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GSE76220

GSE GEO
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Gene 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
  1. 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).
  2. Aligned reads were assigned to a custom annotation of human genes [36], [48], and gene expression values were calculated as RPKMs [28].
  3. Control versus sALS patient datasets were compared in a pairwise fashion, calculating ratio fold-changes for all possible 117 disease versus control pairs.
  4. 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.
  5. 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)

GSE76220_ALS_LCM_MPR_gene_expression.txt.gz Download
GSE76220_ALS_LCM_RPKM.txt.gz Download
GEO Samples (21)
GSM1977027 GSM1977028 GSM1977029 GSM1977030 GSM1977031 GSM1977032 GSM1977033 GSM1977034 GSM1977035 GSM1977036 GSM1977037 GSM1977038 GSM1977039 GSM1977040 GSM1977041 GSM1977042 GSM1977043 GSM1977044 GSM1977045 GSM1977046 GSM1977047

Dataset Citations (1)

Transcriptome-pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS.
PMID 29881994 · 2018 · Acta neuropathologica
Florian Krach, Ranjan Batra, Emily C Wheeler, Anthony Q Vu, Ruth Wang, Kasey Hutt, Stuart J Rabin, Michael W Baughn, Ryan T Libby, Sandra Diaz-Garcia, Jennifer Stauffer, Elaine Pirie, Shahram Saberi, Maria Rodriguez, Assael A Madrigal, Zacharias Kohl, Beate Winner, Gene W Yeo, John Ravits

SRA Experiments (21) and Runs (21)

Total: 16199 MB
SRX1494374 SRP067645 RNA-Seq SINGLE
GSM1977027: 10_Control; Homo sapiens; RNA-Seq
Sample: SRS1217219
BioProject: PRJNA306659
BioSample: SAMN04359416
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038253 21117915 1055895750 511.23 10C.fastq.gz, SRR3038253, SRR3038253.sralite SRA
SRX1494375 SRP067645 RNA-Seq SINGLE
GSM1977028: 65_Control; Homo sapiens; RNA-Seq
Sample: SRS1217218
BioProject: PRJNA306659
BioSample: SAMN04359417
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038254 30222648 1511132400 766.33 65C.fastq.gz, SRR3038254, SRR3038254.sralite SRA
SRX1494376 SRP067645 RNA-Seq SINGLE
GSM1977029: 78_Control; Homo sapiens; RNA-Seq
Sample: SRS1217217
BioProject: PRJNA306659
BioSample: SAMN04359418
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038255 22359173 1117958650 531.08 78C.fastq.gz, SRR3038255, SRR3038255.sralite SRA
SRX1494377 SRP067645 RNA-Seq SINGLE
GSM1977030: 39_Control; Homo sapiens; RNA-Seq
Sample: SRS1217216
BioProject: PRJNA306659
BioSample: SAMN04359419
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038256 35390202 1769510100 1019.99 39C.fastq.gz, SRR3038256, SRR3038256.sralite SRA
SRX1494378 SRP067645 RNA-Seq SINGLE
GSM1977031: 67_Control; Homo sapiens; RNA-Seq
Sample: SRS1217215
BioProject: PRJNA306659
BioSample: SAMN04359420
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038257 35702384 1785119200 1028.64 67C.fastq.gz, SRR3038257, SRR3038257.sralite SRA
SRX1494379 SRP067645 RNA-Seq SINGLE
GSM1977032: 76_Control; Homo sapiens; RNA-Seq
Sample: SRS1217214
BioProject: PRJNA306659
BioSample: SAMN04359421
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038258 36089192 1804459600 1082.75 76C.fastq.gz, SRR3038258, SRR3038258.sralite SRA
SRX1494380 SRP067645 RNA-Seq SINGLE
GSM1977033: 44_Control; Homo sapiens; RNA-Seq
Sample: SRS1217213
BioProject: PRJNA306659
BioSample: SAMN04359422
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038259 30616734 1530836700 861.28 44C.fastq.gz, SRR3038259, SRR3038259.sralite SRA
SRX1494381 SRP067645 RNA-Seq SINGLE
GSM1977034: 88_Control; Homo sapiens; RNA-Seq
Sample: SRS1217212
BioProject: PRJNA306659
BioSample: SAMN04359423
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038260 22359173 1117958650 531.08 88C.fastq.gz, SRR3038260, SRR3038260.sralite SRA
SRX1494382 SRP067645 RNA-Seq SINGLE
GSM1977035: 60_sALS; Homo sapiens; RNA-Seq
Sample: SRS1217211
BioProject: PRJNA306659
BioSample: SAMN04359424
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038261 30508179 1525408950 777.28 60A.fastq.gz, SRR3038261, SRR3038261.sralite SRA
SRX1494383 SRP067645 RNA-Seq SINGLE
GSM1977036: 62_sALS; Homo sapiens; RNA-Seq
Sample: SRS1217210
BioProject: PRJNA306659
BioSample: SAMN04359425
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038262 31944963 1597248150 828.25 62A.fastq.gz, SRR3038262, SRR3038262.sralite SRA
SRX1494384 SRP067645 RNA-Seq SINGLE
GSM1977037: 63_sALS; Homo sapiens; RNA-Seq
Sample: SRS1217209
BioProject: PRJNA306659
BioSample: SAMN04359426
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038263 29643723 1482186150 751.51 63A.fastq.gz, SRR3038263, SRR3038263.sralite SRA
SRX1494385 SRP067645 RNA-Seq SINGLE
GSM1977038: 84_sALS; Homo sapiens; RNA-Seq
Sample: SRS1217208
BioProject: PRJNA306659
BioSample: SAMN04359427
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038264 11331121 566556050 241.45 84A.fastq.gz, SRR3038264, SRR3038264.sralite SRA
SRX1494386 SRP067645 RNA-Seq SINGLE
GSM1977039: 89_sALS; Homo sapiens; RNA-Seq
Sample: SRS1217207
BioProject: PRJNA306659
BioSample: SAMN04359428
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038265 19885546 994277300 471.69 89A.fastq.gz, SRR3038265, SRR3038265.sralite SRA
SRX1494387 SRP067645 RNA-Seq SINGLE
GSM1977040: 21_sALS; Homo sapiens; RNA-Seq
Sample: SRS1217206
BioProject: PRJNA306659
BioSample: SAMN04359429
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038266 34754975 1737748750 987.53 21A.fastq.gz, SRR3038266, SRR3038266.sralite SRA
SRX1494388 SRP067645 RNA-Seq SINGLE
GSM1977041: 34_sALS; Homo sapiens; RNA-Seq
Sample: SRS1217205
BioProject: PRJNA306659
BioSample: SAMN04359430
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038267 32978331 1648916550 930.78 34A.fastq.gz, SRR3038267, SRR3038267.sralite SRA
SRX1494389 SRP067645 RNA-Seq SINGLE
GSM1977042: 79_sALS; Homo sapiens; RNA-Seq
Sample: SRS1217204
BioProject: PRJNA306659
BioSample: SAMN04359431
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038268 36101437 1805071850 1043.39 79A.fastq.gz, SRR3038268, SRR3038268.sralite SRA
SRX1494390 SRP067645 RNA-Seq SINGLE
GSM1977043: 82_sALS; Homo sapiens; RNA-Seq
Sample: SRS1217203
BioProject: PRJNA306659
BioSample: SAMN04359432
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038269 34575411 1728770550 981.57 82A.fastq.gz, SRR3038269, SRR3038269.sralite SRA
SRX1494391 SRP067645 RNA-Seq SINGLE
GSM1977044: 16_sALS; Homo sapiens; RNA-Seq
Sample: SRS1217202
BioProject: PRJNA306659
BioSample: SAMN04359433
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038270 30899786 1544989300 884.93 16A.fastq.gz, SRR3038270, SRR3038270.sralite SRA
SRX1494392 SRP067645 RNA-Seq SINGLE
GSM1977045: 27_sALS; Homo sapiens; RNA-Seq
Sample: SRS1217201
BioProject: PRJNA306659
BioSample: SAMN04359434
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038271 26241715 1312085750 722.16 27A.fastq.gz, SRR3038271, SRR3038271.sralite SRA
SRX1494393 SRP067645 RNA-Seq SINGLE
GSM1977046: 48_sALS; Homo sapiens; RNA-Seq
Sample: SRS1217200
BioProject: PRJNA306659
BioSample: SAMN04359435
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038272 11632246 581612300 299.36 48A.fastq.gz, SRR3038272, SRR3038272.sralite SRA
SRX1494394 SRP067645 RNA-Seq SINGLE
GSM1977047: 85_sALS; Homo sapiens; RNA-Seq
Sample: SRS1217199
BioProject: PRJNA306659
BioSample: SAMN04359436
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: Human Lumbar spinal cord motor neurons
cell type: Laser Capture microdissected MNs from post-mortem spinal cord
Original files (1)
Human Lumbar spinal cord motor neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3038273 32710741 1635537050 946.28 85A.fastq.gz, SRR3038273, SRR3038273.sralite SRA

Linked Publications (2)

Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis.
Acta neuropathologica · 2022
Transcriptome-pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS.
Acta neuropathologica · 2018

Data Files (25)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— 10C.fastq.gz RNA-Seq 511.2 MB link
— 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
— 39C.fastq.gz RNA-Seq 1020.0 MB link
— 44C.fastq.gz RNA-Seq 861.3 MB link
— 48A.fastq.gz RNA-Seq 299.4 MB link
— 60A.fastq.gz RNA-Seq 777.3 MB link
— 62A.fastq.gz RNA-Seq 828.2 MB link
— 63A.fastq.gz RNA-Seq 751.5 MB link
— 65C.fastq.gz RNA-Seq 766.3 MB link
— 67C.fastq.gz RNA-Seq 1.0 GB link
— 76C.fastq.gz RNA-Seq 1.1 GB link
— 78C.fastq.gz RNA-Seq 531.1 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
— 88C.fastq.gz RNA-Seq 531.1 MB link
— 89A.fastq.gz RNA-Seq 471.7 MB link
— SRR3038260 RNA-Seq 531.1 MB link
— SRR3038263 RNA-Seq 751.5 MB link
— SRR3038264 RNA-Seq 241.4 MB link
— SRR3038265 RNA-Seq 471.7 MB link