title: 201516250050_R02C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: IL-22+ T cells _Riok2hKO_rep2

status: Public on Apr 14 2021

type: SRA

city: CAMBRIDGE

first: Meromit

last: Singer

state: MASSACHUSETTS

address: 415 main st, ROOM 6031

country: USA

institute: Broad Institute of MIT and Harvard

library_source: transcriptomic

data_processing:
rsem-1.2.8
Genome_build: mm10
Supplementary_files_format_and_content: TPM matrix

molecule: total RNA

organism: Mus musculus

source_name: Th22 cells

growth_protocol: Single-cell suspensions of mouse spleens were prepared by pressing tissue through a 70-mm cell strainer followed by red blood cell lysis using PharmLyse. Total splenic CD4+ T cells were isolated using CD4 T cell isolation kit (Miltenyi Biotec). Enriched CD4+ T cells were then incubated with fluorochrome-conjugated antibodies to CD4, CD8, CD25, CD62L, and CD44 to purify naïve CD4+ T cells using fluorescence activated cell sorting (FACS). In the presence of 1 mg/mL plate-bound anti-CD3e and soluble 1 mg/mL anti-CD28, T cells were cultured in the presence of 30 ng/mL IL-6, 20 ng/mL IL-23, 20 ng/mL IL-1b, 10 mg/mL anti-IL-4, 10 mg/mL anti-IFN-g, 400 nM FICZ to generate TH22 cells.

extract_protocol:
5000 IL-22+ (CD4+IL-22(tdtomato)+) cells were FACS sorted directly into TLC Buffer (Qiagen) with 1% beta-mercaptoethanol. For the preparation of libraries, cell lysates were thawed and RNA was purified with 2.2x RNAClean SPRI beads (Beckman Coulter Genomics) without final elution. The RNA captured beads were air-dried and processed immediately for RNA secondary structure denaturation (72˚C for three minutes) and cDNA synthesis. SMART-seq2 was performed on the resultant samples following the published protocol with minor modifications in the reverse transcription (RT) step. A 15 µL reaction mix was used for subsequent PCR and performed 10 cycles for cDNA amplification. The amplified cDNA from this reaction was purified with 0.8x Ampure SPRI beads (Beckman Coulter Genomics) and eluted in 21ul TE buffer. We used 0.2ng cDNA and one-eighth of the standard Illumina NexteraXT (Illumina FC-131-1096) reaction volume to perform both the tagmentation and PCR indexing steps. Uniquely indexed libraries were pooled and sequenced with NextSeq 500 high output V2 75 cycle kits (Illumina FC-404-2005) and 38 × 38 paired-end reads on the NextSeq 500 instrument. Reads were aligned to the mouse mm10 transcriptome using Bowtie, and expression abundance TPM estimates were obtained using RSEM.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: genotype

tag: age

value: 10 wks

tag: cell type

value: IL-22+ T cells


title: APL331

city: Shanghai

first: Niu

last: Qiao

address: 197 Rui Jin Er Road

department: National Research Center for Translational Medicine (Shanghai)

country: China

institute: Shanghai Jiao Tong University

data_processing:
The HISAT2 was used to align the raw RNA-seq sequences to the hg19 human reference genome. Transcript counts table files were generated using the HTSeq htseq-count subprogram with the GENCODE annotation database and processed with the BAM files created using the Hisat2.
All gene expression data from the RNA-seq experiment were normalized using the variance-stabilizing transformation in the DESeq2. Differentially expressed genes (DEGs) were obtained using the DESeq2 R package. Genes and samples were clustered using the ward.D or the ward.D2 method, and distance was calculated on the basis of the Euclidean or Pearson’s correlation coefficient in the R gplots (version 3.0.1.1) package.
The raw sequence variants of the APL RNA-seq samples without WES samples (n = 144) were called in accordance with the GATK forum-recommended analysis pipeline. The driver mutation sites from the RNA-seq only samples were reported on sites available in the WES data. The detailed screening of the candidate driver gene mutations was carried out in accordance with our previously published procedures.
The FusionCatcher was used to find somatic fusion genes, such that at least 2 split and 3 spanning reads were in the analyzed RNA-seq data.
The IPA was applied to find out whether DEGs were controlled by the same upstream regulator or by the same pathway. The gene set enrichment analysis (GSEA) was performed using the GSEA (version 3.0) with MSigDB-hallmark (H) and MSigDB-curated gene sets. For GSEA, all measured genes with phenotype labels of high and low risks were used. The GO functional and the KEGG pathway analyses were used for enrichment analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression matrix

organism: Homo sapiens

source_name: Bone marrow mononuclear cells, APL patients

extract_protocol:
Bone marrow mononuclear cells from 18 centers were isolated after Ficoll–Isopaque density gradient centrifugation. Genomic mRNA were extracted from the patients’ BM using the AllPrep PowerFecal RNA Kit in accordance with the manufacturer’s instructions. After additional enrichment by purification with Ficoll, BM blasts were over 80%.
The DNase I-treated total RNA preparations were qualitatively validated by Agilent RNA 6000 Nano Kit with the 2100 Bioanalyzer system, and libraries were prepared using the KAPA RNA HyperPrep kit in accordance with the manufacturer’s instructions (KAPA). High-throughput sequencing was performed on the NovaSeq 6000 platform (Illumina, San Diego, CA, USA) in accordance with the manufacturer’s paired-end 2 × 150 bp protocol.

tag: tissue

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

value: Male


title: IL-22+ T cells _Riok2hKO_rep1


title: IL-22+ T cells _Riok2hKO_rep4


title: APL330

value: Female


title: IL-22+ T cells _WT_rep5


title: 201516240031_R04C01_Nonsmoker

city: Research Triangle Park

first: Dana

last: Hancock

state: NC

address: 3040 E Cornwallis Rd

institute: RTI  International

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

source_name: nucleus accumbens

extract_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.

value: control

tag: sex (m, male; f, female)

value: M

tag: ancestry (cauc, caucasian; aa, african american)

value: CAUC

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

value: TRUE


title: IL-22+ T cells _Riok2hKO_rep5


title: APL329


title: 201516250032_R02C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: APL328

tag: tissue

tag: disease state

tag: gender

tag: age


title: 201516250042_R02C01_Nonsmoker

tag: sex (m, male; f, female)

value: F

tag: ancestry (cauc, caucasian; aa, african american)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)


title: IL-22+ T cells _WT_rep4

tag: strain

tag: genotype

tag: cell type


title: IL-22+ T cells _WT_rep2


title: IL-22+ T cells _WT_rep1


title: 201516280047_R05C01_Smoker

tag: current smoking status

value: case

tag: age at death

value: AA

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)


title: hair follicle stem cells at anagen, scRNA-Seq, Rep1

city: Ithaca

first: Tudorita

last: Tumbar

state: NY

address: 526 Campus Rd

department: Molecular biology and genetics

institute: Cornell University

description: Hair follicle stem cells were FACS sorted using CD34 and K14 promoter driven H2BGFP

data_processing:
The raw data files were demultiplexed to generate the sample-specific FASTQ files, which were aligned to the mouse reference genome (mm10-3.0.0) using the 10X Genomics Cell Ranger pipeline (v3.1.0)
The raw scRNA-seq data was processed using Cell Ranger from the 10X platform to generate an expression matrix that was further analyzed in R using the Seurat package version 3.1
Principle Component Analysis (PCA) was performed on the gene expression matrix using the least number of principal components (PCs) that could be used to explain the majority of the variance in the data
The PCA embeddings were used by Harmony to integrated the datasets. Unsupervised shared nearest neighbor (SNN) clustering was done on the Harmony integrated Seurat object
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: feature.tsv, barcode.tsv and matrix.mtx files for each sample

source_name: Hair follicles

extract_protocol:
Hair follicle stem cells were FACS sorte using CD34 and K14 promoter driven H2BGFP
Single-cell 3′ cDNA libraries generation using Chromium Single Cell 3′ gel bead and library Kit v3, following the manufacturer’s protocols (10x Genomics)

tag: tissue

value: Skin

tag: age

value: Post natal day 32

value: wild type

value: Hair follicle stem cells


title: APL327

tag: disease state

tag: gender


title: APL326


title: 201516240054_R02C01_Nonsmoker

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: IL-22+ T cells _Riok2hKO_rep3

tag: strain

tag: genotype

value: 10 wks

tag: cell type


title: 201516240040_R02C01_Smoker

tag: current smoking status

tag: age at death

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)


title: mouse_3m_cardiac_batch1_scRNA

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

institute: Sun Yat-sen University

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Raw sequencing data was demultiplexed, debarcoded, mapped to Cell Ranger pre-built mm10 genome, and counted following the Cell Ranger v.2.2.0 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R.
Genome_build: Cell Ranger pre-built mm10 reference
Supplementary_files_format_and_content: one csv file containing raw count values for the high-quality cells in the sample

source_name: cardiac

growth_protocol: The mouse were raised and maintained under standard laboratory conditions.

extract_protocol:
The adult murine heart was digested by gentle perfusing using Langendorff apparatus, and cardiac cells from ventricle were obtained. To balance the proportion of cardiomyocytes and non-myocytes, the majority of cardiomyocytes were depleted by low speed centrifuge. Single live cells were enriched by flow cytometry and subjected to scRNA-seq using 10X Chromium platform.
Libraries were prepared using Chromium Single Cell 3’ Library and Gel Bead Kit v.2 and Chromium i7 Multiplex kit.

tag: tissue

value: heart

tag: age

value: 10-12 weeks


title: APL325

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender


title: IL-22+ T cells _WT_rep3

value: IL-22+ T cells


title: 201516280005_R08C01_Nonsmoker

value: control

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: APL323

value: Female


title: 201516280060_R08C01_Nonsmoker

tag: current smoking status

tag: age at death

value: CAUC

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)


title: hair follicle stem cells at anagen, scRNA-Seq, Rep2

tag: strain

tag: tissue

tag: age

tag: genotype

tag: cell type


title: Chronic NAc 1h rep1

city: Jerusalem

first: Ami

last: Citri

address: Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

description:
Chronic_NAc_1h_rep1
NAC4_exp17_0222
3’RNA-seq
counts.csv

data_processing:
PCR duplicates were removed using Unique molecular identifiers (UMIs).
PolyA tail was trimmed from the 3' end of the reads (if exists).
Reads were aligned to the mouse genome (GRCm38) using STAR.
HTseq tool was used in order to count the number of reads for each gene.
Genome_build: GRCm38
Supplementary_files_format_and_content: counts.csv: Matrix table with raw gene counts for every gene and every sample.

source_name: Brain, Chronic 1h

extract_protocol:
Collection of tissue samples and RNA-extraction (using Trizol reagent) were performed as previously described (Turm et al., 2014; Mukherjee et al., 2018).
100ng of RNA was used for first strand cDNA preparation with RT primers containing barcodes and UMI. The cDNA was further processed for double-stranded DNA synthesis followed by incubation with Tn5 tagmentation enzyme. The fragmented dsDNA was amplified with forward primer contains Illumina P5-Read1 sequence and reverse primer containing the P7-Read2 sequence. R2 fastq files include 8 bps of unique molecular identifiers (UMIs) and the R1 files include the sequencing data of the fragment.

value: Brain

tag: brain structure

value: nucleus accumbens

tag: cocaine treatment

value: Chronic

tag: timepoint


title: Chronic NAc 4h rep1

description:
Chronic_NAc_4h_rep1
NAC8_exp17_0222
3’RNA-seq
counts.csv

source_name: Brain, Chronic 4h


title: Chronic NAc 0h rep1

description:
Chronic_NAc_0h_rep1
NAC1_exp17_0222
3’RNA-seq
counts.csv

source_name: Brain, Chronic 0h


title: Chronic NAc 2h rep2

description:
Chronic_NAc_2h_rep2
NAC7_exp17_0222
3’RNA-seq
counts.csv

source_name: Brain, Chronic 2h


title: Chronic NAc 1h rep2

description:
Chronic_NAc_1h_rep2
NAC5_exp17_0222
3’RNA-seq
counts.csv


title: APL322

tag: disease state

tag: gender

value: Male


title: Chronic NAc 2h rep1

description:
Chronic_NAc_2h_rep1
NAC6_exp17_0222
3’RNA-seq
counts.csv


title: Chronic NAc 0h rep2

description:
Chronic_NAc_0h_rep2
NAC2_exp17_0222
3’RNA-seq
counts.csv


title: Chronic LH 4h rep2

description:
Chronic_LH_4h_rep2
LH9_exp17_0255
3’RNA-seq
counts.csv

value: lateral hypothalamus


title: 201516240040_R05C01_Nonsmoker

tag: sex (m, male; f, female)

value: M

tag: ancestry (cauc, caucasian; aa, african american)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

value: TRUE

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: APL321

tag: tissue

tag: age


title: Chronic LH 4h rep1

description:
Chronic_LH_4h_rep1
LH8_exp17_0255
3’RNA-seq
counts.csv

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: Chronic NAc 4h rep2

description:
Chronic_NAc_4h_rep2
NAC9_exp17_0222
3’RNA-seq
counts.csv


title: Chronic LH 2h rep2

description:
Chronic_LH_2h_rep2
LH7_exp17_0255
3’RNA-seq
counts.csv


title: 201516240007_R03C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)


title: APL320

tag: disease state

tag: gender


title: 201516250030_R08C01_Nonsmoker

tag: ancestry (cauc, caucasian; aa, african american)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)


title: Chronic LH 1h rep1

description:
Chronic_LH_1h_rep1
LH4_exp17_0255
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: APL324

tag: age


title: APL319


title: Chronic LH 1h rep2

description:
Chronic_LH_1h_rep2
LH5_exp17_0255
3’RNA-seq
counts.csv


title: Chronic LH 2h rep1

description:
Chronic_LH_2h_rep1
LH6_exp17_0255
3’RNA-seq
counts.csv


title: 201516260029_R04C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: 201516260030_R01C01_Nonsmoker

tag: ancestry (cauc, caucasian; aa, african american)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)


title: Chronic LH 0h rep1

description:
Chronic_LH_0h_rep1
LH1_exp17_0255
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: Chronic LH 0h rep2

description:
Chronic_LH_0h_rep2
LH2_exp17_0255
3’RNA-seq
counts.csv


title: APL318

tag: disease state

tag: gender

tag: age


title: Chronic LCtx 4h rep1

description:
Chronic_LCtx_4h_rep1
PFC8_exp17_0222
3’RNA-seq
counts.csv

value: limbic cortex


title: 201516260029_R02C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)


title: 201516280022_R08C01_Nonsmoker

tag: ancestry (cauc, caucasian; aa, african american)

value: AA

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: Chronic LCtx 1h rep2

description:
Chronic_LCtx_1h_rep2
PFC5_exp17_0222
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: Chronic LCtx 2h rep2

description:
Chronic_LCtx_2h_rep2
PFC7_exp17_0222
3’RNA-seq
counts.csv


title: APL317

tag: disease state

tag: gender

tag: age


title: Chronic LCtx 2h rep1

description:
Chronic_LCtx_2h_rep1
PFC6_exp17_0222
3’RNA-seq
counts.csv


title: 201516280040_R06C01_Smoker

tag: current smoking status

value: case

tag: age at death

tag: sex (m, male; f, female)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)


title: Chronic LCtx 0h rep2

description:
Chronic_LCtx_0h_rep2
PFC2_exp17_0222
3’RNA-seq
counts.csv


title: Chronic LCtx 0h rep1

description:
Chronic_LCtx_0h_rep1
PFC1_exp17_0222
3’RNA-seq
counts.csv


title: Chronic DS 4h rep4 run0230

description:
Chronic_DS_4h_rep4_run0230
STR9_exp17_0230
3’RNA-seq
counts.csv

value: dorsal striatum


title: APL316

value: Bone Marrow


title: 201516260028_R06C01_Nonsmoker

value: F

tag: ancestry (cauc, caucasian; aa, african american)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: Chronic LCtx 1h rep1

description:
Chronic_LCtx_1h_rep1
PFC4_exp17_0222
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: APL314

tag: disease state

value: acute promyelocytic leukemia

tag: gender

tag: age


title: APL315


title: APL312


title: 201516240054_R06C01_Smoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)


title: 201516260008_R03C01_Nonsmoker

value: control

tag: ancestry (cauc, caucasian; aa, african american)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: Chronic DS 4h rep4 run0194

description:
Chronic_DS_4h_rep4_run0194
STR9_exp17_0194
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: APL311

tag: disease state

tag: gender

value: Female

tag: age


title: Chronic DS 4h rep3 run0230

description:
Chronic_DS_4h_rep3_run0230
STR8_exp17_0230
3’RNA-seq
counts.csv


title: Chronic DS 4h rep2

description:
Chronic_DS_4h_rep2
STR14_exp16_0230
3’RNA-seq
counts.csv


title: Chronic DS 4h rep3 run0194

description:
Chronic_DS_4h_rep3_run0194
STR8_exp17_0194
3’RNA-seq
counts.csv


title: Chronic DS 4h rep1

description:
Chronic_DS_4h_rep1
STR13_exp16_0230
3’RNA-seq
counts.csv


title: Chronic DS 2h rep5 run0230

description:
Chronic_DS_2h_rep5_run0230
STR7_exp17_0230
3’RNA-seq
counts.csv


title: APL310


title: Chronic DS 2h rep5 run0194

description:
Chronic_DS_2h_rep5_run0194
STR7_exp17_0194
3’RNA-seq
counts.csv


title: 201516250050_R08C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

value: CAUC

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)


title: Chronic DS 2h rep4 run0230

description:
Chronic_DS_2h_rep4_run0230
STR6_exp17_0230
3’RNA-seq
counts.csv

value: Brain


title: 201516250010_R05C01_Nonsmoker

tag: ancestry (cauc, caucasian; aa, african american)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: Chronic DS 2h rep4 run0194

description:
Chronic_DS_2h_rep4_run0194
STR6_exp17_0194
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: APL309

tag: disease state

tag: gender

tag: age


title: APL308


title: Chronic DS 2h rep2

description:
Chronic_DS_2h_rep2
STR12_exp16_0230
3’RNA-seq
counts.csv


title: 201516240018_R02C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)


title: APL307


title: APL306


title: Chronic DS 2h rep1

description:
Chronic_DS_2h_rep1
STR11_exp16_0230
3’RNA-seq
counts.csv


title: Chronic DS 1h rep4 run0230

description:
Chronic_DS_1h_rep4_run0230
STR5_exp17_0230
3’RNA-seq
counts.csv


title: Chronic DS 1h rep4 run0194

description:
Chronic_DS_1h_rep4_run0194
STR5_exp17_0194
3’RNA-seq
counts.csv


title: 201516250029_R08C01_Nonsmoker

tag: ancestry (cauc, caucasian; aa, african american)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: Chronic DS 1h rep3 run0230

description:
Chronic_DS_1h_rep3_run0230
STR4_exp17_0230
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: APL305

tag: disease state

tag: gender

tag: age


title: Chronic DS 1h rep2

description:
Chronic_DS_1h_rep2
STR7_exp16_0230
3’RNA-seq
counts.csv


title: Chronic DS 1h rep3 run0194

description:
Chronic_DS_1h_rep3_run0194
STR4_exp17_0194
3’RNA-seq
counts.csv


title: APL304


title: 201516280060_R06C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)


title: Chronic DS 1h rep1

description:
Chronic_DS_1h_rep1
STR5_exp16_0230
3’RNA-seq
counts.csv


title: Chronic DS 0h rep4 run0230

description:
Chronic_DS_0h_rep4_run0230
STR2_exp17_0230
3’RNA-seq
counts.csv


title: 201516280047_R04C01_Nonsmoker

tag: ancestry (cauc, caucasian; aa, african american)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: Chronic DS 0h rep4 run0194

description:
Chronic_DS_0h_rep4_run0194
STR2_exp17_0194
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: APL303

tag: disease state

tag: gender

tag: age


title: Chronic DS 0h rep3 run0230

description:
Chronic_DS_0h_rep3_run0230
STR1_exp17_0230
3’RNA-seq
counts.csv


title: 201516240009_R05C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)


title: 201516280040_R01C01_Nonsmoker

tag: ancestry (cauc, caucasian; aa, african american)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: 201516250012_R01C01_Nonsmoker

tag: current smoking status

tag: age at death


title: Chronic DS 2h rep3

description:
Chronic_DS_2h_rep3
STR9_exp16_0230
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: Chronic DS 0h rep1

description:
Chronic_DS_0h_rep1
STR1_exp16_0230
3’RNA-seq
counts.csv


title: Chronic DS 0h rep2

description:
Chronic_DS_0h_rep2
STR4_exp16_0230
3’RNA-seq
counts.csv


title: APL301

tag: disease state

tag: gender

tag: age


title: APL302


title: Chronic Amy 4h rep1

description:
Chronic_Amy_4h_rep1
AMG8_exp17_0255
3’RNA-seq
counts.csv

value: amygdala


title: APL300


title: Chronic Amy 2h rep1

description:
Chronic_Amy_2h_rep1
AMG6_exp17_0255
3’RNA-seq
counts.csv

value: Chronic


title: Chronic Amy 2h rep2

description:
Chronic_Amy_2h_rep2
AMG7_exp17_0255
3’RNA-seq
counts.csv


title: Chronic Amy 1h rep2

description:
Chronic_Amy_1h_rep2
AMG5_exp17_0255
3’RNA-seq
counts.csv


title: 201516240019_R08C01_Nonsmoker

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)


title: 201516240041_R06C01_Smoker

tag: current smoking status

tag: age at death

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: 201516250045_R07C01_Nonsmoker

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)


title: APL299

tag: tissue

tag: disease state

tag: gender

value: Male

tag: age


title: 201516280022_R01C01_Nonsmoker

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)


title: APL298


title: 201516260055_R03C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)


title: Chronic DS 0h rep3 run0194

description:
Chronic_DS_0h_rep3_run0194
STR1_exp17_0194
3’RNA-seq
counts.csv

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: Chronic Amy 1h rep1

description:
Chronic_Amy_1h_rep1
AMG4_exp17_0255
3’RNA-seq
counts.csv

tag: tissue


title: Chronic Amy 0h rep2

description:
Chronic_Amy_0h_rep2
AMG2_exp17_0255
3’RNA-seq
counts.csv


title: Chronic Amy 0h rep1

description:
Chronic_Amy_0h_rep1
AMG1_exp17_0255
3’RNA-seq
counts.csv


title: Challenge NAc 4h rep4

description:
Challenge_NAc_4h_rep4
NAC15_exp18_0215
3’RNA-seq
counts.csv

source_name: Brain, Challenge 4h

value: nucleus accumbens

value: Challenge


title: APL297

tag: disease state

tag: gender

tag: age


title: 201516240007_R01C01_Nonsmoker

tag: sex (m, male; f, female)

value: M

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

value: TRUE

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: APL295


title: 201516250030_R02C01_Nonsmoker

tag: current smoking status

tag: age at death

value: AA

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)


title: Challenge NAc 4h rep3

description:
Challenge_NAc_4h_rep3
NAC14_exp18_0215
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: 201516250030_R01C01_Nonsmoker

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: 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)


title: Challenge NAc 4h rep2

description:
Challenge_NAc_4h_rep2
NAC13_exp18_0006
3’RNA-seq
counts.csv


title: Challenge NAc 4h rep1

description:
Challenge_NAc_4h_rep1
NAC12_exp18_0006
3’RNA-seq
counts.csv


title: APL294

tag: disease state

tag: gender

tag: age


title: Chronic Amy 4h rep2

description:
Chronic_Amy_4h_rep2
AMG9_exp17_0255
3’RNA-seq
counts.csv


title: 201516260008_R08C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: Challenge NAc 2h rep4

description:
Challenge_NAc_2h_rep4
NAC9_exp18_0006
3’RNA-seq
counts.csv

source_name: Brain, Challenge 2h

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: Challenge NAc 2h rep3

description:
Challenge_NAc_2h_rep3
NAC8_exp18_0006
3’RNA-seq
counts.csv


title: Challenge NAc 2h rep2

description:
Challenge_NAc_2h_rep2
NAC11_exp18_0215
3’RNA-seq
counts.csv


title: APL293


title: 201516260008_R02C01_Nonsmoker

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: 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)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)


title: Challenge NAc 1h rep4

description:
Challenge_NAc_1h_rep4
NAC7_exp18_0215
3’RNA-seq
counts.csv

source_name: Brain, Challenge 1h


title: APL292

tag: disease state

tag: gender

tag: age


title: Challenge NAc 2h rep1

description:
Challenge_NAc_2h_rep1
NAC10_exp18_0215
3’RNA-seq
counts.csv


title: 201516240034_R01C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: Challenge NAc 1h rep3

description:
Challenge_NAc_1h_rep3
NAC6_exp18_0006
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: APL291


title: Challenge NAc 1h rep2

description:
Challenge_NAc_1h_rep2
NAC5_exp18_0215
3’RNA-seq
counts.csv


title: 201516250010_R04C01_Nonsmoker

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: 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)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)


title: Challenge NAc 0h rep2

description:
Challenge_NAc_0h_rep2
NAC2_exp18_0006
3’RNA-seq
counts.csv

source_name: Brain, Challenge 0h


title: Challenge NAc 0h rep1 run0215

description:
Challenge_NAc_0h_rep1_run0215
NAC1_exp18_0215
3’RNA-seq
counts.csv


title: APL290

tag: disease state

tag: gender

tag: age


title: Challenge NAc 1h rep1

description:
Challenge_NAc_1h_rep1
NAC4_exp18_0006
3’RNA-seq
counts.csv


title: 201516250030_R05C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: 201516240031_R02C01_Nonsmoker

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)


title: Challenge LH 4h rep2

description:
Challenge_LH_4h_rep2
LH14_exp18_0215
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

value: lateral hypothalamus

tag: cocaine treatment

tag: timepoint


title: APL289

tag: disease state

tag: gender

tag: age


title: Challenge LH 4h rep1

description:
Challenge_LH_4h_rep1
LH12_exp18_0006
3’RNA-seq
counts.csv


title: Challenge NAc 0h rep1 run0006

description:
Challenge_NAc_0h_rep1_run0006
NAC1_exp18_0006
3’RNA-seq
counts.csv


title: APL288


title: 201516260029_R08C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: 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)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)


title: APL287


title: 201516260030_R06C01_Smoker

value: case

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: Challenge LH 1h rep2

description:
Challenge_LH_1h_rep2
LH7_exp18_0215
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: Challenge LH 2h rep2

description:
Challenge_LH_2h_rep2
LH9_exp18_0006
3’RNA-seq
counts.csv


title: Challenge LH 2h rep1

description:
Challenge_LH_2h_rep1
LH8_exp18_0006
3’RNA-seq
counts.csv


title: Challenge LH 1h rep1

description:
Challenge_LH_1h_rep1
LH4_exp18_0006
3’RNA-seq
counts.csv


title: Challenge LH 0h rep1 run0215

description:
Challenge_LH_0h_rep1_run0215
LH3_exp18_0215
3’RNA-seq
counts.csv


title: Challenge LH 0h rep1 run0006

description:
Challenge_LH_0h_rep1_run0006
LH3_exp18_0006
3’RNA-seq
counts.csv


title: Challenge LCtx 4h rep3

description:
Challenge_LCtx_4h_rep3
PFC15_exp18_0215
3’RNA-seq
counts.csv

value: limbic cortex


title: 201516280040_R08C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)


title: 201516260008_R07C01_Nonsmoker

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: 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)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)


title: Challenge LCtx 4h rep2

description:
Challenge_LCtx_4h_rep2
PFC14_exp18_0215
3’RNA-seq
counts.csv


title: APL284

value: Bone Marrow

tag: disease state

tag: gender

tag: age


title: APL285

tag: tissue

value: acute promyelocytic leukemia


title: 201516260028_R05C01_Nonsmoker

value: control

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: Challenge LCtx 2h rep3

description:
Challenge_LCtx_2h_rep3
PFC8_exp18_0006
3’RNA-seq
counts.csv

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: APL283


title: Challenge LCtx 2h rep4

description:
Challenge_LCtx_2h_rep4
PFC9_exp18_0006
3’RNA-seq
counts.csv


title: APL286

value: Female


title: 201516240041_R08C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)


title: Challenge LCtx 2h rep2

description:
Challenge_LCtx_2h_rep2
PFC11_exp18_0215
3’RNA-seq
counts.csv

tag: tissue


title: APL281

tag: disease state

tag: gender

tag: age


title: Challenge LCtx 4h rep1

description:
Challenge_LCtx_4h_rep1
PFC12_exp18_0006
3’RNA-seq
counts.csv


title: Challenge LCtx 1h rep2

description:
Challenge_LCtx_1h_rep2
PFC5_exp18_0215
3’RNA-seq
counts.csv


title: Challenge LCtx 1h rep3

description:
Challenge_LCtx_1h_rep3
PFC6_exp18_0006
3’RNA-seq
counts.csv


title: APL279


title: 201516240018_R06C01_Nonsmoker

value: CAUC

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: APL280


title: Challenge LCtx 1h rep1

description:
Challenge_LCtx_1h_rep1
PFC4_exp18_0006
3’RNA-seq
counts.csv

value: Brain

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: APL278


title: Challenge LCtx 0h rep2

description:
Challenge_LCtx_0h_rep2
PFC3_exp18_0215
3’RNA-seq
counts.csv


title: Challenge LCtx 0h rep1 run0215

description:
Challenge_LCtx_0h_rep1_run0215
PFC1_exp18_0215
3’RNA-seq
counts.csv


title: Challenge LCtx 0h rep1 run0006

description:
Challenge_LCtx_0h_rep1_run0006
PFC1_exp18_0006
3’RNA-seq
counts.csv


title: APL277


title: Challenge DS 4h rep4

description:
Challenge_DS_4h_rep4
STR13_exp18_0230
3’RNA-seq
counts.csv

value: dorsal striatum


title: 201516260019_R04C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)


title: 201516250032_R06C01_Nonsmoker

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)


title: APL276

tag: tissue

tag: disease state

tag: gender

tag: age


title: Challenge DS 4h rep2 run0230

description:
Challenge_DS_4h_rep2_run0230
STR15_exp18_0230
3’RNA-seq
counts.csv

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: Challenge LCtx 2h rep1

description:
Challenge_LCtx_2h_rep1
PFC10_exp18_0215
3’RNA-seq
counts.csv


title: Challenge DS 4h rep2 run0194

description:
Challenge_DS_4h_rep2_run0194
STR15_exp18_0194
3’RNA-seq
counts.csv


title: Challenge LCtx 1h rep4

description:
Challenge_LCtx_1h_rep4
PFC7_exp18_0215
3’RNA-seq
counts.csv


title: APL274


title: 201516280047_R07C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: APL275


title: 201516280022_R05C01_Smoker

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)


title: Challenge DS 4h rep1 run0194

description:
Challenge_DS_4h_rep1_run0194
STR14_exp18_0194
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: APL273

tag: disease state

tag: gender

tag: age


title: Challenge DS 2h rep4

description:
Challenge_DS_2h_rep4
STR9_exp18_0230
3’RNA-seq
counts.csv


title: 201516260008_R05C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

value: F

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: 201516280005_R03C01_Nonsmoker

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)


title: APL272

tag: tissue

tag: disease state

tag: gender

value: Male

tag: age


title: 201516240009_R04C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)


title: Challenge DS 2h rep2 run0194

description:
Challenge_DS_2h_rep2_run0194
STR11_exp18_0194
3’RNA-seq
counts.csv

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: Challenge DS 2h rep2 run0230

description:
Challenge_DS_2h_rep2_run0230
STR11_exp18_0230
3’RNA-seq
counts.csv


title: Challenge DS 2h rep3

description:
Challenge_DS_2h_rep3
STR8_exp18_0230
3’RNA-seq
counts.csv


title: 201516260019_R07C01_Nonsmoker

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: Challenge DS 2h rep1 run0230

description:
Challenge_DS_2h_rep1_run0230
STR10_exp18_0230
3’RNA-seq
counts.csv

tag: tissue


title: APL271

tag: disease state

tag: gender

tag: age


title: Challenge DS 2h rep1 run0194

description:
Challenge_DS_2h_rep1_run0194
STR10_exp18_0194
3’RNA-seq
counts.csv


title: APL270


title: Challenge DS 1h rep3

description:
Challenge_DS_1h_rep3
STR4_exp18_0230
3’RNA-seq
counts.csv


title: Challenge DS 4h rep3

description:
Challenge_DS_4h_rep3
STR12_exp18_0230
3’RNA-seq
counts.csv


title: 201516250032_R01C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)


title: 201516240042_R03C01_Nonsmoker

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)


title: Challenge DS 4h rep1 run0230

description:
Challenge_DS_4h_rep1_run0230
STR14_exp18_0230
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: Challenge DS 1h rep2 run0194

description:
Challenge_DS_1h_rep2_run0194
STR7_exp18_0194
3’RNA-seq
counts.csv


title: Challenge DS 1h rep2 run0230

description:
Challenge_DS_1h_rep2_run0230
STR7_exp18_0230
3’RNA-seq
counts.csv


title: APL269

tag: disease state

tag: gender

tag: age


title: Challenge DS 1h rep1 run0194

description:
Challenge_DS_1h_rep1_run0194
STR5_exp18_0194
3’RNA-seq
counts.csv


title: Challenge DS 1h rep1 run0230

description:
Challenge_DS_1h_rep1_run0230
STR5_exp18_0230
3’RNA-seq
counts.csv


title: APL268


title: 201516250029_R02C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: 201516280040_R02C01_Nonsmoker

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)


title: Challenge DS 0h rep1 run0230

description:
Challenge_DS_0h_rep1_run0230
STR1_exp18_0230
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: 201516250032_R04C01_Smoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)


title: Challenge DS 0h rep2 run0230

description:
Challenge_DS_0h_rep2_run0230
STR3_exp18_0230
3’RNA-seq
counts.csv


title: 201516260028_R04C01_Nonsmoker

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: Challenge DS 0h rep1 run0194

description:
Challenge_DS_0h_rep1_run0194
STR1_exp18_0194
3’RNA-seq
counts.csv


title: Challenge DS 0h rep2 run0194

description:
Challenge_DS_0h_rep2_run0194
STR3_exp18_0194
3’RNA-seq
counts.csv


title: APL266

tag: disease state

tag: gender

tag: age


title: 201516250042_R04C01_Smoker

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)


title: 201516280022_R07C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)


title: Challenge Amy 4h rep3

description:
Challenge_Amy_4h_rep3
AMY12_exp18_0006
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

value: amygdala

tag: cocaine treatment

tag: timepoint


title: Challenge DS 1h rep4

description:
Challenge_DS_1h_rep4
STR6_exp18_0230
3’RNA-seq
counts.csv

value: Challenge


title: Challenge Amy 4h rep2

description:
Challenge_Amy_4h_rep2
AMY15STARS_exp18_0215
3’RNA-seq
counts.csv


title: Challenge Amy 4h rep1

description:
Challenge_Amy_4h_rep1
AMY14_exp18_0215
3’RNA-seq
counts.csv


title: Challenge Amy 4h rep4

description:
Challenge_Amy_4h_rep4
AMY13_exp18_0006
3’RNA-seq
counts.csv


title: 201516260028_R01C01_Nonsmoker

value: M

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: APL265

tag: disease state

tag: gender

tag: age


title: Challenge Amy 2h rep4

description:
Challenge_Amy_2h_rep4
AMY9_exp18_0006
3’RNA-seq
counts.csv


title: Challenge Amy 2h rep3

description:
Challenge_Amy_2h_rep3
AMY8_exp18_0006
3’RNA-seq
counts.csv


title: 201516240054_R03C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

value: TRUE


title: APL263

tag: tissue


title: Challenge DS 0h rep3

description:
Challenge_DS_0h_rep3
STR2_exp18_0230
3’RNA-seq
counts.csv

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: 201516240054_R08C01_Nonsmoker

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: APL262

tag: disease state

tag: gender

tag: age


title: Challenge Amy 2h rep2

description:
Challenge_Amy_2h_rep2
AMY11_exp18_0215
3’RNA-seq
counts.csv


title: APL267


title: APL261


title: 201516260028_R03C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

value: AA

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)


title: APL260

tag: tissue


title: APL259


title: Challenge Amy 1h rep4

description:
Challenge_Amy_1h_rep4
AMY6_exp18_0006
3’RNA-seq
counts.csv

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: APL264


title: APL258


title: 201516280005_R05C01_Nonsmoker

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: Challenge Amy 0h rep3

description:
Challenge_Amy_0h_rep3
AMY2_exp18_0006
3’RNA-seq
counts.csv


title: Challenge Amy 1h rep2

description:
Challenge_Amy_1h_rep2
AMY7_exp18_0215
3’RNA-seq
counts.csv


title: Challenge Amy 1h rep3

description:
Challenge_Amy_1h_rep3
AMY4_exp18_0006
3’RNA-seq
counts.csv


title: Challenge Amy 0h rep2

description:
Challenge_Amy_0h_rep2
AMY3_exp18_0215
3’RNA-seq
counts.csv


title: Challenge Amy 0h rep1 run0006

description:
Challenge_Amy_0h_rep1_run0006
AMY1_exp18_0006
3’RNA-seq
counts.csv


title: 201516250042_R08C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)


title: Challenge Amy 0h rep1 run0215

description:
Challenge_Amy_0h_rep1_run0215
AMY1_exp18_0215
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment


title: Acute NAc 4h rep2

description:
Acute_NAc_4h_rep2
NAC15_exp20_0010
3’RNA-seq
counts.csv

source_name: Brain, Acute 4h

value: nucleus accumbens

value: Acute

tag: timepoint


title: Challenge Amy 2h rep1

description:
Challenge_Amy_2h_rep1
AMY10_exp18_0215
3’RNA-seq
counts.csv


title: Acute NAc 4h rep3

description:
Acute_NAc_4h_rep3
NAC16_exp20_0010
3’RNA-seq
counts.csv


title: 201516250045_R03C01_Nonsmoker

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)


title: APL257

tag: disease state

tag: gender

tag: age


title: APL256


title: Acute NAc 2h rep3

description:
Acute_NAc_2h_rep3
NAC9_exp20_0010
3’RNA-seq
counts.csv

source_name: Brain, Acute 2h


title: 201516240042_R06C01_Smoker

tag: current smoking status

value: case

tag: age at death

tag: sex (m, male; f, female)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: 201516260055_R05C01_Smoker

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)


title: APL254

tag: tissue

value: Bone Marrow

tag: disease state


title: Acute NAc 4h rep1

description:
Acute_NAc_4h_rep1
NAC13_exp20_0010
3’RNA-seq
counts.csv

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: Acute NAc 2h rep2

description:
Acute_NAc_2h_rep2
NAC12_exp20_0010
3’RNA-seq
counts.csv


title: APL255

value: acute promyelocytic leukemia

tag: gender

tag: age


title: 201516240031_R07C01_Nonsmoker

tag: current smoking status

value: control

tag: age at death

tag: sex (m, male; f, female)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)


title: Acute NAc 2h rep1

description:
Acute_NAc_2h_rep1
NAC10_exp20_0010
3’RNA-seq
counts.csv


title: 201516260019_R06C01_Nonsmoker

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: Challenge Amy 1h rep1

description:
Challenge_Amy_1h_rep1
AMY5_exp18_0215
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: Acute NAc 1h rep3

description:
Acute_NAc_1h_rep3
NAC7_exp20_0010
3’RNA-seq
counts.csv

source_name: Brain, Acute 1h


title: Acute NAc 1h rep2

description:
Acute_NAc_1h_rep2
NAC6_exp20_0010
3’RNA-seq
counts.csv


title: Acute NAc 1h rep4

description:
Acute_NAc_1h_rep4
NAC8_exp20_0010
3’RNA-seq
counts.csv


title: APL253

tag: disease state

tag: gender

tag: age


title: 201516240031_R08C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)


title: Acute NAc 0h rep1

description:
Acute_NAc_0h_rep1
NAC1_exp20_0010
3’RNA-seq
counts.csv

source_name: Brain, Acute 0h


title: APL249

value: Female


title: 201516260008_R06C01_Smoker

tag: ancestry (cauc, caucasian; aa, african american)

value: CAUC

tag: rin (rna integrity number)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: APL252

tag: tissue

tag: disease state

tag: gender

tag: age


title: Acute NAc 1h rep1

description:
Acute_NAc_1h_rep1
NAC5_exp20_0010
3’RNA-seq
counts.csv

value: Brain

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: 201516240042_R07C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: 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)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)


title: APL248


title: Acute LH 1h rep2

description:
Acute_LH_1h_rep2
LH6_exp20_0255
3’RNA-seq
counts.csv

value: lateral hypothalamus


title: Acute NAc 0h rep4

description:
Acute_NAc_0h_rep4
NAC4_exp20_0010
3’RNA-seq
counts.csv


title: APL250


title: 201516240019_R07C01_Smoker

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: 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)


title: Acute NAc 0h rep3

description:
Acute_NAc_0h_rep3
NAC3_exp20_0010
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: Acute LH 1h rep1

description:
Acute_LH_1h_rep1
LH5_exp20_0255
3’RNA-seq
counts.csv


title: Acute NAc 0h rep2

description:
Acute_NAc_0h_rep2
NAC2_exp20_0010
3’RNA-seq
counts.csv


title: 201516250012_R03C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)