title: N_I_S7

description:
CD4 T cell differentiation, activation and analysis: 12 x 104 freshly sorted allogeneic naïve CD4+ T cells were co-cultured with activated pDCs (DC/T cell ratio of 1:6) in round-bottom 96-wells culture plates for 6 days. Were described, MitoTempo (MT – 50 μM – SantaCruz Biotechnology) or anti-PD1 antibody (clone EH12.2H7 – 10 μg/ml - Biolegend) were added during the co-culture. As a control, 12 x 104 naïve CD4+ T cells were activated with 1 μl of Dynabeads human T cell activator CD3/CD28 (Thermo Fisher) for 6 days (referred in the text as “Th0”). For intracellular cytokine staining, primed CD4+ T cells were re-stimulated with 50 ng/ml PMA, 2 μg/ml Ionomycin and GolgiPlug (BD Biosciences) for 5 h. Cells were then stained with a combination of anti-IL10 and IFNγ mAbs (BD Biosciences) with Cytofix/Cytoperm Fixation and Permeabilization Solution (BD Biosciences) following the manufacturer’s instructions. For re-stimulation experiments, 5 x 104 primed (CFSElow) CD4+ T cells or sorted SLE patient CD4+ T cells were re-stimulated with 10 μg/ml of plate-bound anti-CD3 (OKT3 - Biolegend) and 2 μg/ml of soluble anti-CD28 mAb (Biolegend) for 24 h. Cytokine levels in the corresponding supernatants were measured with Flex Set Kit (BD Biosciences). For HIF1α intracellular staining, CD4+ T cells were stained with anti-HIF-1α antibody (Biolegend) with Foxp3 fix/perm buffer set (Biolegend) following the manufacturer’s instructions. Dead cells were excluded from the analysis by labeling with LIVE/DEAD fixable Aqua (Thermo Fisher) prior to fixation/permeabilization.
project1.csv
cDNA3277

value: I


title: A_III_S6

status: Public on Sep 26 2018

type: SRA

city: Dallas

first: Nicole

last: Baldwin

address: 3434 Live Oak St

country: USA

institute: Baylor Research Institute

description:
CD4 T cell differentiation, activation and analysis: 12 x 104 freshly sorted allogeneic naïve CD4+ T cells were co-cultured with activated pDCs (DC/T cell ratio of 1:6) in round-bottom 96-wells culture plates for 6 days. Were described, MitoTempo (MT – 50 μM – SantaCruz Biotechnology) or anti-PD1 antibody (clone EH12.2H7 – 10 μg/ml - Biolegend) were added during the co-culture. As a control, 12 x 104 naïve CD4+ T cells were activated with 1 μl of Dynabeads human T cell activator CD3/CD28 (Thermo Fisher) for 6 days (referred in the text as “Th0”). For intracellular cytokine staining, primed CD4+ T cells were re-stimulated with 50 ng/ml PMA, 2 μg/ml Ionomycin and GolgiPlug (BD Biosciences) for 5 h. Cells were then stained with a combination of anti-IL10 and IFNγ mAbs (BD Biosciences) with Cytofix/Cytoperm Fixation and Permeabilization Solution (BD Biosciences) following the manufacturer’s instructions. For re-stimulation experiments, 5 x 104 primed (CFSElow) CD4+ T cells or sorted SLE patient CD4+ T cells were re-stimulated with 10 μg/ml of plate-bound anti-CD3 (OKT3 - Biolegend) and 2 μg/ml of soluble anti-CD28 mAb (Biolegend) for 24 h. Cytokine levels in the corresponding supernatants were measured with Flex Set Kit (BD Biosciences). For HIF1α intracellular staining, CD4+ T cells were stained with anti-HIF-1α antibody (Biolegend) with Foxp3 fix/perm buffer set (Biolegend) following the manufacturer’s instructions. Dead cells were excluded from the analysis by labeling with LIVE/DEAD fixable Aqua (Thermo Fisher) prior to fixation/permeabilization.
project1.csv
cDNA3276

library_source: transcriptomic

data_processing:
Sequences were aligned with HISAT2, duplicates removed with Samtools, and counts generated with HTSeq using the annotations from Gencode V20. Genes identified as globins, ribosomal RNAs, and pseudogenes were removed.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: csv; raw counts

molecule: total RNA

organism: Homo sapiens

source_name: T-cells

growth_protocol: Blood samples were obtained from patients fulfilling the diagnosis of SLE according to the criteria established by the American College of Rheumatology. Healthy pediatric controls were children visiting the clinic either for reasons not related to autoimmunity or for surgery not associated with any inflammatory diseases

extract_protocol:
Total RNA was isolated using the RNeasy kit (Qiagen)
Total RNA was converted to cDNA using 20 ng RNA as input for the Ovation RNA-Seq System V2, and barcoded Illumina library constructs were produced using Ovation Ultralow Library System V2 (NuGEN Technologies) following the manufacturer’s instructions. Library fragment size and molar concentration were determined using Agilent High Sensitivity DNA Chip on 2100 Bioanalyzer, and quantitative PCR data were obtained by the KAPA BioSystems Library Quantification qPCR Kit for Illumina Platform on a Viia7 Real-Time PCR System (Thermo Fisher Scientific). RNA-seq libraries were sequenced on the Illumina HiSeq 2500 sequencing system using SBS v3 chemistry and two high-output flow cells targeting 70–80 million 2 × 75 paired-end reads per library.

treatment_protocol: Cell isolation: For pDC isolation, the total dendritic cell fraction was obtained from healthy buffy coats by magnetic cell sorting with pan-DC Enrichment Kit (Stem Cell Technology). Highly pure (>99%) pDCs (Lin- HLADR+ CD11c- CD123+) were then isolated from this fraction by FACS sorting. Fresh peripheral blood naïve CD4 T cells (>99% pure) were isolated using Total CD4 T cell enrichment kit (Stem Cell Technology) followed by cell sorting as CD4+ CD45RA+ CD45RO- cells. Naïve CD4+ T cells where labeled with 5 μM carboxy-fluorescein diacetate succinimidyl ester (CFSE; Thermo Fisher) following the manufacturer’s instructions. Were described, primed (CFSElow) CD4+ T cells were sorted from pDC/CD4 T cell co-cultures at day 6. 7ADD and anti-CD123 antibody were used to remove dead cells and contaminating pDCs, respectively (Extended Data Fig. 2a). For B cell isolation, positively selected CD19+ B cells (Stem Cell Technology) were stained with anti-IgD APC, anti-CD27 PE and anti-CD19 FITC and then sorted as IgD+CD27−CD19+ cells (naïve) or IgD-CD27+CD19+ cells (memory). For blood CD4+ T cell subset sorting, frozen PBMCs from SLE patients were stained with anti-CD4 PE-Cy7, anti-CXCR5 AlexaFluor 647, anti-CD45RA APC-H7, anti-PD1 Brilliant Violet 421, anti-CD3 V500 and anti-CXCR3 Brilliant Violet 785. Then, CXCR3+ PD1low CD4+ T cells, CXCR3- PD1hi CD4+ T cells, CXCR3+ PD1hi CD4+ T cells populations were sorted from the CD3+ CD4+ CD45RA- CXCR5- cells fraction. CD3+ CD4+ CD45RA− CXCR5+ CD4+ T cells (Tfh cells) were also sorted for comparison.    CD4 T cell differentiation, activation and analysis: 12 x 104 freshly sorted allogeneic naïve CD4+ T cells were co-cultured with activated pDCs (DC/T cell ratio of 1:6) in round-bottom 96-wells culture plates for 6 days. Were described, MitoTempo (MT – 50 μM – SantaCruz Biotechnology) or anti-PD1 antibody (clone EH12.2H7 – 10 μg/ml - Biolegend) were added during the co-culture. As a control, 12 x 104 naïve CD4+ T cells were activated with 1 μl of Dynabeads human T cell activator CD3/CD28 (Thermo Fisher) for 6 days (referred in the text as “Th0”). For intracellular cytokine staining, primed CD4+ T cells were re-stimulated with 50 ng/ml PMA, 2 μg/ml Ionomycin and GolgiPlug (BD Biosciences) for 5 h. Cells were then stained with a combination of anti-IL10 and IFNγ mAbs (BD Biosciences) with Cytofix/Cytoperm Fixation and Permeabilization Solution (BD Biosciences) following the manufacturer’s instructions. For re-stimulation experiments, 5 x 104 primed (CFSElow) CD4+ T cells or sorted SLE patient CD4+ T cells were re-stimulated with 10 μg/ml of plate-bound anti-CD3 (OKT3 - Biolegend) and 2 μg/ml of soluble anti-CD28 mAb (Biolegend) for 24 h. Cytokine levels in the corresponding supernatants were measured with Flex Set Kit (BD Biosciences). For HIF1α intracellular staining, CD4+ T cells were stained with anti-HIF-1α antibody (Biolegend) with Foxp3 fix/perm buffer set (Biolegend) following the manufacturer’s instructions. Dead cells were excluded from the analysis by labeling with LIVE/DEAD fixable Aqua (Thermo Fisher) prior to fixation/permeabilization.     Proliferation assay: CD4 T cell proliferation was measured by resazurin reduction, as previously described3. Briefly, primed (CFSElow) CD4+ T cells were seeded at 5 × 105 cells and re-stimulated with 10 μg/ml of plate-bound anti-CD3 (OKT3) and 2 μg/ml of soluble anti-CD28 mAbs. After incubation for 20 h, medium supplemented with 40 μM resazurin was added for an additional 4 hr. Resazurin reduction to resorufin was measured fluorometrically using a SpectraMax M5 (Molecular Devices). Results obtained were expressed in fluorescence arbitrary units (AU). Alternatively, proliferation was assessed by flow cytometry using the Click-IT EdU Proliferation Kit, according to the manufacturer’s instructions (Thermo Fisher).     In vitro Tfh cell generation: Human Tfh cells were generated as previously described. Briefly, after overnight stimulation of naive CD4+ T cells with Dynabeads human T cell activator CD3/CD28 (Thermo Fisher) in complete RPMI medium, cells were transferred to 96-well plates coated with anti-CD3 and supplemented with 2 μg/ml of soluble anti-CD28 mAb (Biolegend), human recombinant IL-23 (25 ng/ml) and human recombinant TGFβ (5 ng/ml). After 4 d cells were collected and used for analysis.

tag: tissue

value: T-cells

tag: subject id

value: III

tag: diagnosis

value: healthy control

tag: cell population (pd1pos=cxcr3+ pd1hi cd4+ t)

tag: treatment

value: CpGA

tag: activation

value: Ox mtDNA generation and pDC activation:Ox mtDNA was generated as previously described. Briefly, healthy neutrophils were pre-incubated with IFNα2β (2000 U/ml; Schering Corp.) for 90 min at 370C and then extensively washed before incubation with anti-RNP IgG (50 μg/ml) purified from SLE patient sera. Neutrophil supernatants were then collected, centrifuged for 10 min at 1400g and stored at -80C. PDCs (5x105 cells/well – 96 U bottom plate) were cultured with 40% v/v Ox mtDNA-containing neutrophil supernatants (referred in the text as “Ox mtDNA”) or with 5 μg/ml of either CpGA (ODN-2216; Invivogen) for 24 h. The volume of Ox mtDNA-containing neutrophil supernatants and the concentration of CpGA were selected based on their capacity to trigger similar levels of IFNα production by pDCs.

tag: project


title: 0_I_S1

description:
CD4 T cell differentiation, activation and analysis: 12 x 104 freshly sorted allogeneic naïve CD4+ T cells were co-cultured with activated pDCs (DC/T cell ratio of 1:6) in round-bottom 96-wells culture plates for 6 days. Were described, MitoTempo (MT – 50 μM – SantaCruz Biotechnology) or anti-PD1 antibody (clone EH12.2H7 – 10 μg/ml - Biolegend) were added during the co-culture. As a control, 12 x 104 naïve CD4+ T cells were activated with 1 μl of Dynabeads human T cell activator CD3/CD28 (Thermo Fisher) for 6 days (referred in the text as “Th0”). For intracellular cytokine staining, primed CD4+ T cells were re-stimulated with 50 ng/ml PMA, 2 μg/ml Ionomycin and GolgiPlug (BD Biosciences) for 5 h. Cells were then stained with a combination of anti-IL10 and IFNγ mAbs (BD Biosciences) with Cytofix/Cytoperm Fixation and Permeabilization Solution (BD Biosciences) following the manufacturer’s instructions. For re-stimulation experiments, 5 x 104 primed (CFSElow) CD4+ T cells or sorted SLE patient CD4+ T cells were re-stimulated with 10 μg/ml of plate-bound anti-CD3 (OKT3 - Biolegend) and 2 μg/ml of soluble anti-CD28 mAb (Biolegend) for 24 h. Cytokine levels in the corresponding supernatants were measured with Flex Set Kit (BD Biosciences). For HIF1α intracellular staining, CD4+ T cells were stained with anti-HIF-1α antibody (Biolegend) with Foxp3 fix/perm buffer set (Biolegend) following the manufacturer’s instructions. Dead cells were excluded from the analysis by labeling with LIVE/DEAD fixable Aqua (Thermo Fisher) prior to fixation/permeabilization.
project1.csv
cDNA3271


title: 0_II_S2

description:
CD4 T cell differentiation, activation and analysis: 12 x 104 freshly sorted allogeneic naïve CD4+ T cells were co-cultured with activated pDCs (DC/T cell ratio of 1:6) in round-bottom 96-wells culture plates for 6 days. Were described, MitoTempo (MT – 50 μM – SantaCruz Biotechnology) or anti-PD1 antibody (clone EH12.2H7 – 10 μg/ml - Biolegend) were added during the co-culture. As a control, 12 x 104 naïve CD4+ T cells were activated with 1 μl of Dynabeads human T cell activator CD3/CD28 (Thermo Fisher) for 6 days (referred in the text as “Th0”). For intracellular cytokine staining, primed CD4+ T cells were re-stimulated with 50 ng/ml PMA, 2 μg/ml Ionomycin and GolgiPlug (BD Biosciences) for 5 h. Cells were then stained with a combination of anti-IL10 and IFNγ mAbs (BD Biosciences) with Cytofix/Cytoperm Fixation and Permeabilization Solution (BD Biosciences) following the manufacturer’s instructions. For re-stimulation experiments, 5 x 104 primed (CFSElow) CD4+ T cells or sorted SLE patient CD4+ T cells were re-stimulated with 10 μg/ml of plate-bound anti-CD3 (OKT3 - Biolegend) and 2 μg/ml of soluble anti-CD28 mAb (Biolegend) for 24 h. Cytokine levels in the corresponding supernatants were measured with Flex Set Kit (BD Biosciences). For HIF1α intracellular staining, CD4+ T cells were stained with anti-HIF-1α antibody (Biolegend) with Foxp3 fix/perm buffer set (Biolegend) following the manufacturer’s instructions. Dead cells were excluded from the analysis by labeling with LIVE/DEAD fixable Aqua (Thermo Fisher) prior to fixation/permeabilization.
project1.csv
cDNA3272

value: II


title: A_I_S4

description:
CD4 T cell differentiation, activation and analysis: 12 x 104 freshly sorted allogeneic naïve CD4+ T cells were co-cultured with activated pDCs (DC/T cell ratio of 1:6) in round-bottom 96-wells culture plates for 6 days. Were described, MitoTempo (MT – 50 μM – SantaCruz Biotechnology) or anti-PD1 antibody (clone EH12.2H7 – 10 μg/ml - Biolegend) were added during the co-culture. As a control, 12 x 104 naïve CD4+ T cells were activated with 1 μl of Dynabeads human T cell activator CD3/CD28 (Thermo Fisher) for 6 days (referred in the text as “Th0”). For intracellular cytokine staining, primed CD4+ T cells were re-stimulated with 50 ng/ml PMA, 2 μg/ml Ionomycin and GolgiPlug (BD Biosciences) for 5 h. Cells were then stained with a combination of anti-IL10 and IFNγ mAbs (BD Biosciences) with Cytofix/Cytoperm Fixation and Permeabilization Solution (BD Biosciences) following the manufacturer’s instructions. For re-stimulation experiments, 5 x 104 primed (CFSElow) CD4+ T cells or sorted SLE patient CD4+ T cells were re-stimulated with 10 μg/ml of plate-bound anti-CD3 (OKT3 - Biolegend) and 2 μg/ml of soluble anti-CD28 mAb (Biolegend) for 24 h. Cytokine levels in the corresponding supernatants were measured with Flex Set Kit (BD Biosciences). For HIF1α intracellular staining, CD4+ T cells were stained with anti-HIF-1α antibody (Biolegend) with Foxp3 fix/perm buffer set (Biolegend) following the manufacturer’s instructions. Dead cells were excluded from the analysis by labeling with LIVE/DEAD fixable Aqua (Thermo Fisher) prior to fixation/permeabilization.
project1.csv
cDNA3274


title: 0_III_S3

description:
CD4 T cell differentiation, activation and analysis: 12 x 104 freshly sorted allogeneic naïve CD4+ T cells were co-cultured with activated pDCs (DC/T cell ratio of 1:6) in round-bottom 96-wells culture plates for 6 days. Were described, MitoTempo (MT – 50 μM – SantaCruz Biotechnology) or anti-PD1 antibody (clone EH12.2H7 – 10 μg/ml - Biolegend) were added during the co-culture. As a control, 12 x 104 naïve CD4+ T cells were activated with 1 μl of Dynabeads human T cell activator CD3/CD28 (Thermo Fisher) for 6 days (referred in the text as “Th0”). For intracellular cytokine staining, primed CD4+ T cells were re-stimulated with 50 ng/ml PMA, 2 μg/ml Ionomycin and GolgiPlug (BD Biosciences) for 5 h. Cells were then stained with a combination of anti-IL10 and IFNγ mAbs (BD Biosciences) with Cytofix/Cytoperm Fixation and Permeabilization Solution (BD Biosciences) following the manufacturer’s instructions. For re-stimulation experiments, 5 x 104 primed (CFSElow) CD4+ T cells or sorted SLE patient CD4+ T cells were re-stimulated with 10 μg/ml of plate-bound anti-CD3 (OKT3 - Biolegend) and 2 μg/ml of soluble anti-CD28 mAb (Biolegend) for 24 h. Cytokine levels in the corresponding supernatants were measured with Flex Set Kit (BD Biosciences). For HIF1α intracellular staining, CD4+ T cells were stained with anti-HIF-1α antibody (Biolegend) with Foxp3 fix/perm buffer set (Biolegend) following the manufacturer’s instructions. Dead cells were excluded from the analysis by labeling with LIVE/DEAD fixable Aqua (Thermo Fisher) prior to fixation/permeabilization.
project1.csv
cDNA3273


title: CD4+Tcells_Ox mtDNA-pDC_III

data_processing:
Quality control of raw reads were analyzed with FASTQC
Quality and adapter trimming by cutadapt
Reads were aligned to the reference human genome using hisat2
Sort bam files by name using samtools
HTSeq-count program was used to quantify total numbers of read counts mapped to genome
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv format, read counts generated by HTSeq-count

growth_protocol: 12 x 10^4 freshly sorted allogeneic naïve CD4+ T cells were co-cultured with activated pDCs (DC/T cell ratio of 1:6) in round-bottom 96-wells culture plates for 6 days. As a control, 12 x 104 naïve CD4+ T cells were activated with 1 ml of Dynabeads human T cell activator CD3/CD28 (Thermo Fisher) for 6 days (referred in the text as “Th0”). Activated (CFSElow) CD4+ T cells were then sorted and analyzed by RNAseq.

extract_protocol:
Total RNA was isolated from cell lysates using a modified protocol for the RNAqueous™ Micro Total RNA Isolation Kit (Thermo Fisher) including on-column DNase digestion and analyzed for quality using the RNA 6000 Pico Kit (Agilent)
Poly-A enriched NGS library construction was performed using the KAPA mRNA Hyper Prep Kit (KAPA Biosystems) using 500ng of input total RNA according to manufacturer’s protocol using 9 amplification cycles. Individual libraries were quantitated via qPCR using the KAPA Library Quantification Kit, Universal (KAPA Biosystems) and equimolar pooled.

tag: cell source

value: in vitro

tag: cell type

tag: conditions

value: Ox mtDNA-pDC

tag: replicate


title: SLE413-PD1POS

description:
project2.csv
cDNA3650

source_name: whole blood

value: whole blood

value: Systemic Lupus Erythematosus (SLE)


title: CD4+Tcells_Ox mtDNA-pDC_II


title: CD4+Tcells_CpGA-pDC_III

value: CpGA-pDC


title: CD4+Tcells_CpGA-pDC_II


title: CD4+Tcells_Th0_III


title: CD4+Tcells_Th0_I


title: CD4+Tcells_Th0_II


title: A_II_S5

description:
CD4 T cell differentiation, activation and analysis: 12 x 104 freshly sorted allogeneic naïve CD4+ T cells were co-cultured with activated pDCs (DC/T cell ratio of 1:6) in round-bottom 96-wells culture plates for 6 days. Were described, MitoTempo (MT – 50 μM – SantaCruz Biotechnology) or anti-PD1 antibody (clone EH12.2H7 – 10 μg/ml - Biolegend) were added during the co-culture. As a control, 12 x 104 naïve CD4+ T cells were activated with 1 μl of Dynabeads human T cell activator CD3/CD28 (Thermo Fisher) for 6 days (referred in the text as “Th0”). For intracellular cytokine staining, primed CD4+ T cells were re-stimulated with 50 ng/ml PMA, 2 μg/ml Ionomycin and GolgiPlug (BD Biosciences) for 5 h. Cells were then stained with a combination of anti-IL10 and IFNγ mAbs (BD Biosciences) with Cytofix/Cytoperm Fixation and Permeabilization Solution (BD Biosciences) following the manufacturer’s instructions. For re-stimulation experiments, 5 x 104 primed (CFSElow) CD4+ T cells or sorted SLE patient CD4+ T cells were re-stimulated with 10 μg/ml of plate-bound anti-CD3 (OKT3 - Biolegend) and 2 μg/ml of soluble anti-CD28 mAb (Biolegend) for 24 h. Cytokine levels in the corresponding supernatants were measured with Flex Set Kit (BD Biosciences). For HIF1α intracellular staining, CD4+ T cells were stained with anti-HIF-1α antibody (Biolegend) with Foxp3 fix/perm buffer set (Biolegend) following the manufacturer’s instructions. Dead cells were excluded from the analysis by labeling with LIVE/DEAD fixable Aqua (Thermo Fisher) prior to fixation/permeabilization.
project1.csv
cDNA3275


title: CD4+Tcells_CpGA-pDC_I


title: CD4+Tcells_Ox mtDNA-pDC_I


title: 9373549117_B-V4-ILARIS-1

status: Public on Sep 17 2018

type: RNA

hyb_protocol: Amplified RNA was hybridized to Illumina HT-12 V4 beadchips following manufacturer's protocols

scan_protocol: using an Illumina Beadstation 500 following manufacturer's protocols

data_processing: Data processing was completed using GenomeStudio version 2011.1 with the Gene Expression Module v1.9.0 (Illumina). After background subtraction the average normalization was conducted using GenomeStudio to rescale the difference in overall intensity to the mean average intensity for all samples across multiple chips.

label: biotin

label_protocol: RNA was isolated using the PerfectPure RNA Blood Kit (5 PRIME) MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion) according to the manufacturer’s instructions. Two and a half micrograms of isolated total RNA was then globin-reduced using the GLOBINclear 96-well format kit (Applied Biosystems/Ambion) according to the manufacturer’s instructions. Total and globin-reduced RNA integrity was assessed using an Agilent 2100 Bioanalyser showing a quality of RNA integrity number of 7–9.5 (Agilent Technologies). RNA yield was assessed using a NanoDrop 1000 spectrophotometer (NanoDrop Products Thermo Fisher Scientific). Biotinylated amplified antisense complementary RNA (cRNA) targets were then prepared from 200 to 250 ng of the globin-reduced RNA using the Illumina CustomPrep RNA amplification kit (Applied Biosystems/Ambion).

growth_protocol: The study included three parts. Part 1 (P1) was a 6-month open-label treatment period in which all patients received canakinumab subcutaneously (300 mg every 6 weeks [q6w] or 4 mg/kg q6w for patients weighing ≤40 kg). Patients who experienced an attack before week 4 received an additional dose of 150 mg (or 2 mg/kg for patients weighing ≤40 kg) at the time of flare and 450 mg q6w (or 6 mg/kg q6w for patients weighing ≤40 kg) thereafter starting at week 6. Patients who experienced an attack between weeks 5 and 6 received a rescue medication (NSAIDs or corticosteroids [0.5 mg/kg for 3 days]) and waited up to week 6 to receive canakinumab (450 mg or 6 mg/kg for patients weighing ≤40 kg). Part 2 (P2) was an up to six months withdrawal period where canakinumab was not given unless the patient had an attack. At P2 completion or at the time of relapse whichever occurred first patients immediately entered part 3 (P3) a 24-month extension period in which patients received the same canakinumab dose administered at the end of P1. Only those patients who completed P1 and P2 were eligible to enter P3.

extract_protocol: Three millilitres of whole blood were collected into Tempus tubes (Applied Biosystems) vigorously mixed immediately after collection and stored between −20 and −80 °C before RNA extraction.

tag: donor id

tag: age (yrs)

tag: gender

value: F

tag: race

value: Caucasian

tag: disease

value: HIDS

tag: visit

tag: days

value: ILARIS


title: pDC-Ox mtDNA-2

hyb_protocol: Biotinylated complementary RNA (cRNA) was hybridized to Illumina Human-6 Beadchip Array version 2

scan_protocol: scanned on Illumina Beadstation 500

data_processing: Fluorescent hybridization signals were assessed with Beadstudio software (Illumina). After background subtraction the average normalization was conducted using GenomeStudio to rescale the difference in overall intensity to the mean average intensity for all samples across multiple chips.

source_name: pDC-Ox mtDNA

label_protocol: Total RNA was isolated using the RNeasy kit (Qiagen), amplified and then labeled with Illumina TotalPrep RNA amplification kit (Invitrogen). Agilent 2100 Analyzer (Agilent Technologies) was used to assess RNA integrity.

extract_protocol: For pDCs isolation, the total dendritic cell fraction was obtained from healthy buffy coats by magnetic cell sorting with pan-DC Enrichment Kit (Stem Cell Technology). Highly pure (>99%) pDCs (Lin- HLADR+ CD11c- CD123+) were then isolated from this fraction by FACS sorting. Fresh peripheral blood naïve CD4 T cells (>99% pure) were isolated using Total CD4 T cell enrichment kit (Stem Cell Technology) followed by cell sorting as CD4+ CD45RA+ CD45RO- cells. Freshly sorted naïve CD4 T cells where then labeled with 5 μM carboxy-fluorescein diacetate succinimidyl ester (CFSE; Thermo Fisher) following the manufacturer’s instructions.

treatment_protocol: PDCs (5x105 cells/well – 96 U bottom plate) were cultured with 40% v/v Ox mtDNA-containing neutrophil supernatants (referred in the text as “Ox mtDNA”) or with 5 μg/ml of either CpGA (ODN-2216; Invivogen) for 24 hr. The volume of Ox mtDNA-containing neutrophil supernatants and the concentration of CpGA were selected based on their capacity to trigger similar levels of IFNα production by pDCs

tag: cell population

value: pDC

value: Ox mtDNA


title: 9373549117_F-V5-ILARIS-1

tag: tissue


title: 9373549117_C-V4-ILARIS-1

value: M


title: pDC-CpGA-1

source_name: pDC-CpGA


title: pDC-Ox mtDNA-3


title: pDC-MEDIA-2

source_name: pDC-MEDIA

value: MEDIA


title: pDC-CpGA-2


title: 9373549117_E-V4-ILARIS-1


title: 9373549114_A-V3-ILARIS-1


title: 9373549117_G-V2_NT-NT-1

value: NT


title: 9373549114_H-HC-HC-1

value: Hispanic

value: HC


title: 9373549117_J-HC-HC-1


title: 9373549117_I-V5-ILARIS-1


title: 9373549114_I-V2_NT-NT-1


title: 9373549114_C-V1_AK-AK-1

value: AK


title: pDC-MEDIA-3


title: 9373549117_A-V5-ILARIS-1


title: pDC-MEDIA-1


title: 9373549114_G-V5-ILARIS-1


title: 9373549117_K-V3-ILARIS-1


title: 9373549109_K-HC-HC-1


title: 9373549114_E-V4-ILARIS-1


title: 9373549117_H-HC-HC-1


title: 9373549117_D-V3-ILARIS-1


title: pDC-Ox mtDNA-1


title: 9373549114_D-V3-ILARIS-1


title: pDC-CpGA-3

value: CpGA


title: 9373549114_K-V2_NT-NT-1


title: 9373549109_B-V2_NT-NT-1


title: 9373549108_K-V5-ILARIS-1


title: 9373549109_J-ATTACK-ATTACK-1

value: ATTACK


title: 9373549109_E-ATTACK-ATTACK-1

value: whole blood


title: 9373549109_I-HC-HC-1


title: 9373549109_G-HC-HC-1


title: 9373549108_L-HC-HC-1


title: 9373549108_I-V1_AK-AK-1


title: 9373549109_A-ATTACK-ATTACK-1


title: 9373549108_A-HC-HC-1


title: 9373549104_L-HC-HC-1


title: 9373549108_E-V1_AK-AK-1


title: 9373549108_H-V3-ILARIS-1


title: 9373549104_E-V4-ILARIS-1


title: 9373549104_B-V1_AK-AK-1


title: 9373549108_B-V1_AK-AK-1


title: 9373549104_G-HC-HC-1


title: 9373549108_D-ATTACK-ATTACK-1


title: 9373549104_K-V2_NT-NT-1


title: 9373549109_H-V5-ILARIS-1


title: 9373549109_C-V3-ILARIS-1


title: 9373549104_H-V2_NT-NT-1


title: 9373549108_G-V2_NT-NT-1


title: 9373549104_F-V1_AK-AK-1


title: 9373549109_L-HC-HC-1


title: 9373549108_F-HC-HC-1


title: 9373549108_C-HC-HC-1


title: 9373549104_J-V3-ILARIS-1


title: 9339657095_H-V4-ILARIS-1


title: 9373549104_A-V3-ILARIS-1


title: 9339657095_J-V3-ILARIS-1


title: 9373549109_D-V4-ILARIS-1


title: 9339657095_K-ATTACK-ATTACK-1


title: 9339657095_E-V1_AK-AK-1


title: 9339657095_F-V2_NT-NT-1


title: 9339657093_J-HC-HC-1


title: JY1779 P37 NT siRNA day 3 EPC

status: Public on Mar 29 2018

city: Houston

first: Maria

last: Szwarc

address: One Baylor Plaza

institute: Baylor College of MEdicine

data_processing:
Raw reads in fastq file format were mapped to human genome hg19 (Human assembly:  GRCh37/hg19;  http://genome.ucsc.edu) through use of the ultrafast universal RNA-seq aligner: Spliced Transcripts Alignment to a Reference (STAR) software
To reduce possible PCR bias, read duplicates were removed with Picard Tools (http://broadinstitute.github.io/picard/).
The number of reads aligned to known genes was determined by the Python-based software package HTSeq
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: txt; 13 columns; "GeneSymbol" and raw count data for each of the 12 samples

source_name: nontargeting siRNA day 3 EPC

growth_protocol: Plated 8x10^4 cells per well in 6-well format. 48 hours allowed for growth before siRNA transfection

extract_protocol:
RNeasy Plus kit (Qiagen Inc., Germantown, MD)
250ng of total RNA as input, the TruSeqTM RNA library preparation kit v2 (Illumina®, Inc., San Diego, CA) was used for mRNA isolation, fragmentation, and subsequent first and second strand DNA synthesis.  The kit also was used for follow up end-repair along with base- and adaptor- ligation before products were purified and then enriched by PCR (15 cycles) to create the cDNA libraries.  The resulting libraries were quantitated using the NanoDropTM spectrometer and fragment size assessed using a DNA 1000 chip on the Agilent 2100 Bioanalyzer. A qPCR assay was performed on the libraries to determine the concentration of adapter-ligated fragments using the Applied Biosystems ViiATM 7 Real-Time PCR System (Thermo Fisher Scientific®) with a KAPA library Quant kit (Kapabiosystems, Inc., Wilmington, MA). Relevant samples were pooled in equimolar amounts and re-quantitated by qPCR. Library pools (27pM) were loaded into a high output flow cell for clonal cluster generation by bridge amplification using the cBot 2 system (Illumina®, Inc.). Indexed paired-end sequencing (2x100bp read lengths) was performed using the ultrahigh-throughput HiSeq 2500 sequencing system (Illumina®, Inc.).

treatment_protocol: nontargeting vs. PLZF siRNA transfection for 48 hours; followed by EPC treatment for 0 or 3 days

value: endometrial stromal cells

tag: sirna

value: nontargeting siRNA

tag: days of epc

value: day 3 EPC

tag: volunteer


title: JY1778 P37 PLZF siRNA day 0 EPC

source_name: PLZF siRNA day 0 EPC

value: PLZF siRNA

value: day 0 EPC


title: 9339657095_L-HC-HC-1

tag: treatment


title: 9339657093_L-ATTACK-ATTACK-1

value: F

value: Caucasian

value: HIDS


title: JY1780 P37 PLZF siRNA day 3 EPC

source_name: PLZF siRNA day 3 EPC


title: 9339657095_C-V5-ILARIS-1

value: ILARIS


title: 9339657095_A-V2_NT-NT-1


title: 9339657093_K-ATTACK-ATTACK-1


title: pDC-0 hrs post CpGB-rep 3

status: Public on Jun 01 2018

hyb_protocol: Standard Illumina hybridization protocol .

scan_protocol: Standard Illumina scanning protocol .

data_processing: Average Normalization per GenomeStudio

source_name: pDC-0 hrs post CpGB

label_protocol: not provided

growth_protocol: pDCs were isolated from healthy donors by sorting as lineage-negative (CD3, CD14, CD15, CD16, CD19, CD20, CD25, CD56, and CD11c) cells using a pDC isolation kit (Miltenyi Biotec) to more than 98% purity.

extract_protocol: RNA isolation was performed using Qiagen RNeasy mini kit according to the manufacturer’s instructions

treatment_protocol: pDCs were stimulated with 0.5 µM of CpGB

value: pDC

tag: hrs post cpgb stimulation


title: pDC-4 hrs post CpGB-rep 3

source_name: pDC-4 hrs post CpGB

tag: cell type


title: JY1774 P35 PLZF siRNA day 0 EPC


title: JY1772 P30 PLZF siRNA day 3 EPC


title: 9339657095_D-V4-ILARIS-1


title: pDC-12 hrs post CpGB-rep 1

source_name: pDC-12 hrs post CpGB


title: pDC-4 hrs post CpGB-rep 2


title: pDC-0 hrs post CpGB-rep 2


title: JY1770 P30 PLZF siRNA day 0 EPC


title: pDC-12 hrs post CpGB-rep 3


title: pDC-8 hrs post CpGB-rep 2

source_name: pDC-8 hrs post CpGB


title: pDC-12 hrs post CpGB-rep 2


title: pDC-4 hrs post CpGB-rep 1


title: pDC-8 hrs post CpGB-rep 1


title: JY1769 P30 NT siRNA day 0 EPC

source_name: nontargeting siRNA day 0 EPC


title: JY1773 P35 NT siRNA day 0 EPC


title: whole blood-RSV-RSVB-BA-12

status: Public on Mar 21 2018

hyb_protocol: Amplified labeled RNA were hybridized overnight to Illumina HumanHT-12 v4 Beadchips (Illumina) following manufacturer's protocols. Following hybridization each chip was washed, blocked and stained following the manufacturer’s protocols.

scan_protocol: Illumina Beadstation 500

data_processing: llumina GenomeStudio software was used to subtract background and scale average samples’ signal intensity

source_name: whole blood-RSV-RSVB-BA

label_protocol: Following extraction, a LabChip GX instrument (Caliper Life Sciences Inc.) was used to measure the RNA Quality Score (RQS) for each sample. RNA concentration was measured using a Nanodrop 8000 (Nanodrop Technologies). Following RNA extraction and quality control analysis, Globin mRNA was depleted from a portion of each total RNA sample using the GLOBINclear™ 96-well format kit (Ambion). This was followed by another round of RQS and concentration determinations for quality control purposes. 250ng of globin reduced RNA from all samples passing quality control were then amplified and labeled using the Illumina® TotalPrep™-96 RNA Amplification Kit (Ambion).

extract_protocol: Blood samples (1-3 mL) were collected in Tempus tubes (Applied Biosystems, CA, USA) and stored at -20°C within 2-4 hours of collection for further processing in batches.

tag: age (in months)

value: M

value: RSV

value: RSVB

tag: rsv genotypes

value: BA

value: blood


title: whole blood-RSV-RSVB-N/A-1

source_name: whole blood-RSV-RSVB-N/A


title: whole blood-RSV-RSVB-BA-8


title: JY1771 P30 NT siRNA day 3 EPC


title: 9373549108_J-V5-ILARIS-1

tag: donor id


title: whole blood-RSV-RSVB-BA-3


title: whole blood-RSV-RSVA-GA5-5

source_name: whole blood-RSV-RSVA-GA5

value: RSVA


title: whole blood-RSV-RSVB-BA-11


title: whole blood-RSV-RSVA-GA5-2


title: whole blood-RSV-RSVB-BA-5


title: whole blood-RSV-RSVB-BA-9


title: whole blood-RSV-RSVA-GA2-43

source_name: whole blood-RSV-RSVA-GA2


title: whole blood-RSV-RSVB-BA-2


title: whole blood-RSV-RSVB-BA-10


title: whole blood-RSV-RSVB-BA-7


title: whole blood-RSV-RSVA-GA5-4


title: whole blood-RSV-RSVA-GA5-1


title: JY1775 P35 NT siRNA day 3 EPC


title: whole blood-RSV-RSVB-BA-1


title: whole blood-RSV-RSVB-BA-6


title: pDC-8 hrs post CpGB-rep 3

tag: replicate


title: whole blood-RSV-RSVA-N/A-1

source_name: whole blood-RSV-RSVA-N/A

tag: gender


title: pDC-0 hrs post CpGB-rep 1


title: whole blood-RSV-RSVA-GA2-42


title: whole blood-RSV-RSVA-GA2-38


title: whole blood-RSV-RSVA-GA2-39


title: whole blood-RSV-RSVA-GA2-35


title: whole blood-RSV-RSVA-GA2-41


title: JY1776 P35 PLZF siRNA day 3 EPC


title: whole blood-RSV-RSVA-GA2-34


title: whole blood-RSV-RSVA-GA2-40


title: whole blood-RSV-RSVA-GA2-37


title: whole blood-RSV-RSVB-BA-4


title: JY1777 P37 NT siRNA day 0 EPC


title: whole blood-RSV-RSVA-GA5-3


title: whole blood-RSV-RSVA-GA2-36


title: whole blood-RSV-RSVA-GA2-27


title: whole blood-RSV-RSVA-GA2-30


title: whole blood-RSV-RSVA-GA2-31


title: whole blood-RSV-RSVA-GA2-25


title: whole blood-RSV-RSVA-GA2-29


title: whole blood-RSV-RSVA-GA2-33


title: whole blood-RSV-RSVA-GA2-22


title: whole blood-RSV-RSVA-GA2-28


title: whole blood-RSV-RSVA-GA2-26


title: whole blood-RSV-RSVA-GA2-19


title: whole blood-RSV-RSVA-GA2-32


title: whole blood-RSV-RSVA-GA2-23


title: whole blood-RSV-RSVA-GA2-15


title: whole blood-RSV-RSVA-GA2-18


title: whole blood-RSV-RSVA-GA2-24


title: whole blood-RSV-RSVA-GA2-9


title: whole blood-RSV-RSVA-GA2-16


title: whole blood-RSV-RSVA-GA2-14


title: whole blood-RSV-RSVA-GA2-17


title: whole blood-RSV-RSVA-GA2-20


title: whole blood-RSV-RSVA-GA2-12


title: whole blood-RSV-RSVA-GA2-21


title: whole blood-RSV-RSVA-GA2-8


title: whole blood-RSV-RSVA-GA2-13


title: whole blood-RSV-RSVA-GA2-3


title: S4-GSE1

status: Public on Feb 28 2018

data_processing:
Fastq files were trimmed using Flexbar to remove 3’ bases with quality score lower than 30
Novoalign+ V2.08.01 was used for alignment
The trimmed reads were mapped to human genome version GRCH38 downloaded from GENCODE using HISAT2] to generate alignment files in bam format.
Samtools name-sorted bam files were processed using htseq-count to summarize gene level counts.
Genome_build: GRCH38 downloaded from GENCODE
Supplementary_files_format_and_content: csv, gene-level counts

source_name: GSE

growth_protocol: Colorectal cancer cell lines HCT116, SW480, SW620, HT29, Caco-2, RKO and LoVo were purchased from American Type Culture Collection (Manassas, VA). All cell lines were tested and authenticated using a panel of genetic and epigenetic markers in June 2017. The cells were grown in Iscove’s Modified Dulbecco’s Medium (IMDM; Gibco, Carlsbad, CA), supplemented with 10% fetal bovine serum, 1% penicillin and streptomycin and maintained at 37˚C in a humidified incubator at 5% CO2.

extract_protocol:
RNA was extracted using miRNeasy Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instruction.
NGS library construction was performed using the TruSeq RNA Library Kit (Illumina) with up to 1 µg of total RNA input according to manufacturer’s protocol. The quality of individual libraries was assessed using the High Sensitivity DNA Kit (Agilent). Libraries were pooled together using a Pippin HT instrument (Sage Science). Efficiency of size selection was assessed using a High Sensitivity DNA Kit (Agilent). Pooled libraries were quantitated via qPCR using the KAPA Library Quantification Kit, Universal (KAPA Biosystems).

treatment_protocol: Unfractionated GSE that includes both small oligomeric (monomers, dimers and trimers) proanthocyanidins and larger polymers, and the OPCs fraction (VX1 extract, Berkem,, France) that is devoid of larger proanthocyanidins were used in this study. For treatments, OPCs and GSE were dissolved in DMSO and diluted to 100 ng/ul in culture medium. Cultures were treated for 18 hrs.

tag: treatment (opc

value: oligomeric proanthocyanidins, gse:grape seed extract):GSE-1

tag: cell line


title: S4-OPC2

source_name: OPC

value: oligomeric proanthocyanidins, gse:grape seed extract):OPC-2


title: S4-GSE2

value: oligomeric proanthocyanidins, gse:grape seed extract):GSE-2


title: S4-OPC1

value: oligomeric proanthocyanidins, gse:grape seed extract):OPC-1


title: S4-C2

source_name: Control

value: oligomeric proanthocyanidins, gse:grape seed extract):Control-2


title: HT-GSE2


title: S4-C1

value: oligomeric proanthocyanidins, gse:grape seed extract):Control-1


title: whole blood-RSV-RSVA-GA2-5

value: F


title: whole blood-RSV-RSVA-GA2-10


title: whole blood-RSV-RSVA-GA2-7


title: whole blood-Control-7

source_name: whole blood-Control

value: Control


title: whole blood-Control-11


title: whole blood-RSV-RSVA-GA2-4


title: whole blood-RSV-RSVA-GA2-1


title: whole blood-Control-8


title: HT-GSE1


title: whole blood-Control-10


title: whole blood-Control-5


title: whole blood-Control-4


title: HT-OPC2


title: whole blood-RSV-RSVA-GA2-6


title: HT-C2


title: HT-C1


title: HCT-C2


title: HCT-OPC1


title: whole blood-Control-2


title: whole blood-Control-6


title: whole blood-Control-1


title: whole blood-Control-9


title: S6-GSE1


title: whole blood-RSV-RSVA-GA2-11


title: S6-OPC1


title: S6-C2


title: HT-OPC1


title: HCT-GSE1


title: HCT-GSE2


title: D-GSE2

value: RKO


title: D-GSE1


title: S6-OPC2


title: HCT-OPC2


title: D-OPC2


title: HCT-C1


title: D-C1


title: whole blood-RSV-RSVA-GA2-2


title: whole blood-Control-3


title: D-C2


title: whole blood-Control-12


title: S6-C1


title: S6-GSE2


title: CXIR66OC21-matched normal mucosa (NM)

status: Public on Feb 14 2018

data_processing:
Novoalign+ V2.08.01 was used for alignment
Read count for each annotated transcript was then derived from mapped reads by Rsubread
Differential expression was determined by DESeq/edgeR
Genome_build: hg19
Supplementary_files_format_and_content: csv file; lncRNAs dysregulated in CRC as determined by edgeR (logFC and p val < 0.02) and DESeq (p val < 0.05)

source_name: frozen mucosal tissue

extract_protocol:
RNA was extracted using miRNeasy Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instruction. Briefly, 700 μL of QIAzol was added to samples and homogenized with a TissueLyser LT (QIAGEN) for RNAlater immersed tissues or by vortexing for 1 minute for cultured cells. After incubation of the homogenate for 5 minutes at room temperature, 140 μL chloroform was added and centrifuged at 12,000g and at 4°C for 15 minutes. Thereafter, transfer the upper aqueous phase to a new tube, and total RNA was extracted and eluted in 60 μL of RNase-free water using QIAcube (QIAGEN).
Illumina TruSeq V2 kit

value: frozen mucosal tissue

tag: tissue type

value: matched normal mucosa (NM)

tag: source id


title: CXIR60OC4-matched normal mucosa (NM)


title: CXIR56SE6-CRC: colorectal cancer

value: CRC:colorectal cancer


title: CXIR66OC21-CRC: colorectal cancer


title: CXIR56SE6-matched normal mucosa (NM)


title: CXIR60OC4-CRC: colorectal cancer


title: HuRCLIP_293T_NoDice_2-20_rep3

status: Public on Jan 19 2018

city: Riverside

first: Fedor

last: Karginov

state: California

address: 900 University Ave

department: MCSB

institute: UC Riverside

description: crosslinked HuR-bound RNA

data_processing:
3' adapter (GTGTCAGTCACTTCCAGCGG) was clipped off and the resulting reads filtered for a length of 20nt or more (4nt random ligation barcode + G + 15nt of insert)
reads that have identical barcode + G + insert (i.e. PCR duplicates) were collapsed to unique reads and filtered for the presence of G at position 5
4nt barcode + G were trimmed off, and remaining insert (peak) sequences collapsed to unique sequences, preserving their count of barcodes (unique 5' ligation events during library construction) as the readcount for quantification
reads were aligned by bowtie2 to the hg19 genome build; unmapped reads were further mapped by Tophat to a transcriptome file combining refseq gene information and lincRNAs; matches with a mapping quality of 20 or more were retained; distinct reads with identical mapping coordinates (i.e. sequencing or allelic variants) were collapsed by readcount
reads were annotated by microRNA, refseq/lincRNA, and repeatmasker annotation positions
combined reads from all conditions were pooled to define peaks using FindPeaks4, and readcounts underneath each peak were re-extracted for each replicate
peak readcounts were filtered for a sum of more than 9 across all replicates, and peak signal and differential signal was computed by DESeq2, and further intersected with external data on mRNA level changes as described
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text, extended .bed file with processed, filtered HuR peak coordinates, annotations, quantification and overlap information

growth_protocol: Cells were grown in DMEM (Corning Cellgro) with 10 % Fetal Bovine Serum (HyClone) and 10 units/ml of Penicillin-Streptomycin (HyClone). Cultured plates were grown in a humidified incubator at 37 °C with 5 % CO2

extract_protocol:
Cells were crosslinked, lysed and immunoprecipitated with antibodies against endogenous HuR as described in the Materials and Methods
The HITS-CLIP (CLIP-seq) protocol for library construction was performed, as described in the Materials and Methods

tag: dicer protein status

value: KO


title: HuRCLIP_293T_NoDice_4-25_rep1

description: crosslinked HuR-bound RNA


title: Ago2CLIP_dsiHuR2_rep5

description: crosslinked Ago2-bound RNA

data_processing:
3' adapter (GTGTCAGTCACTTCCAGCGG) was clipped off and the resulting reads filtered for a length of 20nt or more (4nt random ligation barcode + G + 15nt of insert)
reads that have identical barcode + G + insert (i.e. PCR duplicates) were collapsed to unique reads and filtered for the presence of G at position 5
4nt barcode + G were trimmed off, and remaining insert (peak) sequences collapsed to unique sequences, preserving their count of barcodes (unique 5' ligation events during library construction) as the readcount for quantification
reads were aligned by bowtie2 to the hg19 genome build; unmapped reads were further mapped by Tophat to a transcriptome file combining refseq gene information and lincRNAs; matches with a mapping quality of 20 or more were retained; distinct reads with identical mapping coordinates (i.e. sequencing or allelic variants) were collapsed by readcount
reads were annotated by microRNA, refseq/lincRNA, and repeatmasker annotation positions
combined reads from all conditions were pooled to define peaks using FindPeaks4, and readcounts underneath each peak were re-extracted for each replicate
peak readcounts were filtered for a sum of more than 15 across all replicates, peaks containing complements to nucleotides 3-7 of the knockdown siRNAs were eliminated to avoid off-targeting artefacts, and peak signal and differential signal was computed by DESeq2, and further intersected with external data on mRNA level changes as described
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text, extended .bed file with processed, filtered Ago2 peak coordinates, annotations, quantification and overlap information

source_name: T-REx-293 cells

extract_protocol:
Cells were crosslinked, lysed and immunoprecipitated with antibodies against endogenous Ago2 as described in the Materials and Methods
The HITS-CLIP (CLIP-seq) protocol for library construction was performed, as described in the Materials and Methods

treatment_protocol: T-REx-293 cells were separately transfected with two distinct siRNAs against HuR, or with a gl3.1 siRNA control. TransIT-TKO (Mirus) transfections with 100nM of siRNA were performed for the first 2 replicates, and calcium phosphate transfections with 25nM siRNA were carried out for the later 3 replicates. For each replicate set, three successive transfections 2 days apart were performed to get sufficient knockdown of HuR.

tag: sirna used

tag: knockdown protein

value: HuR


title: Ago2CLIP_dsiHuR5_rep1

description: crosslinked Ago2-bound RNA


title: HuRCLIP_293T_NoDice_2-20_rep2

description: crosslinked HuR-bound RNA


title: HuRCLIP_293T_rep1

description: crosslinked HuR-bound RNA

value: WT


title: Ago2CLIP_gl3.1_rep4

description: crosslinked Ago2-bound RNA

value: luciferase (control, not present)


title: HuRCLIP_293T_NoDice_4-25_rep3

description: crosslinked HuR-bound RNA


title: Ago2CLIP_dsiHuR2_rep1

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_gl3.1_rep3

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_dsiHuR2_rep2

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_dsiHuR2_rep3

description: crosslinked Ago2-bound RNA


title: HuRCLIP_293T_NoDice_2-20_rep1

description: crosslinked HuR-bound RNA


title: Ago2CLIP_gl3.1_rep2

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_dsiHuR5_rep3

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_dsiHuR5_rep2

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_dsiHuR5_rep4

description: crosslinked Ago2-bound RNA


title: HuRCLIP_293T_NoDice_4-25_rep2

description: crosslinked HuR-bound RNA


title: HuRCLIP_293T_rep3

description: crosslinked HuR-bound RNA


title: Ago2CLIP_dsiHuR2_rep4

description: crosslinked Ago2-bound RNA


title: HuRCLIP_293T_rep2

description: crosslinked HuR-bound RNA


title: Ago2CLIP_gl3.1_rep5

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_dsiHuR5_rep5

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_gl3.1_rep1

description: crosslinked Ago2-bound RNA


title: HIDS_Patient2_RPMI_d1_RNAseq

status: Public on Jan 08 2018

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 data.
ChIP-seq reads were aligned to the hg19 genome assembly using bwa. For peak calling the BAM files were first filtered to remove the reads with mapping quality less than 15, followed by fragment size modeling (http://code.google.com/p/phantompeakqual-tools/). The peak calling algorithm MACS2 http://github.com/taoliu/MACS/) was used to detect the binding sites for the three studied histone marks at p-value of 10-10. H3K4me1 peaks were called using the broad setting of MACS2 while H3K27ac and H3K4me3 were called using the default (narrow) setting.
Library strategy: RNA-seq. MMSEQ package was used to infer gene expression levels. Reads were mapped to human gene annotation using Bowtie1 (Ensemble release 68).
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq files are in bigWig format, DownSampled to make all files the same read depth. RNA files are in a .gene.mmseq format, containing counts per gene.

source_name: HIDS monocyte cultured in media (RPMI) for 24 hours

growth_protocol: Monocytes were negatively selected from peripheral blood and grown in culture for 6 days, with 24 hours exposure to RPMI (media only) or Mevalonate (to induce trained immuniy) and then fixed for ChIP or placed in Trizol for RNA.

extract_protocol:
RNA was extracted using the RNEasy mini kit. ChIP was performed using BLUEPRINT protocols.
Libraries were prepared using the KAPA hyperprep kit.

treatment_protocol: For ChIP-seq: Purified cells were fixed with 1% formaldehyde (Sigma) at a concentration of approximately 10 million cells/ml. Fixed cell preparations were sonicated using a Diagenode Bioruptor UCD-300 for 3x 10 minutes (30 seconds on; 30 seconds off). 33 µl of chromatin was used for immunoprecipitation.

value: Monocyte

tag: treatment protocol

value: cultured in media (RPMI) for 24 hours

tag: disease

value: Hyper IgD Syndrome (HIDS)

tag: tissue

value: Adult Peripheral Blood

tag: donor

tag: chip antibody


title: HIDS_Patient3_LPS_d1_RNAseq

source_name: HIDS monocyte cultured in media (RPMI) with 10ng/mL LPS for 24 hours

tag: cell type


title: HIDS_Patient3_RPMI_d1_RNAseq


title: HIDS_Patient3_unstim_RNAseq

source_name: HIDS monocyte sample from peripheral blood of healthy volunteer


title: HIDS_Patient2_LPS_d1_RNAseq

value: cultured in media (RPMI) with 10ng/mL LPS for 24 hours


title: HIDS_Patient1_RPMI_d1_RNAseq


title: HIDS_Control3_LPS_d1_RNAseq

source_name: Control monocyte cultured in media (RPMI) with 10ng/mL LPS for 24 hours

value: healthy


title: HIDS_Control2_LPS_d1_RNAseq


title: HIDS_Control1_LPS_d1_RNAseq


title: MevT_Mevalonate_Mf2_RNAseq

data_processing:
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 data.
ChIP-seq reads were aligned to the hg19 genome assembly using bwa (https://github.com/lh3/bwa). For peak calling the BAM files were first filtered to remove the reads with mapping quality less than 15, followed by fragment size modeling (https://github.com/kundajelab/phantompeakqualtools). The peak calling algorithm MACS2 http://github.com/taoliu/MACS/) was used to detect the binding sites for the three studied histone marks at p-value of 10-10. H3K4me1 peaks were called using the broad setting of MACS2 while H3K27ac  were called using the default (narrow) setting.
Library strategy: RNA-seq. MMSEQ package was used to infer gene expression levels. Reads were mapped to human gene annotation using Bowtie1 (Ensemble release 68).
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq files are in bigWig format, DownSampled to make all files the same read depth. RNA files are in a .gene.mmseq format, containing counts per gene.

source_name: Adult Human Peripheral Blood

value: Monocytes cultured for 24 hours in mevalonate, followed by 5 days in media (RPMI)


title: HIDS_Control1_Unstim_H3K27ac

library_source: genomic

molecule: genomic DNA

source_name: Control monocyte sample from peripheral blood of healthy volunteer

value: Rabbit polyclonal anti-H3K27ac (Diagenode, cat. # pAb-196-050)


title: HIDS_Control2_Unstim_H3K27ac


title: HIDS_Control2_unstim_RNAseq


title: HIDS_Patient2_Unstim_H3K27ac

source_name: Monocyte from peripheral blood of HIDS patients


title: MevT_Mevalonate_Mf6_RNAseq


title: HIDS_Patient1_unstim_RNAseq


title: HIDS_Control1_RPMI_d1_RNAseq

source_name: Control monocyte cultured in media (RPMI) for 24 hours


title: HIDS_Control1_unstim_RNAseq


title: MevT_RPMI_Mf1_RNAseq

value: Monocytes cultured for 6 days in media (RPMI) only


title: HIDS_Control3_unstim_RNAseq


title: HIDS_Control3_RPMI_d1_RNAseq


title: HIDS_Patient1_LPS_d1_RNAseq


title: HIDS_Patient3_Unstim_H3K27ac


title: MevT_RPMI_Mf5_H3K4me1

value: Rabbit polyclonal anti-H3K4me1 (Diagenode, cat. # pAb-003-050)


title: MevT_Mevalonate_Mf6_H3K4me1


title: HIDS_Control3_Unstim_H3K27ac


title: HIDS_Control2_RPMI_d1_RNAseq


title: MevT_Mevalonate_Mf2_H3K4me1


title: HIDS_Patient1_Unstim_H3K27ac


title: MevT_Mevalonate_Mf6_H3K27ac


title: MevT_RPMI_Mf5_H3K27ac


title: HIDS_Patient2_unstim_RNAseq


title: MevT_RPMI_Mf5_RNAseq


title: MevT_RPMI_Mf1_H3K4me1


title: MevT_Mevalonate_Mf2_H3K27ac


title: BCG_Donor28_v1_H3K27ac

description: Before BCG vaccine

data_processing:
Illumina Casava software 1.8.2 used for basecalling of Hiseq2000 data.
ChIP-seq reads were aligned to the hg19 genome assembly using bwa. For peak calling, the BAM files were first filtered to remove the reads with mapping quality less than 15, followed by fragment size modeling (https://code.google.com/archive/p/phantompeakqualtools/). The peak calling algorithm MACS2 (http://github.com/taoliu/MACS/) was used to detect the binding sites for the three studied histone marks at p-value of 10-10. H3K4me1 peaks were called using the broad setting of MACS2, while H3K27ac and H3K4me3 were called using the default (narrow) setting.
RNA-seq: MMSEQ package was used to infer gene expression levels. Reads were mapped to human gene annotation using Bowtie1 (Ensembl release 68).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: RNA files are in a .gene.mmseq.txt format, containing counts per gene.
Supplementary_files_format_and_content: ChIP-seq files are in bigWig format, DownSampled to make all files the same read depth.

growth_protocol: Monocytes were negatively selected from peripheral blood and immediately fixed for ChIP or placed in Trizol for RNA.

extract_protocol:
RNA was extracted using the RNeasy mini kit.
ChIP was performed using BLUEPRINT protocols.
Libraries were prepared using the KAPA hyperprep kit.

tag: disease status

value: Healthy

tag: treatment

tag: time point

value: Baseline


title: BCG_Donor29_v2_H3K27ac

description: 1 month after BCG vaccine

value: Bacillus Calmette-Guérin (BCG) vaccine

value: 1 month


title: MevT_RPMI_Mf1_H3K27ac


title: BCG_Donor28_v2_H3K27ac

description: 1 month after BCG vaccine


title: BCG_Donor18_V1_H3K27ac

description: Before BCG vaccine


title: RNA_Donor24_baseline

description: Before BCG vaccine


title: RNA_Donor29_baseline

description: Before BCG vaccine


title: RNA_Donor28_baseline

description: Before BCG vaccine


title: RNA_Donor29_BCG_1_month

description: 1 month after BCG vaccine


title: RNA_Donor20_BCG_1_month

description: 1 month after BCG vaccine


title: BCG_Donor18_V2_H3K27ac

description: 1 month after BCG vaccine


title: BCG_Donor15_V2_H3K27ac

description: 1 month after BCG vaccine


title: RNA_Donor28_BCG_1_month

description: 1 month after BCG vaccine


title: BCG_Donor15_V1_H3K27ac

description: Before BCG vaccine


title: RNA_Donor20_baseline

description: Before BCG vaccine


title: BCG_Donor20_v1_H3K27ac

description: Before BCG vaccine


title: RNA_Donor23_BCG_1_month

description: 1 month after BCG vaccine


title: BCG_Donor9_V2_H3K27ac

description: 1 month after BCG vaccine


title: BCG_Donor7_V2_H3K27ac

description: 1 month after BCG vaccine


title: BCG_Donor20_V2_H3K27ac_B

description: 1 month after BCG vaccine


title: BCG_Donor7_V1_H3K27ac

description: Before BCG vaccine


title: RNA_Donor18_baseline

description: Before BCG vaccine


title: RNA_Donor18_BCG_1_month

description: 1 month after BCG vaccine


title: BCG_Donor29_v1_H3K27ac

description: Before BCG vaccine


title: RNA_Donor24_BCG_1_month

description: 1 month after BCG vaccine


title: BCG_Donor9_V1_H3K27ac

description: Before BCG vaccine


title: Donor4_RNA_RPMI_24_hours

status: Public on Dec 08 2017

data_processing:
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 data.
Library strategy: RNA-seq. MMSEQ package was used to infer gene expression levels. Reads were mapped to human gene annotation using Bowtie1 (Ensemble release 68).
Genome_build: hg19
Supplementary_files_format_and_content: RNA files are in a .gene.mmseq format, containing counts per gene.

growth_protocol: Monocytes were negatively selected from peripheral blood and exposed for 24 hours to RPMI (media only) or uric acid (to induce trained immuniy) and then placed in Trizol for RNA.

extract_protocol:
RNA was extracted using the RNEasy mini kit.
Libraries were prepared using the KAPA hyperprep kit.

treatment_protocol:
Uric acid or media, and exposed to lipopolysaccharide
Monocytes cultured for 24 hours in media (RPMI) only

tag: diagnosis


title: Donor4_RNA_RPMI_24_hours_LPS_4h

treatment_protocol:
Uric acid or media, and exposed to lipopolysaccharide
Monocytes cultured for 24 hours in media (RPMI) only and exposed to LPS for 4 hours


title: Donor3_RNA_Uric_acid_24_hours_LPS_4h

treatment_protocol:
Uric acid or media, and exposed to lipopolysaccharide
Monocytes cultured for 24 hours with Uric Acid and exposed to LPS for 4 hours


title: Donor4_RNA_Uric_acid_24_hours

treatment_protocol:
Uric acid or media, and exposed to lipopolysaccharide
Monocytes cultured for 24 hours with Uric Acid


title: Donor4_RNA_Uric_acid_24_hours_LPS_4h


title: Donor4_RNA_Monocyte_T0

treatment_protocol:
Uric acid or media, and exposed to lipopolysaccharide
Monocytes at time 0 (1 hour attachment to plate)


title: Donor2_RNA_Uric_acid_24_hours


title: Donor3_RNA_RPMI_24_hours_LPS_4h


title: Donor3_RNA_RPMI_24_hours


title: Donor1_RNA_RPMI_24_hours_LPS_4h


title: Donor1_RNA_Uric_acid_24_hours_LPS_4h


title: RNA_Donor23_baseline

description: Before BCG vaccine


title: Donor2_RNA_RPMI_24_hours_LPS_4h


title: Donor1_RNA_RPMI_24_hours


title: Donor1_RNA_Monocyte_T0


title: Donor2_RNA_Uric_acid_24_hours_LPS_4h


title: Donor2_RNA_RPMI_24_hours


title: Donor1_RNA_Uric_acid_24_hours


title: Donor3_RNA_Monocyte_T0


title: Donor2_RNA_Monocyte_T0


title: 12_Z13_1_d5_Zika

status: Public on Oct 11 2017

city: Los Angeles

first: Bennett

last: Novitch

address: 650 Charles E Young Dr. S, CHS 66-200

department: Department of Neurobiology

institute: University of California, Los Angeles

data_processing:
RNAseq reads were aligned to the hg38 genome assembly using STAR_2.4.0j with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: cortical organoids_Zika_5d

extract_protocol:
Human cortical organoids were lysed in QIAzol reagents and RNA was extracted following manufacturer’s instructions (the miRNeasy Micro Kit, Qiagen).
the KAPA stranded mRNA-Seq kits (KAPA Biosystems)

value: Human cerebral organoids

tag: infected with

value: Zika

tag: timepoint

value: 5 days of post infection


title: 17_Z13_2_d5_Control

source_name: cortical organoids_mock_5d

value: Control


title: 16_Z13_2_d3_Zika

source_name: cortical organoids_Zika_3d

value: 3 days of post infection


title: 18_Z13_2_d5_Zika


title: 15_Z13_2_d3_Control

source_name: cortical organoids_mock_3d


title: 11_Z13_1_d5_Control


title: 10_Z13_1_d3_Zika


title: Donor3_RNA_Uric_acid_24_hours

value: Monocyte


title: 9_Z13_1_d3_Control


title: 5_Z12_d5_Control


title: 6_Z12_d5_Zika


title: 4_Z12_d3_Zika


title: 3_Z12_d3_Control


title: D-OPC1

source_name: OPC

tag: treatment (opc

value: oligomeric proanthocyanidins, gse:grape seed extract):OPC-1

tag: cell line

value: RKO


title: D98-2

description: Cortical Organoids Donor: 1 DiffWk: 14 Replicate: 2

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: Log2 normalization and quantile normalization.

label_protocol: Biotin

extract_protocol: Human cortical organoids were lysed in QIAzol reagents and RNA was extracted following manufacturer’s instructions (the miRNeasy Micro Kit, Qiagen).

tag: tissue type

value: Cortical Organoids

tag: donorid

tag: diffwk

tag: rin

tag: batch


title: D98-1

description: Cortical Organoids Donor: 1 DiffWk: 14 Replicate: 1


title: SYS-130_sIA_HKSE_6h [V2 manifest]

status: Public on Sep 18 2017

data_processing:
The data were normalized using average normalization in GenomeStudio’s gene expression module.
Please note that data were analyzed using both V1 manifest (pre-Oct 2010) or the V2 manifest (post-Oct 2010).
Matrix non-normalized data is the raw data computed from the chip by GenomeStudio.

source_name: whole blood_sIA_HKSE_6h

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep kit for Illumina arrays.

extract_protocol: 3mls of whole blood was collected into Tempus tubes (Applied Biosystems, Foster City, CA, USA), vigorously mixed immediately after collection, and stored between −20°C and −80°C before RNA extraction. RNA was isolated from Training Set samples using 1.5mls whole blood and the PerfectPure RNA Blood kit (5 PRIME Inc, Gaithersburg, MD, USA)

treatment_protocol: Ligands were diluted in medium (RPMI 1640 with GlutaMax, Thermo Fisher  Scientific, Grand Island, NY, USA) and aliquoted into 2 mL polypropylene  96-well plates (Greiner Bio-One, Monroe, NC, USA). Blood was drawn in the  morning into the BD Vacutainers containing ACD anticoagulant (BD, Franklin  Lakes, NJ, USA). Time between blood draw and culture setup was less than  2h. Blood and appropriately diluted ligands were mixed in 1:1 ratio in  total volume of 1 mL/well and incubated for 6h at 37oC/5% CO2. After the culture, blood was mixed and  100 uL aliquot set aside for activation marker phenotyping and  intracellular cytokine staining (ICS) for IL-1b. The plate was then  centrifuged at 12,000 x g/15  and 400 mL of plasma aliquoted and stored at  -80oC until the Luminex analysis. The pellet was the  lysed with Tempus  solution (Tempus blood RNA tubes, Thermo Fisher Scientific) in 2:1 ratio  and stored at -20oC until the RNA extraction.

tag: donor id

tag: subject status

value: Systemic onset juvenile idiopathic arthritis (sJIA)

value: inactive

value: Anakinra

value: sIA

tag: stimulus

value: HKSE

tag: tissue

value: whole blood


title: SYS-188_sIA_HKSE_6h [V2 manifest]


title: D35-1

description: Cortical Organoids Donor: 1 DiffWk: 5 Replicate: 1


title: SYS-188_sIA_HKSA_6h [V2 manifest]

source_name: whole blood_sIA_HKSA_6h

value: HKSA


title: D56-1

description: Cortical Organoids Donor: 1 DiffWk: 8 Replicate: 1


title: D35-3

description: Cortical Organoids Donor: 1 DiffWk: 5 Replicate: 3


title: D98-3

description: Cortical Organoids Donor: 1 DiffWk: 14 Replicate: 3


title: SYS-206_sIA_CpG-C_6h [V2 manifest]

source_name: whole blood_sIA_CpG-C_6h

value: CpG-C


title: SYS-188_sIA_LTA_6h [V2 manifest]

source_name: whole blood_sIA_LTA_6h

value: LTA


title: SYS-206_sIA_R848_6h [V2 manifest]

source_name: whole blood_sIA_R848_6h


title: SYS-130_sIA_HKSA_6h [V2 manifest]


title: D77-3

description: Cortical Organoids Donor: 1 DiffWk: 11 Replicate: 3


title: D77-2

description: Cortical Organoids Donor: 1 DiffWk: 11 Replicate: 2


title: SYS-206_sIA_HKSE_6h [V2 manifest]


title: SYS-188_sIA_R848_6h [V2 manifest]


title: D35-2

description: Cortical Organoids Donor: 1 DiffWk: 5 Replicate: 2


title: D56-2

description: Cortical Organoids Donor: 1 DiffWk: 8 Replicate: 2


title: D77-1

description: Cortical Organoids Donor: 1 DiffWk: 11 Replicate: 1


title: SYS-188_sIA_Medium_6h [V2 manifest]

source_name: whole blood_sIA_Medium_6h

value: Medium


title: SYS-206_sIA_HKSA_6h [V2 manifest]


title: D56-3

description: Cortical Organoids Donor: 1 DiffWk: 8 Replicate: 3


title: SYS-206_sIA_Medium_6h [V2 manifest]


title: SYS-130_sIA_LPS_6h [V2 manifest]

source_name: whole blood_sIA_LPS_6h

value: LPS


title: SYS-188_sIA_LPS_6h [V2 manifest]


title: SYS-130_sIA_R848_6h [V2 manifest]


title: SYS-206_sIA_R837_6h [V2 manifest]

source_name: whole blood_sIA_R837_6h


title: SYS-206_sIA_LTA_6h [V2 manifest]


title: SYS-188_sIA_CpG-C_6h [V2 manifest]


title: SYS-130_sIA_LTA_6h [V2 manifest]


title: H-391_healthy pediatric_R837_6h [V2 manifest]

source_name: whole blood_healthy pediatric_R837_6h

value: healthy pediatric


title: SYS-130_sIA_Medium_6h [V2 manifest]


title: H-390_healthy pediatric_CpG-C_6h [V2 manifest]

source_name: whole blood_healthy pediatric_CpG-C_6h


title: SYS-130_sIA_CpG-C_6h [V2 manifest]


title: H-389_healthy pediatric_LPS_6h [V2 manifest]

source_name: whole blood_healthy pediatric_LPS_6h


title: H-391_healthy pediatric_R848_6h [V2 manifest]

source_name: whole blood_healthy pediatric_R848_6h


title: H-389_healthy pediatric_R848_6h [V2 manifest]


title: H-391_healthy pediatric_CpG-C_6h [V2 manifest]


title: H-391_healthy pediatric_HKSE_6h [V2 manifest]

source_name: whole blood_healthy pediatric_HKSE_6h


title: H-389_healthy pediatric_HKSE_6h [V2 manifest]


title: SYS-206_sIA_LPS_6h [V2 manifest]


title: H-390_healthy pediatric_LTA_6h [V2 manifest]

source_name: whole blood_healthy pediatric_LTA_6h


title: H-393_healthy pediatric_Medium_6h [V2 manifest]

source_name: whole blood_healthy pediatric_Medium_6h


title: H-391_healthy pediatric_HKSA_6h [V2 manifest]

source_name: whole blood_healthy pediatric_HKSA_6h


title: H-390_healthy pediatric_Medium_6h [V2 manifest]


title: H-389_healthy pediatric_LTA_6h [V2 manifest]


title: H-390_healthy pediatric_R848_6h [V2 manifest]


title: H-393_healthy pediatric_LTA_6h [V2 manifest]


title: H-393_healthy pediatric_R848_6h [V2 manifest]


title: H-391_healthy pediatric_LTA_6h [V2 manifest]


title: H-391_healthy pediatric_Medium_6h [V2 manifest]


title: H-390_healthy pediatric_HKSE_6h [V2 manifest]


title: H-389_healthy pediatric_CpG-C_6h [V2 manifest]


title: H-390_healthy pediatric_HKSA_6h [V2 manifest]


title: H-389_healthy pediatric_Medium_6h [V2 manifest]


title: H-390_healthy pediatric_LPS_6h [V2 manifest]


title: H-393_healthy pediatric_LPS_6h [V2 manifest]


title: H-393_healthy pediatric_CpG-C_6h [V2 manifest]


title: H-389_healthy pediatric_R837_6h [V2 manifest]


title: H-389_healthy pediatric_HKSA_6h [V2 manifest]


title: H-393_healthy pediatric_HKSA_6h [V2 manifest]


title: H-393_healthy pediatric_R837_6h [V2 manifest]


title: SYS-201_sAU_HKSE_6h [V2 manifest]

source_name: whole blood_sAU_HKSE_6h

value: active

value: untreated

value: sAU


title: H-393_healthy pediatric_HKSE_6h [V2 manifest]


title: SYS-200_sAU_HKSA_6h [V2 manifest]

source_name: whole blood_sAU_HKSA_6h


title: H-390_healthy pediatric_R837_6h [V2 manifest]


title: H-287_healthy pediatric_Medium_6h [V2 manifest]


title: SYS-200_sAU_R848_6h [V2 manifest]

source_name: whole blood_sAU_R848_6h


title: H-287_healthy pediatric_CpG-C_6h [V2 manifest]


title: SYS-200_sAU_CpG-C_6h [V2 manifest]

source_name: whole blood_sAU_CpG-C_6h


title: H-287_healthy pediatric_R837_6h [V2 manifest]


title: SYS-201_sAU_R848_6h [V2 manifest]


title: SYS-201_sAU_LPS_6h [V2 manifest]

source_name: whole blood_sAU_LPS_6h


title: H-287_healthy pediatric_HKSE_6h [V2 manifest]


title: H-287_healthy pediatric_LPS_6h [V2 manifest]


title: H-386_healthy pediatric_CpG-C_6h [V2 manifest]


title: SYS-200_sAU_LPS_6h [V2 manifest]


title: SYS-201_sAU_Medium_6h [V2 manifest]

source_name: whole blood_sAU_Medium_6h


title: SYS-200_sAU_R837_6h [V2 manifest]

source_name: whole blood_sAU_R837_6h


title: SYS-201_sAU_LTA_6h [V2 manifest]

source_name: whole blood_sAU_LTA_6h


title: SYS-201_sAU_HKSA_6h [V2 manifest]


title: SYS-201_sAU_CpG-C_6h [V2 manifest]


title: H-386_healthy pediatric_R848_6h [V2 manifest]


title: H-287_healthy pediatric_LTA_6h [V2 manifest]


title: H-386_healthy pediatric_R837_6h [V2 manifest]


title: H-287_healthy pediatric_HKSA_6h [V2 manifest]


title: SYS-200_sAU_HKSE_6h [V2 manifest]


title: SYS-200_sAU_LTA_6h [V2 manifest]


title: H-386_healthy pediatric_HKSA_6h [V2 manifest]


title: BD1658_healthy adult_Medium_6h [V2 manifest]

source_name: whole blood_healthy adult_Medium_6h

value: healthy adult


title: BD3038_healthy adult_IL-17A/F_6h [V2 manifest]

source_name: whole blood_healthy adult_IL-17A/F_6h


title: H-287_healthy pediatric_R848_6h [V2 manifest]


title: BD1350_healthy adult_PMA/I_6h [V2 manifest]

source_name: whole blood_healthy adult_PMA/I_6h

value: PMA/I


title: BD3045_healthy adult_TNFalpha_6h [V2 manifest]

source_name: whole blood_healthy adult_TNFalpha_6h

value: TNFalpha


title: H-386_healthy pediatric_LTA_6h [V2 manifest]


title: SYS-200_sAU_Medium_6h [V2 manifest]

value: Systemic onset juvenile idiopathic arthritis (sJIA)


title: BD1658_healthy adult_CpG-C_6h [V2 manifest]

source_name: whole blood_healthy adult_CpG-C_6h


title: BD1350_healthy adult_R848_6h [V2 manifest]

source_name: whole blood_healthy adult_R848_6h


title: H-386_healthy pediatric_HKSE_6h [V2 manifest]

source_name: whole blood_healthy pediatric_HKSE_6h


title: SYS-201_sAU_R837_6h [V2 manifest]


title: H-386_healthy pediatric_Medium_6h [V2 manifest]

source_name: whole blood_healthy pediatric_Medium_6h


title: BD3041_healthy adult_IL-18_6h [V2 manifest]

source_name: whole blood_healthy adult_IL-18_6h


title: BD1635_healthy adult_R837_6h [V2 manifest]

source_name: whole blood_healthy adult_R837_6h


title: BD1350_healthy adult_CpG-C_6h [V2 manifest]


title: H-386_healthy pediatric_LPS_6h [V2 manifest]

source_name: whole blood_healthy pediatric_LPS_6h


title: BD1837_healthy adult_TNFalpha_6h [V2 manifest]


title: BD1350_healthy adult_IL-1beta_6h [V2 manifest]

source_name: whole blood_healthy adult_IL-1beta_6h


title: BD1837_healthy adult_TLR8L_6h [V2 manifest]

source_name: whole blood_healthy adult_TLR8L_6h


title: BD1658_healthy adult_IFNalpha_6h [V2 manifest]

source_name: whole blood_healthy adult_IFNalpha_6h

value: IFNalpha


title: BD1737_healthy adult_Medium_6h [V2 manifest]


title: BD1858_healthy adult_IL-18_6h [V2 manifest]


title: BD1277_healthy adult_CpG-C_6h [V2 manifest]


title: BD1635_healthy adult_Medium_6h [V2 manifest]


title: BD1768_healthy adult_R848_6h [V2 manifest]


title: BD1312_healthy adult_Medium_6h [V2 manifest]


title: BD1277_healthy adult_LPS_6h [V2 manifest]

source_name: whole blood_healthy adult_LPS_6h


title: BD1277_healthy adult_Medium_6h [V2 manifest]


title: BD1768_healthy adult_IFNalpha_6h [V2 manifest]


title: BD1658_healthy adult_R837_6h [V2 manifest]


title: BD1635_healthy adult_Flagellin_6h [V2 manifest]

source_name: whole blood_healthy adult_Flagellin_6h

value: Flagellin


title: BD1737_healthy adult_LPS_6h [V2 manifest]


title: BD1312_healthy adult_LTA_6h [V2 manifest]

source_name: whole blood_healthy adult_LTA_6h


title: BD1858_healthy adult_IL-17A/F_6h [V2 manifest]


title: BD1312_healthy adult_PMA/I_6h [V2 manifest]


title: BD1635_healthy adult_PGN_6h [V2 manifest]

source_name: whole blood_healthy adult_PGN_6h

value: PGN


title: BD1768_healthy adult_Medium_6h [V2 manifest]

source_name: whole blood_healthy adult_Medium_6h

value: whole blood


title: BD1277_healthy adult_PGN_6h [V2 manifest]


title: BD1737_healthy adult_CpG-C_6h [V2 manifest]


title: BD1063_healthy adult_Medium_6h [V2 manifest]


title: BD1768_healthy adult_LPS_6h [V2 manifest]


title: BD1858_healthy adult_IL-1beta_6h [V2 manifest]


title: BD1063_healthy adult_R848_6h [V2 manifest]


title: BD1768_healthy adult_PGN_6h [V2 manifest]


title: BD1063_healthy adult_Flagellin_6h [V2 manifest]


title: BD1837_healthy adult_IFNgamma_6h [V2 manifest]

source_name: whole blood_healthy adult_IFNgamma_6h

value: IFNgamma


title: BD1658_healthy adult_PGN_6h [V2 manifest]


title: BD1737_healthy adult_LTA_6h [V2 manifest]


title: BD3045_healthy adult_Medium_6h [V2 manifest]


title: BD3045_healthy adult_IL-1beta_6h [V2 manifest]


title: BD1635_healthy adult_R848_6h [V2 manifest]


title: BD3038_healthy adult_TNFalpha_6h [V2 manifest]

source_name: whole blood_healthy adult_TNFalpha_6h


title: BD1768_healthy adult_IL-1beta_6h [V2 manifest]


title: BD1837_healthy adult_Medium_6h [V2 manifest]


title: BD1350_healthy adult_Medium_6h [V2 manifest]


title: BD3041_healthy adult_TNFalpha_6h [V2 manifest]


title: BD1768_healthy adult_LTA_6h [V2 manifest]


title: BD1350_healthy adult_Flagellin_6h [V2 manifest]


title: BD1312_healthy adult_PGN_6h [V2 manifest]


title: BD1658_healthy adult_Flagellin_6h [V2 manifest]


title: BD1858_healthy adult_TLR8L_6h [V2 manifest]


title: BD1658_healthy adult_LPS_6h [V2 manifest]


title: BD1635_healthy adult_LPS_6h [V2 manifest]


title: BD1350_healthy adult_LTA_6h [V2 manifest]


title: BD1635_healthy adult_CpG-C_6h [V2 manifest]

source_name: whole blood_healthy adult_CpG-C_6h

value: CpG-C


title: BD3045_healthy adult_IL-18_6h [V2 manifest]


title: BD3038_healthy adult_Medium_6h [V2 manifest]


title: BD1063_healthy adult_R837_6h [V2 manifest]


title: BD1063_healthy adult_LTA_6h [V2 manifest]

value: LTA


title: BD1350_healthy adult_PGN_6h [V2 manifest]


title: BD1858_healthy adult_IFNgamma_6h [V2 manifest]


title: BD1312_healthy adult_CpG-C_6h [V2 manifest]


title: BD1768_healthy adult_PMA/I_6h [V2 manifest]

source_name: whole blood_healthy adult_PMA/I_6h


title: BD1312_healthy adult_IFNalpha_6h [V2 manifest]


title: BD1858_healthy adult_Medium_6h [V2 manifest]

value: Medium


title: BD1837_healthy adult_IL-1beta_6h [V2 manifest]


title: BD1658_healthy adult_LTA_6h [V2 manifest]


title: BD1277_healthy adult_Flagellin_6h [V2 manifest]


title: BD3045_healthy adult_IFNgamma_6h [V2 manifest]


title: BD1635_healthy adult_IFNalpha_6h [V2 manifest]


title: BD3041_healthy adult_IL-1beta_6h [V2 manifest]


title: BD3038_healthy adult_IL-1beta_6h [V2 manifest]


title: BD3041_healthy adult_Medium_6h [V2 manifest]


title: BD1635_healthy adult_LTA_6h [V2 manifest]


title: BD1737_healthy adult_R837_6h [V2 manifest]


title: BD1063_healthy adult_PGN_6h [V2 manifest]


title: BD1768_healthy adult_Flagellin_6h [V2 manifest]


title: BD3041_healthy adult_IFNgamma_6h [V2 manifest]


title: BD1658_healthy adult_R848_6h [V2 manifest]

source_name: whole blood_healthy adult_R848_6h


title: BD1737_healthy adult_PGN_6h [V2 manifest]


title: BD1277_healthy adult_LTA_6h [V2 manifest]


title: BD1312_healthy adult_LPS_6h [V2 manifest]

value: LPS


title: BD1063_healthy adult_PMA/I_6h [V2 manifest]


title: BD3038_healthy adult_TLR8L_6h [V2 manifest]


title: BD1635_healthy adult_PMA/I_6h [V2 manifest]


title: BD1277_healthy adult_IL-1beta_6h [V2 manifest]


title: BD1277_healthy adult_PMA/I_6h [V2 manifest]


title: BD1277_healthy adult_R837_6h [V2 manifest]


title: BD1635_healthy adult_IL-1beta_6h [V2 manifest]


title: BD1063_healthy adult_IFNalpha_6h [V2 manifest]


title: BD1350_healthy adult_IFNalpha_6h [V2 manifest]


title: BD1768_healthy adult_CpG-C_6h [V2 manifest]


title: BD3038_healthy adult_IFNgamma_6h [V2 manifest]


title: BD1063_healthy adult_LPS_6h [V2 manifest]


title: BD1277_healthy adult_IFNalpha_6h [V2 manifest]


title: BD1837_healthy adult_IL-18_6h [V2 manifest]


title: BD1837_healthy adult_IL-17A/F_6h [V2 manifest]

source_name: whole blood_healthy adult_IL-17A/F_6h


title: BD1063_healthy adult_CpG-C_6h [V2 manifest]


title: BD1312_healthy adult_IL-1beta_6h [V2 manifest]


title: BD1737_healthy adult_R848_6h [V2 manifest]


title: BD1277_healthy adult_R848_6h [V2 manifest]


title: BD1768_healthy adult_R837_6h [V2 manifest]


title: BD1312_healthy adult_R837_6h [V2 manifest]


title: SYS-90_sIU_R848_6h [V1 manifest]

data_processing:
The data were normalized using average normalization in GenomeStudio’s gene expression module.
Please note that data were analyzed using either V1 manifest (pre-Oct 2010) or the V2 manifest (post-Oct 2010) as indicated in the sample title.
Matrix non-normalized data is the raw data computed from the chip by GenomeStudio.

source_name: whole blood_sIU_R848_6h

value: inactive

value: sIU


title: BD1350_healthy adult_R837_6h [V2 manifest]

source_name: whole blood_healthy adult_R837_6h


title: BD1858_healthy adult_TNFalpha_6h [V2 manifest]


title: SYS-109_sIU_CpG-C_6h [V1 manifest]

source_name: whole blood_sIU_CpG-C_6h

value: untreated


title: BD1737_healthy adult_Flagellin_6h [V2 manifest]


title: BD3041_healthy adult_TLR8L_6h [V2 manifest]


title: BD1350_healthy adult_LPS_6h [V2 manifest]


title: BD3045_healthy adult_TLR8L_6h [V2 manifest]


title: BD3038_healthy adult_IL-18_6h [V2 manifest]

source_name: whole blood_healthy adult_IL-18_6h


title: BD1312_healthy adult_R848_6h [V2 manifest]


title: SYS-110_sIA_R837_6h [V1 manifest]

source_name: whole blood_sIA_R837_6h

value: Anakinra

value: sIA


title: SYS-110_sIA_LTA_6h [V1 manifest]

source_name: whole blood_sIA_LTA_6h


title: SYS-53_sIU_R837_6h [V1 manifest]

source_name: whole blood_sIU_R837_6h


title: BD1312_healthy adult_Flagellin_6h [V2 manifest]

source_name: whole blood_healthy adult_Flagellin_6h

value: healthy adult


title: SYS-53_sIU_HKSA_6h [V1 manifest]

source_name: whole blood_sIU_HKSA_6h

value: HKSA


title: SYS-110_sIA_R848_6h [V1 manifest]

source_name: whole blood_sIA_R848_6h

value: Systemic onset juvenile idiopathic arthritis (sJIA)


title: SYS-180_sIA_Medium_6h [V1 manifest]

source_name: whole blood_sIA_Medium_6h


title: SYS-109_sIU_HKSE_6h [V1 manifest]

source_name: whole blood_sIU_HKSE_6h

value: HKSE


title: SYS-110_sIA_CpG-C_6h [V1 manifest]

source_name: whole blood_sIA_CpG-C_6h


title: SYS-13_sIU_LTA_6h [V1 manifest]

source_name: whole blood_sIU_LTA_6h


title: SYS-180_sIA_LTA_6h [V1 manifest]


title: SYS-90_sIU_R837_6h [V1 manifest]


title: SYS-60_sIU_CpG-C_6h [V1 manifest]


title: SYS-110_sIA_HKSE_6h [V1 manifest]

source_name: whole blood_sIA_HKSE_6h


title: SYS-180_sIA_HKSE_6h [V1 manifest]


title: SYS-13_sIU_CpG-C_6h [V1 manifest]


title: SYS-110_sIA_HKSA_6h [V1 manifest]

source_name: whole blood_sIA_HKSA_6h


title: SYS-60_sIU_LPS_6h [V1 manifest]

source_name: whole blood_sIU_LPS_6h


title: SYS-53_sIU_HKSE_6h [V1 manifest]


title: SYS-180_sIA_LPS_6h [V1 manifest]

source_name: whole blood_sIA_LPS_6h


title: SYS-13_sIU_HKSE_6h [V1 manifest]


title: SYS-90_sIU_LPS_6h [V1 manifest]


title: SYS-180_sIA_R837_6h [V1 manifest]


title: SYS-90_sIU_LTA_6h [V1 manifest]


title: SYS-60_sIU_HKSA_6h [V1 manifest]


title: SYS-60_sIU_R837_6h [V1 manifest]


title: SYS-13_sIU_Medium_6h [V1 manifest]

source_name: whole blood_sIU_Medium_6h


title: SYS-53_sIU_LPS_6h [V1 manifest]


title: SYS-60_sIU_R848_6h [V1 manifest]

source_name: whole blood_sIU_R848_6h


title: SYS-90_sIU_HKSA_6h [V1 manifest]


title: SYS-13_sIU_HKSA_6h [V1 manifest]


title: SYS-53_sIU_LTA_6h [V1 manifest]


title: SYS-109_sIU_HKSA_6h [V1 manifest]


title: SYS-53_sIU_R848_6h [V1 manifest]


title: SYS-109_sIU_LPS_6h [V1 manifest]


title: SYS-180_sIA_R848_6h [V1 manifest]


title: SYS-110_sIA_LPS_6h [V1 manifest]


title: SYS-60_sIU_LTA_6h [V1 manifest]


title: SYS-109_sIU_R837_6h [V1 manifest]


title: SYS-109_sIU_R848_6h [V1 manifest]


title: SYS-90_sIU_CpG-C_6h [V1 manifest]

source_name: whole blood_sIU_CpG-C_6h


title: SYS-60_sIU_HKSE_6h [V1 manifest]


title: SYS-13_sIU_R848_6h [V1 manifest]


title: SYS-180_sIA_CpG-C_6h [V1 manifest]


title: SYS-90_sIU_HKSE_6h [V1 manifest]


title: SYS-109_sIU_LTA_6h [V1 manifest]


title: SYS-13_sIU_LPS_6h [V1 manifest]


title: SYS-13_sIU_R837_6h [V1 manifest]


title: SYS-90_sIU_Medium_6h [V1 manifest]


title: SYS-53_sIU_Medium_6h [V1 manifest]


title: SYS-53_sIU_CpG-C_6h [V1 manifest]


title: SYS-109_sIU_Medium_6h [V1 manifest]


title: SYS-110_sIA_Medium_6h [V1 manifest]


title: BD1635_healthy adult_HKSE_6h [V1 manifest]

source_name: whole blood_healthy adult_HKSE_6h


title: SYS-60_sIU_Medium_6h [V1 manifest]


title: BD1277_healthy adult_Medium_6h [V1 manifest]

source_name: whole blood_healthy adult_Medium_6h


title: BD1277_healthy adult_IFNalpha_6h [V1 manifest]

source_name: whole blood_healthy adult_IFNalpha_6h

value: IFNalpha


title: BD1277_healthy adult_CpG-C_6h [V1 manifest]

source_name: whole blood_healthy adult_CpG-C_6h


title: BD1350_healthy adult_IFNalpha_6h [V1 manifest]


title: BD1350_healthy adult_R848_6h [V1 manifest]

source_name: whole blood_healthy adult_R848_6h


title: BD1277_healthy adult_HKSA_6h [V1 manifest]

source_name: whole blood_healthy adult_HKSA_6h


title: BD1277_healthy adult_Flagellin_6h [V1 manifest]

source_name: whole blood_healthy adult_Flagellin_6h

value: Flagellin


title: BD1635_healthy adult_IL-1beta_6h [V1 manifest]

source_name: whole blood_healthy adult_IL-1beta_6h

value: whole blood


title: BD1635_healthy adult_Medium_6h [V1 manifest]


title: BD1350_healthy adult_PGN_6h [V1 manifest]

source_name: whole blood_healthy adult_PGN_6h

value: PGN


title: BD1277_healthy adult_LTA_6h [V1 manifest]

source_name: whole blood_healthy adult_LTA_6h


title: BD1635_healthy adult_HKSA_6h [V1 manifest]


title: BD1350_healthy adult_HKSE_6h [V1 manifest]


title: BD1635_healthy adult_Flagellin_6h [V1 manifest]


title: BD1277_healthy adult_R837_6h [V1 manifest]

source_name: whole blood_healthy adult_R837_6h


title: BD1350_healthy adult_LPS_6h [V1 manifest]

source_name: whole blood_healthy adult_LPS_6h


title: BD1635_healthy adult_LTA_6h [V1 manifest]


title: BD1277_healthy adult_PGN_6h [V1 manifest]


title: BD1277_healthy adult_HKSE_6h [V1 manifest]


title: SYS-68_exvivo

data_processing:
Sequences were aligned with HISAT2 (Kim et al., 2015)
Duplicates removed with Samtools (Li et al., 2009)
Counts generated with HTSeq (Anders et al., 2015) using the annotations from Gencode V20 (Harrow et al., 2012)
Genes identified as globins, rRNAs, and pseudogenes were removed.
Differential expression analysis was performed using DESeq2 (Love et al., 2014). For ex vivo analysis, the design matrix was defined by design=~disease. For 6h stimulation analysis, the design matrix was defined by design=~stimulus + disease + stimulus:disease.
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited count matrix from HTSeq

source_name: Monocytes

extract_protocol:
Monocytes were sorted from frozen PBMC on a BD Influx cell sorter (BD Biosciences). After sorting, cells were lysed ex vivo or resuspended in complete RPMI with 10% FCS at 1x106 cells/mL and stimulated in 96-well flat-bottom plates for 6 or 24h ± LPS. Monocyte viability, assessed by FACS, decreased slightly with culture time and stimulation: median viability (IQR) ex vivo, at 6h medium, 6h LPS, 24h medium and 24h LPS was 98.3% 482 (1.7), 97% (2.2), 93.9% (5.2), 91.7% (4.5) and 90.7% (12.3), respectively. There were no differences in viability between healthy and sJIA monocytes. After incubation, supernatants were collected and cells were lysed with RLT buffer supplemented with 1% β-mercaptoethanol (Qiagen, Valencia, CA, USA) for RNA-Seq analysis. RNA from cell suspensions was purified using the RNAqueous-Micro Total RNA Isolation Kit (Thermo Fisher Scientific). RNA integrity was assessed using RNA 6000 Pico or RNA 6000 Nano assay on Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA concentration and purity were assessed using the NanoDrop 8000 (Thermo Fisher Scientific). All procedures were performed according to the manufacturer’s instructions.
Total RNA was converted to cDNA using 20 ng of RNA as input for the Ovation RNA-Seq System V2, and barcoded Illumina library constructs were produced using Ovation Ultralow Library System V2 (NuGEN Technologies, San Carlos, CA, USA) following the manufacturer’s instructions. Library fragment size and molar concentration were determined using Agilent High Sensitivity DNA Chip on 2100 Bioanalyzer, and qPCR data obtained by KAPA BioSystems Library Quantification qPCR Kit for Illumina Platform (Kapa Biosystems, Wilmington, MA, USA) on Viia7 Real-Time PCR System (Thermo Fisher Scientific). RNA-Seq libraries were sequenced on the Illumina HiSeq 2500 sequencing system, using SBS v3 chemistry and two high-output flow cells targeting 70-80 million 2X75 paired-end reads per library.

value: Monocytes

tag: cdna

value: exvivo

tag: donor

tag: disease

value: SYS

tag: group


title: SYS-37_exvivo

tag: treatment


title: BD1350_healthy adult_CpG-C_6h [V1 manifest]

value: CpG-C

tag: timepoint


title: BD1350_healthy adult_IL-1beta_6h [V1 manifest]


title: BD1277_healthy adult_R848_6h [V1 manifest]


title: SYS-208_exvivo


title: SYS-205_exvivo


title: BD1635_healthy adult_LPS_6h [V1 manifest]

value: LPS


title: BD1350_healthy adult_Medium_6h [V1 manifest]

value: Medium


title: SYS-192_exvivo


title: BD1635_healthy adult_PGN_6h [V1 manifest]


title: SYS-180_exvivo


title: BD1635_healthy adult_IFNalpha_6h [V1 manifest]


title: SYS-177_exvivo


title: BD1350_healthy adult_Flagellin_6h [V1 manifest]


title: BD1277_healthy adult_LPS_6h [V1 manifest]


title: BD1350_healthy adult_R837_6h [V1 manifest]


title: BD1350_healthy adult_HKSA_6h [V1 manifest]


title: BD1635_healthy adult_CpG-C_6h [V1 manifest]


title: BD1350_healthy adult_LTA_6h [V1 manifest]

value: LTA


title: BD1635_healthy adult_R837_6h [V1 manifest]


title: H-398_exvivo

value: H


title: H-394_exvivo


title: SYS-37_medium

value: medium

value: invitro


title: SYS-180_LPS


title: SYS-37_LPS


title: H-391_exvivo


title: H-394_LPS


title: SYS-208_LPS


title: SYS-177_LPS


title: H-391_LPS


title: BD1635_healthy adult_R848_6h [V1 manifest]

value: healthy adult


title: SYS-68_medium


title: SYS-205_LPS


title: H-397_LPS


title: SYS-68_LPS


title: H-396_exvivo


title: H-392_exvivo


title: H-398_LPS


title: SYS-205_medium


title: SYS-208_medium


title: SYS-177_medium


title: SYS-180_medium


title: H-398_medium


title: H-394_medium


title: H-397_medium


title: H-391_medium


title: Control_67F

status: Public on Jun 10 2017

city: London

first: Rachel

last: Lai

address: Du Cane Road

department: Infectious Disease

country: United Kingdom

institute: Imperial College London

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using 75 Percentile Shift using GeneSpring GX 13.0 software

label: Biotin

source_name: Control

label_protocol: Biotinylated cRNA were prepared with Life Technologies' Illumina TotalPrep-96 RNA Amplification kit

growth_protocol: Whole blood from patients were drawn into Paxgene Blood Tubes directly and stored at -20C until RNA extraction

extract_protocol: RNA from whole blood was extracted using Paxgene Blood RNA kit according the manufacturer's protocol. Quality control was performed with Agilent Bioanalyser.

value: Control


title: Control_91F

treatment_protocol: Whole blood from patients were drawn into Paxgene Blood Tubes directly and stored at -20C until RNA extraction


title: Control_100F


title: Control_112F


title: Control_95F


title: Control_98F


title: Control_49F


title: Control_77F


title: Control_15F


title: Control_58F


title: Control_10F


title: Control_109F


title: Control_14F


title: Control_13F


title: Control_57F


title: Control_2F


title: Control_94F


title: TBM-IRIS_88D_TBM Diagnosis

data_processing: The data were normalised using 75 Percentile Shift using GeneSpring GX 13.1 software

source_name: TBM Diagnosis

value: TBM-IRIS


title: Non-IRIS_9D_TBM Diagnosis

value: Non-IRIS


title: TBM-IRIS_81D_TBM Diagnosis


title: Non-IRIS_6D_TBM Diagnosis


title: Non-IRIS_37D_TBM Diagnosis


title: Non-IRIS_36D_TBM Diagnosis


title: TBM-IRIS_90D_TBM Diagnosis


title: Non-IRIS_87D_TBM Diagnosis


title: TBM-IRIS_93D_TBM Diagnosis


title: Non-IRIS_66D_TBM Diagnosis


title: TBM-IRIS_63D_TBM Diagnosis


title: Non-IRIS_40D_TBM Diagnosis


title: TBM-IRIS_24D_TBM Diagnosis


title: Non-IRIS_5D_TBM Diagnosis


title: TBM-IRIS_73D_TBM Diagnosis


title: Non-IRIS_96D_TBM Diagnosis


title: TBM-IRIS_65D_TBM Diagnosis


title: TBM-IRIS_59D_TBM Diagnosis


title: TBM-IRIS_22D_TBM Diagnosis


title: TBM-IRIS_47D_TBM Diagnosis


title: Non-IRIS_26D_TBM Diagnosis


title: TBM-IRIS_60D_TBM Diagnosis


title: Non-IRIS_53D_TBM Diagnosis


title: TBM-IRIS_28D_TBM Diagnosis


title: TBM-IRIS_1D_TBM Diagnosis


title: Non-IRIS_54D_TBM Diagnosis


title: Non-IRIS_18D_TBM Diagnosis


title: Non-IRIS_64D_TBM Diagnosis


title: TBM-IRIS_116D_TBM Diagnosis


title: BD1277_healthy adult_IL-1beta_6h [V1 manifest]


title: TBM-IRIS_88S_2wpTBRx


title: Non-IRIS_110D_TBM Diagnosis


title: TBM-IRIS_93S_2wpTBRx


title: Non-IRIS_104D_TBM Diagnosis


title: TBM-IRIS_90S_2wpTBRx


title: TBM-IRIS_81S_2wpTBRx


title: TBM-IRIS_24S_2wpTBRx


title: TBM-IRIS_22S_2wpTBRx


title: Non-IRIS_96S_2wpTBRx


title: Non-IRIS_66S_2wpTBRx


title: Non-IRIS_102D_TBM Diagnosis


title: TBM-IRIS_28S_2wpTBRx


title: Non-IRIS_5S_2wpTBRx


title: TBM-IRIS_60S_2wpTBRx


title: TBM-IRIS_47S_2wpTBRx


title: Non-IRIS_87S_2wpTBRx


title: TBM-IRIS_59S_2wpTBRx


title: TBM-IRIS_114S_2wpTBRx


title: TBM-IRIS_73S_2wpTBRx


title: Non-IRIS_53S_2wpTBRx


title: TBM-IRIS_1S_2wpTBRx


title: TBM-IRIS_114D_TBM Diagnosis


title: Non-IRIS_54S_2wpTBRx


title: Non-IRIS_6S_2wpTBRx


title: Non-IRIS_9S_2wpTBRx


title: TBM-IRIS_63S_2wpTBRx


title: TBM-IRIS_116S_2wpTBRx


title: Non-IRIS_40S_2wpTBRx


title: Non-IRIS_37S_2wpTBRx


title: Non-IRIS_26S_2wpTBRx


title: Non-IRIS_110S_2wpTBRx


title: Non-IRIS_104S_2wpTBRx


title: Non-IRIS_18S_2wpTBRx


title: TBM-IRIS_65S_2wpTBRx


title: Non-IRIS_36S_2wpTBRx


title: Non-IRIS_64S_2wpTBRx


title: TBM-IRIS_93I_IRIS Diagnosis


title: TBM-IRIS_73I_IRIS Diagnosis


title: TBM-IRIS_88I_IRIS Diagnosis


title: TBM-IRIS_59I_IRIS Diagnosis


title: TBM-IRIS_47I_IRIS Diagnosis


title: TBM-IRIS_90I_IRIS Diagnosis


title: TBM-IRIS_22I_IRIS Diagnosis


title: TBM-IRIS_1I_IRIS Diagnosis


title: TBM-IRIS_81I_IRIS Diagnosis


title: TBM-IRIS_63I_IRIS Diagnosis


title: Non-IRIS_102S_2wpTBRx


title: TBM-IRIS_65I_IRIS Diagnosis


title: TBM-IRIS_116I_IRIS Diagnosis


title: TBM-IRIS_60I_IRIS Diagnosis


title: TBM-IRIS_24I_IRIS Diagnosis


title: TBM-IRIS_114I_IRIS Diagnosis


title: Non-IRIS_87N_2wpART


title: Non-IRIS_96N_2wpART


title: Non-IRIS_6N_2wpART


title: Non-IRIS_40N_2wpART


title: Non-IRIS_66N_2wpART


title: Non-IRIS_5N_2wpART


title: 1009_D60_Flu10_DC3

status: Public on May 22 2017

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequences were aligned with TopHat2, duplicates were removed using Picard (picard.sourceforge.net/) and counts were generated by HTSeq using the annotations from Gencode V19.
Genes identified as globins, rRNAs, and pseudogenes were removed.  The alignment files were converted to BAM format by using SAMtools
Genome_build: hg19
Supplementary_files_format_and_content: .txt format; transcripts with raw counts <30 across all the samples were removed from downstream analysis.  Raw counts were normalized to log2 transformed Counts Per Million (logCPM)

source_name: Apheresis sorted dendritic cells

extract_protocol:
Purified cells were lysed in QIAzol for RNA sequencing analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols for Illumina® TruSeq™ RNA Sample Preparation V2 kit

treatment_protocol: Leukapheresis samples were collected and enriched for dendritic cells by negative depletion of CD3, CD9, CD14, CD16, CD19, CD34, CD56, CD66b and glycophorin A using magnetic beads with a Human Pan-DC Pre-Enrichment Kit (StemCell Technologies) for dendritic cells. Enriched DCs were stained with the following antibodies: Lin 1-FITC (CD3, CD8, CD14, CD16, CD19, CD20, CD56 and NKp46), CD11c-Pacific Blue, CD303 (BDCA2) -PE (all from BD), CD1c-PE-Cy7 (BioLegend, San Diego, CA), BDCA-3(CD141)-APC (Miltenyi Biotec, San Diego, CA), HLA-DR-Pacific Orange (Invitrogen),  and CD2-ECD (Beckman Coulter, CA).  Four DC subsets were purified: CD1c+ DCs, CD141+ DCs, BDCA2+CD2+ pDCs and BDCA2+CD2- pDCs.

tag: cell type

value: BDCA2+CD2- pDCs

value: Blood

tag: time point

value: Steady state


title: 1006_D60_Flu10_DC4

value: BDCA2+CD2+ pDCs


title: Non-IRIS_54N_2wpART


title: Non-IRIS_9N_2wpART


title: 1009_D60_Flu10_DC2

value: CD141+ DCs


title: Non-IRIS_53N_2wpART


title: Non-IRIS_37N_2wpART


title: Non-IRIS_64N_2wpART


title: Non-IRIS_102N_2wpART


title: Non-IRIS_36N_2wpART


title: Non-IRIS_18N_2wpART


title: 1006_D60_Flu10_DC2


title: 1005_D60_Flu10_DC3


title: 1005_D60_Flu10_DC4


title: 1005_D60_Flu10_DC2


title: 1006_D60_Flu10_DC1

value: CD1c+ DCs


title: Non-IRIS_26N_2wpART


title: Non-IRIS_110N_2wpART


title: 1009_D60_Flu10_DC4


title: 1009_D60_Flu10_DC1


title: 1006_D60_Flu10_DC3


title: Non-IRIS_104N_2wpART


title: 1005_D60_Flu10_DC1


title: HC5-whole blood-healthy control-healthy control

status: Public on Jan 18 2017

hyb_protocol: Labeled cRNA was hybridized overnight to HumanHT-12 V4 BeadChip arrays (Illumina).

scan_protocol: Following hybridization, each chip was washed, blocked, stained, and scanned on an Illumina BeadStation 500 following the manufacturer's protocols and iScan Control Software v3.3.28 (library v3.8.117).

data_processing:
Data was Global Average Normalized per Illumina GenomeStudio, all signal <10 has been set to 10.
The data in the non-normalized data matrix is the raw data computed from the chip by GenomeStudio.

source_name: whole blood, healthy control

label_protocol: Amplification and labeling used the Illumina TotalPrep RNA Amplification Kit (Ambion).

growth_protocol: Blood samples were collected in Tempus tubes (Applied Biosystems), vigorously mixed and stored at -80oC.

extract_protocol: Total RNA was isolated using the MagMAX RNA Isolation Kit for Blood RNA Tubes (Ambion/ Life Technologies). RNA integrity was assessed using Caliper (Perkin Elmer). Isolated total RNA was globin-reduced (GLOBINclear, Ambion/Life Technologies).

treatment_protocol: None.

value: whole blood

tag: condition

value: healthy

tag: treatment group

value: healthy control

tag: organ system

tag: match degree

tag: response

value: healthy control (HC)

tag: age (yr)

tag: gender

value: M

tag: race

value: White

tag: ethnicity

value: non-Hispanic (NH)


title: HC4-whole blood-healthy control-healthy control

tag: tissue


title: HC7-whole blood-healthy control-healthy control

value: F

value: Caucasian

tag: donor


title: HC2-whole blood-healthy control-healthy control

tag: disease


title: HC8-whole blood-healthy control-healthy control


title: PS-19-whole blood-chronic graft-vs-host disease-cycle 3; day 1

source_name: whole blood, chronic graft-vs-host disease, bortezomib, cycle 3, day 1

value: steroid-refractory chronic graft-vs-host disease

value: bortezomib

value: cycle 3; day 1

value: myelodisplastic syndrome

value: eyes, gut

value: 6 out of 6

value: near complete response


title: LR-15-whole blood-chronic graft-vs-host disease-30 day post dose

source_name: whole blood, chronic graft-vs-host disease, bortezomib, 30 day post dose

value: 30 day post dose

value: acute myelogenous leukemia

value: joints

value: stable disease


title: PC-14-whole blood-chronic graft-vs-host disease-baseline

source_name: whole blood, chronic graft-vs-host disease, bortezomib, baseline

value: whole blood

value: baseline

value: chronic lymphocytic leukemia

value: skin

value: not evaluable


title: JC-13-whole blood-chronic graft-vs-host disease-baseline

value: eyes, skin

value: 6 out of 8

value: partial response

value: M

value: African-American

value: non-Hispanic (NH)


title: SR-17-whole blood-chronic graft-vs-host disease-cycle 3; day 1

value: steroid-refractory chronic graft-vs-host disease

value: bortezomib

value: cycle 3; day 1

value: acute lymphocytic leukemia

value: 6 out of 6

value: Caucasian


title: JD-16-whole blood-chronic graft-vs-host disease-baseline

value: whole blood

value: acute myelogenous leukemia


title: HC1-whole blood-healthy control-healthy control

value: healthy

value: healthy control

value: healthy control (HC)


title: SK-21-whole blood-chronic graft-vs-host disease-baseline

value: baseline

value: skin

value: F


title: SK-21-whole blood-chronic graft-vs-host disease-cycle 3; day 1

value: partial response


title: PS-19-whole blood-chronic graft-vs-host disease-30 day post dose

value: 30 day post dose

value: myelodisplastic syndrome

value: eyes, gut

value: near complete response


title: MD-18-whole blood-chronic graft-vs-host disease-30 day post dose

value: steroid-refractory chronic graft-vs-host disease

value: bortezomib

value: eyes

value: stable disease

value: non-Hispanic (NH)


title: MM-20-whole blood-chronic graft-vs-host disease-cycle 3; day 1

value: whole blood

value: cycle 3; day 1

value: myelofibrosis

value: 6 out of 6

value: Asian


title: SR-17-whole blood-chronic graft-vs-host disease-baseline

value: baseline

value: acute lymphocytic leukemia

value: skin

value: M

value: Caucasian


title: MD-18-whole blood-chronic graft-vs-host disease-cycle 3; day 1

value: acute myelogenous leukemia

value: F


title: MD-18-whole blood-chronic graft-vs-host disease-baseline

value: steroid-refractory chronic graft-vs-host disease


title: HC3-whole blood-healthy control-healthy control

value: healthy

value: healthy control

value: healthy control (HC)


title: PS-19-whole blood-chronic graft-vs-host disease-baseline

value: bortezomib

value: myelodisplastic syndrome

value: eyes, gut

value: near complete response

value: non-Hispanic (NH)


title: DW-12-whole blood-chronic graft-vs-host disease-baseline

value: whole blood

value: 6 out of 6

value: not evaluable


title: HC6-whole blood-healthy control-healthy control


title: MM-20-whole blood-chronic graft-vs-host disease-30 day post dose

value: 30 day post dose

value: myelofibrosis

value: skin

value: stable disease

value: Asian


title: PC-14-whole blood-chronic graft-vs-host disease-30 day post dose

value: steroid-refractory chronic graft-vs-host disease

value: chronic lymphocytic leukemia

value: F

value: Caucasian


title: DW-12-whole blood-chronic graft-vs-host disease-30 day post dose

value: bortezomib

value: acute myelogenous leukemia

value: M


title: JD-16-whole blood-chronic graft-vs-host disease-cycle 3; day 1

value: cycle 3; day 1


title: JD-16-whole blood-chronic graft-vs-host disease-30 day post dose

value: non-Hispanic (NH)


title: BF-11-whole blood-chronic graft-vs-host disease-baseline

value: whole blood

value: baseline

value: skin,eyes,gut


title: AH-10-whole blood-chronic graft-vs-host disease-baseline

value: acute lymphocytic leukemia

value: eyes, skin

value: 6 out of 6

value: near complete response


title: BF-11-whole blood-chronic graft-vs-host disease-30 day post dose

value: 30 day post dose

value: not evaluable


title: AH-10-whole blood-chronic graft-vs-host disease-cycle 3; day 1

value: steroid-refractory chronic graft-vs-host disease


title: CS-07-whole blood-chronic graft-vs-host disease-cycle 3; day 1

value: gut,skin

value: complete response


title: SC-02-whole blood-chronic graft-vs-host disease-30 day post dose

value: bortezomib

value: non-Hodgkins lymphoma

value: skin, eyes, pulmonary

value: progression

value: F

value: Caucasian


title: SC-02-whole blood-chronic graft-vs-host disease-baseline

value: whole blood

value: baseline

value: non-Hispanic (NH)