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Sample GSM1679648 Query DataSets for GSM1679648
Status Public on Jan 15, 2016
Title C_0002 [reanalysis of GSM1580869]
Sample type SRA
Source name BA9 prefrontal cortex
Organism Homo sapiens
Characteristics tissue: brain (BA9 prefrontal cortex)
gender: male
post-mortem interval (pmi): 2
rna integrity number (rin): 7.7
age at death: 73
proteomics study: yes
proteomics sv1: -0.1521250874
proteomics sv2: -0.22833302
proteomics sv3: 0.140254512
microarray study: C_2
Extracted molecule polyA RNA
Extraction protocol QIAzol, Qiagen miRNeasy kit
Illumina TruSeq RNA Sample Prep Kit, mRNA
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description RNA-Seq data in GEO (GSE64977), Microarray data in ArrayExpress (E-MTAB-812)
Data processing RNA-Seq: Bases were called with the Illumina CASAVA 1.7 pipeline
RNA-Seq: mRNA-Seq reads were aligned against UCSC hg19 genome build with tophat 2.0.1, parameters --read-mismatches=3 --read-edit-dist=3 --max-multihits=20 --splice-mismatches=1 --microexon-search --coverage-search --mate-inner-dist=50 --mate-std-dev=50 –num-threads=8
RNA-Seq: Aligned reads were counted against the Gencode v17 gene annotation using htseq-count in the HTSeq package with –mode=intersection-nonempty
RNA-Seq: Genes that were not protein coding (PCG) were filtered from further analysis
RNA-Seq: Genes were filtered from further analysis that had more than half of both PD and Control samples with zero counts
RNA-Seq: Differential expression between PD and controls was assessed using DESeq2 v1.4.0
genome build: hg19
proteomics: MS/MS and MS/MS/MS spectra were searched against the human IPI database (Version 3.87) from the European Bioinformatics Institute using the SEQUEST algorithm, with modifications permitted to allow the detection of oxidized Met (+16), carboxyamidomethylated Cys (+57), and phosphorylated Ser, Thr and Tyr (+80)
proteomics: The raw proteomics data for 3,558 unique gene symbols were normalized in R using two steps: 1) an intra-experimental (within plex) variation step – for each sample, each protein’s raw signal was normalized to the total ion intensity of the protein within the plex, and 2) an inter-experimental (across plexes) variation step – for each sample, each protein’s normalized value from step 1) was transformed by dividing it to the mean of all normalized values of the protein obtained in step 1) of all 24 samples.
proteomics: The Surrogate Variable Analysis (SVA) method implemented in the sva R package (v3.10.0) was used to eliminate latent noise in the data not explained by the categorical factors, including batch effects. Three significant surrogate variables (SVs) were identified for the proteomics data.
proteomics: The limma R package was used for statistical analysis of differential abundance, using a linear model fit including the 3 SVs for the contrast between the PD and the control groups.
proteomics: The protein abundance p-values were adjusted for multiple comparisons using the q-value method; a gene was considered to be significantly different between PD and control samples if it had an adjusted q-value < 0.05.
processed data files format and content: Processed files contain: normalized counts for all samples (mlpd_PCG_DESeq2_norm_counts.txt) and differential expression values (mlpd_DESeq2_diffexp_pmi_age_rin_default.txt) from DESeq2 for protein-coding genes (PCG), in tab delimited format; normalized protein abundance data for 3,558 gene symbols with information about the proteomics samples included in the four 6-plex experiments (proteomics_dataset.RData - objects contained are "expdata", "genename", and "normdata"; the gene order in "genename" corresponds to the gene order in "normdata")
Submission date May 11, 2015
Last update date Jan 15, 2016
Contact name Alexandra Dumitriu
Organization name Boston University
Department Neurology
Street address 72 East Concord Street
City Boston
ZIP/Postal code 02118
Country USA
Platform ID GPL11154
Series (1)
GSE68719 mRNA-Seq expression and MS3 proteomics profiling of human post-mortem BA9 brain tissue for Parkinson Disease and neurologically normal individuals
Reanalysis of GSM1580869
BioSample SAMN03651527
SRA SRX1022857

Supplementary data files not provided
Processed data is available on Series record
Raw data provided as supplementary file

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