title: A calcium- and calpain-dependent pathway determines the response to lenalidomide in myelodysplastic syndromes

status: Public on Jun 08 2016

city: Columbia

first: Jing

last: Fang

state: SC

address: 715 Sumter Street

department: Drug Discovery and Biomedical Sciences

institute: University of South Carolina

summary: Despite the high response rates of individuals with myelodysplastic syndrome (MDS) with deletion of chromosome 5q (del(5q)) to treatment with lenalidomide (LEN) and the recent identification of cereblon (CRBN) as the molecular target of LEN, the cellular mechanism by which LEN eliminates MDS clones remains elusive. Here we performed an RNA interference screen to delineate gene regulatory networks that mediate LEN responsiveness in an MDS cell line, MDSL. We identified GPR68, which encodes a G-protein-coupled receptor that has been implicated in calcium metabolism, as the top candidate gene for modulating sensitivity to LEN. LEN induced GPR68 expression via IKAROS family zinc finger 1 (IKZF1), resulting in increased cytosolic calcium levels and activation of a calcium-dependent calpain, CAPN1, which were requisite steps for induction of apoptosis in MDS cells and in acute myeloid leukemia (AML) cells. In contrast, deletion of GPR68 or inhibition of calcium and calpain activation suppressed LEN-induced cytotoxicity. Moreover, expression of calpastatin (CAST), an endogenous CAPN1 inhibitor that is encoded by a gene (CAST) deleted in del(5q) MDS, correlated with LEN responsiveness in patients with del(5q) MDS. Depletion of CAST restored responsiveness of LEN-resistant non-del(5q) MDS cells and AML cells, providing an explanation for the superior responses of patients with del(5q) MDS to LEN treatment. Our study describes a cellular mechanism by which LEN, acting through CRBN and IKZF1, has cytotoxic effects in MDS and AML that depend on a calcium- and calpain-dependent pathway.

overall_design: Loss of function screen was performed with GeneNetTM Lentiviral shRNA Libraries (System Biosciences, S12XXB-1) and analyzed by GeneNet Library Data Analysis Software (System Biosciences) according to the manufacturer. Briefly, VSV-G pseudotyped lentiviral particles targeting ~47,000 transcripts in the human genome according to the NCBI RefSeq database (GRCh38.p6) were transduced into 2 x 10^6 MDSL cells with MOI at 0.5–1. Within this range, each cell that has been successfully transduced is expected to contain only one copy of a given shRNA construct. Three days post transduction, GFP+ transduced MDSL cells were purified for drug selection with DMSO or 10 μM LEN for seven days. 5 x 10^6 viable MDSL cells were then isolated for RNA extraction. After two rounds of PCR, the amplified cDNA corresponding to the unique shRNA hairpins were labeled with biotin. After removing the sense strands, the biotin-labeled antisense strands were used as hybridization targets for Human Genome U133+2.0 GeneChip® Arrays (Affymetrix, #900470). GeneNet Library Data Analysis Software (System Biosciences) was used to generate expression values for individual shRNAs by comparing the background corrected and normalized signal values for each shRNA in LEN treated and control samples. The list of enriched shRNAs was calculated based on the absolute mean difference of expression values of shRNAs in LEN versus control treated replicate samples. Only shRNAs with > 1.5-fold enrichment were further considered. P values were calculated based on the biological replicates of individual shRNA clones using Student’s t-test. To further narrow the list of hits for adjusted P values, False Discovery Rate (FDR) was applied.

first: Xiaona

last: Liu

first: Lyndsey

last: Bolanos

first: Brenden

last: Barker

first: Carmela

last: Rigolino

first: Agostino

last: Cortelezzi

first: Esther

last: Oliva

first: Maria

last: Cuzzola

first: Leighton

last: Grimes

first: Celia

last: Fontanillo

first: Kakajan

last: Komurov

first: Kyle

middle: T

last: MacBeth

first: Daniel

last: Starczynowski


title: Transcriptomic profiling of Melon necrotic spot virus-infected melon plants revealed virus strain and plant cultivar-specific alterations (cotyledons)

status: Public on Jun 07 2016

city: Murcia

first: Cristina

middle: Gómez

last: Aix

address: Campus universitario de Espinardo

country: Spain

institute: CEBAS

summary:
Viruses are among the most destructive and difficult to control plant pathogens. Melon (Cucumismelo L.) has become the model species for the agriculturally important Cucurbitaceae family. Approaches that take advantage of recently developed genomic tools in melon are being extremely useful for understanding viral pathogenesis and can contribute to the identification of target genes to breed new resistant cultivars. In this work, we have used a recently described melon microarray for transcriptome profiling of two melon cultivars infected with two strains of Melon necrotic spot virus (MNSV) that only differ on their 3´-untranslated regions. Tissues of melon plants from cultivars Out of 7566 and 7074 genes deregulated by MNSV-Mα5 and MNSV-Mα5/3’264, 1851 and 1356, respectively, were strain-specific. Likewise, MNSV-Mα5/3’264 specifically deregulated 2925 and 1618 genes in Planters Jumbo and Tendral, respectively. Thus, significantly affected GO categories were clearly different for the different virus/host combinations. Grouping genes according to their patterns of expression allowed the identification of two groups specifically deregulated by MNSV-Mα5/3’264 with respect to MNSV-Mα5 in Tendral, and one group antagonistically regulated in Planters Jumbo vs. Tendral after MNSV-Mα5/3’264 infection. Genes in these three groups belong to a diversity of functional classes, and no obvious regulatory commonalities were identified. When data on MNSV-Mα5/Tendral infections were compared to equivalent data on cucumber mosaic virus or watermelon mosaic virus infections, cytokinin-O-glucosyltransferase2 was identified as the only gene deregulated by the three viruses, with infections dynamics correlating with the amplitude of transcriptome remodeling.  Both common and strain-specific changes, as well as common but also cultivar-specific changes, have been identified by profiling transcriptomes of plants from two melon cultivars infected with two MNSV strains. No obvious regulatory features shared among deregulated genes have been identified, pointing toward regulation through differential functional implications.
Viruses are among the most destructive and difficult to control plant pathogens. Melon (Cucumismelo L.) has become the model species for the agriculturally important Cucurbitaceae family. Approaches that take advantage of recently developed genomic tools in melon are being extremely useful for understanding viral pathogenesis and can contribute to the identification of target genes to breed new resistant cultivars. In this work, we have used a recently described melon microarray for transcriptome profiling of two melon cultivars infected with two strains of Melon necrotic spot virus (MNSV) that only differ on their 3´-untranslated regions. Tissues of melon plants from cultivars Out of 7566 and 7074 genes deregulated by MNSV-Mα5 and MNSV-Mα5/3’264, 1851 and 1356, respectively, were strain-specific. Likewise, MNSV-Mα5/3’264 specifically deregulated 2925 and 1618 genes in Planters Jumbo and Tendral, respectively. Thus, significantly affected GO categories were clearly different for the different virus/host combinations. Grouping genes according to their patterns of expression allowed the identification of two groups specifically deregulated by MNSV-Mα5/3’264 with respect to MNSV-Mα5 in Tendral, and one group antagonistically regulated in Planters Jumbo vs. Tendral after MNSV-Mα5/3’264 infection. Genes in these three groups belong to a diversity of functional classes, and no obvious regulatory commonalities were identified. When data on MNSV-Mα5/Tendral infections were compared to equivalent data on cucumber mosaic virus or watermelon mosaic virus infections, cytokinin-O-glucosyltransferase2 was identified as the only gene deregulated by the three viruses, with infections dynamics correlating with the amplitude of transcriptome remodeling.  Both common and strain-specific changes, as well as common but also cultivar-specific changes, have been identified by profiling transcriptomes of plants from two melon cultivars infected with two MNSV strains. No obvious regulatory features shared among deregulated genes have been identified, pointing toward regulation through differential functional implications.

overall_design: The microarray contained 75,000 probes based on a previously validated microarray [Mascarell-Creus et al. 2009] but arranged in a modified 4-plex design, covering 17,443 melon unigenes derived from expressed sequence tags. These unigenes represent 10,649 genes in the melon genome (38% of the total predicted genes). A total of 30 cotyledons samples were submitted, hybridize and used to normalize the data.

first: C

last: Gómez-Aix

first: L

last: Pascual

first: J

last: Cañizares

first: M

middle: A

last: Sánchez-Pina

last: Aranda


title: Gene expression profile associated with a cytostatic does of mifepristone in ovarian cancer cells by microarray analysis

status: Public on Jun 09 2016

city: Vermillion

first: Kathleen

middle: M

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

country: USA

institute: University of South Dakota

summary:
Goal of the experiment:  To examine differential gene expression in three ovarian cancer cell lines in the absence and presence of mifepristone.

Brief description of the experiment:
Hypothesis:  The gene expression profile associated with a cytostatic response to Mifepristone will be similar between ovarian cancer cells regardless of their p53 status or sensitivity to Cisplatin.
Aim:  Evaluate the modifications in gene expression profile in ovarian cancer cells in response to a cytostatic concentration of Mifepristone against those in logarithmic phase of growth (Vehicle). Compare the gene expression profile of cells with different genetic backgrounds as well as between those with identical genetic backgrounds but different sensitivities to Cisplatin.
Cell Types: SKOV-3 as null p53 and semi-resistant to Cisplatin, OV2008 cells as wild type p53 and hyper-sensitive to Cisplatin , OV2008/C13 cells as wild type p53 and resistant to Cisplatin.
Conditions: Cells from three different passages were cultured in T25 flasks. The starting number of cells was 250,000 or 500,000, however cells were left to grow for 48 hr or 24 hr respectively before to start the treatment with Mifepristone 8.6 µg/ml (20 µM) or DMSO (vehicle) for 24 hr.

overall_design:
Experimental design:  Three cell lines of ovarian cancer cells were grown in culture:  SK-OV-3, OV2008, and OV2008/C13.  Three different passages of cells of each cell line were used for each treatment (vehicle control and mifepristone) (n=3).    Total RNA was extracted from ovarian cancer cells and processed for hybridization to Codelink Whole Human Genome microarrays.

Quality control steps:  The cRNA that was synthesized from each passage of each cell line was used for hybridization to a single CodeLink (Applied Microarrays, Tempe, AZ) whole human genome microarray.  Only one sample was hybridized with each slide and only one dye (Alexa 647) was used so no dye swaps were necessary.  Bacterial control spikes were used as per manufacturer's instructions.

Samples used, extract preparation and labeling:
The origin of each biological sample:  The samples were ovarian cancer cell lines.

Manipulations of biological samples and protocols used:  Cells were in log phase of growth (60-70% confluent) when treatment was initiated.  Cells were treated with vehicle (DMSO) or with 20 micromolar mifepristone for 24 hours.

Experimental factor:  treatment with vehicle or with 20 micromolar mifepristone for 24 hours

Technical protocols:  One ml TRI reagent was added to the cultured ovarian cancer cells.  Bromochloropropane and sodium acetate were added and the samples were centrifuged to separate the phases.  The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen) (Eyster and Brannian, Meth Molec Biol 2010;590:71-89).  The purity and quantity of RNA were evaluated by spectrophotometry and agarose gel electrophoresis.

	Labeled cRNA was prepared using the MessageAmp II-Biotin enhanced kit (Ambion).  1.0 microgram of total ovarian cancer cell RNA was mixed with bacterial control RNA spikes and primed with T7 oligo(dT) primer for 10 min at 70C.  (The bacterial control spikes included araB, entF, fixB, gnd, hisB, and leuB.)  The first strand of cDNA was synthesized with first strand buffer, dNTP mix, RNase inhibitor, and reverse transcriptase for 2 h at 42C.  The second strand cDNA synthesis reaction was prepared using second strand buffer, dNTP mix, DNA polymerase mix, and RNase H; the reaction was carried out for 2h at 16C.  The double-stranded cDNA was purified on QIAquick columns (Qiagen) and the eluent was dried down in a SpeedVac concentrator.  The double-stranded cDNA was resuspended in a mixture containing T7 reaction buffer, T7 ATP, T7 GTP, T7 UTP, T7 CTP, biotin-11-UTP, and T7 enzyme mix for the synthesis of cRNA.  The cRNA synthesis reaction was terminated after 14h at 37C by purifying the cRNA on RNA extraction columns.  The concentration of cRNA was determined by spectrophotometry.

Hybridization procedures and parameters:  10 micrograms of cRNA was mixed with fragmentation buffer and heated to 94C for 20 min.  The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the CodeLink Whole Human Genome microarray slides, and hybridized for 18 hours at 37C.
	The slides were washed in 0.75x TNT (Tris-HCl, NaCl, Tween-20) at 46C for 1h then incubated with streptavidin-Alexa 647 fluorescent dye for 30 min at room temperature.  The Alexa fluor was prepared in TNB blocking buffer (0.1M Tris-HCl, 0.15M NaCL, 0.5% NEN Blocking Reagent-PerkinElmer)  The slides were then washed 4 times for 5 min each in 1x TNT and twice in 0.05% Tween 20 for 5 sec each.  The slides were dried by centrifugation and scanned in an Axon GenePix 4000B scanner.

Keywords:  ovarian cancer, cell lines, mifepristone, RU486

middle: B

last: Hapon

first: Carlos

middle: D

last: Gamarra Luques

first: Eduardo

last: Callegari

first: Alicia

last: Goyeneche

last: Telleria


title: Regulation of gene expression by light in the fungus Mucor circinelloides

status: Public on Jun 06 2016

first: Victoriano

last: Garre

state: Murcia

address: Facultad de Biología. Campus de Espinardo

department: Genetics and Microbiology

institute: University of Murcia

summary: Transcriptional profiling of wild-type strain (R7B) of the fungus Mucor circinelloides comparing control mycelia grown for 18 hours in the dark with mycelia grown in the same conditions and illuminated with white light for 20 min. Goal was to identify genes regulated by a pulse of white light.

overall_design: Two-condition experiment, light-induced mycelia vs. dark-grown mycelia. Biological replicates: 3 control replicates, 3 light-induced replicates.

first: Sergio

last: López-García

first: Santiago

last: Torres-Martínez


title: microRNA analysis of infantile hemangioma, lymphatic malformation, and skin

city: Seattle

first: Graham

last: Strub

state: WA

address: 1959 NE Pacific St

institute: University of Washington

summary: Surgical specimens from children with infantile hemangioma or lymphatic malformations, as well as healthy appearing adjacent skin, were analyzed by microarray analysis of microRNA expression. Unsupervised hierarchical clustering was performed to identify microRNAs that were differentially expressed in IH compared to lymphatic malformations and skin

overall_design: 19 patients who underwent surgical excision of either a lymphatic malformation or infantile hemangioma were used in the study. 5 patients have multiple samples on the array and these duplicates are from different regions of the excised tissue or separate lesions as indicated. Tissue was snap frozen in liquid nitrogen and used for RNA extraction

first: Andrew

last: Kirsh

first: Mark

last: Whipple

first: Winston

last: Kuo

first: Rachel

last: Keller

first: Raj

last: Kapur

first: Jonathan

last: Perkins

last: Majesky


title: Gene expression analysis of cardiac-specific calreticulin transgenic mice

status: Public on Jun 03 2016

city: Edmonton

first: Marek

last: Michalak

state: Alberta

address: 87 Avenue

department: Biochemistry

country: Canada

institute: University of Alberta

summary:
Investigation of global genome gene expression changes in cardiac-spcifically overexpressed calreticulin mice in 8-10 weeks-old male mice, compared to age and gender matched control mice
The characteristics of the transgenic mice analyzed in this study are further discribed in Calreticulin Induces Dilated Cardiomyopathy, PLOS ONE 2013; 8(2): e56387

overall_design: A MM9 Expression Array (12 x 135K) chip study using total RNA isolated from the heart of three biological calreticulin transgenic mice and three biological control mice

first: Dukgyu

last: Lee


title: Characterization of aldehyde dehydrogenase 1 high ovarian cancer cells: Towards targeted stem cell therapy [FNAR-C1]

status: Public on Jun 02 2016

city: Baltimore

first: Richard

middle: J

last: Jones

state: MD

address: 1650 Orleans St.

institute: Johns Hopkins University School of Medicine

summary:
Objective: The cancer stem cell (CSC) paradigm hypothesizes that successful clinical eradication of CSCs may lead to durable remission for patients with ovarian cancer.  Despite mounting evidence in support of ovarian CSCs, their phenotype and clinical relevance remain unclear.  We and others have found high aldehyde dehydrogenase 1 (ALDHhigh) expression in a variety of normal and malignant stem cells, and sought to better characterize ALDHhigh cells in ovarian cancer.
Methods: We compared ALDHhigh to ALDHlow cells in two ovarian cancer models representing distinct subtypes: FNAR-C1 cells, derived from a spontaneous rat endometrioid carcinoma, and the human SKOV3 cell line (described as both serous and clear cell subtypes).  We assessed these populations for stem cell features then analyzed expression by microarray and qPCR.
Results: ALDHhigh cells displayed CSC properties, including: smaller size, quiescence, regenerating the phenotypic diversity of the cell lines in vitro, lack of contact inhibition, nonadherent growth, multi-drug resistance, and in vivo tumorigenicity.  Microarray and qPCR analysis of the expression of markers reported by others to enrich for ovarian CSCs revealed that ALDHhigh cells of both models showed downregulation of CD24, but inconsistent expression of CD44, KIT and CD133.  However, the following drugable targets were consistently expressed in the ALDHhigh cells from both models: mTOR signaling, her-2/neu, CD47 and FGF18 / FGFR3.
Conclusions: Based on functional characterization, ALDHhigh ovarian cancer cells represent an ovarian CSC population.  Differential gene expression identified drugable targets that have the potential for therapeutic efficacy against ovarian CSCs from multiple subtypes.

overall_design: FNAR-C1 rat ovarian cancer cells were sorted into Aldefluor high and Aldefluor low populations.  Analysis was performed in triplicate.  Aldefluor low cells served as the reference cells for fold-change analysis.

first: Allison

middle: C

last: Sharrow

first: Wayne

last: Yu


title: Human serum-derived protein removes the need for coating in defined human pluripotent stem cell culture

city: Nottingham

first: Sara

last: Pijuan-Galitó

address: University Park

department: STEM Centre for Biolomolecular Sciences

country: United Kingdom

institute: University of Nottingham

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

summary: Reliable, scalable and time-efficient culture methods are required to fully realize the clinical and industrial applications of human pluripotent stem (hPS) cells. Here we present a completely defined, xeno-free medium that supports long-term propagation of hPS cells on uncoated tissue-culture plastic. The medium consists of the Essential 8 (E8) formulation supplemented with Inter-α-inhibitor (IαI), a human serum-derived protein, recently demonstrated to activate key pluripotency pathways in mouse PS cells. IαI efficiently induces attachment and long-term growth of both embryonic and induced hPS cell lines when added as a soluble protein to the medium at seeding. IαI-supplementation efficiently supports adaptation of feeder-dependent hPS cells to xeno-free conditions, clonal growth as well as single-cell survival in the absence of Rho-associated kinase inhibitor (ROCKi). This time-efficient and simplified culture method paves the way for large-scale, high-throughput hPS cell culture, and will be valuable for both basic research and commercial applications.

overall_design: SNP genotyping with Illumina HumanOmniExpressExome-array version 8v1-2_A, encompassing >964.000 single nucleotide polymorphism (SNP)-markers, were performed by the SNP&SEQ technology Platform in Uppsala (www.genotyping.se), according to the manufacturer’s instructions. Each of the four hPS cell lines (i.e. H181, H207, HUES1 and K2C) were analyzed in three separate SNP-array experiments for the 12 samples described here. A first analysis was performed after 2-5 passages of growth for initial reference (4 samples), and subsequently, two analyses were performed per cell line after 16-21 passages in E8:VN or E8:IαI culture (8 samples). The CN-calls of the autosomal chromosomes were illustrated using the Nexus-software.

last: Pijuan-Galito

first: Christoffer

last: Tamm

first: Jens

last: Schuster

first: Maria

last: Sobol

first: Lars

last: Forsberg

first: Catherine

middle: L

last: Merry

first: Cecilia

last: Anneren

first: Tomas

last: Axelsson


title: Light and BcLTF2-dependent gene expression profiles in the phytopathogenic fungus Botrytis cinerea

status: Public on Jun 01 2016

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

country: France

institute: INRAE

summary: Full transcriptomes of the Botrytis cinerea wild-type strain B0510 and the null-mutant deltaBcLTF2, cultured in continuous darkness or submitted to a light stimulation, were compared to identify light- or/and BcLTF2-dependent genes.

overall_design: The Botrytis cinerea wild-type strain and the null-mutant deltaBcLTF2  were cultured for 54h in continuous darkness ; then, cultures were exposed for 60 min to light before harvest (L) or were harvested after additional 60 min darkness (D). 4 replicates were performed. The 12 total-RNA samples (4 conditions* 3 replicates) were used for hybridization on NimbleGen 4plex gene expression arrays (20,885 gene models from Botrytis cinerea with three 60-mer probes per gene).

first: Julia

last: Schumacher

first: Kim

last: Cohrs

last: Simon

first: Muriel

last: Viaud


title: The fission yeast Schizosaccharomyces pombe: H3K9me2, Erh1-GFP and CFP-Mmi1 ChIP-chip

status: Public on Jun 15 2016

city: Bethesda

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

type: Genome binding/occupancy profiling by genome tiling array

summary: ChIP-chip analyses of H3K9me2 (in WT, erh1∆, mmi1∆ and ccr4∆), Erh1-GFP (in WT and mmi1∆) and CFP-Mmi1 (in WT)

overall_design: H3K9me2: WT vs erh1∆, WT vs mmi1∆ and WT vs ccr4∆; Erh1-GFP: WT vs mmi1∆; CFP-Mmi1 in WT, Biological replicates: 2

first: Tomoyasu

last: Sugiyama

first: Venkata

middle: R

last: Chalamcharla

first: Gobi

last: Thillainadesan

first: Vanivilasini

last: Balachandran

first: Jothy

last: Dhakshnamoorthy

middle: I


title: In vitro proteomic expression changes in Ewing sarcoma cell lines after IGF-1R or IGF-1R/IR blockade

city: Houston

first: Joseph

middle: A.

last: Ludwig

state: Texas

department: Sarcoma Medical Oncology

institute: UT-MD-Anderson Cancer Center

summary: Ewing Sarcoma is caused by a pathognomonic genomic translocation that places an N-terminal EWSR1 gene in approximation with one of several ETS genes (typically FLI1). This aberration, in turn, alters the transcriptional regulation of more than five hundred genes and perturbs a number of critical pathways that promote oncogenesis, cell growth, invasion, and metastasis. Among them, translocation-mediated up-regulation of the insulin-like growth factor receptor 1 (IGF-1R) and mammalian  target of rapamycin (mTOR) are of particular importance since they work in concert to facilitate IGF-1R expression and ligand-induced activation, respectively, of proven importance in ES transformation. When used as a single agent in Ewing sarcoma therapy, IGF-1R or mTOR inhibition leads to rapid counter-regulatory effects that blunt the intended therapeutic purpose. Therefore, identify new mechanisms of resistance that are used by Ewing sarcoma to evade cell death to single-agent IGF-1R inhibition might suggest a number of therapeutic combinations that could improve its clinical activity.

overall_design: TC32 and TC71 ES clones with acquired resistance to OSI-906 or NVP-ADW-742 were generated by maintaining the corresponding parental cell lines with increasing concentrations of the agents (up to 2.3 μM for OSI-906, 1.5 μM for NVP-ADW-742) for 7 months. All parental and acquired drug resistant cell lines were tested twice per year for mycoplasma contamination using the MycoAlert Detection Kit (Lonza Group Ltd.) according to the manufacturer’s protocol and validated using short-tandem repeat fingerprinting with an AmpFLSTR Identifier kit as previously described. Herein, we determine subtle differences in acquired mechanism of resistance by two promising small molecule inhibitors of IGF-1R/IR-α. OSI-906, which inhibits IGF-1R and IR, and NVP-ADW-742, which inhibits only IGF-1R, were evaluated using in vitro assays to decipher the mechanism(s) by which IGF-1R inhibition induces drug resistance in Ewing sarcoma cells.  The preparation of extracted proteins from sensitive and acquired resistant Ewing sarcoma cells to OSI-906 and NVP-ADW-742 for reverse-phase protein lysate array (RPPA) analysis were prepared using the same array. Lysates were processed, spotted onto nitrocellulose-coated FAST slides, probed with 115 validated primary antibodies, and detected using a DakoCytomation-catalyzed system with secondary antibodies. MicroVigene software program (VigeneTech) was used for automated spot identification, background correction, and individual spot-intensity determination. Expression data was normalized for possible unequal protein loading, taking into account the signal intensity for each sample for all antibodies tested. Log2 values were media-centered by protein to account for variability in signal intensity by time and were calculated using the formula log2 signal – log2 median. Principal component analysis was used to check for a batch effect and feature-by-feature two-sample t-tests were used to assess differences between sensitive and resistant cell lines to drug treatments. We also used feature-by-feature one-way analysis of variance (ANOVA) followed by the Tukey test to perform pair comparisons for all groups. Beta-uniform mixture models were used to fit the resulting p value distributions to adjust for multiple comparisons. The cutoff p values and number of significant proteins were computed for several different false discovery rates (FDRs).  Biostatistical analyses comparing two groups were performed using an unpaired t-test with Gaussian distribution followed by the Welch correction. To distinguish between treatment groups, we used one-way ANOVA with the Geisser-Greenhouse correction. Differences with p values <0.05 were considered significant. Within clustered image maps (CIM), unsupervised double hierarchical clustering used the Pearson correlation distance and Ward’s linkage method as the clustering algorithm to link entities (proteins) and samples.

first: Salah-Eddine

last: Lamhamedi-Cherradi

first: Brian

last: Menegaz

first: Vandhana

last: Ramamoorthy


title: In vivo proteomic expression changes in EW5 Ewing sarcoma xenografts after IGF-1R and/or mTOR blockade

summary: Ewing Sarcoma is caused by a pathognomonic genomic translocation that places an N-terminal EWSR1 gene in approximation with one of several ETS genes (typically FLI1). This aberration, in turn, alters the transcriptional regulation of more than five hundred genes and perturbs a number of critical pathways that promote oncogenesis, cell growth, invasion, and metastasis. Among them, translocation-mediated up-regulation of the insulin-like growth factor receptor 1 (IGF-1R) and mammalian  target of rapamycin (mTOR) are of particular importance since they work in concert to facilitate IGF-1R expression and ligand-induced activation, respectively, of proven importance in ES transformation. When used as a single agent in Ewing sarcoma therapy, IGF-1R or mTOR inhibition leads to rapid counter-regulatory effects that blunt the intended therapeutic purpose. Therefore, identify new mechanisms of resistance that are used by Ewing sarcoma to evade cell death to single-agent IGF-1R or mTOR inhibition might suggest a number of therapeutic combinations that could improve their clinical activity.

overall_design: Male non-obese diabetic (NOD)-SCID-IL-2Rgnull mice were used to generate EW5 explants (2 mm). Mice bearing subcutaneous tumors were randomized into treatment and control groups when their tumors reached a diameter of 6 mm and received ridaforolimus (MK-8669, mTOR inhibitor, 5mg/kg per dose, once weekly), dalotuzumab (MK-0646, IGF-1R inhibitor monoclonal antibody, 0.5mg IP twice weekly), a placebo control (sterile buffer) or a combination of both treatments. Animals were treated either until their tumors reached 1500 mm3 in volume. RPPA profiling of EW5 xenografts treated in vivo either with MK-0646, MK-8669, control and combination and compared each other were performed simultaneously using the same array. Lysates were processed, spotted onto nitrocellulose-coated FAST slides, probed with 179 validated primary antibodies, and detected using a DakoCytomation-catalyzed system with secondary antibodies. MicroVigene software program (VigeneTech) was used for automated spot identification, background correction, and individual spot-intensity determination. Expression data was normalized for possible unequal protein loading, taking into account the signal intensity for each sample for all antibodies tested. Log2 values were media-centered by protein to account for variability in signal intensity by time and were calculated using the formula log2 signal – log2 median. Principal component analysis was used to check for a batch effect and feature-by-feature two-sample t-tests were used to assess differences between treatment and control groups. We also used feature-by-feature one-way analysis of variance (ANOVA) followed by the Tukey test to perform pair comparisons for all groups. Beta-uniform mixture models were used to fit the resulting p value distributions to adjust for multiple comparisons. The cutoff p values and number of significant proteins were computed for several different false discovery rates (FDRs).  Biostatistical analyses comparing two groups were performed using an unpaired t-test with Gaussian distribution followed by the Welch correction. To distinguish between treatment groups, we used one-way ANOVA with the Geisser-Greenhouse correction. Differences with p values <0.05 were considered significant. Within clustered image maps (CIM), unsupervised double hierarchical clustering used the Pearson correlation distance and Ward’s linkage method as the clustering algorithm to link entities (proteins or genes) and samples.


title: Altered microRNA profiles in cumulus cells isolated from PCOS patients

city: Shanghai

first: Xin

last: Huang

state: Shanghai

address: No.2699 Gaoke east road

department: Reproductive Medicine Centre

country: China

institute: Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine

summary: To identify the altered miRNA expression profiles of PCOS patients, the differentially expressed miRNAs were identified from cumulus cells of PCOS patients by comparing to that of normal women.

overall_design: Case-control study that involved 18 women with PCOS and 18 women without PCOS (control). The miRNA expression profiles of cumulus cells were identified by miRNA array.

first: Cuifang

last: Hao


title: Transcriptomic profiling of Melon necrotic spot virus-infected melon plants revealed virus strain and plant cultivar-specific alterations (leaf)

first: Cristina

last: Aix

overall_design: The microarray contained 75,000 probes based on a previously validated microarray [Mascarell-Creus et al. 2009] but arranged in a modified 4-plex design, covering 17,443 melon unigenes derived from expressed sequence tags. These unigenes represent 10,649 genes in the melon genome (38% of the total predicted genes). A total of 22 leaf samples were submitted, hybridize and used to normalize the data but only 15 were used for the analisys.

first: C

last: Gómez-Aix

first: L

last: Pascual

first: J

last: Cañizares

first: M

last: Sánchez-Pina

last: Aranda


title: Bovine  cumulus cells transcriptome in relation with oocyte chromatin configuration of the germinal vesicle

status: Public on Apr 04 2016

city: Milann

first: Cecilia

last: Dieci

address: Via Celoria 10

department: Department of Health, Animal Science and Food Safety

country: Italy

institute: University of Milan

summary: Gene expression analysis in cc from COCs with different chromatin configuration (GV0-3)

overall_design: Bovine cumulus cells (4 biological replicates) were collected and grouped according to the oocyte different chromatin configuration of the germinal vesicle described by Lodde et al. 2007. Four GV stages corresponding to the state of chromatin condensation were used (GV0; GV1; GV2 and GV3). Multiple microarray comparisons were performed. First a reference design (GV0 as a reference) was used for a total of three comparisons (GV0 vs GV1; GV0 vs GV2 and GV0 vs GV3) .

first: Valentina

last: Lodde

first: Rémi

last: Labrecque

first: Isabelle

last: Dufort

first: Marc-André

last: Sirard

first: Alberto

last: Luciano


title: Profiling ethylene-responsive genes expressed in the latex of Hevea brasiliensis using cDNA microarray

city: Danzhou

first: Zhiyi

last: Nie

state: Hainan

address: Baodao New Village

department: Rubber Research Institute

institute: Chinese Academy of Tropical Agricultural Sciences

summary: Ethylene is commonly used as a latex stimulant of Hevea brasiliensis by application of ethephon (chloro-2-ethylphosphonic acid); however, the molecular mechanism by which ethylene increases latex production is not clear. To better understand the effects of ethylene stimulation on the laticiferous cells of rubber trees, a latex expressed sequence tag (EST)-based complementary DNA microarray containing 2973 unique genes (probes) was first developed and used to analyze the latex gene expression changes at three different time-points after ethephon treatment: 8, 24 and 48 h. Transcript levels of 163 genes were significantly altered with fold-change values ≥ 2 or ≤ –2 (q-value < 0.05) in ethephon-treated compared with control rubber trees. Of the 163 genes, 92 were up-regulated and 71 down-regulated. The microarray results were further confirmed using real-time quantitative reverse transcript-PCR for 20 selected genes.

overall_design: Analysis used the 8, 24 or 48 h control latex RNA samples comparison to the ET stimulated 8, 24 or 48 h latex RNA samples.  Each sample included three independent biological replicates, and each replicate comprised the latex collected from six trees.

first: Rizhong

last: Zeng


title: In vitro proteomic expression changes in Ewing sarcoma cell lines after mTOR blockade

first: Joseph

last: Ludwig

summary: Ewing Sarcoma is caused by a pathognomonic genomic translocation that places an N-terminal EWSR1 gene in approximation with one of several ETS genes (typically FLI1). This aberration, in turn, alters the transcriptional regulation of more than five hundred genes and perturbs a number of critical pathways that promote oncogenesis, cell growth, invasion, and metastasis. Among them, translocation-mediated up-regulation of the insulin-like growth factor receptor 1 (IGF-1R) and mammalian  target of rapamycin (mTOR) are of particular importance since they work in concert to facilitate IGF-1R expression and ligand-induced activation, respectively, of proven importance in ES transformation. When used as a single agent in Ewing sarcoma therapy, IGF-1R or mTOR inhibition leads to rapid counter-regulatory effects that blunt the intended therapeutic purpose. Therefore, identify new mechanisms of resistance that are used by Ewing sarcoma to evade cell death to single-agent mTOR inhibition might suggest a number of therapeutic combinations that could improve its clinical activity.

overall_design: TC32 and TC71 ES clones with acquired resistance to ridaforolimus (MK8669, mTOR inhibitor) were generated by maintaining the corresponding parental cell lines with increasing concentrations of the agents (up to 50 μM using ridaforolimus) for 7 months. All parental and acquired drug resistant cell lines were tested twice per year for mycoplasma contamination using the MycoAlert Detection Kit (Lonza Group Ltd.) according to the manufacturer’s protocol and validated using short-tandem repeat fingerprinting with an AmpFLSTR Identifier kit as previously described. Herein, we determine subtle differences in acquired mechanism of resistance by promising small molecule inhibitor of mTOR, were evaluated using in vitro assays to decipher the mechanism(s) by which IGF-1R inhibition induces drug resistance in Ewing sarcoma cells.  The preparation of extracted proteins from sensitive and acquired resistant Ewing sarcoma cells to ridaforolimus for reverse-phase protein lysate array (RPPA) analysis were prepared using the same array. Lysates were processed, spotted onto nitrocellulose-coated FAST slides, probed with 115 validated primary antibodies, and detected using a DakoCytomation-catalyzed system with secondary antibodies. MicroVigene software program (VigeneTech) was used for automated spot identification, background correction, and individual spot-intensity determination. Expression data was normalized for possible unequal protein loading, taking into account the signal intensity for each sample for all antibodies tested. Log2 values were media-centered by protein to account for variability in signal intensity by time and were calculated using the formula log2 signal – log2 median. Principal component analysis was used to check for a batch effect and feature-by-feature two-sample t-tests were used to assess differences between sensitive and resistant cell lines to drug treatments. We also used feature-by-feature one-way analysis of variance (ANOVA) followed by the Tukey test to perform pair comparisons for all groups. Beta-uniform mixture models were used to fit the resulting p value distributions to adjust for multiple comparisons. The cutoff p values and number of significant proteins were computed for several different false discovery rates (FDRs).  Biostatistical analyses comparing two groups were performed using an unpaired t-test with Gaussian distribution followed by the Welch correction. To distinguish between treatment groups, we used one-way ANOVA with the Geisser-Greenhouse correction. Differences with p values <0.05 were considered significant. Within clustered image maps (CIM), unsupervised double hierarchical clustering used the Pearson correlation distance and Ward’s linkage method as the clustering algorithm to link entities (proteins) and samples.

first: Salah-Eddine

last: Lamhamedi-Cherradi

first: Brian

last: Menegaz

last: Ramamoorthy


title: The non-CG methylation is cell-type specific and conserved between human and mouse [Third-party reanalysis]

status: Public on Sep 01 2016

city: Beijing

first: Weilong

last: Guo

address: Intergrated Science Building

institute: Peking University

type: Methylation profiling by high throughput sequencing

summary: The non-CG methylations are abundant in several mammalian cell types, while their biological functions are largely unknown. We gathered 51 DNA methylomes in both human and mouse, covering brain neuron cells, embryonic stem (ES) and induced pluripotent stem (iPS) cells, primordial germ cells (PGC) and oocytes. Then a two-dimensional comparison on non-CG methylation was carried out across cell types and species. We employed an unbiased sub-motif prediction method and identified CW (W can be A or T) as the representative non-CG methylation context. We further showed mCW was significantly distinct from CC methylation (mCC) in both context and genomic distribution. Our studies on sequence preferences and genomic region enrichment revealed that mCW was cell-type specific and conserved between human and mouse. We reported young long interspersed nuclear elements-1 (LINE-1) elements tended to be deprived of mCW in brain for both species. Interestingly, both human Alu elements and mouse B1 elements were found to prefer high mCW at specific loci during evolution. Additionally, we reported a peak of CG methylation (mCG) at the promoter of young LINE-1 element in PGC, in contrast to the global CG demethylation. Lastly, we confirmed strand-skewed non-CG methylation in mouse ES intronic region, and showed the strand-specific distributions of mCW in LINE elements are also cell-type specific and conserved. Our findings indicate that mCW is conserved in species, dynamically regulated during development, and likely to guide the evolution of transposon elements.

sample_organism:
Homo sapiens
Mus musculus

overall_design:
In this study, 41 samples were re-aligned from raw sequencing data using BS-Seeker2.
The raw data available from the samples associated with the following Series:
GSE11034
GSE30199
GSE30206
GSE34864
GSE37202
GSE42923
GSE46644
GSE46710
GSE49828
GSE51239
GSE52331
GSE56650
GSE61330
GSE61457
GSE63394
GSE63818
The accession numbers of the re-analyzed GEO Samples (GSMnnnnn; associated with each processed data file) are indicated in the 'complete_metadata.xls'.
Please note that several raw data files are downloaded directly from SRA, DDBJ (https://trace.ddbj.nig.ac.jp), European Nucleotide Archive, and the public accession numbers for the raw data associated with each processed data file are indicated in the  'complete_metadata.xls' as well.
The 'DATA PROCESSING PIPELINE' section (in the  'complete_metadata.xls') describes the re-analysis details.

first: Michael

last: Zhang

first: Hong

last: Wu


title: MicroRNA expression profiling of CCl4-induced liver fibrosis in Mus musculus

status: Public on Mar 22 2016

city: Pusan

first: Jeongeun

last: Hyun

address: Pusandaehak-ro 63-beon gil

country: South Korea

institute: Pusan National University

summary: To investigate the differences in microRNA expression profiles between fibrotic and normal livers, we performed microRNA microarrays for total RNA extracts isolated from mouse livers treated with carbontetrachloride (CCl4) or corn-oil for 10 weeks (n=3/group). MicroRNAs were considered to have significant differences in expression level when the expression difference showed more than two-fold change between the experimental and control groups at p<0.05. We found that 12 miRNAs were differentially expressed in CCl4-induced fibrotic liver.

overall_design: To induce chronic liver fibrosis, seven-week-old mice received 0.6 ml/kg body weight of carbon-tetrachloride (CCl4) dissolved in corn-oil by intraperitoneal (i.p.) injection, twice a week for 10 weeks (n=3). As a control, same number of mice was injected with equal volume of corn-oil for 10 weeks.

first: Youngmi

last: Jung


title: Aspergillus fumigatus: Control vs. Deletion mutant

status: Public on Jun 11 2016

city: Daejeon

first: Kwang-Soo

last: Shin

department: Life Science

institute: Daejeon University

summary:
RGS protein encoding genes gprK and rgsC deletion mutant microarray
To identify the function of RGSs of A. fumigatus

overall_design: Biological replicates: WT vs. three deletion mutants, independently grown and harvested. One replicate per array

first: Jae-Hyuk

last: Yu


title: Expression analysis of the fungus Ustilago maydis WT strain FB2 (a2b2) at different pH values

status: Public on Feb 23 2016

city: Irapuato

first: José

last: Ruiz-Herrera

state: Guanajuato

address: Libramiento Norte Carretera Irapuato León Kilómetro 9.6, Carretera Irapuato León.

department: Ingeniería Genética

country: Mexico

institute: CINVESTAV, Irapuato, México

summary:
Elicidate the changes of the transcriptional program response of U. maydis WT strain (a2b2) when transfered from neutrality to acidic or alkaline medium
The mutants strains CL211 and GP25 used as controls as well as the WT strain are described in Martínez-Espinoza et al., 1997; 2004;González-Prieto et al., 2014 and Banuett & Herskowitz, 1989 respectively.

overall_design: High density-one color arrays from Nimblegen were used according to a design from Scott Gold from University of Georgia. The design has five different oligonucleotides of 60 bp in lenght in duplicate, representing each one of the 6883 gene of the U. maydis genome.

first: Juan

last: Cervantes-Montelongo

first: Elba

last: Aréchiga-Carbajal


title: Circular RNA cFUT8 acts as an epithelial–mesenchymal transition trigger in liver cancer.

status: Public on Feb 26 2016

first: Chong

last: Li

address: NO.15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: Using the highly sensitive cricRNA array, we screened 13617 circRNAs abundant in the human liver cancer and Adjacent normal liver tissues, and the function of differentially expressed circRANs were analyzed by bioinformatics. The results revealed that cFUT8 controls epithelial–mesenchymal transition in liver cancer by cFUT8/miR-548c-3p/FUT8 axis.

overall_design: In this study, three cases of liver cancer samples were used to acquire the circRNA expression profiling, and qRT-PCR was employed to confirm the results of circRNA microarrays. The functions of the differentially expressed circRNA were analyzed by bioinformatics methods. Finally, through in vivo and ex vivo experiments，the “cFUT8/miR-548c-3p/FUT8 axis” was found to control epithelial–mesenchymal transition in liver cancer


title: Prenatal exposure to bisphenol A, genistein and indole-3-carbinol on early mammary gland development and carcinogenesis in female Sprague-Dawley offspring

city: Barretos

first: Lucas

middle: Tadeu

last: Bidinotto

state: SP

address: Antenor Duarte Vilela, 1331

country: Brazil

institute: Barretos Cancer Hospital

summary: Rodent studies have indicated that gestational and perinatal bisphenol A (BPA) exposure increase the risk of developing breast cancer during adulthood. In contrast, some dietary compounds such as genistein (GEN) and indole 3-carbinol (I3C) present potential protective effects against inducing hormone-dependent cancers, including that of the mammary gland. Thus, we aimed to evaluate the role of these dietary compounds on early mammary gland development and carcinogenesis in female Sprague-Dawley offspring. Pregnant Sprague-Dawley (SD) rats were treated with BPA at 25 or 250µg/kg b.w./day by gavage from gestational day (GD) 10 to 21 with or without dietary GEN (250 mg/kg chow, ~5.5 mg/kg b.w./day) or I3C (2000 mg/kg chow, ~45.0 mg/kg b.w./day). At post-natal day (PND) 21, some female offspring from different litters were euthanized for mammary gland development and gene expression analyses while other female offspring received a single dose of N-methyl-N-nitrosourea (MNU) for mammary carcinogenesis initiation. The findings this study indicated the prenatal exposure to BPA, GEN and I3C did not significantly alter ductal elongation, number of terminal end buds (TEB) or cell proliferation, and estrogen receptor alpha (ER-α) immunostaining expression in epithelial mammary cells at PND 21. BPA treatment modulated the expression of several genes, but these changes were not associated with a dose dependent response. Dietary GEN and I3C treatment causally and consistent with the mammary gland structures outcomes. Besides, maternal BPA exposure associated with dietary GEN and I3C did not alter the susceptibility to the mammary cancer development in adulthood when the carcinogen was administered in a window of immature mammary gland development.

first: Tony

middle: F

last: Grassi

first: Glenda

middle: N

last: da Silva

first: Bruna

last: Rossi

first: Maria

last: Quinalha

first: Laura

last: Kass

first: Mónica

last: Muñoz-de-Toro

first: Luís

last: Barbisan


title: High-throughput phenotyping of lung cancer somatic mutations [main experiment]

status: Public on Jun 28 2016

city: Cambridge

first: Jesse

middle: S.

last: Boehm

address: 415 Main Street

institute: Broad Institute

summary: Recent genome sequencing efforts have identified millions of somatic mutations in cancer. However, the functional impact of most variants is poorly understood. Here we characterize 194 somatic mutations identified in primary lung adenocarcinomas using L1000 high-throughput gene-expression assays followed by expression-based variant impact phenotyping (eVIP), a method that uses gene expression changes to distinguish impactful from netural somatic mutations. This series represents the main experiment of the study where 8 replicates of wild-type and mutant ORFs are introduced into A549 cell lines.

overall_design: An ORF library containing wild-type and mutated versions of genes found to be mutated in lung cancer are introduced in A549 cell lines and measurements are made using the L1000 high-throughput gene-expression assay. These are done with 8 replicate experiemnts. The data are processed through a computational system, that converts raw fluorescence intensities into differential gene expression signatures. The data at each stage of the pre-processing are available: (LXB) - raw, unprocessed flow cytometry data from Luminex scanners. One LXB file is generated for each well of a 384-well plate, and each file contains a fluorescence intensity value for every observed analyte in the well. (Q2NORM) - gene expression profiles of directly measured landmark transcripts. Normalized using invariant set scaling followed by quantile normalization. (Z-SCORES) - signatures with differentially expressed genes computed by robust z-scores for each profile relative to control (relative to plate population as control)

first: Angela

last: Brooks

first: Alice

middle: H

last: Berger

first: Xiaoyun

last: Wu

first: Matthew

last: Meyerson

middle: S


title: A conserved factor Dhp1/Rat1/Xrn2 triggers premature transcription termination and nucleates heterochromatin to promote gene silencing [ChIP-chip]

status: Public on Jan 05 2016

first: Shiv

last: Grewal

summary:
Occupancy profiling of lysine 9 dimethylated histone H3 in fission yeast.
Occupancy profiling of Red1, Mtl1, and Mmi1 proteins in fission yeast.

overall_design: Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of  lysine 9 dimethylated histone H3, Red1, Mtl1, and Mmi1 proteins from asynchronous culture of fission yeast.

first: Venkata

last: Chalamcharla

first: H

last: Diego Folco

first: Jothy

last: Dhakshnamoorthy


title: Engineering Corynebacterium glutamicum for fast production of lysine and pipecolic acid

status: Public on Mar 30 2016

city: Bielefeld

first: Fernando

last: Pérez

state: Deutschland

address: Laue Str.

country: Germany

institute: Herr

summary: The Gram-positive soil bacterium Corynebacterium glutamicum is widely used in industrial fermentative processes for the production of amino acids. The world production of L-lysine has surpassed 2 million tons per year. Glucose is taken up into the C. glutamicum cell by the phosphotransferase system PTS which can be replaced and/or enhanced by a permease and a glucokinase. Heterologous expression of the gene for the high-affinity glucose permease from Streptomyces coelicolor and of the Bacillus subitilis glucokinase gene fully compensated for the absence of the PTS in hpr strains and strains grew as fast with glucose as C. glutamicum wild type. Growth of PTS-positive strains with glucose was accelerated when the endogenous inositol permease IolT2 and the glucokinase from Bacillus subtilis were overproduced using plasmid pEKEx3-IolTBest. When the genome-reduced C. glutamicum strain GRLys1 carrying additional in-frame deletions of sugR and ldhA to derepress glycolytic and PTS genes and to circumvent formation of L-lactate as by-product was transformed with this plasmid, a 40% higher L-lysine titer and a 30% higher volumetric productivity as compared to GRLys1(pEKEx3) resulted. The non-proteinogenic amino acid pipecolic acid (L-PA), a precursor of immunosuppressants, peptide antibiotics or piperidine alkaloids, can be derived from L-lysine. To enable production of L-PA by the L-lysine producing strain, the L-Lysine dehydrogenase gene lysDH from Silicibacter pomeroyi and the endogenous pyrroline 5-carboxylate reductase gene proC were expressed as synthetic operon. This enabled C. glutamicum to L-PA with a yield of 0.49 ± 0.03 gg-1 and a volumetric productivity of 0.04 ± 0.00 gL-1h-1.To the best of our knowledge, this is the first fermentative process for the production of L-PA.

overall_design: Two conditions tested, 200 mM NaCl Vs 200 mM pipecolic supplemented in the culture medium, control experiments done with the addition of 200mM of NaCl. Four technical replicates.

middle: P

last: García

first: Petra

last: Peters-Wendisch

first: Volker

last: Wendisch


title: C. elegans pdf-1 gene knockout effect

status: Public on Jan 04 2016

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: This study aims to quantify the effect of pdf-1 gene knockout in the nematode Caenorhabditis elegans at the RNA level. Gene expression of pdf-1 (lsc27) mutant animals is compared to wild type gene (N2) expression. RNA levels of all differentially expressed genes have been verified by means of qPCR on idependent samples.

overall_design: For each condition, four biologically independent samples of approximately 12000 young adult worms are analysed. Samples were compared in dye-swap.

first: Liesbet

last: Temmerman

first: Ellen

last: Meelkop

first: Tom

last: Janssen

first: Nick

last: Suetens

first: Liliane

last: Schoofs


title: Global miRNA expression is temporally correlated with acute kidney injury in mice

status: Public on Nov 18 2015

city: Harbin

first: Wenliang

last: Zhu

state: Heilongjiang

address: Xuefu road 194

department: 1Institute of Clinical Pharmacology

institute: The Second Affiliated Hospital of Harbin Medical University

summary: MicroRNAs (miRNAs) are negative regulators of gene expression and protein abundance. Current evidence showed implication of miRNAs in acute kidney injury (AKI) that led to obviously increased morbidity and mortality. Herein, we investigated whether miRNAs be initiative regulators showing responsibility for pathological development of AKI.

overall_design: Alteration in global miRNA expression profile was detected by miRNA microarray technique after renal bilateral ischemia reperfusion injury (IRI) surgery at 6, 12, 24, and 48 hour (n = 8 per time point). Additionally, Sham-operated mice was established as controls, which underwent the same surgical procedure without placement of the vascular clamp.


title: Bacillus licheniformis isolated from Korean traditional food resources enhances the lifespan of Caenorhabditis elegans through serotonin signaling

status: Public on Nov 05 2015

city: Jeonju

first: Younghoon

last: Kim

address: 567 Baekje-Daero, Deokjin-Gu

department: Department of Animal Science

institute: Chonbuk National University

summary:
The C. elegans lifespan in the presence of Bacillus licheniformis caused induction of a large number of genes associated with anti-aging activiy including beta-oxidation
Inaddition, these results indicate the B. licheniformis enhances the lifespan of Caenorhabditis elegans through serotonin signaling

overall_design: Two-condition experiment, C. elegans with B. lichemiformis 141 or E. coli OP50 (conrol) for 24 h. For preparing the total RNA, C. elegans were exposed to 20 mg of bacterial lawn in NGN agar for 24 h.

first: Mi

last: Park

first: Sangnam

last: Oh


title: Ciprofloxacin triggers L-glutamate production by Corynebacterium glutamicum

status: Public on Jan 26 2016

first: Dorit

last: Lubitz

address: Universitätsstraße 25

institute: University of Bielefeld

summary: Ciprofloxacin, an inhibitor of bacterial gyrase and topoisomerase IV, was shown to inhibit growth of C. glutamicum with concomitant excretion of L-glutamate. C. glutamicum strains overproducing L-lysine, L-arginine, L-ornithine, and putrescine, respectively, produced L-glutamate instead of the desired amino acid when exposed to ciprofloxacin. Even in the absence of the putative L-glutamate exporter gene yggB, ciprofloxacin effectively triggered L-glutamate production. When C. glutamicum wild type was cultivated under nitrogen-limiting conditions, 2-oxoglutarate rather than L-glutamate was produced as consequence of exposure to ciprofloxacin. Transcriptome analysis revealed that ciprofloxacin increased RNA levels of genes involved in DNA synthesis, repair and modification. Enzyme assays showed that 2-oxoglutarate dehydrogenase activity was decreased due to ciprofloxacin addition. Here, it was shown for the first time that production of L-glutamate by C. glutamicum may be triggered by an inhibitor of DNA synthesis and L-glutamate titers of up to 37 ± 1 mM and a substrate specific L-glutamate yield of 0.13 g/g were reached.

overall_design: The gene expression was analyzed in the C. glutamicum WT strain. Direct comparison and analysis of expression response to 4 µg/ml ciprofloxacin addition in CGXII minimal medium with 10 g/L glucose.


title: Insulin-Like Growth Factor Receptor 1 and Mammalian Target Of Rapamycin Blockade: Novel Mechanisms of Resistance and Synergistic Drug Combinations for Ewing Sarcoma

first: Joseph

last: Ludwig

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

overall_design: Refer to individual Series


title: The long noncoding RNA ASNR suppresses Bcl-2 mRNA degradation in apoptosis through affecting nuclei-cytoplasmic transportation of AUF1

status: Public on Nov 15 2015

first: Guifeng

last: Wei

state: Beijing

address: 15 Datun Road

summary: Many long noncoding transcripts are involved in cancer progression. Here, we utilized high-throughput microarray to compare the transcriptome alterations between the Lnc_ASNR knockdown or control in RKO cell lines. Two independent siRNAs were designed against the Lnc_ASNR cDNA sequence. Thus, we identified 111 genes which were expressionally changed. Moreover, GSEA analysis suggested apoptosis related pathway were markedly associated with Lnc_ASNR-reuglated genes. The present study indicated that Lnc_ASNR regulated specific genes in cancer progression.

overall_design: RKO cells with Lnc_ASNR knockdown and control. Three biological replicates of each condition were analyzed on Agilent microarray.

first: J

last: Chen

first: L

last: Liu

first: G

first: W

last: Wu

first: H

last: Luo

last: Yuan

first: R


title: Transcriptional profiling of C. elegans aptf-1(gk7954) mutant in pretzel-stage embryos.

status: Public on Sep 22 2015

city: Goettingen

first: Michal

last: Turek

address: Am Fassberg 11

department: Sleep and Waking

institute: Max Planck Institute for Biophysical Chemistry

summary: To investigate which genes are up- or down-regulated by aptf-1 transcription factor in C. elegans, aptf-1(gk794) mutants pretzel-stage embryos were used to performe whole genome microarray expression profiling using the C. elegans (V2) Gene Expression Microarray, 4x44K from Agilent Technologies.

overall_design: Approximately 3000 pretzel-stage embryos were used per sample. As a control we have used N2 C. elegans wild type strain. Mutant condition (aptf-1(gk794)) and control (N2) were done in four replicates.

first: Henrik

last: Bringmann

first: Gabriela

last: Salinas-Riester


title: Genome-wide maps of nuclear lamina interactions in AML12 cells.

status: Public on Nov 30 2015

first: Bo

last: Wen

address: 130 DongAn Road

department: Institutes of Biomedical Sciences

institute: Fudan University

summary: We have used microarrays to identify LaminB1 occupancy signal in AML12 cell using the DamID protocol.

overall_design: We have performed DamID-chip on AML12 cell with four biological replicates.

first: Yuhua

last: Fu

first: Feng

last: Zhang

first: Hao

first: Pin

last: Lv


title: Stress and juvenility in maize

status: Public on Oct 24 2015

city: Iowa City

first: Erin

last: Irish

state: IA

address: 129 E. Jefferson St.

department: Biology

institute: University of Iowa

summary: As maize (Zea mays) plants undergo vegetative phase change from juvenile to adult, they both exhibit heteroblasty, an abrupt change in patterns of leaf morphogenesis, and gain the ability to produce flowers.  Both processes are under the control of microRNA 156, whose levels decline at the end of the juvenile phase.  Gain of ability to flower is conferred by expression of miR156 targets that encode Squamosa Promoter-Binding (SBP) transcription factors, which when derepressed in the adult phase induce the expression of MADS-box transcription factors that promote maturation and flowering.  What gene expression differences underlie heteroblasty, as well as what regulates miR156 levels, remain open questions. Here, we compare gene expression in primordia that will develop into juvenile or adult leaves to identify genes that define these two developmental states and may influence vegetative phase change. In comparisons among successive leaves at the same developmental stage of plastochron 6, three-fourths of approximately 1,100 differentially expressed genes were more highly expressed in primordia of juvenile leaves. This juvenile set was enriched in photosynthetic genes, particularly those associated with cyclic electron flow at photosystem I, and in genes involved in oxidative stress and retrograde redox signaling. Pathogen- and herbivory-responsive pathways including jasmonic acid and salicylic acid were also up-regulated in juvenile primordia and indeed, exogenous application of jasmonic acid both delayed the appearance of adult traits and the decline of miR156 levels in maize seedlings. The successful amelioration of stress signals thus plays an important role in inducing vegetative phase change in maize.

overall_design: 12 untreated samples (8mm primordia of leaves 1-12) and 1 treated sample (leaf 5 primordium, 15mM JA treatment). 2 or more technical replicates per sample

first: E

first: B

last: Beydler


title: Identification of two mutations increasing the methanol tolerance of Corynebacterium glutamicum

status: Public on Aug 01 2015

first: Lennart

middle: Hendrik

last: Leßmeier

address: Universitätsstr. 25

institute: Bielefeld University

summary: Background: Methanol is present in most ecosystems and may also occur in industrial applications, e.g. as an impurity of carbon sources such as technical glycerol. Methanol often inhibits growth of bacteria, thus, methanol tolerance may limit fermentative production processes.   Results: The methanol tolerance of the amino acid producing soil bacterium Corynebacterium glutamicum was improved by genetic adaption in the presence of methanol. The resulting strain Tol1 exhibited significantly increased growth rates in the presence of up to 1 M methanol. However, neither transcriptional changes nor increased enzyme activities of the linear methanol oxidation pathway were observed, which was in accordance with the finding that tolerance to the downstream metabolites formaldehyde and formate was not improved. Genome sequence analysis of strain Tol1 revealed two point mutations potentially relevant to enhanced methanol tolerance: one leading to the amino acid exchange A165T of O-acetylhomoserine sulfhydrolase MetY and the other leading to shortened CoA transferase Cat (Q342*). Introduction of either mutation into the genome of C. glutamicum wild type increased methanol tolerance and introduction of both mutations into C. glutamicum was sufficient to achieve methanol tolerance almost indistinguishable from that of strain Tol1.  Conclusion: The methanol tolerance of C. glutamicum can be increased by two point mutations leading to amino acid exchange of O-acetylhomoserine sulfhydrolase MetY and shortened CoA transferase Cat. Introduction of these mutations into producer strains may be helpful when using carbon sources containing methanol as component or impurity.

overall_design: The gene expression was analyzed in the methanol tolerant strain Tol1 in comparison to the C. glutamicumWT. Direct comparison in LB complex medium and analysis of expression response to methanol addition in mCGXII minimal medium with 100 mM glucose.

first: Volker

last: Wendisch


title: miRNA profile in mice lung after influenza A infection

status: Public on Jun 22 2015

first: Meng

last: Guo

address: No. 415, Fengyang Road, Huangpu District

department: Organ transplantation center

institute: ShangHai Changzheng Hospital

summary: The regulation of host defense against influenza A viruses (IAVs) infection has attracted much attention, especially for type I interferon (IFN)-mediated innate response. Here we revealed that miR-93 expression was significantly downregulated in Alveolar epithelial type II cells (AT2) upon IAVs infection through RIG-I/JNK pathway. Inhibition of miR-93 was found to suppress host antiviral innate response by facilitating type I IFN effector signaling, and JAK1 was identified to be directly targeted by miR-93. Importantly, in vivo administration of miR-93 antagomiR significantly inhibited miR-93 expression and markedly suppressed IAVs infection, which in turn prevented the death of IAVs infected mice. Hence, the inducible downregulation of miR-93 suppress IAVs infection by upregulation IFN-JAK-STAT effector pathway, and in vivo inhibition of miR-93 bears considerable therapeutic potential for suppressing IAVs infection.

overall_design: The miRNA profiling in mice lung was measured at 24 and 36 hours after gave each mouse 50µl of influenza A (50 µl of 10-6 TCID50/µl) via retropharyngeal instillation. Three mice were performed at each time (24 or 36 hours) and RNA from different donors was mixed before determination.

first: Quanxing

last: Wang


title: Exploring the role of sigma factor gene expression on production by Corynebacterium glutamicum: sigma factor H and FMN as example

status: Public on Jun 20 2015

first: Hironori

last: Taniguchi

summary: Bacteria are known to cope with environmental changes by using alternative sigma factors binding to RNA polymerase core enzyme. Sigma factor is one of the targets to modify transcription regulation in bacteria and to influence production capacities. In this study, the effect of overexpressing all annotated sigma factor genes on C. glutamicum WT was assayed using an IPTG inducible plasmid system and different IPTG concentrations. It was revealed that growth was severely decreased when sigD or sigH were overexpressed with IPTG concentrations higher than 50 μM. Overexpression of sigH led to an obvious phenotypic change, a yellow-colored supernatant. HPLC analysis revealed that riboflavin was excreted to the medium when sigH was overexpressed and DNA Microarray analysis confirmed increased expression of riboflavin biosynthesis genes. In addition, genes for enzymes of the pentose phosphate pathway and for enzymes dependent on FMN, FAD or NADPH as cofactor were upregulated when sigH was overexpressed. To test if sigH overexpression can be exploited for production of riboflavin-derived FMN or FAD, the endogenous gene for bifunctional riboflavin kinase/FMN adenyltransferase was co-expressed with sigH from a plasmid. Balanced expression of sigH and ribF improved accumulation of riboflavin (19.8 ± 0.3 μM) and allowed for its conversion to FMN (33.1 ± 1.8 μM) in the supernatant. While a proof-of-concept was reached, conversion was not complete and titers were not high. This study revealed that inducible and gradable overexpression of sigma factor genes is an interesting approach to switch gene expression profiles and to discover untapped potential of bacteria for chemical production.

overall_design: Endogenous sigma factor gene, sigH, was overexpressed in C. glutamicum ATCC13032 from IPTG inducible vector, pEKEx3. Two different concentration of IPTG (10 μM and 15 μM) was used for induction of SigH expression.


title: Transcriptional profiling of C. elegans aptf-1(gk7954) mutant in L4 sleep stage.

summary: To investigate which genes are up- or down-regulated during L4 sleep in C. elegans mutant aptf-1(gk794) we performed whole genome microarray expression profiling using the C. elegans (V2) Gene Expression Microarray, 4x44K from Agilent Technologies.

overall_design: Approximately 200 sleeping L4 worms were used per sample. As a control we have used N2 C. elegans wild type strain. Mutant condition (aptf-1(gk794)) and control (N2) were done in four replicates.


title: Expression analysis of p53-/- and p53-/-, Ha-RasV12-transformed MEFs upon E4F1 gene inactivation

status: Public on Apr 01 2015

city: Montpellier

first: Claude

last: Sardet

address: 208 rue des Apothicaires

department: Inserm U1194 - Université de Montpellier - Institut Régional du Cancer de Montpellier (ICM)

institute: Institut de Recherche en Cancérologie de Montpellier (IRCM)

summary: E4F1 is a ubiquitously expressed zinc-finger protein of the Gli-Kruppel family that was first identified, more than 30 years ago, as a cellular target of the adenoviral oncoprotein E1A13S (Ad type V), required for transcriptional regulation of adenoviral genes. In order to identify the p53-independent program controlled by E4F1, we performed microarray analyses in p53 KO and p53 KO; Ha-RasV12-transformed mouse embryonic fibroblasts (MEFs) in wild type and E4F1-inactivated cells.

overall_design: To address p53-independent E4F1 transcriptome, a 12 chip array study has been realized using total RNA recovered from wild-type (E4F1+/flox, CRE infected; odd Samples) MEFs and E4F1-depleted (E4F1-/flox, CRE infected; even Samples) MEFs in p53-/- (Samples 1 to 12) and p53-/-, Ha-RasV12 background (Samples 13 to 24). p53-/- MEFs were derived from 13.5-day mouse embryos. Transformed p53-/- MEFs were generated by infection with a recombinant retrovirus encoding for Ha-RasV12. Three independent biological replicates of wild-type and knock-out MEFs for E4F1 have been used on the two genetic backgrounds.

first: Geneviève

last: Rodier

first: Olivier

last: Kirsh


title: Gene expression profile of C. elegans worms when mekk-3 is knocked down by RNAi

status: Public on Dec 01 2014

city: New Delhi

first: Arnab

last: Mukhopadhyay

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

summary: We have discovered a novel gene, mekk-3/idr-1, which when knocked down by RNAi dramatically increases life span. In order to understand how this gene works, we performed microarray analysis to compare the gene expression profiles of control and mekk-3/idr-1 RNAi-grown worms.

overall_design: Gene expression profile of wild type N2 worms on mekk-3/idr-1 RNAi w.r.t to control RNAi worms. Total RNA was isolated from L4 larvae. Two independent biological samples for each RNAi were analyzed.

first: Manish

last: Chamoli


title: High resolution Hi-C analysis in S. pombe reveals fundamental elements of genome architecture [ChIP-chip]

status: Public on Oct 22 2014

city: Bethesda

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

institute: NCI

summary:
ChIP-chip analyses of Psc3 in wild-type and mutant fission yeast cells.
Eukaryotic genomes are folded into three-dimensional structures that govern diverse hromosomal procsses.  Studeis in Drosophila and mammals have revealed large self-associating tomological domains whose borders are enriched in cohesin/CTCF factors that are required for long-range intrations.  However, mechanisms governing higher-order folding of chromatin fivbers and the exact function of cohesin in this process remain poor understood.  Here we perform Hi-C to explore the organization of the Schizosaccharomyces pombe genome at high-resolution, which despite its small size comprises fundamental features found in higher eukaryotes.  Our analyses reveal that in addition to determinants of Rabl-like chromosome architecture, smaller locally interacting regions of chromatin, referred to as globules, are a distinctive features of S. pombe chromosome organization.  This feature of chromatin architecture requires a function of cohesin distinct from its role in sister chromatid cohesion.  Cohesin is enriched at globule boundaries and its loss causes disruption of local globule structure and global chromosome territories.   Heterochromatin, which selectively loads cohesin at specific loci including pericentromric and subtelomeric domains, is dispensable for globule formation but uniquely impacts genome organization through chromatin compaction by enforcing Rabl configuration.

overall_design: Genome-wide distribution of Psc3 were determined by ChIP-chip analysis in wild-type and mutant fission yeast cells.

first: Takeshi

last: Mizuguchi


title: MicroRNA (miRNA) expression profile in Huh7 cells treated with siRNA targeting nuclear factor 90 (siNF90)

status: Public on Mar 31 2015

city: Nankoku

first: Shuji

last: Sakamoto

state: Kochi

address: Oko-cho, Kohasu

department: Science Research Center

country: Japan

institute: Kochi University

summary: Our previous study has showed that complex of NF90 and nuclear factor 45 (NF45) (NF90-NF45) inhibits miRNA biogenesis through negative regulation of primary-miRNA processing step. On the other hand, miRNAs, the biogenesis of which is regulated by NF90-NF45 in hepatocellular carcinoma, are not clear. Thus, to identify the miRNAs, we performed a miRNA array using RNAs extracted from control Huh7 cells and the cells depleted of NF90.

overall_design: Comparison of miRNA expression profile in one non-targeting control siRNA (siNTC)- or two independent siNF90-treated Huh7 cells.


title: Expression profiling of breast cancer samples from Institut Curie (Maire cohort) -- BrainArray CDF

status: Public on Jan 23 2015

city: PARIS

first: Thierry

last: Dubois

address: 26 rue d’Ulm

department: Recherche Center

institute: Institut Curie

summary: Transcriptome analysis of 130 breast cancer samples (41 TNBC ; 30 Her2 ; 30 Luminal B and 29 Luminal A), 11 normal breast tissue samples and 14 TNBC cell lines.

overall_design: This dataset contains 178 arrays. 153 arrays were used to analyze 130 unique breast cancer samples from as many patients and 23 technical duplicates. In addition 11 “Normal” samples from healthy breast tissue obtained from mammoplasty are included, as well as a collection of 14 breast cancer cell lines. Data production involved different array batches and hybridation series which were accounted for in the pre-processing of the data.


title: From transcriptomics to phenomics to reveal adaptation response of Lactobacillus plantarum C2 in plant substrates

status: Public on Apr 24 2015

city: BARI

first: pasquale

last: filannino

address: Via Amendola, 165/A

department: Dipartimento di Scienze del Suolo

institute: Università degli Studi di Bari “Aldo Moro”

summary: The aim of the study was to determine biological relevance of differentially expressed genes in Lactobacillus plantarum C2 during fermentation of plant substrates. Whole-transcriptome analysis based on customized microarray profiles has been used to determine altered transcription patterns in L. plantarum C2.

overall_design: L. plantarum C2 was grown (24 h at 30°C) and stored ( 21 days at 4°C) in carrot or pineapple juices to mimic the chemical composition of the respective raw matrices. De Man, Rogosa and Sharpe broth was used as the control medium for optimal growth. Samples were analyzed at the late exponential phase of growth and after storage

first: Pasquale

last: Filannino

first: Raffaella

last: Di Cagno

first: Maria

last: De Angelis

first: Marco

last: Gobbetti


title: High resolution Hi-C analysis in S. pombe reveals fundamental elements of genome architecture [microarray CGH]

department: LBMB

type: Genome variation profiling by genome tiling array

summary: Eukaryotic genomes are folded into three-dimensional structures that govern diverse hromosomal procsses.  Studeis in Drosophila and mammals have revealed large self-associating tomological domains whose borders are enriched in cohesin/CTCF factors that are required for long-range intrations.  However, mechanisms governing higher-order folding of chromatin fivbers and the exact function of cohesin in this process remain poor understood.  Here we perform Hi-C to explore the organization of the Schizosaccharomyces pombe genome at high-resolution, which despite its small size comprises fundamental features found in higher eukaryotes.  Our analyses reveal that in addition to determinants of Rabl-like chromosome architecture, smaller locally interacting regions of chromatin, referred to as globules, are a distinctive features of S. pombe chromosome organization.  This feature of chromatin architecture requires a function of cohesin distinct from its role in sister chromatid cohesion.  Cohesin is enriched at globule boundaries and its loss causes disruption of local globule structure and global chromosome territories.   Heterochromatin, which selectively loads cohesin at specific loci including pericentromric and subtelomeric domains, is dispensable for globule formation but uniquely impacts genome organization through chromatin compaction by enforcing Rabl configuration.

overall_design: microarray CGH analysis in mutant fission yeast cell; Copy number change in rad21-K1 were examined by comparative genomic hybridization analysis.


title: Heterochromatin assembly and transcriptome repression by Set1 in coordination with a class II histone deacetylase

status: Public on Dec 12 2014

city: Chestnut Hill

first: Hugh

last: Cam

state: MA

address: Higgins Hall Room 355, 140 Commonwealth Avenue

institute: Boston College

type: Genome binding/occupancy profiling by array

summary: Gene expression profiling of S. pombe set1/COMPASS/H3K4 mutants, atf1 and set1 atf1 deletion mutants, set1 clr3 deletion mutants; ChIP-chip tiling microarray profiling of S. pombe Set1, Atf1, H3K4me3 in wt/atf1 deletion mutants, H3K9me2 in wt/set1 clr3 deletion mutants

overall_design: Custom Agilent 60mer microarrays were used to assay gene expression in set1/COMPASS mutants in combination with atf1 and clr3 mutants, and to profile genome-wide binding of Set1, Atf1, H3K4me3 and H3K9me2 in S. pombe cells  (two-color mutant vs. wildtype, ChIP vs. input experiments).

first: David

last: Lorenz


title: Differential gene expression in the spleen among crossbred beef steers with divergent gain and feed intake phenotypes.

status: Public on Oct 30 2015

city: Clay Center

first: Amanda

middle: K

last: Lindholm-Perrry

state: NE

address: State Spur 18D

department: NEMRU

institute: USMARC

summary:
Steer spleen transcriptome
Evaluation of the naturally occurring transcriptome variation in the spleen among beef steers with divergent gain and feed intake phenotypes.

overall_design: The transcriptomes of the spleen were examined for expression differences that contribute to cattle feed efficiency.

last: Lindholm-Perry


title: miRNA profiles of brain glioma stem cells and normal neural stem cells

status: Public on Jul 30 2014

city: beijing

first: Shuang

last: Liu

address: Navy General Hospital PLA

institute: Navy General Hospital

summary: A human microarray comprising 1658 human genome probes was used to evaluate the specific expression of miRNA  between brian glioma stem cells (GSC) and normal neural stem cells (NSC).

overall_design:
2 total RNA samples are analyzed, brian glioma stem cells (GSC) and normal neural stem cells (NSC).
cell type: brain glioma stem cells: GSC_1, GSC_2, GSC_3 ; cell line: normal neural stem cells: NSC_1, NSC_2, NSC_3
biological replicate: NSC_1, NSC_2, NSC_3; biological replicate: GSC_1, GSC_2, GSC_3


title: C. elegans gene expression in response to Salmonella enterica infection and recovery by Tetracycline treatment

status: Public on Jul 26 2014

city: Durham

first: Brian

last: Head

state: NC

address: Box 3580 DUMC

department: Molecular Genetics and Microbiology

institute: Duke University Medical Center

summary:
(Part 1) Gene expression profiles of C. elegans in response to a 120 hour S. enterica infection. Synchronized larval stage 1 (L1) animals were exposed to S. enterica SL1344 for 36, 72, 96, or 120 hours. As an uninfected control, synchronized L1 animals were exposed to E. coli OP50 for 36 hours.
(Part 2) Gene expression profiles of C. elegans in response to Tetracycline-mediated recovery from 72 hour and 96 hour S. enterica infections. Synchronized L1 animals were exposed to S. enterica SL1344 for 72 hours and then shifted to E. coli HT115 plus Tetracycline plates for 24 hours to resolve the infection. Synchronized L1 animals were exposed to S. enterica SL1344 for 96 hours and then shifted to E. coli HT115 plus Tetracycline plates for 24 hours to resolve the infection.

overall_design: Samples include 36 hours on OP50 (36hOP), 36 hours on SL1344 (36hSL), 72 hours on SL1344 (72hSL), 96 hours on SL1344 (96hSL), 120 hours on SL1344 (120hSL), 72 hours on SL1344 plus 24 hours on HT115-Tet (96hHT), 96 hours on SL1344 plus 24 hours on HT115-Tet (120hHT). Duplicate biological samples were included for each timepoint. 14 total samples. Agilent C. elegans expression microarray (GPL14144).

first: Alejandro

last: Aballay


title: Brain glioma stem cells and normal neural stem cells

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

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

overall_design: Refer to individual Series.


title: Transcriptome profiles of brain glioma stem cells and normal neural stem cells

summary: A human cDNA microarray comprising 29,187 human genome probes was used to evaluate the transcriptional changes between brian glioma stem cells (GSC) and normal neural stem cells (NSC).

overall_design:
There were 6 samples that were analyzed, 3 samples were from glioma stem cells and the other 3 samples form normal neural stem cells were controls.
cell type: brain glioma stem cells:GSC_H004, GSC_H005, GSC_H006 ; cell line: normal neural stem cells: NSC_H001, NSC_H002, NSC_H003
biological replicate: NSC_H001, NSC_H002, NSC_H003; biological replicate: GSC_H004, GSC_H005, GSC_H006


title: Time Course of Gene Expression in the Substantia Nigra in Response to Intrastriatal 6-hydroxydopamine in the rat.

status: Public on Jun 21 2014

city: Grand Rapids

first: Jack

middle: W

last: Lipton

state: MI

address: 333 Bostwick Ave.

department: TSMM

institute: Michigan State University

summary:
The 6-hydroxydopamine (6OHDA) rat model of parkinsonism is among the first, and most commonly used, animal models of Parkinson’s disease. It provides insight into the compensatory changes that occur in the brain after dopamine (DA) neuron degeneration. In order to better define the consequences of substantia nigra DA neuron loss on the neural and glial populations during and following nigrostriatal degeneration, tissue was collected and evaluated from the substantia nigra of 6OHDA or vehicle treated, or naïve rats at 1, 2, 4, 6 & 16 weeks.
Comprehensive gene expression analysis was conducted to detect significant differences in gene expression. Comparisons were conducted within the same treatment groups over time as well as across treatments within the same post-treatment interval. Longitudinal expression patterns were parsed using a k-means clustering algorithm as a method for finding patterns indicative of neuronal loss, upregulation in response to lesion or surgical damage exclusive of lesion.

overall_design: Tissue was collected from the substantia nigra of 6OHDA treated, sham and naïve rats at 1, 2, 4, 6 & 16 weeks post-treatment.  A unilateral striatal lesion was employed that results in a 99% striatal DA reduction and an 80% loss of DA neurons in the substantia nigra.  6OHDA lesions were confirmed via catecholamine quantitation by HPLC. RNA integrity was assessed with an Agilent 2100 Bioanalyzer with minimum RIN acceptance criteria of 8.0. Multidimensional plots and Pearson Correlations were used to establish group/treatment homogeneity.  Tissue was subjected to comprehensive gene expression analysis using the Affymetrix Rat Gene 1.0ST array.

first: Timothy

last: Collier

first: Nicholas

middle: M

last: Kanaan

first: Allyson

last: Cole-Strauss

first: Caryl

middle: E

last: Sortwell

first: Kathy

middle: A

last: Steece-Collier

first: Fredric

last: Manfredsson

first: Zachary

last: Mattingly

first: Emeline

middle: G

last: Tolod-Kemp


title: Yeast X-Chromosome Associated Protein 5 (Xap5) Functions with H2A.Z to Suppress Aberrant Transcripts [ChIP-chip]

status: Public on Jul 01 2014

city: Davis

first: Shajahan

last: Anver

state: CA

address: 1002 LSA, One Shields Av

department: Plant Biology

institute: University of California Davis

summary: Comparison of occupancy profiling of Xap5 and H2A.Z/Pht1 in fission yeast.

overall_design: Agilent 60mer array was used to analyze DNA recovered by chromatin immunoprecipitation of Xap5 from fission yeast culture.

first: Assen

last: Roguev

first: Martin

last: Zofall

first: Nevan

middle: J

last: Krogan

first: Shiv

last: Grewal

first: Stacey

middle: L

last: Harmer


title: Expression Profiles of Primary Mouse Hepatocytes treated with Cyclosporin A and solvent control [miRNA]

status: Public on Jul 24 2014

city: Maastricht

first: Wim

last: Van den Hof

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

summary: The microRNA changes induced in Primary Mouse Hepatocytes of C57Bl6-mice by Cyclosporin A after treatment for 24h and 48h

overall_design: The study investigated differential microRNA expression in Primary Mouse Hepatocytes following 24 and 48 hours of exposure to Cyclosporin A and solvent. Three biological replicates per compound/six per solvent. In total 24 arrays .


title: Caenorhabditis elegans N2: Control vs. Lysinibacillus sphaericus-fed

status: Public on Apr 01 2014

city: Seoul

first: Junhyeok

last: Go

address: Sinchon-dong, Seodaemun-gu

institute: Yonsei university

summary: Transcriptional profiling of Caenorhabditis elegans comparing control E. coli OP50-fed C. elegans with L. sphaericus-fed C. elegans

overall_design: Two-condition experiment,  E. coli OP50-fed C. elegans vs. L. sphaericus-fed C. elegans

first: Sang

last: Yoon


title: Expression profiling of microRNAs in Bovine ovarian follicular development

status: Public on Jun 15 2014

city: Midlothian

first: Xavier

last: Donadeu

address: Easter Bush

institute: Roslin Institute, University of Edinburgh

summary: The study aimed to identify miRNAs expression profiles associated with growth and regression of dominant-size follicles in bovine. Follicles and corpora lutea (CL, from days 1 to 4 of the estrous cycle) were collected from abattoir ovaries and their status (healthy/atretic) was assessed by measuring steroid levels and aromatase expression. Total RNA was isolated from whole follicles at different developmental stages and from CL. An heterologous microarray (Exiqon, Denmark) approach followed by RT-qPCR validation (Qiagen, UK) was used to identify and compare miRNA profiles between large healthy follicles (diameter, 13–16 mm, n=6) and each of small (4–8 mm, n=6 pools of follicles), large atretic folllicles (13-16 mm, n=6) and CL (n=6) . RNA from the above groups was hybridized to the miRCURY LNA™ microRNA Hi-Power Labeling Kit,Hy3™/Hy5™ (Exiqon) and hybridized on the miRCURY LNA™ microRNA Array (6th gen).  A total of 17 and 57 microRNAs were differentially expressed (> 2 fold, adj. P-value < 0.05) between Large Healthy and each of Small and Large Atretic follicles, respectively, a fraction of which corresponded to registered bovine miRNA sequences.  A subset of 5 bovine miRNAs (miR-144, miR-202,vmiR-451, miR-652, miR-873) were confirmed by qPCR to be upregulated in Large Healthy follicles, were enriched in mural granulosa cells and their predicted targets mapped to genes involved in follicular cell proliferation and differentiation, suggesting an involvemet of this subset of microRNAs in ovarian follicle development. Moreover, a total of 11 and 22 unique miRNAs were up- and down-regulated, respectively (≥ 2.5 fold; adjusted P-value < 0.01), in corpora lutea relative Large Healthy follicles, including an upregulated cluster, miR-183-96-182, which was shown to be involved in luteal cell proliferation and steroidogenesis

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Six biological replicates per developmental stage (total of 24 samples) were used in a double dye microRNA microarray experiment. Samples were distributed among slides so that each experimental group was represented at least once in each slide. For each gene, mean normalized intensities (n= 6 biological replicates/group) were compared between follicle stages (SF vs LHF, LHF vs LAF and LHF vs CL).

first: F

middle: X

first: Sadanand

middle: D

last: Sontakke


status: Public on May 01 2014

city: College Station

first: Luis

middle: Humberto

last: Reyes

address: 3122 TAMU

department: Chemical Engineering

institute: Texas A&M University

summary:
Transcriptome analysis of isolated hyper-producer carotenoids mutants obtained via adaptive evolution.  Transcriptome of isolated strains was compared with the ancestral strain as reference.
To emulate evolution experiments, the cells were grown in YPD until late-exponential phase.

overall_design: Three biological replicas of 4 samples vs reference (sample SM12 contains 4 replicas).  Location of the samples in the two microarrays are described below.

first: Katy

middle: C

last: Kao

first: Jose

last: Gomez


title: miRNAs regulated by Gadd45a during somatic cell reprogramming

status: Public on Apr 22 2014

city: Guangzhou

first: Keshi

last: Chen

address: 190 Kai Yuan Avenue

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Science

summary: Gadd45a can enhance somatic cell reprogramming significantly. To explore the roles of  Gadd45a playing in reprogramming, we performed miRNA microarray to identify miRNAs and signals pathways that regulated by Gadd45a.

overall_design: miRNAs expression of MEFs was measured at day8 in reprogramming. Four samples were set: MEFs infected with SKO plus Flag, MEFs infected with SKO plus Gadd45a, MEFs infected with SKOM plus Flag and MEFs infected with SKOM+Ga.

first: Qi

last: Long

first: Xingguo

last: Liu


title: Expression Profiles of Primary Mouse Hepatocytes treated with Cyclosporin A and solvent control

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

overall_design: Refer to individual Series


title: Rif1 regulates initiation timing of late replication origins throughout the S. cerevisiae genome [array]

status: Public on Jun 01 2014

city: Los Angeles

first: Jared

last: Peace

state: CA - California

address: 1050 Childs Way RRI 203

department: Molecular and Computational Biology

institute: University of Southern California

summary: Chromosomal DNA replication involves the coordinated activity of hundreds to thousands of replication origins.  Individual replication origins are subject to epigenetic regulation of their activity during S-phase, resulting in differential efficiencies and timings of replication initiation during S-phase.  This regulation is thought to involve chromatin structure and organization into timing domains with differential ability to recruit limiting replication factors.  Rif1 has recently been identified as a genome-wide regulator of replication timing in fission yeast and in mammalian cells.  However, previous studies in budding yeast have suggested that Rif1’s role in controlling replication timing may be limited to subtelomeric domains and derives from its established role in telomere length regulation.  We have analyzed replication timing by analyzing BrdU incorporation genome-wide, and report that Rif1 regulates the timing of late/dormant replication origins throughout the S. cerevisiae genome.  Analysis of pfa4∆ cells, which are defective in palmitoylation and membrane association of Rif1, suggests that replication timing regulation by Rif1 is independent of its role in localizing telomeres to the nuclear periphery.  Intra-S checkpoint signaling is intact in rif1∆ cells, and checkpoint-defective mec1∆ cells do not comparably deregulate replication timing, together indicating that Rif1 regulates replication timing through a mechanism independent of this checkpoint.  Our results indicate that the Rif1 mechanism regulates origin timing irrespective of proximity to a chromosome end, and suggest instead that telomere sequences merely provide abundant binding sites for proteins that recruit Rif1.  Still, the abundance of Rif1 binding in telomeric domains may facilitate Rif1-mediated repression of non-telomeric origins that are more distal from centromeres.

overall_design:
30 total samples: (6 samples - BrdU- HU arrest 45min with 2 replicates, strains: WT, rif1 delta, pfa4 delta) (12 samples -S-phase BrdU time course with 2 replicates at 25 and 35 min, strains: WT, rif1 delta, mec1_100)
(12 samples - S-phase BrdU time course with 2 replicates at 25 and 35 min, strains: sml1 delta, sml1 delta rif1 delta, sml1 delta mec1 delta)

first: Anna

last: Ter-Zakarian

first: Oscar

last: Aparicio


title: Estrogen-like activity and dual roles in cell signaling of brefeldin A

status: Public on Jan 01 2014

city: Tokyo

first: zhu

last: yun

address: takanawa 4-21-12

institute: scinet company

summary: Comparing the expression profiles of the genes in response to 17b-estradiol (E2) and brefeldin A (BFA)

overall_design: Two-condition experiment, E2- or BFA-treated vs. control cells. Two biological replicates, independently grown and harvested. Two replicates per array.

first: Yun

last: Zhu

first: Ryoiti

last: Kiyama


title: Comparison of Gametocyte producer 3D7-A subclone E5 to the gametotcyte nonprodcer strain F12 and pfap2-g deletion mutant

status: Public on Nov 06 2013

city: New York

first: Bjorn

middle: FC

last: Kafsack

state: NY

address: 1300 York Avenue

department: Microbiology & Immunology

institute: Weill Cornell Medicine

summary: Identify differentially expressed genes across the 48h intraerythrocytic development cycle of gametocyte non-producers of P. falcuparum

overall_design: two-color comparison to a common labeled reference pool

middle: F

first: Manuel

last: Llinas


title: Estrogen-like activity and dual roles in cell signaling of an Agaricus blazei Murrill mycelia-dikaryon extract

summary: Comparing the expression profiles of the genes in response to 17b-estradiol (E2) and Agaricus blazei extract (ABE)

overall_design: Two-condition experiment, E2- or ABE-treated vs. control cells. 2 to 3 biological replicates, independently grown and harvested. Two to three replicates per array.


title: Transcriptome profiling of Lactococcus garvieae strains in response to growth temperature

status: Public on Nov 04 2013

city: Madrid

first: Mónica

last: Aguado-Urda

address: Avda. Puerta de Hierro s/n

department: Animal Health

institute: Complutense University of Madrid

summary: Analysis of the changes in the transcriptome of two different Lactococcus garvieae strains (21881 & 8831) at different temperatures of growth (18/37 ºC)

overall_design: Reference design experiment  comparing samples of 21881 and 8831 strains of Lactoccocus garvieae, with three biological replicates for each condition grown at 18 and 37 degrees Celsius. The results were referenced to a equimolar mixture of both strains grown at 29 degrees Celsius

first: Monica

first: Alicia

last: Gibello

first: Maria

last: Blanco

first: Victoria

last: Lopez-Alonso

last: Fernández-Garayzabal

first: Guillermo

middle: H

last: Lopez-Campos


title: Effects of TNF-alpha blocking in sorted Th17 cells from co-cultures of human CD4-positive and CD14-positive cells

status: Public on Nov 01 2013

city: Måløv

first: Klaus Stensgaard

last: Frederiksen

address: Novo Nordisk Park F9.1.07

department: Molecular Genetics

country: Denmark

institute: Novo Nordisk A/S

summary: Human CD4+ T cells and CD14+ monocytes from healthy donors were co-cultured with anti-CD3 for three days in the presence or absence of TNF-alpha mAb (Adalimumab). Classical Th17 cells (Th17) or those generated in the presence of the inhibitor (iTh17) were then sorted and analyzed by full transcriptome microarray analysis.

overall_design: A total of 18 samples consisting of paired samples from 9 healthy volunteers were compared. Sorted Th17 cells from co-cultures containing either Adalimumab (1 microgram/ml) or not were obtained from each of the donors, and compared by full transcriptome profiling.

first: Klaus

middle: S

first: Hayley

last: Evans

first: Leonie

last: Taams