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Accession Number: GSE18823 Platform: GPL7266: Agilent-011842 Magnaporthe grisea Oligo Microarray G4137A (Probe Name version) Organism: Magnaporthe grisea Published on 2018-01-05 Summary: The identification of genes regulated by the transcription factor Bip1 during appressorial development. The rice blast fungus Magnaporthe grisea develops melanized appressoria with high turgor pressure that inject the fungus into epidermal host cells. A screen for M. grisea non-pathogenic mutants recovered mutant M763 with reduced penetration efficiency and infectious growth. Complementation analysis identified a gene inactivated in M763 that encodes a novel basic leucine zipper (bZIP) transcription factor named Bip1 (B-ZIP Involved in Pathogenesis1). Deletion of Bip1 by targeted replacement generated non-pathogenic mutants that are unable to infect rice or barley. These mutants develop melanized appressoria that are unable to penetrate intact or wounded host leaves. Bip1 mRNA was detected in fungal spores, appressoria and infected leaves but not in mycelia, while a BIP1:GFP fusion was detected only in nuclei of mature appressoria. Genome wide transcriptome analysis identified 44 genes down regulated in Δbip1:hph appressoria. Most of these genes (77%) are specifically expressed in appressoria and encode enzymes involved in secondary metabolism (11), secreted proteins and enzymes (18) and G-Protein Coupled Receptors (GPCRs) (5). Promoters of BIP1 down-regulated genes share a similar GCN4/bZIP DNA binding motif (TGACTC). Gel shift assays showed that the motifs from 6 of the 7 promoters tested bind to recombinant BIP1 in vitro, including MGG_08381.5 from the ACE1 locus. Mutation of BIP1 binding sites in the MGG_08381.5 promoter significantly reduced its appressorium specific expression. Molecular and biochemical studies confirmed that BIP1 controls the expression of a distinct set of M. grisea genes in the appressorium, revealing a novel regulatory network involved in early stages of fungal infection that activates a diverse gene expression program resulting in a “shock and awe” impact on the plant host. Overall Design: Two condition experiment, wt P1.2 vs. delta bip1 at 24 h post-inoculation on Teflon. Three biological replicates, four technical replicates per biological replicate consisting of two slides plus two dye-swapped slides. Contact: Name: Andrew Tag Organization: Texas A&M University Laboratory: Laboratory for Functional Genomics Deparment: Biology Address: 3258 TAMU College Station TX 77843-3258 USA Email: atag@bio.tamu.edu Organization: Agilent Technologies Address: Palo Alto CA 94304 USA Email: cag_sales-na@agilent.com Phone: 877-424-4536 Web-Link: www.agilent.com
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Accession Number: GSE45979 Platform: GPL6480: Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version) GPL13359: Agilent-020097 E. coli Gene Expression Microarray (Probe Name version) Organism: Homo sapiens Published on 2018-01-05 Summary: We conducted comparative gene co-expression network (GCN) analyses of two O113:H21 STEC strains: EH41, reference strain, isolated from hemolytic-uremic syndrome patient in Australia, and Ec472/01, isolated from cattle feces in Brazil. These strains were cultured in fresh or in Caco-2 cell conditioned media. GCN analyses were also accomplished for cultured Caco-2 cells exposed to EH41 or Ec472/01. Differential transcriptome profiles for EH41 and Ec472/01 were not significantly changed by exposure to fresh or Caco-2 conditioned media. Conversely, global gene expression comparison of both strains cultured in conditioned medium revealed a gene set exclusively expressed in EH41, which includes the dicA putative virulence factor regulator. Network analysis showed that this set of genes constitutes an EH41 specific transcriptional module. The GCNs of Caco-2 cells exposed to EH41 or to Ec472/01 presented a major transcriptional module containing many hubs related to inflammatory response that was not found in the GCN of control cells. Moreover, EH41 seems to cause gene network dysregulation in Caco-2. Therefore, EH41 virulence may be derived from its capacity for dysregulating enterocyte genome functioning and its enhanced enteric survival due to slow growth. Overall Design: [EH41]: Caco-2 transcriptomic profiles after 3 hrs of interaction with STEC strain EH41 and without interaction (control) were compared in order to identify differentially expressed transcripts [EC472]: Caco-2 transcriptomic profiles after 3 hrs of interaction with STEC strain EC472/01 and without interaction (control) were compared in order to identify differentially expressed transcripts [COND]: STEC transcriptomic profiles after 3 hrs incubation in conditioned Caco-2 cell medium: STEC strain EH41 (isolated from patient with HUS) and STEc strain EC472/01 (isolated from cattle) were compared in order to identify differentially expressed transcripts [FRESH]: STEC transcriptomic profiles after 3 hrs incubation in fresh medium: STEC strain EH41 (isolated from patient with HUS) and STEc strain EC472/01 (isolated from cattle) were compared in order to identify differentially expressed transcripts Contact: Name: Carlos Alberto Moreira-Filho Organization: Faculdade de Medicina da Universidade de Sao Paulo Laboratory: LIM36 Deparment: Departments of Pediatrics Address: Av. Dr. Eneas Carvalho de Aguiar 647 Sao Paulo SP Brazil Email: carlos.moreira@hc.fm.usp.br Phone: 55-11-26618606 Organization: Agilent Technologies Address: Palo Alto CA 94304 USA Email: cag_sales-na@agilent.com Phone: 877-424-4536 Web-Link: www.agilent.com
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Accession Number: GSE66665 Platform: GPL11154: Illumina HiSeq 2000 (Homo sapiens) Organism: Homo sapiens Published on 2018-01-04 Summary: Abstract: Argonaute-2, the primary effector molecule of the RNA Induced Silencing Complex, loads both canonical miRNAs and a wide variety of other non-canonical miRNA-like species that enable base pair mediated transcript regulation. Here, using ultra-deep RNA immunoprecipitation and sequencing of nuclear and cytoplasmic hAGO2 in human breast cancer-derived MCF-7 cells, we have identified over one thousand novel AGO2-associated small RNAs. These include a wide variety of isomiRs, in excess of 100 mirtron loci and H/ACA snoRNA and HY3 repeat-derived small RNAs. Unexpectedly, we also discovered 298 AGO2-loaded exon-derived miRNAs (emiRs). These conserved small RNAs are encoded within protein-coding exons and 3’UTRs, have a 5’ end adenosine bias (in contrast to the 5’ U observed in canonical miRNAs), are DICER-1 dependent, processed from mature mRNAs post-splicing and derived from a wide variety of genes involved in differentiation and development including SOX4, JUN, c-MYC and AGO2 itself. We find evidence of emiR expression in human brain and other peripheral tissues, and demonstrate that human emiRs are conserved and detected in murine Ago2 small RNA libraries. Five human emiR loci coincide with known Mendelian disease-causing mutations, and the expression of emiRs is altered in human breast cancer, which may indicate that these species can play a role in disease etiology and progression. We propose that emiRs are the small RNA complement to the competing endogenous RNA (ceRNA) system. Overall Design: Small RNAs and AGO2-bound small RNAs and in whole cell, nuclear and cytoplasmic compartments of MCF-7 cells. Contact: Name: Selene Lizbeth Fernandez-Valverde Organization: University of Queensland Deparment: School of Biological Sciences Address: Goddard Building 8 University of Queensland Brisbane QLD Australia Email: selene.fernandez.valverde@gmail.com Organization: GEO Address: USA
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Accession Number: GSE80020 Platform: GPL19168: Illumina MiSeq (Escherichia coli K-12) Organism: Escherichia coli K-12 Published on 2018-01-03 Summary: Recently, we developed an in vivo technology to draw the interacting map of a specific small regulatory RNA (sRNA). We called it MAPS for MS2-affinity purification coupled with RNA sequencing. Using this technology, we already revealed the targetome of RyhB, RybB and DsrA, three well-characterized sRNAs in Escherichia coli. In this study, we perform MAPS with RprA sRNA. Overall Design: Identification of RNAs co-purified with MS2-RprA in a rne131 ΔrprA strain. RprA (without MS2) was used as control. Contact: Name: Eric Massé Organization: Université de Sherbrooke Laboratory: Eric Massé Lab Deparment: Biochemistry Address: 3201, Jean Mignault Sherbrooke Québec Canada Email: eric.masse@usherbrooke.ca Organization: GEO Address: USA
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Accession Number: GSE89620 Platform: GPL17021: Illumina HiSeq 2500 (Mus musculus) Organism: Mus musculus Published on 2018-01-03 Summary: By comparing Sirt6-silenced YAMC cells to siControl-transfected YAMC cells, we found that there were 916 and 1,026 differentially expressed genes in the naïve and TNF-a treatment conditions respectively. We also found that there were 302 genes that were co-expressed differentially in both naïve and TNF-a treatment conditions between Sirt6-silenced and siControl-transfected YAMC cells. Overall Design: YAMC cells were transfected with Sirt6 siRNA (siSirt6, 50 nM) and negative control siRNA (siControl, 50 nM) respectively using lipofectamine 2000. Forty-eight hours after transfections, the cells were cultured with medium containing TNFa (100 ng/mL) and medium alone respectively for additional 24 h. At the end of treatments, cells were harvested for RNA extraction followed by RNA-seq transcriptome analysis. Contact: Name: Fangyi Liu Organization: Children's research institute of Chicago Laboratory: Tan Lab Deparment: Center for Intestinal and Liver inflammation Research Address: 2430 N Halsted St Chicago IL 60614 USA Email: msliufangyi@gmail.com Organization: GEO Address: USA
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Accession Number: GSE94530 Platform: GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110) Organism: Escherichia coli str. K-12 substr. W3110 Published on 2018-01-03 Summary: Peptides have great potential to combat antibiotic resistance. While many platforms can screen peptides for their ability to bind to target cells, there are virtually no platforms that directly assess the functionality of peptides. This limitation is exacerbated when identifying antimicrobial peptides, since the phenotype, death, selects against itself, and has caused a scientific bottleneck confining research to only a few naturally occurring classes of antimicrobial peptides. We have used this seeming dissonance to develop Surface Localized Antimicrobial displaY (SLAY); a platform that allows screening of unlimited numbers of peptides of any length, composition, and structure in a single tube for antimicrobial activity. Using SLAY, we screened ~800,000 random peptide sequences for antimicrobial function and identified thousands of active sequences doubling the number of known antimicrobial sequences. SLAY hits present with different potential mechanisms of peptide action and access to areas of antimicrobial physicochemical space beyond what nature has evolved. Overall Design: As proof of concept, we used high-throughput sequencing (mi-seq) to identify a defined subset of surface expressed peptides with antimicrobial activity against E. coli. Samples include a non-induced and an 3 induced samples taken at 2, 3, and 4 hours post-induction in duplicate. Please note that the Miseq run was a much smaller set of peptides than the Hiseq run. Also the miseq run had samplings at 0, 2, 3 and 4 hours rather than just 0 and 4 hours in the Hiseq. Downstream analysis was the same. Contact: Name: Bryan Davies Organization: University of Texas at Austin Address: 2506 Speedway Austin TX 78712 USA Email: bwdavies@utexas.edu Organization: GEO Address: USA
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Accession Number: GSE107450 Platform: GPL21061: Agilent-039494 8x60k Human Whole Genome Microarray Gene expression (Probe name version) Organism: Homo sapiens Published on 2018-01-03 Summary: This microarray experiment was performed for identifying the signaling pathways that could be differentially regulated in response to changes in the pigmentation levels in human melanocytes. Melanocytes were either treated with pigmentation inducing agent or depigmenting compound targeting tyrosinase (key enzyme involved in the melanogenesis). The samples were then processed for analyzing the differentially regulated signaling pathway by performing microarray on agilent platform. The pathway enrichment analysis was executed on DAVID software. The plot has been generated using the average enrichment score for the pathways under similar category of function. Interestingly, along with the expected melanogenic and cAMP pathways, we observed differential regulation of Ca2+ signaling during pigmentation. We then performed several experiments for evaluating the contribution of cytoplasmic and endoplasmic reticulum (ER) Ca2+ homeostasis to pigmentation. After extensive studies in in vitro and in vivo pigmentation models, we demonstrate a critical role for ER Ca2+ sensor, STIM1 protein in the process of pigmentation. Taken together, we performed the microarray experiment for identifying potential pathways wherein Ca2+ homeostasis came out as one of the several hits. We then specifically studied cytoplasmic and endoplasmic reticulum (ER) Ca2+ homeostasis and identified a novel regulator of pigmentation based on several lines of evidences including in vivo model system Overall Design: Melanocytes were treated with differentially pigmenting agents Tyrosine (the substrate of pigmentation to increase pigmentation), Phenylhiourea( a inhibitor of tyrosinase enzyme involved during pigment synthesis to suppress pigment syntheis) for 48 hours in culture media. All treatments were given 24 hours post seeding the cells in T25 flasks. Contact: Name: Rajender Motiani Organization: CSIR-IGIB Laboratory: SYSTEMS BIOLOGY Deparment: SKIN BIOLOGY Address: CSIR-IGIB, SUKHDEV VIHAR, MATHURA ROAD DELHI, OPPOSITE SUKHDEV VIHAR BUS DEPOT, ADJACENT TO CRRI DELHI-110020 Delhi Delhi India Email: rajmotiani@igib.in Phone: +91-9717427369 Name: Genotypic technology Organization: Genotypic Technology Address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE Bangalore Karnataka India Email: genomics@genotypic.co.in
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Accession Number: GSE108660 Platform: GPL19612: Agilent-062918 OE Human lncRNA Microarray V4.0 028004 [Probe Name version] Organism: Homo sapiens Published on 2018-01-03 Summary: To investigate the expression profiles of long non-coding RNAs (lncRNAs) in atrial fibrillation (AF), atrial tissues from 5 AF patients and 5 non-AF patients that were collected for lncRNA expression microarray analyses to explore the role of lncRNA in the pathogenesis of AF.rhythm (SR) patients with rheumatic heart valvular disease,we have employed Overall Design: Five specimens of right auricular dextra were obtained from patients of rheumatic heart valve disease with permanent AF and with SR respectively. Expression profiling of lncRNA and mRNA were performed on SurePrint G3 Human Gene Expression 8x60K v2 Microarray, and the functions of lncRNAs were predicted by gene ontology analysis (GO analysis), kyoto Encyclopedia of Genes and Genomes analysis(KEGG analysis). Contact: Name: Peng Liu Organization: GeneBang Address: YiZhou Road 1800 ChengDu China Email: sxliulian2012@gmail.com Phone: 18030608041 Name: Feilin Cao Organization: Wenzhou Medical University Deparment: Department of Surgical Oncology, Taizhou Hospital, Address: No.150 Ximen Road Taizhou Zhejiang China Email: tzyyrjk@hotmail.com
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Accession Number: GSE106331 Platform: GPL17021: Illumina HiSeq 2500 (Mus musculus) Organism: Mus musculus Published on 2018-01-03 Summary: The ability of induced pluripotent stem cells (iPSCs) to differentiate into all adult cell types makes them attractive for basic research and regenerative medicine applications, but it remains unknown when and how this hallmark of the pluripotent state is established. Here, we pinpoint the acquisition of developmental pluripotency in a suitable reprogramming system and show that nascent iPSCs abruptly and without extensive maturation period in culture become capable of generating all tissues upon injection into preimplantation embryos. Strikingly, the developmental potential of nascent iPSCs is comparable to or even surpasses that of high-quality established pluripotent cells. Further functional assays as well as genome-wide transcriptional and chromatin analyses suggest that cells acquiring developmental pluripotency exhibit a unique combination of molecular and functional properties that distinguish them from canonical pluripotency states. These include reduced clonal self-renewal potential and the elevated expression of transcriptional regulators of postimplantation development. Our observations close an important gap in our understanding of induced pluripotency and provide an improved roadmap of cellular reprogramming with ramifications for the biomedical use of iPSCs. Overall Design: ATAC-seq cells at four stages (MEF, Stage 1 or day 6, Stage 2 or day 6+4 and established iPSCs) in triplicate. Cells (except MEFs) were sorted for Oct4-GFP+ Contact: Name: Matthias Stadtfeld Organization: NYU School of Medicine Address: 540 First Avenue Skirball Lab 4-1 New York 10016 USA Organization: GEO Address: USA
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Accession Number: GSE94531 Platform: GPL21530: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. W3110) GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110) Organism: Escherichia coli str. K-12 substr. W3110 Published on 2018-01-03 Summary: This SuperSeries is composed of the SubSeries listed below. Overall Design: Refer to individual Series Contact: Name: Bryan Davies Organization: University of Texas at Austin Address: 2506 Speedway Austin TX 78712 USA Email: bwdavies@utexas.edu Organization: GEO Address: USA
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