Z-DNA underlies the target choice of Aire by facilitating promoter poising [ChIPmentation]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 10 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
- 10 samples: 2 × WT_NELF_Chipmentation vs 2 × Aire_KO_NELF_Chipmentation vs 2 × WT_DMSO_Aire_Chipmentation vs 2 × WT_Topotecan_Aire_ChipmentationGroups 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
- AIRE relies on Z-DNA to flag gene targets for thymic T cell tolerizationNature · 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 GSE224554_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 PRJNA934447 and SRA study SRP424169. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 4 replicated groups read from 10 sample titles; they account for 8 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.
- GSM7025891 WT_NELF_Chipmentation_rep1 WT_NELF_Chipmentation
- GSM7025892 WT_NELF_Chipmentation_rep2 WT_NELF_Chipmentation
- GSM7025893 Aire_KO_NELF_Chipmentation_rep1 Aire_KO_NELF_Chipmentat…
- GSM7025894 Aire_KO_NELF_Chipmentation_rep2 Aire_KO_NELF_Chipmentat…
- GSM7025895 Input_Chipmentation_for_NELF_rep1
- GSM7025896 WT_DMSO_Aire_Chipmentation_rep1 WT_DMSO_Aire_Chipmentat…
- GSM7025897 WT_DMSO_Aire_Chipmentation_rep2 WT_DMSO_Aire_Chipmentat…
- GSM7025898 WT_Topotecan_Aire_Chipmentation_rep1 WT_Topotecan_Aire_Chipm…
- GSM7025899 WT_Topotecan_Aire_Chipmentation_rep2 WT_Topotecan_Aire_Chipm…
- GSM7025900 Input_Chipmentation_for_Aire_rep1
- GSE224551 Z-DNA underlies the target choice of Aire by facilitating promoter poising [ATAC-seq] 10 samples shares z-dna, facilitating, underlies, promoter, poising, target, choice
- GSE224557 Z-DNA underlies the target choice of Aire by facilitating promoter poising 78 samples shares z-dna, facilitating, underlies, promoter, poising, target, choice
- GSE224556 Z-DNA underlies the target choice of Aire by facilitating promoter poising [RNA-seq] 30 samples shares z-dna, facilitating, underlies, promoter, poising, target, choice
- 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 facilitating, promoter
- GSE295991 Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at meiotic promoters in mice 32 samples shares facilitating, promoter
- GSE296438 Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at the promoters of genes expressed during meiosis [scRNA-seq & scATAC-seq] 10 samples shares facilitating, promoter
- GSE291987 Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization [RNA-Seq] 23 samples shares z-dna
- GSE270508 In vivo CRISPR screen reveals interplay of epigenetic regulators underlies kinetics of hepatobiliary reprogramming [CUT&Tag] 183 samples shares underlies
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.