metadata table for encode components of bedbase

metadata table for encode components of bedbase

meta_2021_03_09

Format

data.frame

Note

A column "cell_type_onto" was added, after searching UBERON, Cell Ontology, Cell Line Ontology for exact matches (module 'cell' in Cell Line Ontology), using ontoProc images in Bioc 3.12.

Examples

names(meta_2021_03_09)
#>  [1] "md5sum"         "sample_name"    "file_name"      "genome"        
#>  [5] "exp_protocol"   "cell_type"      "target"         "data_source"   
#>  [9] "file_acc"       "format"         "format_type"    "description"   
#> [13] "cell_type_onto"
head(meta_2021_03_09)
#>                             md5sum sample_name          file_name genome
#> 1 8ff1591e21c370133fbdbd544d850b7a    encode_1 ENCFF003QKM.bed.gz   hg38
#> 2 b7c93b26aa70bdda10ad0c1f7adc67e5    encode_2 ENCFF850BBV.bed.gz   hg38
#> 3 6a49ac34d6926a8ae6623ee3ac566048    encode_3 ENCFF488KZB.bed.gz   hg38
#> 4 665650f5fe8db5a78733127f72e62695    encode_4 ENCFF452DAM.bed.gz   hg38
#> 5 948ca6b287b4b9c17d5cdbe00ef0cfb1    encode_5 ENCFF805AOR.bed.gz   hg38
#> 6 91c2f7ceb852450b1d9a162f5175d57c    encode_6 ENCFF899YUP.bed.gz   hg38
#>       exp_protocol                cell_type   target data_source    file_acc
#> 1 Histone ChIP-seq skeletal muscle myoblast H3K36me3      ENCODE ENCFF003QKM
#> 2 Histone ChIP-seq skeletal muscle myoblast H3K36me3      ENCODE ENCFF850BBV
#> 3 Histone ChIP-seq skeletal muscle myoblast H3K36me3      ENCODE ENCFF488KZB
#> 4 Histone ChIP-seq skeletal muscle myoblast H3K36me3      ENCODE ENCFF452DAM
#> 5      TF ChIP-seq                     K562    RBBP5      ENCODE ENCFF805AOR
#> 6      TF ChIP-seq                     K562    RBBP5      ENCODE ENCFF899YUP
#>   format format_type
#> 1    bed  narrowPeak
#> 2    bed  narrowPeak
#> 3    bed  narrowPeak
#> 4    bed  narrowPeak
#> 5    bed  narrowPeak
#> 6    bed  narrowPeak
#>                                                   description cell_type_onto
#> 1 H3K36me3 Histone ChIP-seq on human skeletal muscle myoblast     CL:0000515
#> 2 H3K36me3 Histone ChIP-seq on human skeletal muscle myoblast     CL:0000515
#> 3 H3K36me3 Histone ChIP-seq on human skeletal muscle myoblast     CL:0000515
#> 4 H3K36me3 Histone ChIP-seq on human skeletal muscle myoblast     CL:0000515
#> 5                             RBBP5 TF ChIP-seq on human K562           <NA>
#> 6                             RBBP5 TF ChIP-seq on human K562           <NA>