DOI: 10.5061/dryad.69p8cz9dj
title: RNA-seq data for LS180 and NCI-H358 Cancer cell lines

description: Despite exciting developments in cancer immunotherapy, its broad
 application is limited by the paucity of targetable antigens on the tumor
 cell surface. As an intrinsic cellular pathway, nonsense-mediated decay
 (NMD) conceals neoantigens through the destruction of the RNA products
 from genes harboring truncating mutations. We developed and conducted a
 high throughput screen, based on the ratiometric analysis of transcripts,
 to identify critical mediators of NMD. This screen revealed disruption of
 kinase SMG1’s phosphorylation of UPF1 as a potent disruptor of NMD. This
 led us to design a novel SMG1 inhibitor, KVS0001, that elevates the
 expression of transcripts and proteins resulting from truncating mutations
 in vivo and in vitro. Most importantly, KVS0001 concomitantly increased
 the presentation of immune-targetable HLA class I-associated peptides from
 NMD-downregulated proteins on the surface of cancer cells. KVS0001
 provides new opportunities for studying NMD and the diseases in which NMD
 plays a role, including cancer and inherited diseases.
description: Whole transcriptome RNA-seq LS180 or
 NCI-H358 cells were run in biological duplicate, treated with DMSO or 5µM
 LY3023414. For RNA extraction, cells were pelleted, frozen in liquid
 nitrogen, and stored at -80<sup>o</sup>C until RNA extraction.
 RNA extraction was performed using a Qiagen AllPrep DNA/RNA Mini Kit
 (Qiagen, Maryland, USA, Cat# 80204) per manufacturer’s instruction with
 cell homogenization and lysis in RLT buffer with a QIAshredder (Qiagen,
 Maryland, USA, Cat# 79656). RNA quality control using Agilent Tapestation
 2200 (Agilent, California, USA, Cat# G2964AA) and the Agilent RNA
 ScreenTape (Agilent, California, USA, Cat# 5067- 5576) with Agilent RNA
 ScreenTape Sample Buffer and Ladder (Agilent, California, USA, Cat# 5067-
 5577, Cat# 5067- 5578) per manufacturer’s instruction. Library prep using
 Illumina RNA library prep kit (Illumina, California, USA, Cat
 #RS-122-2001) and sequenced on an Illumina HiSeq 4000 150 cycle paired-end
 using manufacturer’s instructions. The data provided here is are the
 unprocessed fastq files from this run.
description: # RNA-seq data for LS180 and NCI-H358 Cancer cell lines
 [https://doi.org/10.5061/dryad.69p8cz9dj](https://doi.org/10.5061/dryad.69p8cz9dj) ## Description of the data and file structure Data is RNA-seq fastq files from paired end 150 cycle NGS on an Illumina Hiseq 4000. There are two cell lines represented, LS180 and NCI-H358. Each were treated with either DMSO or the drug LY3023414. Both cell lines were treated, library prepared, and sequenced as biological replicates in duplicate, as indicated by a -1 and -2 in their file names. Both index and read files are included in this data set. ### Files and variables #### File: 9-H358-LY-1\_S9\_L002\_I1\_001.fastq.gz **Description:** NCI-H358 cell line treated with LY3023414 biological replicate 1 #### File: 10-H358-LY-2\_S10\_L002\_I1\_001.fastq.gz **Description:** NCI-H358 cell line treated with LY3023414 biological replicate 2 #### File: 11-H358-DMSO-1\_S11\_L002\_I1\_001.fastq.gz **Description:** NCI-H358 cell line treated with DMSO biological replicate 1 #### File: 12-H358-DMSO-2\_S12\_L002\_I1\_001.fastq.gz **Description:** NCI-H358 cell line treated with DMSO biological replicate 2 #### File: 10-H358-LY-2\_S10\_L002\_R1\_001.fastq.gz **Description:** NCI-H358 cell line treated with LY3023414 biological replicate 2 #### File: 11-H358-DMSO-1\_S11\_L002\_R1\_001.fastq.gz **Description:** NCI-H358 cell line treated with DMSO biological replicate 1 #### File: 12-H358-DMSO-2\_S12\_L002\_R1\_001.fastq.gz **Description:** NCI-H358 cell line treated with DMSO biological replicate 2 #### File: 15-LS180-DMSO-1\_S15\_L002\_I1\_001.fastq.gz **Description:** LS180 cell line treated with DMSO biological replicate 1 #### File: 9-H358-LY-1\_S9\_L002\_R1\_001.fastq.gz **Description:** NCI-H358 cell line treated with LY3023414 biological replicate 1 #### File: 15-LS180-DMSO-1\_S15\_L002\_R1\_001.fastq.gz **Description:** LS180 cell line treated with DMSO biological replicate 1 #### File: 13-LS180-LY-1\_S13\_L002\_I1\_001.fastq.gz **Description:** LS180 cell line treated with LY3023414 biological replicate 1 #### File: 14-LS180-LY-2\_S14\_L002\_I1\_001.fastq.gz **Description:** LS180 cell line treated with LY3023414 biological replicate 2 #### File: 16-LS180-DMSO-2\_S16\_L002\_I1\_001.fastq.gz **Description:** LS180 cell line treated with DMSO biological replicate 2 #### File: 13-LS180-LY-1\_S13\_L002\_R1\_001.fastq.gz **Description:** LS180 cell line treated with LY3023414 biological replicate 1 #### File: 14-LS180-LY-2\_S14\_L002\_R1\_001.fastq.gz **Description:** LS180 cell line treated with LY3023414 biological replicate 2 #### File: 16-LS180-DMSO-2\_S16\_L002\_R1\_001.fastq.gz **Description:** LS180 cell line treated with DMSO biological replicate 2 ## Code/software No specific software required, use standard programs for reviewing fastq data. ## Access information Other publicly accessible locations of the data: * None Data was derived from the following sources: * Data directly from an Illumina Hiseq 4000 instrument, not processed.