Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

Nature Methods

Volumn 11, Issue 1, 2014, Pages 73-78

  He, Housheng Hansen ^a,b,c,d,e   Meyer, Clifford A ^a,c   Hu, Sheng'En Shawn ^c,f   Chen, Mei Wei ^c   Zang, Chongzhi ^a,c   Liu, Yin ^c,f   Rao, Prakash K ^c   Fei, Teng ^a,b,c   Xu, Han ^a,c   Long, Henry ^c   Liu, X Shirley ^a,c   Brown, Myles ^b,c  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c DANA FARBER CANCER INSTITUTE   (United States)

^d PRINCESS MARGARET HOSPITAL   (Canada)

^e UNIVERSITY OF TORONTO   (Canada)

^f TONGJI UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE I; DNA FRAGMENT; ESTROGEN RECEPTOR; GLUCOCORTICOID RECEPTOR; MICROCOCCAL NUCLEASE; NAKED DNA; NUCLEOTIDE; TRANSCRIPTION FACTOR CTCF; ANDROGEN RECEPTOR; CHROMATIN; NUCLEOSOME; PROTEIN P53; TP53 PROTEIN, HUMAN; TRANSCRIPTION FACTOR;

ANIMAL CELL; ARTICLE; BASE PAIRING; BINDING SITE; CANCER CELL CULTURE; CHROMATIN IMMUNOPRECIPITATION; DNA BINDING MOTIF; DNA CLEAVAGE; DNA FOOTPRINTING; DNA SEQUENCE; DNA STRAND; ENHANCER REGION; HISTONE MODIFICATION; HUMAN; HUMAN CELL; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROSTATE CANCER; PROTEIN DNA INTERACTION; PROTEIN MOTIF; CHEMISTRY; CHROMATIN; FEMALE; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; K562 CELL LINE; MALE; MCF 7 CELL LINE; PROCEDURES; TUMOR CELL LINE; CELL STRAIN K 562; CELL STRAIN MCF 7; METHODOLOGY;

AMINO ACID MOTIFS; BINDING SITES; CELL LINE, TUMOR; CHROMATIN; DEOXYRIBONUCLEASE I; FEMALE; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HUMANS; K562 CELLS; MALE; MCF-7 CELLS; NUCLEOSOMES; NUCLEOTIDES; RECEPTORS, ANDROGEN; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS; TUMOR SUPPRESSOR PROTEIN P53;

EID: 84894613651     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.2762     Document Type: Article

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