Multiome analysis of tumors isolated from Apc cKO; Kras-mutant animals
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- 12 samples: 12 samples, each with a distinct title — no replicated groupsGroups 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 GSE301967_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 PRJNA1287795 and SRA study SRP598770. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 12 sample titles: 12 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.
- GSM9092929 Apc_KO_Kras_G12D_rep1_atac
- GSM9092930 Apc_KO_Kras_G12D_rep2_atac
- GSM9092931 Apc_KO_Kras_Q61R_rep1_atac
- GSM9092932 Apc_KO_Kras_WT_rep1_atac
- GSM9092933 Apc_KO_Kras_WT_rep2_atac
- GSM9092934 Apc_KO_Kras_WT_rep3_atac
- GSM9092935 Apc_KO_Kras_G12D_rep1_gex
- GSM9092936 Apc_KO_Kras_G12D_rep2_gex
- GSM9092937 Apc_KO_Kras_Q61R_rep1_gex
- GSM9092938 Apc_KO_Kras_WT_rep1_gex
- GSM9092939 Apc_KO_Kras_WT_rep2_gex
- GSM9092940 Apc_KO_Kras_WT_rep3_gex
- GSE303719 SnRNAseq of tumors isolated from Apc cKO; Kras-mutant animals 12 samples shares kras-mutant, isolated, animals
- GSE301970 Multiome analysis of Kras-mutant intestinal epithelium 10 days post-recombination 20 samples shares kras-mutant, multiome
- GSE327960 Transcription profiles of mouse microglia isolated by FACS from WT and Grn KO animals, separated by lipofuscin levels [hex001110] 24 samples shares isolated, animals
- GSE309545 Inflammatory signaling differentially changes chromatin accessibility and gene expression of the PD-associated kinase LRRK2 between human and mice [multiome mouse] 64 samples shares multiome
- GSE155577 Gene expression data from epithelial and mesenchymal tumor cells isolated from E-A14 mouse mammary tumors grown in immunodeficient and immunocompetent mice 26 samples shares isolated
- GSE318068 eIF4G2-mediated Translation Initiation of Histone Modifiers is Essential for Intestinal Stem Cell Maintenance and Differentiation [Multiome] 16 samples shares multiome
- GSE318722 10X Genomics Multiome Assay (GEX + ATAC) of hypothalamic preoptic area in prenatally androgenized and control prepubertal female mice. 16 samples shares multiome
- GSE236258 Trametinib sensitizes KRAS-mutant lung adenocarcinoma tumors to PD-1/PD-L1 axis blockade via Id1 downregulation 15 samples shares kras-mutant
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.