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Single Cell Analysis Reveals The Essential Role of TGFbeta Pathway in Shaping Immune-suppressive Microenvironment and Promoting CRPC Development (bulk RNA-Seq)

GSE270743 Mus musculus (mouse) Single-cell RNA-seq 48 samples Submitted 2024/11/29 Platform GPL18480
At a glance

Single-cell RNA-seq · mouse · 48 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Mus musculus (mouse)
Samples
48 samples: 14 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.
Summary (written by the submitters)
To understand the dynamic changes of different cell populations within the Pten-null prostate cancer model in response to ADT, we carried out scRNA-seq transcriptome analysis on CD45- and CD45+ FACS-sorted cells from Pten-null intact (CP), early-(nmCRPC-4wks) and late-(nmCRPC-12wks) stage castrated prostates, respectively.
Read the full summary ↓
To systematically investigate the effects of androgen deprivation therapy (ADT) on the cellular landscapes of primary and nmCRPC as well as intra- and extra-tumoral immune cells and their functional status at single cell level, we conducted scRNA-seq on CD45+ cells from bone marrow, blood, spleen and thymus of intact, early- and late-stage castrated Pten-null mice.
This dataset
Open GSE270743 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE270743_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1128106 and SRA study SRP516005. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
14 conditions, mostly in triplicate
Epithelial cells from prostate, Castration at… ×5 Fibroblasts from prostate, Castration at 10th… ×5 CaP2 cells, Control, ×4 CaP8 cells, Control, ×4 CaP2 cells, FGF9, ×3 CaP2 cells, FGF9 + TGFβ, ×3 CaP2 cells, TGFβi + TGFβ, ×3 CaP2 cells, TGFβ, ×3 +6 more

Supports a between-group comparison across 48 samples.

How we read this: 14 replicated groups read from 48 sample titles; they account for 48 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.

Samples in this study

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.