RNA-seq and ONT full-length transcriptome profiling of HCT116 and WiDr cells treated with DMSO, GSK025, or GSK715
RNA-seq (gene expression) · human · 19 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
- 19 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.
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 GSE335198_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 PRJNA1477555 and SRA study SRP708910. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 19 samples.
How we read this: 7 replicated groups read from 19 sample titles; they account for 19 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.
- GSM9807973 HCT116 DMSO RNA-seq replicate 1 HCT116 DMSO RNA-seq
- GSM9807974 HCT116 DMSO RNA-seq replicate 2 HCT116 DMSO RNA-seq
- GSM9807975 HCT116 DMSO RNA-seq replicate 3 HCT116 DMSO RNA-seq
- GSM9807976 HCT116 GSK025 RNA-seq replicate 1 HCT116 GSK025 RNA-seq
- GSM9807977 HCT116 GSK025 RNA-seq replicate 2 HCT116 GSK025 RNA-seq
- GSM9807978 HCT116 GSK025 RNA-seq replicate 3 HCT116 GSK025 RNA-seq
- GSM9807979 HCT116 GSK715 RNA-seq replicate 1 HCT116 GSK715 RNA-seq
- GSM9807980 HCT116 GSK715 RNA-seq replicate 2 HCT116 GSK715 RNA-seq
- GSM9807981 HCT116 GSK715 RNA-seq replicate 3 HCT116 GSK715 RNA-seq
- GSM9807982 WiDr DMSO RNA-seq replicate 1 WiDr DMSO RNA-seq
- GSM9807983 WiDr DMSO RNA-seq replicate 2 WiDr DMSO RNA-seq
- GSM9807984 WiDr DMSO RNA-seq replicate 3 WiDr DMSO RNA-seq
- GSM9807985 WiDr GSK715 RNA-seq replicate 1 WiDr GSK715 RNA-seq
- GSM9807986 WiDr GSK715 RNA-seq replicate 2 WiDr GSK715 RNA-seq
- GSM9807987 WiDr GSK715 RNA-seq replicate 3 WiDr GSK715 RNA-seq
- GSM9807988 WiDr DMSO ONT full-length cDNA sequencing replicate 1 WiDr DMSO ONT full-leng…
- GSM9807989 WiDr DMSO ONT full-length cDNA sequencing replicate 2 WiDr DMSO ONT full-leng…
- GSM9807990 WiDr GSK715 ONT full-length cDNA sequencing replicate 1 WiDr GSK715 ONT full-le…
- GSM9807991 WiDr GSK715 ONT full-length cDNA sequencing replicate 2 WiDr GSK715 ONT full-le…
- GSE306466 RNA-seq of dTAG-NUDT21 HCT116 cells treated with DMSO+JTE-607 or dTAGV1+JTE-607. 8 samples shares hct116, dmso, rna-seq, treated
- GSE168618 Whole transcriptomes analyses of HGC-27 cell line treated with control DMSO, disulfiram, thiram or CX-6258 4 samples shares dmso, ont, treated
- GSE333738 Genome-wide mapping of human H4K20me3 in the HN-SCC-151 HPV-negative head and neck squamous cell carcinoma cells treated with DMSO or the SUV420H1 inhibitor A-196/siNC (control) or siSUV420H1 siRNAs. 24 samples shares dmso, ont, treated
- GSE336726 KDM5A CUT&RUN profiling of MCF7 cells treated with abemaciclib or DMSO control 5 samples shares dmso, ont, treated
- GSE254323 RNA-seq of colorectal cancer cell line HCT116 and DLD-1 cells treated with PRIMA-1met or oxaliplatin or combination therapy 24 samples shares hct116, rna-seq, treated
- GSE232612 RNA-seq on DMSO or MAK683 treated cancer cells and xenograft tumor samples 24 samples shares dmso, rna-seq, treated
- GSE300831 RNA-seq of Immortalized RAFLS treated with TNFα for 24h and DMSO or celastrol derivatives for 4h in human 12 samples shares dmso, rna-seq, treated
- GSE211773 RNA-seq in human neuroblastoma SK-N-BE(2)-C cells treated with DMSO, TSA or E6R 9 samples shares dmso, rna-seq, treated
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.