CUT&RUN of alveolar macophages sorted bronchoalveolar lavage fluid (BALF) isolated from naive mice or mice recovered from SARS-CoV-2 (mouse-adapted strain MA10)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 20 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
- 20 samples: 5 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
- Antiviral innate immune memory in alveolar macrophages following SARS-CoV-2 infection ameliorates secondary influenza A virus diseaseImmunity · 2024
Read the full summary ↓
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 GSE266968_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 PRJNA1108857 and SRA study SRP506325. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 5 replicated groups read from 20 sample titles; they account for 10 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.
- GSM8257541 Alveolar macrophages, naïve_1_H3K4me1 Alveolar macrophages, n…
- GSM8257542 Alveolar macrophages, naïve_2_H3K4me1 Alveolar macrophages, n…
- GSM8257543 Alveolar macrophages, recovered_1_H3K4me1 Alveolar macrophages, r…
- GSM8257544 Alveolar macrophages, recovered_2_H3K4me1 Alveolar macrophages, r…
- GSM8257545 Alveolar macrophages, recovered_3_H3K4me1 Alveolar macrophages, r…
- GSM8257546 Alveolar macrophages, naïve_1_H3K4me3 Alveolar macrophages, n…
- GSM8257547 Alveolar macrophages, naïve_2_H3K4me3 Alveolar macrophages, n…
- GSM8257548 Alveolar macrophages, recovered_1_H3K4me3 Alveolar macrophages, r…
- GSM8257549 Alveolar macrophages, recovered_2_H3K4me3 Alveolar macrophages, r…
- GSM8257550 Alveolar macrophages, recovered_3_H3K4me3 Alveolar macrophages, r…
- GSM8257551 Alveolar macrophages, naïve_1_H3K27Ac
- GSM8257552 Alveolar macrophages, naïve_2_H3K27Ac
- GSM8257553 Alveolar macrophages, recovered_1_H3K27Ac
- GSM8257554 Alveolar macrophages, recovered_2_H3K27Ac
- GSM8257555 Alveolar macrophages, recovered_3_H3K27Ac
- GSM8257556 Alveolar macrophages, naïve_1_IgG
- GSM8257557 Alveolar macrophages, naïve_2_IgG
- GSM8257558 Alveolar macrophages, recovered_1_IgG
- GSM8257559 Alveolar macrophages, recovered_2_IgG
- GSM8257560 Alveolar macrophages, recovered_3_IgG
- GSE289642 Noncanonical PRC2 chromatin association reveals a key role of EZHIP in intergenerational epigenetic memory transition [ChIP-Seq, Cut & Run] 107 samples shares cut, run
- GSE303384 Mechanism of maintenance and establishment of repression by the Mtg16 tumor suppressor [CUT&RUN, ChIP-Seq] 92 samples shares cut, run
- GSE306261 Astrocyte glucocorticoid receptor signaling restricts neuronal plasticity [CUT&RUN] 50 samples shares cut, run
- GSE313359 Hippocampal estrogen levels, receptor types and epigenetics contribute to sex-specific memory-vulnerabilities to concurrent acute stresses [Cut & Run] 45 samples shares cut, run
- GSE292333 H2AK119ub1-MLL2 counteraction underlies heritable H3K27me3 formation in oocytes [CATCH-seq and CUT&RUN] 44 samples shares cut, run
- GSE298002 Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [CUT&Run] 38 samples shares cut, run
- GSE274875 A mutant ASXL1-EHMT complex contributes to heterochromatin dysfunction in clonal hematopoiesis and chronic monomyelocytic leukemia [Cut & Run] 38 samples shares cut, run
- GSE293129 Enhancer rewiring orchestrates inflammation and loss of cell identity during muscle stem cell aging [CUT&RUN] 36 samples shares cut, run
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.