ライフサイエンスコーパス: paired-end

1 as for incomplete overlap among reads (e.g. paired-end).

2 y for any level up to, and including, 100 bp paired-end.

3 nstructs potential splicing paths connecting paired ends.

4 We used paired-end 101 bp reads and trimmed them to simulate dif

5 Our data set is produced using the paired-end analysis of transcription start sites (PEAT)

6 Paired-end and coverage information is used to predict S

7 ear-complete genomes, assembled de novo with paired-end and long-mate-pair (8 kb) libraries were firs

8 cing detection is unquestionably improved by paired-end and longer reads.

9 This workflow enables the analysis of both paired-end and single-end ChIP-Seq reads, with or withou

10 Also, the comprehensiveness of a paired-end approach enabled the discovery of 12 previous

11 Not only did a paired-end approach provide a greater dynamic range in c

12 ified threshold, and supplements that with a paired-end approach to identify larger variants that are

13 higher sensitivity and specificity than the paired-end approach when the inner distance between read

14 current bioinformatics tools heavily rely on paired-end approaches and overlook the importance of rea

15 urately estimate the PCR duplication rate on paired-end as well as single-end read datasets which con

16 le error-corrected sequences; it can process paired-end as well as single-end reads.

17 Users submit a bedpe (paired-end BED format) file containing the locations and

18 (BED), bedGraph and Browser Extensible Data Paired-End (BEDPE).

19 Further analysis of paired-end BES and approximately 1.0 Mb sequences from n

20 transcript connectivity information through paired-end cDNA sequencing.

21 computational analysis on a strand-specific paired-end ChIP-exo (termed as ChIP-ePENS) data of FOXA1

22 We generated 101 bps paired-end ChIP-seq data for many transcription factors

23 relative to O. sativa by combining data from paired-end clone alignments to the O. sativa reference g

24 fivefold coverage of the human genome by the paired-end clones.

25 All DKA compounds inhibited paired end complex (PEC) formation in which the nucleopr

26 eat (TIR)-specific binding and assembly of a paired end complex, and cleavage of the 5'-end of the TI

27 observed for the OE is caused by a defect in paired ends complex (PEC) formation resulting from the o

28 Crystallographic analyses of the paired-end complex (PEC) formed from precleaved transpos

29 1 A resolution crystal structure of the Mos1 paired-end complex containing the pre-cleaved left IR se

30 he catalytic domain provides a model for the paired-end complex formed between a dimer of Mos1 transp

31 hitecture of this pre-second strand cleavage paired-end complex supports our proposal that second str

32 izes all steps during NHEJ within the stable paired-end complex to limit end processing and associate

33 nd Arg(62) are required for formation of the paired ends complexes when the transposon is attached to

34 The sequencing depth of Illumina paired end data obtained with a Wolbachia capture system

35 em correlated well with that for an Illumina paired end data set used to detect LGT in Wolbachia-depl

36 es and duplicates, generates strand-specific paired-end data and is highly reproducible.

37 In addition, paired-end data were assembled and analyzed using a comm

38 the commercial software was used to assemble paired-end data, and resolved assemblies were used to pe

39 can detect fusion events in both single- and paired-end datasets from either RNA-Seq or gDNA-Seq stud

40 We illustrate PING using two paired-end datasets from Saccharomyces cerevisiae and co

41 Paired-end deep sequencing identified more than 200 de n

42 Here, we used paired-end deep sequencing of mRNA to identify genes tha

43 extension (SHAPE) chemistry with multiplexed paired-end deep sequencing of primer extension products.

44 After PCR, we applied paired-end deep sequencing to read the two barcodes and

45 sis tools, and indicated clear advantages of paired-end designs in several aspects such as alignment

46 porates various cues from read alignment and paired-end distance distribution, as well as a sequence

47 enomic fusions and breakpoints from targeted paired-end DNA sequencing data, we developed Fusion And

48 e block organization of a cancer genome from paired-end DNA sequencing data.

49 ei with a modified protocol for constructing paired-end DNA sequencing libraries to map both nucleoso

50 Here, we used a fosmid-based, paired-end DNA sequencing strategy to identify 68 full-l

51 otein-DNA complexes into the supernatant for paired-end DNA sequencing.

52 structural variant identification, including paired-end DNA sequencing/mapping and array comparative

53 Through novel statistical modeling of paired-end DNA-sequencing data using blood-derived DNA f

54 ome sequence as input and outputs artificial paired-end FASTQ files containing Phred quality scores.

55 es be ribodepleted and sequenced in a 100 bp paired end format with a minimum of 40 million reads per

56 SV) that detects SVs with high accuracy from paired-end high-throughput genomic sequencing data and p

57 By analyzing paired-end high-throughput sequence data from polytene l

58 ution that permits users to merge and filter paired end illumina reads.

59 a were assembled into c. 22,000 isotigs, and paired-end Illumina reads for phosphorus-starved (P-) an

60 We mapped nucleosome occupancy by paired-end Illumina sequencing in C. elegans embryonic c

61 Paired-end Illumina sequencing of ssDNA revealed interge

62 nd is compatible with standard and multiplex paired-end Illumina sequencing.

63 ur rounds of antigen selections by multiplex paired-end Illumina sequencing.

64 bacterial 16S ribosomal RNA was subjected to paired-end Illumina sequencing.

65 ion PCR, and interrogated by high-throughput paired-end Illumina sequencing.

66 llite loci from short sequence reads without paired-end information.

67 raph, weighted by a bin-packing strategy and paired-end information.

68 encing data, especially when they exceed the paired-end insert size.

69 without prior WGA using an NEBNext Ultra II paired-end kit, which requires a very small amount of in

70 generate high-quality large-insert (680 bp) paired-end libraries using a range of 50 pg to 50 ng of

71 The use of paired-end libraries with a fragment size shorter than t

72 Given paired-end mapped reads, and a candidate high-copy regio

73 Paired end mapping of chromosomal fragments has been use

74 We introduce high-throughput and massive paired-end mapping (PEM), a large-scale genome-sequencin

75 These paired-end mapping patterns reveal a greater diversity a

76 d been aligned, we identify and interpret 21 paired-end mapping patterns, which we validate by PCR.

77 onal methods can be adapted to identify most paired-end mapping patterns.

78 orithm (HYDRA) to localize SV breakpoints by paired-end mapping, and a general approach for the genom

79 ed to call short insertion variants based on paired-end mapping.

80 Using paired-end massively parallel sequencing of cDNA (RNA-se

81 n is choosing one based on read overlaps and paired-end (mate-pair) reads.

82 as well as next-generation sequencing with "paired-end" methods, has enabled a whole-genome analysis

83 gestion of chromatin, can be sequenced using paired-end mode next-generation technology.

84 st tumors, SnowShoes-FTD was used to analyze paired-end mRNA-Seq data from a panel of estrogen recept

85 developed for fusion transcript detection in paired-end mRNA-Seq data, employs multiple steps of fals

86 Here, we use paired-end next-generation RNA sequencing (RNA-seq) to c

87 ent to the nucleotide level within single or paired-end NGS data.

88 rger that combines the rescue and capture of paired ends of 3-kb fragments, massive 454 sequencing, a

89 g de novo assembly of massive short (90 bp), paired-end or single-end reads.

90 It aligns paired-end (PE) reads and preassembled contigs or scaffo

91 Designed for libraries of paired-end (PE) reads, GBS-SNP-CROP maximizes data usage

92 ted it to deep sequencing using the Illumina paired-end protocol and analysis using public and custom

93 age read length and the variety of available paired-end protocols.

94 enetic relationships) or the availability of paired end read libraries.

95 The RNA-seq paired-end read (PER) protocol samples transcript fragme

96 _DETECTION is able to detect DDs purely from paired-end read alignments.

97 n protocol artifacts (biotin junction reads, paired-end read contamination, chimeras, etc.) and prese

98 It provides a complementary paired-end read homology search tool to HMMER.

99 omal locations were assigned on the basis of paired-end read information and/or by RFLP mapping.

100 hes for CNV detection are primarily based on paired-end read mapping (PEM) as reported previously by

101 Second, we present a sequence-to-PRG paired-end read mapping algorithm that enables accurate

102 ce coverage overviews, variant highlighting, paired-end read mark-up, GFF3-based feature tracks and p

103 taneously uses split read signal, discordant paired-end read signal, read depth signal and the fragme

104 analyzed using a combination of single read, paired-end read, and long read RNA sequencing.

105 The paired end reads of MSLL and HMPR clones were shown to b

106 l sequence of insertion events from Illumina paired end reads.

107 upports multiplexed primer pools, single- or paired-end reads and emerging technologies that use sing

108 Our tool, BRAT, supports single and paired-end reads and handles input files containing read

109 BRAT is faster, maps more unique paired-end reads and has higher accuracy than existing p

110 ation data analysis that supports single and paired-end reads and includes a tool for estimation of m

111 Using 100 bp paired-end reads and minimal manual curation, we produce

112 are scheme for paired-end reads) for merging paired-end reads and provides users the option to qualit

113 to build 'virtual libraries' of mate pairs, paired-end reads and single-ended reads.

114 a platform, merging and quality filtering of paired-end reads are essential first steps in data analy

115 uring this stage, contigs assembled from the paired-end reads are merged into bigger chains called sc

116 t Program), which can align both single- and paired-end reads as short as 14 nt and of arbitrarily lo

117 sitioning analyses, or the ability to subset paired-end reads by groups of insert size that can conta

118 inversion breakpoints using next-generation paired-end reads derived from D. melanogaster isofemale

119 t exploited the mate constraints provided by paired-end reads from either platform to build larger co

120 end the length of short reads by overlapping paired-end reads from fragment libraries that are suffic

121 , a whole-genome shotgun (WGS) sequencing of paired-end reads from plasmids and fosmids were assemble

122 Our method transforms large numbers of paired-end reads into a much smaller number of longer 's

123 cing technology, using high-quality Illumina paired-end reads mapped onto the long reads.

124 ng to the human genome 550 million 2 x 76 bp paired-end reads per hour on a modest 12-core server, wh

125 t longer reads are more informative and that paired-end reads produce better results than single-end

126 transcriptome construction from 3.03 billion paired-end reads revealed 606,880 unique contigs annotat

127 ility by generating >30,000 Escherichia coli paired-end reads separated by 1, 2, or 3 kb using in sit

128 the African puff adder Bitis arietans using paired-end reads sequenced on Illumina's MiSeq platform.

129 entional de novo assembler and alignments of paired-end reads to assemble cyclic sequences likely to

130 We present a method for using paired-end reads to find fusion transcripts without requ

131 tal, 142.2 million uniquely mapped 64-100-bp paired-end reads were generated on the Illumina GA II yi

132 Other features include automatic support for paired-end reads with arbitrary insert sizes.

133 FiT invokes CASPER (context-aware scheme for paired-end reads) for merging paired-end reads and provi

134 mate pair orientation and insert length (for paired-end reads), sequencing coverage, read alignment a

135 nstruction by incorporating information from paired-end reads, and demonstrate its utility on simulat

136 e genomes and linkage of contigs provided by paired-end reads, as well as the ensemble of both.

137 os: it is able to handle both single-end and paired-end reads, it does not rely on the presence of ca

138 RMAP software package are tools for mapping paired-end reads, mapping using more sophisticated use o

139 m that automatically generates bidirectional paired-end reads, pinpointing the position of modified n

140 the following: whole-genome sequencing using paired-end reads, single-nucleotide polymorphism (SNP) g

141 e using massively parallel pyrosequencing of paired-end reads, that UCYN-A has a photofermentative me

142 6-50 bps), long (75-100 bps), single-end, or paired-end reads, the impact of these read parameters on

143 Tedna uses Illumina paired-end reads, the most widely used sequencing techno

144 When using short 100 bp paired-end reads, we found that using mixtures of insert

145 from both exon-exon junctions and discordant paired-end reads.

146 on sequencing platform to generate 100 bases paired-end reads.

147 put data, including both single-stranded and paired-end reads.

148 nts using comparative genome information and paired-end reads.

149 plit-read mapping within focal regions using paired-end reads.

150 ated RNA-Seq datasets, which contained 75 nt paired-end reads.

151 s for soft-masked alignments and overlapping paired-end reads.

152 rect for sequencing errors using overlapping paired-end reads.

153 named Short-Pair that is designed for short paired-end reads.

154 costs with increasing read-lengths and true paired-end reads.

155 gerprint (as k-mers) profiles of the RNA-Seq paired-end reads.

156 er long reads (longer than 100 bp) or joined paired-end reads.

157 on an Illumina Miseq, generating 20 million paired-end reads.

158 rom whole genome resequencing datasets using paired-end reads.

159 res favourably to that obtained from regular paired-end reads.

160 antly related taxa using a single library of paired-end reads: aTRAM, automated Target Restricted Ass

161 -throughput sequencing (total of 354,505,167 paired-ended reads).

162 We design an efficient algorithm, called Paired-end Reconstruction of Genome Organization (PREGO)

163 Here, we used paired end RNA sequencing (RNA-seq) to explore the trans

164 Paired-end RNA sequencing (RNA-Seq) was used to explore

165 Here, we use strand-specific paired-end RNA sequencing (ssRNA-seq) data from 376 canc

166 Analyses of 126 paired-end RNA sequencing libraries, spanning nine time

167 Here, using high-throughput, paired-end RNA sequencing, we generated an isoform-level

168 ntreated conditions) and developed tools for paired-end RNA-seq alignment and ASE analysis.

169 ective of this study was to compare parallel paired-end RNA-Seq and microarray data generated on 5-az

170 detection algorithms have been developed for paired-end RNA-seq data but their performance has not be

171 Using paired-end RNA-Seq data from breast cancer cell lines, F

172 expressed SNVs (eSNVs) from non-directional paired-end RNA-Seq data.

173 vel fusion detection tool, FusionQ, based on paired-end RNA-Seq data.

174 thod to quantify exon inclusion levels using paired-end RNA-seq data.

175 e by multifaceted analysis starting from raw paired-end RNA-seq data: gene expression levels, quality

176 tion of mRNA fragment length distribution in paired-end RNA-seq greatly improved estimation of altern

177 Performing paired-end RNA-Seq of the breast cancer cell line MCF-7

178 We applied a tailored paired-end RNA-seq protocol to specifically probe the po

179 use kallisto to analyze 30 million unaligned paired-end RNA-seq reads in <10 min on a standard laptop

180 transcripts from transcriptional analysis of paired-end RNA-seq.

181 Using a paired-end RNA-sequencing approach, we report the discov

182 e-transposon fusions in standard single- and paired-end RNA-sequencing data.

183 Using paired-end RNAseq method, we performed a transcriptome a

184 ements, such as viral genome integration, in paired-end sequence data.

185 . tularensis subsp. holarctica, we have used paired-end sequence mapping (PESM) to identify regions o

186 sassembly errors and their breakpoints using paired-end sequence reads and optical mapping data.

187 lcitrant to subcloning and suggests that the paired-end-sequenced fosmid libraries could prove to be

188 When a clone's paired end sequences fall in different contigs, the cont

189 was designed to include a high proportion of paired end sequences of various size selected inserts, f

190 A single "lane" of paired-end sequences (2 x 76 bp) provides a good synteni

191 a method to optimally map chimpanzee fosmid paired-end sequences against the human genome to systema

192 Fosmid paired-end sequences and DNA fingerprints from a query g

193 We analysed 22.9 Gb of paired-end sequences and identified and scored >3000 hig

194 ere we produce a draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC seq

195 se contigs into sequence scaffolds using the paired-end sequences derived from large-insert DNA libra

196 y, it is possible to reliably produce 300 bp paired-end sequences for RNA expression analysis.

197 High concordance between the assembly and paired-end sequences from 62,758 BAC clones provides str

198 Using paired-end sequences from bacterial artificial chromosom

199 Fosmid paired-end sequences in the WGS assembly provide anchori

200 ses of metagenomic sequence data and 600,000 paired-end sequences of bacterial 16S rRNA gene were gen

201 Paired-end sequences were assembled and used for structu

202 with a second genome (represented by fosmid paired-end sequences) to detect intermediate-sized struc

203 ng of random-primed products and (2) 2-sided paired-end sequences.

204 ranscriptome on Illumina GAIIX platform with paired end sequencing for obtaining short reads.

205 Massively parallel paired-end sequencing allowed identification of a cytoge

206 Paired-end sequencing allows circumventing the shortness

207 Using complementary experiments by capture/paired-end sequencing and FISH experiments, various type

208 Mate pair protocols add to the utility of paired-end sequencing by boosting the genomic distance s

209 Paired-end sequencing conflicts reveal differences in re

210 data, such as single-end sequencing data or paired-end sequencing data can accommodate to detect SV.

211 We apply the presented techniques to paired-end sequencing data from pancreatic tumors and co

212 pe novel Numt insertions using whole genome, paired-end sequencing data.

213 method versus those that were "observed" in paired-end sequencing data.

214 th high precision from standard, short-read, paired-end sequencing datasets.

215 Paired-end sequencing is a common approach for identifyi

216 ts in cancer genomes, and integrate aCGH and paired-end sequencing measurements of structural variant

217 An alternative paired-end sequencing method using interstrand DNA photo

218 recently developed technique, based on deep paired-end sequencing of lightly digested chromatin, to

219 xes in Saccharomyces cerevisiae, obtained by paired-end sequencing of micrococcal nuclease-resistant

220 Our genome-wide paired-end sequencing of nucleosomal DNA reveals that th

221 We have used paired-end sequencing of yeast nucleosomal DNA to obtain

222 We have shown previously, using paired-end sequencing of yeast nucleosomes, that major c

223 s from circulating memory B cells with 2x250 paired-end sequencing on the Illumina MiSeq platform.

224 16S rRNA amplicon sequencing using paired-end sequencing on the MiSeq platform from Illumin

225 oach compares the physical distances between paired-end sequencing reads of a library of a wild-type

226 riation using next-generation, short-insert, paired-end sequencing reads.

227 Paired-end sequencing revealed that single-end data unde

228 Here we use a paired-end sequencing strategy to identify somatic rearr

229 Here we describe a paired-end sequencing strategy, which enables more robus

230 Although paired-end sequencing technologies are commonly used for

231 ow sorted and sequenced by Illumina (Solexa) paired-end sequencing to an average depth of 11x or 20x,

232 nomic fusion events, we applied whole-genome paired-end sequencing to identify structural alterations

233 inverse PCR generates a jumping library for paired-end sequencing with 101-base reads.

234 lls from 3 patients for whole transcriptome, paired-end sequencing with an average depth of 112 milli

235 Methyl-MAPS (methylation mapping analysis by paired-end sequencing) method.

236 -seq (Multiplexed *OH Cleavage Analysis with paired-end sequencing) with mutate-and-map secondary str

237 ch are converted to a sequencing library for paired-end sequencing.

238 ing the genome by 112.6-fold was obtained by paired-end sequencing.

239 hen perform affinity purification of TFs and paired-end sequencing.

240 -Seq data combined with either single-end or paired-end sequencing.

241 on of chromothripsis, which was confirmed by paired-end sequencing.

242 re targeted and sampled with 454 or Illumina paired-end sequencing.

243 -CGH and may be interpreted as insertions by paired-end sequencing.

244 benefitting from the current availability of paired-end sequencing.

245 20-bp barcode is constructed, and decoded by paired-end sequencing.

246 -generation library preparation for Illumina paired-end sequencing.

247 amplicons >500 bp using Illumina short read paired-end sequencing.

248 on library in preparation for Illumina Miseq paired-end sequencing.

249 based on micrococcal nuclease digestion and paired-end sequencing.

250 e deletions and medium-sized insertions from paired-end short reads.

251 Here, we describe using the overlap of paired-end, short sequence reads to identify error-prone

252 ied EWT to the analysis of chromosome 1 from paired-end shotgun sequence data (30x) on five individua

253 ves as the read length increases with 100 bp paired-end showing the best performance.

254 However, paired-end strategies do not accurately predict precise

255 Based on chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing data, we used CRISP

256 oinformatics approach to analyze chromosomal paired-end tag (ChromPET) sequence data and demonstrate

257 We generated single-end tag (SET) and paired-end tag (PET) ChIP-Seq data for sigma(7)(0) facto

258 878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeti

259 Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) is a robust method

260 Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) is an established m

261 erformed chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) of the cohesin subu

262 n advanced chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) strategy to compreh

263 We used chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) to comprehensively

264 resolution chromatin interaction analysis by paired-end tag sequencing of P300, we observed agonist-i

265 g 4C and chromatin interaction analysis with paired-end tag sequencing), and fluorescence in situ hyb

266 hrough a chromatin interaction analysis with paired-end tagging approach using an antibody that prima

267 e original ChIA-PET protocol generates short paired-end tags (2 x 20 base pairs (bp)) to detect two g

268 ng-read ChIA-PET, in which the length of the paired-end tags is increased (up to 2 x 250 bp).

269 Using the paired-end transcriptome sequencing approach, we observe

270 ional gene fusions in cancer by evaluating a paired-end transcriptome sequencing strategy.

271 Last, we successfully used paired-end transcriptome sequencing to detect previously

272 Here we used paired-end transcriptome sequencing to explore the lands

273 Here we used paired-end transcriptome sequencing to screen ETS rearra

274 Using paired-end transcriptome sequencing, we identified recur

275 y cataloguing chimeras within a sample using paired-end transcriptome sequencing.

276 We demonstrated paired-end TSS analysis to be a powerful method to uncov

277 A extraction, optimized library preparation, paired-end WGS, and an in-house-developed bioinformatics

278 verified Hepatitis B Virus chimeras within a paired-end Whole Genome Sequencing hepatocellular carcin

279 Paired-end whole transcriptome sequencing provides evide

280 Paired-end whole-genome NGS was performed on the Illumin

281 ng non-reference TE insertions from Illumina paired-end whole-genome sequencing data.

282 called, for assembling genome sequence using paired-end whole-genome shotgun reads.