Effects of GLI1, GLI3, and GLI1/3 knockdown on rhematoid arthritis synovial fibroblasts stimulated with TNF-alpha
RNA-seq (gene expression) · human · 15 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
- 15 samples: 5 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
- Reciprocal Regulation of GLI1 and GLI3 Fine Tunes the Pathogenic Behavior of Synovial Fibroblasts in Rheumatoid ArthritisInternational journal of rheumatic diseases · 2026
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 GSE329806_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 PRJNA1461869 and SRA study SRP697147. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 5 replicated groups read from 15 sample titles; they account for 15 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.
- GSM9711596 siCtrl_Veh1 siCtrl_Veh
- GSM9711597 siCtrl_Veh2 siCtrl_Veh
- GSM9711598 siCtrl_Veh3 siCtrl_Veh
- GSM9711599 siCtrl_T1 siCtrl_T
- GSM9711600 siCtrl_T2 siCtrl_T
- GSM9711601 siCtrl_T3 siCtrl_T
- GSM9711602 siGLI1_T1 siGLI1_T
- GSM9711603 siGLI1_T2 siGLI1_T
- GSM9711604 siGLI1_T3 siGLI1_T
- GSM9711605 siGIL3_T1 siGIL3_T
- GSM9711606 siGIL3_T2 siGIL3_T
- GSM9711607 siGIL3_T3 siGIL3_T
- GSM9711608 siGLI1_3_T1 siGLI1_3_T
- GSM9711609 siGLI1_3_T2 siGLI1_3_T
- GSM9711610 siGLI1_3_T3 siGLI1_3_T
- GSE328951 The embryonic origins of site-specific arthritis; Bulk RNA sequencing of CD34+(Pi16+) fibroblasts stimulated with TNF and IL1b. 24 samples shares fibroblasts, stimulated, arthritis
- GSE298908 Positionally distinct interferon-stimulated dermal immune-acting fibroblasts promote neutrophil recruitment in Sweet's syndrome [RNA-seq] 113 samples shares fibroblasts, stimulated
- GSE315599 Primary human fibroblasts and keratinocytes stimulated with IL-17A and/or TNF 32 samples shares fibroblasts, stimulated
- GSE304266 Bulk RNA‑seq of IMR90 fibroblasts in IR‑induced senescence with siRNA knockdowns of CCND1, CDK4, CDK6 and controls 21 samples shares fibroblasts, knockdown
- GSE316921 Effects of SLC2A1 knockdown in intrahepatic cholangiocarcinoma (ICC) cancer-associated fibroblasts (CAFs) on endothelial sprouting under normal and hypoxic conditions 12 samples shares fibroblasts, knockdown
- GSE299256 Positionally distinct interferon-stimulated dermal immune-acting fibroblasts promote neutrophil recruitment in Sweet's syndrome. 116 samples shares fibroblasts, stimulated
- 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
- GSE275647 Role of Cancer-Associated Fibroblasts in Prognostic Stratification of Advanced-Stage Gastric Cancer through Interacting with Endothelial and Malignant Epithelial Cells [AGC RNA-seq] 216 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.