GEO series

Ancestry-Specific Structural Variation at 17q21.31 Reveals a Novel H1 Sub-Haplotype and Functional Effects on Tau Biology

GSE328854 Homo sapiens (human) RNA-seq (gene expression) 102 samples Submitted 2026/05/31 Platform GPL34382Platform GPL28352Platform GPL34678

At a glance

RNA-seq (gene expression) · human · 102 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: 102 samples: 102 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.

Summary (written by the submitters)

This study investigates how structural variation at the 17q21.31 locus influences MAPT transcript diversity across ancestries and cellular contexts. The locus contains the H1 and H2 haplotypes, which differ by a large inversion and are associated with distinct risks for neurodegenerative disease. To characterize ancestry- and haplotype-specific tau isoform expression, targeted long-read Iso-Seq was performed on human postmortem brain tissue samples from caudate and Middle Frontal Gyrus, as well as induced pluripotent stem cell–derived neurons and astrocytes.

Read the full summary ↓

Samples represented multiple haplotype groups and ancestries, including a newly identified African-enriched H1 sub-haplotype (H1_A). Full-length transcript sequencing was used to identify known and novel MAPT isoforms, quantify relative isoform usage, and compare splicing patterns across tissues and cell types. These data provide a resource for understanding how population-specific genomic structure at 17q21.31 may shape tau biology and neurodegenerative disease susceptibility.

This dataset

Open GSE328854 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 GSE328854_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 PRJNA1456894 and SRA study SRP694156. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

102 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 102 sample titles: 102 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.

Samples in this study

GSM9690926 HBCC_2542 WT Caudate
GSM9690927 HBCC_2542 WT Middle Frontal Gyrus
GSM9690928 1992_30 WT Caudate
GSM9690929 HBCC_3134 WT Caudate
GSM9690930 HBCC_3134 WT Middle Frontal Gyrus
GSM9690931 NDBB023_7_8 WT Caudate
GSM9690932 NDBB023_2_2 WT Middle Frontal Gyrus
GSM9690933 HBCC_1887 WT Caudate
GSM9690934 HBCC_1887 WT Middle Frontal Gyrus
GSM9690935 2021_51 WT Caudate
GSM9690936 2021_51 WT Middle Frontal Gyrus
GSM9690937 274 WT Caudate
GSM9690938 274 WT Middle Frontal Gyrus
GSM9690939 BJSIPS WT Astrocytes
GSM9690940 1995_78 WT Caudate
GSM9690941 NDBB057_6_8 WT Caudate
GSM9690942 NDBB057_2_1 WT Middle Frontal Gyrus
GSM9690943 51069 WT Astrocytes
GSM9690944 NDBB021_4_5 WT Caudate
GSM9690945 NDBB021_4_6 WT Middle Frontal Gyrus
GSM9690946 NDBB331_7_4 WT Caudate
GSM9690947 NDBB331_5_2 WT Middle Frontal Gyrus
GSM9690948 51048 WT Astrocytes
GSM9690949 2019_50 WT Caudate
GSM9690950 6734 WT Caudate
GSM9690951 50975 WT Astrocytes
GSM9690952 HBCC_859 WT Caudate
GSM9690953 HBCC_859 WT Middle Frontal Gyrus
GSM9690954 HBCC_1111 WT Caudate
GSM9690955 HBCC_1111 WT Middle Frontal Gyrus
GSM9690956 HBCC_2543 WT Caudate
GSM9690957 HBCC_2543 WT Middle Frontal Gyrus
GSM9690958 HBCC_846 WT Caudate
GSM9690959 HBCC_846 WT Middle Frontal Gyrus
GSM9690960 HBCC_1314 WT Caudate
GSM9690961 HBCC_1314 WT Middle Frontal Gyrus
GSM9690962 2021_119 WT Caudate
GSM9690963 2021_119 WT Middle Frontal Gyrus
GSM9690964 2020_54_1 WT Caudate
GSM9690965 NDBB024_5_6 WT Caudate

+ 62 more — browse all 102 samples with per-sample file links →

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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.