Bulk RNA-seq of dorsolateral prefrontal cortex tissue collected during deep brain stimulation neurosurgery in obsessive-compulsive disorder and neurological controls
RNA-seq (gene expression) · human · 10 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
- Homo sapiens (human)
- Samples
- 10 samples: 8 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 GSE328351_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 PRJNA1454822 and SRA study SRP692704. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 10 sample titles: 8 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.
- GSM9679743 DLPFC tissue from OCD subject 01
- GSM9679744 DLPFC tissue from OCD subject 02
- GSM9679745 DLPFC tissue from OCD subject 03 sample A
- GSM9679746 DLPFC tissue from OCD subject 03 sample B
- GSM9679747 DLPFC tissue from Control subject 01
- GSM9679748 DLPFC tissue from Control subject 02 sample A
- GSM9679749 DLPFC tissue from Control subject 02 sample B
- GSM9679750 DLPFC tissue from Control subject 03
- GSM9679751 DLPFC tissue from Control subject 04 sample A
- GSM9679752 DLPFC tissue from Control subject 04 sample B
- GSE174409 Transcriptional alterations in dorsolateral prefrontal cortex and nucleus accumbens implicate neuroinflammation and synaptic remodeling in opioid use disorder 80 samples shares dorsolateral, prefrontal, disorder
- GSE54568 Expression data from human brain dorsolateral prefrontal cortex - including control samples and samples with major depression disorders (30 samples BA9_F) 30 samples shares dorsolateral, prefrontal, disorder
- GSE54567 Expression data from human brain dorsolateral prefrontal cortex - including control samples and samples with major depression disorders (28 samples BA9_M) 28 samples shares dorsolateral, prefrontal, disorder
- GSE307537 Tissue Block-Resolved Spatiotemporal Transcriptomic Atlas of Human Fetal Brainstem Reveals Gene Modules and Paradigms Linked to Neurological Disorders 107 samples shares neurological, disorder
- GSE292759 High-Throughput Drug Discovery for a Rare Neurological Disorder: Uncovering a Novel Therapeutic Opportunity for the 19q12 Autism Spectrum Disorder [DRUGseq] 68 samples shares neurological, disorder
- GSE308457 Microglia-like cells derived from patients with obsessive-compulsive disorder and social anxiety disorder 37 samples shares obsessive-compulsive, disorder
- GSE271268 Gene expression analysis in obsessive-compulsive disorder with and without comorbid neurodevelopmental disorders 28 samples shares obsessive-compulsive, disorder
- GSE292760 High-Throughput Drug Discovery for a Rare Neurological Disorder: Uncovering a Novel Therapeutic Opportunity for the 19q12 Autism Spectrum Disorder [post treatment entrectinib patient data] 10 samples shares neurological, disorder
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.