMAP-263, clone 2, visceral tropism
Leishmania infantum LiLEM75 = MHOM/FR/78/LEM 75, clone X, cutaneous tropism
E0111:B4 = lipopolysaccharide (LPS, Escherichia coli, Sigma)

first: Philippe

last: Holzmuller

last: Nirdé

first: Frédéric

last: Vezilier

first: Bruno

last: Bucheton

last: Chuchana


title: Gene expression changes upon Lamin A and Lamin B2 depletion in a diploid colorectal cancer cell line - DLD1

city: Pune

first: Kundan

last: Sengupta

state: Maharashtra

address: Dr. Homi Bhabha Road, Pashan

department: Biology

country: India

institute: Indian Institute of Science Education and Research (IISER) Pune

summary: Small interfering RNA (siRNA) mediated depletion of Lamin A/C and Lamin B2 was performed in a diploid colorectal cancer cell line - DLD1 with an aim to identify transcription deregulation across the genome.

overall_design: To elucidate transcription changes upon Lamin A/C and Lamin B2 depletion, siRNA mediated knockdown was performed in three biological replicates at a concentration of 100nM and for a duration of 48 hours.

first: Devika

last: Ranade


title: Comparison of gene expression in wild-type and rpl-1 Arabidopsis inflorescence apices

status: Public on Sep 22 2016

city: NORWICH

first: Robert

last: Sablowski

state: Norfolk

address: The John Innes Centre

department: CDB

institute: JIC

summary: The Arabidopsis thaliana REPLUMLESS gene (RPL), also known as PENNYWISE (PNY) and BELLRINGER (BLR) encodes a BEL1-like TALE homeodomain (BLH) transcription factor that controls multiple aspects of meristem and floral development, including meristem maintenance, phyllotaxis, the transition to flowering, stem development and floral organ patterning [1-3]. As part of a screen for genes that mediate the function of RPL in the processes above, we compared gene expression in inflorescence apices of wild-type (Landsberg-erecta) and the rpl-1 mutant [2].     1. Byrne, M.E., Groover, A.T., Fontana, J.R., and Martienssen, R.A. (2003). Development 130, 3941-3950.  2. Roeder, A.H.K., Ferrandiz, C., and Yanofsky, M.F. (2003). Current Biology 13, 1630-1635.  3. Smith, H.M.S., and Hake, S. (2003).  Plant Cell 15, 1717-1727.

overall_design:
Plants were grown in a controlled environment room at 20-22 °C, 16 h light (100 µE) until they flowered and the inflorescences were around 12 cm tall. Immediately after dissecting the terminal 1-2 cm of the inflorescences (1-2 g per sample, three biological replicates each for wild-type Landsberg-erecta and rpl-1 [1]), RNA was extracted with Trizol (Sigma) and purified using QIAGEN RNAeasy columns (QIAGEN) according to the manufacturer's instructions. Probes were prepared from 10 µg total RNA using a standard Affymetrix protocol (GeneChip © 3’  IVT Express kit) and hybridised to Affymetrix AGROMONICS1 oligonucleotide arrays. Data were normalized and analyzed statistically with the affylmGUI package (http://bioinf.wehi.edu.au/affylmGUI/about.html) using LIMMA (Linear Models for MicroArray data) [2] with a chip description format (CDF) file for the AGRONOMICS1 array and TAIR10 [3].
1. Roeder, A.H.K., Ferrandiz, C., and Yanofsky, M.F. (2003). Current Biology 13, 1630-1635.
2. Smyth, G.K. (2005). Limma: linear models for microarray data. In Bioinformatics and computational biology solutions using R and Bioconductor. (Springer), pp. 397-420.
3. Müller, M., Patrignani, A., Rehrauer, H., Gruissem, W., and Hennig, L. (2012). Plant Methods 8, 1.

first: Stefano

last: Bencivenga


title: CyAbrB2 contributes to the transcriptional regulation of low CO2 acclimation in Synechocystis sp. PCC 6803

status: Public on Sep 19 2016

first: Stephan

last: Klähn

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

summary: Acclimation to low CO2 conditions in cyanobacteria involves the coordinated regulation of genes mainly encoding components of the carbon concentration mechanism (CCM). Making use of several independent microarray datasets a core set of CO2-regulated genes was defined for the model strain Synechocystis sp. PCC 6803. On the transcriptional level, the CCM is mainly regulated by the well-characterized transcriptional regulators NdhR and CmpR, whereas the role of an additional regulatory protein, namely cyAbrB2 belonging to the widely distributed AbrB regulator family that was originally characterized in the genus Bacillus, is less defined. Here we present results of transcript profiling of the wild type and a ΔcyabrB2 mutant of Synechocystis sp. PCC 6803 after shifts from high CO2 (5% in air, HC) to low CO2 (0.04%, LC). Evaluation of the transcriptomic data revealed that cyAbrB2 is involved in the regulation of several CCM-related genes such as sbtA/B, ndhF3/ndhD3/cupA and cmpABCD under LC conditions, but apparently acts supplementary to the main regulators. Under HC conditions, cyAbrB2 deletion changes the expression of photosystem II subunits, light-harvesting components, and Calvin-Benson-Bassham cycle enzymes.

overall_design: We analyzed gene expression in Synechocystis sp. PCC 6803 WT as well as a ΔcyabrB2 mutant at HC (5% CO2) and 24h after shift to LC (air). For the WT six biological replicates were analyzed for each sampling point; the ∆cyAbrb2 mutant was analyzed in duplicates.

first: Isabel

last: Orf

first: Doreen

last: Schwarz

first: Aaron

last: Kaplan

first: Joachim

last: Kopka

first: Wolfgang

last: Hess

first: Martin

last: Hagemann


title: Genome-wide profiling of hypothalamus, cerebellum, striatum, and frontal cortex across young, middle-aged, and aged mice

status: Public on Sep 20 2016

city: Omaha

first: Stephen

middle: John

last: Bonasera

state: Nebraska

address: 3028 Durham Research Center

department: Internal Medicine

country: USA

institute: University of Nebraska Medical Center

summary:
We describe age-related molecular and neuronal changes that disrupt mobility or energy balance based on brain region and genetic background. Compared to young mice, aged C57BL/6 mice exhibit marked locomotor (but not energy balance) impairments. In contrast, aged BALB mice exhibit marked energy balance (but not locomotor) impairments. Age-related changes in cerebellar or hypothalamic gene expression accompany these phenotypes. Aging evokes upregulation of immune pattern recognition receptors and cell adhesion molecules. However, these changes do not localize to microglia, the major CNS immunocyte. Consistent with a neuronal role, there is a marked age-related increase in excitatory synapses over the cerebellum and hypothalamus. Functional imaging of these regions is consistent with age-related synaptic impairments. These studies suggest that aging reactivates a developmental program employed during embryogenesis where immune molecules guide synapse formation and pruning. Renewed activity in this program may disrupt excitatory neurotransmission, causing significant behavioral deficits.
keywords: aging, C57BL/6, BALB, CBA, hypothalamus, cerebellum, striatum, frontal cortex

overall_design:
In our cited manuscript, we examined age-associated changes in gene expression in two mouse strains (C57BL/6, BALB) at three ages (2-3 mo, 12-13 mo, 21-24 mo), and at two sites (whole tissue hypothalamus and cerebellum). Biological replicates were as follows: BALB hypothalamus, 2-3 mo, n=7; 12-13 mo, n=5; 20-23 mo, n=6; C57BL/6 hypothalamus, 2-3 mo, n=5; 22-24 mo, n=5; BALB cerebellum, 2-3 mo, n=5; 12-13 mo, n=6, 21-23 mo, n=4; C57BL/6 cerebellum, 2-3 mo, n=4, 12-13 mo, n=2, 21-23 mo, n=6. We also provide additional unpublished data describing age-related changes in gene expression for the frontal cortex of 2-3 mo (n=8) and 15-16 mo old (n=8) female BALB mice, for the striatum of 2-3 mo old (n=3), 12-13 mo old (n=5), and 21-23 mo old (n=5) male BALB mice, and for the hypothalamus of 2-3 mo old (n=7), 12-13 mo old (n=5), and 21-23 mo old (n=8) male CBA mice.
--------------------------------------
The authors are unable to locate the raw data for the following 8 samples:
BALB-frontalcortex-young-3
BALB-frontalcortex-young-5
BALB-frontalcortex-young-6
BALB-frontalcortex-young-7
BALB-frontalcortex-old-1
BALB-frontalcortex-old-3
BALB-frontalcortex-old-4
BALB-frontalcortex-old-7

However, the authors state that this has the complete data for the manuscript.

middle: J

first: Jyothi

last: Arikkath

first: Michael

middle: D

last: Boska

first: Tammy

last: Chaudoin

first: Nicholas

middle: W

last: DeKorver

first: Evan

last: Goulding

first: Traci

last: Hoke

first: Vahid

last: Mojtahedzedah

first: Crystal

last: Reyelts

first: Balasrinivasa

last: Sajja

first: A

middle: K

last: Schenk

first: Laurence

last: Tecott

first: Tiffany

last: Volden


title: Transcriptomic data to assess hexavalent chromium mode of action in mice and rats [mouse]

city: Chapel Hill

first: Julia

last: Rager

state: NC

address: 135 Dauer Drive, CB 7431

institute: UNC

summary: In order to evaluate the mechanisms underlying hexavalent chromium (Cr(VI)) responses, mice and rats were treated with varying concentrations of Cr(VI) in drinking water, as sodium dichromate dihydrate (SDD). Potential transcriptomic responses were evaluated through microarray analysis.

overall_design:
Mice and rats were exposed to varying concentration of Cr(VI) through drinking water for either 7 or 90 days. Animals were sacrificed on days 8 and 91, respectively, and tissue samples were collected from the small intestine (i.e. duodenum and jejunum) and oral mucosa (palate). Tissue samples were processed and total RNA analyzed using Agilent 4x44K Whole Genome Microarrays.
Please note that two-dye Agilent arrays were used but only Cy3 signal was processed.

first: Chad

last: Thompson

first: Mark

last: Harris


title: A network including TGFβ/Smad4, Gata2 and p57 regulates proliferation of mouse hematopoietic stem/progenitor cells [expression]

status: Public on Sep 01 2016

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

summary:
Transforming growth factor-β (TGFβ) is a potent inhibitor of hematopoietic stem cell (HSC) proliferation. However, the precise mechanism for this effect is unknown. Here, we have identified the transcription factor Gata2, previously described as an important regulator of HSC function, as an early and direct target gene for TGFβ-induced Smad signaling in hematopoietic stem and progenitor cells (HSPCs). Interestingly, TGFβ-induced Gata2 upregulation is critical for subsequent transcriptional activation of the TGFβ signaling effector molecule p57 and resulting growth arrest of HSPCs. Importantly, both Gata2 and p57 are abundantly expressed in freshly isolated highly purified HSCs, demonstrating the relevance of this circuit in HSC regulation within the HSC niche. Our results connect key molecules involved in HSC self-renewal and reveal a functionally relevant network regulating proliferation of primitive hematopoietic cells.
To identify early gene targets of TGFβ signaling in hematopoietic progenitor cells, we performed high-throughput gene expression profiling of a primitive murine hematopoietic cell line. One of the revealed target genes was the transcription factor Gata2, which became the base for the rest of the study.

overall_design: Three independent RNA harvests were separately analyzed. Untreated cells were used as controls to the 10ng/ml TGFb-treated cells.

first: Matilda

last: Billing

first: Stefan

last: Karlsson


title: JNK1 Ablation in Mice Confers Long-term Metabolic Protection from Diet-Induced Obesity at the Cost of Increased Skin Oxidative Damage

city: Trento

first: Alessandro

last: Provenzani

address: via delle regole 101

department: CIBIO

institute: University of Trento

summary:
Obesity and insulin resistance are associated with oxidative stress, which may be implicated in their progression. The kinase JNK1 emerged as a promising drug target for the treatment of obesity and type-2 diabetes. However, JNK1 is a key mediator of the oxidative stress response, promoting either cell dead or survival depending on magnitude and context of its activation. Furthermore, JNK inactivation shortens lifespan in drosophila and c. elegans. To learn on the safety and efficacy of long-term JNK inhibition in vertebrates, we investigated mice lacking JNK1 (JNK1-/-) exposed over a long period to an obesogenic high-fat diet (HFD).
JNK1-/- mice chronically fed an HFD developed more skin oxidative damage because of reduced catalase expression, but also showed sustained protection from obesity, adipose tissue inflammation, steatosis, and insulin resistance, paralleled by decreased oxidative damage in fat and liver. We conclude that JNK1 is a relatively safe drug target for obesity-related diseases.

overall_design: RNA was collected from liver, skin and epididymal fat tissues from JNK1 KO mice and WT mice fed in high fat diet. Each condition was run in quadruplicate

first: Barbara

last: Becattini

first: Fabio

last: Zani

first: Lucia

last: Radici

first: Ludovic

last: Breasson

first: Vito

middle: G

last: D'Agostino

first: Min-Kyung

last: Choo

first: Jin

middle: M

last: Park

first: Giovanni

last: Solinas

first: Tarcisio

last: Fedrizzi

first: Michael

last: Pancher


title: Expression analysis of Danio Rerio strain AB liver over 2 diurnal cycle

city: Houston

first: Ghislain

last: Breton

state: TX

address: 6431 Fannin St MSB 4.216

department: Integrative Biology & Pharmacology

institute: McGovern Medical School

summary: Investigation of diurnal gene expression in liver over the course of 2 days at 4hr interval.

overall_design: A single slide 12-array design for 3 pooled liver samples from 3-6 months old male Zebrafish starting from 7AM (LD24) (light ON) until 3AM (LD68) 44 hours later (light OFF). Light/dark cycle 14:10


title: Gene expression signatures for murine alveolar type II lung epithelial cells after tumor bearing

status: Public on Aug 10 2016

city: Shanghai

first: Liu

last: Yanfang

address: 800 Xiangyin Road

department: Immunology

country: China

institute: Second Military Medical University

summary: To determine the influence of primary tumors on pre-metastatic lungs, we have employed whole genome microarray expression profiling as a discovery platform to identify gene signatures of alveolar type II epithelial cells (AT-II) in TLR3 deficient mice (Tlr3-/-) and wide-type (WT) littermates with tumor bearing. We subcutaneously inoculated Tlr3-/- and WT mice with Lewis lung carcinoma (LLC). Two weeks later, lung tissues from Tlr3-/- and WT mice were dissociated and AT-II cells were sorted. AT-II cells from mice without tumor bearing were set as controls.

overall_design: Primary tumor induced gene expression in AT-II cells from Tlr3-/- and WT mice was measured at 2 weeks after tumor inoculation subcutaneously. AT-II cells from mice without tumor bearing were set as controls.

first: Xuetao

last: Cao

first: Yanfang

last: Liu


title: Expression profiling of mural granulosa cells after heat-stress (HS) vs. pair-fed (PF) conditions

city: Dummerstorf

first: Jens

last: Vanselow

address: Wilhelm-Stahl-Allee 2

department: Reproductive Biology

institute: Leibniz Institute for Farm Animal Biology

summary: High environmental temperatures induce detrimental effects on various reproductive processes in cattle. According to the predicted global warming the number of days with unfavorable ambient temperatures will further increase. The objective of this study was to investigate effects of acute heat stress during the late pre-ovulatory phase on morphological, physiological and molecular parameters of dominant follicles in cycling cows during lactation. Eight German Holstein cows in established lactation were exposed to heat stress (28°C) or thermoneutral conditions (15°C) with pair-feeding for four days. After synchronization growth of dominant follicles was monitored by ultrasonogrphy, and 21 hrs after an induced pre-ovulatory LH surge antral steroid hormones and granulosa cell-specific gene expression profiles were determined. The data showed that the pre-ovulatory growth of dominant follicles and the estradiol, but not the progesterone concentrations tended to be slightly affected. mRNA microarray and hierarchical cluster analysis revealed distinct expression profiles in granulosa cells derived from heat stressed compared to pair-fed animals. Among the 255 affected genes heatstress-, stress- or apoptosis associated genes were not present. But instead, we found up-regulation of genes essentially involved in G-protein coupled signaling pathways, extracellular matrix composition, and several members of the solute carrier family as well as up-regulation of FST encoding follistatin. In summary, the data of the present study show that acute pre-ovulatory heat stress can specifically alter gene expression profiles in granulosa cells, however without inducing stress related genes and pathways and suggestively can impair follicular growth due to affecting the activin-inhibin-follistatin system.

overall_design: German Holstein cows in established lactation were exposed to heat stress (28°C) or thermoneutral conditions (15°C) with pair-feeding for four days.  21 hrs after an induced pre-ovulatory LH surge antral steroid hormones and granulosa cell-specific gene expression profiles were determined.

first: Torsten

last: Viergutz

first: Björn

last: Kuhla


title: Effect of Notch signal inhibition on chicken neural retina in spreading culture

status: Public on Aug 31 2016

city: Takatsuki

first: Hisato

last: Kondoh

state: Osaka

address: Murasakicho 1-1

country: Japan

institute: Biohistory Research Hall

summary: We investigated the effect of Notch signal inhibition on the embryonic E8 neural retina cells concerning expression of various regulatory genes.

overall_design: E8 neural retina cultures were treated with DAPT (Notch signal inhibitor) or DMSO (solvent control) from day 2 to day 12 of culturing, and each duplicate samples were analyzed.

first: Hideaki

last: Iida


title: Differential response of normal and tumor cells to nucleosome depletion

city: Helsinki

first: Maria

last: Sokolova

address: Viikinkaari 5

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

summary: Gene-expression in siRNA treated U2OS and hTERT-RPE1 cells showed that CASP8AP2, NPAT and HINFP do not regulate expression of each other, and do not have any common target genes, except histones. Most histone genes are downregulated in U2OS cells following loss of CASP8AP2, NPAT or HINFP. In normal cells, highly-expressed histone genes were downregulated, albeit less than in tumor cells following loss of CASP8AP2. The p53 target genes were upregulated relatively late, clearly after the changes in expression of histone genes were observed.

overall_design: U2OS and hTERT-RPE1 cells were treated with CASP8AP2, NPAT,  HINFP or control siRNA in duplicates or triplicates and collected for RNA purification on 1st, 2nd and 3d days.


title: Aquaporin gene therapy corrects Sjogren's syndrome phenotype in mice

status: Public on Jul 20 2016

city: Bethesda

first: John

last: Chiorini

state: MD

address: Building 10/Room 1A21

department: NIDCR

institute: NIH

summary: Primary Sjögren’s syndrome (pSS) is a chronic autoimmune disease that is estimated to affect 35 million people worldwide. Currently, no effective treatments exist for Sjögren’s syndrome, and there is a limited understanding of the physiological mechanisms associated with xerostomia and hyposalivation. The present work revealed that aquaporin 5 expression, a water channel critical for salivary gland fluid secretion, is regulated by bone morphogenetic protein 6. In- creased expression of this cytokine is strongly associated with the most common symptom of primary Sjögren’s syndrome, the loss of salivary gland function. This finding led us to develop a novel ther- apy in the treatment of Sjögren’s syndrome by increasing the water permeability of the gland to restore saliva flow. Our study demon- strates that the targeted increase of gland permeability not only resulted in the restoration of secretory gland function but also re- solved the hallmark salivary gland inflammation and systemic inflam- mation associated with disease. Secretory function also increased in the lacrimal gland, suggesting this local therapy could treat the sys- temic symptoms associated with primary Sjögren’s syndrome.

overall_design:
Human salivary gland cells were grown in culture in the presence or absence of BMP-6 at concentractions of 0.1 ng/mL, 6.0 ng/mL or 150 ng/mL.  The study includes 12 samples, with 6 negative controls without BMP6 treatment and two biological replicates for each BMP6 treatment group.

**Please note that the data (both raw and normalized data) have been updated on Jan 4, 2017 to fix the errors made during the initial submission**

first: Zhennan

last: Lai


title: 4T1 breast cancer cells: SPARC knock down vs. Control

status: Public on Jun 29 2016

city: Córdoba

first: Cristobal

last: Fresno

state: Córdoba

address: Av. Armada Argentina 3555

department: UA AREA CS. SOC. Y HUM

country: Argentina

institute: CONICET-Universidad Católica de Córdoba

summary: Comparative analysis of the transcriptome of 4T1 cells stably transduced with a lentiviral vector expressing a siRNA against murine SPARC (4T1-C18) with 4T1 control cells stably transduced with a lentiviral vector expressing a scramble sequence (4T1-SCR).

overall_design: Two-condition experiment, 4T1-C18 vs. 4T1-SCR cells. Biological replicates: 4 SPARC knock down, 4 control, independently grown in vitro and harvested. One replicate per array.  Microarrays were hybridized in three different days.

first: Leandro

middle: N

last: Güttlein

first: Lorena

last: Benedetti

first: Cristóbal

first: Raúl

last: Spallanzani

first: Sabrina

middle: F

last: Mansilla

first: Cecilia

last: Rotondaro

first: Ximena

middle: L

last: Raffo Iraolagoitia

first: Leonardo

last: Sganga

first: Edgardo

last: Salvatierra

first: Alicia

middle: I

last: Bravo

first: Elmer

last: Fernández

first: Vanesa

last: Gottifredi

first: Norberto

last: Zwirner

first: Andrea

middle: S

last: Llera

first: Osvaldo

last: Podhajcer


title: 4T1 breast tumors: SPARC knock down primary tumors vs. Control primary tumors vs. Lung metastasis foci

summary: Comparative analysis of the transcriptome of primary tumors generated from 4T1 cells transduced with a lentiviral vector expressing a siRNA against murine SPARC (4T1-C18), primary tumors generated from 4T1 cells transduced with a lentiviral vector expressing a scramble sequence (4T1-SCR) or lung metastasis foci from 4T1-SCR tumor-bearing mice (4T1-SCR MTTS).

overall_design: Three experimental conditions, 4T1-C18, 4T1-SCR and 4T1-SCR MTTS. Biological replicates: 4  4T1-C18, 4 4T1-SCR, 4 4T1-SCR MTTS independently grown in different mice. 2 days-old tumors and 30 days old lung foci. One replicate per array.  All microarrays were processed the same day


title: SPARC knock down

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

overall_design: Refer to individual Series


title: Transcriptional analysis of oxidative-stressed bean nodules elicited by Rhizobium etli expressing an heterologous globin (VHb)

status: Public on Jun 15 2016

city: Cuernavaca

first: Mario

last: Ramírez

state: Morelos

address: Avenida Universidad S/N

department: Functional Genomics of Eukaryotes

country: Mexico

institute: Centro de Ciencias Genomicas-UNAM

summary: A wide range of environmental stresses lead to an elevated production of reactive oxygen species (ROS) in plant cells thus resulting in oxidative stress. The biological nitrogen fixation in the legume - Rhizobium symbiosis is at high risk of damage from oxidative stress. Common bean (Phaseolus vulgaris) active nodules exposed to the herbicide Paraquat (1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate) that generates ROS accumulation, showed a reduced nitrogenase activity and ureide content. We analyzed the global gene response of stressed nodules using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST). The experimental design, based on circular hybridizations, included four conditions as, with two independent biological replicates and three technical replicates for each conditions. A total of 2418 differentially expressed genes (DEG) were identified among the different combinations. Our results showed good correspondence among both the GO term and the MapMan enrichment analyses highlighting DEG from PQ-treated nodules assigned to the functional super-categories: trans-membrane transport, hormone signal transduction, stress response, and regulation.

platform_organism:
Glycine max
Phaseolus vulgaris

overall_design: In this work we analyzed the effect of VHb-expressing R. etli CE3 in the symbiosis of common bean plants under oxidative stress experimentally generated by the addition of PQ  for 48 hours. We analyzed the transcript profile, via microarray hybridization, using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST).

first: Roberto

last: Ferrarini

first: Francesca

last: Sparvoli

first: Bianca

last: Castiglioni

first: Paola

last: Cremonesi

first: Dario

last: Panzeri

first: Alessandra

last: Stella

first: Francesco

last: Strozzi

first: Georgina

last: Hernández


title: caArray_liu-00251: TCGA Analysis of RNA Expression for Glioblastoma Multiforme

status: Public on May 27 2016

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary: TCGA Analysis of RNA Expression for Glioblastoma Multiforme Using Affymetrix HT_HG-U133A

overall_design:
liu-00251
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HT_HG-U133A
Organism: Homo sapiens (ncbitax)
Tissue Sites: Brain
Material Types: cell, organism_part, synthetic_RNA, total_RNA, solid_tumor
Disease States: GLIOBLASTOMA MULTIFORME, NOT SPECIFIED


title: The FtsH3 protease is an epistatic master regulator of the iron and phosphate stress responses in the cyanobacterium Synechocystis sp. PCC 6803

status: Public on Jun 14 2016

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

institute: University of Freiburg

summary: Regulation of gene expression is a sophisticated process leading to the activation or suppression of genes due to adaptation to environmental stimuli. The membrane-embedded FtsH proteases conserved in bacteria, chloroplasts and mitochondria, are involved in such regulation. The genome of the cyanobacterium Synechocystis sp. PCC 6803 encodes four FtsH homologues FtsH1-4, functioning in the form of oligomeric complexes. Homologue FtsH3 is bound in two hetero-oligomeric complexes, FtsH1/FstH3 and/or FtsH2/FtsH3, respectively. Previous data showed that the FtsH1/FtsH3 complex is involved in the acclimation of cells to iron deficiency by controlling the availability of the transcriptional regulator Fur (Sll0567). To gain more comprehensive insight into the physiological role of FtsH hetero-complexes, we carried out genome-wide expression profiling of a mutant conditionally depleted in FtsH3, grown under nutrient sufficiency and iron depletion. Our results show, that besides Fur, also the SufR and Pho regulons belong to the set of genes controlled by FtsH. Moreover, by combining the transcriptome data with in silico prediction we identified novel targets of Fur in Synechocystis PCC 6803. Fur tends to evoke mostly repression, but also appears to activate some target genes.

overall_design: We monitored the global gene expression in a conditional Synechocystis PCC6083 ftsH knockdown strain (FtsHdown) (Boehm et al., 2012) and a control strain (WT) at standard conditions and at iron depletion. The presence of ammonia to induced the conditional knockdown. Each sample was done in biological replicates.

first: Vendula

last: Krynická

first: Miguel

last: Hernández-Prieto

first: Wolfgang

last: Hess

first: Matthias

middle: E

last: Futschik

first: Josef

last: Komenda


title: Microarray analysis of gene expression in Dnmt3a-knockdown macrophages.

status: Public on May 30 2016

city: shang hai

first: Qian

last: Zhang

address: xiangyin road 800

institute: Second military medical university

summary: To measure the gene expression profile in Dnmt3a-knockdown macrophages

overall_design: Gene expression after 48hr in  Control or Dnmt3a siRNA transfected peritoneal macrophages

first: Li

last: Xia

first: Cao

middle: X

last: Tao


title: Prefrontal cortex gene expression signature in autistic BTBR mice

status: Public on May 18 2016

first: Yuri

last: Bozzi

address: via Sommarive 9

department: CIBIO - Centre for Integrative Biology

summary: Autism spectrum disorders (ASD) are characterized by a high degree of genetic heterogeneity. Genomic studies identified common pathological processes underlying the heterogeneous clinical manifestations of ASD, and transcriptome analyses revealed that gene networks involved in synapse development, neuronal activity and immune function are deregulated in ASD. Mouse models provide unique tools to investigate the neurobiological basis of ASD. Here we used the BTBR (BTBR T+ Itpr3tf/J) ASD mouse model to identify conserved ASD-related molecular signatures.

overall_design: Gene expression in the BTBR mouse prefrontal cortex was measured by microarrays and compared to the gene expression profile of C57Bl6/J controls (5 months old, n= 3 mice per group).

first: Giovanni

last: Provenzano

first: Laura

last: Ricceri

first: Maria

last: Scattoni


title: Hippocampal gene expression signature in autistic BTBR mice

overall_design: Gene expression in the BTBR mouse hippocampus was measured by microarrays and compared to the gene expression profile of C57Bl6/J controls (5 months old, n= 4 mice per group).


title: Gene expression analysis of inositol hexakisphosphate kinase 1 (IP6K1) knockout mouse embryonic fibroblasts

status: Public on May 16 2016

city: Hyderabad

first: Rashna

last: Bhandari

state: Telangana

address: Bldg 7, Gruhakalpa, 5-4-399/B Nampally

institute: Centre for DNA Fingerprinting and Diagnostics

summary: To investigate the biological significance of IP6K1 function we compared the gene expression profile of two mouse embryonic fibroblast (MEF) cell lines each derived from Ip6k1+/+ and Ip6k1-/- embryos. Results reveal downregulation of several biological processes upon the loss of IP6K1.

overall_design: Organism : Mus musculus , Agilent Gene Expression Whole Genome Mouse 4x44k (AMADID: 14868). Two biological replicates each of Ip6k1+/+ and Ip6k1-/- MEFs


title: Hippocampal gene expression signature following inflammation in epileptic mice

status: Public on May 03 2016

summary: We used a systemic inflammatory challenge in animals with chronic mesial temporal lobe epilepsy to identify novel molecular pathways involved in seizure regulation. Mice were first rendered epileptic by a single intrahippocampal injection of kainic acid (KA). After a period of two-three weeks, mice developed spontaneous seizures and then received a single intraperitoneal injection of lipopolysaccharide (LPS) to mimic systemic inflammation, or saline as a control. Gene expression analysis by microarrays was then performed on hippocampal RNA samples extracted 4 and 24 hours after LPS or saline treatment (n=3 samples per treatment group).

overall_design: Inflammation-induced gene expression in the epileptic mouse hippocampus was measured at 4 and 24 hours after intraperitoneal injection of lipopolysaccharide (LPS; L5886, Sigma; from Salmonella enterica, serotype abortus equi; 100 micrograms/kg in PBS) or saline (SAL).  Three animals per treatment group  were analyzed at each time point (4 or 24 hours).

first: Sacha

last: Genovesi

first: Chiara

last: Cerri

first: Matteo

last: Caleo


title: Microarray analysis to unravel the function of C-terminus domain of EBF1 by gain-of function approach

status: Public on May 09 2016

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: To study the function of C-terminus domain of EBF1, a gain-of function microarray analysis was performed by transducing Empty, Ebf1wt and Ebf1DC expressing vectors into Ebf1-/- progenitor cells.

overall_design: Freshly prepared Ebf1−/− c-Kit+ fetal liver cells were transduced with  pmys-Empty-IRES-GFP, pmys-EBF1wt-IRES-GFP and pmys-EBF1DC-IRES-GFP. EBF1wt- or EBF1ΔC-transduced cells were sorted as early pro-B cells (GFP+CD19+BP1−Thy1−Mac1−NK1.1−CD3−). vector-transduced cells were sorted as only GFP+.

first: Sören

last: Boller

first: Duygu

last: Akbas

first: Rudolf

last: Grosschedl


title: Role of smooth muscle cell autophagy in atherosclerosis

status: Public on May 07 2016

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Study of the effect of autophagy inhibition on smooth muscle cell function and atherosclerotic plaque stability

overall_design: The study searches for differences in gene expression in SMCs from the aorta of mice between two mouse strains (Atg7+/+ SM22α-Cre+ and Atg7F/F SM22α-Cre+). For each strain, two biological replicates were collected. The cells were cultured in DMEM/F-12 medium supplemented with 10% FBS. Cells from passage 4 untill 10 were used for experiments. Two-color arrays were run, each time comparing a replicate from one strain to a replicate from the other strain. For each array we added a dye swap, giving a total of four arrays.

first: Mandy

middle: O

last: Grootaert

first: Wim

last: Martinet

first: Dorien

last: Schrijvers


title: caArray_meyer-00180: TCGA GBM: Analysis of Gene Expression for Glioblastoma Multiforme Using Affymetrix HT_HG-U133A (Broad)

status: Public on Jun 09 2016

first: Mervi

last: Heiskanen

overall_design:
meyer-00180
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HT_HG-U133A
Organism: Homo sapiens (ncbitax)
Tissue Sites: Brain, Brain
Material Types: cell, organism_part, normal_tissue, organism_part, solid_tumor, synthetic_RNA, total_RNA, solid_tumor
Disease States: GLIOBLASTOMA MULTIFORME, Glioblastoma Multiforme


title: Gene expression change in Keap1 knockdown (KD) mice in kidneys of ischemia-reperfusion injury (IRI)

status: Public on Apr 01 2016

city: Sendai

first: Masahiro

last: Nezu

state: Miyagi

address: 2-1 Seiryo-cho, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University School of Medicine

summary: We analyzed differences in IRI kidneys between WT and Keap1 KD mice (= Nrf2-activated mice).  To identify Nrf2-target genes or metabolic genes in kidneys, we examined the mRNA expression profile both in normal (uninjured) and IRI kidneys (at day1 after unilateral IRI) from mice

overall_design: We performed microarray analyses using 1)  Injured kidneys at day 1 after unilateral IRI,  and 2)  intact kidneys from mice which did not undergo UIRI.  Samples were harvested from Keap1 KD mice and WT mice, n = 2 each,

first: Tomokazu

last: Souma

first: Norio

last: Suzuki

first: Masayuki

last: Yamamoto


title: Dual role of the adaptive immune system in liver injury and hepatocellular carcinoma  development

status: Public on Apr 21 2016

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: To identify pro-tumorigenic signaling cascades in livers of Fah-/- mice, gene expression patterns were compared between tumor prone Fah-/- mice and immunocompromised mice in which tumor development was found to be reduced

overall_design: Gene set enrichment analysis (GSEA) comparing hepatic Fah(-/-) cells  [tumor:Fah_off, Fah_2xoff/on] vs FCR (normal, inflamed liver: FCR_100%, FCR_2xoff/on)

first: J

last: Endig

first: R

first: S

last: Marhenke

first: A

last: Vogel


title: Gene Regulation by microRNA-16 forced expression in ErbB-2 positive murine breast cancer cells.

status: Public on May 04 2016

city: Ciudad Autónoma de Buenos Aires

first: Patricia

middle: Virginia

last: Elizalde

state: Ciudad Autónoma de Buenos Aires

address: Vuelta de Obligado 2490

institute: Instituto de Biología y Medicina Experimental

summary: miR-16 is a potent tumor suppressor in ErbB-2 positive breast cancer. The primary objetive of this study was to identify previously uncharacterized putative mRNA targets of miR-16 in ErbB-2 postitive breast cancer cells. To achieve our objective we studied the effects of exogenously expressed miR-16 on the gene expression profile of primary cultures of ErbB-2 positive murine breast cancer tumors. The C4HD tumor line displays high levels of estrogen receptor and progesterone receptor, overexpresses ErbB-2 and ErbB-3, exhibits low ErbB-4 levels, and lacks EGF-R expression.

overall_design: Primary cultures of the C4HD murine breast tumor were transfected with a miR-16 precursor (pre-miR-16) or a scrambled sequence (pre-miR-Control) that does not form any known mammalian miRNA. Three biological replicates were obtained for each experimental condition.

middle: V

first: John

middle: A

last: Cidlowski

first: Leandro

last: Venturutti

first: Martín

last: Rivas


title: Differential gene expression in the liver among crossbred beef steers with divergent gain and feed intake phenotypes

status: Public on Mar 31 2016

city: Clay Center

first: Amanda

last: Lindholm-Perrry

state: NE

address: State Spur 18D

department: NEMRU

institute: USMARC

summary:
Steer liver transcriptome
Evaluation of the naturally occurring transcriptome variation in liver among beef steers with divergent gain and feed intake phenotypes.

overall_design: The transcriptomes of liver were examined for expression differences that contribute to cattle feed efficiency.

last: Lindholm-Perry


title: Microarray analysis to unravel the function of C-terminus domain of EBF1 by replacement approach

first: Senthilkumar

last: Ramamoorthy

summary: To unravel the function of C-terminus domain of EBF1, a replacement microarray analysis was performed by transducing Ebf1wt and Ebf1DC expressing vectors intoA-MuLV transformed pro-B (Ebf1fl/fl;RERTCre) cells.

overall_design: A-MuLV transformed Ebf1fl/fl RERTCre pro-B cells were treated with 2μM 4-hydroxy-tamoxifen (4-OHT) 24h after transduction. Five days after treatment, cells were sorted as GFP+. More than two week later, the replacement was validated by IB and the cells were used for downstream analyses. As control, mock-transduced cells were harvested four days after tamoxifen treatment before cell death was observed.

first: Sören

last: Boller

first: Rudolf

last: Grosschedl


title: Gene expression signature for highly liver metastatic colon cancer cell line

status: Public on Mar 30 2016

city: Columbia

first: Maria Marjorette

middle: Ociones

last: Pena

state: SC

address: 715 Sumter St. CLS 401

department: Biological Sciences

institute: University of South Carolina

summary: The goal was to identify genes that promote liver metastasis of colorectal cancer. Microarray analysis was performed to compare gene expression and altered biological pathways between a poorly metastatic CT26 cell line as compared to an isogenic highly metastatic CT26 FL3 cell line that was isolated by in vivo selection in an orthotopic mouse model of colon cancer metastasis to the liver.

overall_design: Gene expression in CT26-FL3 and parental CT26 cells were determined using the Agilent platform.  Four independent samples each were analyzed.

first: Maria

last: Peña

first: James

middle: C

last: Ryan

first: Diego

last: Altomare


title: Nrf2 suppresses macrophage inflammatory response by blocking proinflammatory cytokine transcription

status: Public on May 12 2016

first: Eri

middle: H

last: Kobayashi

address: 2-1 Seiryo-machi, Aobaku

institute: Tohoku University Graduate School of Medicine

summary: Nrf2 (NF-E2-related factor-2) transcription factor regulates oxidative/xenobiotic stress response and also represses inflammation. However, the mechanisms how Nrf2 alleviates inflammation are still unclear. Here, we demonstrate that Nrf2 interferes with lipopolysaccharide-induced transcriptional upregulation of proinflammatory cytokines, including IL-6 and IL-1β. ChIP-seq and ChIP-qPCR analyses revealed that Nrf2 binds to the proximity of these genes in macrophages and inhibits RNA Pol II recruitment. Further, we found that Nrf2-mediated inhibition is independent of the Nrf2 binding motif and reactive oxygen species level. Murine inflammatory models further demonstrated that Nrf2 interferes with IL6 induction and inflammatory phenotypes in vivo. Thus, contrary to the widely accepted view that Nrf2 suppresses inflammation through redox control, we demonstrate here that Nrf2 opposes transcriptional upregulation of proinflammatory cytokine genes. This study identifies Nrf2 as the upstream regulator of cytokine production and establishes a molecular basis for an Nrf2-mediated anti-inflammation approach.

overall_design: Gene expression in BMDMs obtained from wild-type and Keap1-CKO mice. In Keap1-CKO (Keap1 flox/flox::LysM-Cre) BMDMs, Nrf2 transcription factor is activated due to Keap1-deficiency. BMDMs were obtained by a culture of bone marrow cells in the presence of M-CSF for7 days. M1-activated BMDMs were obtained by stimulation with LPS and IFNg for 6 hours, while M2-activated BMDMs were obtained by a stimulation with IL-4 for 6 hours. Two independent BMDM cultures were performed, and each experiment contains samples obtained from one wild-type and one Keap1-CKO mice, respectively.

first: Takafumi

last: Suzuki

first: Ryo

last: Funayama

first: Takeshi

last: Nagashima

first: Makiko

last: Hayashi

first: Takashi

last: Moriguchi

first: Keiko

last: Nakayama

first: Masayuki

last: Yamamoto


title: MuRF1 regulation of Fenofibrate’s induction of spontaneous cardiac hypertrophy in vivo.

status: Public on Mar 01 2016

city: Chapel Hill

first: Monte

middle: Shaw

last: Willis

address: 103 Mason Farm Road, MBRB 2340B

department: Pathology & Laboratory Medicine

institute: University of North Carolina

summary: MuRF1 -/- w/ Fenofibrate treatment leads to the reduction of proteolytic and fibrolytic enzymes, increasing hypertrophy

overall_design: Four strain-matched groups of 3-8 week old mice were investigated: 1) MuRF1 -/- Fenofibrate feed;  2) MuRF1 -/- chow feed; 3) MuRF1 +/+ Fenofibrate feed; 4) MuRF1 +/+ chow feed  at two time points: 1) 3 weeks; 2) 8 Weeks  Biological replicates: Two to three per condition.  Hearts harvested.  One replicate per array.

first: Gopal

last: Desai

first: Traci

last: Parry

first: Luge

last: Li

first: Natalie

last: Stanley

first: Pamela

last: Lockyer

first: Cam

last: Patterson

first: Jonathan

last: Schisler


title: Expression profiles of mouse NK cell subsets

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

institute: University Hospital Regensburg

summary: It is known that NK cells are a heterogeneous population of functionally distinct NK cell subsets. Here we report on different genomic, phenotypic and functional properties of four murine NK cell subsets distinguished by CD117 (c-kit), CD27 and CD11b expression.

overall_design: Gene expression was measured in NK cell subsets freshly sorted from murine C57Bl/6 splenocytes. Two to three different batches were analysed.

first: Evelyn

last: Ullrich


title: Characterizing the molecular features of ERG-positive tumors in primary and castration resistant prostate cancer

status: Public on Feb 01 2016

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: This study examined ERG expression in primary PCa and CRPC. We have identified altered levels of inflammatory mediators associated with ERG expression and a novel ERG-associated protein, DCLK1, which may play a role in primary PCa progression to metastatic CPRC.

overall_design: Custom Agilent 44K whole human genome expression oligonucleotide microarrays were used to profile 20 LuCaP PCa xenograft line, 11 radical prostatectomies and 45 CRPC metastases from 32 patients. RNA was amplified prior to hybridization against a common reference pool of prostate tumor cell lines.

first: Martine

middle: P

last: Roudier

first: Brian

middle: R

last: Winters

first: Hung-Ming

last: Lam

first: Xiaotun

last: Zhang

first: Roger

first: Lisly

last: Chéry

first: Lawrence

middle: D

last: True

first: Celestia

last: Higano

first: Bruce

last: Montgomery

first: Paul

last: Lange

first: Linda

last: Snyder

first: Shiv

last: Srivistava

first: Eva

last: Corey

first: Robert

last: Vessella

first: Peter

last: Nelson

first: Aykut

last: Üren

first: Colm

last: Morrissey


title: Cardiomyocyte-specific Nitric Oxide Synthase 3 Overexpression in Pressure-Overloaded Left Ventricle.

status: Public on Jan 15 2016

first: Rekin's

last: Janky

summary:
Aims: Cardiomyocyte-specific nitric oxide synthase 3 (NOS3) overexpression reduces left ventricular (LV) remodelling after myocardial infarction in mice, but its effect on sustained LV pressure-overload remains incompletely understood. We investigated LV structural and functional adaptation to elevated afterload in mice with cardiomyocyte-restricted NOS3 overexpression (NOS3TG) and wild type littermates (WT).
Methods and Results: Hemodynamic indices, cardiac hypertrophy and interstitial fibrosis were measured 10 weeks after transverse aortic constriction (TAC). After 10 weeks TAC, NOS3TG had better preserved systolic function (maximum rates of pressure development normalized to maximal pressure 77±6 versus 65±2 ms-1, P=0.05), reduced heart weight-body weight ratio (HW/BW, 5.0±0.3 versus 5.8±0.1, P<0.05), and cardiomyocyte width than WT (14.9±0.4 vs 16.7±0.2 ?m, P<0.05). After 10 weeks TAC, a 44k cDNA chip-based microarray analysis was validated using real time PCR and revealed significantly altered expression pattern of genes involved in cellular growth, matrix remodelling, and inflammation between genotypes.
Conclusions: Cardiomyocyte-restricted NOS3 overexpression attenuates TAC-induced hypertrophy via autocrine inhibition of cardiomyocyte cell growth, but does not mitigate myocardial fibrosis. The subsequent diastolic dysfunction suggests that inhibition of matrix producing cells during hypertrophic stress is necessary to prevent functional and structural deterioration of the pressure-overloaded heart.

overall_design: Left ventricular mRNA expression profiles were compared between alpha-myosin heavy chain driven nitric oxide synthase 3 (alpha-MHC-NOS3) transgenic and wild type (WT) littermate mice at baseline and 10 weeks after transversal aortic constrcition-induced pressure-overload. Biological repeats: n=4, two males and two females, for each group and condition. Transgenic mice were backcrossed for seven generations (F7) to a C57Bl/6 N background and age and weight matched animals were used for microarray experiments.

last: Pokreisz

first: Glenn

last: Marsboom

first: Pieter

last: Vermeersch

first: Sara

last: Vandenwijngaert

first: Marijke

last: Pellens

first: Hilde

last: Gillijns

last: Van Hummelen

first: Rudy

last: van Eijsden

first: Zsolt

last: Szelid

first: Jan

last: D'Hooge

first: Kenneth

last: Bloch

first: Stefan

last: Janssens


title: Activation of Wnt/β-catenin Signaling Blocks Monocyte-Macrophage Differentiation Through Antagonizing PU.1-Targeted Gene Transcription

status: Public on Apr 06 2016

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary: We have shown that β-catenin overexpression induced blockage of monocyte-macrophage differentiation by inhibiting PU.1-targeted gene transcription including Egr2 expression in myeloid progenitor cells. Our results suggest that compromised PU.1-targeted gene transcription induced by β-catenin overexpression, at least partially, may mediate a pathogenic role of β-catenin in myeloid leukemia.

overall_design: PUER cells were infected with retrovirus expressing beta-catenin-S33Y or control vector MIGR1. Five days after infection,  the GFP positive cells were sorted by flow cytometry, and were treated  with  4-OHT to induce the expression of PU.1. Total RNA was exacted from cell samples and purified by RNeasy Micro kit (Qiagen). cRNAs were generated and hybridized to the mouse whole genome 4×44K arrays according to manufacturer’s instructions (Agilent Technologies).

first: Yue

last: Sheng

first: Wen

last: Ju

first: Howard

last: Ozer

first: Xiaohong

last: Qiao

first: Zhijian

last: Qian


title: PIE cell line: Control vs. ETEC treated or Immunobiotic treated

status: Public on Jan 22 2016

city: San Miguel de Tucumán

first: Julio

last: Villena

state: Tucumán

address: Chacabuco 145

institute: CERELA-CONICET

summary: We investigate the transcriptome response of porcine intestinal epitheliocyte cell line (PIE cells) to the challenge with heat-stable Enterotoxigenic Escherichia coli (ETEC) pathogen-associated molecular patterns (PAMPs) and, the changes induced by Lactobacillus jensenii TL2937 in that response. The transcriptome approach allowed us to obtain a global overview of the immune and immune related genes involved in response of PIE cells to heat-stable ETEC PAMPs. The most remarkable changes in PIE cells after heat-stable ETEC PAMPs challenge were observed in chemokines expressions, followed by cell adhesion molecules and, complement and coagulation cascades factors. We also confirmed that L. jensenii TL2937 differently modulates gene expression in ETEC PAMPs-challenged PIE cells. The microarray gene expression profiles clearly demonstrated that an anti-inflammatory effect was triggered by the immunobiotic strain in PIE cells. The main outcome from the study was the differential regulation of chemokines (CCL8, CXCL5, CXCL9, CXCL10 and CXCL11), complement factors (C1R, C1S, C3 and CFB) and, coagulation system proteins (Tissue factor) expression by L. jensenii TL2937. PIE cells treated with the negative control Lactobacillus plantarum TL2766 showed a transcriptomic response similar to ETEC PAMPs-challenged PIE cells.

overall_design: PIE cells were cultured for 3 days, L. jensenii TL2937 or L. plantarum TL2766 were added to cell cultures and 48 hours latercells were washed to eliminate bacteria. Non-bacteria treated PIE cells were used as controls.  Then cells were stimulated with ETEC PAMPs  for 12 hours for microarray studies. Groups: unchallenged PIE cells, PIE cells + ETEC PAMPs, PIE cells + TL2937 + ETEC PAMPs, PIE cells + TL2766 + ETEC PAMPs. One replicate for each group.

first: H

last: Kobayashi

first: L

last: Albarracin

first: J

last: Kitazawa


title: Gene expression data from lung of mice infected with H5N1 or H1N1 virus

status: Public on Jan 12 2016

city: Beijing

first: Yanli

last: Zhang

state: BEIJING

address: No.5 Dongdansantiao

institute: Chinese Academy of Medical Sciences, Peking Union Medical College

summary: To find the different host response during H5N1 and H1N1 infection, we have employed whole genome microarray expression profiling as a discovery platform to identify genes differentially expressed in mouse lungs infected by H5N1 and H1N1 virus. BALB/c mice were infected with live H5N1 virus , live H1N1 virus, or inactivated H5N1 virus or allantoic fluid (AF) for 24 h.

overall_design: Mice were  intra-tracheally  inoculated with 106 TCID50 of live H5N1 virus or an identical volume of inactivated H5N1 virus , 106 TCID50 of live H1N1 virus, or allantoic fluid (AF). After 24 hours, lungs were taken for RNA extraction and hybridization on Agilent microarrays.H5N1 and H1N1 virus induced gene expression in mouse was measured. This experiment was performed with 3 mice in each group.

first: Jun

last: Tang

first: Ning

last: Yang

first: Yang

last: Sun

first: Chengyu

last: Jiang


title: Molecular Characterization of Spontaneously Transformed Epithelial Murine Colon Cell Lines as a Model of Human Colorectal Neoplasia

status: Public on Jan 01 2016

city: Bethesda

first: Hesed

middle: Maria

last: Padilla-Nash

address: 50 South Drive

department: Genetics Branch

institute: NCI

type:
Expression profiling by array
Genome variation profiling by array

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

overall_design: Refer to individual Series


title: Molecular Characterization of Spontaneously Transformed Epithelial Murine Colon Cell Lines as a Model of Human Colorectal Neoplasia (expression)

summary:
To characterize a series of mouse colon cells that have become spontaneously transformed over time in order to identify the chromosomal and genomic alterations that take place during the development of tumorigenesis.
Colorectal cancer is the third common malignancy in the United States. The stepwise progression from adenoma to carcinoma is accompanied by specific genomic alterations.  Existing mouse models of human colon cancer have been induced by chemicals, viruses, or through genetic manipulation.   Presented here is a unique mouse model of spontaneous transformation designed to identify the sequential steps of tumorigenesis.     Normal epithelial colon cells were selectively isolated from the large intestine from eight different isogenic five-six week old C57BL/6 mice.  Primary colon cells were grown in vitro with reduced serum concentration. The cells were sequentially recovered from culture based on distinct morphological changes: first, when the cells were in the pre-immortal stage and established as adherent cultures; second, as the cells bypassed crisis, increased their mitotic activity and became immortal; third, at early transformation, as the cells first formed foci; fourth, mid-transformed where the cells had higher proliferation rates in later passages; and finally, late transformed with  rapid proliferation, contact inhibition, and multiple foci. The cells within each stage were analyzed using the molecular cytogenetic techniques of spectral karyotyping (SKY) and array comparative genomic hybridization (aCGH), and gene expression profiling.  The late transformed cells were injected into nude mice to assess their tumorigenic potential.      Spectral karyotyping revealed many recurrent structural and numerical aberrations, specifically in the late transformed cells.  Loss of chromosome 4 is a consistent chromosomal aberration observed in all stages of the transformed colon cells, as well as in other tissues during the process of spontaneous transformation. Array CGH identified a pattern of gains and losses, and showed deletions of APC and Trp53 as well as a gain of Kras similar that observed in human colorectal cancer.  Gene expression profiling identified the deregulation of several genes known to be involved in the progression of human colon cancer.   Tumors resulted from three of the eight late transformed cultures confirming tumorigenic potential. Ultimately, the molecular characterization of spontaneously transformed murine epithelial colon cells indeed recapitulated the step wise progression of human colon cancer, and will prove to be an invaluable system in which to test potential rational intervention strategies.

overall_design: Mouse colon epithelial cells were isolated from the colon of 8 isogenic C57BL\6 mice. These cells were grown in reduced serum and over time spontaneously became immortal and transformed. Our objective is to compare these changes to those that occur during human colon cancer development.

first: Nicole

last: McNeil

middle: M

last: Hu

first: Thomas

last: Ried


title: Gene expression profiles in the liver of obese AIM+/+ and AIM-/- mice

status: Public on Dec 23 2015

city: Kisarazu

first: Osamu

last: Ohara

state: Chiba

address: 2-6-7 Kazusa-Kamatari

department: Technology Development

institute: Kazusa DNA Research Institute

summary: To elucidate differential preventive roles of the blood apoptosis inhibitor of macrophage (AIM)  protein in fat deposition and hepatocarcinoma development, we have performed microarray analysis to assess putative difference in expression of genes related to carcinnogenesis in the liver of AIM+/+ and AIM-/- fed a high-fat diet (HFD) for various periods.

overall_design: RNA was isolated from the liver of AIM+/+ and AIM-/- mice fed an HFD for 0, 6, 12, and 20 weeks, and analyzed by microarray.

first: Satoko

last: Arai

first: Toru

last: Miyazaki

first: Kazuhiro

last: Sato


title: ERK activation, gene dysregulations and cell transformation at submicromolar doses of Cr6+ in C3H10T1/2 and BALB/c 3T3 cells: interaction with Lipoic acid

status: Public on Dec 31 2015

city: Lucknow

first: Dr Sushil

last: Kumar

state: Uttar Pradesh

address: M G Marg

department: Environmental Carcinogenesis

institute: Indian Institute of Toxicology Research

summary:
The molecular mechanism of Cr6+ carcinogenicity is not well understood. Studies advocate a key involvement of the altered cytogenomics and dysregulated pathways in Cr6+ toxicity. However, the dissimilarity in expression of genes and pathways in cells transformed by Cr6+ has led us to supplement more data on the subject. We report here genomics of cells transformed after acute exposure to submicromolar (0.01or1µM) test doses of Cr6+; the non-cytotoxic submicromolar test concentrations transformed the mammalian cells; the characteristic gain of anchorage independent growth potential was demonstrable in soft agar assay. C3H10T1/2 and BALB/c 3T3 cell transformation assay has been used which is established in literature as the in vitro carcinogenesis test system.
Gene expression profile of the transformed cells was found to be dysregulated at both the toxicant doses. PARP1 gene was significantly up regulated and SFN, MTIF2, IRGQ, RAVER2, SLC2A6, MLLT3, EPB4.1L3, JAK1, RALGPS1, EXTL3, PRMT6, PREB, SERPINE1, MORC4 genes were significantly down regulated commonly at two test concentrations. These genes were found to be involved in tumour suppression, DNA repair, cell cycle control, energy metabolism and biosynthesis.Cr6+ also induced MAPK signalling via ERK phosphorylation. Activation of ERK signalling, dysregulation of gene expressions, and cell transformation was prevented by alpha lipoic acid (LA) in equimolar concentrations.
The acute exposure to submicromolar concentrations of Cr6+ can induce cell transformation and gene dysregulations in mammalian cell. The influenced genes are crucial for progression of Cr6+ toxicity and their mitigation by LA shows critical role of redox reactions in Cr6+ toxicity.

overall_design:
Agilent one-color experiment,Organism: Mus musculus ,Agilent-Whole Genome Mouse 4x44k (AMADID: 14868)  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)
C3H10T1/2  cells treated with 1uM or 0.01uM Cr(V1)

first: Akanksha

last: Nigam

first: Sushil


title: MicroRNA expression profile of primary prostate cancer stem cells as a source of biomarkers and therapeutic targets

city: Tampere

first: Antti

last: Ylipää

address: Korkeakoulunkatu 1

institute: Tampere University of Technology

summary: MicroRNA (miRNA) expression profiles were generated from prostate epithelial sub-populations, enriched from patient-derived benign prostatic hyperplasia (BPH, n=5), Gleason 7 treatment naïve prostate cancer (PCa, n=5) and castration-resistant prostate cancer (CRPC, n=3). Microarray expression was validated in an independent patient cohort (n=10). The analyses show that miRNA expression in epithelial sub-populations (e.g. stem cells) clustered together, irrespective of pathological status. We also discovered concordance between the miRNA expression profiles of unfractioned CRPCs, human embryonic stem cells (SCs), and prostate epithelial SCs (both, benign and malignant).  miR-548c-3p was chosen as a candidate miRNA from this group to explore its utility as a CRPC biomarker and/or therapeutic target. Overexpression of miR-548c-3p was confirmed in cancer SCs (8-fold, p<0.05) and unfractionated CRPCs (1.8-fold, p<0.05). Enforced overexpression of miR-548c-3p in differentiated cells induced stem-like properties (p 0.01) and radioresistance (p<0.01). Re-analyses of published studies further revealed that miR-548c-3p is significantly overexpressed in CRPC (p<0.05) and is associated with poor recurrence-free survival (p<0.05), suggesting that miR-548c-3p is a functional biomarker for prostate cancer aggressiveness. Our results validate the prognostic and therapeutic relevance of miRNAs for advanced prostate cancer management, whilst demonstrating that resolving cell-type and differentiation-specific differences is essential to obtain clinical relevant miRNA expression profiles.

overall_design: There are 42 samples in total: 15 benign prostatic hyperplasia, 15 prostate cancers, 9 treatment-resistant prostate cancer. There are stem cells, transit amplifying cells and committed basal cells dissected from each sample. Three PrEC samples of each three cell types can be used as reference.

first: Jayant

middle: K

last: Rane

first: Mauro

last: Scaravilli

first: Davide

last: Pellacani

first: Vincent

last: Mann

first: Matthew

last: Simms

first: Matti

last: Nykter

first: Anne

middle: T

last: Collins

first: Tapio

last: Visakorpi

first: Norman

middle: J

last: Maitland


title: Gene expression of mice over-expressing secretoglobin 3A2 in lung

city: bethesda

first: yan

last: cai

state: maryland

address: 9000 rockville pike

department: NCI

institute: NIH

summary: Secretoglobin (SCGB) 3A2 is a cytokine-like secretory protein and is predominantly expressed in airway epithelial cells. While SCGB3A2 is known to have anti-inflammatory, growth factor, and anti-fibrotic activities, its roles in lung homeostasis and diseases are still elusive. In order to obtain an insight into these roles, a transgenic mouse line over-expressing SCGB3A2 in the lung using the human surfactant protein-C promoter was established.

overall_design: non-treated Condition. Biological replicates: 4WT,4TG samples.

first: Yan

last: Cai

first: Takeshi

last: Tomita

first: Taketomo

last: Kido


title: Analyses of lung early responses to RSV in the neonatal environment reveal key roles for DC and type I IFN in controlling immunopathologic imprinting.

status: Public on Dec 21 2015

city: Jouy en Josas

first: Aude

last: Remot

address: Domaine de Vilvert

department: VIM

institute: INRA

summary: The gene expression profile of neonatal versus adult lung, 2 days after an RSV or mock infection was analyzed using whole mouse genome agilent microarrays.

overall_design: Total lung RNA were extracted, labeled with Cy3 and hybridized on Agilent G4122F slides. We used 4 biological replicates per condition.

first: Luc

last: Jouneau

first: Catherine

last: Dubuquoy

first: Stefan

last: Bouet

first: Jérome

last: Lecardonnel

first: Emmanuelle

last: Rebours

first: Claire

last: Cherbuy

first: Agnès

last: Petit-Camurdan

first: Sabine

last: Riffault

first: Delphyne

last: Descamps

first: Daphné

last: Laubreton


title: The 1918 PB2 protein, not HA, enhances the virulence of an avian influenza virus closely related to the 1918 pandemic virus through the inhibition of wnt signaling.

first: Michael

last: Katze

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: The purpose of this experiment was to understand the pathogenic role of individual 1918 genes on the host response to the 1918 pandemic influenza virus.  We examined reassortant avian viruses nearly identical to the pandemic 1918 virus (1918-like avian virus) carrying either the 1918 HA or PB2 gene. Both genes enhanced 1918-like avian virus replication, but only the mammalian host adaptation of the 1918-like avian virus through reassortment of the 1918 PB2 led to increased lethality in mice. We demonstrate that 1918 PB2 enhances immune and inflammatory responses concomitant with increased cellular infiltration in the lung.  We also show that 1918 PB2 expression results in the repression of both canonical and non-canonical Wnt signaling pathways which are crucial for inflammation mediated lung regeneration and repair.

overall_design: Five- to six-week-old female BALB/c mice (Jackson Laboratory) were used for the experiments. Isoflurane-anesthetized mice were intranasally inoculated with tenfold serial dilutions (three mice per dilution) of 1918, 1918-like avian, 1918 PB2/avian and 1918 HA/avian viruses. The dose required to kill 50% of mice (MLD50) was calculated using the Reed-Muench method. For analysis of virus growth and microarray profiling mice were intranasally inoculated with 10^4 PFU of virus (n=4/virus/timepoint) or PBS (n=3/timepoint). At days 1, 2 and 4 after infection, lungs were harvested from the infected mice. Lungs were processed for RNA extraction for microarray studies and virus titer determination.

first: Adriana

last: Forero

first: Jennifer

last: Go

first: Tokiko

last: Watanabe

first: Gongxun

last: Zhong

first: Nicolas

last: Tchitchek

first: Christian

last: Selinger

first: Juliet

last: Morrison

first: Laurence

last: Josset

first: Jean

last: Chang

first: Yoshihoro

last: Kawaoka


title: Profile of mouse Lewis lung carcinoma LLC1 cell line cultivated in 2-dimensional or 3-dimensional cell culture enriched with laminin rich extracellular matrix proteins

status: Public on Dec 10 2015

city: Vilnius

first: Vaidotas

last: Stankevicius

state: Lithuania

address: Santariskiu 1

country: Lithuania

institute: National Cancer Institute

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


title: Gene expression profile of mouse Lewis lung carcinoma cell line cultivated in 2-dimensional or 3-dimensional cell culture enriched with laminin rich extracellular matrix proteins.

summary: Obvious advantages of 3D cell culture model are the cell morphology better reflecting tissue cell morphology, the formation of zones of i) active proliferation, ii) quiescent viable cell zone and iii) necrotic zone, as well as formation of nutrition, oxygen and drug gradients better reflecting cellular environment in tissue. Nevertheless the 3D cultures are a model still not resembling full complexity of tumor tissue environment in vivo. Few obvious limitations of 3D cell cultures as cancer research model are the lack of vasculature, host immune response and other cell-cell interactions that occur between cancer and stromal cells in tumors. Recognized advantages and limitations of the 3D cell culture models, however do not suggest directly the areas of cancer biology where 3D models could be applied with highest success. Hence detailed analysis at the molecular level of 2D/3D cell cultures and tumors in vivo are needed to unlock the power of 3D cell culture model.  In order to elucidate which biological pathways of cancer cells in tumors are best resembled by the 3D cell culture model we have analyzed whole genome gene expression changes in mouse LLC1 cell line when cultured in 2D or laminin rich ECM 3D system.

overall_design: RNA was isolated 48h after growing in two different cell culture systems.

first: V

first: K

last: Suziedelis


title: KLF15- and glucocorticoid-dependent transcriptional responses in mouse muscle.

status: Public on Dec 01 2015

city: San Francisco

first: Saptarsi

last: Haldar

address: 1650 Owens St

institute: Gladstone Institute of Cardiovascular Disease

summary: Excessive or sustained glucocorticoid (GC) exposure causes muscle wasting. Paradoxically, moderate or transient GC exposure elicits ergogenic effects, evidenced by their widespread use as doping agents by endurance athletes and poorly understood efficacy in Duchenne muscular dystrophy (DMD), a genetic muscle wasting disease. While mechanisms underlying GC-mediated muscle wasting are well defined, the molecular basis for the latter remains unknown. In this arm of our studies, Wild-type (WT) and Klf15-/- (KO) mice were given the potent GC receptor agonist dexamethasone (dex) and quadriceps tissue was subjected to transcript expression profiling by cDNA microarrays.

overall_design: Total RNA was isolated from the quadriceps of KLF15 WT and KO mice 8 hours after treatment with dexamethasone or vehicle (4 animals per group) and hybridized to single-color Agilent 4x44K arrays to determine transcriptional responses to glucocorticoids and their dependence on KLF15 expression.

first: Alexander

last: Morrison-Nozik


title: The sRNA NsiR4 is involved in nitrogen assimilation control in cyanobacteria by targeting glutamine synthetase inactivating factor IF7

status: Public on Oct 20 2015

city: Freiburg

first: Stephan

last: Klähn

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

institute: University of Freiburg

summary: Glutamine synthetase (GS), a key enzyme in biological nitrogen assimilation, is regulated in multiple ways in response to varying nitrogen sources and levels. Here we show a small regulatory RNA, NsiR4 (nitrogen stress induced RNA 4), which plays an important role in the regulation of GS in cyanobacteria. NsiR4 expression in the unicellular Synechocystis sp. PCC 6803 and in the filamentous, nitrogen-fixing Anabaena sp. PCC 7120 is stimulated through nitrogen-limitation via NtcA, the global transcriptional regulator of genes involved in nitrogen metabolism. NsiR4 is widely conserved throughout the cyanobacterial phylum, suggesting a conserved function. In silico target prediction, transcriptome profiling upon pulse overexpression and site-directed mutagenesis experiments using a heterologous reporter system showed that NsiR4 interacts with the 5’UTR of gifA mRNA, which encodes glutamine synthetase inactivating factor IF7. In Synechocystis, we observed an inverse relationship between the levels of NsiR4 and the accumulation of IF7 in vivo. This NsiR4-dependent modulation of gifA (IF7) mRNA accumulation influenced the glutamine pool and thus NH4+ assimilation via glutamine synthetase. As a second target, we identified ssr1528, a hitherto uncharacterized nitrogen-regulated gene. Competition experiments between wild type and an NsiR4 knock-out mutant showed that the lack of NsiR4 led to decreased acclimation capabilities of Synechocystis towards oscillating nitrogen levels. These results suggest a role for NsiR4 in the regulation of nitrogen metabolism in cyanobacteria, especially for the adaptation to rapid changes in available nitrogen sources and concentrations. NsiR4 is the first identified bacterial sRNA regulating the primary assimilation of a macronutrient.

overall_design: We compared gene expression of Synechocystis sp. PCC 6803 WT with strains showing overexpressed (NsiR4oex) or abolished (∆nsiR4) and re-estbalished (∆nsiR4::oex) NsiR4 expression. For each strain, 2 biological replicates were analyzed. All cultures were supplemented with 2 µM CuSO4 and after 12 hours samples were taken for RNA extraction.

first: Christoph

last: Schaal

first: Jens

last: Georg

first: Desirée

last: Baumgartner

first: Gernot

last: Knippen

first: Martin

last: Hagemann

first: Alicia

last: Muro-Pastor

first: Wolfgang

last: Hess


title: gene expression analysis in Pbx1; Emx1-cre mutant cortex at embryonic day 15.5

status: Public on Nov 10 2015

city: san francisco

first: olga

last: golonzhka

state: CA

address: 1550 4th street

department: psychiatry

institute: UCSF

summary: the goal of the study was to compare gene expression between control and Pbx1; Emx1-cre mutant corteces at e15.5

overall_design: E15.5 whole cortex was dissected for the analysis. Control embryo genotype was Pbx1F/+. Mutant embryo genotype was Pbx1F/-; Emx1-cre. 4 corteces of each genotype were used for the analysis: 4 controls and 4 mutants, 8 samples total.

first: John

middle: L

last: Rubenstein

first: Olga

last: Golonzhka


title: gene expression analysis in Pbx1; Emx1-cre mutant cortex at embryonic day 12.5

summary: the goal of the study was to compare gene expression between control and Pbx1; Emx1-cre mutant corteces at e12.5

overall_design: E12.5 whole cortex was dissected for the analysis. Control embryo genotype was Pbx1F/+. Mutant embryo genotype was Pbx1F/-; Emx1-cre. 4 corteces of each genotype were used for the analysis: 4 controls and 4 mutants, 8 samples total.


title: Murine chondrocytes: Control vs Ad-Epas1 infected

status: Public on Oct 02 2015

city: Gwangju

first: Jang-Soo

last: Chun

department: School of Life Science

country: South Korea

institute: Gwangju institute of science and technology

summary: Transcriptional profiling of mouse chondrocytes comparing chondrocytes infected with empty adenovirus and Epas1 adenovirus. RNA was extracted from each chondrocytes. We used microarrays to determine the effect of Epas1 overexpression on chondrocytes and identify the noble regulatory molecules during osteoarthritic pathogenesis.

overall_design: Two-condition experiment, Mock vs. Ad-Epas1 chondrocytes. Biological replicates: 4 mock adenoviral infected replicates, 4 Ad-Epas1 infected replicates.

first: Je-Hwang

last: Ryu


title: Gene expression of mouse intestine treated with azoxymethane and/or St. John's wort

status: Public on Oct 01 2015

first: yan

last: cai

summary:
The aim of this study was to examine the effects of dietary supplementation of St John’s wort extract on azoxymethane-induced colorectal carcinogenesis in mice. Microarray data showed atttenuation of NF-kB and ERK-mediated pathway in colon epithelium by St. Jone's wort suggesting that the anti-inflammatory effect is a possible cancer-preventing mechanism induced by St. Jone's wort.
Gene expression will be compared between mice with the control vs. St. Jone's wort.

overall_design: Six-condition experiment, CSN vs SSN vs CAN vs SAN vs CAT vs.SAT Biological replicates: 3CSN, 3SSN, 3CAN, 3SAN, 3CAT and 3SAT samples.

first: Soumen

last: Manna

first: Naoki

last: Tanaka

first: Yan

last: Cai

first: Tsutomu

last: Matsubara

first: Frank

last: Gonzalez


title: Gene expression of hepatocyte-specific Mcl-1 ko mice

status: Public on Dec 07 2015

city: Zürich

first: Yannick

last: Boege

address: Schmelzbergstrasse 12

department: Institute for Surgical Pathology

country: Switzerland

institute: UniversityHospital Zürich

summary:
Gene expression from livers of knock-out, hemizygous and wild-type mice at the age of , 8 and 12 months. Including tumor and non-tumor tissue of the same animals.
AlbCre negative littermates were used as wild type controls.

overall_design: The hepatic gene expression of mice carrying a hepatocyte specific deletion of the anti-apoptotic protein Mcl-1 was analyzed at various age. Expression was compared between knock-out, hemizygous and wild-type littermates as well as between tumor and corresponding non-tumor tissue.

last: Böge

first: Mathias

last: Heikenwälder


title: microRNA-mediated GALNT3 upregulation facilitates mucin production and viral replication in influenza A virus-infected respiratory epithelial cells

status: Public on Dec 08 2015

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Viral infections affecting the upper or lower respiratory tract induce mucin production in the epithelial surfaces of the respiratory cells. However, a little is known about how mucins are produced on the surfaces of respiratory epithelial cells and affects viral replication. In the course of the investigation of the cellular responses in the early stage of Influenza A virus (IAV) infection, we found that two miRNAs, miR-221 and miR-17-3p, which target the mRNA of GalNAc transferase 3 (GALNT3), are rapidly down-regulated as early as 1.5 h post-infection.

overall_design: To understand the early host cell responses to the IAV infection, we performed miRNA microarray analysis using a human alveolar adenocarcinoma cell line, A549 cells, infected with influenza A/Puerto Rico/8/34 H1N1 (PR8) virus. We isolated the cellular RNAs at 0.5, 1.5 and 4.5 h post-infection and detected significant changes in the global profile of miRNA expression after infection with IAV. mouse embryonic fibroblasts. Each sample was run in duplicate.

first: Tomoyuki

last: Honda


title: Transcriptome profiling of Arabidopsis thaliana leaves infected with Botrytis cinerea at different times of the day

city: York

first: Katherine

last: Denby

address: Department of Biology

institute: University of York

summary: Arabidopsis thaliana exhibits differential susceptibility to the fungal pathogen Botrytis cinerea depending on the time of day that infection occurs. We hypothesised that this is driven by teh circadian clock and that differences in the amplitude or speed of the plant defence response will underlie the difference in susceptiblity. A major component of the defence response is transcriptional reprogramming, hence we investigated whether the transcriptional response to B. cinerea infection differs following inoculation at subjective dawn or night (the points of greatest difference in susceptiblity) under constant light conditions.

overall_design: Arabidopsis thaliana (ecotype Col-0) plants were grown for four weeks under 16h:8h light:dark conditions and then moved into constant light 24 hours prior to infection. Detached leaves were inoculated with Botrytis cinerea spores (5 x 104 spores mL-1) or mock-inoculated at subjective dawn or subjective night. Leaves were harvested for transcriptome profiling at 18 and 22 hours after inoculation. Four individual leaves were pooled for one sample. Two technical replicates were carried out for each sample. Gene expression was analysed using NimbleGen 12 x 135K microarrays, designed for the TAIR10 genome. Data was normalised using the Robust Multichip Averaging algorithm.

first: Robert

last: Ingle


title: 2,3,7,8-Tetrachlorodibenzo-p-Dioxin (TCDD) Alters Lipid Metabolism and Depletes Immune Cell Populations in the Jejunum of C57BL/6 Mice

city: East Lansing

first: Timothy

last: Zacharewski

state: Michigan

address: 603 Wilson Road

department: BMB

institute: Michigan State University

summary: Dose-dependent jejunal epithelial gene expression was examined following repeated exposure (every 4 days for 28 days) to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). These data were used to examine the effect of repeated TCDD exposure on jejunal differential gene expression, in order to investigate the role of the jejunum in TCDD-elicited steatohepatitis in C57BL/6.

overall_design: Three biological replicates for each dose (0.01, 0.03, 0.1, 0.3, 1, 3, 10, 30) of TCDD and sesame oil vehicle

first: Kelly

last: Fader

first: Rance

last: Nault

first: Dustin

last: Ammendolia

first: Jack

last: Harkema

first: Kurt

last: Williams

middle: B

last: Crawford

first: Norbert

middle: E

last: Kaminski

first: Dave

last: Potter

first: Bonnie

last: Sharratt


title: KLF15

first: Saptarsi

last: Haldar

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

overall_design: Refer to individual Series


title: Integrated transcriptomic and metabolomic characterization of the low-carbon response using an ndhR mutant of Synechocystis sp. PCC 6803

first: Stephan

last: Klähn

summary: The acquisition and assimilation of inorganic carbon (Ci) represents the largest flux of inorganic matter in photosynthetic organisms, and, hence it is tightly controlled. We studied the Ci-dependent transcriptional and metabolic regulation in the Synechocystis sp. PCC 6803 wild type compared to a DndhR mutant that is defective in the main transcriptional repressor for Ci acquisition genes, NdhR (CcmR). The analysis revealed that many protein-coding genes, which are normally repressed in presence of high CO2 concentrations (HC), were already strongly expressed in ∆ndhR, whereas other genes were strongly down-regulated in mutant cells pointing towards a possible activating role of NdhR. A conserved NdhR-binding motif was identified in the promoters of de-repressed genes. Interestingly, the expression of some NdhR-regulated genes remained further inducible under low CO2 conditions (LC) indicating the involvement of additional, NdhR-independent Ci-regulatory mechanisms. Intriguingly, we also found the expression of 52 asRNAs and 34 potential ncRNAs affected by Ci supply, but most of them appear not to be regulated by NdhR and thus could contribute to NdhR-independent carbon-regulation. In contrast to the transcriptome, the metabolome in ∆ndhR cells appeared similar to that of wild-type cells under HC conditions. This observation and the delay of the metabolic responses to the LC-shift in ∆ndhR, specifically the lack of transient increases in intermediates of photorespiratory pathways comprising 2-phosphoglycolate, glycolate and glycine, supports the hypothesis that the deregulation of gene expression in the DndhR mutant successfully pre-acclimates cyanobacterial cells under HC conditions to a low Ci supply.

overall_design: We analyzed gene expression in Synechocystis sp. PCC 6803 WT as well as a ndhR mutant at HC (5% CO2) as well as 3h and 24h after shift to LC (air). For each strain (WT/∆ndhR) and each sampling point, 2 biological replicates were analyzed, however, the ∆ndhR mutant at 24h after LC shift was analyzed in triplicates.

first: Isabel

last: Orf

first: Doreen

last: Schwarz

first: Jasper

last: Matthiessen

first: Joachim

last: Kopka

first: Wolfgang

last: Hess

first: Martin

last: Hagemann


title: The Tsk2/+ mouse fibrotic phenotype is due to a gain-of-function mutation in the PIIINP segment of the Col3a1 gene

status: Public on Sep 24 2015

city: Hanover

first: Michael

last: Whitfield

state: New Hampshire

address: 710 Remsen 74 College Street

department: Genetics

institute: Geisel School of Medicine at Dartmouth

summary: Systemic sclerosis (SSc) is a polygenic, autoimmune disorder of unknown etiology,  characterized by the excessive accumulation of extracellular matrix (ECM) proteins, vascular  alterations, and autoantibodies. The tight skin (Tsk)2/+ mouse model of SSc demonstrates signs  similar to SSc including tight skin and excessive deposition of dermal ECM proteins. By linkage  analysis, we mapped the Tsk2 gene mutation to less than 3 megabases on chromosome 1. We  performed both RNA sequencing of skin transcripts and genome capture DNA sequencing of the  region spanning this interval in Tsk2/+ and wild-type littermates. A missense point mutation in  the procollagen III amino terminal propeptide segment (PIIINP) of Col3a1 was found to be the  best candidate for Tsk2, so both in vivo and in vitro genetic complementation tests were used to  prove that this Col3a1 mutation is the Tsk2 gene. All previously documented mutations in the  human Col3a1 gene are associated with Ehlers-Danlos syndrome, a connective tissue disorder  that leads to a defect in type III collagen synthesis. The Tsk2 point mutation is the first  documented gain-of-function mutation associated with Col3a1, which leads instead to fibrosis.  This discovery provides insight into the mechanism of skin fibrosis manifested by Tsk2/+ mice.

overall_design: For the transfection experiment, three Col3a1 knockout fibroblast transfected with WT Col3a1 samples and three Col3a1 knockout fibroblast transfected with Tsk2 Col3a1 samples were used. For the 4-week female, three WT mice and three Tsk2 total skin RNA were used.

first: Kristen

last: Long

first: Zhenghui

last: Li

first: Chelsea

last: Burgwin