The receptor protein tyrosine phosphatase PTPRK promotes intestinal repair and catalysis-independent tumor suppression
RNA-seq (gene expression) · human · 25 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)
- Samples
- 25 samples: 5 conditions, mostly with about 5 replicates eachGroups 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
- The receptor protein tyrosine phosphatase PTPRK promotes intestinal repair and catalysis-independent tumour suppressionJournal of cell science · 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 GSE254156_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 PRJNA1068645 and SRA study SRP485724. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 25 samples.
How we read this: 5 replicated groups read from 25 sample titles; they account for 25 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.
- GSM8035149 CS_rep1 CS
- GSM8035150 CS_rep2 CS
- GSM8035151 CS_rep3 CS
- GSM8035152 CS_rep4 CS
- GSM8035153 CS_rep5 CS
- GSM8035154 KO_rep1 KO
- GSM8035155 KO_rep2 KO
- GSM8035156 KO_rep3 KO
- GSM8035157 KO_rep4 KO
- GSM8035158 KO_rep5 KO
- GSM8035159 Rescue_rep1 Rescue
- GSM8035160 Rescue_rep2 Rescue
- GSM8035161 Rescue_rep3 Rescue
- GSM8035162 Rescue_rep4 Rescue
- GSM8035163 Rescue_rep5 Rescue
- GSM8035164 Rescue_rep6 Rescue
- GSM8035165 RQ_rep1 RQ
- GSM8035166 RQ_rep2 RQ
- GSM8035167 RQ_rep3 RQ
- GSM8035168 RQ_rep4 RQ
- GSM8035169 WT_rep1 WT
- GSM8035170 WT_rep2 WT
- GSM8035171 WT_rep3 WT
- GSM8035172 WT_rep4 WT
- GSM8035173 WT_rep5 WT
- GSE250614 Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst 225 samples shares suppression, promotes
- GSE246293 Astrocyte-driven suppression of tumor-specific T-cell immunity in glioblastoma 102 samples shares suppression
- GSE244945 NOTCH1 reverses immune suppression in small cell lung cancer through reactivation of STING [RNA-seq] 69 samples shares suppression
- GSE322659 Nitric Oxide Synthase 2-Dependent Metabolic Dysregulation, Immunosuppression, and Genomic Instability in Metastatic Triple-Negative Breast Cancer 24 samples shares suppression
- GSE270903 Hypoxic Memory Mediates Prolonged Tumor Intrinsic Type I Interferon Suppression to Promote Breast Cancer Progression 8 samples shares suppression
- GSE244947 NOTCH1 reverses immune suppression in small cell lung cancer through reactivation of STING 87 samples shares suppression
- GSE270431 Neutrophils recruited by NKX2-1 suppression via activation of CXCLs/CXCR2 axis promote lung adenocarcinoma progression 12 samples shares suppression
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.