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Table 1 Overview of ChIP-seq and RNA-seq sequencing data for the rat (BN and SHR), for the mouse (male and female), for the myoblast (MB) dataset from [ 36 ], and for the ENCODE cell lines

From: histoneHMM: Differential analysis of histone modifications with broad genomic footprints

Data Replicate Total number Mapped
   of reads reads
H3K27me3 BN 1 69,047,384 54,415,680
H3K27me3 BN 2 82,631,022 70,349,074
H3K27me3 BN 3 70,920,377 60,263,098
H3K27me3 SHR 1 62,894,736 49,966,171
H3K27me3 SHR 2 68,439,111 58,495,532
H3K27me3 SHR 3 68,419,655 58,433,557
Input BN 1 14,104,386 12,833,263
Input BN 2 15,381,807 14,172,254
Input BN 3 61,276,324 58,969,661
Input SHR 1 16,049,419 14,700,053
Input SHR 2 18,586,414 16,910,655
Input SHR 3 74,035,329 70,234,582
RNA-seq BN 1 168,796,774 121,417,255
RNA-seq BN 2 162,380,800 123,606,276
RNA-seq BN 3 170,100,328 129,078,242
RNA-seq BN 4 161,444,260 117,512,826
RNA-seq BN 5 144,182,176 105,095,363
RNA-seq SHR 1 164,552,150 118,500,162
RNA-seq SHR 2 166,005,952 126,920,455
RNA-seq SHR 3 149,525,162 108,870,073
RNA-seq SHR 4 120,844,554 85,337,460
RNA-seq SHR 5 138,124,004 99,015,155
H3K9me3 female 1 13,306,841 8,708,647
H3K9me3 female 2 7,860,660 3,942,578
H3K9me3 female 3 7,092,019 3,553,617
H3K9me3 male 1 12,091,621 6,274,126
H3K9me3 male 2 7,195,641 3,514,546
H3K9me3 male 3 5,703,768 2,786,109
Input 1 10,458,196 6,714,959
Input 2 4,304,875 1,940,625
Input 3 3,586,754 1,559,414
Input 4 4,482,286 1,947,833
Input 5 3,680,479 1,535,794
Input 6 14,922,773 11,291,654
RNA-seq female 1 6,245,431 4,367,593
RNA-seq female 2 13,093,629 9,257,763
RNA-seq male 1 14,086,627 11,311,584
RNA-seq male 2 8,098,083 6,476,421
MB H3K27me3 1 9,453,468 9,421,380
MB H3K27me3 2 9,924,308 9,875,240
MB H3K27me3 3 10,316,946 10,262,585
MB input 1 9,798,009 9,780,084
MB input 2 9,807,040 9,789,125
MB input 3 7,351,896 7,340,980
MB input 4 12,350,738 12,324,079
H1 H3K09me3 1 32,382,686 22,900,208
H1 H3K09me3 2 41,645,083 27,715,874
H1 H3K27me3 1 8,342,672 6,434,801
H1 H3K27me3 2 15,963,714 12,146,581
H1 H3K27me3 3 19,825,041 10,943,029
H1 H3K27me3 4 17,600,144 5,009,090
H1 H3K27me3 5 11,715,209 7,194,836
H1 H3K27me3 6 14,948,211 8,705,091
H1 H3K27me3 7 13,277,331 5,472,352
H1 H3K36me3 1 24,086,746 13,669,344
H1 H3K36me3 2 16,739,261 13,164,807
H1 H3K79me2 1 29,740,715 24,616,670
H1 H3K79me2 2 45,788,899 35,599,680
H1 input 1 13,876,810 10,813,095
H1 input 2 16,581,567 7,681,001
H1 RNA-seq 1 250,790,392 140,719,829
H1 RNA-seq 2 214,202,680 114,403,031
K562 H3K27me3 1 19,297,190 12,210,065
K562 H3K27me3 2 22,830,589 12,119,288
K562 H3K36me3 1 26,973,698 14,803,144
K562 H3K36me3 2 17,501,267 10,393,298
K562 H3K79me2 1 31,690,813 22,740,997
K562 H3K79me2 2 21,245,046 13,669,674
K562 H3K9me3 1 21,099,652 15,816,227
K562 H3K9me3 2 46,226,003 33,939,687
K562 input 1 27,579,809 19,570,350
K562 RNA-seq 1 227,177,516 134,666,953
K562 RNA-seq 2 238,106,630 158,075,847
  1. Mapped reads refers to the number of uniquely mapped reads after removal of likely PCR duplicates.