Abstract：
:Multiplexed high-throughput pyrosequencing is currently limited in complexity (number of samples sequenced in parallel), and in capacity (number of sequences obtained per sample). Physical-space segregation of the sequencing platform into a fixed number of channels allows limited multiplexing, but obscures available sequencing space. To overcome these limitations, we have devised a novel barcoding approach to allow for pooling and sequencing of DNA from independent samples, and to facilitate subsequent segregation of sequencing capacity. Forty-eight forward-reverse barcode pairs are described: each forward and each reverse barcode unique with respect to at least 4 nt positions. With improved read lengths of pyrosequencers, combinations of forward and reverse barcodes may be used to sequence from as many as n(2) independent libraries for each set of 'n' forward and 'n' reverse barcodes, for each defined set of cloning-linkers. In two pilot series of barcoded sequencing using the GS20 Sequencer (454/Roche), we found that over 99.8% of obtained sequences could be assigned to 25 independent, uniquely barcoded libraries based on the presence of either a perfect forward or a perfect reverse barcode. The false-discovery rate, as measured by the percentage of sequences with unexpected perfect pairings of unmatched forward and reverse barcodes, was estimated to be <0.005%.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Parameswaran P,Jalili R,Tao L,Shokralla S,Gharizadeh B,Ronaghi M,Fire AZdoi
10.1093/nar/gkm760subject
Has Abstractpub_date
2007-01-01 00:00:00pages
e130issue
19eissn
0305-1048issn
1362-4962pii
gkm760journal_volume
35pub_type
杂志文章abstract：:EcoRI digestion of total mouse DNA yields a prominant 1.3 kb fragment amounting to between 1 and 2% of the mouse genome. The majority of the 1.3 kb EcoRI fragments have a single Bg1II site 800 bp from one end. This EcoRI-Bg1II sequence family shows HindIII and HaeIII sequence heterogeneity. We have cloned representati...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.21.5031
更新日期：1980-11-11 00:00:00
abstract：:Base excision repair (BER), which is initiated by DNA N-glycosylase proteins, is the frontline for repairing potentially mutagenic DNA base damage. The NTHL1 glycosylase, which excises DNA base damage caused by reactive oxygen species, is thought to be a tumor suppressor. However, in addition to NTHL1 loss-of-function...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky162
更新日期：2018-05-18 00:00:00
abstract：:We examined the 3'-flanking regions required for accurate 3'-end formation of wheat histone H3 mRNA using gene expression in transformed sunflower cells. The introduction of mutations into the conserved sequence AATGGAAATG in the 3'-flanking region of plant histone genes, located 22 bp upstream from the polyadenylatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.6.1052
更新日期：1994-03-25 00:00:00
abstract：:The RNA Editing Database (REDIdb) is an interactive, web-based database created and designed with the aim to allocate RNA editing events such as substitutions, insertions and deletions occurring in a wide range of organisms. The database contains both fully and partially sequenced DNA molecules for which editing infor...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl793
更新日期：2007-01-01 00:00:00
abstract：:The gene for human apolipoprotein (apo) A-II has been isolated from a human genomic DNA library. The cloned fragment was approximately 14 kilobase-pair (kb) long, and extended about 9.0 kb upstream as well as 3.5 kb downstream from the apoA-II gene, which was contained within a 3.1 kb HindIII fragment of human DNA. Th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.12.4597
更新日期：1985-06-25 00:00:00
abstract：:The RNA of a deleted strain (lacking Src gene) of an avian sarcoma virus (ASV) was examined by a newly developed immunoelectron microscopic procedure which uses anti-nucleotide antibodies as probes. After denaturation of the RNA and reaction with a high affinity, highly specific anti-7-methylguanosine-5'-phosphate (an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.19.4485
更新日期：1980-10-10 00:00:00
abstract：:The HIV RT and Protease Sequence Database is an online relational database that catalogs evolutionary and drug-related human immunodeficiency virus (HIV) reverse transcriptase (RT) and protease sequence variation (http://hivdb.stanford.edu). The database contains a compilation of nearly all published HIV RT and protea...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.1.346
更新日期：2000-01-01 00:00:00
abstract：:Next-generation sequencing allows now the sequencing of small RNA molecules and the estimation of their expression levels. Consequently, there will be a high demand of bioinformatics tools to cope with the several gigabytes of sequence data generated in each single deep-sequencing experiment. Given this scene, we deve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp347
更新日期：2009-07-01 00:00:00
abstract：:Digestion of isolated Friend erythroleukemic cell nuclei with DNase I under conditions which selectively destroy the DNA of transcriptionally "active" genes releases into the supernatant fraction proteins of the non-histone "High Mobility Group" (HMGs). Two of these, HMG-14 and HMG-17(identified by solubility in trich...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.9.1947
更新日期：1980-05-10 00:00:00
abstract：:Reliable prediction of orthology is central to comparative genomics. Approaches based on phylogenetic analyses closely resemble the original definition of orthology and paralogy and are known to be highly accurate. However, the large computational cost associated to these analyses is a limiting factor that often preve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq953
更新日期：2011-03-01 00:00:00
abstract：:Scanning tunneling microscopy (STM) reveals nanometer scale details of hydrated DNA but the interpretation of the images is controversial because of substrate artifacts and the lack of a theory for image contrast. We demonstrate that we have overcome these problems by identifying five DNA samples by their STM images a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.25.5896
更新日期：1993-12-25 00:00:00
abstract：:DNA strand exchange, the central step of homologous recombination, is considered to occur approximately independently of DNA sequence content. However, certain prokaryotic and eukaryotic genomic loci display either an enhanced or reduced frequency of genetic exchange. Here we show that the Homo sapiens DNA strand exch...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl355
更新日期：2006-05-24 00:00:00
abstract：:Saccharomyces cerevisiae Pif1 (ScPif1) is known as an ATP-dependent DNA helicase that plays critical roles in a number of important biological processes such as DNA replication, telomere maintenance and genome stability maintenance. Besides its DNA helicase activity, ScPif1 is also known as a single-stranded DNA (ssDN...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz541
更新日期：2019-08-22 00:00:00
abstract：:The detailed conformational features and dynamics of the naturally occurring deoxyribotrinucleoside diphosphates d-TpTpT and d-TpTpC have been investigated at 20 degrees C and 80 degrees C in aqueous solution by nuclear magnetic resonance spectroscopy. The observed NMR parameters indicate that the conformational prope...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.11.4399
更新日期：1978-11-01 00:00:00
abstract：:The entire intervening sequence of Tetrahymena thermophila ribosomal DNA has been determined. It is 413 nucleotides long and has the same splice junctions as those in T. pigmentosa. There is 93% homology between the intervening sequences in the two species, and 100% homology between their adjacent 26S RNA coding regio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.9.2809
更新日期：1982-05-11 00:00:00
abstract：:Apolipoprotein B (apoB) mRNA editing is a nuclear event that minimally requires the RNA substrate, APOBEC-1 and APOBEC-1 Complementation Factor (ACF). The co-localization of these macro-molecules within the nucleus and the modulation of hepatic apoB mRNA editing activity have been described following a variety of meta...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl417
更新日期：2006-07-04 00:00:00
abstract：:Escherichia coli mRNA translation is facilitated by sequences upstream and downstream of the initiation codon, called Shine-Dalgarno (SD) and downstream box (DB) sequences, respectively. In E.coli enhancing the complementarity between the DB sequences and the 16S rRNA penultimate stem resulted in increased protein acc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.4.970
更新日期：2001-02-15 00:00:00
abstract：:The 338.5 kb of the Escherichia coli genome described here together with previously described segments bring the total of contiguous finished sequence of this genome to > 1 Mb. Of 319 open reading frames (ORFs) found in this 338.5 kb segment, 147 (46%) are potential new genes. The positions of several genes which had ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.12.2105
更新日期：1995-06-25 00:00:00
abstract：:One of the most intensively studied chromatin binding factors is HP1α. HP1α is associated with silenced, heterochromatic regions of the genome and binds to H3K9me3. While H3K9me3 is necessary for HP1α recruitment to heterochromatin, it is becoming apparent that it is not sufficient suggesting that additional factors a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky632
更新日期：2018-10-12 00:00:00
abstract：:Using circular dichroism spectroscopy, UV absorption spectroscopy and polyacrylamide gel electrophoresis, we studied conformational properties of guanine-rich DNA strands of the fragile X chromosome repeats d(GGC)n, d(GCG)n and d(CGG)n, with n = 2, 4, 8 and 16. These strands are generally considered in the literature ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh179
更新日期：2004-01-12 00:00:00
abstract：:The side chains of the 20 types of amino acids, owing to a large extent to their different physical properties, have characteristic distributions in interior/surface regions of individual proteins and in interface/non-interface portions of protein surfaces that bind proteins or nucleic acids. These distributions have ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm231
更新日期：2007-07-01 00:00:00
abstract：:A 30 nt RNA with a sequence designed to form an intramolecular triple helix was analyzed by one-and two-dimensional NMR spectroscopy and UV absorption measurements. NMR data show that the RNA contains seven pyrimidine-purine-pyrimidine base triples stabilized by Watson-Crick and Hoogsteen interactions. The temperature...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.14.2841
更新日期：1996-07-15 00:00:00
abstract：:Yeast tRNA Val 1 alkylation with 2', 3'-O-4-(N-2-chloroethyl-N-methylamino) benzylidene d(pC-G)-A proceeds at 20 degrees - 30 degrees C in the complementary complexes which are formed by d(pC-G)-A greater than RC1 binding to 3 sequences of tRNA Val 1 : psi-C-G58 in the T loop, C-G40 at the 3'-side of the anticodon loo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.5.1609
更新日期：1977-01-01 00:00:00
abstract：:The molecular structure of the DNA double helix has been known for 60 years, but we remain surprisingly ignorant of the balance of forces that determine its mechanical properties. The DNA double helix is among the stiffest of all biopolymers, but neither theory nor experiment has provided a coherent understanding of t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt808
更新日期：2013-12-01 00:00:00
abstract：:PKR is a doubled-stranded RNA-dependent protein kinase which is implicated in the regulation of several cellular processes, including cell proliferation. PKR undergoes phosphorylation and activation in mouse embryonic 3T3-F442A cells in response to endogenous RNA(s). Activation of PKR is related to growth and differen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.13.2672
更新日期：1997-07-01 00:00:00
abstract：:In order to facilitate the direct computation of the sizes of DNA fragments separated by gel electrophoresis, we have written and evaluated programmes for the Hewlett-Packard 41C programmable calculator. The sizes estimated for DNA fragments of known length using some of these programmes were found to be more accurate...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.1part2.845
更新日期：1984-01-11 00:00:00
abstract：:A study of the activity of deoxyribonucleotide-substituted analogs of the hammerhead domain of RNA catalysis has led to the design of a 14mer oligomer composed entirely of deoxyribonucleotides that promotes the cleavage of an RNA substrate. Characterization of this reaction with sequence variants and mixed DNA/RNA oli...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.20.4092
更新日期：1995-10-25 00:00:00
abstract：:A simple and efficient method is described to introduce structurally pre-determined mutations into recombinant genomes of filamentous phage M13. The method rests on gapped duplex DNA (gdDNA) molecules of the phage M13 genome as the key intermediate. In this gdDNA, the (+) and the (shorter) (-) strand carry different g...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.24.9441
更新日期：1984-12-21 00:00:00
abstract：:DNA restriction fragments located 5' to the human c-myc gene display anomalous electrophoretic mobility on polyacrylamide gels. Computer modeling of the c-myc flanking DNA suggests that the slow-moving DNA fragments spanning nucleotides -1690 to -1054 (relative to c-myc promoter P1) and -718 to -452 form large left ha...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.7.2819
更新日期：1989-04-11 00:00:00
abstract：:Dramatic improvements in ribozyme mimics have been achieved by employing the principles of small molecule catalysis to the design of macromolecular, biomimetic reagents. Ribozyme mimics derived from the ligand 2,9-dimethylphenanthroline (neocuproine) show at least 30-fold improvements in efficiency at sequence-specifi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.10.2199
更新日期：2001-05-15 00:00:00
