Nanopore long-read RNA sequencing in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed HeLa cells
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: 6 conditions, mostly in duplicateGroups 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
- De novo assembly of nuclear stress bodies rearranges and enhances NFIL3 to restrain acute inflammatory responsesCell · 2025
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 GSE277764_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 PRJNA1163900 and SRA study SRP534081. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 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.
- GSM8529146 nanopore_polya_plus_UN_rep1 nanopore_polya_plus_UN
- GSM8529147 nanopore_polya_plus_UN_rep2 nanopore_polya_plus_UN
- GSM8529148 nanopore_polya_plus_HS_rep1 nanopore_polya_plus_HS
- GSM8529149 nanopore_polya_plus_HS_rep2 nanopore_polya_plus_HS
- GSM8529150 nanopore_polya_plus_SA_rep1 nanopore_polya_plus_SA
- GSM8529151 nanopore_polya_plus_SA_rep2 nanopore_polya_plus_SA
- GSM8529152 nanopore_ribo_minus_UN_rep1 nanopore_ribo_minus_UN
- GSM8529153 nanopore_ribo_minus_UN_rep2 nanopore_ribo_minus_UN
- GSM8529154 nanopore_ribo_minus_HS_rep1 nanopore_ribo_minus_HS
- GSM8529155 nanopore_ribo_minus_HS_rep2 nanopore_ribo_minus_HS
- GSM8529156 nanopore_ribo_minus_SA_rep1 nanopore_ribo_minus_SA
- GSM8529157 nanopore_ribo_minus_SA_rep2 nanopore_ribo_minus_SA
- GSE278916 RNA sequencing in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed HeLa,HUVEC and THP-1 cells 18 samples shares untreated, arsenite, stressed, sodium, shock, heat
- GSE280712 TSA-sequencing in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed HeLa cells 8 samples shares untreated, arsenite, stressed, sodium, shock, heat
- GSE280307 ATAC-sequencing in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed THP-1 cells 6 samples shares untreated, arsenite, stressed, sodium, shock, heat
- GSE293661 A nanopore long-read transcriptome in pancreatic cancer cells 20 samples shares long-read, nanopore
- GSE312820 Effect of cantharidin sodium treatment on gene expression in AGS and MKN1 gastric cancer cell lines (treated vs. untreated groups) 12 samples shares untreated, sodium
- GSE223088 Long-read nanopore sequencing (Nanopore-seq) of PQBP1 knockdown in ovarian cancer cells 6 samples shares long-read, nanopore
- GSE293395 Nanopore long-reads sequencing of hepatitis A virus RNAs 6 samples shares long-read, nanopore
- GSE226080 Nanopore long-read sequencing from Nutlin-3a-treated MCF-7 cells 2 samples shares long-read, nanopore
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.