title: Differential Molecular Effects of Imiglucerase and Velaglucerase Alfa in Gaucher Disease Mice [Affymetrix]

summary: Gaucher disease type 1 is an inborn error of metabolic disease with the defective activity of the lysosomal enzyme acid b-glucosidase (GCase). Enzyme replacement/reconstitution therapy (ERT), infusions with purified recombinant GCases, is efficacious in reversing hematologic, hepatic, splenic, and bony disease manifestations in Gaucher type 1 patients. However, the tissue specific molecular events in Gaucher disease and their response to therapy are not known yet. To explore the molecular events underlying GCase treatment, we evaluated the tissue-specific gene expression profiles and molecular responses in our Gaucher disease mouse model, which were treated with two FDA approved commercially available GCases, imiglucerase (imig) and velaglucerase alfa (vela). Using microarray and mRNA-Seq techniques, differentially expressed genes (DEGs) were identified in the spleen and liver by the direct comparison of imig- vs. vela-treated mice. Among them three gene expression networks were derived from these spleens: 1) cell division/proliferation, 2) hematopoietic system and 3) inflammatory/macrophage response. Our study showed the occurrence of differential molecular pathophysiologic processes in the mice treated with imig compared with vela even though these two biosimilars had the same histological and biochemical efficacy

overall_design: 9V/null mice (Gaucher mouse model) were injected weekly via tail vein with 60U/kg/wk of imig or vela for 8 wks and were sacrificed one week after the injection for RNA isolation from different tissues like liver, lung and spleen.

first: Mehdi

first: Gregory

last: Grabowski


title: Cell Reprogramming experiment (reprogramming cardiac fibroblasts into cardiomyocytes)

status: Public on Jul 26 2013

city: San Francisco

first: Gladstone

last: Bioinformatics

state: CA

address: 1650 Owens St

department: Data Science and Biotechnology

country: USA

institute: Gladstone Institutes

summary: Cells were reprogrammed from cardiac fibroblasts to cardiomyocytes, in various conditions. These are the iCM cells (induced cardiomyocytes). There are both human and mouse arrays here, as seen below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Microarrays were used to measure the overall degree to which cellular repogramming was successful, by comparing the reprogrammed cells to reference populations of cardiomyocytes (CMs) and cardiac fibroblasts (CFs).

first: Jidong

last: Fu

first: Li

last: Quan


title: The gene expression upon dominant negative form of GAS2 (GAS2DN) in MEG-01 cells

status: Public on Jul 25 2013

city: ShangHai

first: BaoHong

last: Liu

address: 100 QinZhou Road

country: China

institute: ShangHai center for bioinformation and technology

summary:
GAS2DN could suppress the growth of chronic myeloid leukemia cells, including K562, MEG-01 and CD34+ cells from patients. In addition, GAS2DN inhibited the tumorigenic ability of MEG-01 cells in nude mice. To understand the molecular insight of this inhibitory effect of GAS2DN, global gene expression were performed.
The control and GAS2DN-transduced MEG-01 cells were used for microarray analysis.

overall_design: Three biological independent extracts of control and GAS2DN-transduced cells were pooled together with equal amount, and then the pooled samples were compared with Affymetrix chips.

first: Yun

last: Zhao


title: Identification of Arabidopsis thaliana PRR7 regulated clock components and circadian outputs through genome-wide binding sites analysis

status: Public on Jul 27 2013

city: East Lansing

first: Tiffany

middle: L

state: Michigan

address: 3260 Molecular Plant Sciences Building

department: Plant Biology

institute: Michigan State University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We identified genome-wide PRR7 targets by conducting chromatin immunoprecipitation combined with high-throughput sequencing.

overall_design: Lines include prr7-3 and prr7-3 PRR7::HA-PRR7 #151, and we conducted immunoprecipitations using an anti-HA antibody.

first: Jenny

last: Carlsson

first: Linsey

last: Newton

first: Tomomi

last: Takeuchi

first: Eva

middle: M

last: Farre


title: Genomic topography of HDACi-induced hyperacetylation of hippocampal chromatin [ChIP-Seq]

status: Public on Jul 09 2013

city: Sant Joan d'Alacant

first: Angel

last: Barco

state: Alicante

address: Av. Santiago Ramón y Cajal

country: Spain

institute: Instituto de Neurociencias (UMH-CSIC)

summary: Histone deacetylase inhibitors (HDACis) have been shown to potentiate hippocampal-dependent memory and synaptic plasticity and to ameliorate cognitive deficits and degeneration in animal models for different neuropsychiatric conditions. However, the impact of these drugs on hippocampal histone acetylation and gene expression profiles at the genomic level, and the molecular mechanisms that underlie their specificity and beneficial effects in neural tissue, remains obscure. Here, we mapped four relevant histone marks (H3K4me3, AcH3K9,14, AcH4K12 and pan-AcH2B) in hippocampal chromatin and investigated at the whole-genome level the impact of HDAC inhibition on acetylation profiles and basal and activity-driven gene expression. HDAC inhibition caused a dramatic histone hyperacetylation that was largely restricted to active loci pre-marked with H3K4me3 and AcH3K9,14. In addition, the comparison of Chromatin immunoprecipitation sequencing and gene expression profiles indicated that Trichostatin A-induced histone hyperacetylation, like histone hypoacetylation induced by histone acetyltransferase deficiency, had a modest impact on hippocampal gene expression and did not affect the transient transcriptional response to novelty exposure. However, HDAC inhibition caused the rapid induction of a homeostatic gene program related to chromatin deacetylation. These results illuminate both the relationship between hippocampal gene expression and histone acetylation and the mechanism of action of these important neuropsychiatric drugs.

overall_design: Examination of 4 different histone modifications in the hippocampus of vehicle (DMSO/Saline) or HDACi TSA (2.4 mg/kg)-treated mice. Samples were obtained 30 min after intraperitoneal administration of either TSA or Vehicle. NOTE: The ChIPseq experiments described here and those presented in the series GSE44854 were performed in paralell. Therefore, some control samples are part of both datasets (GSM1062434, GSM1062437, GSM1062441 and GSM1062442).

first: Jose

middle: P

last: LOPEZ-ATALAYA

last: BARCO


title: Gene expression profiling of neural HDAC inhibition

overall_design: We performed transcriptional profiling of hippocampal samples from willd-type and cbp+/- mice (C57/DBA F1 hybrid females). Treatments consisted in intraperioneal treatment with HDACi TSA (2.4 mg/kg) o vehicle (DMSO/Saline). Samples were obtained 75 min after TSA administration. Novelty consisted of placing an individual animal in a white plexiglas square box containing plastic tubing and small toys for 1h. For TSA and Novelty condition animals were injected with TSA and 15 min later were allowed to exploration in the Novelty paradigm. We obtained quintuplicate (standar housing) and triplicate (novelty; TSA; and novelty + TSA) samples containing total RNA from the hippocampi of 3-4 three-month old females of either genotype (cbp+/- and wild-type mice) (in total >100 mice were used in the experiment). NOTE: The microarray experiments described here and those presented in the series GSE30880 were performed in paralell. Therefore, control samples (wt and cbp+/-) are part of both datasets.

last: Lopez-Atalaya


title: microRNA Dysregulation in Human Prostate Cancer Cell Model (M12 and P69)

status: Public on Aug 15 2013

city: Richmond

first: William

middle: Thomas

last: Budd

state: VA

address: 401 College Street Room 1-112

department: Department of Biochemistry and Molecular Biology

institute: Virginia Commonwealth University

summary: An isogenic prostate cancer cell model was used to profile miRNA changes that contribute to the tumorigenic state of prostate cancer. P69 cells are an SV40 large T antigen immortalized cell line that is poorly tumorigenic and non-metastatic. The M12 derivative was derived from an in vivo selection process using nude, athymic mice. Immortalized cells were cultured and used to extract RNA and probed against the human miRNA panel from Exiqon. There were a total of 186 miRNAs that were at least two fold differentially regulated .

overall_design: Two human prostate cancer cell lines were used to evaluate miRNA expression differences contributing to oncogenesis. Two replicates were performed and the data presented as the mean fold difference between P69 and M12.

middle: T

first: Sarah

last: Seashols

first: Danielle

last: Weaver

first: Cyriac

last: Joseph

first: Zendra

last: Zehner


title: Comparative transcriptome analysis of various adipose depots in Hanwoo

city: Seoul

first: HYEONGMIN

last: KIM

address: Seoul National Univ., Daehak-dong, Gwanak-gu,

department: College of Agriculture Sciences

country: South Korea

institute: Seoul National University

type: Expression profiling by high throughput sequencing

summary:
*Background: Adipocytes mainly function as energy storage and endocrine cells.  The amount and distribution of fat are important factor that influence the meat quality in the beef industry.  Fat depot can be found around internal organ (ometal), beneath the skin (subcutaneous), and between muscles (intramuscular).  Different adipose depot showed the biological and genetic difference depending on their location.  This inter-depot variation might be influenced by the inherent genetic programing for development of adipose depots.  In this study, we used RNA-seq data to investigate the difference in transcriptome of various adipose depots in Hanwoo.
*Results: Using RNA-seq, we identified 5797, 2156, and 5455 DEGs in the comparison between OI, OS, and IS respectively (FDR<0.01) and found 853, 48, and 979 DEGs specific to subcutaneous, intramuscular and omental fat respectively.  DEGs in intramuscular fat were highly enriched the metabolism related pathways compared to other fat depots. DEGs specific to the omental fat is significantly enriched in PPAR signaling pathway and cell-junction related pathway.  In subcutaneous fat, cytokine-cytokine receptor interaction with chemokines (CXC and CC subfamily) was the most significantly enriched the pathways.  Interestingly, melanogenesis pathway was associated with the subcutaneous depot.  Even though the adipose tissues shared the same pathways for adipocyte differentiation, the regulation of genes were different based on the depot.
*Conclusions: We comparatively analyzed the transcripome profile from different adipose tissues using NGS and identified DEGs between adipose depot and specific to depot in Hanwoo animals.  The functional annotation analysis of DEGs found that transcriptome profile difference in various adipose tissue of intramuscular, subcutaneous, and ometal fat.

overall_design: whole mRNA sequencing profiles of nine Korean native cattle (nine profiles of omental fat tissue, nine profiles of intramuscular fat tissue, nine profiles of subcutaneous fat tissue and eight profiles of muscle tissue)

first: Hyun-Jeong

last: Lee

first: Mi

last: Jang

first: Heebal

last: Kim

first: Bo-Young


title: Comparing gene expression in CD5+CD1dhigh and CD5-CD1dhigh B cells

status: Public on Jun 30 2013

city: Ann Arbor

first: Matthew

last: Klinker

state: MI

address: 109 Zina Pitcher Place, 4368

institute: University of Michigan

summary:
We have previously observed that regulatory B cells expressing the apoptosis-inducing surface molecule Fas ligand were enriched in the B cell fraction denoted by a surface phenotype of CD5+CD1dhigh. To identify potential growth factors, transcriptional regulators, or surface markers that might better characterize regulatory B cells, we compared global gene expression by microarray in two B cells subsets isolated by FACS.
Splenocytes from 20 DBA/1 male mice were harvested, pooled, and CD19+ B cells were isolated by positive selection using MACS. B cells were then stained for CD5 and CD1d and sorted by FACS into CD5+CD1dhigh and CD5-CD1dhigh populations.

overall_design: Single replicates of both CD5+CD1dhigh and CD5-CD1dhigh B cells from pooled mouse splenocytes were isolated and assay using the Affymetrix GeneChip Mouse 430 2.0 Array.

first: Steven

middle: K

last: Lundy

middle: W


title: Genomic targets, and histone acetylation and gene expression profiling of neural HDAC inhibition

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

overall_design: Refer to individual Series


title: Giardia lamblia WB: 5'5npac control vs pPTopoII

city: Taipei

first: Chin-Hung

last: Sun

address: Department of Parasitology, College of Medicine, National Taiwan University

department: Department of Parasitology

country: Taiwan

summary: Transcriptional profiling of Giardia lamblia WB comparing control 5'5npac cells with pPTopoII cells.

overall_design: Two-condition experiment 5'5npac cells with pPTopoII cells.


title: Plasma miRNA profiling of nasopahryngeal carcinoma patients

status: Public on Jul 02 2013

city: Guangzhou

first: juan

last: lu

address: guangzhou da dao bei No. 1838

department: Department of ENT

institute: Nanfang hospital

summary: We performed miRNA microarray analysis to find differentially expressed miRNAs between nasopharyngeal carcinoma patients and normal control subjects

overall_design: In this study, 20 nasopharyngeal carcinoma patients and 10 normal control subjects were selected to collect plasma samples and perform miRNA microarray profiling

first: Juan

last: Lu


title: Gene expression microarray analysis on hippocampus of Schnurri-2 knockout and wild-type control mice

status: Public on Aug 13 2013

city: Toyoake

first: Juzoh

last: Umemori

address: 1-98 Kutsukakecho, Dengakugakubo

country: Japan

institute: Fujita Health University

summary: Schnurri-2 (Shn-2), an NF-kappa B site-binding protein, tightly binds to the enhancers of major histocompatibility complex (MHC) class I genes and inflammatory cytokines, which have been shown to harbor common variant single nucleotide polymorphisms associated with schizophrenia. Shn-2 knockout mice show behavioral abnormalities that strongly resemble those of schizophrenics. We performed gene expression microarray analysis of hippocampi from Shn-2 knockout and wild-type control mice.

overall_design: Hippocampal RNA isolated from four Shn-2 knockout and four control wild-type mice were compared.

first: Keizo

last: Takao


title: Analysis of miR-203 regulated genes during IFNalpha treatment

status: Public on Jun 20 2013

city: Evanston

first: William

last: Buggele

state: IL

address: 2200 Campus Dr.

institute: Northwestern University

summary: The goal of this experiment was to determine gene expression changes during IFNα treatment as the result of expression or inhibition of miR-203 in A549 cells.

overall_design: The gene expression profiling experiment was performed with 4 groups (mock infected, IFNα treated, IFNα treated in the presence of exogenous miR-203, and IFNα treated in the presence of miR-203 inhibitor) with 3 biological replicates for each group.  Total RNA was purified from A549 cells that were untreated of treated with IFNα (1000 units/mL) alone or in the presence of miR-203 mimic or inhibitor for 10 hours.

middle: A


title: Histone deacetylation-dependent and -independent transcriptional dysregulation in early-onset polyglutamine disease

first: Angel

last: Barco

summary: Transcriptional dysregulation is an important early feature of polyglutamine diseases. One of its proposed causes is defective neuronal histone acetylation, but important aspects of this hypothesis, such as the precise genomic topography of acetylation deficits and the relationship between transcriptional and acetylation alterations at the whole-genome level, remain unknown. The new techniques for the mapping of histone posttranslational modifications at genomic scale enable such global analyses and are challenging important assumptions concerning the role of specific histone modifications in gene expression. We examined here the genome-wide correlation of histone acetylation and gene expression defects in a mouse model of early-onset Huntington’s disease. Our analyses identified hundreds of loci that were hypoacetylated for H3K9,14 and H4K12 in the chromatin of these mice. Surprisingly, few genes with altered transcript levels in mutant mice showed significant changes in these acetylation marks and vice versa. Our screen, however, identified a subset of genes in which H3K9,14 deacetylation and transcriptional dysregulation concur. Genes in this group were consistently affected in different brain areas, mouse models and tissue from patients, which suggests a role in the etiology of this pathology. Overall, the combination of histone acetylation and gene expression screenings demonstrates that histone deacetylation and transcriptional dysregulation are two early, largely independent, manifestations of polyglutamine disease and suggests that additional epigenetic marks or mechanisms are required for explaining the full range of transcriptional alterations associated with this disorder.

overall_design: Examination of 2 different histone modifications in the hippocampus of wild-type and HD mice (PrP-htt-N171-82Q (Schilling et al., 1999)). Samples were obtained from 10 week old mice.

first: Jose

last: LOPEZ-ATALAYA

first: Luis

last: VALOR

last: BARCO


title: Gene expression profile of N171-HD82Q hippocampus and cerebellum.

summary:
Transcriptional dysregulation is an important early feature of polyglutamine diseases. One of its proposed causes is defective neuronal histone acetylation, but important aspects of this hypothesis, such as the precise genomic topography of acetylation deficits
and the relationship between transcriptional and acetylation alterations at the whole-genome level, remain unknown. We examined here the genome-wide correlation of histone acetylation and gene expression defects in a mouse model of early-onset Huntington’s disease.

overall_design: Hippocampi and cerebella were dissected from 10- and 20-weeks old transgenic mice alongside with wild-type littermates. Total RNA was extracted and hybridized to Affymetrix MoGene 1.0 ST arrays. One array consisted on a pool of 3-4 RNA samples and three arrays were used per condition (genotype-tissue-age).  This is the gene expression component of the study only.

last: Valor

last: Lopez-Atalaya


title: Genomic landscape of transcriptional and epigenetic dysregulation in a mouse model of early onset Huntington's disease


title: Early transcriptional changes in Zea mays seedlings exposed to Z-3-hexenol

status: Public on Jun 15 2013

city: San Antonio

first: Jurgen

last: Engelberth

state: Texas

address: One UTSA Circle

department: Biology

institute: University of Texas at San Antonio

summary: Z-3-Hexenol and other green leaf volatiles have been known to induce defense-related gene expression. Here we investigated the early transcriptional changes in response to Z-3-hexenol.

overall_design: 3-week-old Zea mays seedling (inbred line B73) was exposed to pure Z-3-hexenol (1.5 μM) in a glass cylinder. Controls were treated likewise without the addition of Z-3-hexenol. Plants were exposed for 20 min and 60 min. The second leaf was then cut and shock-frozen in liquid N2 and then stored at -85°prior to RNA extraction. 3 individual leaves were pooled for 1 biological replicate. 3 biological replicates were performed for each treatment, with one dye swap (second sample).


title: Bj_indole-3-acetic acid 1 mM vs. non-treatment

status: Public on Jun 01 2013

city: Arlington

first: Woo-Suk

last: Chang

state: TX

address: 501 S. Nedderman Dr. , Life Science Building 216

institute: University of Texas at Arlington

summary: Transcriptional profiling of mid-logarithmic phase cultures exposed to a 1 mM shock treatment of indole-3-acetic acid for 3 hours.

overall_design: Three independent biological replicates were prepared for cells shocked with 1 mM  indole-3-acetic acid during growth and for non-treated cells. A total 6 arrays which includes dye swap were analyzed.

first: Andrew

middle: J

last: Donati

first: Hae-In

last: Lee


title: Peripheral blood mononuclear cell gene expression in chronic obstructive pulmonary disease

status: Public on May 06 2013

city: Denver

first: Grant

last: Hughes

state: CO

address: 1400 Jackson St

institute: University of Colorado/National Jewish

summary:
Expression data were generated on 136 subjects from the COPDGene® study using Affymetrix microarrays. Multiple linear regression with adjustment for covariates (gender, age, body mass index, family history, smoking status, pack years) was used to identify candidate genes and Ingenuity Pathway Analysis was used to identify candidate pathways.
Candidate genes identified included those that play a role in the immune system, inflammatory responses, and sphingolipid metabolism. Many of our final candidate genes also show an association with related disease phenotypes such as emphysema, gas trapping, and 6-minute walk distance.

overall_design: 42 control subjects and 94 subjects with varying severity of COPD had PBMC gene expression profiles generated.  All subjects are non-hispanic white, current or former smokers.

first: Russell

last: Bowler

first: Katerina

last: Kechris

first: Timothy

last: Bahr


title: Crosstalk between renal tumor suppressors: FLCN contributes to VHL tumor suppressing activity in renal cancer

status: Public on May 20 2013

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary:
Renal cancer accounts for 2% to 3% of all adult malignancies in the US. In 2011 more than 64,770 new cases and 13,000 deaths were reported and the incidence is steadily increasing by 2.5% per year. Clear cell renal carcinoma (ccRCC) represents the majority (85% to 90%) of adult kidney cancers and is the most malignant. This cancer is characterized by an early loss of the von Hippel-Lindau tumor suppressor (VHL) on short arm of chromosome 3 in the majority of tumors (80%).  It is a classic knowledge that loss of VHL results in an increased accumulation and activity of the hypoxia-inducible transcription factor (HIF), which in turns activates expression of genes promoting tumor growth. In that respect, induction of angiogenic factors induces blood flow through the tumors and delivery of nutrients and oxygen to cancer cells, while induction of genes inducing anaerobic glycolysis supports adaptation to reduced nutrients availability and shifts towards metabolic pathways promoting tumor growth. Recently we have discovered another tumor suppressing pathway regulated by VHL. We found that VHL is a major regulator of the process of macroautophagy (autophagy) (ref).  We identified that VHL induces expression of a microRNA, miR-204, which in turn inhibits activity of a major regulator required for the formation of autophagosome, LC3B.  LC3B-mediated autophagy is necessary for the ccRCC tumor growth, and inhibition of this process by VHL and miR-204 significantly contributes to the tumor suppression. Most importantly, we discovered that VHL by inhibiting activity of HIF, induced expression and activity of an LC3B paralog, LC3C. In contrast to LC3B, LC3C acts as a tumor suppressor, indicating the specificity and complexity of different autophagic programs. Integrating these novel data with the established role of VHL in regulating angiogenesis produces a more global picture of VHL as a master tumor suppressor that regulates nutrient access for renal cancer cells from both extracellular and intracellular sources.
In the process of searching for other genes induced by VHL that could participate in the tumor suppressing activity of VHL, we discovered that reconstitution of VHL in RCC cells induces enrichment of genes expressed from the Smith-Magenis locus (SM), located on the short arm of chromosome 17p11.2. Smith-Magenis syndrome is a complex neurobehevioural disorder, characterized by intellectual impairment, craniofacial and skeletal anomalies and sleep disturbance. Recently, deletions or mutations of one specific gene in the SM locus, RAI1, (retinoic acid induced 1), were shown to be responsible for the syndrome. Interestingly, this locus contains another kidney tumor suppressor gene, folliculin (FLCN), of which activity is lost in the genetic dominant disorder, Birt-Hogg-Dube syndrome (BHD). BHD is characterized by skin fibrofolliculomas, pulmonary cysts and spontaneous pneumothorax, as well as renal cancer of mixed histological types, including chromophobe, oncocytic, clear cell and papillary type. Here we show that VHL regulates expression of FLCN, and in turn FLCN contributes to the VHL-mediated suppression of tumor growth.

overall_design: Two-condition experiment, VHL(-) vs. VHL(+). 4 biological replicates in each group. Two dual-channel arrays with VHL(+) on Cy5 and VHL(-) on Cy3, and two dual-channel arrays with flipped samples.

first: Prabhat

last: Bastola

first: Yiwen

last: Startton

first: Olga

last: Mikhaylova

first: Emily

last: Kellner

first: Ying

last: Yi

first: Maureen

last: Startor

first: Jacek

last: Biesiada

first: Jarek

last: Meller

first: Maria

middle: F

last: Czyzyk-Krzeska


title: ChIP-chip data for transcription factor binding in white and opaque cell types of Candida albicans

status: Public on May 01 2013

first: Aaron

last: Hernday

state: Ca

institute: UC San Francisco

type: Genome binding/occupancy profiling by genome tiling array

summary:
The human fungal pathogen Candida albicans can switch between two phenotypic cell types, termed “white” and “opaque.” Both cell types are heritable for many generations, and the switch between the two types occurs epigenetically, that is, without a change in the DNA sequence of the genome. Previous work identified six key transcriptional regulators important for white-opaque switching: Wor1, Wor2, Wor3, Czf1, Efg1, and Ahr1. In this work, we use a combination of genetic and genome-wide approaches to explore the topology of the transcriptional network that specifies each of the two cell types, and governs the ability to switch between them. In particular, we use a combination of genome-wide chromatin immunoprecipitation and gene expression profiling to determine the direct and indirect regulatory interactions that form the switch network. The six regulators are arranged together in a complex transcriptional network, and we propose that the topology of this network is responsible for both the epigenetic maintenance of the white and opaque states and for the switching between them.
Chromatin IP's were performed using the protocol described by Hernday et al (Methods Enzymol. 2010;470:737-58. ).  Briefly, log phase cultures were crosslinked with formaldehyde prior to cell lysis, chromatin shearing, and transcription-factor immunoprecipitation.  Recovered DNA was amplified, dye-coupled, and competitively hybridized to a 244k-probe tiling array with a non-enriched genomic DNA reference.

overall_design: Immunoprecipitated chromatin was hybridized against a non-enriched genomic DNA reference to identify transcription-factor binding sites


title: Impact of sucrose on the tolerance of phenanthrene-phytoremediation

status: Public on Jun 28 2013

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary:
au10-04_phytoremediation; impact of sucrose on the tolerance of phenanthrene
Effect of phenanthrene and sucrose - We test 3 conditions plants non-treated (C or t0), plants treated with phenanthrene (P) and plants tread with phenanthrene and sucrose (S).
The plants were grown on MS/2 media for 17 days and then transferred on the corresponding condition. We took a sample of 30 plants at different times (0, 30 min, 2h, 4h, 8h and 24h).

overall_design: 22 dye-switch - treated vs untreated comparison

first: Richard

last: Berthome

first: Delphine

last: Gey

first: Sandrine

last: Balzergue

first: Abdelhack

last: El Amrani

first: Anne-sophie

last: Dumas

first: Marie-Laure

last: Martin-Magniette


title: Expression changes between  C. albicans white and opaque cell types and mutant strains

type: Expression profiling by genome tiling array

summary: The goal of this study is to characterize the transcriptional regulatory network that controls white-opaque cell-type switching in Candida albicans.  This dataset includes microarrays comparing expression levels in wild-type white and opaque cell types, as well as 6 different transcription factor deletion strains.  All samples were hybridized against a common mixed reference to allow for comparison between any two datasets within this study.

overall_design:
Gene expression arrays were performed on wild-type and transcription factor deletion white and opaque a/a cell types .  High and low intensity scans were performed.  Background and saturated spots were filtered out, as indicated by null.  Data from each scan was normalized by lowess normalization to enable transformation across any pair of datasets.  All data presented are log2 ratios of Cy5/Cy3
Each sample was hybridized against a mixed reference sample to allow for transformation between any of the individual samples (white vs. opaque, wild-type vs. mutant)


title: Identification of miR-203 Regulated Genes During Sendai Virus Infection

first: William

last: Buggele

summary: The goal of this experiment was to determine gene expression changes during Sendai virus infection as the result of expression or inhibition of miR-203 in A549 cells.

overall_design: The gene expression profiling experiment was performed with 4 groups (mock infected, Sendai virus infected, Sendai virus infeceted in the presence of exogenous miR-203, and Sendai virus infected in the presence of miR-203 inhibitor) with 3 biological replicates for each group.  Total RNA was purified from A549 cells that were mock infected or infected with Sendai virus (Cantell strain, 5pfu/cell) alone or in the presence of miR-203 mimic or inhibitor for 10 hours.


title: A genome-wide methylation study on essential hypertension in young African American Males

city: Augusta

first: Xiaoling

last: Wang

state: GA

address: 1120 15th streeet

department: Pediatrics

institute: Medical College of Georgia

summary: We performed a genome wide methylation scan using the Illumina HumanMethylation27 BeadChip on DNAs extracted from the leukocytes of 8 hypertensive cases and 8 normotensive age-matched controls. All subjects were African American males aged 14-23 years.

overall_design: Bisulphite converted DNA from the 16 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2


title: Unusual DNA packaging characteristics in endo-reduplicated C. elegans oocytes defined by in vivo accessibility to an endogenous nuclease activity

status: Public on Jul 01 2013

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: NJ

address: Nelson Labs A125, 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

summary: We describe DNA-surface interactions in activated C. elegans oocytes that are revealed through the activity of an endogenous nuclease. Our analysis began with an unexpected observation that a majority (>50%) of DNA from C. elegans fer-1 oocytes can be recovered in fragments of  ~500 base pairs or shorter, cleaved at regular intervals (10-11nt) along the DNA helix. In some areas of the genome, cleavage patterns in the endoreduplicated oocytes appear consistent from cell-to-cell, indicating coherent rotational positioning of the DNA in chromatin. Particularly striking in this analysis are arrays of sensitive sites with a periodicity of ~10bp that persist for several hundred base pairs of genomic DNA, longer than a single nucleosome core.  Genomic regions with a strong bias toward a 10-nt periodic occurrence of A(n)/T(n) (so-called PATC regions) appear to exhibit a high degree of rotational constraint in endo-cleavage phasing, with a strong tendency for the periodic A(n)/T(n) sites to remain on the face of the helix protected from nuclease digestion. Overall, the present analysis provides evidence for an unusual structure in C. elegans oocytes in which genomic DNA and associated protein structures are coherently linked.

overall_design: Examine endocleavage pattern in C. elegans fer-1 oocyte chromatin

middle: G

first: Barbara

last: Goszczynski

first: James

middle: D

last: McGhee

first: Andrew

middle: Z

last: Fire


title: The plasticity of the grapevine berry transcriptome

status: Public on Apr 11 2013

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:
Background: Phenotypic plasticity refers to the range of phenotypes a single genotype can express as a function of its environment. These phenotypic variations are attributable to the effect of the environment on the expression and function of genes influencing plastic traits. We investigated phenotypic plasticity in grapevine by comparing the berry transcriptome in a single clone of the vegetatively-propagated common grapevine species Vitis vinifera cultivar Corvina through three consecutive growth years cultivated in 11 different vineyards in the Verona area of Italy.

Results: Most of the berry transcriptome clustered by year of growth rather than common environmental conditions or viticulture practices, and transcripts related to secondary metabolism showed high sensitivity towards different climates, as confirmed also by metabolomic data obtained from the same samples. When analyzed in 11 vineyards during one growth year, the environmentally-sensitive berry transcriptome comprised 5% of protein-coding genes and 18% of the transcripts modulated during berry development. Plastic genes were particularly enriched in ontology categories such as transcription factors, translation, transport and secondary metabolism. Specific plastic transcripts were associated with groups of vineyards sharing common viticulture practices or environmental conditions, and plastic transcriptome reprogramming was more intense in the year characterized by extreme weather conditions. We also identified a set of genes that lacked plasticity, showing either constitutive expression or similar modulation in all berries.

Conclusions: Our data reveal candidate genes potentially responsible for the phenotypic plasticity of grapevine and provide the first step towards the characterization of grapevine transcriptome plasticity under different agricultural systems.

overall_design: Vitis vinifera cultivar Corvina clone 48 berries were harvested from different vineyards, each located in one of the three most important wine production macro-areas of the Verona region: Bardolino, Valpolicella and Soave, on the basis of the site geographical coordinates. For each of the selected vineyards, specific environmental conditions (altitude and type of soil) and farming and agricultural practices used (training system, rows facing direction, planting layout, vineyard age and rootstock type) were recorded. Vineyards were selected in order to maximize differences in locations and in microenvironmental and farming conditions. Berries were harvested at three different developmental stages: véraison, mid-ripening and harvest; each sample was collected in three biological replicates, to cover the whole vineyard variability. The same sampling procedure had been repeated over three consecutive vintages (2006, 2007 and 2008).

first: Silvia

last: Dal Santo

first: Giovanni

middle: B

last: Tornielli

first: Sara

last: Zenoni

first: Lorenzo

last: Farina

first: Andrea

last: Anesi

first: Flavia

last: Guzzo

first: Massimo

last: Delledonne

first: Mario

last: Pezzotti


title: Characterization of SOC1’s central role in flowering by the identification of its upstream and downstream regulators

status: Public on Apr 09 2013

city: Tuebingen

first: Felix

last: Ott

address: Spemannstr. 35-39

country: Germany

institute: Max Planck Institute for Developmental Biology

summary: The transition from vegetative to reproductive development is one of the most important phase changes in the plant life cycle. This step is controlled by various environmental signals that are integrated at the molecular level by so-called floral integrators. One such floral integrator in Arabidopsis (Arabidopsis thaliana) is the MADS domain transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). Despite extensive genetic studies, little is known about the transcriptional control of SOC1, and we are just starting to explore the network of genes under the direct control of SOC1 transcription factor complexes. Here, we show that several MADS domain proteins, including SOC1 heterodimers, are able to bind SOC1 regulatory sequences. Genome-wide target gene analysis by ChIP-seq confirmed the binding of SOC1 to its own locus and shows that it also binds to a plethora of flowering-time regulatory and floral homeotic genes. In turn, the encoded floral homeotic MADS domain proteins appear to bind SOC1 regulatory sequences. Subsequent in planta analyses revealed SOC1 repression by several floral homeotic MADS domain proteins, and we show that, mechanistically, this depends on the presence of the SOC1 protein. Together, our data show that SOC1 constitutes a major hub in the regulatory networks underlying floral timing and flower development and that these networks are composed of many positive and negative autoregulatory and feedback loops. The latter seems to be crucial for the generation of a robust flower-inducing signal, followed shortly after by repression of the SOC1 floral integrator.

overall_design: A. thaliana SOC1 ChIP-seq w. control, 3 replicates

first: Richard

last: Immink

first: David

last: Posé

last: Ferrario

first: Kerstin

last: Kaufmann

first: Felipe

last: Leal Valentim

first: Stefan

last: de Folter

first: Froukje

last: van der Wal

first: Aalt

last: van Dijk

first: Markus

last: Schmid

first: Gerco

middle: C

last: Angenent


title: Global epigenomic reconfiguration during mammalian brain development

status: Public on Jul 03 2013

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Whole-genome single-base resolution methylcytosine and hydroxymethylcytosine maps reveal profound changes that occur during frontal cortex development in humans and mice.

overall_design: MethylC-Seq, TAB-Seq, RNA-Seq and hmC-IP (CMS-IP and biotin-glucosyl tagging) from Homo sapiens and Mus musculus frontal cortex tissue and neural sorted cell populations. Additionally, MethylC-Seq was performed on the HUES6 embryonic stem cell line (Homo sapiens).

first: Ryan

last: Lister


title: An Epigenetic Component of Hematopoietic Stem Cell Aging Amenable to Reprogramming Into a Young State

status: Public on Mar 06 2013

city: Lund

first: Martin

last: Wahlestedt

address: Klinikgatan 26

department: Divison of Molecular Hematology

country: Sweden

institute: Lund University

summary: Aging of hematopoietic stem cells (HSCs) leads to several functional changes, including alterations affecting self-renewal and differentiation. While it is well established that many of the age-induced changes are intrinsic to HSCs, less is known about the stability of this state. Here, we entertained the hypothesis that HSC aging is driven by the acquisition of permanent genetic mutations. To examine this issue at a functional level in vivo, we applied induced pluripotent stem (iPS) cell reprogramming of aged hematopoietic progenitors and allowed the resulting aged-derived iPS cells to reform hematopoiesis via blastocyst complementation. Next, we functionally characterized iPS-derived HSCs in primary chimeras and following the transplantation of 're-differentiated' HSCs into new hosts; the gold standard to assess HSC function. Our data demonstrate remarkably similar functional properties of iPS-derived and endogenous blastocyst-derived HSCs, despite the extensive chronological and proliferative age of the former. Our results therefore favor a model in which an underlying, but reversible, epigenetic component is a hallmark of HSC aging rather than being driven by an increased DNA mutation burden.

overall_design: Hematopoietic stem cells (HSC) have been sorted out from young and aged steady-state mice, and from recipients transplanted with young and aged bone marrow. Generated iPS and commercially available ES cells were also sorted and analyzed.

first: Gudmundur

middle: L

last: Norddahl

first: Gerd

last: Sten

first: Amol

last: Ugale

first: Mary-Ann

last: Frisk

first: Ragnar

last: Mattsson

first: Tomas

last: Deierborg

first: Mikael

last: Sigvardsson

last: Bryder


title: sRNA profiles of control adults, postdauer adults, larva L3, and dauer stages of C. elegans

status: Public on Apr 05 2013

city: BOSTON

first: NELSON

last: LAU

state: MA

address: 72 E Concord St K219, Dept of Biochemistry

department: Biochemistry and Cell Biology

institute: Boston University Chobanian & Avedisian School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Early environmental experiences and life histories profoundly influence adult phenotypes via as yet poorly understood mechanisms. We previously showed that wild-type adult C. elegans that transiently passed through the stress-induced dauer larval stage (post-dauers) exhibit different gene expression patterns, genome-wide chromatin structure, and life history traits when compared to adults that bypassed the dauer stage (controls). Here we show that endogenous small inhibitory RNAs (endo-siRNAs) and siRNA pathways may mediate developmental history-dependent phenotypic diversity. Deep sequencing of small RNA libraries show changes in endo-siRNA levels in post-dauer as compared to control animals, and meta analyses indicate that specific endo-siRNA pathways are targets of developmental history-dependent reprogramming. We demonstrate that mutations in specific endo-siRNA pathways affect the expected gene expression and chromatin state changes in post-dauer animals, and also disrupt their increased brood size phenotype. We find that the chromatin state and endo-siRNA distribution in dauers is also distinct and suggest that this remodeling in dauers provides a template for the subsequent establishment of adult post-dauer profiles. Together, our results imply a critical mechanistic role for endo-siRNA pathways in mediating early experience-dependent phenotypic divergence in adults, and suggest that regulation of these pathways contribute to increased fitness via non-genetic mechanisms.

overall_design: We deep-sequenced small RNA libraries from 2 biological replicates each of control and postdauer adults, and one biological each of larval L3 and dauer stages.

first: Sarah

middle: E

last: Hall

first: Gung-wei

last: Chirn

first: Nelson

last: Lau

first: Piali

last: Sengupta


title: Expression data from High-grade prostate cancer cells

status: Public on Mar 12 2013

city: Nankoku

first: Kenji

last: Tamura

state: Kochi

address: Kohasu, Oko-cho

department: Urology

institute: Kochi University

summary: To identify molecules to serve as diagnostic markers for high-grade prostate cancer (PC) and targets for novel therapeutic drugs, we investigated the gene expression profiles of high-grade PCs using a cDNA microarray combined with laser microbeam microdissection.

overall_design: For this study, we collected 10 frozen specimens from high-grade PCs with high PSA levels and high Gleason score (GS) in clinically using prostatic needle biopsy. All needle biopsy specimens were at clinical stages T2 to T4 with or without N1 and M1 and their GS were 8-9. Moreover, all 10 patients had not received androgen ablation therapy. Simultaneously, normal prostate (NP) epithelial cells were also microdissected from five non-prostate cancer (BPH) patients. These NP cells from five males were used as a normal mixture control for our cDNA microarray analysis.

first: Hirofumi

last: Satake

first: Taro

last: Shuin


title: Gene expression changes in C57Bl/6 and CD16-/- murine bone-marrow derived dendritic cells (BMDCs) following overnight stimulation with OVA or OVA-immune complex

status: Public on Feb 20 2013

city: Chicago

first: Melissa

middle: Yuwono

last: Tjota

department: Department of Medicine

institute: University of Chicago

summary: Atopic asthma is a chronic inflammatory disease of the lungs that is commonly associated with a Th2 response. The role of allergen-specific IgG in the initiation and development of allergic airway inflammation is still poorly understood; however, a receptor of IgG-immune complexes, CD16, has been demonstrated to promote augmentation of Th2 responses. To identify what genes downstream of CD16 signaling may be contributing to development of a Th2 response, we use ovalbumin (OVA) as our model antigen and compared wildtype and CD16-/- BMDCs that were treated overnight with OVA or OVA-immune complex.

overall_design: C57Bl/6 and CD16-/- BMDCs were treated for 24 hours with OVA or OVA-immune complex and then analyzed for gene expression changes.

first: Anne

middle: I

last: Sperling


title: Creation of differentiation-specific genomic maps of human epidermis through laser capture microdissection

status: Public on Jan 30 2013

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: We sought to understand the differences between the basal and suprabasal layers of normal human skin epidermis.

overall_design: Comparison of transcriptomes among basal epidermis, suprabasal epidermis, whole epidermis, and reticular dermis

first: Nicholas

last: Gulati

first: James

last: Krueger

last: Suárez-Fariñas

first: Hiroshi

last: Mitsui


title: Small RNA profiling during Sendai virus infection

status: Public on Jun 10 2013

first: William

last: Buggele

institute: Northwestern University

summary: Small RNAs were profiled during Sendai virus infection of human A549 cells to identify changes in microRNA abundance during the cellular antiviral response.

overall_design: Examination of microRNA abundance during Sendai virus infection.

first: Curt

middle: M

last: Horvath


title: Effect of GDF3 on NCCIT cells

status: Public on Feb 27 2013

city: Berlin

first: Karolina

last: Tykwinska

state: Berlin

address: Gustav-Meyer-Allee 25

institute: TU Berlin

summary: The aim of the study was to characterize the role of GDF3 in NCCIT cells as a model of cancer stem cells. The NCCIT cells were stimulated for 3h with (1) 100ng/mL and (2) 300ng/mL GDF3, (3) 300ng/mL Nodal and (4) 100ng/mL GDF3 + 300ng/mL Nodal and compared to unstimulated control. Additionally a stable, lentiviral knockdown of GDF3 was performed in NCCIT cells and the transciption profile of these cells was compared to cells transduced with mock-virus.

overall_design: 5 conditions, 1 biological replicate each

first: Mark

last: Rosowski

first: Roland

last: Lauster


title: Zucker Diabetic Fatty (ZDF) Rat Study - Diaphragm vs. Sternohyoid

status: Public on May 12 2014

city: Cleveland

first: Erik

last: van Lunteren

address: 10701 East Boulevard

department: Pulmonary 111J(W)

institute: Cleveland VA Medical Center

summary: Type 2 diabetes differs from type 1 diabetes in its pathogenesis. Type 1 diabetic diaphragm has altered gene expression which includes lipid and carbohydrate metabolism, ubiquitination and oxidoreductase activity. The objectives of the present study were to assess respiratory muscle gene expression changes in type 2 diabetes and to determine whether they are greater for the diaphragm than an upper airway muscle. Diaphragm and sternohyoid muscle from Zucker diabetic fatty (ZDF) rats were analyzed with Affymetrix gene expression arrays. The two muscles had 97 and 102 genes, respectively, with at least ±1.5-fold significantly changed expression with diabetes, and these were assigned to gene ontology groups based on over-representation analysis. Several significantly changed groups were common to both muscles, including lipid metabolism, carbohydrate metabolism, muscle contraction, ion transport and collagen, although the number of genes and the specific genes involved differed considerably for the two muscles. In both muscles there was a shift in metabolism gene expression from carbohydrate metabolism toward lipid metabolism, but the shift was greater and involved more genes in diabetic diaphragm than diabetic sternohyoid muscle. Groups present in only diaphragm were blood circulation and oxidoreductase activity. Groups present in only sternohyoid were immune & inflammation and response to stress & wounding, with complement genes being a prominent component. In conclusion, type 2 diabetes-induced gene expression changes in respiratory muscles has both similarities and differences relative to previous data on type 1 diabetes gene expression. Furthermore, the diabetic alterations in gene expression differ between diaphragm and sternohyoid.

overall_design: 18-week-old Zucker diabetic fatty rats: 6 normal and 5 diabetic diaphragms and sternohyoids.

first: Michelle

last: Moyer


title: Differential neutrophil gene expression in early bovine pregnancy

status: Public on Jan 31 2013

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

summary: Background: In food production animals, especially cattle, the diagnosis of gestation is an important issue because the timing of gestation has direct effects on the running of farms. Various methods have been used to detect gestation, but none of them are ideal because of problems with the timing of detection, or the accuracy, simplicity, or cost of the method, etc. A new method for detecting gestation, which involves assessing interferon-tau-related gene expression in peripheral blood leucocytes (PBL), was recently proposed. PBL fractionation methods were used to examine whether the expression profiles of various PBL populations could be used as reliable diagnostic markers of bovine gestation.  Methods: PBL were collected on days 0 (just before artificial insemination), 7, 14, 17, 21, and 28 of gestation. The gene expression levels of the PBL were assessed with microarray analysis and/or quantitative real-time reverse transcription (q)-PCR. PBL fractions were collected with flow cytometry or density gradient cell separation using Histopaque 1083 or Ficoll-Conray solution. The expression levels of four interferon-tau-related genes, interferon-stimulated protein 15 kDa (ISG15), myxovirus-resistance (Mx) 1 and 2, and 2'-5'-oligoadenylate synthetase (OAS1), were then analysed in each fraction until day 28 of gestation using qPCR.  Results: Miroarray analysis detected 72 and 28 genes significantly higher in whole PBL on days 14 and 21 of gestation compare to those on day 0, respectively. They involved interferon-tau responded genes. The expression levels of these genes increased with the progression of gestation. In the flow cytometry experiment, on day 14 all of the genes displayed significantly higher expression levels in the granulocyte fraction than the other fractions, and their expression levels gradually decreased until day 28 of gestation. Strong correlations were observed between the expression levels of the four genes in the granulocyte fractions obtained with flow cytometry and density gradient separation.   Conclusions: The expression profile of the four abovementioned genes could be a useful diagnostic biomarker of bovine gestation. Assessing the expression levels of ISG15, Mx1, Mx2 and OAS1 in a granulocyte fraction obtained with density gradient separation is a practical way of detecting gestation in cows within three weeks of insemination.

overall_design: Gene expression profiles were analyzed in the peripheral blood leucocytes at days 0 (n=5), 14 (n=3) and 21 (n=5) after artificial insemination in cow.

first: Kazuyoshi

last: Hashizume


title: Effect of dietary vitamin B6 on white adipose tissue

status: Public on Jan 12 2013

city: Higashi-Hiroshima

first: Yanaka

last: Noriyuki

address: Kagamiyama 1-4-4

department: Graduate School of Biosphere Science

institute: Hiroshima University

summary: Transcriptional profiling of mouse white adipose tissues The objective of this study is to explore the relationship between vitamin B6 activity and chronic inflammation of white adipose tissue in mice fed a high-fat diet. Twenty-four CD-1 mice were divided into two groups (n = 12) and fed either a 1 mg pyridoxine (PN) HCl /kg diet or a 35 mg PN HCl /kg diet for 8 weeks. We isolated total RNA from epididymal white adipose tissue of each group and compared gene expression profiles by DNA microarray data analysis.

overall_design: Noriyuki Yanaka

first: Haruna

last: Suehiro

first: Yohei

last: Sanada


title: Genome wide binding sites of the Arabidopsis B3 domain protein FUSCA3

status: Public on Jan 11 2013

city: Lexington

first: Sharyn

last: Perry

state: KY

address: 1405 Veterans Dr.

department: Plant and Soil Sciences

institute: University of Kentucky

summary:
FUSCA3 (FUS3) is a B3 domain transcription factor that is a member of the LEAFY COTYLEDON (LEC) group of genes. The LEC genes encode proteins that also include LEC2, a B3 domain factor related to FUS3, and LEC1, a CCAAT box binding factor. LEC1, LEC2 and FUS3 are essential for plant embryo development. We report ChIP-chip experiments using the Affymetrix tiling array to globally map binding sites for FUS3.
Fangfang Wang and Sharyn E. Perry (2013) Plant Physiology preview

overall_design: FUSCA3 was expressed by the native promoter and included a C-terminal 10x-c-myc tag. This transgene was able to rescue the fus3-3 mutant. A second transgene (35S:AGL15) was present to allow establishment of stable somatic embryo cultures. ChIP was performed using anti-c-myc antibody (Myc-Tag (9B11) Mouse mAb; Cell Signaling 2276S) on tissue expressing FUS3-myc (three biological replicates) and on three controls of tissue expressing FUS3 (no epitope tag).

first: Fangfang

last: Wang


title: Transcriptional reprogramming by root knot and migratory nematode infection in rice

status: Public on Jan 10 2013

city: Brussels

first: Simon

middle: Lieven Imanuel Johannes

last: Denil

address: Laarbeeklaan 101

department: University Hospital Brussels

country: Belgium

institute: VUB/ULB

summary: In this study  a comparison was made between the local transcriptional changes at two time points upon root knot (Meloidogyne graminicola) and migratory nematode (Hirschmanniella oryzae) infection in rice. Using mRNA-Seq we have characterized specific and general responses of the root challenged with these endoparastic root nematodes with very different modes of action. Root knot nematodes induce major developmental reprogramming of the root tip, where they force the cortical cells to form multinucleate giant cells, resulting in gall-development. Our results show that root knot nematodes force the plant to produce and transfer nutrients, like sugars and amino acids, to this tissue. Migratory nematodes, on the other hand, induce the expression of proteins involved in plant death and oxidative stress, and obstruct the normal metabolic activity of the root. While migratory nematode infection also causes upregulation of biotic stress-related genes early in the infection, the root knot nematodes seem to actively suppress the local defence  of the plant root. This is exemplified by a downregulation of genes involved in the salicylic acid and ethylene pathways. Interestingly, hormone pathways usually involved in plant development, were strongly induced (auxin and gibberellin) or repressed (cytokinin) in the galls. In addition, thousands of novel transcriptionally active regions as well as highly expressed nematode transcripts were detected in the infected root tissues. These results uncover previously unrecognized nematode-specific expression profiles and provide an interesting starting point to study the physiological function of many yet unannotated transcripts potentially targeted by these nematodes.

overall_design: 2 or 3 biological replicates of nematode infected roots and root tips and their respective controls were sampled at two time points (1 biological replicate contains pooled tissue from 6 plants)

first: Tina

last: Kyndt

first: Annelies

last: Haegeman

first: Geert

last: Trooskens

first: Lander

last: Bauters

first: Tim

last: De Meyer

first: Wim

last: Van Criekinge

first: Godelieve

last: Gheysen


title: Effect of hypoxia on Mycobacterium tuberculosis-host phagocyte interactions

status: Public on May 22 2013

city: Covington

first: Smriti

last: Mehra

state: LA

address: 18703 Three Rivers Road, 2-209

institute: TNPRC

summary: Mtb appears to have developed specialized biomolecular infrastructure to survive and persist within granulomas, where it is subjected to a diverse set of stress conditions. One of these stress conditions is hypoxia. We hypothesized that host cell response is radically altered with hypoxia stressed Mtb and designed in-vitro experiments to study this phenomenon. Hypoxia-stressed as well as aerobically grown Mtb were used to infect rhesus macaque bone marrow derived macrophages (Rh-BMDMs) and the host global transcriptional response compared.

overall_design: Using 4 x44 k Agilent arrays specific for rhesus macaque genome, we tested in biological duplicate the effect of aerogically grown Mtb on rhesus macaque BMDMs and compared this to the corresponding effect of the hypoxia-conditioned Mtb on rhesus macaque BMDMs


title: MicroRNA expression in lineage specific hematopoiesis

status: Public on Jan 04 2013

city: Bethesda

first: Jennifer

last: Barb

state: MD

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

summary: MicroRNA plays a critical role in a wide variety of biological processes and regulate genes associated with different biological processes such as development, proliferation, apoptosis, stress response, and tumourigenesis. Profiling miRNA expression during differentiation of embryonic stem cells will help to understand the regulation pathway of differentiation, which in turn may elucidate disease mechanisms. In human hematopoiesis that requires a tight control of gene expression, lineage-specific transcription factors have long been known to act as key regulators of gene expression in multiple cell-fate decisions that govern cell differentiation. Given the important role of miRNAs in development and differentiation, it would be beneficial to elucidate the role of miRNAs in hematopoiesis for identifying novel drug targets.  We undertook the current study of examining the expression of miRNA expression in CD34+ before and after differentiation into erythropoietic, granulopoietic and megakaryocytic  cells using Affymetrix V 2.0 miRNA genechips. We identified 388 probesets representing 140 miRNAs, snoRNAs and stemloop RNAs to be significantly altered during lineage specific differentiation of CD34+ cells.  Of these differentially expressed miRNAs with functional roles in cellular growth and proliferation, differentiation and apoptosis, 16 downregulated miRNAs were found to overlap between the E, M and G groups, hsa-miR150 was significantly downregulated and hsa-miR 210 and hsa-miR-1260b were found to be uniquely upregulated during granulopoiesis while hsa-miR486 was found to be upregulated during erythropoiesis and downregulated in megakaryopoiesis. Megakaryopoitic differentiation specifically resulted in significant down regulation of many miRNAs such as mir -150, mir -155, mir-15, mir-181, mir-221 that seem to play critical roles in the regulation of  B and T cell differentiation . An integrated analysis of the differentially expressed miRNA and mRNA identified specific gene targets that are regulated by the significantly altered micro RNAs during lineage specific hematopoiesis. We believe that this study would enhance our understanding of the role of miRNA in lineage specific gene expression.

overall_design:
CD34+ cells were compared to differentiated Erythropoitic, granulopoietic and megakaryopoiteic groups to identify differentially expressed microRNAs
Human hematopoietic progenitor cells

first: P

last: Liu

first: Y

last: Yan

first: R

first: J

last: Munson

first: N

last: Raghavachari


title: Comparisons of transcriptome among several human iPSC clones derived from different origin and different donors

status: Public on Jan 01 2013

city: kyoto

first: Junya

last: Toguchida

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

institute: Kyoto University

summary: Genetically matched human iPSCs from different origins were generated using bone marrow stromal cells and dermal fibroblasts of the same donor, and the global gene expression profile were analyzed.

overall_design: Comparison of gene expressions among 14 iPS clones, 4 and 4 were derived from bone marrow stromal cells(BM), 2 and 4 were from dermal skin fibroblasts(SF) of donor90 and 91, respectively.


title: Transcriptional response of bovine macrophages after infection with two Argentinean Mycobacterium bovis isolates

status: Public on Nov 28 2012

city: Buenos Aires

first: Marcelo

middle: Abel

last: Soria

address: Ave. San Martin 4453

country: Argentina

institute: University of Buenos Aires. College of Agronomy

summary:
Infection of cattle with Mycobacterium bovis causes severe financial hardship in many countries, in addition to presenting a health risk for humans. As an intracellular pathogen, M. bovis, adapted to survive and thrive within the intramacrophage environment. However, little is known about expression patterns in the macrophage, particularly in the bovine host.
In this study, DNA microarray analysis was used to detect genes expressed in Holstein bovine macrophages derived from peripheral blood mononuclear cells infected during four hours with two Argentinean strains of M. bovis, a virulent strain, 04-303 and an attenuated strain, 534. Genes encoding antrax toxin receptor, cell division and apoptosis regulator, ankyrin proteins that are found within the membrane associated cytoskeleton, protein of cell differentiation and regulators of endocytic traffic of membrane were more strongly expressed in infected macrophages.

overall_design: Blood from healthy Holstein bovines was taken in sterile conditions and peripheral blood mononuclear cells (PBMC) were separated from heparinized blood. PBMCs were used to prepare ten independent cultures which were incubated at 37C for one week in RPMI 1640 complete medium supplemented with 10% of autologous plasma. Four cultures were infected with viable cells of M. bovis virulent strain 04-303, four with avirulent strain 534 and two were left as uninfected controls. Four hours post infection, the cells were scraped, lysed. RNA was extracted, labeled and hybridized to ten Affymetrix Bovine Genome arrays.

first: Karina

last: Caimi

first: Fabiana

last: Bigi


title: UC San Diego_Friedmann_Kang_ESD3_Neuronal Differentiation

status: Public on Nov 22 2012

first: Tae Hyuk

last: Kang

state: CA

address: 9500 Gilman Drive # 0634

institute: University of California, San Diego

summary: The overall gene expression pattern of HPRT knockdown murine D3 stem cells during neuronal differentiation was invesitigated by microarray based gene expression analysis and the results were interpreted by GO, GSEA and signaling pathway analyses with GeneSpring GX and PANTHER Classification System.

overall_design: For microarray experiment, total RNAs from replicated HPRT knockdown and control cultures were pooled and the microarray experiment with each pooled sample was triplicated, respectively.

first: Tae

middle: H

first: Theodore

last: Friedmann


title: Polyphenols from olive mill waste affect biofilm formation and motility in Escherichia coli K12

status: Public on Nov 09 2012

city: Legnaro

first: Lisa

last: Carraro

state: Padova

address: Viale dell'Università 16, Agripolis

department: Department of Comparative Biomedicine and Food Science

institute: University of Padova

summary: Genome-wide transcriptional analysis was performed on E. coli K12 exposed to 1 mg/ml of olive vegetation water phenolic extract (OVWPE) in planktonic condition.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Three groups of samples were considered: P group (three replicate cultures with OVWPE extract diluted in ethanol 20%), E group (three replicate cultures with ethanol 20% alone) C group (three control replicate cultures). 1 ml of VWPE extract (1 mg/ml), 1 ml of ethanol 20% and 1 ml of LB broth were added respectively to the three groups when the OD600 of each culture reached 0.4. Cultures were sampled (2 ml) at the time of treatment (t1), 20 (t2) and 40 (t3) minutes after treatment.

first: Barbara

last: Cardazzo


title: Heat and copper induced mRNA changes in mussels

status: Public on Oct 31 2012

city: Chott-Mariem

first: Mohamed

last: Banni

state: Sousse

address: Route Touristique

department: Life sciences

country: Tunisia

institute: Higher Institut of Agronomy

summary:
Transcriptional profiling of the digestive gland tissue of female mussel Mytilus galloprovincialis exposed to copper along with a temperature gradient
Background: Global warming is a major factor that may affect biological organization, especially in marine ecosystems and in coastal areas that are particularly subject to anthropogenic pollution. We evaluated the effects of simultaneous changes in temperature and copper concentrations on lysosomal membrane stability of the blue mussel Mytilus galloprovincialis (Lam.). Temperature and copper exerted additive effects on lysosomal membrane stability, exacerbating the toxic effects of metal cations present in non-physiological concentrations. Mussel lysosomal membrane stability was positively related toscope for growth, indicating possible effects of increasing temperature on mussel populations in metal-polluted areas. To clarify the molecular response to environmental stressors, we used a cDNA microarray with 1,700 sequences to measure the relative transcript abundances in the gills of mussels exposed to copper (40µg/L) and a temperature gradient (16°C, 20°C, and 24°C). In animals exposed only to heat stress, hierarchical clustering of the microarray data revealed three main clusters, which were largely dominated by down-regulation of translation-related differentially expressed genes, drastic up-regulation of folding protein-related genes, and genes involved in chitin metabolism. The response of mussels exposed to copper at 24° C was characterized by an opposite pattern of the genes involved in translation, most of which were up-regulated, as well asthe down-regulation of genes encoding heat shock proteins and microtubule-based movement proteins. Our data provide novel information on the transcriptomic modulations in mussels facing temperature increases and high copper concentrations; these data highlight the risk of marine life exposed to toxic chemicals in the presence of temperature increases due to climate change.

overall_design: Digestive gland tissue from individual animals in different experimental conditions were analyzed in a complete loop design. Dual color competitive hybridizations (Control “16°C” vs “20°C” vs “24°C” vs “16°C+Cu”, “20°C” vs “24°C” vs “20°C+Cu”, “24°C” vs “24°C+Cu”, “16°C+Cu” vs”20°C+Cu” vs “24°C+Cu”; “20°C+Cu” vs “24°C+Cu”) including label swap. Single individuals. Four biological replicates. One replicate per array.

first: BANNI

last: Mohamed

first: NEGRI

last: Alessandro

first: VIARENGO

last: Aldo


title: UC San Diego Friedmann Kang Neuronal Differentiation DSD3 SNM

status: Public on Dec 10 2012

city: La Jolla

department: Pediatrics

summary: The gene expression pattern of spherical neural masses (SNM) derived from HPRT knockdown murine D3 stem cells during neuronal differentiation to final neurons was invesitigated by RNA-Seq based gene expression analysis and the results were interpreted by GO, GSEA and signaling pathway analyses with Avadis NGS and PANTHER Classification System.

overall_design: For RNA-Seq experiment, total RNAs of HPRT knockdown and control SNMs were extracted time-sequentially during the SNM differentiation such as differentiation-day 0, 1, 2, 3, 4, 6, 8, 10, 12, and 14 to final neurons, and each prepared library applied to the HiSeq 2000 sequencer of Illumina for 50 cycles of single lane run.


title: Prolactin-induced protein (PIP) regulates proliferation of luminal A type breast cancer cells in a hormone-independent manner

status: Public on Oct 29 2012

city: Los Angeles

first: sanjeev

middle: k

last: baniwal

address: 2220 Alcazar street

department: Orthopaedics

institute: University of Southern California

summary: RNA was extracted from cells using Aurum Total RNA kit from Bio-Rad Laboratories, Inc., Hercules, CA following the manufacturer’s recommendations. Gene expression profiling was performed using the BeadChip HumanHT-12 v4 Expression kit from Illumina®, which contains 47,231 gene-probes (Illumina® Inc., San Diego, CA). The raw signal intensities were imported and analyzed using the GenomeStudio® data software.  After background subtraction and normalization, the signal intensity values were exported to the Partek® genomics expression analysis suite using “Partek's Report Plug-in” option in the GenomeStudio® software. Differentially expressed genes in the dox- versus vehicle-treated samples were identified using the “gene expression” workflow in the Partek® software.

overall_design: T47D cells hoaboring a doxycycline inducible shPIP construct were treated for 24 or 48 hours with 250 ng/mL of doxycycline and their mRNAs analyzed in biological triplicates (a total of 12 samples) using Illumina‘s HumanHT-12 v4 BeadChips.  The samples for each time point comprised of three  samples each for doxycycline or equal volume of water as vehicle control.

first: Sanjeev

middle: K

last: Baniwal


title: Virus-misplaced host protein activates innate immunity

status: Public on Oct 03 2012

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Discrimination between self vs. non-self and adequate response to infection and tissue damage are fundamental functions of the immune system. The rapid and global spread of known and emerging viruses is a testament that the timely detection of viral pathogens that reproduce within host cells, presents a formidable challenge to the immune system. To gain access to a proper reproductive niche, many pathogens travel via the host vasculature and therefore become exposed to humoral factors of the innate immune system. Although a cascade of coagulation factors plays a fundamental role in host defense for “living fossils” such as horseshoe crabs (Xiphosurida spp), the role of the coagulation system in activation of innate responses to pathogens in higher organisms remains unclear. When human type C adenovirus (HAdv) enters the circulation, 240 copies of coagulation factor X (FX) bind to the virus particle with picomolar affinity. Here, using molecular dynamics flexible fitting (MDFF) and high resolution cryo-electron microscopy (cryo-EM), we defined the interface between the HAdv5 hexon protein and FX at pseudo-atomic level. Based on this structural data, we introduced a single amino acid substitution, T424A, in the hexon that completely abrogated FX interaction with the virus. In vivo genome-wide transcriptional profiling revealed that FX-binding-ablated virus failed to activate a distinct network of the early response genes, whose expression depends on transcription factor NFKB1. Deconvolution of the signaling network responsible for early gene activation showed that the FX-HAdv complex triggers MyD88/TRIF/TRAF6 signaling upon activation of toll-like receptor 4 (TLR4) that serves as a principal sensor of FX-virus complex in vivo. Our study implicates host factor “decoration” of the virus as a mechanism to trigger innate immune sensor that respond to a misplacement of coagulation FX from the blood into intracellular macrophage compartments upon virus entry into the cell. Our results further the mounting evidence of evolutionary conservation between the coagulation system and innate immunity.

overall_design: Two strains of mice, C57BL/6, and Il1r1-/- deficient. Mice were challenged with wild type HAdv5 or HAdv5-based vectors.

first: Richard

middle: P

last: Beyer

first: Nelson

last: DiPaolo

first: Konstantin

last: Doronin

first: Justin

middle: W

last: Flatt

first: Oleksandr

last: Kalyuzhniy

first: Theodor

last: Bammler

first: Federico

last: Farin

first: Phoebe

last: Stewart

first: Dmitry

last: Shayakhmetov


title: TFPI alpha and beta regulate mRNAs involved in cancer biology and in the immune system

status: Public on Oct 08 2012

city: Oslo

first: Nina

last: Iversen

address: Kirkeveien 166

department: Dept. of Medical Genetics

country: Norway

institute: Oslo University Hospital

summary: Emerging evidences indicate a new role of TFPI in cancer biology. We recently reported that both isoforms of TFPI induced apoptosis and inhibited proliferation of cancer cells. The signaling pathway(s) mediating the effects of TFPI is, however, presently still unclear. Our goal was to further investigate the cellular processes affected by TFPI and to get insight into the molecular mechanisms involved in the effects of TFPI, using a global gene expression study approach. TFPIa or TFPIb cDNA were transfected into SK-BR-3 breast cancer cells for stable overexpression. Global mRNA and microRNA (miRNA) expressions were measured and functional annotation of the differentially expressed genes and miRNAs according to gene ontology terms was conducted. Selected results were validated using qRT-PCR and Western blot. Overexpression of TFPIa or TFPIb resulted in a 6.4- and 17-fold increase in TFPI protein levels, respectively. A total of 242 and 801 mRNA transcripts and 120 and 46 miRNAs were differentially expressed in cells overexpressing TFPIa or TFPIb, respectively. Overexpression of either isoform significantly affected the expression of genes involved in cell development (apoptosis, cell movement, migration, invasion, colony formation, growth, and adhesion) and immune response. Network analyses revealed biological interactions between these genes and implied that several of the genes may be involved in both processes. Functional cluster analyses indicated altered activity of the epidermal growth factor receptor (EGFR), small GTPases, and the NFkB and JAK/STAT cascades. Integrated mRNA-miRNA analyses showed that up to 46 and 252 genes differentially expressed in cells overexpressing TFPIa or TFPIb, respectively, may have been regulated by miRNAs. Overexpression of TFPI in breast cancer cells affected the expression of mRNAs and miRNAs involved in processes facilitating cancer cell growth and immunologic response, probably by signal transduction involving the EGFR pathway.

overall_design:
Total RNA was isolated from SK-BR-3 breast cancer cells stably transfected with TFPIalpha or TFPIbeta cDNA, or with an empty vector for control. RNA was obtained from three independent isolations, yielding three biological replicates of each of the three samples.
Mean expression data from cells overexpressing TFPIalpha or TFPIbeta were compared to mean data from cells transfected with an empty vector.

first: Benedicte

last: Stavik

first: Grethe

last: Skretting

first: Ole

last: Olstad

first: Marit

last: Sletten

first: Magnus

middle: D

last: Vigeland

first: Per

last: Sandset


title: Age-associated DNA methylation increases in mouse pancreatic islets suggest an epigenetic drift toward the exocrine pancreas epigenome

status: Public on Dec 03 2014

city: Houston

first: Ge

last: Li

state: TX

address: 1100 Bates St.

institute: Baylor College of Medicine

summary: Early postnatal overnutrition causes persistent dysregulation of endocrine pancreas function. We used genome-scale DNA methylation profiling in the suckling-period small litter (SL) mouse model to test whether this occurs via persistent epigenetic changes in pancreatic islets. Although SL islets showed DNA methylation changes directly after weaning and in adulthood, few of these were present at both ages, contrary to our hypothesis. Most interestingly, we discovered that genomic regions that are hypermethylated in exocrine relative to endocrine pancreas tend to gain methylation in islets during aging. Focusing on a subset of genes relevant to β cell function, we showed that these methylation differences are strongly correlated with expression. Together, our results provide the novel insight that DNA methylation changes that occur as islets age indicate an overall epigenetic drift toward the exocrine pancreas epigenome. These concerted shifts in the islet methylome could contribute to the age-associated decline in endocrine pancreas function.

overall_design: Pancreatic islets were isolated from P21/P180 SL or C mice. To ensure purity of islets, 3 rounds of manual picking were performed in each samples. Whole pancreas samples, ~98% of which is exocrine pancreas, were used as exocrine pancreas. There are 5 mice per group.

first: Tihomira

last: Petkova

first: Eleonora

last: Laritsky

first: Noah

last: Kessler

first: Maria

middle: S

last: Baker

first: Shaoyu

last: Zhu

first: Robert

middle: A

last: Waterland


title: Increased levels of aneuploidy and deregulation of ploidy controlling genes are associated with maintained cultures of hMSC

status: Public on Oct 30 2012

city: MADRID

first: Juan

middle: C

last: Estrada

state: MADRID

address: MELCHOR FERNANDEZ ALMAGRO 3

department: REGENERATIVE CARDIOLOGY

institute: CNIC

summary: Human mesenchymal stem cells (hMSC) are being successfully evaluated for the treatment of a wide range of pathological conditions, including graft versus host disease (GVHD), bone and cartilage degeneration, complex fistula and myocardial infarction. Many of these clinical trials use hMSC, which have been previously expanded in vitro for 8-12 weeks under pro-oxidative “standard” cell culture conditions. These conditions could have negative effects over genetic stability and promote mutations and chromosomal abnormalities. Our FISH (Fluorescence in situ hybridization) analysis shows that aneuploidy is not unusual phenomenon in conventional cultures of hMSC and that it progressively increases with the passages. We further demonstrate that senescence is linked to transcriptional deregulation of a set of genes that have been previously implicated in cancer and ploidy control. Overexpression of hTERT reversed the deregulation of these ploidy control genes and maintained the basal levels of ploidy even during long-term culture, through its canonical function of telomere elongation and by reducing the levels of oxidative stress. We propose that the high levels of aneuploidy and deregulation of these genes would be relevant biomarkers of senescence in standard cultures of hMSC.

overall_design: We compared the RNA expression profiles of adipose tissue-derived human mesenchymal stem cells cultured in standard cell culture condition at passages 2 with the same primary cell lines cultured by 21 passages. A total of four independent samples were used.

first: Yaíma

last: Torres

first: Alberto

last: Benguría

first: Ana

last: Dopazo

first: Lucrecia

last: Carrera-Quintanar

first: Enrique

last: Roche

last: Samper

first: Antonio

last: Bernad


title: Modulation of the osteosarcoma expression phenotype by miRNAs [Illumina]

status: Public on Oct 16 2012

first: Heidi

middle: Maria

last: Namløs

address: PO Box 4953 Nydalen

department: Institute for cancer research, The Norwegian Radium Hospital

summary:
Background: Osteosarcomas are the most common primary malignant tumors of bone and show multiple and complex genomic aberrations. miRNAs are non-coding RNAs capable of regulating gene expression at the post transcriptional level, and miRNAs and their target genes may represent novel therapeutic targets or biomarkers for osteosarcoma. In order to investigate the involvement of miRNAs in osteosarcoma development, global microarray analyses of a panel of 19 human osteosarcoma cell lines was performed.
Principal findings: We identified 177 miRNAs that were differentially expressed in osteosarcoma cell lines relative to normal bone. Among these, miR-126/miR-126*, miR-142-3p, miR-150, miR-223, miR-486-5p and members of the miR-1/miR-133a, miR-144/miR-451, miR-195/miR-497, and miR-206/miR-133b clusters were found to be downregulated in osteosarcoma cell lines. All miRNAs in the paralogous clusters miR-17-92, miR-106b-25 and miR-106a-92 were overexpressed. Furthermore, the upregulated miRNAs included miR-9/miR-9*, miR-21*, miR-31/miR-31*, miR-196a/miR-196b, miR-374a and members of the miR-29, miR-130/301 families. The most interesting inversely correlated miRNA/mRNA pairs in osteosarcoma cell lines included miR-9/TGFBR2 and miR-29/the p85α regulatory subunit of PI3K. PTEN mRNA correlated inversely with miR-92a and members of the miR-17 and miR-130/301 families. Expression profiles of selected miRNAs were confirmed in clinical samples. A set of miRNAs, miR-1, miR-18a, miR-18b, miR-19b, miR-31, miR-126, miR-142-3p, miR-133b, miR-144, miR-195, miR-223, miR-451 and miR-497 was identified with an intermediate expression level in osteosarcoma clinical samples compared to osteoblasts and bone, which may reflect the differentiation level of osteosarcoma relative to the undifferentiated osteoblast and fully differentiated normal bone.
Significance: This study provides an integrated analysis of miRNA and mRNA in osteosarcoma, and gives new insight into the complex genetic mechanisms of osteosarcoma development and progression.

overall_design: 19 osteosarcoma cell lines, 4 normal bones used as controls. No replicates. The group of osteosarcomas are compared to the group of normal bones.

first: Leonardo

last: Meza-Zepeda

first: Tale

last: Barøy

first: Ingrid

last: Østensen

first: Stine

last: Kresse

first: Marieke

middle: L

last: Kuijjer

first: Massimo

last: Serra

first: Horst

last: Bürger

first: Anne-Marie

last: Cleton-Jansen

first: Ola

last: Myklebost


title: The Diagnostic Value of Salivary microRNA in Esophageal Cancer

city: Guangzhou

first: Zijun

last: Xie

address: No.106,zhongshan 2nd round

institute: Guangdong General Hospital

summary: Tissue microRNAs (miRNAs) can detect cancers and predict prognosis. Several recent studies reported that tissue, plasma, and saliva miRNAs share similar expression profiles. In this study, we investigated the diagnostic value of salivary miRNAs (including whole saliva and saliva supernatant) for detection of esophageal cancer.

overall_design: By Agilent microarray, six deregulated miRNAs from whole saliva samples from seven patients with esophageal cancer and three healthy controls were selected. The six selected miRNAs were subjected to validation of their expression levels by RT-qPCR using both whole saliva and saliva supernatant samples from an independent set of 39 patients with esophageal cancer and 19 healthy controls.

last: Li


title: A macrophage autonomous alpha4beta1integrin-Syk-Rac2 signaling axis controls macrophage differentiation, tumor growth and metastasis

status: Public on Oct 02 2012

city: San Diego

first: Lei

last: Bao

address: 3855 Health Sciences Drive

department: Cancer Center

institute: UCSD

summary: Macrophages, play an essential role in promoting tumor growth by affecting angiogenesis, immune suppression, invasion and metastasis. The signal transduction events within macrophages which encode the complex cascade of events required for tumor growth and polarization of macrophages are poorly understood. We have discovered an ECM dependent signaling pathway in macrophages that regulates M2 macrophage differentiation, tumor growth, invasion and metastasis. We provide direct evidence that a macrophage autonomous, α4β1 integrin dependent Syk-Rac2 signaling axis acts in concert with the p110 isoform (PTEN-PI-3 kinase pathway) to control metastasis.

overall_design: Bone marrow derived macrophages from five wild type and five Rac2 -/- mutant C57BL mice.

first: Shweta

last: Joshi

first: Alok

middle: R

last: Singh

first: Muamera

last: Zulcic

first: Karen

last: Messer

first: Donald

last: Durden


title: Expression data from the neural crest cells isolated from mouse cardiac outflow tract at E10.5

status: Public on Oct 01 2012

city: shanghai

first: yunfu

last: sun

state: shanghai

address: 150 jimo road, pudong new district

department: school of medicine

institute: tongji university

summary:
Neural crest defects lead to congenital heart disease involving outflow tract (OFT) malformation. Integrin-linked-Kinase (ILK) plays important roles in multiple cellular processes and embryogenesis. ILK is expressed in neural crest cells (NCC), but its role in NCC and OFT morphogenesis remains unknown.
We used microarrays to detail the global programme of gene expression underlying the morphogenesis of the cardiac neural crest and outflow tract.

overall_design: The outflow tract of control and ILK mutant mouse embryos at E10.5 were dissected and dissociated. Neural crest cells were FACS sorted and used for RNA extraction and hybridization on Affymetrix microarrays.

first: Xingqun

last: Liang

first: Ju

last: Chen

first: Yunfu

last: Sun


title: Modulation of the osteosarcoma expression phenotype by miRNAs [Agilent]

first: Heidi

last: Namløs

first: Leonardo

last: Meza-Zepeda

first: Tale

last: Barøy

first: Ingrid

last: Østensen

first: Stine

last: Kresse

last: Kuijjer


title: Discovery of a Novel Human Polyomavirus in Acute Diarrheal Samples from Children

city: San Francisco

first: Charles

last: Chiu

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

summary: By unbiased deep sequencing, we identified a novel, highly divergent polyomavirus, provisionally named MX polyomavirus (MXPyV), in stool samples from children. From Mexico, 12 samples (out of 96) were positive for MxPyV by MXPyV-specific PCR. We used the ViroChip microarray and PCR to screen these 12 samples for co-infection with common diarrheal viruses. Six of 12 MxPyV-positive diarrheal samples tested negative by the ViroChip and PCR, and the other 6 samples were positive for at least one known diarrheal virus.

overall_design: The ViroChip microarray (version 5.0, Viro5AG-60K platform, GPL15905) was used to screen RNA extracts from MX polyomavirus (MXPyV)-positive pediatric diarrheal samples from Mexico for common diarrheal viruses.

middle: Y

first: Guixia

last: Yu


title: Modulation of the osteosarcoma expression phenotype by miRNAs

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

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

overall_design: Refer to individual Series


title: The effect of over-expression of PRR5-VP in Arabidopsis seedlings

status: Public on Sep 20 2012

city: Yokohama

first: Norihito

last: Nakamichi

address: Suehiro1-7-22, Tsurumi

department: Plant Science Center

institute: RIKEN

summary: PRR5 transcription factor acts in the circadian clock system. To elucidate regulated genes by PRR5, Chimeric protein PRR5-VP, which activates direct target genes of PRR5, was over-expressed in Col-0. Microarray analsysis was performed using these plants with Affymetrix ATH1 genechip.

overall_design: PRR5-VP expressing plants and its parental plants (accession Col-0, described as Wild) were grown under 12 hr light / 12 hr dark conditions, and harvested at ZT6(6 hr after light on), ZT12, and ZT18

first: Hitoshi

last: Sakakibara


title: Transcriptional profile of sustained ligand-activated preconditioning in pre- and post-ischemic myocardium

city: Gold Coast

first: Kevin

middle: John

last: Ashton

state: QLD

address: University Drive

department: Health Sciences & Medicine

country: Australia

institute: Bond University

summary: Analysis of left venticular myocardium following morphine-induced sustained ligand activated preconditioning (SLP). Results provide insight into the molecular pathways affected by morphine-induced SLP in the pre- and post-ischemic heart.

overall_design: Total RNA obtained from isolated ventricular myocardium subjected to 5 days of morphine induced sustained ligand activated preconditioning (SLP) compared to placebo control ventricular myocardium, tissue collected pre- and post-ischemia (n=6/group).

middle: J

first: Amanda

last: Tupicoff

first: Grant

last: Williams-Pritchard

first: Can

last: Kiessling

first: John

last: Headrick

first: Jason

middle: N

last: Peart


title: Genome-wide maps of PRR5 binding loci in Arabidopsis thaliana

summary: PRR5 transcription factor acts in the circadian clock system. To elucidate bound genes by PRR5, Chimeric protein FLAG-PRR5-GFP, was expressed under PRR5 promoter in Col-0 (PRR5pro:FLAG-PRR5-GFP/prr5). ChIP was performed using anti-GFP antibody (ab290;Abcam), which was bound to Dynabeads Protein G (100-03D;Life technologies), and ChIP DNA and input DNA were analyzed by Illumina GA II.

overall_design: ChIP and input sequence reads were compared to find out PRR5 binding sites


title: The transcriptional landscape and mutational profile of lung adenocarcinoma

status: Public on Sep 06 2012

first: Won-Chul

last: Lee

address: 1881 East Road

institute: MD Anderson Cancer Center

summary:
Understanding the molecular signatures of cancer is important to apply appropriate targeted therapies. Here we present the first large scale RNA sequencing study of lung adenocarcinoma demonstrating its power to identify somatic point mutations as well as transcriptional variants such as gene fusions, alternative splicing events and expression outliers. Our results reveal the genetic basis of 200 lung adenocarcinomas in Koreans including deep characterization of 87 surgical specimens by transcriptome sequencing. We identified driver somatic mutations in cancer genes including EGFR, KRAS, NRAS, BRAF, PIK3CA, MET and CTNNB1. New cancer genes, such as LMTK2, ARID1A, NOTCH2 and SMARCA4, were also suggested as candidates for novel drivers in lung adenocarcinoma. We found 45 fusion genes, 8 of which were chimeric tyrosine kinases involving ALK, RET, ROS1, FGFR2, AXL and PDGFRA. Of 17 recurrent alternative splicing events, we identified exon 14 skipping in the proto-oncogene MET as highly likely to be a cancer driver. The number of somatic mutations and expression outliers varied markedly between individual cancers and was strongly correlated with smoking history of cancer patients. In addition, we identified genomic blocks where genes were frequently up- or down-regulated together that could be explained by copy number alterations in the cancer tissue. We also found an association between lymph node metastasis and somatic mutations in TP53. Our findings broaden our understanding of lung adenocarcinoma and may also lead to new diagnostic and therapeutic approaches.
* Raw data files were submitted to EBI-SRA under accession number ERP001058.

overall_design: RNA-Seq for 87 lung adenocarcinomas and 77 adjacent normal tissues

first: Jeong-Sun

last: Seo

first: Young

last: Ju


title: Transcriptional Signatures as a Disease-Specific and Predictive Inflammatory Biomarker for Type 1 Diabetes [T1D_114]

status: Public on Sep 01 2012

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary: The complex milieu of inflammatory mediators associated with many diseases is often too dilute to directly measure in the periphery, necessitating development of more sensitive measurements suitable for mechanistic studies, earlier diagnosis, guiding selection of therapy, and monitoring interventions.  Previously, we determined that plasma of recent-onset (RO) Type 1 diabetes (T1D) patients induce a proinflammatory transcriptional signature in fresh peripheral blood mononuclear cells (PBMC) relative to that of unrelated healthy controls (HC). Here, using an optimized cryopreserved PBMC-based protocol, we analyzed larger RO T1D and HC cohorts. In addition, we examined T1D progression by looking at longitudinal, pre-onset and longstanding T1D samples.

overall_design: UPN727 cells were stimulated with autologous plasma (n=7), unrelated healthy control plasma (n=44), recent onset T1D plasma (n=46), longstanding T1D plasma (n=11), or longitudinal series plasma (n=6 time points) from pre/post onset. Gene expression analysis was performed in order to evaluate the transcriptional signature associated with T1D.

first: Hara

last: Levy

first: Xujing

last: Wang

first: Mary

last: Kaldunski

first: Shuang

last: Jia

first: Joanna

last: Kramer

first: Scott

last: Pavletich

first: Melissa

last: Reske

first: Mike

last: Quasney

last: Dahmer

first: Jack

last: Gorski


title: Global transcriptional analysis of S. mutans sugar transporters in biofilm

city: Miami

first: Dragana

last: Ajdic

state: Florid

address: 1600 NW 10th Ave, RMSB 2023

department: Dermatology

institute: University of Miami

summary:
In this study we showed that one PTS of S. mutans is specific for biofilm mode of growth in the presence of sucrose.
Our data indicates that this PTS is involved in transport and metabolism of disaccharides and possibly oligosaccharides synthesized by GtfI and GtfSI.

overall_design:
Global transcriptional patterns were obtained in different growth modes on specific carbohydrates (glucose, sucrose  and nigerose). To assure reproducibility of the data, the cultures were always grown to the same optical density for RNA extraction, cDNA synthesis and hybridization on Affymetrix microarrays. Multiple conditions were analyzed with 2 or 6 replicates for each.
Carbohydrate response in different growth modes.

first: Zhiyun

last: Chen


title: Adipose Tissue MicroRNAs as Regulators of CCL2 Production in Human Obesity [miRNA data]

status: Public on Aug 13 2012

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

institute: Karolinska

summary: We used an unbiased systems biology approach to study the regulation of gene expression in human adipose tissue focusing on inflammation. We show that microRNAs play a major role as regulators of CCL2 production in obesity.

overall_design: Abdominal subcutaneous adipose needle biopsies were obtained from women (n=56) with a wide variation in BMI. From the biopsies, total RNA was isolated and labelled using the FlashTag biotin HSR labeling kit (Genisphere Inc., Hatfield, PA) according to the supplier's protocol. The labelled samples were placed in a hybridization cocktail mix containing 4% formamide and hybridised overnight to Affymetrix miRNA Arrays (Affymetrix Inc.) following the indicated Genisphere protocol. The arrays were washed, stained and scanned in an Affymetrix GCS 3000 scanner. Signal intensities and present calls were generated by using the microRNA QC tool by Affymetrix.

first: Niklas

last: Mejhert

first: Erik

last: Arner


title: Adipose Tissue MicroRNAs as Regulators of CCL2 Production in Human Obesity [gene expression]

overall_design: Abdominal subcutaneous adipose needle biopsies were obtained from women (n=56) with a wide variation in BMI. From the biopsies we prepared and hybridised biotinylated complementary RNA to GeneChip Human Gene 1.0 ST Arrays (Affymetrix Inc., Santa Clara, CA),  labelled RNA to Affymetrix miRNA arrays, and bisulphite converted DNA to Illumina Infinium HumanMethylation27 beadchips using standardised protocols (Affymetrix Inc., Illumina Inc.) . Subsequent analyses of gene expression was performed using the Affymetrix GeneChip Operating Software version 1.4. To allow comparisons of transcript levels between samples, all samples were subjected to an all-probeset scaling-to-target signal of 100.

first: Peter


title: Transcriptomic comparison of serotype M1 S. pyogenes

status: Public on Aug 21 2012

city: St Lucia

middle: G

last: Maamary

address: Cooper Road

department: School of Chemistry and Molecular Biosciences

institute: University of Queensland

summary: S. pyogenes strains were compared with the intact covRS form of the globally disseminated M1T1 clone to track transcriptomic changes engendered during the emergence of the M1T1 clone. The  mutant covRS form of the M1T1 clone was included as a transcriptomic outlier and to provide a context for the magnitude of transcriptional shifts detected within the isolate set examined.

overall_design: Microarray was performed on RNA extracted from mid-logarithmic phase S. pyogenes grown in Todd-Hewitt with 1% yeast extract in vitro. Experiments were performed using a single color method. Each sample was labelled with Cy3 and hybridized to separate arrays. Each strain was analysed in 3 biological replicates. cDNA hybridized to JCVI PFGRC Streptococcus pyogenes v2 oligo arrays. Only probed representing the core M1 genome were used for analysis.

first: Timothy

last: Barnett

first: Mark

last: Walker


title: Adipose Tissue MicroRNAs as Regulators of CCL2 Production in Human Obesity

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

platform_organism:
Homo sapiens
synthetic construct


title: Miniature pigs tooth germ tissue: four different developing stages

status: Public on Aug 03 2012

city: Beijing

first: Ang

last: Li

address: Tian Tan Xi Li No.4

institute: Capital Medical University School of Stomatology

summary: The miRNAs expression profile of four typical stages of tooth development, embryonic day 35 (E35), E45, E50, and E60, which cover the major morphological and physiological changes in pig tooth germ growth and development throughout pregnancy, including the bud, cap, early bell, and late bell stages.

overall_design: Four-condition experiment: E35 vs. E45 vs. E50 vs. E60. Biological replicates: 3, independently removed under a microscope. Four replicates per array.

first: Songling

last: Wang