title: GSU1771_Glass_rep2

description:
WTvsGSU1771_Glass.txt
gsu1771_4

value: biofilm grown on glass support in NBAF medium for 48 h at 25 oC


title: RNAseq Mutant Untreated replicate-2

status: Public on Jun 19 2023

type: SRA

city: Adelaide

first: John

last: Toubia

address: Frome Rd

country: Australia

institute: Centre for Cancer Biology

description: Immortalized fetal liver cells from βc-/-βIL-3 mice

library_source: transcriptomic

data_processing:
Reads were mapped against the mouse reference genome (mm10) using the STAR spliced alignment algorithm version 2.6.1d with default parameters and --chimSegmentMin 20, --quantMode GeneCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file of gene expression

molecule: total RNA

organism: Mus musculus

source_name: RNAseq Mutant Untreated

growth_protocol: FDH cell lines expressing wild-type IL3Ra or IL3Ra P248L and bc were grown in IMDM + 10% heat-inactivated fetal bovine serum + penicillin-streptomycin + doxycycline + mouse SCF (100 ng/ml)

extract_protocol:
RNA was extracted from 10^6 cells/condition using the Ambion mirVana miRNA isolation kit with phenol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: FDH cell lines expressing wild-type IL3Ra or IL3Ra P248L and bc were washed twice with PBS prior to plating in IMDM + 10% heat-inactivated fetal bovine serum + penicillin-streptomycin + IL-3 (100 ng/ml) and incubated for 2 or 5 days.

tag: strain

value: BALB/c

tag: strain background

tag: genotype/variation

value: bc-/- mice transduced with IL3Ra P248L and bc

tag: cell type

value: Immortalized fetal liver cells

tag: passages

value: mouse fetal liver cells from E14.5; Experiment performed for cell lines at passages 10-12


title: Rattus norvegicus_male_tibialis anterior_21 months_rep2

city: Tarrytown

first: Kun

last: Xiong

state: NY

address: 777 Old Saw Mill River Road

department: Molecular Profiling and Data Science

country: USA

institute: Regeneron Pharmaceuticals

data_processing:
Sequencing reads were processed with ArrayStudio RNA-seq pipeline to quantify gene expression levels
Assembly: B6.0
Supplementary files format and content: tab-delimited text files include raw counts for each sample

organism: Rattus norvegicus

source_name: tibialis anterior

growth_protocol: Male and female C57BL/6J mice were purchased from Jackson Laboratory (USA) at various ages and maintained at Regeneron animal holding facilities for ~12 weeks prior to tissue collection under specific pathogen free (SPF) conditions. Mice were housed in groups of 5 per cage with controlled temperature and light (22℃, 12-h light/12-h dark cycle: lights on at 0600h/lights off at 1800h) and with ad libitum access to food (PicoLab Rodent Diet 20, Lab Supply) and water. Male Sprague Dawley (SD) rats were purchased at 3-4 weeks of age from Envigo (Indianapolis, USA) and aged at Envigo under specific pathogen free (SPF) conditions. Rats were imported to New York Medical College animal holding facilities 8-12 weeks prior to tissue collection. Once imported, rats were housed two per cage at the SPF facility with controlled temperature and light (22℃, 12-h light/12-h dark cycle: lights on at 0600h/lights off at 1800h) and with ad libitum access to food (2014 Teklad Global 14% Protein diet, Envigo) and water.

extract_protocol:
Tissue collection occurred over several months and tissues from the same age group (n = 8-12 per group) were collected on the same day between 9am and 1pm. Prior to tissue collection, mice were killed by CO2 asphyxiation. Diaphragm, gastrocnemius, soleus, and tibialis anterior muscles were preserved in RNA later and stored at -80℃. RNA was extracted from tissues preserved in RNA later using MagMax-96 Total RNA isolation kit (Thermo Fisher). The RNA concentration was quantified using NanoDrop Spectrophotometer (NanoDrop Technologies) and the integrity assessed using Fragment Analyzer (Agilent).
The RNA concentration was quantified using NanoDrop Spectrophotometer (NanoDrop Technologies) and the integrity assessed using Fragment Analyzer (Agilent). Strand specific total RNA-seq libraries were prepared using Kapa RNA HyperPrep kit (Roche) with Fastselect rRNA HMR ribosome RNA removal kit (Qiagen).

tag: tissue

value: tibialis anterior

value: Sprague Dawley

tag: Sex

value: male

tag: time

value: 21 months


title: Mus musculus_male_gastrocnemius_27 months_rep6

data_processing:
Sequencing reads were processed with ArrayStudio RNA-seq pipeline to quantify gene expression levels
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: gastrocnemius

value: gastrocnemius

value: 27 months


title: GSU1771_Glass_rep1

city: Mexico

first: Leticia

last: Vega

state: Mexico

address: Circuito Ext s/n

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

description:
WTvsGSU1771_Glass.txt
gsu1771_3

data_processing:
Illumina bcl2fastq software were used for basecalling
Reads were aligned to the GCF_000007985.2/ASM798v2 genome assembly using smalt
The number of reads falling in the genes  were counted using coveragebed software and normalized with DESeq2 software
Assembly: GCF_000007985.2
Supplementary files format and content: tab-delimited text file includes the differential expression results of DESeq2 and raw and normalized counts  for each sample.

organism: Geobacter sulfurreducens

source_name: DL1 with gsu1771-deletion

growth_protocol: G. sulfurreducens biofilms grown on glass supports were grown in NBAF medium at 25 oC for 48 hours. The planktonic cells were separated from the biofilm that grew at the bottom of the culture tube. On the other hand, biofilms of G. sulfurreducens grown on graphite electrodes were separated from microbial fuel cells poised at 60 mV versus Ag/AgCl as the electron acceptor operated for 2 weeks. In the MFC, to grow G. sulfurreducens, FWAF medium was used.

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen) following the manufacturer's instructions, and residual DNA was removed by DNaseI treatment (Thermo Scientific). RNA samples were quantified using the NanoDrop 200c (Thermo Scientific) and examined with an Agilent 2100 Bioanalyzer.
cDNA libraries were constructed using the TruSeq Stranded mRNA kit (Illumina) following the manufacturer´s protocol. The cDNA libraries were purified with the Zymoclean Gel DNA Recovery Kit (Zymo Research).

treatment_protocol: The cells present in the biofilms were resuspended in 1 mL of NBAF and incubated with 100 uL of RNAlater. Cells were pelleted by centrifugation and frozen at -70 oC until use.

value: bacterial cell

tag: genotype

tag: treatment


title: Mus musculus_male_gastrocnemius_27 months_rep5


title: Chronic Beryllium Disease 2

type: genomic

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado - Anschutz Medical Campus

hyb_protocol: per Manufacturer Instructions

scan_protocol: per Manufacturer Instructions

data_processing: .idat files were processed using default parameters in the sesame R package.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Bronchoalveolar lavage cells from: Chronic Beryllium Disease 2

label_protocol: per Manufacturer Instructions

growth_protocol: Cells were stored in RLT buffer at –80°C

extract_protocol: genomic DNA and RNA were extracted using Qiagen AllPrep DNA/RNA extraction mini kit

tag: diagnosis

value: CBD

value: M

tag: age

tag: race

value: White

tag: hispanic

value: No

tag: smoker

value: Never

tag: tlc

tag: fvc

tag: dlco

tag: white_blood_cell_count (x 10^6)

tag: slide

tag: array


title: RNAseq Mutant Untreated replicate-1

tag: strain

tag: strain background

tag: genotype/variation

tag: cell type

tag: passages


title: Rattus norvegicus_male_tibialis anterior_21 months_rep12

tag: tissue

tag: Sex

tag: time


title: RNAseq Wild Type IL-3 Treated Day5 replicate-3

source_name: RNAseq Wild Type IL-3 Treated Day5

value: bc-/- mice transduced with wild-type IL3Ra and bc


title: WT_Glass_rep1

description:
WTvsGSU1771_Glass.txt
WT_1

source_name: DL1 wild-type strain

tag: genotype

value: Wild type

tag: treatment

value: biofilm grown on glass support in NBAF medium for 48 h at 25 oC


title: WT_Glass_rep2

description:
WTvsGSU1771_Glass.txt
WT_2


title: RNAseq Wild Type IL-3 Treated Day5 replicate-2

value: BALB/c

value: Immortalized fetal liver cells


title: Mus musculus_male_gastrocnemius_27 months_rep7


title: Rattus norvegicus_male_tibialis anterior_21 months_rep10

value: tibialis anterior


title: Mus musculus_male_gastrocnemius_27 months_rep3


title: Mus musculus_male_gastrocnemius_27 months_rep4


title: Mus musculus_male_gastrocnemius_27 months_rep2


title: PP13A08B low dose IV BCG wk12

city: Stanford

first: Yiran

middle: E

last: Liu

state: CA

address: 291 Campus Drive

institute: Stanford University

data_processing:
We trimmed reads with Cutadapt and performed quality control checks with FastQC before aligning to the Macaca mulatta genome (mmul_10) using kallisto. We removed genes in the globin family, genes that were unannotated, and genes with fewer than 5 reads in over two-thirds of all samples. We applied DESeq2’s variance stabilizing transformation to generate normalized expression values.
Assembly: mmul10
Supplementary files format and content: Tab-delimited text file containing a matrix with normalized expression values for all samples

organism: Macaca mulatta

source_name: Whole Blood

extract_protocol:
Whole blood was collected in PAXgene blood RNA tubes (Qiagen) and stored at -80C for batch processing at end of study. RNA was extracted using the PAXgene Blood RNA Tube kit (PreAnalytiX) as instructed. Globin mRNA was removed using GLOBINclear Kit (Life Technologies) and remaining mRNA concentration and quality was measured on an Agilent Bioanalyzer using an Agilent nano 6000 kit.
Illumina-ready libraries were generated using NEBNext Ultra II RNA Preparation reagents (New England BioLabs).

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: low

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

value: tntc

tag: log grans_nx

tag: protect outcome


title: Rattus norvegicus_male_tibialis anterior_21 months_rep1

tag: strain

value: Sprague Dawley

value: male

value: 21 months


title: PP13A08B low dose IV BCG wk4


title: RNAseq Wild Type IL-3 Treated Day5 replicate-1

tag: strain background

tag: genotype/variation

tag: cell type

tag: passages

value: mouse fetal liver cells from E14.5; Experiment performed for cell lines at passages 10-12


title: RNAseq Wild Type IL-3 Treated Day2 replicate-3

source_name: RNAseq Wild Type IL-3 Treated Day2


title: Mus musculus_male_gastrocnemius_27 months_rep1

tag: tissue

value: gastrocnemius

tag: Sex

tag: time

value: 27 months


title: PP13A08B low dose IV BCG wk2

tag: animal id

tag: pitt id


title: RNAseq Wild Type IL-3 Treated Day2 replicate-2


title: Mus musculus_male_gastrocnemius_27 months_rep0


title: Rattus norvegicus_male_tibialis anterior_21 months_rep0


title: PP13A08B low dose IV BCG d2

tag: bcg dose_log10

tag: dose group


title: RNAseq Wild Type IL-3 Treated Day2 replicate-1


title: Mus musculus_male_gastrocnemius_24 months_rep9

value: 24 months


title: OBC high dose IV BCG wk12

value: OBC

value: high

tag: timeafterbcg

tag: total mtb_cfu

value: protected


title: Rattus norvegicus_male_tibialis anterior_18 months_rep8

value: 18 months


title: Rattus norvegicus_male_tibialis anterior_21 months_rep11


title: RNAseq Wild Type Untreated replicate-3

source_name: RNAseq Wild Type Untreated

value: BALB/c

value: bc-/- mice transduced with wild-type IL3Ra and bc


title: Mus musculus_male_gastrocnemius_24 months_rep8


title: RNAseq Wild Type Untreated replicate-2

value: Immortalized fetal liver cells


title: Mus musculus_male_gastrocnemius_24 months_rep7


title: OBC high dose IV BCG wk4

value: Whole Blood

tag: log mtb_cfu

tag: grans nx


title: OBC high dose IV BCG d2

tag: log grans_nx

tag: protect outcome


title: Mus musculus_male_gastrocnemius_24 months_rep6

tag: strain


title: Rattus norvegicus_male_tibialis anterior_18 months_rep5

value: tibialis anterior


title: Rattus norvegicus_male_tibialis anterior_18 months_rep7


title: RNAseq Wild Type Untreated replicate-1

tag: strain background

tag: genotype/variation


title: Mus musculus_male_gastrocnemius_24 months_rep5


title: Rattus norvegicus_male_tibialis anterior_18 months_rep6


title: OBC high dose IV BCG pre

value: pre


title: Rattus norvegicus_male_tibialis anterior_18 months_rep9

value: Sprague Dawley


title: Mus musculus_male_gastrocnemius_24 months_rep4

value: male


title: Flies, Double mutant , Rep3

city: Bethesda

first: Richard

last: Youle

state: MD

address: 35 Convent Drive, 2C917

department: Surgical Neurology Branch

institute: National Institute of Neurological Disorders and Stroke, NIH

description: in "merged_gene_counts.txt" Column 11

data_processing:
Seq pipeline was originally adapted from nf-core/rnaseq pipeline v1.4.2 (https://github.com/nf-core/rnaseq).
Quality control of reads performed with FastQC v0.11.9
Adapter and low-quality sequences were trimmed from raw reads using Trim Galore! v0.6.6
Trimmed reads were aligned to the reference genome using STAR v2.6.1d
BAM file filtering and indexing was carried out using SAMtools v1.9
RNAseq library quality control was implemented using RSeQC v4.0. and QualiMap v2.2.2-dev
Duplicate reads were marked using Picard tools v2.23.9
Library complexity was estimated using Preseq v2.0.3
Duplication rate quality control was performed using dupRadar v1.18.0
Reads were assigned to genes using featureCounts v2.0.1
Quality control and analysis results plots were visualized using MultiQC v1.9
Differential gene expression analysis was completed using DESeq2 v1.28.0  DESeq2 v1.28.0 ; DESeq2 FDR cutoff 0.05; DESeq2 Log2FC cutoff 0.585
Assembly: BDGP6 (GCA_000001215.4)
Supplementary files format and content: "merged_gene_counts.txt" ; matrix file containing raw read counts. Columns are indicated above
Supplementary files format and content: "zr6381_AM_Processed Data.xlsx" : Contains normalized read counts for all samples as well as the results of DESeq2 analyses on multiple spreadsheet pages: 1: "Normalized Counts", 2: "DESeq  WT vs Park",  3: "DESeq  WT vs Sting",  4: "DESeq  WT vs Double",  5: "DESeq  Sting vs Double",  6: "DESeq  Park vs Double",

organism: Drosophila melanogaster

source_name: Entire fly lysate - 10 flies

growth_protocol: Flies were raised in identifcal conditions (25°C normal L:D cycle) for 4 days following eclosion

extract_protocol:
Direct-zol RNA Miniprep kit (Zymo Research P/N R2050), with DNAseI on column treatment
Zymo-Seq RiboFree Total RNA Library Kit- After extraction, all steps, including ribosomal RNA depletion, were performed by Zymo Research Services, using their Total-RNA-Seq protocol

value: Entire fly lysate - 10 flies

tag: age

value: 4-5 days p. eclosion

tag: developmental stage

value: Adult

tag: genotype

value: sting[delta-RG5]; park[25]


title: Flies, Double mutant , Rep2

description: in "merged_gene_counts.txt" Column 6

tag: tissue

tag: Sex


title: Rattus norvegicus_male_tibialis anterior_18 months_rep3

tag: time


title: Flies, Double mutant , Rep1

description: in "merged_gene_counts.txt" Column 8


title: Mus musculus_male_gastrocnemius_24 months_rep3

value: gastrocnemius

value: 24 months


title: O1K high dose IV BCG wk12

tag: animal id

tag: pitt id

tag: bcg dose_log10

value: high


title: O1K high dose IV BCG wk4

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

value: protected


title: Mus musculus_male_gastrocnemius_24 months_rep2


title: Rattus norvegicus_male_tibialis anterior_18 months_rep11

value: 18 months


title: Rattus norvegicus_male_tibialis anterior_18 months_rep2


title: OBC high dose IV BCG wk2

value: OBC

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx


title: O1K high dose IV BCG wk2

tag: protect outcome


title: Flies, sting , Rep2

description: in "merged_gene_counts.txt" Column 10


title: Flies, sting , Rep1

description: in "merged_gene_counts.txt" Column 5


title: Rattus norvegicus_male_tibialis anterior_18 months_rep4

tag: strain


title: Flies, park , Rep3

description: in "merged_gene_counts.txt" Column 7

tag: age


title: ARS2 3'UTR siRNA - TET treated - rep1

city: Aarhus

first: Jerome

middle: O

last: Rouviere

address: Universitetsbyen 81

country: Denmark

institute: Aarhus University

data_processing:
Raw sequence reads from RNA-seq experiments quality checked using FastQC (Babraham Bioinformatics group).
Reads were then trimmed for adaptors and filtered using Trim Galore (Babraham Bioinformatics group).
Trimmed reads were mapped to Hg38, using Hisat2 (Kim et al., 2019) in paired-end mode.
Mapped files were sorted and checked for pairing using Samtools (Danecek et al., 2021).
Reads were then deduplicated using MarkDuplicates (Picard – Broad Institute) and further filtered to keep only unique mappers by using Samtools (Danecek et al., 2021).
Finally, reads were converted to bigwig (bw) files normalized to library sizes (Reads per Millions) using bamCoverage (Deeptools – Ramirez et al., 2016). A binning of 5 was used.
An additional set of bw tracks, normalized to size factors is also provided. These data were processed identically, but the normalization factor used for bw files generation with bamCoverage is a size factor calculated with DEseq2 (Love et al., 2014) based on counts measured on mapped data using HTSeq-counts (Putri et al., 2022)
Assembly: Hg38
Supplementary files format and content: stranded bigwig (bw) files

source_name: cervix

growth_protocol: HeLa cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
RNA was extracted using TRIzol (Ambion) and then further treated with TURBO DNAse (Ambion), according to manufacturer’s recommendations
Library construction and sequencing was a paid service from the Beijing Genome Institute (BGI) which performed rRNA depletion followed by strand-specific library preparation and PE100 sequencing on DNBSEQ equipment

treatment_protocol: Two rounds of transfections were performed. The first transfections were performed using SilentFect (final dilution 1:1000) in RPMI 1640 medium. One day after transfection, cells were mock treated or transfected using Lipofectamine 3000 with a plasmid expressing ARS2 WT or ZnF-mut under TET promoter. Two days after the first transfection, the media was changed, and the siRNA transfection was repeated using Lipofectamine 3000 (final dilution 1:1000) in RPMI 1640 medium. siRNAs were used at a final concentration of 15 nM of each siRNA. 4h after the second round of siRNA transfection, cells were treated with Tetracycline (sigma) at a final concentration of 250ng/ml. 24 hours after the second round of transfections, cells were harvested.

value: cervix

tag: cell line

value: HeLa Kyoto

tag: cell type

value: epithelial

tag: treatment

value: ARS2 3'UTR siRNA - TET 250 ng/ml for 18-20h


title: O1K high dose IV BCG pre

tag: tissue

value: Whole Blood

value: pre


title: Rattus norvegicus_male_tibialis anterior_18 months_rep1

value: tibialis anterior

value: Sprague Dawley

tag: Sex

value: male

tag: time


title: Flies, park , Rep2

description: in "merged_gene_counts.txt" Column 9

value: Entire fly lysate - 10 flies

value: 4-5 days p. eclosion

tag: developmental stage

value: Adult

tag: genotype


title: Mus musculus_male_gastrocnemius_24 months_rep0

value: gastrocnemius

value: 24 months


title: Mus musculus_male_gastrocnemius_21 months_rep7

value: 21 months


title: Mus musculus_male_gastrocnemius_24 months_rep1


title: Rattus norvegicus_male_tibialis anterior_18 months_rep10

value: 18 months


title: Rattus norvegicus_male_tibialis anterior_12 months_rep9

value: 12 months


title: Mus musculus_male_gastrocnemius_21 months_rep6


title: HCZ low dose IV BCG wk12

tag: animal id

value: HCZ

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: low


title: HCZ low dose IV BCG wk4

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: Rattus norvegicus_male_tibialis anterior_18 months_rep0

tag: strain


title: Flies, wild-type , Rep3

description: in "merged_gene_counts.txt" Column 12

tag: age


title: Flies, park , Rep1

description: in "merged_gene_counts.txt" Column 4


title: O1K high dose IV BCG d2

value: high

tag: log grans_nx

tag: protect outcome

value: protected


title: Mus musculus_male_gastrocnemius_21 months_rep5

tag: tissue


title: Flies, wild-type , Rep2

description: in "merged_gene_counts.txt" Column 14

tag: Sex


title: Mus musculus_male_gastrocnemius_21 months_rep4

tag: time


title: Rattus norvegicus_male_tibialis anterior_12 months_rep7


title: HCZ low dose IV BCG d2

value: Whole Blood


title: HCZ low dose IV BCG wk2


title: Rattus norvegicus_male_tibialis anterior_12 months_rep8


title: Mus musculus_male_gastrocnemius_21 months_rep3


title: Rattus norvegicus_male_tibialis anterior_12 months_rep6


title: HCZ low dose IV BCG pre

value: pre


title: HAR low dose IV BCG wk12

value: HAR


title: Mus musculus_male_gastrocnemius_21 months_rep2


title: Rattus norvegicus_male_tibialis anterior_12 months_rep5

value: tibialis anterior

value: Sprague Dawley


title: HAR low dose IV BCG wk4


title: Rattus norvegicus_male_tibialis anterior_12 months_rep4

value: male


title: Mus musculus_male_gastrocnemius_21 months_rep1


title: Rattus norvegicus_male_tibialis anterior_12 months_rep2


title: HAR low dose IV BCG wk2


title: Rattus norvegicus_male_tibialis anterior_12 months_rep3


title: Mus musculus_male_gastrocnemius_18 months_rep6


title: Flies, wild-type , Rep1

description: in "merged_gene_counts.txt" Column 13

value: Entire fly lysate - 10 flies

value: 4-5 days p. eclosion

tag: developmental stage


title: HAR low dose IV BCG pre


title: Rattus norvegicus_male_tibialis anterior_12 months_rep11


title: TCF4_ihtc-03_input

city: nanjing

first: yuanyuan

last: wang

address: 818 Tianyuan E Rd, Nanjing, JIANGSU

country: China

institute: nanjing medical university

library_source: genomic

data_processing:
The sequencing of precipitated DNA of hMGEOs using Illumina Hiseq X-10 (2X150). Sequenced reads were mapped to the human genome (hg38) using BWA software (version 0.7.5a-r405). Only the uniquely mapped reads were retained for further analyses. Peak calling for TCF4 in ihtc-03 was carried out using PeakSeq (version v.1.1, with options "target_FDR 0.05, max_Qvalue 0.05") on the TCF4 ChIP file against the input file and further retains the peak with input reads ≥ 5 as the significant enrichment peak. Genome-wide signal coverage tracks were computed using DeepTools (version 3.3.0, bamCoverage), and visualized in the Integrative Genome Browser (IGV, version 2.8.0).
Assembly: hg38
Supplementary files format and content: bed (ChIP-Seq peak file)

growth_protocol: Stem cells were detached by dispase (Life Technologies) to form embryoid bodies (EB) and then cultured in the neural induction medium (NIM), containing 490 mL DMEM/F12 medium, 5 mL of minimum essential medium non-essential amino acids (MEM-NEAA) (Gibco), 5 mL of N2 supplement (Gibco) for 7 days. Half the NIM medium were changed out every day from day 1 to day 6. After floating for 7 days, EBs were attached on vitronectin coated surfaces. Rosette structures could be formed during the period from day 10 to day 15. Half the NIM medium were changed out every other day from day 10 to day 15. On day 16, neuroepithelial containing rosette clones were detached and neuroepithelial cells gradually formed neurospheres. Neurospheres were continuously floated in NIM, and changed half the NIM medium every other day. For ventral differentiation, 500 nmol/L smoothened agonist (SAG, Millipore, Germany) was added from day 10 to day 40. From day 0 to day 10, BMP inhibitor DMH1 (Tocris Bioscience, UK) and TGF-β inhibitor SB431542 (StemGent, Cat.No.04-0010) were added. Properly developed neurospheres were collected on day 40 for follow-up ChIP experiments.

extract_protocol:
ChIP assay was conducted on hMGEOs derived from ihtc-03 cell lines. According to the manufacturer's instructions, libraries of ChIP DNA were prepared using the ChIP Kit (Millipore, Lot No. 17-10086). ChIP assay was performed using anti-TCF4 antibody (Santa Cruz Biotechnology, USA, Lot No. sc-393407X; dilution 1:1000) .  We followed ENCODE guidelines for anti-TCF4 antibody validation.
Library construction were performed by Annoroad genomic company (China).

tag: cell line

tag: chip antibody


title: Mus musculus_male_gastrocnemius_18 months_rep5

value: gastrocnemius


title: Rattus norvegicus_male_tibialis anterior_12 months_rep10


title: TCF4_ihtc-03_CHIPSeq

value: TCF4 (Santa Cruz Biotechnology, #sc-393407X)


title: DGLF low dose IV BCG wk12

tag: animal id

value: DGLF

tag: pitt id


title: HAR low dose IV BCG d2

tag: bcg dose_log10

tag: dose group


title: S48.SLE.BM4.X8

city: Melbourne

first: Katherine

last: Monaghan

state: Victoria

address: 30 Flemington Rd, Parkville

department: Research and Development

institute: CSL Limited

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 2.17.1.14 pipeline was used to generate the sequence data.
Sequenced reads were mapped to human reference genome GRCh38.p12 using star (v2.6.1)13 with default parameters except for the --quantMode TranscriptomeSAM setting.
Reads were summarized at the gene level using featureCounts tool from the Subread package (v1.6.4)14, in a strand-specific manner.

source_name: Blood

extract_protocol:
RNA extraction was done with Qiagen RNeasy plus mini kit (Cat#74134/74136)
-RNA was extracted in batched as cell pellets from each group of donors were frozen together in 96 well plates
-The plates were removed from the freezer at thawed at 4°C (approx. 1 hour) and stored at 4°C for the day while different wells had RNA extracted
-The cell pellets in 125 μl RNAprotect were mixed up and down and moved into 1.5 ml microfuge tube (eppendorf). -Cells were pelleted by centrifuging for 5 mins at 5000 x g.
-The SN was then aspirated
-RNA was then extracted using the manufacturer’s instructions from step 2, Briefly-
-The pellets were loosened by flicking
-Cells were then disrupted with RLT plus buffer by adding 350 μl RLT plus buffer and vortexing to mix.
-Cells were then homogenised by pipetting sample on a QIAshredder column and centrifuging 2 mins at full speed -The lysate was transferred to a gDNA eliminator spin column and centrifuge for 30s at 10,000 x g, collect flow through (can repeat spin if membrane has any remaining liquid)
-350 μl 70% ethanol was added and mixed well by pipetting (adjust volume if ethanol if some lysate lost in previous steps)
-Sample and any precipitate was transferred to a RNeasy spin column, close the lid gently and centrifuge for 15 sec at 10,000 x g, discard flow through
-700 μl buffer RW1 was added to the column, close the lid gently and centrifuge for 15 sec at 10,000 x g, flow through discarded
-500 μl buffer RPE was added to the column, close the lid gently and centrifuge for 15 sec at 10,000 x g, flow through discarded
-500 μl buffer RPE was added to the column, close the lid gently and centrifuge for 2 mins at 10,000 x g, collection tube and flow through discarded
-Column placed in new 2 ml collection tube, lid of spin column opened, spin at full speed for 5 mins, collection tube and flow through discarded
-RNeasy spin column placed in a new 1.5 ml collection tube, 30 μl RNase free water (warmed to 55°C) was added directly to the centre of the spin column and incubated for 10 mins, then centrifuged for 1 min at 16,000 x g
-An additional 10 μl RNase free water was added, then centrifuged for 1 min at 16,000 x g – approx. 35 μl will be eluted for potential RNAseq
-Eluted RNA was immediately stored at -80°C and shipped for sequencing for RNAseq frozen on dry ice
RNA libraries were prepared for sequencing using standard Illumina protocols for polyA extraction for samples from stimulated cells.

value: Blood

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

value: SLE

tag: gender

value: F

tag: diagnosis

tag: ethnicity

value: Caucasian

tag: sledai

tag: drug

tag: stimulus

tag: stimdescription

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: S48.SLE.BM4.X7

tag: tissue

tag: age

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: S48.SLE.BM4.X5

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: S48.SLE.BM4.X6

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: S48.SLE.BM4.X9

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_male_gastrocnemius_18 months_rep4

tag: strain

tag: Sex

tag: time

value: 18 months


title: Rattus norvegicus_male_tibialis anterior_12 months_rep1

value: tibialis anterior

value: Sprague Dawley

value: male

value: 12 months


title: Mus musculus_male_gastrocnemius_18 months_rep3

value: gastrocnemius


title: Mus musculus_male_gastrocnemius_21 months_rep0

value: 21 months


title: Rattus norvegicus_male_tibialis anterior_12 months_rep0


title: DGLF low dose IV BCG wk2

value: Whole Blood

tag: animal id

value: DGLF

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: low

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome

value: protected


title: S48.SLE.BM4.X3

value: Blood

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

value: SLE

tag: gender

value: F

tag: diagnosis

tag: ethnicity

value: Caucasian

tag: sledai

tag: drug

tag: stimulus

value: 10% SLE patient #4 sera


title: Arabidopsis normal 6mA IP rep1

city: Fuzhou

first: mao

last: fei

state: Fujian

address: Shangxiadianlu NO.15

department: National Engineering Research Center of JUNCAO

institute: Fujian Agriculture and Forestry University

data_processing:
The reads of raw data were trimmed according to adapt sequence using cutadapt (v1.1) . then the clean data were mapped to Arabidopsis genome (TAIR10) using bowtie, the parameter of maximum insert size was reset to 1000. Only unique reads were used to detect 6mA enrichment region by SCIER (v1.1) (using parameters redundancy threshold = 1 window size (bp) = 200 fragment size = 100 effective genome fraction = 0.74 gap size (bp) = 200 FDR = 0.01). Overlapping peaks (at least 1 bp overlap) between 2 biological replicates of a sample were retained for next analyses. DESeq2 (1.24.0) [41] was used to compare all 6mA region from normal and cold stress with the consideration of sample variation. Differential regions with p value < 0.05 (false discovery rate<0.05) were considered significant (DMRs)
The sequencing data were mapped to the Arabidopsis genome with matching annotation by tophat (v2.1.1)]using default parameters. The expression value (FPKM) of each gene were calculated with cufflinks (v2.1.1). And cuffdiff (v2.1.1) was used to calculate the fold change of gene expression and FDR. Differential expression genes (DEGs) with false discovery rate < 0.05 were considered significant.
Assembly: Arabidopsis genome (TAIR10)  Rice (Tigr7)
Supplementary files format and content: Processed data were stored in bigWig files and xlsx files.

organism: Arabidopsis

source_name: leaves

growth_protocol: Arabidopsis thaliana Col-0 was grown in a growth chamber at 22℃ under long day conditions (16 h light/8 h dark) with a light intensity of 100 µmol m-2 sec-1.Rice was grown in a growth chamber at 28°C under long-day conditions (16 h light/8 h dark) with a light intensity of 200 µmol m-2 sec-1 for 2 weeks.

extract_protocol:
gDNA of Arabidopsis and rice were extracted by using a DNAsecure Plant Kit (TIANGEN, Cat. DP320-03) according to its procedures. Isolated gDNA was sonicated into 200-400 bp with Biorupter UCD-600, followed by end repair, 3′-adenylation, and adaptor ligation according to NEB Next Ultra Ⅱ DNA Library Prep Kit for Illumina (E764S, NEB). The ligated DNA was denatured at 95°C for 10 min and chilled on ice for 10 min. 10 µl of denatured DNA was saved as input. 1µg DNA was incubated with 3 µg of anti-m6A antibody (202-003, Synaptic Systems) at 4°C for 6 h in 1×IP buffer (10 mM Tris-HCl PH 7.4, 150 mM NaCl, 0.1% IGEPAL CA-630). Dynabeads Protein A (10001D, Invitrogen) was washed twice with 1×IP buffer and pre-blocked in 0.5 ml 1×IP buffer with 20 µg/µl BSA for 2 h at 4°C. After pre-blocked beads were washed twice with 1×IP buffer, the DNA-antibody mixture was added to beads, rotating overnight at 4°C. The beads were washed 4 times with 1×IP buffer. Methylated DNA was eluted twice by 100 ml elution buffer containing N6-methyladenosine 5’-monophosphatesodium salt (M2780, Sigma) at 4°C for 1 h. Eluted DNA was combined, then added to 20ml of 3 M NaOAc (PH 5.3), 500 ml ethanol, and 0.5 ml glycogen. The mixture was frozen at -80°C overnight, and centrifuged. The precipitated DNA was dissolved in 20 ml ddH2O, followed by 8-10 cycles PCR amplification. The PCR product was purified by VAHTS DNA clean beads (N411-01, Vazyme). Sequencing was conducted by the Illumina NovaSeq6000 platform with 150-bp paired-end reads at Jiangbei New Area Biopharmaceutical Public Service Platform Co., Ltd. (Nanjing, China).
RNA-seq and 6mA-IP-seq

treatment_protocol: In arabidopsis, 3-week-old plants were transfer to 4℃ for 24 h. In rice, 2-week-old seedlings were transferred to 4°C for 6 days.

tag: tissue

value: leaves

tag: treatment

value: CK


title: Mus musculus_male_gastrocnemius_18 months_rep2

tag: strain

tag: Sex

tag: time

value: 18 months


title: DGLF low dose IV BCG d2

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx


title: Rattus norvegicus_male_soleus_9 months_rep9

source_name: soleus

value: soleus

value: Sprague Dawley

value: male

value: 9 months


title: Mus musculus_male_gastrocnemius_18 months_rep1

value: gastrocnemius


title: Rattus norvegicus_male_soleus_9 months_rep8


title: DGLF low dose IV BCG pre

value: Whole Blood

value: DGLF

value: pre

tag: protect outcome


title: Mus musculus_male_gastrocnemius_18 months_rep0


title: S48.SLE.BM4.X1

value: Blood

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

tag: stimdescription

value: Untreated and Unstimulated


title: DGJR low dose IV BCG wk12

tag: tissue

tag: animal id

value: DGJR

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: low

tag: timeafterbcg


title: Rattus norvegicus_male_soleus_9 months_rep7

tag: strain

tag: Sex

tag: time


title: S48.SLE.BM4.X13

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

value: SLE

value: F

value: Caucasian

tag: stimulus

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: DGLF low dose IV BCG wk4

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome

value: protected


title: DGJR low dose IV BCG wk4

tag: tissue

tag: animal id

tag: pitt id


title: Mus musculus_male_gastrocnemius_12 months_rep6

value: 12 months


title: Mus musculus_male_gastrocnemius_18 months_rep7

value: male

value: 18 months


title: S48.SLE.BM4.X12

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

tag: stimdescription

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: DGJR low dose IV BCG wk2

value: Whole Blood

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg


title: Rattus norvegicus_male_soleus_9 months_rep6

value: soleus

tag: strain

value: Sprague Dawley

tag: Sex

tag: time

value: 9 months


title: S48.SLE.BM4.X4

value: Blood

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: stimulus

value: 10 ug/ml LPS


title: S48.SLE.BM4.X11

tag: tissue

tag: gender

tag: diagnosis

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: Mus musculus_male_gastrocnemius_12 months_rep5

value: gastrocnemius


title: Rattus norvegicus_male_soleus_9 months_rep4


title: DGJR low dose IV BCG d2

tag: animal id

value: DGJR

tag: pitt id

value: low

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome


title: S48.SLE.BM4.X10

value: Disease

value: SLE

value: F

tag: age

tag: ethnicity

value: Caucasian

tag: sledai

tag: drug

tag: stimdescription

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_soleus_9 months_rep3

tag: strain

tag: Sex

value: male

tag: time


title: Mus musculus_male_gastrocnemius_12 months_rep4

tag: tissue

value: 12 months


title: S48.SLE.BM4.X2

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: stimulus

value: 0.25 uM CpGc


title: S48.SLE.362.X9

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_male_gastrocnemius_12 months_rep3


title: Rattus norvegicus_male_soleus_9 months_rep2

value: soleus

value: Sprague Dawley


title: Mus musculus_male_gastrocnemius_12 months_rep7


title: DGJB high dose IV BCG wk12

value: Whole Blood

tag: animal id

value: DGJB

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: high

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome

value: protected


title: S48.SLE.362.X8

tag: tissue

value: Blood

tag: donorid

tag: age

tag: ethnicity

tag: sledai

tag: drug

tag: stimdescription

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_soleus_9 months_rep11

tag: strain

tag: Sex

tag: time

value: 9 months


title: DGJB high dose IV BCG wk4

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group


title: Mus musculus_male_gastrocnemius_12 months_rep2

value: gastrocnemius


title: Rattus norvegicus_male_soleus_9 months_rep5


title: S48.SLE.362.X7

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

value: SLE

tag: gender

value: F

tag: diagnosis

tag: stimulus

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_soleus_9 months_rep10

tag: tissue

value: male


title: Mus musculus_male_gastrocnemius_12 months_rep0

value: 12 months


title: Mus musculus_male_gastrocnemius_12 months_rep1


title: S48.SLE.362.X5

tag: donorid

tag: age

tag: ethnicity

value: Caucasian

tag: sledai

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: S48.SLE.362.X6

tag: drug

tag: stimdescription

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_soleus_9 months_rep0

value: soleus

tag: strain

value: Sprague Dawley

tag: Sex

tag: time


title: Mus musculus_male_diaphragm_6 months_rep7

source_name: diaphragm

value: diaphragm

value: 6 months


title: Rattus norvegicus_male_soleus_9 months_rep1


title: DGJB high dose IV BCG d2

value: Whole Blood

tag: animal id

value: DGJB

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: high

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome

value: protected


title: S48.SLE.362.X4

tag: tissue

value: Blood

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: stimulus

value: 10 ug/ml LPS


title: DGJB high dose IV BCG pre

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: pre


title: DGJB high dose IV BCG wk2

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: Rattus norvegicus_male_soleus_6 months_rep9

tag: tissue

tag: strain

tag: Sex

value: male

tag: time


title: DGJR low dose IV BCG pre

value: DGJR

value: low

tag: log grans_nx

tag: protect outcome


title: S48.SLE.362.X3

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: SLE

tag: gender

value: F

tag: diagnosis

tag: age

value: Caucasian

tag: sledai

tag: drug

tag: stimdescription

value: 10% SLE patient #4 sera


title: DGIT low dose IV BCG wk12

tag: animal id

value: DGIT

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: Mus musculus_male_diaphragm_6 months_rep5

tag: tissue

value: diaphragm

tag: strain

tag: Sex

tag: time

value: 6 months


title: Mus musculus_male_diaphragm_6 months_rep6


title: Rattus norvegicus_male_soleus_6 months_rep8

value: soleus

value: Sprague Dawley


title: DGIT low dose IV BCG wk4

value: Whole Blood

tag: log grans_nx

tag: protect outcome


title: Rattus norvegicus_male_soleus_6 months_rep7


title: Mus musculus_male_diaphragm_6 months_rep4


title: S48.SLE.362.X2

value: Blood

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: stimulus

value: 0.25 uM CpGc


title: DGIT low dose IV BCG wk2

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: S48.SLE.362.X1

tag: tissue

tag: donorid

tag: group

value: Disease

tag: drug

tag: stimdescription

value: Untreated and Unstimulated


title: Rattus norvegicus_male_soleus_6 months_rep6

tag: strain

tag: Sex

value: male

tag: time


title: DGIT low dose IV BCG d2

tag: log grans_nx

tag: protect outcome


title: S48.SLE.362.X13

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: stimulus

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_male_diaphragm_6 months_rep3

tag: tissue


title: Mus musculus_male_diaphragm_6 months_rep2


title: Rattus norvegicus_male_soleus_6 months_rep5


title: S48.SLE.362.X12

tag: donorid

tag: group

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_soleus_6 months_rep4


title: DGHR low dose IV BCG wk12

tag: animal id

value: DGHR

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: low

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: Mus musculus_male_diaphragm_6 months_rep1

tag: strain

tag: Sex

tag: time


title: DGIT low dose IV BCG pre

value: pre

tag: log grans_nx

tag: protect outcome


title: Rattus norvegicus_male_soleus_6 months_rep3


title: DGHR low dose IV BCG wk4


title: Rattus norvegicus_male_soleus_6 months_rep2


title: Mus musculus_male_diaphragm_6 months_rep0


title: S47.SLE.BM4.X9

tag: diseasenormal

tag: diseasegroup

value: SLE

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

value: Asian

tag: sledai

tag: drug

tag: stimulus

tag: stimdescription

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_male_diaphragm_27 months_rep9

tag: tissue

value: diaphragm

value: 27 months


title: Mus musculus_male_diaphragm_27 months_rep8


title: Rattus norvegicus_male_soleus_6 months_rep11

value: soleus

value: Sprague Dawley

value: 6 months


title: DGHR low dose IV BCG wk2

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: S47.SLE.BM4.X8

value: Blood

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

tag: gender

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: DGHR low dose IV BCG pre

tag: log grans_nx

tag: protect outcome


title: Rattus norvegicus_male_soleus_6 months_rep10

tag: strain

tag: Sex

value: male

tag: time


title: S47.SLE.BM4.X7

tag: tissue

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

tag: stimulus

tag: stimdescription

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_soleus_6 months_rep1


title: DGGG low dose IV BCG wk12

tag: animal id

value: DGGG

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: low

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: S47.SLE.BM4.X6

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: SLE

tag: gender

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_male_diaphragm_27 months_rep6

tag: tissue

tag: strain

tag: Sex

tag: time


title: Mus musculus_male_diaphragm_27 months_rep5


title: S48.SLE.362.X11

value: F

tag: diagnosis

tag: age

tag: ethnicity

value: Caucasian

tag: sledai

tag: drug

tag: stimulus

tag: stimdescription

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_soleus_6 months_rep0


title: S47.SLE.BM4.X5

value: Asian

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: DGGG low dose IV BCG wk4

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome


title: Rattus norvegicus_male_soleus_27 months_rep9

tag: tissue

value: soleus

tag: strain

value: Sprague Dawley

tag: Sex

tag: time

value: 27 months


title: DGGG low dose IV BCG wk2

value: Whole Blood


title: S47.SLE.BM4.X4

value: Blood

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 10 ug/ml LPS


title: S48.SLE.362.X10

tag: stimulus

tag: stimdescription

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: Mus musculus_male_diaphragm_27 months_rep4

value: diaphragm

value: male


title: Mus musculus_male_diaphragm_27 months_rep3


title: DGGG low dose IV BCG d2

tag: animal id

value: DGGG

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: low

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome


title: DGHR low dose IV BCG d2

tag: tissue

value: DGHR


title: Rattus norvegicus_male_soleus_27 months_rep8

tag: strain

tag: Sex

tag: time


title: DGGG low dose IV BCG pre

value: pre


title: Rattus norvegicus_male_soleus_27 months_rep7


title: Mus musculus_male_diaphragm_27 months_rep2


title: S47.SLE.BM4.X2

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: SLE

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 0.25 uM CpGc


title: Rattus norvegicus_male_soleus_27 months_rep6

value: soleus


title: Mus musculus_male_diaphragm_27 months_rep1


title: DGFV low dose IV BCG wk12

tag: animal id

value: DGFV

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: S47.SLE.BM4.X1

tag: tissue

tag: donorid

tag: group

value: Asian

tag: stimulus

tag: stimdescription

value: Untreated and Unstimulated


title: Mus musculus_male_diaphragm_27 months_rep0

tag: strain

tag: Sex

tag: time

value: 27 months


title: DGFV low dose IV BCG wk4

value: Whole Blood

tag: log grans_nx

tag: protect outcome


title: Rattus norvegicus_male_soleus_27 months_rep5

value: Sprague Dawley


title: DGFV low dose IV BCG wk2

tag: animal id

tag: pitt id


title: S47.SLE.BM4.X12

value: Blood

tag: diseasenormal

value: Disease

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_soleus_27 months_rep3

tag: tissue

value: male


title: DGFV low dose IV BCG d2

tag: bcg dose_log10

tag: dose group

value: low

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: Rattus norvegicus_male_soleus_27 months_rep2

tag: strain

tag: Sex

tag: time


title: S47.SLE.BM4.X11

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: stimulus

tag: stimdescription

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: DGFV low dose IV BCG pre

tag: animal id

tag: pitt id

value: pre

tag: log grans_nx

tag: protect outcome


title: Mus musculus_male_diaphragm_24 months_rep7

tag: tissue

value: diaphragm

value: 24 months


title: S47.SLE.BM4.X10

value: SLE

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: Mus musculus_male_diaphragm_24 months_rep8

tag: strain

tag: Sex

tag: time


title: Mus musculus_male_diaphragm_24 months_rep6


title: Rattus norvegicus_male_soleus_27 months_rep11

value: soleus


title: Rattus norvegicus_male_soleus_27 months_rep10


title: DGFT low dose IV BCG wk12

value: DGFT

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

value: tntc


title: S47.SLE.362.X9

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: Asian

tag: stimulus

tag: stimdescription

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: DGFT low dose IV BCG wk4

tag: tissue

value: Whole Blood

tag: animal id

tag: pitt id

tag: log grans_nx

tag: protect outcome


title: Mus musculus_male_gastrocnemius_6 months_rep1

value: gastrocnemius

tag: strain

tag: Sex

tag: time

value: 6 months


title: S47.SLE.BM4.X3

value: Blood

value: Disease

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 10% SLE patient #4 sera


title: S47.SLE.BM4.X13

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: DGFT low dose IV BCG wk2

tag: tissue

tag: animal id

tag: bcg dose_log10

tag: dose group

value: low

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: Rattus norvegicus_male_soleus_27 months_rep4

tag: strain

value: Sprague Dawley

tag: Sex

value: male

tag: time

value: 27 months


title: S47.SLE.362.X7

value: SLE

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: stimulus

tag: stimdescription

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_soleus_27 months_rep1

tag: tissue

value: soleus


title: Mus musculus_male_diaphragm_24 months_rep9

value: diaphragm

value: 24 months


title: S47.SLE.362.X8

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: Asian

tag: drug

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: DGFT low dose IV BCG d2

value: Whole Blood

tag: animal id

value: DGFT

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

value: tntc

tag: log grans_nx

tag: protect outcome


title: Mus musculus_male_diaphragm_24 months_rep3

tag: strain

tag: Sex

tag: time


title: Rattus norvegicus_male_soleus_27 months_rep0

tag: tissue


title: S47.SLE.362.X6

value: Blood

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: stimulus

tag: stimdescription

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: DGFT low dose IV BCG pre

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: low

tag: timeafterbcg

value: pre

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: Rattus norvegicus_male_soleus_24 months_rep9

tag: tissue

tag: strain

value: Sprague Dawley

tag: Sex

value: male

tag: time


title: Mus musculus_male_diaphragm_24 months_rep1


title: Mus musculus_male_diaphragm_24 months_rep2


title: DFV9 high dose IV BCG wk12

value: high

tag: log grans_nx

tag: protect outcome

value: protected


title: Rattus norvegicus_male_soleus_24 months_rep8

value: soleus


title: Mus musculus_male_diaphragm_24 months_rep5

value: diaphragm


title: Mus musculus_male_diaphragm_24 months_rep0

value: 24 months


title: DFV9 high dose IV BCG wk4


title: Mus musculus_male_diaphragm_24 months_rep4


title: Rattus norvegicus_male_soleus_24 months_rep6


title: Rattus norvegicus_male_soleus_24 months_rep7


title: S47.SLE.362.X2

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: SLE

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

value: Asian

tag: sledai

tag: drug

value: 0.25 uM CpGc


title: Mus musculus_male_diaphragm_21 months_rep6

value: 21 months


title: Mus musculus_male_diaphragm_21 months_rep5


title: Rattus norvegicus_male_soleus_24 months_rep5


title: DFV9 high dose IV BCG d2

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: S47.SLE.362.X1

tag: tissue

value: Blood

tag: donorid

tag: group

value: Disease

tag: stimulus

tag: stimdescription

value: Untreated and Unstimulated


title: DFV9 high dose IV BCG wk2

tag: log grans_nx

tag: protect outcome


title: Mus musculus_male_diaphragm_21 months_rep4

tag: strain

tag: Sex

tag: time


title: Rattus norvegicus_male_soleus_24 months_rep4


title: S47.SLE.362.X13

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_soleus_24 months_rep3

tag: tissue

value: Sprague Dawley


title: DFR4 high dose IV BCG wk12

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

value: tntc


title: S47.SLE.362.X5

tag: donorid

tag: group

tag: diseasenormal

tag: stimulus

tag: stimdescription

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: DFV9 high dose IV BCG pre

value: high

value: pre

tag: log grans_nx

tag: protect outcome

value: protected


title: Mus musculus_male_diaphragm_21 months_rep3

value: diaphragm

tag: strain

tag: Sex

value: male

tag: time


title: S47.SLE.362.X4

tag: tissue

tag: diseasegroup

value: SLE

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 10 ug/ml LPS


title: DFR4 high dose IV BCG wk4

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: Mus musculus_male_diaphragm_21 months_rep2

tag: strain

tag: Sex

tag: time

value: 21 months


title: S47.SLE.362.X12

tag: tissue

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

value: Asian

tag: stimulus

tag: stimdescription

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: S47.SLE.362.X11

value: Blood

value: Disease

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: S47.SLE.362.X3

value: 10% SLE patient #4 sera


title: DFR4 high dose IV BCG wk2

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

value: tntc

tag: log grans_nx

tag: protect outcome


title: Rattus norvegicus_male_soleus_24 months_rep2

tag: tissue

value: soleus

tag: strain

value: Sprague Dawley

tag: Sex

tag: time

value: 24 months


title: S47.SLE.362.X10

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: stimulus

tag: stimdescription

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_soleus_24 months_rep11

value: male


title: DFR4 high dose IV BCG d2

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: high

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: Rattus norvegicus_male_soleus_24 months_rep1

tag: tissue

tag: strain

tag: Sex

tag: time


title: Mus musculus_male_diaphragm_18 months_rep5

value: diaphragm

value: 18 months


title: DFR4 high dose IV BCG pre

value: pre

tag: log grans_nx

tag: protect outcome


title: S46.SLE.BM4.X9

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: SLE

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

value: Caucasian

tag: sledai

tag: drug

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: DFN5 low dose IV BCG wk12

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: low

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: S46.SLE.BM4.X8

tag: tissue

value: Blood

tag: donorid

tag: group

value: Disease

tag: stimulus

tag: stimdescription

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_male_diaphragm_21 months_rep0

tag: strain

tag: Sex

tag: time

value: 21 months


title: S46.SLE.BM4.X7

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_soleus_24 months_rep0

value: soleus

value: Sprague Dawley

value: 24 months


title: DFN5 low dose IV BCG wk4

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome


title: Rattus norvegicus_male_soleus_21 months_rep9

tag: tissue

tag: strain

tag: Sex

value: male

tag: time


title: Mus musculus_male_diaphragm_18 months_rep3

value: diaphragm

value: 18 months


title: Mus musculus_male_diaphragm_18 months_rep2


title: S46.SLE.BM4.X6

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: SLE

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: stimulus

tag: stimdescription

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_soleus_21 months_rep7


title: Mus musculus_male_diaphragm_18 months_rep1


title: Mus musculus_male_diaphragm_21 months_rep1


title: DFN5 low dose IV BCG d2

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: DFN5 low dose IV BCG wk2

tag: tissue

tag: log grans_nx

tag: protect outcome


title: DFN5 low dose IV BCG pre

value: pre


title: Rattus norvegicus_male_soleus_24 months_rep10

tag: strain

tag: Sex

tag: time


title: Rattus norvegicus_male_soleus_21 months_rep6


title: S46.SLE.BM4.X4

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

value: Caucasian

tag: sledai

tag: drug

value: 10 ug/ml LPS


title: S46.SLE.BM4.X3

value: Blood

value: Disease

tag: stimulus

tag: stimdescription

value: 10% SLE patient #4 sera


title: Mus musculus_male_diaphragm_18 months_rep4

tag: tissue


title: DFM3 low dose IV BCG wk4

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: low

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome

value: protected


title: DFM3 low dose IV BCG wk12


title: S46.SLE.BM4.X1

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

value: Untreated and Unstimulated


title: S46.SLE.BM4.X2

tag: tissue

tag: ethnicity

tag: sledai

tag: drug

tag: stimulus

tag: stimdescription

value: 0.25 uM CpGc


title: Rattus norvegicus_male_soleus_21 months_rep5

value: soleus

tag: strain

value: Sprague Dawley

tag: Sex

tag: time

value: 21 months


title: DFM3 low dose IV BCG wk2

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome


title: S46.SLE.BM4.X5

tag: tissue

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: SLE

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: DFM3 low dose IV BCG d2

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group


title: S46.SLE.BM4.X12

tag: drug

tag: stimulus

tag: stimdescription

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: DFM3 low dose IV BCG pre

tag: tissue

tag: timeafterbcg

value: pre

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome


title: S46.SLE.BM4.X11

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

value: F

tag: diagnosis

tag: age

value: Caucasian

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: S46.SLE.BM4.X10

value: Blood

value: Disease

tag: ethnicity

tag: sledai

tag: drug

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: DFA4 low dose IV BCG wk4

tag: tissue

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: low


title: S46.SLE.362.X9

tag: stimulus

tag: stimdescription

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: S46.SLE.BM4.X13

tag: donorid

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_soleus_21 months_rep8

value: soleus

tag: strain

tag: Sex

value: male

tag: time


title: DFA4 low dose IV BCG wk12

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome


title: Rattus norvegicus_male_soleus_21 months_rep4

tag: tissue

value: Sprague Dawley

value: 21 months


title: DFA4 low dose IV BCG wk2

value: Whole Blood

tag: animal id


title: DFA4 low dose IV BCG d2

tag: pitt id


title: DFA4 low dose IV BCG pre

tag: bcg dose_log10


title: Mus musculus_male_diaphragm_12 months_rep4

value: diaphragm

value: 12 months


title: Mus musculus_male_diaphragm_12 months_rep3


title: Mus musculus_male_diaphragm_12 months_rep6


title: Mus musculus_male_diaphragm_12 months_rep2


title: Mus musculus_male_diaphragm_18 months_rep0

value: 18 months


title: Mus musculus_male_diaphragm_12 months_rep5


title: S46.SLE.362.X8

tag: group

tag: diseasenormal

tag: diseasegroup

value: SLE

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: S46.SLE.362.X6

value: Blood

tag: donorid

value: Caucasian

tag: stimulus

tag: stimdescription

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: S46.SLE.362.X7

value: Disease

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_soleus_18 months_rep8

tag: strain

tag: Sex

tag: time


title: Rattus norvegicus_male_soleus_21 months_rep11

tag: tissue


title: Rattus norvegicus_male_soleus_21 months_rep2


title: Rattus norvegicus_male_soleus_21 months_rep0


title: Rattus norvegicus_male_soleus_21 months_rep10


title: Rattus norvegicus_male_soleus_21 months_rep3


title: Rattus norvegicus_male_soleus_18 months_rep7


title: Rattus norvegicus_male_soleus_18 months_rep9


title: Rattus norvegicus_male_soleus_21 months_rep1


title: Mus musculus_female_tibialis anterior_6 months_rep4

value: tibialis anterior

value: female

value: 6 months


title: Mus musculus_female_tibialis anterior_6 months_rep7


title: Mus musculus_male_diaphragm_12 months_rep1

value: male


title: Mus musculus_female_tibialis anterior_6 months_rep5


title: Mus musculus_female_tibialis anterior_6 months_rep6


title: Mus musculus_male_diaphragm_12 months_rep0


title: A9V105 high dose IV BCG wk12

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: high

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome

value: protected


title: S46.SLE.362.X5

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_soleus_18 months_rep6

tag: tissue

value: soleus

tag: strain

value: Sprague Dawley

tag: Sex

tag: time


title: Mus musculus_female_tibialis anterior_6 months_rep3


title: A9V105 high dose IV BCG wk2

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: A9V105 high dose IV BCG wk4

tag: log grans_nx

tag: protect outcome


title: Mus musculus_female_tibialis anterior_6 months_rep1


title: S46.SLE.362.X3

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: SLE

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

tag: stimulus

tag: stimdescription

value: 10% SLE patient #4 sera


title: Rattus norvegicus_male_soleus_18 months_rep5

tag: tissue

tag: strain

tag: Sex

tag: time

value: 18 months


title: S46.SLE.362.X4

value: Blood

value: Caucasian

tag: sledai

tag: drug

value: 10 ug/ml LPS


title: Rattus norvegicus_male_soleus_18 months_rep4


title: A9V105 high dose IV BCG d2

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome


title: Mus musculus_female_tibialis anterior_6 months_rep2

value: tibialis anterior


title: Rattus norvegicus_male_soleus_18 months_rep3


title: A14V013 high dose IV BCG wk12


title: A14V013 high dose IV BCG wk4


title: Rattus norvegicus_male_soleus_18 months_rep11


title: S46.SLE.362.X12

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: stimulus

tag: stimdescription

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: S46.SLE.362.X13

tag: tissue

tag: sledai

tag: drug

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_soleus_18 months_rep10

tag: strain

tag: Sex

value: male

tag: time


title: A9V105 high dose IV BCG pre

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: high

tag: timeafterbcg

value: pre

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome

value: protected


title: Mus musculus_female_tibialis anterior_27 months_rep7

value: female

value: 27 months


title: Mus musculus_female_tibialis anterior_27 months_rep9


title: Mus musculus_female_tibialis anterior_6 months_rep0

value: 6 months


title: S46.SLE.362.X11

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: SLE

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

tag: stimulus

tag: stimdescription

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_tibialis anterior_27 months_rep8

tag: tissue

tag: strain

tag: Sex

tag: time


title: A14V013 high dose IV BCG wk2

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: S46.SLE.362.X1

value: Blood

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

value: Caucasian

tag: sledai

tag: drug

value: Untreated and Unstimulated


title: Rattus norvegicus_male_soleus_18 months_rep1

tag: tissue

value: soleus

tag: strain

value: Sprague Dawley

tag: Sex

tag: time

value: 18 months


title: A14V013 high dose IV BCG pre

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: log grans_nx

tag: protect outcome


title: S46.SLE.362.X2

tag: donorid

tag: group

value: Disease

tag: age

tag: ethnicity

tag: stimulus

tag: stimdescription

value: 0.25 uM CpGc


title: Rattus norvegicus_male_soleus_18 months_rep2

value: male


title: Rattus norvegicus_male_soleus_18 months_rep0


title: Mus musculus_female_tibialis anterior_27 months_rep5

value: tibialis anterior


title: A12V158 high dose IV BCG wk12

value: high

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: S46.SLE.362.X10

tag: tissue

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: sledai

tag: drug

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: S45.SLE.BM4.X9

tag: donorid

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_tibialis anterior_27 months_rep3

tag: strain

tag: Sex

value: female

tag: time

value: 27 months


title: Rattus norvegicus_male_soleus_12 months_rep8

value: 12 months


title: Mus musculus_female_tibialis anterior_27 months_rep4


title: Rattus norvegicus_male_soleus_12 months_rep7


title: A12V158 high dose IV BCG d2

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: log grans_nx

tag: protect outcome


title: S45.SLE.BM4.X7

tag: tissue

value: Blood

tag: group

value: SLE

value: F

tag: age

tag: ethnicity

tag: stimulus

tag: stimdescription

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: S45.SLE.BM4.X8

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

value: Caucasian

tag: sledai

tag: drug

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_soleus_12 months_rep6

value: soleus

tag: strain

value: Sprague Dawley

tag: Sex

tag: time


title: A12V158 high dose IV BCG pre

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

value: pre

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx


title: Mus musculus_female_tibialis anterior_27 months_rep6

tag: tissue

value: tibialis anterior


title: S45.SLE.BM4.X6

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

tag: gender

tag: age

tag: ethnicity

tag: stimulus

tag: stimdescription

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: S45.SLE.BM4.X5

tag: diagnosis

tag: sledai

tag: drug

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: A12V119 low dose IV BCG wk12

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: low

tag: timeafterbcg

tag: total mtb_cfu

tag: protect outcome


title: Mus musculus_female_tibialis anterior_27 months_rep1

tag: tissue

tag: strain

tag: Sex

value: female

tag: time

value: 27 months


title: Mus musculus_female_tibialis anterior_27 months_rep0


title: Rattus norvegicus_male_soleus_12 months_rep5

value: male

value: 12 months


title: A12V119 low dose IV BCG wk4

value: Whole Blood

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx


title: S45.SLE.BM4.X4

value: Blood

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: SLE

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

tag: stimulus

tag: stimdescription

value: 10 ug/ml LPS


title: Mus musculus_female_tibialis anterior_24 months_rep9

tag: tissue

value: 24 months


title: Rattus norvegicus_male_soleus_12 months_rep9

value: soleus

tag: strain

value: Sprague Dawley


title: A12V158 high dose IV BCG wk2

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: high

tag: timeafterbcg

tag: total mtb_cfu

tag: protect outcome


title: A12V119 low dose IV BCG wk2

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx


title: Rattus norvegicus_male_soleus_12 months_rep4

tag: Sex

tag: time


title: S45.SLE.BM4.X3

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

value: Caucasian

tag: sledai

tag: drug

value: 10% SLE patient #4 sera


title: S45.SLE.BM4.X2

tag: tissue

tag: stimulus

tag: stimdescription

value: 0.25 uM CpGc


title: Rattus norvegicus_male_soleus_12 months_rep3

tag: strain


title: Mus musculus_female_tibialis anterior_27 months_rep2

value: tibialis anterior

value: female


title: Mus musculus_female_tibialis anterior_24 months_rep8


title: Rattus norvegicus_male_soleus_12 months_rep2

value: male


title: Mus musculus_female_tibialis anterior_24 months_rep7


title: S45.SLE.BM4.X1

value: Untreated and Unstimulated


title: Rattus norvegicus_male_soleus_12 months_rep10

value: 12 months


title: Mus musculus_female_tibialis anterior_24 months_rep6


title: Rattus norvegicus_male_soleus_12 months_rep11


title: A12V095 low dose IV BCG wk12

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: low

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome

value: protected


title: A12V095 low dose IV BCG wk4


title: A12V119 low dose IV BCG pre

value: pre


title: Mus musculus_female_tibialis anterior_24 months_rep5

tag: Sex

tag: time

value: 24 months


title: Mus musculus_female_tibialis anterior_24 months_rep4


title: S45.SLE.BM4.X13

value: Blood

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: SLE

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_soleus_12 months_rep1

tag: tissue

value: soleus

tag: strain

value: Sprague Dawley


title: S45.SLE.BM4.X11

value: Disease

value: Caucasian

tag: stimulus

tag: stimdescription

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: S45.SLE.BM4.X12

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_male_diaphragm_27 months_rep7

value: diaphragm

value: male

value: 27 months


title: Rattus norvegicus_male_soleus_12 months_rep0

value: 12 months


title: A12V095 low dose IV BCG wk2

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: low

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome

value: protected


title: A12V095 low dose IV BCG d2


title: S45.SLE.BM4.X10

value: Blood

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: A12V119 low dose IV BCG d2

tag: tissue

tag: animal id

tag: pitt id


title: Mus musculus_female_tibialis anterior_24 months_rep2

value: tibialis anterior

tag: strain

tag: Sex

value: female

tag: time

value: 24 months


title: A12V095 low dose IV BCG pre

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

value: pre

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: S45.SLE.362.X9

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

value: SLE

value: F

tag: sledai

tag: drug

tag: stimulus

tag: stimdescription

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_gastrocnemius_9 months_rep9

tag: tissue

value: gastrocnemius

tag: strain

value: Sprague Dawley

value: 9 months


title: A12V066 high dose IV BCG wk12

tag: animal id

tag: pitt id

value: high

tag: log grans_nx

tag: protect outcome


title: Rattus norvegicus_male_gastrocnemius_9 months_rep8

tag: Sex

value: male

tag: time


title: S45.SLE.362.X8

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

value: Caucasian

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_gastrocnemius_9 months_rep7


title: Mus musculus_female_tibialis anterior_24 months_rep1


title: Rattus norvegicus_male_gastrocnemius_9 months_rep6


title: Mus musculus_female_tibialis anterior_21 months_rep7

value: 21 months


title: S45.SLE.362.X7

value: Blood

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: A12V066 high dose IV BCG wk2

value: Whole Blood

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

value: protected


title: A12V066 high dose IV BCG wk4

tag: tissue

tag: animal id

tag: pitt id

tag: log grans_nx

tag: protect outcome


title: S45.SLE.362.X6

tag: gender

tag: diagnosis

tag: age

tag: sledai

tag: drug

tag: stimulus

tag: stimdescription

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: S45.SLE.362.X5

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

tag: ethnicity

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_tibialis anterior_21 months_rep6

tag: tissue

value: tibialis anterior

tag: strain

tag: Sex

value: female

tag: time


title: A12V066 high dose IV BCG d2

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome


title: Mus musculus_female_tibialis anterior_21 months_rep5


title: Rattus norvegicus_male_gastrocnemius_9 months_rep4

value: gastrocnemius


title: Rattus norvegicus_male_gastrocnemius_9 months_rep5

value: Sprague Dawley


title: S45.SLE.362.X4

tag: donorid

tag: group

tag: diseasenormal

value: SLE

tag: gender

value: F

tag: diagnosis

tag: age

tag: sledai

tag: drug

tag: stimulus

tag: stimdescription

value: 10 ug/ml LPS


title: Mus musculus_female_tibialis anterior_24 months_rep3

tag: tissue

tag: strain

tag: Sex

tag: time

value: 24 months


title: A12V066 high dose IV BCG pre

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: high

tag: timeafterbcg

value: pre

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: A12V062 low dose IV BCG wk12

value: low

tag: log grans_nx

tag: protect outcome


title: S45.SLE.362.X3

value: Blood

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

value: Caucasian

tag: sledai

tag: drug

value: 10% SLE patient #4 sera


title: Rattus norvegicus_male_gastrocnemius_9 months_rep3

tag: tissue

tag: strain

tag: Sex

value: male

tag: time

value: 9 months


title: Mus musculus_female_tibialis anterior_21 months_rep3

value: 21 months


title: A12V062 low dose IV BCG wk4

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

value: protected


title: S45.SLE.362.X2

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

tag: gender

tag: diagnosis

tag: stimulus

tag: stimdescription

value: 0.25 uM CpGc


title: Mus musculus_female_tibialis anterior_24 months_rep0

tag: tissue

value: tibialis anterior

tag: strain

tag: Sex

value: female

tag: time


title: Rattus norvegicus_male_gastrocnemius_9 months_rep2

value: gastrocnemius

value: Sprague Dawley


title: Rattus norvegicus_male_gastrocnemius_9 months_rep11


title: S45.SLE.362.X1

value: SLE

value: F

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: Untreated and Unstimulated


title: Mus musculus_female_tibialis anterior_21 months_rep2


title: Mus musculus_female_tibialis anterior_21 months_rep1


title: Rattus norvegicus_male_gastrocnemius_9 months_rep10


title: A12V062 low dose IV BCG d2

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: low

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome


title: S45.SLE.362.X13

tag: tissue

value: Blood

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

value: Caucasian

tag: stimulus

tag: stimdescription

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: A12V062 low dose IV BCG pre

tag: animal id

tag: pitt id

tag: bcg dose_log10

value: pre


title: S45.SLE.362.X12

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_tibialis anterior_18 months_rep6

tag: strain

tag: Sex

tag: time

value: 18 months


title: Mus musculus_female_tibialis anterior_21 months_rep0

tag: tissue

value: 21 months


title: Rattus norvegicus_male_gastrocnemius_9 months_rep0

value: male

value: 9 months


title: Rattus norvegicus_male_gastrocnemius_9 months_rep1


title: A12V058 high dose IV BCG wk12

value: Whole Blood

tag: dose group

value: high

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome


title: Mus musculus_female_tibialis anterior_18 months_rep5

value: tibialis anterior

value: female


title: S45.SLE.362.X11

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

value: SLE

tag: gender

tag: diagnosis

tag: stimulus

tag: stimdescription

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_tibialis anterior_21 months_rep4

tag: strain

tag: Sex

tag: time


title: A12V058 high dose IV BCG wk4

tag: tissue

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg


title: S45.SLE.362.X10

tag: donorid

value: F

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_gastrocnemius_6 months_rep9

value: gastrocnemius

value: Sprague Dawley

value: 6 months


title: A12V062 low dose IV BCG wk2

value: low

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome

value: protected


title: Mus musculus_female_tibialis anterior_18 months_rep4

tag: strain

tag: Sex

tag: time

value: 18 months


title: Rattus norvegicus_male_gastrocnemius_6 months_rep8

tag: tissue

value: male


title: A12V058 high dose IV BCG wk2

tag: animal id

tag: pitt id

tag: bcg dose_log10


title: Mus musculus_female_tibialis anterior_18 months_rep3


title: S44.SLE.BM4.X9

value: Blood

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

value: Asian

tag: stimulus

tag: stimdescription

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: A12V058 high dose IV BCG d2

value: Whole Blood

tag: dose group

value: high

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx


title: Rattus norvegicus_male_gastrocnemius_6 months_rep7

tag: tissue

tag: strain

tag: Sex

tag: time


title: Mus musculus_female_tibialis anterior_18 months_rep2

value: tibialis anterior

value: female


title: Rattus norvegicus_male_gastrocnemius_6 months_rep6


title: Rattus norvegicus_male_gastrocnemius_6 months_rep5


title: Rattus norvegicus_male_gastrocnemius_6 months_rep4


title: Mus musculus_female_tibialis anterior_18 months_rep0


title: S44.SLE.BM4.X8

tag: donorid

tag: group

value: Disease

value: SLE

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: A12V057 low dose IV BCG wk4

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: protect outcome


title: A12V057 low dose IV BCG wk12

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu


title: S44.SLE.BM4.X7

tag: tissue

tag: diseasenormal

tag: diseasegroup

tag: gender

value: F

tag: diagnosis

tag: stimulus

tag: stimdescription

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_gastrocnemius_6 months_rep2

value: gastrocnemius

tag: strain

value: Sprague Dawley

tag: Sex

tag: time

value: 6 months


title: A12V057 low dose IV BCG d2

tag: animal id

tag: pitt id

value: low

tag: grans nx

tag: log grans_nx

value: protected


title: S44.SLE.BM4.X4

value: Blood

tag: donorid

tag: group

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 10 ug/ml LPS


title: A12V057 low dose IV BCG wk2

tag: tissue

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: protect outcome


title: Mus musculus_female_tibialis anterior_12 months_rep5

tag: strain

tag: Sex

tag: time

value: 12 months


title: Mus musculus_female_tibialis anterior_18 months_rep1

value: 18 months


title: Mus musculus_female_tibialis anterior_12 months_rep6


title: Rattus norvegicus_male_gastrocnemius_6 months_rep0

value: male


title: Mus musculus_female_tibialis anterior_12 months_rep7

value: tibialis anterior


title: S44.SLE.BM4.X6

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

value: Asian

tag: stimulus

tag: stimdescription

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: S44.SLE.BM4.X3

tag: donorid

tag: group

value: Disease

value: SLE

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 10% SLE patient #4 sera


title: S44.SLE.BM4.X5

tag: tissue

value: F

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_gastrocnemius_6 months_rep1

value: gastrocnemius

value: Sprague Dawley


title: A12V057 low dose IV BCG pre

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: low

tag: timeafterbcg

value: pre

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome


title: A12V058 high dose IV BCG pre

value: high


title: Mus musculus_female_tibialis anterior_12 months_rep4

tag: strain

tag: Sex

value: female

tag: time

value: 12 months


title: A12V053 high dose IV BCG wk12

value: protected


title: S44.SLE.BM4.X1

value: Blood

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: stimulus

tag: stimdescription

value: Untreated and Unstimulated


title: Rattus norvegicus_male_gastrocnemius_27 months_rep9

tag: tissue

value: male

value: 27 months


title: A12V053 high dose IV BCG wk4

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: Mus musculus_female_tibialis anterior_12 months_rep3

value: tibialis anterior

tag: strain

tag: Sex

tag: time


title: Rattus norvegicus_male_gastrocnemius_6 months_rep3

value: 6 months


title: Mus musculus_female_tibialis anterior_12 months_rep2


title: A12V053 high dose IV BCG wk2

tag: log grans_nx

tag: protect outcome


title: S44.SLE.BM4.X12

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

value: SLE

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

value: Asian

tag: sledai

tag: drug

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_gastrocnemius_27 months_rep8

tag: tissue

value: gastrocnemius

value: Sprague Dawley


title: A12V053 high dose IV BCG d2

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: high

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: Mus musculus_female_tibialis anterior_12 months_rep1

tag: strain

tag: Sex

value: female

tag: time

value: 12 months


title: Rattus norvegicus_male_gastrocnemius_27 months_rep7


title: Mus musculus_female_tibialis anterior_12 months_rep0


title: S44.SLE.BM4.X11

value: Blood

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: stimulus

tag: stimdescription

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_gastrocnemius_27 months_rep6

tag: tissue

value: male


title: S44.SLE.BM4.X2

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 0.25 uM CpGc


title: S44.SLE.BM4.X10

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: A12V053 high dose IV BCG pre

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

value: pre

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome

value: protected


title: S44.SLE.362.X9

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

value: SLE

tag: gender

tag: diagnosis

tag: stimulus

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: A12V044 high dose IV BCG wk12

tag: tissue

tag: animal id


title: Rattus norvegicus_male_gastrocnemius_27 months_rep4

tag: strain

tag: Sex

tag: time

value: 27 months


title: Mus musculus_female_soleus_6 months_rep7

value: soleus

value: 6 months


title: Rattus norvegicus_male_gastrocnemius_27 months_rep5

value: gastrocnemius

value: Sprague Dawley


title: S44.SLE.BM4.X13

value: F

tag: age

tag: ethnicity

value: Asian

tag: sledai

tag: drug

tag: stimdescription

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: S44.SLE.362.X8

value: Blood

tag: donorid

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: A12V044 high dose IV BCG wk2

value: Whole Blood

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: high

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome


title: A12V044 high dose IV BCG d2

tag: tissue

tag: animal id


title: Mus musculus_female_soleus_6 months_rep5

tag: strain

tag: Sex

value: female

tag: time


title: A12V044 high dose IV BCG wk4


title: Mus musculus_female_soleus_6 months_rep6


title: Rattus norvegicus_male_gastrocnemius_27 months_rep3

value: male


title: Rattus norvegicus_male_gastrocnemius_27 months_rep2


title: S44.SLE.362.X6

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

tag: stimulus

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_soleus_6 months_rep4


title: Rattus norvegicus_male_gastrocnemius_27 months_rep10


title: Mus musculus_female_soleus_6 months_rep3


title: A12V044 high dose IV BCG pre

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

value: pre

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx


title: Rattus norvegicus_male_gastrocnemius_27 months_rep1

tag: tissue

tag: strain

tag: Sex

tag: time

value: 27 months


title: Mus musculus_female_soleus_6 months_rep2

value: soleus


title: A11V075 high dose IV BCG wk12

tag: animal id

tag: protect outcome

value: protected


title: Mus musculus_female_soleus_6 months_rep1

value: 6 months


title: A11V075 high dose IV BCG wk4


title: S44.SLE.362.X3

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: SLE

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: stimdescription

value: 10% SLE patient #4 sera


title: Mus musculus_female_soleus_6 months_rep0


title: S44.SLE.362.X2

value: F

value: Asian

tag: drug

tag: stimulus

value: 0.25 uM CpGc


title: S44.SLE.362.X7

tag: tissue

value: Blood

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: A11V075 high dose IV BCG d2

value: Whole Blood

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: high

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx


title: Mus musculus_female_soleus_27 months_rep8

tag: strain

tag: Sex

value: female

tag: time


title: S44.SLE.362.X13

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_gastrocnemius_24 months_rep6

tag: tissue

value: gastrocnemius

value: Sprague Dawley

value: male

value: 24 months


title: Rattus norvegicus_male_gastrocnemius_24 months_rep7


title: A11V075 high dose IV BCG pre

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

value: pre

tag: protect outcome

value: protected


title: Mus musculus_female_soleus_27 months_rep6

value: soleus

tag: strain

tag: Sex

value: 27 months


title: Mus musculus_female_soleus_27 months_rep7

tag: time


title: Rattus norvegicus_male_gastrocnemius_24 months_rep5


title: 13N026 low dose IV BCG wk12

value: low

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx


title: 13N026 low dose IV BCG wk4


title: S44.SLE.362.X1

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: SLE

tag: gender

value: F

tag: diagnosis

value: Asian

tag: sledai

tag: drug

tag: stimulus

tag: stimdescription

value: Untreated and Unstimulated


title: S44.SLE.362.X5

tag: tissue

value: Blood

tag: age

tag: ethnicity

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: S44.SLE.362.X12

value: Disease

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: S44.SLE.362.X4

value: 10 ug/ml LPS


title: S44.SLE.362.X11

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_gastrocnemius_27 months_rep0

value: gastrocnemius

tag: strain

value: Sprague Dawley

tag: Sex

value: male

tag: time


title: Mus musculus_female_soleus_27 months_rep5

value: female


title: Rattus norvegicus_male_gastrocnemius_24 months_rep4

value: 24 months


title: 13N026 low dose IV BCG wk2

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome

value: protected


title: S44.SLE.362.X10

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: SLE

tag: gender

tag: diagnosis

tag: sledai

tag: drug

tag: stimulus

tag: stimdescription

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_soleus_27 months_rep4

tag: tissue

value: soleus

tag: strain

tag: Sex

tag: time

value: 27 months


title: Rattus norvegicus_male_gastrocnemius_24 months_rep3


title: Rattus norvegicus_male_gastrocnemius_24 months_rep8


title: Rattus norvegicus_male_gastrocnemius_24 months_rep2


title: Mus musculus_female_soleus_27 months_rep9


title: A11V075 high dose IV BCG wk2

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: high

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: 13N026 low dose IV BCG d2

value: low

tag: log grans_nx

tag: protect outcome


title: S43.SLE.BM4.X9

value: Blood

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

value: Caucasian

tag: sledai

tag: drug

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_soleus_27 months_rep3

tag: tissue

tag: strain

tag: Sex

tag: time


title: Rattus norvegicus_male_gastrocnemius_24 months_rep1

value: gastrocnemius

value: Sprague Dawley


title: 13N026 low dose IV BCG pre

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

value: pre

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: S43.SLE.BM4.X8

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: stimulus

tag: stimdescription

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_soleus_27 months_rep2

tag: tissue

tag: strain

tag: Sex

value: female

tag: time


title: 13N025 high dose IV BCG wk12

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: log grans_nx

tag: protect outcome

value: protected


title: Rattus norvegicus_male_gastrocnemius_24 months_rep0

value: male

value: 24 months


title: S43.SLE.BM4.X7

tag: donorid

tag: group

value: SLE

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_soleus_27 months_rep1

value: soleus

value: 27 months


title: S43.SLE.BM4.X6

value: Blood

tag: diseasenormal

value: Disease

tag: diseasegroup

tag: gender

tag: diagnosis

tag: stimulus

tag: stimdescription

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_gastrocnemius_21 months_rep8

tag: tissue

tag: strain

tag: Sex

tag: time

value: 21 months


title: Mus musculus_female_soleus_27 months_rep0


title: 13N025 high dose IV BCG wk4

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: high

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome


title: 13N025 high dose IV BCG wk2


title: S43.SLE.BM4.X5

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

value: Caucasian

tag: sledai

tag: drug

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_gastrocnemius_21 months_rep6

tag: tissue

value: gastrocnemius

tag: strain

value: Sprague Dawley

tag: Sex

tag: time


title: Rattus norvegicus_male_gastrocnemius_21 months_rep7


title: S43.SLE.BM4.X4

tag: stimulus

tag: stimdescription

value: 10 ug/ml LPS


title: Mus musculus_female_soleus_24 months_rep7

value: female


title: Rattus norvegicus_male_gastrocnemius_21 months_rep5

value: male


title: 13N025 high dose IV BCG pre

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

value: pre

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome

value: protected


title: S43.SLE.BM4.X3

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: SLE

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 10% SLE patient #4 sera


title: S43.SLE.BM4.X2

tag: tissue

value: Blood

value: Disease

tag: stimulus

tag: stimdescription

value: 0.25 uM CpGc


title: 13N023 high dose IV BCG wk12

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: high

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu


title: Mus musculus_female_soleus_24 months_rep6

value: soleus

tag: strain

tag: Sex

tag: time

value: 24 months


title: 13N023 high dose IV BCG wk4

tag: grans nx

tag: log grans_nx

tag: protect outcome


title: S43.SLE.BM4.X1

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

value: Caucasian

tag: sledai

tag: drug

value: Untreated and Unstimulated