Inhibition of DUSP18 impairs cholesterol biosynthesis and promotes anti-tumor immunity in colorectal cancer
RNA-seq (gene expression) · human · 12 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Topic
- Colorectal cancerThis series is part of our curated briefing on it.
- Samples
- 12 samples: 3 × HCT116 cells, shCt vs 3 × HCT116 cells, shDusp18 vs 3 × MC38 cells, shCt vs 3 × MC38 cells, shdusp18Groups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Inhibition of DUSP18 impairs cholesterol biosynthesis and promotes anti-tumor immunity in colorectal cancerNature communications · 2024
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE264145_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1101055 and SRA study SRP502141. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM8212823 HCT116 cells, shCt_1 HCT116 cells, shCt
- GSM8212824 HCT116 cells, shCt_2 HCT116 cells, shCt
- GSM8212825 HCT116 cells, shCt_3 HCT116 cells, shCt
- GSM8212826 HCT116 cells, shDusp18_1 HCT116 cells, shDusp18
- GSM8212827 HCT116 cells, shDusp18_2 HCT116 cells, shDusp18
- GSM8212828 HCT116 cells, shDusp18_3 HCT116 cells, shDusp18
- GSM8212829 MC38 cells, shCt_1 MC38 cells, shCt
- GSM8212830 MC38 cells, shCt_2 MC38 cells, shCt
- GSM8212831 MC38 cells, shCt_3 MC38 cells, shCt
- GSM8212832 MC38 cells, shdusp18_1 MC38 cells, shdusp18
- GSM8212833 MC38 cells, shdusp18_2 MC38 cells, shdusp18
- GSM8212834 MC38 cells, shdusp18_3 MC38 cells, shdusp18
- GSE250000 Bulk RNA-sequencing of transduced colorectal cancer cell line HCT-116 and breast cancer cell line MCF-7 overexpressing full-lenght p53β or p53β-stop-lost. 4 samples same disease briefing · shares colorectal
- GSE12032 Inherent gene signature of stage II and III colorectal cancer leads in individual recurrence 198 samples same disease briefing · shares colorectal
- GSE109308 Single-cell transcriptomic survey of adenomatous polyposis patients with germline APC mutations 97 samples same disease briefing
- GSE110009 Single cell transcriptome landscape of primary and metastatic tumor in colon cancer 76 samples same disease briefing
- GSE287355 An EZH2—SREBP2 axis promotes cholesterol biosynthesis and represents a noncanonical vulnerability in tumorigenesis 79 samples shares biosynthesis, cholesterol, promotes
- GSE264730 Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity 203 samples shares inhibition, immunity
- GSE312944 Inhibition of METTL3 by STC-15 induces RNA misprocessing that results in dsRNA formation and activates innate immunity 140 samples shares inhibition, immunity
- GSE294827 A plastic EMP1⁺ to LGR5⁺ cell state conversion as a therapeutic bypass to KRAS-G12D inhibition in metastatic colorectal cancer 81 samples shares inhibition, colorectal
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.