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First multiomics association study of trace element and mineral concentration and RNA sequencing profiles in human cancers

GSE277467 Homo sapiens (human) RNA-seq (gene expression) 85 samples Submitted 2024/09/21 Platform GPL21290
At a glance

RNA-seq (gene expression) · human · 85 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
85 samples: 39 × CC vs 2 × NC vs 2 × LS vs 2 × CC_20Groups 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.
Summary (written by the submitters)
The integration of various types of omics data is an important trend of contemporary molecular oncology. In this regard, high-throughput analysis of trace and essential elements in cancer biosamples is an emerging field that has not yet been sufficiently addressed. For the first time, we simultaneously obtained RNA sequencing gene expression and mass spectrometry essential and trace element profiles for a set of human cancer samples.
Read the full summary ↓
The biosamples were formalin-fixed, paraffin-embedded primary tumor tissue blocks: 67 for colorectal cancer patients and 17 for different solid cancer types. The levels of 45 trace elements and minerals, Ag, Al, As, Au, B, Ba, Be, Bi, Ca, Cd, Co, Cr, Cu, Fe, Ga, Ge, Hg, I, K, La, Li, Mg, Mn, Mo, Na, Ni, P, Pb, Pd, Pt, Rb, Sb, Sc, Se, Si, Sn, Sr, Te, Ti, Tl, Zn, U, V, W, Zr, were assessed using inductively-coupled plasma mass-spectrometry. The expression levels were profiled for 36596 known human genes, and the activation levels were assessed for 10520 intracellular molecular pathways. For the concentrations of essential elements Ca, Cu, Fe, K, Mg, Na, P, and Zn we detected statistically significant correlations on both gene expression and pathway activation levels, both for colorectal cancer and for pan-cancer level of data analysis. We hope the first-in-class database provided here will be a valuable resource for multiomics cancer research.
This dataset
Open GSE277467 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 GSE277467_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 PRJNA1160473 and SRA study SRP532690. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
39 × CC vs 2 × NC vs 2 × LS vs 2 × CC_20

Supports a between-group comparison across 45 samples.

How we read this: 4 replicated groups read from 85 sample titles; they account for 45 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.

Samples in this study

+ 45 more — browse all 85 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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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.