NG00178 - Multi-brain region mRNA-seq of sporadic ALS patients with pTDP-43 pathological staging

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Description

Post-mortem fresh-frozen brain tissue was obtained for 22 sporadic amyotrophic lateral sclerosis (ALS) cases and 11 neurologically healthy control participants from Sydney Brain Bank and the New South Wales Brain Tissue Resource Centre. ALS cases were clinically diagnosed according to El Escorial criteria and were classified as sporadic based on the absence of a family history of neurodegenerative disease. ALS patients were confirmed to not carry a pathogenic repeat expansion in C9orf72, an intermediate or pathogenic repeat expansion in ATXN2 or a pathogenic variant in SOD1. ALS patients underwent post-mortem pTDP-43 pathological staging by an experienced neuropathologist. ALS patients were classified as stage 1 (n=6), stage 2 (n=7), stage 3 (n=2) or stage 4 (n=7) pTDP-43 pathology.

RNA was isolated from fresh-frozen post-mortem brain tissue using the AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany) as previously described (PMID: 34939123). RNA integrity was measured using the Agilent RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer system (Agilent Technologies, Santa Clara, CA). All sequenced samples had an RNA integrity number (RIN) ≥ 6. RNA-seq libraries were prepared from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina, CA, USA). Sequencing was performed on an Illumina NovaSeq 6000 platform (151bp paired-end reads) generating raw sequencing reads in FASTQ format (Macrogen, South Korea). Samples had an average read depth of 27 million paired-end reads (range: 20 – 45 million).

Sample Summary per Data Type

Sample Set	Accession	Data Type	Number of Samples
ALS mRNA Sequencing	snd10119	mRNA Sequencing	165

Available Filesets

Name	Accession	Latest Release	Description
ALS mRNA Sequencing	fsa000137	NG00178.v1	Fastq Files, Phenotypes, Readme

View the File Manifest for a full list of files released in this dataset.

The first release (April 24, 2025) includes 22 sporadic ALS patients with pTDP-43 pathological staging and 11 non-neurological controls. For each individual, five brain regions were examined (n=165 samples total): motor cortex (pTDP-43 inclusions always present), prefrontal cortex and hippocampus (pTDP-43 inclusions sometimes present), and occipital cortex and cerebellum (pTDP-43 inclusions rarely present). Samples had an average read depth of 27 million 151bp paired-end reads (range: 20 - 45 million).

Sample Set	Accession Number	Number of Subjects	Number of Samples
ALS mRNA Sequencing	snd10119	33	165

Consent	Number of Subjects
GRU-IRB-PUB	33

Total number of samples: 33

Female 14 42.4 %

Male 19 57.6 %

Amyotrophic Lateral Sclerosis (ALS)
Control	55	166.7%
Case	110	333.3%

NG00178 – Multi-brain region mRNA-seq of sporadic ALS patients with pTDP-43 pathological staging

Overview

Description

Sample Summary per Data Type

Available Filesets

Sample information

Related Studies

Cohorts

Consent Levels

Acknowledgement

Acknowledgment statement for any data distributed by NIAGADS:

For investigators using any data from this dataset:

For investigators using Multi-region brain transcriptomic analysis of amyotrophic lateral sclerosis reveals widespread RNA alterations and substantial cerebellum involvement (sa000068) data:

Related Publications

Total number of samples: 33