Time-dependent gene expression patterns in injured brains of WT and LRRK2 G2019S mice.
RNA-seq (gene expression) · mouse · 16 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
- 16 samples: 8 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.
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 GSE215277_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 PRJNA889526 and SRA study SRP402048. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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.
- GSM6631038 WT intact - biol rep1 WT intact - biol
- GSM6631039 WT intact - biol rep2 WT intact - biol
- GSM6631040 GS intact - biol rep1 GS intact - biol
- GSM6631041 GS intact - biol rep2 GS intact - biol
- GSM6631042 WT ATP 6 h - biol rep1 WT ATP 6 h - biol
- GSM6631043 WT ATP 6 h - biol rep2 WT ATP 6 h - biol
- GSM6631044 GS ATP 6 h - biol rep1 GS ATP 6 h - biol
- GSM6631045 GS ATP 6 h - biol rep2 GS ATP 6 h - biol
- GSM6631046 WT ATP 3 d - biol rep1 WT ATP 3 d - biol
- GSM6631047 WT ATP 3 d - biol rep2 WT ATP 3 d - biol
- GSM6631048 GS ATP 3 d - biol rep1 GS ATP 3 d - biol
- GSM6631049 GS ATP 3 d - biol rep2 GS ATP 3 d - biol
- GSM6631050 WT ATP 15 d - biol rep1 WT ATP 15 d - biol
- GSM6631051 WT ATP 15 d - biol rep2 WT ATP 15 d - biol
- GSM6631052 GS ATP 15 d - biol rep1 GS ATP 15 d - biol
- GSM6631053 GS ATP 15 d - biol rep2 GS ATP 15 d - biol
- GSE246117 Parkinson’s-linked LRRK2-G2019S derails AMPAR trafficking, mobility and composition in striatum with cell-type and subunit specificity 6 samples shares g2019s, lrrk2
- GSE271781 Molecular and spatial transcriptomic classification of midbrain dopamine neurons and their alterations in a LRRK2G2019S model of Parkinson’s disease 4 samples shares g2019s, lrrk2
- GSE283183 LRRK2 G2019S mutation incites increased cell-intrinsic neutrophil effector functions and intestinal inflammation in a model of infectious colitis. 4 samples shares g2019s, lrrk2
- GSE283666 Gut Commensal Parabacteroides goldsteinii mitigates LRRK2 Parkinsonism through reducing neuroinflammation and multifaceted effects on gut homeostasis [RNA-seq] 54 samples shares lrrk2
- GSE265833 Single cell RNA sequencing reveals limited effects of Lrrk2 genotype in a mouse model of acute CNS inflammation 18 samples shares lrrk2
- GSE212059 Effect of depletion of Lrrk2 on mice acute kidney injury 12 samples shares lrrk2
- GSE294140 PFF induce LRRK2-Mediated Rab5 Phosphorylation Triggering Lysosomal Dysfunction and Neuronal Senescence [RNA-Seq] 8 samples shares lrrk2
- GSE284454 Gut commensal Parabacteroides goldsteinii mitigates LRRK2 Parkinsonism by reducing neuroinflammation and enhancing gut homeostasis 8 samples shares lrrk2
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.