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Sample GSM5237809 Query DataSets for GSM5237809
Status Public on Apr 14, 2021
Title 201516260055_R07C01_Nonsmoker
Sample type SRA
 
Source name nucleus accumbens
Organism Homo sapiens
Characteristics current smoking status: control
age at death: 26.95140315
sex (m, male; f, female): F
ancestry (cauc, caucasian; aa, african american): AA
rin (rna integrity number): 7.5
salmon_mapping_pct (salmon software read mapping percentage): 60.18769476
exon_mapping_pct (hisat2 software read mapping percentage to exonic regions): 64.894177
intron_mapping_pct (hisat2 software read mapping percentage to intronic regions): 27.174797
intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions): 7.9310282
mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes): 5.789385346
ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes): 0.004258897
chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry): 1.027604678
chry_pc1 (principal component 1 from pca on variance-stablized median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry): -18.63514454
effective_seq_depth (number of reads successfully mapped by salmon): 39316199
shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10): 6.74352706
nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts): TRUE
sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex): TRUE
nac_assigned_sex_for_missing (imputed sex for individuals without a self-reported sex value (f = female, m = male). the imputation is based on chry gene expression counts): NA
Extracted molecule total RNA
Extraction protocol Genomic DNA and RNA were concurrently extracted from dissected postmortem nucleus accumbens tissue using the Qiagen AllPrep DNA/RNA Mini Kit (Cat No./ID: 80204).
RNA expression was profiled on the Illumain HiSeq 3000 platform using the manufacturer's protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing QC metrics for potential exclusion include: sex discrepancy based on k-means clustering of PC1 values from chrY gene expression PCA, missing value for self-reported sex, RIN score <6, effective sequencing depth <10 read pairs, overall mapping rate<30%, intergenic mapping rate > 30%, overall mapping rate < 50%, Shannon diversity index < 5.92596, overall mapping rate <50%, mitochondrial proportion of gene counts <0.20, rRNA mapping proportion < 0.01
Genome alignment performed with HISAT2. Transcript quantification performed with Salmon.
Genome_build: GRCh38
Supplementary_files_format_and_content: Salmon output: counts, tpm, transcript lengths
 
Submission date Apr 12, 2021
Last update date Apr 14, 2021
Contact name Dana Hancock
E-mail(s) dhancock@rti.org
Phone 9195416701
Organization name RTI International
Street address 3040 E Cornwallis Rd
City Research Triangle Park
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL21290
Series (1)
GSE171936 Genome-wide RNA-sequencing differences in nucleus accumbens of smokers vs. nonsmokers
Relations
BioSample SAMN18723188
SRA SRX10592552

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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