title: 201516250010_R02C01_Nonsmoker

value: CAUC

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: APL140

status: Public on Apr 14 2021

type: SRA

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

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Bone marrow mononuclear cells, APL patients

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

tag: tissue

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

value: Female

tag: age


title: Sample 46_VC_H2O_A_Rep 1

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

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

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

tag: cell type

value: Human lymphoblastoid cell line

tag: chemical

tag: concentration


title: A5-LPS_IFNg_TNF_Etan

city: Worcester

first: Jing

last: Wang

state: MA

address: 100 Research Drive

country: USA

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.

value: M0 macropahges

tag: treatment

value: LPS+IFNg+TNF+etanercept


title: APL139


title: Sample 45_VC_H2O_B_Rep 3


title: Sample 44_VC_H2O_B_Rep 2


title: Sample 55_VC_Methanol_Rep 1

value: Methanol


title: APL138


title: 201516240041_R04C01_Smoker

city: Research Triangle Park

first: Dana

last: Hancock

state: NC

address: 3040 E Cornwallis Rd

institute: RTI  International

data_processing:
QC metrics for potential exclusion include: sex discrepancy based on k-means clustering of PC1 values from chrY gene expression PCA, missing value for self-reported sex, RIN score <6, effective sequencing depth <10 read pairs, overall mapping rate<30%, intergenic mapping rate > 30%, overall mapping rate < 50%, Shannon diversity index < 5.92596, overall mapping rate <50%, mitochondrial proportion of gene counts <0.20, rRNA mapping proportion < 0.01
Genome alignment performed with HISAT2. Transcript quantification performed with Salmon.
Genome_build: GRCh38
Supplementary_files_format_and_content: Salmon output: counts, tpm, transcript lengths

source_name: nucleus accumbens

extract_protocol:
Genomic DNA and RNA were concurrently extracted from dissected postmortem nucleus accumbens tissue using the Qiagen AllPrep DNA/RNA Mini Kit (Cat No./ID: 80204).
RNA expression was profiled on the Illumain HiSeq 3000 platform using the manufacturer's protocol.

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)

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 42_VC_Ethanol_Rep 3

value: Ethanol


title: Sample 43_VC_H2O_B_Rep 1


title: APL137

tag: tissue

tag: disease state

tag: gender

tag: age


title: 201516240019_R06C01_Nonsmoker

value: control

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: 201516240054_R04C01_Nonsmoker

tag: current smoking status

tag: age at death

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

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

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)


title: Sample 40_VC_Ethanol_Rep 1

tag: cell line

tag: cell type

tag: chemical

tag: concentration


title: Sample 39_HDACi_Entinostat_Rep 3

description:
External validation compound
HDACi_Ent_D1_333_S45

value: Entinostat

value: 50 µM

tag: vehicle solvent control

value: VC_DMSO_B_Rep 3


title: 201516240019_R03C01_Nonsmoker

value: F

value: CAUC

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: 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 37_HDACi_Entinostat_Rep 1

description:
External validation compound
HDACi_Ent_D1_324_S36

value: VC_DMSO_B_Rep 1


title: APL135

tag: tissue

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

value: Female

tag: age


title: Sample 36_VC_DMSO_B_Rep 3

value: Human lymphoblastoid cell line

value: DMSO


title: APL136

value: Male


title: Sample 48_VC_H2O_A_Rep 3


title: APL134


title: 201516240009_R02C01_Nonsmoker

tag: current smoking status

tag: age at death

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

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

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

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: Sample 35_VC_DMSO_B_Rep 2

tag: cell line

tag: cell type

tag: chemical

tag: concentration


title: 201516250012_R04C01_Nonsmoker

value: M

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: 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: 201516260029_R01C01_Smoker

tag: current smoking status

value: case

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)


title: APL132

tag: tissue

tag: disease state

tag: gender

tag: age


title: APL133


title: 201516250029_R06C01_Nonsmoker

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

value: TRUE


title: Sample 31_VC_DMSO_A_Rep 1

tag: cell line

tag: cell type

tag: chemical

tag: concentration


title: Sample 32_VC_DMSO_A_Rep 2


title: 201516240007_R04C01_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: intron_mapping_pct (hisat2 software read mapping percentage to intronic 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: 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 41_VC_Ethanol_Rep 2

value: Ethanol


title: Sample 29_Plate 1_Universal human reference RNA_Rep 1

description:
Plate #1 control
HDACi_ctrl_UHRR_332_S44

source_name: Plate 1_Universal human reference RNA

tag: sample type

value: Universal human reference RNA


title: 201516250010_R01C01_Nonsmoker

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

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

tag: 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)


title: Sample 30_Plate 1_Universal human reference RNA_Rep2

description:
Plate #1 control
HDACi_ctrl_UHRR_340_S52


title: Sample 26_Plate 1_Human brain total RNA_Rep 2

description:
Plate #1 control
HDACi_ctrl_HBTR_356_S68

source_name: Plate 1_Human brain total RNA

value: Human brain total RNA


title: Sample 38_HDACi_Entinostat_Rep 2

description:
External validation compound
HDACi_Ent_D1_325_S37

tag: cell line

tag: cell type

tag: chemical

value: Entinostat

tag: concentration

value: 50 µM

tag: vehicle solvent control

value: VC_DMSO_B_Rep 2


title: Sample 24_Non-HDACi_Campthothecin_Rep 3

description:
TGx-HDACi Reference compound
HDACi_CPT_D1_306_S18

value: Campthothecin

value: VC_DMSO_A_Rep 3


title: 201516250045_R06C01_Nonsmoker

tag: current smoking status

tag: age at death

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

value: F

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

tag: 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: APL131

tag: tissue

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

value: Female

tag: age


title: Sample 23_Non-HDACi_Campthothecin_Rep 2

description:
TGx-HDACi Reference compound
HDACi_CPT_D1_298_S10

tag: cell line

value: Human lymphoblastoid cell line

value: VC_DMSO_A_Rep 2


title: APL128

value: Male


title: Sample 21_Non-HDACi_Cisplatin_Rep 3

description:
TGx-HDACi Reference compound
HDACi_Cisp_D1_354_S66

tag: cell type

value: Cisplatin

value: 80 µM


title: Sample 25_Plate 1_Human brain total RNA_Rep 1

description:
Plate #1 control
HDACi_ctrl_HBTR_348_S60

tag: sample type


title: Sample 22_Non-HDACi_Campthothecin_Rep 1

description:
TGx-HDACi Reference compound
HDACi_CPT_D1_290_S2

tag: chemical

tag: concentration

value: VC_DMSO_A_Rep 1


title: 201516280022_R04C01_Nonsmoker

tag: current smoking status

value: control

value: M

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

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

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

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

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

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: APL130

tag: tissue

tag: disease state

tag: gender

tag: age


title: 201516260008_R01C01_Smoker

value: case

tag: age at death

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

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

value: AA

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: Sample 33_VC_DMSO_A_Rep 3

tag: cell line

tag: cell type

tag: chemical

value: DMSO

tag: concentration


title: APL129


title: APL127


title: Sample 20_Non-HDACi_Cisplatin_Rep 2

description:
TGx-HDACi Reference compound
HDACi_Cisp_D1_346_S58

tag: vehicle solvent control


title: Sample 19_Non-HDACi_Cisplatin_Rep 1

description:
TGx-HDACi Reference compound
HDACi_Cisp_D1_338_S50


title: 201516250012_R08C01_Nonsmoker

tag: current smoking status

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

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

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

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

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

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

tag: nac_assigned_sex_for_missing (imputed sex for individuals without a self-reported sex value (f = female, m = male). the imputation is based on chry gene expression counts)


title: Sample 34_VC_DMSO_B_Rep 1


title: APL126

tag: tissue

tag: disease state

tag: gender

tag: age


title: Sample 16_Non-HDACi_Cadmium chloride_Rep 1

description:
TGx-HDACi Reference compound
HDACi_CdCl2_D1_315_S27

source_name: TK6_Non-HDACi_Cadmium chloride

tag: cell line

tag: cell type

tag: chemical

value: Cadmium chloride

tag: concentration

value: 50 µM

value: VC_H2O_A_Rep 1


title: Sample 17_Non-HDACi_Cadmium chloride_Rep 2

description:
TGx-HDACi Reference compound
HDACi_CdCl2_D1_323_S35

tag: vehicle solvent control

value: VC_H2O_A_Rep 2


title: Sample 18_Non-HDACi_Cadmium chloride_Rep 3

description:
TGx-HDACi Reference compound
HDACi_CdCl2_D1_331_S43

value: Human lymphoblastoid cell line

value: VC_H2O_A_Rep 3


title: 201516280060_R07C01_Nonsmoker

tag: current smoking status

tag: age at death

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

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

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

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

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

tag: chry_pc1 (principal component 1 from pca on variance-stablized median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

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

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


title: 201516240031_R06C01_Nonsmoker

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

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

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

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

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

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

tag: nac_assigned_sex_for_missing (imputed sex for individuals without a self-reported sex value (f = female, m = male). the imputation is based on chry gene expression counts)


title: APL125

tag: tissue

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

value: Male

tag: age


title: Sample 13_Non-HDACi_Bleomycin_Rep 1

description:
TGx-HDACi Reference compound
HDACi_Ble_D1_313_S25

tag: cell line

tag: cell type

tag: chemical

value: Bleomycin

tag: concentration

value: 10 µg/mL

tag: vehicle solvent control


title: APL124

value: Female


title: Sample 14_Non-HDACi_Bleomycin_Rep 2

description:
TGx-HDACi Reference compound
HDACi_Ble_D1_321_S33


title: 201516280047_R03C01_Nonsmoker

tag: current smoking status

value: control

tag: age at death

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

value: F

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

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

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

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

tag: chry_pc1 (principal component 1 from pca on variance-stablized median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

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

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


title: Sample 15_Non-HDACi_Bleomycin_Rep 3

description:
TGx-HDACi Reference compound
HDACi_Ble_D1_329_S41


title: APL123

tag: tissue

tag: disease state

tag: gender

tag: age


title: Sample 12_HDACi_Apicidin_Rep 3

description:
TGx-HDACi Reference compound
HDACi_Api_D1_335_S47

tag: cell line

tag: cell type

tag: chemical

value: Apicidin

tag: concentration

value: 1 µg/mL

value: VC_DMSO_A_Rep 3


title: APL122


title: Sample 11_HDACi_Apicidin_Rep 2

description:
TGx-HDACi Reference compound
HDACi_Api_D1_327_S39

tag: vehicle solvent control

value: VC_DMSO_A_Rep 2


title: APL121


title: ChIp-seq_Pfhmgb1_rep2

city: shanghai

first: meng

last: liu

address: 1239,SiPing Road

institute: TongJi University

description:
ChIp-seq_Pfhmgb1_rep2
PfHMGB1-R-IP_rep2.bw
PfHMGB1_peaks_rep2.bed

library_source: genomic

data_processing:
Low-quality and the adaptor sequences were trimmed from the reads using cutadapt (v1.18) with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20. Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Bowtie2 (v2.3.4.3) with parameters: -N 0 --no-discordant --no-mixed --no-unal. The Samtools (v1.9) was used to transfer the mapping results from sam format to position sorted bam format. Next, the duplicated reads were removed by markdup from sambamba (v0.6.8). Then, the bam files were converted to bigwig files using bamCoverage from the deeptools suite (v3.1.3) with parameters: --normalizeUsing RPKM --binSize 25. The bigwig files from ChIP sample were normalized to input sample by bigwigCompare from the deeptools suite (v3.1.3) with parameters: --pseudocount 1 for further analysis. The Integrative Genomics Viewer (IGV) was used to show the signal of histone modification in certain genomic region in a track view.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: *bw: IGV enrichment.
Supplementary_files_format_and_content: *bed: PfHMGB1 binding sites.

molecule: genomic DNA

organism: Plasmodium falciparum

growth_protocol: P. falciparum 3D7strain with 2% hematocrit was cultured in medium containing 10.44g/L RPMI-1640, 25mM HEPES, 10% Albumax I, 20μg/ml gentamicin, 0.1 mM hypoxanthine, a gas phase with 5% O2, 3% CO2 at 37 °C. Parasites were synchronized by 5% sorbitol and a 40%/70% Percoll gradient centrifugation.

extract_protocol:
Nuclei were isolated by Lysis Buffer and Dounce homogenization, followed by sonication to generate 200–600 bp fragments in length on the highest power setting for 10-20 min at 30s intervals. Protein-DNA complexes are selectively immunoprecipitated using  2 μg of mouse anti-Ty1(Sigma) and mouse IgG (Sigma) as control. Formaldehyde induced cross-links are reversed with NaCl and DNA extracted using Proteinase K and MinElute PCR purification kit (Qiagen, 28006).
The ChIP DNAs were used to prepare sequencing libraries, including end-repair (Invitrogen No.16123), adding protruding 3’ A base (NEB No.M0212L), adapter ligation(NEB No.M2200L), size selection with Ampure beads (for 250 bp inserts) and amplification of libraries(KAPA Biosystems KB2500) (PCR program: 1 min at 98 ℃ followed by 12 cycles of 10 s at 98 ℃, 1 min at 65 ℃; finally extended 5 min at 65 ℃). Amplified libraries were cleand with Ampure beads
The library were sequenced on an Illumina HiSeq Xten systerm with PE150 strategy.

treatment_protocol: Synchronized parasites at ring stage were cross-linked with 1% paraformaldehyde for 10 min, stopped with 0.125 M glycine for 5min and released with 0.15% saponin.

tag: development stage

value: Ring

tag: strain

value: Pf 3D7

tag: antibody

value: rabbit anti-GFP(abcam)

tag: genotype

value: wild type

tag: host

value: Homo sapiens


title: 201516240018_R05C01_Smoker

tag: current smoking status

value: case

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)

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: 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: HiC_Pfhmgb1_KO_rep3

description:
HiC_Pfhmgb1_KO_rep3
KO_2000_iced.matrix

data_processing:
The adaptor and low-quality sequences were trimmed from the reads using cutadapt(v1.18). Then the clean reads were processed (i.e., mapping, filtering, pairing, removing duplicates and normalizing) using HiC-Pro package(v2.11.1) as described. In brief, each end of read pairs was mapped to Plasmodium falciparum 3D7 genome (Pf 3D7 v32) using bowtie2 with default parameters in HiC-Pro configure files. The alignment results were saved in a bam format file, respectively. On the basis of the alignment results, the reads were re-paired to remove singleton, multi-hits, low-MAPQ and unmapped reads. The pairable reads were assigned to DpnII restriction fragments for filtering dangling-end, self-circle ligation and PCR duplicates. The raw contact matrix was generated for each sample of each replicate at a resolution of 10-kb and then normalized using the iterative correction and eigenvector decomposition (ICE) method to correct for experimental and technical biases.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: *matrix: Normalized contact matrix at 2kb resolution of HiC sequencing data for different samples.
Supplementary_files_format_and_content: 2k_abs.bed: Contact region.

extract_protocol:
Parasites were lysed in 5 ml ice-cold lysis buffer with rotation for 1 h at 4 °C and washed twice with PBS and once with 1×NEBuffer 2. Pelleted nuclei was resuspended with 300 μl H2O, 44 μl of 10×NEBuffer 2 and  38 μl of 1% SDS at 65 °C water bath 10 minutes and reaction was terminated by addition of T44 μl of 10% Triton X-100. To fragment DNA, 350 U endonucleases DpnII (NEB,R0543M) was added to the reaction at 37 °C overnight. Digested DNA was filled in the restriction fragment overhangs with Klenow (NEB,M0210L) and marked the DNA ends with biotin. Chromatin was then ligated with T4 DNA ligase(NEB) for 4 h at 16 °C, reversed with proteinase K and purified with  phenol:chloroform and ethanol protocol. After removal of biotin from un-ligated ends with T4 DNA polymerase (NEB,  M0203L), DNA was sonicated to reduce their size to 300-500 bp.
To prepare biotinylated DNA, sheared DNA were immobilized on Dynabeads M-280 Streptavidin at room temperature for 1 h with rotation. The process of ends repair, A-tailing and adaptor ligation referring to ChIP library, the Hi-C library was amplified 6-10 cycles and the PCR product was loaded to 2% agarose and size selected 300-600bp band.
The library were sequenced on an Illumina HiSeq Xten system with PE150 strategy.

tag: development stage

tag: strain

tag: digestion enzyme

value: DpnII

tag: genotype

value: Pfhmgb1 Knock Down

tag: host


title: HiC_Pfhmgb1_ctrl

description:
HiC_Pfhmgb1_ctrl
Ctrl_2000_iced.matrix

value: wildtype vector


title: Sample 9_Non-HDACi_Antimycin A_Rep 3

description:
TGx-HDACi Reference compound
HDACi_Ant_D1_311_S23

source_name: TK6_Non-HDACi_Antimycin A

tag: cell line

tag: cell type

value: Human lymphoblastoid cell line

tag: chemical

value: Antimycin A

tag: concentration

tag: vehicle solvent control


title: Sample 10_HDACi_Apicidin_Rep 1

description:
TGx-HDACi Reference compound
HDACi_Api_D1_319_S31

value: Apicidin

value: VC_DMSO_A_Rep 1


title: 201516280060_R01C01_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)

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: APL120

tag: tissue

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

value: Male

tag: age


title: Sample 8_Non-HDACi_Antimycin A_Rep 2

description:
TGx-HDACi Reference compound
HDACi_Ant_D1_303_S15

tag: cell line

tag: cell type

tag: chemical

tag: concentration

tag: vehicle solvent control

value: VC_DMSO_A_Rep 2


title: ChIp-seq_Pfhmgb1_rep1

description:
ChIp-seq_Pfhmgb1_rep1
PfHMGB1-R-IP_rep1.bw
PfHMGB1_peaks_rep1.bed

tag: development stage

value: Ring

tag: strain

value: Pf 3D7

tag: antibody

value: rabbit anti-GFP(abcam)

tag: genotype

value: wild type

tag: host

value: Homo sapiens


title: ChIp-seq_input_rep2

description:
ChIp-seq_input_rep2
Input_rep2.bw


title: 201516250050_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: 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: 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: 201516240018_R07C01_Nonsmoker

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: APL118

tag: tissue

tag: disease state

tag: gender

value: Female

tag: age


title: APL119


title: 201516250012_R05C01_Nonsmoker

tag: current smoking status

tag: age at death

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

value: F

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

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)


title: 201516260030_R05C01_Nonsmoker

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)


title: ChIp-seq_input_rep1

description:
ChIp-seq_input_rep1
Input_rep1.bw

tag: development stage

tag: strain

tag: genotype

tag: host


title: Sample 6_Non-HDACi_5-Fluorouracil_Rep 3

description:
TGx-HDACi Reference compound
HDACi_5-FU_D1_381_S93

tag: cell line

tag: cell type

value: Human lymphoblastoid cell line

tag: chemical

tag: concentration

value: 25 µg/mL

tag: vehicle solvent control

value: VC_DMSO_A_Rep 3


title: Sample 5_Non-HDACi_5-Fluorouracil_Rep 2

description:
TGx-HDACi Reference compound
HDACi_5-FU_D1_373_S85


title: 201516250030_R04C01_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: 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: ChIp-seq_IgG_rep2

description:
ChIp-seq_IgG_rep2
IgG_rep2.bw

tag: development stage

tag: strain

tag: antibody

value: rabbit IgG (abcam)

tag: genotype

tag: host


title: Sample 7_Non-HDACi_Antimycin A_Rep 1

description:
TGx-HDACi Reference compound
HDACi_Ant_D1_295_S7

tag: cell line

tag: cell type

tag: chemical

value: Antimycin A

tag: concentration

tag: vehicle solvent control

value: VC_DMSO_A_Rep 1


title: APL117

tag: tissue

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

value: Male

tag: age


title: ChIp-seq_IgG_rep1

description:
ChIp-seq_IgG_rep1
IgG.bw

value: Ring

value: Pf 3D7

value: wild type


title: APL115


title: Sample 4_Non-HDACi_5-Fluorouracil_Rep 1

description:
TGx-HDACi Reference compound
HDACi_5-FU_D1_365_S77


title: APL116


title: ChIp-seq_wt_IgG_rep2

data_processing:
Low-quality and the adaptor sequences were trimmed from the reads using cutadapt (v1.18) with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20. Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Bowtie2 (v2.3.4.3) with parameters: -N 0 --no-discordant --no-mixed --no-unal. The Samtools (v1.9) was used to transfer the mapping results from sam format to position sorted bam format. Next, the duplicated reads were removed by markdup from sambamba (v0.6.8). Then, the bam files were converted to bigwig files using bamCoverage from the deeptools suite (v3.1.3) with parameters: --normalizeUsing RPKM --binSize 25. The bigwig files from ChIP sample were normalized to input sample by bigwigCompare from the deeptools suite (v3.1.3) with parameters: --pseudocount 1 for further analysis. The Integrative Genomics Viewer (IGV) was used to show the signal of histone modification in certain genomic region in a track view.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: *.bed: HM bindings sites.

extract_protocol:
Nuclei were isolated by Lysis Buffer and Dounce homogenization, followed by sonication to generate 200–600 bp fragments in length on the highest power setting for 10-20 min at 30s intervals. Protein-DNA complexes are selectively immunoprecipitated using 3 µg of Rabbit anti-H3K9me3 antibody (Abcam, ab8898), 3 μg of Rabbit anti-H3K9Ac antibody (Millipore, 07-352), or rabbit IgG (Sigma) as control. Formaldehyde induced cross-links are reversed with NaCl and DNA extracted using Proteinase K and MinElute PCR purification kit (Qiagen, 28006).
The ChIP DNAs were used to prepare sequencing libraries, including end-repair (Invitrogen No.16123), adding protruding 3’ A base (NEB No.M0212L), adapter ligation(NEB No.M2200L), size selection with Ampure beads (for 250 bp inserts) and amplification of libraries(KAPA Biosystems KB2500) (PCR program: 1 min at 98 ℃ followed by 12 cycles of 10 s at 98 ℃, 1 min at 65 ℃; finally extended 5 min at 65 ℃). Amplified libraries were cleand with Ampure beads
The library were sequenced on an Illumina HiSeq Xten systerm with PE150 strategy.

treatment_protocol: synchronized parasites at ring stage were cross-linked with 1% paraformaldehyde for 10 min, stopped with 0.125 M glycine for 5min and released with 0.15% saponin.

value: rabbit IgG (Sigma)

value: Homo sapiens


title: APL114


title: Sample 3_Non-HDACi_2-Deoxy-D-glucose_Rep 3

description:
TGx-HDACi Reference compound
HDACi_2-DG_D1_383_S95

value: 20 µM

value: VC_H2O_A_Rep 3


title: 201516280005_R07C01_Nonsmoker

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)

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)

value: TRUE


title: 201516260030_R03C01_Nonsmoker

value: control

value: F

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 2_Non-HDACi_2-Deoxy-D-glucose_Rep 2

description:
TGx-HDACi Reference compound
HDACi_2-DG_D1_375_S87

tag: cell line

tag: cell type

value: Human lymphoblastoid cell line

tag: chemical

tag: concentration

tag: vehicle solvent control

value: VC_H2O_A_Rep 2


title: 201516280040_R05C01_Smoker

tag: current smoking status

value: case

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)


title: ChIp-seq_wt_IgG_rep1

tag: development stage

tag: strain

tag: antibody

tag: genotype

tag: host


title: APL113

tag: tissue

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

tag: age


title: Sample 1_Non-HDACi_2-Deoxy-D-glucose_Rep 1

description:
TGx-HDACi Reference compound
HDACi_2-DG_D1_367_S79

tag: cell line

tag: cell type

tag: chemical

tag: concentration

tag: vehicle solvent control

value: VC_H2O_A_Rep 1


title: 201516250029_R03C01_Nonsmoker

tag: current smoking status

tag: age at death

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

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

tag: rin (rna integrity number)

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

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

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

tag: 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: ChIp-seq_wt_h3k9me3_rep2

description:
ChIp-seq_wt_h3k9me3_rep2
G7N-R_h3k9me3_rep2.bed

tag: development stage

value: Ring

tag: strain

value: Pf 3D7

tag: antibody

value: Rabbit anti-H3K9me3 antibody (Abcam, ab8898)

tag: genotype

tag: host


title: 201516240041_R05C01_Smoker

tag: current smoking status

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)


title: T0901317-pulsed, IL-4-treated macrophages rep3

city: Frankfurt

first: Ryan

middle: G

last: Snodgrass

address: Theodor-Stern-Kai 7, building 74

department: Institute of Biochemistry I

country: Germany

institute: Goethe-University Frankfurt

description: 3 hr Tx/24 hr Tx

data_processing:
Illumina-generated FASTQ files were processed using the Lexogen QuantSeq 3´ mRNA-Seq integrated data analysis pipeline on the BlueBee on-line platform
Within the integrated data analysis pipeline, reads were trimmed using bbduk v35.92, were mapped to the hg38 human genome assembly using STAR Aligner v2.5.2a with modified ENCODE settings, and gene-specific read counts were determined by HTSeq-count v0.6.0.
Genome_build: hg38 human genome assembly
Supplementary_files_format_and_content: read counts as text documents

source_name: human monocyte-derived macrophages

growth_protocol: Human monocytes derived from individual donors were differentiated into naïve macrophages with RPMI 1640 medium containing 5% AB-positive human serum for 7 days. .

extract_protocol:
Library preparation of 500 ng RNA was performed using the Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina.
Libraries were sequenced (single-end, 75 cycles) using the High Output Kit v2 on an Illumina NextSeq 500 sequencer.

treatment_protocol: Naive macrophages were pulsed with T0901317 (1 µM) for 3 hours, then media was aspirated and cells were polarized to alternatively activated macrophages with IL-4 (5 ng/ml) or IL-13 (10 ng/ml) for 24 hours

tag: cell type

value: macrophage

tag: treatment

tag: concentration

value: 1 microM/5 ng/ml


title: APL112

tag: tissue

tag: disease state

tag: gender

value: Male

tag: age


title: APL110

value: Female


title: ChIp-seq_wt_h3k9ac_rep2

description:
ChIp-seq_wt_h3k9ac_rep2
G7N-R_h3k9ac_rep2.bed

tag: development stage

tag: strain

tag: antibody

value: Rabbit anti-H3K9Ac antibody (Millipore, 07-352)

value: wild type

value: Homo sapiens


title: 201516260055_R01C01_Smoker

tag: current smoking status

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)

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: T0901317-pulsed, IL-4-treated macrophages rep2

description: 3 hr Tx/24 hr Tx

tag: cell type

tag: treatment

tag: concentration


title: 201516280005_R06C01_Nonsmoker

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: APL108

tag: tissue

tag: disease state

tag: gender

tag: age


title: T0901317-pulsed, IL-4-treated macrophages rep1

description: 3 hr Tx/24 hr Tx


title: ChIp-seq_wt_h3k9ac_rep1

description:
ChIp-seq_wt_h3k9ac_rep1
G7N-R_h3k9ac_rep1.bed

tag: development stage

tag: strain

tag: antibody

tag: genotype

tag: host


title: ChIp-seq_Pfhmgb1_KO_IgG_rep2

value: rabbit IgG (Sigma)

value: Pfhmgb1 Knock Down


title: ChIp-seq_Pfhmgb1_KO_IgG_rep1


title: APL107

value: Bone Marrow

value: acute promyelocytic leukemia


title: T0901317-pulsed, IL-13-treated macrophages rep3

description: 3 hr Tx/24 hr Tx

tag: cell type

tag: treatment

value: 1 microM/10 ng/ml


title: T0901317-pulsed, IL-13-treated macrophages rep2

description: 3 hr Tx/24 hr Tx

tag: concentration


title: 201516260028_R02C01_Nonsmoker

tag: current smoking status

tag: age at death

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

value: CAUC

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

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

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

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

tag: chry_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: 201516260029_R07C01_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)


title: ChIp-seq_wt_h3k9me3_rep1

description:
ChIp-seq_wt_h3k9me3_rep1
G7N-R_h3k9me3_rep1.bed

tag: development stage

value: Ring

tag: strain

value: Pf 3D7

tag: antibody

value: Rabbit anti-H3K9me3 antibody (Abcam, ab8898)

tag: genotype

tag: host


title: APL106

tag: tissue

tag: disease state

tag: gender

tag: age


title: ChIp-seq_Pfhmgb1_KO_h3k9me3_rep2

description:
ChIp-seq_Pfhmgb1_KO_h3k9me3_rep2
Pfhmgb1_KO_h3k9me3_rep2.bed


title: T0901317-pulsed, IL-13-treated macrophages rep1

description: 3 hr Tx/24 hr Tx

tag: cell type

value: macrophage

tag: treatment

tag: concentration


title: APL104

value: Female


title: IL-4-treated macrophages rep3

description: 24 hr Tx

value: 5 ng/ml


title: 201516250010_R03C01_Nonsmoker

tag: current smoking status

tag: age at death

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

value: M

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)

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: ChIp-seq_Pfhmgb1_KO_h3k9ac_rep2

description:
ChIp-seq_Pfhmgb1_KO_h3k9ac_rep2
Pfhmgb1_KO_h3k9ac_rep2.bed

tag: development stage

tag: strain

tag: antibody

value: Rabbit anti-H3K9Ac antibody (Millipore, 07-352)

tag: genotype

tag: host

value: Homo sapiens


title: IL-4-treated macrophages rep2

description: 24 hr Tx

tag: cell type

tag: treatment

tag: concentration


title: ChIp-seq_Pfhmgb1_KO_h3k9ac_rep1

description:
ChIp-seq_Pfhmgb1_KO_h3k9ac_rep1
Pfhmgb1_KO_h3k9ac_rep1.bed


title: APL103

tag: tissue

tag: disease state

tag: gender

tag: age


title: IL-4-treated macrophages rep1

description: 24 hr Tx


title: APL101


title: 201516280017_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)

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)

value: TRUE


title: HiC_wt_rep2

description:
HiC_wt_rep2
WT_2000_iced.matrix

extract_protocol:
Parasites were lysed in 5 ml ice-cold lysis buffer with rotation for 1 h at 4 °C and washed twice with PBS and once with 1×NEBuffer 2. Pelleted nuclei was resuspended with 300 μl H2O, 44 μl of 10×NEBuffer 2 and  38 μl of 1% SDS at 65 °C water bath 10 minutes and reaction was terminated by addition of T44 μl of 10% Triton X-100. To fragment DNA, 350 U endonucleases DpnII (NEB,R0543M) was added to the reaction at 37 °C overnight. Digested DNA was filled in the restriction fragment overhangs with Klenow (NEB,M0210L) and marked the DNA ends with biotin. Chromatin was then ligated with T4 DNA ligase(NEB) for 4 h at 16 °C, reversed with proteinase K and purified with  phenol:chloroform and ethanol protocol. After removal of biotin from un-ligated ends with T4 DNA polymerase (NEB,  M0203L), DNA was sonicated to reduce their size to 300-500 bp.
To prepare biotinylated DNA, sheared DNA were immobilized on Dynabeads M-280 Streptavidin at room temperature for 1 h with rotation. The process of ends repair, A-tailing and adaptor ligation referring to ChIP library, the Hi-C library was amplified 6-10 cycles and the PCR product was loaded to 2% agarose and size selected 300-600bp band.
The library were sequenced on an Illumina HiSeq Xten systerm with PE150 strategy.

tag: development stage

tag: strain

tag: digestion enzyme

value: DpnII

tag: genotype

value: wild type

tag: host


title: APL099

tag: tissue

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

tag: age


title: IL-13-treated macrophages rep3

description: 24 hr Tx

tag: cell type

tag: treatment

tag: concentration

value: 10 ng/ml


title: 201516280022_R03C01_Nonsmoker

tag: current smoking status

tag: age at death

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

value: F

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

tag: rin (rna integrity number)

tag: 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: 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: IL-13-treated macrophages rep2

description: 24 hr Tx

tag: cell type


title: MKN-28 cells, PTBP1-KO

city: Guangzhou

first: Min

last: Deng

address: 78 Hengzhigang Road

institute: Affiliated Cancer Hospital & Institute of Guangzhou Medical University

description: PTBP1 knockout  MKN-28 cells

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using hisat v2.1.0 with default parameter
Sequence quality was examined using the FastQC software (version 0.11.7). Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using hisat v2.0.4 with default parameter.
The transcript abundances for each sample was estimated with StringTie (v1.2.3), and the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0).
Differential gene expression analysis was done using R package DESeq2 v1.24.0
Genome_build: Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Tab-delimited text file includes FPKMs for each sample.

source_name: Gastric cancer cell line

growth_protocol: Cells grown and maintained in RPMI 1640 medium (Gibco, USA) containing penicillin (100 units/ml) and streptomycin (100 µg/ml). Cultures were incubated in a humidified environment at 5% CO2 and 37°C.

extract_protocol:
Total RNA was isolated from PTBP1 knockout or control MKN28 cells using TRIZOL reagent(Invitrogen,Camarillo,USA) following the manufacturer's instructions, and PolyA RNA was subsequently purified from total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MKN-28 cells were infected with lentivirus expressing both Cas9 enzyme and sgRNA targeting PTBP1 or control, and single cells were isolated 48 h after infection by FACS (BD FACS Aria III) into 96-well plates. Independent clones were allowed to grow for 3 weeks.

tag: cell line

value: Gastric cancer

tag: genotype

value: PTBP1 knockout


title: APL105

tag: tissue

tag: disease state

tag: gender

value: Male

tag: age


title: IL-13-treated macrophages rep1

description: 24 hr Tx

value: macrophage

tag: treatment

tag: concentration


title: 201516240040_R08C01_Nonsmoker

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: 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: MKN-28 cells, Control

description: Control  MKN-28 cells

tag: cell line

tag: cell type

tag: genotype

value: Control


title: APL097

tag: tissue

tag: disease state

tag: gender

tag: age


title: HiC_Pfhmgb1_RC_rep2

description:
HiC_Pfhmgb1_RC_rep2
RC_2000_iced.matrix

tag: development stage

value: Ring

tag: strain

value: Pf 3D7

tag: digestion enzyme

value: Pfhmgb1 Rescue

tag: host


title: HiC_Pfhmgb1_RC_rep1

description:
HiC_Pfhmgb1_RC_rep1
RC_2000_iced.matrix

value: Homo sapiens


title: T0901317-pulsed macrophages rep3

description: 3 hr Tx

tag: treatment

tag: concentration

value: 1 microM


title: APL096


title: HiC_Pfhmgb1_KO_rep2

description:
HiC_Pfhmgb1_KO_rep2
KO_2000_iced.matrix

value: DpnII

value: Pfhmgb1 Knock Down


title: T0901317-pulsed macrophages rep2

description: 3 hr Tx


title: FOSL1 control-siRNA

city: Richmond

first: Jiong

last: Li

state: Virginia

address: 800 E Leigh Street, suite 212

institute: VCU

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.2.0.
The unique mapped reads was used for peak calling by MACS2 with default setting
Supplementary_files_format_and_content: bedGraph files and big wig files

source_name: Head and neck squamous cell carcinoma cells

growth_protocol: 10% FBS in DMEM

extract_protocol:
ChIP DNA was purified using QIAquick PCR Purification Kit (Qiagen, cat#28106). 10–50 ng of ChIP DNA for each sample was sonicated and used for the ligation of barcoded NEB adapters.
ChIP-seq libraries were generated using NEBNext® Ultra# II DNA Library Prep Kit (NEB, #E7103S) following the manufacturer’s instructions.

treatment_protocol: SCC1 cells were treated with FOSL1 siRNA or with control siRNA for 48 hours.

value: SCC1 cells

tag: chip antibody

value: FOSL1 rabbit antibody (Cell Signaling, cat#5281)

value: control-siRNA


title: APL094

value: Bone Marrow

value: acute promyelocytic leukemia


title: HiC_Pfhmgb1_KO_rep1

description:
HiC_Pfhmgb1_KO_rep1
KO_2000_iced.matrix


title: WNT rep3 [OD24]

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

data_processing:
According to Illumina protocol, the libraries underwent 101-bp paired-end sequencing using an Illumina NovaSeq (S4).. Basecalls performed using CASAVA version 1.8.2
For each read, the first 6 and the last nucleotides were trimmed to the point where the Phred score of an examined base fell below 20 using in-house scripts. If, after trimming, the read was shorter than 45 bp, the whole read was discarded.
Trimmed reads were mapped to the Neurospora crassa OR74A reference genome (FungiDB release 43) with hisat2 v2.1.0 indicating that reads correspond to the reverse complement of the transcripts. Alignments with quality score below 20 were excluded from further analysis.
Gene counts were produced with stringtie v1.3.3b and the python script “prepde.py” provided in the package. Stringtie was limited to reads matching the reference annotation.
Genome_build: Neurospora crassa OR74A (FungiDB release 43)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Neurospora crassa

source_name: hyphae

growth_protocol: Strains were grown in either liquid or solid (supplemented with 1.5% agar) Vogel's minimal medium with 1.5% (w/v) sucrose (Vs) as described by Davis, 2000) or is available at http://www.fgsc.net/Neurospora/NeurosporaProtocolGuide.htm.

extract_protocol:
RNA extraction, DNase treatment, cDNA and RT PCR (primers are listed in Table 2) were performed as previously described (Herold and Yarden, 2017).
For purified total RNA collected from samples, strand-specific sequencing libraries were produced following the Illumina TruSeq stranded protocol.

treatment_protocol: For cell wall stress induction, relevant cultures were supplemented with 10-5 M Nikkomycin Z, for the last hour prior to RNA extraction.

value: wildtype

tag: rna immunoprecipitation

value: total

tag: agent

value: Nikkomycin Z

tag: fraction

value: total RNA


title: HiC_wt_rep1

description:
HiC_wt_rep1
WT_2000_iced.matrix

value: wild type


title: MED1 FOSL1-siRNA

tag: cell line

value: MED1 rabbit antibody (Bethyl, cat#A300-793A)


title: T0901317-pulsed macrophages rep1

description: 3 hr Tx

tag: cell type

value: macrophage


title: APL093

value: Male


title: APL098


title: MED1 control-siRNA


title: untreated macrophages rep3

description: no Tx

value: untreated


title: APL091


title: APL090


title: FOSL1 FOSL1-siRNA


title: untreated macrophages rep2

description: no Tx


title: WPT rep3 [OD23]

value: pull-dow

tag: genotype

value: pull-down RNA


title: APL088

tag: tissue


title: APL089

tag: disease state

value: Female


title: WNT rep1 [OD20]


title: WPT rep2 [OD21]


title: WNT rep2 [OD22]


title: APL087

tag: gender


title: C_R2

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

data_processing:
Illumina RTAv2 software was used for basecalling
Raw reads were trimmed using Trim Galore! (Galaxy version 0.4.2) to remove low-quality reads and adaptor sequence.
Libraries were mapped to the hg38 and dm3 genome assemblies using Bowtie2 (Galaxy version 2.2.6.2).
Duplicates and reads mapping to the Broad Institute's blacklist (Encode Project Consortium, 2012) were discarded. Remaining reads were extended by 250 bp for downstream analyses. Replicates were merged for plotting and downstream analyses.
Genome_build: hg38 and dm3
Supplementary_files_format_and_content: Bedgraph files contain either RPM, RRPM or RRPM, n+1, log-transformed read counts for merged replicates (R1+R2) of ChIP-seq datasets from 10 Kb windows with a 5 Kb step.

source_name: U2OS cells

growth_protocol: U2OS were grown in DMEM with 10 % heat-inactivated FBS and 1 % penicillin/streptomycin under Blasticidin (5 µg/ml) selection and additionally Hygromycin B (100 µg/ml) selection for cell lines with pcDNA5-FRT-TO integration at 37 °C with 5 % CO2. Drosophila S2 cells (male) were grown in M3+BPYE media: Shields and Sang M3 Insect Medium, KHCO3, yeast extract, bactopeptone, 10 % heat-inactivated FBS and 1X penicillin/streptomycin at 25 °C with 5 % CO2.

extract_protocol:
Cells were processed using the truChIP Chromatin Shearing Kit (Covaris, 520127) following manufacturer’s instructions. 20 million nuclei were sonicated in 1mL tubes using a Covaris M220 to obtain chromatin frgament size of 250-500bp. Sonicated chromatin was centrifuged at 14,000 rpm at 4ºC for 10 minutes and the supernatant was isolated for subsequent steps. In parallel, Drosophila S2 cells were ﬁxed, lysed and sonicated as described above. U2OS input chromatin was mixed with Drosophila S2 chromatin (1.5% of total chromatin) after sonication. Chromatin associated to DNAJC9-MYC-Flag was obtained by incubating sonicated chromatin with anti FLAG antibody.
Libraries were costructed using the KAPA Hyperprep kit following manufacturer’s instruction, except that 1.25 µM of Illumina compatible indexed adapters (Pentabase) were ligated to A-tailed DNA.

treatment_protocol: Protein expression was induced in media with Tetracycline (2 µg/ml, 48 hrs) in DMEM, 10 % FBS and 1 % P/S.

tag: overexpressed protein

tag: spike-in

value: YES

tag: antibodies

value: FLAG:Sigma, F7425; H2Av:Active Motif, 39715


title: APL109

tag: age


title: 4AJ_R2

value: DNAJC9-MYC-Flag 4AJ mutant


title: WPT rep1 [OD19]

tag: strain


title: APL086

value: Bone Marrow


title: J_R2

value: DNAJC9-MYC-Flag J mutant


title: INPUT

value: DNAJC9-MYC-Flag WT


title: GNT rep3 [OD18]

value: total


title: untreated macrophages rep1

description: no Tx

tag: treatment


title: GPT rep3 [OD17]

value: Nikkomycin Z


title: GNT rep2 [OD16]

value: total RNA


title: APL085

value: acute promyelocytic leukemia


title: 4AJ_R1


title: C_R1


title: APL083


title: GPT rep2 [OD15]


title: APL078


title: APL079


title: APL077


title: WT_R1


title: WT_R2


title: J_R1


title: Merb 2 h rep2

city: Madrid

first: Felipe

last: Cortés Ledesma

state: Madrid

address: Melchor Fernández Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v1.2.0 with parameter -m 1.
Differentially expressed genes were identified using DEseq2 (Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550. doi: 10.1186/s13059-014-0550-8).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample and were computed using custom R scripts that made use of the Bioconductor libraries bamsignals and edgeR.
Supplementary_files_format_and_content: bigWig files were generated using bamCoverage function from deepTools v2.4.1 with parameters --binSize 50 –normalizeUsingRPKM. Refs: Mammana A, Helmuth J (2019). bamsignals: Extract read count signals from bam files. R package version 1.18.0, https://github.com/lamortenera/bamsignals . McCarthy DJ, Chen Y, Smyth GK (2012). “Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.” Nucleic Acids Research, 40(10), 4288-4297. doi: 10.1093/nar/gks042. Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research (2016). doi:10.1093/nar/gkw257

source_name: retinal pigment epithelium

growth_protocol: RPE-1 cells were serum starved by 48h incubation in Dulbecco's Modified Eagle’s Medium (DMEM) F-12 (Sigma) supplemented with penicillin, streptomycin and 0.1% Fetal Bovine Serum (FBS) (Sigma) at 37ºC in 5% CO2.

extract_protocol:
Total RNA was isolated with the RNeasy kit from Qiagen following instructions from the manufacturer.
cDNA libraries were prepared with TruSeq Stranded mRNA (Illumina) using 150ng of total RNA.

treatment_protocol: RPE-1 cells were treated with vehicle (DMSO) for 30 minutes or merbarone (200μM) for 30 or 120 minutes.

value: hTERT RPE-1

tag: genotype/variation

value: wild type

value: Merbarone, 2 h


title: APL076

value: Male


title: WNU rep3 [OD12]

value: wildtype


title: WPU rep3 [OD11]

value: pull-dow

value: pull-down RNA


title: WNU rep2 [OD10]


title: Merb 2 h rep1


title: GPT rep1 [OD13]


title: APL075


title: WPU rep2 [OD9]


title: Untreated rep2

value: Untreated


title: APL074


title: APL084

value: Female


title: WNU rep1 [OD8]


title: APL071


title: WPU rep1 [OD7]


title: TOP2A Untreated rep1

description: processed data file: chip_top2a_peaks.bed

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v1.2.0 with parameter -m 1.
For the computation of ChIP-seq binding sites (peaks), we merged the corresponding replicates and used MACS2 (Zhang et al., 2008) with option “-q 0.01”. Then, only peaks showing a fold change over the control sample greater than 3 were kept. Since untreated and vehicle POLII ChIP-seq samples showed similar profiles, we treated them as replicates and merged them together. Ref: Zhang et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol (2008) vol. 9 (9) pp. R137.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files were generated using bamCoverage function from deepTools v2.4.1 with parameters --binSize 50 --extendReads TRUE –normalizeUsingRPKM. Ref: Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research (2016). doi:10.1093/nar/gkw257
Supplementary_files_format_and_content: bed files include peaks.

extract_protocol:
To prepare chromatin, RPE-1 cells were fixed by adding formaldehyde to a final concentration of 1% and incubated at 37ºC for 10 min. Immunoprecipitation was performed as previously described (Jimeno-González et al. 2015).
Libraries were prepared by ChIPmentation as described by Schmidl et al. 2015 using NEBNext HF Polymerase and sequenced using Illumina NextSeq 500.

treatment_protocol: RPE-1 cells were treated with vehicle (DMSO) for 30 minutes or merbarone (200μM) for 30 or 60 minutes.

tag: chip antibody

value: TOP2A (ab52934, Abcam)


title: IgG Untreated

value: Negative IgG


title: GPU rep1 [OD2]

tag: rna immunoprecipitation


title: APL069

value: Bone Marrow


title: GPU rep2 [OD4]

tag: agent


title: APL063


title: APL061


title: IgG Merb

value: Merbarone


title: APL060


title: APL058


title: IgG DMSO

value: DMSO


title: APL059


title: GPU rep1 [OD1]

tag: fraction


title: POLII Untreated rep3

description: processed data file: chip_polII_peaks.bed

tag: cell line

value: Rpb1-NTD (D8L4Y, Cell Signaling)


title: POLII Untreated rep2


title: APL055


title: maternal COVID placenta 4 (COVID4)

city: New Haven

first: Scott

middle: Dean

last: Pope

state: Connecticut

address: 300 Cedar St

department: Immunobiology

institute: Yale School of Medicine

data_processing:
FASTQ files from HiSeq 2500 were analyzed using Kallisto v0.46.1 using the “-b 100 and -t 20” options to obtain transcript abundances in TPM and estimated counts. The kallisto index used during transcript quantification was built (31bp k-mer length) from the Homo sapiens transcriptome GRCh38 downloaded as a FASTA file from Ensembl (Ensembl.org). Transcripts were annotated using the Bioconductor package biomaRt v2.40.5 in R v3.6.2.
Read counts for individual transcripts were summarized for gene-level analysis using the Bioconductor package tximport v1.12.3 with default parameters.
Differential expression analysis was performed using DESeq2 v1.24.0 with default parameters, comparing samples by maternal SARS-CoV-2 status.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts for all gene and all samples
Supplementary_files_format_and_content: csv of differential expression analysis (DESeq2)

source_name: Placenta

extract_protocol:
Villi were dissected from fresh placental tissue and rinsed three times in PBS. Villous samples were homogenized and centrifuged before RNA isolation using the Qiagen RNAeasy Mini Kit.
RNA libraries were prepared for sequencing following rRNA depletion using standard Illumina protocols

value: placental villi

value: postnatal day 0 / full term

value: maternal SARS-CoV-2+

value: placenta SARS-CoV-2 negative


title: maternal COVID placenta 5 (COVID5)


title: maternal COVID placenta 6 (COVID6)


title: POLII Untreated rep1

value: hTERT RPE-1

value: wild type


title: APL054

value: acute promyelocytic leukemia


title: POLII Merb 1 h rep2

description: processed data file: chip_polII_merb_1h_peaks.bed

value: Merbarone, 1 h


title: TOP2A Untreated rep2


title: Untreated rep1


title: GPU rep3 [OD5]

value: pull-dow

value: pull-down RNA


title: maternal COVID placenta 3 (COVID3)

value: placenta SARS-CoV-2 positive


title: APL070

value: Male


title: GPU rep2 [OD3]


title: POLII Merb 1 h rep1


title: ChIp-seq_Pfhmgb1_KO_h3k9me3_rep1

description:
ChIp-seq_Pfhmgb1_KO_h3k9me3_rep1
Pfhmgb1_KO_h3k9me3_rep1.bed

tag: development stage

value: Ring

value: Pf 3D7

tag: antibody

value: Rabbit anti-H3K9me3 antibody (Abcam, ab8898)

value: Pfhmgb1 Knock Down

tag: host

value: Homo sapiens


title: control placenta 3 (ctrl3)

tag: tissue

value: placental villi

tag: disease state

value: healthy control


title: APL051

value: Bone Marrow

tag: gender

value: Female


title: POLII Merb 30 min rep3

description: processed data file: chip_polII_merb_30m_peaks.bed

value: hTERT RPE-1

value: Merbarone, 30 min

value: Rpb1-NTD (D8L4Y, Cell Signaling)


title: maternal COVID placenta 2 (COVID2)

value: postnatal day 0 / full term

value: maternal SARS-CoV-2+

value: placenta SARS-CoV-2 negative


title: APL053

value: acute promyelocytic leukemia


title: APL052


title: POLII Merb 30 min rep2

value: wild type


title: APL050

value: Male


title: control placenta 2 (ctrl2)


title: POLII Merb 30 min rep1


title: POLII DMSO rep3

value: DMSO


title: APL049


title: APL048


title: POLII DMSO rep2


title: POLII DMSO rep1


title: APL046


title: M26_rep2

first: Yuanxiao

last: Tang

address: Dongchuan Road 800

data_processing:
Reads were sorted using index.
Reads were aligned to hg19 using TopHat.
The expression levels were calculated using the Cufflinks software.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_fpkm.txt: Tab-delimited text files include FPKM values for each Sample.

source_name: HEK293T cells

growth_protocol: HEC-1-B were cultured in MEM (Hyclone), supplemented with 10% (v/v) FBS, 2 mM GlutaMAX (Gibco), 1 mM sodium pyruvate (Sigma), and 1% penicillin-streptomycin. HEK293T cells were cultured in DMEM/High glucose (Hyclone), supplemented with 10% (v/v) FBS. Cells were maintained at 37 °C in a 5% (v/v) CO2 incubator.

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol Reagent (Ambion).
RNA-Seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocol.

treatment_protocol: The shGFP or shNRSF3 plasmid was transfected into HEK293T cells with the psPAX2 and pMD2.G helper plasmids (Addgene) using Lipofectamine 2000 to produce lentiviral particles. HEK293T cells or HEC-1-B cells were infected with the virus in the presence of 8 μg/mL polybrene (Sigma). Puromycin (Sigma) was added to a final concentration of 2 μg/mL to select the infected cells. Fresh puromycin-containing medium was changed every other day. Cells were collected for assays at 5 days post infection. For monoclones, HEC-1-B cells or HEK293T cells at ~80% confluency was transfected with Cas9 (0.6 μg) and sgRNA (1.2 μg) expressing plasmids by Lipofectamine 2000 in a 12-well plate. 2 days post transfection, puromycin was added to a final concentration of 2 μg/mL. Four days later, cells were changed to fresh medium without puromycin and cultured for another ten days. The cells were diluted and plated in 96-well plates with approximately one cell per well. Two weeks later, single cell clones were screened for target deletion by PCR.

tag: cell type

value: kidney

value: fetus

value: HS5-1 NRSE -/- monocolon


title: M36_rep2


title: APL045

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.


title: Mg Rep3

city: Heidelberg

first: Annika

last: Guse

address: Im Neuenheimer Feld 230

department: Centre for Organismal Studies

institute: Heidelberg University

description: Exaiptasia pallida (Aiptasia)

data_processing:
Paired-end reads were mapped to the Aiptasia genome version GCF_001417965.1 using HISAT2 version 2.1.0 at default settings, except -X 2000 --no-discordant --no-unal --no-mixed.
Host-derived transcripts were quantified in Trinity v2.5.1 using salmon v0.10.2 at default settings.
Differentially expressed genes between clustered different conditions were detected using DEseq2 (log2-fold change > 2; false-discovery-rate < 0.01) from raw read counts.
Genome_build: GCF_001417965.1
Supplementary_files_format_and_content: .xlsx file contains normalized TMM values for each gene for each replicate.

molecule: polyA RNA

organism: Exaiptasia diaphana

source_name: cells containing M. gaditana from Aiptasia larvae infected with Microchlopopsis gaditana

growth_protocol: Aiptasia larvae were maintained at ~300 larvae per ml in glass beakers in 0.22 µm filter-sterilized artificial sea water (FASW) at 26ºC and exposed to a 12L:12D cycle. M. gaditana were grown in cell culture flasks in 0.22 µm filter-sterilized 1X Daigo’s IMK medium (398-01333, Nihon Pharmaceutical Co. Ltd., Tokyo, Japan) on a 12h light:12h dark (12L:12D) cycle under 20–25 µmol m−2 s−1 of photosynthetically active radiation (PAR) at 18 °C.

extract_protocol:
Following collection of cells, these were lysed in 4.3 µl lysis buffer (0.2 % TritonX-100, 1U/µl Protector RNase inhibitor (3335399001, Sigma-Aldrich Co. LLC), 1.25 µM oligo-dT30VN, and 2.5 mM dNTP mix), and flash-frozen in liquid nitrogen.
Sequencing libraries were prepared following the SmartSeq2 protocol (Picelli et al., 2014). Briefly, full-length polyA+ mRNA was reverse transcribed using SuperScript II Reverse Transcriptase (18064014, Sigma-Aldrich Co. LLC), followed by pre-amplification of cDNA over 21 PCR cycles using KAPA HiFi Hotstart Ready Mix (07958935001, Roche Diagnostics International AG, Rotkreuz, Switzerland). cDNA libraries were then prepared for Illumina sequencing using the Nextera XT sequencing kit (FC-131-1096, Illumina, Inc., San Diego, CA, USA) and sequenced on NextSeq500 with 75 bp paired-end sequencing.

treatment_protocol: Following washing in calcium and magnesium-free artificial sea water (FMF-SW), ectodermal tissue was removed in 0.5 % Pronase and 1% sodium thio glycolate in CMF-SW. The endodermal tissue was macerated and the respective cells (aposymbiotic or containing M. gaditana) were collected using a microcapillary needle.

value: CC7 x F003

value: endoderm

tag: symbiotic state of larvae

value: infected with M. gaditana

tag: symbiotic state of isolated cells

value: containing M. gaditana

tag: age of larvae at start of infection

tag: duration of infection

tag: age at time of sampling

tag: number of cells per replicate

value: 4 M. gaditana containing cells


title: Mg Rep2

description: Exaiptasia pallida (Aiptasia)

tag: strain

value: 3 M. gaditana containing cells & 1 aposymbiotic cell


title: APL047

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

value: Bone Marrow

tag: age


title: Mg Rep1

description: Exaiptasia pallida (Aiptasia)

value: 2 M. gaditana containing cells & 1 aposymbiotic cell


title: 293T_wt_rep2

tag: genotype/variation


title: M26_rep1

tag: cell line


title: 293T_wt_rep1


title: Mg-Apo Rep3

description: Exaiptasia pallida (Aiptasia)

source_name: aposymbiotic cells from Aiptasia larvae infected with Microchlopopsis gaditana

value: aposymbiotic


title: APL042

source_name: Bone marrow mononuclear cells, APL patients


title: APL044

value: Female


title: Mg-Apo Rep2

description: Exaiptasia pallida (Aiptasia)


title: control placenta 1 (ctrl1)

value: placental villi

value: postnatal day 0 / full term

value: healthy control

value: placenta SARS-CoV-2 negative


title: APL041

value: acute promyelocytic leukemia

value: Male


title: APL043


title: M47_rep1

source_name: HEC-1-B cells

value: endometrium

tag: disease

value: adenocarcinoma

value: HS5-1 NRSE -/- monocolon


title: 201516260019_R03C01_Nonsmoker

source_name: nucleus accumbens

tag: current smoking status

value: control

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: 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)

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: M36_rep1

tag: cell line

tag: cell type

value: kidney

tag: age

value: fetus

tag: genotype/variation


title: M46_rep2

tag: disease


title: M47_rep2


title: APL040

tag: tissue

value: Bone Marrow

tag: disease state

tag: gender


title: symsym rep5

description:
Sample 15
Aiptasia
processed data file: TMM_all_replicates.xlsx

data_processing:
Paired-end reads were mapped to the Aiptasia genome version GCF_001417965.1 using HISAT2 version 2.1.0 at default settings, except -X 2000 --no-discordant --no-unal --no-mixed.
Host-derived transcripts were quantified in Trinity v2.5.1 using salmon v0.10.2 at default settings.
Principal component analysis of gene expression across all samples was conducted using the perl script PtR supplied with Trinity based on raw expression counts. Based on principal component analysis, for further analysis, samples apoapo rep1, 3, 4, and aposym rep2, 3, 4, 5 were used in further analysis as the condition "aposymbiotic cells", and samples symsym rep1, 2, 3, and 4 were used as condition "symbiotic cells".
Differentially expressed genes between clustered symbiotic and aposymbiotic samples were detected using DEseq2 (log2-fold change > 2; false-discovery-rate < 0.01) from raw read counts.
Genome_build: GCF_001417965.1
Supplementary_files_format_and_content: TMM_all_replicates.xlsx file contains normalized TMM values for each gene for each replicate.

source_name: symbiotic cells from symbiotic Aiptasia larvae

growth_protocol: Aiptasia larvae were maintained at ~300 larvae per ml in glass beakers in 0.22 µm filter-sterilized artificial sea water (FASW) at 26ºC and exposed to a 12L:12D cycle. B. minutum were grown in cell culture flasks in 0.22 µm filter-sterilized 1X Daigo’s IMK medium (398-01333, Nihon Pharmaceutical Co. Ltd., Tokyo, Japan) on a 12h light:12h dark (12L:12D) cycle under 20–25 µmol m−2 s−1 of photosynthetically active radiation (PAR) at 26 °C.

treatment_protocol: Following washing in calcium and magnesium-free artificial sea water (FMF-SW), ectodermal tissue was removed in 0.5 % Pronase and 1% sodium thio glycolate in CMF-SW. The endodermal tissue was macerated and the respective cells (symbiotic or aposymbiotic) were collected using a microcapillary needle.

tag: strain

value: CC7 x F003

value: endoderm

tag: symbiotic state of larvae

value: symbiotic

tag: symbiotic state of isolated cells

tag: age of larvae at start of infection

tag: duration of infection

tag: age at time of sampling

tag: number of cells per replicate


title: HEC_wt_rep2

value: wild type


title: APL039

value: Female


title: symsym rep4

description:
Sample 14
Aiptasia
processed data file: TMM_all_replicates.xlsx


title: APL038

value: acute promyelocytic leukemia