GEO series
The malignant trajectory from the notochord to chordoma and the role of the TBXT rs2305089 germline single nucleotide polymorphism
GSE277707
Homo sapiens (human)
Single-nucleus RNA-seq
36 samples
Submitted 2025/03/28
Platform GPL24676
At a glance
Single-nucleus RNA-seq · human · 36 samples
- What it is
- Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Homo sapiens (human)
- Samples
- 36 samples: 12 conditions, mostly in triplicateGroups 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 TBXT rs2305089 SNP links the benign notochordal cell tumour and chordomaThe Journal of pathology · 2025
Summary (written by the submitters)
The rare bone cancer chordoma and its putative precursor the Benign Notochordal Cell Tumor (BNCT) express the notochordal transcription factor, TBXT. The aim of this study was to elucidate the role of rs2305089 germline single nucleotide polymorphism in TBXT in the pathogenesis of chordoma. A radiological and genotyping association study demonstrated that BNCTs are associated with chordomas (P<0.001) and with the rs2305089 polymorphism (P=0.002).
Read the full summary ↓
We then engineered mesoderm/notochord models which differed only by their rs2305089 genotype. Expression of TBXT was higher and the gene regulatory network activated by TBXT was enriched in heterozygous compared to wild type cell lines. Heterozygous cell lines displayed enrichment of Wnt/beta-catenin and epithelial mesenchymal transition pathways while wild type cell lines were enriched for metabolic pathways and MTORC1 signalling. Moreover, the variant A allele induced faster cell migratory capacity together with changes in the expression of endoplasmic reticulum and intracellular transport mediators, thus suggesting that rs2305089 regulates notochord vacuoles as lysosome-related organelles in the aberrant regression of the notochord. In conclusion, we show for the first time that the rs2305089 variant allele is associated not only with chordoma but also with the BNCT and provide functional evidence that this SNP regulates notochordal cell differentiation in the pathogeneis of BNCTs and chordomas.
Published in
Usher I, O'Donnell P, Ligammari L et al.
· The Journal of pathology 2025
· PMID 40323130
· doi:10.1002/path.6427
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 GSE277707_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1163402 and SRA study SRP533916. Searching any of these in the dataset finder brings you back here.
Study design
12 conditions, mostly in triplicate
rs2305089 heterozygous mesoderm cell line 1 a… ×3
rs2305089 heterozygous mesoderm cell line 2 a… ×3
rs2305089 heterozygous mesoderm cell line 3 a… ×3
rs2305089 wild type mesoderm cell line 1 at 4… ×3
rs2305089 wild type mesoderm cell line 2 at 4… ×3
rs2305089 wild type mesoderm cell line 3 at 4… ×3
rs2305089 heterozygous MSC cell line 1 at 72 … ×3
rs2305089 heterozygous MSC cell line 2 at 72 … ×3
+4 more
Supports a between-group comparison across 36 samples.
How we read this: 12 replicated groups read from 36 sample titles; they account for 36 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
- GSM8528107 rs2305089 heterozygous mesoderm cell line 1 at 48 hours, replicate 1 rs2305089 heterozygous …
- GSM8528108 rs2305089 heterozygous mesoderm cell line 1 at 48 hours, replicate 2 rs2305089 heterozygous …
- GSM8528109 rs2305089 heterozygous mesoderm cell line 1 at 48 hours, replicate 3 rs2305089 heterozygous …
- GSM8528110 rs2305089 heterozygous mesoderm cell line 2 at 48 hours, replicate 1 rs2305089 heterozygous …
- GSM8528111 rs2305089 heterozygous mesoderm cell line 2 at 48 hours, replicate 2 rs2305089 heterozygous …
- GSM8528112 rs2305089 heterozygous mesoderm cell line 2 at 48 hours, replicate 3 rs2305089 heterozygous …
- GSM8528113 rs2305089 heterozygous mesoderm cell line 3 at 48 hours, replicate 1 rs2305089 heterozygous …
- GSM8528114 rs2305089 heterozygous mesoderm cell line 3 at 48 hours, replicate 2 rs2305089 heterozygous …
- GSM8528115 rs2305089 heterozygous mesoderm cell line 3 at 48 hours, replicate 3 rs2305089 heterozygous …
- GSM8528116 rs2305089 wild type mesoderm cell line 1 at 48 hours, replicate 1 rs2305089 wild type mes…
- GSM8528117 rs2305089 wild type mesoderm cell line 1 at 48 hours, replicate 2 rs2305089 wild type mes…
- GSM8528118 rs2305089 wild type mesoderm cell line 1 at 48 hours, replicate 3 rs2305089 wild type mes…
- GSM8528119 rs2305089 wild type mesoderm cell line 2 at 48 hours, replicate 1 rs2305089 wild type mes…
- GSM8528120 rs2305089 wild type mesoderm cell line 2 at 48 hours, replicate 2 rs2305089 wild type mes…
- GSM8528121 rs2305089 wild type mesoderm cell line 2 at 48 hours, replicate 3 rs2305089 wild type mes…
- GSM8528122 rs2305089 wild type mesoderm cell line 3 at 48 hours, replicate 1 rs2305089 wild type mes…
- GSM8528123 rs2305089 wild type mesoderm cell line 3 at 48 hours, replicate 2 rs2305089 wild type mes…
- GSM8528124 rs2305089 wild type mesoderm cell line 3 at 48 hours, replicate 3 rs2305089 wild type mes…
- GSM8528125 rs2305089 heterozygous MSC cell line 1 at 72 hours, replicate 1 rs2305089 heterozygous …
- GSM8528126 rs2305089 heterozygous MSC cell line 1 at 72 hours, replicate 2 rs2305089 heterozygous …
- GSM8528127 rs2305089 heterozygous MSC cell line 1 at 72 hours, replicate 3 rs2305089 heterozygous …
- GSM8528128 rs2305089 heterozygous MSC cell line 2 at 72 hours, replicate 1 rs2305089 heterozygous …
- GSM8528129 rs2305089 heterozygous MSC cell line 2 at 72 hours, replicate 2 rs2305089 heterozygous …
- GSM8528130 rs2305089 heterozygous MSC cell line 2 at 72 hours, replicate 3 rs2305089 heterozygous …
- GSM8528131 rs2305089 heterozygous MSC cell line 3 at 72 hours, replicate 1 rs2305089 heterozygous …
- GSM8528132 rs2305089 heterozygous MSC cell line 3 at 72 hours, replicate 2 rs2305089 heterozygous …
- GSM8528133 rs2305089 heterozygous MSC cell line 3 at 72 hours, replicate 3 rs2305089 heterozygous …
- GSM8528134 rs2305089 wild type MSC cell line 1 at 72 hours, replicate 1 rs2305089 wild type MSC…
- GSM8528135 rs2305089 wild type MSC cell line 1 at 72 hours, replicate 2 rs2305089 wild type MSC…
- GSM8528136 rs2305089 wild type MSC cell line 1 at 72 hours, replicate 3 rs2305089 wild type MSC…
- GSM8528137 rs2305089 wild type MSC cell line 2 at 72 hours, replicate 1 rs2305089 wild type MSC…
- GSM8528138 rs2305089 wild type MSC cell line 2 at 72 hours, replicate 2 rs2305089 wild type MSC…
- GSM8528139 rs2305089 wild type MSC cell line 2 at 72 hours, replicate 3 rs2305089 wild type MSC…
- GSM8528140 rs2305089 wild type MSC cell line 3 at 72 hours, replicate 1 rs2305089 wild type MSC…
- GSM8528141 rs2305089 wild type MSC cell line 3 at 72 hours, replicate 2 rs2305089 wild type MSC…
- GSM8528142 rs2305089 wild type MSC cell line 3 at 72 hours, replicate 3 rs2305089 wild type MSC…
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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.