BHLHE40 Orchestrates TL1A-Driven ILC3 Effector Programs and RORγt⁺ APC-Mediated Tolerance.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 40 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
- 40 samples: 12 conditions, mostly in triplicateGroups 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.
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 GSE325199_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 PRJNA1438985 and SRA study SRP537730. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 36 samples.
How we read this: 12 replicated groups read from 40 sample titles; they account for 36 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.
- GSM8563968 Bhlhe40 het_un 1 Bhlhe40 het_un
- GSM8563969 Bhlhe40 het_un 2 Bhlhe40 het_un
- GSM8563970 Bhlhe40 het_un 3 Bhlhe40 het_un
- GSM8563971 Bhlhe40 ko_un1 Bhlhe40 ko_un
- GSM8563972 Bhlhe40 ko_un2 Bhlhe40 ko_un
- GSM8563973 Bhlhe40 ko_un3 Bhlhe40 ko_un
- GSM8563974 Bhlhe40 het_TL1A 1 Bhlhe40 het_TL1A
- GSM8563975 Bhlhe40 het_TL1A 2 Bhlhe40 het_TL1A
- GSM8563976 Bhlhe40 het_TL1A 3 Bhlhe40 het_TL1A
- GSM8563977 Bhlhe40 ko_TL1A 1 Bhlhe40 ko_TL1A
- GSM8563978 Bhlhe40 ko_TL1A 2 Bhlhe40 ko_TL1A
- GSM8563979 Bhlhe40 ko_TL1A 3 Bhlhe40 ko_TL1A
- GSM9234024 Bhlhe40 het_IL23 1 Bhlhe40 het_IL23
- GSM9234025 Bhlhe40 het_IL23 2 Bhlhe40 het_IL23
- GSM9234026 Bhlhe40 het_IL23 3 Bhlhe40 het_IL23
- GSM9234027 Bhlhe40 ko_IL23 1 Bhlhe40 ko_IL23
- GSM9234028 Bhlhe40 ko_IL23 2 Bhlhe40 ko_IL23
- GSM9234029 Bhlhe40 ko_IL23 3 Bhlhe40 ko_IL23
- GSM9240734 un 1 un
- GSM9240735 un 2 un
- GSM9240736 un 3 un
- GSM9240737 TL1A 1 TL1A
- GSM9240738 TL1A 2 TL1A
- GSM9240739 TL1A 3 TL1A
- GSM9597755 mesenteric lymph nodes single cells from Bhlhe40 het mice
- GSM9597756 mesenteric lymph nodes single cells from Bhlhe40 ko mice
- GSM9597757 mesenteric lymph nodes single cells from Bhlhe40 het mice treaed with agonist DR3
- GSM9597758 mesenteric lymph nodes single cells from Bhlhe40 ko mice treated with agonist DR3
- GSM9601104 Bhlhe40 Het_un_1 Bhlhe40 Het_un
- GSM9601105 Bhlhe40 Het_un_2 Bhlhe40 Het_un
- GSM9601106 Bhlhe40 Het_un_3 Bhlhe40 Het_un
- GSM9601107 Bhlhe40 KO_un_1 Bhlhe40 KO_un
- GSM9601108 Bhlhe40 KO_un_2 Bhlhe40 KO_un
- GSM9601109 Bhlhe40 KO_un_3 Bhlhe40 KO_un
- GSM9601110 Bhlhe40 Het_TL1A_1 Bhlhe40 Het_TL1A
- GSM9601111 Bhlhe40 Het_TL1A_2 Bhlhe40 Het_TL1A
- GSM9601112 Bhlhe40 Het_TL1A_3 Bhlhe40 Het_TL1A
- GSM9601113 Bhlhe40 KO_TL1A_1 Bhlhe40 KO_TL1A
- GSM9601114 Bhlhe40 KO_TL1A_2 Bhlhe40 KO_TL1A
- GSM9601115 Bhlhe40 KO_TL1A_3 Bhlhe40 KO_TL1A
- GSE279193 BHLHE40 Orchestrates TL1A-Driven ILC3 Effector Programs and RORγt⁺ APC-Mediated Tolerance 24 samples shares bhlhe40, ilc3, ror, orchestrates, apc-mediated, tl1a-driven, tolerance, effector
- GSE325341 BHLHE40 Orchestrates TL1A-Driven ILC3 Effector Programs and RORγt⁺ APC-Mediated Tolerance [ATAC-Seq] 12 samples shares bhlhe40, ilc3, ror, orchestrates, apc-mediated, tl1a-driven, tolerance, effector
- GSE274081 A distinct cis-regulatory element is required for ILC3s to maintain intestinal tolerance through amplifying RORγt expression [scRNA-seq] 2 samples shares ilc3, ror, tolerance
- GSE233908 Transcription factor TCF1 binds Rorgt and orchestrates a regulatory network that determines homeostatic Th17 cell state 21 samples shares ror, orchestrates
- GSE278157 A hierarchical Rorc(γt) cis-regulatory cascade orchestrates differentiation of RORγt⁺ innate immune cells [ATAC-seq] 40 samples shares ror, orchestrates
- GSE278516 A hierarchical Rorc(γt) cis-regulatory cascade orchestrates differentiation of RORγt⁺ innate immune cells [BulkRNA-seq_ChILP] 23 samples shares ror, orchestrates
- GSE233905 Transcription factor TCF1 binds Rorgt and orchestrates a regulatory network that determines homeostatic Th17 cell state [ATAC-seq] 13 samples shares ror, orchestrates
- GSE316584 MicroRNA-224 Orchestrates the BMP Pathway and Represents a New Therapeutic Target for Pulmonary Arterial Hypertension 9 samples shares ror, orchestrates
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.