Malaria pigment hemozoin-induced chromatin remodeling of mouse hematopoietic stem and progenitor cells, granulocyte-macrophage progenitors, and bone marrow monocytes
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- 12 samples: 6 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
- Persistent bone marrow hemozoin accumulation confers a survival advantage against bacterial infection via cell-intrinsic Myd88 signalingCell reports · 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 GSE224160_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 PRJNA929994 and SRA study SRP420305. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 12 sample titles; they account for 12 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.
- GSM7016842 HSPC_PBS_1 HSPC_PBS
- GSM7016843 HSPC_PBS_2 HSPC_PBS
- GSM7016844 HSPC_Plas_1 HSPC_Plas
- GSM7016845 HSPC_Plas_2 HSPC_Plas
- GSM7016846 GMP_PBS_1 GMP_PBS
- GSM7016847 GMP_PBS_2 GMP_PBS
- GSM7016848 GMP_Plas_1 GMP_Plas
- GSM7016849 GMP_Plas_2 GMP_Plas
- GSM7016850 Monocyte_PBS_1 Monocyte_PBS
- GSM7016851 Monocyte_PBS_2 Monocyte_PBS
- GSM7016852 Monocyte_Plas_1 Monocyte_Plas
- GSM7016853 Monocyte_Plas_2 Monocyte_Plas
- GSE272588 Multipotent progenitors with distinct origins, clonal lineage fates, transcriptomes, and surface markers yield two hematopoietic trees 605 samples shares hematopoietic, progenitors, progenitor
- GSE266188 Profiling of gene expression, histone marks, chromatin accessibility, and DNA methylation in myeloid progenitors expressing H3WT, H3K4M, H3K27M, or H3K4M/K27M for 2 weeks [CUT&Tag] 36 samples shares progenitors, progenitor, chromatin
- GSE268058 PPARγ-dependent Remodeling of Translational Machinery in Adipose Progenitors is Impaired in Obesity 24 samples shares progenitors, remodeling, progenitor
- GSE310548 Distinct contributions of Etv2+ and Flk1+ progenitors to endothelial, hematopoietic, and cardiac lineages [RNA-seq] 21 samples shares hematopoietic, progenitors, progenitor
- GSE267192 PPARγ-dependent Remodeling of Translational Machinery in Adipose Progenitors is Impaired in Obesity [scRNA-seq] 12 samples shares progenitors, remodeling, progenitor
- GSE239738 Histone modification in dendritic cell progenitors and dendritic cells 42 samples shares progenitors, progenitor
- GSE318940 Smarca4 coordinates chromatin accessibility and metabolic programs to sustain hematopoietic stem cell function 25 samples shares hematopoietic, chromatin
- GSE245399 ATAC-seq analysis of early T cell progenitors from various gene deficient mice 12 samples shares progenitors, progenitor
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.