Signal-responsive transcription factors cooperate to establish alveolar macrophage identity
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 42 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
- 42 samples: 8 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.
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 GSE243165_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 PRJNA1016453 and SRA study SRP460294. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 21 samples.
How we read this: 8 replicated groups read from 42 sample titles; they account for 21 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.
- GSM7780058 Imm_KO2 Imm_KO
- GSM7780059 Imm_KO3 Imm_KO
- GSM7780060 Imm_KO4 Imm_KO
- GSM7780061 mAM_KO1 mAM_KO
- GSM7780062 mAM_KO2 mAM_KO
- GSM7780063 mAM_KO3 mAM_KO
- GSM7780064 mAM_KO4 mAM_KO
- GSM7780065 mAM_WT1 mAM_WT
- GSM7780066 mAM_WT2 mAM_WT
- GSM7780067 mAM_WT3 mAM_WT
- GSM7780068 mAM_WT4 mAM_WT
- GSM7780087 AMs, KO1_2 AMs, KO1
- GSM7780088 AMs, KO1_3 AMs, KO1
- GSM7780089 AMs, KO2 AMs, KO
- GSM7780090 AMs, KO3 AMs, KO
- GSM7780091 AMs, WT1_2 AMs, WT1
- GSM7780092 AMs, WT1_3 AMs, WT1
- GSM7780093 AMs, WT3 AMs, WT
- GSM7780094 AMs, WT4 AMs, WT
- GSM7780095 AMs, H3
- GSM7780096 AMs, INPUT
- GSM7780097 AMs, WTA
- GSM7780098 AMs, WTG
- GSM7780099 AMs, KOA
- GSM7780100 AMs, KOG
- GSM7780101 AMs, INPUT for RXR HT-ChIPmentation
- GSM8070569 s6, input
- GSM8070570 s7, ChIPmentation
- GSM8070571 s8, input
- GSM8070572 s9, ChIPmentation
- GSM9393774 RBPJ_k1
- GSM9393775 Input_k1
- GSM9393776 RBPJ_k2_AMS1
- GSM9393777 Input_k2_AMS1 Input_k2_AMS
- GSM9393778 PPARG_k1
- GSM9393779 Input-k1
- GSM9393780 PPARG_k2_AMS2
- GSM9393781 Input_k2_AMS2 Input_k2_AMS
- GSM9393899 H3K27Ac_k1
- GSM9393900 Input, k1
+ 2 more — browse all 42 samples with per-sample file links →
- GSE200323 Establishment of chromatin architecture interplays with embryo hypertranscription 158 samples shares transcription, establish
- GSE283382 N6-methyladenosine modulate second cell fate decision by enhancing mRNA stability of pivotal transcription factors during primitive endoderm development [TBLC_RNAseq] 98 samples shares transcription, factors
- GSE282280 DNA methylation-sensitive transcription factors and bivalency orchestrate transposon expression in the absence of DNA methylation. 93 samples shares transcription, factors
- GSE324864 HP1B and H3K9me3 Regulate Olfactory Receptor Choice and 2 Transcriptional Identity [ChIP-seq] 28 samples shares transcription, identity
- GSE245648 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [RNA-seq_BMDM] 24 samples shares transcription, macrophage
- GSE303772 Ontogenically distinct alveolar macrophages mediate cigarette smoke-induced inflammation and damage [RNA-Seq] 24 samples shares macrophage, alveolar
- GSE281001 The C3-C3aR axis modulates trained immunity in alveolar macrophages 8 samples shares macrophage, alveolar
- GSE294389 BMAL1 and YAP cooperate to hijack enhancers and promote inflammation in the aged epidermis 131 samples shares cooperate
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.