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| Status |
Public on Apr 14, 2021 |
| Title |
201516250042_R07C01_Smoker |
| Sample type |
SRA |
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| Source name |
nucleus accumbens
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| Organism |
Homo sapiens |
| Characteristics |
current smoking status: case
age at death: 43.67430983
sex (m, male; f, female): M
ancestry (cauc, caucasian; aa, african american): CAUC
rin (rna integrity number): 8.8
salmon_mapping_pct (salmon software read mapping percentage): 41.44207571
exon_mapping_pct (hisat2 software read mapping percentage to exonic regions): 47.709489
intron_mapping_pct (hisat2 software read mapping percentage to intronic regions): 41.914615
intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions): 10.3758999
mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes): 4.623294501
ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes): 0.016892284
chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry): 254.8300003
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): 5.283476319
effective_seq_depth (number of reads successfully mapped by salmon): 25122195
shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10): 6.922618707
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 |
SAMN18723218 |
| SRA |
SRX10592557 |
| 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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