Table 1 Sequencing read alignment statistics for PRO-seq and ChIP-exo data sets.
From: Epigenetic and transcriptional profiling of triple negative breast cancer
ChIP target | Antibody | Replicate | SRA identification | Read Length | Total Mapped Reads | Uniquely Mapped Reads | Unique Mapping Rate |
|---|---|---|---|---|---|---|---|
PRO-seq | Â | 1 | SRX4485383 | 50 | 46,406,885 | 35,062,933 | 76% |
2 | SRX4485400 | 75 | 87,474,762 | 43,763,320 | 50% | ||
TOTAL | Â | Â | 133,881,647 | 78,826,253 | Â | ||
Pol2 | sc899 (Santa Cruz) | 1 | SRX4485384 | 50 | 82,965,774 | 63,381,472 | 76% |
2 | SRX4485397 | 50 | 32,051,539 | 24,838,833 | 77% | ||
TOTAL | Â | Â | 115,017,313 | 88,220,305 | Â | ||
H2A.Z | 07-594 (EMD Milipore) | 1 | SRX4485385 | 50 | 9,783,691 | 6,506,998 | 67% |
2 | SRX4485398 | 50 | 41,880,546 | 31,974,125 | 76% | ||
TOTAL | Â | Â | 51,664,237 | 38,481,123 | Â | ||
H3K4me3 | ab8580 (Abcam) | 1 | SRX4485387 | 50 | 37,105,094 | 30,487,398 | 82% |
2 | SRX4485404 | 75 | 76,560,088 | 59,872,974 | 78% | ||
TOTAL | Â | Â | 113,665,182 | 90,360,372 | Â | ||
H3K4me2 | ab7766 (Abcam) | 1 | SRX4485388 | 50 | 28,077,305 | 21,915,585 | 78% |
2 | SRX4485401 | 75 | 74,333,953 | 58,377,458 | 79% | ||
TOTAL | Â | Â | 102,411,258 | 80,293,043 | Â | ||
H3K4me1 | ab8895 (Abcam) | 1 | SRX4485389 | 50 | 43,663,792 | 32,717,084 | 75% |
2 | SRX4485402 | 50 | 37,395,250 | 28,813,014 | 77% | ||
TOTAL | Â | Â | 81,059,042 | 61,530,098 | Â | ||
H3K27Ac | ab4729 (Abcam) | 1 | SRX4485390 | 50 | 32,203,255 | 17,535,368 | 54% |
2 | SRX4485395 | 50 | 43,865,531 | 31,734,234 | 72% | ||
TOTAL | Â | Â | 76,068,786 | 49,269,602 | Â | ||
H3K9Ac | ab4441 (Abcam) | 1 | SRX4485392 | 50 | 30,684,340 | 26,874,881 | 88% |
2 | SRX4485394 | 50 | 16,339,334 | 14,037,513 | 86% | ||
TOTAL | Â | Â | 47,023,674 | 40,912,394 | Â | ||
H3K27me3 | 07-449 (EMD Millipore) | 1 | SRX4485391 | 50 | 36,950,654 | 29,977,079 | 81% |
2 | SRX4485396 | 75 | 37,579,106 | 32,496,728 | 86% | ||
TOTAL | Â | Â | 74,529,760 | 62,473,807 | Â | ||
H4K20me1 | ab9051 (Abcam) | 1 | SRX4485399 | 75 | 79,587,575 | 62,260,072 | 78% |
2 | SRX4485393 | 75 | 44,993,047 | 36,175,837 | 80% | ||
TOTAL | Â | Â | 124,580,622 | 98,435,909 | Â | ||
CTCF | 07-729 (EMD Millipore) | 1 | SRX4485386 | 75 | 65,862,116 | 48,218,698 | 73% |
2 | SRX4485403 | 75 | 61,974,400 | 52,856,699 | 85% | ||
TOTAL | Â | Â | 127,836,516 | 101,075,397 | Â |
