Bulk RNA sequencing of quadricep in wildtype and Foxp3-DTR mice in synthetic material implant fibrosis
RNA-seq (gene expression) · mouse · 10 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
- 10 samples: 5 × WT control, vs 5 × Treg depleted,Groups 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 GSE306145_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 PRJNA1309585 and SRA study SRP610684. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 2 replicated groups read from 10 sample titles; they account for 10 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.
- GSM9194035 WT control, replicate 1 WT control,
- GSM9194036 WT control, replicate 2 WT control,
- GSM9194037 WT control, replicate 3 WT control,
- GSM9194038 WT control, replicate 4 WT control,
- GSM9194039 WT control, replicate 5 WT control,
- GSM9194040 Treg depleted, replicate 1 Treg depleted,
- GSM9194041 Treg depleted, replicate 2 Treg depleted,
- GSM9194042 Treg depleted, replicate 3 Treg depleted,
- GSM9194043 Treg depleted, replicate 4 Treg depleted,
- GSM9194044 Treg depleted, replicate 5 Treg depleted,
- GSE306146 Bulk RNASeq of Stromal Subsets in Wildtype and GD T cell-deficent Mice in Biomaterial Implant Fibrosis 16 samples shares wildtype, material, fibrosis, implant, bulk
- GSE306147 Single-cell RNA/TCR-seq of T cells from murine muscle injury and foreign body response to synthetic biomaterial implants 15 samples shares synthetic, material, implant
- GSE269404 Engineering Programmable Material-To-Cell Pathways Via Synthetic Notch Receptors To Spatially Control Cellular Phenotypes In Multi-Cellular Constructs 30 samples shares synthetic, material
- GSE269373 Engineering Programmable Material-To-Cell Pathways Via Synthetic Notch Receptors To Spatially Control Cellular Phenotypes In Multi-Cellular Constructs [RNA-seq] 22 samples shares synthetic, material
- GSE335106 Bulk RNAseq analysis of wildtype and Pim1-/- macrophages 12 samples shares wildtype, bulk
- GSE272235 Gene expression profile at single cell level of all CD45+ cells infiltrating B16-SIY-dsRed syngeneic tumors implanted subcutaneously after 26 days of tumor growth in Wildtype and PRKCD KO bone marrow engrafted animals 8 samples shares wildtype, implant
- GSE269381 Engineering Programmable Material-To-Cell Pathways Via Synthetic Notch Receptors To Spatially Control Cellular Phenotypes In Multi-Cellular Constructs [snRNA-seq] 8 samples shares synthetic, material
- GSE296151 Identifying and Exploiting Combinatorial Synthetic Lethality by Characterizing Adaptive Kinome Rewiring of EGFRvIII-driven Glioblastoma 80 samples shares synthetic
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.