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Generation of an oligonucleotide array for analysis of gene expression in Chlamydomonas reinhardtii

Stephan Eberhard, Monica Jain, Chung Soon Im, Steve Pollock, Jeff Shrager, Yuan Lin, Andrew S. Peek, Arthur R. Grossman
2005 Current Genetics  
The desired characteristics of microarrays (intense signals, hybridization specificity and extensive coverage of the transcriptome) were not fully met by the previous Chlamydomonas reinhardtii microarray  ...  After developing a protocol for selecting a high-quality unigene set representing all known expressed sequences, oligonucleotides were designed and a microarray with $10,000 unique array elements ($70  ...  This work was supported by NSF Grant MCB 0235878 awarded to ARG.  ... 
doi:10.1007/s00294-005-0041-2 pmid:16333659 fatcat:kwiu675nhna6texizg3kazf76u

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome

Jia Qian Wu, Jiang Du, Joel Rozowsky, Zhengdong Zhang, Alexander E Urban, Ghia Euskirchen, Sherman Weissman, Mark Gerstein, Michael Snyder
2008 Genome Biology  
We analyzed annotated known gene regions, but primarily we focused on novel transcriptionally active regions (TARs), which were previously identified by high-density oligonucleotide tiling arrays and on  ...  Results: We have interrogated the transcribed loci in 420 selected ENCyclopedia Of DNA Elements (ENCODE) regions using rapid amplification of cDNA ends (RACE) sequencing.  ...  JQ Wu is supported by NIH Ruth L Kirschstein National Research Service Award and an NIH training grant. M Snyder and M Gerstein are partially supported by the grants from the NIH.  ... 
doi:10.1186/gb-2008-9-1-r3 pmid:18173853 pmcid:PMC2395237 fatcat:tjrdkrhlxbf4zfqtttuwjsicwy

Head and neck squamous cell carcinoma transcriptome analysis by comprehensive validated differential display

A Carles, R Millon, A Cromer, G Ganguli, F Lemaire, J Young, C Wasylyk, D Muller, I Schultz, Y Rabouel, D Dembélé, C Zhao (+6 others)
2005 Oncogene  
We report here the HNSCC transcriptome that was determined by exhaustive differential display (DD) analysis coupled with validation by different methods on the same patient samples.  ...  The resulting 820 nonredundant sequences were analysed by high throughput bioinformatics analysis. Human proteins were identified for 73% (596) of the DD sequences.  ...  Macroarray blots Production of the cDNA array MAB were prepared by spotting double dots of cDNAs onto positively charged nylon membranes (Amersham).  ... 
doi:10.1038/sj.onc.1209203 pmid:16261155 fatcat:pp2xccwthvg4jfrcmoiysjmyxa

Potential pitfalls in microRNA profiling

Pauline Chugh, Dirk P. Dittmer
2012 Wiley Interdisciplinary Reviews - RNA  
post-transcriptionally influence a wide range of cellular processes such as the host response to viral infection, innate immunity, cell cycle progression, migration, and apoptosis through the inhibition of target  ...  ACKNOWLEDGMENTS This work is supported by NIH grant CA019014 to D.P.D. and P.C. is a recipient of a T32 award T32-CA009156-37.  ...  One approach is to use rigorous thresholding, by only including the 50 most abundant miRNAs in an experiment in cross-platform comparison.  ... 
doi:10.1002/wrna.1120 pmid:22566380 pmcid:PMC3597218 fatcat:5e5tvhbk4refdiwfbgi465ut6e

AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets

H. Liu, B. R. Zeeberg, G. Qu, A. G. Koru, A. Ferrucci, A. Kahn, M. C. Ryan, A. Nuhanovic, P. J. Munson, W. C. Reinhold, D. W. Kane, J. N. Weinstein
2007 Bioinformatics  
That technology is based on the concept of a probe set. Individual probes within a probe set were originally designated by Affymetrix to hybridize with the same unique mRNA transcript.  ...  About 65.6% of the probe sets on the HG-U133A chip were affected by the remapping.  ...  For example, Carter (2005) redefined Affymetrix probe sets by sequence overlap with cDNA microarray probes to reduce cross-platform inconsistencies in cancer-associated gene expression measurements.  ... 
doi:10.1093/bioinformatics/btm360 pmid:17660211 fatcat:3wko2x7qjjgq7d23styndpla7u

An improved analysis methodology for translational profiling by microarray

Thomas Sbarrato, Ruth V. Spriggs, Lindsay Wilson, Carolyn Jones, Kate Dudek, Amandine Bastide, Xavier Pichon, Tuija Pöyry, Anne E. Willis
2017 RNA: A publication of the RNA Society  
This work was funded by grants from the Medical Research Council programme (T.S., L.A.W., R.S., A.B., T.P., and A.E.W.), the Wellcome Trust (X.P.), and the Core Medical Research Council Toxicology Unit  ...  Preparation of fluorescently labeled cDNA for microarray hybridization and data analysis Microarrays used were Agilent 8×60k Human Gene Expression arrays (Agilent Technologies LDA UK Ltd.).  ...  This can be achieved by using normalization approaches that make appropriate use of within-array housekeeping genes (selected by the user), internal controls (introduced on the array), or Spike-In (added  ... 
doi:10.1261/rna.060525.116 pmid:28842509 pmcid:PMC5648029 fatcat:o4ykarb4pnhczc375tkjb6tsam

Genome-Scale Probe and Primer Design with PRIMEGENS [chapter]

Gyan Prakash Srivastava, Dong Xu
2007 Msphere  
Such design is especially useful for constructing cDNA or oligo microarray to minimize cross hybridization.  ...  PRIMEGENS can also be used for designing primers to amplify a segment of a unique target gene using RT-PCR.  ...  In cDNA microarray, typically each spot on the array contains sequence segment of a specific gene, which is amplified by PCR.  ... 
doi:10.1007/978-1-59745-528-2_8 pmid:17951795 fatcat:v5jv2z55iva6rj5aspmw6wizzq

The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont

E. Tisserant, A. Kohler, P. Dozolme-Seddas, R. Balestrini, K. Benabdellah, A. Colard, D. Croll, C. Da Silva, S. K. Gomez, R. Koul, N. Ferrol, V. Fiorilli (+29 others)
2011 New Phytologist  
We generated a set of 25 906 nonredundant virtual transcripts (NRVTs) transcribed in germinated spores, extraradical mycelium and symbiotic roots using Sanger and 454 sequencing.  ...  Our results illuminate the genetic basis of symbiosis-related traits of the most ancient lineage of plant biotrophs, advancing future research on these agriculturally and ecologically important symbionts  ...  We would like to thank Nicolas Corradi for helpful discussions on the meiotic genes, and three anonymous referees for their insightful comments and suggestions.  ... 
doi:10.1111/j.1469-8137.2011.03948.x pmid:22092242 fatcat:fy3k4hs3kbhcjhgvs727hvymry

Impact of experience-dependent and -independent factors on gene expression in songbird brain

J. Drnevich, K. L. Replogle, P. Lovell, T. P. Hahn, F. Johnson, T. G. Mast, E. Nordeen, K. Nordeen, C. Strand, S. E. London, M. Mukai, J. C. Wingfield (+6 others)
2012 Proceedings of the National Academy of Sciences of the United States of America  
The brain region from which tissue was taken had the greatest influence on gene expression profile, affecting the majority of signals measured by 18,848 cDNA spots on the microarray.  ...  The data were also analyzed using weighted gene coexpression network analysis, followed by gene ontology analysis.  ...  The SoNG Initiative was supported by Public Health Service Grant R01 NS 045264.  ... 
doi:10.1073/pnas.1200655109 pmid:23045667 pmcid:PMC3477375 fatcat:ic2lyrhajfbfnkzg4yl6pizr3a

Transcriptomes and pathways associated with infectivity, survival and immunogenicity in Brugia malayi L3

Ben-Wen Li, Amy C Rush, Makedonka Mitreva, Yong Yin, David Spiro, Elodie Ghedin, Gary J Weil
2009 BMC Genomics  
This study has improved our understanding of molecules involved in parasite invasion and immune evasion, potential targets of protective immunity, and molecules required for parasite growth and development  ...  Conclusion: Changes in gene expression that normally occur during culture under conditions that support L3 development and molting are prevented or delayed by radiation.  ...  Acknowledgements The Brugia malayi Microarray Consortium worked together to plan and finance construction of the array.  ... 
doi:10.1186/1471-2164-10-267 pmid:19527522 pmcid:PMC2708187 fatcat:wtme3tmhybbnhjuubrifk22qyi

A burst of segmental duplications in the genome of the African great ape ancestor

Tomas Marques-Bonet, Jeffrey M. Kidd, Mario Ventura, Tina A. Graves, Ze Cheng, LaDeana W. Hillier, Zhaoshi Jiang, Carl Baker, Ray Malfavon-Borja, Lucinda A. Fulton, Can Alkan, Gozde Aksay (+8 others)
2009 Nature  
As a second approach, we designed a specialized oligonucleotide microarray (1 probe/585 bp) targeted to primate SDs (Table 1 ) and performed array comparative genomic hybridization (arrayCGH) between species  ...  By this criterion, we characterized 73 Mbp corresponding to the duplications identified in at least one of the four primate species, correcting for copy number in each primate (Methods).  ...  Interspecific array comparative genomic hybridization As a second validation approach, we performed cross-species array comparative genomic hybridization to confirm lineage-specific duplications and to  ... 
doi:10.1038/nature07744 pmid:19212409 pmcid:PMC2751663 fatcat:cgmdtanbijatngqx32adfaluyu

Genetic Regulation of Gene Expression During Shoot Development in Arabidopsis

R. DeCook
2005 Genetics  
SFPs may alter the hybridization efficiency between cDNAs from one ecotype with probes of another ecotype. In genome scans, five eQTL hot spots were found with significant marker-by-gene linkages.  ...  Using oligonucleotide array data from 30 recombinant inbred lines derived from a cross of Columbia and Landsberg erecta ecotypes, the Arabidopsis genome was scanned for marker-by-gene linkages or so-called  ...  These are SFPs within the probe sets that may alter the hybridization efficiency of cDNA made from the RNA of one ecotype to the probe of another ecotype.  ... 
doi:10.1534/genetics.105.042275 pmid:15956669 pmcid:PMC1456214 fatcat:numt6ak2ojc6nk3z3pz4xzo4eu

Functional Genomics of the Chicken--A Model Organism

L. A. Cogburn, T. E. Porter, M. J. Duclos, J. Simon, S. C. Burgess, J. J. Zhu, H. H. Cheng, J. B. Dodgson, J. Burnside
2007 Poultry Science  
Functional genomics focuses on understanding the function and regulation of genes and gene products on a global or genome-wide scale.  ...  Comprehensive analysis of this large expressed sequence tag collection and a set of ∼20K full-length cDNA sequences indicate that the transcriptome of the chicken represents approximately 20,000 genes.  ...  Regardless of the delivery method, one must choose specific~19-nt targets within the gene to be silenced.  ... 
doi:10.1093/ps/86.10.2059 pmid:17878436 fatcat:hz5qfoja5befpiev7w32riwltq

The Wellcome Trust Sanger Institute

Christian Duffin
2015 Nursing Standard  
Image SAM: The Image SAM protocol washes the hybridized Sentrix™ array matrix (SAM) and images the array on the Sherlock™-1000 array scanner.  ...  The address sequences are used as probes on the universal array and have been selected to not cross hybridise with each other or with sequences in the human genome.  ...  Take a new 384 well plate and add 2µl of PCR/SAP product from row A into row A and row I, continue with 2µl of product from row B into row B and row J, and so on until 2µl have been taken out of row H  ... 
doi:10.7748/ns.29.22.30.s35 pmid:25627520 fatcat:qwoywdsh75hofiulvjys4ktzny

Summaries of National Science Foundation-Sponsored Arabidopsis 2010 Projects and National Science Foundation-Sponsored Plant Genome Projects That Are Generating Arabidopsis Resources for the Community

F. M. Ausubel
2002 Plant Physiology  
In addition, by choosing a T-DNA launching line in which the T-DNA has landed next to a small gene of interest, one can easily saturate a small, targeted region of the chromosome with transposon insertions  ...  Therefore, the MPSS sequence data provide quantitative or "digital" expression information for the entire "transcriptome," avoiding problems inherent in microarray analysis such as cross hybridization,  ...  These proteins then will be identified by mass spectrometric techniques to provide a database of Ub pathway targets.  ... 
doi:10.1104/pp.900034 fatcat:uqugi42ma5hk5fx4mge7upq5ui
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