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Literature DB >> 32398051

APEC: an accesson-based method for single-cell chromatin accessibility analysis.

Bin Li¹, Young Li¹, Kun Li¹, Lianbang Zhu¹, Qiaoni Yu¹, Pengfei Cai¹, Jingwen Fang^1,2, Wen Zhang¹, Pengcheng Du¹, Chen Jiang¹, Jun Lin¹, Kun Qu^3,4.

Abstract

The development of sequencing technologies has promoted the survey of genome-wide chromatin accessibility at single-cell resolution. However, comprehensive analysis of single-cell epigenomic profiles remains a challenge. Here, we introduce an accessibility pattern-based epigenomic clustering (APEC) method, which classifies each cell by groups of accessible regions with synergistic signal patterns termed "accessons". This python-based package greatly improves the accuracy of unsupervised single-cell clustering for many public datasets. It also predicts gene expression, identifies enriched motifs, discovers super-enhancers, and projects pseudotime trajectories. APEC is available at https://github.com/QuKunLab/APEC.

Entities: CellLine Chemical Disease Gene Species

Keywords: Accesson; Cell clustering; Pseudotime trajectory; Regulome; scATAC-seq

Mesh：

Year: 2020 PMID： 32398051 PMCID： PMC7218568 DOI： 10.1186/s13059-020-02034-y

Source DB: PubMed Journal: Genome Biol ISSN： 1474-7596 Impact factor: 13.583

79 in total

1. Erg is required for self-renewal of hematopoietic stem cells during stress hematopoiesis in mice.

Authors: Ashley P Ng; Stephen J Loughran; Donald Metcalf; Craig D Hyland; Carolyn A de Graaf; Yifang Hu; Gordon K Smyth; Douglas J Hilton; Benjamin T Kile; Warren S Alexander
Journal: Blood Date: 2011-06-14 Impact factor: 22.113

2. The landscape of accessible chromatin in mammalian preimplantation embryos.

Authors: Jingyi Wu; Bo Huang; He Chen; Qiangzong Yin; Yang Liu; Yunlong Xiang; Bingjie Zhang; Bofeng Liu; Qiujun Wang; Weikun Xia; Wenzhi Li; Yuanyuan Li; Jing Ma; Xu Peng; Hui Zheng; Jia Ming; Wenhao Zhang; Jing Zhang; Geng Tian; Feng Xu; Zai Chang; Jie Na; Xuerui Yang; Wei Xie
Journal: Nature Date: 2016-06-15 Impact factor: 49.962

3. CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus.

Authors: Erik Splinter; Helen Heath; Jurgen Kooren; Robert-Jan Palstra; Petra Klous; Frank Grosveld; Niels Galjart; Wouter de Laat
Journal: Genes Dev Date: 2006-09-01 Impact factor: 11.361

4. Impairment of T cell development in deltaEF1 mutant mice.

Authors: Y Higashi; H Moribe; T Takagi; R Sekido; K Kawakami; H Kikutani; H Kondoh
Journal: J Exp Med Date: 1997-04-21 Impact factor: 14.307

5. Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.

Authors: Hannah A Pliner; Jonathan S Packer; José L McFaline-Figueroa; Darren A Cusanovich; Riza M Daza; Delasa Aghamirzaie; Sanjay Srivatsan; Xiaojie Qiu; Dana Jackson; Anna Minkina; Andrew C Adey; Frank J Steemers; Jay Shendure; Cole Trapnell
Journal: Mol Cell Date: 2018-08-02 Impact factor: 17.970

6. T-cell apoptosis detected in situ during positive and negative selection in the thymus.

Authors: C D Surh; J Sprent
Journal: Nature Date: 1994-11-03 Impact factor: 49.962

7. The TCF-1 and LEF-1 transcription factors have cooperative and opposing roles in T cell development and malignancy.

Authors: Shuyang Yu; Xinyuan Zhou; Farrah C Steinke; Chengyu Liu; Shann-Ching Chen; Oksana Zagorodna; Xuefang Jing; Yoshifumi Yokota; David K Meyerholz; Charles G Mullighan; C Michael Knudson; Dong-Mei Zhao; Hai-Hui Xue
Journal: Immunity Date: 2012-10-25 Impact factor: 31.745

8. Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility.

Authors: Sarah K Denny; Dian Yang; Chen-Hua Chuang; Jennifer J Brady; Jing Shan Lim; Barbara M Grüner; Shin-Heng Chiou; Alicia N Schep; Jessika Baral; Cécile Hamard; Martine Antoine; Marie Wislez; Christina S Kong; Andrew J Connolly; Kwon-Sik Park; Julien Sage; William J Greenleaf; Monte M Winslow
Journal: Cell Date: 2016-06-30 Impact factor: 41.582

APEC: an accesson-based method for single-cell chromatin accessibility analysis.

1. Erg is required for self-renewal of hematopoietic stem cells during stress hematopoiesis in mice.

2. The landscape of accessible chromatin in mammalian preimplantation embryos.

3. CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus.

4. Impairment of T cell development in deltaEF1 mutant mice.

5. Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.

6. T-cell apoptosis detected in situ during positive and negative selection in the thymus.

7. The TCF-1 and LEF-1 transcription factors have cooperative and opposing roles in T cell development and malignancy.

8. Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility.

9. cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data.

10. Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq.

Review 1. Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq.

2. Development of double-positive thymocytes at single-cell resolution.

3. simATAC: a single-cell ATAC-seq simulation framework.

4. TooManyPeaks identifies drug-resistant-specific regulatory elements from single-cell leukemic epigenomes.

5. Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA.