Foxp3 depends on Ikaros for control of regulatory T cell gene expression and function
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 72 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
- 72 samples: 56 distinct titles, 8 of them repeatedGroups 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
- Foxp3 depends on Ikaros for control of regulatory T cell gene expression and functioneLife · 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 GSE200179_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 PRJNA823549 and SRA study SRP367600. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 18 samples read as cases, 36 as controls.
How we read this: Read from 72 sample titles: 56 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.
- GSM6019836 ATAC-Seq - Treg Ikzf1 conditional knockout ex vivo stimulated 1
- GSM6019837 ATAC-Seq - Treg Ikzf1 conditional knockout ex vivo stimulated 2
- GSM6019838 ATAC-Seq - Treg Ikzf1 conditional knockout ex vivo stimulated 3
- GSM6019839 ATAC-Seq - Treg Ikzf1 conditional knockout ex vivo 1
- GSM6019840 ATAC-Seq - Treg Ikzf1 conditional knockout ex vivo 2
- GSM6019841 ATAC-Seq - Treg Ikzf1 conditional knockout ex vivo 3
- GSM6019842 ATAC-Seq - Treg WT ex vivo stimulated 1
- GSM6019843 ATAC-Seq - Treg WT ex vivo stimulated 2
- GSM6019844 ATAC-Seq - Treg WT ex vivo stimulated 3
- GSM6019845 ATAC-Seq - Treg WT ex vivo 1
- GSM6019846 ATAC-Seq - Treg WT ex vivo 2
- GSM6019847 ATAC-Seq - Treg WT ex vivo 3
- GSM6019848 Treg Ikzf1 conditional knockout ex vivo 1 Foxp3_chip
- GSM6019849 Treg Ikzf1 conditional knockout ex vivo 2 Foxp3_chip
- GSM6019850 Treg Ikzf1 conditional knockout ex vivo 3 Foxp3_chip
- GSM6019851 Treg Ikzf1 conditional knockout ex vivo 1 Foxp3_input
- GSM6019852 Treg Ikzf1 conditional knockout ex vivo 2 Foxp3_input
- GSM6019853 Treg Ikzf1 conditional knockout ex vivo 3 Foxp3_input
- GSM6019854 Treg WT ex vivo 1 Foxp3_chip
- GSM6019855 Treg WT ex vivo 2 Foxp3_chip
- GSM6019856 Treg WT ex vivo 3 Foxp3_chip
- GSM6019857 Treg WT ex vivo 1 Foxp3_input
- GSM6019858 Treg WT ex vivo 2 Foxp3_input
- GSM6019859 Treg WT ex vivo 3 Foxp3_input
- GSM6019860 Naïve CD4 T cell from WT mice ex vivo 1 Ikaros_chip
- GSM6019861 Naïve CD4 T cell from WT mice ex vivo 2 Ikaros_chip
- GSM6019862 Naïve CD4 T cell from WT mice ex vivo 3 Ikaros_chip
- GSM6019863 Naïve CD4 T cell from WT mice ex vivo 1 Ikaros_input
- GSM6019864 Naïve CD4 T cell from WT mice ex vivo 2 Ikaros_input
- GSM6019865 Naïve CD4 T cell from WT mice ex vivo 3 Ikaros_input
- GSM6019866 Treg WT ex vivo 1 Ikaros_chip
- GSM6019867 Treg WT ex vivo 2 Ikaros_chip
- GSM6019868 Treg WT ex vivo 3 Ikaros_chip
- GSM6019869 Treg WT ex vivo 1 Ikaros_input
- GSM6019870 Treg WT ex vivo 2 Ikaros_input
- GSM6019871 Treg WT ex vivo 3 Ikaros_input
- GSM6019872 Naïve CD4 T cell from Treg Ikzf1cko mice ex vivo 1 H3K27ac_chip
- GSM6019873 Naïve CD4 T cell from Treg Ikzf1cko mice ex vivo 2 H3K27ac_chip
- GSM6019874 Naïve CD4 T cell from Treg Ikzf1cko mice ex vivo 3 H3K27ac_chip
- GSM6019875 Naïve CD4 T cell from Treg Ikzf1cko mice ex vivo 1 H3K27ac_input
+ 32 more — browse all 72 samples with per-sample file links →
- GSE305064 FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry [mouse_Tconv_ChIP-seq] 15 samples shares foxp3, regulatory, depends
- GSE267884 Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [scMultiome] 16 samples shares foxp3, regulatory
- GSE267967 Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for functional differentiation of Treg cells [RNA-seq] 26 samples shares foxp3, regulatory
- GSE149674 Dynamic Foxp3-chromatin interaction controls tunable Treg cell function 94 samples shares foxp3, control
- GSE267882 Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [ChIP-Seq] 34 samples shares foxp3, regulatory
- GSE267881 Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [ATAC-Seq] 30 samples shares foxp3, regulatory
- GSE297451 Temporal and Context-Dependent Requirements for the Transcription Factor Foxp3 in Regulatory T Cell Development and Maintenance [RNA-seq] 70 samples shares foxp3, regulatory
- GSE311963 CD38 endows local antigen-specific Foxp3+ Treg cells with stress resilience for compartmentalized control of CNS inflammation 68 samples shares foxp3, control
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.