title: 201516240042_R04C01_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: 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 LH 4h rep2

status: Public on Apr 14 2021

type: SRA

city: Jerusalem

first: Ami

last: Citri

address: Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

description:
Acute_LH_4h_rep2
LH16_exp20_0255
3’RNA-seq
counts.csv

library_source: transcriptomic

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.

molecule: total RNA

organism: Mus musculus

source_name: Brain, Acute 4h

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.

tag: tissue

value: Brain

tag: brain structure

value: lateral hypothalamus

tag: cocaine treatment

value: Acute

tag: timepoint


title: Acute LH 4h rep1

description:
Acute_LH_4h_rep1
LH15_exp20_0255
3’RNA-seq
counts.csv


title: Acute LH 2h rep2

description:
Acute_LH_2h_rep2
LH12_exp20_0255
3’RNA-seq
counts.csv

source_name: Brain, Acute 2h


title: Acute LH 2h rep1

description:
Acute_LH_2h_rep1
LH11_exp20_0255
3’RNA-seq
counts.csv


title: 201516260055_R02C01_Smoker

city: Research Triangle Park

first: Dana

last: Hancock

state: NC

address: 3040 E Cornwallis Rd

country: USA

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

organism: Homo sapiens

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.

tag: current smoking status

value: case

tag: age at death

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

value: F

value: CAUC

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: 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)

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: APL246

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

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.

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

value: Female

tag: age


title: 201516280022_R06C01_Nonsmoker

value: control

value: M

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: 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: APL243

tag: tissue

value: Male


title: Acute LCtx 1h rep2

description:
Acute_LCtx_1h_rep2
PFC8_exp20_0250
3’RNA-seq
counts.csv

source_name: Brain, Acute 1h

tag: brain structure

value: limbic cortex

tag: cocaine treatment

tag: timepoint


title: Acute LH 0h rep2

description:
Acute_LH_0h_rep2
LH2_exp20_0255
3’RNA-seq
counts.csv

source_name: Brain, Acute 0h


title: Acute LH 0h rep1

description:
Acute_LH_0h_rep1
LH1_exp20_0255
3’RNA-seq
counts.csv


title: Acute LCtx 0h rep1

description:
Acute_LCtx_0h_rep1
PFC2_exp20_0250
3’RNA-seq
counts.csv


title: APL244


title: APL245


title: 201516240034_R06C01_Smoker

tag: current smoking status

tag: age at death

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

value: AA

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: 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)


title: APL241

tag: disease state

tag: gender

tag: age


title: Acute DS 4h rep2 run0194

description:
Acute_DS_4h_rep2_run0194
STR14_exp20_0194
3’RNA-seq
counts.csv

value: dorsal striatum


title: APL238


title: Acute LCtx 4h rep1

description:
Acute_LCtx_4h_rep1
PFC13_exp20_0250
3’RNA-seq
counts.csv


title: 201516250042_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: 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: 201516260055_R04C01_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)


title: Acute LCtx 2h rep1

description:
Acute_LCtx_2h_rep1
PFC9_exp20_0250
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: APL242

tag: disease state

tag: gender

tag: age


title: Acute LCtx 2h rep2

description:
Acute_LCtx_2h_rep2
PFC10_exp20_0250
3’RNA-seq
counts.csv


title: 201516250029_R07C01_Nonsmoker

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: 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: Acute LCtx 1h rep1

description:
Acute_LCtx_1h_rep1
PFC7_exp20_0250
3’RNA-seq
counts.csv


title: 201516260030_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: 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: Acute DS 2h rep4 run0090

description:
Acute_DS_2h_rep4_run0090
STR9_exp20_0090
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: Acute LCtx 0h rep3

description:
Acute_LCtx_0h_rep3
PFC4_exp20_0250
3’RNA-seq
counts.csv


title: Acute LCtx 0h rep2

description:
Acute_LCtx_0h_rep2
PFC3_exp20_0250
3’RNA-seq
counts.csv


title: 201516280047_R01C01_Nonsmoker

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


title: APL234

tag: disease state

tag: gender

tag: age


title: APL233


title: Acute DS 1h rep4 run0194

description:
Acute_DS_1h_rep4_run0194
STR8_exp20_0194
3’RNA-seq
counts.csv


title: APL240


title: Acute DS 1h rep4 run0090

description:
Acute_DS_1h_rep4_run0090
STR8_exp20_0090
3’RNA-seq
counts.csv


title: 201516240041_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: 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: Acute DS 4h rep3

description:
Acute_DS_4h_rep3
STR15_exp20_0090
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: Acute DS 4h rep2 run0090

description:
Acute_DS_4h_rep2_run0090
STR14_exp20_0090
3’RNA-seq
counts.csv


title: APL237


title: Acute DS 1h rep3 run0194

description:
Acute_DS_1h_rep3_run0194
STR7_exp20_0194
3’RNA-seq
counts.csv


title: 201516280060_R04C01_Nonsmoker

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: 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: Acute DS 1h rep1

description:
Acute_DS_1h_rep1
STR5_exp20_0090
3’RNA-seq
counts.csv


title: Acute DS 4h rep1 run0194

description:
Acute_DS_4h_rep1_run0194
STR13_exp20_0194
3’RNA-seq
counts.csv


title: 201516280060_R03C01_Smoker

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


title: Acute DS 4h rep4

description:
Acute_DS_4h_rep4
STR16_exp20_0090
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment


title: Acute DS 4h rep1 run0090

description:
Acute_DS_4h_rep1_run0090
STR13_exp20_0090
3’RNA-seq
counts.csv

tag: timepoint


title: 201516240041_R07C01_Nonsmoker

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: 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 DS 2h rep4 run0194

description:
Acute_DS_2h_rep4_run0194
STR9_exp20_0194
3’RNA-seq
counts.csv


title: APL235

tag: disease state

tag: gender

tag: age


title: APL236


title: 201516280017_R07C01_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: 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 DS 2h rep2

description:
Acute_DS_2h_rep2
STR11_exp20_0090
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: Acute DS 2h rep3

description:
Acute_DS_2h_rep3
STR12_exp20_0090
3’RNA-seq
counts.csv


title: Acute DS 2h rep1 run0194

description:
Acute_DS_2h_rep1_run0194
STR10_exp20_0194
3’RNA-seq
counts.csv


title: 201516260019_R01C01_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: 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: APL340

tag: disease state

tag: gender

tag: age


title: Acute DS 2h rep1 run0090

description:
Acute_DS_2h_rep1_run0090
STR10_exp20_0090
3’RNA-seq
counts.csv


title: APL226


title: APL232


title: 201516260008_R04C01_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: 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 DS 1h rep3 run0090

description:
Acute_DS_1h_rep3_run0090
STR7_exp20_0090
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: APL231


title: 201516240040_R06C01_Smoker

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: 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 DS 1h rep2

description:
Acute_DS_1h_rep2
STR6_exp20_0090
3’RNA-seq
counts.csv


title: APL230

tag: disease state

tag: gender

tag: age


title: Acute DS 0h rep4 run0090

description:
Acute_DS_0h_rep4_run0090
STR4_exp20_0090
3’RNA-seq
counts.csv


title: Acute Amy 1h rep2

description:
Acute_Amy_1h_rep2
AMG6_exp20_0255
3’RNA-seq
counts.csv

value: amygdala


title: Acute Amy 2h rep1

description:
Acute_Amy_2h_rep1
AMG11_exp20_0255
3’RNA-seq
counts.csv

value: Brain


title: 201516250029_R04C01_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: 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: APL229

tag: tissue


title: Acute DS 0h rep4 run0194

description:
Acute_DS_0h_rep4_run0194
STR4_exp20_0194
3’RNA-seq
counts.csv

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: APL224


title: Acute DS 0h rep3 run0090

description:
Acute_DS_0h_rep3_run0090
STR3_exp20_0090
3’RNA-seq
counts.csv


title: 201516240042_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: 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 Amy 0h rep2

description:
Acute_Amy_0h_rep2
AMG2_exp20_0255
3’RNA-seq
counts.csv


title: 201516240018_R04C01_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: Acute DS 0h rep3 run0194

description:
Acute_DS_0h_rep3_run0194
STR3_exp20_0194
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment


title: APL222

tag: disease state

tag: gender

tag: age


title: APL228


title: A6-LPS_IFNg_TNF_Cert

city: Worcester

first: Jing

last: Wang

state: MA

address: 100 Research Drive

institute: AbbVie

data_processing:
Fastq files were first processed by cutadapt (version 1.14) to remove adapter sequences.
RNA-seq reads were aligned to the human genome (GRCh38.85) with STAR (version 2.5.0a).
Gene counts were derived from the number of uniquely aligned unambiguous reads by featureCount from Rsubread R package (version 1.28.0).
Genome_build: GRCh38.85
Supplementary_files_format_and_content: count data

source_name: peripheral blood mononuclear cells (PBMC)

growth_protocol: Monocytes were suspended at 106 cell/ml and stimulated with M-CSF (20 ng/ml) in completed RPMI 1640 medium for 7 days to obtain M0 Mφ.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA library preparation from total RNA was conducted following the manufacturer’s protocol for the SMARTer Stranded Total RNA-Seq Kit V2-Pico.

treatment_protocol: TNFα alone (100 ng/ml) or pre-formed TNF-anti-TNF complexes (anti-TNF agents, 10 ug/ml) were added into the medium containing LPS (10 ng/ml) plus IFN-γ (20 ng/ml) cocktails for M1  differentiation.

tag: cell type

value: M0 macropahges

tag: treatment

value: LPS+IFNg+TNF+certolizumab


title: Acute DS 0h rep2

description:
Acute_DS_0h_rep2
STR2_exp20_0090
3’RNA-seq
counts.csv

value: Acute

tag: timepoint


title: Acute DS 0h rep1

description:
Acute_DS_0h_rep1
STR1_exp20_0090
3’RNA-seq
counts.csv


title: APL220


title: 201516260030_R07C01_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: 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: 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: APL219

tag: tissue

tag: disease state


title: A2-LPS_IFNg_TNF

value: LPS+IFNg+TNF


title: 201516260019_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)

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


title: APL227

tag: gender

tag: age


title: Acute Amy 4h rep2

description:
Acute_Amy_4h_rep2
AMG16_exp20_0255
3’RNA-seq
counts.csv

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: 201516250032_R08C01_Nonsmoker

value: F

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


title: D6-LPS_IFNg_TNF_Cert

tag: cell type

tag: treatment


title: D5-LPS_IFNg_TNF_Etan

value: LPS+IFNg+TNF+etanercept


title: 201516260029_R03C01_Smoker

tag: current smoking status

value: case

tag: age at death

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

value: CAUC

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

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: Acute Amy 4h rep1

description:
Acute_Amy_4h_rep1
AMG15_exp20_0255
3’RNA-seq
counts.csv

tag: tissue

tag: brain structure

tag: cocaine treatment

tag: timepoint


title: D3-LPS_IFNg_TNF_IgG

value: LPS+IFNg+TNF+IgG


title: APL214

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

tag: age


title: 201516240040_R01C01_Nonsmoker

value: control

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


title: C7-M0

tag: cell type

tag: treatment

value: untreated


title: APL213

tag: tissue

value: Male


title: Acute Amy 2h rep2

description:
Acute_Amy_2h_rep2
AMG12_exp20_0255
3’RNA-seq
counts.csv

value: Brain

tag: brain structure

value: amygdala

tag: cocaine treatment


title: C6-LPS_IFNg_TNF_Cert

value: M0 macropahges

value: LPS+IFNg+TNF+certolizumab


title: 201516250045_R04C01_Smoker

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

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: C5-LPS_IFNg_TNF_Etan


title: APL225

tag: disease state

tag: gender

value: Female

tag: age


title: 201516280047_R02C01_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: 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: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)


title: C4-LPS_IFNg_TNF_Ada

tag: cell type

tag: treatment

value: LPS+IFNg+TNF+adalimumab


title: 201516260030_R04C01_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: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)


title: C3-LPS_IFNg_TNF_IgG


title: APL211

tag: tissue

tag: disease state

tag: gender

tag: age


title: Acute Amy 1h rep1

description:
Acute_Amy_1h_rep1
AMG5_exp20_0255
3’RNA-seq
counts.csv

tag: brain structure

tag: cocaine treatment

value: Acute

tag: timepoint


title: APL212


title: Acute Amy 0h rep1

description:
Acute_Amy_0h_rep1
AMG1_exp20_0255
3’RNA-seq
counts.csv


title: 17-M0


title: e12.5 cervical motor neurons

city: Taipei

first: Jun-An

last: Chen

address: 128 Academia Road, Section 2

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

data_processing:
The raw Bcl files output from Illumina sequencers were processed with 10X Genomics Cell Ranger Pipeline (v3.1). The scRNA-seq data were demultiplexed into FASTQ files, mapped to mouse reference genome (mm10) using STAR aligner, filtered and counted for barcode and UMI.
The generated cell barcode and gene expression matrix were further analysed using Seurat (v2.3.4). Cells fitting quality control criteria of 1300-8000 genes, <72200 unique molecular identifiers (UMI) and <10% mitochondria-associated UMIs were retained for analysis. Filtered dataset were log-normalized, scaled and selected for highly variable genes for principal component analysis. Significant principal components (PCs) were determined using Jackstraw test and Elbow plot (PC:40 for whole dataset; PC:30 for LMC only). Cells were clustered using the default Louvain algorithm. Clusters identities were assigned based on expression of known markers.
Genome_build: mm10
Supplementary_files_format_and_content: csv file of normalized gene expression for all cells which passed the quality control criteria.
Supplementary_files_format_and_content: tsv file containing gene features of cells
Supplementary_files_format_and_content: tsv file containing cell features of cells
Supplementary_files_format_and_content: mtx file containing expression matrix of all cells collected

molecule: polyA RNA

source_name: e12.5 mouse spinal motor neurons at cervical segment (C2-T1)

extract_protocol:
Spinal cords from cervical segment were dissected in L15 medium and cells were dissociated using enzymatic (papain) and mechanical approach, following manufacturer's instruction (Neural Tissue Dissociation Kit (P) and gentleMACS dissociator, Miltenyi Biotec). Cell suspension was filtered through 70µm strainer and subjected to FACS under 45 psi to enrich GFP-positive cells . Collected cells were centrifuged at 1000rpm for 5 minutes and resuspended in 1%FBS supplemented DMEM. Cells viability and concentration was determined using Countess II Automated Cell Counter. Cells were loaded into 10x Chromium Controller using Single Cell 3' v3.1 reagents for single cell isolation.
scRNA-seq libraries were generated following manufacturer's instruction (10X Genomics, Chromium Single Cell 3’ v3.1) and sequenced using a NextSeq 500/550 platform with pair-ended reads (PE150: Read 1: 28 bp; Read 2: 122 bp). A total of 6193 cells were sequenced up to 79k mean reads per cell.

tag: strain

value: B6.Cg-Tg(Hlxb9-GFP)1Tmj/J MGI:J:88764

tag: developmental stage

tag: tissue/cell type


title: 201516280040_R04C01_Nonsmoker

tag: current smoking status

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

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: 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: 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: 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: 201516240031_R03C01_Nonsmoker

tag: age at death

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

value: F

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: 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: 15-LPS_IFNg_TNF_Etan

tag: cell type

tag: treatment

value: LPS+IFNg+TNF+etanercept


title: A7-M0


title: APL221

tag: tissue

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

tag: age


title: APL201


title: 13-LPS_IFNg_TNF_IgG

value: LPS+IFNg+TNF+IgG


title: APL200


title: Sample 128_HDACi_Trichostatin A_Rep 3

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description:
TGx-HDACi Reference compound
HDACi_TSA_3_17_S17

data_processing:
library strategy: TempO-Seq
Initial quality assessment was performed using negative controls (water only) and reference standards (human universal reference RNA and human brain total RNA) included on every TempO-Seq plate. We confirmed very little signal (< 0.3%) from samples with no cells/RNA. The BCL files were converted to FASTQ files and the reads were demultiplexed using bcl2fastq v. 2.20.0.42. The FASTQ files were processed using the “pete. star. Script_v3.0” (BioSpyder). The script uses star v.2.5 and the qCount function from QuasR to align the reads and to extract the feature counts specified in a Gene Transfer Format (GTF) file from the aligned reads, respectively.
Using R 3.4.1, the read counts of all samples were normalized as counts per million (CPM) (Law et al. 2014).
Supplementary_files_format_and_content: Text file with counts per million (CPM) for each gene

source_name: TK6_HDACi_Trichostatin A

growth_protocol: TK6 cells were cultured in suspension in a T75 flask in RPMI1640 medium supplemented with 10% v/v heat-inactivated horse serum, 2 mM L-glutamine, and 1 mM sodium pyruvate at 37ºC in 5% CO2. The cell density was maintained between 1x10^5 cells/mL and 1x10^6 cells/mL.

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy Mini kit. Quality was assessed using High Sensitiy RNA ScreenTapes on an Agilent TapeStation. RNA integrity number (RIN) of all samples was above 7.5.
The Templated Oligo-Sequencing (TempO-Seq) Human Whole Transcriptome Assay kit (BioSpyder, Carlsbad, CA) was used to generate sequencing libraries using total RNA from TK6 cells following the manufacturer's protocol. An input of 100ng was used from each RNA sample.

treatment_protocol: Prior to exposure, cells were plated in 6-well plates with 5 mL of 3x10^5 cells/mL suspension in each well. Cells were exposed to each chemical prepared in their respective vehicle solvent (1% v/v). After 4 hours, cells were rinsed once with PBS and lysed in TempO-Seq lysis buffer. RNA was extracted using a Qiagen RNeasy Mini kit. The exposure was performed on three separate occasions to produce three replicates of each sample.

tag: cell line

value: Human lymphoblastoid cell line

tag: chemical

value: Trichostatin A

tag: concentration

tag: vehicle solvent control

value: VC_DMSO_C_Rep 3


title: APL199

value: Male


title: Sample 127_HDACi_Trichostatin A_Rep 2

description:
TGx-HDACi Reference compound
HDACi_TSA_2_9_S9

value: VC_DMSO_C_Rep 2


title: 201516250045_R01C01_Smoker

tag: current smoking status

value: case

value: M

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

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: 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: 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: 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: A4-LPS_IFNg_TNF_Ada

tag: cell type

value: M0 macropahges

tag: treatment

value: LPS+IFNg+TNF+adalimumab


title: APL198

tag: tissue

tag: disease state

tag: gender

value: Female

tag: age


title: Sample 126_HDACi_Trichostatin A_Rep 1

description:
TGx-HDACi Reference compound
HDACi_TSA_1_1_S1

tag: cell line

tag: chemical

tag: concentration

tag: vehicle solvent control

value: VC_DMSO_C_Rep 1


title: A1-LPS_IFNg

value: LPS+IFNg


title: APL218


title: D7-M0

value: untreated


title: 201516240009_R06C01_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: 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: 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: Sample 124_Non-HDACi_Thapsigargin_Rep 2

description:
External validation compound
HDACi_Thap_2_81_S81

tag: cell type

value: Thapsigargin


title: 201516280005_R01C01_Nonsmoker

value: control

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: 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: APL216

tag: tissue

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

tag: age


title: D4-LPS_IFNg_TNF_Ada

tag: treatment


title: A3-LPS_IFNg_TNF_IgG

value: LPS+IFNg+TNF+IgG


title: APL197


title: 201516250030_R07C01_Smoker

tag: current smoking status

tag: age at death

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

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

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


title: APL215

value: Male


title: D1-LPS_IFNg

tag: cell type


title: 201516240009_R01C01_Smoker

value: case

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)

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: APL196

tag: tissue

tag: disease state

tag: gender

tag: age


title: D2-LPS_IFNg_TNF

tag: treatment

value: LPS+IFNg+TNF


title: Sample 121_Plate 2_Universal human reference RNA_Rep 1

description:
Plate #2 control
HDACi_Ref_RNA_24_S24

source_name: Plate 2_Universal human reference RNA

tag: sample type

value: Universal human reference RNA


title: 201516280047_R08C01_Nonsmoker

tag: current smoking status

tag: age at death

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

value: F

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

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: 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: C2-LPS_IFNg_TNF

tag: cell type

value: M0 macropahges


title: C1-LPS_IFNg


title: 16-LPS_IFNg_TNF_Cert

value: LPS+IFNg+TNF+certolizumab


title: APL209


title: APL210


title: 14-LPS_IFNg_TNF_Ada

value: LPS+IFNg+TNF+adalimumab


title: 12-LPS_IFNg_TNF


title: 201516260030_R02C01_Nonsmoker

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)

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: Sample 117_Non-HDACi_Methotraxate_Rep 1

description:
External validation compound
HDACi_MTX_1_77_S77

tag: cell line

value: Human lymphoblastoid cell line

tag: chemical

value: Methotraxate

tag: concentration

tag: vehicle solvent control

value: VC_DMSO_C_Rep 1


title: 11-LPS_IFNg

tag: treatment

value: LPS+IFNg


title: 201516250012_R06C01_Nonsmoker

tag: current smoking status

value: control

tag: age at death

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)

value: TRUE

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


title: APL191

tag: tissue

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

tag: age


title: 201516280047_R06C01_Smoker

value: case

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)

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: 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: Sample 125_Non-HDACi_Thapsigargin_Rep 3

description:
External validation compound
HDACi_Thap_3_89_S89

tag: cell line

tag: cell type

tag: chemical

value: Thapsigargin

tag: concentration

tag: vehicle solvent control

value: VC_DMSO_C_Rep 3


title: 201516240019_R05C01_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: salmon_mapping_pct (salmon software read mapping percentage)

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

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


title: Sample 113_Non-HDACi_GSK-J4_Rep 2

description:
External validation compound
HDACi_GSKJ4_2_15_S15

value: 10 µM

value: VC_DMSO_C_Rep 2


title: 201516250010_R06C01_Smoker

value: F

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: 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: Sample 123_Non-HDACi_Thapsigargin_Rep 1

description:
External validation compound
HDACi_Thap_1_73_S73

tag: cell line

tag: cell type

tag: chemical

tag: concentration


title: 201516240019_R02C01_Nonsmoker

tag: current smoking status

tag: age at death

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

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: 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: Sample 122_Plate 2_Universal human reference RNA_Rep2

description:
Plate #2 control
HDACi_Ref_RNA_40_S40

tag: sample type

value: Universal human reference RNA


title: 201516240018_R03C01_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: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

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


title: APL195

tag: tissue

tag: disease state

tag: gender

value: Male

tag: age


title: Sample 112_Non-HDACi_GSK-J4_Rep 1

description:
External validation compound
HDACi_GSKJ4_1_7_S7

tag: cell line

tag: cell type

value: Human lymphoblastoid cell line

tag: chemical

tag: concentration

tag: vehicle solvent control


title: Sample 111_Non-HDACi_Garcinol_Rep 3

description:
External validation compound
HDACi_Gar_3_70_S70

value: Garcinol

value: 5 µM


title: APL190


title: APL189


title: Sample 118_Non-HDACi_Methotraxate_Rep 2

description:
External validation compound
HDACi_MTX_2_85_S85

value: Methotraxate


title: 201516250012_R02C01_Nonsmoker

tag: current smoking status

value: control

tag: age at death

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

value: CAUC

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)

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: 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: Sample 109_Non-HDACi_Garcinol_Rep 1

description:
External validation compound
HDACi_Gar_1_54_S54

value: VC_DMSO_C_Rep 1


title: Sample 110_Non-HDACi_Garcinol_Rep 2

description:
External validation compound
HDACi_Gar_2_62_S62


title: 201516250012_R07C01_Nonsmoker

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

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

value: TRUE

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


title: APL181

tag: tissue

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

value: Female

tag: age


title: Sample 106_Non-HDACi_3-Deazaneplanocin_Rep 1

description:
External validation compound
HDACi_DZNep_1_74_S74

tag: cell line

tag: cell type

tag: chemical

value: 3-Deazaneplanocin A

tag: concentration

value: 2 µM

tag: vehicle solvent control


title: APL179


title: Sample 108_Non-HDACi_3-Deazaneplanocin_Rep 3

description:
External validation compound
HDACi_DZNep_3_90_S90

value: VC_DMSO_C_Rep 3


title: 201516250029_R05C01_Nonsmoker

tag: current smoking status

tag: age at death

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

value: F

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)

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: 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: 201516240040_R07C01_Nonsmoker

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

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

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

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


title: 201516240034_R08C01_Smoker

tag: current smoking status

value: case

tag: age at death

value: FALSE


title: Sample 107_Non-HDACi_3-Deazaneplanocin_Rep 2

description:
External validation compound
HDACi_DZNep_2_82_S82

tag: cell line

tag: cell type

value: Human lymphoblastoid cell line

tag: chemical

tag: concentration

tag: vehicle solvent control

value: VC_DMSO_C_Rep 2


title: Sample 102_VC_DMSO_C_Rep 3

value: DMSO


title: Sample 104_Non-HDACi_Docetaxel_Rep 2

description:
External validation compound
HDACi_Doc_2_37_S37

value: Docetaxel

value: 50 nM


title: Sample 114_Non-HDACi_GSK-J4_Rep 3

description:
External validation compound
HDACi_GSKJ4_3_23_S23

value: 10 µM


title: Sample 105_Non-HDACi_Docetaxel_Rep 3

description:
External validation compound
HDACi_Doc_3_45_S45


title: APL177

tag: tissue

tag: disease state

tag: gender

tag: age


title: Sample 99_Non-HDACi_Arabinofuranosyl cytidine_Rep 3

description:
External validation compound
HDACi_AraC_3_46_S46

source_name: TK6_Non-HDACi_Arabinofuranosyl cytidine

value: Arabinofuranosyl cytidine

value: 25 µM


title: Sample 100_VC_DMSO_C_Rep 1


title: Sample 101_VC_DMSO_C_Rep 2


title: 201516250045_R02C01_Nonsmoker

value: control

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

value: M

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

value: CAUC

tag: rin (rna integrity number)

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)

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: 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: APL176

value: Bone Marrow

value: acute promyelocytic leukemia

value: Male


title: APL175


title: 201516260028_R07C01_Smoker

tag: current smoking status

value: case

tag: age at death

value: F

value: AA

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


title: APL174

tag: tissue

tag: disease state

tag: gender

value: Female

tag: age


title: Sample 98_Non-HDACi_Arabinofuranosyl cytidine_Rep 2

description:
External validation compound
HDACi_AraC_2_38_S38

tag: cell line

tag: cell type

value: Human lymphoblastoid cell line

tag: chemical

tag: concentration

tag: vehicle solvent control

value: VC_DMSO_C_Rep 2


title: Sample 97_Non-HDACi_Arabinofuranosyl cytidine_Rep 1

description:
External validation compound
HDACi_AraC_1_30_S30

value: VC_DMSO_C_Rep 1


title: 201516240054_R01C01_Nonsmoker

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

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

tag: rin (rna integrity number)

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)

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: 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: APL173

tag: tissue

tag: disease state

tag: gender

tag: age


title: Sample 96_HDACi_Valproic acid_Rep 3

description:
External validation compound
HDACi_VPA_D1_377_S89

source_name: TK6_HDACi_Valproic acid

tag: cell line

tag: cell type

tag: chemical

value: Valproic acid

tag: concentration

value: VC_H2O_B_Rep 3


title: Sample 103_Non-HDACi_Docetaxel_Rep 1

description:
External validation compound
HDACi_Doc_1_29_S29

value: Docetaxel

value: 50 nM

tag: vehicle solvent control


title: Sample 94_HDACi_Valproic acid_Rep 1

description:
External validation compound
HDACi_VPA_D1_361_S73

value: VC_H2O_B_Rep 1


title: Sample 93_HDACi_Vorinostat_Rep 3

description:
TGx-HDACi Reference compound
HDACi_Vor_D1_310_S22

value: Vorinostat

value: 10 µM

value: VC_DMSO_B_Rep 3


title: APL171

value: Bone Marrow

value: acute promyelocytic leukemia


title: Sample 92_HDACi_Vorinostat_Rep 2

description:
TGx-HDACi Reference compound
HDACi_Vor_D1_302_S14

value: VC_DMSO_B_Rep 2


title: APL170


title: 201516240009_R08C01_Nonsmoker

tag: current smoking status

value: control

tag: age at death

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: 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)

value: TRUE

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


title: 201516240034_R07C01_Nonsmoker

value: CAUC

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)

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: 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: Sample 89_Non-HDACi_Vinblastine_Rep 2

description:
TGx-HDACi Reference compound
HDACi_Vin_D1_326_S38

tag: cell line

tag: cell type

value: Human lymphoblastoid cell line

tag: chemical

value: Vinblastine

tag: concentration

value: 200 ng/mL

tag: vehicle solvent control

value: VC_DMSO_A_Rep 2


title: Sample 90_Non-HDACi_Vinblastine_Rep 3

description:
TGx-HDACi Reference compound
HDACi_Vin_D1_334_S46

value: VC_DMSO_A_Rep 3


title: Sample 86_Non-HDACi_Tunicamycin_Rep 2

description:
TGx-HDACi Reference compound
HDACi_Tun_D1_370_S82

value: Tunicamycin

value: 2.5 µg/mL


title: Sample 85_Non-HDACi_Tunicamycin_Rep 1

description:
TGx-HDACi Reference compound
HDACi_Tun_D1_362_S74

value: VC_DMSO_A_Rep 1


title: APL166

tag: tissue

tag: disease state

tag: gender

value: Female

tag: age


title: APL168


title: Sample 87_Non-HDACi_Tunicamycin_Rep 3

description:
TGx-HDACi Reference compound
HDACi_Tun_D1_378_S90


title: 201516240018_R01C01_Nonsmoker

tag: current smoking status

tag: age at death

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

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

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


title: Sample 84_HDACi_Trichostatin A_Rep 3_excl

description:
TGx-HDACi Reference compound (excluded from study)
HDACi_TSA_D1_307_S19

tag: cell line

tag: cell type

tag: chemical

value: Trichostatin A

tag: concentration


title: APL165

tag: tissue

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

value: Male


title: Sample 95_HDACi_Valproic acid_Rep 2

description:
External validation compound
HDACi_VPA_D1_369_S81

value: Valproic acid

tag: vehicle solvent control

value: VC_H2O_B_Rep 2


title: 201516280040_R07C01_Smoker

tag: current smoking status

value: case

tag: age at death

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

value: M

value: CAUC

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)

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: 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: 201516250029_R01C01_Nonsmoker

value: control

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


title: APL158

tag: tissue

tag: disease state

tag: gender

tag: age


title: APL172


title: Sample 82_HDACi_Trichostatin A_Rep 1_excl

description:
TGx-HDACi Reference compound (excluded from study)
HDACi_TSA_D1_291_S3

tag: cell line

tag: cell type

value: Human lymphoblastoid cell line

tag: chemical

tag: concentration

tag: vehicle solvent control


title: Sample 83_HDACi_Trichostatin A_Rep 2_excl

description:
TGx-HDACi Reference compound (excluded from study)
HDACi_TSA_D1_299_S11

value: VC_DMSO_A_Rep 2


title: 201516250032_R03C01_Nonsmoker

tag: current smoking status

tag: age at death

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

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

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)

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: 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: Sample 81_HDACi_Tacedinaline_Rep 3

description:
TGx-HDACi Reference compound
HDACi_Tac_D1_357_S69

value: Tacedinaline

value: VC_DMSO_B_Rep 3


title: Sample 91_HDACi_Vorinostat_Rep 1

description:
TGx-HDACi Reference compound
HDACi_Vor_D1_294_S6

value: Vorinostat

value: 10 µM

value: VC_DMSO_B_Rep 1


title: 201516250050_R05C01_Nonsmoker

value: F

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


title: Sample 80_HDACi_Tacedinaline_Rep 2

description:
TGx-HDACi Reference compound
HDACi_Tac_D1_349_S61

tag: cell line

tag: cell type

tag: chemical

tag: concentration

tag: vehicle solvent control

value: VC_DMSO_B_Rep 2


title: Sample 79_HDACi_Tacedinaline_Rep 1

description:
TGx-HDACi Reference compound
HDACi_Tac_D1_341_S53


title: Sample 88_Non-HDACi_Vinblastine_Rep 1

description:
TGx-HDACi Reference compound
HDACi_Vin_D1_318_S30

value: Vinblastine

value: 200 ng/mL

value: VC_DMSO_A_Rep 1


title: Sample 78_HDACi_Sodium butyrate_Rep 3

description:
TGx-HDACi Reference compound
HDACi_Sodbuty_D1_379_S91

source_name: TK6_HDACi_Sodium butyrate

value: Sodium butyrate

value: 4 mM

value: VC_H2O_B_Rep 3


title: Sample 77_HDACi_Sodium butyrate_Rep 2

description:
TGx-HDACi Reference compound
HDACi_Sodbuty_D1_371_S83

value: VC_H2O_B_Rep 2


title: 201516240054_R05C01_Nonsmoker

tag: current smoking status

value: control

tag: age at death

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

value: M

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

value: CAUC

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)

value: TRUE


title: 201516260055_R06C01_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: 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: 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: 201516250042_R05C01_Nonsmoker

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


title: Sample 76_HDACi_Sodium butyrate_Rep 1

description:
TGx-HDACi Reference compound
HDACi_Sodbuty_D1_363_S75

tag: cell line

tag: cell type

value: Human lymphoblastoid cell line

tag: chemical

tag: concentration

tag: vehicle solvent control

value: VC_H2O_B_Rep 1


title: APL155

tag: tissue

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

value: Male

tag: age


title: Sample 74_HDACi_Scriptaid_Rep 2

description:
TGx-HDACi Reference compound
HDACi_Scr_D1_297_S9

value: Scriptaid

value: 50 µM

value: VC_DMSO_B_Rep 2


title: Sample 75_HDACi_Scriptaid_Rep 3

description:
TGx-HDACi Reference compound
HDACi_Scr_D1_305_S17

value: VC_DMSO_B_Rep 3


title: 201516240007_R06C01_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: 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_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: APL153

value: Female


title: Sample 73_HDACi_Scriptaid_Rep 1

description:
TGx-HDACi Reference compound
HDACi_Scr_D1_289_S1

tag: cell line

tag: cell type

tag: chemical

tag: concentration

value: VC_DMSO_B_Rep 1


title: Sample 71_HDACi_Suberohydroxamate_Rep 2

description:
TGx-HDACi Reference compound
HDACi_SBHA_D1_304_S16

value: Suberohydroxamic acid

tag: vehicle solvent control


title: Sample 72_HDACi_Suberohydroxamate_Rep 3

description:
TGx-HDACi Reference compound
HDACi_SBHA_D1_312_S24


title: APL152

tag: tissue

tag: disease state

tag: gender

tag: age


title: 201516240018_R08C01_Smoker

tag: current smoking status

value: case

tag: age at death

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: 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: APL150


title: Sample 70_HDACi_Suberohydroxamate_Rep 1

description:
TGx-HDACi Reference compound
HDACi_SBHA_D1_296_S8

tag: cell line

tag: cell type

tag: chemical

tag: concentration


title: Sample 68_HDACi_Pracinostat_Rep 2

description:
External validation compound
HDACi_Pra_D1_328_S40

value: Pracinostat

value: 2 µM

tag: vehicle solvent control


title: APL151

tag: tissue

tag: disease state

tag: gender

tag: age


title: Sample 69_HDACi_Pracinostat_Rep 3

description:
External validation compound
HDACi_Pra_D1_336_S48


title: Sample 67_HDACi_Pracinostat_Rep 1

description:
External validation compound
HDACi_Pra_D1_320_S32


title: 201516250050_R07C01_Smoker

tag: current smoking status

tag: age at death

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

value: M

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

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: 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: APL149


title: 201516280017_R04C01_Smoker

value: F

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: 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: Sample 66_HDACi_Panobinostat_Rep 3

description:
TGx-HDACi Reference compound
HDACi_Pan_D1_330_S42

tag: cell line

tag: cell type

value: Human lymphoblastoid cell line

tag: chemical

value: Panobinostat

tag: concentration

tag: vehicle solvent control


title: Sample 65_HDACi_Panobinostat_Rep 2

description:
TGx-HDACi Reference compound
HDACi_Pan_D1_322_S34


title: 201516240007_R02C01_Nonsmoker

tag: current smoking status

value: control

tag: age at death

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: APL156

tag: tissue

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

value: Male

tag: age


title: 201516280060_R02C01_Smoker

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)

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: Sample 63_HDACi_Oxamflatin_Rep 3

description:
TGx-HDACi Reference compound
HDACi_Oxa_D1_358_S70

tag: cell line

tag: cell type

tag: chemical

value: Oxamflatin

tag: concentration

value: 1 µM

tag: vehicle solvent control

value: VC_DMSO_A_Rep 3


title: APL157

tag: tissue

tag: disease state

tag: gender

value: Female

tag: age


title: Sample 62_HDACi_Oxamflatin_Rep 2

description:
TGx-HDACi Reference compound
HDACi_Oxa_D1_350_S62

value: VC_DMSO_A_Rep 2


title: Sample 61_HDACi_Oxamflatin_Rep 1

description:
TGx-HDACi Reference compound
HDACi_Oxa_D1_342_S54

value: VC_DMSO_A_Rep 1


title: APL147


title: 201516260019_R05C01_Smoker

tag: current smoking status

value: case

tag: age at death

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: 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: 201516240019_R04C01_Smoker

value: F

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)

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: APL146

tag: tissue

tag: disease state

tag: gender

tag: age


title: APL148


title: Sample 59_HDACi_Mocetinostat_Rep 2

description:
TGx-HDACi Reference compound
HDACi_Mo_D1_374_S86

tag: cell line

tag: cell type

tag: chemical

value: Mocetinostat

tag: concentration

value: 25 µM

tag: vehicle solvent control

value: VC_DMSO_B_Rep 2


title: Sample 58_HDACi_Mocetinostat_Rep 1

description:
TGx-HDACi Reference compound
HDACi_Mo_D1_366_S78

value: Human lymphoblastoid cell line

value: VC_DMSO_B_Rep 1


title: APL145

value: Bone Marrow


title: 201516240034_R02C01_Nonsmoker

tag: current smoking status

value: control

tag: age at death

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

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

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: 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)

value: TRUE


title: Sample 57_VC_Methanol_Rep 3

value: Methanol


title: Sample 56_VC_Methanol_Rep 2


title: Sample 54_Non-HDACi_Hydroxyurea_Rep 3

description:
TGx-HDACi Reference compound
HDACi_HU_D1_309_S21

value: Hydroxyurea

value: VC_H2O_A_Rep 3


title: 201516240054_R07C01_Smoker

value: CAUC

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)

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: 201516240041_R01C01_Nonsmoker

tag: current smoking status

tag: age at death


title: APL144

tag: tissue

tag: disease state

value: acute promyelocytic leukemia

tag: gender

value: Male

tag: age


title: Sample 64_HDACi_Panobinostat_Rep 1

description:
TGx-HDACi Reference compound
HDACi_Pan_D1_314_S26

tag: cell line

tag: cell type

tag: chemical

value: Panobinostat

tag: concentration

value: 2 µM

tag: vehicle solvent control


title: APL143

value: Female


title: 201516240007_R08C01_Smoker

value: case

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: 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)


title: APL142

tag: tissue

tag: disease state

tag: gender

tag: age


title: Sample 52_Non-HDACi_Hydroxyurea_Rep 1

description:
TGx-HDACi Reference compound
HDACi_HU_D1_293_S5

tag: cell line

tag: cell type

value: Human lymphoblastoid cell line

tag: chemical

tag: concentration

value: VC_H2O_A_Rep 1


title: Sample 53_Non-HDACi_Hydroxyurea_Rep 2

description:
TGx-HDACi Reference compound
HDACi_HU_D1_301_S13

tag: vehicle solvent control

value: VC_H2O_A_Rep 2


title: Sample 51_HDACi_HC toxin_Rep 3

description:
External validation compound
HDACi_HCT_D1_355_S67

source_name: TK6_HDACi_HC toxin

value: HC toxin

value: 20 ng/mL

value: VC_Methanol_Rep 3


title: Sample 50_HDACi_HC toxin_Rep 2

description:
External validation compound
HDACi_HCT_D1_347_S59

value: VC_Methanol_Rep 2


title: APL141

value: Bone Marrow


title: Sample 49_HDACi_HC toxin_Rep 1

description:
External validation compound
HDACi_HCT_D1_339_S51

value: VC_Methanol_Rep 1


title: 201516280022_R02C01_Nonsmoker

tag: current smoking status

value: control

tag: age at death

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

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

value: AA

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

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: Sample 60_HDACi_Mocetinostat_Rep 3

description:
TGx-HDACi Reference compound
HDACi_Mo_D1_382_S94

value: Mocetinostat

value: 25 µM

value: VC_DMSO_B_Rep 3


title: Sample 47_VC_H2O_A_Rep 2