title: Chicken family BC1 1998: transcriptome profiling used for QTL/eQTL detection

city: Rennes

first: Le MIGNON

last: Guillaume

address: 65 rue de Saint Brieuc

institute: INRA

summary: The family concerns 44 offspring of the sire BC1 n°1998 (produced from a F1 male obtained by-intercrossing two fat (FL) and lean (LL) meat-type chicken lines that divergently selected on fatness [Leclercq et al 1980] mated with 8 LL females. Hepatic transcriptomic profiles were obtained using a chicken 20K oligochips (ARK-genomics). The 44 chickens were fed ad libitum using a conventional starter diet (0-3 weeks: 12.8 MJ of metabolizable energy) and then a growing broiler diet (4-9 weeks: 13.0 Mj of metabolizable energy). Light/dark periods were 24h light for the first 2 days, then 14h light/10h night up to slaughtering. At 4 weeks of age, blood samples were collected for DNA extraction and genotyping. At 9 weeks of age, the birds were fed ad libitum for 4 hours minimum after overnight fasting and then weighed and sacrificed by electrical stunning in the experimental processing plant (Station de Recherches Avicoles, Inra, Nouzilly, France). Following sacrifice, livers were collected, quickly frozen in liquid nitrogen and stored at −80°C until RNA extraction for transcriptome analyses

overall_design: Five micrograms of total RNA from each sample were labelled with Cy5 and then hybridized to the microarray with a same Cy3-labeled reference probe. The reference RNA pool was made from an equal amount of RNA derived from all liver samples.

first: Guillaume

last: Le Mignon

first: Sandrine

last: Lagarrigue


title: Isolation and expression profiling of circulating tumor cells in breast cancer patients part 3

status: Public on Dec 18 2014

city: Los Angeles

first: Vasu

last: Punj

state: CA

address: Biggy Street

country: USA

institute: USC

summary:
We developed a method to isolate pure circulating tumor cells (CTC). RNA from such CTCs isolated from the peripheral blood of metastatic breats cnacer patients and gene expression was performed using cDNAmicroarray.
we used cDNA array  to compare  gene expression of CTCs with normal epithelial and breast tumor samples

overall_design: CTCs vs. breast tumors

first: Julie

middle: E

last: Lang

first: Janet

middle: H

last: Scott

first: Christopher

middle: M

last: Haqq

first: Denise

last: Wolf

first: Petr

last: Novak

first: Laura

middle: J

last: Esserman

last: Van't Veer

first: John

middle: W

last: Park


title: Isolation and expression profiling of circulating tumor cells in breast cancer patients part 2

overall_design: normal peripheral blood, normal epithelium, and CTCs


title: Toxicogenomic profiling in the whole zebrafish embryo after exposure to reference hepatotoxicants.

status: Public on Dec 16 2014

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

summary:
Zebrafish embryos have been proposed as an attractive alternative model system for hepatotoxicity testing.
In this study we determined gene expression responses after exposure to reference hepatotoxicants and controls to identify biomarkers for hepatotoxicity.

overall_design: 188 samples; hepatotoxic compounds at 3 concentrations and with multiple replicates; negative controls at single concentration and with multiple replicates; water (DSW) and 0.2% DMSO vehicle control.

first: Marja

last: Driessen


title: Isolation and expression profiling of circulating tumor cells in breast cancer patients part 1

summary:
We developed a method to isolate pure circulating tumor cells (CTC). RNA from such CTCs isolated from the peripheral blood of metastatic breast cancer patients and gene expression was performed using cDNAmicroarray.
we used cDNA array  to compare  gene expression of CTCs with normal epithelial and breast tumor samples

overall_design: normal blood vs. breast tumor


title: Gene expression profiles of acetaminophen, isoniazid, and paraquat treated C57BL/6 mice

first: Alexa

last: Vitins

address: P.O. Box 1

institute: RIVM

summary: Toxicogenomics (tgx) is used as a tool to identify mechanisms and markers of necrosis in C57BL/6 mice treated by oral gavage using acetaminophen (APAP), isoniazid (INZ), and paraquat (PQ). Critical doses for tgx analysis were derived from a 25 day dose range finding study.  For tgx analysis, livers of mice were collected 1 and 2 days after a single compound dose of 168.75, 225, and 300 mg/kg bw for APAP; 12.5, 25, and 50 mg/kg bw for PQ; and 22, 44, and 88 mg/kg bw for INZ.  All samples were diluted in water.

overall_design: For the toxicogenomics study, samples were as followed: five mice per low, medium, and high dose group at 1 day, and five mice in the high dose group at 2 days. One set of vehicle controls (n=5) per day was used. The total number of samples was 70.

middle: P

first: Anne

middle: S

last: Kienhuis

first: Ewoud

middle: N

last: Speksnijder

first: Marianne

last: Roodbergen

first: Leo

last: van der Ven


title: Regulation of alkaloid biosynthesis by miRNAs in opium poppy

status: Public on Dec 15 2014

city: Çankırı

first: tugba

last: gurkok

address: Uluyazı

department: biology

country: Turkey

institute: Çankırı Karatekin University

summary:
MicroRNAs (miRNA) are ~21 nucleotide long, small endogenous non-coding RNAs that functioning in regulation of gene expression found in many eukaryotes. In this study, small RNA libraries of opium poppy from four different tissues (leaf, root, capsule, stem) were sequenced using high-throughput next generation Illumina sequencing (Solexa) technology to investigate potential mode of actions of miRNAs in alkaloid biosynthesis.
A total of 27 opium poppy miRNAs which have roles in regulation of alkaloid biosynthesis were identified in this study.

overall_design: A six chip study using miRNA isolated from four separate tissues (capsule, leaf, stem, root). small RNA libraries of opium poppy tissues were sequenced using high-throughput next generation Illumina sequencing (Solexa) technology to investigate potential mode of actions of miRNAs in alkaloid biosynthesis.  Furthermore, the novel opium poppy miRNAs were also confirmed by a direct small RNA cloning strategy. The microarray platform were performed to measure and analyze the mirnome of the different opium poppy tissues.

first: Hatice

last: Böke

first: Esma

last: Özhüner

first: Mine

last: Türktaş

first: İskender

last: Parmaksız

first: Sebahattin

last: Özcan

first: Turgay

last: Unver


title: Genome-wide recruitment profile of Tat protein on cellular genes in HIV-1 infected T-cells

city: Pune

first: Debashis

last: Mitra

state: Maharashtra

address: Ganeshkhind

country: India

institute: National Centre for Cell Science

type: Genome binding/occupancy profiling by genome tiling array

summary: HIV-1 Tat is a multifunctional protein, that in addition to its primary function of transactivating viral transcription also tends to modulate cellular gene expression, the molecular mechanism of which remains to be clearly elucidated. We have reported earlier NFκB enhancer binding activity of Tat and proposed its potential role in regulation of cellular gene expression. In the present study, we have analysed genome wide occupancy of Tat protein in HIV-1 infected cells. Our results identify an entire spectrum of binding sites of Tat protein on chromatin and also reveal that Tat is recruited majorly on gene promoters indicating its possible involvement in the regulation of cellular gene expression.

overall_design: Agilent two-color ChIP-on-Chip experiment, Organism: Homo sapiens ,Genotypic Technology designed Custom Human Promoter 244k ChIP-on-chip Array (AMADID-019469)

first: Neeru

last: Dhamija

first: Beena

last: Pillai

first: Jayashree

last: Ladha


title: Gene expression regulated by Transparent Testa16 in Brassica napus

status: Public on Dec 13 2014

city: Edmonton

first: Guanqun

last: Chen

state: Alberta

address: University of Alberta

department: Department of Agricultural, Food & Nutritional Science

country: Canada

institute: University of Alberta

summary: To broadly identify genes regulated by Transparent Testa16 in Brassica napus

overall_design: In order to broadly identify genes regulated by BnTT16s, microarray technology was employed to compare gene expression levels in developing seeds (2-DAP) of Bntt16 RNAi and wild-type plants.

first: Wei

last: Deng

first: Fred

last: Peng

first: Randall

last: Weselake


title: Isolation and expression profiling of circulating tumor cells in breast cancer patients

first: Vasu

last: Punj

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

overall_design: Refer to individual Series


title: Time course of serum starved ARPE19 cells

city: Bethesda

first: Katherine

middle: MacLean

last: Peterson

state: MD

address: Building 6 Room 107B

institute: NEI, NIH

summary: Cells from the human retina pigment epithilium cell line, ARPE-19, were cultured in media supplemented with 10% fetal bovine serum.  Then, the supplemented media was replaced with serum free media.  Cells were collected and RNA prepared from the serum free cultures on days 0, 1, 3, 5, and 7.  Changes in gene expression were calculated using the day0 sample for reference.

overall_design: The analysis compared RNAs from serum supplemented cultures to cultures grown in serum free media for 1, 3, 5, or 7 days.  Each array was hybridized to a day0 sample and one of the serum free day samples.  Each serum free day was hybridized to four arrays in a dye swap pattern.  The time course was repeated three times.

first: Sanghamitra

last: Mishra

first: Graeme

last: Wistow

first: Alan

last: Berger


title: The effects of serum starvation on APRE-19 and HEK293T cells on gene expression


title: Comparison of HEK293T cells grown in serum supplemented media to cells serum starved for 3 days

summary: HEK293T cells grown to confluence in media +10% fetal bovine serume.  Media was removed and replaced with serum free media, and cultured for 3 days.  RNA was harvested from day0 (serum supplemented), control, and day3 (serum starved) cultures, experiment.

overall_design: The analysis compared RNAs from serum supplemented cultures to cultures grown in serum free media for 3 days.  Each array was hybridized to a day0 sample and a day3 serum starved sample.  There are a total of four arrays with 2 arrays each for dye swap.


title: Defining glioma subtypes based on robust transcriptional patterns from 16 prior studies

status: Public on Dec 21 2014

city: Salt Lake City

first: Sanghoon

last: Lee

state: Utah

address: 15 North Medical Drive East

department: Biochemistry

institute: University of Utah

type:
Expression profiling by array
Third-party reanalysis

summary:
The purpose of our study was to define robust glioma subtypes by applying rigorous preprocessing and validation steps to 1,952 microarray samples aggregated from public data repositories for 16 prior studies. We evaluated each sample for quality-control issues, normalized high-quality samples using the Single-Channel Array Normalization (SCAN) algorithm (PMID:  22959562), corrected for probe-composition biases and inter-platform variability, and adjusted for intra- and inter-study batch effects. The deposited data in GEO include the 1,841 microarray samples that passed quality control tests, and underwent normalization and batch effect adjustment.

Where available, we retrieved treatment, histological and clinical data, such as tumor grade, histopathology, age-at-diagnosis, and survival time after diagnosis for these samples. Using a training/testing validation design, we identified six transcriptional subtypes in the training set, and evaluated clinically observable characteristics in the test set. Three of our clusters contained a heterogeneous mix of histopathological subtypes and tumor grades. We evaluated age, survival, and treatment patterns across our test samples and observed highly significant differences among the clusters. We also observed the potential to use gene expression patterns to further understanding of the biological mechanisms that drive gliomagenesis for each subtype. Our findings provide clinical and biological insights that may not be apparent with alternative approaches or smaller data sets, and our approach serves as an example for gene-expression meta-analyses that can be applied to other complex diseases.

relation:
Affiliated with: GSE1993
Affiliated with: GSE4271
Affiliated with: GSE4412
Affiliated with: GSE7696
Affiliated with: GSE8692
Affiliated with: GSE16011
Affiliated with: GSE19728
Affiliated with: GSE21354
Affiliated with: GSE24072
Affiliated with: GSE45921

overall_design:
Total 1,841 microarray samples aggregated from public data repositories from 16 prior studies were used to define six robust glioma subtypes by applying rigorous preprocessing and validation steps.

We collected raw microarray data from publicly available repositories for histologically defined glioma patients. We downloaded 11 of the data sets from general-purpose databases—either NCBI GEO (http://ncbi.nlm.nih.gov/geo) or ArrayExpress (http://www.ebi.ac.uk/arrayexpress) —and 5 of the data sets from disease-focused databases.  We focused on data sets that used the Human Genome U133A and U133 Plus 2.0 Affymetrix platforms because they constitute the majority of available microarray samples that have been used to profile glioma patients, and these two Affymetrix platforms have many overlapping probes.

Step 1: We performed quality control tests, SCAN normalization and batch effect adjustment. We excluded low-quality samples.

Step 2: We separated data sets into training and testing sets according to clinical data availability. Unsupervised clustering analysis and internal validation was performed on the training data to determine an optimal cluster size.

Step 3: Cluster Assignment for the test data set was performed and clinical characteristics across transcriptional clusters were examined.

Results are reported as normalized log2 signal intensity which was mapped to human 12,078 Entrez Gene IDs from the Human Genome U133A and U133 Plus 2.0 Affymetrix platforms probe-set IDs (File: GSE55918_Matrix_GliomaClusteringAnalysis.txt).

first: Stephen

last: Piccolo

first: Kristina

last: Allen-Brady


title: Global analysis of photosynthesis transcriptional regulatory networks [Expression profiling]

city: Madison

first: Timothy

last: Donohue

state: WI

address: 1552 University Avenue

department: Bacteriology

institute: University of Wisconsin - Madison

summary: To gain a deeper understanding of the transcription factors that regulate photosynthesis in Rhodobacter sphaeroides global gene expression analysis was used to determine the expression profiles of the deletion mutants of 4 transcription factors (FnrL, PrrA, CrpK and RSP_2888) known or predicted to be involved in the regulation of photosynthesis.

overall_design: Microarray analysis conducted for deletion strains of 4 transcription factors known or predicted to be involved in the regulation of photosynthesis in Rhodobacter sphaeroides using the R. sphaeroides Affymetrix gene chip. These deletion mutant expression profiles were compared to that of wild type cells to determine differentially expressed genes regulated by these transcription factors.

first: Saheed

last: Imam


title: mTORC1 regulates microRNA biogenesis in mouse bone marrow hematopoietic stem and progenitor cells

status: Public on Dec 11 2014

city: Chengdu

first: Chong

state: Sichuan

address: 17 Renmin S. Road-No. 3

department: State Key Laboratory of Biotherapy

country: China

institute: Sichuan University

summary:
mTOR senses nutrient and energy status to regulate cell survival and metabolism in response to environmental changes. Surprisingly, targeted mutation of Tsc1, a negative regulator of mTORC1, caused a broad reduction in miRNAs due to Drosha degradation. mTOR activation increased expression of Mdm2, which is hereby identified as the necessary and sufficient ubiquitin E3 ligase for Drosha.  Drosha was induced by nutrient and energy deprivation and conferred resistance to glucose deprivation.  Using a high throughput screen of a miRNA library, we identified 4 miRNAs that were necessary and sufficient to protect cells against glucose deprivation-induced apoptosis.  These miRNA was regulated by glucose through the mTORC1-MDM2- Drosha axis.  Taken together, our data reveal an mTOR-Mdm2-Drosha pathway in mammalian cells that broadly regulates miRNA biogenesis as a response to alteration in cellular environment.
mTOR activation by Tsc1 knockout causes a global decrease in both miRNA and pre-miRNA in mouse hematopoietic stem and progenitor cells(HSPCs).

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Tsc1(flox/flox) mice with conditional alleles for inactivating Raptor in C57BL/6 background were used for this study.  Age (10 weeks old) and sex (all female)-matched Ctrl (Mx1-Cre-, 4 mice) and cKO (Mx1-Cre+, 4 mice) littermates were treated with 400 μg polyinosinic:polycytidylic acid (pIpC, 2mg/ml in 1xDPBS, Sigma-Aldrich) 7 times every other day by intraperitoneal injection (i.p.) to induce targeted gene deletion. At 10 days post pIpC treatment, bone marrow HSPCs (Lin-cKit+Sca1+) were purified with BD FACSAria. Total RNA isolation was performed with TRIzol (Invitrogen) according to manufacturer’s instructions. RNA labeling and hybridization for miRNA expression profiling on miRNA microarray chips were performed as described (Liu, C.G., Calin, G.A., Volinia, S., and Croce, C.M. (2008). MicroRNA expression profiling using microarrays. Nat Protoc 3, 563-578).
genotype: Tsc1f/f, Mx1-Cre- (Cre negative Ctrl):WT LSK 1, WT LSK 2, WT LSK 3, WT LSK 4
genotype: Tsc1f/f, Mx1-Cre+ (Cre positive cKO): KO LSK 1, KO LSK 2, KO LSK 3, KO LSK 4
biological replicate: WT LSK 1, WT LSK 2, WT LSK 3, WT LSK 4
biological replicate: KO LSK 1, KO LSK 2, KO LSK 3, KO LSK 4

first: Peiying

last: Ye

first: Yu

last: Liu

first: Fei

last: Tang

first: Qi

last: Wu

first: Xiang

last: Wang

first: Chang-Gong

first: Xiuping

first: Runhua

first: Yang

first: Pan

last: Zheng


title: mTORC1 regulates microRNA biogenesis in mouse embryonic fibroblast cells

status: Public on Dec 12 2014

last: Chen

summary:
mTOR senses nutrient and energy status to regulate cell survival and metabolism in response to environmental changes.  Surprisingly, targeted mutation of Tsc1, a negative regulator of mTORC1, caused a broad reduction in miRNAs due to Drosha degradation.In contrast, when the activated mTOR level is repressed by its inhibitor rapamycin, the repression of miRNA is released. mTOR activation increased expression of Mdm2, which is hereby identified as the necessary and sufficient ubiquitin E3 ligase for Drosha.  Drosha was induced by nutrient and energy deprivation and conferred resistance to glucose deprivation.  Using a high throughput screen of a miRNA library, we identified 4 miRNAs that were necessary and sufficient to protect cells against glucose deprivation-induced apoptosis.  These miRNA was regulated by glucose through the mTORC1-MDM2- Drosha axis.  Taken together, our data reveal an mTOR-Mdm2-Drosha pathway in mammalian cells that broadly regulates miRNA biogenesis as a response to alteration in cellular environment.
mTOR activation by Tsc1 knockout cause repression of both miRNA and pre-miRNA in mouse embryonic fibroblasts (MEFs)

overall_design:
Tsc1-/- MEF cells were treated with vehicle or rapamycin (R, 5nM) for 4 days before harvesting, while Tsc1+/+ cells were only treated with vehicle for 4 days. Total RNA isolation was performed with TRIzol (Invitrogen) according to manufacturer’s instructions. RNA labeling and hybridization for miRNA expression profiling on miRNA microarray chips were performed as described (Liu, C.G., Calin, G.A., Volinia, S., and Croce, C.M. (2008). MicroRNA expression profiling using microarrays. Nat Protoc 3, 563-578).
genotype: Tsc1+/+: Tsc1+/+_1, Tsc1+/+_2, Tsc1+/+_3, Tsc1+/+_4, Tsc1+/+_5
genotype: Tsc1-/-:Tsc1-/-_1, Tsc1-/-_2, Tsc1-/-_3, Tsc1-/-_4, Tsc1-/-_5, Tsc1-/-_R_1, Tsc1-/-_R_2, Tsc1-/-_R_3, Tsc1-/-_R-4, Tsc1-/-_R_5
biological replicate: Tsc1+/+_1, Tsc1+/+_2, Tsc1+/+_3, Tsc1+/+_4, Tsc1+/+_5
biological replicate: Tsc1-/-_1, Tsc1-/-_2, Tsc1-/-_3, Tsc1-/-_4, Tsc1-/-_5
biological replicate: Tsc1-/-_R_1, Tsc1-/-_R_2, Tsc1-/-_R_3, Tsc1-/-_R_4, Tsc1-/-_R_5


title: The Mycobacterium tuberculosis Clp Gene Regulator is Required for in vitro Reactivation from Hypoxia-induced Dormancy

city: San Antonio

first: Deepak

last: Kaushal

state: TX

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

summary: The isogenic Mtb:ΔRv2745c mutant is significantly more sensitive normoxia conditions after a period of hypoxia, relative to wild-type Mtb, implicating a role for ClgR in response to reactivation, in vivo. Both hypoxia and reaeration treatment led to dysregulation of the σH regulon in the isogenic mutant, Mtb:ΔRv2745c. Induction of clgR in Mtb did lead to Clp protease induction, indicating that clgR plays a role in differntially activating downstream genes in a condition dependent manner. Disruption of genes involved in the dosR regulon, the Enduring Hypoxia Response, lipid synthesis, and mycolic acid synthesis also occurred in the knock out, implicating clgR as a possible regulator of downstream signaling cascades that facilitate Mtb survival. There was also a differnetial response of genes that are known Clp protease targets, in addition to potential Clp protease targets that had similar induction patterns as known Clp protease targets.

platform_organism:
Mycobacterium tuberculosis CDC1551
Mycobacterium tuberculosis H37Rv

overall_design: At different time points, following hypoxia (day 1, day 5, and day 7) and reaeration (1 hour, 4 hour, 6 hour, 12 hour, 24 hour, and 48 hour) treatments M. tuberculosis CDC1551 cultures, RNA was extracted and labeled with Cy5. RNA was also extracted from pre-hypoxia (t=0) time points and labeled with Cy3. These samples were cohybridized on M. tuberculosis CDC1551 whole genome microarrays using biological triplicate samples (i.e. samples derived from three distinct cultures and treatments) and thus three unique datasets were generated for each of the three time points for Mtb. Similar experiments were performed for an isogenic Rv2745c (clgR) mutant in Mtb CDC1551 which was generated by allelic exchange.

first: Amanda

last: McGillivray


title: Sperm miRNA expression differences between bulls consuming toxic and non-toxic tall fescue seed

status: Public on Dec 10 2014

city: Clemson

first: Scott

middle: L

last: Pratt

state: SC

address: 138 Poole Ag Center

institute: Clemson University

summary: The objectives of our study were to identify microRNA (miRNA) present in bovine sperm and to evaluate the effects of fescue toxicosis on sperm miRNA expression.

overall_design: Angus bulls were assigned to treatments of either toxic or non-toxic fescue seed diets. Semen was collected and subjected to microRNA (miRNA) isolation after 126 days. Three bull's sperm miRNA samples from each treatment group were chosen and pooled for deep sequencing. Sequencing results were used to create a custom microarray for miRNA comparison between groups. LC Sciences was used as a service provider for the sequencing and custom microarray.

first: Heather

last: Stowe


title: Global Genome Analysis of the Downstream Binding Targets of Testis Determining Factor SRY and SOX9

status: Public on Dec 05 2014

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

type: Genome binding/occupancy profiling by array


title: Global Genome Analysis of the Downstream Binding Targets of Testis Determining Factor SRY and SOX9 [SOX9 ChIP]

summary: A major event in mammalian male sex determination is the induction of the testis determining factor Sry and its downstream gene Sox9. The current study provides one of the first genome wide analyses of the downstream gene binding targets for SRY and SOX9 to help elucidate the molecular control of Sertoli cell differentiation and testis development. A modified ChIP-Chip analysis using a comparative hybridization was used to identify 71 direct downstream binding targets for SRY and 109 binding targets for SOX9. Interestingly, only 5 gene targets overlapped between SRY and SOX9. In addition to the direct response element binding gene targets, a large number of atypical binding gene targets were identified for both SRY and SOX9. Bioinformatic analysis of the downstream binding targets identified gene networks and cellular pathways potentially involved in the induction of Sertoli cell differentiation and testis development. The specific DNA sequence binding site motifs for both SRY and SOX9 were identified. Observations provide insights into the molecular control of male gonadal sex determination.

overall_design: The current study provides one of the first genome wide analyses of the downstream gene binding targets for SRY and SOX9 to help elucidate the molecular control of Sertoli cell differentiation and testis development.  At embryonic day 13 (E13) of pregnancy rats were euthanized and embryonic gonads were collected for chromatin. A modified ChIP-Chip analysis using a comparative hybridization was used to identify direct downstream binding targets for SRY and for SOX9. Then, bioinformatic analysis of the downstream binding targets was done to identify gene networks and cellular pathways that are potentially involved in the induction of Sertoli cell differentiation and testis development.

first: Ramji

last: Bhandari

first: Md

last: Haque


title: Global Genome Analysis of the Downstream Binding Targets of Testis Determining Factor SRY and SOX9 [SRY ChIP]


title: A modular analysis reveals that kinase-associated gene groups are involved in taurolithocholic acid 3-sulfate (TLC-S)-induced biological processes of AR42J cells

status: Public on Dec 09 2014

city: Harbin

first: Xue

middle: dong

last: bo

state: Heilongjiang

address: 23 Youzheng Street

institute: The First Affiliated Hospital of Harbin Medical University

summary: Background: Bile acids can act on pancreatic acinar cells and induce intracellular trypsinogen activation, but the underlying molecular  mechanism remains unknown.The present study aimed to investigate taurolithocholic acid 3-sulfate (TLC-S)-induced alterations of gene groups in AR42J cells using a modular analysis.Methods: After the pancreatic acinar AR42J cells were stimulated by TLC-S for 20 min, gene chip technology was applied to identify genes that were differentially expressed. Subsequently, the regulatory sub-networks of genetic interactions among the differentially expressed genes were constructed using the protein–protein interaction (PPI) network. Finally, the CFinder software was utilized to generate genetic modules, which were then subjected to a functional enrichment analysis.Results: The gene chip assay demonstrated that the expression levels of 1124 genes were upregulated and that those of 498 genes were downregulated in the TLC-S

overall_design: The cells were divided into two groups: the control group and the treatment group. The cells in the control group did not receive the treatment, while the cells in the treatment group were stimulated by TLC-S (200 μM/L) for 20 min.


title: microRNA expression profile in peri-implantation porcine embryos

city: Olsztyn

first: Monika

last: Kaczmarek

address: Tuwima 10

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

summary: Recently, microRNAs (miRNAs) have emerged as new players in the fine tuning of embryo development and implantation in mammals via posttranscriptional gene regulation mechanisms. Applying custom made multispecies arrays we aimed to analyze expression profile of microRNAs in peri-implantation porcine conceptuses/trophoblasts to identify their potential role at the maternal-fetal interface during the critical period of maternal recognition of pregnancy and implantation.

platform_organism:
Homo sapiens
Sus scrofa
Bos taurus
Mus musculus

overall_design: miRNA expression profiles were analyzed in samples collected from embryos or trophoblast on Days 10, 11, 12, 16 and 20 of pregnancy. Each group was represented by five to nine samples.

first: Kamil

last: Krawczynski

first: Stefan

last: Bauersachs


title: Complex in vivo RNA-seq analysis reveal reprogramming of Yersinia from virulent to persistent mode during infection [microarray II]

city: Umea

first: Kemal

last: Avican

address: Building 6L

department: Department of Molecular Biology

country: Sweden

institute: Umea University

summary: Whole transcriptome assessment of the Yersinia pseudotuberculosis strain YPIII grown under aerobic or anaerobic conditions to stationary phase.

overall_design: Y. pseudotuberculosis YPIII was grown at 25°C in LB medium supplemented with 10 g/l glucose and 0.2 M HEPES buffer under aeration or under anaerobic growth conditions (in a nitrogen atmosphere) on a rotary shaker. Total RNA was extracted using SV Total RNA Isolation System (Promega). The samples were treated with RNase-free DNase (Roche Applied Science) and the quality of the RNA was confirmed by the lack of PCR amplification of the hns gene and by using an Agilent 2100 Bioanalyzer.

first: Ann

last: Heroven

last: Beckstette

first: Petra

last: Dersch


title: Transcriptome analysis of zebrafish heart exposed to sorafenib

status: Public on Dec 04 2014

city: Tsu

first: Yuhei

last: Nishimura

state: Mie

address: 2-174 Edobashi

department: Integrative Pharmacology

country: Japan

institute: Mie University Graduate School of Medicine

summary: Sorafenib is associated with cardiac adverse effects, including left ventricular dysfunction. However, the precise mechanism remains unclear. Here, we aimed to establish the genes responsible for this cardiotoxicity using zebrafish. A pigmentless zebrafish line expressing green fluorescent protein in the heart were treated with or without sorafenib. In vivo fluorescent cardiac imaging revealed that the ventricular dimension of the longitudinal axis in zebrafish treated with sorafenib was significantly lower than in those without sorafenib. Transcriptome analysis of zebrafish hearts revealed that expression of stanniocalcin1 (stc1) in zebrafish treated with sorafenib was significantly lower than that without sorafenib treatment. We were able to demonstrate that the ventricular dimension of the longitudinal axis in stc1 morphant was significantly smaller than that of control zebrafish and that forced expression of stc1 normalized the decrease in ventricular diameter in stc1 morphant and zebrafish treated with sorafenib. These data suggest that stc1 is the gene responsible for sorafenib-induced cardiotoxicity.

overall_design: Gene expression regulated by sorafenib in zebrafish at 4 dpf was measured. Four independent experiments were performed for each group.

first: Miko

last: Kawabata

first: Toshio

last: Tanaka


title: Complex in vivo RNA-seq analysis reveal reprogramming of Yersinia from virulent to persistent mode during infection [microarray I]

summary: Whole transcriptome assessment of the Yersinia pseudotuberculosis strain YPIII grown under aerobic or anaerobic conditions to exponential phase.


title: Transcriptome of Legionella pneumophila rpoS mutant in water

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

institute: McGill University

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

summary:
Legionella pneumophila is a water-borne pathogen, and thus survival in the aquatic environment is central to its transmission to humans. Hence, identifying genes required for its survival in water could help prevent Legionnaires’ disease outbreaks. In the present study, we investigate for the first time the role of the sigma factor RpoS in promoting the survival in water, where L. pneumophila experiences total nutrient deprivation.
The rpoS mutant showed a significant survival defect compared to the wild-type strain in defined water medium (DFM). Then, we analyzed the transcriptome of the rpoS mutant during exposure to water using whole genome microarray analysis. We found that RpoS negatively affects the expression of several genes, including genes required for replication, cell division, translation and transcription, suggesting that the mutant fails to shutdown major metabolic programs.

sample_organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

overall_design: The WT and rpoS mutant were grown to exponential phase in rich AYE broth, washed three times in DFM (NaCl 0.5 g/L, KH2PO40.2 g/L, KCl 0.5 g/L, pH=6.9) and resuspended in DFM at an OD600 of 0.1, After 24h exposure, RNA was extracted.

first: Hana

last: Trigui

first: Paulina

last: Dudyk

first: Jinrok

last: Oh

first: Jong-In

last: Hong


title: Transcriptome profiling of plaque macrophages during atherosclerosis regression

city: Corvallis

first: Stephen

last: Ramsey

state: OR

address: Dryden Hall 208A

department: Biomedical Sciences

institute: Oregon State University

summary: We have carried out a systems biology investigation of regulators controlling arterial plaque macrophage transcriptional changes in response to lipid lowering, in the Reversa mouse model of plaque regression in which poly I:C injections induce recombination-mediated inactivation of Mttp in the liver and (when combined with a switch to chow diet) restore normal lipid levels in an Ldlr-/-Apob100/100 mouse (Lieu et al., 2003, Circulation, v.107(9), pp.1315-21). Twenty-four Reversa mice (12 males, 12 females) were maintained on Western diet for 16 weeks and given injections of either poly I:C or vehicle (saline) and then switched to normal chow. At seven days after the last injection, animals were sacrificed and CD68+ macrophages were isolated from the aortic root plaque using laser-capture microdissection. An additional two Ldlr-/- animals (male) were treated with poly I:C and CD68+ aortic root plaque macrophages were obtained, as a control group for effects of poly I:C independent of Mttp inactivation. RNA isolated from each of the 26 samples was reverse-transcribed, amplified, fragmented, labeled, and then hybridized to the Affymetrix Mouse Exon Array 1.0 ST GeneChip. Probe intensities were analyzed using transcript-level probesets for gene expression profiling, and for each mouse transcript represented on the microarray, a two-factor model (sex and treatment) was used for the analysis of the 24 samples from the Reversa mice, to test for a significant effect of the poly I:C (vs. saline) treatment.

overall_design: Four-week-old Reversa (or for the control group, Ldlr-/-) mice were weaned onto a Western diet for 16 weeks to establish aortic plaque and then switched to a chow diet and injected (i.p.) every other day, for a total of four injections, with either poly I:C or vehicle (saline, only for Reversa mice). In the Reversa mouse, poly I:C is rapidly taken up by the liver where it induces the MX1:Cre transgene, resulting in recombination at the loxP-flanked Mttp alleles and consequent silencing of Mttp expression (Lieu et al., ibid). Animals were sacrificed for arterial tissue collection at seven days after the last poly I:C injection. Hearts were harvested, aortic roots were frozen sectioned, and guide slides were immunostained for CD68. CD68+ cells were isolated by laser capture microdissection and RNA was reverse-transcribed, amplified, fragmented, labeled, and hybridized to the Affymetrix Mouse Exon Array 1.0 ST GeneChip. GeneChips were analyzed for differential expression (between the poly I:C and saline sample groups derived from the Reversa mouse) using transcript-level probesets from the CustomCDF project and using a two-factor model (sex and treatment) with empirical Bayes variance estimates (Limma).

first: S

middle: A

first: Y

last: Vengrenyuk

first: E

last: Gold

first: I

last: Podolsky

first: A

last: Aderem

last: Fisher


title: Snf1 is involved in the aberrant cell cycle induction in cdc14-3 mutant upon NaCl stress in S. cerevisiae

status: Public on Dec 03 2014

city: madison

first: Audrey

last: Gasch

state: wi

address: 425G Henry mall

department: genetics

institute: university of wisconsin, madison

summary:
Transcriptome profiling of cdc14-3 and cdc14-3_snf1 mutants at non-permissive temp (35C) for 90min or 2hr followed by 30min NaCl stress.
The experiment showed the aberrant cell cycle induction in cdc14-3 mutants upon NaCl response is abrogated with snf1 deletion in cdc14-3 background.

overall_design: Two-color fluorescence arrays reporting on mRNA abundance in strains before and at 30 min after a shock with 0.7M NaCl

first: Yi-Hsuan

last: Ho


title: WT + DOX vs tetO:HAL3 vhs3 + DOX

status: Public on Dec 02 2014

city: Cerdanyola del Vallès

first: David

last: Canadell

address: IBB, Campus UAB

country: Spain

institute: UAB

summary: Maintenance of ion homeostatic mechanisms is essential for living cells, including the budding yeast S. cerevisiae. Whereas the impact of changes in phosphate metabolism on metal ion homeostasis has been recently examined, the inverse effect is still largely unexplored. We show here that depletion of potassium from the medium or alteration of diverse regulatory pathways controlling potassium uptake, such as the Trk1 potassium transporter or the Pma1 H+-ATPase, trigger a response that mimics that of phosphate (Pi) deprivation, exemplified by accumulation of the high-affinity Pi transporter Pho84. This response is mediated by and requires the integrity of the PHO signaling pathway. Removal of potassium from the medium does not alter the amount of total or free intracellular Pi, but is accompanied by decreased in the ATP and ADP levels and a rapid depletion of cellular polyphosphates. Therefore, our data do not support the notion of Pi being the major signaling molecule triggering phosphate-starvation responses. We also observe that cells with compromised potassium uptake cannot grow under limiting Pi conditions. The link between potassium and phosphate homeostasis reported here could explain the invasive phenotype, characteristic of nutrient deprivation, observed in potassium-deficient yeast cells.

overall_design: Wild type JA100 (control) and tetO:HAL3 vhs3 strains were inoculated in synthetic complete medium and grown for 15 h in the presence of 100 µg/ml of doxycycline. Data from 3 microarrays experiments was combined, 2 biological replicates with dye-swapping of Replicate1.

first: Asier

last: González

first: Carlos

last: Casado

first: Joaquín

last: Ariño


title: Real-time quantitative PCR analysis of microRNA from lung adenocarcinoma cell lines

city: Houston

first: Amin

last: mOMIN

address: 6767 Bertner Ave

department: Clinical cancer prevention

institute: MD anderson cancer center

summary: An integrated approach combining genomics, proteomics, DNA methylation and microRNA analysis with functional profiling to define molecular features associated with epithelial to mesenchymal transition (EMT) states.

overall_design: qRT-PCR analysis of microRNA expression.


title: Coordination and interconnectivity in the inferred stress-activated signaling network from yeast

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

overall_design: Refer to individual Series


title: Detecting the effects of Cd and PCBs by means of a non-invasive transcriptomic approach in laboratory- and wild-contaminated European eels (Anguilla anguilla)

status: Public on Dec 01 2014

city: Arcachon

first: lucie

last: baillon

address: place du docteur Peyneau

country: France

institute: université de Bordeaux UMR ePOC

summary:
Our main objectives were: 1) to test whether the caudal fin may be used to detect the effects of pollutant exposure by means of DNA microarray; 2) to test whether the fin may be used to detect the effects of pollutants in wild contaminated fish; 3) to investigate the mechanisms of toxicity for Cd metal.
Detecting and unraveling specific effects of contaminants in a multi-stress field context remain a major challenge in ecotoxicology. The aim of this study was to apply a previously developed DNA microarray comprising 1000 candidate genes on caudal fin clips in order to assess the usefulness of a non-invasive method in ecotoxicogenomic studies in the European eel. Fin gene expression patterns of eels exposed in laboratory to Cd or a PCBs mixture were compared to test whether fin clips may be used to detect effects of these contaminants. Then, gene transcription profiles of wild fish from 3 sampling sites with differing contamination levels were compared to experimental exposures to test whether fin could detect and unravel the in situ effects of these contaminants. Also, transcriptomic profiles from liver and caudal fin of eels experimentally exposed to Cd were compared to test whether fins may be used to investigate the toxicity mechanisms of this metal. Our results showed distinct fin transcription profiles in response to Cd or PCBs exposure. In addition, the transcription profiles of eels from the most contaminated site clustered with the laboratory-exposed fish. Finally, gene transcription patterns from caudal fin and liver in Cd-exposed eels showed significant differences between the two organs and only 16 common genes were identified. Many of these genes were found to be involved in tissue development and in epigenetic mechanisms. This study thus demonstrates the applicability and usefulness of performing gene transcription assays on non-invasive tissue sampling in order to assess the effect of Cd and PCBs on the transcriptome of fish.

platform_organism:
Anguilla anguilla
Anguilla rostrata

overall_design: Comparison between laboratory-controls and fish laboratory-exposed to PCBs contamination at 50 and 300ng.g-1 and Cd at 4µg.L-1 were performed using a common reference (named in raw data reference, colored with cyanine 5)  on microarray; cluster analysis between eels from laboratory and wild fish from Garonne-Gironde continuum using the same reference were also performed, comparison between fish exposed to Cd and control fish from caudal fin and liver microarrays using also the common reference described earlier was then performed.

first: Lucie

last: Baillon

first: Fabien

last: Pierron

first: Jennifer

last: Oses

first: Eric

last: Normandeau

first: Pauline

last: Pannetier

first: Patrice

last: Couture

first: Pierre

last: Labadie

first: Hélène

last: Budzinski

first: Patrick

last: Lambert

first: Louis

last: Bernatchez

first: Magalie

last: Baudrimont


title: miRNA expression profiles of cloned CD4+ and CD8+ T cells infected or not by HTLV-1 in vivo

city: Lyon

first: Céline

last: Vernin

address: 46 allée d'Italie

institute: ENS

summary: To address whether changes in miRNA expression accompany cell-associated replication of HTLV-1 in vivo, we carried out the miRNA expression profiling of CD4+ and CD8+ T-cells derived from naturally HTLV-1 infected individuals with no clinical sign of malignancy. T-cell clones were obtained by limiting dilution culture of PBMCs of HTLV-1 carriers. miRNA expression was assessed by Agilent V3 miRNA array according to the manufacturer's instructions.

overall_design: miRNA expression profiles of cloned CD4+ and CD8+ T-cells (carrying or not HTLV-1) derived from naturally HTLV-1 infected individuals.

first: Franck

last: Mortreux


title: Transcriptome profiling of responses of mouse peritoneal macrophages to oxLDL

first: Stephen

last: Ramsey

summary: The goal of this study was to profile transcriptional changes of mouse peritoneal macrophages during foam cell formation induced by the atherogenic lipoprotein, oxidized LDL (oxLDL)

overall_design: Resident peritoneal macrophages were isolated from female C57BL/6J mice at 8-12 weeks of age, by intraperitoneal lavage, and purified by triple-washing to retain adherent cells. Macrophages were incubated with either 25 ug/mL CuSO4-oxidized human LDL (or vehicle) for 24 h, and then total RNA was isolated using TRIzol. Microarray profiling was carried out using the Affymetrix Mouse Exon Array 1.0 ST GeneChip and analyzed using the Affymetrix algorithms PLIER and DABG, using transcript-level and exon-level probesets from the CustomCDF project that were based on Ensembl transcript/exon definitions. Differential expression testing was performed using Limma.

first: Elizabeth

last: Gold

first: Irina

last: Podolsky

first: Alan

last: Aderem


title: miRNA expression in blood of 15 schizophrenia patients and 15 healthy controls

city: Wuxi

first: Fuquan

last: Zhang

address: 156 Qianrong Rd

institute: Wuxi mental health center

summary:
The study profiles genome-wide miRNA expression in blood from 15 early-onset SZ (EOS) cases and 15 healthy controls. A total of 1070 miRNAs were detected by the microarrays in our samples.
We profiles miRNA expression in 15 schizophrenia samples and 15 healthy controls to explore the alteration of miRNAs in schizophrenia.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Human betaherpesvirus 5
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: 15 schizophrenia samples and 15 healthy controls were used to acquire blood expression profiles of a total of 1065 unique miRNAs

first: Yong

last: Xu


title: Transcriptional response to tetanus toxoid in pigs with divergent temperament (High-Reactive vs. Low-Reactive) [day 14]

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

summary: in vivo microarray study of transcriptional changes in porcine peripheral blood mononuclear cells (PBMCs) during the immune response to tetanus vaccination.

overall_design: Per temperament group, 23 pigs were collected for expression profiling. High-Reactive vs. Low-Reactive.

first: Eduard

last: Muráni

first: Siriluck

last: Ponsuksili

first: Michael

last: Oster

first: Mathias

last: Scheel


title: Transcriptional response to tetanus toxoid in pigs with divergent temperament (High-Reactive vs. Low-Reactive) [day 0]


title: Inferring the stress-activated signaling network in yeast through multi-omic data integration

first: Audrey

last: Gasch

summary: Transcriptome profiling of yeast mutant strains responding to 0.7M NaCl treatment for 30  minutes. This study identified affected genes in each mutant and used it to computationally infer the complete NaCl-activated signaling network in yeast.

overall_design: Two-color fluorescence arrays reporting on mRNA abundance in strains before and at 30 min after a shock with 0.7M NaCl, hybridized to yeast tile-genome Nimblegen arrays

first: James

last: Hose

first: Elisha

middle: Y

last: Ho

first: Matt

last: MacGilvray

first: Jessica

last: Will


title: Molecular diversity of breast cancers at the time of endocrine resistance [microRNA]

city: Cambridge

first: Alexey

last: Larionov

state: Cambridgeshire

address: Box 238, Lv 6 Addenbrooke's Treatment Centre, Cambridge BioMedical Campus

department: School of Clinical Medicine

country: United Kingdom

institute: The University of Cambridge

summary:
Dataset containing micro-RNA expression profiles of breast cancers at the time of endocrine resistance. It has been used to correlate micro-RNA and mRNA expressions and to identify two distinctive phenotypes with different expression of micro-RNA gens.

Please note that the tumor samples are clinically quite homogeneous: all are post-menopausal ER+ve breast cancers, endocrine treated and growing on treatment. The main purpose of collecting these data was not to compare transcriptional profiles with clinical parameters, but rather to use the micro-RNA expression profiles of these clinically homogeneous tumours for (i) identifying intrinsic subgroups within endocrine resistance and (ii) for relating micro-RNA and mRNA expressions. However, the relevant clinical data was also provided as Series supplementary file (ClinicalData_AL28Jan2014.xlsx).

overall_design: micro-RNA extracted from 56 fresh-frozen clinical biopsies of breast cancer at the time of endocrine resistance has been profiled with Illumina Human v1 MicroRNA expression beadchip.


title: Long noncoding RNAs in human Neuroblastoma BE(2)-C Cells

city: Randwick, Sydney

first: Tao

last: Liu

state: NSW

address: Lowy Cancer Research Centre UNSW

country: Australia

institute: Children's Cancer Institute Australia

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

summary:
Transcriptional profiling of long noncoding RNAs in human neuroblastoma BE(2)-C after transfection with control siRNA or N-Myc siRNA
We analysed which long nocoding RNAs were N-Myc targets.

overall_design: Neuroblastoma BE(2)-C cells were transfected with control siRNA or N-Myc siRNA. RNA was extracted from the cells 30 hours after siRNA transfections, and subjected to differential gene expression studies with NCode™ Human Non-coding RNA Microarray from In vitrogen.

first: Pei

first: Bernard

last: Atmadibrata


title: Transcriptomic profiling of the DTT induced ER-stress response in Plasmodium falciparum

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

institute: Genotypic Technology

summary: Plasmodium falciparum lacks the homologs of UPR machinery and is unable to upregulate the known targets of UPR. Therefore, we have carried out microarray analysis to identify novel unfolded protein response (UPR) target genes in this parasite.

overall_design: Agilent one-color experiment, Organism: Plasmodium falciparum, Custom Microarray Gene Expression Plasmodium falciparum 8x15k designed by Genotypic Technology Private Limited (AMADID: 022127), Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Utpal

last: Tatu

first: Shweta

last: Chaubey

first: Manish

last: Grover


title: Transcriptional response to tetanus toxoid in pigs with divergent temperament (High-Reactive vs. Low-Reactive) [day 140]

first: Klaus

last: Wimmers

overall_design: Per temperament group, 24 pigs were collected for expression profiling. High-Reactive vs. Low-Reactive.

first: Eduard


title: Transcriptional response to tetanus toxoid in pigs with divergent temperament (High-Reactive vs. Low-Reactive) [day 28]

last: Muráni

first: Siriluck

first: Michael


title: mRNA expression in RNase deletion mutants of Thermus thermophilus HB8

city: Toyonaka

first: Hiromasa

last: Ohyama

address: Machikaneyamachou 1-1

institute: Osaka University

summary: We analyzed the expression profile of RNase deletion strains of Thermus thermophils HB8. Keywords: cell type comparison

overall_design: The T. thermophilus HB8 wild-type strain and disruptants were cultured in TT medium at 70°C until the cells reached to OD600 of 0.8 (log phase) or to stationary phase.  In the case of TTHA0137, TTHA0540 and TTHA1817 log phase samples, an equal volume of hot medium was added to the culture.  In the other disruptants, cultures were added to an equal volume of 100% ethanol and stored at -80°C.  Total RNA was extracted from these frozen cells by following the same procedure as described previously (Shinkai et al. 2007) with the exception that the RNA was resuspended in 20 μL of water after ethanol precipitation.  The cDNA was synthesized with SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA) in the presence of the RNase inhibitor SUPERase (Ambion, Austin, TX) and 6-base random primers (Invitrogen).  The cDNA was fragmented with 35 units of DNase I (GE Healthcare, Amersham, UK) at 37°C for 10 min; after inactivation at 98°C for 10 min, the cDNA fragments were labeled with the GeneChip DNA labeling reagent (Affymetrix, Santa Clara, CA), using terminal transferase, according to the manufacturer's instructions (Affymetrix). The 3'-terminally labeled cDNA (2 μg) was hybridized to a TTHB8401a520105F GeneChip (Affymetrix), which contained probe sets of 25-mer oligonucleotides representing 2238 ORFs and 1096 intergenic regions.  The procedure was basically the same as that described previously with the exception that 20 μg of herring sperm DNA (Promega) was added to the hybridization mixture (Shinkai et al. 2007).  The array was automatically washed and stained with streptavidin-phycoerythrin (Invitrogen) using a GeneChip Fluidics Station 450XP (Affymetrix).  The probe array was then scanned with a GeneChip Scanner 3000 (Affymetrix).  To determine the mRNA expression level in disruptants relative to that in wild-type, the image data for the three samples in each disruptant and growth phase were processed. The expression intensity of each of the 2238 ORFs for the three wild-type strains was evaluated using image data and scaled by means of the one-step Tukey's biweight algorithm using GeneChip Operating Software version 1.0 (Affymetrix).  Scaled probe value was calculated as Sc = 500 according to Statistical Algorithms Description Document (Affymetrix).

first: H

first: T

last: Sakai

first: Y

last: Agari

first: K

last: Fukui

first: N

last: Nakagawa

first: A

last: Shinkai

first: R

last: Masui

first: S

last: Kuramitsu


title: Early and late changes in gene and miRNA expression after hepatitis B or C infection in human hepatocyte chimeric mice [tissue_mRNA]

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Changes in gene and microRNA expression 10 days and 8 weeks after infection with hepatitis B and C virus and with or without interferon administration was determined in human hepatocyte chimeric mice.

overall_design:
68 immunodeficient human hepatocyte chimeric mice were allocated into 8 experimental groups. 25 mice were infected with HBV, 22 were infected with HCV, and 21 were reserved as controls. 5 HBV-infected mice and 5 HCV-infected mice were sacrificed at 10 days. Half of the remaining mice were injected with interferon prior to sacrifice, and all mice were sacrificed at 8 weeks.

Please note that only 44 serum samples and 51 tissue samples (out of 68 samples) were included in the study due to RNA degradataion and contamination.

first: Kazuaki

last: Chayama


title: Aberrant expression of miRNAs in the liver carcinogenesis from NASH

sample_organism:
Homo sapiens
Mus musculus

first: Yoshimasa

last: Saito


title: Transcriptional response to tetanus toxoid in pigs with divergent temperament


title: Pancreatic cancer cell exosomal microRNA as diagnostic marker

city: Heidelberg

first: Shijing

last: Yue

address: Im Neuenheimer Feld 365

department: Tumor cell biology

institute: University hospital Heidelberg

summary: Pancreatic cancer has a dismal prognosis partly due to late diagnosis, where a reliable non-invasive diagnosis is urgently wanted. We here explored, whether serum-derived PaCa exosomes may provide a diagnostic means and microRNA may be advantageous. Exosomes were collected from the serum of 133 patients with pancreatic cancer, 22 patients with non-malignant pancreatic tumors, 25 patients with chronic pancreatitis and 20 healthy donors. Exosomes were isolated by ultracentrifugation and used qRT-PCR for miRNA quantification and miRCURY LNA microRNA Array for miRNA analysis.

overall_design: Exosomes isolated from human serum or human pancreatic cancer cell lines culture supernatant. Healthy exosomes and serum were pooled from 10 healthy donors. Patient exosomes and serum were pooled from 12 pancreatic cancer patients. Pancreatic cancer cell culture supernatant exosome was pooled from 9 human cancer cell lines. MicroRNA isolated from serum and exosomes for miRCURY LNA microRNA Array assay. To find out the candidates for pancreatic cancer diagnosis, we compared the expression profile of healthy, patient, and cancer cell culture supernatant exosomal MicroRNA.

first: Margot

last: Zöller


title: Sex differences on the effect of Testosterone in songbirds

status: Public on Nov 30 2014

city: Seewiesen-Starnberg

first: Carolina

last: Frankl-Vilches

state: Bavaria

address: Eberhard-Gwinner-Str. 6a

department: Behavioural Neurobiology

institute: Max Planck Institute for Ornithology

summary: In this data set, we compare the expression data of the song nuclei from canaries treated with testosterone to untreated animals to identify gender specific stimulated gene expression. The gene expression profiles were compared to specie specific sexual dimorphic expressions.

overall_design:
A total of 12 HVCs isolated from treated and untreated animals were compared. The differential expression was analyzed by ChipInspector using the group-wise exhaustive analysis with False Discovery Rate set to zero and 10-significant probe minimum coverage.
ChipInspector carries out significance analysis on the single probe level. Normalized probe set level data not provided for individual Sample records.

first: C

last: Bakker

first: M

last: Gahr


title: Human lncRNA NRAV regulates antiviral response by modulating ISGs expression during influenza A virus infection

status: Public on Nov 26 2014

city: Beijing

first: jing

last: ouyang

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute of microbiology, Chinese Academy of Sciences

summary: Human lncRNA NRAV-overexpression in A549 cells was found to increase the influenza virus WSN replication. To discover the mechanism underlying this promotion by NRAV, genome-wide mRNA expression was measured by using microarray. Thousands of genes were differentially expressed and some ISGs were down-regulated.

overall_design: Human lncRNA NRAV-overexpressioning A549 cells (Test) and empty vector control cells were infected with influenza virus A/WSN/33 (H1N1) for 16 hours at a MOI of 3. Six total RNA samples from three independent experiments were extracted and used for mRNA microarray.

first: Jing

last: Ouyang

first: Ji

last: Chen


title: Gene Expression Profiling in Pachyonychia Congenita Skin

status: Public on Nov 16 2014

city: Santa Cruz

first: Yuan

last: Cao

state: CA

address: 2161 Delaware Ave., Suite D

institute: Transderm Inc

summary: Pachyonychia congenita (PC) is a skin disorder resulting from mutations in keratin genes (KRT) 6A, KRT6B, KRT6C, KRT16, and KRT17 genes. One of the major symptoms is painful plantar keratoderma. The pathogenic sequelae resulting from the keratin mutations remain unclear.   To better understand PC pathogenesis.RNA profiling was performed on biopsies taken from PC-involved and uninvolved plantar skin of seven PC (-K6a, -K6b, -K16, -K17) patients as well as from control volunteers. Protein profiling was generated from tape-stripping samples.   A comparison of PC-involved skin biopsies to adjacent uninvolved plantar skin identified 112 differentially-expressed mRNAs common to patient groups harboring keratin protein (K) 6 and K16 mutations. Among these mRNAs, 25 encode structural proteins including keratins, small proline-rich and late cornified envelope proteins, 20 are related to metabolism and 16 encode proteases, peptidases, and their inhibitors including kallikrein-related peptidases (KLKs) and serine protease inhibitors (SERPINs). mRNAs were also identified to be differentially expressed only in K6 (81) or K16 (141) patient samples. Furthermore, 13 mRNAs were identified that may be involved in pain including nociception and neuropathy. Protein profiling, comparing three K6a plantar tape-stripping samples to non-PC controls, showed changes in the PC corneocytes similar, but not identical, to the mRNA analysis.   Many differentially-expressed genes identified in PC-involved skin encode components critical for skin barrier homeostasis including keratinocyte proliferation, differentiation, cornification, and desquamation. The profiling data provide a foundation for unraveling the pathogenesis of PC and identifying targets for developing effective PC therapeutics.

overall_design: Two-condition experiment, Involved vs. Uninvolved Pachyonychia Congenita Skin for seven different patients and controls.  HPR are the initials of the patient used as a control.

first: Yu-An

first: Robyn

last: Hickerson

first: Brandon

last: Seegmiller

first: Dmitry

last: Grapov

first: Maren

last: Gross

first: Marc

middle: R

last: Bessette

first: Brett

last: Phinney

first: Manuel

last: Flores

first: Tycho

last: Speaker

first: Annaleen

last: Vermeulen

first: Albert

last: Bravo

first: Anna

last: Bruckner

first: Mary

last: Schwartz

first: Robert

last: Rice

first: Roger

last: Kaspar


title: Profiling of Esg genomic binding in the Drosophila midgut with DamID

status: Public on Nov 18 2014

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

institute: Imperial College London

summary: Tissue stem cells divide asymmetrically to self-renew and generate differentiated progeny to maintain tissue homeostasis. Escargot (Esg) is a transcriptional repressor that is expressed in multiple stem cell populations in Drosophila melanogaster. Reduced esg function in intestinal stem cells (ISCs) causes a loss of ISCs and a biased differentiation of the daughter enteroblasts (EBs) toward the enteroendocrine (EE) cell fate. Loss of esg leads to an upregulation of differentiation factors and reduced Notch activity within EBs, indicating that Esg is a pivotal regulator of homeostasis in the intestine, supporting self-renewal to maintain a healthy stem cell pool as well as differentiation of progenitor cells. To identify potential transcriptional targets that mediate these phenotypes, in vivo DamID was used to generate the data deposited herein.

overall_design: 3 biological relicates were performed for Esg (with one dye-swap).

first: Mariano

last: Loza-Coll

middle: D

first: Andrea

last: Brand

first: D

last: Jones


title: Expression data from uterus of high vs low prolificacy Iberian x Meishan F2 sows at 30-32 days of gestation

city: Bunyola

last: Tomas Sangenis

state: Mallorca

address: recinte Hosp. Joan-March, ctra soller Km 12

department: Infection and Immunity

institute: Fundacio d'Investigacio Sanitaria Illes Balears (FISIB)

summary: An F2 cross between two highly divergent porcine breeds for most productive traits, including prolificacy, was generated. F2 sows were classified as of high or low prolificacy based on phenotypic records of four consecutive parities (total number of piglets born and number of piglets born alive were recorded). At the fifth gestation, sows were slaughtered at day 30-32 of gestation, and the number of corpora lutea and number of embryos were registered. Samples from different tissues were snap frozen in liquid nitrogen for further studies. Uterus samples were used for total RNA extraction and hybridized on the affymetrix porcine genechip for comparison between high and low prolificacy F2 sows.

overall_design: Uterus samples from five high and 9 low prolificacy Iberian x Meishan F2 sows were hybridized to the affymetrix porcine genechip for determination of differential gene expression.

first: Ingrid

middle: B

last: Ortega

middle: T

last: Sangenis

first: Armand

last: Bonastre


title: CGH of stages 10B and 13 amplifying follicle cells to determine the effect SuUR has on replication fork progression

status: Public on Nov 10 2014

first: Terry

middle: L.

last: Orr-Weaver

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

type: Genome variation profiling by genome tiling array

summary:
Comparative genomic hybridization was performed to compare amplificaiton gradients in genomic DNA derived from stage 13 egg chambers of wild-type, suppressor of under-replication (SuUR) mutant and SuUR overexpression, compared with 0-2hr diploid embryo gDNA.
Comparative genomic hybridization was performed to compare amplificaiton gradients in genomic DNA derived from stage 10B egg chambers of wild-type, compared with 0-2hr diploid embryo gDNA.

overall_design:
CGH of stage 13 egg chambers relative to diploid early embryonic samples for four different Drosophila strains
CGH of stage 10B egg chambers relative to diploid early embryonic samples for the wild type Oregon R Drosophila strain

first: Jared

last: Nordman


title: Profile of differential expression and DNA methylation status in choriodecidua of women affected with severe endometriosis [Gene Expression]

city: Paris

first: Céline

last: Méhats

address: 24 rue du Faubourg St jacques

institute: Inserm

summary:
Endometriosis is a common gyncological disease that affects 10-20% of women in child-bearing age. It is defined by the presence of endometrial tissues outside the uterus. The causes remain elusive, but the endometrium of these patients differs profoundly from that of disease-free subjects.
During pregnancy, the maternal-fetal interface is built onto decidualized endometrium. We investigated whether this interface is normal when the subjects suffer of endometriosis and showed remarkly properties of eutopic endometrium from endometriosis-affected women to spontaneously develop endometriotic-like lesions within direct contact to non-uterine tissues.

overall_design: Microarray analysis was conducted on three distinct pools of three choriodecidua RNAs from women suffering of severe endometrosis and three distinct pools of healthy choriodecidua from eighteen pregnant women in total. These women were delivered at term by cesarean sectionfor feto-pelvic disproportion or scarred uterus, after an uncomplicated pregnancy.

first: Louis

last: Marcellin

first: Sébastien

last: Jacques


title: Rapid neurogenesis through transcriptional activation in human stem cell (miRNA)

status: Public on Nov 07 2014

city: La Jolla

first: Nathan

last: Lewis

department: Pediatrics

institute: University of California, San Diego

summary: Advances in cellular reprogramming and stem cell differentiation now enable ex vivo studies of human neuronal differentiation. However, it remains challenging to elucidate the underlying regulatory programs because differentiation protocols are laborious and often result in low neuron yields. Here, we overexpressed two murine Neurogenin transcription factors in human induced pluripotent stem cells, and obtained neurons with bipolar morphology in four days at greater than 90% purity. The high purity enabled mRNA and microRNA expression profiling during neurogenesis, thus revealing the genetic programs involved in the transition from stem cell to neuron. The miRNA profiles were then analyzed to identify the miRNAs involved in the differentiation of the neurons.

overall_design: Nanostring nCounter was used to profile miRNAs of iPS cells (PGP1) at 0, 1, 3, and 4 days post- doxycycline induction of murine NGN1 and NGN2.

first: B

last: Volker

first: N


title: Transcriptome analysis of chicken ES, blastodermal, primordial germ cells, embryonic fibroblasts and monocytic cells

status: Public on Nov 01 2014

city: Bron

first: Bertrand

middle: Pierre-Yves

last: PAIN

address: 18, Avenue du  Doyen Lépine

institute: U1208, INSERM

summary: The comparative transcriptomic analysis of chicken stem cells defines a chicken set of pluripotency associated genes that is almost coincident with mammalian pluripotency-assocaited genes.  A total of 5944 differentially expressed unique identifiers (target IDs) were defined for CEF, 5942 for BM2  cells, 4550 for cES, 5465 for PGC and 5522 for cBC.

overall_design: Chicken Blastodermal cells (cBC) were taken from stage IX-XII (Eyal-Giladi & Kochav, 1976) embryos,chicken embryonic stem (cES) cells were  established, amplified on inactivated STO feeder cells in proliferative medium containing cytokines and growth factors as described (Pain et al., 1996, Lavial et al., 2007). Long term cultured primordial germ cells (PGCs) were derived from 48h embryonic blood and maintained as described (McDonald et al., 2010). The non-tumorigenic BM2 monocytic cell line was grown as described (Solari et al., 1996). Primary chicken Embryonic fibroblasts (CEF) were prepared from 11-12 day old embryos according to  standard protocols (Gandrillon et al., 1987), maintained and homogenised for 3-4 passages before being used as a somatic cell control. RNAs were extracted using Trizol (Invitrogen) according to the manufacturer and microarray analysis performed in biological triplicate.

first: Christian

last: Jean

first: Clément

last: Mazoyer

last: Pain


title: Inhibition of zygotic DNA repair in trout: transcriptome analysis of the offspring

status: Public on Oct 29 2014

city: Rennes

first: Julien

last: Bobe

address: Campus de Beaulieu

institute: Institut National de la Recherche Agronomique

summary: Zygotic repair of paternal genome is a key event after fertilization. Spermatozoa accumulate DNA single and double strand breaks during spermatogenesis and can suffer additional damage before fertilization by different factors, including cryopreservation. Fertilization with DNA damaged spermatozoa (DDS) is considered to promote implantation failures and abortions, but also long term effects in the progeny that could be related to a defective repair. Base excision repair (BER) pathway is considered the most active in zygotic DNA repair, but healthy oocytes contain enzymes for all repairing pathways. In this study the effects of the inhibition of the BER pathway in the zygote, were analyzed on the progeny obtained after fertilization with differentially DDS. Massive gene expression (37.394 transcripts) was analyzed after hatching using microarrays. Trout oocytes are easily fertilized with DDS and the high prolificacy allows obtaining live progeny even with a high rate of abortions. Results showed that DDS, even if increased the number of abortions, provided normal progeny. Nevertheless, the zygotic inhibition of PARP, upstream the BER pathway, result 810 differentially expressed genes (DEGs) after hatching. DEGs are related to DNA repair, apoptosis, telomere maintenance or growth and development, revealing a scenario of impaired DNA damage signalization and repair. Down-regulation of the apoptotic cascade was noticed, suggesting a selection of embryos tolerant to residual DNA damage during embryo development. Our results suggest a high zygotic capacity to repair paternal DNA damage and reveals changes in the progeny from defective repairing zygotes whose long term consequences should be deeply analyzed

overall_design: Gene expression was analyzed in trout larvae one day after hatching obtained from differentially DNA damaged sperm with or without zygotic inhibition of the BER pathway of DNA repair. Eggs from two females were pooled and fertilized with sperm fresh (F samples) or cryopreserved using different procedures (LDL and EY samples).  Ten min later two batches from each sperm kind were treated with 3-aminobenzamide (3AB) to inhibit the PARP activity. Ten larvae per each one of the 6 treatments (3sperm kind x 2 zygotic treatments) were analyzed after pooling RNA. Four replicates per treatment were done fertilizing eggs from the same females with sperm from 4 different males.

first: Cristina

last: Fernéndez-Déz

first: Silvia

last: González-Rojo

first: Jérôme

last: Montfort

first: Aurelie

last: Le Cam

first: Vanesa

last: Robles

first: Serafín

last: Pérez-Cerezalez

first: Maria

last: Herráez


title: Identifying targets of DSX with DamID-chip

status: Public on Oct 30 2014

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary: We have used microarrays to identify DSX occupancy signal in adult female fatbody using the DamID protocol.

overall_design: We have performed DamID-chip on adult female fatbody with three biological replicates.

first: Emily

last: Clough

first: Erin

last: Jimenez

first: Yoo-Ah

last: Kim

first: Cale

last: Whitworth

first: Megan

last: Neville

first: Leonie

last: Hempel

first: Hania

last: Pavlou

first: Zhen-Xia

last: Chen

first: David

last: Sturgill

first: Ryan

last: Dale

first: Harold

middle: E

last: Smith

first: Teresa

middle: M

last: Przytycka

first: Stephen

last: Goodwin

first: Mark

last: Van Doren


title: Sex-specific gene expression profiles of Aedes aegypti 24 hr pupal heads

status: Public on Oct 27 2014

city: South Bend

first: Molly

middle: Duman

last: Scheel

state: IN

address: 1234 Notre Dame Ave.

institute: Indiana University School of Medicine

summary: Custom microarrays were used to examine global differences in female vs. male gene expression in the developing pupal head of the dengue vector mosquito Aedes aegypti.

overall_design: RNA was extracted from the heads of male and female 24 hr pupae.  20 male or female heads were pooled for each of four replicates.  Hybridization experiments were performed on the Nimblegen Aedes aegypti 12-plex microarray design: 090305_Aedes_aegypti_TEfam_expr.ndf.  Four unique replicates and two repeat replicates were assessed in the hybridization experiment.

first: Michael

last: Tomchaney

last: Duman-Scheel


title: Human meniscus from late stages of osteoarthritis - Comparisons: diseased vs. less diseased samples

status: Public on Oct 20 2014

city: Göttingen

first: Silvia

last: von der Heyde

address: Humboldtalle 32

department: Medical Statistics

institute: University Medical Center Göttingen

summary: Meniscus samples were taken from eight patients. Four patients were less diseased (LD) than the other four (D). Microarrays were used to detect differential gene expression between these two groups.

overall_design: Differential expression analysis: diseased (D) vs. less diseased (LD) samples. Biological replicates: 4 diseased, 4 less diseased. One replicate per array.

first: Nicolai

last: Miosge

first: Boris

last: Schminke

first: Hayat

last: Muhammad


title: ChIP-on-chip with anti-RBPj antibody from embryonic AGM E11.5

status: Public on Oct 22 2014

city: Barcelona

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

institute: Institut Hospital del Mar d'Investigacions Mèdiques

summary: Hematopoietic Stem Cells (HSC) are originated during embryonic development from endothelial-like cells located in the ventral side of the dorsal aorta around day E10-12 of murine development. This region is called AGM for Aorta/Gonad/Mesonephros refering to the tissues around the hemogenic aorta. Hematopoiesis depends on the Notch pathway and the identification of Notch-targets is important for the understanding of blood origin.

overall_design: Hematopoietic Stem Cells (HSCs) specification occurs in the embryonic aorta and requires Notch activation, however which are the elements regulated by Notch that control this process are mainly unknown. Here, we took a genome-wide approach to identify putative direct Notch targets by precipitating the chromatin that binds to the Notch partner RBPj in the Aorta-Gonad-Mesonephros (AGM) tissue from E11.5 mouse embryos. This assay revealed 701 gene promoter regions as candidates to be regulated by Notch in the AGM. Chromatin was obtained from a pool of 40 dissected AGMs at E11.5. Chromatin immunoprecipitation (ChIP) was performed as previously described (Aguilera et al, PNAS 2004) with minor modifications. In brief, cross-linked chromatin was sonicated for 10 minutes, medium-power, 0.5-interval; with a Bioruptor (Diagenode) and precipitated with anti-RBPJ (Chu and Bresnick, 2004). After crosslinkage reversal, DNA was used as a template for PCR or for array hybridization. Mouse promoter chip on chip microarray SET (Agilent) was used to identify RBPj targets. It covers 70,000 best identified gene regions with a-5.5 kb to + 2.5 kb range, and has on average 25 probes per gene with an average probe to probe distance of 200 bp. The ChIP-on-chip was performed with dye swaps and one IgG control was brought along. Enrichment analysis was done by comparing the precipitation normalized dye swap signal with input control signal.

first: Lluis

last: Espinosa


title: HPL-2 in GW638 (met-2 set-25) MxEmb

status: Public on Oct 11 2014

first: Susan

last: Strome

address: 1156 High St.

department: Molecular, Cell, and Developmental Biology

institute: UC Santa Cruz

summary: ChIP-chip of HPL-2 in met-2 set-25 C. elegans mixed-stage embryo

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: GW638; Developmental Stage: Mixed-stage Embryo; Genotype: met-2(n4256) set-25(n5021); Sex: population predominantly Hermaphrodites perhaps with some Males; NUMBER OF REPLICATES: 2; EXPERIMENTAL FACTORS:  temperature 20

first: Jacob

last: Garrigues


title: inra12-01_mut-flg-FLG-OoPTIMICE

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: ra12-01_mut_flg - inra12-01_mut-flg - Analysis of flg22-induced transcriptional changes in oxi1, OXI1oe, pti1-4, CA-MPK4 and ice1 mutant lines - 2 weeks seedlings compared for their transcriptome after a 30min mock or 1µM flg22 treatment.

overall_design: 27 dye-swap - gene knock in (transgenic)

first: Heribert

last: Hirt

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Expression profiling in PFR40 (hpl-2) mutant early embryo

summary: Identification of genes significantly misregulated in hpl-2 mutant early embryo compared to wild-type early embryo

overall_design: 4 replicates of total RNA from hpl-2 mutant early embryo was compared to 4 replicates of total RNA from wild-type early embryo [GSE58759] obtained from PMID 20824077.


title: Testosterone effects on the HVC transcriptome of adult female European robins (Erithacus rubecula)

status: Public on Nov 03 2014

first: Carolina

last: Frankl-Vilches

summary: Female European robins routinely sing during the winter season, a time when they defend feeding territories and also show elevated circulating testosterone levels. We used wild female European robins captured during fall to examine the effects of testosterone administration on the transcriptome of the song control nucleus HVC (proper name).

overall_design:
Robins were caught during fall, housed at short day cycles in sound-proofed recoding boxes and songs were recorded continously. A testosterone-teated robin was sacrificed one day after detection of the first high amplitude notes with a frequency above 15 kHz. Therefore, duration of testosterone treatment varied between samples. An individual of the control group was sacrificed on the same day to ensure a time-matched sampling of individuals from both groups. The differential gene expression in the HVC of 5 control and  6 testosterone birds was analyzed using the group-wise exhaustive analysis with False Discovery Rate set to zero and 10-significant probe minimum coverage.
ChipInspector carries out significance analysis on the single probe level. Normalized probe set level data not provided for individual Sample records. Processed data is available on Series record.

first: C

first: A

last: Bakker

first: F

last: Dittrich


title: HP1 in C. elegans

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

overall_design: Refer to individual Series


title: Comparative analysis of different cortical interneuron groups.

status: Public on Oct 07 2014

city: New York

first: Miho

last: Nakajima

state: New York

address: 1230 York Ave.

institute: The Rockefeller University

summary:
GABAergic interneuron in the cortex comprise a very heterogenous group. and it is critical to identify discrete interneuron types to understand how their contributions to behavior can be modulated by external and internal cues. However, molecular difinition of these interneuron cell groups has been difficult.  Comparative analysis of different interneuron subtypes can provide us new candidate marker genes which could target more specific interneuｒon cell group. Here we identify oxytocin responsive novel class of interneuron through our comparative analysis.
We employed the bacTRAP strategy, which uses BAC transgenic mice expressing EGFP-tagged ribosomal protein L10a in specific cell populations, to affinity purify polysome-bound mRNAs from Nek7, Dlx1, Cort, Htr3a, Oxtr expressing cortical interneurons. We show that Oxtr expressing cells are a subtype of somatostatin positive interneurons.

overall_design: Three independent TRAP replicates were collected and total RNA from the immunoprecipitates or flow-through (input) whole cortex lysates were amplified and hybridized. Data were normalized with the GCRMA algorithm and replicates were averaged across conditions. We recommend filtering data to remove probe sets with normalized expression values less than 50 in at least one condition. Because the Nek7 BAC labels non-neuronal cells, we recommend to delete astrocytes and oligodendrocytes genes from the list using GSE13379 data.

first: Andreas

last: Görlich

first: Nathaniel

last: Heintz


title: Mitochondrial ATP Synthase Subunit d Interacts with TOR Signaling and Dietary Macronutrients to Modulate Proteostasis and Lifespan in Drosophila

status: Public on Oct 02 2014

city: Baltiimore

first: Sige

last: Zou

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

summary: Diet composition is a critical determinant of lifespan and nutrient imbalance is detrimental health. However, how nutrients interact with genetic factors to modulate lifespan remains elusive. We investigated how diet composition influences mitochondrial ATP synthase subunit d (ATPsyn-d) in modulating lifespan in Drosophila. ATPsyn-d knockdown extended lifespan in females fed low carbohydrate-to-protein (C:P) diets, but not the high C:P ratio diet. We also measured changes in the genome-wide expression profile induced by ATPsyn-d knockdown.  Lifespan extension induced by ATPsyn-d knockdown was associated with increased resistance to oxidative stress, transcriptional changes in metabolism, proteostasis and immune genes, reduced protein damage and aggregation, and reduced phosphorylation of S6K and ERK in TOR and MAPK signaling, respectively. Our data reveal a link among diet, mitochondria, MAPK and TOR signaling in aging and stresses the importance of considering genetic background and diet composition in implementing interventions for promoting healthy aging.

overall_design: Eight experimental samples from the heads of 14-day old actin-GSG>UAS-ATPsyn-d-RNAi females treated with and without RU486 were labeled with Cy3 and analyzed using custom printed long oligo microarrays. Samples from wild type Canton S flies were labeled with Cy5 and used as the common reference for all microarray experiments.

first: X

last: Sun

first: S


title: Evolution of Context Dependent Regulation by Expansion of Feast/Famine Regulatory Proteins [expression]

city: Seattle

first: Christopher

last: Plaisier

state: Washington

address: 401 Terry Avenue North

institute: Institute for Systems Biology

summary:
We validated context dependent regulation by two FFRPs AsnC and VNG1237C by deleting the FFRP and testing the effect on downstream target genes.
For validtion of AsnC condition specific regulation we grew wild-type and delta-AsnC in the presence of 4mM paraquat (PQ) and samples at 1 and 160 minutes post addition of this sub-lethal dose of PQ. For validation of VNG1237C we grew wild-type and delta-VNG1237C in a standard growth curve sampling at OD 0.18 and 1.15.

overall_design: The asnC deletion strain (∆asnC) and the control ∆ura3 strain were grown in 4mM paraquat (PQ) and were sampled at 1 and 160 minutes after PQ addition. Sampling timing for ∆VNG1237C was designed such that the starting ODs were as similar as possible and once an OD of 1.17 was reached for ∆ura3 the ∆VNG1237C was sampled at this same time point.

first: Nitin

middle: S

last: Baliga


title: Evolution of Context Dependent Regulation by Expansion of Feast/Famine Regulatory Proteins [ChIP-chip]

status: Public on Oct 03 2014

summary: Chromatin immunoprecipitation and microarray hybridization (ChIP-chip) experiments were carried out for all 8 FFRPs in H. salinarum NRC-1.

overall_design: To study the FFRP localization in both nutrient-replete and -deplete conditions, all strains were grown in CDM and genomic DNA of samples was harvested in both early log phase and late log phase. DNA from FFRP-bound regions was collected through c-Myc-tagged protein complexes and unenriched non-IP DNA were each labeled and hybridized to the whole genome tiling array.


title: APR2 mapping

status: Public on Oct 01 2014

city: Shanghai

first: Daiyin

last: Chao

address: 300 Fenglin Road

department: Shanghai Institute of Plant Physiology and Ecology

institute: Shanghai Institutes for Biological Sciences

summary: ABSTRACT: Natural variation allows the investigation of both the fundamental functions of genes and their role in local adaptation. As one of the essential macronutrients, sulfur is vital for plant growth and development, and also for crop yield and quality. Selenium and sulfur are assimilated by the same process, and although plants do not require selenium, plant-based selenium is an important source of this essential element for animals. Here, we report the use of linkage mapping in synthetic F2 populations, and complementation to investigate the genetic architecture of variation in total leaf sulfur and selenium concentrations in a diverse set of Arabidopsis thaliana accessions. We identify in accessions collected from Sweden and the Czech Republic two variants of the enzyme adenosine 5-phosphosulfate reductase 2 (APR2) with strongly diminished catalytic capacity. APR2 is a key enzyme in both sulfate and selenate reduction and its reduced activity in the loss-of-function allele apr2-1 and the two A. thaliana accessions Hodon¨ªn (Hod) and Shahdara (Sha), leads to a lowering of sulfur flux from sulfate into the reduced sulfur compounds, cysteine and glutathione, and into proteins, concomitant with an increase in the accumulation of sulfate in leaves. We conclude from our observation, and the previously identified weak allele of APR2 from the Sha accession collected in Tadjikistan, that the catalytic capacity of APR2 varies by four orders of magnitude across the A. thaliana species range, driving significant differences in sulfur and selenium metabolism. The selective benefit, if any, of this large variation remains to be explored.

overall_design:
genomic hybridization bulked segregant analysis
Hybridizations from a set of Bulk Segregant analysis. We measured the elemental profile of 328 F2 plants from a cross between the high sulfur and selenium Arabidopsis thaliana accession Hod and the Col-0 accession, data available at www.ionomicshub.org <http://www.ionomicshub.org>). Leaves from the 57 highest and 61 lowest sulfur and selenium accumulating plants (calculated as a percentage of the Col-0 accumulation in the same growth tray) were pooled and the genomic DNA was extracted using Qiagen kits.


title: aCGH: Human SUM149-Luc triple-negative Inflammatory Breast Cancer cell line versus its metabolically adaptable variants MA1 and MA2

city: Houston

first: Anthony

last: Lucci

state: Texas

address: 1515 Holcombe Blvd

department: Surgical Oncology

institute: UT MD Anderson Cancer Center

summary: CGH array of MA1 and MA2 variant cells as compared to the parental SUM149-Luc breast cancer cell line. The MA1 and MA2 variants were isolated based on the ability of rare cancer cells to survive and grow without adding glutamine in culture medium. To gain insight into the characteristic of metabolically adaptable MA cells that enables them to survive severe metabolic challenge, i.e., prolonged lack of glutamine and other challenges [Singh et al., PLoS ONE 7: e36510, 2012], we analyzed CGH array to compare these cells with the parental SUM149-Luc (luciferase-transfected) cells. We analyzed two independently selected cell populations, one from 0.5 million parental cells (designated MA1) and one from 1 million parental cells (designated MA2).

overall_design: Comparing the MA1 and MA2 variants to the common parental SUM149-Luc cell line. One sample each.

first: Balraj

last: Singh


title: Evolution of Context Dependent Regulation by Expansion of Feast/Famine Regulatory Proteins


title: MicroRNA expression in the glomerulus of C57BL/6 mice and B6.MRLc1 glomerulonephritis mice

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

institute: Toray Industries,Inc.

summary: In isolated glomeruli by beads-perfusion methods, microRNA (miRNA) expression was analyzed in healthy C57BL/6 and B6.MRLc1 glomerulonephritis mice. The expression of 1,135 miRNAs was examined, and up-regulated or down-regulated miRNA was determined. These results provide a basical information of molecular pathology in glomerulonephritis.

overall_design: The glomeruli were collected from female C57BL/6 (n=3, 9-month-old, healthy control) and female B6.MRLc1 (n=3, 14-month-old, early stage of glomerulonephritis; n=3, 9-month-old, late stage of glomerulonephritis). The total RNA sample was purified, and total 1,135 microRNA expression was compared among healthy, early stage, and late stage.

first: Osamu

last: Ichii


title: HPL-2 in PFR40 (hpl-2) early embryo

city: Santa Cruz

first: Susan

last: Strome

summary: ChIP-chip of HPL-2 in hpl-2 C. elegans early embryo

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: PFR40; Developmental Stage: Early Embryo; Genotype: hpl-2(tm1489); Sex: population predominantly Hermaphrodites perhaps with some Males; NUMBER OF REPLICATES: 1; EXPERIMENTAL FACTORS:  temperature 20

first: Jacob

last: Garrigues


title: Expression analysis in intestinal mucosa of genes under association peaks in celiac disease

status: Public on Sep 30 2014

city: Leioa

first: Jose Ramon

last: Bilbao

state: Outside the US or Canada

address: Bº Sarriena

department: Genetics, Physical Anthropology and Animal Physiology

institute: University of the Basque Country (UPV/EHU)

summary: Celiac disease is a chronic immune-mediated disorder with an important genetic component. To date, there are 57 independent association signals from 39 non-HLA loci, and a total of 66 candidate genes have been proposed. We aimed to scrutinize the functional implication of 45 of those genes by analyzing their expression in the disease tissue of celiac patients (at diagnosis/treatment) compared to non-celiac controls.

overall_design: The sample set consisted of 15 CD children at diagnosis (on a gluten-containing diet, with CD associated antibodies, atrophy of intestinal villi and crypt hyperplasia), and the same patients in remission after being treated with GFD for >2 years (asymptomatic, antibody negative, and normalized intestinal epithelium at that time), plus 15 tissue samples from non-celiac individuals not suffering from inflammation at the time of endoscopy used as controls

first: Leticia

last: Plaza-Izurieta

first: Nora

last: Fernandez-Jimenez

first: Iñaki

last: Irastorza

first: Amaia

last: Jauregi-Miguel

first: Irati

last: Romero-Garmendia

first: Juan

middle: C

last: Vitoria

first: Jose


title: Comparing bacterial community composition of healthy and dark-spot-affected Siderastrea siderea in Florida and the Caribbean.

city: Berkeley

first: Yvette

last: Piceno

address: 1 Cyclotron Rd., MS 70A-3317

department: Ecology

institute: LBNL

summary: Coral disease is one of the major causes of reef degradation and therefore of concern to management and conservation efforts. Dark Spot Syndrome (DSS) was described in the early 1990’s as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease, since they can also be caused by physical injury in some species. The most commonly affected species in the Caribbean is the massive starlet coral Siderastrea siderea. We sampled this species in two geographic locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies with normal pigmentation and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip™ G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, however the amplicon pools were overwhelmed by coral 18S rRNA genes from S. siderea. Unlike a similar study on a white-plague-like disease, S. siderea samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and Vibrios, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in S. siderea is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the healthy scleractinian coral S. siderea.

platform_organism: Bacteria Archaea

overall_design: 17 samples, coral tissue punches from healthy and also from dark-spot-affected Siderastrea Siderea coral in the Virgin Islands and the Dry Tortugas National Parks was collected for comparison of associated bacterial communities

first: Christina

last: Kellogg

first: Lauren

last: Tom

first: Todd

middle: Z

last: DeSantis

first: Michael

last: Gray

first: Gary

middle: L

last: Andersen


city: Natanya

first: Tal

middle: Haim

last: Hasson

address: Hatrufa 12

department: Analytical R&D

country: Israel

institute: Teva Pharmaceuticals

summary: For decades, policies regarding generic medicines have sought to provide patients with economical access to safe and effective drugs, while encouraging the development of new therapies. This balance is becoming more challenging for physicians and regulators as biologics and non-biological complex drugs (NBCDs) such as glatiramer acetate demonstrate remarkable efficacy, because generics for these medicines are more difficult to assess. We sought to develop computational methods that use transcriptional profiles to compare branded medicines to generics, robustly characterizing differences in biological impact. We combined multiple computational methods to determine whether differentially expressed genes result from random variation, or point to consistent differences in biological impact of the generic compared to the branded medicine. We applied these methods to analyze gene expression data from mouse splenocytes exposed to either branded glatiramer acetate or a generic. The computational methods identified extensive evidence that branded glatiramer acetate has a more consistent biological impact across batches than the generic, and has a distinct impact on regulatory T cells and myeloid lineage cells. In summary, we developed a computational pipeline that integrates multiple methods to compare two medicines in an innovative way. This pipeline, and the specific findings distinguishing branded glatiramer acetate from a generic, can help physicians and regulators take appropriate steps to ensure safety and efficacy.

overall_design:
Glatiramoid samples for SPL cell activation were grouped into four categories: 1) Verified GA, which included GA-RS (22 biological samples) and GA drug product (GA-DP, 34 biological samples from 30 batches) manufactured by Teva; 2) Deliberately Modified GA (DM-GA; 9 biological samples), which included glatiramoids made by Teva that were similar to GA but modified in a variety of ways: prepared with different ingredients (e.g., missing a constituent amino acid); prepared with the same amino acids in the same molar ratio as GA, but with defined amino acid sequences and different molecular weights (referred to as peptide markers TV-35 and TV-66); synthesized by a different process (e.g., changing acetolytic cleavage conditions, alternating polymerization initiator); exposed to destabilizing conditions (e.g., degradation by acid, base, and heat); 3) Unverified Glatiramoids, which included 4 biological samples, TV-5010 and 3 glatiramoids synthesized to be similar to GA but not manufactured using the Teva-patented manufacturing process; and 4) Unverified Generic GA, which included samples from 2 glatiramoids (“GA-Q” 11 biological samples from 5 different batches, and 2 “GA-C” samples from a single batch) marketed as generic GA manufactured by companies other than Teva.

Please note that GSE61901 is another series on the same data as GSE40566.  GSE61901 includes the individual  technical replicates, and was utilized for the manuscript: Towfic F, Funt JM, Fowler KD, Bakshi S et al. Comparing the biological impact of glatiramer acetate with the biological impact of a generic. PLoS One 2014;9(1):e83757. PMID: 24421904.  GSE40566 was preprocessed to average the technical replicates, and was utilized for the manuscript: Bakshi S, Chalifa-Caspi V, Plaschkes I, Perevozkin I et al. Gene expression analysis reveals functional pathways of glatiramer acetate activation. Expert Opin Ther Targets 2013 Apr;17(4):351-62. PMID: 23469939.

first: Shlomi

last: Bakshi

first: V

last: Caspi

first: I

last: Plaschkes

last: Perevozkin


title: Microrray expression data of Osteoarthritis synovial fibroblasts (OASF) transfected with TBX5

city: Schlieren

first: Emmanuel

last: Karouzakis

address: Wagistrasse 14/3.OG

department: Center of Experimental Rheumatology

country: Switzerland

institute: University Hospital Zurich

summary:
TBX5 is hypomethylated in Rheumatoid Arthritis synovial fibroblasts (RASF). Hypomethylation increased the TBX5 expression in RASF.
We performed a microarray expression analysis upon TBX5 overexpression to find TBX5  molecular targets.TBX5 belongs to the T-box transcription factor family all of which possess a T-box DNA binding domain in their sequence. It has been shown to play an important role in tissue development and cancer.

overall_design: We were interested in identifying a possible role of TBX5 overexpression in RA. To that end, OASF were transfected with pcDNA3.1(+)_TBX5 or pcDNA3.1(+) empty vector as a negative control. After 48h, RNA was extracted  and cDNA was generated by reverse transcription. The labeled cDNA was hybridized to the Affymetrix microarray.

first: Michel

last: Neidhart