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PiR-hsa-4447944 serves as an oncogenic mediator in prostate cancer and promotes the development of castration resistance by inhibiting NEFH expression

GSE248169 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2024/07/17 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 12 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
12 samples: 3 × LNCaP-piR-Ctrl vs 3 × LNCaP-piR-hsa-4447944 vs 3 × 22RV1-piR-Ctrl vs 3 × 22RV1-piR-hsa-4447944Groups 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
PiRNA-4447944 promotes castration-resistant growth and metastasis of prostate cancer by inhibiting NEFH expression through forming the piRNA-4447944-PIWIL2-NEFH complexInternational journal of biological sciences · 2024
Summary (written by the submitters)
PiR-hsa-4447944 showed a significantly higher expression level in both CRPC tissues and CRPC cell lines. Functionally, piR-hsa-4447944 overexpression conferred, whereas piR-hsa-4447944 suppression inhibited castration resistance ability in vitro and in vivo. Enforced piR-hsa-4447944 expression in vitro promoted PCa cells migration and invasion, as well as reduced cell apoptosis.
Read the full summary ↓
To explore the potential targets of piR-hsa-4447944, two PCa cells 22RV1 and LNCaP were transfected with control or piR-hsa-4447944 mimic, and then the extracted total RNA was used for mRNA sequencing and bioinformatic analysis.
Published in
PiRNA-4447944 promotes castration-resistant growth and metastasis of prostate cancer by inhibiting NEFH expression through forming the piRNA-4447944-PIWIL2-NEFH complex
Peng Q, Chen Y, Xie T et al. · International journal of biological sciences 2024 · PMID 38993562 · doi:10.7150/ijbs.96173
This dataset
Open GSE248169 in finder → Find more human RNA-seq datasets → Prostate cancer landscape →
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 GSE248169_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: 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 PRJNA1041862 and SRA study SRP472643. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38993562) ↗
Study design
3 × LNCaP-piR-Ctrl vs 3 × LNCaP-piR-hsa-4447944 vs 3 × 22RV1-piR-Ctrl vs 3 × 22RV1-piR-hsa-4447944

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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
More Prostate cancer datasets

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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.