title: Expression profile of Arabidopsis DEFLs in pistils and developing siliques

status: Public on Apr 10 2014

city: Minneapolis

first: Kevin

last: Silverstein

state: MN

address: 599 Walter Library, 117 Pleasant St SE

department: Minnesota Supercomuting Institute

institute: Universtiy of Minnesota

summary: The aim of the project is to determine the expression profile of Arabidopsis DEFL during sexual reproduction, in particular seed development. To this aim, we generated a customised Affymetrics array that was hybridized with labeled cDNA synthetised from total RNA.

overall_design: Plant were grown in a control environment chamber and were pollinated manually to precisely generate different stages of seed development. Samples were collected in tripicates.

first: Mesfin

last: Tesfaye

first: Liliana

last: Costa

first: Kathryn

last: VandenBosch

first: Jose

last: Gutierrez-Marcos


title: Dynamic gene expression by putative hair-cell  progenitors during regeneration in the  zebrafish lateral line

status: Public on Apr 01 2014

city: New York

first: Aaron

middle: B

last: Steiner

state: NY

address: 1230 York Ave, Box 314

department: Laboratory of Sensory Neuroscience

country: USA

institute: The Rockefeller University

summary:
Hearing loss is most commonly caused by the destruction of mechanosensory hair cells in the ear. This condition is usually permanent: Despite the presence of putative hair-cell progenitors in the cochlea, hair cells are not naturally replenished in adult mammals. Unlike those of the mammalian ear, the progenitor cells of nonmammalian vertebrates can regenerate hair cells through- out life. The basis of this difference remains largely unexplored but may lie in molecular dissimilarities that affect how progenitors respond to hair-cell death.
We analyzed gene expression in hair-cell progenitors of the lateral-line system. We developed a transgenic line of zebrafish called alpl:mCherry that expresses a red fluorescent protein in the presumptive hair-cell progenitors known as mantle cells. Fluorescence-activated cell sorting from the skins of transgenic larvae, followed by microarray-based expression analysis, revealed a constellation of transcripts that are specifically enriched in these cells versus hair cells and non-fluorescent skin cells. Gene expression analysis after hair-cell ablation uncovered a cohort of genes that are differentially regulated early in regeneration, suggesting possible roles in the response of progen- itors to hair-cell death. These results provide a resource for studying hair-cell regeneration and the biology of sensory progenitor cells.

overall_design: Two sets of analyses were performed. The first compared baseline expression levels in four sorted cell types from two different transgenic lines of zebrafish, alpl:mCherry;pou4f3:GFP and alpl:mCherry:ET20. alpl:mCherry;pou4f3:GFP larvae express GFP in hair cells and mCherry in mantle cells. alpl:mCherry:ET20 larvae express GFP in most mantle cells and mChery in all mantle cells. The four cell types compared were GFP+ hair cells, mCherry+ mantle cells, mCherry+/GFP+ mantle cells from  alpl:mCherry:ET20 larvae, and non-fluorescent (NF) cells. Two hair-cell, five mCherry+ mantle cell, four mCherry+/GFP+ mantle cell, and six NF cell samples were analyzed. This excludes a few samples that were discardced based on failure to cluster by principal component analysis. A second analysis, separately imported, compared gene expression in mCherry+ mantle cells and NF cells at four time points following chemical ablation of hair cells with copper sulfate. These were one, three, five, and eleven hours after treatment (hpCu). Untreated samples served as controls. For mCherry+ cells, five untreated and four each of 1 hpCu, 3 hpCu, 5 hpCu and 11 hpCu were analyzed. For NF cells, six untreated, seven 1 hpCu, and four each of 3 hpCu, 5 hpCu and 11 hpCu samples were analyzed. Untreated mCherry+ and NF cells were shared between both analyses.

first: Taeryn

last: Kim

first: Victoria

last: Cabot

first: A

middle: J

last: Hudspeth


title: The Mi-2 homolog, Mit1, actively positions nucleosomes within heterochromatic domains to suppress transcription

status: Public on Apr 08 2014

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

type: Expression profiling by genome tiling array

summary: Nucleosome positioning is both active and passive and regulates access to the genome for replication, transcription and repair. Here we report that Mit1, a subunit of the fission yeast SHREC complex similar to Mi-2/NuRD, regulates transcription at regions of heterochromatin by positioning nucleosomes to preclude access to RNA Polymerase II. Purified Mit1 is a nucleosome remodeling factor capable of mobilizing histone octamers on short DNA fragments and requires ATP hydrolysis and chromatin tethering domains to remodel nucleosomes and silence transcription. We propose that SHREC is recruited to heterochromatin to mobilize nucleosomes onto unfavorable positions to prevent spurious transcription within heterochromatin.

overall_design: RNA samples were prepared from biological duplicates of WT and mit1∆::NatMX6 fission yeast to compare transcript levels using the Affymetrix GeneChip S.pombe Tiling 1.0FR microarray.

middle: M

last: Creamer

first: Janet

middle: F

last: Partridge

middle: A


title: Blood Transcriptome analysis of wild common bottlenose dolphins (Tursiops truncatus) from the South-East of the United States

status: Public on Mar 26 2014

city: Ferrara

first: Annalaura

last: Mancia

address: via L.Borsari, 46

department: Life Sciences and Biotechnology

country: Italy

institute: University of Ferrara

summary: To validate the oligo array and to investigate the impact of the environmental stressors on dolphin health at transcriptomic level

overall_design: Collection of blood samples from wild animals in 4 different geographic locations of the South East of the United States


title: Inheritance patterns and stability of DNA methylation variation in maize near-isogenic lines

city: St. Paul

first: Steve

middle: R

last: Eichten

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

type: Methylation profiling by genome tiling array

summary: DNA methylation is a chromatin modification that contributes to epigenetic regulation of gene expression.  The inheritance patterns and trans-generational stability of 962 differentially methylated regions (DMRs) were assessed in a panel of 71 near-isogenic lines (NILs) derived from maize (Zea mays) inbred lines B73 and Mo17.  The majority of DMRs exhibit inheritance patterns that would be expected for local (cis) inheritance of DNA methylation variation such that DNA methylation level was coupled to local genotype.  There are few examples of DNA methylation that exhibit trans-acting control or paramutation-like patterns.  The cis-controlled DMRs provided an opportunity to study the stability of inheritance for DNA methylation variation.  There was very little evidence for alterations of DNA methylation levels at the cis-controlled DMRs during NIL population development.  DNA methylation level was associated with local genotypes in all of the >30,000 examined cases except one.  Additionally, the majority of the DMRs were not associated with small RNA.  Together, our results suggest that a significant portion of DNA methylation variation in maize exhibits cis-controlled inheritance patterns, is highly stable and does not require active programming by small RNAs for maintenance.

overall_design: Methylation profiles in seedling tissue of maize near-isogenic lines (NILs) derived from B73 and Mo17 using a custom 12x270K NimbleGen array.

first: Qing

last: Li

first: Peter

last: Hermanson

first: Nathan

last: Springer


title: Transcriptional adaptation of Eurotium rubrum to hypersalinity

status: Public on Mar 25 2014

city: Bayreuth

first: Alfons

last: Weig

address: Universitaetsstrasse 30

department: Genomics and Bioinformatics

country: Germany

institute: University of Bayreuth

summary: Long-term transcriptional adaptation was investigated by comparative transcriptome analysis of E. rubrum grown at different salt concentrations.

overall_design: E. rubrum mycelia were grown at low, medium and high salt media. Salt concentrations are expressed in percentage of Dead Sea Water (DSW) salt content. Comparative data analysis was performed using transcription profiles at medium salt concentrations as the reference.

first: Tamar

last: Kis-Papo


title: Suckling piglets: Control vs. weaned piglets

status: Public on May 01 2014

city: Shanghai

first: Lihui

last: Zhu

state: Shanghai

address: 800 Dongchuang Road

department: School of Agriculture and Biology

country: China

institute: Shanghai Jiaotong University

summary: Transcriptional profiling of 25d old piglets comparing control untreated suckling jejunum with weaned piglets' jejunum. The goal was to gain new insight into the interaction between weaning and intestinal function.A keen interest is paid in deciphering expression changes of apoptosis or cell cycle control genes.  The statistical analysis of gene ontology revealed that most of these altered genes are metabolic-related enzymes and regulators which may involved in the biological regulation, developmental process, and cellular process. Weaning also causes alterations in various immune response pathways. Results likely indicate that weaning induced cell cycle arrest, enhanced apoptosis, and inhibited cell proliferation.

overall_design: Two-condition experiment, suckling control piglets' jejunum vs. weaned piglets' jejunum. Biological replicates: 4 control replicates, 4 weaned replicates.

first: Jianxiong

last: Xu


title: Expression data for Paramecium sexually reactive cells from type 7 and type 8

status: Public on Mar 14 2014

city: Villerubanne

first: Jean-François

last: Gout

address: 43 Bld du 11 Novembre 1918

country: France

institute: Laboratoire Biométrie et Biologie Evolutive

summary: We used microarrays to find differentially expressed genes between reactive cells of mating type 7 and 8

overall_design: Total RNA was extracted from sexually reactive cells of both mating types.

first: Eric

last: Meyer


title: ChIP-chip of E. coli K-12 MG1655 with antibody against ArcA-8myc or Fnr-8myc under various conditions.

status: Public on Feb 27 2014

city: La Jolla

first: Bernhard

last: Palsson

state: CA

address: 9500 Gilman Dr.

institute: University of California San Diego

type: Genome binding/occupancy profiling by genome tiling array

summary: Determining how facultative anaerobic organisms sense and direct cellular responses to electron acceptor availability has been a subject of intense study. However, even in the model organism Escherichia coli, established mechanisms only explain a small fraction of the hundreds of genes that are regulated during shifts in electron acceptor availability. Here we propose a qualitative model that accounts for the full breadth of regulated genes by detailing how two global transcription factors (TFs), ArcA and Fnr of E. coli, sense key metabolic redox ratios and act on a genome-wide basis to regulate anabolic, catabolic, and energy generation pathways. We first fill gaps in our knowledge of this transcriptional regulatory network by carrying out ChIP-chip and gene expression experiments to identify 463 regulatory events. We then interfaced this reconstructed regulatory network with a highly curated genome-scale metabolic model to show that ArcA and Fnr regulate > 80% of total metabolic flux and 96% of differential gene expression across fermentative and nitrate respiratory conditions. Finally, based on the data we propose a feedforward with feedback trim regulatory scheme by showing extensive repression of catabolic genes by ArcA and extensive activation of chemiosmotic genes by Fnr. We further corroborated this regulatory scheme by showing a 0.71 r2 (p < 1e-6) correlation between changes in metabolic flux and changes in regulatory activity across fermentative and nitrate respiratory conditions. We also are able to relate the proposed model to a wealth of previously generated data by contextualizing the existing transcriptional regulatory network.

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

overall_design:
We integrated transcription factor binding regions and mRNA transcript abundance to elucidate the ArcA and Fnr regulons experimentally. To measure transcription factor binding at a genome scale, we employed a ChIP-chip method to derivative strains of  E. coli K-12 MG1655 harboring ArcA-8myc or Fnr-8myc under various conditions.
The E. coli strains harboring Fnr-8myc and ArcA-8myc were generated as described previously [PMID 16454042].
A 12 chip study with two different strains under two different culture conditions.

first: Stephen

last: Federowicz

first: Donghyuk

last: Kim

first: Byung-Kwan

last: Cho

middle: O


title: Transcriptomic analysis of (Group I) Clostridium botulinum ATCC 3502 cold shock response

status: Public on Feb 24 2014

city: Helsinki

first: Marita

last: Isokallio

address: PO Box 66

country: Finland

institute: University of Helsinki

summary: Profound understanding of the mechanisms foodborne pathogenic bacteria utilize in adaptation to the environmental stress they encounter during food processing and storage is of paramount importance in design of control measures. Chill temperature is a central control measure applied in minimally processed foods; however, data on the mechanisms the foodborne pathogen Clostridium botulinum activates upon cold stress are scarce. Global gene expression analysis on the C. botulinum ATCC 3502 strain upon temperature downshift from 37 °C to 15 °C was performed to identify the cold-responsive gene set of this organism. Significant up- or down-regulation of 16 and 11 genes, respectively, was observed already 1 h after the cold shock. At 5 h after the temperature downshift, 199 and 210 genes were up- and down-regulated, respectively. Thus, the cold shock rapidly affected the expression of a gene set of a relatively small size, indicating a targeted acute response to cold shock, whereas extensive metabolic remodeling took place after prolonged exposure to cold. Induction of genes related to fatty acid biosynthesis, oxidative stress response, and iron uptake and storage was observed, in addition to mechanisms previously characterized as cold-tolerance related in bacteria. Furthermore, induction of several uncharacterized DNA-binding transcriptional regulator-encoding genes was observed, suggesting involvement of novel regulatory mechanisms in the cold shock response of C. botulinum. The role of such regulatory proteins, CBO0477 and CBO0558A, in cold tolerance of C. botulinum ATCC 3502 was demonstrated by the deteriorated growth of mutants of the respective genes at 17 °C.

overall_design: C. botulinum ATCC 3502 wild type cold-shocked vs. pre-cold-shock; 3 replicates; growth at 37C in TPGY broth batch culture and subjected to cold shock to 15C; sampling at mid-log growth phase before cold shock, and 1 h and 5 h after temperature downshift to 15C (= 3 time points). Dye-swapped hybridization.

first: Elias

last: Dahlsten

first: Panu

last: Somervuo

first: Miia

last: Lindström

first: Hannu

last: Korkeala


title: Selective amputation of the pharynx identifies a FoxA-dependent regeneration program in planaria

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

summary: Planarian flatworms can regenerate every organ after amputation. Adult pluripotent stem cells drive the ability to regenerate, but how injury activates these cells and directs them into the appropriate lineages is not understood. To study the regeneration response in a simplified context, we selectively induced the ejection of the planarian pharynx by briefly exposing animals to sodium azide followed by microarray analysis. Tissue surrounding the wound site was examined at 6, 12, 18, 24, 48, and 72 hours post amputation by comparison to tissue isolated immediately after amputation (time zero). Stem cells are required for the regeneration process, and can be eradicated by exposure to radiation. A parallel time course was also performed on worms that had been irradiated with 10k rads of gamma irradiation.

overall_design: Two time courses consisting of irradiated or unirradiated worms following chemical amputation of the pharynx. Tissue samples taken at 6, 12, 18, 24, 48 and 72 hours are each compared to a reference sample at time zero. The experiment was performed in triplicate for a total of 42 samples on 36 arrays.

first: Carolyn

middle: E

last: Adler

first: Sean

last: McKinney

first: A

last: Sanchez Alvarado


title: Evolutionarily conserved C-terminal region of TAF9 is critical for SAGA and TFIID recruitment to promoters and transcriptional activation

status: Public on Feb 21 2014

city: New Delhi

first: Krishnamurthy

last: Natarajan

state: Delhi

address: 314/325, School of life sciences, JNU

department: School of life sciences

country: India

institute: Jawaharlal Nehru University

summary: TFIID and SAGA complexes play a critical role in RNA Polymerase II dependent activated transcription. Although the two regulatory complexes are recruited to promoters by activation domain-interactions, the contribution of the different subunits or the different domains of the individual subunits is not completely understood. Taf9 is a shared subunit in TFIID and SAGA and has an N-terminal H3-like histone fold domain and a highly conserved C-terminal domain, Taf9-CTD. In this study, we have uncovered an essential role for the Taf9-CTD in transcriptional activation. The Taf9-CTD was not essential for the histone-fold mediated interaction with Taf6, SAGA and TFIID integrity or Gcn4 interaction with SAGA.  Transcriptome profiling performed under Gcn4 activating conditions showed that the Taf9-CTD is required for expression of ~17% of the yeast genome and provides a coactivator function to recruit TFIID and SAGA complexes to the promoters in vivo during transcriptional activation.  Integrated genome-wide data analysis showed that the Taf9-CTD is required for activation of promoters bound by several transcription factors indicating a broad role for Taf9-CTD in promoter occupancy of TFIID or SAGA complexes.  Interestingly, only a subset of the promoters seemed to be dependent on the Taf9-CTD for assembly of the pre-initiation complex indicating redundancy in activator targets to assemble PIC in vivo.  Together these results indicate that evolutionarily conserved domains in shared subunits of TFIID and SAGA have a pervasive role in genome-wide transcription.

overall_design: This GEO series consists of 14 microarray hybridizations using the Agilent two-color experiment with the Agilent Custom Saccharomyces cerevisiae 8x15k gene expression array.  Four biological replicates each for the wild-type (TAF9), the mutant taf9-tCRD2 strain treated or untreated with SM, and the wild-type (TAF9) versus mutant taf9-tCRD2 treated with SM hybridized as dye-swapped replicates. Two biological replicates for wild-type (SPT20) vs spt20D strains treated with SM, and hybridized as dye-swapped replicates to identify the fraction of SAGA dependent genes  under amino-acid starvation conditions.  The overall aim was to identify genes dependent on the conserved C-terminal region domain of TAF9 and determine their dependence on the SAGA subunit Spt20 for expression.

first: K

first: Malika

last: Saint


title: Identifying mRNA Sequence Elements for Target Recognition by Human Argonaute Proteins

status: Public on Feb 19 2014

city: Toronto

first: Zhaolei

last: Zhang

state: ONTARIO

address: 160 College St

department: Molecular Genetics, Computer Science

country: Canada

institute: University of Toronto

summary: It is commonly known that mammalian microRNAs guide the RNA-induced silencing complex (RISC) to target mRNAs through the seed-pairing rule. However, recent experiments by co-immunoprecipitating the argonaute proteins (AGOs), the central catalytic component of RISC, have consistently revealed extensive AGO-associated mRNAs lacking seed complementarity with microRNAs. We herein test the hypothesis that AGO has its own binding preference within target mRNAs, independent of guide microRNAs. By systematically analyzing the data from in vivo cross-linking experiments with human AGOs, we have identified a structurally accessible and evolutionarily conserved region (~10 nucleotides) that alone can accurately predict AGO-mRNA associations, independent of the presence of microRNA binding sites. Within this region, we further identified an enriched motif that is also consistently present in several independent AGO-immunoprecipitation datasets. We used RNAcompete to enumerate the RNA-binding preference of human AGO2 to all possible 7-mer RNA sequences, and validated our motif in vitro. These findings reveal a novel function of AGOs as sequence-specific RNA-binding proteins, which may aid microRNAs in recognizing their targets with high specificity.

overall_design: Here, we analyze the RNA-binding preference of human Argonaute 2 protein using RNAcompete assay

first: Jingjing

last: Li

first: TaeHyung

first: Razvan

last: Nutiu

first: Debashish

last: Ray

first: Timothy

last: Hughes


title: The Lung Microbiome of HIV-infected Pneumonia Patients in Sub-Saharan Africa

status: Public on Feb 20 2014

city: San Francisco

first: Shoko

last: Iwai

address: 513 Parnassus Ave.

department: Medicine

institute: University of California San Francisco

summary:
Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome were significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population.

Please note that the data from the comparable cohort of patients in the USUS data was published as supplemental material of PMID: 22760045 but not submitted to GEO

The 'patient_info.txt' contains 12 clinical, 7 immunological and 3 microbiological variables for each patient.

platform_organism: Bacteria Archaea

overall_design: The G2 PhyloChip microarray platform (commercially available from Second Genome, Inc.) was used to profile bacteria in lower airway samples from 60 subjects

first: Susan

middle: V

last: Lynch

first: Laurence

last: Huang


title: Transcriptome analysis in rice smos1 mutant

status: Public on Mar 01 2014

city: Nagoya

first: Koichiro

last: Aya

state: Aichi

address: Furo-cho, Chikusa-ku

department: Bioscience and Biotechnology Center

country: Japan

institute: Nagoya University

summary: In this study, we identified a new rice loss-of-function mutant, small organ size1 (smos1), that decreases the final size of various organs due to decreased cell size and abnormal microtubule orientation. SMOS1 encodes an unusual APETALA2 (AP2)-type transcription factor with an imperfect AP2 domain, and its product belongs to the basal AINTEGUMENTA (ANT) lineage, including WRINKLED1 (WRI1) and ADAP. SMOS1 expression was induced by exogenous auxin treatment, and the auxin response element (AuxRE) of the SMOS1 promoter acts as a cis-motif through interaction with auxin response factor (ARF). Furthermore, a functional fluorophore-tagged SMOS1 was localized to the nucleus, supporting the role of SMOS1 as a transcriptional regulator for organ size control. Microarray analysis showed that the smos1 mutation represses expression of several genes involved in microtubule-based movement and DNA replication.

overall_design: Expression profiling with the rice 44K-Agilent microarray was conducted using RNAs extracted from the leaf sheaths of WT and smos1 mutant. Each dataset was obtained from three biological replicates.

first: Matsuoka

last: Makoto


title: The distribution of genomic variations in human iPSCs is related to replication timing reorganization during reprogramming [NimbleGen]

status: Public on Mar 28 2014

city: Rochester

first: Hu

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

type: Genome variation profiling by genome tiling array

summary: Cell fate change involves significant genome reorganization, including change in replication timing, but how these changes are related to genetic variation has not been examined. To study how change in replication timing that occurs during reprogramming impacts the copy number variation (CNV) landscape, we generated genome-wide replication timing profiles of induced pluripotent stem cells (iPSCs) and their parental fibroblasts. A significant portion of the genome changes replication timing as a result of reprogramming, indicative of overall genome reorganization. We found that early and late replicating domains in iPSCs are differentially affected by copy number gains and losses, and that in particular CNV gains accumulate in regions of the genome that change to earlier replication during the reprogramming process. This differential relationship was present irrespective of reprogramming method. Overall, our findings reveal a functional association between reorganization of replication timing and the CNV landscape that emerges during reprogramming.

overall_design: 3 cell lines, all in duplicates

first: Junjie

last: Lu

first: Takayo

last: Sasaki


title: microRNA (miRNA) expression analysis of developmental retinoic acid exposure in zebrafish

status: Public on Feb 15 2014

city: Corvallis

first: Robert

middle: L

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

summary: Investigation of microRNA expression profile of 12, 24, 36 and 48 hours post-fertilization Danio rerio embryos developmentally exposed to retinoic acid.

overall_design: A twelve chip study using total RNA recovered from pools of 75 tropical 5D zebrafish embryos at 12, 24, 36, and 48 hours post fertilization (hpf). Embryos were exposed to control embryo medium or 5 nM retinoic acid from 6-24 hpf, with two biological replicates per condition. Control samples were pooled and hybridized to a single array. 12 miRZebrafish arrays (based on MirBase release 12.0) were used to measure the expression level of 218 mature miRNA from Danio rerio.

first: J

last: Franzosa

first: S

last: Bugel

first: T

last: Tal

middle: K

last: La Du

middle: C

last: Tilton

last: Waters


title: Meiotic recombination cold spots in chromosomal cohesion sites [ChIP-chip]

status: Public on Mar 31 2014

city: Suita

first: Masaru

last: Ito

state: Osaka

address: Yamadaoka 3-2

institute: Osaka University

summary: Meiotic chromosome architecture called “axis-loop structures” and histone modifications have been demonstrated to regulate the Spo11-dependent formation of DNA double-strand breaks (DSBs) that trigger meiotic recombination. Using genome-wide chromatin immunoprecipitation (ChIP) analyses followed by deep sequencing, we compared the genome-wide distribution of the axis protein Rec8 (the kleisin subunit of meiotic cohesin) with that of oligomeric DNA covalently bound to Spo11, indicative of DSB sites. The frequency of DSB sites is overall constant between Rec8 binding sites. However, DSB cold spots are observed in regions spanning ±0.8 kb around Rec8 binding sites. The axis-associated cold spots are not due to exclusion of Spo11 localization from the axis, since ChIP experiments revealed that substantial Spo11 persists at Rec8 binding sites during DSB formation. Spo11 fused with Gal4 DNA binding domain (Gal4BD-Spo11) tethered in close proximity (≤0.8 kb) to Rec8 binding sites hardly forms meiotic DSBs, in contrast with other regions. In addition, H3K4 tri-methylation (H3K4me3) remarkably decreases at Rec8 binding sites. These results suggest that reduced histone H3K4me3 in combination with inactivation of Spo11 activity on the axis discourages DSB hot spot formation.

overall_design: ChIP-chip analysis of Rec8 on fission yeast meiotic chromosomes

first: Kazuto

last: Kugou

first: Jeffrey

last: Fawcett

first: Sachiko

last: Mura

first: Sho

last: Ikeda

first: Hideki

last: Innan

first: Kunihiro

last: Ohta


title: Gene Expression of Kidney from FHH and Nr4a1 Deficient Rats

status: Public on Feb 06 2014

city: Jackson

first: Michael

last: Garrett

state: MS

address: 2500 North State Street

department: Pharmacology

institute: University of Mississippi Medical Center

summary: Nr4a1 deficient rats (Nr4a1-/-) were developed using the fawn hooded hypertensive rat (FHH), which provided a genetic background susceptible to kidney injury. Both groups of animals were evaluated for blood pressure, proteinuria, renal function, and whole transcriptome gene pathway changes. Gene expression profiling was performed at week 8, 16, and 24 using kidney from FHH and Nr4a1-/- rats. To identify differentially expressed gene between FHH and Nr4a1-/-  two statistical methods were utilized: (1) FWER (family-wise error rate) procedure, p<0.05 and fold-change ±1.2 or greater; and/or (2) Benjamani and Hochberg FDR (false discovery rate) using p<0.05, and fold-change ±1.2 or greater.  Two-way ANOVA using a p<0.01 or lower was performed to identify strain X time interaction effects between groups. Gene networks and functional analysis were evaluated through the use of Ingenuity Pathways Analysis .

overall_design: FHH and Nr4a1-/- rats were grown to 8, 16, and 24 weeks of age and kidney tissue was harvested for transcriptome analysis (n=3 replicates/ per group/ time)

first: Michae


title: Integrated analysis of microRNA and mRNA expression and association with HIF binding in MCF-7 cells under hypoxia [miRNA]

status: Public on Feb 13 2014

city: Oxford

first: Carme

last: Camps

address: Roosevelt Drive

country: United Kingdom

institute: Wellcome Trust Centre for Human Genetics/ U. of Oxford

summary:
Purpose: We aimed to investigate in depth the regulation of microRNA expression by hypoxia in the breast cancer cell line MCF-7, establish the relationship between microRNA expression and HIF binding sites, pri-miRNA transcription and microRNA processing gene expression.
Methods: microRNA sequencing data and gene expression microarray data were generated from MCF-7 cells submitted to an hypoxia timecourse (16h, 32h and 48h at 1% Oxygen). Data was integrated to 500 published high-stringency HIF binding sites identified in MCF-7 cells.
Results: We identified 41 microRNAs significantly up- and 28 down- regulated, of which 38 mature and 20 star forms are reported in conjunction with hypoxia for the first time. HIF-1α and HIF-2α binding sites within 50kb distance of microRNA loci were found by integration of HIF ChIP-seq data, showing overall association between binding sites and up-regulation. Gene expression profiling analysis showed no full coordination between pri-miRNA and microRNA expression, pointing towards additional levels of regulation. Several transcripts playing a role in microRNA processing were found regulated by hypoxia, of which two were HIF dependent.
Conclusions: The data support the hypothesis that microRNA expression under hypoxia is regulated at transcriptional and post-transcriptional level. HIF is involved at both levels, regulating the transcription of certain microRNAs and also the expression of key elements of the microRNA processing pathway.

overall_design: MicroRNA expression profiles of MCF-7 exposed to hypoxia (1% Oxygen) for 16h (2 replicates), 32h (3 replicates) and 48h (3 replicates) and to normoxia (3 replicates) were generated using Agilent miRNA microarrays. This data was used to validate the microRNA-seq data included in this study.

first: Jiannis

last: Ragoussis


title: Chemical allergen-induced perturbations of the mouse lymph node DNA methylome

status: Public on Feb 07 2014

city: Basel

first: Arne

last: Mueller

address: Klybeckstrasse 141

country: Switzerland

institute: Novartis Pharma

summary: Epigenetic regulation of gene expression plays a pivotal role in the orchestration of immune responses and may determine the vigor, quality, or longevity of such responses. Chemical allergens can be divided into two categories: skin sensitizing chemicals associated with allergic contact dermatitis, and chemicals that cause sensitization of the respiratory tract and occupational asthma. In mice these are characterized by different T helper (Th) cell responses. To explore the regulation and maintenance of these divergent responses, mice were exposed to 2,4-dinitrochlorobenzene (DNCB; a contact allergen) or trimellitic anhydride (TMA; a respiratory allergen). DNA from draining lymph nodes was processed for methylated DNA immunoprecipitation (MeDIP) followed by hybridization to a whole-genome DNA promoter array. 6319 differently methylated regions (DMR) were identified following DNCB treatment, while 2178 DMRs were measured following TMA treatment, with approximately half of the TMA DMR common to DNCB. When limited to promoter region-associated DMR, 637 genes were uniquely associated with DNCB induced DMR but only 164 genes were unique to TMA DMR. Promoter-associated DMR unique to either DNCB or TMA were generally hypomethylated whereas DMR common to both allergens tended to be hypermethylated. Pathway analyses highlighted a number of immune related pathways, including chemokine and cytokine signalling. These data demonstrate that chemical allergen exposure results in characteristic patterns of DNA methylation indicative of epigenetic regulation of the allergic response.

overall_design: Comparison of methylation profiles from allergens  2,4-dinitrochlorobenzene (DNCB; a contact allergen) and trimellitic anhydride (TMA; a respiratory allergen) or vehicle acetone:olive oil (AOO).

first: Victoria

last: Chapman

first: Tulipan

last: Zollinger

first: Rémi

last: Terranova

first: Jonathan

last: Moggs

first: Ian

last: Kimber

first: Rebecca

last: Dearman


title: Production of cytokines by CD4+CAR+ T-cells in spleens

city: Manchester

first: Dominic

middle: Graham

last: Rothwell

state: Manchester

address: Wilmslow Road

department: CEP

institute: University of Manchester

summary: The aim of the study was to compare and contrast cytokine production by CD4+ chimeric antigen receptor + T-cells and putative myeloid derived suppressor cell populations (CD11b+Gr-1 hi and lo) in the spleens of Balb/c mice which had received a transfer of CD19 specific second-generation CAR T-cells 56 days previously following cyclophosphamide pre-conditioning.

overall_design: Splenocytes from four individual mice were pooled, incubated with antibodies to CD4, CD34 (CAR), CD11b, Gr-1 and sorted using flow cytometric cell sorting for CD4+CD34+, Gr-1 and the negative cell fraction. Total RNA was isolated and samples loaded in duplicate in the array. Data was normalized to global expression levels.

middle: G

first: Eleanor

last: Cheadle


title: Stochastic genome-nuclear lamina interactions: Modulating roles of Lamin A and BAF

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

summary: The nuclear lamina (NL) is a filamentous layer lining the inner-nuclear-membrane (INM) that aids in the organization of the genome in large domains of low transcriptional activity. Recently, it was shown that the single-cell genome-NL interactions are much more dynamic than previously anticipated, which challenges the concept of the NL as a safe guard for transcriptional repressed genes. Here we discuss the role of the NL in light of these new findings and introduce Lamin A and BAF as potential modulators of LAD positioning

overall_design: BAF-chromatin and Lamin B2-chromatin interactions were assayed in human HT1080 by DamID on Nimblegen microarrays, with two biological replicates each, that were hybridized in a dye-swap design.

first: Jop

last: Kind


title: Profiling hepatic microRNAs in zebrafish: Fluoxetine exposure mimics a fasting response that targets AMP-activated protein kinase (AMPK)

city: Ottawa

first: Paul

last: Craig

state: Ontario

address: 30 Marie Curie

department: Biology

institute: University of Ottawa

summary: Recent evidence has suggested that fluoxetine, a serotonin-reuptake inhibitor and emerging environmental contaminant, can have non-targeted effects on metabolism in fish exposed to this waterborne pollutant. Using the highest, environmentally relevant, detectable level of fluoxetine (540 ng/L) we examined the impact of fluoxetine on the miRNA profile in the liver of zebrafish that were both fed and fasted for a period of 7 days. These results were further compared to the miRNA profile of zebrafish fasted and fed for 7 days, which were not exposed to fluoxetine. Results indicated that several miRNA that were involved with downregulating genes/pathways in response to fasting were also upregulated in fish exposed to fluoxetine, irrespective to fasting or feeding. These results suggest fluoxetine can have non-targeted effects on metabolic pathways mediated through miRNA expression. Furthermore, specific miRNA (dre-let-7d & dre-miR-140-5p) were found to target the catalytic subunit (AMPKa1 & AMPKa2, respectively) of AMP-Kinase, a master regulator of metabolism. Using predictive software and qPCR validation, combined with the expression profile of these two miRNA, we were able to establish a significant relationship between the expression of these specific miRNA to the downregulation of AMPKa subunit under the influence of 540 ng/L fluoxetine.

overall_design: Adult, female zebrafish were either fed or fasted for 7 days with and without the presense of 540 ng/L fluoxetine, and livers extracted and miRNA purified for miRNA microaary experiment.

first: Vance

last: Trudeau

first: Thomas

last: Moon


title: Corrinoid salvaging and remodeling by Dehalococcoides mccartyi strain 195 in a defined consortium containing a corrinoid-producer Pelosinus fermentans strain R7

status: Public on Feb 05 2014

city: Urbana

first: Yujie

last: Men

address: 205 N Mathews Ave

institute: University of Illinois at Urbana-Champaign

summary:
Differental gene expression of three consortia: Dhc195/DVH with exogenous cobalamin, Dhc195/DVH/PF with exogenous cobalamin, Dhc195/DVH/PF without exogenous cobalamin
Acronyms: Dhc195: Dehalococcoides mccartyi strain 195; DVH: Desulfovibrio vulgaris Hildenborough; PF: Pelosinus fermentans strain R7

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

platform_organism:
Dehalococcoides mccartyi BAV1
Dehalococcoides mccartyi 195
Dehalococcoides mccartyi CBDB1
Dehalococcoides mccartyi VS

overall_design: The total RNA of cells in the three consortia extracted at exponential growth phase of Dhc195 was dechlorinated to VC was applied on the microarray to query the transcript levels of Dhc195 genes

first: Erica

last: Seth

first: Shan

last: Yi

first: Robert

middle: H

last: Allen

first: Michiko

last: Taga

first: Lisa

last: Alvarez-Cohen


title: HuMiChip analysis of 86 samples from different body sites

status: Public on Feb 04 2014

city: Norman

first: Qichao

last: Tu

state: OK

address: 101 David L Boren Blvd

institute: University of Oklahoma

summary: HuMiChip was used to analyze human oral and gut microbiomes, showing significantly different functional gene profiles between oral and gut microbiome.

overall_design: The results were used to demonstarte the usefulness of applying HuMiChip to human microbiome studies.


title: Expression data measured by Nanostring of monocyte-derived dendritic cells from healthy individuals stimulated with LPS, influenza, or IFN-beta, or left unstimulated

city: Cambridge

first: Nir

last: Hacohen

state: MA

address: 7 Cambridge Center

institute: Broad Institute

summary: Variation in individuals' responses to environmental factors is believed to influence susceptibility to complex diseases in humans. The genetic basis of such variation is poorly understood. We measured gene expression from resting and stimulated dendritic cells (DCs) derived from the peripheral blood of healthy individuals. We stimulated the primary DCs with E. coli lipopolysaccharide (LPS), influenza virus or the cytokine IFNβ, and associated genetic variation between individuals with the observed variation in gene expression and gene induction.

overall_design: We collected peripheral blood from each human donor. We isolated peripheral blood mononuclear cells by Ficoll, and magnetically sorted them for CD14+CD16- monocytes. We then differentiated the monocytes into monocyte-derived dendritic cells (MoDCs) by culturing the cells for 7 days with GM-CSF and IL-4. We stimulated the cells with E. coli lipopolysaccharide (LPS) for 2.5 hr or 5 hr, influenza (PR8 dNS1) for 10 hr, or recombinant IFN-beta for 6.5 hr. Finally, we lysed the cells and ran Nanostring on the lysates.

first: Chun

last: Ye

first: Mark

middle: N

last: Lee

first: Aviv

last: Regev


title: Expression analysis of INA6 cells permanently cultured in presence of IL-6

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells have been permanently cultured in presence of IL-6. Transcriptome-wide expression data was assessed by using TileShuffle (Otto C, Reiche K, Hackermüller J. "Detection of differentially expressed segments in tiling array data". Bioinformatics. 2012 Jun 1;28(11):1471-9. Epub 2012 Apr 6.).

overall_design: We analyzed one Affymetrix Human Tiling 1.0R set

first: Jörg

last: Hackermüller

first: Christian

last: Otto

first: Nadine

last: Hösler

first: Katja

last: Brocke-Heidrich

first: Levin

last: Böhlig

first: Katharina

last: Kasack

first: Peter

last: Ahnert

first: Wolfgang

last: Krupp

first: Kurt

last: Engeland

last: Stalder

first: Friedemann

last: Horn


title: Expression analysis of INA6 cells after IL-6 restimulation

summary: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Transcriptome-wide expression data was assessed by using TileShuffle (Otto C, Reiche K, Hackermüller J. "Detection of differentially expressed segments in tiling array data". Bioinformatics. 2012 Jun 1;28(11):1471-9. Epub 2012 Apr 6.).


title: Differential expression analysis of HFF cells in G0 phase compared to cells in G2

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

overall_design: Refer to individual Series


title: Expression analysis of INA6 cells after IL-6 withdrawal

summary: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Transcriptome-wide expression data was assessed by using TileShuffle (Otto C, Reiche K, Hackermüller J. "Detection of differentially expressed segments in tiling array data". Bioinformatics. 2012 Jun 1;28(11):1471-9. Epub 2012 Apr 6.).


title: Expression analysis of HFF cells in S phase

summary: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide expression in S phase was assessed by using TileShuffle (Otto C, Reiche K, Hackermüller J. "Detection of differentially expressed segments in tiling array data". Bioinformatics. 2012 Jun 1;28(11):1471-9. Epub 2012 Apr 6.).


title: Expression analysis of HFF cells in G1 phase

summary: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide expression in G1 phase was assessed by using TileShuffle (Otto C, Reiche K, Hackermüller J. "Detection of differentially expressed segments in tiling array data". Bioinformatics. 2012 Jun 1;28(11):1471-9. Epub 2012 Apr 6.).


title: Expression analysis of HFF cells in G2 phase

summary: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide expression in G2 phase was assessed by using TileShuffle (Otto C, Reiche K, Hackermüller J. "Detection of differentially expressed segments in tiling array data". Bioinformatics. 2012 Jun 1;28(11):1471-9. Epub 2012 Apr 6.).


title: Expression analysis of HFF cells in G0 phase

summary: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide expression in G0 phase was assessed by using TileShuffle (Otto C, Reiche K, Hackermüller J. "Detection of differentially expressed segments in tiling array data". Bioinformatics. 2012 Jun 1;28(11):1471-9. Epub 2012 Apr 6.).


summary: Expression and differential expression analysis of astrocytoma patient samples (WHO grades I and III) and primary glioblastoma (WHO grade IV). Expression and differential expression was assessed by using an Agilent custom microarray (244K). The custom array contains probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway by employing TAS (Kampa et al. "Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22". Genome Research, 14:331-42, 2004).  In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe set 014850.

overall_design: We analyzed four arrays each for astrocytoma patient samples of grade I, grade III and grade IV.


title: Expression and differential expression analysis in INA6 cells

summary: Expression and differential expression analysis of custom probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway.  In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe sets 014850. INA6 cells restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours.

overall_design: We analyzed three arrays each for INA6 cells after 13 hours of IL-6 withdrawal and cells restimulated with IL-6 for 1 hour


title: Differential expression analysis of HFF cells in G0 phase compared to cells in G1


title: Differential expression analysis of INA6 cells


title: MicroRNA microarray analysis in nasal NK/T-cell lymphoma cell lines

status: Public on Feb 01 2014

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Gene expression profiling of 1,211 microRNAs in nasal NK/T-cell lymphoma cell lines

overall_design: Gene expression profiling of 1,211 microRNAs in three nasal NK/T-cell lymphoma cell lines, EBV-negative NK-cell line and normal NK cells

first: Yuki

last: Komabayashi

first: Kan

last: Kishibe


title: Differential expression analysis of HFF cells in S phase compared to cells in G2


title: Differential expression analysis of HFF cells in G1 phase compared to cells in S


title: Expression analysis of colorectal carcinoma cells with defunct P53 (D53wt cells)

summary: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct P53 on Affymetrix Human Tiling 1.0 array set. Transcriptome-wide expression data was assessed by using TileShuffle (Otto C, Reiche K, Hackermüller J. "Detection of differentially expressed segments in tiling array data". Bioinformatics. 2012 Jun 1;28(11):1471-9. Epub 2012 Apr 6.).


title: Constitutively active STAT5 recruits p53 to alternative transcriptional targets in myeloid cancers

city: Montpellier

first: Michael

last: Girardot

state: France

address: 1919 route de Mende

institute: IGMM CNRS UMR5535

summary:
In several cancer types, STAT (Signal transducer and activator of transcription) transcription factors are constitutively activated. We previously identified a target gene, LPP/miR-28 (LIM domain containing preferred translocation partner in lipoma), induced by constitutive activation of STAT5, but not by transient cytokine-activated STAT5. Here, we demonstrate in transformed hematopoietic cells that binding of both STAT5B and p53 to chromatin is required for transcriptional activity of an alternative LPP/miR-28 promoter.

Using a genome-wide approach, we identified 463 genomic positions at promoter regions where STAT5B and p53 are co-localized on the chromatin. At these positions, p53 chromatin binding is dependent on persistent STAT5B activation. The transcriptional activity of selected promoters bound by STAT5B and p53 was significantly changed upon STAT5 or p53 inhibition, and the transcription of these target genes is frequently altered in platelets of myeloproliferative neoplasm patients harboring mutations constitutively activating STAT5. These data suggest that the constitutive STAT5 activation recruits p53 in cancer cells and thereby activates oncogenic transcriptional programs.

overall_design: STAT5B and p53 ChIP-chip with or without JAK2 inhibition (ruxolitinib) to inhibit STAT5 phosphorylation and DNA binding.


title: Differential expression analysis of colorectal carcinoma cells (D53wt)


title: MicroRNAs in bovine adipose tissue: genomic context, expression and function

city: Edmonton

first: Josue

middle: Moura

last: Romao

state: Alberta

address: 116 St. and 85 Ave.

department: AFNS

institute: University of Alberta

summary: MicroRNAs (miRNAs) are small non-coding RNAs found to regulate several biological processes including adipogenesis. Understanding adipose tissue regulation is critical for beef cattle as fat is an important determinant of beef quality and nutrient value . This study analyzed the association between genomic context characteristics of miRNAs with their expression and function in bovine adipose tissue. Twenty-four subcutaneous adipose tissue biopsies were obtained from eight British-continental crossbred steers  at 3 different time points . Total RNA was extracted and miRNAs were profiled using a miRNA microarray with expression further validated by qRT-PCR. A total of 224 miRNAs were detected of which 155 were expressed in all steers (n=8), and defined as the core miRNAs of bovine subcutaneous adipose tissue. Core adipose miRNAs varied in terms of genomic location (59.5% intergenic, 38.7% intronic, 1.2% exonic, and 0.6% mirtron), organization (55.5% non-clustered and 44.5% clustered), and conservation (49% highly conserved, 14% conserved and 37% poorly conserved). Clustered miRNAs and highly conserved miRNAs were more highly expressed (p<0.05) and had more predicted targets than non-clustered or less conserved miRNAs (p<0.001). A total of 34 miRNAs were coordinately expressed, being part of six identified relevant networks. Two intronic miRNAs (miR-33a and miR-1281) were shown to have coordinated expression with their host genes which are involved in lipid metabolism, suggesting these miRNAs may also play a role in regulation of lipid metabolism/adipogenesis of bovine adipose tissue. Furthermore, a total of 17 bovine specific miRNAs were predicted to be involved in the regulation of energy balance in adipose tissue. These findings improve our understanding on the behavior of miRNAs in the regulation of bovine adipogenesis and fat metabolism as it reveals that miRNA expression patterns and functions are associated with miRNA genomic organization and conservation in bovine adipose tissue.

overall_design: In this study, a total of 24 subcutaneous adipose tissue samples were analyzed by microRNA microarrays. The samples were derived from eight steers at three different ages (12, 13.5 and 15 months).

first: Weiwu

last: Jin

first: Maolong

last: He

first: Tim

last: McAllister

first: Le-Luo

last: Guan


title: RNAi mediates post-transcriptional repression of gene expression in fission yeast Schizosaccharomyces pombe [Affymetrix]

status: Public on Jan 23 2014

city: Huddinge

first: Agata

last: Smialowska

address: Halsovagen 7

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

summary: RNA interference (RNAi) is a gene silencing mechanism conserved from fungi to mammals. Small interfering RNAs are products and mediators of the RNAi pathway and act as specificity factors in recruiting effector complexes. The Schizosaccharomyces pombe genome encodes one of each of the core RNAi proteins, Dicer, Argonaute and RNA-dependent RNA polymerase (dcr1, ago1, rdp1). Even though the function of RNAi in heterochromatin assembly in S. pombe is established, its role in controlling gene expression is elusive. Here, we report the identification of small RNAs mapped anti-sense to protein coding genes in fission yeast. We demonstrate that these genes are up-regulated at the protein level in RNAi mutants, while their mRNA levels are not significantly changed. We show that the repression by RNAi is not a result of heterochromatin formation. Thus, we conclude that RNAi is involved in post-transcriptional gene silencing in S. pombe.

overall_design: Total RNA from wild type, dcr1Δ and rpd1Δ cells; 3 biological replicates for each strain.

first: Ingela

last: Djupedal

first: Jingwen

last: Wang

first: Per

last: Kylsten

last: Swoboda

first: Karl

last: Ekwall


title: Mesenchymal Stem Cells (MSCs): Control vs. PTH-stimulated

summary: Transcriptional profiling of human MSCs comparing control MSCs with parathyroid hormone (PTH)-stimulated MSCs. PTH-stimulated MSCs were treated with 0.1 nM recombinant human PTH (N-terminal fragment, amino acids 1-34) for 48 hours. Human MSCs were isolated from a bone marrow sample obtained from a healthy adult volunteer.

overall_design: Two-condition experiment: control MSCs vs. PTH-stimulated MSCs. 1 control MSCs and 1 PTH-stimulated MSCs.

first: Hisayuki

last: Yao

first: Yasuo

last: Miura

first: Taira

last: Maekawa


title: Expression profiling in Human Umbilical Vein Endothelial Cells (HUVEC)

status: Public on Jan 07 2014

first: Tobias

last: Heckel

address: Grenzacherstr. 124

department: pRED

institute: Roche

summary:
Whole transcriptome gene expression profiling of Normal -(HUVEC) Human Umbilical Vein Endothelial Cells
The HUVEC gene expression results analyzed in this study are further described in Kustermann S. et al. (2014) A real-time impedance based screening assay for drug induced vascular leakage.

overall_design: A NimbleGen Homo sapiens Expression Array [100718_HG18_opt_expr] study using total RNA recovered from HUVECs grown until 80% confluency. Each microarray measures the expression level of 23,611 genes using 45,033 probe sets with three 60-mer probes (PM) per probe set. Each probe set is represented once on the array.


title: miRNA-mediated post-transcriptional regulation of gene expression in ABR17 transgenic Arabidopsis thaliana under salt stress

status: Public on Jan 31 2014

city: Cleveland

first: Sanjay

last: Gupta

state: Ohio

address: 10900 Euclid Avenue

department: Department of Urology

institute: Case Western Reserve University

summary: Micro RNAs (miRNAs) are a class of small endogenous RNAs conserved in eukaryotic organisms including plants. They suppress gene expression post-transcriptionally in many different biological processes. Previously, we reported salinity-induced changes in gene expression in transgenic Arabidopsis thaliana plants that constitutively expressed a pea abscisic acid-responsive (ABR17) gene. In the current study, we used a microarray to investigate the role of miRNA-mediated post-transcriptional gene regulation in these same transgenic plants in the presence and absence of salinity stress. We identified nine miRNAs that were significantly modulated due to ABR17 gene expression, and seven miRNAs that were modulated in response to salt stress. The target genes regulated by these miRNAs were identified using starBase (sRNA target Base) Degradome analysis and through 5' RNA Ligase Mediated-Rapid Amplification of cDNA Ends (RLM-RACE). Our findings revealed miRNA:mRNA interactions comprising regulatory networks of Auxin Response Factor (ARF), ARGONAUTE 1, (AGO1), Dicer-like proteins 1 (DCL1), Squamosa Promoter Binding (SPB), NAC, APETALA 2 (AP2), Nuclear Factor-Y (NFY), RNA binding proteins, Arabidopsis thaliana vacuolar phyrophosphate 1 (AVP1) and Pentatricopetide repeat (PPR) in ABR17 transgenic A. thaliana, which control physiological, biochemical and stress signalling cascades due to the imposition of salt stress. Our results are discussed within the context of the effect of the transgene, ABR17, and the roles miRNA expression may play in mediating plant responses to salinity.

overall_design: In this miRNA-microarray experiment, a total of 4 samples were analyzed with their 3 biological replicates. Two samples, WT and ABR17 control (without salt treatment), were used as reference controls.

first: Shiv

middle: S

last: Verma

first: Nat

last: Kav


title: microRNA expression profiling of human colorectal cancer cell lines: HRT-18 vs. Caco-2

status: Public on Jan 13 2014

city: Vienna

first: Michael

last: Karbiener

address: Benatzkygasse 2-6 / G

department: Global Pathogen Safety

country: Austria

institute: Takeda

summary: MicroRNAs regulate the biological aggressiveness of colorectal cancer (CRC) cells and might serve as potential prognostic factors and therapeutic targets. In this study, we therefore globally profiled microRNAs associated with aggressive growth in CRC cells, in an attempt to identify novel prognostic biomarkers in CRC patients. In detail, two different CRC cell lines (Caco-2 and HRT-18) with completely different growth rates and different E-cadherin expression were profiled for differences in more than 1000 human microRNAs by using microarray technology.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Two-condition experiment, HRT-18 vs. Caco-2. Biological replicates: 3, independently grown and harvested. On each array, one BR of HRT-18 cells was directly compared to one BR of Caco-2 cells (serving as reference sample). All hybridizations were repeated with reversed dye assignment (dye-swap) as technical replicates.

first: Marcel

last: Scheideler


title: Regulation of exon definition and apoptosis by the Ewing's Sarcoma Protein

status: Public on Jan 01 2014

city: Rome

first: Maria Paola

last: Paronetto

address: Piazza Lauro de Bosis, 6

department: Department of Health Sciences

institute: University of Rome "Foro Italico"

summary:
The Ewing's Sarcoma Protein EWS belongs to the TET family (FUS/TLS, EWS, TAF15) of RNA and DNA binding proteins, implicated in DNA transcription, pre-mRNA splicing and maintenance of genome integrity. To identify in vivo RNA targets of EWS we performed a combinatorial approach of CLIP-Seq
In this dataset, we include the expression data obtained from three biological replicates of HeLa cells transfected with either scrambled or siEWS oligonucleotides. These data allowed us to identify 805 genes affected at the expression level by EWS knockdown, of which 395 upregulated and 410 downregulated. Moreover, HJAY identified 206 differentially regulated alternative splicing events in 114 genes.

overall_design: Three biological replicates were labeled and hybridized onto Affymetrix HJAY

first: M

first: J

last: Valcarcel


title: Expression data from primary mouse hepatocytes treated with Diclofenac

status: Public on Jan 22 2014

city: Leiden

first: Steven

last: Wink

state: Zuid Holland

address: Einsteinweg 55

department: Division of Toxicology

institute: LACDR

summary: Drug-induced liver injury (DILI) is an important clinical problem. Here we used a genomics approach to establish the critical drug-induced toxicity pathways that act in synergy with the pro-inflammatory cytokine tumor necrosis factor  (TNF) to cause cell death of liver HepG2 cells. Transcriptomics of the cell injury stress response pathways initiated by two hepatoxicants, diclofenac and carbamazepine, revealed the endoplasmic reticulum (ER) stress/translational initiation signaling and Nrf2 antioxidant signaling as two major affected pathways, which was similar to that observed for the majority of ~80 DILI compounds in primary human hepatocytes. The ER stress was primarily related to PERK and ATF4 activation and subsequent expression of CHOP, which was all independent of TNFα signaling. Identical ATF4 dependent transcriptional programs were observed in primary human hepatocytes as well as primary precision cut human liver slices. Targeted RNA interference studies revealed that while ER stress signaling through IRE1α and ATF6 acted cytoprotective, activation of the ER stress protein kinase PERK and subsequent expression of CHOP was pivotal for the onset of drug/TNF-induced apoptosis. While inhibition of the Nrf2-dependent adaptive oxidative stress response enhanced the drug/TNF cytotoxicity, Nrf2 signaling did not affect CHOP expression. Both hepatotoxic drugs enhanced expression of the translational initiation factor EIF4A1, which was essential for CHOP expression and drug/TNF-mediated cell killing. Our data support a model in which enhanced drug-induced translation initiates PERK-mediated CHOP signaling in an EIF4A1 dependent manner, thereby sensitizing towards caspase-8-dependent TNF induced apoptosis.

overall_design: 4 biological  replicates of Diclofenac and 6 biological replicates of vehicle.  46 hours after isolation, cells were exposed to either 300 µM DCF or the solvent DMSO for 24 hours.

first: Lisa

last: Fredriksson

first: Bram

last: Herpers

first: Giulia

last: Benedetti

first: Mackenzie

last: Hadi

first: Hans

last: de Bont

first: Geny

last: Groothuis

first: Mirjam

last: Luijten

first: Erik

last: Danen

first: Marjo

last: de Graauw

first: John

last: Meerman

first: Bob

last: van de Water


title: Expression analysis of colorectal carcinoma cells (D53wt) stably transfected with tetracycline responsive wild type P53

first: Kristin

last: Reiche

summary: Whole transcriptome expression analysis of colorectal carcinoma cells stably transfected with tetracycline responsive wild type P53 on Affymetrix Human Tiling 1.0 array set. Transcriptome-wide expression data was assessed by using TileShuffle (Otto C, Reiche K, Hackermüller J. "Detection of differentially expressed segments in tiling array data". Bioinformatics. 2012 Jun 1;28(11):1471-9. Epub 2012 Apr 6.).

first: Jörg

last: Hackermüller

first: Christian

last: Otto

first: Nadine

last: Hösler

first: Katja

last: Brocke-Heidrich

first: Levin

last: Böhlig

first: Katharina

last: Kasack

first: Peter

last: Ahnert

first: Wolfgang

last: Krupp

first: Kurt

last: Engeland

last: Stalder

first: Friedemann

last: Horn


title: EDCs gene expression profile in MCF7 cells

status: Public on Dec 31 2013

city: Houston

first: Anne

middle: Chinenye

last: Katchy

state: Texas

address: 3605 Cullen Blvd, Room 3021

department: CNRCS, Biology and Biochemistry

institute: University of Houston

summary: Endocrine disrupting chemicals (EDCs) are compounds that disrupt normal hormonal signaling. Examples are Xenoestrogens (e.g BPA) and Phytoestrogens (e.g isoflavones).

overall_design: Comparison of EDC treated versus vehicle treated MCF7 parental cells. Each comparison in technical and biological duplicate.

first: Caroline

last: Pinto

first: Philip

last: Jonsson

first: Trang

last: Vu

first: Marchela

last: Pandelowa

first: Jan-Åke

last: Gustafsson

first: Maria

last: Bondesson

first: Cecilia

last: Williams


title: Centromeric H2B monoubiquitination promotes noncoding transcription and chromatin integrity

status: Public on Jan 29 2014

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

institute: Karolinska Inst

summary: Functional centromeres are essential for proper cell division. Centromeres are established largely by epigenetic processes resulting in incorporation of the histone H3 variant CENP-A. Here, we demonstrate the direct involvement of H2B monoubiquitination, mediated by RNF20 in humans or Brl1 in Schizosaccharomyces pombe, in centromeric chromatin maintenance. Monoubiquinated H2B (H2Bub1) is needed for this maintenance, promoting noncoding transcription, centromere integrity and accurate chromosomal segregation. A transient pulse of centromeric H2Bub1 leads to RNA polymerase II–mediated transcription of the centromere’s central domain, coupled to decreased H3 stability. H2Bub1-deficient cells have centromere cores that, despite their intact centromeric heterochromatin barriers, exhibit characteristics of heterochromatin, such as silencing histone modifications, reduced nucleosome turnover and reduced levels of transcription. In the H2Bub1-deficient cells, centromere functionality is hampered, thus resulting in unequal chromosome segregation. Therefore, centromeric H2Bub1 is essential for maintaining active centromeric chromatin.

overall_design:
ChIP: In total 17 samples; 15 ChIP DNA files (7 different conditions) 2 Input files. Cnp1_WT_input.bar (antibody against Cnp1 in strains Hu303, Hu29 (WT) (Cnp1_Hu303.CEL, AS_10.CEL) vs input (JW_1.CEL, JW_2_2.CEL)); Cnp1_Hu2640_WT.bar (antibody against Cnp1 in strain Hu2640 (htb1K119R) (Cnp1_Hu2640_A.CEL, Cnp1_Hu2640_B.CEL) vs strains Hu303, Hu29 (WT) (Cnp1_Hu303.CEL, AS_10.CEL)); Cnp1_Hu2640_input.bar (antibody against Cnp1 in strain Hu2640 (htb1K119R) (Cnp1_Hu2640_A.CEL, Cnp1_Hu2640_B.CEL)  vs input (JW_1.CEL, JW_2_2.CEL)); H2Bub1_Hu303_input.bar (antibody against H2Bub1 in strain Hu303 (WT) (H2Bub1_Hu303_A.CEL, H2Bub1_Hu303_B.CEL) vs input (JW_1.CEL, JW_2_2.CEL)); H3_WT_input.bar (antibody against H3 in strains Hu303, Hu29 (WT) (H3_Hu303.CEL, As_12.CEL) vs input (JW_1.CEL, JW_2_2.CEL); H3_Hu2640_WT.bar (antibody against H3 in strain Hu2640 (htb1K119R) (H3_Hu2640_A.CEL, H3_Hu2640_B.CEL, H3_Hu2640_C.CEL) vs strains Hu303, Hu29 (WT) (H3_Hu303.CEL, AS_12.CEL)); H3_Hu2640_input.bar (antibody against H3 in strain Hu2640 (htb1K119R) (H3_Hu2640_A.CEL, H3_Hu2640_B.CEL, H3_Hu2640_C.CEL) vs input (JW_1.CEL, JW_2_2.CEL)); H3K9me2_Hu303_input.bar (antibody against H3K9me2 in strains Hu303, Hu29 (WT) (H3K9me2_Hu303.CEL, AS_6.CEL) vs input (JW_1.CEL, JW_2_2.CEL)); H3k9me2_Hu2640_Hu303.bar (antibody against H3K9me2 in strain Hu2640 (htb1K119R) (H3K9me2_Hu2640_A.CEL, H3K9me2_Hu2640_B.CEL) vs strain Hu303, Hu29 (WT) (H3K9me2_Hu303.CEL, AS_6.CEL)); H3K9me2_Hu2640_input.bar (antibody against H3K9me2 in strain Hu2640 (htb1K119R) (H3K9me2_Hu2640_A.CEL, H3K9me2_Hu2640_B.CEL)  vs input (JW_1.CEL, JW_2_2.CEL)).

RNA: 4 RNA samples: 2 replicates of WT RNA (RNA_Hu303_A.CEL, RNA_Hu303_B.CEL) and 2 replicates of htb1-K119R RNA (RNA_Hu2640_A.CEL, RNA_Hu2640_B.CEL).

first: Laia

last: Sadeghi

first: Lee

last: Siggens

first: J

middle: P

last: Svensson


title: Gene-expression profiles of archived section of formalin-fixed paraffin-embedded (AS-FFPE) liver and tumor tissues from hepatocellular carcinoma patients

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary:
Background and Aims
Formalin-fixed, paraffin-embedded (FFPE) tissue is the most commonly available form of archived clinical specimens, which are often stored as thin sections on glass slides. RNA isolated from such archived section (AS) of FFPE tissue is more degraded compared to freshly cut (FC) FFPE section because of prolonged air exposure. In this study, we evaluated performance of transcriptome profiling-based disease classification in AS-FFPE tissue.
Methods
Genome-wide gene-expression profiles of AS-FFPE tissues of 83 hepatocellular carcinoma (HCC) and 47 liver cirrhosis samples were generated by using whole-genome DASL assay (Illumina), and compared with the profiles previously produced by using FC tissue sections from the same FFPE blocks. Quality of the profiles and performance of gene signature-based class prediction were systematically evaluated.
Results
RNA quality and assay reproducibility of AS-FFPE RNA were comparable to intermediate ~ poor quality FC-FFPE samples (R2 as high as 0.93). Gene-expression signal was detected in lower number of probes in AS FFPE samples compared to FC-FFPE samples (proportion of probes with present signal (%P-call): 10%~60% and 70%~90% in AS- and FC-FFPE profiles, respectively). Based on %P-call quality threshold of 20%, 64/88 (77%) HCC and 37/48 (77%) liver profiles were judged as having relatively good quality data with comparable inter-sample correlation. Inter-sample correlation coefficient, as a measure to detect outlier profiles due to poor RNA quality, was also lower in AS-FFPE (0.4~0.9) compared to FC-FFPE (0.6~1.0).  In the genome-wide profiling analysis, previously identified molecular subclasses of HCC tumors were reproduced in 67/83 (81%) samples, which was improved to 43/48 (90%) samples when we focused on statistically confident predictions (p<0.05). A 186-gene prognostic signature in liver cirrhosis was reproduced in 32/47 (68%) samples, which was slightly improved to 11/16 (69%) when focused on statistically significant predictions.
Conclusions
We observed decay of genome-wide transcriptional profiles in AS-FFPE tissues in quantitative manner. However, disease classification was still possible, which suggests potential of AS-FFPE material for clinical diagnosis and prognosis.

overall_design:
FFPE tissue sections (10 micron-thick) sliced from 5~16-year-old FFPE blocks and archived for 6~7 years on glass slide
Gene-expression profiles of archived section of formalin-fixed paraffin-embedded (AS-FFPE) liver tissues from HCC patients: 47 samples
Gene-expression profiles of archived section of formalin-fixed paraffin-embedded (AS-FFPE) tumor tissues from HCC patients: 83 samples

first: Xintong

last: Chen


title: Comparison between GT and rre37 overexpressed strains of cyanobacteria

status: Public on Nov 30 2013

city: Kawasaki

first: Takashi

last: Osanai

address: 1-1-1, Higashimita, Tamaku

department: School of Agriculture

institute: Meiji University

summary: Rre37 activates sugar catabolism in a unicelluar cyanobacterium Synechocystis sp. PCC6803. We constructed rre37-overexpressing strain, named ROX370, by introducing the rre37 genes fusing psbAII promoter by homologous recombination. The transcript profiles of parental wild-type strain GT and ROX370 were compared by microarray CyanoChip (Takrara bio.). Experiments were performed by three times with biologically independent RNA. The results showed that genes for the oxidaditive pentose phosphate pathway and glycogen catabolism were induced by rre37 overexpression.

overall_design: Total RNAs from three independent wild-type (GT) and three independent rre37-overexpression strains were differently labeled by Cy3 or Cy5, followed by hybridyzation on CyanoChip.


title: Characterization and in vivo functional analysis of the Schizosaccharomyces pombe ICln gene

status: Public on Dec 05 2013

first: johann

last: Soret

address: 1919, route de Mende

department: Institut de Genetique Moleculaire

institute: CNRS

summary: During the early steps of snRNP biogenesis, the Survival of Motor Neuron (SMN) complex acts together with the methylosome, an entity formed by the pICln protein, WD45 and the PRMT5 methyltransferase. To expand our understanding of pICln and SMN functional relationships in vivo, we performed a genetic analysis of an uncharacterized S. pombe pICLn homologue. Although not essential, the S. pombe ICln protein is important for optimal yeast cell growth. The human pICln gene complements the icln∆ slow growth phenotype demonstrating that the identified SpICln sequence represents the bona fide human homolog. Consistent with the role inferred for human pICln using in vitro experiments, we found that the SpICln protein is required for optimal production of the spliceosomal snRNPs and for efficient splicing in vivo. Genetic interaction approaches demonstrate furthermore that modulation of ICln activity is unable to compensate for defects induced by SMN mutations, and reciprocally. Using a genome-wide approach and RT-PCR validation tests, we show also that splicing is altered differentially in icln∆ cells. Our data are consistent with the emerging view that splice site selection and spliceosome kinetics is highly dependent on the concentration of core spliceosomal components.

overall_design: RNA from ΔIcln mutant (2 replicates) vs RNA from wild type cells (2 replicates)

first: Adrien

last: Barbarossa

first: Etienne

last: Antoine

first: Henry

last: Neel

first: Thierry

last: Gostan

first: Johann

first: Rémy

last: Bordonné


title: Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe [Affymetrix]

status: Public on Nov 25 2013

city: Salamanca

first: Luis

last: Quintales

address: Calle Zacarías González, 2

department: Universidad de Salamanca / CSIC

country: Spain

institute: Instituto de Biología Funcional y Genómica (IBFG)

summary: Mononucleosomal DNA analysis of atf1D and pcr1D mutants of Schizosaccharomyces pombe and transcription analysis of exponential wild type 972 h-, atf1D, pcr1D and mitotic diploid pat1.114, and synchronous diploid pat1.114 at 0h, 3h and 5h into meiosis

overall_design: Mononucleosomal DNA vs. genomic input DNA in wildtype 972 h-, atf1D and pcr1D mutants of S. pombe was hybridized to Affymetrix GeneChip 1.0FR tiling microarrays (GPL7715). Total RNA for genome-wide transcription analysis from exponential wild type 972 h-, atf1D, pcr1D and mitotic diploid pat1.114 cells, and from synchronous diploid pat1.114 at 0h, 3h and 5h into meiosis was hybridized to the same microarrays.

first: Ignacio

last: Soriano

first: Francisco

last: Antequera


title: Transcriptional response of Schizosaccharomyces pombe to 5-Fluorouracil (5FU)

status: Public on Nov 14 2013

summary: We use high-density tiling DNA microarray technology to obtain the specific transcriptome-wide response induced by 5-Fluorouracil (5FU) in the eukaryotic model Schizosaccharomyces pombe.

overall_design: Schizosaccharomyces pombe cultures with 5FU added to a final concentration of 500 μM. Incubation was allowed to proceed for 0, 15, 60 and 240 minutes.Two biological replicates each.

first: Laura

last: Mojardín

first: Javier

last: Botet

first: Sergio

last: Moreno

first: Margarita

last: Salas


title: Expression data from rhesus macaque colon, jejunum, and lung

status: Public on Nov 01 2013

city: Davis

first: Michael

last: George

state: CA

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

summary:
The mucosa that lines the respiratory and gastrointestinal (GI) tracts is an important portal of entry for pathogens and provides the frontline of immune defense against HIV infection. Using the simian immunodeficiency virus (SIV) rhesus macaque model, we have performed a comparative analysis of host gene expression in the lung and GI mucosa in response to SIV infection and antiretroviral therapy.
Microarrays were used to characterize changes in gene expression in the colonic, jejunal, and pulmonary (lung) mucosa that occur during chronic SIV infection in the presence or absence of antiretroviral therapy.

overall_design: Colon, jejunum, and lung tissues from healthy uninfected macaques and macaques with chronic stage SIV infection (+/- therapy) were used for RNA extraction and hybridization on Affymetrix microarrays.

middle: D


title: Phosphate starvation/sufficient treatment of rice seedling

status: Public on Nov 23 2013

city: Tsukuba

first: Youko

last: Oono

state: Ibaraki

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

summary: We compared our mRNA-seq expression data with that from Rice 44K oligomicroarray, and about 95.5% (root) and 95.4% (shoot) transcripts supported by the array were confirmed expression both by the array and by mRNA-seq.

overall_design:
Three-condition experiment, non-treatment vs. phosphate starvation/sufficient treatment of rice seedling. Biological replicates: 3 non-treatment replicates, 3  phosphate starvation/sufficient treatment replicates.
*** This submission represents the microarray component of the study

last: Matsumoto


title: Direct Conversion of Human Fibroblasts into Neuronal Restricted Progenitors

status: Public on Oct 24 2013

city: Guangzhou

first: Qingjian

last: Zou

state: Guangdong

address: 190 Kaiyuan Street, Guangzhou Science district

institute: Guangzhou Institutes of Biomedicine and Health, CAS

summary: Neuronal restricted progenitors (NRPs) represent a type of transitional intermediate cells that lie between multipotent neural progenitors (NPs) and terminal differentiated neurons during neurogenesis. These NRPs have the ability to self-renew and differentiate into neurons, but not into glial cells, which is considered as an advantage for cellular therapy of human neurodegenerative diseases. However, difficulty in the extraction of highly purified NPRs from normal nervous tissue prevents further studies and applications. In this study, we reported conversion of human fetal dermal fibroblasts into human induced neuronal restricted progenitors (hiNRPs) in seven days by using just three defined factors: Sox2, c-Myc, and either Brn2 or Brn4. The hiNRPs exhibited distinct neuronal characteristics, including cell morphology, multiple neuronal markers expression, self-renewal capacity, and genome-wide transcriptional profile. Moreover, hiNRPs were able to differentiate into various terminal neurons with functional membrane properties, but not glial cells. Direct generation of hiNRPs from somatic cells will provide a new source of cells for cellular replacement therapy of human neurodegenerative diseases.

overall_design: This is a general expression microarray design (NimbleGen platform). It includes 5 samples.

first: Quanmei

last: Yan

first: Liangxue

last: Lai


title: Development of micoRNA expression signatures for invasive ductal breast carcinoma

status: Public on Sep 28 2013

city: Padappai

first: Parvathi

last: MVS

address: near BDO office

department: Genetic toxicology

institute: International institute of biotechnology and toxicology

summary: To further develop gene expression approach to miRNA biomarker discovery, we have employed miRNA microarray expression profiling as a discovery platform to identify miRNA with the potential to regulated the gene expression signatures in the process of tumor development. Human FFPE tissues from grade 1, 2 and 3 were used to profile miRNA.  The miRNA targeted  genes were also studied for expression along with the selected miRNA, from this signature  in the same RNA samples by real-time PCR, confirming the selected miRNA has regulatory action on the target gene expression.

overall_design: miRNA were profiled with less number of samples from each grade using miRNa microarray hybridization. Confirmation of the expression was carried out with more (20 from each grade)number of samples and targetted gene expression regulation was confirmed using RT PCR.

first: Balakrishna

last: Murthy


title: Expression analysis of Chlamydomonas reinhardtii exposed to silver

status: Public on Oct 01 2013

city: Duebendorf

first: Smitha

last: Pillai

address: Ueberlandstrasse 133

institute: Eawag

summary: Chlamydomonas reinhardtii exposed to various concentrations of silver

overall_design: For this experiment,C. reinhardtii were exposed to (4) different concentrations of silver, as biological triplicates


title: Gene expression of soybean roots inoculated with wild-type and type III secretion mutant strains of Bradyrhizobium elkanii

status: Public on Sep 17 2013

city: Fuchu

first: Shin

last: OKAZAKI

state: Tokyo

address: 3-5-8 Saiwaicho

institute: Tokyo University of Agriculture and Technology

summary: To dissect differences in gene expression profile of soybean roots inoculated with wild-type and type III secretion mutant rhizobia, we have employed microarray analysis. Seeds of soybeans (Glycine max L. cv. Enrei and its non-nodulating line En1282) were surface-sterilized and germinated at 25 °C for 2 days and were transferred to a plant box (CUL-JAR300; Iwaki, Tokyo, Japan) containing sterile vermiculite watered with B&D nitrogen-free medium (Broughton and Dilworth 1971). One day after transplant, each seedling was inoculated with Bradyrhizobium elkanii USDA61, its type III secretion mutant BerhcJ or sterilized water (mock treatment). Plants were cultivated in a growth chamber at 25°C and 70% humidity with a daytime of 16 h followed by a nighttime of 8 h. To determine the gene expression, RNA was extracted from the roots 8 days after inoculation.

overall_design: Gene expression in soybean roots inoculated with Bradyrhizobium elkanii USDA61, its type III secretion mutant BerhcJ or sterilized water (mock treatment) was measured 8 days after inoculation. Three independent experiments were performed at each inoculation.

last: Okazaki


title: Adipose subtype-selective recruitment of TLE3 in thermogenic gene programs

status: Public on Sep 27 2013

city: Los Angeles

first: Claudio

last: Villanueva

address: 610 Charles E. Young Drive East Box 957239

department: Integrative Biology and Physiology

institute: UCLA

summary:
Transcriptional effectors of white adipocyte-selective gene expression have not been described. TLE3 is a white-selective cofactor that acts reciprocally with the brown-selective cofactor Prdm16 to specify lipid storage and thermogenic gene programs.
When expressed at elevated levels in brown fat, TLE3 counters Prdm16, suppressing brown-selective genes and inducing white-selective genes, resulting in impaired fatty acid oxidation and thermogenesis. To further test the functional consequences of the changes in BAT phenotype in aP2-TLE3 Tg mice, we challenged them with cold exposure at 4C. aP2-TLE3 Tg mice had an impaired ability to respond to cold exposure compared to littermate control mice, as evidenced by a marked drop in core body temperature.

overall_design: Transgenic mice expressing TLE3 from the aP2 enhancer and wild type mice were housed individually without food and bedding immediately before the start of experiments. Mice were allowed free access to water and placed at 4C for 5 hours while core body temperature was monitored every hour using a rectal probe. For microarray experiments of BAT, RNA was extracted and pooled from 4 mice in each group.

first: Peter

last: Tontonoz


title: Gene expression profiling of five diffuse large B-cell lymphoma (DLBCL) cell lines, DHL4, DHL6, LY7, HBL1 and U2932, treated with the SYK inhibitor, R406

status: Public on Aug 31 2013

city: Boston

first: Stefano

last: Monti

address: 72 East Concord st. E-613B

department: Medicine

institute: Boston University

summary: The five DLBCL cell lines were treated with R406 to assess the signature of SYK inhibition. In previous studies, R406 decreased the proliferation and induced apoptosis of these surface Ig+ cell lines. In the previous studies, R406 inhibited the autophosphorylation of SYK 525/526 and SYK-dependent phosphorylation of BCR signaling components such as BLNK.

overall_design: RNA samples from five DLBCL cell lines treated with R406 or vehicle (DMSO) alone for 0, 6, or 24 hours were profiled in triplicate on Affymetrix HT_HG-U133plust2 chips.

first: Linfeng

last: Chen

first: Shipp

last: Margaret


title: Telomeric repeats facilitate CENP-A incorporation via telomere binding proteins

status: Public on Aug 22 2013

first: Karl

last: Ekwall

summary: The histone H3 variant, CENP-ACnp1, is normally assembled upon canonical centromeric sequences, but there is no apparent obligate coupling of sequence and assembly, suggesting that centromere location can be epigenetically determined. To explore the tolerances and constraints on CENP-ACnp1 deposition we investigated whether certain locations are favoured when additional CENP-ACnp1 is present in fission yeast cells.  Our analyses show that additional CENP-ACnp1 accumulates within and close to heterochromatic centromeric outer repeats, and over regions adjacent to rDNA and telomeres. The use of minichromosome derivatives with unique DNA sequences internal to chromosome ends shows that telomeres are sufficient to direct CENP-ACnp1 deposition. However, chromosome ends are not required as CENP-ACnp1 deposition also occurs at telomere repeats inserted at an internal locus and correlates with the presence of H3K9 methylation near these repeats. The Ccq1 protein, which is known to bind telomere repeats and recruit telomerase, was found to be required to induce H3K9 methylation and thus promote the incorporation of CENP-A near telomere repeats.  These analyses demonstrate that at non-centromeric chromosomal locations the presence of heterochromatin influences the sites at which CENP-A is incorporated into chromatin and thus, potentially the location of centromeres.

overall_design: For CENP-A/Cnp1 chromatin immunoprecipitation: DNA immunoprecipitated with anti-Cnp1 serum using chromatin extracts from mutants and wild type control cells in biological duplicates normalized to input DNA from each strain.

first: Araceli

last: Castillo

first: Alison

last: Pidoux

first: Sandra

last: Catania

first: Mickaël

last: Durand-Dubief

first: Eun

last: Choi

first: Georgina

last: Hamilton

first: Robin

last: Allshire


title: Clinical Monoclonal B lymphocytosis versus Rai 0 Chronic Lymphocytic Leukemia: a comparison of the cellular, molecular, cytogenetic features and clinical course in a prospective multicenter study [miRNA]

status: Public on Aug 30 2013

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

summary: Prospective series of 136 clinical monoclonal B lymphocytosis (cMBL) and 216 chronic lymphocytic leukemia (CLL) Rai 0 patients, were investigated in this study. While the distribution of CD38 and ZAP-70 positivity was similar, IGHV-mutated cases were more frequent among cMBL (P = 0.005). A Cox multivariate analysis on the whole patient cohort showed that cMBL condition was predictive of longer PFS, while CD38 expression and IGHV-unmutated status and CD38 expression correlated significantly with a shorter PFS in cMBL and Rai0-CLL, respectively. Trisomy 12, 11q- and 17p- abnormalities were scanty and of no predictive value in both conditions. Notably, gene and miRNA expression profiling showed no significant differences between cMBL and Rai0-CLL. Furthermore, similar gene and miRNA expression signatures were found in cMBL and Rai0-CLL according to the IGHV gene mutational status: that is, unmutated cases had different signatures from mutated cases, irrespectively of the cMBL or CLL condition. Overall, our study based on a prospective series of patients indicates that no major biological differences exist in cMBL compared to Rai0-CLL, suggesting that this two entities mainly differ for the initial size of the monoclonal cell population which may reflect in the longer time for clonal expansion.

overall_design: This series of microarray experiments contains the microRNA profiles of purified B-cell chronic lymphocytic leukemia (B-CLL) cells obtained from 150 patients (Binet stage A) including 39 cMBL and 111 Rai0-CLL. Peripheral blood mononuclear cells from CLL patients were isolated by Ficoll-Hypaque (Seromed, Biochrom KG, Berlin, Germany) density-gradient centrifugation. For gene and miRNA expression profiling experiments CLL cells were enriched by negative selection with the EasySep-Human B cell enrichment kit without CD43 depletion (Stem Cell Technologies) using the fully automated protocol of immunomagnetic cell separation with RoboSepTM (Stem Cell Technologies). The proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence with antibodies for CD19 FITC, CD23 PE and CD5 PC5. 500 nanograms of total RNA was processed in accordance with the manufacturer's protocols (Agilent Technologies) to generate Cy3-labelled RNA, which were purified on chromatography columns (Micro Biospin 6, Bio-Rad, Hercules, CA) and then hybridized on an Agilent microarray (G4470B) at 55C for 17 hr in a rotating oven. Images at 5 um resolution were generated using an Agilent scanner G2505B. The Feature Extraction 10.7.3.1 software (Agilent Technologies) was used to obtain the microarray raw-data. The raw gTotalGeneSignal has been recalculated using the procedures described in Agilent Feature Extraction Software version 10.1 manual. Non-human probes, miRNAs flagged as 'absent' (i.e. expressed below background levels) throughout the whole dataset and miRNAs expired according to Sanger miRBase Release 15 (April 2010) were discarded, and a quantile normalization was applied on raw data using the aroma.light package for Bioconducor. The data were then converted to obtain positive values throughout the dataset, at a minimum value of 1, and log2 transformed.

first: Morabito

last: Fortunato

first: Mosca

last: Laura

first: Cutrona

last: Giovanna

first: Tuana

last: Giacomo

first: Ferracin

last: Manuela

first: Zagatti

last: Barbara

first: Fabris

last: Sonia

first: Matis

last: Serena

first: Gentile

last: Massimo

first: Recchia

last: Anna

first: Bossio

last: Sabrina

first: D

first: Ilariucci

last: Fiorella

first: Musolino

last: Caterina

first: Molica

last: Stefano

last: Francesco

first: Tassone

last: Pierfrancesco

first: Negrini

first: Ferrarini

last: Manlio

first: Neri

last: Antonino


title: Potential Biomarkers of Long-term Benefit from Single-agent Trastuzumab or Lapatinib in HER2-positive Metastatic Breast Cancer

status: Public on Oct 25 2013

city: Barcelona

first: Aleix

last: Prat

address: Passeig Vall d´Hebron 119

department: Translational Genomics

institute: VHIO

summary:
Gene expression data of HER2+ breast tumor samples
Increasing evidence indicates that a subset of patients with HER2-positive breast cancer may achieve significant clinical benefit with anti-HER2 targeted therapy without chemotherapy. Thus, identification of biomarkers of long-term benefit from anti-HER2 agents is needed, especially in the metastatic setting. In the HERLAP study (NCT00842998), patients with HER2-positive metastatic breast cancer were randomized to trastuzumab or lapatinib as first-line therapy. Patients showing radiological signs of tumor regression after 8 weeks of treatment were allowed to continue on single agent anti-HER2 therapy until disease progression. Chemotherapy was added to anti-HER-2 therapy in patients failing to achieve tumor regression at the 8-week evaluation and those progressing at any time. Expression analysis of 105 selected genes was performed from formalin-fixed paraffin-embedded in 17 primary tumor samples. The research-based PAM50 intrinsic subtypes were also identified. The association of the expression of each biomarker with clinical outcome endpoints was evaluated. Nineteen patients were enrolled. In 4 patients (21.1%) we observed disease control lasting longer than 12 months with single agent anti-HER2 therapy (range 14.9-38.8 months). High expression of 17q12-21 amplicon genes HER2 and GRB7, and the PAM50 HER2-enriched intrinsic profile, were found significantly associated with 8-week overall response rate and with the duration of disease control during single agent anti-HER2 therapy. Conversely, high expression of luminal-related genes such as PGR, MDM2 or PIK3CA, or the PAM50 luminal intrinsic profile, was found associated with reduced benefit from single agent anti-HER2 therapy. Conclusions: Our data indicate that gene expression-based biomarkers can identify patients with HER2-positive metastatic breast cancer that benefit substantially from single agent chemo-free anti-HER2 targeted therapy.

overall_design: In the study presented here, a well-defined cohort of 21 breast cancer cases from the HERLAP trial, was used to acquire expression profiles of a total of 105 unique genes

first: Maurizio

last: Scaltriti


title: MIRnome Profiling of Hereditary Pheochromocytoma and Paraganglioma Reveals Specific Signatures According to Primary Mutation: Possible Implications in the Differentiation Status of Tumor Cells

status: Public on Jul 02 2013

city: Madrid

first: Mercedes

last: Robledo

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics Program

institute: Spanish National Cancer Research Centre (CNIO)

summary: Pheochromocytoma (PCC) and paraganglioma (PGL) are rare neuroendocrine neoplasias of neural crest origin. They can be part of several syndromes, and their mRNA profile is dependent on genetic background, but questions related to clinical behavior or even main location remain unanswered. MicroRNAs are key modulators of target genes through translational repression, mRNA degradation, or both, and therefore they could resolve some of these issues. To determine the role microRNAs play in tumorigenesis and progression of PCC/PGL, as well as to identify microRNA biomarkers specifically related to different PCC/PGL genetic classes known so far, we characterized microRNA profiles in a large series of frozen tumors with germline mutations in SDHD, SDHB, VHL, RET, NF1, and TMEM127 genes through microarray analysis. We identified microRNA signatures specific to, as well as common among, the genetic classes of PCC/PGLs, and the best candidate microRNAs (miR-122, miR-126*, miR-129*, miR-133b, miR-137, miR-183, miR-210, miR-382, miR-488, miR-885-5p, and miR-96) were validated in an independent series of formalin-fixed paraffin-embedded PCC/PGL samples by qRT-PCR. MicroRNA-137, -96/183, and -143/145 expression in PCC/PGLs correlated inversely with the differentiation status of tumor cells. MicroRNA-210, -382, and -380 could modulate pseudohypoxic cellular response in VHL-deficient PCC/PGL. MicroRNA-193b, -365, and -424 were commonly downregulated among all genetic classes, suggesting their involvement in cell cycle control and differentiation. Herein, we demonstrate that PCC/PGLs have different microRNA profiles according to the underlying primary mutation, suggesting they could be used as specific biomarkers and add information on the etiology of these tumors.

overall_design: For this study, we employed the Agilent-019118 Human miRNA Microarray 2.0 G4470B (with Labeling kit: Agilent miRNA labeling reagent and Hybridization Kit, Cat # 5190-0408) to perform microRNA expression profiling on a large series of 54 fresh-frozen tissue samples, including a total of 48 genetically characterized pheochromocytomas (n=37) and paragangliomas (n=11) (8 SDHB-related tumors, 4 SDHD-related tumors, 14 Ret-related tumors, 12 VHL-related tumors, 4 NF1-related tumors, 3 TMEM127-related tumors, and 3 familial pheochromocytoma (FPCC) samples), and 6 normal adrenal medulla. Normalization of array data was performed applying the robust multiarray average (RMA) method using the AgiMicroRna package in Bioconductor.  RMA normalization, by default, merges replicates of each probe and produces an Eset with a single value for each microRNA.

first: Aguirre

middle: A

last: de Cubas

first: Elena

last: López-Jiménez