Z-DNA underlies the target choice of Aire by facilitating promoter poising [ATAC-seq]
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: 5 conditions, mostly in duplicateGroups 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 GSE224551_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 PRJNA934444 and SRA study SRP424168. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 5 replicated groups read from 10 sample titles; they account for 10 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.
- GSM7025865 B6_NOD_F1_WT_mTEC_GFP_ATAC_rep1 B6_NOD_F1_WT_mTEC_GFP_A…
- GSM7025866 B6_NOD_F1_WT_mTEC_GFP_ATAC_rep2 B6_NOD_F1_WT_mTEC_GFP_A…
- GSM7025867 B6_WT_mTEC_GFP_ATAC_rep1 B6_WT_mTEC_GFP_ATAC
- GSM7025868 B6_WT_mTEC_GFP_ATAC_rep2 B6_WT_mTEC_GFP_ATAC
- GSM7025869 NOD_WT_mTEC_GFP_ATAC_rep1 NOD_WT_mTEC_GFP_ATAC
- GSM7025870 NOD_WT_mTEC_GFP_ATAC_rep2 NOD_WT_mTEC_GFP_ATAC
- GSM7025871 B6_PBS_Aire_KO_mTEC_ATAC_rep1 B6_PBS_Aire_KO_mTEC_ATAC
- GSM7025872 B6_PBS_Aire_KO_mTEC_ATAC_rep2 B6_PBS_Aire_KO_mTEC_ATAC
- GSM7025873 B6_Spermidine_Aire_KO_mTEC_ATAC_rep1 B6_Spermidine_Aire_KO_m…
- GSM7025874 B6_Spermidine_Aire_KO_mTEC_ATAC_rep2 B6_Spermidine_Aire_KO_m…
- GSE224554 Z-DNA underlies the target choice of Aire by facilitating promoter poising [ChIPmentation] 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
- 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, atac-seq
- GSE339197 Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome [Regulators_KD_CutnTag] 44 samples shares promoter, choice
- GSE339202 Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome [Xist-Tsix-perturbations_CutnTag] 42 samples shares promoter, 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
- GSE339196 Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome [TX-Maged1-2tag_CutnTag] 12 samples shares promoter, choice
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.