title: N-DP

city: hong kong

first: wenwei

last: tu

address: L7-55, lab block, 21 sassoon road.

department: Paediatrics & Adolescent Medicine

country: Hong Kong

institute: University of Hong Kong

data_processing: All the downstream analyses were based on the good-quality clean reads and mapped to mouse genome (ftp://ftp.ensembl.org/pub/release-81/gtf/mus_musculus/) by TopHat v2.0.9 and Cufflinks v2.1.1.

source_name: NKp46+NKG2A+ NK cells

extract_protocol:
Total RNA of distinct NK subsets was isolated by Qiagen RNA isolation kit and treated with RNase-free DNase I (New England Biolabs, MA, USA), to remove contaminating genomic DNA.
The cDNAs are then fragmented by nebulization and the standard Illumina protocol is followed thereafter, to create the mRNA-seq library.
Clean reads were obtained by removing reads containing adapter or poly-N and low-quality reads.

treatment_protocol: 4-5 weeks old C57BL/6N mice were treated with sub-lethal dose of PR8 virus (25μl, 10^3.5TCID50), i.n. 1-2 months later, completely recovered mice were sacrificed and spleen NKp46+NKG2A+ NK cell subsets were purified by magnetic beads isolation kit followed with flow cytometry sorting

value: spleen

tag: cell type

value: primary cells

tag: mouse strain


title: 200397540086_R05C02: genomic DNA from whole Blood

status: Public on Dec 31 2020

type: genomic

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

country: United Kingdom

institute: University of Exeter

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) protocol with the exception that 7ul of bisulfite treated material was input into the whole genome amplicifaction reaction instead of 4ul.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing: Data was imported using the R package methylumi methylumIDAT function. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions.

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood - EDTA tube

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit  (Zymo Research) according to the manufacturer’s standard protocol.

extract_protocol:
DNA from a Case extracted using Gentra Autopure method
Genomic DNA was extracted from frozen  blood samples using either Gentra Autopure or Phenol-Chloroform method.

tag: Sex

value: F

value: Schizophrenia

tag: status

value: Case

tag: age


title: 200397540086_R04C02: genomic DNA from whole Blood


title: L-DP

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue


title: RNAseq_34384

city: Boston

first: Peter

last: Castaldi

state: Massachusetts

address: 181 Longwood Ave

country: USA

institute: Brigham and Women's Hospital

description:
gene_TMM_counts.csv
exon_TMM_counts.csv
isoform_TMM_counts.csv

data_processing:
alignment: STAR, 2-pass
gene quantification: Salmon v0.12.0 and tximport
exon quantification: Rsubread v1.32.2
isoform quantification: Salmon v0.12.0
Genome_build: HG38 (GTF: Ensembl Homo_sapiens.GRCh38.94.gtf.gz)
Supplementary_files_format_and_content: count matrices

source_name: blood

extract_protocol:
Total RNA was extracted from PAXgene TM Blood RNA tubes using the Qiagen PreAnalytiX PAXgene Blood miRNA Kit (Qiagen, Valencia, CA).
Globin reduction and cDNA library preparation for total RNA was performed with the Illumina TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina, Inc., San Diego, CA).

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: M-DP

tag: cell type


title: TC6: Treatment HT29 rep2

city: Bangkok

first: Nakarin

last: Kitkumthorn

address: Yothee road

department: Oral Biology

country: Thailand

institute: Mahidol University

data_processing:
The quality of the raw sequencing reads were assessed with the FastQC v.0.11.2 software. The raw sequencing reads were subjected to trimming process with Trimmomatic v.0.32 software. The surviving paired-end reads were aligned to the Homo sapiens reference genome (Ensembl GRCh38 genome) with HISAT2 v.2.1.0 software. The alignment files were analyzed individually with the StringTie version 1.3.3b software to detect and quantify previously known transcripts. Invidual annotation files generated from transcript assembly process were merged together parsimoniously using StringTie version 1.3.3b. With the merged annotation file.
The expression unit calculated is FPKM, Fragments Per Kilobase Million. Besides, differential expression (DE) analysis was performed according to the given comparison groups . The expression fold change between each comparison group were calculated and log-transformed. Multiple output files were generated by DESeq2 version 1.16.1 and the detail files information are described in the table of result files below. Significant DE genes or transcripts (p-value < 0.05) were extracted for each comparison groups and cancer type.
Genome_build: HG19
Supplementary_files_format_and_content: ID, Gene_id, FPKM of each sample, fold change and P-value of each gene

source_name: RCF3 treated with HT29

growth_protocol: The colon cancer cell lines were grown with DMEM medium (Gibco BRL, USA) supplemented with 10% FBS at 37 ºc 5 % CO2 in culture flask. The cells were harvested at 80% confluence by using 0.05% Trypsin (with 0.5 mM EDTA) and washed by using phosphate buffer saline (PBS). All of this were used for maintaining cells.

extract_protocol:
PBMCs were collected from Transwell culture six well plates and RNA was harvested using Trizol reagent.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®). The poly(A) mRNA isolation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified (by AxyPrep Mag PCR Clean-up (Axygen)) double-stranded cDNA was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer ( Agilent Technologies, Palo Alto, CA, USA ) , and quantified by Qubit 2.0 Fluorometer ( Invitrogen, Carlsbad, CA, USA ).

treatment_protocol: Indirect or co-culture colon cancer cell lines with PBMCs from healthy were performed in Transwell culture six well plates (Costar, France). The colon cancer cell lines were seeded into plate (106 cells) with DMEM in experiment wells but not in control wells and then incubated overnight at 37 ºc 5 % CO2. The PBMCs from healthy were plated on permanent membrane culture of Transwell (2 × 106 cells) and incubated for 4 hours at 37 ºc 5 % CO2.

value: PBMC

tag: treatment

value: co-cultured with cell line HT29

tag: gender

value: Female


title: 200397540086_R02C02: genomic DNA from whole Blood

source_name: Blood - buffy coat

extract_protocol:
DNA from a Control extracted using Gentra Autopure method
Genomic DNA was extracted from frozen  blood samples using either Gentra Autopure or Phenol-Chloroform method.

tag: Sex

value: M

value: Control

tag: status


title: RNAseq_68876

tag: age


title: RNAseq_51164

tag: batch


title: H-DP

tag: tissue

tag: mouse strain


title: TC2: Treatment SW480 rep2

source_name: RCM2 treated with SW480

value: co-cultured with cell line SW480

value: Male


title: TC3: Treatment SW480 rep3

source_name: RCM3 treated with SW480


title: 200397540086_R01C02: genomic DNA from whole Blood


title: 200397540086_R06C01: genomic DNA from whole Blood

value: Schizoaffective Disorder


title: TC4: Treatment HT29 rep1

source_name: RCF1 treated with HT29


title: RNAseq_50428

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)


title: TC1: Treatment SW480 rep1

source_name: RCM1 treated with SW480


title: RCM3: Control Male rep3

source_name: Male PBMC


title: LNCAP_ENZ_2

city: Cleveland

first: Sanjay

last: Gupta

state: Ohio

address: 10900 Euclid Avenue

department: Department of Urology

institute: Case Western Reserve University

description:
Single -end sequence reads
LNCaP_Enzudata_text

data_processing:
Illumina HiSeq 1000 reads were trimmed and clipped for quality control in Trimmomatic v0.27.
Read quality was checked for each sample using FastQC v0.10.1.
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm10 reference genome and the GENCODE transcript annotation vM10
Supplementary_files_format_and_content: FastaQ files were generated

source_name: Prostate Cancer cells

growth_protocol: The LNCaP parent cell lines and LNCaP-ENZU (resistance) cell lines were cultured in RPMI-1640 media, contained 10%FBS. The cell lines were maintained in a 5% CO2 atmosphere at 37 °C.

extract_protocol:
Total RNA was extracted from LNCaP parental and LNCaP-ENZU (resistance) cells treated with enzalutamide (10uM), using RNA RNeasy kit (Qiagen).
1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.
The quality of total RNA integrity (RIN) was assessed using an RNA 6000 nanochip (Agilent technologies, Lexington, MA) on a Bioanalyzer 2100 (Agilent Technologies). Libraries were prepared using the Illumina TruSeq Stranded Total RNA sample preparation kit according to the manufacturer’s protocol. 50 bp single-end sequencing was performed on pooled libraries using an Illumina HiSeq 2500 platform. Sequencing reads generated were assessed for quality using FastQC. The library preps and sequencing were performed in the Genomics Core Facility at Case Western Reserve University. Differential expression was determined using Cufflinks v2.2.1. Differentially expressed genes (DEGs) were identified using a multiple testing corrected q-value < 0.05.

treatment_protocol: LNCaP  cells were recurrently exposed to increasing concentrations of enzalutamide (1-20μM) by passage in complete cell culture medium containing enzalutamide. In each concentration of enzalutamide, the cells were grown in RPMI 1640 (GE Healthcare) for a week allowing them to acclimatize and propagate for a minimum of six months. The resistant cells generated from 20 µM enzalutamide were maintained in media containing 5 µM enzalutamide, referred to as LNCaP enzalutamide resistant cells.

value: AR-sensitive human prostate adenocarcinoma cells

tag: passages

tag: sample type

value: Metastatic

tag: cell

value: non-neuroendocrine phenotype


title: CONT_LNT_MIR503HG_1

city: Edinburgh

first: Julie

last: Rodor

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

institute: UNIVERSITY OF EDINBURGH

data_processing:
Fastq files obtained from GENEWIZ
Gene quantification (read count and normalised expression value as FPKM) was obtained using RSEM 1.3.0 (options: -bowtie2 -forward-prob 0 -paired-end), based on GENCODE annotation version 26 (primary assembly).
Genome_build: GRCh38
Supplementary_files_format_and_content: txt file with FPKM

source_name: HUVEC

growth_protocol: Primary endothelial cells (HUVEC #C2519A, HPAEC #CC-2530) were purchased from Lonza (Basel) and maintained in endothelial cell growth medium (EGM-2 BulletKit™) (Lonza) supplemented with foetal bovine serum (FBS) (10%, Life Technologies) and Penicillin-Streptomycin (100U/ml) (Gibco).

extract_protocol:
Total RNA isolation was performed using the miRNEasy Mini Kit (Qiagen), according to the manufacturer’s instructions, including on column DNAse digestion.
polyA stranded libraries were prepared and sequenced in HiSeq Illumina at an average of 20M paired end reads (2x150bp) per sample by GENEWIZ.

treatment_protocol: To induce EndMT, Endothelial cells were plated at a density of 5x104 cells/well in collagen coated 6-well culture plates and were treated with TGF-β2 (10 ng/ml, PeproTech) and IL-1β (1ng/ml, PeproTech) in for 7 consecutive day in EGM-2 BulletKit™ supplemented with 10% FBS and refreshed every 24 hours. For MIR503HG overexpression, MIR503HG isoform 2 sequence was cloned into the LNT/SFFV-MCS plasmid. Lentiviral vectors were produced by triple transient transfection of HEK293T cells with a packaging plasmid (pCMV∆8.74), a plasmid encoding the envelope of vesicular stomatitis virus (VSVg) (pMDG) (Plasmid Factory) and pLNT/SFFV-MCS plasmid employing polyethylenimine (PEI; Sigma-Aldrich) as previously described (Ballantyne et al, 2016). Transduction was performed over a period of 24 hours on a 70% confluent HUVEC on collagen coated 6-well cell culture plate. A negative control (LNT_CT) or lncRNA containing lentivirus (LNT_MIR503HG) was added to each well at a multiplicity of infection (MOI) of 5. After 24 hours cells were used.

value: No


title: RCM2: Control Male rep2


title: 200397540086_R05C01: genomic DNA from whole Blood


title: LNCAP_ENZ_1


title: RNAseq_60783

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: 200397540086_R04C01: genomic DNA from whole Blood

tag: Sex

tag: status


title: RNAseq_15933

tag: batch

tag: age

tag: basophil percent


title: heart RNA

city: Guangzhou

first: Yan

last: Liao

state: Guangdong

address: the NO.2nd Zhongshan Road

department: Zhongshan School of Medicine

country: China

institute: Sun Yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, mapped to mm8 whole genome using CLC Genomics Workbench
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using CLC Genomics Workbench
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Mesenchymal stem cells

growth_protocol: Heart-derived Nestin+ cells were cultured in a 2:1 mixture of DMEM/F12 (1:1) and IMDM (Gibco, USA) containing 20 ng/ml EGF (Peprotech, USA), 20 ng/ml bFGF (Peprotech, USA), 1% N2 (Invitrogen, USA), 2% B27 (Invitrogen, USA), 4 ng/ml Cardiotrophin-1 (CT-1; Peprotech, USA), 0.1 mM β-mercaptoethanol (Invitrogen, USA), 1% L-glutamine (Sigma Aldrich, USA) and 100 IU/ml penicillin/streptomycin (Invitrogen, USA). The cells were cultured at 37℃ under 5% CO2 and propagated every 3 days. Bone-marrow-derived Nestin+ cells were  cultured in growth medium as reported previously [Nature. 2010 Aug 12;466(7308):829-34.].

extract_protocol:
The RNA of cultured cells (Passage 10) were harvested using Trizol reagent, and 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: Heart


title: BM RNA

value: Bone marrow


title: 200397540086_R03C02: genomic DNA from whole Blood

extract_protocol:
DNA from a case extracted using Gentra Autopure method
Genomic DNA was extracted from frozen  blood samples using either Gentra Autopure or Phenol-Chloroform method.

value: case


title: 200397540086_R03C01: genomic DNA from whole Blood

value: F


title: RNAseq_99975

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)


title: RCF3: Control Female rep2

source_name: Female PBMC

tag: treatment

tag: gender


title: RNAseq_17976

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: 200397540086_R02C01: genomic DNA from whole Blood

value: Schizophrenia


title: RCF1: Control Female rep1

value: PBMC


title: RCM1: Control Male rep1


title: LNCAP_1

tag: cell type

tag: passages

tag: sample type

tag: cell


title: 200397540086_R01C01: genomic DNA from whole Blood

tag: Sex

tag: status


title: LNCAP_ENZ_0


title: RNAseq_46143

tag: batch

tag: age

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: Treatment HN4 rep2

data_processing:
The quality of the raw sequencing reads were assessed with the FastQC v.0.11.2 software. The raw sequencing reads were subjected to trimming process with Trimmomatic v.0.32 software. The surviving paired-end reads were aligned to the Homo sapiens reference genome (Ensembl GRCh38 genome) with HISAT2 v.2.1.0 software. The alignment files were analyzed individually with the StringTie version 1.3.3b software to detect and quantify previously known transcripts. Individual annotation files generated from transcript assembly process were merged together parsimoniously using StringTie version 1.3.3b. With the merged annotation file.
The expression unit calculated is FPKM, Fragments Per Kilobase Million. Besides, differential expression (DE) analysis was performed according to the given comparison groups . The expression fold change between each comparison group were calculated and log-transformed. Multiple output files were generated by DESeq2 version 1.16.1 and the detail files information are described in the table of result files below. Significant DE genes or transcripts (p-value < 0.05) were extracted for each comparison groups and cancer type.
Genome_build: HG19
Supplementary_files_format_and_content: ID, Gene_id, FPKM of each sample, fold change and P-value of each gene

source_name: RCF3 treated with HN4

growth_protocol: The Head and Neck cancer cell lines (HN cell lines) were grown with DMEM medium (Gibco BRL, USA) supplemented with 10% FBS at 37 ºc 5 % CO2 in culture flask. The cells were harvested at 80% confluence by using 0.05% Trypsin (with 0.5 mM EDTA) and washed by using phosphate buffer saline (PBS). All of this were used for maintaining cells.

treatment_protocol: Indirect or co-culture HN cell lines with PBMCs from healthy were performed in Transwell culture six well plates (Costar, France). The HN cell lines were seeded into plate (106 cells) with DMEM in experiment wells but not in control wells and then incubated overnight at 37 ºc 5 % CO2. The PBMCs from healthy were plated on permanent membrane culture of Transwell (2 × 106 cells) and incubated for 4 hours at 37 ºc 5 % CO2.

value: co-cultured with cell line HN4


title: LNCAP_0


title: 200397540049_R06C02: genomic DNA from whole Blood


title: Treatment HN4 rep1

source_name: RCF1 treated with HN4


title: RNAseq_10376

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: basophil percent


title: 200397540049_R05C02: genomic DNA from whole Blood


title: Treatment HN17 rep3

source_name: RCM3 treated with HN17

tag: treatment

value: co-cultured with cell line HN17


title: RNAseq_26158

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: 200397540049_R04C02: genomic DNA from whole Blood

value: M

value: Case


title: 200397540049_R03C02: genomic DNA from whole Blood


title: RNAseq_78849


title: Treatment HN17 rep1

source_name: RCM1 treated with HN17

tag: cell type


title: LNCAP_2

tag: passages

tag: sample type

tag: cell


title: 200397540049_R02C02: genomic DNA from whole Blood

source_name: Blood - EDTA tube

tag: Sex

tag: status


title: 200397540049_R01C02: genomic DNA from whole Blood

tag: age


title: RNAseq_22659

source_name: blood

tag: batch

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_40361

tag: current smoker

tag: eosinophil percent

tag: monocyte percent


title: RNAseq_58887

tag: pack years

tag: gender (1=male, 2=female)

tag: basophil percent


title: 200397540049_R06C01: genomic DNA from whole Blood

value: Control


title: 200397540049_R05C01: genomic DNA from whole Blood


title: RNAseq_02199

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: Control Female rep2

tag: cell type

tag: treatment


title: RNAseq_42185


title: Treatment HN17 rep2

source_name: RCM2 treated with HN17


title: RNAseq_16251


title: Control Female rep1


title: 200397540049_R04C01: genomic DNA from whole Blood

source_name: Blood - buffy coat


title: RNAseq_83344


title: 200397540049_R03C01: genomic DNA from whole Blood


title: Control Male rep3


title: RNAseq_03071


title: hir1_t8_3

city: Vienna

first: Sabrina

last: Jenull

address: Dr. Bohrgasse 9/2

country: Austria

institute: Max Perutz Labs

data_processing:
Quality control of raw reads with fastQC (AndrewsS, 2010)
Reads were trimmed via cutadapt with a quality score threshold of 30.
Reads were mapped onto the Assembly 22 of the haploid C. albicans genome using NextGenMap (Sedlazeck, Bioinfromatics, 2013) with only keeping aligned reads with a mapping quality higher than 30.
Optical read duplicates were removed using the Picard tool and ribosomal RNA reads were removed with BEDtools intersect.
Reads per gene ID were counted using htseq count (AndersS, Bioinformatics, 2014) using the current C.albicans annotation file (.gff; C_albicans_SC5314_version_A22-s07-m01-r88; http://www.candidagenome.org) and used for differential gene analysis with edgeR (RobinsonMD, Bioinformatics, 2010).
Genome_build: Assembly 22
Supplementary_files_format_and_content: tab delimited .txt files containing the output of the htseq analysis (read counts) and Excel table (.xlsx) of the edgeR analysis result.

organism: Candida albicans

source_name: fungal cells

growth_protocol: Cells were either grown at YPD for approx. 16 hours at 30 °C with constant shaking (200 rpm) or washed 2 times with dH2O after overnight growth in YPD, re-inoculated in yeast carbon base (YCB) medium supplemented with 0.1 % BSA to a final OD600 of 0.5 and grown further for 4 hours (t4) or 8 hours (t8) at 30 °C with constant shaking (200 rpm).

extract_protocol:
RNA was isolated using Trizol and glass bead lysis after which RNA was precipitated and DNase treated followed by a column purification step. The quality of DNase-treated RNA was analyzed on a Bioanalyzer RNA Nano Chip (Agilent).
Total DNase treated RNA was submitted to the Next Generation Sequencing Facilty from the Vienna Biocenter Core Facilities for mRNA library preparation (rRNA removal).

tag: growth

value: YCB-BSA grown 8 hours

tag: strain background

tag: genotype

value: homozygous deletion of HIR1


title: 200397540049_R02C01: genomic DNA from whole Blood

tag: Sex

tag: status

tag: age


title: Control Male rep2


title: RNAseq_11008

tag: batch

tag: neutrophil percent

tag: lymphocyte percent


title: hir1_t8_2


title: Donor16_06h_StimVcl [3999545109_L]

type: RNA

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

hyb_protocol: 50 ng of the obtained biotinylated cRNA samples was hybridized onto the Illumina HumanHT-12 v4 as per manufacturer's instructions.

scan_protocol: The samples were scanned using the Illumina iScan array scanner. There were no deviations from the Illumina protocol.

data_processing: Data were processed using R/Bioconductor (the lumi package), Raw data were transformed using a Variance Stabilizing Transformation, and normalized with the robust spline normalization algorithm. Probes were selected which fulfilled the criteria of Illumina probe detection p-value of <0.01.

label: biotin

source_name: Primary keratinocytes, stimulated, vehicle, 6hrs

label_protocol: The Illumina TotalPrep-96 RNA Amplification Kit was used to generate Biotin labeled (biotin-16-UTP), amplified cRNA starting from 200ng total RNA.

growth_protocol: Normal human epidermal keratinocytes were extracted from foreskin tissue and cultured in Epilife keratinocyte media (Life Technologies, Paisley, UK) supplemented with human keratinocyte growth supplement (Life Technologies, Paisley, UK) and penicillin, streptomycin amphotericin B (Lonza Biologics, Switzerland).

extract_protocol: Total RNA isolated using the Machery Nagel Nucleospin kit following the manufacturer’s protocol, RNA integrity was checked using Agilent Bioanalyser.

treatment_protocol: Keratinocytes were pre-incubated in the presence or absence of I-BET151 (1µM) (GlaxoSmithKline, Stevenage, UK) and/or DMSO (I-BET151 vehicle - 1:1200) for 1h, prior to stimulation with TNF⍺ (10ng/ml) + IL-17A (100ng/ml) (TNF⍺ + IL-17) (Immunotools, Friesoythe, Germany), unless indicated.

tag: donor

value: Primary keratinocytes

tag: stimulation

tag: bet inhibition

value: DMSO

tag: treatment group

value: StimVcl

tag: timepoint


title: Donor17_24h_StimVcl [3999545109_I]

source_name: Primary keratinocytes, stimulated, vehicle, 24hrs


title: Donor28_24h_StimVcl [3999545109_K]


title: Donor15_24h_StimVcl [3999545109_G]


title: Donor06_06h_StimVcl [3999545109_D]


title: Donor21_24h_StimOnly [3999545109_E]

source_name: Primary keratinocytes, stimulated, none, 24hrs

value: StimOnly


title: 200397540049_R01C01: genomic DNA from whole Blood


title: Donor18_24h_StimOnly [3999545109_J]


title: Donor10_24h_Unstim [3999545109_F]

source_name: Primary keratinocytes, none, none, 24hrs

value: Unstim


title: RNAseq_43578

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: hir1_t8_1

tag: growth

tag: strain background

tag: genotype


title: 200397540051_R06C02: genomic DNA from whole Blood

tag: Sex

tag: status

tag: age


title: Control Male rep1

source_name: Male PBMC

tag: cell type

tag: treatment


title: RNAseq_83644

tag: batch

tag: neutrophil percent

tag: lymphocyte percent


title: 200397540051_R05C02: genomic DNA from whole Blood


title: 200397540051_R04C02: genomic DNA from whole Blood


title: Donor18_24h_StimVcl [3999545109_C]

tag: donor

tag: stimulation

tag: bet inhibition

tag: treatment group

tag: timepoint


title: wt_t8_3

value: wild type


title: Donor17_06h_StimVcl [3999545109_B]


title: wt_t8_2


title: RNAseq_14993

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: wt_t8_1

tag: growth

tag: strain background

tag: genotype


title: 200397540051_R03C02: genomic DNA from whole Blood

tag: Sex

tag: status

tag: age


title: RNAseq_07942

tag: batch

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_02972

tag: current smoker


title: RNAseq_67846

tag: pack years


title: hir1_t4_3

value: YCB-BSA grown 4 hours


title: 200397540051_R02C02: genomic DNA from whole Blood


title: Donor20_06h_StimOnly [3999545085_K]

source_name: Primary keratinocytes, stimulated, none, 6hrs

tag: donor

tag: cell type

tag: stimulation

tag: bet inhibition

tag: treatment group

tag: timepoint


title: hir1_t4_2

tag: growth


title: Donor16_24h_Unstim [3999545109_A]


title: 200397540051_R01C02: genomic DNA from whole Blood


title: RNAseq_17208

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: RNAseq_77445

tag: batch

tag: age

tag: neutrophil percent


title: Donor21_06h_StimVcl [3999545085_L]


title: hir1_t4_1

tag: strain background

tag: genotype


title: 200397540051_R06C01: genomic DNA from whole Blood

tag: Sex

tag: status


title: wt_t4_3


title: RNAseq_27922

tag: current smoker

tag: pack years

tag: lymphocyte percent


title: 200397540051_R05C01: genomic DNA from whole Blood


title: 200397540051_R04C01: genomic DNA from whole Blood


title: RNAseq_08449


title: Donor10_24h_StimOnly [3999545085_I]

tag: donor

tag: cell type

tag: stimulation

tag: bet inhibition

tag: treatment group

tag: timepoint


title: wt_t4_2

tag: growth


title: wt_t4_1


title: 200397540051_R03C01: genomic DNA from whole Blood

value: F


title: RNAseq_68101

tag: batch

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: hir1_t0_3

value: YPD grown overnight

tag: strain background

tag: genotype


title: Donor21_06h_StimOnly [3999545085_J]


title: RNAseq_32654

tag: current smoker

tag: pack years

tag: age

tag: neutrophil percent

tag: lymphocyte percent


title: 200397540051_R01C01: genomic DNA from whole Blood

tag: Sex

value: Schizophrenia

tag: status


title: Donor16_06h_StimCpd [3999545085_H]

source_name: Primary keratinocytes, stimulated, treated, 6hrs

tag: donor

tag: cell type

tag: stimulation

tag: bet inhibition

value: BET Inhibitor (I-BET151)

tag: treatment group

value: StimCpd

tag: timepoint


title: hir1_t0_2

tag: growth


title: 200397540051_R02C01: genomic DNA from whole Blood


title: Donor20_24h_Unstim [3999545085_F]


title: 200397540038_R06C02: genomic DNA from whole Blood

value: M


title: Donor18_24h_StimCpd [3999545085_E]

source_name: Primary keratinocytes, stimulated, treated, 24hrs


title: hir1_t0_1


title: wt_t0_3


title: RNAseq_16052

tag: batch

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: RNAseq_96082

tag: current smoker

tag: pack years

tag: age

tag: neutrophil percent

tag: lymphocyte percent


title: 200397540038_R05C02: genomic DNA from whole Blood

tag: Sex

tag: status


title: RNAseq_40763


title: wt_t0_2

tag: strain background

tag: genotype


title: RNAseq_53540


title: 200397540038_R04C02: genomic DNA from whole Blood

extract_protocol:
DNA from a Case extracted using Phenol-Chloroform method
Genomic DNA was extracted from frozen  blood samples using either Gentra Autopure or Phenol-Chloroform method.

value: Schizoaffective Disorder

value: Case


title: Donor28_06h_StimOnly [3999545085_D]

tag: donor

tag: cell type

tag: stimulation

tag: bet inhibition

tag: treatment group

tag: timepoint


title: wt_t0_1

tag: growth


title: RNAseq_45917

tag: batch

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: Donor26_06h_Unstim [3999545085_G]

source_name: Primary keratinocytes, none, none, 6hrs


title: 200397540038_R03C02: genomic DNA from whole Blood

tag: Sex

tag: status

tag: age


title: 200397540038_R02C02: genomic DNA from whole Blood

value: Control


title: Donor06_24h_Unstim [3999545109_H]

tag: donor


title: Donor21_06h_Unstim [3999545085_B]

tag: cell type


title: Donor19_24h_StimOnly [3999545085_C]

tag: stimulation


title: RNAseq_78195

tag: current smoker

tag: pack years

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_03145

tag: batch


title: Donor28_24h_StimOnly [3999545075_L]

tag: bet inhibition

tag: treatment group

tag: timepoint


title: Donor06_06h_Unstim [3999545075_K]


title: RNAseq_44232

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: eosinophil percent


title: 200397540038_R06C01: genomic DNA from whole Blood

tag: Sex

tag: status


title: Donor16_06h_Unstim [3999545075_J]

tag: donor


title: 200397540038_R05C01: genomic DNA from whole Blood

tag: age


title: RNAseq_48452

tag: monocyte percent

tag: basophil percent


title: 200397540038_R04C01: genomic DNA from whole Blood


title: Donor01_06h_Unstim [3999545085_A]

tag: cell type

tag: stimulation


title: RNAseq_89179

tag: current smoker

tag: pack years

tag: neutrophil percent

tag: lymphocyte percent


title: Donor26_24h_StimCpd [3999545075_I]

tag: bet inhibition

tag: treatment group

tag: timepoint


title: 200397540038_R03C01: genomic DNA from whole Blood


title: RNAseq_80830

tag: batch

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: 200397540038_R02C01: genomic DNA from whole Blood

tag: Sex

tag: status


title: RNAseq_02471

tag: age

tag: eosinophil percent

tag: monocyte percent


title: RNAseq_58258

tag: basophil percent


title: 200397540038_R01C02: genomic DNA from whole Blood


title: 200397540038_R01C01: genomic DNA from whole Blood


title: 200379120017_R05C02: genomic DNA from whole Blood


title: RNAseq_87570

tag: current smoker


title: RNAseq_20033

tag: pack years


title: 200379120017_R04C02: genomic DNA from whole Blood

value: case


title: RNAseq_54943

tag: neutrophil percent


title: 200379120017_R03C02: genomic DNA from whole Blood

extract_protocol:
DNA from a control extracted using Gentra Autopure method
Genomic DNA was extracted from frozen  blood samples using either Gentra Autopure or Phenol-Chloroform method.

value: control


title: RNAseq_06513

tag: lymphocyte percent


title: 200379120017_R02C02: genomic DNA from whole Blood


title: RNAseq_71390


title: Donor26_24h_Unstim [3999545075_G]

tag: donor

tag: cell type

value: Primary keratinocytes

tag: stimulation

tag: bet inhibition


title: Donor19_06h_StimOnly [3999545075_D]

tag: treatment group

tag: timepoint


title: Donor10_24h_StimCpd [3999545075_F]


title: lmn_Y59C_cec4_b

city: Basel

first: Susan

last: Gasser

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
For each genotype the RNA-seq data from two biological replicate samples from the L1 stage were mapped to the C. elegans genome (ce10) using the R package QuasR v1.22.0 (www.bioconductor.org/packages/2.12/bioc/html/QuasR.html). QuasR includes the short read aligner bowtie using the parameters "-m 1 --best --strata --phred33-quals" to consider only uniquely mapping reads (command: "proj <-qAlign("samples.txt","BSgenome. Celegans.UCSC.ce10")") and subsequently extract count tables of reads mapping within exon gene annotation from WormBase (WS220).
To normalize for sequencing depth, each sample was divided by the total number of reads and multiplied by the average library size. Transformation into log2 space was performed after the addition of a pseudocount of 8 in order to minimize large changes in expression caused by low count numbers. The various count tables used throughout this study were normalized separately.
The EdgeR package v 3.24.0 was used to determine fold changes (Fc) and false discovery rates (FDR) of differential transcript abundances.
Genome_build: ce10

organism: Caenorhabditis elegans

source_name: L1 larval stage sorted for non green (no balancer)

growth_protocol: Worms were expanded on 15cm peptone rich plates with OP50. Synchronized L1 larvae were obtained by hyopchlorite treatment of gravid adults to recover eggs. Eggs were left to hatch 16h at room temperature in M9 buffer and then re-feed with OP50 for 2.5 hours. Before RNA extraction, worms were washed 3x in M9 and re-suspended in 100μl of M9, 400μl of Trizol® (Ambion) and snap-frozen in liquid nitrogen.

extract_protocol:
After 3x in M9, L1 worms were re-suspended in 100μl of M9, 400μl of Trizol® (Ambion) and snap-frozen in liquid nitrogen. Extraction of RNA used 4 freeze-thaw cycles from liquid nitrogen to a 42 °C heat bath, followed by the addition of 200 μl of Trizol® to each sample. Vigorous vortexing at RT in 5 cycles (30 sec vortex, 30 sec on ice), was followed by 5 min at RT. RNA extraction was with 140 μl chloroform, vigorous shaking for 15 sec, and 2 min. The samples were centrifuged at 12000 rcf at 4 °C, and the aqueous phases were transferred to fresh tubes. An equal volume of 70 % EtOH was added slowly and the homogeneous mixture was transferred to a Qiagen RNeasy spin column (RNeasy kit, QIAGEN 74104).
Library preparation for the L1 samples was performed with the TrueSeq Total RNA preparation kit, stranded (Illumina).  The quality of the resulting libraries was assessed with an Agilent Bioanalyzer and concentrations were measured with a Qubit fluorometer prior to pooling. 50 bp single-end sequencing was done on an Illumina HiSeq 2500.

tag: strain

tag: genotype


title: 200379120017_R01C02: genomic DNA from whole Blood

tag: Sex

tag: status


title: lmn_Y59C_cec4_a


title: Donor16_06h_StimOnly [3999545075_E]


title: Donor20_06h_StimCpd [3999545075_H]


title: lmn_Y59C_b


title: RNAseq_02843

tag: batch

tag: age

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: eosinophil percent


title: Donor21_06h_StimCpd [3999545075_A]


title: 200379120017_R06C02: genomic DNA from whole Blood


title: Donor06_24h_StimVcl [3999545075_C]

value: DMSO

value: StimVcl


title: Donor01_06h_StimCpd [3999545060_K]


title: Donor19_24h_StimVcl [3999545060_I]


title: 200379120017_R06C01: genomic DNA from whole Blood


title: Donor19_24h_StimCpd [3999545060_L]


title: RNAseq_83681

tag: current smoker

tag: pack years

tag: neutrophil percent

tag: lymphocyte percent

tag: monocyte percent

tag: basophil percent


title: lmn_Y59C_a


title: Donor26_24h_StimOnly [3999545075_B]

tag: donor

tag: cell type

tag: stimulation

tag: bet inhibition

tag: treatment group

value: StimOnly

tag: timepoint


title: RNAseq_16965

tag: batch

tag: age


title: cec4_b

tag: strain

tag: genotype


title: 200379120017_R04C01: genomic DNA from whole Blood

tag: Sex

tag: status


title: Donor15_06h_Unstim [3999545060_G]

value: Unstim


title: RNAseq_29638

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: eosinophil percent


title: RNAseq_13772

tag: neutrophil percent

tag: lymphocyte percent

tag: monocyte percent

tag: basophil percent


title: cec4_a


title: 200379120017_R03C01: genomic DNA from whole Blood


title: 200379120017_R02C01: genomic DNA from whole Blood


title: RNAseq_72962


title: lmn_WT_a

value: wild-type, Bristol


title: 200379120017_R05C01: genomic DNA from whole Blood

value: F


title: 200379120017_R01C01: genomic DNA from whole Blood


title: RNAseq_24709


title: 200379120030_R06C02: genomic DNA from whole Blood


title: 200379120030_R05C02: genomic DNA from whole Blood


title: RNAseq_54523


title: VERO_P2V_3

city: ANN ARBOR

first: Shasha

last: Li

state: MI

address: 1109 Maiden Ln, ct apt 104

institute: University of Michigan

description: vero cell P2V treatment

data_processing:
The FastQC  tools and fastx_trimmer wrapped in fastx toolkit were used to trim low-quality bases (Q<20) and adapter for raw sequences. Cleaned RNA-seq reads were mapped to the reference chlorocebus sabaeus genome ChlSab1.1 (GCA_000409795.2) by HISAT2 (v2.1.0)[14]. Duplicated reads for pair-end data were removed by SAMtools (v1.5)[15]. Counts for each gene were obtained by using HTseq. DESeq2 were used to identify differentially expressed genes between experimental groups [16]. False Discovery Rate (FDR q-value) was calculated by adjusting P-values with the Benjamini-Hochberg method. Genes with FDR q-value < 0.05 and |Log2 (Fold change)| > 1 were considered as differential expressed genes.
Genome_build: chlorocebus sabaeus genome ChlSab1.1 (GCA_000409795.2)
Supplementary_files_format_and_content: .txt, counts

organism: Chlorocebus sabaeus

source_name: vero cell P2V treatment

growth_protocol: Vero E6 cells (1.5×107 cells/flask) were plated in T75 culture flasks for 24h.

extract_protocol:
Cells were harvested and mRNA was isolated by using TRIzon (Invitrogen).
The libraries were constructed by using the NEBNext Ultra™ RNA Library Prep Kit for Illumina (NEB) standard protocols.

treatment_protocol: Cells were treated with GX_P2V (2019-nCoVr at MOI = 0.01), CEP (5 uM), or CEP and virus, and then cultured for another 72h.

tag: treatment

value: vero cell P2V treatment

tag: cell line

value: Vero E6


title: 200379120030_R04C02: genomic DNA from whole Blood

value: Schizophrenia

tag: age


title: Donor01_06h_StimOnly [3999545060_E]

tag: donor

tag: cell type

tag: stimulation

tag: bet inhibition

tag: treatment group

tag: timepoint


title: lmn_WT_b

tag: strain

tag: genotype


title: VERO_P2V_2

description: vero cell P2V treatment


title: Donor21_24h_StimVcl [3999545060_F]


title: VERO_P2V_1

description: vero cell P2V treatment


title: Donor16_24h_StimOnly [3999545060_H]


title: Donor17_24h_StimCpd [3999545060_D]

value: BET Inhibitor (I-BET151)

value: StimCpd


title: Donor17_06h_StimCpd [3999545060_B]


title: VERO_CEP_P2V_2

description: vero cell CEP treatment first, then P2V treatment


title: RNAseq_08348

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: RNAseq_01685

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: 200379120030_R02C02: genomic DNA from whole Blood

tag: Sex

value: M

tag: status

tag: age


title: RNAseq_04646


title: Donor18_06h_Unstim [3999545060_A]

tag: donor

tag: cell type

tag: stimulation

tag: bet inhibition

tag: treatment group

tag: timepoint


title: VERO_CEP_P2V_1

source_name: vero cell CEP treatment first, then P2V treatment

tag: treatment

tag: cell line


title: RNAseq_89190

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: RNAseq_99950

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: VERO_CEP_P2V_3

value: vero cell CEP treatment first, then P2V treatment


title: Donor21_24h_Unstim [3999545060_C]

tag: donor

tag: cell type

tag: stimulation


title: Donor19_24h_Unstim [3999545044_L]

tag: bet inhibition

tag: treatment group

tag: timepoint


title: VERO_CEP_3

description: vero cell CEP treatment

source_name: vero cell CEP treatment

tag: treatment

value: vero cell CEP treatment

tag: cell line


title: Donor20_24h_StimCpd [3999545044_K]


title: 200379120030_R01C02: genomic DNA from whole Blood

source_name: Blood - EDTA tube

tag: Sex

tag: status

value: case

tag: age


title: 200379120030_R03C02: genomic DNA from whole Blood

value: Control


title: RNAseq_99049

source_name: blood

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: 200379120030_R06C01: genomic DNA from whole Blood

source_name: Blood - buffy coat


title: 200379120030_R05C01: genomic DNA from whole Blood

value: Case


title: Donor20_24h_StimVcl [3999545044_J]

tag: donor

value: Primary keratinocytes

value: DMSO


title: VERO_CEP_1

description: vero cell CEP treatment


title: RNAseq_68599

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: Donor01_24h_StimOnly [3999545044_I]

tag: cell type

tag: stimulation

tag: bet inhibition

tag: treatment group

value: StimOnly

tag: timepoint


title: VERO_CEP_2

description: vero cell CEP treatment

tag: treatment

tag: cell line


title: 200379120030_R03C01: genomic DNA from whole Blood

tag: Sex

tag: status

tag: age


title: 200379120030_R04C01: genomic DNA from whole Blood


title: VERO_2

description: vero cell no treatment

source_name: vero cell no treatment

value: vero cell no treatment


title: 200379120030_R02C01: genomic DNA from whole Blood


title: RNAseq_78485

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: RNAseq_42126

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: 200379120030_R01C01: genomic DNA from whole Blood


title: RNAseq_39317


title: Donor06_06h_StimCpd [3999545044_G]

tag: donor

tag: cell type

tag: stimulation

tag: bet inhibition

tag: treatment group

tag: timepoint


title: VERO_1

description: vero cell no treatment

tag: treatment

tag: cell line


title: Donor28_24h_StimCpd [3999545044_E]


title: Donor10_06h_StimCpd [3999545044_F]


title: Donor10_06h_StimOnly [3999545044_H]


title: RNAseq_51501

tag: batch

tag: current smoker

tag: pack years

tag: age


title: Sample_MP-Bla98

city: Edmonton

first: Graham

last: Plastow

state: Alberta

address: 1400 College Plaza, 8215 - 112 Street

department: Agricultural, Food & Nutritional Science

country: Canada

institute: University of Alberta

data_processing:
Briefly, the raw reads with quality score < 15 were filtered, and then mapped to bovine genome (UMD3.1, https://bovinegenome.elsiklab.missouri.edu/downloads/UMD_3.1) using the Tophat2 software. The number of reads uniquely aligned to each gene was calculated using HTSeq-count.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Bos taurus

source_name: Blood

extract_protocol:
Total RNA was extracted from the PAXgene Blood RNA tube using PAXgene Blood miRNA Kit (QIAGEN Inc., Hilden, Germany) based on the manufacturer’s instructions. The Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA) and Nanodrop 2000 (Thermo Scientific, Wilmington, DE, USA) were applied to assess the quantity and quality of RNA, respectively
Only samples with RNA integrity value > 7.5 were used for library construction and RNA-Sequencing (totally 24 of 49 overlapping samples among entry, pulled, and close-out stages stages).
Total RNA was purified using poly-T oligo-attached magnetic beads and mRNA libraries were constructed using the TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, CA, USA).

tag: Stage

value: Pulled stage

tag: animal id

value: animal 24

tag: tissue

value: blood

tag: Sex

value: male


title: RNAseq_41132

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: Donor20_24h_StimOnly [3999545060_J]

tag: donor

tag: cell type

tag: stimulation

tag: bet inhibition

tag: treatment group

tag: timepoint


title: 200379120154_R05C02: genomic DNA from whole Blood

value: F

value: Schizophrenia

tag: status

tag: age


title: RNAseq_09989

tag: batch

tag: current smoker

tag: pack years


title: 200379120154_R06C02: genomic DNA from whole Blood

tag: Sex


title: RNAseq_01851

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent


title: Donor26_06h_StimOnly [3999545044_C]


title: VERO_3

description: vero cell no treatment

tag: treatment

tag: cell line

value: Vero E6


title: Sample_MP-Bla84

tag: Stage

tag: animal id

value: animal 23

tag: tissue


title: 200379120154_R04C02: genomic DNA from whole Blood

value: M


title: Sample_MP-Bla74

value: animal 22


title: Sample_MP-Bla72

value: animal 21


title: 200379120154_R03C02: genomic DNA from whole Blood


title: RNAseq_89886

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: Donor19_06h_StimCpd [3999545044_D]

tag: donor

tag: cell type

tag: stimulation

tag: bet inhibition

value: BET Inhibitor (I-BET151)

tag: treatment group

value: StimCpd

tag: timepoint


title: Sample_MP-Bla71

value: animal 20

tag: Sex


title: Donor17_06h_StimOnly [3999545044_B]

value: Primary keratinocytes


title: Donor01_24h_StimCpd [3999545044_A]


title: Donor15_24h_Unstim [3999545040_L]

value: Unstim


title: RNAseq_43554

tag: batch

tag: current smoker

tag: pack years

tag: age

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent


title: 200379120154_R02C02: genomic DNA from whole Blood

value: Control

tag: status


title: RNAseq_16162

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: Sample_MP-Bla70

tag: Stage

value: Pulled stage

tag: animal id

value: animal 19

tag: tissue


title: Sample_MP-Bla69

value: animal 18

value: blood

tag: Sex


title: 200379120154_R06C01: genomic DNA from whole Blood


title: RNAseq_50713

tag: batch


title: 200379120154_R01C02: genomic DNA from whole Blood


title: 200379120154_R05C01: genomic DNA from whole Blood


title: RNAseq_63099

tag: current smoker


title: Sample_MP-Bla67

value: animal 17

value: male


title: Sample_MP-Bla6

value: animal 16


title: 200379120154_R04C01: genomic DNA from whole Blood

value: Schizophrenia

value: Case


title: Sample_MP-Bla58

value: animal 15


title: RNAseq_50634

tag: pack years


title: RNAseq_69677

tag: age


title: RNAseq_28786

tag: gender (1=male, 2=female)


title: Sample_MP-Bla55

value: animal 14


title: 200379120154_R02C01: genomic DNA from whole Blood

value: M

value: Schizophreniform Disorder


title: Sample_MP-Bla48

value: animal 13


title: 200379120154_R01C01: genomic DNA from whole Blood

value: F


title: Sample_MP-Bla41

value: animal 12


title: RNAseq_04003

tag: race (1=white, 2=black)


title: 200379120112_R06C02: genomic DNA from whole Blood


title: RNAseq_03333

tag: fev1 % predicted


title: Sample_MP-Bla39

value: animal 11


title: 200379120112_R05C02: genomic DNA from whole Blood

value: Control


title: Donor28_24h_Unstim [3999545040_H]

tag: donor

tag: cell type

value: Primary keratinocytes

tag: stimulation

tag: bet inhibition

tag: treatment group

value: Unstim

tag: timepoint


title: Donor01_24h_StimVcl [3999545040_K]

source_name: Primary keratinocytes, stimulated, vehicle, 24hrs

value: DMSO

value: StimVcl


title: RNAseq_68624

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: Donor19_06h_Unstim [3999545040_E]


title: Donor18_24h_StimVcl [3999545040_J]


title: Donor16_24h_StimVcl [3999545040_D]


title: Donor26_24h_StimVcl [3999545040_G]


title: Sample_MP-Bla30

tag: Stage

value: Pulled stage

tag: animal id

value: animal 10

tag: tissue

value: blood

tag: Sex

value: male


title: Donor06_24h_StimOnly [3999545040_C]

source_name: Primary keratinocytes, stimulated, none, 24hrs

value: StimOnly


title: Donor01_24h_Unstim [3999545040_I]

source_name: Primary keratinocytes, none, none, 24hrs


title: 200379120154_R03C01: genomic DNA from whole Blood

value: Schizophrenia

tag: status

value: Case

tag: age


title: Donor16_24h_StimCpd [3999545040_F]

tag: donor

value: BET Inhibitor (I-BET151)

value: StimCpd


title: RNAseq_41077

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: Sample_MP-Bla26

value: animal 9


title: 200379120112_R03C02: genomic DNA from whole Blood

value: F


title: RNAseq_43213

tag: neutrophil percent

tag: lymphocyte percent


title: Sample_MP-Bla17

value: animal 8


title: 200379120112_R02C02: genomic DNA from whole Blood

value: M

value: Control


title: RNAseq_44265

tag: eosinophil percent

tag: monocyte percent


title: Donor28_06h_Unstim [3999545040_A]

tag: cell type

value: Primary keratinocytes

tag: stimulation

tag: bet inhibition

tag: treatment group

value: Unstim

tag: timepoint


title: Donor17_24h_Unstim [3999545040_B]


title: Sample_MP-Bla147

tag: Stage

tag: animal id

value: animal 7

tag: tissue

tag: Sex


title: 200379120112_R04C02: genomic DNA from whole Blood

tag: status

tag: age


title: Donor21_24h_StimCmp [3999538083_L]

tag: donor


title: Donor19_06h_StimVcl [3999538083_J]

source_name: Primary keratinocytes, stimulated, vehicle, 6hrs

value: DMSO

value: StimVcl


title: 200379120112_R01C02: genomic DNA from whole Blood

description: Sample was excluded from the final analysis due to low quality

value: Schizophrenia (Galway CP)

value: case


title: RNAseq_99564

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: basophil percent


title: 200379120112_R06C01: Meth Control

source_name: Meth control

extract_protocol:
Fully methylated control sample
Genomic DNA was extracted from frozen  blood samples using either Gentra Autopure or Phenol-Chloroform method.


title: Sample_MP-Bla145

value: Pulled stage

value: animal 6

value: blood

value: male


title: RNAseq_44174

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: RNAseq_61499


title: RNAseq_91139


title: Donor06_24h_StimCmp [3999538083_I]

tag: cell type

tag: stimulation

tag: bet inhibition

value: BET Inhibitor (I-BET151)

tag: treatment group

value: StimCpd

tag: timepoint


title: 200379120112_R04C01: genomic DNA from whole Blood

tag: Sex

tag: status

tag: age


title: Sample_MP-Bla134

tag: Stage

tag: animal id

value: animal 4

tag: tissue


title: Donor10_06h_Unstim [3999538083_K]

tag: donor


title: Sample_MP-Bla144

value: animal 5


title: 200379120112_R03C01: genomic DNA from whole Blood

value: F

value: Schizophrenia

value: Case


title: 200379120112_R05C01: genomic DNA from whole Blood

value: Control


title: RNAseq_01245

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: basophil percent


title: Donor18_06h_StimCmp [3999538083_H]

source_name: Primary keratinocytes, stimulated, treated, 6hrs

tag: cell type

value: Primary keratinocytes

tag: stimulation

tag: bet inhibition


title: RNAseq_50102

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: 200379120112_R02C01: genomic DNA from whole Blood

tag: Sex

value: M

tag: status

tag: age


title: RNAseq_30823

tag: batch


title: 200379120112_R01C01: genomic DNA from whole Blood


title: Sample_MP-Bla10

tag: Stage

tag: animal id

value: animal 1

tag: tissue


title: RNAseq_23521

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: Sample_ME-Bla98

value: Entry stage

value: animal 24


title: 200379120023_R06C02: genomic DNA from whole Blood


title: 200379120023_R05C02: genomic DNA from whole Blood


title: Sample_ME-Bla72

value: animal 21


title: Sample_MP-Bla108

value: Pulled stage

value: animal 2


title: RNAseq_52228

tag: fev1 % predicted

tag: basophil percent


title: Sample_MP-Bla117

value: animal 3

value: blood

value: male


title: Donor10_24h_StimVcl [3999538083_F]

tag: donor

tag: cell type

tag: stimulation

tag: bet inhibition

value: DMSO

tag: treatment group

value: StimVcl

tag: timepoint


title: Sample_ME-Bla71

value: animal 20

tag: Sex


title: 200379120023_R03C02: genomic DNA from whole Blood

value: Schizophrenia

tag: status

tag: age


title: Donor17_24h_StimOnly [3999538083_G]

value: StimOnly


title: Donor18_06h_StimVcl [3999538083_E]


title: Donor15_06h_StimCmp [3999538083_D]

value: BET Inhibitor (I-BET151)

value: StimCpd


title: 200379120023_R02C02: genomic DNA from whole Blood

value: M

value: Case


title: RNAseq_02367

tag: batch

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: 200379120023_R01C02: genomic DNA from whole Blood

value: Control


title: Sample_ME-Bla70

tag: Stage

value: Entry stage

tag: animal id

value: animal 19

tag: tissue


title: Donor28_06h_StimCmp [3999538083_B]

tag: donor

value: Primary keratinocytes


title: Donor01_06h_StimVcl [3999538083_C]

tag: cell type


title: 200379120023_R04C02: genomic DNA from whole Blood

value: F

value: Schizoaffective Disorder


title: Sample_ME-Bla69

value: animal 18

value: blood


title: RNAseq_62657

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: basophil percent


title: Sample_ME-Bla84

value: animal 23

tag: Sex

value: male


title: Donor10_06h_StimVcl [3999538083_A]

tag: stimulation

tag: bet inhibition

value: DMSO

tag: treatment group

value: StimVcl

tag: timepoint


title: RNAseq_26780

tag: batch

tag: age

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: Donor20_06h_StimVcl [3999538079_K]

tag: donor

tag: cell type


title: RNAseq_74383

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)


title: 200379120023_R06C01: genomic DNA from whole Blood

tag: status


title: 200379120023_R05C01: genomic DNA from whole Blood

tag: Sex


title: RNAseq_13966

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: basophil percent


title: Sample_ME-Bla6

tag: Stage

tag: animal id

value: animal 16

tag: tissue


title: Donor20_06h_Unstim [3999538079_L]

tag: stimulation

tag: bet inhibition

tag: treatment group

value: Unstim

tag: timepoint


title: Sample_ME-Bla67

value: animal 17


title: Donor18_06h_StimOnly [3999538079_J]

source_name: Primary keratinocytes, stimulated, none, 6hrs

tag: donor

value: StimOnly


title: 200379120023_R04C01: genomic DNA from whole Blood

tag: age


title: RNAseq_53179

tag: batch

tag: current smoker

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: Sample_ME-Bla58

value: animal 15

tag: Sex


title: 200379120023_R03C01: genomic DNA from whole Blood

value: M

value: Control

tag: status


title: RNAseq_34378

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: basophil percent


title: RNAseq_22756


title: Sample_ME-Bla55

tag: Stage

value: Entry stage

tag: animal id

value: animal 14

tag: tissue


title: 200379120023_R02C01: genomic DNA from whole Blood

value: Schizophrenia

value: Case

tag: age


title: RNAseq_14318

tag: batch


title: 200379120023_R01C01: genomic DNA from whole Blood


title: Donor17_06h_Unstim [3999538079_H]

source_name: Primary keratinocytes, none, none, 6hrs

tag: donor

tag: cell type

value: Primary keratinocytes

tag: stimulation

tag: bet inhibition

tag: treatment group

tag: timepoint


title: Sample_ME-Bla48

value: animal 13

value: blood

tag: Sex


title: RNAseq_96985

tag: current smoker

tag: pack years

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: Donor26_06h_StimCmp [3999538079_E]

value: BET Inhibitor (I-BET151)

value: StimCpd


title: RNAseq_62102

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: basophil percent


title: Sample_ME-Bla41

tag: Stage

tag: animal id

value: animal 12

tag: tissue

value: male


title: Donor15_06h_StimOnly [3999538079_G]

tag: donor

tag: cell type

tag: stimulation

tag: bet inhibition


title: Donor28_06h_StimVcl [3999538079_I]

value: DMSO

tag: treatment group

value: StimVcl

tag: timepoint


title: Sample_ME-Bla39

value: animal 11

tag: Sex


title: Donor15_24h_StimOnly [3999538079_F]

value: StimOnly


title: 200379120008_R06C02: genomic DNA from whole Blood

value: M

tag: status

tag: age


title: RNAseq_42423

tag: batch

tag: current smoker

tag: pack years

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: 200379120008_R05C02: genomic DNA from whole Blood

value: Control


title: Sample_ME-Bla30

tag: Stage

value: Entry stage

tag: animal id

value: animal 10

tag: tissue


title: Sample_ME-Bla74

value: animal 22


title: RNAseq_19829

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: basophil percent


title: 200379120008_R04C02: genomic DNA from whole Blood

tag: Sex

value: Schizophrenia

value: Case


title: Donor15_06h_StimVcl [3999538079_D]

tag: donor

tag: cell type

value: Primary keratinocytes

tag: stimulation

tag: bet inhibition

tag: treatment group

tag: timepoint


title: Donor06_06h_StimOnly [3999538079_C]


title: Sample_ME-Bla26

value: animal 9

value: blood


title: Sample_ME-Bla17

value: animal 8


title: 200379120008_R03C02: genomic DNA from whole Blood

tag: status

tag: age


title: RNAseq_12225

tag: batch

tag: current smoker

tag: pack years

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: 200379120008_R02C02: genomic DNA from whole Blood


title: RNAseq_69351

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: basophil percent


title: Donor15_24h_StimCmp [3999538079_A]

source_name: Primary keratinocytes, stimulated, treated, 24hrs

tag: donor

tag: cell type

tag: stimulation

value: BET Inhibitor (I-BET151)

value: StimCpd


title: Donor26_06h_StimVcl [3999538079_B]

tag: bet inhibition

value: DMSO

tag: treatment group

tag: timepoint


title: Sample_ME-Bla147

tag: Stage

tag: animal id

value: animal 7

tag: tissue

tag: Sex

value: male


title: 200379120008_R01C02: genomic DNA from whole Blood

tag: status

tag: age


title: CD4 T cells, N172

city: Vancouver

first: Pascal

last: Lavoie

state: BRITISH COLUMBIA

address: 950 West 28th Avenue

institute: BC Children's Hospital

hyb_protocol: The RNA-loaded BeadChip was hybridized in the illumina Hybridization Oven for 18 hours at 58oC and followed by wash steps and Cy3-Streptavidin bind to analytical probes step.

scan_protocol: BeadChip information from the Illumina HiScan SQ was extracted for each chip using Illumina software.

data_processing: Data were analyzed using R. Data was preprocessed by quantile normalization and log2 transformation. Probes that were non-expressed (based on their detection p-values) were removed. For differential gene analyses, linear models were fit using limma. Probes with FDR <0.05 were considered differentially expressed.

label: Biotin

source_name: Neonate naïve CD4 T cells

label_protocol: The biotin-labeled cRNA was performed by illumina TotalPrep RNA Amplification kit.cRNA was quantified using NanoDrop 2000 sepectrophometer and the size distribution of cRNA was evaluated using Agilient 2100 Bioanalyzer.

growth_protocol: Naïve CD4 T cells (CD3/CD4+, CD25/CD45RO-, CCR7+) were Fluorescent Activated Cell Sorted (FACS)-isolated from peripheral or cord blood.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini Kit and cleaned & concentrated using Zymo Research RNA Clean & Concentrator-5 kit. RNA was quantified using NanoDrop™ 1000 spectrophotometer, and its integrity was determined using the Agilent 2100 Bioanalyzer.

tag: developmental stage

value: Neonate

value: cord blood

value: naïve CD4 T cells

tag: stimulation condition

value: unstimulated


title: RNAseq_25769

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: CD4 T cells, N173

tag: cell type


title: 200379120008_R06C01: genomic DNA from whole Blood

value: F

value: Control


title: Sample_ME-Bla145

tag: Stage

value: Entry stage

tag: animal id

value: animal 6


title: RNAseq_29552

tag: fev1 % predicted

tag: basophil percent


title: RNAseq_34211

tag: age


title: Sample_ME-Bla144

value: animal 5

tag: tissue

tag: Sex


title: 200379120008_R05C01: genomic DNA from whole Blood

value: M

tag: status


title: Sample_ME-Bla134

value: animal 4

value: blood


title: 200379120008_R04C01: genomic DNA from whole Blood

extract_protocol:
DNA from a Case extracted using Gentra Autopure method
Genomic DNA was extracted from frozen  blood samples using either Gentra Autopure or Phenol-Chloroform method.

value: Schizophrenia

value: Case


title: RNAseq_89556

extract_protocol:
Total RNA was extracted from PAXgene TM Blood RNA tubes using the Qiagen PreAnalytiX PAXgene Blood miRNA Kit (Qiagen, Valencia, CA).
Globin reduction and cDNA library preparation for total RNA was performed with the Illumina TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina, Inc., San Diego, CA).

tag: batch

tag: current smoker


title: Sample_ME-Bla117

value: animal 3


title: RNAseq_18296

tag: pack years

tag: gender (1=male, 2=female)


title: 200379120008_R03C01: genomic DNA from whole Blood


title: Sample_ME-Bla108

value: animal 2


title: RNAseq_81522

tag: race (1=white, 2=black)

tag: neutrophil percent


title: 200379120008_R02C01: genomic DNA from whole Blood


title: Sample_ME-Bla10

value: animal 1

value: male


title: RNAseq_74226

tag: lymphocyte percent

tag: eosinophil percent


title: 200379120008_R01C01: genomic DNA from whole Blood


title: Sample_MC-Bla98

value: Close out stage

value: animal 24


title: CD4 T cells, N171

tag: developmental stage

value: Neonate

value: cord blood

tag: cell type

value: naïve CD4 T cells

tag: stimulation condition

value: unstimulated


title: 200379120009_R06C02: genomic DNA from whole Blood

value: F

value: Control


title: Sample_MC-Bla72

tag: Stage

tag: animal id

value: animal 21


title: Sample_MC-Bla84

value: animal 23


title: RNAseq_43488

tag: age

tag: fev1 % predicted

tag: monocyte percent

tag: basophil percent


title: 200379120009_R05C02: genomic DNA from whole Blood

extract_protocol:
DNA from a case extracted using Phenol-Chloroform method
Genomic DNA was extracted from frozen  blood samples using either Gentra Autopure or Phenol-Chloroform method.

tag: Sex

value: M

tag: status

value: case


title: CD4 T cells, N165

tag: tissue


title: CD4 T cells, N166


title: CD4 T cells, N188


title: RNAseq_50361

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)


title: 200379120009_R03C02: genomic DNA from whole Blood

extract_protocol:
DNA from a Control extracted using Gentra Autopure method
Genomic DNA was extracted from frozen  blood samples using either Gentra Autopure or Phenol-Chloroform method.


title: CD4 T cells, N186


title: CD4 T cells, N185


title: CD4 T cells, N184


title: CD4 T cells, N187


title: 200379120009_R04C02: genomic DNA from whole Blood

value: Schizoaffective Disorder

value: Case


title: RNAseq_67325

tag: race (1=white, 2=black)

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent


title: RNAseq_64665


title: 200379120009_R02C02: genomic DNA from whole Blood

value: Schizophrenia


title: RNAseq_11605


title: Sample_MC-Bla74

tag: Stage

value: animal 22

value: blood


title: CD4 T cells, A300

source_name: adult naïve CD4 T cells

tag: developmental stage

value: adult

value: peripheral blood

tag: cell type

tag: stimulation condition


title: CD4 T cells, N169

value: Neonate


title: Sample_MC-Bla70

value: Close out stage

tag: animal id

value: animal 19

value: male


title: CD4 T cells, N174

value: cord blood

value: naïve CD4 T cells

value: unstimulated


title: 200379120009_R01C02: genomic DNA from whole Blood

tag: age


title: CD4 T cells, A299


title: Sample_MC-Bla71

value: animal 20

tag: Sex


title: Sample_MC-Bla69

value: animal 18


title: CD4 T cells, A294


title: RNAseq_92488

tag: fev1 % predicted

tag: monocyte percent

tag: basophil percent


title: 200379120009_R06C01: genomic DNA from whole Blood

value: F

value: Control

tag: status


title: 200379120009_R05C01: genomic DNA from whole Blood

value: Case


title: Sample_MC-Bla67

value: animal 17

tag: tissue


title: RNAseq_86912

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)


title: RNAseq_98104

tag: race (1=white, 2=black)

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent


title: 200379120009_R04C01: genomic DNA from whole Blood


title: Sample_MC-Bla6

tag: Stage

value: animal 16


title: RNAseq_80305


title: CD4 T cells, A287

tag: developmental stage

tag: cell type

tag: stimulation condition


title: CD4 T cells, A286


title: 200379120009_R03C01: genomic DNA from whole Blood

tag: Sex

tag: age


title: Sample_MC-Bla55

tag: animal id

value: animal 14

value: blood


title: RNAseq_17874

tag: fev1 % predicted

tag: monocyte percent

tag: basophil percent


title: RNAseq_19900

tag: batch

tag: current smoker


title: 200379120009_R01C01: genomic DNA from whole Blood

tag: status


title: Sample_MC-Bla48

value: animal 13

tag: tissue


title: Sample_MC-Bla41

value: animal 12


title: RNAseq_87437

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: neutrophil percent


title: 200379120066_R06C02: genomic DNA from whole Blood

value: M


title: RNAseq_38732

tag: lymphocyte percent

tag: eosinophil percent


title: 200379120066_R05C02: genomic DNA from whole Blood


title: Sample_MC-Bla39

tag: Stage

value: Close out stage

value: animal 11


title: RNAseq_78629


title: 200379120066_R04C02: genomic DNA from whole Blood

tag: Sex

value: Schizoaffective Disorder

value: case


title: RNAseq_91630

tag: age


title: Sample_MC-Bla30

tag: animal id

value: animal 10

value: male


title: 200379120066_R03C02: genomic DNA from whole Blood

value: Schizophrenia


title: RNAseq_91924

tag: fev1 % predicted


title: Sample_MC-Bla26

value: animal 9


title: CD4 T cells, A318

tag: developmental stage

value: adult

value: peripheral blood

tag: cell type

value: naïve CD4 T cells

tag: stimulation condition

value: unstimulated


title: CD4 T cells, A316


title: CD4 T cells, A298


title: CD4 T cells, A296


title: CD4 T cells, A314


title: RNAseq_17370

tag: batch

tag: current smoker

tag: monocyte percent

tag: basophil percent


title: 200379120009_R02C01: genomic DNA from whole Blood

tag: status

value: Case


title: Sample_MC-Bla147

value: animal 7

tag: tissue

value: blood


title: Sample_MC-Bla58

value: animal 15


title: 200379120066_R01C02: genomic DNA from whole Blood

value: M


title: RNAseq_76796

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: neutrophil percent


title: Sample_MC-Bla145

tag: Stage

value: Close out stage

value: animal 6

tag: Sex


title: CD4 T cells, A317


title: 200379120066_R06C01: genomic DNA from whole Blood

value: Control

tag: age


title: CD4 T cells, A319


title: Sample_MC-Bla144

tag: animal id

value: animal 5


title: 200379120066_R02C02: genomic DNA from whole Blood

value: F


title: 200379120066_R04C01: genomic DNA from whole Blood


title: 200379120066_R03C01: genomic DNA from whole Blood


title: Sample_MC-Bla17

value: animal 8

value: male


title: Sample_MC-Bla117

value: animal 3


title: RNAseq_83952

tag: fev1 % predicted

tag: lymphocyte percent

tag: eosinophil percent


title: RNAseq_68528

tag: batch


title: Sample_MC-Bla108

value: animal 2


title: RNAseq_36760

tag: current smoker


title: 200379120066_R02C01: genomic DNA from whole Blood

value: Schizophrenia


title: 200379120066_R01C01: genomic DNA from whole Blood


title: 200379120053_R06C02: genomic DNA from whole Blood


title: RNAseq_32815

tag: monocyte percent


title: RNAseq_58087

tag: basophil percent


title: 200379120066_R05C01: genomic DNA from whole Blood

tag: status


title: Sample_MC-Bla10

value: animal 1

tag: tissue


title: 200379120053_R05C02: genomic DNA from whole Blood


title: 200379120053_R04C02: genomic DNA from whole Blood


title: RNAseq_78279

tag: pack years


title: Sample_MC-Bla134

value: animal 4


title: RNAseq_21865

tag: gender (1=male, 2=female)


title: 200379120053_R02C02: genomic DNA from whole Blood


title: RNAseq_30827

tag: race (1=white, 2=black)


title: RNAseq_76111

tag: neutrophil percent


title: 200379120053_R06C01: genomic DNA from whole Blood

value: Schizophrenia (Galway PRCL SZ)

value: Case


title: RNAseq_26571


title: RNAseq_20959


title: RNAseq_90066


title: 200379120053_R05C01: genomic DNA from whole Blood


title: 200379120053_R04C01: genomic DNA from whole Blood


title: RNAseq_35523


title: 200379120053_R03C02: genomic DNA from whole Blood


title: RNAseq_56736


title: 200379120053_R03C01: genomic DNA from whole Blood


title: 200379120053_R02C01: genomic DNA from whole Blood


title: RNAseq_74269


title: 200379120053_R01C02: genomic DNA from whole Blood


title: RNAseq_97888


title: 200379120053_R01C01: genomic DNA from whole Blood


title: RNAseq_28081


title: 2nd Techn. replicate laterne vs.WTCy5/Cy3

city: Wien

first: Thomas

last: Nussbaumer

address: Althanstraße 14

institute: Computational Systems Biology

description:
Tech.replic. of Biol replic.2
RS.267_120612_251505910578_S01_GE2_107_Sep09_1_2

hyb_protocol: For the fragmentation 825ng of the Cy3-labelled/Cy5-labelled sample were mixed with 11 µl blocking agent and filled to 52.8 µl with nuclease-free H2O. After addition of 10µl 25x fragmentation buffer the reaction was incubated at 60ºC for 30 min and afterwards 55µl GEX Hyb buffer were added and the sample was hybridized with the Agilent microarrays. Washing was according to the suppliers (Agilent) instructions i.e. the slide washed with wash buffer1 for 1min, transferred to wash buffer2 (37ºC) for 1min, washed in acetonitrile for 1min and in drying solution for another 1min. The the slide was dried in darkness for 15min.

scan_protocol: The scanning of the Agilent microarrays was performed by IMGM services (München, Martinsried) with the following parameters. scan area (61 X 21.6 mm), Scan resolution 5 µm, Sum scanning mode : singe pass, Dye channel: Red and green, Green PMT: XDR Hi 100%; XDR Lo 10%, Red PMT XDR Hi 100%; XDR Lo 10%.

data_processing:
Data processing was performed by IMGM services (München, Martinsried) using Agilent Feature Extraction Software (FeatureExtractor_Version: 10.7.3.1)
RG <- backgroundCorrect(RG, method="normexp", offset=50)
MA <- normalizeWithinArrays(RG, method="loess")

organism: Arabidopsis thaliana

source_name: homozygous pid enp mutant_seedling

label_protocol:
Spike-In internal standards were generated according to the suppliers Instructions. Briefly 900ng of RNA in 8.3µl H2O were mixed with 1.2µl T7 promoter and 2µl spike-A or spike-B for Cy3- and Cy5-labbeled samples respectively and incubated 65ºC, 10 min, and 4ºC for 5min. Then cDNA synthesis was performed with 4µl 5X 1st strand buffer, 2µl 0.1M DDT, 1µl 10mM dNTP, 1µl MML V-RT, 0.5µl RNase Out and 11.5 µl Spike-in sample incubated at 40ºC for 2 hrs, 65ºC for 15 min and 4ºC for 5 min.
For cRNA synthesis 60µl of the master mix (15.3 µl nuclease-free H2O, 20 µl 4x transcription buffer, 6µl 0.1M DTT, 8 µl NTP mix, 6.4 µl 50% PEG, 0.5 µl RNase out, 0.6 µl inorganic pyrophosphatase, 0.8 µl T7 RNA polymerase, Cy3-CTP or Cy5-CTP respectively) were mixed with the cDNA synthesis sample and incubated 2 hrs at 40ºC. Then the labelled cRNA was purified with a Quiagen mini spin kit according to the manufactures instructions.

growth_protocol: Seeds were surface sterilsed, placed on H2O Agar plates with 100µg/ml Ampicillin, incubated for 2 days at 8C and transferred to a  growth chamber.

extract_protocol: Four independent pools of seedlings were used shock frozen separately. Total RNA was isolated using the Quiagen Rneasy Plant Mini Kit following the manufacture´s instructions. Quality of the RNA was determined with the Bioanalyzer (Agilent). Only samples with a RNA Integration Number (RIN) higher than 8 were taken for further analysis.

treatment_protocol: Seedlings were grown at 18C under constant light for exactly 4 days. During this time the plates were vertically placed on a stand and their position was randomly changed daily in order to adjust for possible light differences.

tag: genotype/variation

value: homozygous pid enp mutant

value: 6th day

value: seedling

tag: seedling

value: wild-type


title: 4th Replicate laterne vs. WT Cy3/Cy5

description:
Biological replicate 4 of 4
RS.267_120612_251505910577_S01_GE2_107_Sep09_1_4

tag: age


title: 1st Replicate laterne vs. WT Cy3/Cy5

description:
Biological replicate 1 of 4
RS.267_120612_251505910577_S01_GE2_107_Sep09_1_1


title: RNAseq_02019


title: 3rd Techn. replicate laterne vs.WT Cy5/Cy3

description:
Tech.replic. of Biol replic.3
RS.267_120612_251505910578_S01_GE2_107_Sep09_1_3


title: 200379120132_R06C02: genomic DNA from whole Blood

source_name: Blood - EDTA tube

tag: Sex

value: M


title: 3rd Replicate laterne vs. WT Cy3/Cy5

description:
Biological replicate 3 of 4
RS.267_120612_251505910577_S01_GE2_107_Sep09_1_3


title: 4th Techn. replicate laterne vs.WT Cy5/Cy3

description:
Tech.replic. of Biol replic.4
RS.267_120612_251505910578_S01_GE2_107_Sep09_1_4


title: 1st Techn.replicate laterne vs. WT Cy5/Cy3

description:
Tech.replic. of Biol replic.1
RS.267_120612_251505910578_S01_GE2_107_Sep09_1_1


title: H. parainfluenzae coculture with S. mitis rep2

city: Kingston

first: Dasith

last: Perera

state: Rhode Island

address: Flagg Rd

institute: University of Rhode Island

data_processing:
paired end alignment using bowtie2
counts generated using htseq-count with parameters -rev -a 1 -m intersection-nonempty
normalization and differential expression analysis carried out using DESeq2
automated workflow can be found at https://github.com/dasithperera-hub/RNASeq-analysis-toolkit
Genome_build: H. parainfluenzae ATCC 33392
Supplementary_files_format_and_content: csv file

organism:
Haemophilus parainfluenzae
Streptococcus mitis

source_name: Bacterial culture

growth_protocol: H. parainfluenzae grown in mono or coculture with mitis aerobically for 22 hours on BHI-YE HP at 37.C, 5% CO2, transferred to fresh media for 4 hours

extract_protocol:
Beadbeating and trizol
RNAtag-Seq (Shishkin AA, Giannoukos G, Kucukural A, et al. Simultaneous generation of many RNA-seq libraries in a single reaction. Nat Methods. 2015;12(4):323-5.)

tag: strain

value: H. parainfluenzae ATCC 33392 and S. mitis NCTC 12261


title: 200379120132_R05C02: genomic DNA from whole Blood

source_name: Blood - buffy coat

value: Control


title: RNAseq_91034

source_name: blood

tag: fev1 % predicted

tag: lymphocyte percent


title: 200379120132_R04C02: genomic DNA from whole Blood

value: F


title: RNAseq_29672

tag: batch

tag: eosinophil percent


title: 200379120132_R03C02: genomic DNA from whole Blood


title: RNAseq_95037

tag: current smoker

tag: monocyte percent


title: H. parainfluenzae coculture with S. mitis rep1


title: 200379120132_R02C02: genomic DNA from whole Blood

tag: status


title: RNAseq_26759

tag: basophil percent


title: RNAseq_44611

tag: pack years


title: RNAseq_83239

tag: gender (1=male, 2=female)


title: 200379120132_R06C01: genomic DNA from whole Blood


title: RNAseq_89171

tag: race (1=white, 2=black)


title: RNAseq_48561

tag: neutrophil percent


title: 2nd Replicate laterne vs. WT Cy3/Cy5

description:
Biological replicate 2 of 4
RS.267_120612_251505910577_S01_GE2_107_Sep09_1_2

tag: genotype/variation

tag: tissue


title: UhAvr1 deletion mutant (cross Uh362 Uhavr1 x Uh364 ΔUhAvr1, 116)_Odessa_48hrs, rep 3

city: Summerland

first: Guus

last: Bakkeren

state: BC

department: Summerland Research and Development Centre

institute: Agriculture & Agri-Food Canada

hyb_protocol: Hybridization of the probes to Affymetrix 22K GeneChip Barley Genome Arrays (#900515) was done for 16 hrs. Washing and staining were performed on a Fluidics Workstation 450/250 (49 Format) according to recommended procedures.

scan_protocol: A GeneChip Scanner 3000 was used following recommended procedures.

data_processing: Data files were analyzed using the 'Flexarray' software, available from Genome Quebec (http://genomequebec.mcgill.ca/FlexArray). The microarray data were normalized using the 'Robust Multi-chip Average' (RMA) method and probe sets showing significant differences in hybridization intensity among treatments were revealed using the empirical Bayes analysis due to Wright and Simon (algorithm EB Wright & Simon) available in the Flexarray software. The probesets were obtained and identified from the 'HarvEST' barley database (http://harvest.ucr.edu/).

organism: Hordeum vulgare

source_name: Odessa barley coleoptiles 48hrs after inoculation with "116" U. hordei teliospores

label_protocol: For microarray analysis, probes were synthesized using the Affymetrix GeneChip 3' IVT Express Kit Assay (Affymetrix, http://www.affymetrix.com): 50 ng polyA mRNA in 3 μl was incubated for 16 hrs for the IVT reaction and biotin labeling for 16 hrs.

growth_protocol: Two barley cultivars, 'Odessa' (ruh1, universal susceptibility) and a differential, 'Hannchen' (Ruh1) were used. Teliospores were produced on cultivar Odessa by crossing and inoculating U. hordei haploid parental strains Uh364 (alias Uh4857-4, MAT-1 UhAvr1) and Uh362 (alias Uh4854-10, MAT-2 Uhavr1), described previously in Linning et al., 2004. Genetics, 166(1):99-111, or Uh362 x Uh364 (delta UhAvr1).

extract_protocol: Total RNA was isolated by grinding frozen coleoptiles with sterile sand and extraction in a solution of phenol-guanidine isothiocyanate ('TRI Reagent', BIO/CAN Scientific). Due to large amounts of polysaccharides, total RNA was re-precipitated in 2 M LiCl at 4oC, resuspended and treated with TURBO DNase (Ambion) for 60 min at 37oC, extracted with phenol/chloroform and precipitated. Messenger RNA was isolated from the purified total RNA using the Dynabeads mRNA Direct Kit (Invitrogen).

treatment_protocol: Dehulled barley seeds were surface sterilized with 70% EtOH followed with 1% bleach, and germinated for 24 hrs at 18oC on sterile filterpaper in the dark. Then inoculated with teliospores by dusting using a sterile paint brush, and left under the same conditions for infection to occur. Coleoptiles were harvested 48 hrs after inoculation, snap-frozen in liquid nitrogen, after seed and roots were quickly removed, and stored at -80oC.

tag: cultivar

value: Odessa

tag: ruh1 status

value: coleoptiles

tag: treatment

value: infection with Ustilago hordei teliospores from a UhAvr1 deletion mutant cross


title: Wild-type cross (Uh362 Uhavr1 x Uh364 UhAvr1, 58)_Odessa_48hrs, rep 3

source_name: Odessa barley coleoptiles 48hrs after inoculation with "58" U. hordei teliospores

value: infection with Ustilago hordei teliospores from a wild-type cross


title: UhAvr1 deletion mutant (cross Uh362 Uhavr1 x Uh364 ΔUhAvr1, 116)_Hannchen_48hrs, rep 2

source_name: Hannchen barley coleoptiles 48hrs after inoculation with "116" U. hordei teliospores

value: Hannchen


title: Wild-type cross (Uh362 Uhavr1 x Uh364 UhAvr1, 58)_Odessa_48hrs, rep 1


title: UhAvr1 deletion mutant (cross Uh362 Uhavr1 x Uh364 ΔUhAvr1, 116)_Odessa_48hrs, rep 1


title: UhAvr1 deletion mutant (cross Uh362 Uhavr1 x Uh364 ΔUhAvr1, 116)_Odessa_48hrs, rep 2


title: 200379120132_R04C01: genomic DNA from whole Blood

tag: Sex

value: Schizophrenia

tag: age


title: Wild-type cross (Uh362 Uhavr1 x Uh364 UhAvr1, 58)_Hannchen_48hrs, rep 3

source_name: Hannchen barley coleoptiles 48hrs after inoculation with "58" U. hordei teliospores


title: RNAseq_39067

tag: batch

tag: fev1 % predicted

tag: lymphocyte percent


title: RNAseq_58489

tag: current smoker

tag: eosinophil percent

tag: monocyte percent


title: 200379120132_R03C01: genomic DNA from whole Blood

extract_protocol:
DNA from a case extracted using Gentra Autopure method
Genomic DNA was extracted from frozen  blood samples using either Gentra Autopure or Phenol-Chloroform method.

tag: status

value: case


title: UhAvr1 deletion mutant (cross Uh362 Uhavr1 x Uh364 ΔUhAvr1, 116)_Hannchen_48hrs, rep 1


title: RNAseq_04556

tag: pack years

tag: gender (1=male, 2=female)

tag: basophil percent


title: Wild-type cross (Uh362 Uhavr1 x Uh364 UhAvr1, 58)_Odessa_48hrs, rep 2


title: 200379120132_R02C01: genomic DNA from whole Blood


title: UhAvr1 deletion mutant (cross Uh362 Uhavr1 x Uh364 ΔUhAvr1, 116)_Hannchen_48hrs, rep 3


title: 200379120132_R01C01: genomic DNA from whole Blood


title: soil_CNT_300_rep3

city: Beijing

first: fan

last: wu

address: NO.5 Yiheyuan Road Haidian District

institute: Peking university

description: functional genes

hyb_protocol: the labeled DNA was hybridized onto the GeoChip 5.0 microarray, then the arrays were washed before scanning

scan_protocol: the arrays were scanned by the NimblGen MS200 Microarry Scanner

data_processing:
ImaGene 6.0 software was used to convert optical signals into digital ones and only those spots automatically scored positively in the raw data were used for downstream analysis. Spots with a signal-to noise ratio below 2.0 were removed. And the raw data were then normalized.
normalized intensity of each detected genes were list in the table.

organism: uncultured soil microorganism

source_name: soil with 300 mg/kg carbon nanomateirals

label_protocol: after amplified, samples were labeled with the fluorescent dye Cy-5 using a random priming method

extract_protocol: genomic DNA was extracted from soil samples and then purified

tag: group

value: CNTs


title: Wild-type cross (Uh362 Uhavr1 x Uh364 UhAvr1, 58)_Hannchen_48hrs, rep 2

tag: tissue


title: 200379120132_R01C02: genomic DNA from whole Blood

data_processing: Data was imported using the R package methylumi methylumIDAT function. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions.

value: Case


title: 200379120132_R05C01: genomic DNA from whole Blood


title: RNAseq_70985

data_processing:
alignment: STAR, 2-pass
gene quantification: Salmon v0.12.0 and tximport
exon quantification: Rsubread v1.32.2
isoform quantification: Salmon v0.12.0
Genome_build: HG38 (GTF: Ensembl Homo_sapiens.GRCh38.94.gtf.gz)
Supplementary_files_format_and_content: count matrices

tag: race (1=white, 2=black)

tag: neutrophil percent


title: soil_CNT_300_rep2

description: functional genes


title: 200379120092_R05C02: genomic DNA from whole Blood


title: Mock control_Hannchen_48hrs, rep 2

source_name: Hannchen barley coleoptiles 48hrs after mock inoculation

tag: cultivar

tag: ruh1 status

tag: treatment

value: mock infection


title: RNAseq_54116

tag: batch

tag: age


title: 200379120092_R04C02: genomic DNA from whole Blood

tag: Sex

value: Schizoaffective Disorder


title: soil_CNT_30_rep3

description: functional genes

source_name: soil with 30 mg/kg carbon nanotubes


title: Mock control_Hannchen_48hrs, rep 3


title: soil_CNT_300_rep1

description: functional genes


title: 200379120092_R06C02: genomic DNA from whole Blood


title: Mock control_Hannchen_48hrs, rep 1


title: RNAseq_55669

tag: current smoker

tag: fev1 % predicted

tag: lymphocyte percent


title: RNAseq_56667

tag: eosinophil percent

tag: monocyte percent


title: RNAseq_17313

tag: pack years

tag: gender (1=male, 2=female)


title: soil_CNT_30_rep1

description: functional genes

tag: group


title: 200379120092_R02C02: genomic DNA from whole Blood

tag: status


title: 200379120092_R01C02: genomic DNA from whole Blood


title: RNAseq_24461

tag: race (1=white, 2=black)

tag: basophil percent


title: soil_CNT_30_rep2

description: functional genes


title: soil_CNM_300_rep3

description: functional genes

value: CNMs


title: RNAseq_57229

tag: neutrophil percent


title: 200379120092_R06C01: genomic DNA from whole Blood

value: control


title: soil_CNM_300_rep2

description: functional genes


title: 200379120092_R05C01: genomic DNA from whole Blood


title: RNAseq_21153


title: soil_CNM_300_rep1

description: functional genes


title: RNAseq_18639


title: soil_CNM_30_rep3

description: functional genes

source_name: soil with 30 mg/kg carbon nanomateirals


title: 200379120092_R02C01: genomic DNA from whole Blood

value: M


title: 200379120092_R01C01: genomic DNA from whole Blood


title: soil_CNM_30_rep2

description: functional genes


title: 200379120092_R03C02: genomic DNA from whole Blood


title: 200379120092_R03C01: genomic DNA from whole Blood

value: Schizophrenia (Galway CP)


title: soil_control_rep3

description: functional genes

source_name: soil without contaminant

value: Control


title: RNAseq_98503


title: 200379120028_R06C02: Meth Control

source_name: Meth control


title: RNAseq_53856


title: RNAseq_89071


title: soil_control_rep2

description: functional genes


title: soil_control_rep1

description: functional genes


title: 200379120028_R04C02: genomic DNA from whole Blood


title: RNAseq_86385


title: RNAseq_07278


title: 200379120028_R05C02: genomic DNA from whole Blood


title: Wild-type cross (Uh362 Uhavr1 x Uh364 UhAvr1, 58)_Hannchen_48hrs, rep 1

tag: cultivar

tag: ruh1 status

tag: tissue


title: RNAseq_67550

tag: batch

tag: age


title: 200379120028_R02C02: genomic DNA from whole Blood

tag: Sex

value: F


title: 200379120028_R03C02: genomic DNA from whole Blood


title: RNAseq_71084

tag: current smoker

tag: fev1 % predicted


title: 200379120092_R04C01: genomic DNA from whole Blood


title: RNAseq_02742

tag: lymphocyte percent

tag: eosinophil percent


title: 200379120028_R06C01: genomic DNA from whole Blood


title: RNAseq_67056

tag: pack years

tag: monocyte percent


title: soil_CNM_30_rep1

description: functional genes

tag: group


title: 200379120028_R04C01: genomic DNA from whole Blood

tag: status


title: RNAseq_02693

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: RNAseq_31123

tag: neutrophil percent

tag: basophil percent


title: 200379120028_R05C01: genomic DNA from whole Blood


title: 200379120028_R03C01: genomic DNA from whole Blood


title: RNAseq_35632


title: RNAseq_72709


title: 200379120028_R02C01: genomic DNA from whole Blood


title: RNAseq_54450


title: 200379120028_R01C01: genomic DNA from whole Blood


title: RNAseq_28115


title: 200379120054_R06C02: genomic DNA from whole Blood


title: RNAseq_77776


title: D7.1 rep2

city: Tulln

first: Silvia

last: Fibi-Smetana

address: Technopark 1A

department: R&D

institute: BIOMIN Holding GmbH

data_processing:
Adapter removal and trimming was performed using Trimmomatic V0.36.
STAR-aligner v020201 was used for alignment to the chicken genomes
Samtools v1.7 were used to sort the BAM files by the read names.
Aligned reads were counted with HTSeq-count v0.6.1.
DESeq2 was used to evaluate differentially expressed genes.
Genome_build: Galgal5

organism: Gallus gallus

source_name: ileum

extract_protocol:
Approximately 30 mg of tissue were disrupted via a bead-beating step, and total RNA was extracted and purified with the RNeasy Mini Kit (Qiagen).
Construction of RNA sequencing libraries was done with the TruSeq Stranded Total RNA Illumina kit including Ribo-Zero Gold

treatment_protocol: Small pieces of the mid-ileum were dissected, placed into 1 mL of RNAlater (Ambion Inc.), stored overnight at 4 °C, and transferred to -80 °C until transcriptomics analysis

value: ileum

value: day 35

value: Avilamycin


title: RNAseq_52649


title: 200379120054_R05C02: genomic DNA from whole Blood

city: Exeter

first: Jonathan

last: Mill

institute: University of Exeter


title: D3.1 rep2


title: 200379120028_R01C02: genomic DNA from whole Blood


title: RNAseq_68118

city: Boston

first: Peter

last: Castaldi

institute: Brigham and Women's Hospital


title: 200379120054_R04C02: genomic DNA from whole Blood


title: RNAseq_03473


title: D2.1 rep2


title: 200379120054_R03C02: genomic DNA from whole Blood


title: RNAseq_17020


title: 200379120054_R02C02: genomic DNA from whole Blood


title: 200379120054_R01C02: genomic DNA from whole Blood


title: A6.1 rep2


title: 200379120054_R06C01: genomic DNA from whole Blood


title: A4.1 rep2


title: RNAseq_86240


title: RNAseq_55341


title: D5.1 rep2


title: 200379120054_R05C01: genomic DNA from whole Blood


title: RNAseq_00810


title: 200379120054_R03C01: genomic DNA from whole Blood


title: D4.1 rep2


title: RNAseq_56288


title: RNAseq_37370


title: A5.1 rep2


title: A3.1 rep2


title: RNAseq_25400


title: 200379120054_R01C01: genomic DNA from whole Blood


title: A7.1 rep2


title: D4.1 rep1


title: D5.1 rep1


title: 200379120054_R02C01: genomic DNA from whole Blood


title: RNAseq_83136


title: 200379120042_R05C02: genomic DNA from whole Blood


title: A5.1 rep1


title: RNAseq_60016


title: 200379120042_R06C02: genomic DNA from whole Blood


title: 200379120042_R04C02: genomic DNA from whole Blood


title: A3.1 rep1


title: 200379120042_R03C02: genomic DNA from whole Blood


title: D7.1 rep1


title: RNAseq_99560


title: D3.1 rep1


title: RNAseq_46555


title: 200379120054_R04C01: genomic DNA from whole Blood


title: 200379120042_R02C02: genomic DNA from whole Blood


title: 200379120042_R01C02: genomic DNA from whole Blood


title: RNAseq_02525


title: D2.1 rep1


title: A7.1 rep1


title: 200379120042_R06C01: genomic DNA from whole Blood


title: RNAseq_85612


title: RNAseq_12631


title: A6.1 rep1


title: 200379120042_R05C01: genomic DNA from whole Blood


title: RNAseq_88570


title: A4.1 rep1


title: RNAseq_65370


title: 200379120042_R04C01: genomic DNA from whole Blood


title: RNAseq_18695


title: 200379120042_R03C01: genomic DNA from whole Blood


title: RNAseq_99800


title: RNAseq_80345


title: 200379120042_R02C01: genomic DNA from whole Blood


title: RNAseq_45061


title: 200379120156_R06C02: genomic DNA from whole Blood


title: RNAseq_75099


title: 200379120156_R05C02: genomic DNA from whole Blood


title: RNAseq_71549


title: RNAseq_26708


title: 200379120156_R04C02: genomic DNA from whole Blood


title: RNAseq_54643


title: 200379120156_R03C02: genomic DNA from whole Blood


title: 200379120156_R02C02: genomic DNA from whole Blood


title: RNAseq_75039


title: RNAseq_11342


title: 200379120156_R01C02: genomic DNA from whole Blood


title: 200379120156_R06C01: genomic DNA from whole Blood


title: RNAseq_17289


title: 200379120042_R01C01: genomic DNA from whole Blood


title: 200379120156_R05C01: genomic DNA from whole Blood

extract_protocol:
DNA from a Case extracted using Phenol-Chloroform method
Genomic DNA was extracted from frozen  blood samples using either Gentra Autopure or Phenol-Chloroform method.


title: 200379120156_R04C01: genomic DNA from whole Blood


title: RNAseq_86997


title: RNAseq_30448


title: 200379120156_R02C01: genomic DNA from whole Blood


title: 200379120156_R01C01: genomic DNA from whole Blood

value: Schizophrenia (Galway PRCL SZ)


title: RNAseq_31723


title: RNAseq_46593


title: 200379120156_R03C01: genomic DNA from whole Blood


title: RNAseq_22286


title: RNAseq_32017


title: 200379120133_R06C02: genomic DNA from whole Blood


title: 200379120133_R05C02: genomic DNA from whole Blood


title: RNAseq_18652


title: RNAseq_27406


title: RNAseq_20390


title: 200379120133_R04C02: genomic DNA from whole Blood


title: 200379120133_R03C02: genomic DNA from whole Blood


title: RNAseq_70092


title: 200379120133_R02C02: genomic DNA from whole Blood


title: RNAseq_40906


title: 200379120133_R06C01: genomic DNA from whole Blood


title: RNAseq_74115


title: RNAseq_98492


title: 200379120133_R01C02: genomic DNA from whole Blood


title: RNAseq_73347


title: 200379120133_R05C01: genomic DNA from whole Blood


title: RNAseq_87612


title: 200379120133_R04C01: genomic DNA from whole Blood


title: 200379120133_R03C01: genomic DNA from whole Blood


title: RNAseq_37123


title: RNAseq_34870


title: RNAseq_72562


title: 200379120133_R02C01: genomic DNA from whole Blood


title: RNAseq_52576


title: 200379120082_R06C02: genomic DNA from whole Blood


title: genomic DNA from adult cancer survivor_EP26

first: Gordon

last: Strathdee

description: Normal PBL sample from adult cancer survivor

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Male

value: peripheral blood

tag: disease state

value: Normal

tag: developmental stage

value: adult


title: genomic DNA from adult cancer survivor_EP27

value: Female

tag: tissue


title: RNAseq_21025

tag: batch

tag: age


title: genomic DNA from adult cancer survivor_EP28


title: 200379120082_R05C02: genomic DNA from whole Blood

tag: Sex


title: genomic DNA from adult cancer survivor_EP32


title: genomic DNA from adult cancer survivor_EP31


title: genomic DNA from adult cancer survivor_EP23


title: genomic DNA from adult cancer survivor_EP21


title: 200379120082_R04C02: genomic DNA from whole Blood

value: Schizophrenia

value: Case


title: RNAseq_29537

tag: current smoker

tag: fev1 % predicted

tag: lymphocyte percent


title: 200379120133_R01C01: genomic DNA from whole Blood


title: genomic DNA from adult cancer survivor_EP29


title: genomic DNA from adult cancer survivor_EP22


title: genomic DNA from adult cancer survivor_EP30


title: RNAseq_60688

tag: pack years

tag: eosinophil percent

tag: monocyte percent


title: 200379120082_R03C02: genomic DNA from whole Blood

tag: status


title: genomic DNA from adult cancer survivor_EP17


title: genomic DNA from adult cancer survivor_EP16


title: genomic DNA from adult cancer survivor_EP14


title: genomic DNA from adult cancer survivor_EP24


title: genomic DNA from adult cancer survivor_EP13


title: genomic DNA from adult cancer survivor_EP12


title: 200379120082_R02C02: genomic DNA from whole Blood


title: genomic DNA from adult cancer survivor_EP20


title: RNAseq_90582

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: RNAseq_84006

tag: neutrophil percent

tag: basophil percent


title: 200379120082_R01C02: genomic DNA from whole Blood

value: Schizoaffective Disorder


title: genomic DNA from adult cancer survivor_EP15

tag: gender

tag: disease state


title: genomic DNA from adult cancer survivor_EP11

tag: tissue

tag: developmental stage


title: RNAseq_44990

tag: batch

tag: age


title: 200379120082_R06C01: genomic DNA from whole Blood

tag: Sex


title: genomic DNA from adult cancer survivor_EP19


title: RNAseq_74977

tag: current smoker

tag: fev1 % predicted


title: 200379120082_R04C01: genomic DNA from whole Blood


title: genomic DNA from adult cancer survivor_EP25


title: genomic DNA from adult cancer survivor_EP6


title: RNAseq_75507

tag: pack years

tag: lymphocyte percent


title: 200379120082_R02C01: genomic DNA from whole Blood


title: RNAseq_53600

tag: eosinophil percent

tag: monocyte percent


title: genomic DNA from adult cancer survivor_EP18


title: 200379120082_R03C01: genomic DNA from whole Blood

tag: status


title: RNAseq_13456

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: RNAseq_26214

tag: neutrophil percent

tag: basophil percent


title: 200379120058_R06C02: genomic DNA from whole Blood


title: 200379120082_R01C01: genomic DNA from whole Blood


title: RNAseq_58757


title: genomic DNA from adult cancer survivor_EP5

tag: gender

tag: disease state