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The whole transcriptome analysis using FFPE and fresh tissue samples identifies the molecular fingerprint of osteosarcoma

GSE253548 Homo sapiens (human) RNA-seq (gene expression) 90 samples Submitted 2024/07/10 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 90 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
OsteosarcomaThis series is part of our curated briefing on it.
Samples
90 samples: 34 conditions, mostly in duplicateGroups 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
The whole transcriptome analysis using FFPE and fresh tissue samples identifies the molecular fingerprint of osteosarcomaExperimental biology and medicine (Maywood, N.J.) · 2024
Summary (written by the submitters)
Osteosarcoma is a form of bone cancer that predominantly impacts osteoblasts, the cells responsible for creating fresh bone tissue. Typical indications include bone pain, inflammation, sensitivity, mobility constraints, and fractures. Utilizing imaging techniques such as X-rays, MRI scans, and CT scans can provide insights into the size and location of the tumor.
Read the full summary ↓
Additionally, a biopsy is employed to confirm the diagnosis. Analyzing genes with distinct expression patterns unique to osteosarcoma can be valuable for early detection and the development of effective treatment approaches. In this research, we conducted a comprehensive examination of the entire transcriptome and pinpointed genes with altered expression profiles specific to osteosarcoma.The study mainly aimed to identify the molecular fingerprint of osteosarcoma. In this study, we processed a total of 90 FFPE samples from PathWest of which 45 were OS and equal number of healthy tissues. RNA was extracted from Paraffin-embedded tissue; RNA was sequenced, the sequencing data was analysed and gene expression was compared to healthy of the same patients. Differentially expressed genes in osteosarcoma derived samples were identified and the functions of those genes were explored. This result was combined to perform meta-analysis with our previous studies based on FFPE and fresh samples. We identified 1,500 identical differentially expressed genes in PathWest osteosarcoma samples when compared with normal tissue sample of the same patients. Meta-analysis with combined fresh issue samples identified 504 differentially expressed genes. IFITM5, MMP13, PANX3, MAGEA6 were some of the most overexpressed genes in osteosarcoma samples while SLC4A1, HBA1, HBB, AQP7 genes were some of the top downregulated genes. Through the metanalysis, 504 differentially expressed genes were identified to be identical among FFPE (105 FFPE samples) and 36 fresh bone samples. These 504 differentially expressed genes can be taken as a molecular fingerprint of osteosarcoma.
Published in
The whole transcriptome analysis using FFPE and fresh tissue samples identifies the molecular fingerprint of osteosarcoma
Poudel BH, Koks S · Experimental biology and medicine (Maywood, N.J.) 2024 · PMID 38966281 · doi:10.3389/ebm.2024.10161
This dataset
Open GSE253548 in finder → Find more human RNA-seq datasets → Osteosarcoma landscape →
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 GSE253548_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 PRJNA1066265 and SRA study SRP484489. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38966281) ↗
Study design
34 conditions, mostly in duplicate
Q02B032169YB ×2 Q05B009812WA ×2 Q08B047467NA ×2 Q09B042936FB ×2 Q10B040965MA ×2 Q11B045903JA ×2 Q12B019249NA ×2 Q12B044305AA ×2 +48 more

Supports a between-group comparison across 68 samples.

How we read this: 34 replicated groups read from 90 sample titles; they account for 68 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

+ 50 more — browse all 90 samples with per-sample file links →

More Osteosarcoma datasets

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.