GEO series

Functionally distinct subset of monocytes in mouse and human blood [RNA-Seq]

GSE148554 Mus musculus (mouse) RNA-seq (gene expression) 48 samples Submitted 2024/04/10 Platform GPL17021Platform GPL21103

At a glance

RNA-seq (gene expression) · mouse · 48 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: 48 samples: 48 samples, each with a distinct title — no replicated groupsGroups 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.

Summary (written by the submitters)

Here, we used an inducible and reversible system to pause myeloid differentiation at a self-renewing state. These cells were clonally isolated and allowed to differentiate to test whether function was clone-specific and clonally restricted. We found that monocytic subsets exist with inherent, restricted capabilities which differ in their capacity to perform traditional monocytic functions.

This dataset

Open GSE148554 in finder → Find more mouse RNA-seq datasets →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE148554_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA625029 and SRA study SRP256269. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

48 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 48 sample titles: 48 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.

Samples in this study

GSM4473488 Clone1_Plus [RNA-Seq]
GSM4473489 Clone2_Plus [RNA-Seq]
GSM4473490 Clone3_Plus [RNA-Seq]
GSM4473491 Clone4_Plus [RNA-Seq]
GSM4473492 Clone5_Plus [RNA-Seq]
GSM4473493 Clone6_Plus [RNA-Seq]
GSM4473494 Clone7_Plus [RNA-Seq]
GSM4473495 Clone8_Plus [RNA-Seq]
GSM4473496 Clone9_Plus [RNA-Seq]
GSM4473497 Clone10_Plus [RNA-Seq]
GSM4473498 Clone11_Plus [RNA-Seq]
GSM4473499 Clone12_Plus [RNA-Seq]
GSM4473500 Clone13_Plus [RNA-Seq]
GSM4473501 Clone15_Plus [RNA-Seq]
GSM4473502 Clone16_Plus [RNA-Seq]
GSM4473503 Clone17_Plus [RNA-Seq]
GSM4473504 Clone18_Plus [RNA-Seq]
GSM4473505 Clone19_Plus [RNA-Seq]
GSM4473506 Clone20_Plus [RNA-Seq]
GSM4473507 Clone21_Plus [RNA-Seq]
GSM4473508 Clone22_Plus [RNA-Seq]
GSM4473509 Clone23_Plus [RNA-Seq]
GSM4473510 Clone24_Plus [RNA-Seq]
GSM4473511 Clone26_Plus [RNA-Seq]
GSM4473512 Clone1_Minus [RNA-Seq]
GSM4473513 Clone2_Minus [RNA-Seq]
GSM4473514 Clone3_Minus [RNA-Seq]
GSM4473515 Clone4_Minus [RNA-Seq]
GSM4473516 Clone5_Minus [RNA-Seq]
GSM4473517 Clone6_Minus [RNA-Seq]
GSM4473518 Clone7_Minus [RNA-Seq]
GSM4473519 Clone8_Minus [RNA-Seq]
GSM4473520 Clone9_Minus [RNA-Seq]
GSM4473521 Clone10_Minus [RNA-Seq]
GSM4473522 Clone11_Minus [RNA-Seq]
GSM4473523 Clone12_Minus [RNA-Seq]
GSM4473524 Clone13_Minus [RNA-Seq]
GSM4473525 Clone15_Minus [RNA-Seq]
GSM4473526 Clone16_Minus [RNA-Seq]
GSM4473527 Clone17_Minus [RNA-Seq]

+ 8 more — browse all 48 samples with per-sample file links →

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Search all mouse RNA-seq datasets in GEO →

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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.