Notch signaling suppresses neuroendocrine differentiation and alters the tumor immune microenvironment in advanced prostate cancer
RNA-seq (gene expression) · mouse · 13 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
- 13 samples: 4 × TKO_Notch_12W_NT vs 2 × TKO_12W_T vs 2 × TKO vs 2 × TKO_NotchGroups 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
- Notch signaling suppresses neuroendocrine differentiation and alters the immune microenvironment in advanced prostate cancerThe Journal of clinical investigation · 2024
Read the full summary ↓
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 GSE235036_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 PRJNA984227 and SRA study SRP444058. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 4 replicated groups read from 13 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.
- GSM7493507 SKO_58W_T2057
- GSM7493508 SKO_45W_T1636
- GSM7493509 SKO_12W_T2001
- GSM7493510 TKO_12W_T2789 TKO_12W_T
- GSM7493511 TKO_12W_T1883 TKO_12W_T
- GSM7493512 TKO_Notch_12W_NT449 TKO_Notch_12W_NT
- GSM7493513 TKO_Notch_12W_NT504 TKO_Notch_12W_NT
- GSM7493514 TKO_Notch_12W_NT505 TKO_Notch_12W_NT
- GSM7493515 TKO_Notch_12W_NT497 TKO_Notch_12W_NT
- GSM7493516 TKO_12 TKO
- GSM7493517 TKO_15 TKO
- GSM7493518 TKO_Notch_10 TKO_Notch
- GSM7493519 TKO_Notch_13 TKO_Notch
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- GSE297048 EZH2 alters aggressive variant prostate cancer subtype evolution, but is not required for neuroendocrine prostate cancer [ChIP-seq] 40 samples shares neuroendocrine, prostate, alters
- GSE271053 A forward genetic screen identifies Sirtuin1 as a driver of neuroendocrine prostate cancer [RNA-Seq] 43 samples shares neuroendocrine, prostate
- GSE264598 Prostate adenocarcinoma transition to neuroendocrine small cell tumors requires ASCL1 12 samples shares neuroendocrine, prostate
- GSE271066 A forward genetic screen identifies Sirtuin1 as a driver of neuroendocrine prostate cancer. 44 samples shares neuroendocrine, prostate
- GSE218178 Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance 183 samples shares microenvironment
- GSE218173 Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance [acid] 150 samples shares microenvironment
- GSE259380 TG6050, an oncolytic vaccinia virus encoding interleukin-12 and anti-CTLA-4 antibody induces tumor regression through profound tumor microenvironment remodeling and strong antitumor adaptive immune response [RNA-seq] 149 samples shares microenvironment
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.