title: Vglutd14cd45_S7_L006

status: Public on Feb 03 2023

city: Cambridge

first: Aviv

last: Regev

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

description:
3'-end
ONC-retina.mtx, ONC-retina_gene.tsv, ONC-retina_cell.tsv, ONC-retina_celltype.tsv

data_processing:
For 10x 3' v2 data, the 10x Genomics Cell Ranger Single Cell Software Suite 2.0.1 was used to perform sample demultiplexing and single cell UMI counting
For 10x 3' v3 data, the 10x Genomics Cell Ranger Single Cell Software Suite 3.1.0 was used to perform sample demultiplexing and single cell UMI counting
Sample alignment to mouse genome GRCm38 with a costumized transcriptome reference using the count function from Cell Ranger software(version 2.1.0, 10X Genomics)
Assembly: GRCm38
Supplementary files format and content: mtx, a gene by cell count matrix in the sparse matrix market format
Supplementary files format and content: cell.tsv, cell names (colname names of the sparse count matrix)
Supplementary files format and content: celltype.tsv, a tab-delimited file with annotated cell type information for each cell
Supplementary files format and content: gene.tsv, gene names (row names of the sparse count matrix)

source_name: Mouse retina

extract_protocol:
Retinas were dissected in oxygenated AMES, digested in papain, and dissociated to single cell suspensions using manual trituration in ovomucoid solution. Eyecups were dissected in HBSS+HEPES and digested in trypsin/EDTA, after which RPE sheets were released by manual shaking into 20% FBS in HBSS+HEPES, and dissociated into single cell suspensions using manual trituration. Single cell suspensions were incubated with anti-CD90, CD45, CD140a and GLAST antibodies (conjugated to various fluorophores) for 10 million cells per 100µl. Cells were sorted using a MoFlo Astrios. Cellular debris, doublets, and dead cells were excluded. Collected cells were loaded into 10X Chromium Single Cell Chips at ~1,000 cells/ul.
Single cell libraries were made with Chromium 3’ V2 or V3 platforms (10X Genomics, Pleasanton, CA) following the manufacturer’s protocols. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina NextSeq 500 or HiSeq X.

treatment_protocol: C57BL/6J and Vglut2:cre;Stp15 mice were used. Retinas were dissected in Ames solution (Sigma-Aldrich; equilibrated with 95% O2/5% CO2 for all use) immediately following enucleation. Eyecups were trypsinized and gently shaken to release RPE cells.

value: Mixed

tag: age

value: 6-8 weeks

tag: strain

value: Vglut2-Cre x STP15

tag: time point

tag: version


title: Vglutd14cd45_S7_L007

type: SRA

state: MA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: Sex


title: Vglutd14cd45_S7_L004


title: Vglutd14cd45_S7_L005


title: CtrlGlast_S3_L004

value: Male

value: Ctrl


title: Vglutd14cd45_S7_L002


title: CtrlGlast_S3_L002


title: CtrlGlast_S3_L001


title: ONCRGCimmune14dR2_S5_L008


title: ONCRGCimmune14dR2_S5_L001


title: ONCRGCimmune14dR1_S4_L008


title: ONCRGCimmune14dR1_S4_L004


title: ONCRGCimmune14dR2_S5_L004


title: ONCRGCimmune14dR2_S5_L002


title: 526_Non-PASC_WT

status: Public on Feb 09 2023

city: San Francisco

first: Kailin

last: Yin

state: California

address: 1650 Owens street

institute: Gladstone Institutes

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh37 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Below are the statistics of mapping the reads to the reference genome.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison. Below are the results of the number of significantly differentially expressed genes for all comparisons provided.
Assembly: hg19
Supplementary files format and content: DEGs file includes normalized counts for each individual sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Total PBMC

growth_protocol: PBMCs were cultered in RPMI 1640 medium containing 10% FBS, 1% penicillin-streptomycin, 1% L-Glu at 37 degree incubator with 5% carbon dioxide supplied.

extract_protocol:
Following incubation, total RNAs were extracted from PBMCs using the AllPrep kit as per manufacturer's instructions (Qiagen).
Briefly, following oligo dT enrichment, fragmentation and random priming, cDNA syntheses was completed. End repair, 5’ phosphorylation and dA-tailing were performed, followed by adaptor ligation, PCR enrichment, and sequencing.

treatment_protocol: No treatments were performed in this project.

tag: pid

tag: lc status

value: Non-LC

value: Female

tag: tissue

value: Total PBMC

tag: cell type

value: PBMC

tag: genotype

value: WT

tag: time (collection_point)

value: 8 months


title: ONCRGCimmune14dR1_S4_L001


title: ONCRGCimmune14dR2_S5_L003


title: 912_Non-PASC_WT


title: ONCRGCimmune14dR1_S4_L002


title: CtrlRGCimmuneR2_S3_L008


title: CtrlRGCimmuneR2_S3_L004


title: ONCRGCimmune14dR1_S4_L003


title: CtrlC57RPECD45RPE_S3_L002

description:
3'-end
eyecup.mtx, eyecup_gene.tsv, eyecup_cell.tsv, eyecut_celltype.tsv

source_name: Mouse eyecup

value: 8 weeks


title: CtrlRGCimmuneR2_S3_L002


title: CtrlRGCimmuneR2_S3_L003


title: CtrlRGCimmuneR2_S3_L001


title: CtrlGlast_S3_L003


title: Vglutd14cd45_S7_L003


title: CtrlRGCimmuneR1_S1_L003


title: CtrlRGCimmuneR1_S1_L004


title: CtrlRGCimmuneR1_S1_L008


title: CtrlC57Cd45Cd140aR1_S3_L002


title: CtrlC57Cd45Cd140aR2_S1_L002


title: CtrlRGCimmuneR1_S1_L001


title: CtrlRGCimmuneR1_S1_L002


title: mnp-20-1405

status: Public on Jan 30 2023

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

molecule: genomic DNA

source_name: CNS tumor tissue

label_protocol: Illumina

extract_protocol: DNA from FFPE tissue was extracted using a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: "material"

value: FFPE tissue

tag: "tumor type"

value: Papillary tumor of pineal region (PTPR)

tag: "patient age (years)"

tag: "patient gender"

value: male

tag: "tumor location"

value: third ventricle


title: mnp-20-0116

value: female

value: pineal region


title: mnp-20-0663

value: Ependymoma, WHO grade III

value: cerebellum


title: AMD19-1891, Dry AMD, snRNAseq

status: Public on Jan 18 2023

city: New Haven

first: Marcello

last: DiStasio

state: CT

address: 300 George St. Rm 353D

department: Pathology

institute: Yale School of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0, 10X Genomics. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-3.0.0
Supplementary files format and content: The data.mtx, genes.csv, and sample_annotations.csv are processed data in aggregate, from all samples, whereas the *_barcodes.tsv.gz, *_features.tsv.gz,  *_matrix.mtx.gz files are for individual samples.

molecule: nuclear RNA

source_name: Retina

extract_protocol:
Globes were placed in RNAlater (ThermoFisher) and transported on ice. Trephine punches (6 mm diameter) were used to isolate samples from the macula in the central retina, located away from the optic disc and major arterioles. For each punch of tissue, the retina was mechanically separated from the underlying retinal pigment epithelium-choroid, snap-frozen on dry ice and stored at -80C. Nuclei were isolated and purified using the Nuclei EZ Prep Nuclei Isolation Kit (Sigma), following the manufacturer’s protocol, with some modification. All procedures were carried out on ice or at 4C. Briefly, frozen retinal tissue was subjected to dounce homogenization (25 times with pestle A followed by 25 times with tight pestle B) using the KIMBLE Dounce Tissue Grinder Set (Sigma) in 2ml EZ Lysis buffer. The sample was transferred to a 15ml tube with an additional 2ml EZ lysis buffer and incubated on ice for 5min. Following incubation, the sample was centrifuged at 500xg, 5min at 4C. Supernatants were discarded, and the isolated nuclei were resuspended in 4ml EZ lysis buffer, incubated for 5min on ice and centrifuged at 500xg for 5min at 4C. Next, the nuclei were washed with 4ml ice-cold Nuclei Suspension Buffer (1X PBS containing 0.01% BSA and 0.1% RNase inhibitor), resuspended in 1ml Nuclei EZ Storage buffer and passed through a 40μM nylon cell strainer. The nuclei suspensions were counted with trypan blue prior to loading on the microfluidics platform.
Isolated nuclei from each macular sample were processed through microfluidics-based single nuclear RNA-seq. Single-cell libraries were prepared using the Chromium 3' v2 and v3 platforms (10X Genomics) following the manufacturer’s protocol. Briefly, single nuclei were partitioned into Gel beads in Emulsion in the 10X Chromium Controller instrument followed by lysis and barcoded reverse transcription of RNA, amplification, shearing and 5' adapter and sample index attachment. On average, ~7000 nuclei were loaded on each channel that resulted in the recovery of ~4000 nuclei.
snRNA-seq

tag: disease state

value: Dry AMD

value: All neurosensory retina cells

value: Retina


title: 10_LXR-bKO_LPS_24h_(LXRa)_rep2

status: Public on Dec 31 2022

city: Madrid

first: ANTONIO

last: CASTRILLO

address: Arturo Duperier 4

department: metabolism and cellular signaling

country: Spain

institute: Instituto Investigaciones Biomedicas Alberto Sols CSIC

library_source: genomic

data_processing:
Basecalls performed using Casava version 1.8.4
For ChIP-Seq, reads were aligned to the mm10 genome using default parameter for bowtie2 (v2.2.9).
Aligned read files were analyzed with HOMER software (v4.9) to find peaks, perform sequence motif finding and other analyses in the study.
Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped.
annotation was performed with HOMER software v4.9 annotatePeaks.pl using default parameters
Assembly: mm10
Supplementary files format and content: Processed files include bed files.

source_name: Bone marrow

growth_protocol: For bone marrow-derived macrophage (BMDM) cell differentiation, bone marrow from femurs and tibias of 8-10 week-old WT or LXRβ-/- mice were isolated and cultured for 7 days in RPMI supplemented with 10% conditioned media from L-929 cells expressing M-CSF and 1% antibiotics (penicillin and streptomycin). To analyze LXRα-dependent response, cells were cultured in RPMI supplemented with 10% FBS, 1% antibiotics (penicillin and streptomycin) and 100 nM of Lipopolysachaaride (LPS). Genome-wide locations of LXRα and H3K27ac acetylation mark were analized in response to treatment with  LPS.

extract_protocol:
Cells were fixed with DSG (2 mM) for 30 minutes and 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Biorruptor plus (Diagenode) and LXR-DNA or H3K27ac-DNA complexes were isolated with indicated antibodies.
to create the sequencing library, DNA was end-repaired and ligated to stem-loop adaptors (DNA Library Prep kit for Illumina (Ref.:#7370) following the manufacture instructions). Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.

value: Bone marrow

tag: cell line

value: Bmdm

value: bone marrow-derived macrophage

value: LXR-bKO

tag: chip antibody

value: A polyclonal antibody raised against LXRα and LXRβ was obtained from their original creators (Pehkonen 2012)

tag: treatment

value: Lipopolysaccharide 100 nM 24 hours


title: 11_LXR-bKO_LPS_24h_(LXRa)_rep3


title: A18-1974, Dry AMD, snRNAseq

description: 10x Genomics

tag: age


title: A20-1257, Wet AMD, snRNAseq

description: 10x Genomics

value: Wet AMD


title: 4_LXR-DKO_LPS_24h_(LXRa)_rep1

value: LXR-DKO


title: 5_LXR-DKO_LPS_24h_(LXRa)_rep2


title: 23_LXR-aKO_LPS_24h_(H3K27ac)_rep3

value: LXR-aKO

value: H3K27ac (Abcam catalog#ab4729)


title: 21_LXR-aKO_LPS_24h_(H3K27ac)_rep1


title: 9_LXR-bKO_LPS_24h_(LXRa)_rep1


title: 22_LXR-aKO_LPS_24h_(H3K27ac)_rep2


title: 17_LXR-WT_LPS_24h_(H3K27ac)_rep3

value: WT


title: Sympathetic neurons from S2 FD iPSCs, day 35, biol rep 4

status: Public on Oct 26 2022

city: Athens GA

first: Nadja

last: Zeltner

state: GA

address: 325 Riverbend road

institute: University of Georgia

data_processing:
All analyses were done on the Galaxy web platform (www.usegalaxy.org)
Low quality bases were trimmed from sequencing reads using Trimmomatic (version 0.38)
Reads were  mapped to the human genome using HISAT2 (version 2.21) using default parameters.
Reads per gene were counted using HTseq (version 0.91) with a minimum alignment quality value of 10.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file, include raw counts per gene

growth_protocol: hPSCs were mainatined on vitronectin in Essential media 8 and differntiated according to Wu et al., JoVE 2020

extract_protocol:
Total RNA was isolated using TRIZOL and purified following manufacturer's protocol.
Libraries were prepared using KAPA’s Stranded mRNA-seq kit (#KK4821) with halved reaction volumes. mRNA was selected using oligo-dT beads, followed by RNA fragmentation and cDNA generation using random hexamer priming.

value: iPSC

value: FD

value: sympathetic neuron differentiation


title: 15_LXR-WT_LPS_24h_(H3K27ac)_rep1


title: Sympathetic neurons from S2 FD iPSCs, day 35, biol rep 3


title: Patient 4, Endometriosis

status: Public on Oct 30 2022

city: Los Angeles

first: Marcos

last: Fonseca

state: CA

address: 8000 Beverly Boulevard

department: Division of Gynecologic Oncology, Department of Obstetrics and Gynecology

institute: Cedars-Sinai Medical Center

description: 10X 3' scRNA-seq

data_processing:
for scRNA-seq: Raw reads were aligned to the hg38 reference genome, UMI (unique molecular identifier) counting was performed using Cell Ranger v.3.1.0 (10X Genomics) pipeline with default parameters. keratin-positive, mesenchymal and endothelial cells were extract from BAM files using cellranger 5.0.1 bamtofastq command.
for visium: Slides were processed by Cedars-Sinai Applied Genomics, Computation and Translational core. Alignment and QC was performed using Space Ranger (version 1.2.1)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Endometriosis

extract_protocol:
For Visium spatial transcriptomics - H&E stained slides were made and reviewed to confirm the presence of endometriosis lesions. Tissue sections were cut by pathology intraoperative consult staff onto Visium slides according to the 10X Genomics Visium spatial tissue preparation guide
10X 3' scRNA-seq, 10X Visium spatial gene expression

tag: patient id

value: Endometriosis

value: tissue

tag: anatomic location

value: Posterior cul-de-sac

tag: tissue type

value: fresh


title: CTRLC57AllOther2_S4_L002

tag: Sex

value: Male

value: 6-8 weeks

tag: strain

tag: time point

value: Ctrl

tag: version


title: 16_LXR-WT_LPS_24h_(H3K27ac)_rep2

tag: tissue

value: Bone marrow

tag: cell type

value: bone marrow-derived macrophage

tag: genotype


title: Sympathetic neurons from S2 FD iPSCs, day 35, biol rep 2


title: Sympathetic neurons from S2 FD iPSCs, day 35, biol rep 1


title: Sympathetic neurons from H9 hESCs, day 35, biol rep 1

value: hESC


title: Sympathetic neurons from H9 hESCs, day 35, biol rep 3


title: Sample 4

status: Public on Oct 13 2022

description: 10x Genomics

source_name: Eutopic Endometrium

extract_protocol: none provided by the submitter

value: Eutopic Endometrium

value: Endometrium


title: sample2

description: 10x Genomics

value: Endometrioma

value: Left ovary


title: Sample 48

status: Public on Oct 11 2022

description: 10x Genomics

source_name: Endometriosis, scRNAseq

extract_protocol: Single cells are captured and barcoded using the 10X Chromium platform (10X Genomics). scRNA-seq libraries were prepared following the instructions from Chromium Single Cell 3ʹ Reagent Kits User Guide (v2 or v3). Briefly, Gel Bead-In EMulsions (GEMs) are generated using single cell preparations. After GEM-RT and cleanup, the cDNA from barcoded single cell RNAs were amplified before quantification using Agilent Bioanalyzer High Sensitivity DNA chips. The single cell 3’ gene expression libraries were constructed and cDNA corresponding to an insertion size of around 350 bp selected. Libraries were quantified using Agilent Bioanalyzer High Sensitivity DNA chips and pooled together to get similar numbers of reads from each single cell before sequencing on the NovaSeq S4 (Novogene).

value: Anterior cul-de-sac


title: Sample 49

description: 10x Genomics

value: Posterior uterus


title: Sample 45

description: 10x Genomics

value: Rectum


title: Sample 44

description: 10x Genomics

value: Endometriosis

value: Left uterosacral ligament


title: Sample 47

description: 10x Genomics

value: tissue

value: Right uterosacral ligament


title: Sample 46

description: 10x Genomics

value: Left ovarian fossa


title: Sample 41

description: 10x Genomics

source_name: Ovary, scRNAseq

value: Ovary


title: Sample 40

description: 10x Genomics

source_name: Eutopic Endometrium, scRNAseq


title: Sample 43

description: 10x Genomics

value: Right ovarian fossa


title: Sample 37

description: 10x Genomics


title: Sample 34

description: 10x Genomics


title: Sample 33

description: 10x Genomics

value: Right ovary


title: Sample 36

description: 10x Genomics


title: Sample 42

description: 10x Genomics

source_name: Endometrioma, scRNAseq

value: Left ovarian cyst


title: Sample 27

description: 10x Genomics

source_name: No endometriosis detected, scRNAseq

value: No endometriosis detected

value: Bladder endometriosis


title: Sample 30

description: 10x Genomics

value: Eutopic Endometrium

value: Endometrium


title: Sample 39

description: 10x Genomics


title: Sample 38

description: 10x Genomics


title: Sample 26

description: 10x Genomics


title: Sample 35

description: 10x Genomics


title: Sympathetic neurons from H9 hESCs, day 35, biol rep 4

value: hESC

value: WT

value: sympathetic neuron differentiation


title: Sample 29

description: 10x Genomics

value: Endometrioma


title: Sample 32

description: 10x Genomics


title: Sample 28

description: 10x Genomics

value: Endometriosis

value: Left pelvic side wall


title: Sample 31

description: 10x Genomics

value: tissue


title: Sample 23

description: 10x Genomics

value: Perirectal fat


title: Sympathetic neurons from H9 hESCs, day 35, biol rep 2


title: Sample 25

description: 10x Genomics

value: Left uterosacral ligament


title: sample3

description: 10x Genomics

source_name: Endometrioma


title: Sample 21

description: 10x Genomics


title: Sample 20

description: 10x Genomics

value: Anterior abdominal wall and cul-de-sac†


title: Sample 19

description: 10x Genomics

value: Left ovarian fossa


title: Sample 17

description: 10x Genomics

value: Rectal serosa


title: Sample 15

description: 10x Genomics

value: Left ovary


title: Sample 13

description: 10x Genomics

value: Right and left uterosacral ligament


title: Sample 14

description: 10x Genomics

value: No endometriosis detected

value: Anterior cul-de-sac and right pelvic side wall†


title: Sample 9

description: 10x Genomics

value: Ovary

value: Right ovary


title: Sample 11

description: 10x Genomics

value: Anterior cul-de-sac


title: Sample 8

description: 10x Genomics

value: Eutopic Endometrium

value: Endometrium


title: Sample 10

description: 10x Genomics

value: Endometriosis

value: Right and left pelvic side wall†


title: M2 THP-1_RNA-seq [MIL-4+IL-13_2]

status: Public on Sep 12 2022

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

country: Australia

institute: Centenary Institute

data_processing:
The original raw data from Illumina CASAVA v1.8 software are transformed to Sequenced Reads by base calling.
Raw reads are filtered to remove reads containing adapters or reads of low quality reads, then were mapped to Ensembl human reference genome (GRCh38.v86) using STAR_2.5.2a.
Gene-level expression was measured using featureCounts (1.5.0-p3).
Differential expression was assessed with Deseq2 (1.22.2)
(108). Differentially enriched mRNAs undergoing translation in the polysomes were identified using Wald statistical test, with fold-change > 1.5 and p <0.05 after Benjamini-Hochberg correction.
Assembly: GRCh38.v86 (Ensembl)
Supplementary files format and content: Excel file including raw counts for M2

source_name: THP-1 M2-like cells (polarised)

growth_protocol: Human THP-1 monocytic cells were maintained in RPMI medium supplemented with 2 mM L-glutamine, 25 mM HEPES, 10% (v/v) FBS, 1 mM sodium pyruvate, 1% (v/v) non-essential amino acids, and 0.1 mg/mL penicillin/streptomycin at 37°C in the presence of 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol. Genomic DNA was extracted using standard phenol-chloroform method.
Poly-A-enriched mRNA libraries were prepared from 2 μg of TURBOTM DNase-treated, total RNA using the TruSeq® Stranded Library Preparation Kit (Illumina), according to the manufacturers’ instructions. mRNA sequencing was performed on each cell population in triplicates by Novogene (China). A total of 100 million paired-end strand-specific reads were sequenced per sample on an Illumina HiSeq® 2500 Platform.Whole-genome bisulphite sequencing (WGBS) was performed on a HiSeq X Ten platform (Illumina) following library preparation using the TruMethyl WG method v.1.9 (Cambridge Epigenetix).

treatment_protocol: 1.5 × 10^7 cells per 75 cm2 culture flask of THP-1 cells were differentiated using phorbol-12-myristate 13-acetate (PMA) into macrophages. Resting macrophages are further polarised into pro-inflammatory macrophages using lipopolysaccharide (LPS) and interferon gamma (IFN-γ). To inhibit nuclear degradation by the RNA exosome, THP-1 macrophages were transfected with 300 nM EXOSC10 siRNA (sense: 5′ – GAAGGCAGCUGAGCAAACAdTdT – 3′, antisense: 5′ – UGUUUGCUCAGCUGCCUUCdTdT). ON-TARGETplus non-targeting siRNA (GE Dharmacon) was used as a negative control.

value: Monocytic cell line


title: Sample 1

description: 10x Genomics

value: Endometrioma

value: tissue


title: M2 THP-1_RNA-seq [MIL-4+IL-13_3]


title: FC687, replicate 2, scRNAseq

status: Public on Sep 06 2022

city: Kaohsiung

first: Kuang-Den

last: Chen

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peripheral blood

extract_protocol:
RNA samples of mononuclear/polymorphnuclear cells are harvested by Tri-zol (Invritrogen, Inc. Faraday Avenue, Carlsbad, CA). (500 μl Tri-zol/600 μl cell lyses buffer for each 1 × 105 cell)
Single-cell RNA-Seq libraries were prepared using GemCode Single-Cell 3’ Gel Bead and Library Kit (now sold as P/N 120262, 1000009, 120267, 10x Genomics). GEM-RT was performed in a Veriti 96-Well Thermal Cycler 2020/7/29 Version1 (Applied Biosystems; Model#: 9902)at 53 °C for 45 min, 85 °C for 5 min, and held at 4 °C.

value: WBC

value: peripheral blood

value: febrile control


title: Sample 7

description: 10x Genomics

value: Posterior cul-de-sac


title: Sample 22

description: 10x Genomics

value: Right parametrium


title: Spleen ST2+ CD44hi Tregs - FK7700

status: Public on Jul 24 2022

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Base-calling was performed using CASAVA v.1.8.2.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Reads were aligned in Galaxy using STAR aligner; duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, STAR, Samtools, and htseq-count.
Genome_build: GRCm38 release 91
Supplementary_files_format_and_content: P239-1_CCLKLANXX_180806_combined_counts.csv is a comma separated value file. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.

source_name: Spleen

extract_protocol:
Tissues (blood, spleen, lungs, abdominal VAT, colon, back skin) were harvested from Foxp3YFP-cre mice.  Single cell suspensions were prepared from tissue samples, and MACS magnetic bead enrichment was performed on spleen and lung samples to enrich CD4 T cells. Treg populations were sorted on a FACS Aria II directly into reaction buffer using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), and reverse transcription was performed followed by PCR amplification to generate full length amplified cDNA.
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries

tag: mouse id

value: Spleen

tag: population

value: ST2+ CD44hi Tregs

value: Male

tag: age (weeks)

tag: # of cells sorted


title: Colon ST2- CD44hi Tregs - FK7700

source_name: Colon

value: Colon

value: ST2- CD44hi Tregs


title: Colon ST2+ CD44hi Tregs - FK7700


title: M2 THP-1_RNA-seq [MIL-4+IL-13_1]

tag: cell line


title: KD1092, replicate 2, scRNAseq

description: 10x Genomics

tag: disease state

value: Kawasaki disease


title: Blood ST2- CD44hi Tregs - FK7700

source_name: Blood

value: Blood


title: Spleen ST2- CD44hi Tregs - FK7700


title: FC665, replicate 1, scRNAseq

description: 10x Genomics


title: Sample 18

description: 10x Genomics

value: Endometriosis

value: Right and left pelvic side wall


title: Sample 16

description: 10x Genomics

value: Left uterosacral ligament


title: Blood ST2+ CD44hi Tregs - FK7700


title: VAT ST2- CD44hi Tregs - FK7700

source_name: Abdominal VAT

value: Abdominal VAT


title: KD1053, replicate 1, scRNAseq

description: 10x Genomics


title: Sample 12

description: 10x Genomics

value: Endometrioma

value: tissue

value: Right ovary


title: Sample 5

description: 10x Genomics

value: Anterior cul-de-sac


title: VAT ST2+ CD44hi Tregs - FK7700


title: Lung ST2+ CD44hi Tregs - FK7700

source_name: Lungs

value: Lungs


title: Lung ST2- CD44hi Tregs - FK7700


title: Lung ST2- CD44lo CD62L+ Tregs - FK7700

value: ST2- CD44lo CD62L+ Tregs


title: Skin ST2- CD44hi Tregs - FK7700

source_name: Skin (back)

value: Skin (back)


title: Spleen ST2- CD44lo CD62L+ Tregs - FK7699

value: Spleen


title: Skin ST2+ CD44hi Tregs - FK7700

value: ST2+ CD44hi Tregs

value: Male


title: Spleen ST2- CD44lo CD62L+ Tregs - FK7700


title: Colon ST2+ CD44hi Tregs - FK7699

value: Colon


title: Colon ST2- CD44hi Tregs - FK7699

value: ST2- CD44hi Tregs


title: VAT ST2+ CD44hi Tregs - FK7699


title: Skin ST2+ CD44hi Tregs - FK7699


title: Blood ST2- CD44hi Tregs - FK7699

value: Blood


title: Skin ST2- CD44hi Tregs - FK7699


title: Lung ST2- CD44hi Tregs - FK7699


title: Lung ST2- CD44lo CD62L+ Tregs - FK7699


title: Lung ST2+ CD44hi Tregs - FK7699


title: Colon ST2+ CD44hi Tregs - FK7698


title: Spleen ST2+ CD44hi Tregs - FK7698


title: Colon ST2- CD44hi Tregs - FK7698


title: Spleen ST2- CD44hi Tregs - FK7698


title: VAT ST2+ CD44hi Tregs - FK7698


title: Blood ST2- CD44hi Tregs - FK7698


title: Spleen ST2+ CD44hi Tregs - FK7699


title: Spleen ST2- CD44hi Tregs - FK7699


title: VAT ST2- CD44hi Tregs - FK7698


title: Skin ST2+ CD44hi Tregs - FK7698


title: Blood ST2+ CD44hi Tregs - FK7698


title: Lung ST2+ CD44hi Tregs - FK7698


title: Spleen ST2+ CD44hi Tregs - FK7697


title: Lung ST2- CD44lo CD62L+ Tregs - FK7698


title: Spleen ST2- CD44lo CD62L+ Tregs - FK7697


title: Lung ST2- CD44hi Tregs - FK7698


title: Colon ST2+ CD44hi Tregs - FK7697


title: VAT ST2- CD44hi Tregs - FK7699


title: Skin ST2- CD44hi Tregs - FK7698


title: Spleen ST2- CD44hi Tregs - FK7697


title: Spleen ST2- CD44lo CD62L+ Tregs - FK7698


title: Colon ST2- CD44hi Tregs - FK7697


title: Blood ST2+ CD44hi Tregs - FK7697


title: VAT ST2+ CD44hi Tregs - FK7697


title: Blood ST2- CD44hi Tregs - FK7697


title: VAT ST2- CD44hi Tregs - FK7697


title: Skin ST2+ CD44hi Tregs - FK7697


title: Skin ST2- CD44hi Tregs - FK7697


title: Lung ST2- CD44hi Tregs - FK7697


title: Lung ST2+ CD44hi Tregs - FK7697


title: Spleen ST2- CD44lo CD62L+ Tregs - FK7696


title: Colon ST2+ CD44hi Tregs - FK7696


title: Spleen ST2+ CD44hi Tregs - FK7696


title: Colon ST2- CD44hi Tregs - FK7696


title: Spleen ST2- CD44hi Tregs - FK7696


title: Blood ST2+ CD44hi Tregs - FK7696


title: Blood ST2+ CD44hi Tregs - FK7699


title: Skin ST2- CD44hi Tregs - FK7696


title: Lung ST2+ CD44hi Tregs - FK7696


title: Lung ST2- CD44lo CD62L+ Tregs - FK7696


title: VAT ST2+ CD44hi Tregs - FK7696


title: Lung ST2- CD44hi Tregs - FK7696


title: VAT ST2- CD44hi Tregs - FK7696


title: Lung ST2- CD44lo CD62L+ Tregs - FK7697


title: Sample 24

description: 10x Genomics

value: Eutopic Endometrium

value: Endometrium


title: Blood ST2- CD44hi Tregs - FK7696


title: Breast Cancer 241

status: Public on Jul 16 2022

type: RNA

city: Brussels

first: Christos

last: Sotiriou

address: Rue Meylemeersch 90

country: Belgium

institute: Institut Jules Bordet – Université Libre de Bruxelles (ULB)

description: Biotinylated cRNA was prepared according to Affymetrix's standard protocols

hyb_protocol: Hybridization was done according to Affymetrix's standard protocols for 96 array plate. The GeneTitan Hybridization, Wash and Stain kit for 3' IVT arrays was used for preparing hybridization mixes

scan_protocol: 96 array plates were scanned using Affymetriix's automated GeneTitan system according to the manufacturer's instructions

data_processing: The probe level intensities were background adjusted using the Robust multi-array analysis (RMA) method followed by quantile normalization as impletemented in the R/Bioconductor package affy. Probe level annotations were obtained from Affymetrix’s website. In particular, we used release 32 of the NetAffx annotation files.

label: biotin

source_name: Breast tumor

extract_protocol: RNA was extracted from FFPE tumor tissue according to the method described in Bohmann et al, Clinical Chemistry 2009

tag: filename

tag: batch

tag: dataset

value: FinHER


title: Breast Cancer 253

label_protocol: Biotinylated cRNA was prepared according to Affymetrix's standard protocols


title: Breast Cancer 246


title: Breast Cancer 250


title: Breast Cancer 248


title: Breast Cancer 233


title: Breast Cancer 1002


title: Breast Cancer 243


title: Skin ST2+ CD44hi Tregs - FK7696


title: Breast Cancer 997


title: Breast Cancer 256


title: Breast Cancer 1005


title: Breast Cancer 979


title: Breast Cancer 990


title: Breast Cancer 989


title: Breast Cancer 996


title: Breast Cancer 966


title: Breast Cancer 962


title: Breast Cancer 986


title: Breast Cancer 974


title: Breast Cancer 991


title: Breast Cancer 226


title: Breast Cancer 948


title: Breast Cancer 982


title: Breast Cancer 955


title: Breast Cancer 951


title: Breast Cancer 965


title: Breast Cancer 969


title: Breast Cancer 238


title: Breast Cancer 943


title: Breast Cancer 945


title: Breast Cancer 934


title: Breast Cancer 947


title: Breast Cancer 941


title: Breast Cancer 940


title: Breast Cancer 927


title: Breast Cancer 939


title: Breast Cancer 928


title: Breast Cancer 923


title: Breast Cancer 932


title: Breast Cancer 907


title: Breast Cancer 911


title: Breast Cancer 908


title: Breast Cancer 905


title: Breast Cancer 894


title: Breast Cancer 880


title: Breast Cancer 976


title: Breast Cancer 872


title: Breast Cancer 884


title: Breast Cancer 886


title: Breast Cancer 859


title: Breast Cancer 876


title: Breast Cancer 871


title: Breast Cancer 867


title: Breast Cancer 897


title: Breast Cancer 860


title: Breast Cancer 847


title: Breast Cancer 845


title: Breast Cancer 849


title: Breast Cancer 863


title: Breast Cancer 854


title: Breast Cancer 839


title: Breast Cancer 834


title: Breast Cancer 842


title: Breast Cancer 858


title: Breast Cancer 843


title: Breast Cancer 832


title: Breast Cancer 828


title: Breast Cancer 836


title: Breast Cancer 831


title: Breast Cancer 829


title: Breast Cancer 815


title: Breast Cancer 800


title: Breast Cancer 822


title: Breast Cancer 785


title: Breast Cancer 827


title: Breast Cancer 824


title: Breast Cancer 936


title: Breast Cancer 792


title: Breast Cancer 793


title: Breast Cancer 783


title: Breast Cancer 773


title: Breast Cancer 757


title: Breast Cancer 795


title: Breast Cancer 771


title: Breast Cancer 801


title: Breast Cancer 767


title: Breast Cancer 765


title: Breast Cancer 772


title: Breast Cancer 753


title: Breast Cancer 763


title: Breast Cancer 750


title: Breast Cancer 736


title: Breast Cancer 739


title: Breast Cancer 734


title: Breast Cancer 768


title: Breast Cancer 745


title: Breast Cancer 749


title: Breast Cancer 755


title: Breast Cancer 721


title: Breast Cancer 719


title: Breast Cancer 716


title: Breast Cancer 712


title: Breast Cancer 718


title: Breast Cancer 709


title: Breast Cancer 698


title: Breast Cancer 727


title: Breast Cancer 717


title: Breast Cancer 697


title: Breast Cancer 684


title: Breast Cancer 682


title: Breast Cancer 674


title: Breast Cancer 695


title: Breast Cancer 696


title: Breast Cancer 685


title: Breast Cancer 673


title: Breast Cancer 671


title: Breast Cancer 660


title: Breast Cancer 656


title: Breast Cancer 675


title: Breast Cancer 683


title: Breast Cancer 648


title: Breast Cancer 899


title: Breast Cancer 669


title: Breast Cancer 651


title: Breast Cancer 642


title: Breast Cancer 644


title: Breast Cancer 635


title: Breast Cancer 634


title: Breast Cancer 639


title: Breast Cancer 631


title: Breast Cancer 628


title: Breast Cancer 615


title: Breast Cancer 616


title: Breast Cancer 614


title: Breast Cancer 606


title: Breast Cancer 607


title: Breast Cancer 608


title: Breast Cancer 623


title: Breast Cancer 618


title: Breast Cancer 581


title: Breast Cancer 580


title: Breast Cancer 590


title: Breast Cancer 579


title: Breast Cancer 582


title: Breast Cancer 572


title: Breast Cancer 563


title: Breast Cancer 573


title: Breast Cancer 561


title: Breast Cancer 558


title: Breast Cancer 557


title: Breast Cancer 657


title: Breast Cancer 603


title: Breast Cancer 588


title: Breast Cancer 605


title: Breast Cancer 553


title: Breast Cancer 542


title: Breast Cancer 554


title: Breast Cancer 546


title: Breast Cancer 547


title: Breast Cancer 548


title: Breast Cancer 555


title: Breast Cancer 528


title: Breast Cancer 527


title: Breast Cancer 534


title: Breast Cancer 518


title: Breast Cancer 533


title: Breast Cancer 529


title: Breast Cancer 517


title: Breast Cancer 545


title: Breast Cancer 499


title: Breast Cancer 505


title: Breast Cancer 516


title: Breast Cancer 504


title: Breast Cancer 509


title: Breast Cancer 494


title: Breast Cancer 501


title: Breast Cancer 506


title: Breast Cancer 498


title: Breast Cancer 496


title: Breast Cancer 491


title: Breast Cancer 475


title: Breast Cancer 454


title: Breast Cancer 489


title: Breast Cancer 477


title: Breast Cancer 677


title: Breast Cancer 441


title: Breast Cancer 458


title: Breast Cancer 466


title: Breast Cancer 460


title: Breast Cancer 453


title: Breast Cancer 437


title: Breast Cancer 443


title: Breast Cancer 445


title: Breast Cancer 483


title: Breast Cancer 414


title: Breast Cancer 419


title: Breast Cancer 415


title: Breast Cancer 396


title: Breast Cancer 431


title: Breast Cancer 658


title: Breast Cancer 693


title: Breast Cancer 393


title: Breast Cancer 387


title: Breast Cancer 386


title: Breast Cancer 412


title: Breast Cancer 384


title: Breast Cancer 492


title: Breast Cancer 391


title: Breast Cancer 405


title: Breast Cancer 428


title: Breast Cancer 390


title: Breast Cancer 377


title: Breast Cancer 374


title: Breast Cancer 373


title: Breast Cancer 381


title: Breast Cancer 356


title: Breast Cancer 361


title: Breast Cancer 372


title: Breast Cancer 340


title: Breast Cancer 331


title: Breast Cancer 336


title: Breast Cancer 316


title: Breast Cancer 333


title: Breast Cancer 342


title: Breast Cancer 311


title: Breast Cancer 358


title: Breast Cancer 343


title: Breast Cancer 315


title: Breast Cancer 349


title: Breast Cancer 302


title: Breast Cancer 295


title: Breast Cancer 307


title: Breast Cancer 280


title: Breast Cancer 300


title: Breast Cancer 290


title: Breast Cancer 297


title: Breast Cancer 284


title: Breast Cancer 289


title: Breast Cancer 271


title: Breast Cancer 266


title: Breast Cancer 276


title: Breast Cancer 269


title: Breast Cancer 217


title: Breast Cancer 360


title: Breast Cancer 218


title: Breast Cancer 257


title: Breast Cancer 279


title: Breast Cancer 215


title: Breast Cancer 287


title: Breast Cancer 270


title: Breast Cancer 263


title: Breast Cancer 275


title: Breast Cancer 216


title: Breast Cancer 186


title: Breast Cancer 273


title: Breast Cancer 222


title: Breast Cancer 192


title: Breast Cancer 183


title: Breast Cancer 195


title: Breast Cancer 206


title: Breast Cancer 203


title: Breast Cancer 198


title: Breast Cancer 202


title: Breast Cancer 184


title: Breast Cancer 213


title: Breast Cancer 169


title: Breast Cancer 204


title: Breast Cancer 146


title: Breast Cancer 147


title: Breast Cancer 137


title: Breast Cancer 165


title: Breast Cancer 133


title: Breast Cancer 140


title: Breast Cancer 132


title: Breast Cancer 160


title: Breast Cancer 167


title: Breast Cancer 162


title: Breast Cancer 148


title: Breast Cancer 164


title: Breast Cancer 120


title: Breast Cancer 126


title: Breast Cancer 131


title: Breast Cancer 135


title: Breast Cancer 124


title: Breast Cancer 123


title: Breast Cancer 161


title: Breast Cancer 163


title: Breast Cancer 143


title: Breast Cancer 134


title: Breast Cancer 177


title: Breast Cancer 182


title: Breast Cancer 149


title: Breast Cancer 142


title: Breast Cancer 107


title: Breast Cancer 117


title: Breast Cancer 113


title: Breast Cancer 105


title: Breast Cancer 94


title: Breast Cancer 81


title: Breast Cancer 100


title: Breast Cancer 52


title: Breast Cancer 82


title: Breast Cancer 68


title: Breast Cancer 59


title: Breast Cancer 106


title: Breast Cancer 91


title: Breast Cancer 90


title: Breast Cancer 96


title: Breast Cancer 34


title: Breast Cancer 44


title: Breast Cancer 101


title: Breast Cancer 39


title: Breast Cancer 83


title: Breast Cancer 62


title: Breast Cancer 76


title: Breast Cancer 65


title: Breast Cancer 99


title: Breast Cancer 75


title: Breast Cancer 35


title: Breast Cancer 53


title: Breast Cancer 40


title: Breast Cancer 30


title: RB31

status: Public on Jun 08 2022

city: Manchester

first: Ian

middle: Edward

last: Prise

state: Select state

address: Oxford Road

country: United Kingdom

institute: University of Manchester

data_processing:
Raw files trimmed with Trimmomatic (v0.36) using defualt settings
Timmed Fastqs aligned with STAR (v2.5.3) using default settings
Aligned reads were sorted and filtered with samtools (v1.3)
Counts were normalized and analysed with Cufflinks (v2.2.1)
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: Normalized FPKMs, .txt

source_name: CD45+ from basal cell carcinoma skin

growth_protocol: After removing subcutaneous fat tissue, skin biopsies were chopped into small pieces, and treated with collagenase 0.5 wunch unit/mL (Liberase TM, Roche Applied Science) for 3-16 hours. At complete digestion, cell suspensions were passed through 70 µm cell strainers, and spun down. Cell suspensions were stained with Fc receptor blocking solution (Human TruStain FcX™), CD45 (2D1), anti-human Lineage cocktail (CD3 (UCHT1), CD14 (HCD14), CD19 (HIB19), CD20 (2H7) and CD56 (HCD56)), CD117 (104D2), FcɛRIα (AER-37) antibodies (all from BioLegend, San Diego, CA) in FACS buffer (Phosphate-buffered saline (PBS), 1% bovine serum albumin (BSA), 2 mM EDTA) for 30 minutes at 4°C. Then cells were washed with PBS, and incubated 20 minutes with live/dead™ blue viability dye to discriminate dead cells (LIVE/DEAD™ Fixable Blue Dead Cell Stain Kit, ThermoFisher Scientific). Cells were washed, resuspended in FACS buffer, and sorted by flow cytometry using the FACS Aria cytometer. After exclusion of dead cells and doublets, CD45+Lin-CD117+ cells were gated and CD45+Lin-CD117+FcɛRIα+ cells were sorted as MCs. The rest of CD45+Lin+CD117+, CD45+Lin+CD117- and CD45+Lin-CD117-cells were sorted as CD45+ cells. 1000 MCs were collected.

extract_protocol:
From cell pellets, total RNA was extracted and cDNA synthesized using the SMART-Seq® kit (Takara Bio USA, Inc.) according to the manufacturer’s protocol
Sequencing libraries were generated using Nextera XT DNA Library Preparation Kits (Illumina, Inc.). The manufacturer’s protocol was modified to accommodate a reduced amount of starting material (100-150 pg). Adapter indices were used to multiplex the libraries, which were pooled prior to cluster generation using a cBot instrument. The loaded flow-cell was then paired-end sequenced (76 + 76 cycles, plus indices) on an Illumina HiSeq4000 instrument. Finally, the output data was demultiplexed (allowing one mismatch) and BCL-to-Fastq conversion performed using Illumina’s bcl2fastq software.

value: CD45+Cells, Excluding Mast Cells

value: Basal Cell Carcinoma Skin


title: Breast Cancer 26


title: Breast Cancer 32


title: RB30


title: RB29


title: RB25

source_name: CD45+ from melanoma skin

value: Melanoma Skin


title: Breast Cancer 19


title: Breast Cancer 27


title: Breast Cancer 18


title: Breast Cancer 28


title: RB32


title: BR46


title: Breast Cancer 17


title: BR45


title: RB27


title: BR44

source_name: CD45+ from healthy skin

value: Healthy Skin


title: BR43


title: Breast Cancer 6


title: BR47


title: RB34


title: RB35


title: RB11

source_name: Mast cells from basal cell carcinoma skin

value: Mast Cells


title: RB26


title: RB12


title: RB10


title: Breast Cancer 9


title: Breast Cancer 4


title: Breast Cancer 3


title: Breast Cancer 16


title: RB9


title: MB7


title: RB36


title: MB5


title: BCC12


title: BCC19


title: BCC11


title: BCC10


title: BCC18


title: MB11

source_name: Mast cells from melanoma skin


title: BCC14


title: RB2


title: RB4


title: BR37

source_name: Mast cells from Healthy skin


title: BR39


title: RB3


title: V16


title: V15


title: V17


title: BR38


title: MB3


title: MB4


title: MB6


title: Sample_9NO2 (B1-9NO2)

status: Public on Mar 15 2022

data_processing:
Base-calling was performed using CASAVA v.1.8.2.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh38 release 77
Supplementary_files_format_and_content: Gern1_CAK30ANXX_170214_combined_counts.csv is a comma separated value file. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.

source_name: Epithelial Cell from ALI Culture

extract_protocol:
Cell lysates were collected in 350 microliters of Buffer RLT, then transferred to Qiashredder tubes and spun 2 minutes at 14,000 rpm in microfuge.  RNA was then isolated using RNeasy Mini Kit (Qiagen #74106)
Illumina TruSeq RNA Seq v2

tag: donor

tag: treatment

value: mock

tag: timepoint


title: Sample_8NO2 (B2-8NO2)


title: Sample_962 (B1-962)

value: 6 h


title: Sample_9242 (B1-9242)


title: Sample_9241 (B1-9241)


title: Sample_8NO1 (B2-8NO1)


title: Sample_8242 (B2-8242)


title: Sample_9NO1 (B1-9NO1)


title: Sample_961 (B1-961)


title: Sample_0NO1 (B0-0NO1)


title: Sample_062 (B0-062)


title: Sample_862 (B2-862)


title: Sample_061 (B0-061)


title: Sample_8241 (B2-8241)


title: Sample_861 (B2-861)


title: Sample_0242 (B0-0242)


title: Sample_0NO2 (B0-0NO2)


title: Breast Cancer 114


title: SN_d1

status: Public on Mar 11 2022

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

department: Department of Medicine

country: Italy

institute: University of Verona

data_processing:
Reads were quality-filtered according the Illumina pipeline
reads were mapped onto the Ensembl human transcriptome (version 96) and quantified at the transcript level using kallisto
transcripts were combined to gene level using tximport packages
Gene counts were normalized among various samples using DESeq2
Gene abundance was indicated as FPKM, and genes with FPKM equal or higher than 1 in at least one sample were considered as expressed and further analysed
Differentially expressed genes were identified using DESeq2, by using as selection parameter an adjusted p-values (padj) lower than 0.01
Genome_build: Ensembl human transcriptome (version 96)
Supplementary_files_format_and_content: tab-delimited text files include sample specific read counts per gene in FPKM

source_name: bone marrow

extract_protocol:
Total RNA was extracted after cell lysis by the RNeasy Mini Kit (Qiagen). To completely remove any possible contaminating DNA, an on-column DNase digestion with the RNase-free DNase set (Qiagen) was performed during total RNA isolation.
Libraries for transcriptome analysis were prepared using Smart-seq2 protocol (PMID: 24056875)

value: segmented neutrophils

value: bone marrow

tag: donor id


title: Sample_0241 (B0-0241)


title: PMN_d6

source_name: blood

value: neutrophil

value: blood


title: SN_d3


title: PMN_d4


title: PMN_d7


title: BC_d3

value: band cells


title: SN_d2


title: BC_d2


title: BC_d1


title: MM_d3

value: metamyelocytes


title: MM_d2


title: MY_d3

value: myelocytes


title: MY_d2


title: MY_d1


title: PM_d2

value: promyelocytes


title: NCP4_d2

value: neutrophil-committed progenitors 4 (NCP4s)


title: NCP4_d3


title: PM_d3


title: PM_d1


title: NCP3_d3

value: neutrophil-committed progenitors 3 (NCP3s)


title: NCP4_d1


title: NCP3_d2


title: NCP2_d2

value: neutrophil-committed progenitors 2 (NCP2s)


title: NCP2_d3


title: NCP2_d1


title: NCP3_d1


title: NCP1_d3

value: neutrophil-committed progenitors 1 (NCP1s)


title: NCP1_d2


title: NCP1_d1


title: lib18616

status: Public on Feb 28 2022

data_processing:
Base-calling was performed automatically by Illumina real time analysis software and demultiplexing was performed on Illumina BaseSpace.
Hard trimming was performed in Galaxy; 1 3'-end base was removed from all reads using the FASTQ Trimmer tool (v1.0.0)
Quality-based trimming was performed in Galaxy; reads were trimmed from both ends using the FASTQ Quality Trimmer tool (v1.0.0) until minimum base quality for each read was >= 30.
Reads were aligned in Galaxy using TopHat (Tophat for Illumina tool, v.1.5.0)
Read counts per Ensembl gene ID were determined in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: NCBIM37
Supplementary_files_format_and_content: raw_counts_P164.txt is a tab-delimited matrix. The first column ("geneName") contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library. Counts have not been filtered or normalized.

source_name: hyperoxic Ly6C lo cells

extract_protocol:
Mononuclear cells of the indicated subtypes were sorted directly into 10ul Smart-Seq (V4) lysis buffer (Clontech).
Following sorting of cells into Smart-Seq (V4) lysis buffer to prepare amplified cDNA, Illumina NexteraXT libraries were prepared following manufacturer's instructions (Illumina).

treatment_protocol: Newborn pups were randomly assigned to the hyperoxic or normoxic (control) condition.

value: lung

tag: strain

tag: developmental stage

value: neonate

tag: litter number

value: Litter 108

value: Ly6C lo

tag: oxygenation


title: lib18613

source_name: hyperoxic dc cells

tag: tissue

tag: cell type

value: dc


title: lib18614

source_name: hyperoxic am cells

value: am


title: lib18612


title: MM_d1

value: bone marrow


title: lib18610


title: lib18611

source_name: hyperoxic Ly6C hi cells

value: Ly6C hi


title: lib18609


title: lib18608

source_name: normoxic Ly6C hi cells

value: ra


title: lib18607

source_name: normoxic am cells


title: lib18604


title: lib18605

source_name: normoxic Ly6C lo cells


title: lib18601

value: Litter 100


title: lib18602

source_name: normoxic dc cells


title: lib18599


title: lib18606


title: lib18600


title: lib18603


title: lib18596


title: lib18615


title: HSC_d3

value: hematopoietic stem/multipotent progenitor (HSCs/MPPs)   cells


title: lib18591


title: lib18592


title: lib18595


title: lib18597


title: lib18593


title: lib18594


title: lib18589

value: Litter 93


title: lib18588


title: lib18585


title: lib18587


title: lib18584


title: lib18581


title: lib18590


title: lib18579


title: lib18580


title: lib18598


title: lib18583


title: lib18578


title: lib18575


title: lib18576


title: P0L1camS2

status: Public on Feb 01 2022

city: Berkeley

first: Karthik

last: Shekhar

address: 101D Gilman Hall

institute: University of California, Berkeley

data_processing:
Sample demultiplexing for each sample mkfastq function from Cell Ranger software(version 2.1.0, 10X Genomics)
Sample alignment to the mouse reference transcriptome (GRCm38) using “cellranger count” with default parameters to obtain a digital gene expression (DGE) matrix (genes x cells) summarizing transcript counts.
Genome_build: GRCm38
Supplementary_files_format_and_content: Csv files including gene expression matrix from all larval samples and all adult samples

source_name: Mouse retina

growth_protocol: Mice were maintained in pathogen-free facilities under standard housing conditions with continuous access to food and water. Animals used in this study include both males and females.

extract_protocol:
Cells from E13, E14, E16, and P0 were incubated for 15 minutes at room temperature with antibodies to Thy1 (also known as CD90) and L1CAM pre-conjugated to the fluorophores APC (ThermoFisher Scientific\#17-0902-82) and PE (Miltenyi Biotec #130-102-243), respectively. Cells were washed with 6ml of  Ames + 4\% BSA, spun down and resuspended at a concentration of $\sim$7 million cells/ml, and calcein blue was added to label metabolically active cells.\\      Viable Thy1 or L1CAM positive cells were sorted using a MoFlo Astrios sorter into $\sim$100$\mu$l of AMES + 4\% BSA.  Sorted cells were spun down a final time and resuspended in PBS + 0.1\% BSA at a concentration of 500-2000 cells/$\mu$l. P5 RGCs were enriched using only CD90, with either magnetic-activated cell sorting (MACS) using large cell columns and CD90 pre-conjugated to microbeads (\#130-042-202 and \#130-049-101, Miltenyi Biotec), fluorescence activated cell sorting (FACS)  with CD90 pre-conjugated to PE/Cy7 (ThermoFisher Scientific \#25-0902-81), or both.
Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of ~30,000 reads per cell.

treatment_protocol: RGCs were enriched from dissociated retinal cells as previously described with minor modifications (Tran et al., 2019)

tag: development stage


title: lib18577


title: P0Cd90S2


title: P0L1camS1


title: E16L1camS2


title: E16L1camS1


title: E16Cd90S2


title: P0Cd90S1


title: E16Cd90S1


title: lib18582


title: E14L1camS2


title: E14L1camS1


title: E14Cd90S2


title: E13L1camS1


title: E14Cd90S1


title: lib18574


title: E13Cd90S1


title: C2PL6V1

status: Public on Jan 02 2022

hyb_protocol: 750 ng of amplified labeled RNA were hybridized overnight to Illumina HT12 V4 beadchips (Illumina, San Diego, CA)

scan_protocol: Following hybridization each chip was washed, blocked, stained, and scanned on an Illumina BeadStation 500 following the manufacturer’s protocols.

data_processing: Illumina GenomeStudio software was used for each sample to subtract background and scale average signal intensity to the global average signal intensity for all samples.

source_name: Whole Blood

label_protocol: 250 ng of RNA from all samples passing quality control were then amplified and labeled using the Illumina TotalPrep-96 RNA amplification kit (Ambion, Austin, TX)

extract_protocol: RNA was isolated using the MagMAX™-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer's instructions

tag: group

value: SLE

tag: sle group 1 2 3

tag: collection date

tag: condition

value: SLE-SevereFlare

tag: years since dx

tag: age

tag: gender

value: F

tag: race

value: Caucasian

tag: country of origin

value: North Africa

tag: sledai

tag: skin

value: N

tag: joints

tag: hemato

tag: renal

value: Y

tag: kidney biopsy

tag: class kb

value: IV

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: neutro percent

tag: lympho

tag: lympho percent

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: acuterenfail

tag: chronickd


title: C2PL42V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

value: M

tag: race

value: Asian

tag: country of origin

value: Vietnam

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: class kb

value: III + V

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: 24h proteinuria

tag: haematuria

tag: leukocyturia

tag: uriry casts

tag: protid

tag: albumin

tag: nephrotic sd

tag: crp

tag: ldh


title: C1PL14V2

tag: group

tag: collection date

tag: condition

value: SLE-mildModerateFlare

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: neutro

tag: neutro percent

tag: lympho

tag: lympho percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: acuterenfail

tag: chronickd


title: C2PL19V3

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: 24h proteinuria

tag: haematuria


title: C2PL3V2

tag: group

tag: collection date

tag: condition

value: SLE-NoFlare

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

value: France

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: neutro

tag: neutro percent

tag: lympho

tag: lympho percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: acuterenfail

tag: chronickd


title: C1PL4V1

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

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tag: kidney biopsy

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tag: cyp

tag: aza

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tag: nsaid

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: 24h proteinuria

tag: haematuria


title: C2PL34V2

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: neutro

tag: neutro percent

tag: lympho

tag: lympho percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: acuterenfail

tag: chronickd


title: C2PL15V2

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

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tag: nsaid

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: 24h proteinuria

tag: haematuria


title: C2PL23V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

value: Chi

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: neutro

tag: neutro percent

tag: lympho

tag: lympho percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: acuterenfail

tag: chronickd


title: C1PL11V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

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tag: hemato

tag: renal

tag: kidney biopsy

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tag: cyp

tag: aza

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tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: 24h proteinuria


title: C2PL7V2

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

value: Black

tag: country of origin

value: Comorres

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: neutro

tag: neutro percent

tag: lympho

tag: lympho percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: acuterenfail

tag: chronickd

tag: haematuria


title: C2PL7V3

tag: group

value: SLE

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: 24h proteinuria


title: C1PL11V3

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: neutro

tag: neutro percent

tag: lympho

tag: lympho percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: acuterenfail

tag: chronickd

tag: haematuria

tag: leukocyturia

tag: uriry casts

tag: protid

tag: albumin

tag: nephrotic sd


title: C2PL20V4

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

value: SLE-SevereFlare

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: class kb

value: III

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: 24h proteinuria


title: C2PL2V4

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

value: F

tag: race

value: Caucasian

tag: country of origin

value: North Africa

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: assa

tag: neutro

tag: neutro percent

tag: lympho

tag: lympho percent

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: acuterenfail

tag: chronickd

tag: haematuria


title: C2PL29V2

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

value: Y

tag: joints

value: N

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: neutro percent

tag: 24h proteinuria


title: C2PL36V3

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

value: Cuba

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: lympho

tag: lympho percent

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: acuterenfail

tag: chronickd

tag: haematuria


title: C2PL11V2

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: neutro percent

tag: 24h proteinuria

tag: leukocyturia

tag: uriry casts

tag: protid

tag: albumin

tag: nephrotic sd


title: C2PL28V3

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: lympho

tag: lympho percent

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: acuterenfail

tag: chronickd

tag: haematuria


title: C1PL13V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: neutro percent

tag: 24h proteinuria


title: C2PL27V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: class kb

value: interstitial nephritis

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: lympho

tag: lympho percent

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: acuterenfail

tag: chronickd


title: C2PL38V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: class kb

value: V

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: neutro percent

tag: 24h proteinuria

tag: haematuria

tag: leukocyturia

tag: uriry casts


title: C2PL34V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: lympho

tag: lympho percent

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: acuterenfail

tag: chronickd


title: C2PL22V3

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c4

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: neutro percent

tag: 24h proteinuria

tag: haematuria

tag: leukocyturia

tag: uriry casts

tag: protid

tag: albumin

tag: nephrotic sd

tag: cholesterol

tag: apsyndrome


title: C1PL5V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

value: SLE-mildModerateFlare

tag: years since dx

tag: age

tag: gender

value: M

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: lympho

tag: lympho percent

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: acuterenfail

tag: chronickd


title: C1PL9V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

value: France

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: class kb

value: IV + V

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: neutro percent

tag: 24h proteinuria

tag: haematuria

tag: leukocyturia

tag: uriry casts


title: C2PL43V2

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: assb

tag: lympho

tag: lympho percent

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: acuterenfail

tag: chronickd


title: C2PL16V2

tag: group

tag: collection date

tag: condition

value: SLE-NoFlare

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: neutro percent

tag: 24h proteinuria

tag: haematuria


title: C2PL31V2

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: assb

tag: lympho

tag: lympho percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: acuterenfail

tag: chronickd

tag: leukocyturia

tag: uriry casts

tag: protid

tag: albumin

tag: nephrotic sd


title: C1PL12V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: neutro percent

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: 24h proteinuria


title: C2PL24V2

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: low c3

tag: low c4

tag: lympho

tag: lympho percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: acuterenfail

tag: chronickd

tag: haematuria

tag: leukocyturia

tag: uriry casts

tag: protid

tag: albumin

tag: nephrotic sd

tag: crp

tag: ldh

tag: asat

tag: alat

tag: bilirubin

tag: alk phos

tag: cholesterol

tag: apsyndrome


title: C2PL3V4

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: neutro percent

tag: lympho

tag: lympho percent

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: 24h proteinuria


title: C2PL25V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

value: Asian

tag: country of origin

value: Philippines

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: acuterenfail

tag: chronickd


title: C2PL11V3

tag: group

value: SLE

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: neutro

tag: neutro percent

tag: lympho

tag: lympho percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: 24h proteinuria

tag: haematuria

tag: leukocyturia

tag: uriry casts

tag: protid

tag: albumin

tag: nephrotic sd


title: C2PL44V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: acuterenfail

tag: chronickd


title: C2PL38V3

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: neutro

tag: neutro percent

tag: lympho

tag: lympho percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: 24h proteinuria


title: C2PL36V2

tag: group

tag: collection date

tag: condition

value: SLE-SevereFlare

tag: years since dx

tag: age

tag: gender

tag: race

value: Black

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: acuterenfail

tag: chronickd

tag: haematuria


title: C2PL18V2

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

value: F

tag: race

value: Caucasian

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: neutro

tag: neutro percent

tag: lympho

tag: lympho percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: 24h proteinuria


title: C2PL42V2

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

value: Vietnam

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

value: Y

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: acuterenfail

tag: chronickd

tag: haematuria

tag: leukocyturia

tag: uriry casts

tag: protid

tag: albumin

tag: nephrotic sd


title: C1PL8V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

value: N

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: neutro

tag: neutro percent

tag: lympho

tag: lympho percent

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: 24h proteinuria


title: C2PL15V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

value: North Africa

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: acuterenfail

tag: chronickd


title: C1PL6V2

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: neutro

tag: neutro percent

tag: lympho

tag: lympho percent

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: 24h proteinuria

tag: haematuria


title: C1PL4V2

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: acuterenfail

tag: chronickd

tag: leukocyturia

tag: uriry casts

tag: protid

tag: albumin


title: C2PL4V2

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: low c3

tag: low c4

tag: neutro percent

tag: lympho

tag: lympho percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: 24h proteinuria

tag: haematuria

tag: nephrotic sd

tag: crp

tag: ldh


title: C2PL31V3

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: a-dsdna antibodies

tag: a-dsd

tag: arnp

tag: asm

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: acuterenfail

tag: chronickd


title: C2PL6V3

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: neutro percent

tag: lympho

tag: lympho percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: 24h proteinuria

tag: haematuria

tag: leukocyturia

tag: uriry casts

tag: protid

tag: albumin

tag: nephrotic sd


title: C2PL3V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: class kb

value: III + V

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: acuterenfail

tag: chronickd


title: C2PL4V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: asm

tag: assa

tag: assb

tag: neutro percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: 24h proteinuria

tag: haematuria

tag: leukocyturia

tag: uriry casts

tag: protid

tag: albumin

tag: nephrotic sd


title: C1PL15V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

value: SLE-mildModerateFlare

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: lympho

tag: lympho percent

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: acuterenfail

tag: chronickd


title: C2PL31V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: class kb

value: V

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: neutro percent

tag: eosino

tag: eosino percent

tag: serum creatinin


title: C1PL13V2

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: lympho

tag: lympho percent

tag: acuterenfail

tag: chronickd

tag: 24h proteinuria

tag: haematuria

tag: leukocyturia

tag: uriry casts

tag: protid

tag: nephrotic sd


title: C1PL10V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: neutro percent

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: eosino

tag: eosino percent

tag: serum creatinin


title: lib18586

tag: tissue

value: lung

tag: strain

tag: developmental stage

value: neonate

tag: litter number

value: Litter 93

tag: cell type

value: dc

tag: oxygenation


title: C2PL1V2

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

value: France

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: neutro percent

tag: lympho

tag: lympho percent

tag: acuterenfail

tag: chronickd

tag: 24h proteinuria

tag: haematuria

tag: leukocyturia

tag: uriry casts

tag: protid

tag: albumin

tag: nephrotic sd


title: C2PL22V2

tag: group

value: SLE

tag: sle group 1 2 3

tag: collection date

tag: condition

value: SLE-NoFlare

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: eosino

tag: eosino percent

tag: serum creatinin


title: C2PL37V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

value: SLE-SevereFlare

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: class kb

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: neutro percent

tag: lympho

tag: lympho percent

tag: acuterenfail

tag: chronickd

tag: 24h proteinuria

tag: haematuria

tag: leukocyturia

tag: uriry casts


title: C2PL7V1

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

value: F

tag: race

value: Black

tag: country of origin

value: Comorres

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: asm

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: eosino

tag: eosino percent

tag: serum creatinin


title: C2PL32V2

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

value: Caucasian

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

value: Y

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: low c3

tag: low c4

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: neutro percent

tag: lympho

tag: lympho percent

tag: acuterenfail

tag: chronickd

tag: 24h proteinuria

tag: haematuria

tag: leukocyturia

tag: uriry casts

tag: protid

tag: albumin

tag: nephrotic sd

tag: crp

tag: ldh

tag: asat

tag: alat

tag: bilirubin

tag: alk phos

tag: cholesterol

tag: apsyndrome


title: C2PL32V5

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

value: North Africa

tag: sledai

tag: skin

value: N

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: neutro percent

tag: lympho

tag: lympho percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: acuterenfail


title: C1PL3V2

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

value: SLE-mildModerateFlare

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: cd4 tcells

tag: cd4 percent

tag: cd8 t cells

tag: cd8 percent

tag: b cells

tag: b cell percent

tag: nk cells

tag: nk cell percent

tag: chronickd

tag: 24h proteinuria


title: C2PL18V1

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: asm

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: neutro

tag: neutro percent

tag: lympho

tag: lympho percent

tag: eosino

tag: eosino percent

tag: serum creatinin

tag: acuterenfail

tag: haematuria


title: C2PL36V4

tag: group

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

tag: country of origin

value: Cuba

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: hcq

tag: hcq mg

tag: nsaid

tag: a-dsdna antibodies

tag: a-dsd

tag: low c3

tag: low c4

tag: arnp

tag: asm

tag: chronickd

tag: 24h proteinuria

tag: leukocyturia

tag: uriry casts

tag: protid

tag: albumin

tag: nephrotic sd


title: C2PL25V2

tag: group

tag: sle group 1 2 3

tag: collection date

tag: condition

tag: years since dx

tag: age

tag: gender

tag: race

value: Asian

tag: country of origin

value: Philippines

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: kidney biopsy

tag: class kb

value: V

tag: ever renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs daily dose

tag: cs mgkg

tag: assa

tag: assb

tag: hb below 12

tag: hb

tag: platelets

tag: leukocytes

tag: leukopenia <3000

tag: serum creatinin

tag: acuterenfail

tag: haematuria

tag: apsyndrome