An atlas of the human liver diurnal transcriptome and its perturbation by hepatitis C virus infection
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 56 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Samples
- 56 samples: 36 × SGroups 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
- An atlas of the human liver diurnal transcriptome and its perturbation by hepatitis C virus infectionNature communications · 2024
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 GSE200812_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA826852 and SRA study SRP370262. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 36 samples.
How we read this: 1 replicated groups read from 56 sample titles; they account for 36 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.
- GSM6044016 3657
- GSM6044017 3907
- GSM6044018 3950
- GSM6044019 4500
- GSM6044020 4695
- GSM6044021 4915
- GSM6044022 S51_H3k27ac
- GSM6044023 S83_H3k27ac
- GSM6044024 S87_H3k27ac
- GSM6044025 S93_H3k27ac
- GSM6044026 S98_H3k27ac
- GSM6044027 S16_Input
- GSM6044028 S65_Input
- GSM6044029 S65_H3k27ac
- GSM6044030 S73_H3k27ac
- GSM6044031 S44_H3k27ac
- GSM6044032 S16_H3k27ac
- GSM6044033 S23_H3k27ac
- GSM6044034 S54_H3k27ac
- GSM6044035 S77_H3k27ac
- GSM6044036 S76781 S
- GSM6044037 S76774 S
- GSM6044038 S76775 S
- GSM6044039 S76766 S
- GSM6044040 S76768 S
- GSM6044041 S76767 S
- GSM6044042 S76776 S
- GSM6044043 S76777 S
- GSM6044044 S76785 S
- GSM6044045 S76763 S
- GSM6044046 S76762 S
- GSM6044047 S76765 S
- GSM6044048 S76797 S
- GSM6044049 S76796 S
- GSM6044050 S76795 S
- GSM6044051 S76764 S
- GSM6044052 S76770 S
- GSM6044053 S76771 S
- GSM6044054 S76794 S
- GSM6044055 S76793 S
+ 16 more — browse all 56 samples with per-sample file links →
- GSE173736 Transcriptional regulation of liver lipotoxicity in non-alcoholic steatohepatitis 52 samples shares hepatitis, liver
- GSE288077 Metabolic dysfunction-associated steatotic liver disease may increase intrahepatic interferon gene signatures in patients with chronic hepatitis B 35 samples shares hepatitis, liver
- GSE189600 Hepatocytes demarcated by EphB2 contribute to the progression of non-alcoholic steatohepatitis 21 samples shares hepatitis
- GSE275942 Estrogen Receptor 1 Signaling in Hepatic Stellate Cells Designates Resistance to Liver Fibrosis 11 samples shares liver
- GSE296748 Dp16 liver transcriptome 78 samples shares liver
- GSE320163 Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity [ATAC-Seq] 377 samples shares perturbation
- GSE320162 Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity [RNA-Seq] 347 samples shares perturbation
- GSE305923 exoWNT3A/RSPO1 improves HE to LPC differentiation, hepatic organoids growth, and different acute and chronic liver injuries. 72 samples shares liver
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.