RUNX2 regulates aberrant collagen gene expression in keloid fibroblasts
RNA-seq (gene expression) · human · 12 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
- 12 samples: 3 × normal skin sample vs 3 × keloid sampleGroups 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.
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE293677_RAW.tar (it can run to tens of gigabytes).
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: 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 PRJNA1245486 and SRA study SRP576097. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 6 samples.
How we read this: 2 replicated groups read from 12 sample titles; they account for 6 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.
- GSM8888283 primary keloid fibroblasts sample1, siControl
- GSM8888284 primary keloid fibroblasts sample2, siControl
- GSM8888285 primary keloid fibroblasts sample3, siControl
- GSM8888286 primary keloid fibroblasts sample1, siRUNX2
- GSM8888287 primary keloid fibroblasts sample2, siRUNX2
- GSM8888288 primary keloid fibroblasts sample3, siRUNX2
- GSM9043023 normal skin sample1 normal skin sample
- GSM9043024 normal skin sample2 normal skin sample
- GSM9043025 normal skin sample3 normal skin sample
- GSM9043026 keloid sample1 keloid sample
- GSM9043027 keloid sample2 keloid sample
- GSM9043028 keloid sample3 keloid sample
- GSE262112 Mechanical stretching of keloid and normal skin fibroblasts 20 samples shares fibroblasts, keloid
- GSE224698 Gene expression profiles of human dermal fibroblasts and human pluripotent stem cells analyzed by bulk RNA-seq 69 samples shares fibroblasts
- GSE251807 Investigation of gene expression changes in normal human dermal fibroblasts after exposure to bone marrow mesenchymal stromal cell secretome 32 samples shares fibroblasts
- GSE305928 Effect of latrunculin A on gene expression in human skin dermal fibroblasts 12 samples shares fibroblasts
- GSE280714 The role of RUNX2 and BHLHE40 in pathologically relevant CD4-positive tissue-resident T-cells in Crohn's disease. (scMultiome) 12 samples shares runx2
- GSE221896 Effect of nimodipine on gene expression during TGF-β induced fibrotic phenotype switching of human orbital fibroblasts 11 samples shares fibroblasts
- GSE301181 Identification of IPF Specific Genes Expressed by Lung Tissue - Derived Fibroblasts Using Next Generation Sequencing 43 samples shares fibroblasts
- GSE237690 Lupus dermal fibroblasts hyper-respond to inflammatory cytokines and exhibit a pro-fibrotic phenotype to TGF-β in patients with scarring skin disease 317 samples shares fibroblasts
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.