GEO series

Molecular effects of arsenic and smokeless tobacco aqueous extract in cultured cells [RNA-seq]

GSE269688 Homo sapiens (human) RNA-seq (gene expression) 44 samples Submitted 2024/12/04 Platform GPL18573

At a glance

RNA-seq (gene expression) · human · 44 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)
Samples: 44 samples: 43 distinct titles, 1 of them repeatedGroups 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: Molecular and cell phenotype programs in oral epithelial cells directed by co-exposure to arsenic and smokeless tobaccobioRxiv : the preprint server for biology · 2024

Summary (written by the submitters)

Chronic arsenic exposure can lead to various health issues including cancer. There has been a growing concern about co-exposure to various prevalent lifestyle habits and their role in the enhancement of arsenic toxicity. Smokeless tobacco (SLT) products are extensively consumed in many South Asian countries, where their use frequently co-occurs with exposure to arsenic from contaminated groundwater.

Read the full summary ↓

To decipher the oral epithelial cell responses to arsenic and SLT alone and in co-exposure, we performed multi-omics analyses of DNA methylome, transcriptomic reprogramming and genotoxic effects in controlled experimental settings. Chronic exposure studies revealed hypomethylation of genes involved in inflammation response and apoptosis, further corroborated by the upregulation of genes involved in these processes due to arsenic and the combined treatment in acute exposure setting. Next, to validate the omics results at the phenotypic level, we observed a dose dependent decrease in cell viability, induction of DNA damage, cell cycle changes, and an increase in apoptotic cells, with the most pronounced effects observed under arsenic and SLT co-exposure conditions. The observed DNA damage was likely the result of apoptosis induction, as chronic exposure experiments based on whole-exome sequencing did not reveal increased mutagenicity following the arsenic and/or SLT exposure. Our integrative omics study provides insights into both chronic and acute responses to arsenic and SLT co-exposure, with both types of responses converging on some of the same mechanisms. We identified large-scale epigenomic and transcriptomic reprograming associated with arsenic and SLT co-exposure, alongside genotoxic effects presumably manifesting as consequences of apoptosis induction. The findings point to a role of arsenic and SLT in altering key molecular responses, especially in the context of the co-exposure, and call for further studies in humans in the areas of exposure, to validate the observed mechanisms.

Published in

Molecular and cell phenotype programs in oral epithelial cells directed by co-exposure to arsenic and smokeless tobacco

Das S, Thakur S, Cahais V et al. · bioRxiv : the preprint server for biology 2024 · PMID 39463997 · doi:10.1101/2024.10.14.618077

This dataset

Open GSE269688 in finder → Find more human RNA-seq datasets →

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.

Series matrix ↓

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 GSE269688_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

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.

Raw reads on ENA ↗

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 PRJNA1123234 and SRA study SRP513542. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39463997) ↗

Study design

43 distinct titles, 1 of them repeated

NOK_RNA_SA_8h_1_S ×2

How we read this: Read from 44 sample titles: 43 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

GSM8324671 NOK_RNA_NA_0h_1_S1
GSM8324672 NOK_RNA_NA_0h_2_S2
GSM8324673 NOK_RNA_SA_2h_1_S3
GSM8324674 NOK_RNA_SA_2h_2_S4
GSM8324675 NOK_RNA_SLT_2h_1_S5
GSM8324676 NOK_RNA_SLT_2h_2_S6
GSM8324677 NOK_RNA_SASLT_2h_1_S7
GSM8324678 NOK_RNA_SASLT_2h_2_S8
GSM8324679 NOK_RNA_SA_4h_1_S9
GSM8324680 NOK_RNA_SA_4h_2_S10
GSM8324681 NOK_RNA_SLT_4h_1_S11
GSM8324682 NOK_RNA_SLT_4h_2_S12
GSM8324683 NOK_RNA_SASLT_4h_1_S13
GSM8324684 NOK_RNA_SASLT_4h_2_S14
GSM8324685 NOK_RNA_SA_8h_1_S15
GSM8324686 NOK_RNA_SA_8h_1_S16
GSM8324687 NOK_RNA_SLT_8h_1_S17
GSM8324688 NOK_RNA_SLT_8h_2_S18
GSM8324689 NOK_RNA_SASLT_8h_1_S19
GSM8324690 NOK_RNA_SASLT_8h_2_S20
GSM8324691 NOK_RNA_NT_8h_1_S21
GSM8324692 NOK_RNA_NT_8h_2_S22
GSM8324693 NOK_RNA_NA_0h_3_S23
GSM8324694 NOK_RNA_NA_0h_4_S24
GSM8324695 NOK_RNA_SA_2h_3_S25
GSM8324696 NOK_RNA_SA_2h_4_S26
GSM8324697 NOK_RNA_SLT_2h_3_S27
GSM8324698 NOK_RNA_SLT_2h_4_S28
GSM8324699 NOK_RNA_SASLT_2h_3_S29
GSM8324700 NOK_RNA_SASLT_2h_4_S30
GSM8324701 NOK_RNA_SA_4h_3_S31
GSM8324702 NOK_RNA_SA_4h_4_S32
GSM8324703 NOK_RNA_SLT_4h_3_S33
GSM8324704 NOK_RNA_SLT_4h_4_S34
GSM8324705 NOK_RNA_SASLT_4h_3_S35
GSM8324706 NOK_RNA_SASLT_4h_4_S36
GSM8324707 NOK_RNA_SA_8h_3_S37
GSM8324708 NOK_RNA_SA_8h_4_S38
GSM8324709 NOK_RNA_SLT_8h_3_S39
GSM8324710 NOK_RNA_SLT_8h_4_S40

+ 4 more — browse all 44 samples with per-sample file links →

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