title: Using the combined analysis of transcripts and metabolites to propose key genes for differential terpene accumulation across two regions

status: Public on Jul 22 2015

city: Beijing

first: Qiu-hong

last: Pan

address: Tsinghua East Road No.17,Haidian district

department: College of Food Science and Nutritional Engineering

institute: China Agriculture University

summary: To obtain an interpretation from the view of transcriptome on distinct metabolite accumulation between ecologically different regions in China, next-generation sequencing technology was performed on E-L 31, 35，36 and 38 stages of Muscat Blanc a Petits Grains grape berries from Changli (CL, eastern) and Gaotai (GT, western). Transcriptome analysis revealed that some key genes involved in terpene synthesis were markedly up-regulated in the CL region. Particularly in the MEP pathway, the expression of VvHDR (1-hydroxy-2-methyl-2-butenyl 4-diphosphate reductase) paralleled with the accumulation of terpenes, which can promote the flow of isopentenyl diphosphate (IPP) into the terpene synthetic pathway. The glycosidically bound monoterpenes accumulated differentially along with maturation in both regions, which is synchronous with the expression of a monoterpene glucosyltransferase gene (VvGT14). Other genes were also found to be related to the differential accumulation of terpenes and monoterpene glycosides in the grapes between regions. Transcription factors that could regulate terpene synthesis were predicted through gene co-expression network analysis. Additionally, the genes involved in abscisic acid (ABA) and ethylene signal responses were expressed at high levels earlier in GT grapes than in CL grapes.

overall_design: cDNA libraries generated from four developmental stages (E-L 31, 35, 36 and 38) of Muscat Blanc a Petits Grains grape berries in two consecutive years from Changli (CL) and Gaotai (GT) in China were sequenced using Illumina HiSeq™ 2000.Only one RNA-seq library was constructed for each of the E-L31 and E-L36 stage samples because of the small amount of high quality RNA acquired, whereas two libraries were constructed for each of the E-L35 and E-L38 stage samples. As a result, a total of 24 libraries were obtained for the two regions within two years.

first: Ya-Qin

last: Wen

first: Gan-Yuan

last: Zhong

first: Yuan

last: Gao

first: Chang-Qing

last: Duan

first: Qiu-Hong


title: Global DNA methylation landscape reveals roles of DNA methylation involved in the regulation of drug metabolizing enzyme [II]

status: Public on Jun 16 2015

city: Yahaba-Cho, Shiwa-Gun

first: Wataru

last: Habano

state: Iwate

address: 2-1-1 Nishitokuta

department: Pharmacodynamics and Molecular Genetics

country: Japan

institute: Iwate Medical University

type: Methylation profiling by genome tiling array

summary: In order to elucidate the role of DNA methylation in the DME gene regulation, global DNA methylation and mRNA expression profiles of human tissues and cell lines were examinde by HumanMethylation450 Bead Chip and SurePrint G3 Human Gene Expression 8×60K v2. We demonstrated DNA methylation landscape of the DME genes in human tissues. Although a fraction of DME genes can be regulated by their DNA methylation, the variable DNA methylation status probably affects drug metabolism and response.

overall_design: Bisulphite converted DNA from the 7 samples were hybridized to the Illumina HumanMethylation450 BeadChip.


title: Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks

status: Public on Jun 05 2015

city: Minneapolis

first: Marissa

last: Macchietto

address: 117 Pleasant Street SE

department: Minnesota Supercomputing Institute

country: USA

institute: University of Minnesota, Minneapolis

type: Expression profiling by high throughput sequencing

summary: Parasitism is a major ecological niche for a variety of nematodes. Multiple nematode lineages have specialized as pathogens, including deadly parasites of insects that are used in biological control. We have sequenced and analyzed the draft genomes and transcriptomes of the entomopathogenic nematode Steinernema carpocapsae and four congeners (S. scapterisci, S. monticolum, S. feltiae, and S. glaseri). We used these genomes to establish phylogenetic relationships, explore gene conservation across species, and identify genes uniquely expanded in insect parasites. Protein domain analysis in Steinernema revealed a striking expansion of numerous putative parasitism genes, including certain protease and protease inhibitor families, as well as fatty acid- and retinol-binding proteins. Stage-specific gene expression of some of these expanded families further supports the notion that they are involved in insect parasitism by Steinernema. We show that sets of novel conserved non-coding regulatory motifs are associated with orthologous genes in Steinernema and Caenorhabditis. We have identified a set of expanded gene families that are likely to be involved in parasitism. We have also identified a set of non-coding motifs associated with groups of orthologous genes in Steinernema and Caenorhabditis involved in neurogenesis and embryonic development that are likely part of conserved protein–DNA relationships shared between these two genera.

sample_organism:
Caenorhabditis elegans
Steinernema carpocapsae
Steinernema feltiae

overall_design: We analyzed the gene expression of a total of 24 RNA-seq samples from 3 nematode species( S. carpocapsae, S. feltiae, and C. elegans) for comparative analysis. We collected the RNA at four developmental time points (mixed embryo, L1, infective juvenile/dauer, young adult) for each species, and two biological replicates per stage.

first: Adler

last: Dillman

first: Camille

last: Porter

first: Alicia

last: Rogers

first: Brian

last: Williams

first: Igor

last: Antoshechkin

first: Ming-Min

last: Lee

first: Zane

last: Goodwin

first: Xiaojun

last: Lu

first: Edwin

middle: E

last: Lewis

first: Heidi

last: Goodrich-Blair

first: Patricia

last: Stock

first: Byron

middle: J

last: Adams

first: Paul

middle: W

last: Sternberg

first: Ali

last: Mortazavi


title: Whole blood microarray analysis of pigs showing extreme phenotypes after a porcine reproductive and respiratory syndrome virus infection [7 dpi]

status: Public on Jun 04 2015

city: East Lansing

first: juan

middle: p

last: steibel

state: MI

address: 1205 I Anthony Hall

institute: Michigan State University

summary: The presence of variability in the response of pigs to Porcine Reproductive and Respiratory Syndrome virus (PRRSv) infection, and recent demonstration of significant genetic control of such responses, leads us to believe that selection towards more disease resistant pigs could be a valid strategy to reduce its economic impact on the swine industry. To find underlying molecular differences in PRRS susceptible versus more resistant pigs, 100 animals with extremely different growth rates and viremia levels after PRRSv infection were selected from a total of 600 infected pigs. A microarray experiment was conducted on whole blood RNA samples taken at 0, 4 and 7 days post infection (dpi) from these pigs. From these data, we examined associations of gene expression with weight gain and viral load phenotypes. The single nucleotide polymorphism (SNP) marker WUR10000125 (WUR) on the porcine 60K SNP chip was shown to be associated with viral load and weight gain after PRRSv infection, and so, additionally, the effect of the WUR10000125 (WUR) genotype was examined. Limited information was obtained through linear modeling of blood gene differential expression (DE) that contrasted pigs with extreme phenotypes, for growth or viral load or between animals with different WUR genotype. However, using network-based approaches, molecular pathway differences between extreme phenotypic classes could be identified. Several gene clusters of interest were found when Weighted Gene Co-expression Network Analysis (WGCNA) was applied to 4dpi contrasted with 0dpi data. The expression pattern of one such cluster of genes correlated with weight gain and WUR genotype, contained numerous immune response genes such as cytokines, chemokines, interferon type I stimulated genes, apoptotic genes and genes regulating complement activation. In addition, Partial Correlation and Information Theory (PCIT) identified differentially hubbed (DH) genes between the phenotypically divergent groups. GO enrichment revealed that the target genes of these DH genes are enriched in adaptive immune pathways. There are molecular differences in blood RNA patterns between pigs with extreme phenotypes or with a different WUR genotype in early responses to PRRSv infection, though they can be quite subtle and more difficult to discover with conventional DE expression analyses. Co-expression analyses such as WGCNA and PCIT can be used to reveal network differences between such extreme response groups.

overall_design: three timepoints from 100 animals are hibridized following a blocked reference design; Blood gene expression of pigs 7 days post infection

first: Juan

last: Steibel

first: Martine

last: Schroyen


title: A Blood Transcriptional Diagnostic Assay for Septicemic Melioidosis

city: Seattle

first: Scott

last: Presnell

state: WA

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

summary: Melioidosis, caused by Gram negative bacteria Burkholderia pseudomallei, is a major type of community-acquired septicemia in Southeast Asia and Northern Australia with high mortality and morbidity rate. More accurate and rapid diagnosis is needed for improving the management of septicemic melioidosis. We previously identified 37-gene candidate signature to distinguish septicemic melioidosis from sepsis due to other pathogens. The aims of this current study were to independently validate our previous biomarker and consolidate gene selection from each of our microarray data set for establishing a targeted assay for the differential diagnosis of melioidosis. Blood samples were collected from patients who presented with severe inflammatory response syndromes from 3 provincial hospitals in Northeast of Thailand during September 2009 and November 2011. Only culture-confirmed sepsis were included in the study (n=166). We generated a new microarray dataset comprising of 29 patients with septicemic melioidosis and 54 patients with sepsis due to other pathogens. Validation of the 37-gene signature using this new dataset demonstrated the prediction accuracy of approximately 80% for detecting type of sepsis. In order to develop a nanoliter-scale high throughput PCR technology, we further identified additional gene signature from this new microarray dataset and by revisiting our published data. Altogether 85 genes including 6 housekeeping genes were selected. Using multi-steps iteration approach we could reduce the number of biomarkers to 12 genes while the performance is comparable to that of the full panel. The high performance (accuracy >70%) of this 12-gene signature could be validated in a second independent set of samples. The 12-gene panel identified by our study provides high performance for the differential diagnosis of septicemic melioidosis. This finding will be useful for improving the management of septicemic melioidosis in term of diagnosis, treatment and follow up.

overall_design:
Total RNA from whole blood obtained from patients with sepsis caused by B.pseudomallei (n=29) or other pathogens (n=54) and uninfected controls (28 healthy and 27 subjects with type 2 diabetes mellitus) were collected. In order to validate the published signature, microarray data were generated from these samples. This dataset was also used for an independent selection of signature for septicemic melioidosis. The same RNA samples were used for validation by a high throughput real-time PCR technique, Fluidigm.
Please note that the non_normalized.txt contains background-subtracted raw data.

first: Prasong

last: Khaenam

first: Surachat

last: Buddhisa

first: Matthew

middle: C

last: Altman

first: Michael

last: Mason

first: Elizabeth

last: Whalen

first: Wattanachai

last: Susaengrat

first: Kimberly

last: O’Brien

first: Quynh-Ahn

last: Nguyen

first: Dimitry

last: Popov

first: Vivian

last: Gersuk

first: Charles

last: Quinn

first: Gregory

last: Bancroft

first: Ganjana

last: Lertmemongkolchai

first: Damien

last: Chaussabel


title: DNA methylation in ductal carcinoma in situ related with future development of invasive breast cancer

status: Public on Jun 01 2015

city: Hanover

first: Kevin

middle: Crowley

last: Johnson

state: NH

address: 72 College Street

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth College

summary: Ductal carcinoma in situ (DCIS) is a heterogeneous, pre-invasive lesion associated with an increased risk for future invasive ductal carcinoma. However, accurate risk stratification for development of invasive disease and appropriate treatment decisions remain clinical challenges. DNA methylation alterations are recognized to be early events in the progression of cancer and represent emerging molecular markers that may predict invasive recurrence more accurately than traditional measures of DCIS prognosis.  We measured DNA methylation of DCIS (n=40) and adjacent normal (n=15) tissues using the Illumina HumanMethylation450 array. We identified locus-specific methylation differences between DCIS and matched adjacent-normal tissue (95,609 CpGs, Q < 0.05). Among 40 DCIS cases 13 later developed invasive disease and we identified 641 CpG sites that exhibited differential DNA methylation (P < 0.01 and medianúΔβú > 0.1) in these cases compared with age-matched subjects without invasive disease over a similar follow up period. The set of differentially methylated CpG loci associated with disease progression was enriched in homeobox-containing genes (P = 1.3E-9) and genes involved with limb morphogenesis (P = 1.0E-05). In an independent cohort, a subset of genes with progression-related differential methylation between DCIS and invasive breast cancer were confirmed. Further, the functional relevance of these genes’ regulation by methylation was demonstrated in early stage breast cancers from The Cancer Genome Atlas database. This work contributes to the understanding of epigenetic alterations that occur in DCIS and illustrates the potential of DNA methylation as markers of DCIS progression.

overall_design: Bisulfite converted DNA from the 55 samples (40 DCIS and 15 adjacent-normal) that were hybridized to the Illumina Infinium 450K Human Methylation beadchip


title: Global DNA methylation landscape reveals roles of DNA methylation involved in the regulation of drug metabolizing enzyme [III]

first: Wataru

last: Habano

overall_design: Bisulphite converted DNA from the 4 samples were hybridized to the Illumina HumanMethylation450 BeadChip (Sample L and SI were examined twice).


title: Pooled mouse macrophage datasets from GEO

status: Public on Aug 03 2019

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

type:
Expression profiling by array
Third-party reanalysis

summary: This is a collection of diverse publicly available mouse macrophage datasets and is also a subset of GSE119085. The datasets belong to GPL1261 platform and all normalized together with samples from GSE119085.

relation:
Reanalysis of: GSM224735
Reanalysis of: GSM224733
Reanalysis of: GSM224734
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Reanalysis of: GSM329260
Reanalysis of: GSM329259
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Reanalysis of: GSM427333
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Reanalysis of: GSM211339
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Reanalysis of: GSM211375
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Reanalysis of: GSM211327
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Reanalysis of: GSM211348
Reanalysis of: GSM211399
Reanalysis of: GSM211322
Reanalysis of: GSM211390
Reanalysis of: GSM211243
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Reanalysis of: GSM211331
Reanalysis of: GSM211245
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Reanalysis of: GSM211281
Reanalysis of: GSM211347
Reanalysis of: GSM211282
Reanalysis of: GSM211386
Reanalysis of: GSM211397
Reanalysis of: GSM211321
Reanalysis of: GSM211285
Reanalysis of: GSM211300
Reanalysis of: GSM211244
Reanalysis of: GSM211394
Reanalysis of: GSM211408
Reanalysis of: GSM211309
Reanalysis of: GSM211311
Reanalysis of: GSM211354
Reanalysis of: GSM211341
Reanalysis of: GSM211356
Reanalysis of: GSM289455
Reanalysis of: GSM289459
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Reanalysis of: GSM289460
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Reanalysis of: GSM117564
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Reanalysis of: GSM117562
Reanalysis of: GSM117567

overall_design: 327 published macrophage samples from 18 different series assayed on the GPL1261 platform were re-analyzed. RMA was used to normalize the CEL files.


title: Whole blood microarray analysis of pigs showing extreme phenotypes after a porcine reproductive and respiratory syndrome virus infection

first: juan

last: steibel

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

overall_design: Refer to individual Series


title: Detection of hypoxia inducible/reducible miRNAs in Hepatocellular Carcinoma cells

status: Public on May 06 2015

city: Hangzhou

first: Chengli

last: Du

state: Zhejiang

address: NO.79 Qingchun Road

country: China

institute: The First Affiliated Hospital of Zhejiang University

summary: To explore the miRNAs mediating the hypoxia in HCC, we design several groups HCC cells exposed to hypoxic conditions for several times and and submit to miRNA microarrays

overall_design: we expose HCC cells to hypoxic conditions for 0 hrs and 8 hrs. Both groups contain 3  independent replicates

first: Jian

last: Wu


title: Whole blood microarray analysis of pigs showing extreme phenotypes after a porcine reproductive and respiratory syndrome virus infection [4 dpi]

overall_design: three timepoints from 100 animals are hibridized following a blocked reference design; Blood gene expression of pigs 4 days post infection

first: Juan

last: Steibel

first: Martine

last: Schroyen


title: 5-FU resistant ESCC

status: Public on Jun 03 2015

city: Kyoto

first: Osamu

last: Kikuchi

address: 54 Shogoin-Kawaharacho Sakyoku

department: Therapeutic Oncology

institute: Kyoto University

type: Genome variation profiling by genome tiling array

summary: TE-5 and 5-FU resistant subline TE-5R

overall_design: TE-5 cells were treated with continuous and step-wise concentrations of 5-FU (1, 2, 5, and 10 μM), and consequently 5-FU-resistant ESCC cells were established and named as TE-5R cells.

first: Shinya

last: Ohashi


title: Pseudomonas aeruginosa PA14 differential gene expression in PA14_69770 mutants

city: Pasadena

first: Dianne

last: Newman

state: CA

address: 1200 E California Blvd, MC 147-75

institute: Caltech

summary: Extremely slow growth imposed by energy limitation is a ubiquitous but poorly understood physiological state for microbes. We used oxygen limitation to impose this state on Pseudomonas aeruginosa and measured newly synthesized proteins using a time-selective proteome labeling method (BONCAT) to identify relevant regulators and metabolic pathways. We further characterized one upregulated protein that has no homology to any known protein domains. This small, acidic protein is post-transcriptionally regulated and physically interacts with RNA polymerase, binding near the secondary channel during transcription elongation, and leading to widespread effects on gene expression. For some genes, the impacts on transcript and protein levels are different, suggesting possible modulation of translation as well. These effects have phenotypic consequences, as deletion of the gene affects biofilm formation, secondary metabolite production, and fitness in fluctuating conditions. Based on these phenotypes, we have designated the protein SutA (survival under transitions).

overall_design: Profiles of rRNA-depleted total RNA from WT, ∆sutA (PA14_69770), and SutA-overexpressing cells grown late exponential phase in minimal medium containing pyruate as the carbon source, in triplicate

first: Megan

last: Bergkessel

first: Brett

middle: M

last: Babin

first: David

middle: A

last: Tirrell

middle: K

first: Michael

last: Sweredoski

first: Sonja

last: Hess


title: Tet1 is a tumor suppressor of hematopoietic maligancy [RRBS]

status: Public on Apr 12 2015

city: New York

first: Luisa

last: Cimmino

address: 550 First Avenue

institute: NYU

type: Methylation profiling by high throughput sequencing

summary: Loss of Tet1 expression causes global 5mC and 5hmC changes in stem and progenitor cells in mice and causes enhanced Pro-B cell self-renewal, increased DNA damage and B-lymphomageneis. In this study we performed reduced representative bisulfite sequencing (RRBS) of DNA from WT and Tet1 KO LSK cells.

overall_design:
DNA methylation sequencing was performed and analyzed using an enhanced reduced representation (ERRBS) methodology as previously described. DNA was extracted from purified LSK cells of 6-month old WT and Tet1 KO mice, Bisulphite treatment was performed using the EZ DNA Methylation Kit (Zymo Research). Libraries were amplified according to illumina protocols and sequenced on an Illumina HiSeq2500 machine
DNA methylation profiling of LSK cells in WT and Tet1 KO mice.


title: Tet1 is a tumor suppressor of hematopoietic malignancy

city: Bronx

first: Yiting

last: Yu

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Epigenetic pathways that regulate DNA methylation and chromatin modifications are frequently found to be dysregulated in human cancers. The TET methylcytosine dioxygenase 1 (TET1) enzyme is an important regulator of hydroxymethylcytosine (5hmC) in embryonic stem cells, neural progenitors,adult cells and reprogrammed cells. Decreased expression of TET proteins and loss of 5hmC has been reported in many tumors, suggesting a critical role for the maintenance of this epigenetic modification in normal cellular function. However, loss of TET1 function in the etiology of cancer has not been directly investigated. Here, we show that deletion of the Tet1 gene promotes the development of B cell lymphoma. Tet1 is required for maintaining normal levels of 5hmC, preventing aberrant DNA hypermethylation and for the regulation of transcriptional programs involved in B-cell lineage specification, chromosome maintenance, and DNA repair. Progenitor B cells in the absence of Tet1 accumulate DNA damage and whole-exome sequencing of Tet1-deficient tumors revealed a high correlation of mutations with those most frequently found in Non-Hodgkin B cell lymphoma (B-NHL) patients. In addition, we show that the TET1 gene is deleted, hypermethylated and transcriptionally silenced in B-NHL patients. These findings provide the first in vivo evidence of TET1 function as a tumor suppressor of hematopoietic malignancy.

overall_design: We did hydroxymethylation tests for two wild type mice and two Tet1 knockout mice.

first: Iannis

last: Aifantis

first: Rudolf

last: Jaenisch


title: Chromatin Immunoprecipitation of HA-tagged PA14_69770 and RpoA in Pseudomonas aeruginosa UCBPP-PA14

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Profiles of genome association of HA-tagged PA14_69770 or RpoA in cells lacking or overexpressing PA14_69770, grown to late stationary phase in minimal medium containing pyruate as the carbon source, in triplicate.


title: SutA is a Transcription Elongation Factor Expressed During Slow Growth in *Pseudomonas aeruginosa*


title: Tet1 is a tumor suppressor of hematopoietic maligancy


title: Tet1 is a tumor suppressor of hematopoietic maligancy [RNA-Seq]

summary: Loss of Tet1 expression causes global 5mC and 5hmC changes in stem and progenitor cells in mice and enhanced pro-B cell self-renewal, increased DNA damage and B-lymphomageneis. In this study we performed whole transciptome analysis using RNA-sequencing in purified long-term HSCs and MPPs. These results revealed that genes regulated byTet1 included Histones, DNA repair enzymes and B-lineage specific factors.

overall_design:
Purified long-term HSCs and MPPs from WT and Tet1 KO mice were used for RNA isolation. RNA was extracted using RNeasy kit (Qiagen) and PolyA selection using oligo-dT beads (Life Technologies) was performed according to the manufacturer’s instructions. Libraries were generated as described before, including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification. RNA libraries were then sequenced on the Illumina HiSeq 2000 using 50bp paired-end reads.
Transcriptome profiling of LT-HSC and MPP cells in WT and Tet1 KO mice


title: Allergenic Can f 1 and its human homologue Lcn-1 direct dendritic cells to induce divergent immunity

status: Public on Apr 08 2015

city: Innsbruck

first: Daniel

last: Bindreither

state: Tirol

address: Innrain 82

department: Division of Molecular Pathophysiology

country: Austria

institute: Medical University Innsbruck

summary: Why and when the immune system skews to Th2 mediated allergic immune responses is still poorly characterized. With two homologous lipocalins, the major respiratory dog allergen Can f 1 and the human endogenous, non-allergenic Lipocalin-1, we investigated their impact on human monocyte derived dendritic cells (DC). The two lipocalins had differential effects on DC according to their allergenic potential. Compared to Lipocalin-1, Can f 1 persistently induced lower levels of the Th1 skewing maturation marker expression, tryptophan breakdown and IL-12 production in DC. As a consequence, T cells stimulated by DC treated with Can f 1 produced more of the Th2 signature cytokine IL-13 and lower levels of the Th1 signature cytokine IFN-γ than T cells stimulated by Lipocalin-1 treated DC. These data were partially verified by a second pair of homologous lipocalins, the cat allergen Fel d 4 and its putative human homologue MUP. Our data indicate that the crosstalk of DC with lipocalins alone has the potential to direct the type of immune response to these particular antigens. A global gene expression analysis further supported these results and indicated significant differences in intracellular trafficking, sorting and antigen presentation pathways when comparing Can f 1 and Lipocalin-1 stimulated DC. With this study we contribute to a better understanding of the induction phase of a Th2 immune response.

overall_design: Comparisons of mDc, Can f 1 and Lcn-1 regulations in dentridic cells

first: Beate

last: Posch

first: Christian

last: Irsara

first: Fabian

last: Gamper

first: Martin

last: Herrmann

first: Dietmar

last: Fuchs

first: Norbert

last: Reider

first: Bernhard

last: Redl

first: Christine

last: Heufler


title: Tet1 is a tumor suppressor of hematopoietic maligancy [array]

summary: Loss of Tet1 expression causes global 5mC and 5hmC changes in stem and progenitor cells in mice and causes enhanced Pro-B cell self-renewal, increased DNA damage and B-lymphomageneis. In this study we performed microarray analysis of total LSK cells from WT and Tet1 KO mice. These results revealed that genes regulated byTet1 in LSKs included Histones, DNA repair enzymes and B-lineage specific factors.

overall_design:
LSK cells were purified from the bone marrow of 6-month old WT and Tet1 KO mice . RNA was extracted using RNeasy kit (Qiagen) and hybridized on Affymetrix microarrays.
Microarray profiling of LSK cells in WT and Tet1 KO mice.


title: Deciphering the RNA landscape by RNAome sequencing

status: Public on Apr 01 2015

city: Maastricht

first: Kasper

last: Derks

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

type: Non-coding RNA profiling by high throughput sequencing


title: Deciphering the RNA landscape by RNAome sequencing [Affymetrix]

summary: Current RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species in an unperturbed manner. We report strand-specific RNAome sequencing that determines expression of small and large RNAs from ribosomal RNA-depleted total RNA in a single sequence run. Since current analysis pipelines cannot reliably analyze small and large RNAs simultaneously, we developed TRAP, Total Rna Analysis Pipeline, a robust interface that is also compatible with existing RNA sequencing protocols. RNAome sequencing quantitatively preserved all RNA classes, allowing cross-class comparisons that facilitates the identification of relationships between different RNA classes. We demonstrate the strength of RNAome sequencing in mouse embryonic stem cells treated with cisplatin. MicroRNA and mRNA expression in RNAome sequencing significantly correlated between replicates and was in concordance with both existing RNA sequencing methods and gene expression arrays generated from the same samples.  Moreover, RNAome sequencing also detected additional RNA classes such as enhancer RNAs, anti-sense RNAs, novel RNA species and numerous differentially expressed RNAs undetectable by other methods. At the level of complete RNA classes, RNAome sequencing also identified a specific global repression of the microRNA and microRNA isoform classes after cisplatin treatment whereas all other classes such as mRNAs were unchanged. These characteristics of RNAome sequencing will significantly improve expression analysis as well as studies on RNA biology not covered by existing methods.

overall_design: 8 mouse embryonic stem cell samples,  control and cisplatin treated, 4 replicates per group

first: Branco

last: Misovic

first: Mirjam

last: van den Hout

first: Christel

last: Kockx

first: Cesar

last: Payan Gomez

first: Rutger

last: Brouwer

first: Harry

last: Vrieling

first: Jan

last: Hoeijmakers

first: Wilfred

last: van IJcken

first: Joris

last: Pothof


title: Effect of FTO (fat mass and obesity-associated) overexpression on gene expression profiling in beta cells

status: Public on Jan 06 2015

city: Nanjing

first: Hong-Qi

last: Fan

state: Jiangsu

address: 300 Guangzhou RD

department: Department of Endocrinology

institute: The First Affiliated Hospital of Nanjing Medical University

summary: We have completed the mouse expression microarray analysis of the 2 samples. Total RNA from each sample was quantified using the NanoDrop ND-1000 and the RNA integrity was assessed using standard denaturing agarose gel electrophoresis. For microarray analysis, Agilent Array platform was employed. The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Mouse Genome Oligo Microarray (4x44K, Agilent Technologies). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 1 out of 2 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes between two samples were identified through fold change filtering. Pathway analysis and GO Analysis were applied to determine the roles of these differentially expressed genes played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable gene expression profiling between samples.

overall_design: beta cell lines (MIN6) were transfected with FTO vector or empty vector. The gene expression profiling of the two samples were performed by expression microarray analysis

first: Bo

last: Zhang


title: Deciphering the RNA landscape by RNAome sequencing [Seq]

overall_design: 8 mouse embryonic stem cell samples, 4 control and 4 cisplatin treated, 4 replicates per group for Affymetrix arrays.  Of these, 6 were used for sequencing and are reported in this Series.


title: Prmt5 is a crucial regulator of muscle stem cell expansion in adult mice

status: Public on Mar 13 2015

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute for Heart and Lung Research

summary: Skeletal muscle stem cells (MuSC), also called satellite cells, are indispensable for maintenance and regeneration of adult skeletal muscles. Yet, a comprehensive picture of the regulatory events controlling the fate of MuSC is missing. Here, we determine the proteome of MuSC to design a loss-of-function screen, and identify 120 genes important for MuSC function including the arginine methyltransferase Prmt5. MuSC-specific inactivation of Prmt5 in adult mice prevents expansion of MuSC, abolishes long-term MuSC maintenance and abrogates skeletal muscle regeneration. Interestingly, Prmt5 is dispensable for proliferation and differentiation of Pax7(+) myogenic progenitor cells during mouse embryonic development, indicating significant differences between embryonic and adult myogenesis. Mechanistic studies reveal that Prmt5 controls proliferation of adult MuSC by direct epigenetic silencing of the cell cycle inhibitor p21. We reason that Prmt5 generates a poised state that keeps MuSC in a standby mode, thus allowing rapid MuSC amplification under disease conditions.

overall_design: RNA from cultured satellite cells on Ion torrent sequencer

first: Thomas

last: Braun

first: Carsten

last: Kuenne

first: Johnny

last: Kim

first: Ting

first: Marcus

last: Krüger

first: Yonggang

last: Zhou

first: Stefan

last: Günther


title: Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction (small RNA-seq)

status: Public on Feb 11 2015

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: Maize anthers, the male reproductive floral organs, express two classes of phased, small interfering RNAs (phasiRNAs). RNA profiling from ten sequential cohorts of staged maize anthers plus mature pollen revealed that 21-nt phased siRNAs (21-phasiRNAs) from 463 loci appear abruptly after germinal and initial somatic cell fate specification and then diminish, while 24-nt phased siRNAs (24-phasiRNAs) from 176 loci coordinately accumulate during meiosis and persist as haploid gametophytes differentiate into pollen. RNA sequencing of anther developmental mutants, together with in situ RNA hybridization detection of phasiRNA biogenesis factors, demonstrated that 21-phasiRNAs and 24-phasiRNAs are independently regulated. Furthermore, 21-phasiRNAs require epidermal cells while 24-phasiRNAs require functional tapetal cells.  Maize phasiRNAs and mammalian PIWI-interacting RNAs (piRNAs) illustrate convergent evolution of small RNAs to support male reproduction.

sample_organism:
Zea mays
Zea mays subsp. mays

platform_organism:
Zea mays
Zea mays subsp. mays

overall_design: Examination of maize phasiRNAs by high throughput sequencing for small RNA profiling

first: Jixian

last: Zhai

first: Han

first: Siwaret

last: Arikit

first: Kun

last: Huang

first: Virginia

last: Walbot


title: Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction


title: Gene expression profiles after infection of rainbow trout with viral hemorrhagic septicemia virus (VHSV)

status: Public on Mar 05 2015

city: Madrid

first: Julio

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

country: Spain

institute: INIA

summary: We describe here transcripts induced after intraperitoneal injection of rainbow trout with 2 different viruses, both belonging to strain 23.75 of viral hemorrhagic septicemia virus (VHSV): a deleted Nv gene (dNV) virus and a wild type (wt) virus. Two days after infection, differentially expressed transcript levels from selected immune-related trout genes were studied in internal organs (spleen and head kidney).

overall_design: Fishes were divided in two groups (3 fishes per group). The first group was intraperitoneally injected with 100000 pfu per trout of dNV VHSV, while the second group was injected with 100000 pfu/trout of wt VHSV. All fishes were sacrificed two days post infection.

first: Eduardo

last: Gómez-Casado

first: Blanca

last: Chinchilla

first: Paloma

last: Encinas


title: Characterization of small RNAs and their targets in soybean (Glycine max)

status: Public on Dec 01 2014

summary: Small RNAs, including microRNAs and their targets, as well as phased secondary siRNAs, were characterized in the soybean genome by deep sequencing of small RNA libraries from a wide range of tissues. The mRNA targets of many of these small RNAs were also validated from many of the same tissues using PARE (Parallel Analysis of RNA Ends) libraries.

overall_design: Small RNA profiling was done by Illumina TruSeq sample preparation followed by high-throughput sequencing using an Illumina HiSeq 2500 at the Delaware Biotechnology Institute. PARE analysis used library construction approaches described in the journal Methods (PubMed ID: 23810899).


title: Somatic CRISPR/Cas9-mediated tumor suppressor disruption enables versatile murine cancer modeling

status: Public on Dec 31 2014

city: HEIDELBERG

first: Paul

middle: A.

last: Northcott

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

summary: Recent cancer genome sequencing studies have identified numerous novel candidate driver genes. In vivo functional investigation of oncogenes using somatic gene transfer has been successfully exploited as a versatile means to validate their pathogenic relevance. In contrast, such functional analyses have been hampered for candidate tumor suppressor genes, e.g. by insufficient knockdown using RNAi-mediated approaches. In order to provide a flexible method for investigating loss-of-function mutations and their potential role in tumorigenesis, we have established CRISPR/Cas9-mediated somatic gene disruption, allowing for in vivo deletion of candidate tumor suppressor genes. We demonstrate the utility of this approach by somatic disruption of the Ptch1 gene in the mouse cerebellum, leading to the formation of medulloblastoma faithfully resembling the SHH-driven subgroup of the disease. This in vivo method for validation of candidate tumor suppressor genes provides a fast and convenient system for the generation of faithful animal models of human cancer.

overall_design: We used gene expression arrays to evaluate the transcriptional profiles of malignant cerebellar tumours generated using CRISPR/Cas9 technology designed to disrupt the Ptch1 tumour suppressor gene in the embryonic and neonatal mouse cerebellum.

first: Jan

last: Gronych


title: miRNA expression profile in HOS cells exposed to sodium fluoride

status: Public on Jan 01 2015

city: Nagpur

first: praveen

middle: Kumar

last: Naoghare

state: Maharashtra

address: CSIR Lab,Nehru Marg

department: Environmental Health Division

country: India

institute: Innovative Life Discoveries

summary: Fluorosis is caused due to excess of fluoride intake over a long period of time. Aberrant change in RUNX2-mediated signaling cascade is one of the decisive steps during the pathogenesis of fluorosis. Till date, role of fluoride on the epigenetic alterations is not studied. In the present study, global expression profiling ofshort non-coding RNAs, in particular   miRNAs and snoRNAs was carried out in NaF treated HOS cells to understand their possible role in the development of fluorosis. RT-PCR and insilico hybridization revealed that miR-124 and miR-155 can be directly involved in the transcriptional regulation of RUNX2 and RANKL genes. Compare to control, C/D box analysis revealed mark elevation in the number of UG dinucleotides and D-box sequences in NaF exposed HOS cells. Herein, we report miR-124 and miR-155 as the new possible players involved in the development of fluorosis.  We also state that the alterations in UG dinucleotides and D-box sequences of snoRNAs could be due to NaF exposure.

overall_design: HOS cells grown on MEM media were treated with sodium fluoride and total RNA was isolated from cells after one month of chronic exposure; Cells grown on six 25mm flask. two replicates of control and two different concentration of exposed samples; two replicate are served as control

first: Atul

middle: P

last: Daiwile

first: S

middle: S

last: Devi

first: Amit

last: Bafana

first: Pravin

first: P

last: Arrigo

first: Hemant

last: Purohit

first: Devendra

last: Parmar

first: K

last: Krishnamurthi


title: Fatal Asthma vs. Control Human Airway Smooth Muscle Transcriptome Changes in Response to Vitamin D or Albuterol

city: Philadelphia

last: Himes

state: PA

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

institute: University of Pennsylvania

summary:
Rationale: Asthma is a chronic inflammatory airway disease. Children with severe asthma have lower levels of vitamin D than children with moderate asthma, and among children with severe asthma, airway smooth muscle (ASM) mass is inversely related to vitamin D levels. Beta2 agonists are a common asthma medication that act partly by targetting the ASM. We used RNA-Seq to characterize the human ASM transcriptome of fatal and asthma vs. contols at baseline and under two treatment conditions.
Methods: The Illumina TruSeq assay was used to prepare 75bp paired-end libraries for ASM cells from white donors, 6 with fatal asthma and 12 control donors under three treatment conditions: 1) no treatment; 2) treatment with a β2-agonist (i.e. Albuterol, 1μM for 18h); 3) treatment with vitamin D 100 nM for 18h). Llibraries were sequenced with an Illumina Hi-Seq 2000 instrument. The Tuxedo Suite Tools were used to align reads to the hg19 reference genome, assemble transcripts, and perform differential expression analysis using the protocol described in https://github.com/blancahimes/taffeta

overall_design: mRNA profiles obtained via RNA-Seq for primary human airway smooth muscle cell lines from fatal asthma or control donors that were treated with vitamin D, albuterol, or were left untreated.

first: Himes

last: Blanca

first: Panettieri

last: Reynold


title: Histone chaperone HIRA orchestrates H4K16ac-decorated dynamic chromatin in senescent cells and is required for suppression of oncogene-induced neoplasia.

status: Public on Nov 26 2014

city: Glasgow

first: Peter

last: Adams

address: Switchback Rd, Bearsden

country: United Kingdom

institute: University of Glasgow, Beatson Institute for Cancer Research

summary: Cellular senescence is a stable proliferation arrest that suppresses tumorigenesis. Histone chaperone HIRA deposits nucleosome-destabilizing histone variant H3.3 into chromatin in a DNA replication-independent manner. Histone H3.3 and a subset of other typically “replication-dependent” core histones were expressed in non-proliferating senescent cells, the latter linked to alternative mRNA splicing and polyadenylation. Senescent cells incorporated newly-synthesized histones into chromatin, partially dependent on HIRA. HIRA and newly-deposited histone H3.3 co-localized at promoters of expressed genes, and their distribution shifted between proliferating and senescent cells, paralleling changes in gene expression. In senescent cells, gene promoters showed exceptional enrichment of a histone acetylation linked to open and dynamic chromatin, H4K16ac. Abundance of H4K16ac depended on HIRA. In the mouse, inactivation of HIRA downregulated H4K16ac and dramatically enhanced oncogene-induced hyperplasia. To conclude, HIRA controls a previously undefined dynamic non-canonical H4K16ac-decorated chromatin landscape in senescence, and also plays an unanticipated role in suppression of oncogene-induced neoplasia.

overall_design: Examination of HIRA protein binding alongside histone modification H4K16ac and H3.3 in proliferating and senescent IMR90 cells

first: Taranjit

last: Rai

first: John

last: Cole

middle: D


title: Expression data from PD32 and PD88 IMR90

middle: D.

summary: IMR90 cells were passaged until replicative senescence and compared with proliferating cells.

overall_design: We used RNA-Seq to detail the global programme of gene expression in human IMR90 replicative induced senescence

first: Tony

last: McBryan


title: Complex Genomic Rearrangements at the PLP1 Locus Include Triplication and Quadruplication

status: Public on Nov 25 2014

city: HOUSTON

first: Christine

middle: R.

last: Beck

state: Texas

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Inverted repeats (IRs) can facilitate structural variation as crucibles of genomic rearrangement. Complex DUP-TRP/INV-DUP rearrangements that contain breakpoint junctions within IRs have been recently associated with both MECP2 duplication syndrome (MIM#300260) and Pelizaeus-Merzbacher disease (PMD, MIM#312080). We investigated 17 unrelated PMD subjects with copy number gains at the PLP1 locus including triplication and quadruplication of specific genomic intervals – 16/17 were found to have a DUP-TRP/INV-DUP rearrangement product. An IR distal to PLP1 facilitates DUP-TRP/INV-DUP formation as well as an inversion structural variation found frequently amongst normal individuals. We show that a homology—or homeology—driven replicative mechanism of DNA repair can apparently mediate template switches within stretches of microhomology. Moreover, we provide evidence that quadruplication, and potentially higher order amplification of a genomic interval, can occur in a manner consistent with rolling circle amplification as predicted by the microhomology mediated break induced replication (MMBIR) model.

overall_design: To determine size, genomic extent and gene content for each rearrangement, we used a customized tiling-path oligonucleotide microarray spanning the Xq22 chromosomal region to query the genomic DNA of 7 males with Pelizaeus-Merzbacher disease, and 5 unaffected or carrier/unaffected family members. A 4x44k Agilent Technologies (Santa Clara, CA) microarray was designed using the Agilent e-array website targeting the region of the genome encompassing the dosage-sensitive PLP1 gene.

middle: R

first: James

last: Lupski


title: Expression data from ER32 and ER32.40HT IMR90

summary: IMR90 cells were infected with pLNC-RAS:ER (from Jesus Gil lab) with retroviral gene transfer. Infected cells were drug selected G418. The cells were induced either with ethanol as control or with 100nM final conc 4-hydroxytamoxifen (sigma H7904) for ectopic expression of protein

overall_design: We used RNA-Seq to detail the global programme of gene expression in human IMR90 oncogene induced senescence


title: Gene Expression in induced Treg cell from CD4+ Naive T cell isolated from miR-31fl/fl/CD4Cre vs Control mice

status: Public on Oct 02 2014

city: Shanghai

first: Lingyun

last: Zhang

address: 280 Chongqing South Road

institute: Shanghai Institute of Immunology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine

summary: A microarray study performed in iTreg of miR-31fl/fl/CD4Cre and control mice to identify genes that are regulated by the miR-31. CD4+ naïve T cells from miR-31fl/fl mice and miR-31fl/flCD4Cre mice were used to induce iTreg in vitro. Four independent experiments were performed.

overall_design: MiR-31fl/fl/CD4Cre mice (6 wk old) and age-matched control mice were sacrificed, and the spleen were removed and teased into cell-single suspensions and filtered through a 40 μm cell strainer. Naïve CD4+CD25-Foxp3gfp-CD62Lhi T cells were sorted by FACSAria III (BD bioscience).The medium used for T cell cultures was RPMI-1640 (Gibco) supplemented with 10% heat-inactivated FBS (Gibco), 2 mM L-glutamine (Gibco), 100 U/ml penicillin, 100 μg/ml streptomycin, and 5 mM β-mercaptoethanol (Gibco). The CD4+ Naïve T cells were stimulated with plate-bound anti-CD3 (5 μg/ml) plus soluble anti-CD28 (2 μg/ml) under iTreg cell differentiation conditions (mTGF-β1, 5 ng/ml and rmIL-2, 40 ng/ml; R&D Systems). After 4 days, harvested cell ,the RNA was extracted in Trizol and then purified using the miRNeasy Micro Kit (Qiagen). This submission shows the data obtained from 3 individual miR-31fl/fl/CD4Cre mice mice measured against 3 control mice.

first: Honglin

last: Wang


title: Methylome of a low-grade invasive GIST

status: Public on Aug 01 2014

city: Heidelberg

first: Henri-Jacques

last: Delecluse

address: Im Neuenheimer Feld 242

department: Pathogenesis of virus-associated tumours

summary: A low-grade invasive gastro-intestinal stromal tumour (GIST) was subjected to whole-genome sequencing as well as methylation profiling using Illumina 450K BeadChip array, in order to determine the minimal set of genomic and epigenomic alterations necessary to trigger the formation of invasive GIST.

overall_design: single-sample study, DNA extracted from fresh frozen tissue.

first: Olaf

last: Klinke


title: Expression data from Human gingival fibroblast transfected with CEMP1

status: Public on Sep 16 2014

city: Cambridge

first: Madeline

last: Lancaster

state: Cambridgeshire

address: Cambridge Biomedical Campus, Francis Crick Avenue

department: Cell Biology Division

institute: MRC Laboratory of Molecular Biology

summary:
Cementum protein 1 (CEMP1) is involved in cell adhesion, cell differentiation, regulates the mineralization processes during cementogenesis, and selects progenitor cells from periodontal ligament.
To determine the gene expression profiling induced by CEMP1 overexpression by non-osteogenic cells such as human gingival fibroblasts  we performed microarrays (Human Gene 1.0 ST, Affymetrix) to identify differentially expressed transcripts (ED) between human gingival fibroblasts (HGF) and those that overexpress CEMP1 (HGF/CEMP1).

overall_design: HGF cells overexpressing CEMP1 and controls were harvested at 3, 7 and 14 days after transfection of CEMP1, three biological replicates were analyzed for each time point and condition for a total of 18 microarrays.

first: Mercedes

last: Bermudez-Cortes

first: Ivan

last: Imaz-Rosshandler

first: Claudia

last: Rangel

first: Gabriela

middle: E

last: Mercado-Celis

first: Higinio

last: Arzate


title: Transcript profiling of Bln1 silenced plants (BSMV-VIGS) relative to empty vector and buffer treated controls in barley-powdery mildew interactions

status: Public on Sep 30 2014

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

institute: Iowa State University

summary: Barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) was used to identify significant new genes in the regulation of host innate immunity.  This experiment was designed to uncover significant changes in Bln1 (Contig12219_at)-silenced plants relative to empty vector and buffer treated controls. Five independent biological replications of a split-plot experimental design were conducted with replications as blocks, treatment with Blumeria graminis f. sp. hordei (Bgh) as the whole-plot factor, and all combinations of genotype (Mla13 and Mla9) and VIGS treatment [Buffer control (mock), BSMV:00 (empty vector), and BSMV:Bln1248] as the split-plot factor for a total of 60 GeneChip hybridizations. Ten seedlings were used as a split-plot experimental unit for each combination of replication, Bgh treatment, genotype, and VIGS treatment.  Plants were grown in a controlled 20°C glasshouse prior to VIGS treatment.  Twelve days after VIGS treatment, half of the plants in each replication were challenged with the compatible Bgh isolate 5874.  Top halves of 5 of the 10 seedling third leaves (about 10 cm) from each split-plot experimental unit were harvested into liquid N2 at 32 hours after inoculation (HAI) - the timepoint with the highest differential Bln1 transcript accumulation (Meng et al. 2009), and after initial establishment of the perihaustorial interface (Caldo et al. 2004).  The remaining 5 leaves were used to record infection phenotype 7 days later.  RNA was isolated for GeneChip hybridization from the 32-HAI samples.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Yan Meng.  The equivalent experiment is BB101 at PLEXdb.]

overall_design: genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: Mock (Buffer Control)(5-replications);  genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:00(5-replications);  genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:Bln1[248](5-replications);  genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: Mock (Buffer Control)(5-replications);  genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: BSMV:00(5-replications);  genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: BSMV:Bln1[248](5-replications);  genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: Mock (Buffer Control)(5-replications);  genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:00(5-replications);  genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:Bln1[248](5-replications);  genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: Mock (Buffer Control)(5-replications);  genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: BSMV:00(5-replications);  genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: BSMV:Bln1[248](5-replications)

first: Yan

last: Meng

first: Roger

last: Wise


title: Weight-reduction by low-fat diet cause differently-expressed circulating microRNAs in obese C57BL/6 mice

status: Public on Sep 03 2014

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

summary: To profile the expression of circulating miRNAs in a mouse model of diet-induced obesity (DIO) with subsequent weight-reduction with low-fat diet (LFD), eighteen C57BL/6 male mice were grouped into three subgroups as: (1) Control: the mice fed with the standard AIN-76A (fat: 11.5 kcal%) diet for 12 wks; (2) DIO: the mice fed with 58 kcal% high-fat diet for 12 wks; (3) DIO+LFD: the mice fed with high-fat diet for 8 wks to induce obesity, then changed to 10.5 kcal% low-fat diet for subsequent 4 wks.

overall_design: C57BL/6 mice were purchased from BioLasco (Taipei, Taiwan). All housing conditions were maintained, and surgical procedures, including analgesia, were performed in an Association for Assessment and Accreditation of Laboratory Animal Care International (AAALAC)-accredited SPF facility according to national and institutional guidelines. In this experiment, eighteen C57BL/6 wild type male mice were randomly grouped into three subgroups (n=6 in each group): (1) Control: the control mice were fed ad libitum a standard AIN-76A (fat: 11.5 kcal%) diet for 12 wks; (2) DIO: the mice were fed ad libitum a 58 kcal% HFD (D12331; Research Diets Inc., New Brunswick, NJ) for 12 wks to induce obesity; (3) DIO+LFD: the mice fed ad libitum a 58 kcal% HFD (D12331) for 8 wks to induce obesity, then continued the feeding of 10.5 kcal% LFD (D 12329; Research Diets Inc.) for additional 4 wks. Weight measurements were performed on a weekly basis to for these three groups of mice. Evaluation of blood glucose levels was performed at the beginning and in the end of the experiment to confirm that the HFD-fed mice developed an obese and insulin resistant phenotype. After the end of experiment at 12w, all mice were killed. The abdominal WAT of each mice was removed and weighted. Paraffin-embedded abdominal WAT was sectioned at 5 μm and stained with hematoxylin and eosin to measure mean adipocyte area. A volume of 1 mL of whole blood was collected into a plain tube and allowed to clot for 1 hour. The sera samples were aliquoted after centrifugation at 3,000 × g for 10 minutes and stored at −80°C until further analysis.

first: Cheng-Shyuan

last: Rau

first: Shao-Chun

last: Wu

first: Johnson

last: Yang


title: Expression data of E13.5 mouse Blood Brain Barrier and lung endothelial cells

status: Public on May 14 2014

city: Boston

first: Meeta

last: Mistry

state: MA

address: 655 Huntington Ave

institute: Harvard School of Public Health

summary:
Following the identification of a critical time window of Blood Brain Barrier formation in the mouse embryo, we aimed to identify genes important for barriergenesis. To this end, we isolated cortical and lung E13.5 endothelial cells and compared expression between the two populations.
The working hypothesis was that endothelial cells which are actively building a barrier would have a uniqe pattern of gene expression that would be detectable in comparison to a non-barrier endothelial population that is also active in vasculogenesis.

overall_design: E13.5 Tie2-GFP embryos were micro-dissected for cortex and lungs. Cortex tissue was carefully cleared of the meninges and choroid plexus. FACS purification of GFP positive cells and GeneChip analysis was applied . All material from a single litter (10-13 embryos) was pooled and considered as a biological replicate. n=4 litters.

first: Ayal

last: Ben-Zvi

first: Chenghua

last: Gu


title: Expression of three hepatocellular carcinoma cell lines with different organ-tropism

status: Public on Jun 30 2014

first: Wei zhong

address: Fenglin Rd 180, Xuhui district

department: Zhongshan Hospital

institute: Fudan University

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

overall_design: Refer to individual Series


title: Gene expression of three hepatocellular carcinoma cell lines with different organ-tropism.

summary: In this study we investigated the gene expression profiling in three HCC cell lines with different organ-tropism.The parent cell line has low metastasis ability in nude mice model. Subclone 1 has higher metastasis ability specific to lung, and subclone 2 has dual metastasis ability to lung and celiac lymph node. We aimed to explore differentially expressed genes involved in process of HCC metastasis and organ-specific metastasis, and identify their biological functions.

overall_design: Examination of different gene expression among the 3 cell types.

first: W

middle: Z

first: J

middle: L

last: Wan

first: Z

middle: H

last: Tao


title: Multipotent mammary cancer stem cells integrate stem cell and clonal expansion theories of tumor progression

status: Public on Sep 12 2014

city: La Jolla

first: Lesley

middle: G

last: Ellies

address: 9500 Gilman Drive

department: Pathology

institute: University of California, San Diego

summary: The diversity of human breast cancer subtypes has led to the hypothesis that breast cancer is a number of different diseases arising from cells at various stages of differentiation. We have derived clonal multipotent metastatic mammary cancer stem cells from the polyomavirus middle T mouse model of breast cancer, that can differentiate into luminal, myoepithelial and alveolar cells. When injected orthotopically at low-density, the resulting tumors express estrogen and progesterone receptors. With continued passage in vivo, the tumor cells undergo additional epigenetic and/or genetic changes that result in upregulation of Her2 expression or clonal expansion of cells that give rise to basal-like or claudin-low tumors. As in human tumors, the more aggressive tumor subtypes express nuclear p53. The temporal sequence of events suggests that contrary to current dogma, multiple tumor subtypes can originate from a single multipotent cancer stem cell that undergoes evolution during tumor progression. Furthermore, these data raise the possibility that a human polyomavirus may be a causative agent in spontaneous forms of human breast cancer.

overall_design: Three spontaneous PyVmT tumors and forty cell line derived tumors were analyzed. To generate cell line derived tumors, 10^6 tumor cells were injected orthotopically into four abdominal mammary fat pads in syngeneic C57Bl/6 female mice. After 6-8 weeks the mice were euthanized and the tumors excised and frozen at -80°C. One tumor per mouse 8-10mm in diameter was used for array analysis. RNA was extracted using the RNeasy kit (Qiagen) with on column DNA removal.

first: Lei

last: Bao

first: Karen

last: Messer


title: RNA-Seq Analysis of Laser-Capture Microdissected Cells of the Developing Central Starchy Endosperm of Maize

status: Public on Jun 17 2014

city: Tucson

first: Ramin

last: Yadegari

state: Arizona

address: 1140 E. South Campus Dr.

department: Plant Sciences

institute: University of Arizona

summary: Endosperm is a product of double fertilization, and provides nutrients and signals to the embryo during seed development in flowering plants. Early stages of endosperm development are critical for the development of its storage capacity through synthesis and accumulation of starch and storage proteins. Here we report on the isolation and sequencing of mRNAs from the central portion of the starchy endosperm of Zea mays (maize) B73 at 6 days after pollination. We detected high correlation among the four biological replicates of RNAs isolated using laser-capture microdissection of the cell type. Because the assayed stage of development precedes the synthesis and accumulation of the major storage proteins and starch in the endosperm, our dataset likely include mRNAs for genes that are involved in control and establishment of these developmental programs.

overall_design: Four replicates of mRNAs from the central portion of starchy endopserm were isolated using laser-capture microdissection and sequenced using the Illumina GAIIx platform.

first: Dhiraj

last: Thakare

first: Ruolin

first: Joshua

last: Steffen

first: Junpeng

last: Zhan

first: Dongfang

last: Wang

first: Richard

middle: M

last: Clark

first: Xiangfeng


title: Core Ileal Transcriptome in Pediatric Crohn Disease

status: Public on Jul 24 2014

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: We report the global pattern of ileal gene expression in a cohort of 359 treatment-naïve pediatric Crohn Disease, Ulcerative Colitis patients and controls. We focus on genes with consistent altered expression in inflamed and unaffected ileum of CD [ileal-involved CD (iCD) and non-invloved ileal CD (cCD)], but not in the ileum of ulcerative colitis or control.

overall_design: Ileal biopsies were obtained during diagnostic colonoscopies of children and adolescents aged less than 17 years, who presented with IBD-like symptoms. All patients underwent baseline colonoscopy and histological characterization; non-IBD controls were those with suspected IBD, but with no microscopic or macroscopic inflammation and normal radiographic, endoscopic, and histologic findings. Biopsies were stored at -80 degrees.

first: Yael

last: Haberman

first: Lee

last: Denson


title: Gene expression profile after injection of rhabdoviral recombinant protein NV [PBS vs. NV]

status: Public on May 05 2014

first: Julio

last: Coll

summary: Due to the common presence of a non-virion NV gene absent from other fish rhabdoviruses, NV-coding rhabdoviruses, such as the viral haemorrhagic septicemia (VHSV), were placed into a new Novirhabdovirus genus. Because conflicting results do exist on the importance of NV for VHSV trout pathogenicity and the NV function is still unclear, the effects of intraperitoneal injection of recombinant NV protein were studied by using home-designed immune-related microarrays from rainbow trout Oncorhynchus mykiss.

overall_design: Trouts were separated in two groups. One group was injected with PBS and it was used as control group. Second group was injected with soluble VHSV non-virion (NV) recombinant protein


title: Transcriptome Analysis of Follicular Helper T cells, Central Memory Precursors, and Terminal Effector Th1 Cells from Wild Type and Stat3fl/fl Cd4cre mice

status: Public on Mar 06 2014

city: New Haven

first: Joe

last: Craft

state: CT

address: 300 Cedar St.

department: Immunobiology

institute: Yale University

summary: Purpose: To compare the transcriptomes of activated CD4 T effector cell populations in the presence and absence of STAT3 at 8 days post-infection using high-throughput RNA sequencing analysis. Methods: Cell sorting of the populations was done using the markers Ly6c and PSGL-1

overall_design: CD4 T cell Ly6c and PSGL-1 population mRNA profiles 8 days post-LCMV infection of wild type (WT) and STAT3fl/fl Cd4cre mice were generated by mRNA sequencing using Illumina HiSeq 2000.

first: John

last: Ray


title: Domains of genomewide gene expression dysregulation in Down syndrome

status: Public on Apr 08 2014

city: Geneva

first: Audrey

last: Letourneau

address: Rue Michel-Servet 1

department: Genetic Medicine and Development

country: Switzerland

institute: University of Geneva Medical School

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: BMP-2-responsive genes in mouse periodontal ligament-derived PDL-L2 cells with and without endoglin knockdown

status: Public on Jan 21 2014

city: Sakai

first: OSAMU

last: ISHIBASHI

address: 1-1 Gakuen-cho, Naka-ku

department: Grad Sch Life & Environmental Sciences

institute: Osaka Prefecture University

summary: This study was designed to identify endoglin (ENG)-dependent BMP2-responsive genes in the mouse fibroblastic cell line PDL-L2.

overall_design: PDL-L2 cells were treated with an siRNA for endoglin (siENG) or a control siRNA (siCont). After 48hr, the cells were exposed to recombinant human BMP-2 (250 ng/ml) or vehicle and cultured for 12 hr.

first: Osamu

last: Ishibashi

first: Hiroyuki

last: Kawashima


title: Domains of genomewide gene expression dysregulation in Down syndrome [RNA-seq]

summary: Trisomy 21 (T21) is the most frequent genetic cause of cognitive impairment. To assess the perturbations of gene expression in T21, and to eliminate the noise of the genomic variability, we studied the transcriptome of fetal fibroblasts from a pair of monozygotic twins discordant for T21. Here we show that the differential expression between the twins is organized in domains along all chromosomes that are either up- or downregulated. These gene expression dysregulation domains (GEDDs) can be defined by the expression level of their gene content, and are well conserved in induced pluripotent stem cells derived from the twins’ fibroblasts. Comparison of the transcriptome of the Ts65Dn mouse model of DS and wild-type, also showed GEDDs along the mouse chromosomes that were syntenic in human. The GEDDs correlate with the lamina-associated (LADs) and replication domains of mammalian cells. The overall LADs position was not altered in trisomic cells. However, the H3K4me3 profile of the trisomic fibroblasts was modified and accurately followed the GEDD pattern. These results suggest that the nuclear compartments of trisomic cells undergo modifications of the chromatin environment influencing the overall transcriptome and that GEDDs may therefore contribute to some T21 phenotypes.

overall_design: mRNA-Seq profiling in Down syndrome: fibroblasts derived from a pair of monozygotic twins discordant for trisomy 21 (4 replicates), iPS cells from the same pair of discordant twins, fibroblasts from a pair of normal monozygotic twins, fibroblasts from 16 unrelated individuals (8 trisomic and 8 euploid controls), fibroblasts from the Ts65Dn mouse model of Down syndrome (1 trisomic mouse and 1 control wt).

first: Federico

middle: A

last: Santoni

first: Ximena

last: Bonilla

last: Sailani

first: David

last: Gonzalez

first: Jop

last: Kind

first: Claire

last: Chevalier

first: Robert

last: Thurman

last: Sandstrom

first: Youssef

last: Hibaoui

first: Konstantin

last: Popadin

first: Emilie

last: Falconnet

first: Maryline

last: Gagnebin

first: Corinne

last: Gehrig

first: Anne

last: Vannier

first: Michel

last: Guipponi

first: Laurent

last: Farinelli

first: Daniel

last: Robyr

first: Marco

last: Garieri

first: Eugenia

last: Migliavacca

first: Christelle

last: Borel

first: Samuel

last: Deutsch

first: Anis

last: Feki

last: Stamatoyannopoulos

first: Yann

last: Herault

first: Bas

last: van Steensel

first: Roderic

last: Guigo

first: Stylianos

last: Antonarakis


title: Extensive oscillatory gene expression during C. elegans larval development [RNA-seq for polyA enriched mRNAs]

status: Public on Mar 01 2014

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute

summary: We report the presence of extensive, transcriptionally controlled oscillations in the C. elegans, developmental transcriptome. Furthermore, using ribosome profiling, we show that these oscillating transcripts are actively translated.

overall_design: Examination of three timecourses that were collected over C. elegans development and analyzed by RNA-seq of mRNA libraries

first: Gert-Jan

last: Hendriks

first: Helge

last: Großhans


title: Extensive oscillatory gene expression during C. elegans larval development


title: LOXs in invasive trophoblasts

status: Public on Dec 04 2013

city: PARIS

first: Severine

middle: Aude

last: Degrelle

address: 4 avenue de l'Observatoire

country: France

institute: INSERM UMRS-1139

summary:
Human placental development is characterized by invasion of extravillous cytotrophoblasts (EVCTs) into the uterine wall during the first trimester of pregnancy. Peroxisome proliferator-activated receptor gamma (PPARG) plays a major role in placental development, and activation of PPARG by its agonists results in inhibition of EVCT invasion in vitro. To identify PPARG target genes, microarray analysis was performed using GeneChip technology on EVCT primary cultures obtained from first-trimester human placentas. Gene expression was compared in EVCTs treated with the PPARG agonist rosiglitazone versus control. A total of 139 differentially regulated genes were identified, and changes in the expression of the following 8 genes were confirmed by reverse transcription-quantitative polymerase chain reaction: a disintegrin and metalloproteinase domain12 (ADAM12), connexin 43 (CX43), deleted in liver cancer 1 (DLC1), dipeptidyl peptidase 4 (DPP4), heme oxygenase 1 (HMOX-1), lysyl oxidase (LOX), plasminogen activator inhibitor 1 (PAI-1) and PPARG. Among the upregulated genes, lysyl oxidase (LOX) was further analyzed. In the LOX family, only LOX, LOXL1 and LOXL2 mRNA expression was significantly upregulated in rosiglitazone-treated EVCTs. RNA and protein expression of the subfamily members LOX, LOXL1 and LOXL2 were analyzed by absolute RT-qPCR and western blotting, and localized by immunohistochemistry and immunofluorescence-confocal microscopy. LOX protein was immunodetected in the EVCT cytoplasm, while LOXL1 was found in the nucleus and nucleolus. No signal was detected for LOXL2 protein. Specific inhibition of LOX activity by beta-aminopropionitrile in cell invasion assays led to an increase in EVCT invasiveness. These results suggest that LOX, LOXL1 and LOXL2 are downstream PPARG targets and that LOX activity is a negative regulator of trophoblastic cell invasion.
Microarray analysis was performed using GeneChip technology in EVCTs isolated from first trimester human placentae. Gene expression in rosiglitazone-treated primary EVCT cultures was compared with matched untreated controls. A total of 175 probe sets identified differentially regulated genes. One of these genes, lysyl oxidase (LOX) which was up-regulated, was further analyzed. Expression of the LOX family was determined by real time Q-PCR, Western blotting, immunohistochemistry and immunofluorescence. LOX, LOXL and LOXL2 mRNA expression was significantly upregulated in PPARg-activated EVCTs. LOX and LOXL2 protein were present throughout the trophoblast cytoplasm, while LOXL was localized to the nucleus and nucleolus. Cell invasion assays on Matrigel Transwells showed that specific inhibition of LOX activity by ß-aminopropionitrile led to an increase in EVCT invasiveness, showing the basal inhibitory effect of LOX and LOX-like in the trophoblastic cells invasion process. Together these results show that LOX family as PPARg-target genes participate to the regulation of trophoblast invasion.

overall_design: Total RNA from EVCT were labelled according to the standard Affymetrix protocol. Five independent targets per treatment vs control were generated and hybridized on a GeneChip.

first: N

last: Segond

first: S

last: Berndt

first: E

last: Clouqueur

first: A

last: Chissey

first: C

last: Rouault

first: B

last: Saubamea

first: P

last: Dessen

first: K

last: Fong

last: Csiszar

first: J

last: Badet

first: D

last: Evain-Brion

first: T

last: Fournier


title: Chickpea Transcriptome Atlas - I

status: Public on Jan 09 2014

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

institute: Jawaharlal Nehru University

summary: In this study, we aim to present a global view of transcriptome dynamics during flower development in chickpea. We generated around 234 million high-quality reads for eight flower development stages (ranging from 16 to 40 million reads for each stage) and 91 million high-quality reads from three vegetative tissues using Illumina high-throughput sequencing GAII platform. Because of non-availability of reference genome sequence, we mapped the reads to chickpea transcriptome comprised of 34,760 transcripts for estimation of their transcriptional activity in different tissue samples. The transcriptome dynamics was studied by comparison of gene expression during flower development stages with vegetative tissues.

overall_design: We collected different tissue samples used in this study and total RNA isolated was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to 34760 chickpea transcripts and reads per kilobase per million (RPKM) was calculated for each gene in all the sample to measure their gene expression. Differential expression analysis was performed using DESeq software. The genes preferentially expression during various stages of flower development as compared to vegetative stages and those with speciifc expression were identified.

first: Vikash

middle: K

last: Singh

first: Rohini

last: Garg


title: cmi_0-8h_embryonic_ChIP-seq

status: Public on Aug 28 2013

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_4967
This submission comes from a modENCODE project of Kevin White. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The White Lab is aiming to map the association of all the Transcription Factors (TF) on the genome of Drosophila melanogaster. One technique that we use for this purpose is chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) utilizing an Illumina next generation sequencing platform. The data generated by ChIP-seq experiments consist basically of a plot of signal intensity across the genome. The highest signals correspond to positions in the genome occupied by the tested TF.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Exd-GFP-13T; Developmental Stage: Embryo 0-8; Genotype: w; PBac{y[+]-attP-3B}VK00033; Sex: Unknown; Transgene: exd genomic coding region with stop codon replaced with GFP;  EXPERIMENTAL FACTORS: Developmental Stage Embryo 0-8; Strain Exd-GFP-13T; Antibody anti-Cmi (target is CG5591)

first: Kevin

last: White

first: Lijia

last: Ma

first: Matthew

last: Slattery


title: Microarray analysis of microRNAs in NPC FFPE tissue samples

status: Public on Jan 13 2014

city: Washington

first: Jeffrey

last: Bethony

state: DC

address: 2300 Eye St. NW.

department: Microbiology, Immunology, and Tropical Medicine

institute: George Washington University

summary: Nasopharyngeal carcinoma (NPC) is a challenging cancer that is rare in the United States but shows exceptionally high incidence in Southern China, Indonesia, and Malaysia. While the hallmark of NPC is striking geographic variation, early detection and clinical management are also critical characteristics of this cancer. The etiology of NPC is complex, involving the interplay of multiple factors, including Epstein Barr Virus (EBV), which appears to play an oncogenic role. While multimodality therapy is the mainstay of treatment for NPC, the impact of this treatment is greatly influenced by the presenting tumor stage, tumor size, nodal involvement, and the histologic subtype classification. Up to 40% percent of NPC cases present at an advanced stage, likely due to its deep location in the lymphatic-rich nasopharynx and its propensity for early lymphatic spread. Recent modifications in the TNM staging schema have attempted to improve prognostic accuracy, but variations in clinical outcome are still reported in patients with the same stage and similar treatment regimens. The various molecular markers developed to monitor disease progression have also proven unreliable. Hence, there is a significant need for a new kind of prognostic biomarker for NPC. Herein different approaches were applied to a set of samples to detect NPC-related miRNAs, potential circulating biomarkers. We have optimized the extraction of total RNA from NPC Formalin-fixed, paraffin-embedded (FFPE) samples and sera from four patients and matched controls and analyzed the miRNA expression profile by microarray, qPCR and RNAseq. The microarray analysis showed that 46 miRNAs were found to be differentially and significantly expressed in carcinogenic tissue compared to healthy tissue. Twenty-three (23) microRNAs were significantly upregulated (21 human microRNAs and 2 EBV miRNAs), whereas 13 were down-regulated.

overall_design: A total of 8 unique samples were analyzed on Agilent human miRNA microarray (miRBase Release 16.0). Of the 8 samples, 4 are from Non-keratinizing NPC tissue. Non-NPC (normal) tissue were taken from 4 individuals that were diagnosed with NPC (2 of which were matched/paired from the NPC case).

first: Jordan

last: Plieskatt

first: Gabriel

last: Rinaldi

first: Yanjun

last: Feng

first: Elizabeth

last: Martínez

first: Samantha

last: Easley

first: Paul

last: Levine

first: Salman

last: Hashmi

middle: J

last: Brindley

first: Jason

last: Mulvenna


title: Expression data from pooled RNA of various ocular tissues

status: Public on Apr 17 2013

city: Iowa City

first: Alex

middle: Handler

last: Wagner

state: Iowa

address: 5315 Seamans Center

department: Biomedical Engineering

institute: University of Iowa

summary:
The normal gene expression profiles of the tissues in the eye are a valuable resource for considering genes likely to be involved with disease processes.  This is based on the assumption that transcript abundances in healthy tissue are correlated to the continued health of that tissue.
Expression values were compared with publically available EST and RNA-sequencing resources.  The estimated gene and exon level abundances are available online on the Ocular Tissue Database.

overall_design: Ten different tissues were obtained from 6 different individuals and RNA was pooled.  The tissues included:  retina, optic nerve head (ONH), optic nerve (ON), ciliary body (CB), trabecular meshwork (TM), sclera, lens, cornea, choroid/RPE and iris.

first: Terry

last: Braun


title: Genome-wide methylation maps for Proliferating and Senescent cells

status: Public on Nov 25 2013

city: Glasgow

first: Peter

last: Adams

address: Switchback Rd, Bearsden

institute: University of Glasgow, Beatson Institute for Cancer Research

summary: Altered DNA methylation and associated destabilization of genome integrity and function is a hallmark of cancer. Replicative senescence imposes a limit on proliferative potential that all cancer cells must bypass. Compared to proliferating cells, senescent cells exhibit marked chromatin re-organization. Here we show by whole-genome single-nucleotide bisulfite sequencing that replicative senescent human cells exhibit widespread alterations in their DNA methylome. These changes are linked to mislocalization of the maintenance DNA methyltransferase (DNMT1) in cells approaching senescence, altered replication-coupled DNA methylation and de-repression of repetitive satellite sequences. Deficiency of DNMT1 triggers chromatin changes characteristic of senescence and expression of satellite sequences. Most importantly, but paradoxically, gains and losses of methylation in replicative senescence are similar to those in cancer, and this ‘reprogrammed’ methylation landscape is largely retained when cells escape or bypass senescence. In sum, altered regulation of DNMT1 in cells approaching replicative senescence contributes to changes in chromatin structure and function. Consequently, if senescent cells escape the proliferative barrier, they already harbor epigenetic changes likely to promote malignancy.

overall_design: Examination of methylation status in IMR90 cells

first: Hazel

last: Cruickshanks

first: Tony

last: McBryan


title: Gene Expression data from 56 lung cancer cell lines

status: Public on May 24 2013

city: Salt Lake City

first: Nader

middle: Nassib

last: El-Chaar

state: Utah

address: 20 South 2030 East

department: Oncological Sciences

institute: University of Utah

summary:
Highlighting the gene expression characteristics of a large panel of lung cancer cell lines.
Microarrays were used to explore and detail the global gene expression profile of 56 lung cancer cell lines

overall_design: Gene expression was measured and recorded on HG-U133A chips in a large panel of lung cancer cell lines under ATCC recommended growth conditions

first: Emily

last: Chenette

first: Joseph

last: Nevins


title: Systematic analysis of palatal transcriptome to identify cleft palate genes within TGFbeta3-knockout mice alleles: RNA-Seq analysis of TGFbeta3 Mice

status: Public on Mar 29 2013

city: OMAHA

first: You

last: Li

state: NE

address: Emile St

department: Department of Genetics, Cell Biology and Anatomy

institute: University of Nebraska Medical Center

summary:
Background: In humans, cleft palate (CP) accounts for one of the largest number of birth defects with a complex genetic and environmental etiology. TGFβ3 has been established as an important regulator of palatal fusion in mice and it has been shown that TGFβ3-null mice exhibit CP without any other major deformities. However, the genes that regulate cellular decisions and molecular mechanisms maintained by the TGFβ3 pathway throughout palatogenesis are predominantly unexplored. Our objective in this study was to analyze global transcriptome changes within the palate during different gestational ages within TGFβ3 knockout mice to identify TGFβ3-associated genes previously unknown to be associated with the development of cleft palate. We used deep sequencing technology, RNA-Seq, to analyze the transcriptome of TGFβ3 knockout mice at crucial stages of palatogenesis, including palatal growth (E14.5), adhesion (E15.5), and fusion (E16.5).
Results: The overall transcriptome analysis of TGFβ3 wildtype mice (C57BL/6) reveals that almost 6000 genes were upregulated during the transition from E14.5 to E15.5 and more than 2000 were downregulated from E15.5 to E16.5. Using bioinformatics tools and databases, we identified the most comprehensive list of CP genes (n = 322) in which mutations cause CP either in humans or mice, and analyzed their expression patterns. The expression motifs of CP genes between TGFβ3+/− and TGFβ3−/− were not significantly different from each other, and the expression of the majority of CP genes remained unchanged from E14.5 to E16.5. Using these patterns, we identified 8 unique genes within TGFβ3−/− mice (Chrng Foxc2, H19, Kcnj13, Lhx8, Meox2, Shh, and Six3), which may function as the primary contributors to the development of cleft palate in TGFβ3−/− mice. When the significantly altered CP genes were overlaid with TGFβ signaling, all of these genes followed the Smad-dependent pathway.
Conclusions: Our study represents the first analysis of the palatal transcriptome of the  mouse, as well as TGFβ3 knockout mice, using deep sequencing methods. In this study, we characterized the critical regulation of palatal transcripts that may play key regulatory roles through crucial stages of palatal development. We identified potential causative CP genes in a TGFβ3 knockout model, which may lead to a better understanding of the genetic mechanisms of palatogenesis and provide novel potential targets for gene therapy approaches to treat cleft palate.

overall_design: Palatal mRNA profiles of wild type (WT), TGFβ3+/-, and TGFβ3-/- mice at E14.5, E15.5, and E16.5 were generated by deep sequencing, in triplicate, using Illumina HiSeq2000

first: Ferhat

last: Ozturk

first: Xiujuan

last: Zhu

first: Chittibabu

last: Guda

first: Ali

last: Nawshad


title: Gene expression profile after injection of recombinant deleted non-virion protein gene (NV) VHSV

status: Public on Aug 17 2013

city: Madrid

first: Julio

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

institute: INIA

summary: The function of the non-virion protein (NV) of the Viral hemorrhagic septicemia virus (VHSV) has been long questioned but it still remains unknown. We report here the differences in gene expression profiles of trouts infected with deleted NV VHSV or wild type VHSV so that it could shed some light on the issue.

overall_design: Eight fingerlings of rainbow trout were used for the experiment. Four of them were injected with deleted NV VHSV and the rest were injected with wild type VHSV as a control. Head kidney and spleen of each trout were collected 2 days post-injection and total RNA was extracted.


title: Human MCF7 cells: Mock control vs. siRNA transfected against calreticulin

status: Public on Feb 26 2013

city: Tehran

first: Mohammadreza

last: Zamanian

state: Tehran

address: Hafez al., Bani Hashem st., Resalat Highway

department: Genetics

country: Iran

institute: Royan Institute

summary: Transcriptional profiling of human MCF7 cells comparing mock control MCF7cells with MCF7cells transfected by siRNA against calreticulin. The latter was shown to be of having significantly decreased expression of calreticulin followed by significant decrease in migrative and invasive potentials of the MCF7 cells. Goal was to determine the effect of calreticulin knockdown on the global gene expression of MCF7 cells.

overall_design: Two-condition experiment, Mock control MCF7 cells vs. calreticulin siRNA knockdown MCF7 cells. Biological replicates: 3 mock control replicates, 3 transfected replicates.

first: Abhi

last: Veeracumarasivam

first: Rozita

last: Rosli


title: Karyotyping using SNP array of  primary uveal melanoma cells, normal uveal melanocytes, neural crest stem cells, embryonic stem cells and uveal melanoma cell lines MUM2B and OCM1A

status: Public on Feb 14 2013

city: Cleveland

first: Li

last: Zhang

address: 9500 Euclid Ave, JJN3

department: Quantitative Health Sciences

institute: CleveLAND CLINIC LERNER COL/MED-CWRU

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

summary: Karyotyping by SNP array of primary uveal melanoma samples, uveal melanoma cell lines and normal controls

overall_design: The Human660WQuad v1.0 DNA Analysis Bead Chip and kit were used for high resolution molecular karyotyping of DNA isolated from snap-frozen primary uveal melanoma tissue isolated from enucleated eyes.

first: Saunthararajah

last: Yogen


title: Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae

status: Public on Jan 29 2013

city: Baltimore

first: Mallory

middle: Ann

last: Freeberg

state: MD

address: 3400 N Charles St

department: Department of Biology

institute: Johns Hopkins University

summary: Protein-RNA interactions are integral components of nearly every aspect of biology including regulation of gene expression, assembly of cellular architectures, and pathogenesis of human diseases. However, studies in the past few decades have only uncovered a small fraction of the vast landscape of the protein-RNA interactome in any organism, and even less is known about the dynamics of protein-RNA interactions under changing developmental and environmental conditions. Here, we describe the gPAR-CLIP (global photoactivatable-ribonucleoside-enhanced crosslinking and immunopurification) approach for capturing regions of the transcriptome bound by RNA-binding proteins (RBPs) in budding yeast. We report over 13,000 RBP crosslinking sites in untranslated regions (UTR) covering 72% of protein-coding transcripts encoded in the genome, confirming 3’ UTRs as major sites for RBP interaction. Comparative genomic analyses reveal that RBP crosslinking sites are highly conserved, and RNA folding predictions indicate that secondary structural elements are constrained by protein binding and may serve as generalizable modes of RNA recognition. Finally, 38% of 3’ UTR crosslinking sites show changes in RBP occupancy upon glucose or nitrogen deprivation, with major impacts on metabolic pathways as well as mitochondrial and ribosomal gene expression. Our study offers an unprecedented view of the pervasiveness and dynamics of protein-RNA interactions in vivo.

overall_design: Duplicate gPAR-CLIP and mRNA-seq libraries were sequenced from yeast strains for each of three conditions: log-phase growth, growth after 2 hour glucose starvation, and growth after 2 hour nitrogen starvation. Additional duplicate mRNA-seq libraries were sequenced from yeast strains grown in the absence of 4-thiouracil. gPAR-CLIP libraries were used to determine regions of mRNA bound by proteins. mRNA-seq libraries served as controls for mRNA abundance. A Puf3p PAR-CLIP library was sequenced to determine how well gPAR-CLIP captured the binding signatures of a single RNA-binding protein.

first: Ting

last: Han

first: James

last: Moresco

first: Andy

last: Kong

first: Yu-Cheng

last: Yang

first: Zhi

last: Lu

first: John

last: Yates

last: Kim