Malaria pigment hemozoin-induced transcriptional remodeling of mouse hematopoietic stem and progenitor cells, granulocyte-macrophage progenitors, and bone marrow monocytes
RNA-seq (gene expression) · mouse · 14 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 14 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
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 GSE224161_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA929995 and SRA study SRP420310. 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 14 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.
- GSM7016854 HSPC_RNA_PBS
- GSM7016855 HSPC_RNA_Plas
- GSM7016856 GMP_RNA_PBS rep1 GMP_RNA_PBS
- GSM7016857 GMP_RNA_PBS rep2 GMP_RNA_PBS
- GSM7016858 GMP_RNA_Plas rep1 GMP_RNA_Plas
- GSM7016859 GMP_RNA_Plas rep2 GMP_RNA_Plas
- GSM7016860 Monocyte_RNA_PBS rep1 Monocyte_RNA_PBS
- GSM7016861 Monocyte_RNA_PBS rep2 Monocyte_RNA_PBS
- GSM7016862 Monocyte_RNA_Plas rep1 Monocyte_RNA_Plas
- GSM7016863 Monocyte_RNA_Plas rep2 Monocyte_RNA_Plas
- GSM7016864 Monocyte_RNA_PBS_CLP rep1 Monocyte_RNA_PBS_CLP
- GSM7016865 Monocyte_RNA_PBS_CLP rep2 Monocyte_RNA_PBS_CLP
- GSM7016866 Monocyte_RNA_Plas_CLP rep1 Monocyte_RNA_Plas_CLP
- GSM7016867 Monocyte_RNA_Plas_CLP rep2 Monocyte_RNA_Plas_CLP
- GSE224160 Malaria pigment hemozoin-induced chromatin remodeling of mouse hematopoietic stem and progenitor cells, granulocyte-macrophage progenitors, and bone marrow monocytes 12 samples shares granulocyte-macrophage, hemozoin-induced, hematopoietic, progenitors, remodeling, progenitor, monocytes, malaria
- 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
- GSE272588 Multipotent progenitors with distinct origins, clonal lineage fates, transcriptomes, and surface markers yield two hematopoietic trees 605 samples shares hematopoietic, progenitors, progenitor
- GSE268058 PPARγ-dependent Remodeling of Translational Machinery in Adipose Progenitors is Impaired in Obesity 24 samples shares progenitors, remodeling, progenitor
- GSE326003 The differentiation of myeloid progenitors is effected by cascading waves of coordinated gene expression that remodel cellular physiology in a characteristic sequence [RNA-seq] 165 samples shares progenitors, progenitor
- GSE289311 Erythropoietin Exposure Impairs B Cell Development and Promotes Myeloid-Imprinted Biphenotypic Progenitors 96 samples shares progenitors, progenitor
- GSE260623 Germline ELP1 deficiency sensitizes cerebellar granule neuron progenitors to SHH medulloblastoma [bulkRNA] 91 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.