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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

26 3CPET does so by combining data from ChIA-PET, transcription factor binding sites, and protei

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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