Choosing a Dataset - bcb420-2025/Clare_Gillis GitHub Wiki

Chosen dataset info:

GEO Accession: GSE251939

Title: Analysis of microisolated frontal cortex excitatory layer III and V pyramidal neurons reveals a neurodegenerative phenotype in individuals with Down syndrome

Date published: Aug 07, 2024

Organism: Homo sapiens

Publications:

  • Alldred MJ, Pidikiti H, Ibrahim KW, Lee SH et al. Analysis of microisolated frontal cortex excitatory layer III and V pyramidal neurons reveals a neurodegenerative phenotype in individuals with Down syndrome. Acta Neuropathol 2024 Aug 6;148(1):16. PMID: 39105932
  • Alldred MJ, Ibrahim KW, Pidikiti H, Chiosis G et al. Down syndrome frontal cortex layer III and layer V pyramidal neurons exhibit lamina specific degeneration in aged individuals. Acta Neuropathol Commun 2024 Nov 27;12(1):182. PMID: 39605035

Contributors: Alldred MJ, Pidikiti H, Ibrahim K, Heguy A, Hoffmann G, Roussos P, Ginsberg SD

Classes:

  • DS-L3: Frontal cortex layer III pyramidal neurons (L3) of individuals with Down Syndrome (DS)
  • DS-L5: Frontal cortex layer V pyramidal neurons (L5) of individuals with Down Syndrome (DS)
  • CTL-L3: Frontal cortex layer III pyramidal neurons (L3) of control individuals without Down Syndrome (CTL)
  • CTL-L5: Frontal cortex layer V pyramidal neurons (L5) of control individuals without Down Syndrome (CTL)

Sample sizes: 12 DS (Down Syndrome) (6M/6F) and 17 CTR (Control) (9M/8F)

Reference Genome: Gencode GRCh38 (includes 78724 total genes)

Number of genes detected: 61906

Number of replicates: 2 (quite low)

Selection process:

A journal entry documenting my process of choosing a dataset for Assignment #1 - Data set selection and initial Processing

The field of research I'm interested in (for BCB430 project) doesn't really incorporate gene expression analysis, so I'm thinking more about experimental conditions that interest me personally.

Condition I'm interested in: Alzheimer's disease.

Search term for GEO Datasets: ("alzheimer disease"[MeSH Terms] OR Alzheimer's[All Fields]) AND "Homo sapiens"[porgn] NOT "single cell"[All Fields] AND "Expression profiling by high throughput sequencing"[Filter]

This retrieved 293 items, so I began by looking through the titles of the datasets to find one that caught my eye. I found this entry: [Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE233208)

I didn't know that there might be a connection between down syndrome and Alzheimer's disease so I am interested in looking into this through a gene expression analysis. Moeover, this dataset is recent (2024) so is likely higher quality than older datasets.