Nuclear PTK7 Interacts with DNA-PK Drives DNA Repair and Immune Evasion in Triple-negative Breast Cancer
RNA-seq (gene expression) · human · 9 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
- Breast cancerThis series is part of our curated briefing on it.
- Samples
- 9 samples: 3 × PTK7NC， vs 3 × PTK7KO1， vs 3 × PTK7KO2，Groups 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.
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 GSE302992_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 PRJNA1293315 and SRA study SRP601769. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 3 replicated groups read from 9 sample titles; they account for 9 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.
- GSM9115288 PTK7NC，rep1 PTK7NC，
- GSM9115289 PTK7NC，rep2 PTK7NC，
- GSM9115290 PTK7NC，rep3 PTK7NC，
- GSM9115291 PTK7KO1，rep1 PTK7KO1，
- GSM9115292 PTK7KO1，rep2 PTK7KO1，
- GSM9115293 PTK7KO1，rep3 PTK7KO1，
- GSM9115294 PTK7KO2，rep1 PTK7KO2，
- GSM9115295 PTK7KO2，rep2 PTK7KO2，
- GSM9115296 PTK7KO2，rep3 PTK7KO2，
- GSE104193 Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-β signalling and malignant features in vitro and in vivo 32 samples same disease briefing
- GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
- GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing
- GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing
- GSE306599 DNA-PK Mediated CRTC2 Phosphorylation Promotes CRTC2 Relocation from Transcription to Repair Complexes Enhancing NHEJ and Suppressing Abscopal Effect [RNA-Seq] 6 samples shares dna-pk, repair
- GSE253744 Phase separation of phospho-HDAC6 drives aberrant chromatin architecture in triple-negative breast cancer [RNA-seq] 22 samples shares triple-negative, drives
- GSE277698 Extracellular Nicotinamide Phosphoribosyltransferase (eNAMPT) Drives Abnormal Pericyte-Rich Vasculature in Triple-Negative Breast Cancer 20 samples shares triple-negative, drives
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.