title: RNAseq_51226


title: Sample M4C4 from D. melanogaster strain MUN-008 (aka MUN24) (Resistant to Copper stress) under Control conditions

status: Public on Dec 31 2020

type: SRA

city: Barcelona

first: Gabriel

middle: Eduardo

last: Rech

address: Passeig Marítim de la Barceloneta 37-49

country: Spain

institute: Consejo Superior de Investigaciones Cientificas - Institute of Evolutionary Biology (CSIC-UPF)

description:
M4C4
Drosophila melanogaster strain MUN-008 (also knows as MUN24)

library_source: transcriptomic

data_processing:
RNA-seq analysis was performed using the rnaseq pipeline (v1.2) from the nf-core community, a nextflow collection of curated bioinformatic pipelines (Di Tommaso et al. 2017; Ewels et al. 2020).
Briefly, sequencing quality was assessed using FastQC (v.0.11.8) (www.bioinformatics.babraham.ac.uk/projects/fastqc). TrimGalore (v.0.5.0) (www.bioinformatics.babraham.ac.uk/projects/trim_galore) was used for adapter removal and Cutadapt (v. 1.18) with default parameters was used for low-quality trimming (Martin 2011). Trimmed reads were mapped to the D. melanogaster genome r6.15 using STAR (v.2.6) (Dobin et al. 2012).
Technical duplications were explored using dupRadar (Sayols et al. 2016). Overall, we found no bias towards high number of duplicates at low read counts, so we did not remove duplicates from the alignments.
We used featureCounts (v.1.6.2) (Liao et al. 2014) for counting the number of reads mapping to genes (reverse-stranded parameter). Gene annotation r6.15.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: extra_and_finalnfcoreResultsSTAR_merged_gene_countsFinal_RMmales.txt: Tab-delimited text file includes RAW COUNTS reads for each sample.

molecule: total RNA

organism: Drosophila melanogaster

source_name: whole body

growth_protocol: Flies were collected in 2015 from different European locations by members of the DrosEU consortium. Flies were inbred for 20 generations. Fly stocks were kept at 25 °C and 65% relative humidity with 12h day and night cycles.

extract_protocol:
RNA was extracted using GenElute™ Mammalian Total RNA Miniprep Kit from 20 whole female flies. RNA samples were treated with DNase I (Thermo Fisher Scientific) following manufacturer’s instructions. RNA concentration was checked with NanoDrop spectrophotometer (NanoDrop Technologies) and quality was assessed with Bioanalyzer.
1.5 µg of total RNA from each sample was used for library preparation and sequencing. Library preparation was performed using the TruSeq Stranded mRNA Sample Prep kit from Illumina following the manufacturer's instructions. Libraries were sequenced using Illumina 125 bp paired-end reads, obtaining between 27 and 41 million reads/sample.

treatment_protocol: Powdered Copper Sulphate (CuSO4) was reconstituted in a 5% sucrose solution. Food dye was added to aid visibility and even dispersal. An identical control solution without CuSO4 was prepared in the same manner. 250μl of the CuSO4 sucrose solution was pipetted onto 70x17mm slips of filter paper, which were then placed into 15ml Falcon tubes (manufacturer, CAT#), containing one ml on 1% agar at the bottom. Papers were allowed to dry for 15 minutes, after which the flies were added. Holes were made in the lids of the falcon tubes before they were re-affixed, to assist respiration. As Drosophila are known to show avoid food with a high concentration of heavy metals (Burke, the parkinsons group. Our prelim data) this assay also allows exposure to copper via contact.

tag: strain

tag: Sex

value: Female

tag: tissue

value: Whole body

tag: copper stress phenotype

value: Resistant

tag: treatment

value: Control


title: Sample M4C2 from D. melanogaster strain MUN-008 (aka MUN24) (Resistant to Copper stress) under Control conditions

description:
M4C2
Drosophila melanogaster strain MUN-008 (also knows as MUN24)


title: RNAseq_64986

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

organism: Homo sapiens

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: age

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

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

tag: fev1 % predicted


title: RNAseq_21887

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: Sample M4D2 from D. melanogaster strain MUN-008 (aka MUN24) (Resistant to Copper stress) under Treated conditions

description:
M4D2
Drosophila melanogaster strain MUN-008 (also knows as MUN24)

tag: strain

value: Copper treated


title: RNAseq_41945


title: Sample M3D3 from D. melanogaster strain MUN-020 (aka MUN33) (Resistant to Copper stress) under Treated conditions

description:
M3D3
Drosophila melanogaster strain MUN-020 (also knows as MUN33)

tag: Sex


title: RNAseq_82655


title: Sample M3D1 from D. melanogaster strain MUN-020 (aka MUN33) (Resistant to Copper stress) under Treated conditions

description:
M3D1
Drosophila melanogaster strain MUN-020 (also knows as MUN33)

tag: tissue


title: Cut and Run H3K9me3 profiling of OSCs with panx knockdown and transfection of control plasmid replicate 1

city: Vienna

first: Jakob

last: Schnabl

state: Vienna

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechnology

library_source: genomic

data_processing:
Library strategy: CUT&RUN
reads were trimmed by removal of the adaptor sequences and to a length of 6-50 bases
reads were mapped to Drosophila melanogaster genome
Genome_build: dm6
Supplementary_files_format_and_content: all mapping and unique mapping bigwig files for sense and antisense

molecule: genomic DNA

source_name: OSCs

growth_protocol: OSCs were grown at 27º C, 2.5% CO2

extract_protocol:
Cut and Run protocol V3
NEBNext Ultra II DNA Library Prep Kit
HiSeqV4

treatment_protocol: siRNA transfection + indicated plasmid transfection

tag: cell type

value: Ovarian Somatic Cells (OSCs)

tag: knock-out or depletion

value: panx depletion

tag: antibody

value: anti-H3K9me3 antibody produced in rabbit (Active Motif Cat# 39161)


title: Sample M4C1 from D. melanogaster strain MUN-008 (aka MUN24) (Resistant to Copper stress) under Control conditions

description:
M4C1
Drosophila melanogaster strain MUN-008 (also knows as MUN24)

tag: copper stress phenotype

tag: treatment


title: RNAseq_18499

tag: batch

tag: current smoker

tag: pack years

tag: age


title: Sample M3D2 from D. melanogaster strain MUN-020 (aka MUN33) (Resistant to Copper stress) under Treated conditions

description:
M3D2
Drosophila melanogaster strain MUN-020 (also knows as MUN33)


title: RNAseq_47200

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

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

tag: fev1 % predicted

tag: neutrophil percent


title: Sample M3C2 from D. melanogaster strain MUN-020 (aka MUN33) (Resistant to Copper stress) under Control conditions

description:
M3C2
Drosophila melanogaster strain MUN-020 (also knows as MUN33)


title: Sample M3C1 from D. melanogaster strain MUN-020 (aka MUN33) (Resistant to Copper stress) under Control conditions

description:
M3C1
Drosophila melanogaster strain MUN-020 (also knows as MUN33)


title: RNAseq_96199

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: RNAseq_95664


title: Sample G4D4 from D. melanogaster strain GIM-012 (aka GIM44) (Resistant to Copper stress) under Treated conditions

description:
G4D4
Drosophila melanogaster strain GIM-012 (also knows as GIM44)

tag: strain

tag: Sex

tag: tissue


title: Sample G4D1 from D. melanogaster strain GIM-012 (aka GIM44) (Resistant to Copper stress) under Treated conditions

description:
G4D1
Drosophila melanogaster strain GIM-012 (also knows as GIM44)

tag: copper stress phenotype


title: Sample G4D2 from D. melanogaster strain GIM-012 (aka GIM44) (Resistant to Copper stress) under Treated conditions

description:
G4D2
Drosophila melanogaster strain GIM-012 (also knows as GIM44)

tag: treatment


title: RNAseq_78276

tag: batch


title: RNAseq_94955

tag: current smoker


title: RNAseq_66906

tag: pack years


title: RNAseq_70085

tag: age


title: RNAseq_40583

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


title: Sample G4C4 from D. melanogaster strain GIM-012 (aka GIM44) (Resistant to Copper stress) under Control conditions

description:
G4C4
Drosophila melanogaster strain GIM-012 (also knows as GIM44)


title: RNAseq_59753

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


title: RNAseq_59610

tag: fev1 % predicted


title: Sample G4C1 from D. melanogaster strain GIM-012 (aka GIM44) (Resistant to Copper stress) under Control conditions

description:
G4C1
Drosophila melanogaster strain GIM-012 (also knows as GIM44)


title: RNAseq_89247

tag: neutrophil percent


title: TL-CDK8i rep 3

city: Lyon

first: Irene

last: Aksoy

address: 18 avenue du Doyen Lepine

country: France

institute: Stem Cell and Brain Research Institute

data_processing:
Samples were sequenced on a NextSeq500 sequencing machine (Illumina) as single-reads of 75bp.
The bcl2fastq conversion software was used for demultiplexing (Illumina) and data trimming was performed using Cutadapt.
Sequencing depth for each sample was about 30 millions of reads.
Reads were then mapped to the Mmul8 rhesus macaque genome using HISAT2 alignment program and quantified with the HTseq script.
Genome_build: Mmul8 macaca mulatta
Supplementary_files_format_and_content: TPM values for each sample

organism: Macaca mulatta

source_name: Rhesus ESCs

growth_protocol: Cells were grown in culture conditions as described in original protocols

extract_protocol:
Cell pellets were lysed in Triizol and subjected to the RNeasy mini kit (Qiagen). 200ng of RNA were used to genrated libraries for sequencing.
The libraries were prepared using 200 ng of RNA with NextFlex Rapid Directional mRNA-Seq kit (Bioo-Scientific).

tag: cell type

value: Rhesus ESCs

tag: type

value: Naive cells

tag: protocol


title: TL-CDK8i rep 2


title: Sample F9D1 from D. melanogaster strain AKA-018 (aka FIN19) (Sensitive to Copper stress) under Treated conditions

description:
F9D1
Drosophila melanogaster strain AKA-018 (also knows as FIN19)

value: Sensitive


title: Sample F9C4 from D. melanogaster strain AKA-018 (aka FIN19) (Sensitive to Copper stress) under Control conditions

description:
F9C4
Drosophila melanogaster strain AKA-018 (also knows as FIN19)


title: RNAseq_51346

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: TL-CDK8i rep 1


title: RNAseq_92395


title: 4i/L/b rep 2


title: Sample D6D2 from D. melanogaster strain JUT-008 (aka DEN62) (Sensitive to Copper stress) under Treated conditions

description:
D6D2
Drosophila melanogaster strain JUT-008 (also knows as DEN62)

tag: strain

tag: Sex

tag: tissue

tag: copper stress phenotype


title: RNAseq_48927

tag: batch

tag: current smoker

tag: pack years


title: 4i/L/b rep 3


title: RNAseq_05474

tag: age

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

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


title: 4i/L/b rep 1

tag: cell type


title: RNAseq_65514

tag: fev1 % predicted

tag: neutrophil percent


title: Sample F9D3 from D. melanogaster strain AKA-018 (aka FIN19) (Sensitive to Copper stress) under Treated conditions

description:
F9D3
Drosophila melanogaster strain AKA-018 (also knows as FIN19)

tag: treatment


title: NHSM-v rep 3

tag: type

tag: protocol

value: NHSM-v


title: RNAseq_91394

description:
gene_TMM_counts.csv
exon_TMM_counts.csv
isoform_TMM_counts.csv

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: Sample D6D1 from D. melanogaster strain JUT-008 (aka DEN62) (Sensitive to Copper stress) under Treated conditions

description:
D6D1
Drosophila melanogaster strain JUT-008 (also knows as DEN62)

tag: strain

tag: Sex

tag: tissue

tag: copper stress phenotype


title: Sample G4C2 from D. melanogaster strain GIM-012 (aka GIM44) (Resistant to Copper stress) under Control conditions

description:
G4C2
Drosophila melanogaster strain GIM-012 (also knows as GIM44)


title: RNAseq_57448

tag: batch

tag: current smoker

tag: pack years

tag: age


title: RNAseq_85631

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

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

tag: fev1 % predicted


title: Sample F9D4 from D. melanogaster strain AKA-018 (aka FIN19) (Sensitive to Copper stress) under Treated conditions

description:
F9D4
Drosophila melanogaster strain AKA-018 (also knows as FIN19)

tag: treatment


title: RNAseq_57285

tag: neutrophil percent


title: NHSM-v rep 2

tag: cell type

tag: type

tag: protocol


title: Sample D6D3 from D. melanogaster strain JUT-008 (aka DEN62) (Sensitive to Copper stress) under Treated conditions

description:
D6D3
Drosophila melanogaster strain JUT-008 (also knows as DEN62)


title: Sample D6C2 from D. melanogaster strain JUT-008 (aka DEN62) (Sensitive to Copper stress) under Control conditions

description:
D6C2
Drosophila melanogaster strain JUT-008 (also knows as DEN62)


title: RNAseq_06205

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: E-NHSM rep 3

value: E-NHSM


title: Sample D6C1 from D. melanogaster strain JUT-008 (aka DEN62) (Sensitive to Copper stress) under Control conditions

description:
D6C1
Drosophila melanogaster strain JUT-008 (also knows as DEN62)

tag: strain

tag: Sex

tag: tissue

tag: copper stress phenotype


title: NHSM-v rep 1


title: E-NHSM rep 2


title: RNAseq_28157

tag: batch

tag: current smoker

tag: pack years

tag: age


title: Sample D6C3 from D. melanogaster strain JUT-008 (aka DEN62) (Sensitive to Copper stress) under Control conditions

description:
D6C3
Drosophila melanogaster strain JUT-008 (also knows as DEN62)

tag: treatment


title: Sample B7D1 from D. melanogaster strain COR-018 (aka BZ37) (Sensitive to Copper stress) under Treated conditions

description:
B7D1
Drosophila melanogaster strain COR-018 (also knows as BZ37)


title: E-NHSM rep 1


title: LCDM (EPS) rep 2

value: LCDM (EPS)


title: RNAseq_52088

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

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

tag: fev1 % predicted

tag: neutrophil percent


title: Sample B7C2 from D. melanogaster strain COR-018 (aka BZ37) (Sensitive to Copper stress) under Control conditions

description:
B7C2
Drosophila melanogaster strain COR-018 (also knows as BZ37)


title: Sample B7C4 from D. melanogaster strain COR-018 (aka BZ37) (Sensitive to Copper stress) under Control conditions

description:
B7C4
Drosophila melanogaster strain COR-018 (also knows as BZ37)


title: Blood, BMI-KM-17-202

type: genomic

city: Kunming

first: Jinlong

last: Huo

state: Yunnan

address: Jin-hei

department: Faculty of Animal Science and Technology

country: China

institute: Yunnan Agricultural University

hyb_protocol: The loaded BeadChip is incubated overnight in the Illumina Hybridization Oven. The amplified and fragmented DNA samples anneal to locus-specific 50-mers (covalently linked to one of up to 300,000 bead types) during hybridization.

scan_protocol: The BeadChip was scanned using iScan system produced by Illumina Inc.

data_processing: BeadStudio (Illumina Inc.) software were used to genotype the SNPs.

label: biotin

organism: Sus scrofa

label_protocol: biotin

extract_protocol: Classic method of phenol-chloroform

treatment_protocol: No treatment

value: blood

tag: breed

value: Banna Mini-pig Inbred Line (BMI)

tag: gender

value: female


title: RNAseq_47899

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: Blood, BMI-KM-7-0820


title: Sample F9C3 from D. melanogaster strain AKA-018 (aka FIN19) (Sensitive to Copper stress) under Control conditions

description:
F9C3
Drosophila melanogaster strain AKA-018 (also knows as FIN19)

tag: strain

tag: Sex

value: Female


title: RNAseq_46688

tag: basophil percent


title: LCDM (EPS) rep 3

tag: cell type

tag: type

tag: protocol


title: RNAseq_96587

tag: batch

tag: current smoker

tag: pack years

tag: age


title: Sample B7D4 from D. melanogaster strain COR-018 (aka BZ37) (Sensitive to Copper stress) under Treated conditions

description:
B7D4
Drosophila melanogaster strain COR-018 (also knows as BZ37)

tag: tissue

value: Whole body

tag: copper stress phenotype

tag: treatment


title: Blood, BMI-KM-18-503

tag: breed

tag: gender

value: male


title: t2iLGöY rep 3


title: RNAseq_70473

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

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

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent


title: Blood, BMI-KM-15-C011


title: Sample B7D3 from D. melanogaster strain COR-018 (aka BZ37) (Sensitive to Copper stress) under Treated conditions

description:
B7D3
Drosophila melanogaster strain COR-018 (also knows as BZ37)

tag: strain

tag: Sex


title: LCDM (EPS) rep 1

tag: cell type

tag: type

tag: protocol


title: Sample B7C1 from D. melanogaster strain COR-018 (aka BZ37) (Sensitive to Copper stress) under Control conditions

description:
B7C1
Drosophila melanogaster strain COR-018 (also knows as BZ37)

value: Control


title: Blood, BMI-KM-6-0704


title: RNAseq_35622

tag: batch

tag: current smoker

tag: pack years

tag: age

tag: monocyte percent

tag: basophil percent


title: t2iLGöY rep 2


title: Sample TOT4 from D melanogaster strain TOM-008 (Sensitive to desiccation), under Treated conditions

data_processing:
Overall, we obtained 1.202 million pair-end sequences for all samples in the experiment. Fastq sequence quality was first assessed using FastQC (v.0.11.8)
Adapter and quality trimming was performed using Cutadapt (v. 1.18) (Martin 2011) with the parameters --quality-cutoff 20, -a AGATCGGAAGAGC and the paired-end option.
Trimmed reads were then mapped to the D. melanogaster genome r6.15 using STAR (v.2.6) (Dobin et al. 2013). On average, 96.3% of the reads mapped to the reference genome. Technical duplications were explored using dupRadar (Sayols et al. 2016).
We then used featureCounts (v.1.6.2) (Liao et al. 2014) for counting the number of reads mapping to genes (reverse-stranded parameter).
Genome_build: dm6
Supplementary_files_format_and_content: Tab-delimited text files include RAW COUNTS reads for each sample.

growth_protocol: Flies were collected in 2015 from different European locations by members of the DrosEU consortium. Flies were inbred for 20 generations, . Fly stocks were kept at 25 °C and 65% relative humidity with 12h day and night cycles.

extract_protocol:
RNA was extracted using GenElute™ Mammalian Total RNA Miniprep Kit from 30 whole female flies, four to six days old, per replicate. RNA samples were treated with DNAse I (Thermo Fisher Scientific) following manufacturer’s instructions. RNA concentration was checked with NanoDrop spectrophotometer (NanoDrop Technologies) and quality was assessed with Bioanalyzer.
1.5 µg of total RNA from each sample was used for library preparation and sequencing. Library preparation was performed using the Truseq Stranded mRNA Sample Prep kit from Illumina following the manufacturer's instructions. Libraries were sequenced using Illumina 125 bp paired-end reads, obtaining between 27 and 41 million reads/sample.

treatment_protocol: In treated conditions,  flies were placed in empty vials and between the cotton and the parafilm, three grams of silica gel (Merck) were placed, so they were starved and desiccated. Control vials were prepared similarly, except that it contained 1mL of 1% agar on the bottom of the vial to prevent desiccation. Agar in the tubes provides hydration but not food source for the control flies (Sinclair et al 2007).

tag: desiccation stress

tag: treatment

value: desiccation stress


title: Sample TOT2 from D melanogaster strain TOM-008 (Sensitive to desiccation), under Treated conditions


title: Blood, BMI-KM-13-01041

tag: tissue

tag: breed

tag: gender


title: RNAseq_43786

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

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

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent


title: Sample TOT1 from D melanogaster strain TOM-008 (Sensitive to desiccation), under Treated conditions

tag: strain


title: RNAseq_68769

tag: batch

tag: current smoker


title: t2iLGöY rep 1

tag: cell type

tag: type

tag: protocol


title: Blood, BMI-KM-8-0830


title: Blood, BMI-KM-5-0708


title: Blood, BMI-KM-11-01040


title: Blood, BMI-KM-4-0614


title: Sample TOC3 from D melanogaster strain TOM-008 (Sensitive to desiccation), under Control conditions

tag: desiccation stress


title: TL2i rep 3


title: RNAseq_82094

tag: pack years

tag: age

tag: monocyte percent

tag: basophil percent


title: Blood, BMI-KM-3-654

tag: tissue

tag: breed

tag: gender


title: TL2i rep 2


title: RNAseq_61222

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

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

tag: fev1 % predicted

tag: neutrophil percent


title: RNAseq_98687

tag: batch

tag: lymphocyte percent

tag: eosinophil percent


title: TL2i rep 1

tag: cell type

tag: type


title: Sample TOC1 from D melanogaster strain TOM-008 (Sensitive to desiccation), under Control conditions

tag: strain

tag: desiccation stress

tag: treatment


title: Sample TOC2 from D melanogaster strain TOM-008 (Sensitive to desiccation), under Control conditions


title: Primed 2 rep 3

value: Primed cells

tag: protocol

value: Primed 3


title: RNAseq_31063

tag: current smoker

tag: pack years

tag: age

tag: monocyte percent

tag: basophil percent


title: Primed 2 rep 2


title: RNAseq_69579

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

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


title: Sample SWT2 from D melanogaster strain LUN-007 (Sensitive to desiccation), under Treated conditions


title: Blood, BMI-KM-9-905

tag: tissue

tag: breed

tag: gender


title: Blood, BMI-Y124


title: Blood, BMI-Y126


title: Blood, BMI-Y145


title: RNAseq_85773

tag: batch

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent


title: Sample SWT4 from D melanogaster strain LUN-007 (Sensitive to desiccation), under Treated conditions

tag: strain

tag: desiccation stress

tag: treatment


title: Primed rep 2

tag: cell type

tag: type

tag: protocol

value: Primed


title: RNAseq_71578

tag: current smoker

tag: pack years

tag: age

tag: monocyte percent

tag: basophil percent


title: RNAseq_61393

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

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


title: Primed rep 3

value: Rhesus ESCs


title: Sample SWC3 from D melanogaster strain LUN-007 (Sensitive to desiccation), under Control conditions


title: Sample SWC2 from D melanogaster strain LUN-007 (Sensitive to desiccation), under Control conditions


title: Sample SWC4 from D melanogaster strain LUN-007 (Sensitive to desiccation), under Control conditions


title: RNAseq_85919

tag: batch

tag: fev1 % predicted


title: Primed rep 1


title: Blood, BMI-Y128

tag: tissue

tag: breed

tag: gender


title: Blood, BMI-Y343


title: Blood, BMI-Y227


title: Blood, BMI-Y344


title: RNAseq_14625

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent


title: Sample SWT1 from D melanogaster strain LUN-007 (Sensitive to desiccation), under Treated conditions

tag: strain

tag: desiccation stress

tag: treatment


title: Sample MUT4 from D melanogaster strain MUN-013 (Sensitive to desiccation), under Treated conditions


title: Primed 2 rep 1

tag: cell type

tag: type

tag: protocol

value: Primed 2


title: Sample MUT3 from D melanogaster strain MUN-013 (Sensitive to desiccation), under Treated conditions

value: Sensitive


title: RNAseq_06683

tag: current smoker

tag: pack years

tag: age

tag: monocyte percent

tag: basophil percent


title: RNAseq_21827

tag: batch

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

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

tag: fev1 % predicted


title: Sample MUT2 from D melanogaster strain MUN-013 (Sensitive to desiccation), under Treated conditions


title: RNAseq_83643

tag: neutrophil percent

tag: lymphocyte percent


title: Blood, BMI-Y402

tag: tissue

tag: breed

tag: gender


title: Sample MUC4 from D melanogaster strain MUN-013 (Sensitive to desiccation), under Control conditions

tag: strain

tag: desiccation stress

tag: treatment


title: Sample G3T3 from D melanogaster strain GIM-012 (Resistant to desiccation), under Treated conditions

value: Resistant


title: Sample MUC3 from D melanogaster strain MUN-013 (Sensitive to desiccation), under Control conditions


title: Sample G3T2 from D melanogaster strain GIM-012 (Resistant to desiccation), under Treated conditions


title: Sample G3T1 from D melanogaster strain GIM-012 (Resistant to desiccation), under Treated conditions


title: Blood, BMI-Y407


title: RNAseq_68201

tag: current smoker

tag: eosinophil percent


title: Blood, BMI-Y434


title: RNAseq_12334

tag: pack years

tag: age


title: Sample MUC2 from D melanogaster strain MUN-013 (Sensitive to desiccation), under Control conditions


title: RNAseq_66940

tag: monocyte percent

tag: basophil percent


title: Blood, BMI-Y406


title: Blood, BMI-Y405


title: Blood, BMI-Y224


title: Blood, BMI-Y346


title: Blood, BMI-0331


title: Blood, BMI-Y433


title: RNAseq_78173

tag: batch

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


title: Sample G2T3 from D melanogaster strain GIM-024 (Resistant to desiccation), under Treated conditions

value: GIM-024 (GIM)


title: Blood, BMI-0473


title: Blood, BMI-0311


title: RNAseq_56249

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

tag: fev1 % predicted


title: Sample G3C3 from D melanogaster strain GIM-012 (Resistant to desiccation), under Control conditions


title: Blood, BMI-01013


title: Sample G3C2 from D melanogaster strain GIM-012 (Resistant to desiccation), under Control conditions


title: RNAseq_99130

tag: neutrophil percent

tag: lymphocyte percent


title: Blood, BMI-0223

tag: tissue

tag: breed


title: RNAseq_62856


title: Blood, BMI-Y436

tag: gender


title: Blood, BMI-Y127


title: Sample G3C1 from D melanogaster strain GIM-012 (Resistant to desiccation), under Control conditions

tag: strain

tag: desiccation stress


title: Sample G2T2 from D melanogaster strain GIM-024 (Resistant to desiccation), under Treated conditions

tag: treatment


title: RNAseq_96267

tag: current smoker

tag: eosinophil percent


title: Sample G2T1 from D melanogaster strain GIM-024 (Resistant to desiccation), under Treated conditions


title: RNAseq_97477

tag: pack years

tag: age


title: Sample G2C2 from D melanogaster strain GIM-024 (Resistant to desiccation), under Control conditions


title: RNAseq_06891

tag: monocyte percent

tag: basophil percent


title: Blood, BMI-0635


title: Blood, BMI-Y144


title: RNAseq_65417

tag: batch

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


title: Sample COT4 from D melanogaster strain COR-023 (Resistant to desiccation), under Treated conditions


title: RNAseq_86030

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


title: Blood, BMI-KM-2-652


title: Sample G2C1 from D melanogaster strain GIM-024 (Resistant to desiccation), under Control conditions


title: RNAseq_53918

tag: fev1 % predicted

tag: neutrophil percent


title: RNAseq_86906

tag: lymphocyte percent


title: Sample COT2 from D melanogaster strain COR-023 (Resistant to desiccation), under Treated conditions


title: RNAseq_52082


title: Sample COT1 from D melanogaster strain COR-023 (Resistant to desiccation), under Treated conditions


title: Sample G2C3 from D melanogaster strain GIM-024 (Resistant to desiccation), under Control conditions


title: RNAseq_51749


title: Sample COC4 from D melanogaster strain COR-023 (Resistant to desiccation), under Control conditions


title: Sample COC3 from D melanogaster strain COR-023 (Resistant to desiccation), under Control conditions


title: RNAseq_73850


title: Blood, BMI-0423

tag: tissue

tag: breed


title: Blood, BMI-0208

tag: gender


title: Blood, BMI-Y348


title: Sample COC2 from D melanogaster strain COR-023 (Resistant to desiccation), under Control conditions

tag: strain

tag: desiccation stress


title: Blood, BMI-KM-1-0508


title: Blood, BMI-C30


title: RNAseq_12169

tag: current smoker


title: RNAseq_49711

tag: eosinophil percent


title: RNAseq_17723

tag: pack years


title: RNAseq_01948

tag: age


title: RNAseq_44815

tag: monocyte percent


title: RNAseq_43373

tag: basophil percent


title: RNAseq_03196

tag: batch


title: RNAseq_18079

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


title: RNAseq_47587

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


title: RNAseq_30424

tag: fev1 % predicted


title: RNAseq_98771

tag: neutrophil percent


title: RNAseq_07767

tag: lymphocyte percent


title: RNAseq_05685


title: RNAseq_09507


title: Serum-derived exosomes from patients resistance to gefitinib - GR rep1

city: Changsha

first: Wen-liang

last: Liu

address: No.139 Renmin middle road

department: Department of thoracic surgery

institute: The second Xiangya hospital, central South university

description:
R1
Raw_gene_counts_matrix.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and ribosomal RNA removed, then mapped to human genome (hg38) using hisat2 (version 2.1.0).
The htseq-count (version 0.9.1) calculated the number of reads that were mapped to known genes.
Differentially expressed genes were identified using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: Blood

extract_protocol:
Exosomes were obtained from the serum of NSCLC patients and cell supernatant using ExoQuick Precipitation Solution (Cat.no EXOQ20A-1, SBI, USA) as described previously.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: sample type

value: Peripheral blood from patients resistance to gefitinib.


title: Serum-derived exosomes from patients resistance to gefitinib - GR rep2

description:
R2
Raw_gene_counts_matrix.txt


title: Serum-derived exosomes from patients sensitive to gefitinib - GS rep3

description:
S3
Raw_gene_counts_matrix.txt

value: Peripheral blood from patients sensitive to gefitinib.


title: Serum-derived exosomes from patients resistance to gefitinib - GR rep4

description:
R4
Raw_gene_counts_matrix.txt


title: Serum-derived exosomes from patients sensitive to gefitinib - GS rep4

description:
S4
Raw_gene_counts_matrix.txt


title: Serum-derived exosomes from patients resistance to gefitinib - GR rep3

description:
R3
Raw_gene_counts_matrix.txt


title: Serum-derived exosomes from patients sensitive to gefitinib - GS rep2

description:
S2
Raw_gene_counts_matrix.txt


title: Blood, BMI-Y432

tag: tissue

value: blood

tag: breed

value: Banna Mini-pig Inbred Line (BMI)


title: RNAseq_61543


title: RNAseq_27477


title: Blood, BMI-Y229

tag: gender


title: Serum-derived exosomes from patients sensitive to gefitinib - GS rep1

description:
S1
Raw_gene_counts_matrix.txt


title: Blood, BMI-C10

value: female


title: Blood, BMI-0915


title: Blood, BMI-0308


title: Blood, BMI-Y341


title: RNAseq_66866


title: RNAseq_31238


title: RNAseq_73867


title: RNAseq_48830


title: MDA231-Combination.12

city: Rochester

first: Mrunal

middle: Kishor

last: Dehankar

state: MN

address: 200 First St. SW

department: Computational genomics

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat (https://ccb.jhu.edu/software/tophat/index.shtml)
Gene counts were generated using Subread featureCounts (http://subread.sourceforge.net/)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include Raw counts and FPKM values for each gene per sample

source_name: Breast Cancer cell line

growth_protocol: Cells were cultured in DMEM supplimented with10% FBS  into a T75 flask.

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Quiagen)
RNA libraries were prepared for sequencing using TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: Three replicates were treated with TGFβ and Alisertib for 48 hrs.

tag: cell type

value: TNBC Cell Line

tag: treatment

value: TGFB+Alisertib for 48 hrs

tag: cell line


title: MDA231-ALIS.9

value: Alisertib for 48 hrs


title: RNAseq_12124

tag: current smoker

tag: pack years

tag: eosinophil percent


title: MDA231-Combination.10


title: MDA231-ALIS.8


title: MDA231-TGFB.6

value: TGFβ for 48 hrs


title: MDA231-ALIS.7


title: MDA231-Combination.11


title: RNAseq_68607

tag: age

tag: monocyte percent

tag: basophil percent


title: RNAseq_01759

tag: batch

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

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


title: MDA-MB-231-CTL.3

value: No Treatment


title: MDA231-TGFB.4


title: RNAseq_10380

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_41176


title: RNAseq_78437


title: RNAseq_91781


title: MDA231-TGFB.5


title: RNAseq_79795


title: RNAseq_38420


title: RNAseq_08928


title: RNAseq_98542


title: RNAseq_02516


title: RNAseq_38402


title: RNAseq_55340


title: RNAseq_32396


title: RNAseq_22308


title: RNAseq_81305


title: MDA-MB-231-CTL.2


title: MDA-MB-231-CTL.1


title: RNAseq_97138


title: RNAseq_60199


title: RNAseq_72639


title: RNAseq_32137


title: HFA570: Fetal single cell RNA sequencing material

city: Montreal

first: Jack

last: Antel

state: Quebec

address: 3801 University, Montreal Neurological Institut

country: Canada

institute: Montreal Neurological Institute

data_processing:
All preprocessing steps were performed using the Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Integration, clustering and differential expression analysis was done using R package Seurat (v3.1)
Genome_build: GRCh38

source_name: Human brain tissue

growth_protocol: For single-cell RNA sequencing, cells were sent for sequencing immediately ex-vivo

extract_protocol:
Single cells were obtained following mechanical and enzymatic (trypsin) dissociation as previously described (Cui et al. 2017). A isotonic Percoll gradient was used to remove myelin. The whole dissociated cell population was collected from the gradient (which sits between the myelin layer and the red blood cell layer), washed 3 times in PBS, and re-suspended at a concentration of 10^6 cells per ml. Fetal cell isolation does not require the percoll gradient step.
Made using the GemCode Single-Cell Instrument (10x Genomics) and Single Cell 3' Library & Gel Bead Kit v2 and Chip Kit (10x Genomics)

value: second trimester fetal

tag: tissue

value: brain


title: HFA567: Fetal single cell RNA sequencing material


title: HFA579: Fetal single cell RNA sequencing material


title: HFA571: Fetal single cell RNA sequencing material


title: RNAseq_78346


title: RNAseq_80349


title: RNAseq_73457


title: RNAseq_41426


title: RNAseq_83587


title: MM_70 (IR-seq)

city: Seoul

first: Sungyoung

last: Lee

address: 101 Daehak-ro

department: Center for Precision Medicine

country: South Korea

institute: Seoul National University Hospital

data_processing:
Library strategy: IR-seq
detected TCR sequences were aligned to the human reference V, D, J and C genes of TCRs using MiXCR version 2.1.9
Overlapping fragmented sequencing reads that were partially aligned were assembled into CDR3-containing contigs
clonotypes and then extracted after sequencing quality score filtering and error correction
TCR repertoires from bulk transcriptome sequencing data were also determined using MiXCR, which uses parameters specifically optimized for RNA-seq to detect sequences with small parts of the TCR region in detail
Genome_build: human reference V, D, J and C genes of TCRs
Supplementary_files_format_and_content: TCR repertoire analysis result files conducted with RNA-Seq data were named starting with "RNA-neg" and "MM-rep" for IR-Seq.

source_name: Bone Marrow (BM)

extract_protocol:
For the isolation of CD138- cells directly from whole BM samples, the mononuclear cell (MNC) layer was first depleted and separated MNCs were then released with MACS buffer followed by incubation with 20 µl of CD138 magnetically labeled microbeads.
RNA libraries were prepared for sequencing using standard Illumina protocols. TCR libraries with molecular barcoded (MBC) adaptors to amplify the T-cell receptor alpha/delta and beta/gamma chains were constructed using the Immunoverse™ kit (ArcherDX) after PCR amplification.

tag: disease state

value: multiple myeloma

tag: sample

tag: Sex

value: male

value: BM

tag: cell sorting

value: 138 negative


title: RNAseq_50954

tag: current smoker


title: MM_72 (IR-seq)


title: MM_71 (IR-seq)


title: RNAseq_88837

tag: pack years


title: MM_68 (IR-seq)


title: MM_7 (IR-seq)


title: MM_67 (IR-seq)


title: RNAseq_72390

tag: eosinophil percent


title: MM_61 (IR-seq)

tag: age


title: RNAseq_93053

tag: monocyte percent


title: MM_50 (IR-seq)


title: RNAseq_99284

tag: basophil percent


title: MM_5 (IR-seq)


title: MM_6 (IR-seq)


title: RNAseq_74278

tag: batch


title: RNAseq_55701

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


title: RNAseq_70840

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


title: RNAseq_16506

tag: fev1 % predicted


title: RNAseq_46386

tag: neutrophil percent


title: MM_49 (IR-seq)


title: RNAseq_96694

tag: lymphocyte percent


title: MM_48 (IR-seq)

tag: tissue


title: MM_47 (IR-seq)

tag: disease state


title: RNAseq_77053


title: MM_46 (IR-seq)

tag: sample


title: MM_44 (IR-seq)

tag: Sex


title: MM_66 (IR-seq)

tag: cell sorting


title: RNAseq_04650

tag: current smoker


title: MM_42 (IR-seq)


title: RNAseq_84413

tag: pack years


title: RNAseq_08560

tag: eosinophil percent


title: MM_41 (IR-seq)

tag: age


title: RNAseq_17517

tag: monocyte percent


title: RNAseq_57046

tag: basophil percent


title: MM_4 (IR-seq)


title: RNAseq_71085

tag: batch


title: MM_39 (IR-seq)


title: MM_38 (IR-seq)


title: RNAseq_95520

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


title: RNAseq_86860

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


title: RNAseq_44829

tag: fev1 % predicted


title: MM_40 (IR-seq)


title: MM_37 (IR-seq)


title: MM_36 (IR-seq)


title: MM_35 (IR-seq)


title: RNAseq_90315

tag: neutrophil percent


title: MM_34 (IR-seq)


title: MM_31 (IR-seq)


title: RNAseq_68492

tag: lymphocyte percent


title: RNAseq_44744


title: RNAseq_42800


title: MM_29 (IR-seq)

tag: tissue


title: MM_19 (IR-seq)

tag: disease state


title: MM_10 (IR-seq)

tag: sample


title: RNAseq_21295


title: RNAseq_18692


title: MM_1 (IR-seq)

tag: Sex


title: RNAseq_54291


title: RNAseq_10938


title: VCaPrev_1

city: Göttingen

first: Oliver

last: Hahn

address: Robert-Koch-Str. 40

department: Department of Urology

country: Germany

institute: University Medical Center Göttingen

data_processing:
Base calling was done using the BaseCaller to bcl files function in the Illumina software.
De-multiplexing was done using bcl2fastq (version 2.17.1.14).
Fastq files were then mapped to the human transcriptome (UCSC HG19) using TopHat2 (version 2.1.0) with very sensitive Bowtie2 settings
Differential gene expression was assessed with the Cuffdiff function of the Cufflinks package (version 2.2.1).
Genome_build: hg19
Supplementary_files_format_and_content: Normalized abundance measurements resulting from cuffdiff analysis of VCaP samples vs. VCaPrev samples

growth_protocol: Cells were cultured in phenol-red free DMEM with 10% fetal bovine serum (both Sigma Aldrich, Taufkirchen, Germany). For the experiments, cells were kept under 35 passages and confluence was kept under 80%.

extract_protocol:
Total RNA was extracted using Trizol extraction and quantified with a Qubit 3 fluorometer. RNA quality was checked on a 1.5% agarose gel. 1 µg of total RNA was then used for library preparation.
Library preparation was done with a total amount of 1 µg RNA per sample using the TruSeq RNA Library Prep Kit v2 (Illumina Inc., San Diego, CA, USA). Size range was verified to be around 280 bp using BioAnalyzer 2100 (Agilent Technologies. Santa Clara, CA, USA). Sequencing was done at the NGS core facility (NIG) at the University Medical Center Göttingen on an Illumina HiSeq 4000 platform

treatment_protocol: Androgen-dependent VCaPrev cells were kept with 1 nM Testosterone over 20 passages. Control cells were grown in normal DMEM media.

tag: cell line background

value: VCaP

tag: cell type

value: prostate cancer cell line

tag: treatment

value: 1 nM testosterone


title: RNAseq_74116

tag: current smoker

tag: pack years

tag: eosinophil percent


title: RNAseq_59091

tag: age

tag: monocyte percent

tag: basophil percent


title: RNAseq_91117

tag: batch

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

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


title: VCaPrev_2


title: RNAseq_50121

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_43329


title: RNAseq_30392


title: RNAseq_72520


title: siFOXA1_plus_IFNα-Rep.3

first: LIGUO

last: WANG

address: 200 1st St SW

department: Division of Computational Biology

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg38) using STAR (2.5.2b)
RseQC was used to calculate gene expression
hg38
FPKM

source_name: prostate

growth_protocol: Cells were maintained at 37°C and 5% CO2 in RPMI 1640 containing 10% fetal bovine serum (FBS) and 1% antibiotic/antimycotic (Thermo Fisher Scientific).FGF-2 (NS expansion medium).

extract_protocol:
RNeasy Mini Kit (Cat No.74104, QIAGEN)
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: LNCaP cells was treated with vehicle (PBS) or 100ng/L IFNα for 24 hours.

value: prostate cancer

tag: passages


title: siFOXA1_plus_siSTAT2_plus_IFNα-Rep.2


title: siFOXA1_plus_siSTAT2_plus_IFNα-Rep.1


title: siFOXA1_plus_IFNα-Rep.2


title: RNAseq_93861


title: siFOXA1_plus_IFNα-Rep.1


title: RNAseq_14122


title: siCon_plus_IFNα-Rep.3


title: RNAseq_71524


title: RNAseq_74045


title: RNAseq_71349


title: siCon_plus_IFNα-Rep.1


title: RNAseq_34155


title: siFOXA1-Rep.3


title: siFOXA1-Rep.2


title: RNAseq_44346


title: RNAseq_04896


title: RNAseq_30015


title: siFOXA1_plus_siSTAT2_plus_IFNα-Rep.3


title: siFOXA1-Rep.1


title: siCon-Rep.2


title: RNAseq_73184


title: siCon-Rep.1


title: RNAseq_56800


title: RNAseq_01707


title: RNAseq_71125


title: RNAseq_00571


title: STAT2-siFOXA1_FOXA1-△αH3_IFNα_positive_Rep.2

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
mm9
wig files were generated using …; Scores represent …

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: LNCaP cells was treated with vehicle (PBS) or 100ng/L IFNα for 6 hours.

tag: chip antibody

value: anti-STAT2 #72604S, Cell Signaling Technology


title: STAT2-siFOXA1_FOXA1△SBR_IFNα_positive_Rep.1


title: siCon_plus_IFNα-Rep.2


title: STAT2-siFOXA1_FOXA1-R261G_IFNα_positive_Rep.2


title: STAT2-siFOXA1_FOXA1△αH3_IFNα_positive_Rep.1


title: STAT2-siFOXA1_FOXA1-R261G_IFNα_positive_Rep.1


title: STAT2-siFOXA1_FOXA1-WT_IFNα_positive_Rep.2


title: RNAseq_26175


title: STAT2-siFOXA1_Vector_IFNα_positive_Rep.2


title: siCon-Rep.3


title: RNAseq_68098


title: RNAseq_44267


title: RNAseq_71182


title: RNAseq_79644


title: STAT2-siFOXA1_Vector_IFNα_positive_Rep.1


title: RNAseq_53232


title: RNAseq_60971


title: STAT2-siFOXA1_FOXA1-WT_IFNα_positive_Rep.1


title: RNAseq_77456


title: STAT2-siFOXA1_FOXA1-△SBR_IFNα_positive_Rep.2


title: RNAseq_56671


title: STAT2-siCon_Vector_IFNα_positive_Rep.2


title: STAT2-siFOXA1_Vector_IFNα_negative_Rep.1


title: RNAseq_95704


title: STAT2-siCon_Vector_IFNα_positive_Rep.1


title: STAT2-siFOXA1_Vector_IFNα_negative_Rep.2


title: STAT2-siCon_Vector_IFNα_negative_Rep.2


title: RNAseq_12068


title: RNAseq_01125


title: RNAseq_83184


title: RNAseq_75062


title: STAT2-siCon_Vector_IFNα_negative_Rep.1


title: IgG-siCon_Vector_IFNα_positive

value: IgG #3900, Cell Signaling Technology


title: RNAseq_76835


title: IgG-siFOXA1_Vector_IFNα_positive


title: RNAseq_74707


title: RNAseq_42798


title: ML_pre ketogenic diet [MUC11748_S67]

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

data_processing:
trimming of adapter sequences using BBDUK k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20
alignment of sequences using STAR against GRCh38.93 --runThreadN 8 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --readFilesCommand zcat --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outFileNamePrefix
counting of reads at gene level using htseq -m intersection-nonempty -s yes -f bam -r pos using  Homo_sapiens.GRCh38.93.gtf
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: ML_pre ketogenic diet

growth_protocol: PBMCs were obtained by density centrifugation (Histopaque 1077, Sigma-Aldrich, St. Louis, MO, USA). A ViCell analyzer (Beckman Coulter, Fullerton, CA, USA) was used to evaluate the cell count and viability. Only samples exceeding a cell viability of 90% were processed further. PBMCs were subjected to cell cultivation in RPMI 1640 (Invitrogen, Carlsbad, CA, USA) containing 10% heat-inactivated fetal calf serum (Biochrom, Berlin, Germany), 1% HEPES (Sigma-Aldrich, St. Louis, MO) and 1% L-glutamine (Life Technologies, Carlsbad, CA, USA).

extract_protocol:
After stimulation, CD3/CD28 Dynabeads were magnetically removed. Pan T cell-, CD4+- and CD8+-cell-isolation was performed by magnetic cell separation (Pan T Cell Isolation Kit, # 130-096-535 | human CD4 MicroBeads, # 130-045-101 | human CD8 MicroBeads, # 130-045-201, Miltenyi Biotec, Bergisch Gladbach, Germany) using an AutoMACS Pro Separator ( # 130-092-545, Miltenyi Biotec, Bergisch-Gladbach, Germany) according to the manufacturer’s instructions. Total RNA was isolated from primary T cells using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA, USA) with subsequent DNase treatment (Turbo DNase, Thermo Fisher Scientific, Waltham, MA, USA) or miRNeasy RNA Isolation Kit (#217004, Quiagen, Hilden, Germany) with on-column DNA digestion. For RNA purification, the Monarch RNA Clean-up Kit (New England Biolabs, Ipswich, MA, USA) was utilized. All isolation procedures have been performed according to the respective manufacturer’s instructions. RNA quantity and purity were measured using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). First-strand cDNA was synthesized from equal amounts of RNA using Superscript III reverse transcriptase (Invitrogen, Carlsbad, CA, USA), random hexamers and oligo(dT) primers.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: T cells were stimulated via the addition of CD3/CD28 Dynabeads (Thermo Fisher Scientific, Waltham, MA, USA) with a bead-to-cell ratio of 1:8 for a duration 24 hours.

tag: subject status

value: Healthy volunteers

tag: treatment/time point

value: pre ketogenic diet

tag: tissue

value: blood

value: PBMCs; CD4+/CD8+ T cells


title: ML_pre ketogenic diet [MUC11746_S65]

tag: cell type


title: CR_post ketogenic diet [MUC11745_S64]

source_name: CR_post ketogenic diet

value: post ketogenic diet


title: RNAseq_75743

tag: current smoker

tag: pack years


title: ML_post ketogenic diet [MUC11747_S66]

source_name: ML_post ketogenic diet


title: RNAseq_80018

tag: age

tag: eosinophil percent


title: RNAseq_08297

tag: monocyte percent

tag: basophil percent


title: CR_pre ketogenic diet [MUC11744_S63]

source_name: CR_pre ketogenic diet


title: CR_post ketogenic diet [MUC11743_S62]


title: RNAseq_06484

tag: batch

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


title: CD_post ketogenic diet [MUC11741_S60]

source_name: CD_post ketogenic diet


title: RNAseq_95575

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


title: RNAseq_01080

tag: fev1 % predicted

tag: neutrophil percent


title: RNAseq_15401

tag: lymphocyte percent


title: CD_post ketogenic diet [MUC11739_S58]


title: RNAseq_42726


title: ML_post ketogenic diet [MUC11749_S68]


title: SiS_post ketogenic diet [MUC11737_S56]

source_name: SiS_post ketogenic diet


title: RNAseq_67270


title: MH_post ketogenic diet [MUC11733_S52]

source_name: MH_post ketogenic diet


title: SiS_pre ketogenic diet [MUC11736_S55]

source_name: SiS_pre ketogenic diet


title: RNAseq_43138


title: RNAseq_31133


title: MH_pre ketogenic diet [MUC11732_S51]

source_name: MH_pre ketogenic diet


title: MH_post ketogenic diet [MUC11731_S50]


title: RNAseq_17957

source_name: blood


title: RNAseq_96234


title: CR_pre ketogenic diet [MUC11742_S61]


title: CD_pre ketogenic diet [MUC11738_S57]

source_name: CD_pre ketogenic diet


title: RNAseq_85456


title: RNAseq_18599


title: GG_pre ketogenic diet [MUC11728_S47]

source_name: GG_pre ketogenic diet


title: RNAseq_23266


title: RNAseq_79502


title: GG_post ketogenic diet [MUC11729_S48]

source_name: GG_post ketogenic diet


title: MH_pre ketogenic diet [MUC11730_S49]


title: CD_pre ketogenic diet [MUC11740_S59]


title: RNAseq_87577


title: RNAseq_08782


title: GG_post ketogenic diet [MUC11727_S46]


title: GG_pre ketogenic diet [MUC11726_S45]


title: RNAseq_64027


title: RNAseq_95590


title: KK_post ketogenic diet [MUC11725_S44]

source_name: KK_post ketogenic diet


title: KK_pre ketogenic diet [MUC11724_S43]

source_name: KK_pre ketogenic diet


title: RNAseq_75029


title: KN_post ketogenic diet [MUC11721_S40]

source_name: KN_post ketogenic diet


title: KK_pre ketogenic diet [MUC11722_S41]


title: RNAseq_55133


title: RNAseq_01285


title: RNAseq_09428


title: KN_pre ketogenic diet [MUC11718_S37]

source_name: KN_pre ketogenic diet


title: KN_pre ketogenic diet [MUC11720_S39]


title: KN_post ketogenic diet [MUC11719_S38]


title: RNAseq_99534


title: RNAseq_37350


title: RNAseq_42829


title: RNAseq_69683


title: RNAseq_26555


title: RNAseq_99255


title: XK_pre ketogenic diet [MUC11712_S31]

source_name: XK_pre ketogenic diet


title: NG_post ketogenic diet [MUC11715_S34]

source_name: NG_post ketogenic diet


title: XK_post ketogenic diet [MUC11713_S32]

source_name: XK_post ketogenic diet


title: RNAseq_30409


title: RNAseq_94204


title: NG_pre ketogenic diet [MUC11714_S33]

source_name: NG_pre ketogenic diet


title: NG_pre ketogenic diet [MUC11716_S35]


title: KK_post ketogenic diet [MUC11723_S42]


title: RNAseq_60502


title: XK_post ketogenic diet [MUC11711_S30]


title: RNAseq_61259


title: RNAseq_61085


title: RNAseq_92665


title: RNAseq_67484


title: NK_post ketogenic diet [MUC11709_S28]

source_name: NK_post ketogenic diet


title: XK_pre ketogenic diet [MUC11710_S29]


title: RNAseq_35763


title: NK_pre ketogenic diet [MUC11708_S27]

source_name: NK_pre ketogenic diet


title: RNAseq_83077


title: RNAseq_53604


title: RNAseq_23154


title: NK_post ketogenic diet [MUC11707_S26]


title: NK_pre ketogenic diet [MUC11706_S25]


title: KjK_pre ketogenic diet [MUC11704_S23]

source_name: KjK_pre ketogenic diet


title: RNAseq_79045


title: TW_post ketogenic diet [MUC11701_S20]

source_name: TW_post ketogenic diet


title: RNAseq_64518


title: lymphoma 1123, rep1

type: RNA

city: Berlin

first: Maja

last: Milanovic

address: Augustenburgerplatz 1

department: Hematology and Oncology

institute: Charite University Medicine, Berlin

description: Gene expression data from primary Emu-myc lymphomas in therapy-naive state or after drug chalenge

hyb_protocol: Following fragmentation, 3 ug of cDNA were hybridized for 16 hr at 45°C on Mouse Gene ST 1.0 Arrays (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner G3000.

data_processing: Affymetrix CEL files were imported into Partek Genomics Suite Software (Version 6.5, Partek Inc., St. Louis, USA) and processed by the implemented RMA workflow (median polish probe set summarization, RMA background correction, quantile normalization).

organism: Mus musculus

source_name: primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice with palpable lymphadenopathy

label_protocol: Biotinylated cDNA was prepared according to the standard WT Expression Kit protocol (Ambion) and GeneChip® WT Terminal Labeling and Hybridization Kit protocol (Affymetrix) using 100 ng total RNA.

growth_protocol: The lymphoma cells from lymph nodes of Emu-myc transgenic mice (explated upon spontaneous lymphoma development) were used directly for RNA extraction, without cell purification or in vitro cultivation.

extract_protocol: The total RNA from aliquots of primary lymphoma cells, explated from lymph nodes of Emu-myc transgenic mice, was prepared using an RNeasy Mini kit (QIAGEN, Valencia, California) according to the manufacturer's instructions.

treatment_protocol: Recipient mice transplanted with primary Emu-myc lymphomas were treated upon palpable lymphoma formation with a single dose Cyclophosphamide (CTX), 300mg/kg body weight, i.p.

tag: strain/background

tag: genotype

value: Emu-myc transgenic

value: primary lymphoma cells from lymph node

tag: treatment

value: CTX 4h


title: lymphoma 1112, rep1

value: native


title: lymphoma 1119, rep1


title: TW_pre ketogenic diet [MUC11700_S19]

source_name: TW_pre ketogenic diet

tag: subject status

tag: treatment/time point

tag: tissue


title: lymphoma 9820, rep1

tag: cell type


title: lymphoma 1127, rep1


title: lymphoma 1135, rep1


title: lymphoma 1126, rep1


title: lymphoma 1113, rep1


title: RNAseq_78109

source_name: blood

tag: current smoker

tag: pack years

tag: age


title: lymphoma 1124, rep1


title: lymphoma 1114, rep1


title: lymphoma 1118, rep1


title: KjK_post ketogenic diet [MUC11705_S24]

source_name: KjK_post ketogenic diet


title: lymphoma 1132, rep1


title: lymphoma 1120, rep1


title: RNAseq_55153

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: TW_post ketogenic diet [MUC11699_S18]


title: RNAseq_86596

tag: batch

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

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


title: TW_pre ketogenic diet [MUC11698_S17]


title: lymphoma 9203, rep1


title: RNAseq_84271

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent


title: lymphoma 9197, rep1

tag: strain/background

tag: genotype

tag: treatment


title: lymphoma 9204, rep1


title: lymphoma 1117, rep1


title: PS_pre ketogenic diet [MUC11696_S15]

source_name: PS_pre ketogenic diet

tag: subject status

tag: treatment/time point

tag: tissue


title: lymphoma 9192, rep1

tag: cell type


title: RNAseq_15381

tag: current smoker

tag: pack years

tag: age


title: RNAseq_46504

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: RS_pre ketogenic diet [MUC11692_S11]

source_name: RS_pre ketogenic diet


title: RS_post ketogenic diet [MUC11691_S10]

source_name: RS_post ketogenic diet


title: PS_pre ketogenic diet [MUC11694_S13]


title: RNAseq_12670

tag: batch

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

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


title: RNAseq_33246

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent


title: RS_post ketogenic diet [MUC11693_S12]


title: JA2_Tissue_b_S88_L004

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

data_processing:
RNASeq data was processed using kallisto (version 0.45.0) and human genome GRCh38 Ensembl version 94 annotation (Homo_sapiens.GRCh38.94.chr_patch_hapl_scaff.gtf). Gene-level TPM values and gene annotations were computed using tximport and biomaRt R package. A custom python script was used to organize the data and log reduced using log2(TPM) if TPM > 1 and TPM - 1 if TPM <= 1.
Genome_build: Genome assembly: GRCh38.p12, Gene annotatiopn: Homo_sapiens.GRCh38.94.chr_patch_hapl_scaff.gtf
Supplementary_files_format_and_content: tab-delimited text files include log2(TPM) if TPM > 1 else TPM - 1 values for each Sample.

source_name: Lung

growth_protocol: Stem cells were isolated from human lung tissue and cultured as 3D organoids. The organoids were broken into single cells and seeded as a monolayer in a 384-well plate.

extract_protocol:
RNA were extracted using the Quick-RNA MicroPrep Kit (Zymo Research, USA) according to the manufacture’s instruction. RNA was converted into cDNA using the qScript™ cDNA SuperMix (Quantabio).
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

tag: condition

value: Tissue

tag: infection

value: Uninfected


title: RNAseq_56890


title: RNAseq_43787


title: RNAseq_97911


title: PS_post ketogenic diet [MUC11697_S16]

source_name: PS_post ketogenic diet

tag: subject status

tag: treatment/time point


title: RNAseq_07353


title: PS_post ketogenic diet [MUC11695_S14]

tag: tissue

tag: cell type


title: lymphoma 9182, rep1

tag: strain/background

tag: genotype

tag: treatment


title: JA2_Tissue_a_S87_L004


title: lymphoma 9189, rep1


title: lymphoma 9186, rep1


title: lymphoma 9188, rep1


title: lymphoma 9183, rep1


title: lymphoma 9190, rep2


title: lymphoma 9184, rep1


title: lymphoma 9195, rep1


title: JA2_org_P1_S83_L004

value: Organoid


title: RNAseq_65702

tag: current smoker

tag: pack years

tag: age

tag: eosinophil percent

tag: monocyte percent


title: JA1_Tissue_a_S85_L004


title: lymphoma 9181, rep1


title: JA1_Tissue_b_S86_L004


title: RNAseq_33697

tag: batch

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

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

tag: fev1 % predicted

tag: basophil percent


title: RS_pre ketogenic diet [MUC11690_S9]

tag: subject status


title: RNAseq_93567

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_85746


title: RNAseq_34530


title: JA1_org_P4_S84_L004

tag: condition

tag: infection


title: JA1_org_P1_S82_L004


title: RNAseq_81748


title: lymphoma 9177, rep1

tag: strain/background

tag: genotype

tag: cell type


title: NCC-RbC-51 Xenograft, rep3

description:
sailaja-2020-cells-expr.txt
Xeno_3

data_processing:
RNASeq data was processed using kallisto (version 0.45.0) and human genome GRCh38 Ensembl version 94 annotation (Homo_sapiens.GRCh38.94.chr_patch_hapl_scaff.gtf). Transcript level TPM values were added together to generate a gene-level TPM value. A custom perl script was used to organize and normalize data using log2(TPM+1).
Genome_build: Genome assembly: GRCh38.p12, Gene annotatiopn: Homo_sapiens.GRCh38.94.chr_patch_hapl_scaff.gtf
Supplementary_files_format_and_content: tab-delimited text file includes log2(TPM+1) values for each Sample

growth_protocol: Retinoblastoma cell line NCC-RbC-51 (Riken, Japan) was maintained in Roswell Park Memorial Institute media (RPMI 1640, Gibco, A10491-01).  These were the cells grown in 2 dimensions on normal tissue culture plate.  The cells grown on graphene sponge were considered as invitro 3-dimensional model for cell growth. PLL was added onto the graphene foam surface in 1:10 (v/v) dilution with sterile water and incubated for 3 h prior to NCC-RbC-51 cell seeding followed by washes with PBS and allowed to dry. Prior to cell seeding on to the scaffold the cells were made into cancer cell clusters as single cell suspensions did not attach well on the foams and they went through the pores and attached to the bottom of the cell culture plate. The NCC-RbC-51 cells under normal culture conditions form grape like clusters of 50-100 cells. These clusters were retained during cell seeding by gentle collection of the cells with minimal media volume (~200μl for 1 cm2 foam).  After incubation time, complete media were supplemented. Caution was taken during media supplementation as sudden jerky movements caused dislodging of the cells from the scaffold. The cells were grown for 72h and taken for global transcriptomic studies by RNA sequencing as tissue culture plate grown cells exhibited increased cell death after this time period.

extract_protocol:
RNA extraction for sequencing experiments were performed using RNeasy Mini Kit (Qiagen, Cat# 74104) then quantified using Qubit RNA Assay HS (Invitrogen, Cat# Q32855). RNA was isolated  from NCC-RbC-51 cells grown on tissue culture plate, graphene sponges and xenograft tissue s(N=3).  RNA purity was checked using QIAxpert and RNA integrity was assessed on TapeStation using RNA ScreenTapes (Agilent, Cat# 5067-5576).
NEB Ultra RNA-Seq Library Prep kit protocol (NEB, E7530L) was used to prepare libraries for total RNA sequencing. RNA (200ng) was depleted ribosomal RNA (rRNA) using biotinylated, target-specific oligos combined with Ribo-Cop rRNA removal beads. Following purification, the ribodepleted RNA was fragmented using divalent cations under elevated temperatures. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase. Second strand cDNA synthesis was performed, using DNA Polymerase I and RNase H enzyme. The cDNA fragments were then subjected to a series of enzymatic steps which repair the ends, tails the 3’ end with a single ‘A’ base, followed by ligation of the adapters. The adapter ligated products were then purified and enriched using the following thermal conditions: initial denaturation 98°C for 30sec; 13 cycles of - 98°C for 10sec, 65°C for 75sec; final extension of 65°C for 5mins. PCR products are then purified and checked for fragment size distribution on TapeStation using D1000 DNA ScreenTapes (Agilent, Cat# 5067-5582).  The adapter sequences used are presented in Supplementary Table 3. Prepared libraries were quantified using Qubit High Sensitivity Assay (Invitrogen, Cat# Q32854). The obtained libraries were pooled and diluted to final optimal loading concentration before cluster amplification on Illumina flow cell. Once the cluster generation is completed, the cluster flow cell is loaded on Illumina HiSeq 4000 instrument to generate 40M, 100bp paired end reads. The raw reads were filtered using Trimmomatic for Quality scores and adapters. Filtered reads were aligned to human genome using splice aware aligner like HISAT2 to quantify reads mapped to each transcript.

treatment_protocol: Normal retina, retinoblastoma, xenografts, cultured cell lines in standard plate and graphene sponge were used to perform RNA-seq.

tag: tissue

value: Xenograft


title: RNAseq_69472

tag: current smoker

tag: pack years

tag: age


title: RNAseq_94784

tag: batch

tag: eosinophil percent

tag: monocyte percent


title: RNAseq_11833

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

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

tag: fev1 % predicted


title: NCC-RbC-51 TC, rep3

description:
sailaja-2020-cells-expr.txt
Plate_BT3

value: Tissue Culture


title: NCC-RbC-51 Xenograft, rep1

description:
sailaja-2020-cells-expr.txt
Xeno_1


title: RNAseq_77812

tag: neutrophil percent

tag: basophil percent


title: NCC-RbC-51 TC, rep2

description:
sailaja-2020-cells-expr.txt
Plate_BT2

tag: condition


title: NCC-RbC-51 TC, rep1

description:
sailaja-2020-cells-expr.txt
Plate_BT1


title: RNAseq_20367

tag: lymphocyte percent


title: NCC-RbC-51 Xenograft, rep2

description:
sailaja-2020-cells-expr.txt
Xeno_2_RNA


title: lymphoma 8775, rep1

tag: strain/background

tag: treatment


title: RNAseq_15515


title: lymphoma 9174, rep1

tag: genotype

tag: cell type


title: lymphoma 9160, rep1


title: NCC-RbC-51 Graphene, rep2

description:
sailaja-2020-cells-expr.txt
GF_BT2

tag: tissue

value: Graphene Sponge Culture


title: lymphoma 9180, rep1


title: lymphoma 8768, rep1


title: lymphoma 8773, rep1


title: lymphoma 8772, rep1


title: NCC-RbC-51 Graphene, rep3

description:
sailaja-2020-cells-expr.txt
GF_BT3


title: lymphoma 8765, rep1


title: NCC-RbC-51 Graphene, rep1

description:
sailaja-2020-cells-expr.txt
GF_BT1


title: lymphoma 8766, rep1


title: lymphoma 9161, rep1


title: Conjunctival melanoma cell-shBACE2-3

city: Shanghai

first: Fanglin

last: He

address: 639 Zhizaoju Rd

institute: Shanghai Ninth People's Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
R software Ballgown was used for RPKM calculation.
Genome_build: Hg19
Supplementary_files_format_and_content: txt files include RPKM values for each Sample

source_name: Derived from  CM patient

growth_protocol: Conjunctival melanoma cells were extracted from conjunctival melanoma and cultured in a 6 mm culture dish with f-12k

extract_protocol:
Conjunctival melanoma cells samples were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Conjunctival melanoma

tag: diagnosis

tag: tumor stage

tag: knockdown


title: RNAseq_96618

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

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: age

tag: eosinophil percent


title: RNAseq_27177

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

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

tag: fev1 % predicted

tag: neutrophil percent

tag: monocyte percent


title: Conjunctival melanoma cell-shBACE2-2


title: RNAseq_68219

tag: lymphocyte percent

tag: basophil percent


title: NG_post ketogenic diet [MUC11717_S36]

source_name: NG_post ketogenic diet

tag: subject status

tag: treatment/time point

tag: cell type


title: lymphoma 8771, rep1

tag: strain/background

tag: genotype

tag: treatment


title: lymphoma 8762, rep1


title: RNAseq_13878

tag: batch

tag: current smoker


title: RNAseq_30016

tag: pack years

tag: age


title: Conjunctival melanoma cell-shBACE2-1

tag: tissue

tag: diagnosis

tag: tumor stage

tag: knockdown


title: RNAseq_23239

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

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

tag: fev1 % predicted

tag: neutrophil percent

tag: eosinophil percent

tag: monocyte percent


title: RNAseq_77378

tag: lymphocyte percent

tag: basophil percent


title: Conjunctival melanoma cell-shNC3

value: control


title: RNAseq_23576


title: Conjunctival melanoma cell-shNC2


title: Conjunctival melanoma cell-shNC1


title: RNAseq_75949


title: lymphoma 8767, rep1

tag: strain/background

tag: genotype

tag: cell type

tag: treatment


title: RNAseq_91991

tag: batch

tag: current smoker

tag: pack years

tag: age


title: RNAseq_44559


title: RNAseq_75621


title: lymphoma 8127, rep1


title: RNAseq_50897


title: lymphoma 8733, rep1


title: RNAseq_16956


title: RNAseq_40422


title: lymphoma 8731, rep1


title: lymphoma 9194, rep1

label_protocol: Biotinylated cDNA was prepared according to the standard WT Expression Kit protocol (Ambion) and GeneChip® WT Terminal Labeling and Hybridization Kit protocol (Affymetrix) using 300 ng total RNA.

growth_protocol: Primary Emu-myc lymphoma cells explated from lymph nodes of transgenic Emu-myc mice upon spontaneous lymphoma development were used directly for RNA extraction, without in vitro cultivation.

tag: lymphoma identifier


title: lymphoma 9201, rep1


title: lymphoma 9173, rep1


title: lymphoma 9205, rep1


title: lymphoma 9193, rep1


title: lymphoma 8754, rep1


title: lymphoma 9178, rep1


title: lymphoma 9196, rep1


title: lymphoma 8753, rep1


title: lymphoma 8778, rep1


title: RNAseq_05392

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


title: lymphoma 8751, rep1


title: RNAseq_07784

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


title: RNAseq_54980

tag: fev1 % predicted


title: RNAseq_85318

tag: neutrophil percent


title: lymphoma 8747, rep1


title: RNAseq_21445

tag: eosinophil percent


title: RNAseq_56029

tag: monocyte percent


title: RNAseq_26192

tag: lymphocyte percent


title: RNAseq_47748

tag: basophil percent


title: RNAseq_52975


title: RNAseq_70796


title: lymphoma 8737, rep1

tag: strain/background


title: lymphoma 8742, rep1

tag: genotype


title: RNAseq_94907


title: lymphoma 8728, rep1

tag: cell type


title: lymphoma 8740, rep1

tag: treatment


title: lymphoma 8082, rep1


title: RNAseq_55315

tag: batch


title: Subject_218_Day 3

city: Baltimore

first: Xu

last: Wang

state: MD

address: 725 W Lombard St

institute: University of Maryland Baltimore

data_processing:
Raw fastq files were analyzed using FastQC v0.11.5 and trimming was performed on raw reads using Trimmomatic v0.35
Reads mapping to the reference genome (GRCh38) was performed on quality-checked and trimmed reads using HISAT2
The overlap of reads with annotation features found in the reference.gtf was calculated using HT-seq v0.6.1
Raw counts were normalized using DESeq2’s function “fpkm” and the expression value of FPKM was used for differential gene expression analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file were generated using DESeq2; Values represent FPKM (fragments per kilobase of exon model per million reads mapped)

source_name: PBMC

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA quality was assessed with the Agilent Bioanalyzer 2100. Only samples with RIN scores above 7 and a minimum total RNA of 200 ng were used for cDNA production.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Human subjects in the Phase I trial received single dose of CD24Fc (240 mg), PBMC samples were collected from human subjects on Day -1 (pre-treatment) and Day 3 (post-treatment) for RNA-sequencing.

tag: tissue

value: PBMC

tag: subject number

tag: time point

value: Day 3 (post-treatment)


title: RNAseq_94127

tag: current smoker

tag: pack years

tag: age


title: lymphoma 8734 rep1

tag: lymphoma identifier


title: Subject_218_Day -1

value: Day -1 (pre-treatment)


title: RNAseq_28767

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

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

tag: fev1 % predicted

tag: neutrophil percent


title: RNAseq_73675

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: Subject_214_Day 3

tag: treatment


title: Subject_214_Day -1


title: RNAseq_24268

tag: batch


title: Subject_211_Day -1

tag: tissue


title: RNAseq_26282


title: Subject_211_Day 3

tag: subject number


title: lymphoma 8744, rep1

tag: strain/background

tag: genotype

tag: cell type


title: Subject_179_Day 3

tag: time point


title: RNAseq_45656

tag: current smoker

tag: pack years

tag: age


title: RNAseq_29188

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

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

tag: fev1 % predicted


title: RNAseq_60537

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent


title: RNAseq_91445

tag: monocyte percent

tag: basophil percent


title: ext_L13376.1_305

first: Maria

last: Reichenbach

address: Thielallee 63

department: Institute for Chemistry and Biochemistry

institute: Freie Universität Berlin

data_processing:
base calling with HCS: HD 3.4.0.38, RTA: 2.7.7, BCL Converter: 2.20.0.422,
data was mapped against the GRCh38 genome obtained from (http://emea.support.illumina.com/sequencing/sequencing_software/igenome.html) using STAR v 2.5.3a (STAR: ultrafast universal RNA-seq aligner.: Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR).
TMM normalization of the read count data was applied
cpm-values were used for GLM-based testing with edgeR (Robinson MD, McCarthy DJ, Smyth GK (2010). “edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.” Bioinformatics, 26(1), 139-140. doi: 10.1093/bioinformatics/btp616.).
Genome_build: GRCh38 genome obtained from (http://emea.support.illumina.com/sequencing/sequencing_software/igenome.html)
Supplementary_files_format_and_content: txt, cpm-values of genes for all 12 samples

source_name: hFOB 1.10, ATCC® CRL-11372™

growth_protocol: Human fetal osteoblast cells (cell line hFOB 1.10, ATCC® CRL-11372™) were cultured in a 1:1 mixture of Dulbeccos’ Modified Eagle’s Medium (DMEM) and Ham’s F12 Medium with 2.5 mM L-glutamine and 8.1 mg/l Phenol Red (Thermo Fischer Scientific, Waltham, USA) supplemented with 10% Fetal Calf Serum (FCS, Biochrom AG, Berlin, Germany) and antibiotics (100 U/ml Penicillin and 0.1 mg/ml Streptomycin, PAN-Biotech GmbH, Aidenbach, Germany, and 0.3 mg/ml G418, Biochrom AG, Berlin, Germany). The cells were grown at a permissive temperature of 33.5°C(55) in a 5% CO2 humidified atmosphere

extract_protocol:
Cellular RNA was isolated using the NucleoSpin® RNA Isolation kit (Macherey-Nagel, Düren, Germany) according to manufacturer’s instructions.
For each experimental condition, three biological replicates were analyzed. After initial quality control using Agilent’s Bioanalyzer, sequencing libraries were prepared from 500ng of total RNA per sample following Roche’s stranded “KAPA RNA HyperPrep” library preparation protocol for single indexed Illumina libraries: First the polyA-RNA fraction was enriched using oligo-dT-probed paramagnetic beads. Enriched RNA was heat-fragmented and subjected to first strand synthesis using random priming. The second strand was synthesized incorporating dUTP instead of dTTP to preserve strand information. After A-tailing Illumina sequencing compatible adapters were ligated. Following bead-based clean-up steps the libraries were amplified using 10 cycles of PCR. Library quality and size was checked with qBit, Agilent Bioanalyzer and qPCR. Sequencing was carried out on an Illumina HiSeq 4000 system in PE75bp mode yielding between 15-23 million fragments per sample.

treatment_protocol: To deplete YAP and TAZ, cells were transfected with ON-TARGETplus SMARTpool human siRNA targeting YAP1 or WWTR1 (L-012200-00-0005 & L-016083-00-0005, Dharmacon, Lafayette, USA). Cells were transfected with a final siRNA concentration of 50 nM using Lipofectamine RNAiMAX (Thermo Fischer Scientific, Waltham, USA). Cells were analyzed 48 hours post-transfection to ensure efficient knockdown.BMP-2 was a generous gift by Prof. W. Sebald (Biozentrum Universität Würzburg, Würzburg, Germany). Generally, cells were starved for 4 hours in media without FCS, then stimulated with 5 nM BMP-2.

value: human fetal osteoblastic cell line

tag: cell line

value: hFOB 1.10, ATCC CRL-11372

tag: sirna

value: YAP/TAZ siRNA

tag: treatment

value: 5nM BMP2


title: ext_L13375.1_304


title: ext_L13373.1_302

value: scrambled siRNA


title: ext_L13374.1_303


title: RNAseq_51186

tag: batch


title: RNAseq_06362


title: ext_L13371.1_300

tag: cell type


title: ext_L13372.1_301


title: ext_L13370.1_299

value: 0nM BMP2


title: RNAseq_51365


title: ext_L13369.1_298


title: Melan-a KRAS G12V R2

city: New York

first: Tyler

last: Hitchman

state: NY

address: 417 E 68th Street

department: HOPP

institute: MSKCC

data_processing:
The sequenced reads from fastq files were mapped to mm9 using STAR version 2.330
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using  Cufflinks suite v2.2.1 (Trapnell Nature biotechnology). We ran cuffquant on each BAM file and then Cuffnorm using upper quartile normalization. Genes were mapped to Ensembl mm9
Please note the RPKM of the same cell type, including duplicates, were combined into a single file.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Melan-a mouse immortalized melanocytes

growth_protocol: Cells were grown in 10% FBS

extract_protocol:
RNA was purified using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: melan-a cells

tag: genotype

value: overexpressing KRAS G12V


title: Melan-a KRAS G12V R1


title: Melan-a GNAQ Q209L R2

value: overexpressing GNAQ Q209L


title: RNAseq_42128

first: Peter

last: Castaldi

address: 181 Longwood Ave

tag: current smoker


title: RNAseq_34913

tag: pack years


title: 3998998121_R06C02: genomic DNA from whole Blood

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.

source_name: Blood - buffy coat

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 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: F

value: Control

tag: status

tag: age


title: Subject_179_Day -1

tag: tissue

tag: subject number

tag: time point


title: ext_L13368.1_297


title: RNAseq_70704

institute: Brigham and Women's Hospital

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

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

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent


title: Melan-a GNAQ Q209L R1


title: 3998998121_R06C01: genomic DNA from whole Blood

value: M


title: CD96- hepatic NK cells

city: Hefei

first: Cheng

last: Sun

state: Anhui

address: 17, Lujiang Road

department: the First Affiliated Hospital of USTC

institute: University of Science and Technology of China

hyb_protocol: Gene ExpressionEach slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructionsHybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US),

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent technologies, Santa Clara, CA, US)settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction

source_name: CD96- hepatic NK cells

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit,OneOne -Color(Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US)

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: liver

value: NK cell

tag: sorted cell type


title: RNAseq_86851

city: Boston

tag: batch

tag: monocyte percent

tag: basophil percent


title: ext_L13367.1_296

tag: cell type

tag: cell line

tag: sirna

tag: treatment


title: RNAseq_74030

tag: current smoker

tag: pack years

tag: age


title: CD96+ hepatic NK cells

source_name: CD96+ hepatic NK cells

tag: tissue


title: 3998998121_R05C02: genomic DNA from whole Blood

source_name: Blood - EDTA tube

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: Schizophrenia

tag: status

value: Case


title: Melan-a R2

tag: genotype

value: Parental


title: RNAseq_65794

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

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

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_03051

tag: batch

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: 3998998121_R05C01: genomic DNA from whole Blood

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


title: 3998998121_R04C02: genomic DNA from whole Blood


title: RNAseq_82432

description:
gene_TMM_counts.csv
exon_TMM_counts.csv
isoform_TMM_counts.csv


title: RNAseq_82526


title: RNAseq_87302


title: 3998998121_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.


title: ext_L13365.1_294

tag: cell type

value: human fetal osteoblastic cell line

tag: cell line

tag: sirna

tag: treatment


title: 482N1

city: sunnyvale

first: Chen-Hua

last: Chuang

address: 963 E homestead rd

institute: amgen

description: TMet/Lymph node

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Using tophat/cuffduf to quantify expression
Genome_build: mm9
Supplementary_files_format_and_content: A single tab-delimited text file, including FPKM values for each Sample

source_name: lung cancer

growth_protocol: We initiated tumors in KrasLSL-G12D/+;p53flox/flox mice with a entiviral-Cre vectors and in vitro culture cancer cells.

extract_protocol:
Total RNA was extracted using the Qiagen RNAase Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tumor samples from defined stages of disease progression

tag: strain

tag: tumor genotype

value: KrasLSL-G12D/+;p53flox/flox (KP)

tag: metastasis status

value: metastatic

tag: tumor location

value: lymph node


title: 394T4

description: TnonMet/Lung

value: non-metastatic

value: lung


title: 368T1

description: TnonMet/Lung


title: 3998998121_R03C01: genomic DNA from whole Blood

tag: Sex

tag: status

tag: age


title: lentiVector OE R3 (RNA-seq)

city: Memphis

first: Mitch

last: Weiss

state: Tennessee

address: 262 Danny Thomas Place

department: Hematology

institute: st jude children's research hospital

description:
RNA.count.all.txt.gz
vector_control-R3

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were aligned and counted by RNA-seq pipeline(WARDEN) at https://www.stjude.cloud/tools.html
Briefly, paired-end reads were aligned to hg19 by STAR and counted by HTSEQ.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for each gene for each sample

growth_protocol: Cells were expanded in StemSpan serum-free expansion medium (SFEM; Stem Cell Technologies) supplemented with 1 µM dexamethasone, 1 µg/mL doxycycline, 50 ng/mL human stem cell factor (SCF), 3 units/mL erythropoietin (EPO), and 1% penicillin–streptomycin.

extract_protocol:
HUDEP-2 cells' RNA was harvested using RLT reagent (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: erythroblast cells

tag: tissue

value: Umbilical Cord blood derived

tag: genotype

value: vector control


title: lentiVector OE R1 (RNA-seq)

description:
RNA.count.all.txt.gz
vector_control-R1


title: lentiVector OE R2 (RNA-seq)

description:
RNA.count.all.txt.gz
vector_control-R2


title: 3998998121_R03C02: genomic DNA from whole Blood

value: F


title: 238N1

description: TMet/Lymph node


title: 3998998121_R02C02: genomic DNA from whole Blood


title: CDT2-V5 OE R3 (RNA-seq)

description:
RNA.count.all.txt.gz
CDT2-V5-R3

value: CDT2-V5 overexpression


title: RNAseq_00298

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

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_41108

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: Melan-a CYSLTR2 L129Q TRAM 24hr R2

data_processing:
The sequenced reads from fastq files were mapped to mm9 (melan-a) and hg19 using STAR version 2.330
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using  Cufflinks suite v2.2.1 (Trapnell Nature biotechnology). We ran cuffquant on each BAM file and then Cuffnorm using upper quartile normalization. Genes were mapped to Ensembl  mm9 or Hg19 genome
Please note the RPKM of the same cell type, including duplicates, were combined into a single file.
Genome_build: mm9/hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was purified using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq per manufacturer's protocol

treatment_protocol: Cells were treated with the indicated drug(s) for indicated times

tag: exogenous expression

value: CYSLTR2 L129Q

tag: treatment

value: 100nM Trametinib


title: 3998998121_R02C01: genomic DNA from whole Blood

tag: Sex

value: Control

tag: status


title: CDT2-V5 OE R1 (RNA-seq)

description:
RNA.count.all.txt.gz
CDT2-V5-R1

tag: cell line

tag: cell type

tag: tissue


title: CDT2-V5 OE R2 (RNA-seq)

description:
RNA.count.all.txt.gz
CDT2-V5-R2

tag: genotype


title: Melan-a R1

value: melan-a cells


title: Melan-a CYSLTR2 L129Q TRAM 24hr R1


title: ext_L13366.1_295

value: hFOB 1.10, ATCC CRL-11372

tag: sirna

value: scrambled siRNA

value: 0nM BMP2


title: Melan-a CYSLTR2 L129Q TRAM 4hr R2


title: RNAseq_90811

tag: batch

tag: current smoker

tag: pack years

tag: age

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


title: 3998998121_R01C02: genomic DNA from whole Blood

value: M

value: Schizophrenia

value: Case


title: BAHD1-V5 OE R3 (RNA-seq)

description:
RNA.count.all.txt.gz
BAHD1-V5-R3

value: BAHD1-V5 overexpression


title: 3998998121_R01C01: genomic DNA from whole Blood


title: RNAseq_79376

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

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent


title: RNAseq_70519

tag: monocyte percent

tag: basophil percent


title: BAHD1-V5 OE R1 (RNA-seq)

description:
RNA.count.all.txt.gz
BAHD1-V5-R1

tag: cell line


title: 3998998212_R06C02: genomic DNA from whole Blood

tag: Sex

tag: status


title: RNAseq_67871


title: 3998998212_R06C01: genomic DNA from whole Blood


title: Bulk-F11KO-6 (RNA-seq)

description:
RNA.count.all.txt.gz
Bulk_F11KO_6

tag: cell type

tag: tissue

tag: genotype

value: FBXO11 Knock out


title: RNAseq_58115

tag: batch

tag: current smoker


title: 3998998212_R05C02: genomic DNA from whole Blood

tag: age


title: 3998998212_R05C01: genomic DNA from whole Blood


title: Melan-a CYSLTR2 L129Q YM 24hr R1

tag: exogenous expression

tag: treatment


title: Bulk-F11KO-5 (RNA-seq)

description:
RNA.count.all.txt.gz
Bulk_F11KO_5

value: erythroblast cells


title: RNAseq_73229

tag: pack years

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

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

tag: fev1 % predicted


title: 3998998212_R04C02: genomic DNA from whole Blood


title: Melan-a CYSLTR2 L129Q YM 4hr R2


title: RNAseq_11383

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: RNAseq_61442

tag: basophil percent


title: Bulk-F11KO-4 (RNA-seq)

description:
RNA.count.all.txt.gz
Bulk_F11KO_4

tag: cell line

tag: cell type

value: Umbilical Cord blood derived


title: Melan-a CYSLTR2 L129Q VEH 24hr R2

value: DMSO


title: Melan-a CYSLTR2 L129Q YM 4hr R1


title: 3998998212_R04C01: genomic DNA from whole Blood

tag: Sex

value: F

tag: status


title: Melan-a CYSLTR2 L129Q TRAM 4hr R1


title: Melan-a CYSLTR2 L129Q VEH 24hr R1


title: RNAseq_99816

tag: batch

tag: current smoker


title: Bulk-F11KO-2 (RNA-seq)

description:
RNA.count.all.txt.gz
Bulk_F11KO_2

tag: tissue

tag: genotype


title: BAHD1-V5 OE R2 (RNA-seq)

description:
RNA.count.all.txt.gz
BAHD1-V5-R2


title: Melan-a CYSLTR2 L129Q VEH 4hr R2

tag: exogenous expression

tag: treatment


title: Melan-a CYSLTR2 L129Q YM 24hr R2


title: RNAseq_97855

tag: pack years

tag: age

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

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


title: Melan-a CYSLTR2 L129Q VEH 4hr R1


title: 3998998212_R03C02: genomic DNA from whole Blood


title: Bulk-F11KO-1 (RNA-seq)

description:
RNA.count.all.txt.gz
Bulk_F11KO_1


title: 3998998212_R03C01: genomic DNA from whole Blood


title: RNAseq_32465

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent


title: 3998998212_R02C02: genomic DNA from whole Blood


title: Bulk-F11KO-3 (RNA-seq)

description:
RNA.count.all.txt.gz
Bulk_F11KO_3

tag: cell line

tag: cell type


title: 3998998212_R02C01: genomic DNA from whole Blood

tag: Sex

tag: status


title: RNAseq_40616

tag: batch

tag: current smoker

tag: monocyte percent

tag: basophil percent


title: 3998998212_R01C02: genomic DNA from whole Blood


title: RNAseq_48703


title: 3998998212_R01C01: genomic DNA from whole Blood


title: Bulk-NT-1 (RNA-seq)

description:
RNA.count.all.txt.gz
Bulk_NT_1

tag: tissue

tag: genotype

value: wild type


title: 3998998140_R06C02: genomic DNA from whole Blood

tag: age


title: RNAseq_21769

tag: pack years

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


title: RNAseq_79439

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

tag: fev1 % predicted


title: RNAseq_38853

tag: neutrophil percent

tag: lymphocyte percent


title: 3998998140_R05C02: genomic DNA from whole Blood


title: 3998998140_R05C01: genomic DNA from whole Blood


title: RNAseq_89910

tag: eosinophil percent


title: RNAseq_97107


title: RNAseq_96002


title: 3998998140_R04C01: genomic DNA from whole Blood


title: RNAseq_50541


title: 3998998140_R03C02: genomic DNA from whole Blood


title: 3998998140_R03C01: genomic DNA from whole Blood


title: RNAseq_96360


title: Bulk-NT-4 (RNA-seq)

description:
RNA.count.all.txt.gz
Bulk_NT_4

tag: cell line

tag: cell type


title: Bulk-NT-2 (RNA-seq)

description:
RNA.count.all.txt.gz
Bulk_NT_2


title: RNAseq_65467


title: RNAseq_83933


title: EndMT_LNT_MIR503HG_3

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: TGFβ2 and IL1β


title: RNAseq_07208


title: 3998998140_R02C02: genomic DNA from whole Blood

tag: Sex

tag: status


title: EndMT_LNT_MIR503HG_2


title: 3998998140_R02C01: genomic DNA from whole Blood


title: 3998998140_R06C01: genomic DNA from whole Blood


title: EndMT_LNT_MIR503HG_1


title: 3998998140_R01C02: genomic DNA from whole Blood


title: RNAseq_46590

tag: batch

tag: current smoker


title: RNAseq_06770

tag: monocyte percent

tag: basophil percent


title: 3998998140_R01C01: genomic DNA from whole Blood


title: EndMT_LNT_Empty_3


title: Bulk-NT-3 (RNA-seq)

description:
RNA.count.all.txt.gz
Bulk_NT_3

tag: tissue

tag: genotype


title: EndMT_LNT_Empty_2


title: 3998998140_R04C02: genomic DNA from whole Blood

tag: age


title: 3998998211_R06C02: genomic DNA from whole Blood


title: RNAseq_09533

tag: pack years

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


title: EndMT_LNT_Empty_1


title: RNAseq_32696

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

tag: fev1 % predicted


title: RNAseq_78042

tag: neutrophil percent

tag: lymphocyte percent


title: 3998998211_R06C01: genomic DNA from whole Blood


title: 3998998211_R05C02: genomic DNA from whole Blood


title: 3998998211_R05C01: genomic DNA from whole Blood


title: EndMT_2

value: No


title: RNAseq_83899

tag: eosinophil percent


title: 3998998211_R04C02: genomic DNA from whole Blood

value: Control


title: EndMT_1


title: RNAseq_60091


title: CONT_LNT_MIR503HG_3


title: RNAseq_51376


title: RNAseq_32262


title: 3998998211_R03C02: genomic DNA from whole Blood


title: CONT_LNT_MIR503HG_2


title: 3998998211_R04C01: genomic DNA from whole Blood


title: RNAseq_71402


title: 3998998211_R02C02: genomic DNA from whole Blood


title: 3998998211_R03C01: genomic DNA from whole Blood


title: RNAseq_75326


title: CONT_LNT_Empty_2


title: CONT_LNT_Empty_3


title: RNAseq_46920


title: 3998998211_R02C01: genomic DNA from whole Blood


title: CONT_LNT_Empty_1


title: RNAseq_57473


title: EndMT_3


title: 3998998211_R01C02: genomic DNA from whole Blood


title: RNAseq_46413


title: 3998998211_R01C01: genomic DNA from whole Blood


title: RNAseq_16058


title: CONT_3


title: CONT_2


title: 200397540086_R06C02: genomic DNA from whole Blood


title: RNAseq_16228


title: CONT_1


title: RNAseq_50925