Thymic epithelial organoids mediate T cell development
RNA-seq (gene expression) · mouse · 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
- Mus musculus (mouse)
- Samples
- 11 samples: 2 × Freshly extracted TECs biol vs 2 × 2D cultured TECs biol vs 2 × TEC organoids D3 biol vs 2 × TEC organoids D7 biolGroups 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
- Thymic epithelial organoids mediate T-cell developmentDevelopment (Cambridge, England) · 2024
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 GSE240698_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 PRJNA1004630 and SRA study SRP454732. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 4 replicated groups read from 11 sample titles; they account for 8 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.
- GSM7707603 Freshly extracted TECs biol rep1 Freshly extracted TECs …
- GSM7707604 Freshly extracted TECs biol rep2 Freshly extracted TECs …
- GSM7707605 2D cultured TECs biol rep1 2D cultured TECs biol
- GSM7707606 2D cultured TECs biol rep2 2D cultured TECs biol
- GSM7707607 TEC organoids D3 biol rep1 TEC organoids D3 biol
- GSM7707608 TEC organoids D3 biol rep2 TEC organoids D3 biol
- GSM7707609 TEC organoids D7 biol rep1 TEC organoids D7 biol
- GSM7707610 TEC organoids D7 biol rep2 TEC organoids D7 biol
- GSM7707611 ORFTOC FTOC - GEX
- GSM7707612 ORFTOC FTOC - TCR
- GSM7707613 ORFTOC FTOC - HTO
- GSE220665 The Transcriptional Cofactor SKI Regulates Medullary Thymic Epithelial Cell Differentiation and Peripheral T Cell Responses 42 samples shares epithelial, thymic
- GSE249753 Age-related epithelial defects limit thymic function and regeneration [single cell; Foxn1Lin] 3 samples shares epithelial, thymic
- GSE333480 METTL3-mediated m6A modification controls Tcra recombination center formation and thymic T cell development 98 samples shares mediate, thymic
- GSE240020 Age-related epithelial defects limit thymic function and regeneration 51 samples shares epithelial, thymic
- GSE319684 Timecourse of FACS sorted Ly6C+ monocytes, tissue resident alveolar macrophages (trAMs), monocyte derived alveolar macrophages (bmAMs) and epithelial cells from SARS-CoV-2 (maVie16) vs. IAV (PR8) infected mouse lungs 176 samples shares epithelial
- GSE308220 Circadian rhythms in microglia mediate early life synaptic development in a sex-specific manner. 75 samples shares mediate
- GSE311286 Analysis of murine normal pancreatic organoids, pancreatitis-derived organoids, and PDAC organoids in complete media and of pancreatitis-derived organoids, and PDAC organoids cultured alone or cocultured with pancreatic stellate cells in reduced media 75 samples shares organoids
- GSE331176 Phagosome-mediated activation of STING by purine and pyrimidine-based bacterial cyclic dinucleotides 380 samples shares mediate
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.