3'UTR-dependent activity of transcription factors and chromatin regulators [RNA-seq]
RNA-seq (gene expression) · human · 21 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
- 21 samples: 7 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.
- Paper
- mRNA 3'UTRs chaperone intrinsically disordered regions to control protein activitybioRxiv : the preprint server for biology · 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 GSE301135_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 PRJNA1284100 and SRA study SRP596002. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 21 samples.
How we read this: 7 replicated groups read from 21 sample titles; they account for 21 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.
- GSM9076148 U2OS cells, GFP only, Rep1 U2OS cells, GFP only,
- GSM9076149 U2OS cells, GFP only, Rep2 U2OS cells, GFP only,
- GSM9076150 U2OS cells, GFP only, Rep3 U2OS cells, GFP only,
- GSM9076151 U2OS cells, GFP-MYC-NU, Rep1 U2OS cells, GFP-MYC-NU,
- GSM9076152 U2OS cells, GFP-MYC-NU, Rep2 U2OS cells, GFP-MYC-NU,
- GSM9076153 U2OS cells, GFP-MYC-NU, Rep3 U2OS cells, GFP-MYC-NU,
- GSM9076154 U2OS cells, GFP-MYC-U, Rep1 U2OS cells, GFP-MYC-U,
- GSM9076155 U2OS cells, GFP-MYC-U, Rep2 U2OS cells, GFP-MYC-U,
- GSM9076156 U2OS cells, GFP-MYC-U, Rep3 U2OS cells, GFP-MYC-U,
- GSM9076157 MCF7 cells, shCtrl, Rep1 MCF7 cells, shCtrl,
- GSM9076158 MCF7 cells, shCtrl, Rep2 MCF7 cells, shCtrl,
- GSM9076159 MCF7 cells, shCtrl, Rep3 MCF7 cells, shCtrl,
- GSM9076160 MCF7 cells, shKDM6A, Rep1 MCF7 cells, shKDM6A,
- GSM9076161 MCF7 cells, shKDM6A, Rep2 MCF7 cells, shKDM6A,
- GSM9076162 MCF7 cells, shKDM6A, Rep3 MCF7 cells, shKDM6A,
- GSM9076163 MCF7 cells, shKDM6A + HA-KDM6A-NU, Rep1 MCF7 cells, shKDM6A + H…
- GSM9076164 MCF7 cells, shKDM6A + HA-KDM6A-NU, Rep2 MCF7 cells, shKDM6A + H…
- GSM9076165 MCF7 cells, shKDM6A + HA-KDM6A-NU, Rep3 MCF7 cells, shKDM6A + H…
- GSM9076166 MCF7 cells, shKDM6A + HA-KDM6A-U, Rep1 MCF7 cells, shKDM6A + H…
- GSM9076167 MCF7 cells, shKDM6A + HA-KDM6A-U, Rep2 MCF7 cells, shKDM6A + H…
- GSM9076168 MCF7 cells, shKDM6A + HA-KDM6A-U, Rep3 MCF7 cells, shKDM6A + H…
- GSE337246 Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [scRNA-Seq organoids] 35 samples shares chromatin, rna-seq
- GSE189357 Spatiotemporal transcriptional atlas of lung adenocarcinoma from adenocarcinoma in situ to invasive carcinoma [scRNA-seq] 9 samples shares transcription, rna-seq
- GSE296192 Hypoxic regulation of chromatin and gene transcription 98 samples shares transcription, chromatin
- GSE302930 Epigenetic Atlas of Bladder Cancer Reveals Master Transcription Factors and Risk-Associated Regulatory Elements in Luminal and Basal-Squamous Molecular Subtypes 92 samples shares transcription, factors
- GSE301298 Functional redundancy between UTY and UTX in regulating the localization of transcription factors involved in pluripotency 88 samples shares transcription, factors
- GSE296190 Hypoxic regulation of chromatin and gene transcription [ChIP-seq] 84 samples shares transcription, chromatin
- GSE293334 Allelic topological centering by transcription factors drives oncogenic multi-enhancer transcriptional regulation [ChIP-seq] 60 samples shares transcription, factors
- GSE296831 Epigenetic Context Defines the Transcriptional Activity of Canonical and Noncanonical NF-kappaB Signaling in Pancreatic Cancer [ChIP-Seq] 48 samples shares transcription, activity
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.