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Status |
Public on Apr 14, 2021 |
Title |
201516260055_R07C01_Nonsmoker |
Sample type |
SRA |
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Source name |
nucleus accumbens
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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
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 3000 |
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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
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Submission date |
Apr 12, 2021 |
Last update date |
Apr 14, 2021 |
Contact name |
Dana Hancock |
E-mail(s) |
dhancock@rti.org
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Phone |
9195416701
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Organization name |
RTI International
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Street address |
3040 E Cornwallis Rd
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City |
Research Triangle Park |
State/province |
NC |
ZIP/Postal code |
27709 |
Country |
USA |
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Platform ID |
GPL21290 |
Series (1) |
GSE171936 |
Genome-wide RNA-sequencing differences in nucleus accumbens of smokers vs. nonsmokers |
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Relations |
BioSample |
SAMN18723188 |
SRA |
SRX10592552 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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