Methods

The two files contain the relaxation rate constants and experimental uncertainties in the relaxation rate constants (1 standard deviation) for deuterium relaxation measurements for 13CH2D methyl group isotopomers in E. coli ribonuclease H protein. The data are recorded at 298 K using 400, 500, 800, and 900 MHz NMR spectrometers. The relaxation measurements are R1, R2, RQ, and RAP, that is, the relaxation rate constants for longitudinal magnetization, transverse magnetization, quadrupolar order, and antiphase magnetization, respectively.

Two reconstructed APOE reference loci on GRCh38.p13 Chr19:44,900,000-44,920,000 including corresponding pEasy Flox fragments of 3.4 kb and 4.4 kb. A reconstructed Pax8-CreERT2 reference loci on GRCm38.p6 chr1: 93570239-93676772.

FreeHi-C Spike-in Simulations on GM12878 replicates 2, 3, 4, and 6 using different proportions of spike-ins which are simulated to different levels of sequencing depths. The spike-in set was determined by comparing four replicates of A549 with four replicates of GM12878 filtered by absolute log2 fold-changes 2.

In this review article, we aimed to provide an overview of the technical aspect used in radiomics analysis in non-small cell lung cancer (NSCLC) and signify the role of 18F-FDG PET/CT-derived radiomics in the diagnosis, prognostication, and therapy response.

Accompanying files Supplementary Data 1: Bash code for all steps from raw reads until peak calling. This file provides the bash code for basic read processing, conversion into crosslink events and peak calling as described in Chapters 3-5.1. Details on the input files, preset variables and external tools required to run this code are listed in Chapters 2.1 and 3.1. Supplementary Data 2: R code for postprocessing of PureCLIP output. This file provides the R code to postprocess the output of PureCLIP peak calling as described in Chapter 5.2. Running this code requires a bed file with ’crosslink sites’ output by PureCLIP (PureCLIP.crosslink_sites_short.bed) and bw files with crosslink events (sampleX.strand.bw). The code to obtain these files is described in Supplementary Data 1. Supplementary Data 3: R code for reproducibility and downstream analysis. This file provides the R code to reproducibility analyses and assignment of genes and transcript regions as described in Chapters 6.1 and 6.2. Running this code requires a bed file with binding sites (e.g. curated PureCLIP output, see Chapter 5), a gtf file with gene/transcript annotations, and bw files with crosslink events in the individual replicates (sampleX.strand.bw, see Chapter4).

This data comprises the full simulation and analysis protocol performed as a part of this work. A README file is contained with a drectory structure and guildlines.

This zip file contains all Matlab scripts involved in the analytical methods in manuscript with a detailed descriptive list in a docx file. It also has a "synapse.txt' file containing all localization coordinates of RIM1/2 and PSD-95 (labeled as 647 and 561, respectively in the channel column) in an example synapse.

The data file has 7 columns and 305 rows containing information for 304 yeast introns, including 24 introns located in 5' UTR: 1. Gene: list the gene name containing individual introns. The first 24 introns are located in 5' UTR of 24 genes. 2. N_EE: number of transcriptomic reads mapped to exon-exon junction sequences 3. N_EI5: number of transcriptomic reads mapped to exon-intron junction sequences at the 5' end 4. N_EI3: number of transcriptomic reads mapped to exon-intron junction sequences at the 3' end 5. L_intron: intron length 6. p_EI5: estimated proportion of EI5 according to Eq. (1) of the manuscript. 7. SE: Splicing efficiency The transcriptomic data are from four files with SRA accessions SRR3440202, SRR3440204, SRR3440206, SRR3440207. They are from BioProject (project accession PRJNA319604). They are the first four of a total of 44 files.

Data sets for ProcartaPlex and QuantiGene Plex assays.

Script of invoking PsolPot module in the latest release of Xplor-NIH (2.46 and later) for the direct refinement of protein structure