title: Male-Dendritic-Cells-rep2

source_name: DC cells sorted from male VAT, replicate 2

value: CD45+TCRb-B220-CD11c+ cells from VAT


title: PBMC_656_ImmEnrich_Alzheimers Disease

status: Public on Mar 22 2024

type: SRA

city: Chicago

first: David

last: Gate

state: IL

address: 303 E Chicago Ave, Chicago, IL 60611

department: Neurology

country: USA

institute: Northwestern University

library_source: transcriptomic

data_processing:
Illumina RTA3 method for base-calling
10xGenomics cellranger pipeline for alignment and filtering (trimming 5' TSO sequence and 3' polyA tail, alignment with STAR, UMI counting, EmptyDrops method for empty droplet removal)
SoupX background contamination removal (S100A8 and S100A9 were used to estimate contamination fraction and counts were adjusted using SoupX::adjustCounts function)
DoubletFinder doublet removal (doublet formation rate of 5.4% based on 10xGenomics multiplet rate estimation, using 12 PCs and pN = 0.25)
Seurat filtering and normalization (filter out cells with >10% mitochondrial reads, retain cells with at least 200 mapped features, retain features with at least 3 mapped cells, counts were then normalized using Seurat's LogNormalize method)
Assembly: hg38
Supplementary files format and content: .rds object of raw gene count matrix for each gene and cell barcode
Supplementary files format and content: .rds object of log-normalized expression matrix for each gene and cell barcode
Library strategy: scRNA-seq + amplification using predesigned gene panel

molecule: polyA RNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

extract_protocol:
PBMCs were pelleted, frozen, and resuspended in PBS with 0.04% BSA before being sorted with Sytox blue live/dead dye
Chromium Next GEM Single Cell 5' v2 + Targeted Gene Expression, Human Immunology panel

tag: tissue

value: Peripheral blood mononuclear cells

tag: Sex

value: female

tag: disease state

value: Alzheimers Disease

tag: genotype

tag: age


title: 193 stem cell condition DMSO treated lane 2

city: London

first: Brigitta

last: Stockinger

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Fastq files were processed using nf-core/rnaseq  3.0 and genome GRCh38 to produce raw gene counts as shown in salmon.merged.gene_counts.tsv
The prefix of a given fastq file name, e.g,, LIE1403A10 corresponds to a sample.  Each sample was run in two lanes, resulting in fastqs LIE1403A10_S38_L007_R1_001.fastq.gz and LIE1403A10_S38_L008_R1_001.fastq.gz.  Raw gene counts for this sample then appear in salmon.merged.gene_counts.tsv in the column LIE1403A10_R1.
Assembly: GRCh38
Supplementary files format and content: tab separated values include raw counts for each sample

molecule: total RNA

source_name: colon organoid

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).  50ng of total RNA was used for the construction of sequencing libraries.
RNA was converted into libraries using the KAPA mRNA HyperPrep kit (Roche) according to the manufacturer’s instructions.

tag: patient organoid line

tag: cell type

value: human colon organoid

value: wt

tag: treatment

value: DMSO treatment


title: PBMC_863_ImmEnrich_Alzheimers Disease

value: male


title: PBMC_1279_ImmEnrich_Healthy Control

value: Healthy Control


title: PBMC_773_ImmEnrich_Alzheimers Disease


title: Male-Dendritic-Cells-rep1

city: Clayton

first: Wei

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

country: Australia

institute: Monash University

data_processing:
The libraries were aligned to the GRCm38/mm10 genome using Rsubread_2.14.1. The mapped read-pairs in each library were assigned to the NCBI RefSeq gene annotation for mm10 (build 38.1) by using featureCounts.
Genes were excluded from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 2 in at least 2 libraries. Counts were quantile normalized with the “voom” function of the limma package and converted to log2 counts per kilobase per million(log2 FKPM).
The log2 FPKM values were provided to the CellPhoneDB program (version 4.1.0) for cell-cell communication analysis. The CellPhoneDB database version 4.0.0 was used for analysis, and interactors having p values less than 0.1 were called as significant.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include log2-FPKM values for each library. The supplementary file, count_table.txt, includes raw read counts for genes in all the libraries.

organism: Mus musculus

source_name: DC cells sorted from male VAT, replicate 1

extract_protocol:
RNA extraction from VAT Treg cells was performed following the manufacturer's instructions using the Qiagen Rneasy mini kit and Rneasy lipid tissue mini kit
Libraries were generated following the manufacturer's protocol using the SMART-Seq mRNA LP, Takara Bio

tag: diet

value: 20-30  week old


title: PBMC_1180_ImmEnrich_Healthy Control


title: Female-Macrophages-rep2

source_name: Macrophages sorted from female VAT, replicate 2

value: CD45+TCRb-B220-CD11b+ cells from VAT


title: 193 stem cell condition CH-223191 treated lane 2

value: CH-223191 treatment


title: 193 stem cell condition CH-223191 treated lane 1


title: PBMC_911_ImmEnrich_Healthy Control


title: Female-Dendritic-Cells-rep2

source_name: DC cells sorted from female VAT, replicate 2


title: PBMC_738_ImmEnrich_Alzheimers Disease


title: PBMC_516_ImmEnrich_Alzheimers Disease


title: PBMC_780_ImmEnrich_Healthy Control


title: PBMC_696_ImmEnrich_Alzheimers Disease


title: at-seed-RNAseq_replicate1_Col_7DAP

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description:
Arabidopsis thaliana seed 7DAP of Columbia-0
TPM.genes.crispRarf.txt

data_processing:
Reads were trimmed by removing the 5 bp from the 5’ end and 20 bp from the 3' end and mapped in a paired-end mode to the Arabidopsis (TAIR10) genome  using using hisat2. Gene expression levels (TPM-transcript per million) were calculated using stringtie.
Assembly: TAIR10
Supplementary files format and content: RNA-seq: expression levels (TPM-transcript per million) are shown for genes in TAIR10 for each condition and replicate.

organism: Arabidopsis thaliana

source_name: AT 7DAP Seed Col

growth_protocol: Seeds were sown on plates containing Murashige and Skoog medium and stratified at 4°C for two days. The plates were transferred to a growth chamber for two weeks (16 h light/8 h dark; 60µmol/s/m²; 22°C). Seedlings were pricked onto soil and grown in phytotron chambers (16 h light/8 h dark; 150µmol/s/m²; 21°C; 70% humidity).

extract_protocol:
RNA extraction was performed using the plant RNeasy Kit from Qiagen. Total RNA was treated with DNAseI. mRNAs were specifically isolated using NEBNext® Poly(A) mRNA Magnetic Isolation Module from NEB (E7490S). The libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645S).
Library construction and sequencing were performed at Novogene on an Illumina Novaseq platform in paired-end mode and with 150bp read length.

treatment_protocol: Anthers were removed from the flowers two days before hand-pollination. Resulting siliques were opened at 4- or 7-DAP and seeds were carefully removed in RNAlater solution.

value: seed


title: Female-Dendritic-Cells-rep1

source_name: DC cells sorted from female VAT, replicate 1


title: PBMC_1273_ImmEnrich_Healthy Control


title: Female-Macrophages-rep1

source_name: Macrophages sorted from female VAT, replicate 1


title: 193 differentiated DMSO treated lane 1

value: differentiated - DMSO treatment


title: PBMC_254_ImmEnrich_Alzheimers Disease


title: 193 differentiated DMSO treated lane 2


title: 193 differentiated CH-223191 treated lane 2

value: differentiated - CH-223191 treatment


title: PBMC_1092_ImmEnrich_Alzheimers Disease


title: Graft-Tregs_2

city: Westmead

first: Brian

middle: S

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

institute: Westmead Institute of Medical Research

description:
SMART-Seq v4 Ultra Low Input RNA Kit
The transplant tolerant model: Porcine-NICC were isolated from pancreases and propagated in culture for 6 days as described previously and in method details. DEREG-mice were transplanted with 4000 IEQ porcine-NICC under their renal capsules as described previously. The DEREG-mice received an intraperitoneal (i.p) dose (500 µg/mouse) of MR-1 (Bioexpress) at days 0, 2, 4 and 6; and a single intraperitoneal dose (500 µg/mouse) of CTLA4-Fc (NS-1, WEHI Antibody Facility, Australia) at day 0 as tolerant-group.

data_processing:
Library sequencing quality was determined using FastQC. Illumina adaptor sequence and low quality read trimming (read pair removed if < 20 base pairs) was performed using Trim Galore. STAR was used to align reads to mouse genome mm10 using ENSEMBL gene annotations as a guide. Read counts data corresponding to ENSEMBL gene annotations were generated using the star flag --quantMode GeneCounts
Assembly: mm10
Supplementary files format and content: text, unstranded, forward and reverse stranded gene counts

source_name: Graft infiltrating cells from transplanted NICC-xenografts under mouse kidney capsule

extract_protocol:
Amplified cDNA for each sample was generated directly from sorted-Tregs using the SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (Takara/Clontech) according to the manufacturer's instructions
Barcoded cDNA libraries were generated with the Nextera XT DNA Library Preparation kit (Illumina) following manufacturer's protocols.
cDNA sequenced with a 2 × 75 bp paired-end protocol with a v3 reagent kit on the Miseq (samples of DLN) and Nextseq 500 instruments (Illumina) (samples of spleen and graft) according to the manufacturer's instructions

tag: time

value: Day 100 post transplantation


title: Graft-Tregs_3

value: Graft infiltrating cells from transplanted NICC-xenografts under mouse kidney capsule


title: 193 stem cell condition DMSO treated lane 1


title: PBMC_1034_ImmEnrich_Alzheimers Disease


title: Graft-Tregs_1


title: PBMC_1055_ImmEnrich_Alzheimers Disease


title: 134 stem cell condition DMSO treated lane 2


title: PBMC_906_ImmEnrich_Alzheimers Disease


title: PBMC_1241_ImmEnrich_Alzheimers Disease


title: SP/CD127highTregs_3

source_name: Mus spleen

value: Mus spleen


title: PBMC_1052_ImmEnrich_Alzheimers Disease

value: Peripheral blood mononuclear cells


title: PBMC_1028_ImmEnrich_Healthy Control


title: PBMC_598_ImmEnrich_Healthy Control


title: SP/CD127highTregs_2


title: 134 stem cell condition CH-223191 treated lane 2


title: 115-5917-1

city: New York City

first: MacIntosh

middle: Grant

last: Cornwell

state: NY

department: School of Medicine

institute: New York University

description:
115-5917-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

data_processing:
Fastq qualtiy assessed via FastQC 0.11.7
Sample contamination assessed via fastqscreen v0.13.0
Fastq files trimmed via Trimmomatic v0.36
Fastq files aligned to the HG38 human genome via STAR v2.7.3a
Reads counted via featurecounts v1.6.3
Assembly: hg38
Supplementary files format and content: Raw count table as a .txt file
Supplementary files format and content: Normalized count table as a .txt file

source_name: whole blood

extract_protocol:
18mLs of whole blood was drawn into 3.2% sodium citrate tubes (BD Vacutainer). Blood was centrifuged to obtain platelet rich plasma, and then depleted of leukocytes and RBCs using StemCell EasySep CD45 and RBC magnetic depletion kits. Purified platelets were pelleted and lysed with 500uL of Qiazol lysis buffer and stored at -80 until ready for RNA extraction. RNA extraction was done by utilizing Zymo Microprep kits (R2062), and stored again at -80 until ready for sequencing.
Sequencing libraries were barcoded and prepared using the Clontech SMART-Seq HT with Nxt HT kit (Takara Bio USA), and libraries sequenced single end on an Illumina NovaSeq 6000

value: whole blood

value: platelet

tag: cohort

value: sle

value: F

tag: ethnicity

value: Non-Hispanic/Latino

tag: race

value: Black or African American

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

value: Predominately Hematologic Activity

tag: progression status

tag: upcr clean


title: PBMC_1160_ImmEnrich_Alzheimers Disease

tag: tissue

tag: Sex

value: male

tag: disease state

value: Alzheimers Disease

tag: genotype

tag: age


title: 116-5929-1

description:
116-5929-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cell type

tag: cohort

tag: ethnicity

tag: race

value: Asian

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

value: Predominately Active Cutaneous Disease


title: SP/CD127highTregs_1

tag: cell type

tag: time

tag: treatment

tag: tissue


title: PBMC_1120_ImmEnrich_Alzheimers Disease

tag: Sex

value: female

tag: disease state

tag: genotype

tag: age


title: 134 stem cell condition CH-223191 treated lane 1

tag: patient organoid line

value: human colon organoid

value: wt

value: CH-223191 treatment


title: SP/CD127-Tregs_3

value: Day 100 post transplantation

value: Mus spleen


title: 134 differentiated DMSO treated lane 2

value: differentiated - DMSO treatment


title: 193 differentiated CH-223191 treated lane 1

value: differentiated - CH-223191 treatment


title: 109-5601-1

description:
109-5601-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

value: whole blood

value: platelet

tag: cohort

value: sle

tag: ethnicity

value: Hispanic/Latino

tag: race

value: White

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

value: Inactive Disease and Either ds-DNA or Low Complement at Enrollment

tag: progression status

tag: upcr clean


title: 108-5821-1

description:
108-5821-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

tag: cohort

tag: age

tag: Sex

value: F

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai


title: 110-9314-1

description:
110-9314-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

tag: cohort

value: control

tag: age

tag: Sex

tag: ethnicity

value: Non-Hispanic/Latino

tag: race

value: Black or African American

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

tag: progression status

tag: upcr clean


title: SP/CD127-Tregs_2

tag: cell type

tag: time

tag: treatment

tag: tissue


title: 134 differentiated DMSO treated lane 1

tag: patient organoid line

value: human colon organoid

tag: genotype


title: SP/CD127-Tregs_1


title: 104-5943-1

description:
104-5943-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

value: Predominately Hematologic Activity


title: 134 differentiated CH-223191 treated lane 2

tag: patient organoid line

tag: cell type

tag: genotype

value: wt

tag: treatment


title: 102-5927-1

description:
102-5927-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

tag: progression status

tag: upcr clean


title: SP/Naïve-Treg_3

tag: cell type

tag: time

value: No transplantation

tag: treatment

value: No

tag: tissue


title: 112-9317-1

description:
112-9317-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai


title: 100-5770-1

description:
100-5770-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

value: Active Musculoskeletal Disease

tag: progression status

tag: upcr clean


title: 104 stem cell condition DMSO treated lane 2

tag: patient organoid line

tag: cell type

tag: genotype

tag: treatment

value: DMSO treatment


title: 111-5200-1

description:
111-5200-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

value: whole blood

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

value: Asian

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai


title: 095-5539-1

description:
095-5539-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

value: platelet

tag: cohort

value: sle

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

tag: progression status

tag: upcr clean


title: 101-5941-1

description:
101-5941-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

value: Predominately Active Cutaneous Disease


title: 107-5686-1

description:
107-5686-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

value: Active Lupus Nephritis

tag: progression status

tag: upcr clean


title: SP/Tolerant-CD4+_2

tag: cell type

value: CD4+ T cell

tag: time

value: Day 100 post transplantation

tag: treatment

tag: tissue

value: Mus spleen


title: 099-5933-1

description:
099-5933-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

tag: age

tag: Sex

value: F

tag: ethnicity

value: Hispanic/Latino

tag: race

value: White

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

value: Inactive Disease


title: SP/Naïve-Treg_2

tag: cell type

tag: time

value: No transplantation

tag: treatment

tag: tissue


title: 084-9307-1

description:
084-9307-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

value: control

tag: age

tag: Sex

tag: ethnicity

value: Non-Hispanic/Latino

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

tag: progression status

tag: upcr clean


title: 081-5826-1

description:
081-5826-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai


title: SP/Naïve-CD4+_3

description:
SMART-Seq v4 Ultra Low Input RNA Kit
The transplant tolerant model: Porcine-NICC were isolated from pancreases and propagated in culture for 6 days as described previously and in method details. DEREG-mice were transplanted with 4000 IEQ porcine-NICC under their renal capsules as described previously. The DEREG-mice received an intraperitoneal (i.p) dose (500 µg/mouse) of MR-1 (Bioexpress) at days 0, 2, 4 and 6; and a single intraperitoneal dose (500 µg/mouse) of CTLA4-Fc (NS-1, WEHI Antibody Facility, Australia) at day 0 as tolerant-group.

tag: cell type

tag: time

tag: treatment

value: No

tag: tissue


title: 094-5385-1

description:
094-5385-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

value: whole blood

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

tag: progression status

tag: upcr clean


title: SP/Naïve-Treg_1

tag: cell type

tag: time

tag: treatment

tag: tissue


title: 104 stem cell condition DMSO treated lane 1

tag: patient organoid line

value: human colon organoid

tag: genotype

value: wt

value: DMSO treatment


title: 089-9310-1

description:
089-9310-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

value: platelet

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai


title: 087-9308-1

description:
087-9308-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

tag: progression status

tag: upcr clean


title: 134 differentiated CH-223191 treated lane 1

tag: patient organoid line

tag: cell type

tag: genotype

tag: treatment

value: differentiated - CH-223191 treatment


title: 104 stem cell condition CH-223191 treated lane 2

value: CH-223191 treatment


title: SP/Tolerant-CD4+_3

value: CD4+ T cell

tag: time

value: Day 100 post transplantation

tag: tissue


title: SP/Naïve-CD4+_2

value: Mus spleen


title: 086-5871-1

description:
086-5871-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

value: sle

tag: age

tag: Sex

value: F

tag: ethnicity

tag: race

value: Asian

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

value: Inactive Disease and Either ds-DNA or Low Complement at Enrollment


title: 104 differentiated CH-223191 treated lane 2

tag: patient organoid line

tag: cell type

tag: genotype

tag: treatment


title: 074-5915-1

description:
074-5915-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

value: White

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

value: Predominately Hematologic Activity

tag: progression status

tag: upcr clean


title: 078-5367-1

description:
078-5367-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

tag: cohort

tag: age

tag: Sex

tag: ethnicity

value: Non-Hispanic/Latino

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

value: Active Lupus Nephritis


title: SP/Naïve-CD4+_1

tag: cell type

tag: time

value: No transplantation

tag: treatment

value: No

tag: tissue


title: 104 stem cell condition CH-223191 treated lane 1

tag: patient organoid line

value: human colon organoid

tag: genotype

value: wt


title: 106-9313-1

description:
106-9313-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

value: whole blood

value: platelet

tag: cohort

value: control

tag: age

tag: Sex

tag: ethnicity

tag: race

value: Black or African American

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

tag: progression status

tag: upcr clean


title: 072-9302-1

description:
072-9302-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai


title: SP/Tolerant-CD4+_1

tag: cell type

value: CD4+ T cell

tag: time

value: Day 100 post transplantation

tag: treatment

tag: tissue

value: Mus spleen


title: 104 differentiated CH-223191 treated lane 1

tag: patient organoid line

tag: genotype

value: differentiated - CH-223191 treatment


title: 104 differentiated DMSO treated lane 2

value: differentiated - DMSO treatment


title: 080-5680-1

description:
080-5680-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

value: sle

tag: age

tag: Sex

value: F

tag: ethnicity

value: Hispanic/Latino

tag: race

value: White

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

tag: progression status

tag: upcr clean


title: 083-5776-1

description:
083-5776-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

tag: cohort

tag: age

tag: Sex

tag: ethnicity

value: Non-Hispanic/Latino

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

value: Inactive Disease


title: SP/Tolerant-CD45+CD4-_3

tag: cell type

value: CD45+CD4- cells

tag: time

tag: treatment

tag: tissue


title: 063-5874-1

description:
063-5874-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

value: Asian

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

tag: progression status

tag: upcr clean


title: 069-9109-1

description:
069-9109-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

value: whole blood

tag: cell type

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai


title: 104 differentiated DMSO treated lane 1

tag: patient organoid line

tag: cell type

value: human colon organoid

tag: genotype

value: wt

tag: treatment


title: WT_D9_3 [ATAC-Seq]

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

library_source: genomic

data_processing:
Raw sequencing data were processed using PEPATAC (Smith et al. 2021; v0.9.5; default parameters) including alignment to the human genome (refdata-cell ranger-atac-GRCh38-1.2.0 assembly provided by 10x Genomics for maximum compatibility with scRNA-seq analyses).
Following initial data processing, all subsequent analyses were performed in R (v4.1.2) using Bioconductor packages.
We removed peaks overlapping blacklisted regions from ENCODE (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz) and merged overlapping peaks across all ATAC-seq datasets to create a common set of consensus genomic regions for subsequent analysis (peak_annot.csv.gz).
Next, we quantified for each input dataset the number of reads overlapping these consensus peaks using featureCounts (Rsubread v2.8.1), see read_counts_raw.csv.gz
Raw read counts were loaded into DESeq2 (v1.34.0; default parameters, design: ~lane+batch+sample_group) for normalization (variance-stabilizing transformation) and differential analysis. In doing so, we estimated count size factors for normalization excluding regions on chromosomes with known chromosomal aberrations (i.e., chr1, chr17) to avoid overcompensation due to differences in global signal strength. Normalized counts are available in read_counts_norm.csv.gz
Assembly: GRCh38
Supplementary files format and content: Comma-separated text files (raw and normalized read counts per peak, annotation of peaks)
Supplementary files format and content: BigWig files summarizing read coverage in genomic bins per sample

molecule: genomic DNA

growth_protocol: hESCs were cultured routinely in feeder-free conditions at 37°C and 5% CO2 in E8 media (made in house adapted from Chen et al 2011) complemented with GlutaMax (Thermo Fisher Scientific) on Vitronectin (Thermo Fisher Scientific) as an attachment substrate. All cell lines were tested regularly for mycoplasma and expression of pluripotency markers. hESC differentiation toward trunk NC and its derivatives was performed using a modified version described in Frith et al. (2018) and Frith & Tsakiridis (2019).

extract_protocol:
20,000 to 50,000 cells were lysed in the transposase reaction mix (12.5 μl 2xTD buffer, 2 μl TDE1 [Illumina], 10.25 μl nuclease-free water, and 0.25 μl 1% digitonin [Promega]) for 30 min at 37 °C.
Following DNA purification with the MinElute kit (Qiagen) eluting in 12 μl, 1 μl of eluted DNA was used in a quantitative PCR (qPCR) reaction to estimate the optimum number of amplification cycles. The remaining 11 μl of each library were amplified for the number of cycles corresponding to the Cq value (i.e., the cycle number at which fluorescence has increased above background levels) from the qPCR using custom Nextera primers. Library amplification was followed by SPRI (Beckman Coulter) size selection to exclude fragments larger than 1,200 bp. Libraries concentration was measured with a Qubit fluorometer (Life Technologies), and libraries were quality checked using a 2100 Bioanalyzer (Agilent Technologies). Libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq 4000 platform in 1x50bp single-end mode.

treatment_protocol: Overexpression of MYCN was induced by supplementing the neural crest media with 100ng/ml of Doxycycline at day 5 (D5) of differentiation in all samples labelled as "17q1qMYCN".

tag: cell line

value: hESC-derived trunk neural crest cells

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: 067-5431-1

description:
067-5431-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

value: platelet

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

value: Inactive Disease and Either ds-DNA or Low Complement at Enrollment

tag: progression status

tag: upcr clean


title: 079-5626-1

description:
079-5626-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai


title: WT_D9_2 [ATAC-Seq]

tag: cell line

tag: cell type

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: SP/Tolerant-CD45+CD4-_2

tag: time

value: Day 100 post transplantation

tag: treatment

tag: tissue

value: Mus spleen


title: WT_D9_1 [ATAC-Seq]


title: H3K27ac_HL_Shox2trac_E125_INACTIVE_rep1

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

description: sorted cells ChIP-seq

data_processing:
TruSeq adapter sequences and bad quality bases were removed using CutAdapt v1.18 (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -q30 -m15). Reads were then mapped to mm39_dsmCherry_P2A_CRE_EYFP custome genome using Bowtie2 v2.3.5.1 with default parameters. Reads were then filtered for a MAPQ≥30 using Samtools view v1.10 and the coverage was obtained after extension of the reads by 200 bp using MACS2 v2.2.7.1 (callpeak --nomodel --call-summits --extsize 200). Coverage was normalized by the number of million tags used by MACS2. broad peak calling was performed by MACS2 using the following parameters --broad --nolambda --broad-cutoff 0.05 --nomodel --gsize mm --extsize 200 -B 2.
Assembly: custom genome: mm39_dsmCherry_P2A_CRE_EYFP
Supplementary files format and content: BigWig + MACS2 broadPeaks

source_name: Embryonic Hindlimb

growth_protocol: Forelimbs and Hindlimbs from E10.5, E11.5, E12.5 and E13.5 Shox2trac embryos were microdissected in PBS. After producing cell suspention, cells were FACS sorted based on the dmCherry and EYFP fluorescent signal.

extract_protocol:
After sorting, cells were centrifuged for 5’ at 400g at 4°C and supernatant was discarded. Cells for ChIP-seq were resuspended in 10% FCS/PBS and fixed in 1% PFA at room temperature. The fixation was blocked by the addition of 1M glycine, cells were isolated by centrifugation (1000g, at 4°C for 8’), resuspended in cold lysis buffer (10 mM Tris, pH 7.5, 10 mM NaCl, 5 mM MgCl2, 1mM EGTA, Protease Inhibitor (Roche, 04693159001)) and incubated on ice for 10’ to isolate the cell nuclei. The nuclei were isolated by centrifugation (1000g, at 4°C for 3’), washed in cold 1X PBS, centrifuged again (1000g, at 4°C for 1’) and stored frozen at -80°C after removal of the PBS supernatant.
500000 fixed nuclei were sonicated to a 200-500bp length with the Bioruptor Pico sonicator (Diagenode). H3K27Ac ChIP was (Diagenode C15410174) was performed as previously described (Lee et al. 2006; Rouco et al. 2021) with the addition of 5mM of Na-Butyrate to all buffers. Libraries were then prepared following the Illumina ChIP TruSeq protocol and sequenced as 50bp single-end reads on an Illumina NovaSeq 6000. Libraries were prepared starting with below <10ng quantities of ChIP-enriched DNA as starting material and processed with the Illumina TruSeq ChIP kit according to manufacturer specifications. Libraries were validated on a Tapestation 2200 (Agilent) and a Qubit fluorimeter (Invitrogen – Thermofisher Scientific). Libraries were pooled at 2 nM and loaded for clustering on a Single-read Illumina Flow cell. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 or an Illumina NovaSeq 6000 sequencer.

tag: background

value: Embryonic Hindlimb

tag: embryonic stage

tag: genotype

tag: facs-sorted status

value: dmCherry-/EYFP-

tag: biological replicate


title: SP/NaiveCD45+CD4-_3

value: No transplantation

value: No


title: 060-5640-1

description:
060-5640-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

value: sle

tag: age

tag: Sex

value: F

tag: ethnicity

value: Hispanic/Latino

tag: race

value: White

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

value: Active Musculoskeletal Disease

tag: progression status

tag: upcr clean


title: H3K27ac_HL_Shox2trac_E125_DECOM_rep1

description: sorted cells ChIP-seq

tag: background

tag: tissue

tag: embryonic stage

tag: genotype

tag: facs-sorted status

value: dmCherry-/EYFP+

tag: biological replicate


title: 061-5657-1

description:
061-5657-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

value: whole blood

tag: cell type

tag: cohort

tag: age

tag: Sex

tag: ethnicity

value: Non-Hispanic/Latino

tag: race

value: Black or African American

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai


title: SP/Tolerant-CD45+CD4-_1

description:
SMART-Seq v4 Ultra Low Input RNA Kit
The transplant tolerant model: Porcine-NICC were isolated from pancreases and propagated in culture for 6 days as described previously and in method details. DEREG-mice were transplanted with 4000 IEQ porcine-NICC under their renal capsules as described previously. The DEREG-mice received an intraperitoneal (i.p) dose (500 µg/mouse) of MR-1 (Bioexpress) at days 0, 2, 4 and 6; and a single intraperitoneal dose (500 µg/mouse) of CTLA4-Fc (NS-1, WEHI Antibody Facility, Australia) at day 0 as tolerant-group.

tag: cell type

value: CD45+CD4- cells

tag: time

tag: treatment

tag: tissue


title: H3K27ac_HL_Shox2trac_E135_INACTIVE_rep1

description: sorted cells ChIP-seq

tag: background

tag: embryonic stage

tag: genotype

tag: facs-sorted status

tag: biological replicate


title: WT_D3_3 [ATAC-Seq]

tag: cell line

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: SP/NaiveCD45+CD4-_1


title: H3K27ac_HL_Shox2trac_E115_DECOM_rep1

description: sorted cells ChIP-seq


title: WT_D3_2 [ATAC-Seq]


title: SP/NaiveCD45+CD4-_2


title: H3K27ac_HL_Shox2trac_E115_INACTIVE_rep1

description: sorted cells ChIP-seq


title: 059-5373-1

description:
059-5373-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

value: platelet

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

tag: progression status

tag: upcr clean


title: 057-5370-1

description:
057-5370-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: pleurisy sledai

value: Predominately Active Cutaneous Disease


title: WT_D3_1 [ATAC-Seq]

tag: cell line

tag: cell type

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: HaCaT SAM 3

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: University of Cincinnati, 160 Panzeca Way

institute: University of Cincinnati

data_processing:
Fastq files for downstream data analysis were automatically generated with Illumina BaseSpace Sequence Hub. Standard bioinformatic analysis was performed with BaseSpace app RNA-Seq Alignment v2.0.2 followed by RNA-Seq Differential Expression app version 1.0.1.
Alignment was performed under 1st strand setting, and analyses used STAR for alignment and Salmon for quantification and assigning Transcripts Per Million (TPM) to genes and transcripts.
The alignment result was used as input to RNA-Seq Differential Expression app for differential expression analysis normalized with DESeq2. Significant genes were selected based on adjusted p-value <0.05.
Assembly: hg38
Supplementary files format and content: Comma separated values after DESeq2 normalizaion

source_name: Skin

extract_protocol:
Poly A RNA was isolated from 1 µg total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA), and enriched with SMARTer Apollo automated NGS library prep system (Takara Bio USA, Mountain View, CA).
The cDNA library was made using the NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs) PCR cycle number of 8, followed by library QC and quantification via real-time qPCR (NEBNext Library Quant Kit, New England BioLabs). The individually indexed libraries were proportionally pooled

tag: tissue

value: Skin

value: HaCaT

value: Keratinocytes

tag: genotype

value: SAM

tag: treatment


title: H3K27ac_FL_Shox2trac_E135_DECOM_rep1

description: sorted cells ChIP-seq

source_name: Embryonic Forelimb

tag: background

value: Embryonic Forelimb

tag: embryonic stage

tag: facs-sorted status

tag: biological replicate


title: 055-5199-1

description:
055-5199-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

value: sle

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

value: Inactive Disease

tag: progression status

tag: upcr clean


title: WT_D19_2 [ATAC-Seq]

tag: cell line

tag: cell type

value: hESC-derived mature sympathoadrenal progenitors

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: HaCaT SAM 1

tag: tissue

tag: genotype

tag: treatment


title: HaCaT SAM 2


title: WT_D19_1 [ATAC-Seq]


title: H3K27ac_HL_Shox2trac_E125_MAINTAIN_rep1

description: sorted cells ChIP-seq

tag: background

value: Embryonic Hindlimb

tag: embryonic stage

tag: facs-sorted status

value: dmCherry+/EYFP+

tag: biological replicate


title: eFL_Shox2Δlate_E145_REP4

description: entire forelimb (bulk) RNA-seq

data_processing:
NextSeq adapter sequences and bad quality bases were removed using CutAdapt v1.18 (-a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -q30 -m15). Unstranded reads were then mapped to the custom genom mm39_dsmCherry_P2A_CRE_EYFP. We used STAR v2.7.2b with a filtered GTF allowing to get a gene quantification simultaneously (--outSAMstrandField intronMotif --sjdbOverhang '99' --sjdbGTFfile $gtfFile --quantMode GeneCounts --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1). FPKM values were determined by Cufflinks v2.2.1 (--max-bundle-length 10000000  --max-bundle-frags 100000000 -- multi-read-correct --library-type “fr-firststrand” --no-effective-length-correction -M MTmouse.gtf). Normalized FPKM were then computed by determining coefficients extrapolated from a set of 1000 house-keeping stably expressed genes, in between the series of compared RNA-seq datasets. Coverage was computed with Bedtools v2.28.0 using uniquely mapped reads (NH:i:1 tag). When indicated, coverage profiles represent an average of the replicates, this was done by dividing each replicate by the number of millions of uniquely mapped reads (for normalization) and calculating the average coverage.
Assembly: custom genome: mm39_dsmCherry_P2A_CRE_EYFP
Supplementary files format and content: BigWig

growth_protocol: Forelimbs and Hindlimbs from E10.5, E11.5, E12.5 and E13.5 Shox2trac embryos were microdissected in PBS. After producing cell suspention, cells were FACS sorted based on the dmCherry and EYFP fluorescent signal. Also entire forelimbs from E10.5, E11.5 and E14.5 Shox2trac embryos, entire forelimbs at E10.5 and E14.5 from Shox2Δearly embryos and entire forelimbs from E11.5 and E14.5 Shox2Δlate embryos were microdissected in PBS and dissociated in a cell suspension.

extract_protocol:
Forelimbs and Hindlimbs sorted cells and entire forelimbs cell suspession were centrifuged for 5’ at 400g at 4°C, supernatant was discarded and cells frozen at -80°C. Total RNA was isolated using the RNeasy Micro Kit (QIAGEN, ID:74004) following manufacturer’s instructions and then stored frozen at -80°C. Total RNA was quantified with a Qubit (fluorimeter from Life Technologies) and RNA integrity assessed with a Bioanalyzer (Agilent Technologies).
The SMART-Seq v4 kit from Clontech, (#634893) was used for the reverse transcription and cDNA amplification according to manufacturer’s specifications, starting with 5 ng of total RNA as input. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina, FC-131-1096. Library molarity and quality was assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled at 2 nM and loaded for clustering on a Single-read Illumina Flow cell for an average of 35 mio reads / library. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 or Illumina NovaSeq 6000 sequencer.

value: entire limb (not sorted)


title: H3K27ac_FL_Shox2trac_E125_DECOM_rep1

description: sorted cells ChIP-seq

value: dmCherry-/EYFP+


title: 134 stem cell condition DMSO treated lane 1

tag: patient organoid line

value: human colon organoid

value: wt

value: DMSO treatment


title: 054-5184-1

description:
054-5184-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

value: whole blood

value: platelet

tag: cohort

tag: age

tag: Sex

value: F

tag: ethnicity

value: Non-Hispanic/Latino

tag: race

value: Asian

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

value: Predominately Hematologic Activity

tag: progression status


title: 053-5173-1

description:
053-5173-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: upcr clean


title: 052-9061-1

description:
052-9061-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

tag: cohort

value: control

tag: age

tag: Sex

tag: ethnicity

value: Hispanic/Latino

tag: race

value: White

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

tag: progression status


title: 058-5323-1

description:
058-5323-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

tag: cohort

value: sle

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

value: Inactive Disease and Either ds-DNA or Low Complement at Enrollment

tag: upcr clean


title: HaCaT shRNA 3

tag: tissue

value: Skin

tag: cell line

value: HaCaT

tag: cell type

value: Keratinocytes

tag: genotype

value: shRNA

tag: treatment


title: HaCaT shRNA 2


title: WT_D14_2 [ATAC-Seq]

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: 051-9107-1

description:
051-9107-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

tag: progression status


title: eFL_Shox2Δlate_E145_REP3

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

value: Embryonic Forelimb

tag: embryonic stage

tag: genotype

tag: facs-sorted status

value: entire limb (not sorted)

tag: biological replicate


title: HaCaT shRNA 1

tag: cell line

tag: cell type

tag: treatment


title: WT_D19_3 [ATAC-Seq]

value: hESC-derived mature sympathoadrenal progenitors

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: eFL_Shox2Δlate_E145_REP1

description: entire forelimb (bulk) RNA-seq


title: eFL_Shox2Δlate_E145_REP2

description: entire forelimb (bulk) RNA-seq


title: 046-9097-1

description:
046-9097-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

value: whole blood

value: platelet

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: upcr clean


title: WT_D0_3 [ATAC-Seq]

tag: cell line

tag: cell type

value: embryonic stem cells (hESC)

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: eFL_Shox2Δlate_E115_REP4

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

tag: embryonic stage

tag: genotype

tag: facs-sorted status

tag: biological replicate


title: WT_D0_2 [ATAC-Seq]


title: 045-5654-1

description:
045-5654-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

tag: age

tag: Sex

value: F

tag: ethnicity

value: Non-Hispanic/Latino

tag: race

value: Asian

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: predominant disease_category

value: Active Lupus Nephritis

tag: progression status


title: WT_D14_3 [ATAC-Seq]

tag: cell line

tag: cell type

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: eFL_Shox2Δlate_E115_REP3

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

tag: embryonic stage

tag: genotype

tag: facs-sorted status

tag: biological replicate


title: WT_D0_1 [ATAC-Seq]


title: 044-5258-1

description:
044-5258-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

tag: age

tag: Sex

tag: ethnicity

value: Hispanic/Latino

tag: race

value: White

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: leukopenia sledai

tag: sledai avail

tag: upcr clean


title: 17q_D9_3 [ATAC-Seq]

tag: cell line

tag: cell type

value: hESC-derived trunk neural crest cells

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: 085-5360-1

description:
085-5360-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cohort

value: sle

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: thrombocytopenia sledai

tag: predominant disease_category

value: Inactive Disease and Either ds-DNA or Low Complement at Enrollment

tag: progression status


title: eFL_Shox2Δlate_E115_REP2

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

tag: embryonic stage

tag: genotype

tag: facs-sorted status

tag: biological replicate


title: 047-5779-1

description:
047-5779-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cell type

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: leukopenia sledai

tag: sledai avail

tag: upcr clean


title: 043-5884-1

description:
043-5884-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

value: Black or African American

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: thrombocytopenia sledai

tag: predominant disease_category

tag: progression status


title: 17q_D9_1 [ATAC-Seq]

tag: cell line

tag: cell type

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: 041-5067-1

description:
041-5067-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: leukopenia sledai

tag: sledai avail

tag: upcr clean


title: WT_D14_1 [ATAC-Seq]

tag: cell line

tag: cell type

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: 17q_D3_3 [ATAC-Seq]


title: eFL_Shox2Δlate_E115_REP1

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

tag: embryonic stage

tag: genotype

tag: facs-sorted status

tag: biological replicate


title: 17q_D9_2 [ATAC-Seq]


title: 039-9014-1

description:
039-9014-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

value: control

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: predominant disease_category

tag: progression status


title: eFL_Shox2trac_E115_REP2

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

value: Embryonic Forelimb

tag: embryonic stage

tag: genotype

tag: facs-sorted status

tag: biological replicate


title: eFL_Shox2trac_E115_REP3

description: entire forelimb (bulk) RNA-seq

value: entire limb (not sorted)


title: 17q_D3_2 [ATAC-Seq]

tag: cell line

tag: cell type

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: eFL_Shox2trac_E115_REP1

description: entire forelimb (bulk) RNA-seq


title: 038-9092-1

description:
038-9092-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: leukopenia sledai

tag: sledai avail

tag: upcr clean


title: eFL_Shox2Δearly_E145_REP4

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

tag: embryonic stage

tag: genotype

tag: facs-sorted status

tag: biological replicate


title: 17q_D3_1 [ATAC-Seq]

tag: cell line

tag: cell type

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: 037-5002-1

description:
037-5002-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: predominant disease_category

tag: progression status


title: 042-5306-1

description:
042-5306-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: leukopenia sledai

tag: sledai avail

value: Inactive Disease

tag: upcr clean


title: 17q_D19_3 [ATAC-Seq]

tag: cell line

tag: cell type

value: hESC-derived mature sympathoadrenal progenitors

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: eFL_Shox2Δearly_E145_REP3

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

tag: embryonic stage

tag: genotype

tag: facs-sorted status

tag: biological replicate


title: Moderate Responder 8 to Etanercept

type: RNA

city: Rouen cedex

first: Celine

last: Derambure

address: 22 Bvd Gambetta

country: France

institute: INSERM U905

hyb_protocol: Hybridization was performed according to the Agilent instructions for Gene Expression Hybridization Kit (catalog number 5188-5242). Samples were applied to microarrays enclosed in Agilent SureHyb hybridization chambers (65°C, 17H). After hybridization, slides were washed and dried in acetonitril.

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction Software (v 10.5.1.1)

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for LOWESS normalization.

source_name: PBMCs

label_protocol: Agilent QuickAmp Labeling kit was used according to the manufacturer instructions (catalog number 5190-0443) with 500ng of total RNA.

extract_protocol: Total RNA from PBMC were extracted using Trizol following manufacturer's instructions.

treatment_protocol: PBMCs from total blood for each patient were isolated by Ficoll and preserved in RNA later at -20°C until total RNA extraction.

tag: gender

value: PBMC

tag: disease state

value: rheumatoid arthritis

tag: treatment

value: methotrexate + etanercept

tag: efficacy

value: moderate response

source_name: PBMCs from 10 healthy donnors

value: healthy

tag: sample type

value: Pool from 5 women and 5 men


title: 036-5883-1

description:
036-5883-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

value: whole blood

tag: cell type

value: platelet

tag: cohort

tag: age

tag: Sex

value: F

tag: ethnicity

value: Hispanic/Latino

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

value: Active Lupus Nephritis

tag: progression status

tag: upcr clean


title: Responder 3 to Etanercept

tag: gender

value: M

tag: cell type

tag: disease state

tag: treatment

tag: efficacy

value: response

tag: sample type


title: Responder 1 to Etanercept


title: Moderate Responder 6 to Etanercept


title: Responder 2 to Etanercept


title: Moderate Responder 7 to Etanercept


title: eFL_Shox2Δearly_E145_REP2

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

value: Embryonic Forelimb

tag: embryonic stage

tag: genotype

tag: facs-sorted status

tag: biological replicate


title: Moderate Responder 4 to Etanercept


title: Moderate Responder 3 to Etanercept


title: 035-5144-1

description:
035-5144-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

value: sle

tag: age

tag: Sex

tag: ethnicity

value: Non-Hispanic/Latino

tag: race

value: Black or African American

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

value: Predominately Hematologic Activity


title: 17q_D19_2 [ATAC-Seq]

tag: cell line

tag: cell type

value: hESC-derived mature sympathoadrenal progenitors

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: Moderate Responder 5 to Etanercept

tag: gender

value: PBMC

tag: disease state

value: rheumatoid arthritis

tag: treatment

value: methotrexate + etanercept

tag: efficacy

tag: sample type


title: eFL_Shox2Δearly_E145_REP1

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

tag: embryonic stage

tag: genotype

tag: facs-sorted status

value: entire limb (not sorted)

tag: biological replicate


title: 17q_D19_1 [ATAC-Seq]

tag: cell line

tag: cell type


title: eFL_Shox2trac_E145_REP5

description: entire forelimb (bulk) RNA-seq


title: 17q_D14_2 [ATAC-Seq]

tag: day

tag: sample group


title: 032-9090-1

description:
032-9090-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

value: whole blood

tag: cohort

value: control

tag: age

tag: Sex

tag: ethnicity

tag: race

value: White

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

tag: progression status

tag: upcr clean


title: Moderate Responder 1 to Etanercept

tag: gender

tag: cell type

tag: disease state

tag: treatment

tag: efficacy

value: moderate response

value: healthy

tag: sample type

value: Pool from 5 women and 5 men


title: eFL_Shox2trac_E145_REP4

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

tag: embryonic stage

tag: genotype

tag: facs-sorted status

tag: biological replicate


title: Moderate Responder 2 to Etanercept

value: M


title: 17q_D14_1 [ATAC-Seq]

tag: cell line

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: Responder 11 to Adalimumab

tag: gender

tag: cell type

value: methotrexate +  adalimumab

value: response


title: 031-9060-1

description:
031-9060-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

value: platelet

tag: cohort

tag: age

tag: Sex

value: F

tag: ethnicity

value: Hispanic/Latino

tag: race

value: More than One Race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

tag: progression status

tag: upcr clean


title: eFL_Shox2trac_E145_REP3

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

value: Embryonic Forelimb

tag: embryonic stage

tag: genotype

tag: facs-sorted status

tag: biological replicate


title: 17q_D0_3 [ATAC-Seq]

tag: cell line

tag: cell type

value: embryonic stem cells (hESC)

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: 030-9089-1

description:
030-9089-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

tag: age

tag: Sex

tag: ethnicity

value: Non-Hispanic/Latino

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail


title: Responder 10 to Adalimumab

tag: gender

tag: cell type

value: PBMC

tag: disease state

value: rheumatoid arthritis

tag: treatment

tag: efficacy

tag: sample type


title: 17q_D0_2 [ATAC-Seq]

tag: cell line

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane