Integrated HPV18 acts as enhancer-like RNA and form phase-separated condensates to promote oncogenic genes expression.
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)
- Samples
- 12 samples: 3 × RNA-seq_HeLa_NT vs 3 × RNA-seq_HeLa_HD vs 3 × RNA-seq_HeLa_ctrlLNA vs 3 × RNA-seq_HeLa_URCLNAGroups 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
- Chimera RNA transcribed from integrated HPV18 genome with adjacent host genomic region promotes oncogenic gene expression through condensate formationGenes to cells : devoted to molecular & cellular mechanisms · 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 GSE249929_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 PRJNA1051147 and SRA study SRP477407. Searching any of these in the dataset finder brings you back here.
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.
- GSM7967293 RNA-seq_HeLa_NT_Rep1 RNA-seq_HeLa_NT
- GSM7967294 RNA-seq_HeLa_NT_Rep2 RNA-seq_HeLa_NT
- GSM7967295 RNA-seq_HeLa_NT_Rep3 RNA-seq_HeLa_NT
- GSM7967296 RNA-seq_HeLa_HD_Rep1 RNA-seq_HeLa_HD
- GSM7967297 RNA-seq_HeLa_HD_Rep2 RNA-seq_HeLa_HD
- GSM7967298 RNA-seq_HeLa_HD_Rep3 RNA-seq_HeLa_HD
- GSM7967299 RNA-seq_HeLa_ctrlLNA_Rep1 RNA-seq_HeLa_ctrlLNA
- GSM7967300 RNA-seq_HeLa_ctrlLNA_Rep2 RNA-seq_HeLa_ctrlLNA
- GSM7967301 RNA-seq_HeLa_ctrlLNA_Rep3 RNA-seq_HeLa_ctrlLNA
- GSM7967302 RNA-seq_HeLa_URCLNA_Rep1 RNA-seq_HeLa_URCLNA
- GSM7967303 RNA-seq_HeLa_URCLNA_Rep2 RNA-seq_HeLa_URCLNA
- GSM7967304 RNA-seq_HeLa_URCLNA_Rep3 RNA-seq_HeLa_URCLNA
- GSE300421 RNA promotes nucleation and oncogenic activity of chromatin-associated condensates [ChIP-Seq] 14 samples shares condensates, oncogenic, promote
- GSE273678 Phase-separated NDF−FACT condensates facilitate transcription elongation on chromatin [ChIP-Seq] 55 samples shares phase-separated, condensates
- GSE275722 Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription [ChIP-seq] 37 samples shares condensates, oncogenic
- GSE275705 Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription [RNA-seq II] 36 samples shares condensates, oncogenic
- GSE275707 Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription [CUT&TAG] 34 samples shares condensates, oncogenic
- GSE275702 Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription [RNA-seq] 20 samples shares condensates, oncogenic
- GSE306285 Disparate Leukemia Mutations Converge on Nuclear Phase-Separated Condensates 12 samples shares phase-separated, condensates
- GSE273679 Phase-separated NDF−FACT condensates facilitate transcription elongation on chromatin [CUT&Run] 11 samples shares phase-separated, condensates
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.