Page 11 - GPD-1-2

Gene & Protein in Disease DNA methylation and gene expression on rats with protein malnutrition

Table 1. Sequence statistics and quality control.
Sample Raw data Valid data Valid ratio (reads) Q20% Q30% GC content%
Read Base Read Base
LPE_1 50,110,990 7.52G 49,585,840 7.44G 98.95 99.78 98.20 55
LPE_2 48,159,708 7.22G 47,586,754 7.14G 98.81 99.74 98.02 54.50
LPE_3 52,007,858 7.80G 51,336,482 7.70G 98.71 99.69 97.96 55.50
LPE_4 40,309,918 6.05G 39,767,412 5.97G 98.65 99.72 98.08 55
LPF_1 49,703,862 7.46G 49,125,664 7.37G 98.84 99.67 97.94 55.50
LPF_2 43,420,462 6.51G 42,969,142 6.45G 98.96 99.72 97.97 55
LPF_3 49,434,484 7.42G 48,855,946 7.33G 98.83 99.76 98.13 55
LPF_4 40,791,036 6.12G 39,541,740 5.93G 96.94 99.89 98.15 54
CON_1 49,544,160 7.43G 47,851,296 7.18G 96.58 99.19 97.24 55
CON_2 45,720,378 6.86G 45,212,860 6.78G 98.89 99.76 98.09 55.50
CON_3 40,445,068 6.07G 39,991,978 6.00G 98.88 99.77 98.06 55
CON_4 46,744,408 7.01G 45,959,300 6.89G 98.32 99.78 98.18 52
LPE: Early-life low-protein group, LPF: Fetal low-protein group, CON: Control group

Table 2. The sequencing raw and trimmed data mapping to the reference genome for each group.
Sample Valid Mapped Unique Multi mapped PE mapped Reads map to Reads map to Non‑splice Splice
reads reads mapped reads reads reads sense strand antisense strand reads reads
LPE_1 49,585,840 47,535,165 25,374,438 22,160,727 44,425,314 16,893,012 17,926,921 9,816,663 25,003,270
(95.86%) (51.17%) (44.69%) (89.59%) (34.07%) (36.15%) (19.80%) (50.42%)
LPE_2 47,586,754 45,554,047 25,821,477 19,732,570 42,853,620 17,176,552 17,944,361 11,322,327 23,798,586
(95.73%) (54.26%) (41.47%) (90.05%) (36.10%) (37.71%) (23.79%) (50.01%)
LPE_3 51,336,482 49,194,876 24,722,802 24,472,074 45,955,892 16,861,421 17,863,308 9,183,794 25,540,935
(95.83%) (48.16%) (47.67%) (89.52%) (32.84%) (34.80%) (17.89%) (49.75%)
LPE_4 39,767,412 38,063,647 20,594,994 17,468,653 35,499,230 13,812,681 14,547,644 8,703,040 19,657,285
(95.72%) (51.79%) (43.93%) (89.27%) (34.73%) (36.58%) (21.88%) (49.43%)
LPF_1 49,125,664 47,138,541 25,090,583 22,047,958 44,623,268 16,832,181 17,251,928 9,062,872 25,021,237
(95.96%) (51.07%) (44.88%) (90.83%) (34.26%) (35.12%) (18.45%) (50.93%)
LPF_2 42,969,142 41,103,823 21,990,657 19,113,166 38,391,118 14,773,806 15,553,045 8,792,928 21,533,923
(95.66%) (51.18%) (44.48%) (89.35%) (34.38%) (36.20%) (20.46%) (50.11%)
LPF_3 48,855,946 46,727,599 25,360,279 21,367,320 43,579,804 16,726,508 17,700,034 10,203,384 24,223,158
(95.64%) (51.91%) (43.74%) (89.20%) (34.24%) (36.23%) (20.88%) (49.58%)
LPF_4 39,541,740 37,913,410 20,566,967 17,346,443 35,434,888 14,135,611 14,275,674 9,322,817 19,088,468
(95.88%) (52.01%) (43.87%) (89.61%) (35.75%) (36.10%) (23.58%) (48.27%)
CON_1 47,851,296 44,924,433 24,842,903 20,081,530 41,396,402 16,611,513 17,424,875 10,739,480 23,296,908
(93.88%) (51.92%) (41.97%) (86.51%) (34.71%) (36.41%) (22.44%) (48.69%)
CON_2 45,212,860 43,239,128 22,380,112 20,859,016 40,178,906 15,072,207 15,858,565 7,861,707 23,069,065
(95.63%) (49.50%) (46.14%) (88.87%) (33.34%) (35.08%) (17.39%) (51.02%)
CON_3 39,991,978 38,283,877 20,607,038 17,676,839 35,748,418 13,794,624 14,535,738 8,268,306 20,062,056
(95.73%) (51.53%) (44.20%) (89.39%) (34.49%) (36.35%) (20.67%) (50.17%)
CON_4 45,959,300 43,757,403 28,236,788 15,520,615 41,800,784 18,267,361 18,722,174 16,610,634 20,378,901
(95.21%) (61.44%) (33.77%) (90.95%) (39.75%) (40.74%) (36.14%) (44.34%)
LPE: Early-life low-protein group, LPF: Fetal low-protein group, CON: Control group

Due to the differences in gene expression number in different expression intervals can be calculated. The
and distribution of gene expression value in the samples, percentage in Table 4 indicates the proportion of the
the sample expression value (FPKM) can be divided into number of genes expressed in the expression interval
different intervals and the number of genes expressed between all the genes expressed in the sample. Coverage

Volume 1 Issue 2 (2022) 5 https://doi.org/10.36922/gpd.v1i2.169