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Table 1 Distribution of mapped reads in different categories of RNAs in the six samples

From: Comprehensive off-target analysis of dCas9-SAM-mediated HIV reactivation via long noncoding RNA and mRNA profiling

Sample_name LTR_Zer1 LTR_Zer2 LTR_L1 LTR_L2 LTR_01 LTR02
3prime_overlapping_ncrna 159 (0.00%) 180 (0.00%) 160 (0.00%) 171 (0.00%) 180 (0.00%) 160 (0.00%)
IG_C_gene 0 (0.00%) 2 (0.00%) 1 (0.00%) 0 (0.00%) 3 (0.00%) 1 (0.00%)
IG_C_pseudogene 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
IG_D_gene 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
IG_J_gene 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
IG_J_pseudogene 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
IG_V_gene 4 (0.00%) 2 (0.00%) 1 (0.00%) 3 (0.00%) 1 (0.00%) 4 (0.00%)
IG_V_pseudogene 0 (0.00%) 0 (0.00%) 3 (0.00%) 1 (0.00%) 0 (0.00%) 1 (0.00%)
Mt_rRNA 1318 (0.00%) 1488 (0.00%) 1734 (0.00%) 1496 (0.00%) 1342 (0.00%) 1779 (0.01%)
Mt_tRNA 644 (0.00%) 637 (0.00%) 692 (0.00%) 784 (0.00%) 603 (0.00%) 668 (0.00%)
TEC 5415 (0.01%) 5636 (0.01%) 5036 (0.01%) 5747 (0.01%) 5685 (0.02%) 5276 (0.02%)
TR_C_gene 32 (0.00%) 21 (0.00%) 23 (0.00%) 29 (0.00%) 36 (0.00%) 26 (0.00%)
TR_D_gene 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
TR_J_gene 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
TR_J_pseudogene 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
TR_V_gene 0 (0.00%) 0 (0.00%) 0 (0.00%) 1 (0.00%) 0 (0.00%) 0 (0.00%)
TR_V_pseudogene 0 (0.00%) 0 (0.00%) 2 (0.00%) 2 (0.00%) 0 (0.00%) 2 (0.00%)
antisense 191,551 (0.52%) 204,790 (0.53%) 178,062 (0.50%) 205,243 (0.50%) 201,319 (0.54%) 189,642 (0.55%)
known_ncrna 0 (0.00%) 0 (0.00%) 1 (0.00%) 0 (0.00%) 1 (0.00%) 1 (0.00%)
lincRNA 738,731 (2.00%) 761,611 (1.97%) 706,213 (1.98%) 702,871 (1.71%) 742,207 (1.99%) 702,377 (2.03%)
miRNA 2479 (0.01%) 2557 (0.01%) 3497 (0.01%) 3299 (0.01%) 1525 (0.00%) 1430 (0.00%)
misc_RNA 1,612,667 (4.37%) 1,593,547 (4.12%) 1,627,962 (4.57%) 1,960,500 (4.76%) 1,343,420 (3.59%) 1,244,791 (3.59%)
non_coding 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
polymorphic_pseudogene 319 (0.00%) 355 (0.00%) 320 (0.00%) 369 (0.00%) 333 (0.00%) 312 (0.00%)
processed_pseudogene 10,437 (0.03%) 10,705 (0.03%) 9812 (0.03%) 11,241 (0.03%) 10,275 (0.03%) 8946 (0.03%)
processed_transcript 196,988 (0.53%) 213,355 (0.55%) 194,373 (0.55%) 229,395 (0.56%) 203,313 (0.54%) 192,191 (0.55%)
protein_coding 32,728,357 34,372,393 31,562,319 36,554,719 33,423,746 30,949,051
(88.74%) (88.92%) (88.65%) (88.74%) (89.42%) (89.36%)
pseudogene 147 (0.00%) 166 (0.00%) 145 (0.00%) 153 (0.00%) 172 (0.00%) 167 (0.00%)
rRNA 32 (0.00%) 44 (0.00%) 38 (0.00%) 62 (0.00%) 46 (0.00%) 44 (0.00%)
sense_intronic 1015 (0.00%) 1032 (0.00%) 1070 (0.00%) 1071 (0.00%) 1035 (0.00%) 1021 (0.00%)
sense_overlapping 14,067 (0.04%) 15,375 (0.04%) 12,765 (0.04%) 14,949 (0.04%) 15,117 (0.04%) 14,014 (0.04%)
snRNA 3417 (0.01%) 3214 (0.01%) 2915 (0.01%) 3858 (0.01%) 3149 (0.01%) 3236 (0.01%)
snoRNA 160 (0.00%) 172 (0.00%) 136 (0.00%) 149 (0.00%) 197 (0.00%) 170 (0.00%)
transcribed_processed_pseudogene 25,420 (0.07%) 26,038 (0.07%) 24,532 (0.07%) 28,196 (0.07%) 25,315 (0.07%) 23,318 (0.07%)
transcribed_unitary_pseudogene 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
transcribed_unprocessed_pseudogene 72,052 (0.20%) 77,671 (0.20%) 69,487 (0.20%) 79,027 (0.19%) 78,124 (0.21%) 73,283 (0.21%)
translated_processed_pseudogene 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
translated_unprocessed_pseudogene 1 (0.00%) 0 (0.00%) 0 (0.00%) 1 (0.00%) 0 (0.00%) 0 (0.00%)
unitary_pseudogene 7892 (0.02%) 8444 (0.02%) 7147 (0.02%) 8507 (0.02%) 8233 (0.02%) 7525 (0.02%)
unprocessed_pseudogene 12,070 (0.03%) 12,228 (0.03%) 11,432 (0.03%) 12,660 (0.03%) 12,177 (0.03%) 11,856 (0.03%)
Others 1,257,539 (3.41%) 1,342,963 (3.47%) 1,185,376 (3.33%) 1,370,001 (3.33%) 1,299,971 (3.48%) 1,201,876 (3.47%)