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Table 1 Read distribution in chicken genome

From: Gene expression profiling of RIP2-knockdown in HD11 macrophages — elucidation of potential pathways (gene network) when challenged with avian pathogenic E.coli (APEC)

Sample TSS_10 kb
(%)
TSS_5 kb (%) TSS_1 kb (%) 5’UTR (%) CDS
(%)
3’UTR (%) TES_1 kb (%) TES_5 kb (%) TES_10 kb (%) Intergenic (%) Intron
(%)
WT_1 817,934 (1.09) 465,652 (0.62) 264,356 (0.35) 1,709,799 (2.29) 44,927,089 (60.14) 3,539,667 (4.74) 894,691
(1.20)
1,329,951 (1.78) 951,088
(1.27)
5,371,654
(7.19)
14,436,393
(19.32)
WT_2 850,628 (1.16) 481,034 (0.65) 266,795 (0.36) 1,783,041 (2.43) 43,890,294 (59.73) 3,326,499 (4.53) 809,810
(1.10)
1,233,127 (1.68) 961,875
(1.31)
5,646,153
(7.68)
14,229,717
(19.37)
WT_3 854,892 (1.16) 484,649 (0.66) 270,098 (0.37) 1,807,517 (2.45) 43,846,172 (59.48) 3,296,988 (4.47) 796,623
(1.08)
1,220,494
(1.66)
969,557
(1.32)
5,770,236
(7.83)
14,400,640
(19.53)
shRIP2_1 901,795 (1.11) 542,484 (0.67) 298,909 (0.37) 1,883,579 (2.31) 48,547,638 (59.62) 4,049,765 (4.97) 913,946
(1.12)
1,340,140
(1.65)
975,162
(1.20)
6,235,343
(7.66)
15,737,712
(19.33)
shRIP2_2 811,832 (1.09) 499,462 (0.67) 276,288 (0.37) 1,758,489 (2.36) 44,794,360 (60.05) 3,562,251 (4.78) 799,364
(1.07)
1,188,481
(1.59)
903,916
(1.21)
5,775,924
(7.74)
14,220,256
(19.06)
shRIP2_3 712,708 (1.08) 435,538 (0.66) 246,408 (0.37) 1,554,302 (2.36) 39,621,169 (60.05) 3,136,809 (4.75) 702,608
(1.06)
1,046,395
(1.59)
807,534
(1.22)
5,049,179
(7.65)
12,662,782
(19.19)
APEC_1 1,200,954 (1.59) 513,130 (0.68) 267,424 (0.35) 1,719,332 (2.27) 42,694,064 (56.42) 3,344,929 (4.42) 903,188
(1.19)
1,368,388
(1.81)
942,420
(1.25)
6,327,762
(8.36)
16,388,478
(21.66)
APEC_2 1,089,300 (1.53) 477,721 (0.67) 254,628 (0.36) 1,636,220 (2.30) 40,618,885 (57.14) 3,027,199 (4.26) 816,604
(1.15)
1,247,046
(1.75)
902,012
(1.27)
5,917,683
(8.33)
15,094,873
(21.24)
APEC_3 1,108,637 (1.52) 486,009 (0.67) 258,748 (0.35) 1,654,734 (2.27) 41,844,050 (57.28) 3,137,449 (4.29) 858,367
(1.17)
1,294,858
(1.77)
923,393
(1.26)
5,923,740
(8.11)
15,564,581
(21.31)
shRIP2 + APEC_1 913,505 (1.13) 530,763 (0.66) 293,283 (0.36) 1,893,473 (2.34) 48,220,437 (59.62) 4,036,600 (4.99) 878,217
(1.09)
1,280,225
(1.58)
776,896
(0.96)
6,356,734
(7.86)
15,702,773
(19.41)
shRIP2 + APEC_2 1,005,052 (1.15) 580,628 (0.66) 322,426 (0.37) 2,117,408 (2.42) 52,630,365 (60.20) 4,073,560 (4.66) 880,221
(1.01)
1,301,687
(1.49)
853,729
(0.98)
6,930,910
(7.93)
16,725,203
(19.13)
shRIP2 + APEC_3 893,086 (1.13) 514,527 (0.65) 287,291 (0.36) 1,876,382 (2.37) 47,741,694 (60.37) 3,806,973 (4.81) 824,719
(1.04)
1,214,147
(1.54)
761,941
(0.96)
6,150,964
(7.78)
15,008,025
(18.98)
  1. WT indicates wild type HD11 cells, shRIP2 represents knockdown of RIP2 HD11 cells, APEC indicates avian pathogenic E. coli; APEC+shRIP2 represents knockdown of RIP2 HD11 cells combined with APEC infection