Dynamic Chromatin Alteration Induces Oncogenic Hijacking by Essential Transcriptional Factors during Medulloblastoma Tumorigenesis [CUT&Tag]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 18 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
- 18 samples: 18 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.
Read the full summary ↓
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 GSE240359_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 PRJNA1003435 and SRA study SRP454017. 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 18 sample titles: 18 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.
- GSM7696730 20211110C-GNP-1-NFIA_S1_R1.fastq.gz
- GSM7696731 20211110C-GNP-1-NFIB_S2_R1.fastq.gz
- GSM7696732 20211110C-GNP-2-NFIA_S4_R1.fastq.gz
- GSM7696733 20211110C-GNP-2-NFIB_S5_R1.fastq.gz
- GSM7696734 20211201C-GNP-NFIA_merged_R1.fastq.gz
- GSM7696735 20211201C-GNP-NFIB_merged_R1.fastq.gz
- GSM7696736 20211110C-Hyperplasia-1-NFIA_S7_R1.fastq.gz
- GSM7696737 20211110C-Hyperplasia-1-NFIB_S8_R1.fastq.gz
- GSM7696738 20211110C-Hyperplasia-2-NFIA_S10_R1.fastq.gz
- GSM7696739 20211110C-Hyperplasia-2-NFIB_S11_R1.fastq.gz
- GSM7696740 20211201C-Hyperplasia-NFIA_merged_R1.fastq.gz
- GSM7696741 20211201C-Hyperplasia-NFIB_merged_R1.fastq.gz
- GSM7696742 20211116C-msTumor-NFIA_S7_R1.fastq.gz
- GSM7696743 20211116C-msTumor-NFIB_S8_R1.fastq.gz
- GSM7696744 20220118C-Mt-NFIA-rep2_S6_R1.fastq.gz
- GSM7696745 20220118C-Mt-NFIB-rep2_S7_R1.fastq.gz
- GSM7696746 20220113C-Mt-NFIA-rep3_S1_R1.fastq.gz
- GSM7696747 20220113C-Mt-NFIB-rep3_S2_R1.fastq.gz
- GSE274493 The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis [CUT&Tag] 46 samples shares cut, chromatin, essential
- GSE304211 H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [CUTnTAG] 128 samples shares cut, chromatin
- GSE298418 MeCP2 stabilizes the glucocorticoid system in active chromatin regions [CUT&Tag] 63 samples shares cut, chromatin
- GSE274875 A mutant ASXL1-EHMT complex contributes to heterochromatin dysfunction in clonal hematopoiesis and chronic monomyelocytic leukemia [Cut & Run] 38 samples shares cut, chromatin
- GSE295964 Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at the promoters of genes expressed during meiosis [CUT&RUN] 13 samples shares cut, chromatin
- GSE255571 Chromatin remodeler CHD7 regulates neurogenic gene expression via controlling chromatin accessibility and modifications of histone marks H3K27me3 and H3K4me3 [Mouse CUT&Tag] 10 samples shares cut, chromatin
- GSE263359 Chromatin Modification Abnormalities by CHD7 and KMT2C Loss Promote Medulloblastoma Progression [ATAC-seq] 11 samples shares medulloblastoma, chromatin
- GSE239470 Condensate-promoting ENL mutation induces tumorigenesis via chromatin remodeling 74 samples shares tumorigenesis, chromatin
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.