title: 043_C6_16_032_PRE_A

status: Public on Feb 28 2022

type: SRA

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

country: USA

institute: La Jolla Institute for Immunology

library_source: transcriptomic

data_processing:
Base-calling with bcl2fastq (v2.20.0.422) with default parameters
Raw reads filtered with fastp (0.20.1)
Aligned with STAR (2.7.3a) with default parameters
Filtering samples with in-house script (https://github.com/vijaybioinfo/quality_control/blob/main/single_cell.R)
Genome_build: GRCh37
Supplementary_files_format_and_content: smartseq2_annotation.txt.gz metadata for 1233 filtered cells
Supplementary_files_format_and_content: smartseq2_counts.txt.gz STAR counts for 2297 cells
Supplementary_files_format_and_content: smartseq2_tpm.txt.gz normalized counts for 2297 cells
Supplementary_files_format_and_content: smartseq2_tpm_filtered.txt.gz normalized counts for 1233 filtered cells

molecule: polyA RNA

organism: Homo sapiens

source_name: Tumor

extract_protocol:
Cells were directly sorted into plates containing 2ul lysis buffer. Perform reverse transcription and PCR pre-amplification. PCR pre-amplified product was purified twice, using 0.8x Ampure-XP beads. 0.3 to 0.5 ng of pre-amplified cDNA was used to generate barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina) in 8µL reaction volume
SMART-Seq2; Libraries were pooled and sequenced on the HiSeq2500 Illumina platform to obtain 50-bp single end reads

tag: tissue

value: Tumor

tag: cell type

value: CD3+ T cells

tag: treatment

value: PRE

tag: sorted fraction


title: 043_C6_16_032_POST_A

value: POST


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title: 072_H9_16_034_POST_B


title: 071_G9_63_033_PRE_A


title: 072_H9_16_032_POST_A


title: 071_G9_63_033_POST_A


title: 072_H9_16_034_POST_C


title: 071_G9_62_030_POST_C


title: 071_G9_62_030_PRE_B


title: 071_G9_62_020_PRE_B


title: 071_G9_62_030_POST_B


title: 071_G9_62_020_PRE_C


title: 071_G9_62_030_POST_A


title: 071_G9_62_020_POST_B


title: 072_H9_16_032_PRE_A


title: 072_H9_62_020_PRE_C


title: 071_G9_62_030_PRE_A


title: 071_G9_62_020_POST_A


title: 071_G9_16_035_PRE_C


title: 071_G9_16_035_PRE_B


title: 072_H9_16_035_POST_A


title: 071_G9_16_035_POST_A


title: 071_G9_16_034_PRE_B


title: 071_G9_16_034_PRE_C


title: 071_G9_16_034_PRE_A


title: 071_G9_16_034_POST_C


title: 015_G2_62_020_POST_B


title: 015_G2_62_020_PRE_B


title: 015_G2_62_020_POST_A


title: 015_G2_16_035_PRE_B


title: 015_G2_16_035_POST_B


title: 015_G2_16_034_PRE_C


title: 015_G2_16_034_POST_C


title: 015_G2_16_034_POST_A


title: 015_G2_16_032_POST_A


title: 014_F2_63_033_PRE_A


title: 014_F2_63_033_POST_A


title: 014_F2_62_030_PRE_B


title: 014_F2_62_030_PRE_A


title: 014_F2_62_030_POST_B


title: 014_F2_62_030_POST_C


title: 014_F2_62_030_POST_A


title: 014_F2_62_020_PRE_B


title: 014_F2_62_020_POST_C


title: 071_G9_16_035_POST_B


title: 071_G9_16_035_PRE_A


title: 015_G2_62_020_POST_C


title: 015_G2_16_032_PRE_A


title: 014_F2_62_020_POST_B


title: 015_G2_16_035_PRE_A


title: 015_G2_16_035_POST_A


title: 014_F2_62_020_PRE_C


title: 014_F2_62_020_POST_A


title: 014_F2_16_035_PRE_B


title: 014_F2_16_035_PRE_A


title: 014_F2_16_035_POST_B


title: 015_G2_16_034_PRE_A


title: 015_G2_16_034_POST_B


title: 015_G2_16_032_POST_B


title: 015_G2_16_034_PRE_B


title: 014_F2_16_035_POST_A


title: 014_F2_16_034_PRE_C


title: 014_F2_16_034_POST_C


title: 014_F2_16_034_PRE_B


title: 014_F2_16_034_PRE_A


title: 014_F2_16_034_POST_A


title: 013_E2_63_033_PRE_A


title: 014_F2_16_032_PRE_A


title: 014_F2_16_032_POST_B


title: 014_F2_16_032_POST_A


title: 013_E2_62_030_PRE_A


title: 013_E2_63_033_POST_A


title: 013_E2_62_030_POST_C


title: 014_F2_16_035_PRE_C


title: 013_E2_62_020_POST_C


title: 013_E2_62_030_POST_A


title: 013_E2_62_030_POST_B


title: 013_E2_62_020_PRE_B


title: 013_E2_16_035_PRE_A


title: 013_E2_16_035_POST_B


title: 013_E2_16_035_POST_A


title: 013_E2_16_034_PRE_C


title: 013_E2_16_034_PRE_B


title: 013_E2_16_034_PRE_A


title: 013_E2_16_034_POST_B


title: 013_E2_16_034_POST_C


title: 013_E2_16_032_PRE_B


title: 014_F2_16_034_POST_B


title: 013_E2_16_034_POST_A


title: 013_E2_16_032_PRE_A


title: 013_E2_62_030_PRE_B


title: 012_D2_63_033_POST_A


title: 012_D2_62_030_POST_C


title: 013_E2_62_020_POST_B


title: 012_D2_62_030_PRE_A


title: 013_E2_62_020_PRE_C


title: 012_D2_63_033_PRE_A


title: 012_D2_62_030_POST_B


title: 012_D2_62_020_PRE_B


title: 012_D2_62_020_PRE_C


title: 012_D2_62_020_POST_C


title: 012_D2_62_030_POST_A


title: 013_E2_16_035_PRE_C


title: 012_D2_62_020_POST_B


title: 013_E2_62_020_POST_A


title: 012_D2_16_035_PRE_A


title: 012_D2_62_020_POST_A


title: 012_D2_16_035_POST_B


title: 012_D2_16_035_PRE_B


title: 012_D2_16_035_POST_A


title: 012_D2_16_034_PRE_A


title: 012_D2_16_034_POST_B


title: 013_E2_16_032_POST_B


title: 012_D2_16_034_POST_C


title: 013_E2_16_032_POST_A


title: 012_D2_62_030_PRE_B


title: 012_D2_16_032_PRE_B


title: 012_D2_16_032_PRE_A


title: 012_D2_16_032_POST_A


title: 011_C2_63_033_PRE_A


title: 011_C2_63_033_POST_A


title: 011_C2_62_030_POST_C


title: 012_D2_16_035_PRE_C


title: 011_C2_62_020_POST_C


title: 011_C2_62_030_PRE_A


title: 011_C2_62_020_PRE_B


title: 011_C2_62_020_PRE_C


title: 011_C2_62_030_POST_A


title: 011_C2_62_030_POST_B


title: 012_D2_16_034_PRE_B


title: 012_D2_16_034_PRE_C


title: 011_C2_16_035_PRE_C


title: 011_C2_62_020_POST_B


title: 011_C2_16_035_PRE_A


title: 011_C2_16_035_PRE_B


title: 011_C2_16_035_POST_B


title: 011_C2_62_020_POST_A


title: 012_D2_16_034_POST_A


title: 011_C2_16_034_PRE_C


title: 011_C2_16_034_PRE_A


title: 011_C2_16_035_POST_A


title: 011_C2_16_034_POST_B


title: 011_C2_16_034_PRE_B


title: 011_C2_16_034_POST_A


title: 012_D2_16_032_POST_B


title: 011_C2_62_030_PRE_B


title: 011_C2_16_032_PRE_A


title: 011_C2_16_032_POST_B


title: 011_C2_16_032_PRE_B


title: 011_C2_16_032_POST_A


title: 010_B2_63_033_PRE_A


title: 010_B2_63_033_POST_A


title: 010_B2_62_030_POST_B


title: 010_B2_62_030_POST_A


title: 010_B2_62_030_PRE_A


title: 010_B2_62_030_PRE_B


title: 010_B2_62_020_PRE_B


title: 010_B2_62_020_POST_A


title: 010_B2_62_020_POST_C


title: 010_B2_16_035_PRE_C


title: 010_B2_16_035_PRE_B


title: 010_B2_62_020_POST_B


title: 010_B2_62_030_POST_C


title: 010_B2_16_035_POST_A


title: 010_B2_16_034_PRE_C


title: 010_B2_62_020_PRE_C


title: 010_B2_16_035_PRE_A


title: 010_B2_16_034_PRE_A


title: 010_B2_16_034_POST_C


title: 010_B2_16_034_POST_B


title: 010_B2_16_032_PRE_B


title: 010_B2_16_032_PRE_A


title: 010_B2_16_034_POST_A


title: 010_B2_16_034_PRE_B


title: 010_B2_16_035_POST_B


title: 010_B2_16_032_POST_B


title: 009_A2_63_033_PRE_A


title: 010_B2_16_032_POST_A


title: 009_A2_63_033_POST_A


title: 009_A2_62_030_PRE_A


title: 009_A2_62_030_PRE_B


title: 009_A2_62_030_POST_C


title: 009_A2_62_020_PRE_C


title: 009_A2_62_030_POST_B


title: 009_A2_62_020_POST_C


title: 009_A2_62_030_POST_A


title: 009_A2_62_020_PRE_B


title: 009_A2_62_020_POST_B


title: 009_A2_16_035_POST_A


title: 009_A2_16_035_POST_B


title: 009_A2_16_035_PRE_B


title: 009_A2_62_020_POST_A


title: 009_A2_16_035_PRE_C


title: 009_A2_16_034_PRE_B


title: 009_A2_16_034_PRE_C


title: 009_A2_16_034_POST_C


title: 009_A2_16_034_POST_B


title: 009_A2_16_034_PRE_A


title: 009_A2_16_032_PRE_B


title: 009_A2_16_032_POST_A


title: 009_A2_16_032_PRE_A


title: 009_A2_16_032_POST_B


title: 008_H1_63_033_PRE_A


title: 009_A2_16_034_POST_A


title: 008_H1_62_030_PRE_B


title: 008_H1_63_033_POST_A


title: 008_H1_62_030_POST_C


title: 008_H1_62_030_POST_B


title: 008_H1_62_020_PRE_C


title: 008_H1_62_030_POST_A


title: 008_H1_62_030_PRE_A


title: 008_H1_62_020_POST_C


title: 008_H1_16_035_PRE_B


title: 008_H1_62_020_POST_B


title: 008_H1_16_035_PRE_C


title: 008_H1_62_020_POST_A


title: 008_H1_16_035_POST_A


title: 008_H1_16_034_PRE_C


title: 008_H1_16_034_PRE_B


title: 008_H1_16_034_PRE_A


title: 008_H1_16_034_POST_B


title: 008_H1_16_034_POST_A


title: 008_H1_16_032_PRE_A


title: 007_G1_63_033_PRE_A


title: 008_H1_16_032_POST_A


title: 007_G1_63_033_POST_A


title: 007_G1_62_030_POST_B


title: 007_G1_62_030_PRE_B


title: 007_G1_62_030_POST_A


title: 007_G1_62_030_PRE_A


title: 007_G1_62_020_PRE_C


title: 007_G1_62_020_PRE_B


title: 007_G1_62_030_POST_C


title: 008_H1_62_020_PRE_B


title: 007_G1_62_020_POST_B


title: 007_G1_62_020_POST_A


title: 007_G1_62_020_POST_C


title: 007_G1_16_034_PRE_A


title: 007_G1_16_034_PRE_C


title: 007_G1_16_034_PRE_B


title: 007_G1_16_035_PRE_B


title: 007_G1_16_035_PRE_C


title: 007_G1_16_035_PRE_A


title: 008_H1_16_035_PRE_A


title: 007_G1_16_035_POST_B


title: 007_G1_16_035_POST_A


title: 007_G1_16_032_PRE_A


title: 007_G1_16_032_POST_A


title: 007_G1_16_034_POST_A


title: 007_G1_16_034_POST_C


title: 007_G1_16_034_POST_B


title: 006_F1_63_033_PRE_A


title: 006_F1_63_033_POST_A


title: 006_F1_62_030_POST_B


title: 006_F1_62_030_PRE_B


title: 006_F1_62_030_POST_C


title: 006_F1_62_020_PRE_C


title: 006_F1_62_020_PRE_B


title: 006_F1_62_030_PRE_A


title: 006_F1_62_030_POST_A


title: 006_F1_62_020_POST_A


title: 006_F1_16_035_PRE_C


title: 006_F1_62_020_POST_B


title: 006_F1_62_020_POST_C


title: 006_F1_16_035_PRE_B


title: 006_F1_16_035_POST_B


title: 006_F1_16_035_PRE_A


title: 006_F1_16_035_POST_A


title: 006_F1_16_034_PRE_C


title: 006_F1_16_034_PRE_A


title: 006_F1_16_034_POST_A


title: 006_F1_16_034_POST_B


title: 006_F1_16_032_POST_B


title: 006_F1_16_034_POST_C


title: 006_F1_16_032_PRE_A


title: 006_F1_16_032_POST_A


title: 006_F1_16_034_PRE_B


title: 005_E1_63_033_PRE_A


title: 005_E1_63_033_POST_A


title: 005_E1_62_030_PRE_A


title: 005_E1_62_030_POST_B


title: 005_E1_62_030_PRE_B


title: 005_E1_62_030_POST_C


title: 005_E1_62_020_PRE_C


title: 005_E1_62_030_POST_A


title: 005_E1_62_020_POST_C


title: 005_E1_62_020_POST_B


title: 005_E1_62_020_POST_A


title: 005_E1_16_035_POST_B


title: 005_E1_62_020_PRE_B


title: 005_E1_16_035_PRE_A


title: 005_E1_16_035_PRE_B


title: 005_E1_16_035_PRE_C


title: 005_E1_16_034_PRE_C


title: 005_E1_16_034_PRE_B


title: 005_E1_16_034_POST_B


title: 005_E1_16_034_PRE_A


title: 005_E1_16_034_POST_A


title: 005_E1_16_032_POST_B


title: 004_D1_62_030_PRE_B


title: 005_E1_16_032_PRE_A


title: 004_D1_63_033_POST_A


title: 005_E1_16_032_PRE_B


title: 005_E1_16_032_POST_A


title: 004_D1_63_033_PRE_A


title: 004_D1_62_030_PRE_A


title: 004_D1_62_030_POST_A


title: 004_D1_62_030_POST_B


title: 004_D1_62_020_PRE_C


title: 004_D1_62_030_POST_C


title: 004_D1_62_020_PRE_B


title: 004_D1_62_020_POST_B


title: 004_D1_62_020_POST_C


title: 004_D1_16_035_PRE_C


title: 004_D1_16_035_PRE_B


title: 005_E1_16_035_POST_A


title: 004_D1_62_020_POST_A


title: 004_D1_16_035_PRE_A


title: 004_D1_16_035_POST_B


title: 004_D1_16_035_POST_A


title: 004_D1_16_034_PRE_C


title: 004_D1_16_034_PRE_B


title: 004_D1_16_034_PRE_A


title: 004_D1_16_034_POST_B


title: 004_D1_16_034_POST_C


title: S_03

type: protein

city: Philadelphia

first: Scott

last: Canna

address: The Children’s Hospital of Philadelphia Department of Pediatrics Philadelphia

institute: Children's Hospital of Philadelphia

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
S_03

hyb_protocol: Somalogic standard protocol

scan_protocol: Somalogic standard protocol

data_processing: Post-normalization, all samples met predefined acceptance criteria and were included in the analysis. A complete description of the normalization and calibration procedures is available at: www.somalogic.com/wp-content/uploads/2017/03/SSM-071-Rev-0-Technical-Note-SOMAscan-Data-Standardization.pdf.

molecule: protein

source_name: SAVI

label_protocol: Somalogic standard protocol

extract_protocol: not provided

value: serum

tag: disease

value: Active SAVI

tag: Sex

value: F

tag: age(year)

tag: hospital

value: NIH

tag: sample quality hemolysis score


title: S_02

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
S_02


title: S_01

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
S_01


title: 004_D1_16_034_POST_A


title: N_02

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
N_02

source_name: NOMID

value: active NOMID


title: 7_13

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
7_13

source_name: PJP

value: PJP colonized

value: Stanford/Chile


title: N_01

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
N_01


title: S_04

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
S_04


title: N_04

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
N_04


title: N_03

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
N_03


title: 7_11

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
7_11


title: 7_10

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
7_10

value: M


title: 004_D1_16_032_POST_A


title: 004_D1_16_032_POST_B


title: 003_C1_63_033_PRE_A


title: 004_D1_16_032_PRE_B


title: 004_D1_16_032_PRE_A


title: N_05

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
N_05


title: 7_08

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
7_08


title: 003_C1_63_033_POST_A


title: 7_05

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
7_05


title: 7_04

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
7_04


title: 7_03

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
7_03


title: 7_06

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
7_06


title: 7_07

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
7_07


title: 003_C1_62_030_PRE_A


title: 003_C1_62_030_PRE_B


title: 003_C1_62_030_POST_C


title: 7_02

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
7_02


title: 003_C1_62_030_POST_A


title: 003_C1_62_030_POST_B


title: 003_C1_62_020_POST_C


title: 003_C1_62_020_PRE_B


title: 6_14

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
6_14

source_name: HPAP

value: PAP

value: CCHMC/Trapnell


title: 003_C1_62_020_POST_A


title: 6_09

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
6_09

source_name: APAP


title: 6_13

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
6_13


title: 6_12

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
6_12


title: 003_C1_16_035_PRE_B


title: 6_08

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
6_08


title: 003_C1_62_020_PRE_C


title: 003_C1_16_035_POST_A


title: 6_07

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
6_07


title: 003_C1_16_035_POST_B


title: 003_C1_16_035_PRE_A


title: 003_C1_16_034_PRE_C


title: 7_01

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
7_01


title: 003_C1_62_020_POST_B


title: 003_C1_16_034_PRE_B


title: 003_C1_16_035_PRE_C


title: 6_10

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
6_10


title: 003_C1_16_034_PRE_A


title: 5_18

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
5_18

source_name: active MAS

value: Active MAS

value: NIHp


title: 6_01

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
6_01


title: 6_02

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
6_02


title: 003_C1_16_034_POST_B


title: 6_05

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
6_05


title: 6_06

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
6_06


title: 6_11

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
6_11


title: 6_04

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
6_04


title: 003_C1_16_032_PRE_A


title: 5_16

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
5_16


title: 003_C1_16_032_POST_B


title: 002_B1_63_033_POST_A


title: 002_B1_63_033_PRE_A


title: 6_03

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
6_03


title: 003_C1_16_032_POST_A


title: 5_14

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
5_14

source_name: NLRC4-MAS, flu shot


title: 5_13

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
5_13


title: 5_15

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
5_15


title: 5_12

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
5_12

source_name: active NOMID-like, MAS


title: 5_10

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
5_10

source_name: AOSD+MAS


title: 5_11

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
5_11


title: 002_B1_62_030_PRE_B


title: 003_C1_16_034_POST_A


title: 5_09

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
5_09

source_name: sJIA+MAS, not nods


title: 5_17

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
5_17


title: 002_B1_62_030_PRE_A


title: 003_C1_16_032_PRE_B


title: 002_B1_62_030_POST_C


title: 002_B1_62_020_PRE_C


title: 002_B1_62_020_PRE_B


title: 002_B1_62_020_POST_C


title: 5_01

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
5_01

source_name: sJIA+MAS

value: CCHMC/Grom


title: 5_02

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
5_02


title: 5_03

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
5_03


title: 5_07

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
5_07


title: 002_B1_62_020_POST_A

value: Tumor


title: 002_B1_62_020_POST_B

value: CD3+ T cells


title: 002_B1_16_035_PRE_C

value: PRE


title: 002_B1_16_035_PRE_B


title: 4_25

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_25

source_name: sJIA no MAS

value: Active sJIA, no MAS


title: 4_24

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_24

source_name: active sJIA no MAS

value: serum


title: 002_B1_62_030_POST_A

value: POST


title: 5_08

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
5_08

value: F


title: 4_21

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_21


title: 4_22

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_22

source_name: Proj 4: act syst, not nods


title: 002_B1_16_035_POST_A


title: 002_B1_16_035_POST_B


title: 002_B1_16_034_PRE_C


title: 5_06

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
5_06


title: 4_20

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_20


title: 5_05

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
5_05

source_name: sJIA-MAS


title: 4_19

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_19


title: 4_18

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_18

value: Stanford


title: 002_B1_16_034_PRE_A


title: 4_16

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_16


title: 002_B1_16_034_POST_A


title: 002_B1_16_035_PRE_A


title: 4_13

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_13


title: 4_23

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_23

value: NIH


title: 4_14

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_14


title: 4_15

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_15


title: 4_12

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_12


title: 002_B1_16_034_PRE_B


title: 001_A1_63_033_POST_A


title: 001_A1_63_033_PRE_A


title: 002_B1_16_032_POST_B


title: 4_10

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_10


title: 4_08

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_08


title: 4_09

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_09

source_name: Proj 4:new onset nods base


title: 001_A1_62_030_POST_C

source_name: Tumor


title: 002_B1_16_034_POST_B


title: 002_B1_16_034_POST_C


title: 001_A1_62_030_PRE_A


title: 4_06

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_06


title: 4_07

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_07


title: 4_04

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_04

source_name: Active


title: 4_05

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_05


title: 002_B1_16_032_PRE_B


title: 4_03

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_03


title: 002_B1_16_032_PRE_A


title: 002_B1_62_030_POST_B


title: 4_02

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_02


title: 001_A1_62_030_POST_B


title: 002_B1_16_032_POST_A


title: 001_A1_62_020_PRE_B


title: 4_11

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_11


title: 4_01

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_01


title: 001_A1_62_030_POST_A


title: 3_34

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_34

source_name: inactive sJIA/MAS

value: Inactive sJIA


title: 001_A1_62_020_PRE_C


title: 3_33

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_33

source_name: inactive?, smoldering


title: 001_A1_62_020_POST_C


title: 001_A1_62_030_PRE_B


title: 001_A1_62_020_POST_B


title: 3_32

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_32

source_name: inactive NLRC4-MAS


title: 001_A1_62_020_POST_A


title: 001_A1_16_035_PRE_C


title: 001_A1_16_035_PRE_B


title: 001_A1_16_035_PRE_A


title: 001_A1_16_035_POST_B


title: 3_30

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_30


title: 3_31

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_31


title: 3_29

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_29


title: 001_A1_16_035_POST_A


title: 001_A1_16_034_PRE_A


title: 001_A1_16_034_PRE_B


title: 3_28

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_28

source_name: inactive NOMID-like


title: 001_A1_16_034_PRE_C


title: 3_26

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_26


title: 001_A1_16_034_POST_C


title: 3_27

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_27


title: 001_A1_16_034_POST_B


title: 3_24

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_24


title: 3_25

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_25


title: 3_23

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_23

source_name: no active disease


title: 001_A1_16_034_POST_A


title: 3_22

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_22


title: 001_A1_16_032_PRE_B


title: 3_21

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_21


title: 3_19

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_19


title: 3_20

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_20


title: 001_A1_16_032_PRE_A


title: 001_A1_16_032_POST_B


title: 3_18

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_18


title: 001_A1_16_032_POST_A


title: 3_14

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_14

source_name: Proj 4: quiet disease


title: 3_15

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_15


title: nmur1_SE_5

city: Spokane

first: Yiyong

last: Liu

state: WA

address: 412 E Spokane Falls Blvd

institute: Washington State University

data_processing:
HiSeq Control Software (HCS v2.2.68) was used for base-calling.
bcl2fastq2 Conversion Software v2.17.1 was used to convert base-calling files to fastq files and to trim adaptors.
Bowtie2 v2.3.4 was used for alignment
htseq-count from HTSeq v0.10.0 was used to quantify genes and transcripts.
DESeq2 v1.22.1 was used for differential gene expression analysis.
Genome_build: UCSC ce10
Supplementary_files_format_and_content: comma-delimited text files including read counts in genes and differential gene expression

molecule: total RNA

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans was cultured under standard conditions and fed E. coli strain HT115.

extract_protocol:
Total RNA was extracted using QIAzol lysis reagent (QIAGEN) and purified with Rneasy Plus Universal Kit (QIAGEN).
Library was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: Synchronized L1 larvae were grown on E. coli HT115 at 20⁰C until they reached young adult stage.  The worms were transferred to NGM plates seeded with E. faecalis or S. enterica for 24 hrs at 25⁰C.  The worms were then collected and washed with M9 buffer.  Total RNA was extracted.

tag: strain/genotype

tag: age

value: 1-day old young adult

tag: infection

value: 24-hrs exposure S. enterica


title: nmur1_SE_4


title: 3_13

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_13


title: 3_16

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_16

value: M


title: 3_17

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_17


title: nmur1_SE_3


title: 3_10

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_10


title: 3_12

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_12


title: nmur1_SE_1


title: N2_SE_4

value: wild-type N2


title: 3_11

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_11


title: N2_SE_3


title: 3_08

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_08

source_name: inactive


title: 3_07

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_07


title: 3_06

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_06


title: nmur1_SE_2


title: 3_09

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_09


title: N2_SE_2


title: 3_05

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_05


title: 3_04

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_04


title: 3_02

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_02


title: nmur1_EF_5

value: 24-hrs exposure E. faecalis


title: N2_SE_1


title: nmur1_EF_4


title: 3_01

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_01


title: nmur1_EF_1


title: nmur1_EF_3


title: N2_EF_5


title: nmur1_EF_2


title: N2_EF_4


title: 2_19

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_19

source_name: Healthy ctrl

value: Controls


title: 2_17

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_17


title: 2_20

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_20


title: 3_03

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
3_03

value: CCHMC/Grom


title: 2_18

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_18


title: 2_21

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_21

source_name: Healthy infant

value: Stanford/Chile


title: 2_22

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_22


title: N2_EF_3


title: nmur1_HT115_4

value: uninfected


title: N2_EF_1


title: nmur1_HT115_5


title: 2_15

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_15


title: 2_12

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_12


title: nmur1_HT115_3


title: N2_EF_2


title: 2_10

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_10


title: 2_14

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_14


title: 2_09

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_09


title: nmur1_HT115_2


title: 2_13

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_13


title: 2_11

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_11


title: nmur1_HT115_1


title: N2_HT115_5


title: 2_08

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_08


title: 2_16

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_16


title: N2_HT115_2


title: N2_HT115_1


title: N2_HT115_4


title: N2_HT115_3


title: 2_03

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_03


title: 2_04

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_04


title: 2_06

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_06


title: 2_02

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_02


title: 2_05

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_05


title: 2_01

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_01


title: 2_07

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
2_07

value: f


title: 1_30

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_30

source_name: sJIA/ILD, CIN-1

value: sJIA-LD


title: 1_28

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_28

source_name: sJIA/ILD

value: serum


title: 1_29

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_29

source_name: sJIA/ILD, paraflu p pulse


title: 1_27

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_27

source_name: sJIA/MAS/ILD


title: 1_26

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_26


title: 1_25

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_25


title: 1_24

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_24


title: 1_23

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_23

source_name: sJIA/subclinical ILD


title: 1_20

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_20


title: 1_21

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_21


title: B786oMST_4_2

city: Xinxiang

first: Ting

last: Zhuang

state: Henan

address: Jinsui Road 601

country: China

institute: Xinxiang Medical University

data_processing:
Illumina hiseq4000 used for basecalling.
Sequence reads were trimmed for adaptor sequence and 3'-end was trimmed by quality, reads were filtered by quality and mapped to GRCh37 using the HISAT2 software
Mapping QC by samtools and picard software
Quantification was done by using Cufflinks to produce gene-level expression values (FPKMs)
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: Cells were cultured in RPMI-1640 with 10% FBS.

extract_protocol:
Cellular RNA was extracted using Qiagen RNA extraction kit (Qiagen; Cat: 74104) according to the manufacturer’s instructions.
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# 0801-0303).

treatment_protocol: Cells were treated with vehicle or 4 μM XMU-MP-1 for 6 hours.

tag: cell line


title: B786oMST_4_3


title: B786oMST_0_3

value: vehicle


title: B786oMST_4_1


title: B786oMST_0_1


title: B786oMST_0_2


title: 1_19

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_19


title: 1_22

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_22

value: F