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Establishment of a human tongue cancer organoid biobank enables early diagnosis, prognosis, and identification of therapeutic targets

GSE145057 Homo sapiens (human) RNA-seq (gene expression) 25 samples Submitted 2024/09/13 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 25 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
Head and neck cancerThis series is part of our curated briefing on it.
Samples
25 samples: 5 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.
Summary (written by the submitters)
Tongue cancer (TC) is the most frequent and a serious type of oral cancer with major clinical challenges such as lymph node metastasis and the appearance of chemotherapy resistant cells. Thus, development of diagnostic and therapeutic strategies to target these malignant cancer cells is urgently required. Here, we describe a novel and highly efficient method to generate human TC organoids, thereby creating a TC organoid biobank with primary and metastatic TC from 28 patients with diverse ages and cancer stages.
Read the full summary ↓
These organoid lines can be expanded, passed, stored frozen for long periods, and they can reproduce original TC tissues in vitro and in xenograft models. The organoids showed different properties among patients with respect to the proliferation capacity and susceptibility to cisplatin, a commonly used chemotherapeutic agent in TC therapy. This suggests that TC organoids are useful for accurate risk grading and predicting the prognosis at early stages of TC, which is difficult to diagnose clinically. Thus, human TC organoids are useful for profiling TCs, which will lead to drug development against metastatic and chemotherapy-resistant TCs.
This dataset
Open GSE145057 in finder → Find more human RNA-seq datasets → Head and neck cancer 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 GSE145057_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 PRJNA605814 and SRA study SRP248010. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 conditions, mostly in duplicate
TumorOrg.P ×8 NormalOrg.P ×4 NormalTissue.P ×2 TumorOrg.P08.CDDPResistant ×2 TumorTissue.P ×2 TumorOrg.P08 ×1 TumorOrg.P03 ×1 TumorOrg.P18 ×1 +4 more

Supports a case/control comparison: 18 samples read as cases, 7 as controls.

How we read this: 5 replicated groups read from 25 sample titles; they account for 18 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
More Head and neck cancer 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.