GEO series
Persistent gene expression and DNA methylation alterations linked to carcinogenic effects of dichloroacetic acid [RNA-seq]
At a glance
DNA methylation · mouse · 78 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Mus musculus (mouse)
- Samples
- 78 samples: 78 samples, each with a distinct title — no replicated groupsGroups 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
- Persistent gene expression and DNA methylation alterations linked to carcinogenic effects of dichloroacetic acidFrontiers in oncology · 2024
Summary (written by the submitters)
Mechanistic understanding of transient exposures that lead to adverse health outcomes will enhance our ability to recognize biological signatures of disease. Here, we measured the transcriptomic and epigenomic alterations due to exposure to the metabolic reprogramming agent, dichloroacetic acid (DCA). Previously, we showed that exposure to DCA increased liver cancer in B6C3F1 mice after continuous or early life exposures similarly over background level.
Read the full summary ↓
Measures from these studies did not support direct cytotoxic, mitogenic, or genotoxic modes-of-action of tumorigenesis. Using archived formalin-fixed liver samples, we utilized modern methodologies to measure gene expression and DNA methylation levels to link to previously generated phenotypic measures. Gene expression was measured by targeted RNA sequencing (TempO-seq 1500+ toxicity panel: 2754 total genes) in liver samples collected from 10-, 32-, 57-, and 78-week old mice exposed to deionized water (controls), DCA continuously at 3.5g/L in drinking water (“Direct” group), or DCA at 3.5g/L for 10-, 32-, or 57-weeks followed by control water (“Stop” groups). Genome-scaled alterations in DNA methylation were measured by Reduced Representation Bisulfite Sequencing (RRBS) at 78-weeks. Transcriptomic changes were most robust with concurrent or adjacent timepoints after exposure stoppage. DNA methylation alterations followed a similar pattern, measuring 2720 and 567 differentially methylated regions (DMRs) in 78-week Direct and 10-week “Stop” DCA exposure groups, respectively. Gene pathway analysis indicated cellular effects linked to increased oxidative metabolism, a primary mechanism of action for DCA, closer to exposure windows especially early in life. Conversely, many gene signatures and pathways reversed patterns later in life and reflected more pro-tumorigenic patterns for both current and prior DCA exposures. DNA methylation patterns linked to early gene pathway perturbations, suggesting persistence in the epigenome and possible regulatory effects. In total, results suggested that liver metabolic reprogramming effects of DCA interact with normal age mechanisms to increase tumor burden with both continuous and prior DCA exposure in the B6C3F1 rodent model.
Published in
Carswell G, Chamberlin J, Bennett BD et al.
· Frontiers in oncology 2024
· PMID 38764585
· doi:10.3389/fonc.2024.1389634
This dataset
Download · which file do I need?
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.
1 · Just have a look
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.
2 · Re-analyse it
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE242661_RAW.tar (it can run to tens of gigabytes).
3 · Start from the raw reads
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: Look for beta-value tables or raw IDAT files among the supplementary files.
Also filed as BioProject PRJNA1013984 and SRA study SRP459128. Searching any of these in the dataset finder brings you back here.
Study design
78 samples, each with a distinct title — no replicated groups
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 78 sample titles: 78 distinct titles with little repetition. 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.
Samples in this study
- GSM7766478 Mouse_ID_13_10 wks DCA
- GSM7766481 Mouse_ID_14_10 wks DCA
- GSM7766482 Mouse_ID_15_10 wks DCA
- GSM7766483 Mouse_ID_16_10 wks DCA
- GSM7766484 Mouse_ID_17_10 wks DCA
- GSM7766485 Mouse_ID_18_10 wks DCA
- GSM7766486 Mouse_ID_19_10 wks DCA, 22 wks drinking water
- GSM7766487 Mouse_ID_20_10 wks DCA, 22 wks drinking water
- GSM7766488 Mouse_ID_21_10 wks DCA, 22 wks drinking water
- GSM7766489 Mouse_ID_22_10 wks DCA, 22 wks drinking water
- GSM7766490 Mouse_ID_23_10 wks DCA, 22 wks drinking water
- GSM7766491 Mouse_ID_24_10 wks DCA, 22 wks drinking water
- GSM7766492 Mouse_ID_25_10 wks DCA, 47 wks drinking water
- GSM7766493 Mouse_ID_26_10 wks DCA, 47 wks drinking water
- GSM7766494 Mouse_ID_27_10 wks DCA, 47 wks drinking water
- GSM7766495 Mouse_ID_28_10 wks DCA, 47 wks drinking water
- GSM7766496 Mouse_ID_29_10 wks DCA, 47 wks drinking water
- GSM7766497 Mouse_ID_30_10 wks DCA, 47 wks drinking water
- GSM7766498 Mouse_ID_31_10 wks DCA, 68 wks drinking water
- GSM7766499 Mouse_ID_32_10 wks DCA, 68 wks drinking water
- GSM7766500 Mouse_ID_33_10 wks DCA, 68 wks drinking water
- GSM7766501 Mouse_ID_34_10 wks DCA, 68 wks drinking water
- GSM7766502 Mouse_ID_35_10 wks DCA, 68 wks drinking water
- GSM7766503 Mouse_ID_36_10 wks DCA, 68 wks drinking water
- GSM7766504 Mouse_ID_37_32 wks DCA
- GSM7766505 Mouse_ID_38_32 wks DCA
- GSM7766506 Mouse_ID_39_32 wks DCA
- GSM7766507 Mouse_ID_40_32 wks DCA
- GSM7766508 Mouse_ID_41_32 wks DCA
- GSM7766509 Mouse_ID_42_32 wks DCA
- GSM7766510 Mouse_ID_43_32 wks DCA, 46 wks drinking water
- GSM7766511 Mouse_ID_44_32 wks DCA, 46 wks drinking water
- GSM7766512 Mouse_ID_45_32 wks DCA, 46 wks drinking water
- GSM7766513 Mouse_ID_46_32 wks DCA, 46 wks drinking water
- GSM7766514 Mouse_ID_47_32 wks DCA, 46 wks drinking water
- GSM7766515 Mouse_ID_48_32 wks DCA, 46 wks drinking water
- GSM7766516 Mouse_ID_49_57 wks DCA
- GSM7766517 Mouse_ID_50_57 wks DCA
- GSM7766518 Mouse_ID_51_57 wks DCA
- GSM7766519 Mouse_ID_52_57 wks DCA
+ 38 more — browse all 78 samples with per-sample file links →
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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.