title: Immediate response of hematopoietic stem cells to low doses of γ-irradiation

status: Public on Feb 26 2016

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

summary: Analysis of highly purified long-term hematopoietic stem cells (LT-HSCs) 2 hours after irradiation at 0Gy, 0.02Gy and 2.5Gy. Results provide insight into the molecular mechanisms underlying LT-HSCs immediate response to low doses of γ-irradiation compared to high doses.

overall_design: Three samples were analyzed and correlated with the control group (0Gy).

first: Sarah

middle: R

last: Moreira

first: Françoise

last: Hoffschir

first: Stéphanie

middle: G

last: Moreno

first: Daniel

last: Lewandowski

first: Hozumi

last: Motohashi

first: Michael

middle: C

last: Joiner

first: Nathalie

last: Gault

first: Paul

middle: H

last: Romeo


title: Long-term effects of low doses of γ-irradiation on hematopoietic stem cells

summary: Analysis of highly purified long-term hematopoietic stem cells (LT-HSCs) irradiated at 0Gy, 0.02Gy, 0.1Gy and 0.5Gy six months after transplantation. Results provide insight into the molecular mechanisms underlying multiple aspects of LT-HSCs premature ageing after low doses of γ-irradiation (0.02Gy).

overall_design: Four samples were analyzed and correlated with the control group (0Gy).


title: Expression Data from Uveal Melanoma patient-derived xenograft and tumor of origin

status: Public on Feb 18 2016

city: Paris Cedex 05

first: Cecile

last: Laurent

address: 26 rue d'ulm

institute: Institut Curie

summary:
We compare the genetic profiles of the primary tumors of uveal melanoma or metastasis to their corresponding xenografts that have been passaged over time.
The study included patient tumors and corresponding xenografts at very early (P1), early (P4), and late (P9) in vivo passages

overall_design: The transcriptome of 16 uveal melanoma patient-derived xenografts models were analyzed using Affymetrix Human Exon 1.0 ST Array

first: Cécile

first: David

last: Gentien

first: Sophie

last: Piperno-Neumann

first: Fariba

last: Némati

first: André

last: Nicolas

first: Bruno

last: Tesson

first: Laurence

last: Desjardins

first: Pascale

last: Mariani

first: Audrey

last: Rapinat

first: Xavier

last: Sastre-Garau

first: Jérôme

last: Couturier

first: Philippe

last: Hupé

first: Leanne

last: de Koning

first: Thierry

last: Dubois

first: Sergio

last: Roman-Roman

first: Marc-Henri

last: Stern

first: Emmanuel

last: Barillot

first: William

last: Harbour

first: Simon

last: Saule

first: Didier

last: Decaudin


title: Immediate and long-term effects of low doses of γ-irradiation on hematopoietic stem cells

first: Florent

last: Dumont

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

overall_design: Refer to individual Series


title: Identity, proliferation capacity, genomic stability and novel senescence markers of mesenchymal stem cells isolated from low volume of human bone marrow

status: Public on Feb 29 2016

city: Vilnius

first: Gabrielis

last: Kundrotas

address: Santariškių str. 1

country: Lithuania

institute: National Cancer Institute


title: Identity, proliferation capacity, genomic stability and novel senescence markers of mesenchymal stem cells isolated from low volume of human bone marrow (III)

summary: Human bone marrow mesenchymal stem cells (hBM-MSCs) hold promise for treating diseases for which currently no therapeutic options exist. High quantities of MSCs are needed, requiring extensive cell expansion in long-term culture. However, the fundamental biological properties of MSCs can be altered by culture conditions. In this study, hBM-MSCs were isolated from residual human bone marrow (hBM) material and expanded to clinically relevant numbers at passage 3-4. The cells had normal morphology, proliferation rate, immunophenotype and karyotype. Despite the chromosomal stability, after additional three passages (P6-P7) hBM-MSCs entered senescence state, confirmed by SA-β-galactosidase staining and paralleling the slower proliferation, altered morphology and imunophenotype. qRT-PCR array profiling revealed 33 out of 420 miRNAs significantly (p <0.05) differentially (≥2 fold) expressed in the late passage cells compared to the early passage cells.

overall_design: qPCR miRNA expression profiling. hBM-MSCs from 3 (1 male and 2 females) adult donors (age 30±7.21 years) were used. Each sample was tested in technical duplicate. 6 samples of early passage (P3-P4) hBM-MSCs were grouped to CONTROL group and 6 samples of late passage (P6-P7) hBM-MSCs were grouped to TEST group. The data were analysed using web-based miScript miRNA PCR Array Data Analysis software (Qiagen)

first: Evelina

last: Gasperskaja

first: Grazina

last: Slapsyte

first: Zivile

last: Gudleviciene

first: Jan

last: Krasko

first: Ausra

last: Strumbryte

first: Regina

last: Liudkeviciene


title: A microarray analysis highlights the role of tetrapyrrole pathways in grapevine responses to stolbur phytoplasma, phloem virus infections and recovered status

status: Public on Feb 19 2016

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

summary: Several systemic diseases affect Vitis vinifera worldwide with important consequent management costs. Phytoplasma and viruses represent the most detrimental pathogens inducing symptoms and metabolic alterations that modify quantitatively the crop production. In the aim to investigate the plant/pathogen interactions, different grapevine samples, naturally affected (in mixed or single infections) by Stolbur phytoplasma (agent of Bois Noir disease) and viruses, in comparison to healthy and recovered controls, to identify the plant response to systemic pathogen infection. The preliminary results showed that expression levels of thousands of genes were altered in infected plants, involving various metabolic pathways.

overall_design:
Total RNA was extracted from central leaf midribs and petioles from different V. vinifera cultivars in different conditions (healthy, infected and recovered). Microarray analyses were conducted using different biological replicates for treatment.
The submitter of this dataset can no longer locate the raw data

first: Federico

last: Punelli

first: Alberto

last: Ferrarini

first: Graziella

last: Pasquini


title: Common lymphoid progenitor-independent pathways of innate and T lymphocyte development

status: Public on Feb 17 2016

city: Vancouver

first: Maryam

last: Ghaedi

state: BC

address: 675 West 10th Avenue

department: Terry Fox Labs

country: Canada

institute: BC Cancer Agency

summary: All lymphocytes are thought to develop from common lymphoid progenitors (CLPs). However, lymphoid-primed multi-potent progenitors (LMPPs) are more efficient than CLPs in differentiating into T cells and group 2 innate lymphoid cells (ILC2s). Here, we have divided LMPPs into CD127− (LMPP-s) and CD127+ (LMPP+s) subsets and compared them with Ly6D− and Ly6D+ CLPs. Adult LMPP+s differentiated into T cells and ILCs more rapidly and efficiently than other progenitors in transplantation assays. The development of T cells and ILC2s is highly active in the neonatal period. Neonatal CLPs are rare and, unlike prominent neonatal LMPP+s, do not efficiently differentiate into T cells and ILC2s. ILC2s generated in the neonatal period are long-lived and persist in adult tissues. These results suggest that some ILCs and T cells may develop from LMPP+s via CLP-independent pathways.

overall_design: Here, we have divided LMPPs into CD127- (LMPP-s) and CD127+ (LMPP+s) subsets and compared them with CLPs.

first: Fumio

last: Takei


title: Relative tRNA abundance in Lactococcus lactis as a function of growth rate and overexpression stress

city: Potsdam

first: Paul

middle: Georg

last: Saffert

state: Brandenburg

address: Karl-Liebknecht Straße 24-25

department: Biochemistry

country: Germany

institute: University of Potsdam

summary: Comparison of overall tRNA level in Lactococcus lactis affected by the growth rate and as a response to the overexpression of the membrane protein OpuA.

overall_design: Lactococcus lactis with growth rate 0.15 h was compared to Lactococcus lactis with growth rates 0.3 h, 0.5 h and 0.6 h. Lactococcus lactis just prior to the induction of the expression of OpuA was compared to Lactococcus lactis after induction of expression of OpuA and to Lactococcus lactis in stationary phase. 2 biological replica.

first: Pranav

last: Puri


title: Transcriptome profiling in five vitally important tissues of Cynomolgus monkeys using customized NimbleGen microarrays

status: Public on Feb 24 2016

city: Basel

first: Tobias

last: Heckel

address: Grenzacherstr. 124

department: pRED

country: Switzerland

institute: Roche

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

summary: Cynomolgus monkeys are well-established translational models for biomedical research and drug testing. To evaluate organ transcriptomes and gene expression variability in Cynomolgus monkeys, we used Customized NimbleGen Microarrays (Design ID: 120419_Cynomolgus_v5_TH_exp_HX12) for genome-wide gene expression profiling on 5 different tissues (heart, kidney, liver, lung, spleen) from 21 Cynomolgus monkeys. Cynomolgus monkey samples were derived from breeding centers located in the Philippines (3 females and 3 males), in Vietnam (2 females and 2 males), in China for animals from Mainland Southeast Asia (3 females), or in Mauritius (4 females and 4 males). Furthermore, genome-wide copy number variation was analyzed in tissue samples from the same animals using a custom NimbleGen 4.2 million probes comparative genomic hybridization (CGH) array to associate CNV genotypes with expression changes of proximal genes.

overall_design:
A NimbleGen customized 12x135K Gene Expression Array [Design ID: 120419_Cynomolgus_v5_TH_exp_HX12] study using total RNA recovered from tissues of drug-naive Cynomolgus monkeys. Each microarray measures the expression level of 22,731 probe sets covering 18,943 genes with six 60-mer probes (PM) per probe set. The number of replicates is 1 - i.e., only one set of probes on the array. The design includes 3420 RANDOM_MK1 control probes for the estimation of the signal threshold and 1536 ERCC probes for ERCC RNA Spike-In Control Mixes.

The gene expression results analyzed in this study are further described in Gschwind A.R. et al. (2016) Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis, under submission.

first: Anjali

last: Singh

first: Ezra

last: Lyon

first: Ulrich

last: Certa


title: Role of the histone demethylase KDM2B in hematopoietic homeostasis and malignancies [Kras background mouse gene expression]

status: Public on Feb 22 2016

city: Washington

first: Alexandros

last: Tzatsos

state: DC

address: 800 22nd St NW SEH 8850

department: GW Cancer Center

country: USA

institute: George Washington University

summary:
Development of the hematopoietic system is dynamically controlled by the interplay of transcriptional and epigenetic networks to determine cellular identity. Those networks are critical for homeostasis and frequently dysregulated in leukemias. We identified histone demethylase Kdm2b as a critical regulator of definitive hematopoiesis and lineage specification of hematopoietic stem and progenitor cells (HSPCs). RNA sequencing in murine HSPCs and genome-wide chromatin immunoprecipitation studies in human leukemias revealed that Kdm2b regulates differentiation, lineage choice, cytokine signaling, and quiescence.
Comparison of gene expression in wild-type and knockout HSPCs

overall_design: We analyzed lineage depleted cells isolated from bone marrow from mice that express oncogenic Kras in the context of knockout and overexpression of Kdm2b in Affymetrxi GeneChip® Mouse Gene 2.0 ST Array

first: Yan

last: Kai


title: Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis

type: Genome variation profiling by genome tiling array


title: microRNA expression profiling  in human gastric cancer

status: Public on Feb 20 2016

city: Haikou

first: Yousheng

last: Huang

state: Hainan

address: The 3rd Xueyuan Road

department: Department of pathology

country: China

institute: Hainan Medical university

summary: Using the highly sensitive miRCURY LNA™ microRNA array, we screened 3100 microRNAs abundant in the human gastric cancer and Adjacent normal gastric mucosa  tissues, and the function of differentially expressed microRNAs were analyzed by bioinformatics. The enrichment results indicated that these microRNAs perhaps participated in the occurrence and development process of gastric cancer.

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

overall_design: In this study, three cases of  gastric cancer were used to acquire the microRNA expression profiling, and qPCR was employed to confirm the results of microRNA chip. The function of the differentially expressed microRNA were analyzed by bioinformatic methods. Finally,compared with the adjacent mormal moucosa tissues，the expression of  99 microRNAs  were up regulated,and 21 microRNAS were down regulated in gastric cancer.qPCR results showed an expression pattern consistent with that of the chip analysis.

first: You

middle: S

last: Xie


title: Identity, proliferation capacity, genomic stability and novel senescence markers of mesenchymal stem cells isolated from low volume of human bone marrow (I)

first: Gabrielis

last: Kundrotas

summary: Human bone marrow mesenchymal stem cells (hBM-MSCs) hold promise for treating diseases for which currently no therapeutic options exist. High quantities of MSCs are needed, requiring extensive cell expansion in long-term culture. However, the fundamental biological properties of MSCs can be altered by culture conditions. In this study, hBM-MSCs were isolated from residual human bone marrow (hBM) material and expanded to clinically relevant numbers at passage 3-4. The cells had normal morphology, proliferation rate, immunophenotype and karyotype. Despite the chromosomal stability, after additional three passages (P6-P7) hBM-MSCs entered senescence state, confirmed by SA-β-galactosidase staining and paralleling the slower proliferation, altered morphology and imunophenotype. qRT-PCR array profiling revealed 3 out of 86 genes significantly (p <0.05) differentially (≥2 fold) expressed in the late passage cells compared to the early passage cells.

overall_design: qPCR gene expression profiling. hBM-MSCs from 3 (1 male and 2 females) adult donors (age 30±7.21 years) were used. Each sample was tested in technical duplicate. 6 samples of early passage (P3-P4) hBM-MSCs were grouped to CONTROL group and 6 samples of late passage (P6-P7) hBM-MSCs were grouped to TEST group. The data were analyzed using web-based RT2 Profiler PCR Array Data Analysis v3.5 software (Qiagen)

first: Evelina

last: Gasperskaja

first: Grazina

last: Slapsyte

first: Zivile

last: Gudleviciene

first: Jan

last: Krasko

first: Ausra

last: Strumbryte

first: Regina

last: Liudkeviciene


title: Genome-wide copy number variation  profiling in Cynomolgus monkeys using customized NimbleGen CGH microarrays

summary:
Cynomolgus monkeys are well-established translational models for biomedical research and drug testing.  Cynomolgus monkeys are outbred species and exhibit substantial levels of genetic variation which can affect the outcome and interpretation of biomedical studies. Copy number variations (CNVs) are a significant source of genetic diversity and a comprehensive understanding of the genomic impact of CNVs on phenotypic traits is limited. A custom 4.2 million probes comparative genomic hybridization (CGH) array (Design-ID:  120405_Cynomolgus5_CGH_UX1) has been designed on the basis of the Cynomolgus monkey genome (Ebeling et al. (2011) Genome Research; PMID: 21862625) to assess  genome-wide copy number variation among Cynomolgus monkeys.  Using Cynomolgus monkey specific NimbleGen CGH Microarrays we profiled the genomes of 21 Cynomolgus monkeys.  Germline DNA from 21 Cynomolgus monkeys with different origin was tested against a Cynomolgus monkey reference. Cynomolus monkey samples were derived from breeding centers located in the Philippines (3 females and 3 males), in Vietnam (2 males and 2 females), in China for animals from Mainland Southeast Asia (3 females), or in Mauritius (4 females and 4 males). Furthermore genome-wide expression profiles were analyzed in 5 vitally important tissue samples (heart, kidney, liver, lung, spleen) from the same animals using a custom Cynomolgus monkey specific NimbleGen gene expression microarray (design ID: 120419_Cynomolgus_v5_TH_exp_HX12) to associate CNV genotypes with expression changes of proximal genes using a cis expression quantitative trait loci (cis-eQTL) mapping approach. Expression data have been deposited at the NCBI Gene Expression Omnibus (GEO) under accession numbers GSE76560.
The array CGH results analyzed in this study are further described in Gschwind A.R. et al. (2016) "Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis". under submission

overall_design: A NimbleGen customized 4.2M Whole-Genome Tiling CGH Array [design ID: 120405_Cynomolgus5_CGH_UX1] study using genomic DNA recovered from tissues of drug-naive Cynomolgus monkeys. The CGH microarray measures the fluorescence intensity ratio of dye-labeled DNA fragments  from test samples relative to a reference across 4.2 million 50-75mer probes spanning the Cynomolgus monkey genome with a median spacing of 598 bp. Germline DNA from 21 Cynomolgus monkeys with different origin was tested against a Cynomolgus monkey reference. The reference was made of DNA from blood samples taken from Cynomolgus monkeys from centers located in Mauritius (25 males). The design includes Labeling Hybridization Control (LHC) probes for the estimation of copy number amplifications and deletions of spike-in 7 kb plasmid DNAs.

first: Sue

last: Olson


title: LPS stimulation of human PBMC-derived macrophages

status: Public on Feb 25 2016

city: Hannover

first: Aravind

last: Tallam

state: Lower Saxony

address: Feodor-Lynen str. 7

department: BIOM

institute: TWINCORE

summary: Immunoresponsive gene 1 (IRG1) is one of the highest induced genes in macrophages under pro-inflammatory conditions and its function has been recently described: it codes for immune-responsive gene 1 protein/cis-aconitic acid decarboxylase (IRG1/CAD), an enzyme catalyzing the production of itaconic acid from cis-aconitic acid, a tricarboxylic acid (TCA) cycle intermediate. Itaconic acid possesses specific antimicrobial properties inhibiting isocitrate lyase, the first enzyme of the glyoxylate shunt, an anaplerotic pathway that bypasses the TCA cycle and enables bacteria to survive on limited carbon conditions. To elucidate the mechanisms underlying itaconic acid production through IRG1 induction in macrophages, we examined the transcriptional regulation of IRG1. Using a combination of literature information, transcription factor prediction models and genome-wide expression arrays, we inferred the regulatory network of IRG1 in mouse and human macrophages.

overall_design: 3 unstimulated (Control) and 3 LPS-stimulated human PBMC-derived macrophages

first: Alessandro

last: Michelucci


title: CCL171, T47D, MDA-MB231 cell lines: stimulation with BMP7 and antagonists

city: Zurich

first: Michal

last: Rajski

address: Winterthurerstrasse 190

department: Institute of Physiology

institute: University of Zurich

summary:
Methods: We used an ex vivo culture model and measured gene expression changes in human lung fibroblasts after stimulation with BMPs and their antagonists using HEEBO microarrays. The in vitro data were correlated with in vivo observations in published expression datasets of human lung adenocarcinomas.  Results: We have systematically analyzed the response to BMP2, BMP4, BMP7 and their antagonists, gremlin and noggin, to define common and specific gene expression patterns. A BMP2 induced gene expression signature was defined, which is specific for stromal fibroblasts. Gene expression profiles from lung adenocarcinoma biopsies were analyzed to determine the prognostic significance of the Fibroblast specific BMP2 induced gene list. This gene list successfully segregated patients with different prognostic outcome in 3 datasets. In a small dataset (Garber et al.) there was a strong trend for a worse prognosis of patients with adenocarcinomas of all stages over-expressing the Fibroblast specific BMP2 induced gene list. In two larger datasets with stage I adenocarcinomas we observed a significantly worse disease-free (p=0.002, Lee et al. and p=0.002, Bhattacharjee et al.) and overall survival (p=0.0002).  Conclusions: The effects of BMPs and their antagonists are heterogeneous in different cell types. The gene expression pattern induced by BMP2 in primary lung fibroblasts may predict outcomes of patients with lung adenocarcinomas.
A stimulus or stress experiment design type is where that tests response of an organism(s) to stress/stimulus. e.g. osmotic stress, behavioral treatment

first: Martin

last: Buess

first: John

last: Matese


title: Human cholangiocarcinoma (CC), ECC (extrahepatic CC) and ICC (intrahepatic CC) cases versus control

city: Heidelberg

first: Dieter

last: Weichenhan

address: Im Neuenheimer Feld 280

department: C010 Epigenomics

institute: DKFZ Heidelberg

type: Methylation profiling by genome tiling array

summary: CpG island methylation profiling of human cholangiocarcinoma, ECC and ICC, cases compared to matched normal controls or to pools of corresponding normal controls. Goal was to identify cholangiocarcinoma-specific differentially methylated regions (DMRs).

overall_design: Highly methylated DNA from cases and controls was enriched by methyl CpG-immunoprecipitation (MCIp) and co-hybridized. DMRs were defined by stepwise stringent criteria such as selecting top 5% vicinal array probes only. ECC- and ICC-specific and common DMRs were identified.


title: CCL171 BMP4 time course

summary:
Methods: We used an ex vivo culture model and measured gene expression changes in human lung fibroblasts after stimulation with BMPs and their antagonists using HEEBO microarrays. The in vitro data were correlated with in vivo observations in published expression datasets of human lung adenocarcinomas.  Results: We have systematically analyzed the response to BMP2, BMP4, BMP7 and their antagonists, gremlin and noggin, to define common and specific gene expression patterns. A BMP2 induced gene expression signature was defined, which is specific for stromal fibroblasts. Gene expression profiles from lung adenocarcinoma biopsies were analyzed to determine the prognostic significance of the Fibroblast specific BMP2 induced gene list. This gene list successfully segregated patients with different prognostic outcome in 3 datasets. In a small dataset (Garber et al.) there was a strong trend for a worse prognosis of patients with adenocarcinomas of all stages over-expressing the Fibroblast specific BMP2 induced gene list. In two larger datasets with stage I adenocarcinomas we observed a significantly worse disease-free (p=0.002, Lee et al. and p=0.002, Bhattacharjee et al.) and overall survival (p=0.0002).  Conclusions: The effects of BMPs and their antagonists are heterogeneous in different cell types. The gene expression pattern induced by BMP2 in primary lung fibroblasts may predict outcomes of patients with lung adenocarcinomas.
Experimental Factor Ontology

overall_design: time series design


title: Expression of CD271 in genetically unstable patient melanomas is highly variable and not linked to tumorigenic potential in an assay-dependent manner

status: Public on Feb 27 2016

city: Parkville

first: Vincent

middle: Dominique

last: Corbin

state: VIC

address: 1G Royal parade

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute

summary: Some cancers are thought to follow a cancer stem cell (CSC) model in which hierarchical and epigenetically determined relationships exist between phenotypically and functionally distinct cells within tumors. In melanoma, for example, CD271/p75/NGFR (nerve growth factor receptor) was found by some groups to be expressed in cells with enriched tumorigenic potential (Boiko et al., 2010; Civenni et al., 2011). However, these observations were not reproduced in highly efficient patient-derived xenograft (PDX) assays (Quintana et al., 2008), in which plastic, nonhierarchical relationships were proposed between CD271- and CD271+ cells (Quintana et al., 2010). Here we confirm that a CD271-based CSC model does not apply to melanoma, regardless of the PDX assay method used. In side-by-side testing of published PDX assays, no consistent differences were seen in CD271 expression or in PDX tumor formation from purified CD271- or CD271+ cells from patient melanomas. Analysis of CD271 in sixty-eight PDX tumors grown from CD271- or CD271+ cells revealed strikingly variable CD271 re-expression patterns, which were not consistent with stable hierarchical or plastic relationships between CD271-defined cell sub-populations. Genotyping of sibling PDX tumors showed extensive (28% - 48%) genomic copy number differences, which were also apparent  (1.4% - 23%) between CD271- and CD271+ cells purified from each of four melanomas, revealing intra-tumoral genetic heterogeneity associated with CD271 expression. Thus, CD271 is not linked reproducibly to tumorigenic potential in melanoma, regardless of the method of melanoma cell isolation, and its expression appears driven by complex and unstable interactions between changing epigenetic and genetic states. Understanding of melanoma biology and the treatment of melanoma patients are unlikely to be advanced by applying a CD271-based CSC model to this disease.

overall_design: To test whether differences in CD271 expression among PDX melanomas grown from CD271- or CD271+ cells could be linked to genetic differences, we genotyped Lin- cells sorted by flow cytometry from four pairs of tumors. Tumors in each pair were grown from aliquots from the same pools of cells, purified according to CD271 expression from patient melanomas 12-1036 and 12-1254. Genomic DNA was extracted from purified Lin- cells from each tumor and subjected to single nucleotide polymorphisms (SNP) genotyping using Illumina Human OmniExpress 715K arrays. To test for genetic differences between CD271- and CD271+ cells within the same tumor, we flow cytometrically-purified CD271- and CD271+ cells from patient (n=1) and PDX (n=4) melanomas, extracted DNA and subjected to SNP genotyping using Illumina 2.58M arrays.

first: Mark

last: Shackleton

first: Anthony

last: Papenfuss


title: Gene expression patterns in allergen-driven CD4 T cell responses from human atopics with or without asthma.

city: Subiaco

last: Bosco

state: WA

address: 100 Roberts Road

institute: Telethon Kids Institute

summary:
PBMC from house dust mite (HDM) sensitized atopics with or without asthma (or nonallergic controls) were cultured in the presence or absence of HDM extract for 24 hours.
At the termination of the cultures, immunomagnetic separation was performed to purify CD4 T cells. Gene expression was profiled on microarrays.

overall_design: The study design consisted of 72 subjects, and two experimental conditions (medium control, HDM stimulation).


title: Identity, proliferation capacity, genomic stability and novel senescence markers of mesenchymal stem cells isolated from low volume of human bone marrow (II)

first: Gabrielis

last: Kundrotas

summary: Human bone marrow mesenchymal stem cells (hBM-MSCs) hold promise for treating diseases for which currently no therapeutic options exist. High quantities of MSCs are needed, requiring extensive cell expansion in long-term culture. However, the fundamental biological properties of MSCs can be altered by culture conditions. In this study, hBM-MSCs were isolated from residual human bone marrow (hBM) material and expanded to clinically relevant numbers at passage 3-4. The cells had normal morphology, proliferation rate, immunophenotype and karyotype. Despite the chromosomal stability, after additional three passages (P6-P7) hBM-MSCs entered senescence state, confirmed by SA-β-galactosidase staining and paralleling the slower proliferation, altered morphology and imunophenotype. qRT-PCR array profiling revealed 10 out of 86 genes significantly (p <0.05) differentially (≥2 fold) expressed in the late passage cells compared to the early passage cells

last: Gasperskaja


title: Omics profiling of 21 novel primary and metastatic colorectal cancer cell lines

city: Singapore

first: Arnoud

last: Boot

state: Singapore

address: 8 college road

country: Singapore

institute: Duke-NUS Medical School

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


title: Primary and adjacent non-malignant tissue samples of 100 HCC patients (miRNA)

first: Thomas

last: Thurnherr

address: 11 Hospital Drive

institute: NCCS

summary: Genome-wide miRNA expression profiles of 100 primary and matched non-malignant tissues of HCC patients from a Singapore patient cohort. HCC is a hetergenous disease and it is important to understand the underlying molecular mechanisms. Here, we studied the role of microRNAs in HCC by integrating microRNA and gene expression profiles of HCC patients.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Profiling of 100 primary and adjacent non-malignant HCC tissue samples on mirXplore two-color miRNA expression microarray. All tissues were collected with approvals from the National Cancer Centre, Singapore; the Research Ethics Review Committee; and signed patient informed consent.

first: Steve

last: Rozen

first: Caroline

last: Lee


title: Transcriptome profile for roots of the rice plants which showed favorable morpho-physiological adaptation when subjected to severe drought stress

city: Los Banos

first: Manish

middle: L

last: Raorane

state: Laguna

address: UP college campus

department: Plant Breeding, Genetics and Biotechnology

country: Philippines

institute: International Rice Research Institute

summary: To understand how OsNAM12.1 over-expression influences the target genes within qDTY12.1 and across the genome to affect root growth, the root transcriptome of Vandana, 481-B, IR64-Tr-E2, and IR64-WT were compared under control and drought conditions.

overall_design: Drought induced gene expression was studied in the roots of the rice plants subjected to severe drought. Seeds of Vandana, 481-B, IR64 and the OsNAM12.1 overexpression line (OsNAM Event 2) were sown in 5 biological replicates in a randomized complete block design for both the well watered and drought stress treatments.

first: Mandy

last: Pueffeld

first: Nese

last: Sreenivasulu

first: Ajay

last: Kohli


title: Development of coregulator-dependent androgen receptor target gene signatures

city: buffalo

first: Dan

last: Wang

state: NY

address: Elm & Carlton Streets

institute: RPCI

summary: To decipher the contribution of coregulators to androgen receptor target gene expression, effect of siRNA-mediated silencing of 18 clinically relevant coregulators on bona fide androgen receptor target gene expression was studied.

overall_design:
Human LNCaP prostate cancer cells were transfected with individual siRNA SmartPools targeting 18 clinically relevant coregulators or a non-targeting siRNA SmartPool. Forty-two hours after transfection, cells were treated with synthetic androgen R1881 (5nM) or vehicle. Three biological replicates were generated per treatment group. Forty-eight hours later, total RNA was isolated and processed for Agilent microarray analysis.
The two normalizer are aliquots from same RNA sample that serves as internal control.

first: Hannelore

last: Heemers


title: microRNA expression profiles of distinct mouse mammary epithelial cell types

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

institute: Walter and Eliza Hall Institute of Medical Research

summary: RNA samples were prepared from freshly sorted mammary cell subpopulations (MaSC/basal-enriched, luminal progenitor, mature luminal and stromal) from five sets of adult mice. High throughput RT-PCR was used to measure the global microRNA expression profiles of each cell subpopulation. The expression profiles were compared between cell subpopulations to gain insight into the regulation of lineage-restricted genes.

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: High throughput RT-PCR profiling of microRNA expression in four mouse mammary cell populations. Samples were collected from pooled mammary gland tissue from a number of mice. Samples were collected at over five different times with tissue from independent sets of mice.

first: Bhupinder

last: Pal

first: Yunshun

last: Chen

first: Geoff

last: Lindeman

first: Jane

last: Visvader


title: Sexual polyploidization in Medicago sativa L.: impact on the phenotype, gene transcription and genome methylation

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

institute: University of Verona

summary: Polyploidization as the consequence of 2n gamete formation is a prominent mechanism in plant evolution. Studying its effects on the genome and its expression has both basic and applied interest. We crossed two diploid (2n=2x=16) M. sativa plants, a subsp. falcata seed parent and a coerulea x falcata pollen parent that produce a mixture of n and 2n eggs and pollen, respectively. Such cross produced full-sib diploid and tetraploid (2n=4x=32) progenies, the latter being the result of bilateral sexual polyploidization (BSP). These unique materials allowed us to investigate the effects of BSP, and separating the effect of intraspecific hybridization from those of polyploidization by comparing 2x with 4x full sib progeny plants.  SSR marker segregation demonstrated tetrasomic inheritance for all chromosomes but one, demonstrating that these neotetraploids are true autotetraploids. BSP brought about increased biomass, earlier flowering, higher seed set and weight, larger leaves with larger cells. Microarray analyses with M. truncatula gene chips showed that several hundred genes, related to diverse metabolic functions, changed their expression level as a consequence of polyploidization. In addition, cytosine methylation increased in 2x but not in 4x hybrids. Our results indicate that sexual polyploidization induce significant transcriptional novelty, possibly mediated in part by DNA methylation, and phenotypic novelty that can be at the base of improved adaptation and reproductive success of tetraploid M. sativa with respect to its diploid progenitor. These polyploidy-induced changes may have promoted the adoption of tetraploid alfalfa in agriculture.

overall_design: Gene expression analysis of leaves  at the vegetative stage of two  Medicago sativa genotypes (PG-F9 and 12P) compared with three F1 diploid lines  and three F1 tetraploid lines originating from crossing PG-F9 x 12P. Three biological replicates were taken for each sample, resulting in a total of twenty-four samples.

first: Daniele

last: Rosellini

first: Nicoletta

last: Ferradini

first: Stefano

last: Allegrucci

last: Capomaccio

first: Elisa

middle: D

last: Zago

first: Paola

last: Leonetti

first: Bachir

last: Balech

first: Riccardo

last: Aversano

first: Domenico

last: Carputo

first: Lara

last: Reale

first: Fabio

last: Veronesi


title: microRNA expression profiles of distinct human mammary epithelial cell types

last: Smyth

summary: RNA samples were prepared from freshly sorted mammary cell subpopulations (MaSC/basal-enriched, luminal progenitor, mature luminal and stromal) from five human donors. High throughput RT-PCR was used to measure the global microRNA expression profiles of each cell subpopulation. The expression profiles were compared between cell subpopulations to gain insight into the regulation of lineage-restricted genes.

overall_design: High throughput RT-PCR profiling of microRNA expression in four mammary cell populations from five human donors.


title: microRNA expression profiles of distinct human and mouse mammary epithelial cell types

sample_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA-dependent repair pathways

status: Public on Feb 15 2016

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

institute: SIB Swiss Institute of Bioinformatics

summary: The mammalian heart has poor regenerative capacity following injury. In contrast, certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA-dependant regulatory circuits in the heart. We identified novel miRNA-dependant networks involved in critical biological pathways, which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart.

overall_design: 2 conditions, 6 biological replicates per condition

first: Stefania

last: Crippa

first: Samir

last: Ounzain

first: Mohammed

last: Nemir

first: Corinne

last: Berthonneche

first: Alexandre

last: Sarre

first: Gaëlle

last: Boisset

first: Keith

last: Harshman

first: Ioannis

last: Xenarios

first: Dario

last: Diviani

first: Daniel

last: Schorderet

first: Thierry

last: Pedrazzini


title: Gene Expression Profiling of human monocytes: Combination Therapy with Anti–CTLA-4 and Anti–PD-1 Leads to Distinct Immunologic Changes In Vivo

status: Public on Feb 16 2016

city: New Haven

first: Rakesh

last: Verma

state: CT

address: 333 Cedar St.

department: Yale Cancer Center

institute: Yale University

summary:
Transcriptome analysis of human peripheral blood monocytes
Combination therapy concurrently targeting PD-1 and CTLA-4 immune checkpoints leads to remarkable antitumor effects. Although both PD-1 and CTLA-4 dampen the T cell activation, the in vivo effects of these drugs in humans remain to be clearly defined.  To better understand biologic effects of therapy, we analyzed blood/tumor tissue from patients undergoing single or combination immune checkpoint blockade. We show that blockade of CTLA-4, PD-1, or combination of the two leads to distinct genomic (changes in gene-expression profile) and functional signatures in vivo in purified human T cells and monocytes.

overall_design: RNA extracted from freshly isolated monocytes from peripheral blood of patients treated with either anti–PD-1 (n = 6), anti–CTLA-4 (n = 5), Combo therapy with anti–PD-1 and anti–CTLA-4 concurrently (Combo, n = 6), and Seq anti–PD-1 in patients with prior anti–CTLA-4 (Seq, n = 3) was analyzed using the Affymetrix GeneChip Human Transcriptome 2.0 exon array. No techinical replicates were performed.


title: Cells Comprising the Prostate Cancer Microenvironment Lack Recurrent Clonal Somatic Genomic Aberrations

status: Public on Feb 12 2016

city: Seattle

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Prostate cancer-associated stroma (CAS) plays an active role in malignant transformation, tumor progression, and metastasis. Molecular analyses of CAS have demonstrated significant changes in gene expression; however, conflicting evidence exists on whether genomic alterations in benign cells comprising the tumor microenvironment (TME) underlie gene expression changes and oncogenic phenotypes. This study evaluates the nuclear and mitochondrial DNA integrity of prostate carcinoma cells, CAS, matched benign epithelium and benign epithelium-associated stroma by whole genome copy number analyses, targeted sequencing of TP53, and fluorescence in situ hybridization. Comparative genomic hybridization (aCGH) of CAS revealed a copy-neutral diploid genome with only rare and small somatic copy number aberrations (SCNAs). In contrast, several expected recurrent SCNAs were evident in the adjacent prostate carcinoma cells, including gains at 3q, 7p, and 8q, and losses at 8p and 10q. No somatic TP53 mutations were observed in CAS. Mitochondrial DNA (mtDNA) extracted from carcinoma cells and stroma identified 23 somatic mtDNA mutations in neoplastic epithelial cells but only one mutation in stroma. Finally, genomic analyses identified no SCNAs, no loss of heterozygosity (LOH) or copy-neutral LOH in cultured cancer-associated fibroblasts (CAFs), which are known to promote prostate cancer progression in vivo.

overall_design: Agilent whole human genome aCGH oligonucleotide microarrays were used to assess copy number aberrations in 79 specimens from 20 patients as well as two pairs of cancer-associated fibroblasts (CAF) and benign/normal associated fibroblasts (NAF). 3 CAF/NAF sample pairs were also assessed for DNA copy number aberrations and copy-neutral LOH using the Infinium HumanOmniExpressExome BeadChip Kit.

first: Daniella

last: Bianchi-Frias

first: Ryan

last: Basom

first: Jeffrey

middle: J

last: Delrow

middle: M

first: Olga

last: Dakhova

first: Xiaoyu

last: Qu

first: Min

last: Fang

first: Omar

middle: E

last: Franco

first: Nolan

last: Ericson

first: Jason

last: Bielas

first: Simon

middle: W

last: Hayward

first: Lawrence

last: True

first: Colm

last: Morrissey

first: Lisha

last: Brown

first: Neil

middle: A

last: Bhowmick

first: David

last: Rowley

first: Michael

last: Ittmann

first: Peter

last: Nelson


title: Identification of MicroRNAs Targeting to Stat3 in RAW264.7 cells

status: Public on Feb 13 2016

city: Shanghai

first: Xiaoping

last: Su

address: 800 Xiangyin Road

institute: National Key Laboratory of Medical Immunology & Institute of Immunology

summary: Purification of mouse mRNAs encoding signal transducer and activator of transcription 3 (Stat3) identified many miRNAs using multiplex miRNA array in RAW264.7 cells.

overall_design: To investigate the miRNAs targeting to mouse Stat3 gene in macrophage cells, we performed a protocol miRIP to affinity purify the miRNAs from an endogenous segment of Stat3 mRNA using nucleic acid hybridization and use multiplex miRNA array to identify the associated miRNAs.

first: Xiang

last: Liu

first: Huamin

last: Wang

first: Xuetao

last: Cao


title: Transcriptional profiling of Coxiella burnetii reveals extensive cell wall remodeling in the small cell variant developmental form

status: Public on Feb 10 2016

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: A hallmark of Coxiella burnetii, the bacterial cause of human Q fever, is a biphasic developmental cycle that generates biologically, ultrastructurally, and compositionally distinct large cell variant (LCV) and small cell variant (SCV) forms. LCVs are replicating, exponential phase forms while SCVs are non-replicating, stationary phase forms. The SCV has several properties, such as a condensed nucleoid and an unusual cell envelope, suspected of conferring enhanced environmental stability. To identify genetic determinants of the LCV to SCV transition, we profiled the C. burnetii transcriptome by microarray at 3 (early LCV), 5 (late LCV), 7 (intermediate forms), 14 (early SCV) and 21 days (late SCV) post-infection (PI) of Vero epithelial cells. Relative to early LCV, genes down-regulated in the SCV were primarily involved with intermediary metabolism. Up-regulated SCV genes included those involved in oxidative stress responses, arginine acquisition, and cell wall remodeling. A striking transcriptional signature of the SCV was induction (>7-fold) of five genes encoding predicted L,D transpeptidases that catalyze nonclassical 3-3 peptide cross-links in peptidoglycan (PG), a modification that can influence several biological traits in bacteria. Accordingly, of cross-links identified, muropeptide analysis showed PG of SCV with 46% 3-3 cross-links as opposed to 16% 3-3 cross-links for LCV. Moreover, cryo-electron microscopy revealed SCV with an unusually dense periplasmic layer that was intimately associated with the outer membrane. In contrast, LCV had a clearly distinguishable periplasm and inner/outer membranes. Collectively, these results indicate the SCV produces a unique transcriptome with a major component directed towards remodeling a PG layer that likely contributes to Coxiella's environmental resistance.

platform_organism:
Coxiella burnetii
Rickettsia rickettsii
Chlamydia muridarum
Chlamydia pneumoniae AR39
Staphylococcus epidermidis RP62A
Staphylococcus epidermidis ATCC 12228
Staphylococcus aureus subsp. aureus MW2
Borreliella burgdorferi B31
Coxiella burnetii RSA 493
Chlamydia caviae GPIC
Chlamydia trachomatis D/UW-3/CX
Staphylococcus haemolyticus JCSC1435
Granulibacter bethesdensis

overall_design: Coxiella Vero time series. Coxiella was profiled at day 3, day 5, day 7, day 14 and day 21 post-infection of Vero epithelial cells.

first: Kelsi

last: Sandoz

last: Popham

first: Paul

last: Beare

first: Daniel

first: Bryan

last: Hansen

first: Vinod

last: Nair

first: Robert

last: Heinzen


title: Gene Expression Profiling of human T cells: Combination Therapy with Anti–CTLA-4 and Anti–PD-1 Leads to Distinct Immunologic Changes In Vivo

first: Rakesh

last: Verma

summary:
Transcriptome analysis of human peripheral blood T cells
Combination therapy concurrently targeting PD-1 and CTLA-4 immune checkpoints leads to remarkable antitumor effects. Although both PD-1 and CTLA-4 dampen the T cell activation, the in vivo effects of these drugs in humans remain to be clearly defined.  To better understand biologic effects of therapy, we analyzed blood/tumor tissue from patients undergoing single or combination immune checkpoint blockade. We show that blockade of CTLA-4, PD-1, or combination of the two leads to distinct genomic (changes in gene-expression profile) andfunctional signatures in vivo in purified human T cells.

overall_design: RNA extracted from freshly isolated T cells from peripheral blood of patients treated with either anti–PD-1 (n = 6), anti–CTLA-4 (n = 5), Combo therapy with anti–PD-1 and anti–CTLA-4 concurrently (Combo, n = 6), and Seq anti–PD-1 in patients with prior anti–CTLA-4 (Seq, n = 3) was analyzed using the Affymetrix GeneChip Human Transcriptome 2.0 exon array. No techinical replicates were performed.


title: Heliothis virescens gene expression on gossypol suppelemented diet, larval gut and rest of body

status: Public on Feb 06 2016

city: Jena

first: Heiko

last: Vogel

address: Hans-Knoell-Strasse 8

department: Dpt. of Entomology

institute: Max Planck Institute for Chemical Ecology

summary: The transcriptional response of H. virescens larvae was analyzed after feeding on gossypol supplemented diet, a toxic secondary metabolite produced in cotton plants, to detect potential detoxification enzymes possibly involved in detoxification of gossypol by H. virescens.

overall_design: A one-color microarray-based gene expression analysis was performed with Cy3 labeled cRNA of gut and rest of the body of H. virescens larvae that fed on 0.32% gossypol and control diet. For each treatment and tissue four biological replicates were used.

first: Corinna

last: Krempl


title: Exvivo Experiment

city: Liverpool

last: Griffiths

address: 8 West Derby Street

country: United Kingdom

institute: Institute of Infection and Global Health, University of Liverpool

summary:
Healthy Kenyan children with (n=10) or without (n=14) a previous history of complicated Plasmodium falciparum infection had aliquots of their whole-blood cultured ex-vivo and either mock infected or infected with Plasmodium falciparum (A4 strain) for 5 (n=24) and 9 hours (n=11).
A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc.
Time: lenght of co-culture
Infection: whole-blood cells cultured ex-vivo in the presence of either uninfected red blood cells or red blood cells infected with Plasmodium falciparum
Disease State: Healthy individuals with (PrevHxMal) or without (NoHxMal) previous exposure to complicated Plasmodium falciparum infection


title: Vietnam Timecourse Experiment

summary:
Gene expression data from Vietnamese subjects admitted to hospital with acute uncomplicated (n=6) or complicated (n=6) Plasmodium falciparum malaria infection had whole-blood samples collected at admission, 1 week later and 1 month later.
Groups of assays that are related as part of a time series.
Disease State: patient with complicated or uncomplicated Plasmodium falciparum malaria infection or Healthy control


title: DNA methylation in the arcuate nucleus of heifers under two nutritional schedules

status: Public on Feb 11 2016

city: College Station

first: Bruna

middle: Rios Coelho

last: Alves

state: TX

address: 2471 TAMU - Department of Animal Sciences

department: Animal Sciences

institute: Texas A&M University

summary: DNA methylation was assessed in genomic DNA obtained from the arcuate nucleus of heifers fed to gain body weight at high (HG, n = 4) and low (LG, n = 4) rates from 4.5 to 8.5 mo of age.  A methyl-CpG binding domain-based (MBD) protein assay was performed to capture fragments of methylated DNA (methylated-enriched DNA). Input (total) and methylated-enriched DNA were labeled with two different dyes and co-hybridized to a custom-designed oligonucleotide array targeted to genes associated with nutritional inputs and the control of puberty. The ratio of the log2 (enriched/input) of the normalized intensities, were determined. Data was analyzed comparing values of HG versus LG heifers.

overall_design:
Two nutritional schedules: HG (n=4 heifers) and LG (n=4 heifers); one array per heifer; methylated enriched DNA (enriched) and total DNA (input) co-hybridyzed into each array
Methylated-enriched DNA obtained from a methyl-CpG binding domain-based (MBD) protein assay

first: Rodolfo

last: Cardoso

first: Ryan

last: Doan

first: Scott

middle: V

last: Dindot

first: Gary

last: Williams

first: Marcel

last: Amstalden


title: Gene expression in tomato in response to Pyrenochaeta lycopersici infection

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary:
Transcriptional changes in greenhouse-grown plants of tomato varieties Monaymaker and Mogeor infected with Pyrenochaeta lycopersici compared to uninfected control plants. The objective of the the study was to give an insight into the establishment of compatible and incompatible interactions between tomato and the pathogen using susceptible (Moneymaker) and resistant (Mogeor) varieties of tomato.

****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Justyna Anna Milc. The equivalent experiment is LE4 at PLEXdb]

overall_design:
genotype: Moneymaker; pathogen infection: infected(2-replications)
genotype: Moneymaker; pathogen infection: uninfected(2-replications)
genotype: Mogeor; pathogen infection: infected(2-replications)
genotype: Mogeor; pathogen infection: uninfected(2-replications)

first: Justyna

last: Milc

first: Nicola

last: Pecchioni


title: Rat cardiomyocyte; control vs celecoxib treatment

status: Public on Feb 05 2016

city: Jinju

first: Dong-hoon

last: Lee

state: Gyeongnam

address: 15 Jinju-daero 816 Beon-gil

department: Convergence Medical Science

country: South Korea

institute: Gyeongsang National University

summary:
Gene expression analysis of celecoxib-treated rat cardiomyocytes vs non-treated rat cardiomyocytes.
Goal of study is to identify changes on genes expression induced by celecoxib. The data analysis focused on genes that might be related to cardiotoxicity; genes expression ion channels and pathways.

overall_design: two control samples vs 6 celecoxib-treated samples. Variables of treatment included two time points (6h or 24h) and three reference concentrations (1, 1/5 and 1/25). Each group had 3 replicates.

first: Dong

first: Cheol

last: Oh


title: Vietnamese malaria patient experiment

first: Michael

summary:
Gene expression data from whole-blood collected from healthy Vietnamese subjects (n=8) or from patients admitted to hospital with acute uncomplicated (n=9) or complicated (n=20) Plasmodium falciparum malaria infection.
A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc.
Disease State: patient with complicated or uncomplicated Plasmodium falciparum malaria infection or Healthy control

first: Stephen

last: Popper


title: Helicoverpa armigera gene expression on gossypol suppelemented diet, larval gut and rest of body

summary: The transcriptional response of H. armigera larvae was analyzed after feeding on gossypol supplemented diet, a toxic secondary metabolite produced in cotton plants, to detect potential detoxification enzymes possibly involved in detoxification of gossypol by H. armigera.

overall_design: A one-color microarray-based gene expression analysis was performed with Cy3 labeled cRNA of gut and rest of the body of H. armigera larvae that fed on 0.016%, 0.16% gossypol and control diet. For each treatment and tissue four biological replicates were used.


title: BET Protein Inhibitor JQ1 Induces Cell Cycle Arrest in Mesenchymal Stem Cells

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

summary:
Efficacy and safety of anticancer drugs are traditionally studied using cancer cell lines and animal models. Recently, a potential anticancer agent, JQ1, an inhibitor of bromodomain and extra terminal (BET) protein, has been shown to promote apoptosis of cancerous cells by arresting them in G1 phase of the cell cycle. However, the effect of JQ1 on normal cells is poorly understood.
In this study, we investigated the safety of JQ1 by using human umbilical cord mesenchymal stem cells (MSCs) as an in vitro model system. Our results indicated that JQ1 induced cell cycle arrest in G1 phase of MSCs, but did not promote apoptosis. Microarray analysis of MSCs treated with JQ1 indicated that it down-regulated genes involved not only in cell cycle regulation but also DNA replication, mitosis, and cell division.
Although many studies have suggested the potential of JQ1 as an anticancer agent, our findings suggest that it caused a deleterious effect on normal cells and may not be safe for anticancer therapy.

overall_design: Human umbilical cord derived MSCs were cultured in vitro and treated with either 100 nM or 500 nM JQ1 for 24 hrs. Gene expression of treated cells was compared to untreated cultured cells.

first: Saeed

last: Alghamdi

first: Irfan

last: Khan

first: Christina

last: McKee

first: Naimisha

last: Beeravolu

first: George

last: Wilson

first: Rasul

last: Chaudhry


title: Plasmodium falciparum infection

last: Griffiths

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


title: Kenyan malaria patient Experiment

summary:
Gene expression data from whole-blood collected from Kenyan children with Plasmodium falciparum malaria infection at acute hospital admission (n=15) and at convalescence (n=9).
A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc.
Disease State: with Plasmodium falciparum malaria infection at acute hospital admission and at convalescence


title: Rat cardiomyocyte: control vs diclofenac treatment

summary:
Gene expression analysis of diclofenac-treated rat cardiomyocytes vs non-treated rat cardiomyocytes.
Goal of study is to identify changes on genes expression induced by diclofenac. The data analysis focused on genes that might be related to cardiotoxicity; genes expression ion channels and pathways.

overall_design: two control samples vs 6 diclofenac-treated samples. Variables of treatment included two time points (6h or 24h) and three reference concentrations (1, 1/5 and 1/25). Each group had 3 replicates.


title: Expression profiling of 22Rv1, DU145, LNCaP and PC3 prostasphere cultures at day 0, 4, 8 and 12 [stem cell]

city: Monterrey

first: Roberto

last: Portillo Lara

state: Nuevo León

address: Ave. Eugenio Garza Sada 2501 Sur Col. Tecnológico

department: División de Biotecnología y Alimentos

country: Mexico

institute: Tecnológico de monterrey

summary: Cancer stem cells (CSCs) drive prostate cancer (PCa) progression and metastasis. These cells exhibit remarkable self-renewal, chemoresistant and invasive potentials, and are thought to participate in the changes in cellular architecture that lead to epithelial-to-mesenchymal transition (EMT). Conventional therapies fail to eliminate CSCs, which results in tumor recurrence and progression to castration resistant PCa (CRPC). Recent evidence suggests that castration itself can induce EMT, which could potentiate the “stemness” and number of CSCs within the tumor. Hence, there is an urgent need for EMT- and CSC-targeted therapies that could prevent progression to CRPC.  22Rv1, DU145, LNCaP, and PC3 cells were grown under sphere-forming conditions standardized in our lab. We have previously demonstrated that these enriched PCa cell lines exhibit phenotypic characteristics associated with CSCs in vivo. Over-expression of the stem-associated CD133 biomarker was determined via flow cytometric analysis. Total RNA was isolated from CD133+ prostasphere-derived cells. Gene expression profiling was carried out using the nCounter NanoString system and three different CodeSets associated with cancer or stem cells. Functional annotation was performed using the over-representation analysis tool from ConsensusPathDB.  Functional annotation analysis of upregulated transcripts suggests that prostasphere-derived cells undergo a transcriptional reprogramming that triggers a major phenotypic shift. These changes are similar to the mesenchymal shift associated with EMT that drives PCa progression to CRPC. Each cell line exhibited distinct expression profiles that are presented and analyzed individually. Furthermore, our analysis revealed over-represented pathways that were common to all cell lines, which are related to the MAPK/ERK, PI3K/AKT, Notch, and Wnt stem cell fate signaling networks.  Transcriptional analysis of induced CSCs not only offers insight into their underlying pathophysiology, but can also be used as a platform for the discovery of therapeutic targets for CSC-specific intervention. In this contribution, we present a flexible in vitro platform for the identification of functionally relevant therapeutic targets, using cell samples with low numbers of malignant stem/progenitors that were enriched in vitro. This approach represents a novel and effective strategy that can be used in the development of therapeutic strategies, which could ultimately be tailored to the biology of individual patients.

overall_design: 22Rv1, DU145, LNCaP and PC3 prostasphere cultures were sampled on Day 4 (P 2), Day 8 (P 3) and Day 12 (P 4), and compared relative to parental monolayers on Day 0 of culture (P 1). Three independent measurements were carried out for monolayers at Day 0 using the CancerReference Kit.  Day 12 prostaspheres were enzymatically dissociated and sorted via MACS using the Anti-CD133/2 (293C3)-PE Antibody (Miltenyi) into CD133+ and CD133- fractions. Total RNA was extracted from CD133+ cells and were analyzed using the nCounter GX Cancer Reference kit, the Stem Cell panel and the custom made ITESM CodeSet (14 genes associated with prostate cancer) from NanoString Technologies. This series contains data for the Stem Cell panel.

first: R

first: M

last: Moisés Alvarez


title: Expression profiling of 22Rv1, DU145, LNCaP and PC3 prostasphere cultures at day 0, 4, 8 and 12 [ITESM]

overall_design: 22Rv1, DU145, LNCaP and PC3 prostasphere cultures were sampled on Day 4 (P 2), Day 8 (P 3) and Day 12 (P 4), and compared relative to parental monolayers on Day 0 of culture (P 1). Three independent measurements were carried out for monolayers at Day 0 using the CancerReference Kit. were sampled Day 12 prostaspheres were enzymatically dissociated and sorted via MACS using the Anti-CD133/2 (293C3)-PE Antibody (Miltenyi) into CD133+ and CD133- fractions. Total RNA was extracted from CD133+ cells and analyzed using the nCounter GX Cancer Reference kit, the Stem Cell panel and the custom made ITESM CodeSet from NanoString Technologies. This series contains data for the ITESM CodeSet.


title: Expression profiling of 22Rv1, DU145, LNCaP and PC3 prostasphere cultures at day 0, 4, 8 and 12


title: A comprehensive study to understand the effects of soil type, soil transplant and landuse changes on soil microbial community and its feedback responses

status: Public on Feb 04 2016

city: beijing

first: zhao

last: mengxin

address: Haidian District Zhongguancun Street

institute: tsinghua university

summary:
The experiment at three long-term agricultural experimental stations (namely the N, M and S sites) across northeast to southeast China was setup and operated by the Institute of Soil Science, Chinese Academy of Sciences. This experiment belongs to an integrated project (The Soil Reciprocal Transplant Experiment, SRTE) which serves as a platform for a number of studies evaluating climate and cropping effects on soil microbial diversity and its agro-ecosystem functioning.
Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of soil type, soil transplant and landuse changes on soil microbial communities, which are key drivers in Earth’s biogeochemical cycles.

overall_design: Eighty one samples were collected from three soil types (Mollisol,Inceptisol,Ultisol) in three sites (Hailun, Fengqiu and Yingtan) along a latitude with reciprocal transplant; With three treatment of bare fallow soil, maize cropping soil and NPK fertilization soil in each site; Three replicates in every treatments.

first: Mengxin

last: Zhao

first: Yunfeng

last: Yang

first: Jizhong

last: Zhou

first: Bo

last: Sun


title: The comparison of MicroRNA profile of the dermis between young and old human

first: Leihong

last: Xiang

address: 12 Wulumuqi Zhong Road

institute: Huashan Hospital, Shanghai Medical College, Fudan University

summary: Skin aging is a process of structural and compositional remolding that can be manifested as wrinkling and sagging. Remarkably, the dermis plays a dominant role in the process of skin aging. Recent studies suggest that microRNAs (miRNAs) may play a role in the regulation of gene expression in organism aging. However, studies about age-related miRNAs in human skin remain limited. In order to obtain an overall view of miRNAs expression in human aged dermis, we have investigated the alteration of microRNAs during aging by examining biopsies of human dermis from 12 young and aged donors, and demonstrated that numerous microRNAs showed significant alteration in dermis tissue.

overall_design: Normal human dermal tissue from 12 consenting individuals. Old group vs young group. Old group: with the age over 60 years old; young group: with the age below 10 years old; each group was constituted of 6 individuals.

first: Tong

last: Li

first: Xianghong

last: Yan

first: Min

last: Jiang


title: Combination of multiomics approach and BCR-ABL based molecular testing: A better way to monitor treatment regimen and  disease progression in Chronic Myeloid Leukemia [OncoScan]

city: Lucknow

first: Neetu

last: Singh

address: Chowk

department: Center for Advance Research

country: India

institute: King George's Medical University

summary:
We screened TKI-treated-CML-samples in different-phases  based on < or >10% copies of BCR-ABL, undetected and control-samples for generating transcriptomics-profile.
Transcriptionally, three clusters were identified which showed correlation with BCR-ABL transcript-levels i.e. <10% copies (I-cluster) , undetectable (II-cluster) and >10% copies (III-cluster).

overall_design: CML-new cases as well as Tyrosiine kinase treated-different phases of CML

first: Anil

last: Tripathi

first: Dinesh

last: sahu

first: Archana

last: Mishra

first: Rebecca

last: Chowdhry

first: Ravi

last: Kant


title: Reactive oxygen species contribute to the bactericidal effects of the fluoroquinolone moxifloxacin in Streptococcus pneumoniae: metabolic pathways involved

city: Majadahonda

first: Antonio

middle: J.

last: Martin-Galiano

state: Madrid

address: Ctra. Majadahonda-Pozuelo, km 2.2

department: Bacterial genetics

country: Spain

institute: Instituto de Salud Carlos III

summary: We studied the transcriptomic response of S. pneumoniae to moxifloxacin, a fluoroquinolone that inhibits DNA gyrase. At 10 × MIC, 30 and 140 responsive genes were detected at 15 and 30 minutes, respectively. Several pathways leading to an increase in pyruvate showed up-regulation. These included 2 genes introducing P-sugars into the glycolysis and 3 out of 7 genes of the glycolysis pathway, which converts fructose-6P to pyruvate. In addition, an increase in acetyl-coA would be expected from the down-regulation of the genes coding for the acetyl-coA carboxylase, and in turn, to a further increase in pyruvate by the up-regulation of formate acetyltransferase. Since pyruvate is converted to hydrogen peroxide (H2O2) by pyruvate oxidase (SpxB), its increase would lead to an equivalent increase in the intracellular amount of H2O2, and in turn, in those of hydroxyl radicals resulting from the Fenton reaction, which damage DNA, lipids and proteins. We observed similar increases in the production of H2O2 and hydroxyl radicals under moxifloxacin treatment. These reactive oxygen species contributed to the lethality of the drug, as showed by the attenuation of its lethality in a strain lacking SpxB. These results support the production of redox alterations by fluoroquinolones and are in agreement with our previous findings showing that levofloxacin, an inhibitor of topoisomerase IV, triggers the transcriptional activation of iron transport genes. Both fluoroquinolones stimulate the Fenton reaction in their mechanism of action, by increasing the amounts of any of their two components: iron by levofloxacin or H2O2 by moxifloxacin.

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

first: María

last: Ferrándiz

first: Adela

middle: G

last: de la Campa


title: Expression analysis of circadian light response in Drosophila recombinant inbred lines (RIL)

status: Public on Feb 09 2016

city: Leicester

first: Eran

last: Tauber

address: University Road

department: Genetics

institute: University of Leicester

summary: The aim of this study was to identify quantitative trait loci (QTL) associated with variation in circadian photosensitivity in Drosophila, by measuring the locomotor response to early night light pulse (Zt15). We used QTL mapping of recombinant inbred lines (RIL), which was followed by microarrays expression comparison of two RI lines which differed significantly in their light response (RIL 104 shows  a strong long phase delay response while  RIL 58  shows a weak light response).

overall_design: Each of the two strains was sampled after light pulse, and without a light pulse (control), totalling 8 samples: 2x lines (L) x treatments (T) x 2 replicates

first: Adeolu

middle: B

last: Adewoye


title: Expression profiling of 22Rv1, DU145, LNCaP and PC3 prostasphere cultures at day 0, 4, 8 and 12 [Cancer Reference]

first: Roberto

last: Portillo Lara

overall_design: 22Rv1, DU145, LNCaP and PC3 prostasphere cultures were sampled on Day 4 (P 2), Day 8 (P 3) and Day 12 (P 4), and compared relative to parental monolayers on Day 0 of culture (P 1). Three independent measurements were carried out for monolayers at Day 0 using the CancerReference Kit.  Day 12 prostaspheres were enzymatically dissociated and sorted via MACS using the Anti-CD133/2 (293C3)-PE Antibody (Miltenyi) into CD133+ and CD133- fractions. Total RNA was extracted from CD133+ cells and analyzed using the nCounter GX Cancer Reference kit, the Stem Cell panel and the custom made ITESM CodeSet from NanoString Technologies.  This series contains the Cancer Reference kit data.

first: R

first: M

last: Moisés Alvarez


title: Osteogenic differentiation-related miRNA expression profile of human mesenchymal stem cells

status: Public on Feb 01 2016

city: Vilnius

first: Kristina

last: Daniunaite

address: Sauletekio Ave. 7

department: Institute of Biosciences

institute: Vilnius University

summary: Mesenchymal stem cells (MSCs) are the multipotent stem cells of adult human tissues that have the ability to replicate with high proliferative rates and are responsible for the tissue renewal and regeneration. Effective osteogenic differentiation of adipose-derived stem cells (ADSCs) encourages clinical application of the cells in bone regeneration. Regeneration of damaged joints is highly dependent on the presence of MSC in synovia. Synovial membrane-derived MSCs (SM-MSCs) show good multi-lineage differentiation potential, low degree of invasiveness, and are considered as an alternative treatment strategy for arthritis-damaged tissues. Studies in MSCs from different sources identified several miRNAs important for osteogenesis. Less is known about the participation of particular miRNAs in osteogenic differentiation of SM-MSCs, the potential source of MSCs for authologous cell therapy in arthritis. In the present study, the changes in miRNA expression profile occurring during osteogenic differentiation were analyzed in human ADSCs and SM-MSCs by microarray-based and quantitative PCR approaches. We aimed at the identification of miRNAs involved in the maintenance of these MSCs and regulation of osteogenic differentiation of ADSCs and SM-MSCs.

overall_design: MiRNA expression profile was analyzed in synovial membrane-derived (SM-MSCs, 3 cell lines) and adipose-derived (ADSCs, 4 cell lines) stem cells differentiated into osteogenic lineage and compared to undifferentiated cells from the same donors. Two ADSCs cell lines of adipogenic differentiation were included for comparison.

first: Sonata

last: Jarmalaite


title: Modifying DNA extraction protocol alters human brain copy number estimation

city: London

first: Christos

last: Proukakis

address: Rowland Hill Street

department: Clinical Neuroscience

institute: UCL Institute of Neurology

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

overall_design: Refer to individual Series


title: Interleukin-6 is a Potential Therapeutic Target in Interleukin-6 Dependent Estrogen Receptor-alpha Positive Breast Cancer [cell lines]

city: Beerse

first: Tine

last: Casneuf

address: Turnhoutseweg 30

department: Oncology Translational Research

country: Belgium

institute: Janssen R&D

summary: Interleukin-6 (IL-6) is an important growth factor for estrogen receptor-alpha (ERα) positive breast cancer, and elevated serum IL-6 is associated with poor prognosis. We firstly demonstrated that pSTAT3 is the primary downstream IL-6 signaling pathway in ERα-positive breast cancer, using ten different breast cancer cell lines.  Three-dimensional cultures of these cell lines were also used to develop a 17-gene IL-6 specific gene signature that could be used to identify IL-6 driven disease. This signature included a variety of genes involved in immune cell function and migration, cell growth and apoptosis, and the tumor microenvironment. To further validate this IL-6 signature, we obtained 36 human ERα-positive breast cancer tumor samples with matched serum for gene expression profiling and determination of an IL-6 pathway activation score (PAS).  Patients with high IL-6 PAS were also enriched for elevated serum IL-6 (>=10 pg/ml).  We then utilized a murine MCF-7 xenograft model to determine the role of IL-6 in ERα-positive breast cancer and potential anti-IL-6 therapy in vivo. When IL-6 was administered in vivo, MCF-7 cells engrafted without the need for estrogen supplementation.  Subsequently, we prophylactically treated mice at MCF-7 engraftment with an anti-IL-6 antibody (siltuximab), fulvestrant or combination therapy.  Siltuximab alone was able to blunt MCF-7 engraftment.  Similarly, when tumors were allowed to grow to 125 mm3 before treatment, siltuximab alone demonstrated tumor regressions in 90% (9/10) of tumors.  Given the established role for IL-6 in ERα+ breast cancer, this data demonstrates the potential for anti-IL-6 therapeutics.

overall_design: Ten ERα-positive breast cancer cell lines, T47D, MDA-MB-134VI, BT474, BT-483, HCC1428, EFM-19, MCF-7, MDA-MB-175-VIIdsRed, MDA-MB-415 and ZR-751, were grown in TME-aligned 3D culture.  After establishment, the cells were grown in triplicate for 6 days in the absence or presence of 10 ng/ml IL-6, which was added on day 1. Sampling was performed on days 4, 5, and 6.  Five additional conditions were investigated in duplicate: (i) 10 ng/ml IL-6 added on day 0 + 50 μg/ml siltuximab added on day 1 (ii) 10 ng/ml IL-6 added on day 1 + 50 μg/ml siltuximab added on day 1 (iii) 50 μg/ml siltuximab added on day 0 (iv) human marrow stromal cell-conditioned media (hMSC-CM) (v) hMSC-CM + 50 μg/ml siltuximab.

first: Tineke

first: Amy

last: Axel

first: Peter

last: King

first: J

last: Alvarez

first: Jillian

last: Werbeck

first: Tinne

last: Verhulst

first: Karin

last: Verstraeten

first: Brett

last: Hall

first: A

last: Sasser


title: Infinium 850k Beadchip analysis of control human brain for copy number mosaicism

summary:
Copy number mosaicism in the human brain has been reported recently by several authors. This experiment was performed to further investigate our preliminary data of apparent widespread deletions in brain DNA, detected in a custom Agilent aCGH designed for Parkinson's disease (PD) genes in both patients and controls, and supported by droplet digital PCR.
To avoid any effect of diseased tissue, we used only controls here. All DNA was freshly extracted. A validated SNP array was chosen to ensure that our results were not due to artefacts specific to the aCGH design used, with SNP array giving the additional advantage of B allele frequency estimation.

overall_design: Seven DNA samples were analysed, from four healthy individuals whose brain had been fresh frozen. The cerebellum and frontal cortex were analysed from three, and the cerebellum only for one.


title: Detection of SNCA duplication aritifical mosaics

summary: To determine sensitivity of a custom 8x60k aCGH design for mosaicism of SNCA gains, a peripheral blood lymphocyte (PBL) DNA sample with a known heterozygous duplication (CN 3, or 50% increase in SNCA) was diluted with a control (wild type, wt) sample (CN 2, screened by MLPA) to create "artifical mosaics" (CN 2.4, 2.3, 2,25, 2.2, 2.15, 2.1). Dilutions, as well as the undiluted heterozygous sample, and the control, were tested, hybridised with Agilent reference DNA.

overall_design: Individual mixed samples ("artifical mosaics"), undliuted duplication carrier, and control, each hybridised against the same Agilent reference DNA.

first: Proukakis

last: Christos


title: Study of the Kluyveromyces lactis Pdr1p regulon

status: Public on Jan 17 2016

city: Bratislava

first: Nora

last: Toth Hervay

address: Ilkovicova 6

country: Slovakia

institute: Deparment of Microbiology and Virology,Faculty of Natural Sciences, Comenius University in Bratislava

summary:
The transcription factor KlPdr1p, belonging to the Zn2Cys6 family, is a central regulator of efflux pump expression in Kluyveromyces lactis. To better understand how KlPDR1-mediated drug resistance is achieved in K. lactis, we used DNA microarrays to identify genes whose expression was affected by deletion or overexpression of the KlPDR1 gene.
All microarray experiments were performed using the 30K Kluyveromyces lactis NRRL Y-1140 microarray (MYcroarray, 5692 Plymouth Road, Ann Arbor, MI 48105, USA).
Exponentially growing (1 x 107 cells ml-1) K. lactis PM6-7A cells (wild-type, PM6-7A/pdr1∆ and the wild-type transformed with multicopy plasmid carrying the gain-of-function allele of KlPDR1* gene) (Balazfyova et al. 2013), were collected and total RNA was isolated using RNeasy midi kit (Qiagen GmbH, Germany). 1 mg of total RNA was linearly amplified and labelled using Amino allyl MessageAmpII aRNA Amplification kit (Ambion, USA) with two different fluorescent dyes; AlexaFluor647 and AlexaFluor555 (Life Technologies, Germany). 4 µg of labelled RNA was hybridized (18 h at 45°C) in 6x SSPE with addition of formamide (10%), tween-20 (0,01%) and microarray-specofoc control oligos (1%, MYcroarray, USA). After washing, microarray images and two-color GPR output files were obtained using the microarray scanner InnoScan 900 and Mapix software version 7.3.1 (Inopsys, France).  The two-color GPR files were processed using the R version 3.0.2 (R Core Team (2014). R: A language and enviroment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org) and functions available in the limma package (Smyth 2005). Briefly,  the two-color GPR files were omported using the read.maimages() function, background-substracted using the “minimum“ method and within-array-normalized using the “loess“ method. The between-array normalisation was achieved using the “Aquantile“ method. For further analysis, only genes with log2FC ˃2 were selected and confirmed using qPCR.

overall_design: Whole K. lactis genome analysis to identify genes whose expression was affected by deletion or overexpression of the KlPDR1 gene. Two two-color microarrays were hybridised as follows: yeast deletion mutant against the wild type control and yeast transformant against the wild-type control.


title: Engineered stomach tissue as a renewable source of functional beta-cells for blood glucose regulation

status: Public on Jan 09 2016

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

summary: The gastrointestinal (GI) epithelium is a highly regenerative tissue with the potential to provide a renewable source of insulin+ cells using cellular reprogramming.  Here, we describe the antral stomach as a previously unrecognized source highly amenable to conversion into functional insulin-secreting cells.  Native antral endocrine cells share a surprising degree of transcriptional similarity with pancreatic beta-cells.  Expression of beta-cell reprogramming factors in vivo converts antral cells efficiently into insulin+ cells with close molecular and functional resemblance to beta-cells.  Our data further indicate that the intestine-expressed Cdx2 acts as a molecular barrier for beta-cell conversion.  Induced GI insulin+ cells can suppress hyperglycemia over at least 6 months and they regenerate rapidly after ablation from the native stem-cell compartment.  Transplantation of bioengineered stomach mini-organs also produced insulin+ cells and suppressed hyperglycemia.  These studies demonstrate the potential of developing engineered stomach tissue as a renewable source of functional beta-cells for glycemic control.

overall_design: Total RNA extracted from primary mouse tissues: Stomach (3 replicates), Duodenum (3 replicates) and Colon (2 replicates)

first: Chaiyaboot

last: Ariyachet

first: Alessio

last: Tovaglieri

first: Guanjue

last: Xiang

first: Jiaqi

last: Lu

first: Manasvi

last: Shah

first: Camilla

last: Richmond

first: Catia

last: Verbeke

first: Juliana

last: Brown

first: Ramesh

last: Shivdasani

first: David

last: Mooney

first: Douglas

last: Melton

first: Qing

last: Xia

middle: T

last: Breault

first: Qiao

last: Zhou


title: Effect of DNA extraction method on brain DNA copy number estimation

first: Christos

last: Proukakis

summary:
We analysed DNA from two brain regions (cerebellum, CER and frontal cortex, FC) from 4 Parkinson's disease (PD) and 4 control brains on a custom design 8x60k Agilent aCGH targeted to PD genes.
All brain DNA samples were hybridised with Agilent sex-matched reference DNA, and three CER samples were hybridised against the FC of the same brain, with a dye swap in one. Male and female reference DNA were hybridised to eachother. The samples were then re-extracted with additional protocols, and hybridisations were performed for two CER samples betwen DNA extracted from the same CER with different protocols, and for one brain between the CER and FC new extraction.

overall_design: DNA from two regions of 8 brains, hybridised to reference DNA or brain DNA from different region / different extraction protocol


title: Microarray profiling of renal medulla / papilla and cortex during postnatal development

status: Public on Jan 12 2016

city: New York City

first: Dr. Yu Leng

last: Phua

state: New York

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

summary: The aim of this study is to establish a comprehensive transcriptome atlas that enables identification of key molecular pathways and morphogenic events regulating postnatal renal medulla/papillary and cortex development. To achieve this, a microarray expression profiling was performed on postnatal day 0-90 renal medulla and cortex obtained from CD1 male mice.

overall_design: Renal medulla and cortex were regionally dissected from postnatal day 0-90 CD1 male mice, and total RNA extracted for microarray expression profiling. Each time point consists of RNA pooled from 4 biological replicates, and an Agilent Bioanalyser test was performed to assess RNA integrity prior to sample pooling. The microarray data was analysed with the use of lumi and limma packages (Bioconductor) in R.

first: Yu

first: Melissa

middle: H

last: Little


title: Honey bee: Apis mellifera syriaca

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

summary: Apis mellifera syriaca is the native honeybee subspecies of Jordan and much of the Middle East. It expresses behavioral adaptations to a regional climate with very high temperatures, nectar dearth in summer, attacks of the Oriental wasp Vespa orientalis and in most cases it is resistant to varroa mites. The Thorax control sample of A. m. syriaca in this experiment was originally collected and stored since 2001 from Wadi Ben Hammad a remote valley in the southern region of Jordan. Using morphometric and Mitochondrial DNA markers it was proved that bees from this area had show higher similarity than other samples collected from the Middle East as represented by reference samples collected in 1952 by Brother Adam. The samples L1-L5 are collected from the National Center for Agricultural Research and Extension breading apiary which was originally established for the conservation of Apis mellifera syriaca. Goal was to use the genetic information in the breeding for varroa resistant bees and to determine the successfulness of this conservation program. Project funded by USAID-MERC grant number: TA-MOU-09-M29-075.

overall_design:
Agilent two-color CGH experiment,Organism: Apis mellifera,Agilent Custom Apis mellifera aCGH, 2X400K(AMADID:035669)  designed by Genotypic Technology Private Limited Labeling kit:  Agilent Genomic DNA labeling Kit (Part Number: 5190-0453)
Jordan Bee legs vs. Syriaca Bee thorax

first: Nizar

last: Haddad

first: Ahmed

last: Batainh

first: Moath

last: Al-Gharaibeh

first: Osama

last: Megdadi

first: Banan

last: Al-Shagour


title: Ssn6 defines a new level of regulation of white-opaque switching in Candida albicans and is required for the stochasticity of the switch

status: Public on Dec 28 2015

city: San Francisco

first: Matthew

last: Lohse

state: CA

address: 44 Vicksburg Street

institute: BioSynesis, Inc.

summary: The human commensal and opportunistic pathogen Candida albicans can switch between two distinct, heritable cell types, named “white” and “opaque,” which differ in morphology, mating abilities, metabolic preferences, and in their interactions with the host immune system. Previous studies revealed a highly interconnected group of transcriptional regulators that control switching between the two cell types. Here, we identify Ssn6, the C. albicans functional homolog of the Saccharomyces cerevisiae transcriptional co-repressor Cyc8, as a new regulator of white-opaque switching. In a or α mating type strains, deletion of SSN6 results in mass switching from the white to the opaque cell type. Transcriptional profiling of ssn6 deletion mutant strains reveals that Ssn6 represses part of the opaque cell transcriptional program in white cells and the majority of the white cell transcriptional program in opaque cells. Genome-wide chromatin immunoprecipitation experiments demonstrate that Ssn6 is tightly integrated into the opaque cell regulatory circuit and that the positions to which it is bound across the genome strongly overlap with those bound by Wor1 and Wor2, previously identified regulators of white-opaque switching. This work reveals the next layer in the white-opaque transcriptional circuitry by integrating a transcriptional regulator that does not bind DNA directly but instead associates with specific combinations of DNA-bound transcriptional regulators.

overall_design: Three independent microarray experiments were performed for each strain. One replicate (Replicate C) used cells grown to mid-log phase in synthetic defined (SD) yeast minimal media supplemented with amino acids and uridine at 25°C. The other two replicates (Replicates A & B) used cells grown in identical conditions but with arginine supplemented into the growth media at a concentration of 2.5 mg/mL to accommodate a growth defect likely associated with the arg- genotype of our a/α strains. Each experimental strain was labeled with Cy5 and analyzed relative to a pooled reference comprised of equal portions of Cy3 labeled aa-cDNA (See Sample records for more details).

first: Liron

last: Noiman


title: Identification of the serum microRNAs (miRNAs) displaying differential levels between hepatocellular carcinoma (HCC) patients and chronic hepatitis B (CHB) controls

city: Guangzhou

first: Xue-Jia

last: Lin

state: Guangdong

address: Xin Gang Xi Road 135#

institute: Sun Yat-sen University

summary: To identify serum miRNAs for the diagnosis of HCC, the profiling of 754 human miRNAs was analyzed in sera from six histopathologically confirmed HCC patients and eight CHB controls, using TaqMan Array Human MicroRNA A+B Cards Set v3.0 (Applied Biosystems, Foster City, CA). Serum miRNAs with differential levels between HCC and CHB were identified by comparing serum miRNA profiling of HCC patients with that of CHB controls.

overall_design: Sera from six HCC patients and eight CHB were subjucted to miRNA array analysis.

first: Shi-Mei

last: Zhuang


title: RING1 links retinoic acid signaling to the early proximal-distal specification of forelimb bud via Meis2 repression (ChIP-chip)

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

type: Genome binding/occupancy profiling by genome tiling array

summary:
Polycomb group (PcG) proteins play a pivotal role in silencing of development-related genes and contribute to maintain various stem and precursor cells and regulate their differentiation. However, it is not well understood how PcG factors regulate dynamic and complex morphogenetic processes particularly in mammals. In this study, we focused on proximal-distal (PD) patterning of forelimb bud to elucidate how PcG factors contribute to regulation of morphogenetic processes that depends on developmental signals. Depletion of RING1 proteins, which are common components of both canonical and variant Polycomb repressive complex-1 (PRC1), led to dramatic deficiencies in forelimb formation.
By using Ring1-deficient forelimb buds, we revealed the early defects in distal specification, which is due to the functional coupling of RING1 and retinoic acid (RA) signaling. RING1 activity is shown to antagonize with RA signals at Meis2 and likely Meis1, which are superior suppressors of distal formation program, in the prospective distal region of outgrowing forelimb bud. This study exhibits a first example showing how PcG factors interplay with developmental signals to mediate compartmentalization of elongating anlagen by regulating the expression of developmental genes.

overall_design: ChIP analysis of mouse E10.5 whole forelimb buds against anti-RING1B antibody.

first: N

last: Yakushiji-Kaminatsui

first: T

first: H

last: Koseki


title: The cytokine DIEDEL and a viral homologue suppress deleterious IMD-dependent gene expression in drosophila

status: Public on Jan 07 2016

city: Strasbourg Cedex

first: Jean-Luc

last: Imler

address: 2, Allée Konrad Roentgen

department: IBMC

country: France

institute: CNRS

summary: Viral infection in Drosophila triggers inducible gene expression, but the function of many of these genes and the biological significance of their induction remain poorly understood. Here, we report the functional characterization of the gene Diedel, which is strongly induced following some viral infections and encodes a 12kDa circulating protein. Diedel mutant flies have reduced viability and succumb rapidly to infection with Sindbis virus. This phenotype is associated with deregulated expression of IMD target genes and is rescued by mutations in the genes imd or IKKg, indicating that Diedel functions as an immunosuppressor cytokine targeting the IMD pathway. Homologues of Diedel are found in the genome of several DNA viruses, providing the first example of virokines in insects. Our results reveal that, besides RNA interference and apoptosis, an NF-kB pathway of inducible defense exerts evolutionary pressure on insect viruses.

overall_design: For each experimental condition (non infected and SINV infected), two biologically independent samples composed of 45 males of w1118 or Diedelcfm null mutant flies were used. Infection has been performed by injecting viral stocks prepared in Tris solution. Flies were then incubated for days at 29°C.

first: Olivier

last: Lamiable

first: Christine

last: Kellenberger

first: Cordula

last: Kemp

first: Laurent

last: Troxler

first: Nadège

last: Pelte

first: Michael

last: Boutros

first: Joao

last: Marques

last: Daeffler

first: Jules

last: Hoffmann

first: Alain

last: Roussel


title: Leukocyte gene expression in a model of perceived social isolation (PSI)

status: Public on Nov 23 2015

city: Los Angeles

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

summary: Differences in basal leukocyte gene expression profiles in macaques classified as showing low, moderate, or high behavioral indications of perceived social isolation (PSI)

overall_design: Gene expression profiling was carried out on peripheral blood mononuclear cell RNA samples collected from 56 adult rhesus macaques classified as showing low, medium, or high behavioral indicators of PSI.  Some analyses additionally controlled for age and RNA indicators of major leukocyte subsets (CD3E, CD3D, CD4, CD8A, CD19, FCGR3A/CD16, NCAM1/CD56, CD14).


title: OG1RF enterococcal cells: wild-type strain (C1) vs. mafR deletion mutant strain (C2)

status: Public on Nov 26 2015

city: Madrid

first: Alicia

last: Bravo

address: Calle Ramiro de Maeztu, 9

department: Centro de Investigaciones Biologicas

institute: CSIC

summary: Transcriptional profiles of strains OG1RF (wild-type) and OG1RFΔmafR (deletion mutant). The goal was to determine the effect of the enterococcal MafR protein on global gene expression

overall_design: Both bacterial strains were grown to mid-log phase in Brain Heart Infusion medium, at 37ºC and without aeration. Replicates 1 (R1) and 2 (R2)

first: Ruiz-Cruz

last: Sofía

first: Espinosa

last: Manuel

first: Goldmann

last: Oliver

first: Bravo

last: Alicia


title: Gene Expression Profile of Deletion RAD50, MRE11, XRS2

status: Public on Dec 31 2015

first: Malathi

last: Srinivasan

address: Allalasandra, GKVK Post, Bellary Road

department: Lipidomic Center

institute: Central Food Technological Research Institute

summary: Deletion mutants of the yeast MRX complex (Rad50, Mre11 and Xrs2) were studied for gene expression levels. Significant difference in expression levels was observed in genes pertaining to DNA damage, cell cycle etc. as compared to the BY4741 wild type.

overall_design: Organism : Saccharomyces cerevisiae , Custom Saccharomyces cerevisiae 8x15k Gene expresssion Microarray (AMADID: 016333) designed by Genotypic Technology Private Limited

first: DHANABALAN

last: KANAGAVIJAYAN

first: MALATHI

last: SRINIVASAN

first: RAM

last: RAJASEKHARAN


title: Leukocyte gene expression as a function of perceived social isolation (PSI): Year 9

summary: Individual differences in basal leukocyte gene expression profiles as a function of perceived social isolation (PSI)

overall_design: Gene expression profiling was carried out on peripheral blood mononuclear cell RNA samples collected from 92 adults in Year 9 of the Chicago Health Aging and Social Relations Study.  Participants were assessed for PSI using the UCLA Loneliness Scale, and were also classified as chronically high in PSI (1/0) based on UCLA Loneliness Scale scores during study years 1-5.  A 1-year lagged value of PSI is also included, and analyses additionally controlled for age at study entry, sex, race/ethnicity (dummy codes for Black and Hispanic), marital status, (log) household income, Body Mass Index (BMI), smoking history, heavy alcohol consumption, depressive symptoms (CESD), perceived stress (PSS), social support (SocSupp), circulating monocyte percentages, and RNA indicators of major leukocyte subsets (CD3E, CD3D, CD4, CD8A, CD19, FCGR3A/CD16, NCAM1/CD56, CD14).


title: Extracellular-signal regulated kinase (Erk1/2), mitogen-activated protein kinase-activated protein kinase 2 (MK2) and tristetraprolin (TTP) comprehensively regulate injury-induced immediate early gene (IEG) response in in vitro liver organ culture.

city: Hannover

first: Doan Duy Hai

last: Tran

state: Niedersachsen

address: Carl-Neubergsstr. 1

department: Institut of physiological Chemistry

institute: Hannover Medical School

summary: Background: Differentiated hepatocytes are long-lived and normally do not undergo cell division, however they have the unique capacity to autonomously decide their replication fate after liver injury. In this context, the key players of liver regeneration immediately after injury have not been adequately studied. Using an in vitro liver culture system, we show that after liver injury, p38 mitogen-activated protein kinase (p38MAPK), mitogen-activated protein kinase-activated protein kinase 2 (MK2)  and extracellular-signal regulated kinase (Erk)1/2  were activated within 15 min and continued to be phosphorylated for more than 2 h. Both p38MAPK and Erk1/2 were activated at the edge of the cut as well as on the liver surface where the mesothelial cell sheet expresses several cytokines. Notably, in human liver Erk1/2 was also activated under the mesothelial cell sheet shortly after liver resections. Furthermore, in in vitro liver slice culture immediate early genes (IEGs) were upregulated within 1-2 h and the S phase marker proliferation-cell-nuclear-antigen (PCNA) appeared 24 h after injury. Although Erk1/2 was activated after injury, in MK2 depleted liver a set of IEGs, such as Dusp1, Cox2, or c-Myc and proliferation marker gene Ki67 were not induced. In addition, in immortalized hepatocyte cells, THLE-2, the same subset of genes was upregulated upon stimulation with lipopolysaccharide (LPS), but not in the presence of MK2 inhibitor. The protein level of tristetraprolin (TTP), a substrate for MK2 that plays a role in mRNA degradation, was increased in the presence of MK2 inhibitor. In this context, the depletion of TTP gene rescued Dusp1, Cox2, or c-Myc upregulation in the presence of MK2 inhibitor. These data imply that MK2 pathway is positively involved in Erk1/2 induced IEG response after liver injury. These data also suggest that in vitro liver culture may be a useful tool for measuring the proliferation potential of hepatocytes in individual liver.

overall_design: In one dual-color microarray hybridization, mRNA expression changes after 2h ex vivo incubation of liver slices were examined.

first: Doan

first: Teruko

last: Tamura


title: Leukocyte gene expression as a function of perceived social isolation (PSI): Year 10

overall_design: Gene expression profiling was carried out on peripheral blood mononuclear cell RNA samples collected from 100 adults in Year 10 of the Chicago Health Aging and Social Relations Study.  Participants were assessed for PSI using the UCLA Loneliness Scale, and were also classified as chronically high in PSI (1/0) based on UCLA Loneliness Scale scores during study years 1-5.  A 1-year lagged value of PSI is also included, and analyses additionally controlled for age at study entry, sex, race/ethnicity (dummy codes for Black and Hispanic), marital status, (log) household income, Body Mass Index (BMI), smoking history, heavy alcohol consumption, depressive symptoms (CESD), perceived stress (PSS), social support (SocSupp), circulating monocyte percentages, and RNA indicators of major leukocyte subsets (CD3E, CD3D, CD4, CD8A, CD19, FCGR3A/CD16, NCAM1/CD56, CD14).