Transcription factor Ikzf1 associates with Foxp3 to repress gene expression in Treg cells and limit autoimmunity and anti-tumor immunity
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 32 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
- 32 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
- Transcription factor Ikzf1 associates with Foxp3 to repress gene expression in Treg cells and limit autoimmunity and anti-tumor immunityImmunity · 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 GSE229592_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 PRJNA955103 and SRA study SRP432419. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 28 samples.
How we read this: 13 replicated groups read from 32 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.
- GSM7165862 WT_Treg_ATAC_rep1 WT_Treg_ATAC
- GSM7165863 IkE5_Treg_ATAC_rep1 IkE5_Treg_ATAC
- GSM7165864 WT_Treg_ATAC_rep2 WT_Treg_ATAC
- GSM7165865 IkE5_Treg_ATAC_rep2 IkE5_Treg_ATAC
- GSM7165878 WT_Treg_Input_histone
- GSM7165879 IkE5_Treg_Input_histone
- GSM7165880 WT_Treg_H3K27ac_rep1 WT_Treg_H3K27ac
- GSM7165881 IkE5_Treg_H3K27ac_rep1 IkE5_Treg_H3K27ac
- GSM7165882 WT_Treg_H3K27ac_rep2 WT_Treg_H3K27ac
- GSM7165883 IkE5_Treg_H3K27ac_rep2 IkE5_Treg_H3K27ac
- GSM7165884 WT_Treg_Input
- GSM7165885 IkE5_Treg_Input
- GSM7165886 WT_Treg_Foxp3_rep1 WT_Treg_Foxp3
- GSM7165887 IkE5_Treg_Foxp3_rep1 IkE5_Treg_Foxp3
- GSM7165888 WT_Treg_p300_rep1 WT_Treg_p300
- GSM7165889 IkE5_Treg_p300_rep1 IkE5_Treg_p300
- GSM7165890 WT_Treg_NFAT1_rep1 WT_Treg_NFAT1
- GSM7165891 IkE5_Treg_NFAT1_rep1 IkE5_Treg_NFAT1
- GSM7165892 WT_Treg_Ikaros_rep1 WT_Treg_Ikaros
- GSM7165893 WT_Treg_Foxp3_rep2 WT_Treg_Foxp3
- GSM7165894 IkE5_Treg_Foxp3_rep2 IkE5_Treg_Foxp3
- GSM7165895 WT_Treg_p300_rep2 WT_Treg_p300
- GSM7165896 IkE5_Treg_p300_rep2 IkE5_Treg_p300
- GSM7165897 WT_Treg_NFAT1_rep2 WT_Treg_NFAT1
- GSM7165898 IkE5_Treg_NFAT1_rep2 IkE5_Treg_NFAT1
- GSM7165899 WT_Treg_Ikaros_rep2 WT_Treg_Ikaros
- GSM7165900 WT_PMA_Treg_1 WT_PMA_Treg
- GSM7165901 WT_PMA_Treg_2 WT_PMA_Treg
- GSM7165902 WT_PMA_Treg_3 WT_PMA_Treg
- GSM7165903 IkE5_PMA_Treg_1 IkE5_PMA_Treg
- GSM7165904 IkE5_PMA_Treg_2 IkE5_PMA_Treg
- GSM7165905 IkE5_PMA_Treg_3 IkE5_PMA_Treg
- GSE245838 Anchored screening identifies transcription factor blueprints underlying dendritic cell diversity and subset-specific anti-tumor immunity [mouse scRNA-seq] 21 samples shares transcription, anti-tumor, immunity
- GSE305064 FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry [mouse_Tconv_ChIP-seq] 15 samples shares foxp3, transcription
- GSE237643 Deletion of the mRNA endonuclease Regnase-1 promotes NK cell anti-tumor activity via OCT2- dependent transcription of Ifng 58 samples shares transcription, anti-tumor
- GSE318514 Organ injury in systemic autoimmunity is mediated by stem-like CD8 T cells arising from tissue-draining lymph nodes 45 samples shares autoimmunity, immunity
- GSE266584 Epigenetic and transcriptional regulation of dendritic cell development and anti-tumor function by HDAC1 34 samples shares transcription, anti-tumor
- GSE245648 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [RNA-seq_BMDM] 24 samples shares transcription, repress
- GSE279310 The circadian clock gene BMAL1 modulates autoimmunity features in lupus 20 samples shares autoimmunity, immunity
- GSE279684 T:B cell cooperation in ectopic lymphoid follicles propagates CNS autoimmunity 11 samples shares autoimmunity, immunity
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.