RNA-seq data for LS180 and NCI-H358 Cancer cell lines
Data files
Mar 04, 2025 version files 25.86 GB
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10-H358-LY-2_S10_L002_I1_001.fastq.gz
255.96 MB
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10-H358-LY-2_S10_L002_R1_001.fastq.gz
3.31 GB
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11-H358-DMSO-1_S11_L002_I1_001.fastq.gz
238.03 MB
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11-H358-DMSO-1_S11_L002_R1_001.fastq.gz
3.08 GB
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12-H358-DMSO-2_S12_L002_I1_001.fastq.gz
232.13 MB
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12-H358-DMSO-2_S12_L002_R1_001.fastq.gz
2.91 GB
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13-LS180-LY-1_S13_L002_I1_001.fastq.gz
231.18 MB
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13-LS180-LY-1_S13_L002_R1_001.fastq.gz
2.84 GB
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14-LS180-LY-2_S14_L002_I1_001.fastq.gz
227.90 MB
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14-LS180-LY-2_S14_L002_R1_001.fastq.gz
2.85 GB
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15-LS180-DMSO-1_S15_L002_I1_001.fastq.gz
246.19 MB
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15-LS180-DMSO-1_S15_L002_R1_001.fastq.gz
2.82 GB
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16-LS180-DMSO-2_S16_L002_I1_001.fastq.gz
254.80 MB
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16-LS180-DMSO-2_S16_L002_R1_001.fastq.gz
2.91 GB
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9-H358-LY-1_S9_L002_I1_001.fastq.gz
257.43 MB
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9-H358-LY-1_S9_L002_R1_001.fastq.gz
3.19 GB
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README.md
3.08 KB
Abstract
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.
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.
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 -80oC 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.