Bulk RNASeq of Stromal Subsets in Wildtype and GD T cell-deficent Mice in Biomaterial Implant Fibrosis
RNA-seq (gene expression) · mouse · 16 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
- Mus musculus (mouse)
- Samples
- 16 samples: 4 × WT_Fibroblast vs 4 × GDKO_Fibroblast vs 4 × WT_Endothelial vs 4 × GDKO_EndothelialGroups 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 GSE306146_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 PRJNA1309588 and SRA study SRP610686. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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.
- GSM9194045 WT_Fibroblast_Rep1 WT_Fibroblast
- GSM9194046 WT_Fibroblast_Rep2 WT_Fibroblast
- GSM9194047 WT_Fibroblast_Rep3 WT_Fibroblast
- GSM9194048 WT_Fibroblast_Rep4 WT_Fibroblast
- GSM9194049 GDKO_Fibroblast_Rep1 GDKO_Fibroblast
- GSM9194050 GDKO_Fibroblast_Rep2 GDKO_Fibroblast
- GSM9194051 GDKO_Fibroblast_Rep3 GDKO_Fibroblast
- GSM9194052 GDKO_Fibroblast_Rep4 GDKO_Fibroblast
- GSM9194053 WT_Endothelial_Rep1 WT_Endothelial
- GSM9194054 WT_Endothelial_Rep2 WT_Endothelial
- GSM9194055 WT_Endothelial_Rep3 WT_Endothelial
- GSM9194056 WT_Endothelial_Rep4 WT_Endothelial
- GSM9194057 GDKO_Endothelial_Rep1 GDKO_Endothelial
- GSM9194058 GDKO_Endothelial_Rep2 GDKO_Endothelial
- GSM9194059 GDKO_Endothelial_Rep3 GDKO_Endothelial
- GSM9194060 GDKO_Endothelial_Rep4 GDKO_Endothelial
- GSE306145 Bulk RNA sequencing of quadricep in wildtype and Foxp3-DTR mice in synthetic material implant fibrosis 10 samples shares wildtype, fibrosis, implant, bulk
- GSE307419 Pulmonary fibroblast subsets demonstrate differentially enriched signaling pathways during fibrosis resolution and repair 26 samples shares fibrosis, subsets
- GSE273123 Aberrant Transitional Alveolar Epithelial Cells Promote Pathogenic Activation of Lung Fibroblasts in Preclinical Fibrosis Modeling (Bulk RNA-Seq) 16 samples shares fibrosis, bulk
- GSE229916 Pericytes and perivascular fibroblasts contribute to central nervous system fibrosis in a region dependent manner 832 samples shares fibrosis
- GSE280554 NNMT promotes tubular senescence and fibrosis in chronic kidney disease 92 samples shares fibrosis
- GSE235623 MERTK inhibition for the treatment of tissue fibrosis [RNA-seq] 86 samples shares fibrosis
- GSE280003 Gpnmb and Spp1 mark a conserved macrophage injury response masking fibrosis-specific programming in the lung 81 samples shares fibrosis
- GSE316023 AI digital pathology as a key tool providing in-depth understanding of the progression and regression of MASH and fibrosis in male mouse models 77 samples shares fibrosis
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.