GSE76220
GSE GEO Potentially relatedGene Expression Signatures of Motor Neuron Populations Isolated from Sporadic ALS
Organism:
Homo sapiens
Platform:
GPL9115
Samples:
21
Experiment Types:
Expression profiling by high throughput sequencing
Submitted:
Dec 21 2015
Last Updated:
Mar 03 2021
Status:
Public on Feb 01 2016
Contact:
Ranjan,,Batra (University of California San Diego)
Relations
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA306659
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP067645
Summary
We used total RNA-sequencing (RNA-seq) to analyze ALS MN-specific gene-expression signatures in laser capture microdissected motor neurons from post-mortem lumbar spinal cords.
Overall Design
To obtain transcriptome-wide gene expression measurements in adult spinal motor neurons (MNs), we performed laser capture microdissection (LCM) of lumbar spinal cord sections from 13 sporadic ALS patients and 9 controls, extracted total RNA, made RNA-seq libraries and sequenced the libraries on Illumina GA II platform
Analysis (5 steps)
View Data Processing
Processing steps for GSE76220
- Raw reads were adaptor-trimmed and aligned to the human genome (UCSC version hg18) using bowtie (parameters: -l 20 -m 5 -k 5 --best -q hg18).
- Aligned reads were assigned to a custom annotation of human genes [36], [48], and gene expression values were calculated as RPKMs [28].
- Control versus sALS patient datasets were compared in a pairwise fashion, calculating ratio fold-changes for all possible 117 disease versus control pairs.
- For Median Percentile Rank (MPR) analysis, each set of fold-changes were sorted and given a percentile rank, and the median percentile rank for each gene was determined and plotted as a histogram.
- The local minima near the down-regulated edge, 0.15 was taken as the down-regulated cutoff, and a mirrored cutoff of 0.85 was taken for the up-regulated cutoff, and these gene sets were used for subsequent GO analysis.
Supplementary Files (2)
Dataset Citations (1)
Potentially Related Publications (1)
This accession was text-mined from the PMC full text of these publications. It may be referenced for comparison or reused from another study rather than generated for them.
Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis.
Acta neuropathologica · 2022
Data Files (10)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | 16A.fastq.gz | RNA-Seq | 884.9 MB | link | |||
| — | 21A.fastq.gz | RNA-Seq | 987.5 MB | link | |||
| — | 27A.fastq.gz | RNA-Seq | 722.2 MB | link | |||
| — | 34A.fastq.gz | RNA-Seq | 930.8 MB | link | |||
| — | 48A.fastq.gz | RNA-Seq | 299.4 MB | link | |||
| — | 79A.fastq.gz | RNA-Seq | 1.0 GB | link | |||
| — | 82A.fastq.gz | RNA-Seq | 981.6 MB | link | |||
| — | 84A.fastq.gz | RNA-Seq | 241.4 MB | link | |||
| — | 85A.fastq.gz | RNA-Seq | 946.3 MB | link | |||
| — | 89A.fastq.gz | RNA-Seq | 471.7 MB | link |