Engineered extrachromosomal oncogene amplifications promote tumorigenesis
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 48 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
- 48 samples: 11 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.
- Paper
- Engineered extrachromosomal oncogene amplifications promote tumorigenesisNature · 2025
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 GSE264006_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 PRJNA1100533 and SRA study SRP501851. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 28 samples.
How we read this: 11 replicated groups read from 48 sample titles; they account for 28 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.
- GSM8208706 NSC_ecMyc_RNAseq_1 NSC_ecMyc_RNAseq
- GSM8208707 NSC_ecMyc_RNAseq_2 NSC_ecMyc_RNAseq
- GSM8208708 NSC_ecMyc_RNAseq_3 NSC_ecMyc_RNAseq
- GSM8208709 NSC_p53_RNAseq_1 NSC_p53_RNAseq
- GSM8208710 NSC_p53_RNAseq_2 NSC_p53_RNAseq
- GSM8208711 NSC_p53_RNAseq_3 NSC_p53_RNAseq
- GSM8208712 MEFsecMdm2_1 MEFsecMdm2
- GSM8208713 MEFsecMdm2_2 MEFsecMdm2
- GSM8208714 MEFsecMdm2_3 MEFsecMdm2
- GSM8208715 MEFs_p53_1 MEFs_p53
- GSM8208716 MEFs_p53_2 MEFs_p53
- GSM8208717 MEFs_p53_3 MEFs_p53
- GSM8208719 HCT116_invMDM2_DN
- GSM8208720 HCT116_invMDM2_low
- GSM8208721 HCT116_invMDM2_med
- GSM8208722 HCT116_ecMDM2_DN
- GSM8208723 HCT116_ecMDM2_high
- GSM8208724 HCT116_ecMDM2_low
- GSM8208725 HCT116_ecMDM2_med
- GSM8208726 NSC_ecMyc_1_week
- GSM8208727 NSC_ecMyc_2_week
- GSM8208728 NSC_ecMyc_3_week
- GSM8208729 NSC_ecMyc_4_week
- GSM8208730 NSC_ecMyc_5_week
- GSM8208731 NSC_ecMyc_no_Cre
- GSM8208732 2_3_KC_IGO_14426_B_10_S251_L004_R1_001.fastq.gz
- GSM8208733 2_3_MZ_IGO_14426_B_3_S257_L004_R1_001.fastq.gz
- GSM8208734 2_3_Ras_MZ_IGO_14426_B_4_S258_L004_R1_001.fastq.gz
- GSM8208735 RK782R_R1.fastq.gz
- GSM8208736 RK783L_R1.fastq.gz
- GSM8208737 RK783R_R1.fastq.gz
- GSM8208738 RK784L_R1.fastq.gz
- GSM8208739 mouse_2_liver_tumor_1 mouse_2_liver_tumo
- GSM8208740 mouse_2_liver_tumor_2 mouse_2_liver_tumo
- GSM8208741 mouse_2_liver_tumor_3 mouse_2_liver_tumo
- GSM8208742 mouse_3_liver_tumor_1 mouse_3_liver_tumo
- GSM8208743 mouse_3_liver_tumor_2 mouse_3_liver_tumo
- GSM8208744 mouse_3_liver_tumor_3 mouse_3_liver_tumo
- GSM8208745 mouse_1_liver_tumor_1 mouse_1_liver_tumo
- GSM8208746 mouse_1_liver_tumor_2 mouse_1_liver_tumo
+ 8 more — browse all 48 samples with per-sample file links →
- GSE239889 VHL loss reprograms the immune landscape to promote an inflammatory myeloid microenvironment in renal tumorigenesis 52 samples shares tumorigenesis, promote
- GSE278268 ALKBH8-Mediated Codon-Specific Translation Promotes Colorectal Tumorigenesis 20 samples shares tumorigenesis, promote
- GSE293919 Longitudinal monitoring of cytoplasmic RBP-RNA interactions and transcriptome in living cells by engineered protein nanocages 424 samples shares engineered
- GSE216391 Engineered T cell therapy for central nervous system injury 230 samples shares engineered
- GSE224832 Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis. 104 samples shares tumorigenesis
- GSE230265 The transcriptional co-repressor Runx1t1 is essential for N-Myc-driven neuroblastoma tumorigenesis 76 samples shares tumorigenesis
- GSE285529 CD133+PD-L1+ cancer cells confer resistance to adoptively transferred engineered macrophage-based therapy in melanoma. 30 samples shares engineered
- GSE277268 Single-Cell RNA Sequencing Reveals Shenbai Granule Retards Colorectal Tumorigenesis by Modulating Cholesterol-Induced Ccl22+ DCs and Tregs Crosstalk 15 samples shares tumorigenesis
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.