Z-DNA underlies the target choice of Aire by facilitating promoter poising [RNA-seq]
RNA-seq (gene expression) · mouse · 30 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 30 samples: 13 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 GSE224556_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA934445 and SRA study SRP424170. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 30 samples.
How we read this: 13 replicated groups read from 30 sample titles; they account for 30 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.
- GSM7025906 B6_NOD_F1_WT_mTEC_GFP_RNA_rep1 B6_NOD_F1_WT_mTEC_GFP_R…
- GSM7025907 B6_NOD_F1_WT_mTEC_GFP_RNA_rep2 B6_NOD_F1_WT_mTEC_GFP_R…
- GSM7025908 B6_NOD_F1_WT_mTEC_GFP_RNA_rep3 B6_NOD_F1_WT_mTEC_GFP_R…
- GSM7025909 B6_WT_mTEC_GFP_RNA_rep1 B6_WT_mTEC_GFP_RNA
- GSM7025910 B6_WT_mTEC_GFP_RNA_rep2 B6_WT_mTEC_GFP_RNA
- GSM7025911 B6_WT_mTEC_GFP_RNA_rep3 B6_WT_mTEC_GFP_RNA
- GSM7025912 B6_Aire_KO_mTEC_GFP_RNA_rep1 B6_Aire_KO_mTEC_GFP_RNA
- GSM7025913 B6_Aire_KO_mTEC_GFP_RNA_rep2 B6_Aire_KO_mTEC_GFP_RNA
- GSM7025914 NOD_WT_mTEC_GFP_RNA_rep1 NOD_WT_mTEC_GFP_RNA
- GSM7025915 NOD_WT_mTEC_GFP_RNA_rep2 NOD_WT_mTEC_GFP_RNA
- GSM7025916 NOD_WT_mTEC_GFP_RNA_rep3 NOD_WT_mTEC_GFP_RNA
- GSM7025917 NOD_Aire_KO_mTEC_GFP_RNA_rep1 NOD_Aire_KO_mTEC_GFP_RNA
- GSM7025918 NOD_Aire_KO_mTEC_GFP_RNA_rep2 NOD_Aire_KO_mTEC_GFP_RNA
- GSM7025919 NOD_Aire_KO_mTEC_GFP_RNA_rep3 NOD_Aire_KO_mTEC_GFP_RNA
- GSM7025920 B6_PBS_WT_mTEC_RNA_rep1 B6_PBS_WT_mTEC_RNA
- GSM7025921 B6_PBS_WT_mTEC_RNA_rep2 B6_PBS_WT_mTEC_RNA
- GSM7025922 B6_Spermidine_WT_mTEC_RNA_rep1 B6_Spermidine_WT_mTEC_R…
- GSM7025923 B6_Spermidine_WT_mTEC_RNA_rep2 B6_Spermidine_WT_mTEC_R…
- GSM7025924 B6_PBS_Aire_KO_mTEC_RNA_rep1 B6_PBS_Aire_KO_mTEC_RNA
- GSM7025925 B6_PBS_Aire_KO_mTEC_RNA_rep2 B6_PBS_Aire_KO_mTEC_RNA
- GSM7025926 B6_Spermidine_Aire_KO_mTEC_RNA_rep1 B6_Spermidine_Aire_KO_m…
- GSM7025927 B6_Spermidine_Aire_KO_mTEC_RNA_rep2 B6_Spermidine_Aire_KO_m…
- GSM7025928 B6_DMSO_WT_mTEC_RNA_rep1 B6_DMSO_WT_mTEC_RNA
- GSM7025929 B6_DMSO_WT_mTEC_RNA_rep2 B6_DMSO_WT_mTEC_RNA
- GSM7025930 B6_Topotecan_WT_mTEC_RNA_rep1 B6_Topotecan_WT_mTEC_RNA
- GSM7025931 B6_Topotecan_WT_mTEC_RNA_rep2 B6_Topotecan_WT_mTEC_RNA
- GSM7025932 B6_Foxn1Cre_Nfe2l2_wt_mTEC_RNA_rep1 B6_Foxn1Cre_Nfe2l2_wt_m…
- GSM7025933 B6_Foxn1Cre_Nfe2l2_wt_mTEC_RNA_rep2 B6_Foxn1Cre_Nfe2l2_wt_m…
- GSM7025934 B6_Foxn1Cre_Nfe2l2_flox_mTEC_RNA_rep1 B6_Foxn1Cre_Nfe2l2_flox…
- GSM7025935 B6_Foxn1Cre_Nfe2l2_flox_mTEC_RNA_rep2 B6_Foxn1Cre_Nfe2l2_flox…
- GSE224557 Z-DNA underlies the target choice of Aire by facilitating promoter poising 78 samples shares z-dna, facilitating, underlies, promoter, poising, target, choice
- 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
- 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
- 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, rna-seq
- GSE291987 Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization [RNA-Seq] 23 samples shares z-dna, rna-seq
- GSE262004 Temporal constraints on enhancer usage and enhancer-promoter connectivity shape the regulation of limb gene transcription [RNA-seq] 99 samples shares promoter, rna-seq
- GSE261066 Transient promoter interactions modulate developmental gene activation [RNA-Seq] 79 samples shares promoter, rna-seq
- GSE296993 H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [RNA-seq of mESC] 50 samples shares underlies, rna-seq
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.