GEO series

Transcriptional response of BMDMs to CRISPR KO of key lysosomal genes [HEX000527]

GSE272357 Mus musculus (mouse) RNA-seq (gene expression) 69 samples Submitted 2026/07/20 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 69 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: 69 samples: 69 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)

WT BMDMs were nucleofected with sgRNA/Cas9 RNPs to induce knockouts of genes encoding lysosomal proteins of interest, and bulk RNA-seq was performed at day 4 and d13 post-CRISPR.

This dataset

Open GSE272357 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 GSE272357_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 PRJNA1136508 and SRA study SRP520277. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

69 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 69 sample titles: 69 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

GSM8399301 Rosa26 KO, 4 hours, replicate 1, Regular protocol [HSA-000027320]
GSM8399302 Rosa26 KO, 4 hours, replicate 2, Regular protocol [HSA-000027321]
GSM8399303 Rosa26 KO, 4 hours, replicate 3, Regular protocol [HSA-000027322]
GSM8399304 Rosa26 KO, 4 hours, replicate 4, Regular protocol [HSA-000027323]
GSM8399305 Rosa26 KO, 4 hours, replicate 5, Regular protocol [HSA-000027324]
GSM8399306 Atp6v1a KO, 4 hours, replicate 1, Regular protocol [HSA-000027325]
GSM8399307 Atp6v1a KO, 4 hours, replicate 2, Regular protocol [HSA-000027326]
GSM8399308 Atp6v1a KO, 4 hours, replicate 3, Regular protocol [HSA-000027327]
GSM8399309 Atp6v1a KO, 4 hours, replicate 4, Regular protocol [HSA-000027328]
GSM8399310 Atp6v1a KO, 4 hours, replicate 5, Regular protocol [HSA-000027329]
GSM8399311 Npc1 KO, 4 hours, replicate 2, Regular protocol [HSA-000027331]
GSM8399312 Npc1 KO, 4 hours, replicate 3, Regular protocol [HSA-000027332]
GSM8399313 Npc1 KO, 4 hours, replicate 4, Regular protocol [HSA-000027333]
GSM8399314 Npc1 KO, 4 hours, replicate 5, Regular protocol [HSA-000027334]
GSM8399315 Pik3c3 KO, 4 hours, replicate 1, Regular protocol [HSA-000027335]
GSM8399316 Pik3c3 KO, 4 hours, replicate 2, Regular protocol [HSA-000027336]
GSM8399317 Pik3c3 KO, 4 hours, replicate 3, Regular protocol [HSA-000027337]
GSM8399318 Pik3c3 KO, 4 hours, replicate 4, Regular protocol [HSA-000027338]
GSM8399319 Pik3c3 KO, 4 hours, replicate 5, Regular protocol [HSA-000027339]
GSM8399320 Ctsd KO, 4 hours, replicate 1, Regular protocol [HSA-000027340]
GSM8399321 Ctsd KO, 4 hours, replicate 2, Regular protocol [HSA-000027341]
GSM8399322 Ctsd KO, 4 hours, replicate 3, Regular protocol [HSA-000027342]
GSM8399323 Ctsd KO, 4 hours, replicate 4, Regular protocol [HSA-000027343]
GSM8399324 Ctsd KO, 4 hours, replicate 5, Regular protocol [HSA-000027344]
GSM8399325 Grn KO, 4 hours, replicate 1, Regular protocol [HSA-000027350]
GSM8399326 Grn KO, 4 hours, replicate 2, Regular protocol [HSA-000027351]
GSM8399327 Grn KO, 4 hours, replicate 3, Regular protocol [HSA-000027352]
GSM8399328 Grn KO, 4 hours, replicate 4, Regular protocol [HSA-000027353]
GSM8399329 Grn KO, 4 hours, replicate 5, Regular protocol [HSA-000027354]
GSM8399330 Trem2 KO, 4 hours, replicate 1, Low-input protocol [HSA-000027355]
GSM8399331 Trem2 KO, 4 hours, replicate 2, Regular protocol [HSA-000027356]
GSM8399332 Trem2 KO, 4 hours, replicate 3, Regular protocol [HSA-000027357]
GSM8399333 Trem2 KO, 4 hours, replicate 4, Regular protocol [HSA-000027358]
GSM8399334 Trem2 KO, 4 hours, replicate 5, Regular protocol [HSA-000027359]
GSM8399335 Rosa26 KO, 13 hours, replicate 1, Regular protocol [HSA-000027360]
GSM8399336 Rosa26 KO, 13 hours, replicate 2, Regular protocol [HSA-000027361]
GSM8399337 Rosa26 KO, 13 hours, replicate 3, Regular protocol [HSA-000027362]
GSM8399338 Rosa26 KO, 13 hours, replicate 4, Regular protocol [HSA-000027363]
GSM8399339 Rosa26 KO, 13 hours, replicate 5, Low-input protocol [HSA-000027364]
GSM8399340 Atp6v1a KO, 13 hours, replicate 1, Low-input protocol [HSA-000027365]

+ 29 more — browse all 69 samples with per-sample file links →

Datasets on a similar topic

GSE327962 Effects of CRISPR-mediated knockout of Mitf, Tfe3 and Tfeb on the transcriptome of mouse BMDMs from WT and Grn KO animals [hex001130] 16 samples shares crispr, bmdms
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GSE272356 Transcriptional response of WT and Trem2 KO BMDMs to lysosomal alkalinization [HEX000434] 12 samples shares lysosomal, bmdms
GSE285351 Genome-wide in vivo CRISPR screens identify GATOR1 as a potent tumor suppressor in MYC-driven lymphomagenesis 35 samples shares crispr
GSE249293 Nonviral CRISPR/Cas9 Mutagenesis for Streamlined Generation of Mouse Lung Cancer Models 12 samples shares crispr
GSE273667 Genome-wide CRISPR screening identifies the E3 ubiquitin ligase HERC1 as a modulator of the response to nucleoside analogs in acute myeloid leukemia 12 samples shares crispr
GSE236826 Rapid CRISPR/Cas12a-based dual-crRNA library screening in high fidelity reveals novel genetic interactions during hepatocarcinogenesis [RNA-Seq] 12 samples shares crispr
GSE334845 Discovery of Tcf7 regulators with clonally-resolved CRISPR screens identifies Trim28 as a mediator of CD8 T cell differentiation in tumors [RNA-Seq] 86 samples shares crispr

Search all mouse RNA-seq datasets in GEO →

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