CisMapper Histone + Expression Panels

Panels

ENCODE Human (hg19)

Description: A panel of human histone modification and gene expression data from the ENCODE project. The tissues are the cell lines listed below. The type of RNA data used to measure expression levels is given below. The histone types used in the panel and the maximum link distance allowed for each histone type are listed below.

Genome Release: hg19

Tissues: A549 Ag04450 Bj Gm12878 H1hesc Helas3 Hepg2 Hmec Hsmm Huvec K562 Mcf7 Nhek Nhlf Sknshra

Expression Data Type: Cage

Histone Modifications: H3k27ac H3k4me3

Maximum Link Distances: 500000 1000

ENCODE Mouse (mm9)

Description: A panel of mouse histone modification and gene expression data from the ENCODE project. The tissues are the listed below (see also Table S1 in the supplement to the paper on CisMapper). The type of RNA data used to measure expression levels is given below. The histone types used in the panel and the maximum link distance allowed for each histone type are listed below.

Genome Release: mm9

Tissues: Bat_MAdult24wks Heart_MAdult8wks Lung_MAdult8wks Spleen_MAdult8wks Bmarrow_MAdult8wks Heart_UE14half Mef_MAdult8wks Testis_MAdult8wks Bmdm_FAdult8wks Kidney_MAdult8wks Mel_MImmortal Thymus_MAdult8wks Cbellum_MAdult8wks Limb_UE14half Olfact_MAdult8wks Wbrain_UE14half Cortex_MAdult8wks Liver_MAdult8wks Plac_FAdult8wks Esb4_ME0 Liver_UE14half Smint_MAdult8wks

Expression Data Type: LongPap

Histone Modifications: H3k27ac H3k04me3

Maximum Link Distances: 500000 1000

Epigenetic Roadmap Human (hg19)

Description: A panel of human histone modification and gene expression data from the Epigenetic Roadmap project (the 57 epigenome subset with E000='Universal Human Reference' omitted). The tissues are the cell lines whose IDs are listed below. The names of the cell lines can be looked up from their IDs at https://egg2.wustl.edu/roadmap/data/byDataType/rna/expression/EG.name.txt. The type of RNA data used to measure expression levels is given below. The histone type used in the panel and the maximum link distance allowed for each histone type are listed below.

Genome Release: hg19

Tissues: E003 E004 E005 E006 E007 E011 E012 E013 E016 E024 E027 E028 E037 E038 E047 E050 E053 E054 E055 E056 E057 E058 E059 E061 E062 E065 E066 E070 E071 E079 E082 E084 E085 E087 E094 E095 E096 E097 E098 E100 E103 E105 E106 E109 E112 E113 E114 E116 E117 E118 E119 E120 E122 E123 E127 E128

Expression Data Type: LongPap

Histone Modifications: H3K27ac

Maximum Link Distances: 500000