Effect of nimodipine on gene expression during TGF-β induced fibrotic phenotype switching of human orbital fibroblasts
RNA-seq (gene expression) · human · 11 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
- 11 samples: 11 samples, each with a distinct title — no replicated groupsGroups 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.
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 GSE221896_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 PRJNA916683 and SRA study SRP415155. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 11 sample titles: 11 distinct titles with little repetition. 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.
- GSM6909095 Human OFs derived from patient 1(A) without nimodipine pretreatment or TGF-β, served as the control group [A_blank]
- GSM6909096 Human OFs derived from patient 2(B),without nimodipine pretreatment or TGF-β, served as the control group [B_blank]
- GSM6909097 Human OFs derived from patient 3(C),without nimodipine pretreatment or TGF-β, served as the control group [C_blank]
- GSM6909098 Human OFs derived from patient 1(A) co-cultured with TGF-β for 24 hours and without nimodipine pretreatment [A_model]
- GSM6909099 Human OFs derived from patient 2(B), co-cultured with TGF-β for 24 hours and without nimodipine pretreatment [B_model]
- GSM6909100 Human OFs derived from patient 3(C), co-cultured with TGF-β for 24 hours and without nimodipine pretreatment [C_model]
- GSM6909101 Human OFs derived from patient 1(A) with nimodipine pretreatment and co-cultured with TGF-β for 24 hours [A_treatment]
- GSM6909102 Human OFs derived from patient 2(B), with nimodipine pretreatment and co-cultured with TGF-β for 24 hours [B_treatment]
- GSM6909103 Human OFs derived from patient 3(C), with nimodipine pretreatment and co-cultured with TGF-β for 24 hours [C_treatment]
- GSM6909104 Human OFs derived from patient 1(A), with nimodipine pretreatment and without TGF-β [A_CCB]
- GSM6909105 Human OFs derived from patient 3(C), with nimodipine pretreatment and without TGF-β [C_CCB]
- GSE282384 Substrate Stiffness Dictates Unique Doxorubicin-induced Senescence-associated Secretory Phenotypes and Transcriptomic Signatures in Human Pulmonary Fibroblasts 12 samples shares fibroblasts, phenotype, induced
- GSE280810 Macrophages expressing chimeric cytokine receptors have an inflammatory phenotype and anti-tumoral activity upon IL-10 or TGFβ stimulation 30 samples shares tgf, phenotype
- GSE272972 Critical role for the TGF-β1/mTORC1 signalling axis in defining the transcriptional identity of CTHRC1+ pathologic fibroblasts in idiopathic pulmonary fibrosis 18 samples shares tgf, fibroblasts
- GSE302114 Mitochondrial One-Carbon Metabolism is Required for TGF-β-Induced Glycine Synthesis and Collagen Protein Production 18 samples shares tgf, induced
- GSE202216 Rhinovirus-induced gene expression patterns that distinguish between neutrophilic asthma and other asthma inflammatory phenotypes in human peripheral blood mononuclear cells 102 samples shares phenotype, induced
- GSE276620 Oncogene induced senescence and senescence-associated secretory phenotype (SASP) determines the efficacy of palbociclib in PIK3CA mutated colorectal cancer 26 samples shares phenotype, induced
- GSE216842 Transcriptomic landscape of human primary stromal cells (fibroblasts, endothelial cells and mesenchymal stem cells) upon therapy-induced senescence (genotoxic chemotherapy） 24 samples shares fibroblasts, induced
- GSE304266 Bulk RNA‑seq of IMR90 fibroblasts in IR‑induced senescence with siRNA knockdowns of CCND1, CDK4, CDK6 and controls 21 samples shares fibroblasts, induced
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.