RARg bookmarking functions in prostate cancer (RNA-Seq)
RNA-seq (gene expression) · human · 18 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
- 18 samples: 6 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.
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 GSE255227_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 PRJNA1073991 and SRA study SRP488548. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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.
- GSM8066833 HPr1-AR_Scr.1 HPr1-AR_Sc
- GSM8066834 HPr1-AR_Scr.2 HPr1-AR_Sc
- GSM8066835 HPr1-AR_Scr.3 HPr1-AR_Sc
- GSM8066836 HPr1-AR_Mir96.1 HPr1-AR_Mir96
- GSM8066837 HPr1-AR_Mir96.2 HPr1-AR_Mir96
- GSM8066838 HPr1-AR_Mir96.3 HPr1-AR_Mir96
- GSM8066839 LNCaP_Scr.1 LNCaP_Sc
- GSM8066840 LNCaP_Scr.2 LNCaP_Sc
- GSM8066841 LNCaP_Scr.3 LNCaP_Sc
- GSM8066842 LNCaP_Mir96.1 LNCaP_Mir96
- GSM8066843 LNCaP_Mir96.2 LNCaP_Mir96
- GSM8066844 LNCaP_Mir96.3 LNCaP_Mir96
- GSM8066845 22RV1_Scr.1 22RV1_Sc
- GSM8066846 22RV1_Scr.2 22RV1_Sc
- GSM8066847 22RV1_Scr.3 22RV1_Sc
- GSM8066848 22RV1_Mir96.1 22RV1_Mir96
- GSM8066849 22RV1_Mir96.2 22RV1_Mir96
- GSM8066850 22RV1_Mir96.3 22RV1_Mir96
- GSE115501 RNA sequencing on circulating tumor cells from prostate cancer patients 136 samples same disease briefing · shares prostate
- GSE222467 The RNA binding proteins LARP4A and LARP4B promote tumour growth and metastasis in prostate cancer and osteosarcoma 12 samples same disease briefing · shares prostate
- GSE300947 A novel six-biomarker panel identified from male breast cancer-associated fibroblasts demonstrates prognostic power for prostate tumors 6 samples same disease briefing · shares prostate
- GSE120181 Human prostate cancer cell line, 22Rv1: Control vs. luteolin treatment 2 samples same disease briefing · shares prostate
- GSE242541 ONECUT2 is a druggable driver of luminal to basal breast cancer plasticity 12 samples same disease briefing
- GSE71008 Plasma extracellular RNA profiles in healthy and cancer patients 192 samples same disease briefing
- GSE297742 Bulk RNA-seq of primary tumor biopsy samples from prostate adenocarcinoma patients 234 samples shares prostate, rna-seq
- GSE319641 RNA-Seq profiling of pre- and on-treatment tumor samples from breast cancer patients enrolled in the NeoTRIP trial. 401 samples shares rna-seq
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.