TABLE 1.
Description of the RNA-seq data sets used in NMDtxDB
| Comparison (vs. control) | Cell line | siRNA KD | CRISPR KO | Sequencing technology |
|---|---|---|---|---|
| HEK_NoKO_SMG5KD_Z023 | HEK 293 | SMG5 | Illumina | |
| HEK_SMG7KO_SMG5KD_Z245 | HEK 293 | SMG5 | SMG7 | Illumina |
| HEK_SMG7KO_SMG6KD_Z245 | HEK 293 | SMG6 | SMG7 | Illumina |
| HEK_SMG7KO_SMG6KD_Z245 | HEK 293 | SMG6 | SMG7 | Nanopore DRS |
| HEK_SMG7KO_SMG5KD_Z319 | HEK 293 | SMG5 | SMG7 | Illumina |
| HEK_SMG7KO_SMG6KD_Z319 | HEK 293 | SMG6 | SMG7 | Illumina |
| HEK_NoKO_SMG6 + SMG7KD_Z023 | HEK 293 | SMG6 + SMG7 | Illumina | |
| HeLa_NoKO_SMG6 + SMG7KD_Z021 | HeLa | SMG6 + SMG7 | Illumina | |
| U2OS_NoKO_SMG6 + SMG7KD | U2OS | SMG6 + SMG7 | Illumina | |
| MCF7_NoKO_SMG6 + SMG7KD | MCF7 | SMG6 + SMG7 | Illumina |
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One single experimental group, HEK_SMG7KO_SMG6KD_Z245, was sequenced with Nanopore and Illumina technology. KDs were compared against a Luciferase (Luc) siRNA for the same cell type, genotype (WT or SMG7 KD), and clone. All samples were sequenced in three biological replicates, except for the Nanopore DRS, which was sequenced with four biological replicates.
