Transcriptomic and Epigenomic Signatures Distinguish High- and Low-Risk Endotypes for Liver Tumor Development
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 307 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
- Mus musculus (mouse)
- Samples
- 307 samples: 292 distinct titles, 15 of them repeatedGroups 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
- Transcriptomic and epigenomic signatures distinguish high- and low-risk endotypes for liver tumor developmentEnvironmental and molecular mutagenesis · 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 GSE272931_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 PRJNA1139313 and SRA study SRP521796. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 307 sample titles: 292 distinct titles with little repetition. 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.
- GSM8414961 Liver_Veh_1M5V_27ac_2018
- GSM8414962 Liver_Veh_2M5V_27ac_2018
- GSM8414963 Liver_Veh_3M5V_27ac_2018
- GSM8414964 Liver_Veh_4M5V_27ac_2018
- GSM8414965 Liver_Veh_5M5V_27ac_2018
- GSM8414966 Liver_Veh_6M5V_27ac_2018
- GSM8414967 Liver_Veh_4M5V_27ac_2021
- GSM8414968 Liver_Veh_5M5V_27ac_2021
- GSM8414969 Liver_Veh_9M5V_27ac_2021
- GSM8414970 Liver_HR_1M5T_27ac_2018
- GSM8414971 Liver_LR_2M5T_27ac_2018
- GSM8414972 Liver_LR_3M5T_27ac_2018
- GSM8414973 Liver_HR_4M5T_27ac_2018
- GSM8414974 Liver_LR_5M5T_27ac_2018
- GSM8414975 Liver_LR_6M5T_27ac_2018
- GSM8414976 Liver_HR_10M5T_27ac_2022
- GSM8414977 Liver_LR_11M5T_27ac_2022
- GSM8414978 Liver_HR_12M5T_27ac_2022
- GSM8414979 Liver_HR_13M5T_27ac_2022
- GSM8414980 Liver_LR_14M5T_27ac_2022
- GSM8414981 Liver_HR_17M5T_27ac_2022
- GSM8414982 Liver_LR_18M5T_27ac_2022
- GSM8414983 Liver_HR_25M5T_27ac_2022
- GSM8414984 Liver_HR_15M5T_27ac_2021
- GSM8414985 Liver_LR_16M5T_27ac_2021
- GSM8414986 Liver_HR_4M5T_27ac_2021
- GSM8414987 Liver_LR_5M5T_27ac_2021
- GSM8414988 Liver_LR_6M5T_27ac_2021
- GSM8414989 Liver_Veh_1M5V_4me1_2018
- GSM8414990 Liver_Veh_2M5V_4me1_2018
- GSM8414991 Liver_Veh_3M5V_4me1_2018
- GSM8414992 Liver_Veh_4M5V_4me1_2018
- GSM8414993 Liver_Veh_5M5V_4me1_2018
- GSM8414994 Liver_Veh_6M5V_4me1_2018
- GSM8414995 Liver_Veh_4M5V_4me1_2021
- GSM8414996 Liver_Veh_5M5V_4me1_2021
- GSM8414997 Liver_Veh_9M5V_4me1_2021
- GSM8414998 Liver_HR_1M5T_4me1_2018
- GSM8414999 Liver_LR_2M5T_4me1_2018
- GSM8415000 Liver_LR_3M5T_4me1_2018
+ 267 more — browse all 307 samples with per-sample file links →
- GSE272927 Transcriptomic and Epigenomic Signatures Distinguish High- and Low-Risk Endotypes for Liver Tumor Development [ChIP-Seq] 217 samples shares distinguish, epigenomic, signatures, endotypes, low-risk, liver
- GSE272929 Transcriptomic and Epigenomic Signatures Distinguish High- and Low-Risk Endotypes for Liver Tumor Development [RNA-Seq liver] 75 samples shares distinguish, epigenomic, signatures, endotypes, low-risk, liver
- GSE272930 Transcriptomic and Epigenomic Signatures Distinguish High- and Low-Risk Endotypes for Liver Tumor Development [RNA-Seq blood] 15 samples shares distinguish, epigenomic, signatures, endotypes, low-risk, liver
- GSE301751 Therapeutic Efficacy, Biomarker Signatures and Translatability of Semaglutide in the Liver Biopsy-Confirmed GAN DIO-MASH Mouse Model (study 7/9) 53 samples shares signatures, liver
- GSE310507 Therapeutic Efficacy, Biomarker Signatures and Translatability of Semaglutide in the Liver Biopsy-Confirmed GAN DIO-MASH Mouse Model (study 6) 24 samples shares signatures, liver
- GSE293636 Genomic and Behavioral Signatures of Selection for Ethanol Preference from the Heterogeneous Stock Collaborative Cross Mice – The Central Nucleus of the Amygdala II 32 samples shares signatures
- GSE268992 Epigenomic preconditioning of peripheral monocytes determines their transcriptional response to the tumor microenvironment 31 samples shares epigenomic
- GSE281967 Functional mapping of epigenomic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes [bullk ATAC-seq] 21 samples shares epigenomic
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.