bulk RNAseq of Ccd18-Co cell line treated with cytokine mix and/or epigenetic modulator
RNA-seq (gene expression) · human · 16 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
- 16 samples: 4 × unstim_dmso vs 4 × combo_dmso vs 4 × combo_belinostat vs 4 × combo_gskj4Groups 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 GSE307519_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 PRJNA1321909 and SRA study SRP618451. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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.
- GSM9225896 unstim_dmso 1 unstim_dmso
- GSM9225897 unstim_dmso 2 unstim_dmso
- GSM9225898 unstim_dmso 3 unstim_dmso
- GSM9225899 unstim_dmso 4 unstim_dmso
- GSM9225900 combo_dmso 13 combo_dmso
- GSM9225901 combo_dmso 14 combo_dmso
- GSM9225902 combo_dmso 15 combo_dmso
- GSM9225903 combo_dmso 16 combo_dmso
- GSM9225904 combo_belinostat 17 combo_belinostat
- GSM9225905 combo_belinostat 18 combo_belinostat
- GSM9225906 combo_belinostat 19 combo_belinostat
- GSM9225907 combo_belinostat 20 combo_belinostat
- GSM9225908 combo_gskj4_21 combo_gskj4
- GSM9225909 combo_gskj4_22 combo_gskj4
- GSM9225910 combo_gskj4_23 combo_gskj4
- GSM9225911 combo_gskj4_24 combo_gskj4
- GSE232076 In vitro reconstitution of epigenetic reprogramming in the human germ line [RNA-Seq] 89 samples shares epigenetic, line
- GSE297046 Human ribomes reveal DNA-embedded ribonucleotides as epigenetic modulators of DNA supercoiling 40 samples shares epigenetic, modulator
- GSE264693 Cytokines drive the formation of memory-like NK cell subsets via epigenetic rewiring and transcriptional mechanisms [ATAC-seq] 39 samples shares epigenetic, cytokine
- GSE294916 IFNγ-induced memory in human macrophages is not sustained by epigenetic changes but the durability of the cytokine itself [CUT&Tag] 28 samples shares epigenetic, cytokine
- GSE300717 RNA-seq and ATAC-seq analysis of 5-azacytidine-treated HepG2 cells reveals epigenetic reactivation of BFL-1 and SQOR in hepatocellular carcinoma 17 samples shares epigenetic, treated
- GSE277909 Epigenetic attenuation of interferon signaling drives aging-related improvements in systemic lupus 271 samples shares epigenetic
- GSE234181 Long-term multi-modal recording reveals epigenetic adaptation routes in dormant breast cancer cells [scRNA-Seq] 184 samples shares epigenetic
- GSE301357 The airway transcriptome in type2 cytokine biomarker-high and -low severe asthma 129 samples shares cytokine
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.