CAGE-seq from Nutlin-3a-treated MCF-7, U2OS, and RPE-1 cells
RNA-seq (gene expression) · human · 20 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
- 20 samples
- 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
- Gene regulation by convergent promotersNature genetics · 2025
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 GSE223512_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 PRJNA926621 and SRA study SRP418722. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 20 more — browse all 20 samples with per-sample file links →
- GSE223513 QuantSeq from Nutlin-3a-treated MCF-7, U2OS, and RPE-1 cells 20 samples shares mcf-7, rpe-1, u2os, nutlin-3a-treated
- GSE250017 ATAC-seq from Nutlin-3a-treated MCF-7 cells 8 samples shares mcf-7, nutlin-3a-treated
- GSE297342 Assessing the Effects of Silver Nanoparticles on ARPE-19 Cells via High-Throughput Phenotypic Profiling with the Cell Painting Assay. 88 samples shares rpe-1
- GSE290998 RNA-sequencing of HCMV-infected ARPE-19 and MCF10A cells 48 samples shares rpe-1
- GSE280432 RNA sequencing of non-targetting ASOs on HEK293 and U2OS cells 36 samples shares u2os
- GSE224502 RNA-Seq profiles of pancreatic adenocarcinoma PANC-1 and osteosarcoma U2OS cells with Pin1 knocking down 18 samples shares u2os
- GSE264653 Effect of MITF depletion on gene expression in U2OS cells 18 samples shares u2os
- GSE241306 Effect of TOP1 knockdown and/or RNase H OE on the transcriptional profile of MCF-7 cells [CEL_Seq] 16 samples shares mcf-7
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.