Transcriptional response of mouse BMDMs to diverse lysosomal stressors [HEX000414]
RNA-seq (gene expression) · mouse · 90 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
- 90 samples: 90 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.
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 GSE272298_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 PRJNA1136059 and SRA study SRP520018. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 90 sample titles: 90 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.
- GSM8397985 DMSO, 1 hour, replicate 1 [HSA-000022153]
- GSM8397986 DMSO, 1 hour, replicate 2 [HSA-000022154]
- GSM8397987 DMSO, 1 hour, replicate 3 [HSA-000022155]
- GSM8397988 DMSO, 1 hour, replicate 4 [HSA-000022156]
- GSM8397989 DMSO, 1 hour, replicate 5 [HSA-000022157]
- GSM8397990 BafA1, 1 hour, replicate 1 [HSA-000022158]
- GSM8397991 BafA1, 1 hour, replicate 2 [HSA-000022159]
- GSM8397992 BafA1, 1 hour, replicate 3 [HSA-000022160]
- GSM8397993 BafA1, 1 hour, replicate 4 [HSA-000022161]
- GSM8397994 BafA1, 1 hour, replicate 5 [HSA-000022162]
- GSM8397995 U18666A, 1 hour, replicate 1 [HSA-000022163]
- GSM8397996 U18666A, 1 hour, replicate 2 [HSA-000022164]
- GSM8397997 U18666A, 1 hour, replicate 3 [HSA-000022165]
- GSM8397998 U18666A, 1 hour, replicate 4 [HSA-000022166]
- GSM8397999 U18666A, 1 hour, replicate 5 [HSA-000022167]
- GSM8398000 VPS34IN-1, 1 hour, replicate 1 [HSA-000022168]
- GSM8398001 VPS34IN-1, 1 hour, replicate 2 [HSA-000022169]
- GSM8398002 VPS34IN-1, 1 hour, replicate 3 [HSA-000022170]
- GSM8398003 VPS34IN-1, 1 hour, replicate 4 [HSA-000022171]
- GSM8398004 VPS34IN-1, 1 hour, replicate 5 [HSA-000022172]
- GSM8398005 E/L/P, 1 hour, replicate 1 [HSA-000022173]
- GSM8398006 E/L/P, 1 hour, replicate 2 [HSA-000022174]
- GSM8398007 E/L/P, 1 hour, replicate 3 [HSA-000022175]
- GSM8398008 E/L/P, 1 hour, replicate 4 [HSA-000022176]
- GSM8398009 E/L/P, 1 hour, replicate 5 [HSA-000022177]
- GSM8398010 MSU, 1 hour, replicate 1 [HSA-000022178]
- GSM8398011 MSU, 1 hour, replicate 2 [HSA-000022179]
- GSM8398012 MSU, 1 hour, replicate 3 [HSA-000022180]
- GSM8398013 MSU, 1 hour, replicate 4 [HSA-000022181]
- GSM8398014 MSU, 1 hour, replicate 5 [HSA-000022182]
- GSM8398015 DMSO, 7 hours, replicate 1 [HSA-000022183]
- GSM8398016 DMSO, 7 hours, replicate 2 [HSA-000022184]
- GSM8398017 DMSO, 7 hours, replicate 3 [HSA-000022185]
- GSM8398018 DMSO, 7 hours, replicate 4 [HSA-000022186]
- GSM8398019 DMSO, 7 hours, replicate 5 [HSA-000022187]
- GSM8398020 BafA1, 7 hours, replicate 1 [HSA-000022188]
- GSM8398021 BafA1, 7 hours, replicate 2 [HSA-000022189]
- GSM8398022 BafA1, 7 hours, replicate 3 [HSA-000022190]
- GSM8398023 BafA1, 7 hours, replicate 4 [HSA-000022191]
- GSM8398024 BafA1, 7 hours, replicate 5 [HSA-000022192]
+ 50 more — browse all 90 samples with per-sample file links →
- GSE272357 Transcriptional response of BMDMs to CRISPR KO of key lysosomal genes [HEX000527] 69 samples shares lysosomal, bmdms
- GSE272356 Transcriptional response of WT and Trem2 KO BMDMs to lysosomal alkalinization [HEX000434] 12 samples shares lysosomal, bmdms
- GSE333520 The flame retardant triphenyl phosphate induces varying responses in genetically diverse mouse induced pluripotent stem cells 436 samples shares diverse
- GSE272288 Transcriptional response of mouse primary microglia to lysosomal alkalinization [HEX000413] 24 samples shares lysosomal
- GSE304115 Bulk RNA-seq of Genetically Diverse Triple-Negative Breast Cancer Mouse Models Treated with Immunotherapy, Chemotherapy, Erlotinib, or Trametinib 309 samples shares diverse
- GSE235987 Enhancer-AAVs allow genetic access to diverse populations of astrocytes and oligodendrocytes across species 2040 samples shares diverse
- GSE310411 Multiomic Profiling of the Liver Across Diets and Age in a Diverse Mouse Population 150 samples shares diverse
- GSE267786 Impact of SLC15A4, TASL and TASL2(Gm6377) deficiency on endolysosomal TLR7 and TLR9 responses 95 samples shares lysosomal
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.