Individual RNA-seq for different prostate cancer cells and Lucap35CR PDX treated by SR8278,JQ1,AZD5153,ENZ or by FOXA1 and NR1D1 gene knockdown or NR1D1 overexpression.
RNA-seq (gene expression) · human · 26 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
- Homo sapiens (human)
- Topic
- Prostate cancerThis series is part of our curated briefing on it.
- Samples
- 26 samples: 26 samples, each with a distinct title — no replicated groupsGroups 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
- Functional inversion of circadian regulator REV-ERBα leads to tumorigenic gene reprogrammingProceedings of the National Academy of Sciences of the United States of America · 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 GSE260725_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 PRJNA1082794 and SRA study SRP492905. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 26 sample titles: 26 distinct titles with little repetition. 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.
- GSM8123021 22RV1_shNR1D1
- GSM8123022 22RV1_shctrl
- GSM8123023 C42B_5uM_SR8278
- GSM8123024 C42B_ENZ
- GSM8123025 C42B_Veh_for_ENZ
- GSM8123026 C42B_Veh_for_SR8278
- GSM8123027 C42B_empty
- GSM8123028 C42B_oe_NR1D1
- GSM8123029 C42B_oe_NR1D1_siFOXA1
- GSM8123030 C42B_oe_NR1D1_sictrl
- GSM8123031 C42B_shNR1D1
- GSM8123032 C42B_shcontrol
- GSM8123033 C42B_siFOXA1
- GSM8123034 C42B_sictrl_for_siFOXA1
- GSM8123035 lucap35cr_comb1
- GSM8123036 lucap35cr_jq1
- GSM8123037 lucap35cr_sr8278
- GSM8123038 lucap35cr_veh
- GSM8279363 RWPE1_SR8278
- GSM8279364 RWPE1_Veh
- GSM8279365 RWPE1_shNR1D1
- GSM8279366 RWPE1_shcontrol
- GSM8279367 hepa16_SR8278
- GSM8279368 hepa16_Veh
- GSM8279369 hepa16_shNR1D1
- GSM8279370 hepa16_shcontrol
- GSE115501 RNA sequencing on circulating tumor cells from prostate cancer patients 136 samples same disease briefing
- GSE222467 The RNA binding proteins LARP4A and LARP4B promote tumour growth and metastasis in prostate cancer and osteosarcoma 12 samples same disease briefing
- GSE242541 ONECUT2 is a druggable driver of luminal to basal breast cancer plasticity 12 samples same disease briefing
- GSE300947 A novel six-biomarker panel identified from male breast cancer-associated fibroblasts demonstrates prognostic power for prostate tumors 6 samples same disease briefing
- GSE71008 Plasma extracellular RNA profiles in healthy and cancer patients 192 samples same disease briefing
- GSE120181 Human prostate cancer cell line, 22Rv1: Control vs. luteolin treatment 2 samples same disease briefing
- GSE245733 HNF4G and FOXA1 are context-specific drivers of pancreatic cancer progression [RNA-seq] 29 samples shares foxa1
- GSE245734 HNF4G and FOXA1 are context-specific drivers of pancreatic cancer progression 225 samples shares foxa1
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.