ライフサイエンスコーパス: ChIA-PET

1 ChIA-PET is a high-throughput mapping technology that re

2 ChIA-PET is rapidly emerging as an important experimenta

3 This unique feature allows ChIA-PET to provide the functional specificity and highe

4 n (ChIP) and chromatin interaction analysis (ChIA-PET), we determined genome-wide SOX2-bound regions

5 P-seq, GRO-seq, STARR-seq, RNA-seq, Hi-C and ChIA-PET data in five human cancer cell lines, we identi

6 reported by Hi-C, promoter capture Hi-C and ChIA-PET experiments and in capturing previously validat

7 n from publicly available datasets (Hi-C and ChIA-PET), and correlated activity links that we infer a

8 on capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome

9 capture (3C) technologies, such as Hi-C and ChIA-PET, have the potential to elucidate the functional

10 enced individuals with LCL-specific Hi-C and ChIA-PET-based chromatin contact maps to uncover one of

11 n proximity-ligation assays, like HiChIP and ChIA-PET, facilitate the accurate identification of long

12 matin binding data in mammary cell lines and ChIA-PET chromatin interaction data from ENCODE, we iden

13 tested on 12 ChIP-seq, ATAC-seq, RNA-seq and ChIA-PET datasets, pyBedGraph is on average 260 times fa

14 sequencing experiments such as ChIP-seq and ChIA-PET that generate coverage files for transcription

15 bined DNaseI hypersensitivity, ChIP-seq, and ChIA-PET technologies to map the promoter-enhancer inter

16 Data interpretation from assays such as ChIA-PET and Hi-C is challenging because the data is lar

17 atin interaction data from protocols such as ChIA-PET, HiChIP and Hi-C provide valuable insights into

18 vailability of orthogonal data types such as ChIA-PET, HiChIP, Capture Hi-C, and high-throughput imag

19 oter capture Hi-C and Hi-Cap data as well as ChIA-PET data from mouse embryonic stem cells to investi

20 RNA polymerase II-associated ChIA-PET data reveal that many groups of MIRs and protei

21 Application of Mango to multiple available ChIA-PET datasets permitted the independent rediscovery

22 by learning the latent relationships between ChIA-PET and two widely used data types: Hi-C and ChIP-s

23 models with contact frequencies observed by ChIA-PET and Hi-C genomic-driven methods to examine the

24 hput assays, including 3C, 4C-Seq, 5C, Hi-C, ChIA-PET and Capture-C.

25 ghly concordant with those detected by Hi-C, ChIA-PET and eQTL analyses at 200 bp resolution.

26 7ac, DNase-seq/ATAC-seq, P300, POLR2A, CAGE, ChIA-PET, GRO-seq, STARR-seq and MPRA).

27 Here, we use ESC cohesin ChIA-PET data to identify the local chromosomal structur

28 sin-associated CTCF-CTCF loops using cohesin ChIA-PET data.

29 We present Mango, a complete ChIA-PET data analysis pipeline that provides statistica

30 hIA-ET in GM12878 and HeLa but also non-CTCF ChIA-PET interactions, including RNA polymerase II (RNAP

31 Current ChIA-PET analysis software packages either fail to corre

32 ors, whole-genome bisulfite sequencing data, ChIA-PET data, and functional data in several biosamples

33 ds of ChIA-PET data generated from different ChIA-PET protocols and also provides quality controls fo

34 We applied ChIA-PET2 to different ChIA-PET datasets, demonstrating its significantly impro

35 ted in the estrogen receptor alpha (ERalpha) ChIA-PET data.

36 lidation of these predictions using existing ChIA-PET and Hi-C data sets showed that RIPPLE accuratel

37 ChIA-PET2 integrates all steps required for ChIA-PET data analysis, including linker trimming, read

38 present Model based Interaction Calling from ChIA-PET data (MICC), an easy-to-use R package to detect

39 3CPET does so by combining data from ChIA-PET, transcription factor binding sites, and protei

40 IAPoP, to detect chromatin interactions from ChIA-PET data.

41 ackage to detect chromatin interactions from ChIA-PET sequencing data.

42 ping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of inter

43 ion factor cooperativity within recent human ChIA-PET enhancer-promoter interaction data.

44 romatin structure data and RNA polymerase II ChIA-PET data from MCF-7 cells did not suggest remote ef

45 Here, we combine proximity ligation in ChIA-PET and transposase accessibility in ATAC-seq into

46 tin interactions using proximity ligation in ChIA-PET, Hi-C, and their derivatives.

47 s, including a hypergeometric model (used in ChIA-PET tool), MICC (used in ChIA-PET2), ChiaSig and ma

48 A subset, of which independent ChIA-PET data are available, is validated to be RNAPII-,

49 interactions through deeper and integrative ChIA-PET data analysis and demonstrates DNA looping pred

50 We leverage ChIA-PET and ChIA-Drop chromatin interaction assays to c

51 High-throughput experiments like ChIA-PET have been developed to map such largely cell-ty

52 High-throughput technologies like ChIA-PET, Hi-C, and their derivatives methods have great

53 e Hi-C and ChIP-seq data, there are not many ChIA-PET datasets available in the literature.

54 e trained our deep models with CTCF-mediated ChIA-PET of GM12878 as ground truth, and the deep networ

55 The main goal of ChIA-PET data analysis is to detect interactions between

56 It supports different kinds of ChIA-PET data generated from different ChIA-PET protocol

57 This multilevel nature of ChIA-PET data offers an opportunity to use multiscale 3D

58 ides quality controls for different steps of ChIA-PET analysis.

59 equirement over 100-fold relative to that of ChIA-PET.

60 le pipeline for analyzing different types of ChIA-PET data from raw sequencing reads to chromatin loo

61 dations for users working with HiChIP and/or ChIA-PET analyses.

62 ur predictions were supported by Hi-C and/or ChIA-PET experiments.

63 tions, which were undetected in the original ChIA-PET paper but were validated by other independent e

64 The original ChIA-PET protocol generates short paired-end tags (2 x 2

65 omparison to the existing software packages, ChIA-PET Tool and ChiaSig revealed that Mango interactio

66 is based on paired-end tag sequencing (PolII ChIA-PET) suggests that this effect is genome wide.

67 earning approach that can accurately predict ChIA-PET interactions by learning the latent relationshi

68 stent with Cohesin extrusion and can predict ChIA-PET CTCF looping interaction measurements with high

69 mputational method for accurately predicting ChIA-PET interactions from Hi-C and ChIP-seq data is nee

70 another computational method for predicting ChIA-PET from Hi-C but using random forests.

71 nce as well as its ability to easily process ChIA-PET raw data.

72 o executes all steps required for processing ChIA-PET datasets, whereas ChiaSig only completes 20% of

73 STACHE recovers a higher number of published ChIA-PET and HiChIP loops as well as loops linking promo

74 user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specif

75 M12878, RAD21 ChIA-PET of GM12878, and RAD21 ChIA-PET of K562.

76 erase II (RNAPII) ChIA-PET of GM12878, RAD21 ChIA-PET of GM12878, and RAD21 ChIA-PET of K562.

77 provide the detailed protocol for long-read ChIA-PET that includes cell fixation and lysis, chromati

78 he original approach by developing long-read ChIA-PET, in which the length of the paired-end tags is

79 ctions, including RNA polymerase II (RNAPII) ChIA-PET of GM12878, RAD21 ChIA-PET of GM12878, and RAD2

80 ction analysis by paired-end tag sequencing (ChIA-PET) can capture genome-wide chromatin interactions

81 lysis followed by paired-end tag sequencing (ChIA-PET) data linked EBV enhancers to 90% of EBV-regula

82 alysis by in-situ Paired-End Tag Sequencing (ChIA-PET) data, we confirmed that SCI sub-compartment pr

83 ction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed

84 ction analysis by paired-end tag sequencing (ChIA-PET) is a method for the genome-wide de novo discov

85 ction Analysis by Paired-End Tag Sequencing (ChIA-PET) is a popular assay method for studying genome-

86 ction analysis by paired-end tag sequencing (ChIA-PET) is a robust method for capturing genome-wide c

87 ction Analysis by Paired-End Tag sequencing (ChIA-PET) is an established method for detecting genome-

88 ion analysis with paired-end tag sequencing (ChIA-PET) of the cohesin subunit SMC1A in developing mou

89 ction analysis by paired-end tag sequencing (ChIA-PET) strategy to comprehensively map higher-order c

90 ction analysis by paired-end tag sequencing (ChIA-PET) to comprehensively identify genome-wide associ

91 ction analysis by paired-end tag sequencing (ChIA-PET), and analysed gene expression in 24 diverse hu

92 ion analysis with paired-end tag sequencing (ChIA-PET), and capture Hi-C.

93 lysis followed by paired-end tag sequencing (ChIA-PET), and genome-wide clustered regularly interspac

94 ction Analysis by Paired-End Tag Sequencing (ChIA-PET).

95 ction analysis by paired-end tag sequencing, ChIA-PET)(3), have revealed topologically associating do

96 Recently, we showed that a single ChIA-PET experiment provides information at all genomic

97 atin interaction analysis by paired-end tag (ChIA-PET) reveals that rhythmic BMAL1 target gene expres

98 atin interaction analysis by paired-end tag (ChIA-PET) sequencing data, we used CRISPR-Cas9 gene edit

99 atin Interaction Analysis by Paired-End Tag (ChIA-PET), in situ Hi-C followed by chromatin immunoprec

100 atin interaction analysis by paired-end tag (ChIA-PET).

101 The ChIA-PET experiments have been applied to explore the ke

102 the general hidden patterns embedded in the ChIA-PET data.

103 A-PET is an accurate tool for predicting the ChIA-PET interactions mediated by various chromatin-asso

104 We have used ChIA-PET interactions that are mediated by cohesin (24 c

105 Using ChIA-PET and Hi-C data derived from human B-lymphocytes,

106 rence 3D genome structure is generated using ChIA-PET data from the GM12878 cell line and SVs data ar

107 ancer-promoter interactions identified using ChIA-PET in mouse ESCs, and confirm previously validated

108 mputational pipeline for 3D simulation using ChIA-PET data.

109 first high-resolution 3D genome mapping via ChIA-PET to capture RNAPII-associated chromatin interact

110 ell lines (K562, MCF7, GM12878) obtained via ChIA-PET, Hi-C, and Hi-CHIP assays.

111 The predictions of ChIPr correlate well with ChIA-PET data in four cell lines.