Gene expression changes in bone marrow dendritic cell progenitors upon acute and chronic LCMV infection
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 24 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
- 24 samples: 20 distinct titles, 2 of them repeatedGroups 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 GSE141640_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 PRJNA594276 and SRA study SRP235228. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 24 sample titles: 20 distinct titles with little repetition. 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.
- GSM4210330 bone marrow DC progenitors, uninfected rep1 (ATAC-seq)
- GSM4210331 bone marrow DC progenitors, uninfected rep2 (ATAC-seq)
- GSM4210332 bone marrow DC progenitors, uninfected rep3 (ATAC-seq)
- GSM4210333 bone marrow DC progenitors, Armstrong rep1 (ATAC-seq)
- GSM4210334 bone marrow DC progenitors, Armstrong rep2 (ATAC-seq)
- GSM4210335 bone marrow DC progenitors, Armstrong rep3 (ATAC-seq)
- GSM4210336 bone marrow DC progenitors, Cl13 rep1 (ATAC-seq)
- GSM4210337 bone marrow DC progenitors, Cl13 rep2 (ATAC-seq)
- GSM4210338 bone marrow DC progenitors, Cl13 rep3 (ATAC-seq)
- GSM4210339 bone marrow DC progenitors, uninfected rep1 (RNA-seq)
- GSM4210340 bone marrow DC progenitors, uninfected rep2 (RNA-seq)
- GSM4210341 bone marrow DC progenitors, uninfected rep3 (RNA-seq)
- GSM4210342 bone marrow DC progenitors, Armstrong rep1 (RNA-seq)
- GSM4210343 bone marrow DC progenitors, Armstrong rep2 (RNA-seq)
- GSM4210344 bone marrow DC progenitors, Armstrong rep3 (RNA-seq)
- GSM4210345 bone marrow DC progenitors, Cl13 rep1 (RNA-seq)
- GSM4210346 bone marrow DC progenitors, Cl13 rep2 (RNA-seq)
- GSM4210347 bone marrow DC progenitors, Cl13 rep3 (RNA-seq)
- GSM5723795 isotype rep1
- GSM5723796 isotype rep2
- GSM5723797 isotype rep3
- GSM5723798 anti-IFNAR rep1
- GSM5723799 anti-IFNAR rep2
- GSM5723800 anti-IFNAR rep3
- GSE224160 Malaria pigment hemozoin-induced chromatin remodeling of mouse hematopoietic stem and progenitor cells, granulocyte-macrophage progenitors, and bone marrow monocytes 12 samples shares progenitors, marrow, bone
- GSE189297 RNA sequencing of wild type or calcineurin-deficient mouse bone marrow-derived dendritic cells stimulated with or without lipoarabinomannan (LAM) from Mycobacterium tuberculosis Aoyama-B 10 samples shares dendritic, marrow, bone
- GSE314874 TOX sustains the longevity and multipotency of CD4 Tprog cells during chronic LCMV infection 16 samples shares lcmv, chronic
- GSE316925 Transcriptome changes in trigeminal ganglia in the mouse chronic constriction injury of the infraorbital nerve model - role of TRPM3. 136 samples shares changes, chronic
- GSE239738 Histone modification in dendritic cell progenitors and dendritic cells 42 samples shares progenitors, dendritic
- GSE237260 Transcriptome Analysis Reveals Gene Expression Changes in a mouse Model of Hyperoxia-induced acute lung injury 12 samples shares changes, acute
- GSE302734 Single-Cell RNA Sequencing Unravels Interactions between Macrophages and Fibroadipogenic Progenitors during Ectopic Bone Formation in FOP Mice 12 samples shares progenitors, bone
- GSE225651 Brain changes in responses of mice to intracerebral hemorrhage at the acute stages 12 samples shares changes, acute
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.