Sample Subject_ID Cell_Type Genotype Age Sex Treatment Total_reads Uniq_Rate Multi_Rate Unmap_Rate Uniq_Mapped_Reads Gene_Rate Ambiguity_Rate No_Feature_Rate Avg_Corr Corr_diff MADScore isOutlier Pct_MT Pct_Top1 Pct_Top10
MG-Sal-WT-1F subject94 Microglia WT 2m F Saline 14163830 88.57 4.26 7.17 12544884 81.07 3.88 15.04 0.75 -0.02 -1.54 N 0 6.4 17.6
MG-Sal-WT-2F subject95 Microglia WT 2m F Saline 15407000 89.76 4.17 6.07 13828849 82.53 3.71 13.76 0.76 -0.01 -1.05 N 0 6.3 17
MG-Sal-WT-3M subject96 Microglia WT 2m M Saline 19455104 90.26 3.94 5.8 17559955 84.92 3.73 11.35 0.76 -0.01 -1.14 N 0 6.2 16.9
MG-Sal-WT-4M subject97 Microglia WT 2m M Saline 17714624 89.03 4.07 6.9 15771723 85.43 3.84 10.72 0.76 -0.01 -0.97 N 0 6.3 17.3
MG-Sal-KO-1F subject98 Microglia KO 2m F Saline 14429702 89.23 4.23 6.54 12875049 79.81 3.65 16.55 0.75 -0.02 -1.56 N 0 5.8 16.9
MG-Sal-KO-2F subject99 Microglia KO 2m F Saline 14120898 89.12 4.22 6.66 12585135 81.35 3.83 14.82 0.75 -0.02 -1.6 N 0 5.9 17.3
MG-Sal-KO-3F subject100 Microglia KO 2m F Saline 15091374 89.91 3.82 6.27 13568037 78.54 3.49 17.97 0.75 -0.03 -2 N 0 5.4 16.1
MG-LPS-WT-10F subject106 Microglia WT 2m F LPS 14991783 86.23 6.03 7.74 12928153 85.54 3.53 10.94 0.78 0.01 0.65 N 0 3.8 14.4
MG-LPS-WT-11F subject107 Microglia WT 2m F LPS 14363456 88.52 5.18 6.3 12714028 85.05 3.41 11.54 0.79 0.01 0.81 N 0 3.7 13.8
MG-LPS-WT-12F subject109 Microglia WT 2m F LPS 17075487 87.98 4.96 7.06 15022723 83.44 3.39 13.17 0.78 0.01 0.66 N 0 3.4 13.3
MG-LPS-WT-5F subject102 Microglia WT 2m F LPS 14263211 88.08 4.97 6.95 12563196 83.59 3.48 12.92 0.77 0 0.05 N 0 3.7 13.4
MG-LPS-WT-6F subject103 Microglia WT 2m F LPS 13451060 88.51 4.8 6.69 11904862 80.37 3.51 16.11 0.77 -0.01 -0.63 N 0 4.2 15.2
MG-LPS-WT-11M subject108 Microglia WT 2m M LPS 15364177 88.8 4.77 6.43 13643895 82.5 3.33 14.16 0.78 0.01 0.47 N 0 3.3 13.6
MG-LPS-WT-1M subject101 Microglia WT 2m M LPS 14911753 89.24 3.82 6.94 13306578 78.74 3.38 17.88 0.74 -0.03 -2.32 N 0 6 16.6
MG-LPS-WT-8M subject104 Microglia WT 2m M LPS 13232750 87.15 5.42 7.43 11532330 83.2 3.45 13.34 0.77 0 0.04 N 0 3.6 13.8
MG-LPS-WT-9M subject105 Microglia WT 2m M LPS 14247389 87.17 5.3 7.53 12419743 86.83 3.67 9.5 0.79 0.02 1.06 N 0 3.6 13.8
MG-LPS-Het-10F subject117 Microglia Het 2m F LPS 18741728 88.15 5.03 6.82 16521215 84.98 3.63 11.39 0.78 0.01 0.63 N 0 4.1 14.5
MG-LPS-Het-6F subject113 Microglia Het 2m F LPS 18019149 87.69 5.4 6.91 15800564 87.71 3.62 8.67 0.79 0.02 1.02 N 0 3.6 14
MG-LPS-Het-9F subject116 Microglia Het 2m F LPS 16395085 89.26 4.69 6.05 14634496 83.75 3.31 12.93 0.78 0.01 0.65 N 0 3 12.5
MG-LPS-Het-3M subject110 Microglia Het 2m M LPS 16451993 87.64 5.7 6.66 14418416 84.58 3.47 11.95 0.78 0.01 0.4 N 0 3.1 14.8
MG-LPS-Het-4M subject111 Microglia Het 2m M LPS 16032627 87.27 5.83 6.9 13991168 87.33 3.64 9.03 0.79 0.02 0.98 N 0 3.8 14.9
MG-LPS-Het-5M subject112 Microglia Het 2m M LPS 16799448 87.54 5.42 7.04 14705795 84.94 3.52 11.54 0.78 0.01 0.46 N 0 3.3 13.3
MG-LPS-Het-7M subject114 Microglia Het 2m M LPS 15475476 89.52 4.15 6.33 13854051 84.16 3.93 11.91 0.76 -0.01 -1.01 N 0 5.7 16.5
MG-LPS-Het-8M subject115 Microglia Het 2m M LPS 16353038 89.16 5.01 5.83 14579682 87.04 3.58 9.37 0.79 0.02 1.11 N 0 3.7 13.5
MG-LPS-KO-12F subject122 Microglia KO 2m F LPS 15651561 88.39 4.98 6.63 13834709 84.57 3.51 11.92 0.78 0.01 0.7 N 0 3.4 13.9
MG-LPS-KO-13F subject123 Microglia KO 2m F LPS 15190526 90.01 4.34 5.65 13672476 88.59 4.2 7.21 0.78 0.01 0.27 N 0 5.9 17.8
MG-LPS-KO-8F subject118 Microglia KO 2m F LPS 15427831 87.83 5.36 6.81 13550917 85.57 3.64 10.79 0.79 0.01 0.84 N 0 3.6 14.7
MG-LPS-KO-9F subject119 Microglia KO 2m F LPS 15020164 88.32 5.08 6.6 13265844 86.91 3.53 9.57 0.79 0.02 0.91 N 0 3.6 13.5
MG-LPS-KO-10M subject120 Microglia KO 2m M LPS 16021540 87.98 5.37 6.65 14096522 85.19 3.68 11.13 0.78 0.01 0.43 N 0 4.1 14.1
MG-LPS-KO-11M subject121 Microglia KO 2m M LPS 15846342 87.68 5.29 7.03 13894167 87.25 3.62 9.13 0.79 0.02 1.25 N 0 3.5 13.5
MG-LPS-KO-14M subject124 Microglia KO 2m M LPS 12799543 87.46 5.35 7.19 11194992 85.01 3.59 11.4 0.78 0.01 0.57 N 0 3.7 13.8
PC-Sal-WT-1F subject125 Peritoneal WT 2m F Saline 15309587 76.21 10.25 13.54 11666911 92.12 3.01 4.87 0.77 0 -0.33 N 0 4.2 15
PC-Sal-WT-2F subject126 Peritoneal WT 2m F Saline 13026263 83.37 7.63 9 10860615 92.51 3.16 4.34 0.77 0 -0.44 N 0 4.8 15.1
PC-Sal-WT-3M subject127 Peritoneal WT 2m M Saline 13420251 85.37 7.34 7.29 11457283 90.61 3.23 6.16 0.78 0.01 0.36 N 0 3.9 14.2
PC-Sal-WT-4M subject128 Peritoneal WT 2m M Saline 13749933 83.75 8.02 8.23 11516042 91.84 3.19 4.97 0.78 0.01 0.25 N 0 3.8 14.2
PC-Sal-KO-1F subject129 Peritoneal KO 2m F Saline 13463794 84.22 7.33 8.45 11339230 92.33 3.44 4.23 0.77 0 -0.25 N 0 4.6 16.2
PC-Sal-KO-2F subject130 Peritoneal KO 2m F Saline 13247855 84.4 7.29 8.31 11181449 92.95 3.34 3.71 0.78 0 0.16 N 0 4.9 16
PC-Sal-KO-3F subject131 Peritoneal KO 2m F Saline 14881902 83.39 8.04 8.57 12409876 91.91 3.32 4.76 0.77 0 -0.37 N 0 7.5 17.5
PC-LPS-WT-10F subject137 Peritoneal WT 2m F LPS 14539690 82.52 8.15 9.33 11998385 92.71 3.07 4.22 0.75 -0.02 -1.41 N 0 2.6 16.7
PC-LPS-WT-11F subject138 Peritoneal WT 2m F LPS 14931683 84.07 7.46 8.47 12553436 91.55 3.35 5.11 0.77 0 -0.33 N 0 5.6 16.4
PC-LPS-WT-12F subject140 Peritoneal WT 2m F LPS 14354036 83.95 7.36 8.69 12050720 92.28 2.95 4.77 0.76 -0.01 -1.08 N 0 5.6 22.8
PC-LPS-WT-5F subject133 Peritoneal WT 2m F LPS 14232601 83.82 7.74 8.44 11929199 91.39 3.1 5.51 0.77 0 -0.19 N 0 2.7 11.7
PC-LPS-WT-6F subject134 Peritoneal WT 2m F LPS 17727513 84.68 7.27 8.05 15012082 92.23 2.96 4.81 0.76 -0.01 -0.96 N 0 4.8 19.6
PC-LPS-WT-11M subject139 Peritoneal WT 2m M LPS 14547045 82.79 8.59 8.62 12044212 93.01 3.11 3.88 0.76 -0.01 -1.15 N 0 4.1 19.8
PC-LPS-WT-1M subject132 Peritoneal WT 2m M LPS 14720474 82.24 9.26 8.5 12105923 91.14 2.95 5.91 0.77 0 0.01 N 0 6.2 19.7
PC-LPS-WT-8M subject135 Peritoneal WT 2m M LPS 14645733 84.78 7.13 8.09 12417129 92.04 2.95 5.01 0.76 -0.01 -0.83 N 0 6 23.5
PC-LPS-WT-9M subject136 Peritoneal WT 2m M LPS 14365891 84.09 7.28 8.63 12079758 92.68 3 4.31 0.77 0 -0.15 N 0 5.2 22.3
PC-LPS-Het-10F subject148 Peritoneal Het 2m F LPS 17552120 82.88 7.91 9.21 14547623 89.99 2.96 7.05 0.76 -0.01 -1.09 N 0 4.9 20.6
PC-LPS-Het-6F subject144 Peritoneal Het 2m F LPS 23062607 83.78 7.51 8.71 19322187 91.18 2.82 6 0.76 -0.02 -1.28 N 0 6.3 22.6
PC-LPS-Het-9F subject147 Peritoneal Het 2m F LPS 15993872 82.94 8.51 8.55 13264910 92.65 3.11 4.24 0.76 -0.01 -0.77 N 0 3.8 18.1
PC-LPS-Het-3M subject141 Peritoneal Het 2m M LPS 13030856 84.03 7.11 8.86 10949232 92.19 2.93 4.88 0.76 -0.01 -0.69 N 0 6.1 24.3
PC-LPS-Het-4M subject142 Peritoneal Het 2m M LPS 16035488 83.7 7.6 8.7 13421856 93.3 2.97 3.73 0.76 -0.01 -1.06 N 0 4.6 19.7
PC-LPS-Het-5M subject143 Peritoneal Het 2m M LPS 20145767 85.2 7.07 7.73 17164366 92.34 3.19 4.47 0.77 0 0.02 N 0 3.4 18.5
PC-LPS-Het-7M subject145 Peritoneal Het 2m M LPS 15000814 83.69 7.77 8.54 12553912 93.88 3.21 2.91 0.78 0.01 0.79 N 0 2.8 13.7
PC-LPS-Het-8M subject146 Peritoneal Het 2m M LPS 14740993 83.7 7.75 8.55 12337729 93.19 2.99 3.82 0.77 0 -0.42 N 0 4.8 20.9
PC-LPS-KO-12F subject153 Peritoneal KO 2m F LPS 23553389 83.33 7.73 8.94 19627097 90.37 3.04 6.59 0.76 -0.01 -0.7 N 0 3.8 16.8
PC-LPS-KO-13F subject154 Peritoneal KO 2m F LPS 17919801 83.97 7.65 8.38 15046805 92.32 3.48 4.2 0.77 0 0.01 N 0 7 16.4
PC-LPS-KO-8F subject149 Peritoneal KO 2m F LPS 13703747 82.36 7.88 9.76 11286390 91.98 3.02 5 0.76 -0.01 -0.83 N 0 4.6 20.3
PC-LPS-KO-9F subject150 Peritoneal KO 2m F LPS 23303529 83.62 7.46 8.92 19486477 93.55 3.73 2.72 0.78 0.01 0.34 N 0 9.7 18.6
PC-LPS-KO-10M subject151 Peritoneal KO 2m M LPS 18811184 83.98 7.84 8.18 15797762 93.22 3.23 3.55 0.78 0.01 0.26 N 0 4 15.1
PC-LPS-KO-11M subject152 Peritoneal KO 2m M LPS 20767813 84.04 7.67 8.29 17453212 92.9 3.02 4.07 0.78 0.01 0.29 N 0 4 19.6
PC-LPS-KO-14M subject155 Peritoneal KO 2m M LPS 20905864 84.36 7.62 8.02 17635180 92.4 3.14 4.46 0.77 0 -0.01 N 0 3.6 18.9
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Total number of sequencing reads from raw fastq file
Percentage of reads uniquely mapped to the reference genome.
Percentage of reads mapped equally well to multiple locations on the reference genome.
Percentage of reads not mapped to the reference genome.
Number of uniquely mapped reads.
Percentage of reads mapped to unique gene region, including Exons, UTRs and Introns.
Percentage of reads mapped to gene-overlapping region and can't be unambiguously assigned to either gene.
Percentage of reads mapped to unannotated genomic regions.
Percentage of mapped reads on Exons.
Percentage of mapped reads on 5' UTR.
Percentage of mapped reads on 3' UTR.
Percentage of mapped reads on Introns.
Percentage of mapped reads on Intergenic regions.
Reads counted by featureCounts (=uniquely mapped read * uniq_rate)
Normalization factor calculated by edgeR
Average correlation where this sample is involved
Avg_Corr : Average correlation where this sample is involved;
Avg_Rest : Average correlation where this sample is NOT involved;
Corr_diff : The difference between Avg_Corr and Avg_Rest.
(1) For each sample, calculate the correlation difference. This is simply a difference between the average of all the pair wise correlations that involve the sample (for the same group) and the average of all the pair wise correlations that do not involve the sample. For example, if we have a, b, c, d for group 1, the correlation difference of sample a is:
The difference of Average (correlation(a, b), correlation(a, c), correlation(a, d)) and Average (correlation(b, c), correlation (b, d), correlation(c, d)). You can see that if sample a is an outlier, then the difference will be negative.
(2) Now we have a vector of values (one for each sample). We simply convert this vector to MAD scores (robust Z-scores) by subtracting the medians then dividing it by median absolute deviations (MAD). We use a standard MAD cutoff (e.g. -5) to determine the outliers.