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Deciphering the functional impact of Alzheimer’s Disease-associated variants in resting and proinflammatory immune cells [crispr]

GSE300841 Homo sapiens (human) RNA-seq (gene expression) 116 samples Submitted 2025/07/02 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 116 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
116 samples: 54 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.
Summary (written by the submitters)
Genome-wide association studies have identified loci associated with Alzheimer’s Disease (AD), but identifying the exact causal variants and genes at each locus is challenging due to linkage disequilibrium and their largely non-coding nature. To address this, we performed a massively parallel reporter assay of 3,576 AD-associated variants in THP-1 macrophages in both resting and proinflammatory states and identified 47 expression-modulating variants (emVars).
Read the full summary ↓
To understand the endogenous chromatin context of emVars, we built an activity-by-contact model using epigenomic maps of macrophage inflammation and inferred condition-specific enhancer-promoter pairs. Intersection of emVars with enhancer-promoter pairs and microglia expression quantitative trait loci allowed us to connect 39 emVars to 76 putative AD risk genes enriched for AD-associated molecular signatures. CRISPR-mediated validation of emVars confirmed the predicted variant-gene relationship. Overall, systematic characterization of AD-associated variants enhances our understanding of the regulatory mechanisms underlying AD pathogenesis.
This dataset
Open GSE300841 in finder → Find more human 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 GSE300841_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 PRJNA1282190 and SRA study SRP595538. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
54 conditions, mostly in duplicate
ADAMTS4_ADAMTS4_Promoter_exp_3 ×2 ADAMTS4_ADAMTS4_Promoter_exp_5 ×2 ADAMTS4_ADAMTS4_Promoter_exp_7 ×2 FCGR3B_FCGR3B_Promoter_exp_7 ×2 FCGR3B_FCGR3B_Promoter_exp_8 ×2 rs4575098_ADAMTS4,FCGR3B_Variant_exp_3 ×2 rs4575098_ADAMTS4,FCGR3B_Variant_exp_7 ×2 HLA-DRB1_HLA-DRB1_Promoter_exp_3 ×2 +54 more

Supports a between-group comparison across 108 samples.

How we read this: 54 replicated groups read from 116 sample titles; they account for 108 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.

Samples in this study

+ 76 more — browse all 116 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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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.