title: JK23: 48hr Chronic wound

city: Riverside

first: Dr Manuela

last: Martins-Green

state: California

address: 900 University Ave

department: Molecular Cell and Systems Biology

institute: University of California

hyb_protocol: The mRNA was analyzed with the nanoString nCounter® Mouse Metabolism Panel. Raw data obtained from the nCounter® was analyzed with nanoString program nSolver to obtain counts, normalize data to positive and negative controls, and perform fold change calculations.

data_processing: WGCNA is a comprehensive method of identifying correlation networks. To identify the constituent nodes/genes in each network, we used 748 gene probes expressed in the nanoString nCounter® dataset. The dataset was not filtered by differential expression. We used the package WGCNA in R and analyzed scale-free topology with a soft threshold value of 10.  Soft threshold values were used to build an adjacency matrix using the Pearson correlation method. The adjacency matrix was then used to identify modules according to the correlated co-expression of the genes. The constituent genes of each module were assigned a ‘module membership’ value which gauged if the gene truly belonged to the module (p<0.05). These modules were then correlated to the experimental conditions (dichotomous matrix of whether the wound tissue was collected from chronic or non-chronic wound) via the module eigengenes. Module eigengenes represent the gene expression profile of each module. The module eigengenes that correlated to each timepoint in chronic and non-CW were then checked for significance (Pearson correlation, p<0.05). The Pearson correlation co-efficient in WGCNA is a measure of correlation of modules to trait or traits of interest which in our case is chronicity of the wound. In each module of genes, potential driver genes (which may influence the expression of other genes in the module and may be the causal factor for chronicity) are the ones which show high gene trait correlation and high module membership. The Pearson correlation co-efficient of module membership is a measure of how much a member gene correlates to the module eigengene. Gene trait significance was calculated for the genes in the significant modules and only genes that showed both significant module membership (p<0.05) and correlation to traits (p<0.05) were used for further analysis.

source_name: Chronic Wound

growth_protocol: All experiments were completed in accordance with federal regulations and University of California policy and all procedures have been approved by the University of California, Riverside Institutional Animal Care and Use Committee (IACUC).

extract_protocol: Wound tissues were collected and stored in RNALater first in 4°C and then in -80°C. Tissues were homogenized with a bead beater for 20 mins and the RNA was extracted with the Zymo RNA extraction kit. Quality of RNA was checked with a Bioanalyzer and samples were normalized to 20 ng/µl before submission to UCI Genomics High Throughput Facility.

treatment_protocol: The db/db -/- mouse model has a knockout mutation in the leptin receptor of the C57BL6 background that makes these mice diabetic and obese. The db/db-/- mice are only used for wounding once they are 5 months-old and weigh ≥ 50 g. This ensures fully diabetic conditions.  For the creation of CW, the mice were treated with catalase and glutathione peroxidase (GPx) inhibitors after 7mm diameter full thickness cutaneous wounds were made. 4,17 Control wounds were treated with phosphate buffer saline (PBS) instead of catalase and GPx inhibitors and remained non-chronic. Non-CW in diabetic mice healed in 20 to 30 days whereas CW remained open for weeks and months, if the mouse survived.  At the time of wound collection, the mice were euthanized with carbon dioxide. Up to 3mm tissue away from the wound margin was excised and immediately frozen on dry ice. Samples were stored at -80°C until subsequent RNA extraction.

value: Chronic Wound

tag: timepoint


title: PA6 7 days mono-cultures FGF2 rep1

status: Public on Sep 05 2021

type: RNA

city: Candiolo

first: Davide

last: Cora'

state: TO

department: Dept. of Oncology

country: Italy

institute: Piemonte Orientale University and IRCCS Candiolo Cancer Institute

description: PA6 cell monolayers cultured for 7 days in serum-free medium in presence of recombinant FGF2

hyb_protocol: 750 ng of cRNA was hybridized on MouseWG-6 v2.0 Expression BeadChip (Illumina Inc.). Array washes were performed using wash buffer

scan_protocol: Hybridized BeadChips were scanned using illumina Array reader

data_processing: Cubic Spline-normalized probe intensity data, togheter with detection p-values, were obtained using the GenomeStudio software v2011.01 (Illumina)

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: PA6 mono-cultures cultured in serum-free medium in presence of recombinant FGF2 for 7 days

label_protocol: Bioinylated cRNA were prepared with Illumina TotalPrep RNA Amplification kit (Life Technologies)

growth_protocol: Murine ES cells were cultured into 6-well plates onto monolayers of stromal PA6 cells in serum-free medium for 7 days and in parallel, PA6 mono-cultures were cultured in serum-free medium for 7 days as well

extract_protocol: Total RNA was extracted from ES/PA6 co-cultures or from PA6 mono-cultures with Trizol reagent (Invitrogen) and purified using the RNeasy total RNA Isolation Kit (Qiagen).

treatment_protocol: For each biological replicate ES/PA6 co-cutlures or PA6 mono-cultures were treated as it follows: one well of ES/PA6 co-cultures and PA6 monocultures untreated, one well of ES/PA6 co-cultures and PA6 monocultures treated with 20 ng/ml of recombinant FGF2, one well of ES/PA6 co-cultures and PA6 monocultures treated with 10 ng/ml of recombinant BMP4

tag: cell lines

tag: growth factors

value: recombinant FGF2 for 3 days


title: JK24: 48hr Chronic wound

country: USA

scan_protocol: The mRNA was analyzed with the nanoString nCounter® Mouse Metabolism Panel. Raw data obtained from the nCounter® was analyzed with nanoString program nSolver to obtain counts, normalize data to positive and negative controls, and perform fold change calculations.

tag: tissue


title: H3K4me3 SET-seq 10^4 cells_Epi_rep1

type: SRA

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

country: China

institute: Zhejiang University

library_source: genomic

data_processing:
Sequencing reads adaptor and low-quality bases were removed by Trim Galore (version 0.6.4) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore)
Filtered transcriptional SET-seq reads were mapped to the mouse reference genome mm9, which excluded mitochondria and random chromosomes, by STAR (version 2.5.4b)(Dobin et al., 2013)
Trimmed epigenomic SET-seq were then mapped to the mouse reference genome mm9 using Bowtie2(Langmead and Salzberg, 2012).PCR duplicates were removed by GATK4 (version 4.1.4.0) (https://github.com/broadinstitute/gatk) with the parameter ‘--REMOVE_DUPLICATES =true’.
Expression matrixes were counted by featureCounts(Liao et al., 2014) (version 2.0.0)
To get the single-cell gene expression matrixes, pipeline tool zUMIs(Parekh et al., 2018) (version 2.7.1c) was used to split reads into each cell by cell-specific barcode and map reads to mouse genome mm9, which excluded mitochondria and random chromosomes. The expression matrixes were analyzed by R package Seurat(Stuart et al., 2019) (version 3.2.1) using genes mapped to both of exons and introns.
Bedtools(Quinlan, 2014) (version 2.92.2) and bedGraphToBigWig (https://www.encodeproject.org/software/bedgraphtobigwig/) (version 4) were used to normalize mapped reads and calculate the coverage of features among the genome with the following parameters ‘genomecov --scaleFactor 10,000,000/mapped_reads_number’.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample of transcriptional SET-seq

molecule: genomic DNA

source_name: Embryonic stem cells

growth_protocol: mESCs were cultured on 0.1% gelatin-coated plates in DMEM medium containing 15% Fetal Bovine Serum, 1% Penicillin/Streptomycin, 1% Glutamax, 0.1 mM 2-mercaptoethanol, 1% MEM nonessential amino acids, 1% sodium pyruvate, and 1,000 U/ml recombinant leukemia inhibitory factor (LIF).

extract_protocol:
The total RNA was extracted by UNIQ-10 Column Total RNA Purification kit (Sangon Biotech). Cells were harvested and then lysed in NE buffer (20 mM HEPES pH 7.5, 0.5 mM KCl, 0.5 mM Spermidine, 0.5% Triton X-100, 20% Glycerol, 1mM PMSF) on ice for 10min.
Bulk libraries preparation was described previously(Kaya-Okur et al., 2019a). Sc-libraries were constructed with a structure similar to True-seq libraries for pooling with other samples as described(Ai et al., 2019a).

treatment_protocol: A localized Wnt3a beads with mESCs were engineered in the 2 cm plates following previous method(Habib et al.). To achieve one cell and one bead contact, mESCs were sed at a low concentration before imaging or collecting. After seeding the cells and Wnt3a beads, samples were collected at around 12 hours.

tag: cell type

tag: strain

tag: treatment

value: untreated

tag: chip antibody

value: H3K4me3 (Cat# ab8580, Abcam)

tag: age


title: PA6 7 days mono-cultures control rep1

description: PA6 cell monolayers cultured for 7 days in serum-free medium in absence of growth factors

source_name: PA6 mono-cultures cultured in serum-free medium in absence of growth factors for 7 days


title: 48_AAV

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

country: France

institute: university Paris Sud11

description: tumor

hyb_protocol: WT plus Affymetrix chemistry

scan_protocol: scan of Clariom S mouse slide on affymetrix microarray station

data_processing: RMA normalization TAC 4.0 software

source_name: AAV

label_protocol: WT plus Affymetrix chemistry

growth_protocol: tranfection with empty vector (AAV) or with PIK3CD (PIK3CD)

extract_protocol: total RNA was extract from the cell culture and a quantity of 100 ng was investigated to start microarray probe synthesis

treatment_protocol: ex vivo  tumor analysis

value: tumor

value: empty vector (AAV)


title: Case17_SNParray

type: genomic

city: Perugia

first: Danika

last: Di Giacomo

address: Piazzale Menghini 0

department: Medicine

institute: University of Perugia

description: Case_17 (UPN#149)

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
Protocol was supported by Affymetrix GeneChip Command Console (AGCC) software. Analysis was performed through Affymetrix Chromosome Analysis (ChAS) software with filters set at 200 Kb dimension for Copy Number Alterations (CNAs) and 10 Mb dimensions for copy neutral loss of heterozygosity (cnLOH). Our data refer to NetAffx Build 32.3 (hg19) database.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

organism: Homo sapiens

source_name: Unsorted Bone Marrow Cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA were extracted from bone marrow cells or periferichal blood cells of patients using All Prep DNA/RNA Mini Kit (Qiagen). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, Bioanalyzer and/or Tapestation visualization (Agilent 2100 Bioanalyzer) and agarose gel electrophoresis.

value: bone marrow

tag: cytogenetics

tag: disease state

value: acute leukemia


title: PA6 7 days mono-cultures control rep2


title: PA6 7 days mono-cultures control rep3


title: ES/PA6 7 days co-cultures BMP4 rep2

description: ES cells co-cultured with stromal PA6 cells for 7 days in serum-free medium in presence of recombinant BMP4

source_name: ES/PA6 co-cultures cultured in serum-free medium in presence of recombinant BMP4 for 7 days

value: recombinant BMP4 for 3 days


title: ES/PA6 7 days co-cultures BMP4 rep1


title: Case11_SNParray

description: Case_11 (UPN#260)


title: H3K4me3 SET-seq 10^3 cells_Epi_rep2


title: Brap-CT__A3-B1-08

city: Bethesda

first: Yuanyi

last: Feng

state: MD

address: 4301 Jones Bridge Road

institute: UNIFORMED SERVICES UNIVERSITY OF THE HEALTH SCIENCES

description: Control

library_source: transcriptomic

data_processing:
The quality of raw sequencing data was assessed using FastQC.
We obtained more than 30 million sequence reads per sample that are uniquely mapped to the mouse reference genome (build mm10).
After alignment of reads, expression levels of individual genes were quantified and estimated using subread::featureCounts.
With the removal of lowly expressed genes using the threshold at least 10 raw read counts, 14,276 out of 21,969 annotated, valid mouse genes were retained for further analysis.
Data were analyzed using several state-of-the-art tools, including DESeq2, edgeR, and Iimma, with a fold change ≥1.5 and FDR < 0.1. We collected overlapped differentially expressed mRNA genes detected with more than one method, and identified 811 differentially expressed genes between BrapcKO and control group.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: df.data.csv: Matrix table with raw gene counts for every gene and every sample.

source_name: cerebral cortex

extract_protocol:
Cerebral cortices were removed, flash frozen in liquid nitrogen, and RNA was extracted and purified using Trizol reagent followed by treatment with TURBO DNase. 1ug of total RNA was used for the construction of sequencing libraries using Illumina Ribo-Zero RNA Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: cerebral cortex

value: 3 month

tag: genotype

value: Brapflox/wt Cre-


title: H3K4me3 SET-seq 10^3 cells_Epi_rep1


title: H3K4me3 SET-seq 10^2 cells_Epi_rep2


title: JK21: 48hr NonChronic wound

source_name: NonChronic Wound

label_protocol: The mRNA was analyzed with the nanoString nCounter® Mouse Metabolism Panel. Raw data obtained from the nCounter® was analyzed with nanoString program nSolver to obtain counts, normalize data to positive and negative controls, and perform fold change calculations.

value: NonChronic Wound


title: Case12_SNParray

description: Case_12 (UPN#462)


title: JK22: 48hr Chronic wound


title: JK20: 48hr NonChronic wound


title: 6_siR50

city: La Jolla

first: Shankar

last: Subramaniam

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California, San Diego

description: Sample 26

data_processing:
Base-calling software (CASAVA v1.8.2)
Omicsoft Sequence Aligner (OSAv2.1.14) was used to trim low quality reads and align reads to   genome build Human.B37.3 using gene model: Ensembl.R66. Default values were used for all OSA parameters except for the following: ReadTrimQuality = 20, ExpressionMeasurement = Count, and SearchNovelExonJunction = True. OSA2 merges transcript counts into gene counts (http://bioinformatics.oxfordjournals.org/content/26/4/493.full).
Data normalization, outlier filtering, and differential expression analysis was conducted using the DESeq2 BioConductor R package using R3.0.3 (as described in http://www.genomebiology.com/2014/15/12/550). Additional p-value (p< 0.01) and fold-change (|FC| > 1.3 ) cutoffs were also used to reduce noise further.
Genome_build: Human B37.7 (GRCh37.p5)
Supplementary_files_format_and_content: comma-separated value file; contains raw gene count output from OSA2 for all samples (columns C -V).

source_name: Endothelial Cells

growth_protocol:
ATCC HUVECs were cultured and transfected with scrambled control or si-HMOX1 according to the Lipofectamine RNAiMAX protocol (13778075; Thermo Fisher, Waltham, MA). 48 hours after transfection, samples were induced with HP and total RNA was isolated in duplicate using the Zymo Direct-zol RNA MiniPrep Kit (R2050).
Pooled HUVECs from ATCC (PCS-100-013) were cultured to near confluence according to ATCC recommendations (http://www.atcc.org/products/all/PCS-100-013.aspx#generalinformation).

extract_protocol:
After treatment with HP, samples were collected in Trizol and RNA was extracted using the Zymo RNA extraction kit.
After isolating total RNA, mRNA was isolated and cDNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Library Prep Kit)

treatment_protocol: All samples (except samples 21 and 22) were treated hydrogen peroxide (HP)

value: Human Umbilical Vascular Endothelial Cells

tag: batch

value: Pooled HUVECs from ATCC (PCS-100-013)

value: siHMOX1 + HP treatment


title: 4_Scr50

description: Sample 24

value: Scrambled + HP treatment


title: 5_siR50

description: Sample 25


title: H3K4me3 SET-seq 10^2 cells_Epi_rep1


title: 3_Scr50

description: Sample 23


title: ES/PA6 7 days co-cultures FGF2 rep1

description: ES cells co-cultured with stromal PA6 cells for 7 days in serum-free medium in presence of recombinant FGF2

source_name: ES/PA6 co-cultures cultured in serum-free medium in presence of recombinant FGF2 for 7 days


title: Case7_SNParray

description: Case_7 (UPN#459)


title: JK19: 48hr NonChronic wound


title: ES/PA6 7 days co-cultures FGF2 rep2


title: Case19_SNParray

description: Case_19 (UPN#461)


title: ES/PA6 7 days co-cultures control rep 2

description: ES cells co-cultured with stromal PA6 cells for 7 days in serum-free medium in absence of growth factors

source_name: ES/PA6 co-cultures cultured in serum-free medium in absence of growth factors for 7 days


title: JK18: 24hr Chronic wound

value: Chronic Wound


title: ES/PA6 7 days co-cultures control rep1


title: 1_ScrNT50

description: Sample 21

value: Scrambled + No Treatment


title: SET-seq_1000_cells_Exp_rep2

value: untreated


title: PA6 3 days mono-cultures BMP4 rep3

description: PA6 cell monolayers cultured for 3 days in serum-free medium in presence of recombinant BMP4

source_name: PA6 mono-cultures cultured in serum-free medium in presence of recombinant BMP4 for 3 days

growth_protocol: Murine ES cells were cultured into 6-well plates onto monolayers of stromal PA6 cells in serum-free medium for 3 days, and in parallel, PA6 mono-cultures were cultured in serum-free medium for 3 days as well


title: SET-seq_1000_cells_Exp_rep1


title: SET-seq_10000_cells_Exp_rep2


title: SET-seq_100_cells_Exp_rep2


title: JK17: 24hr Chronic wound


title: Case20_SNParray

description: Case_20 (UPN#467)


title: JK16: 24hr Chronic wound


title: JK15: 24hr NonChronic wound


title: JK13: 24hr NonChronic wound


title: PA6 3 days mono-cultures BMP4 rep1


title: PA6 3 days mono-cultures BMP4 rep2


title: SET-seq_10000_cells_Exp_rep1


title: PA6 3 days mono-cultures FGF2 rep3

description: PA6 cell monolayers cultured for 3 days in serum-free medium in presence of recombinant FGF2

source_name: PA6 mono-cultures cultured in serum-free medium in presence of recombinant FGF2 for 3 days

value: recombinant FGF2 for 3 days


title: PA6 3 days mono-cultures FGF2 rep2


title: JK14: 24hr NonChronic wound


title: 2_ScrNT50

description: Sample 22


title: PA6 3 days mono-cultures control rep3

description: PA6 cell monolayers cultured for 3 days in serum-free medium in absence of growth factors

source_name: PA6 mono-cultures cultured in serum-free medium in absence of growth factors for 3 days


title: SET-seq_10_cells_Exp_rep1


title: SET-seq_100_cells_Exp_rep1


title: Brap-cKO__A3-B1-04

description: BrapcKO

value: Brapflox/ko Cre+


title: JK12: 12hr Chronic wound


title: SET-seq_10_cells_Exp_rep2


title: JK11: 12hr Chronic wound


title: Case18_RNAseq

description: Case_18 (UPN#147)

data_processing:
Reads were aligned against the human genome (GRCh38/hg38) using Star 2.6.0a
Read counts per gene were generated using HTseq 0.9.1
DESeq2 was used for differential expression analysis
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include counts generated for each Sample

extract_protocol:
RNA were extracted from bone marrow cells of patients using All Prep DNA/RNA Mini Kit (Qiagen).
Libraries were prepared following the Illumina TruSeq® Stranded mRNA Sample Preparation Guide (Low Sample protocol).

value: Unsorted Bone Marrow Cells


title: JK09: 12hr NonChronic wound


title: vitro-37℃-30mins_rep2


title: PA6 3 days mono-cultures FGF2 rep1


title: JK10: 12hr Chronic wound


title: Case10_SNParray

description: Case_10 (UPN#460)

value: bone marrow


title: ES/PA6 3 days co-cultures BMP4 rep3

description: ES cells co-cultured with stromal PA6 cells for 3 days in serum-free medium in presence of recombinant BMP4

source_name: ES/PA6 co-cultures cultured in serum-free medium in presence of recombinant BMP4 for 3 days


title: PA6 3 days mono-cultures control rep1


title: vitro-37℃-15mins_rep2


title: JK06: 6hr Chronic wound


title: JK08: 12hr NonChronic wound


title: Case11_RNAseq

description: Case_11 (UPN#260)


title: PA6 3 days mono-cultures control rep2


title: ES/PA6 3 days co-cultures BMP4 rep2


title: JK07: 12hr NonChronic wound


title: vitro-37℃-30mins_rep1


title: vitro-37℃-15mins_rep1


title: Case12_RNAseq

description: Case_12 (UPN#462)


title: vitro-37℃-10mins_rep1


title: ES/PA6 3 days co-cultures FGF2 rep3

description: ES cells co-cultured with stromal PA6 cells for 3 days in serum-free medium in presence of recombinant FGF2

source_name: ES/PA6 co-cultures cultured in serum-free medium in presence of recombinant FGF2 for 3 days


title: ES/PA6 7 days co-cultures FGF2 rep3


title: Case17_RNAseq

description: Case_17 (UPN#149)


title: JK05: 6hr Chronic wound

source_name: Chronic Wound


title: Case10_RNAseq

description: Case_10 (UPN#460)


title: ES/PA6 3 days co-cultures BMP4 rep1


title: vitro-37℃-10mins_rep2


title: JK04: 6hr Chronic wound


title: vitro-37℃-5mins_rep1


title: vitro-37℃-5mins_rep2


title: Case9_RNAseq

description: Case_9 (UPN#145)


title: vitro-16℃-30mins_rep2


title: Case8_RNAseq

description: Case_8 (UPN#143)


title: JK03: 6hr NonChronic wound


title: JK01: 6hr NonChronic wound


title: ES/PA6 3 days co-cultures FGF2 rep1


title: ES/PA6 3 days co-cultures FGF2 rep2


title: ChIP-input

city: jinan

first: Shourong

last: Wang

address: 44 Wenhua Xi Road

institute: Shandong University

data_processing:
Sequenced reads were generated by base calling using the Illumina standard pipeline
Adaptor and low-quality bases were trimmed with cutadap(version:1.9.3)
the clean reads was mapped to hg19 whole genome using bowtie2 v2.2.4
MACS(v1.4.3 )was used to perform peak calling
Genome_build: hg19
Supplementary_files_format_and_content: peak text file

extract_protocol:
Cells were lysed and protein-DNA complexes were isolated with antibody.
Antibody immunoprecipitation DNA was quantified with QubitTM (Thermo Fisher Scientifc,USA) and Agilent 2200 TapeStation (Agilent Technologies, USA). The DNA library building kit from NEB corporation was used to construct the sequencing library.

tag: cell line

value: serous ovarian cancer cell line

tag: antibody

value: input


title: Case7_RNAseq

description: Case_7 (UPN#459)


title: Ovary OHSS+Drug rep2

city: Shanghai

first: Wenzhi

last: LI

address: No. 639, Zhizaoju Road, Huangpu District, Shanghai, China

department: Department of Assisted Reproduction

institute: Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (Trimmomatic, v0.36), then mapped to mm8 whole genome using HISAT2(v2.1.0).
StringTie(v1.3.3b) and known gene models were used to evaluate gene expression.
Supplementary_files_format_and_content: raw counts

source_name: Ovary

extract_protocol:
Ovaries were removed, flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina (12301ES96, YEASEN) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ICR

value: Ovary

tag: model

value: OHSS

tag: agent

value: Nintedanib (bibf1120)


title: Ovary OHSS rep2


title: ChIP-POLR2A


title: Ovary OHSS+Drug rep1


title: Case3_RNAseq

description: Case_3 (UPN#457)


title: vitro-16℃-15mins_rep2

source_name: Embryonic stem cells


title: vitro-16℃-10mins_rep2


title: ChIP-Flag-USP39


title: Case4_RNAseq

description: Case_4 (UPN#141)


title: Ovary OHSS rep1


title: Case2_RNAseq

description: Case_2 (UPN#456)


title: Case1_RNAseq

description: Case_1 (UPN#455)


title: Ovary COH rep2


title: vitro-16℃-10mins_rep1


title: vitro-16℃-15mins_rep1


title: Ovary COH rep1


title: ES/PA6 3 days co-cultures control rep 3

description: ES cells co-cultured with stromal PA6 cells for 3 days in serum-free medium in absence of growth factors

source_name: ES/PA6 co-cultures cultured in serum-free medium in absence of growth factors for 3 days


title: ERT590_BTZ_4h_rep3_combined

first: Emily

last: Troemel

address: 4202 Bonner Hall, 9500 Gilman #0349

department: Cell and Developmental Biology

description: Bortezomib treated for 4 h

data_processing:
Reads were aligned to WS235 using Rsubreads in R studio
Reads were counted using Featurecounts in Galaxy
Differential expression analyses were performed using limma-voom in Galaxy
Genome_build: Wormbase Release WS235
Supplementary_files_format_and_content: Matrix table of normalized counts from lima-voom

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Wild-type and ERT590 (zip-1(jy13)) animals were grown on NGM plates with E. coli OP50-1 at 20°C for 48 h, and then treated with DMSO or bortezomib (final c=20 µM) for 0.5 h or 4 h.

extract_protocol:
Total RNA was extracted using TriReagent (Sigma-Aldrich) and cleaned using RNAeasy (Qiagen) column purification. RNA quality was assesed using Tapestation analysis.
TruSeq Stranded mRNA (Illumina) prep kit

treatment_protocol: Animals were treated on NGM plates with DMSO or bortezomib disolved in M9 buffer (final bortezomib concentration 20 µM); after all liquid was absorbed by agarose, plates were incubated at 20°C for 0.5 h or 4h.

value: Whole animal


title: vitro-16℃-5mins_rep2


title: vitro-16℃-30mins_rep1


title: ChIP-Seq_TS543_input

city: Singapore

first: Roberto

last: Tirado-Magallanes

email: e0056363@nus.edu.sg, rtmag4@gmail.com

state: Singapore

address: 14 Medical Dr

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
ChIP-seq data quality was monitored via FASTQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were filtered based on quality and adapter sequences were removed from the ChIP-Seq experiments using Trim_galore (https://github.com/FelixKrueger/TrimGalore) with the default options.
The resulting fastq files were aligned to the human reference genome (hg19) using STAR (Dobin et al., 2013) with the following parameters: "--alignIntronMax 1", "--outFilterMismatchNoverLmax 0.09", "--alignMatesGapMax 2000", "--outFilterMultimapNmax 1", "--alignEndsType EndToEnd"; the rest of the options were set to the default.
Picard-tools MarkDuplicates was used to remove read duplicates.
Bam files were converted to bigWig for visualization purposes using deepTools (Ramirez  et al,Nucleic acids research,  2014) normalizing by library size and transforming the values to "counts per million".
Genome_build: hg19
Supplementary_files_format_and_content: BigWig format; two experimental conditions.

source_name: Cancer stem cells

growth_protocol: The GSCs were cultured in human neural stem cell Maintenance Media (Millipore), 1% Penicillin-Streptomycin (PS) supplemented with EGF and  FGF (20 ng/ml each) to maintain stemness.

extract_protocol:
GSC cells were cross-linked with 1% formaldehyde for 10 min at room temperature. The cells were lysed using SDS Lysis buffer for ChIP (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8). The lysate was then sonicated for 25 cycles at 30% amplitude (15 s ON and 45 s OFF). The sonicated samples were then diluted in ChIP dilution buffer (0.01% SDS, 1% Triton-X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8, 167 mM NaCl) and used for the immunoprecipitation with anti-H3K4me3 (Abcam, Ab8580), or H3K27ac (Abcam, Ab4729) beads. After an over-night incubation with antibody, the bound DNA was washed sequentially with low salt wash buffer (0.1% SDS, 1% Triton X 100, 2 mM EDTA, 20 mM Tris-HCl pH 8, 150 mM NaCl), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, 500 mM NaCl), LiCl wash buffer (0.25 M LiCl, 1% NP40, 1%deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8) and TE wash buffer (10 mM Tris-HCl pH 8, 1 mM EDTA) to remove non-specific sequences and eluted in the elution buffer (84 mg NaHCO3, 1 ml 10% SDS, 9 ml H2O). Then the samples were reverse cross-linked using NaCl at 65°C overnight. The eluted DNA was purified and used for library preparation.
Briefly, end repair with NEBNext End Repair enzyme (NEB, E6050) and clean-up with 2.4x volume AMPure XP beads (Beckman Coulter, A63880). A-tailing with Klenow Fragment (3'?5' exo-, NEB, M0212) and purified with 2.4x volume AMPure XP beads. Adapter ligation reactions contained annealed universal adapter and T4 rapid ligase (NEB, B0202) and clean-up with 1.8x volume AMPure XP beads. Chromatin was amplified using KAPA Real-time Library Amplification Kit (KAPABIOSYSTEMS, KK2701) with universal primer and barcoded primer. Amplified chromatin was purified with QIAquick Gel Extraction Kit (Qiagen).

value: Glioblastoma patient derived cancer stem cell

tag: passage


title: ES/PA6 3 days co-cultures control rep1

tag: cell lines


title: 16h_2

description:
16 hours post HP treatment
Sample 20

growth_protocol:
ATCC HUVECs were cultured to near confluence and treated with 0.5 mM HP in duplicate. Samples were collected at 0 (control), 1, 2, 4, 6, 8, 10, 12, 14, and 16 hour time points. Total RNA was purified and concentrated using the Zymo Quick-RNA mini prep and RNA Clean & Concentrator kits (Zymo Research, #R1054 and #1015).
Pooled HUVECs from ATCC (PCS-100-013) were cultured to near confluence according to ATCC recommendations (http://www.atcc.org/products/all/PCS-100-013.aspx#generalinformation).

value: Human Umbilical Vascular Endothelial Cells

value: Pooled HUVECs from ATCC (PCS-100-013)

tag: time

value: 16 hours post HP treatment


title: ERT590_BTZ_4h_rep1_combined

description: Bortezomib treated for 4 h

tag: tissue


title: ChIP-Seq_TS543_H2AZ

tag: cell type


title: ES/PA6 3 days co-cultures control rep 2

tag: growth factors


title: 16h_1

description:
16 hours post HP treatment
Sample 19


title: ERT590_BTZ_4h_rep2_combined

description: Bortezomib treated for 4 h

tag: strain


title: vitro-RNA-30pg_rep2

tag: treatment

tag: chip antibody


title: JK02: 6hr NonChronic wound

value: NonChronic Wound

tag: timepoint


title: ChIP-Seq_TS543_H3K4me3


title: vitro-RNA-3ng_rep2

value: untreated

tag: age


title: ERT590_DMSO_4h_rep3_combined

description: DMSO treated for 4 h

tag: genotype


title: vitro-RNA-30pg_rep1


title: ERT590_DMSO_4h_rep2_combined

description: DMSO treated for 4 h


title: 14h_1

description:
14 hours post HP treatment
Sample 17

tag: batch

value: 14 hours post HP treatment


title: ERT590_DMSO_4h_rep1_combined

description: DMSO treated for 4 h


title: vitro-16℃-5mins_rep1


title: N2_BTZ_4h_rep3_combined

description: Bortezomib treated for 4 h

value: Wild type


title: Case9_SNParray

description: Case_9 (UPN#145)

source_name: Unsorted Bone Marrow Cells

tag: cytogenetics

tag: disease state

value: acute leukemia


title: ChIP-Seq_TS543_H3K27ac

tag: antibody


title: 12h_1

description:
12 hours post HP treatment
Sample 15

value: 12 hours post HP treatment


title: TS543 SN-3

data_processing:
RNA-seq data quality was monitored via FASTQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapters and overrepresented sequences have been removed using cutadapt software (https://cutadapt.readthedocs.io/ en/stable/).
Further reads preprocessing was performed by Trimmomatic (version 0.36) with the parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50.
Mapping of RNA-seq reads was done using STAR_2.5.0a (Dobin et al., 2013) with default parameters for RNA-seq data; the human ENSEMBL gene annotation model (GRCh37).
RSEM software (Li and Dewey, 2011)  were used to quantify the gene-level expression.
Genome_build: hg19
Supplementary_files_format_and_content: txt format; TPM values for two experimental conditions with 3 replicates each.

source_name: TS543 SN

extract_protocol:
Tree days after treatment, cells were harvested and total RNA were extracted with RNeasy® Micro Kit (Qiagen).
A modified NEBNext RNA Ultra protocol is used to prepare the libraries for mRNA sequencing. The first step is selectively purifying the poly-A containing mRNA molecules using oligo-dT attached magnetic beads. Following purification, the mRNA is fragmented using divalent cations under elevated temperature. Next, the cDNA is synthesized using Reverse transcriptase and random hexamers in a first strand synthesis reaction. Subsequently, the cDNA is converted to double stranded cDNA in a DNA polymerase based reaction. These DNA molecules are then subjected to a series of enzymatic steps for end repair, A-Tailing and ligation with NEB adapters. Finally, these adapter ligated molecules are enriched in a limited cycle PCR with indexed primers and purified using AMPure beads to create final cDNA library for sequencing.

treatment_protocol: TS543 cells were treated with either 5 uM DMSO or 5 uM of sulconazole nitrate.

tag: cell line

value: Sulconazole


title: vitro-RNA-3ng_rep1


title: N2_BTZ_4h_rep2_combined

description: Bortezomib treated for 4 h


title: 14h_2

description:
14 hours post HP treatment
Sample 18


title: TS543 SN-1

tag: passage


title: TS543 SN-2


title: 10h_1

description:
10 hours post HP treatment
Sample 13

value: 10 hours post HP treatment


title: TS543 DMSO-3

source_name: TS543 DMSO

value: DMSO


title: vitro-RNA-300ng_rep2


title: 8h_2

description:
8 hours post HP treatment
Sample 12

source_name: Endothelial Cells

value: 8 hours post HP treatment


title: 10h_2

description:
10 hours post HP treatment
Sample 14


title: 8h_1

description:
8 hours post HP treatment
Sample 11


title: TS543 DMSO-2


title: N2_DMSO_4h_rep2_combined

description: DMSO treated for 4 h


title: N2_DMSO_4h_rep3_combined

description: DMSO treated for 4 h


title: vitro-Tn5-100ng/µl_rep2


title: Case6_SNParray

description: Case_6 (UPN#151)

value: bone marrow


title: TS543 DMSO-1


title: vitro-Tn5-100ng/µl_rep1


title: Case8_SNParray

description: Case_8 (UPN#143)


title: vitro-RNA-300ng_rep1


title: 6h_2

description:
6 hours post HP treatment
Sample 10

value: 6 hours post HP treatment


title: Case3_SNParray

description: Case_3 (UPN#457)


title: vitro-Tn5-50ng/µl_rep1


title: N2_DMSO_4h_rep1_combined

description: DMSO treated for 4 h

value: Whole animal


title: vitro-Tn5-25ng/µl_rep2


title: 4h_2

description:
4 hours post HP treatment
Sample 8

value: 4 hours post HP treatment


title: Zebrafish larvae WT-acrolein-treated-rep5

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Genome_build: GRCz11
Supplementary_files_format_and_content: TPM abundance estimates and raw counts generated with kallisto.

organism: Danio rerio

growth_protocol: Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.

extract_protocol:
Larvae were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

treatment_protocol: 6 replicates were treated with acrolein from 24 hours after post fertilization to 120 hours after post fertilization.

value: WT

value: Acrolein

value: Larvae


title: ERT590_BTZ_05h_rep3_combined

description: Bortezomib treated for 0.5 h


title: ERT590_BTZ_05h_rep1_combined

description: Bortezomib treated for 0.5 h


title: vitro-Tn5-50ng/µl_rep2


title: 6h_1

description:
6 hours post HP treatment
Sample 9

value: Human Umbilical Vascular Endothelial Cells

value: Pooled HUVECs from ATCC (PCS-100-013)


title: ERT590_DMSO_05h_rep3_combined

description: DMSO treated for 0.5 h


title: Zebrafish larvae WT-acrolein-treated-rep3


title: Zebrafish larvae WT-acrolein-treated-rep6


title: vitro-Tn5-25ng/µl_rep1

value: untreated


title: Case4_SNParray

description: Case_4 (UPN#141)


title: Case2_SNParray

description: Case_2 (UPN#456)


title: 4h_1

description:
4 hours post HP treatment
Sample 7


title: ERT590_DMSO_05h_rep2_combined

description: DMSO treated for 0.5 h


title: ERT590_BTZ_05h_rep2_combined

description: Bortezomib treated for 0.5 h


title: TIPE1-KO

city: Jinan

first: xiao

middle: lei

last: Ren

address: 44 Wenhua  Xi Road

department: School of Basic Medical Science

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: macrophages

growth_protocol: BMDMs were isolated from the femur and tibia from mice with the indicated genotype and cultured with DMEM added 100ng/ml M-CSF for 5 days

extract_protocol:
Total RNA was extracted from cell  by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: celltype

value: macrophages


title: 2h_1

description:
2 hours post HP treatment
Sample 5

tag: time

value: 2 hours post HP treatment


title: 1h_2

description:
1 hour post HP treatment
Sample 4

value: 1 hour post HP treatment


title: Zebrafish larvae WT-acrolein-treated-rep1

tag: tissue


title: Zebrafish larvae WT-acrolein-treated-rep4


title: IgG SET-seq 10000 cells_epi_rep2

tag: cell type


title: Zebrafish larvae WT-rep6

source_name: Zebrafish larvae WT_larvae

value: Ctrl


title: 2h_2

description:
2 hours post HP treatment
Sample 6


title: 1h_1

description:
1 hour post HP treatment
Sample 3


title: N2_BTZ_05h_rep3_combined

description: Bortezomib treated for 0.5 h

value: Wild type


title: Zebrafish larvae WT-acrolein-treated-rep2


title: Zebrafish larvae WT-rep5


title: Case1_SNParray

description: Case_1 (UPN#455)

value: acute leukemia


title: IgG SET-seq 10000 cells_epi_rep1


title: WT

value: wild type


title: Zebrafish larvae WT-rep4


title: Control_1

description:
control (0 hour)
Sample 1

value: control (0 hour)


title: N2_BTZ_05h_rep1_combined

description: Bortezomib treated for 0.5 h


title: H3K27me3 SET-seq 10000 cells_Epi_2_rep2

value: H3K27me3 (Cat# 9733, Cell Singaling Technology)


title: Ligation based RNA seq_rep2


title: ERT590_DMSO_05h_rep1_combined

description: DMSO treated for 0.5 h

value: Whole animal


title: H3K27me3 SET-seq 1000 cells_Epi_2_rep2


title: N2_DMSO_05h_rep2_combined

description: DMSO treated for 0.5 h


title: Zebrafish larvae WT-rep2


title: N2_DMSO_05h_rep3_combined

description: DMSO treated for 0.5 h


title: H3K27me3 SET-seq 10000cells_Epi_2_rep1


title: Ligation based RNA seq_rep1


title: N2_DMSO_05h_rep1_combined

description: DMSO treated for 0.5 h


title: Zebrafish larvae WT-rep3


title: C3

city: Gui'yang

first: hu

middle: li

last: juan

address: 116 Baoshan North Road, Guiyang City, Guizhou Province, China

institute: Guizhou Normal University

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
The FPKM (Fragments per Kilobase of transcript per Million mapped reads) was calculated
The GO annotations for the DEGs in leaf were determined by using Blast2GO
Genome_build: No reference genome

organism: Sinapis alba

source_name: root

extract_protocol:
The leaves and roots were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: root

tag: Stage

value: 45 days after planting

value: Cadmium treatment group


title: Zebrafish larvae WT-rep1

value: WT

value: Larvae


title: C2


title: H3K27me3 SET-seq 1000cells_Epi_2_rep1

tag: strain


title: H3K27me3 SET-seq 100 cells_Epi_2_rep1

tag: treatment


title: G3

value: root in the control group


title: Zebrafish larvae akr1a1a-KO-rep5

source_name: Zebrafish larvae akr1a1a-KO_larvae


title: H3K27me3 SET-seq 10 cells_Epi_2_rep2

value: untreated

tag: chip antibody


title: N2_BTZ_05h_rep2_combined

description: Bortezomib treated for 0.5 h


title: C1


title: Zebrafish larvae akr1a1a-KO-rep6


title: H3K27me3 SET-seq 10 cells_Epi_2_rep1


title: 12h_2

description:
12 hours post HP treatment
Sample 16

value: Human Umbilical Vascular Endothelial Cells

value: Pooled HUVECs from ATCC (PCS-100-013)

value: 12 hours post HP treatment


title: Zebrafish larvae akr1a1a-KO-rep3

value: Ctrl


title: H3K27me3 SET-seq 100 cells_Epi_2_rep2


title: Zebrafish larvae akr1a1a-KO-rep4


title: retina_db/db_ZT18_rep3

description:
db_db_night_V3B
Gene expression data from retina of diabetic (db/db) mice at ZT18.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 21 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary.

source_name: neuronal retina, diabetic, dark-adapted

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Mice (BKS.Cq-Dock7m +/+ Leprdb/J) were kept under light/dark (LD) 12:12 cycles under standard laboratory conditions (illumination with 200 lux at cage level during the day, 20 ± 1°C, water and food ad libitum).

extract_protocol: Using the Qiagen RNeasy Mini Kit RNA was extracted from retina samples according to the manufacturer's instructions.

value: db/db

value: Retina

value: Adult


title: H3K27me3 SET-seq 10000cells_Epi_1_rep1


title: G1


title: G2


title: Control_2

description:
control (0 hour)
Sample 2

value: control (0 hour)


title: H3K27me3 SET-seq 1000 cells_Epi_1_rep2

value: H3K27me3 (Cat# 9733, Cell Singaling Technology)


title: Zebrafish larvae akr1a1a-KO-rep2


title: Bull_3

city: Hefei

first: Ibrar

middle: Muhammad

last: Khan

address: 1Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, Collage of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China, 230036

department: Animal Science

institute: Anhui Agricultural University

data_processing:
Putative Identification and Coding Potential of CircRNAs  l: Putative circRNAs were identified by filtration of anonymous transcripts. To reduce the rates of false positives; the assembled transcripts were filtrated to gain putative circRNAs by the following steps: i) the transcripts have more than one exon were selected, ii) transcripts having more than 200 bp in length, and free from exon region overlapping were desired, iii) transcripts with high expression levels where FPKM value was more than 2 log2 (fold change).
Bioinformatics Analysis of Gene Ontology (GO) and KEGG The GO term analysis and classification provides significant source genes that are involved in different biological functions, and DE circRNA genes were employed by the GO-seq R package (Young et al., 2010). All source genes in the pathways and the background genes were charted to the GO terms in the database (http://www.geneontology.org/). The GO terms with corrected (p<0.05) were recognized as relatively enriched by DE genes according to the definition of the hyper-geometric test. The significance analysis of the term enrichment was corrected by FDR, and the corrected p-value (Q-value) was obtained (Ashburner et al., 2000). The KEEG pathway-based study further elaborated the explanation of source genes and their biological functions (http://www.genome.jp).:
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: FPKM

organism: Bos taurus

growth_protocol: Animals and Samples Collection: Three physically healthy individuals (n = 3) of two different age groups, andrologically mature bulls (3±0.014 years) and immature calves (3±0.24 months), were selected for the current study

extract_protocol:
RNA Isolation, Quantification and Qualification: Total RNA was isolated from the testis samples using Trizol reagent (Takara, Beijing, China) in sterile conditions and treated with DNase I enzyme to remove endogenous DNA contamination according to the manufacturer’s protocol.
cDNA Library Construction for CircRNAs Sequencing Analysis: A total of 3 μg RNA from each testis sample was used to construct the cDNA libraries using the NEB-Next® Ultra-TM RNA Library Prep Kit for Illumina® (NEB, USA). Novogene constructed a chain-specific library by removing ribosomal RNA (Parkhomchuk et al., 2009). First, the ribosomal RNA was removed from the total RNA, and then RNA was divided into many short slices of 250–300 bp. The first cDNA strand manufactured from the fragmented RNA was used as the template strand, and random oligonucleotides were used as primers. subsequently, the RNA strand was degraded with RNase H, and then the second cDNA strand was manufactured along with dNTPs (dATP, dGTP, dUTP, and dCTP) using the DNA polymerase I system

value: Testicular

tag: group

value: andrologically mature bulls (3 plus or minus 0.014 years)

value: Untreated


title: H3K27me3 SET-seq 100 cells_Epi_1_rep2

tag: age


title: Zebrafish larvae akr1a1a-KO-rep1

tag: genotype


title: retina_db/db_ZT18_rep2

description:
db_db_night_U3B
Gene expression data from retina of diabetic (db/db) mice at ZT18.


title: retina_db/+_ZT6_rep3

description:
db_day_V2A
Gene expression data from retina of non-diabetic (db/+) mice at ZT6.

source_name: neuronal retina, non-diabetic, light-adapted

value: db/+


title: retina_db/+_ZT18_rep3

description:
db_night_V2B
Gene expression data from retina of non-diabetic (db/+) mice at ZT18.

source_name: neuronal retina, non-diabetic, dark-adapted


title: CD1

source_name: leaves

value: leaves

value: 45 days after planting

value: Cadmium treatment group


title: H3K27me3 SET-seq 1000cells_Epi_1_rep1

value: untreated


title: CD2


title: H3K27me3 SET-seq 10000 cells_Epi_1_rep2


title: Bull_2


title: CK3

value: Leaf in the control group


title: Bull_1


title: H3K27me3 SET-seq 100 cells_Epi_1_rep1


title: Calf_3

value: immature calves (3 plus or minus 0.24 months)


title: CK2


title: Calf_2


title: H3K27me3 SET-seq 10 cells_Epi_1_rep2


title: retina_db/db_ZT6_rep3

description:
db_db_day_V3A
Gene expression data from retina of diabetic (db/db) mice at ZT6.

source_name: neuronal retina, diabetic, light-adapted


title: Calf_1


title: retina_db/+_ZT6_rep2

description:
db_day_U2A
Gene expression data from retina of non-diabetic (db/+) mice at ZT6.


title: H3K27me3 SET-seq 10 cells_Epi_1_rep1

source_name: Embryonic stem cells


title: CD3


title: CK1


title: N2_BTZ_4h_rep1_combined

description: Bortezomib treated for 4 h

value: Wild type

value: Whole animal


title: 2396_PDC_EPI CELLS

status: Public on Sep 04 2021

city: Irvine

first: Farah

last: Rahmatpanah

state: CA

address: Medical sciences C

department: Pathology

institute: UCI

description: 2396_PDC_EPI CELLS(normalized)

data_processing:
Aligned to reference genomes from Ensemble with Strand NGS 3.1
Reads  filtered on duplicates to remove PCR artifacts
Used Reads Per Kilo Million (RPKM) method in Strand NGS program
Normalization of reads was performed using Audic Claverie Test (AC) test
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited normalized reads per kilo-million for each sample

source_name: PDC_EPI CELLS

growth_protocol: Each Sample was cultured with and without Epithelial cells in the culture.

extract_protocol:
Total RNA was isolated from cultured PDC cells from four individuals using FFPE RNA/DNA purification plus kit (Cat # 54300, Norgen Biotek Corp) with minor modifications
Prepared using standard Illumina protocols

tag: subject age

tag: ethnicity

value: white/nonhispanic

tag: gender

value: F

value: Peripheral blood

value: plasmacytoid dendritic cell (PDC)

tag: cocultured with

value: air liquid interface differentiated bronchial epithelial cells (PBEC)

tag: molecule subtype

value: oligo-captured sequence from total RNA


title: 5090_PDC_EPI CELLS

description: 5090_PDC_EPI CELLS(normalized)

value: M


title: 4384_PDC

source_name: PDC

value: white/hispanic


title: 5090_PDC


title: 2396_PDC


title: 4019_PDC_EPI CELLS

description: 4019_PDC_EPI CELLS(normalized)


title: 4019_PDC


title: post-pharyngeal fragments, eqx16h5

city: Cambridge

first: Peter

middle: W

last: Reddien

state: MA

address: 9 Cambridge Center

department: MIT Biology

institute: Whitehead Institute for Biomedical Research

description:
equinox_reads_collapsed_v6_reorder.txt
equinox_DEseq_Table.xlsx

data_processing:
Sequenced reads from both lanes were concatenated and quality trimmed using cutadapt v1.8 with parameteres -m 20 -q 30,30 and mapped to the ddv4 transcriptome using Bowtie v1.2 with parameter --best.
Raw read counts were generated with Samtools v1.6 idxstats and transcripts from different isoforms were summed (sum of counts for dd_v4_Smed_XXX_Y_Z for all Z)
Differential expression was determined with DESeq
Dresden S. mediterranea Transcriptome Assembly (ddv6, Rozanski et al, Nucleic Acids Research 2019)
Genome_build: Tab-separated text and excel spreadsheet files

molecule: polyA RNA

organism: Schmidtea mediterranea

source_name: anterior facing wound fragment

growth_protocol: Animals fed liver mixed with dsRNA 2 times twice per week. Cut 7 days after 8th feeding

extract_protocol: KapaHyper mRNA-Seq Kit Illumina Platform (KapaBiosystems)

treatment_protocol: Total RNA extracted from anterior facing wound fragments with 750 uL of TriZOL reagent with 5 wounds per replicate. Quantified by Qubit and Agilent Bioanalyser.

value: 16 hpa

tag: RNAi

value: equinox

tag: RNAi feedings

value: 8 feedings


title: post-pharyngeal fragments, eqx24h5

tag: time

value: 24 hpa


title: post-pharyngeal fragments, eqx24h4


title: post-pharyngeal fragments, eqx48h2

value: 48 hpa


title: post-pharyngeal fragments, eqx24h3


title: post-pharyngeal fragments, eqx48h3


title: retina_db/db_ZT6_rep2

description:
db_db_day_U3A
Gene expression data from retina of diabetic (db/db) mice at ZT6.

value: db/db

tag: tissue

value: Retina

value: Adult


title: retina_db/+_ZT18_rep2

description:
db_night_U2B
Gene expression data from retina of non-diabetic (db/+) mice at ZT18.

value: db/+


title: post-pharyngeal fragments, eqx48h1


title: retina_db/db_ZT6_rep1

description:
db_db_day_P3A
Gene expression data from retina of diabetic (db/db) mice at ZT6.


title: retina_db/+_ZT6_rep1

description:
db_day_P2A
Gene expression data from retina of non-diabetic (db/+) mice at ZT6.


title: post-pharyngeal fragments, eqx24h2


title: post-pharyngeal fragments, eqx48h5


title: post-pharyngeal fragments, eqx24h1


title: post-pharyngeal fragments, eqx16h3


title: retina_db/db_ZT18_rep1

description:
db_db_night_P3B
Gene expression data from retina of diabetic (db/db) mice at ZT18.


title: 4384_PDC_EPI CELLS

description: 4384_PDC_EPI CELLS(normalized)

tag: cell type


title: post-pharyngeal fragments, eqx16h4


title: post-pharyngeal fragments, eqx48h4


title: post-pharyngeal fragments, eqx6h5

value: 6 hpa


title: post-pharyngeal fragments, eqx16h1


title: retina_db/+_ZT18_rep1

description:
db_night_P2B
Gene expression data from retina of non-diabetic (db/+) mice at ZT18.


title: post-pharyngeal fragments, eqx6h4


title: post-pharyngeal fragments, eqx6h2


title: post-pharyngeal fragments, eqx6h1

value: 3 hpa


title: post-pharyngeal fragments, eqx3h4


title: post-pharyngeal fragments, eqx3h2


title: post-pharyngeal fragments, eqx3h1

value: 0 hpa


title: post-pharyngeal fragments, eqx3h5


title: post-pharyngeal fragments, eqx3h3


title: post-pharyngeal fragments, eqx0h2


title: post-pharyngeal fragments, u2224h5


title: post-pharyngeal fragments, u2248h4


title: post-pharyngeal fragments, u2248h2


title: post-pharyngeal fragments, eqx0h1


title: post-pharyngeal fragments, u2224h1


title: post-pharyngeal fragments, u2248h1


title: post-pharyngeal fragments, eqx0h3


title: post-pharyngeal fragments, u2248h3


title: post-pharyngeal fragments, u2216h2


title: post-pharyngeal fragments, u2216h5


title: post-pharyngeal fragments, u2224h2


title: post-pharyngeal fragments, u2224h3


title: post-pharyngeal fragments, u2216h3


title: post-pharyngeal fragments, u2224h4


title: post-pharyngeal fragments, u2216h1


title: post-pharyngeal fragments, eqx6h3


title: post-pharyngeal fragments, u226h5


title: post-pharyngeal fragments, u226h4


title: post-pharyngeal fragments, eqx16h2


title: post-pharyngeal fragments, eqx0h5


title: post-pharyngeal fragments, u226h3


title: post-pharyngeal fragments, u226h2


title: post-pharyngeal fragments, u223h2


title: post-pharyngeal fragments, u223h1


title: post-pharyngeal fragments, u2216h4


title: post-pharyngeal fragments, u220h4


title: post-pharyngeal fragments, u226h1


title: post-pharyngeal fragments, bmp_48h_1

description:
bmp_reads_collapsed_v6_reorder.txt
bmp_DEseq_Table.xlsx

data_processing:
Basecalling was performed by Illumina CASAVA 1.9
Sequenced reads from both lanes were concatenated and quality trimmed using cutadapt v1.8 with parameteres -m 20 -q 30,30 and mapped to the ddv4 transcriptome using Bowtie v1.2 with parameter --best.
Raw read counts were generated with Samtools v1.6 idxstats and transcripts from different isoforms were summed (sum of counts for dd_v4_Smed_XXX_Y_Z for all Z)
Differential expression was determined with DESeq
Genome_build: Dresden S. mediterranea Transcriptome Assembly (ddv6, Rozanski et al, Nucleic Acids Research 2019)
Supplementary_files_format_and_content: Tab-separated text and Excel spreadsheet files

growth_protocol: Standard planarian culture conditions

extract_protocol:
Total RNA extracted from anterior facing wound fragments with 750 uL of TriZOL reagent with 5 wounds per replicate. Quantified by Qubit and Agilent Bioanalyser.
KapaHyper mRNA-Seq Kit Illumina Platform (KapaBiosystems)

treatment_protocol: Animals fed liver mixed with dsRNA 2 times twice per week. Cut 7 days after 4th feeding

value: 4 feedings


title: post-pharyngeal fragments, u223h5


title: post-pharyngeal fragments, bmp_48h_2


title: post-pharyngeal fragments, bmp_48h_4


title: post-pharyngeal fragments, bmp_48h_3


title: post-pharyngeal fragments, bmp_24h_5


title: post-pharyngeal fragments, bmp_24h_2


title: post-pharyngeal fragments, bmp_24h_3


title: post-pharyngeal fragments, bmp_16h_5


title: post-pharyngeal fragments, u223h3


title: post-pharyngeal fragments, bmp_16h_4


title: post-pharyngeal fragments, u220h1


title: post-pharyngeal fragments, bmp_48h_5


title: post-pharyngeal fragments, u220h3


title: post-pharyngeal fragments, bmp_16h_1


title: post-pharyngeal fragments, bmp_16h_3


title: post-pharyngeal fragments, bmp_16h_2


title: post-pharyngeal fragments, bmp_24h_1


title: post-pharyngeal fragments, bmp_6h_5


title: post-pharyngeal fragments, u223h4


title: post-pharyngeal fragments, u220h5


title: post-pharyngeal fragments, u220h2


title: post-pharyngeal fragments, bmp_3h_5


title: post-pharyngeal fragments, bmp_24h_4


title: post-pharyngeal fragments, bmp_6h_1


title: post-pharyngeal fragments, bmp_6h_3


title: post-pharyngeal fragments, bmp_3h_3


title: post-pharyngeal fragments, u22_48h_5


title: post-pharyngeal fragments, bmp_6h_2


title: post-pharyngeal fragments, bmp_0h_5


title: post-pharyngeal fragments, u22_24h_5


title: post-pharyngeal fragments, u22_48h_1


title: post-pharyngeal fragments, bmp_0h_4


title: post-pharyngeal fragments, u22_48h_4


title: post-pharyngeal fragments, u22_24h_3


title: post-pharyngeal fragments, bmp_0h_2


title: post-pharyngeal fragments, bmp_3h_2


title: post-pharyngeal fragments, bmp_6h_4


title: post-pharyngeal fragments, bmp_0h_3


title: post-pharyngeal fragments, u22_16h_3


title: post-pharyngeal fragments, bmp_3h_4


title: post-pharyngeal fragments, u22_16h_4


title: post-pharyngeal fragments, u22_16h_2


title: post-pharyngeal fragments, u22_48h_2


title: post-pharyngeal fragments, u22_24h_2


title: post-pharyngeal fragments, bmp_0h_1


title: post-pharyngeal fragments, u22_24h_4


title: post-pharyngeal fragments, u22_16h_5


title: post-pharyngeal fragments, u22_16h_1


title: post-pharyngeal fragments, u22_48h_3


title: post-pharyngeal fragments, u22_6h_4


title: post-pharyngeal fragments, u22_6h_2


title: post-pharyngeal fragments, u22_24h_1


title: post-pharyngeal fragments, u22_6h_5


title: post-pharyngeal fragments, u22_6h_3


title: post-pharyngeal fragments, bmp_3h_1


title: post-pharyngeal fragments, u22_0h_3


title: post-pharyngeal fragments, u22_0h_4


title: post-pharyngeal fragments, u22_0h_2


title: post-pharyngeal wound fragments, 18h_anterior_facing_unc22

data_processing:
Basecalling was performed by Illumina CASAVA 1.9
Sequenced reads from all lanes were mapped using the standard 10x based mapping strategy (Cell Ranger) using the dd_v6 transcriptome in the context of the Smes genome as the gtf file. This allows for summing of isoforms during the mapping step.
Raw read counts are then expressed through three files (barcodes, features, matrix) which can be loaded in Seurat for further analysis.
Genome_build: Dresden S. mediterranea Transcriptome Assembly (ddv6, Rozanski et al, Nucleic Acids Research 2019), Smes genome (Grohme et al, Nature 2018)
Supplementary_files_format_and_content: sparse matrices from cell ranger pipeline

source_name: anterior facing post-pharyngeal wound fragment

extract_protocol:
Sorted x-insensitve cells were loaded onto the 10x v3 platform, allowing for RNA capture. An estimated 16000 cells were loaded based on FACS counts. Quantified by Agilent Bioanalyser.
Sorted x-insensitve cells were loaded onto the 10x v3 platform, resulting in library creation. Quantified by Agilent Bioanalyser.

treatment_protocol: Animals fed liver, which for one condition was mixed with dsRNA, 2 times twice per week. Cells were cut and collected 7 days after the 4th feeding.

value: 18 hpa

value: unc-22 (4 feedings)

value: propidium iodide low


title: post-pharyngeal fragments, u22_6h_1


title: post-pharyngeal fragments, u22_3h_2


title: post-pharyngeal fragments, u22_3h_4


title: post-pharyngeal fragments, u22_3h_1


title: post-pharyngeal fragments, u22_3h_5


title: GRA415A767

city: London

first: Anne

last: OGarra

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Insititue

description: Control

data_processing:
Trimmomatic v0.36 was used to remove the adapters and filter raw reads below 36 bases long.The filtered reads were aligned to the Homo sapiens genome Ensembl GRCh38 (release 95) using HISAT2 v2.1.0 with default settings and RF rna-strandedness. The mapped and aligned reads were quantified to obtain the gene-level counts using HtSeq v0.6.1 with default settings and reverse strandedness
Raw readcounts were processed using the bioconductor package DESeq2 v.1.12.4 in R v.3.5.1 and normalized using the DESeq method to remove the library-specific artefacts. Genes with 5 read counts or more in at least 12 samples were considered and normalized with variance stabilizing transformation to obtain normalized log2 gene expression values.
Genome_build: Ensembl GRCh38 (release 95)
Supplementary_files_format_and_content: VST log2 normalised expression values. Rows = genes; Columns = samples.

source_name: Blood

extract_protocol:
Total RNA was isolated, from blood from tuberculosis progressors and Treatment reponse cohorts, and IGRA-ve healthy controls simultaneously, from 1ml whole blood using the MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit . Globin RNA was depleted from the total RNA (1.5–2 μg) using the human GLOBINclear kit.
Samples (200 ng) with an RQS > 6 were used to prepare a cDNA library using the TruSeq Stranded mRNA HT Library Preparation Kit (Illumina). The tagged libraries were sized and quantitated in duplicate (Agilent TapeStation system) using D1000 ScreenTape and reagents (Agilent), normalised, pooled and then clustered using the HiSeq® 3000/4000 PE Cluster Kit (Illumina). The libraries were imaged and sequenced on an Illumina HiSeq 4000 sequencer using the HiSeq® 3000/4000 SBS kit (Illumina) at a minimum of 25 million paired-end reads (100 bp) per sample

tag: patient id

tag: subgroup

value: Control

value: M

tag: igra

value: Neg

tag: resistance

value: British Indian

value: UK Born


title: post-pharyngeal wound fragments, 18h_anterior_facing

tag: strain

value: no RNAi


title: post-pharyngeal fragments, u22_0h_1


title: GRA415A765

description: Control

tag: group

value: South Asia (ISC)

value: Foreign Born

tag: age


title: post-pharyngeal wound fragments, 18h_posterior_facing

source_name: posterior facing post-pharyngeal wound fragment


title: GRA415A768

description: Control


title: GRA415A757

description: Control


title: GRA415A760

description: Control

value: F


title: GRA415A756

description: Control


title: GRA415A759

description: Control


title: GRA415A758

description: Control


title: GRA415A764

description: Control


title: GRA415A762

description: Control


title: GRA415A753

description: Control


title: GRA415A763

description: Control


title: post-pharyngeal fragments, u22_3h_3


title: post-pharyngeal fragments, u22_0h_5


title: GRA415A755

description: Control


title: GRA415A747

description: Control

value: South Asia (Sri Lanka)


title: GRA415A748

description: Control


title: GRA415A750

description: Control


title: GRA415A742

description: Control


title: GRA415A751

description: Control


title: GRA415A752

description: Control


title: post-pharyngeal wound fragments, 6h_calcein

value: 6 hpa

value: calcein medium and high


title: GRA415A743

description: Control


title: GRA415A744

description: Control


title: GRA415A746

description: Control

value: East African (Kenya)


title: GRA415A740

description: Control


title: GRA415A766

description: Control


title: GRA415A741

description: Control


title: GRA415A749

description: Control


title: GRA415A739

description: Control

value: Central Europe (Germany)


title: GRA415A738

description: Control


title: GRA415A736

description: Control


title: GRA415A734

description: Control


title: GRA415A737

description: Control


title: GRA415A733

description: Control


title: GRA415A732

description: Control


title: GRA415A730

description: Control


title: GRA415A735

description: Control


title: post-pharyngeal wound fragments, 0h

source_name: post-pharyngeal wound fragment

value: 0 hpa


title: GRA415A728

description: Other TB Progressor

value: Other TB Progressor

value: weaker

value: Negative

value: Positive

value: Pos

value: FS

value: Europe (Portugal)


title: GRA415A727

description: Other TB Progressor


title: GRA415A726

description: Other TB Progressor


title: GRA415A725

description: Other TB Progressor


title: GRA415A731

description: Control

value: Control

value: M

value: Neg


title: GRA415A722

description: Other TB Progressor

value: Incipent TB

value: F

value: Foreign Born


title: GRA415A723

description: Other TB Progressor

value: Subclinical TB


title: GRA415A721

description: Other TB Progressor


title: GRA415A720

description: Other TB Progressor


title: GRA415A718

description: Other TB Progressor

value: similar

value: East African (Tanazia)


title: GRA415A717

description: Other TB Progressor


title: GRA415A714

description: Other TB Progressor


title: GRA415A715

description: Other TB Progressor


title: GRA415A719

description: Other TB Progressor


title: GRA415A712

description: Other TB Progressor


title: GRA415A713

description: Other TB Progressor


title: GRA415A716

description: Other TB Progressor


title: GRA415A711

description: PTB Culture Positive

value: PTB Culture Positive

value: PTB

value: Northeast Europe (Lithuania)


title: GRA415A709

description: PTB Culture Positive

value: Negative


title: GRA415A729

description: Control

value: East African (Kenya)


title: GRA415A710

description: PTB Culture Positive

value: Positive

value: Pos


title: GRA415A708

description: PTB Culture Positive


title: GRA415A702

description: PTB Culture Positive

value: British

value: UK Born


title: GRA415A706

description: PTB Culture Positive

value: M


title: GRA415A703

description: PTB Culture Positive

value: PTB_Sampled before diagnosis

value: Clinical TB


title: GRA415A707

description: PTB Culture Positive


title: GRA415A704

description: PTB Culture Positive


title: GRA415A701

description: PTB Culture Positive

value: F


title: GRA415A724

description: Other TB Progressor

value: Other TB Progressor

value: weaker

value: FS

value: Europe (Portugal)

value: Foreign Born


title: GRA415A697

description: PTB Culture Positive

value: PTB Culture Positive

value: PTB

value: similar


title: GRA415A698

description: PTB Culture Positive


title: GRA415A700

description: PTB Culture Positive


title: GRA415A694

description: PTB Culture Positive


title: GRA415A693

description: PTB Culture Positive


title: GRA415A705

description: PTB Culture Positive

value: Negative

value: Northeast Europe (Lithuania)


title: GRA415A699

description: PTB Culture Positive

value: Positive

value: Pos


title: GRA415A695

description: PTB Culture Positive

value: British

value: UK Born


title: GRA415A754

description: Control

value: Control

value: Neg

value: British Indian


title: GRA415A696

description: PTB Culture Positive

value: F


title: GRA415A690

description: Difficult TB Cases

value: Difficult TB Cases

value: weaker

value: M

value: South Asia (ISC)


title: GRA415A682

description: PTB Culture Positive

value: PTB Culture Positive

value: Foreign Born


title: GRA415A679

description: PTB Culture Positive

value: PTB


title: GRA415A681

description: PTB Culture Positive


title: GRA415A685

description: Difficult TB Cases

value: Negative


title: GRA415A691

description: Difficult TB Cases


title: GRA415A676

description: PTB Culture Positive


title: GRA415A692

description: Difficult TB Cases


title: GRA415A677

description: PTB Culture Positive


title: GRA415A688

description: Difficult TB Cases


title: GRA415A684

description: Difficult TB Cases


title: GRA415A686

description: Difficult TB Cases


title: GRA415A689

description: Difficult TB Cases


title: GRA415A683

description: PTB Culture Positive


title: GRA415A680

description: PTB Culture Positive


title: GRA415A687

description: Difficult TB Cases


title: GRA415A675

description: PTB Culture Positive


title: GRA415A669

description: PTB Culture Positive


title: GRA415A671

description: PTB Culture Positive


title: GRA415A670

description: PTB Culture Positive


title: GRA415A674

description: PTB Culture Positive


title: GRA415A672

description: PTB Culture Positive


title: GRA415A678

description: PTB Culture Positive


title: GRA415A664

description: PTB Culture Positive

value: Southeast Europe (Romania)


title: GRA415A668

description: PTB Culture Positive

value: Positive


title: GRA415A673

description: PTB Culture Positive

value: Pos


title: GRA415A663

description: PTB Culture Positive


title: GRA415A662

description: PTB Culture Positive


title: GRA415A667

description: PTB Culture Positive


title: GRA415A665

description: PTB Culture Positive

value: PTB_Sampled before diagnosis

value: Clinical TB


title: GRA415A655

description: PTB Culture Positive

value: South Africa


title: GRA415A657

description: PTB Culture Positive


title: GRA415A659

description: PTB Culture Positive


title: GRA415A653

description: PTB Culture Positive


title: GRA415A654

description: PTB Culture Positive


title: GRA415A649

description: PTB Culture Positive


title: GRA415A666

description: PTB Culture Positive


title: GRA415A660

description: PTB Culture Positive


title: GRA415A656

description: PTB Culture Positive


title: GRA415A661

description: PTB Culture Positive


title: GRA415A648

description: PTB Culture Positive


title: GRA415A641

description: PTB Culture Positive

value: similar

value: East African (Somalia)


title: GRA415A639

description: Virulent TB Strain

value: Outbreak TB strain

value: F

value: FS

value: British

value: UK Born


title: GRA415A645

description: PTB Culture Positive

value: PTB Culture Positive


title: GRA415A637

description: Virulent TB Strain

value: weaker


title: GRA415A647

description: PTB Culture Positive

value: PTB

value: Foreign Born


title: GRA415A651

description: PTB Culture Positive


title: GRA415A643

description: PTB Culture Positive


title: GRA415A652

description: PTB Culture Positive


title: GRA415A634

description: Virulent TB Strain

value: Negative


title: GRA415A650

description: PTB Culture Positive

value: Positive


title: GRA415A635

description: Virulent TB Strain

value: Pos


title: GRA415A630

description: Virulent TB Strain

value: Incipent TB


title: GRA415A642

description: PTB Culture Positive


title: GRA415A631

description: Virulent TB Strain


title: GRA415A646

description: PTB Culture Positive


title: GRA415A636

description: Virulent TB Strain


title: GRA415A632

description: Virulent TB Strain

value: Clinical TB


title: GRA415A640

description: PTB Culture Positive


title: GRA415A626

description: PTB Culture Positive

value: M

value: South Asia (ISC)


title: GRA415A658

description: PTB Culture Positive

value: Southeast Europe (Romania)


title: GRA415A628

description: PTB Culture Positive

value: similar


title: GRA415A633

description: Virulent TB Strain

value: Outbreak TB strain

value: F


title: GRA415A622

description: PTB Culture Positive


title: GRA415A623

description: PTB Culture Positive


title: GRA415A644

description: PTB Culture Positive

value: East African (Somalia)


title: GRA415A625

description: PTB Culture Positive


title: GRA415A621

description: PTB Culture Positive


title: GRA415A629

description: Virulent TB Strain

value: FS

value: British

value: UK Born


title: GRA415A619

description: PTB Culture Positive

value: PTB Culture Positive

value: PTB


title: GRA415A618

description: PTB Culture Positive

value: Foreign Born


title: GRA415A624

description: PTB Culture Positive

value: Positive


title: GRA415A638

description: Virulent TB Strain

value: weaker

value: Negative

value: Pos


title: GRA415A614

description: PTB Culture Positive


title: GRA415A610

description: PTB Culture Positive


title: GRA415A616

description: PTB Culture Positive


title: GRA415A613

description: PTB Culture Positive


title: GRA415A607

description: PTB Culture Positive

value: PTB_Sampled before diagnosis

value: Clinical TB


title: GRA415A627

description: PTB Culture Positive

value: M

value: South Asia (ISC)


title: GRA415A605

description: Other TB Progressor

value: Other TB Progressor


title: GRA415A603

description: Other TB Progressor

value: F


title: GRA415A615

description: PTB Culture Positive


title: GRA415A617

description: PTB Culture Positive

value: similar


title: GRA415A599

description: Other TB Progressor


title: GRA415A612

description: PTB Culture Positive


title: GRA415A620

description: PTB Culture Positive


title: GRA415A595

description: Other TB Progressor

value: Subclinical TB


title: GRA415A608

description: PTB Culture Positive


title: GRA415A602

description: Other TB Progressor

value: British


title: GRA415A606

description: Other TB Progressor

value: UK Born


title: GRA415A611

description: PTB Culture Positive

value: PTB Culture Positive


title: GRA415A591

description: PTB Culture Positive

value: PTB

value: East African (Zimbabwe)


title: GRA415A604

description: Other TB Progressor

value: Positive


title: GRA415A601

description: Other TB Progressor

value: weaker


title: GRA415A587

description: PTB Culture Positive

value: Negative


title: GRA415A588

description: PTB Culture Positive

value: Pos

value: Foreign Born


title: GRA415A598

description: Other TB Progressor


title: GRA415A597

description: Other TB Progressor


title: GRA415A582

description: PTB Culture Positive


title: GRA415A580

description: PTB Culture Positive


title: GRA415A592

description: PTB Culture Positive


title: GRA415A600

description: Other TB Progressor


title: GRA415A590

description: PTB Culture Positive


title: GRA415A594

description: PTB Culture Positive


title: GRA415A577

description: PTB Culture Positive


title: GRA415A576

description: PTB Culture Positive


title: GRA415A609

description: PTB Culture Positive


title: GRA415A596

description: Other TB Progressor


title: GRA415A589

description: PTB Culture Positive


title: GRA415A583

description: PTB Culture Positive


title: GRA415A575

description: PTB Culture Positive


title: GRA415A569

description: PTB Culture Positive


title: GRA415A584

description: PTB Culture Positive


title: GRA415A581

description: PTB Culture Positive


title: GRA415A567

description: PTB Culture Positive


title: GRA415A565

description: PTB Culture Positive


title: GRA415A593

description: PTB Culture Positive


title: GRA415A579

description: PTB Culture Positive


title: GRA415A574

description: PTB Culture Positive


title: GRA415A564

description: PTB Culture Positive

value: PTB_Sampled before diagnosis

value: Clinical TB


title: GRA415A563

description: Virulent TB Strain

value: Outbreak TB strain

value: M


title: GRA415A572

description: PTB Culture Positive

value: South Asia (ISC)


title: GRA415A586

description: PTB Culture Positive

value: similar


title: GRA415A578

description: PTB Culture Positive


title: GRA415A566

description: PTB Culture Positive


title: GRA415A571

description: PTB Culture Positive


title: GRA415A558

description: Virulent TB Strain


title: GRA415A556

description: Virulent TB Strain


title: GRA415A560

description: Virulent TB Strain


title: GRA415A561

description: Virulent TB Strain


title: GRA415A550

description: PTB Culture Positive


title: GRA415A562

description: Virulent TB Strain


title: GRA415A573

description: PTB Culture Positive


title: GRA415A568

description: PTB Culture Positive


title: GRA415A542

description: PTB Culture Positive


title: GRA415A545

description: PTB Culture Positive


title: GRA415A544

description: PTB Culture Positive


title: GRA415A555

description: Virulent TB Strain


title: GRA415A557

description: Virulent TB Strain


title: GRA415A570

description: PTB Culture Positive


title: GRA415A549

description: PTB Culture Positive


title: GRA415A585

description: PTB Culture Positive


title: GRA415A546

description: PTB Culture Positive


title: GRA415A559

description: Virulent TB Strain


title: GRA415A547

description: PTB Culture Positive


title: GRA415A536

description: Virulent TB Strain


title: GRA415A534

description: Virulent TB Strain


title: GRA415A535

description: Virulent TB Strain


title: GRA415A531

description: Virulent TB Strain


title: GRA415A541

description: Virulent TB Strain


title: GRA415A530

description: Virulent TB Strain


title: GRA415A540

description: Virulent TB Strain


title: GRA415A539

description: Virulent TB Strain


title: GRA415A554

description: Virulent TB Strain


title: GRA415A537

description: Virulent TB Strain


title: GRA415A553

description: Virulent TB Strain


title: GRA415A522

description: Difficult TB Cases

value: Difficult TB Cases

value: F


title: GRA415A523

description: Difficult TB Cases


title: GRA415A521

description: Difficult TB Cases


title: GRA415A520

description: Difficult TB Cases


title: GRA415A548

description: PTB Culture Positive

value: British

value: UK Born


title: GRA415A532

description: Virulent TB Strain


title: GRA415A533

description: Virulent TB Strain


title: GRA415A516

description: Virulent TB Strain


title: GRA415A526

description: Virulent TB Strain


title: GRA415A515

description: Virulent TB Strain


title: GRA415A528

description: Virulent TB Strain


title: GRA415A517

description: Virulent TB Strain


title: GRA415A524

description: Difficult TB Cases

value: PTB


title: GRA415A513

description: Virulent TB Strain


title: GRA415A525

description: Difficult TB Cases


title: GRA415A552

description: Virulent TB Strain


title: GRA415A543

description: PTB Culture Positive

value: PTB Culture Positive


title: GRA415A551

description: PTB Culture Positive

value: Positive


title: GRA415A511

description: Virulent TB Strain


title: GRA415A519

description: Virulent TB Strain

value: weaker


title: GRA415A518

description: Virulent TB Strain

value: Negative


title: GRA415A507

description: Virulent TB Strain

value: Subclinical TB

value: Pos


title: GRA415A504

description: Virulent TB Strain


title: GRA415A502

description: Virulent TB Strain


title: GRA415A501

description: Virulent TB Strain


title: GRA415A503

description: Virulent TB Strain


title: GRA415A529

description: Virulent TB Strain


title: GRA415A510

description: Virulent TB Strain


title: GRA415A514

description: Virulent TB Strain


title: GRA415A499

description: Virulent TB Strain


title: GRA415A498

description: Virulent TB Strain


title: GRA415A494

description: Virulent TB Strain


title: GRA415A495

description: Virulent TB Strain


title: GRA415A527

description: Virulent TB Strain


title: GRA415A505

description: Virulent TB Strain


title: GRA415A493

description: Virulent TB Strain


title: GRA415A491

description: Virulent TB Strain


title: GRA415A508

description: Virulent TB Strain


title: GRA415A487

description: Virulent TB Strain


title: GRA415A482

description: Virulent TB Strain


title: GRA415A500

description: Virulent TB Strain


title: GRA415A497

description: Virulent TB Strain


title: GRA415A509

description: Virulent TB Strain


title: GRA415A496

description: Virulent TB Strain


title: GRA415A474

description: PTB Culture Positive

value: East African (Zambia)

value: Foreign Born


title: GRA415A478

description: PTB Culture Positive

value: Southeast Europe (Romania)


title: GRA415A489

description: Virulent TB Strain

value: Outbreak TB strain

value: M


title: GRA415A476

description: PTB Culture Positive


title: GRA415A512

description: Virulent TB Strain


title: GRA415A490

description: Virulent TB Strain

value: similar


title: GRA415A473

description: PTB Culture Positive


title: GRA415A488

description: Virulent TB Strain


title: GRA415A469

description: PTB Culture Positive


title: GRA415A506

description: Virulent TB Strain


title: GRA415A466

description: PTB Culture Positive

value: South Asia (Pakistan)


title: GRA415A465

description: PTB Culture Positive

value: F


title: GRA415A485

description: Virulent TB Strain

value: British


title: GRA415A538

description: Virulent TB Strain

value: UK Born


title: GRA415A483

description: Virulent TB Strain


title: GRA415A460

description: PTB Culture Positive

value: PTB


title: GRA415A462

description: PTB Culture Positive

value: PTB Culture Positive


title: GRA415A484

description: Virulent TB Strain

value: Positive


title: GRA415A479

description: PTB Culture Positive


title: GRA415A481

description: Virulent TB Strain


title: GRA415A477

description: PTB Culture Positive


title: GRA415A455

description: PTB Culture Positive


title: GRA415A457

description: PTB Culture Positive


title: GRA415A475

description: PTB Culture Positive


title: GRA415A454

description: PTB Culture Positive


title: GRA415A486

description: Virulent TB Strain


title: GRA415A452

description: PTB Culture Positive


title: GRA415A461

description: PTB Culture Positive


title: GRA415A492

description: Virulent TB Strain


title: GRA415A451

description: PTB Culture Positive


title: GRA415A449

description: PTB Culture Positive


title: GRA415A480

description: PTB Culture Positive


title: GRA415A445

description: PTB Culture Positive

value: weaker

value: South Asia (ISC)


title: GRA415A471

description: PTB Culture Positive

value: Negative


title: GRA415A467

description: PTB Culture Positive

value: Pos


title: GRA415A438

description: Virulent TB Strain


title: GRA415A453

description: PTB Culture Positive


title: GRA415A450

description: PTB Culture Positive


title: GRA415A458

description: PTB Culture Positive


title: GRA415A463

description: PTB Culture Positive


title: GRA415A435

description: Virulent TB Strain


title: GRA415A468

description: PTB Culture Positive

value: East African (Zambia)


title: GRA415A436

description: Virulent TB Strain


title: GRA415A437

description: Virulent TB Strain


title: GRA415A431

description: Virulent TB Strain


title: GRA415A443

description: PTB Culture Positive

value: Foreign Born


title: GRA415A447

description: PTB Culture Positive

value: PTB_sampled before diagnosis

value: Clinical TB


title: GRA415A446

description: PTB Culture Positive


title: GRA415A444

description: PTB Culture Positive


title: GRA415A459

description: PTB Culture Positive


title: GRA415A440

description: PTB Culture Positive


title: GRA415A441

description: PTB Culture Positive


title: GRA415A439

description: PTB Culture Positive


title: GRA415A448

description: PTB Culture Positive

value: M


title: GRA415A425

description: PTB Culture Positive

value: similar

value: East African (Somalia)


title: GRA415A434

description: Virulent TB Strain

value: Outbreak TB strain

value: F


title: GRA415A433

description: Virulent TB Strain

value: British

value: UK Born


title: GRA415A424

description: PTB Culture Positive

value: PTB Culture Positive

value: PTB


title: GRA415A432

description: Virulent TB Strain

value: Positive


title: GRA415A430

description: Virulent TB Strain


title: GRA415A427

description: Virulent TB Strain

value: Subclinical TB


title: GRA415A429

description: Virulent TB Strain

value: Negative


title: GRA415A442

description: PTB Culture Positive

value: weaker

value: Pos

value: South Asia (ISC)


title: GRA415A418

description: PTB Culture Positive

value: PTB_sampled before diagnosis

value: Foreign Born


title: GRA415A417

description: Virulent TB Strain

value: M


title: GRA415A420

description: PTB Culture Positive

value: similar


title: GRA415A426

description: PTB Culture Positive

value: East African (Somalia)


title: GRA415A414

description: Virulent TB Strain

value: Outbreak TB strain


title: GRA415A422

description: PTB Culture Positive


title: GRA415A408

description: Virulent TB Strain


title: GRA415A419

description: PTB Culture Positive

value: Clinical TB


title: GRA415A411

description: Virulent TB Strain

value: British


title: GRA415A409

description: Virulent TB Strain

value: UK Born


title: GRA415A407

description: Virulent TB Strain


title: GRA415A410

description: Virulent TB Strain


title: GRA415A428

description: Virulent TB Strain

value: F


title: GRA415A415

description: Virulent TB Strain

value: PTB


title: GRA415A421

description: PTB Culture Positive

value: PTB Culture Positive

value: Positive


title: GRA415A404

description: PTB Culture Positive

value: Negative

value: British Indian


title: GRA415A416

description: Virulent TB Strain

value: Pos


title: GRA415A413

description: Virulent TB Strain


title: GRA415A406

description: PTB Culture Positive

value: weaker


title: GRA415A403

description: PTB Culture Positive


title: GRA415A398

description: Difficult TB Cases

value: Difficult TB Cases

value: East African (Uganda)


title: GRA415A396

description: Difficult TB Cases

value: M

value: Foreign Born


title: GRA415A412

description: Virulent TB Strain

value: similar


title: GRA415A395

description: TB Drug Resistance

value: TB Drug Resistance

value: R, H

value: Northeast Europe (Lithuania)


title: GRA415A399

description: PTB Culture Positive

value: UK Born


title: GRA415A392

description: TB Drug Resistance

value: PTB_sampled before diagnosis

value: Clinical TB


title: GRA415A402

description: PTB Culture Positive

value: PTB Culture Positive

value: PTB


title: GRA415A401

description: PTB Culture Positive

value: Negative

value: Positive


title: GRA415A397

description: Difficult TB Cases

value: Pos


title: GRA415A394

description: TB Drug Resistance


title: GRA415A400

description: PTB Culture Positive

value: weaker

value: British Indian


title: GRA415A405

description: PTB Culture Positive


title: GRA415A388

description: PTB Culture Positive

value: South Asia (ISC)


title: GRA415A389

description: PTB Culture Positive

value: M


title: GRA415A387

description: PTB Culture Positive

value: Foreign Born


title: GRA415A386

description: PTB Culture Positive


title: GRA415A385

description: PTB Culture Positive


title: GRA415A391

description: PTB Culture Positive


title: GRA415A390

description: PTB Culture Positive


title: GRA415A383

description: Difficult TB Cases

value: Difficult TB Cases

value: F

value: West African (Nigeria)


title: GRA415A381

description: Other TB Progressor

value: Other TB Progressor

value: East Africa (Somalia)


title: GRA415A378

description: Other TB Progressor


title: GRA415A376

description: Other TB Progressor


title: GRA415A384

description: Difficult TB Cases


title: GRA415A379

description: Other TB Progressor


title: GRA415A380

description: Other TB Progressor


title: GRA415A423

description: PTB Culture Positive

value: similar

value: East African (Somalia)


title: GRA415A372

description: Other TB Progressor

value: Subclinical TB


title: GRA415A368

description: PTB Culture Positive

value: PTB Culture Positive

value: PTB


title: GRA415A377

description: Other TB Progressor

value: Negative

value: Positive


title: GRA415A371

description: PTB Culture Positive

value: Pos


title: GRA415A393

description: TB Drug Resistance

value: TB Drug Resistance

value: R, H

value: Northeast Europe (Lithuania)


title: GRA415A364

description: PTB Culture Positive

value: M

value: Foreign Born


title: GRA415A374

description: Other TB Progressor

value: F


title: GRA415A365

description: PTB Culture Positive


title: GRA415A369

description: PTB Culture Positive


title: GRA415A367

description: PTB Culture Positive


title: GRA415A363

description: PTB Culture Positive


title: GRA415A366

description: PTB Culture Positive


title: GRA415A370

description: PTB Culture Positive


title: GRA415A360

description: PTB Culture Positive

value: South Asia (Bangladesh)


title: GRA415A359

description: PTB Culture Positive


title: GRA415A362

description: PTB Culture Positive


title: GRA415A355

description: PTB Culture Positive


title: GRA415A358

description: PTB Culture Positive


title: GRA415A361

description: PTB Culture Positive


title: GRA415A375

description: Other TB Progressor

value: Other TB Progressor


title: GRA415A349

description: Difficult TB Cases

value: Difficult TB Cases


title: GRA415A353

description: Difficult TB Cases

value: similar


title: GRA415A357

description: PTB Culture Positive


title: GRA415A351

description: Difficult TB Cases

value: East African (Somalia)


title: GRA415A350

description: Difficult TB Cases


title: GRA415A346

description: Difficult TB Cases


title: GRA415A354

description: PTB Culture Positive


title: GRA415A344

description: PTB Culture Positive

value: weaker

value: Central Africa (Cameroon)


title: GRA415A352

description: Difficult TB Cases

value: PTB


title: GRA415A343

description: PTB Culture Positive

value: PTB Culture Positive

value: Negative


title: GRA415A342

description: PTB Culture Positive

value: Positive

value: Pos


title: GRA415A347

description: Difficult TB Cases


title: GRA415A348

description: Difficult TB Cases


title: GRA415A337

description: PTB Culture Positive


title: GRA415A331

description: PTB Culture Positive

value: South Asia (ISC)


title: GRA415A330

description: PTB Culture Positive


title: GRA415A341

description: PTB Culture Positive


title: GRA415A329

description: PTB Culture Positive


title: GRA415A345

description: PTB Culture Positive


title: GRA415A332

description: PTB Culture Positive


title: GRA415A338

description: PTB Culture Positive


title: GRA415A334

description: PTB Culture Positive


title: GRA415A336

description: PTB Culture Positive


title: GRA415A328

description: PTB Culture Positive


title: GRA415A327

description: PTB Culture Positive


title: GRA415A340

description: PTB Culture Positive


title: GRA415A333

description: PTB Culture Positive


title: GRA415A322

description: PTB Culture Positive


title: GRA415A324

description: PTB Culture Positive


title: GRA415A335

description: PTB Culture Positive


title: GRA415A325

description: PTB Culture Positive


title: GRA415A339

description: PTB Culture Positive


title: GRA415A321

description: PTB Culture Positive


title: GRA415A326

description: PTB Culture Positive


title: GRA415A320

description: PTB Culture Positive


title: GRA415A319

description: PTB Culture Positive


title: GRA415A318

description: PTB Culture Positive


title: GRA415A317

description: PTB Culture Positive


title: GRA415A315

description: PTB Culture Positive


title: GRA415A356

description: PTB Culture Positive


title: GRA415A313

description: PTB Culture Positive


title: GRA415A312

description: PTB Culture Positive


title: GRA415A314

description: PTB Culture Positive


title: GRA415A308

description: PTB Culture Positive


title: GRA415A323

description: PTB Culture Positive


title: GRA415A304

description: PTB Culture Positive


title: GRA415A305

description: PTB Culture Positive


title: GRA415A306

description: PTB Culture Positive


title: GRA415A307

description: PTB Culture Positive


title: GRA415A311

description: PTB Culture Positive


title: GRA415A303

description: PTB Culture Positive


title: GRA415A302

description: PTB Culture Positive


title: GRA415A299

description: PTB Culture Positive


title: GRA415A296

description: PTB Culture Positive


title: GRA415A301

description: PTB Culture Positive


title: GRA415A316

description: PTB Culture Positive


title: GRA415A293

description: Difficult TB Cases


title: GRA415A295

description: PTB Culture Positive


title: GRA415A294

description: Difficult TB Cases


title: GRA415A298

description: PTB Culture Positive


title: GRA415A292

description: Difficult TB Cases


title: GRA415A309

description: PTB Culture Positive


title: GRA415A310

description: PTB Culture Positive


title: GRA415A291

description: Difficult TB Cases


title: GRA415A290

description: Difficult TB Cases


title: GRA415A300

description: PTB Culture Positive


title: GRA415A297

description: PTB Culture Positive


title: GRA415A285

description: Other TB Progressor

value: H

value: Central Europe (Poland)


title: GRA415A284

description: Other TB Progressor

value: Foreign Born


title: GRA415A287

description: Other TB Progressor

value: F


title: GRA415A286

description: Other TB Progressor


title: GRA415A283

description: Other TB Progressor

value: Clinical TB


title: GRA415A280

description: Difficult TB Cases

value: M

value: British

value: UK Born


title: GRA415A278

description: Difficult TB Cases

value: Difficult TB Cases

value: similar


title: GRA415A282

description: Difficult TB Cases


title: GRA415A281

description: Difficult TB Cases


title: GRA415A279

description: Difficult TB Cases


title: GRA415A277

description: Difficult TB Cases


title: GRA415A276

description: Difficult TB Cases


title: GRA415A275

description: Difficult TB Cases


title: GRA415A273

description: Difficult TB Cases


title: GRA415A272

description: Difficult TB Cases


title: GRA415A289

description: Difficult TB Cases

value: PTB_sampled before diagnosis


title: GRA415A274

description: Difficult TB Cases

value: PTB


title: GRA415A269

description: Difficult TB Cases


title: GRA415A268

description: Difficult TB Cases


title: GRA415A271

description: Difficult TB Cases


title: GRA415A266

description: Difficult TB Cases


title: GRA415A270

description: Difficult TB Cases


title: GRA415A288

description: Other TB Progressor

value: Other TB Progressor


title: GRA415A265

description: Difficult TB Cases


title: GRA415A263

description: Difficult TB Cases


title: GRA415A264

description: Difficult TB Cases


title: GRA415A373

description: Other TB Progressor

value: Subclinical TB

value: Negative

value: East Africa (Somalia)


title: GRA415A262

description: Difficult TB Cases

value: Positive

value: Pos


title: GRA415A267

description: Difficult TB Cases


title: GRA415A259

description: PTB Culture Positive

value: PTB Culture Positive

value: South Asia (ISC)


title: GRA415A260

description: PTB Culture Positive

value: F

value: Foreign Born


title: GRA415A253

description: PTB Culture Positive


title: GRA415A256

description: PTB Culture Positive


title: GRA415A251

description: PTB Culture Positive


title: GRA415A254

description: PTB Culture Positive


title: GRA415A261

description: PTB Culture Positive


title: GRA415A258

description: PTB Culture Positive


title: GRA415A248

description: PTB Culture Positive

value: M

value: East African (Somalia)


title: GRA415A250

description: PTB Culture Positive


title: GRA415A247

description: PTB Culture Positive


title: GRA415A255

description: PTB Culture Positive


title: GRA415A242

description: PTB Culture Positive


title: GRA415A246

description: PTB Culture Positive


title: GRA415A243

description: PTB Culture Positive


title: GRA415A234

description: PTB Culture Positive


title: GRA415A240

description: PTB Culture Positive


title: GRA415A245

description: PTB Culture Positive


title: GRA415A236

description: PTB Culture Positive


title: GRA415A249

description: PTB Culture Positive

value: Clinical TB


title: GRA415A230

description: PTB Culture Positive


title: GRA415A237

description: PTB Culture Positive


title: GRA415A244

description: PTB Culture Positive


title: GRA415A231

description: PTB Culture Positive


title: GRA415A252

description: PTB Culture Positive


title: GRA415A228

description: PTB Culture Positive


title: GRA415A227

description: PTB Culture Positive


title: GRA415A239

description: PTB Culture Positive


title: GRA415A257

description: PTB Culture Positive


title: GRA415A238

description: PTB Culture Positive


title: GRA415A235

description: PTB Culture Positive


title: GRA415A226

description: PTB Culture Positive


title: GRA415A225

description: PTB Culture Positive


title: GRA415A222

description: PTB Culture Positive


title: GRA415A224

description: PTB Culture Positive


title: GRA415A233

description: PTB Culture Positive


title: GRA415A229

description: PTB Culture Positive


title: GRA415A219

description: PTB Culture Positive


title: GRA415A241

description: PTB Culture Positive


title: GRA415A218

description: PTB Culture Positive


title: GRA415A232

description: PTB Culture Positive


title: GRA415A209

description: PTB Culture Positive


title: GRA415A216

description: PTB Culture Positive


title: GRA415A211

description: PTB Culture Positive


title: GRA415A221

description: PTB Culture Positive


title: GRA415A204

description: PTB Culture Positive


title: GRA415A203

description: PTB Culture Positive


title: GRA415A214

description: PTB Culture Positive


title: GRA415A205

description: PTB Culture Positive


title: GRA415A217

description: PTB Culture Positive


title: GRA415A215

description: PTB Culture Positive


title: GRA415A208

description: PTB Culture Positive


title: GRA415A207

description: PTB Culture Positive


title: GRA415A210

description: PTB Culture Positive


title: GRA415A197

description: PTB Culture Positive


title: GRA415A223

description: PTB Culture Positive


title: GRA415A199

description: PTB Culture Positive


title: GRA415A206

description: PTB Culture Positive


title: GRA415A202

description: PTB Culture Positive


title: GRA415A220

description: PTB Culture Positive


title: GRA415A212

description: PTB Culture Positive


title: GRA415A192

description: PTB Culture Positive


title: GRA415A201

description: PTB Culture Positive


title: GRA415A191

description: PTB Culture Positive


title: GRA415A198

description: PTB Culture Positive


title: GRA415A188

description: PTB Culture Positive


title: GRA415A196

description: PTB Culture Positive


title: GRA415A185

description: PTB Culture Positive


title: GRA415A195

description: PTB Culture Positive


title: GRA415A186

description: PTB Culture Positive


title: GRA415A194

description: PTB Culture Positive


title: GRA415A183

description: PTB Culture Positive


title: GRA415A189

description: PTB Culture Positive


title: GRA415A187

description: PTB Culture Positive


title: GRA415A193

description: PTB Culture Positive


title: GRA415A178

description: PTB Culture Positive

value: British

value: UK Born


title: GRA415A200

description: PTB Culture Positive


title: GRA415A213

description: PTB Culture Positive


title: GRA415A190

description: PTB Culture Positive


title: GRA415A175

description: PTB Culture Positive


title: GRA415A172

description: PTB Culture Positive


title: GRA415A184

description: PTB Culture Positive


title: GRA415A177

description: PTB Culture Positive


title: GRA415A179

description: PTB Culture Positive


title: GRA415A176

description: PTB Culture Positive


title: GRA415A182

description: PTB Culture Positive