Extended Data Fig. 1: Quality control for IVT RNA samples.
From: Systematic calibration of epitranscriptomic maps using a synthetic modification-free RNA library
a-c) LC-MS/MS detection and quantification of m5C in two commercial NTPs samples. Data are presented as mean values + /- SD (n = 3). ND, not detected. d) Quantification of three RNA modifications (m6A, m5C and m1A) in cellular mRNA and IVT RNA derived from HEK293T cells. Data are presented as mean values + /- SD (n = 3). e) The accumulation percentage curves of recapitulated genes in IVT RNA library. Different threshold (reads count ≥2, 5, 10) were used to determine whether one gene could be reproduced in IVT RNA library. f) Reads coverage across the genes which are grouped by their lengths. g-h) Gene counts, lengths, GC contents, and expression levels (TPM log10 value) for different groups of genes. Genes are grouped in respect to their expression changes or existences in two libraries derived from HEK293T (g) and mESCs (h). The number of each group of genes are indicated on the top-left panel. none: unchanged genes; up: up-regulated genes in IVT RNA library; down: down-regulated genes in IVT RNA library; mRNAmiss: gene specifically present in IVT RNA library but not in cellular mRNA library; IVTmiss: gene specifically present in cellular mRNA library but not in IVT RNA library. Box boundaries represent 25th and 75th percentiles; center line represents the median; whiskers indicate ±1.5× interquartile range (IQR). i) SNVs and Indels identified in cellular mRNA and IVT RNA libraries derived from HEK293T cells. Data are presented as mean values of two replicates. IVT unique indicates SNVs or Indels specifically present in the IVT RNA library.
