title: Picea_P3_P2_bark_phloem

city: Vancouver

first: Dr. Kermit

last: Ritland

state: BC

address: 2424 Main Mall

department: Forest Sciences

country: Canada

institute: University of British Columbia

description: Interior spruce Bark and the attached phloem tissues were separated from the inner layers of the shoots, sampled from mature trees grown under the same environment at the Tree Breeding and Improvement Station, Prince George, BC.

hyb_protocol: A series of 45 microarray hybridizations from the bark/phloem sources of tissue are performed in accordance with the chain design of Albouyeh and Ritland (2009). The slides were pre-washed twice in 0.1% SDS at room temperature for 5 min., followed by two 2 min. washes in MilliQ-H2O, 3 min. at 95ºC in MilliQ-H2O, and dried by centrifugation (3 min at 2000 rpm in an IEC Centra CL2 centrifuge with rotor IEC 2367-00 in 50 mL conical tube). The cDNA probe was heat-denatured at 80ºC for 10 min, maintained at 65ºC prior to adding to a microarray slide that heated to 55ºC, and covered with a 22 x 60 x 1.5 mm glass coverslip.  First hybridization (cDNA hybdridization) used the ingredients of Genisphere Array350 kit (Genisphere, Hatfield, USA): 2X SDS Buffer; LNA dT blocker; nuclease-free water together with 2 ug of salmon tests DNA (Invitrogen).  The incubation condition for cDNA hybridization was 16h at 60ºC. The slide was washed in 2x SSC, 0.2% SDS at room temperature for 5 min to remove the coverslip, followed by 15 min at 65ºC in the same solution, and three washes (5 min. each) in 2x SSC at room temperature, and three washes (5 min. each) in 0.2x SSC at room temperature, and dried by centrifugation.  Second hybridization (3DNA hybridization) used the ingredients of Genisphere Array350 kit (Genisphere, Hatfield, USA): 2X SDS buffer; Cy3 3DNA dendrimer; Cy5 3DNA dendrimer; and nuclease-free water.  Incubation condition for 3DNA hybridization was 3 h at 60ºC, followed by washing and drying as described for the first hybridization.

scan_protocol: The slide was scanned using ScanArray Express (Perkin Elmer, Foster City, USA).The Cy3 and Cy5 cyanine fluors were excited with laser at 543 nm and 633 nm respectively. Scanning was consistently done with 90% laser power. The optimal photomultiplier tube (PMT) gain was set at the dynamic range of 60%<PMT<80% to minimize background intensity, and maximize the signal intensity while the number of saturated spots, excluding human positive spikes and GFP orientation marker, not exceeding 5% of each subgird . Fluorescent intensity data were quantified using the ImaGene 6 software (Biodiscovery, El Segundo, USA).

data_processing: Data were processed using ImaGene software (BioDiscovery, Inc., El Segundo, CA, USA). Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from 45 microarray hybridizations of the bark/phloem tissue sources were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) between arrays. Expression ratios of maternal parent and offspring combinations of this single parent –offspring regression framework will be used to determine the heritability (h^2) for the expression of the genes of interest.

organism: Picea engelmannii x Picea glauca

source_name: P3: 3rd Parent

label_protocol: Used Genisphere Array350 kit (Genisphere, Hatfield, USA) following the manufacturer protocol: 40 micrograms of total RNA for reverse transcription; Superscript II reverse transcriptase (Invitrogen); 5.0 pmole/ul RT Primer for Cy3/Alexa Fluor 546 or Cy5/Alexa Fluor 647; Cy5/Alexa Fluor 647 dye-labeled; hydrolyzed in 0.5 M NaOH / 0.05 M EDTA at 65ºC for 15 min; and neutralized in 1 M Tris-HCl (pH 7.5).

extract_protocol: Total RNA extraction used the protocol described by Kolosova et al. (2004) Biotechniques 36: 821-824. The extracted RNA was quantified and quality checked using spectrophotometry and agarose gel electrophoresis; in respect to the wavelength of maximum absorption at 260 nm and 280 nm and the presence of sharp bright bands of 28s and 18s ribosomal subunits at ~4.5 kb and ~1.9 kb on 1% agarose gel.

treatment_protocol: Specimen (bark/phloem sources of tissue) pooled from various shoots of the individual tree was flash-frozen on the field by liquid nitrogen and kept in -80 ºC freezer until extraction.

value: interior bark and phloem tissues

value: mature trees

tag: location

source_name: P2: 2nd Parent

label_protocol: Label protocol Used Genisphere Array350 kit (Genisphere, Hatfield, USA) following the manufacturer protocol: 40 micrograms of total RNA for reverse transcription; Superscript II reverse transcriptase (Invitrogen); 5.0 pmole/ul RT Primer for Cy3/Alexa Fluor 546 or Cy5/Alexa Fluor 647; Cy3/Alexa Fluor 546 dye-labeled; hydrolyzed in 0.5 M NaOH / 0.05 M EDTA at 65ºC for 15 min; and neutralized in 1 M Tris-HCl (pH 7.5).


title: Picea_P11_O11_bark_phloem

status: Public on Jul 15 2010

type: RNA

molecule: total RNA

source_name: P11: 11th Parent

tag: tissue

tag: developmental stage

value: Tree Breeding and Improvement Station, Prince George, BC

source_name: O11: 11th Offspring


title: Picea_O3_P2_bark_phloem

source_name: O3: 3rd Offspring


title: BRCA1 Breast tumor 60034 1922058668_A DNA

status: Public on Jul 16 2010

type: genomic

city: Brisbane

first: Nic

last: Waddell

address: St Lucia

country: Australia

institute: Queensland Centre for Medical Genomics

hyb_protocol: Standard Illumina hybridization protocol to CNV370 duo beadarrays

scan_protocol: Standard Illumina scanning protocol

data_processing: The samples were preprocessed in Illumina's Genomestudio

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: kConFab

label_protocol: Standard Illumina Infinium protocol

extract_protocol: Frozen sections of 10 um were macrodissected with a needle to ensure that the neoplastic content was >75%. DNA was extracted by the salting-out method followed by a phenol chloroform extraction

value: Breast Tumour

tag: mutation status


title: Picea_O6_P5_bark_phloem

source_name: O6: 6th Offspring

source_name: P5: 5th Parent


title: Picea_P2_O2_bark_phloem

source_name: O2: 2nd Offspring


title: Picea_P1_P15_bark_phloem

source_name: P1: 1st Parent

source_name: P15: 15th Parent

label_protocol: Used Genisphere Array350 kit (Genisphere, Hatfield, USA) following the manufacturer protocol: 40 micrograms of total RNA for reverse transcription; Superscript II reverse transcriptase (Invitrogen); 5.0 pmole/ul RT Primer for Cy3/Alexa Fluor 546 or Cy5/Alexa Fluor 647; Cy3/Alexa Fluor 546 dye-labeled; hydrolyzed in 0.5 M NaOH / 0.05 M EDTA at 65ºC for 15 min; and neutralized in 1 M Tris-HCl (pH 7.5).


title: Picea_O2_P1_bark_phloem


title: Picea_P5_P4_bark_phloem

source_name: P4: 4th Parent


title: Picea_P7_P6_bark_phloem

source_name: P7: 7th Parent

source_name: P6: 6th Parent


title: RM11a_ypd_r2

type: mixed

city: Cambridge

first: Jason

last: Funt

state: MA

address: 7 Cambridge Center

department: Biology

country: USA

institute: MIT

description: 251507210429_200909151218_S01_GE2_105_Dec08_RNAvgDNA_1_4

hyb_protocol: Standard Agilent protocols (5.7) for Agilent-015072 Yeast Oligo Microarray 4x44K G2519F

data_processing: Agilent Feature Extraction version 10.5.1.1 with dye rank correlation normalization disabled.

organism: Saccharomyces cerevisiae

source_name: RM11a YPD

label_protocol: Indirect total RNA labeling

extract_protocol: Qiagen Yeast RNA extraction

tag: strain

source_name: BY4741 DNA

value: progenitor


title: RM11a_ypd_r1

description: 251507210429_200909151218_S01_GE2_105_Dec08_RNAvgDNA_1_3

scan_protocol: Standard Agilent protocols (5.7) for Agilent-015072 Yeast Oligo Microarray 4x44K G2519F


title: BRCA1 Breast tumor 71067 1922058541_A DNA


title: BY4741_ypd_r2

description: 251507210429_200909151218_S01_GE2_105_Dec08_RNAvgDNA_1_2

source_name: BY4741 YPD


title: BRCAx Breast tumor 41413 1922058697_A DNA

value: BRCAx


title: BRCA2 Breast tumor 00864 1922058396_A DNA


title: Picea_P1_O1_bark_phloem

source_name: O1: 1st Offspring


title: Picea_P14_O14_bark_phloem

source_name: P14: 14th Parent

source_name: O14: 14th Offspring


title: Picea_P15_O15_bark_phloem

source_name: O15: 15th Offspring


title: BRCAx Breast tumor 70425 1922058428_A DNA


title: Dreducens_fermentation_T2_R3

city: Neuchâtel

first: Pilar

last: Junier

address: Rue Emile-Argand 11

department: Institute of Biology

country: Switzerland

institute: University of Neuchâtel

description: This sample is of Desulftomaculum reducens MI-1 growing by fermentation of pyruvate. It is the third of four biological replicates used in this experiment, each from separate cultures. RNA extracted in late exponential phase (T2= 30 hours)

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Desulforamulus reducens MI-1

source_name: Desulfotomaculum reducens MI-1

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Standard anaerobic conditions were used throughout the study (Balch et al., 1979). Widdel low phosphate (WLP) medium, modified from Widdel and Bak (1992), was used for all the experiments. The constituents of the WLP medium were as follows (per liter): NH4Cl, 0.25 g; CaCl2.2H2O, 0.1 g; MgCl2.6H2O, 0.5 g; NaCl, 5 g; KCl, 0.5 g; and KH2PO4, 0.03 g, vitamins and trace elements. The medium was dispensed in 100 mL volumes into 200 mL glass serum bottles and autoclaved. The following solutions were added from sterile anaerobic stocks (final concentration): yeast extract, 0.05%; NaHCO3, 30 mM; 1,4-piperazinediethane sulfonic acid disodium salt monohydrate (PIPES), 20 mM; pyruvic acid, 20 mM (unless indicated otherwise). The final pH of the medium was 7.2 ± 0.2.  All cultures were grown in a 100% N2 atmosphere.

extract_protocol: The cultures were sampled (16 mL) for RNA extraction at the time point targeted for the expression analysis.  Samples were collected in a RNAse-free 50 mL Falcon tube by centrifugation at 7000xg for 7 minutes and resuspended in 400 µL of 3 mg/ml lysozyme in TE buffer (pH 8.0) and mixed by vortexing. After digestion for 10 minutes at room temperature 1.4 mL of Buffer RLT (Qiagen) containing freshly added 0.01% vol/vol β-mercaptoethanol, was added to the sample and mixed vigorously by vortexing. The homogenized cell lysates were stored at –80oC. After all the samples were collected, the cell lysates were thawed for 15 min at 37 oC in a water bath to dissolve salts. The samples were separated into four equal aliquots of 450 µL. RNA extraction was carried out using the RNeasy extraction kit (Qiagen) with on column DNAse treatment (Qiagen). The quantity and quality of the RNA were evaluated with a Nanodrop spectrophotometer (Thermo Scientific). RNA from the four aliquots was combined and precipitated using 0.1 volume of 1M sodium acetate and 2.5 volumes cold 95% ethanol, incubating overnight at –20oC. RNA was collected by centrifugation for 15 min at 12,000xg at 4oC and washed with 75% ethanol. RNA was dried at 37oC for 20 min and resuspended in 30 µL RNAse free water. RNA concentration and quality were re-measured using the Nanodrop and the Bioanalyzer (Agilent). A total of 20 µg of total RNA per sample was sent to Nimblegen Systems (Roche) for cDNA synthesis, labeling with Cy3, and hybridization onto a custom-designed 4x77K microarrays

treatment_protocol: For experiments with U(VI) and sulfate, 100 µM U(VI) (as uranyl acetate) and 20 mM sulfate (as Na2SO4) were added, respectively.

tag: growth condition

value: Pyruvate fermentation

tag: time


title: BY4741_ypd_r1

description: 251507210429_200909151218_S01_GE2_105_Dec08_RNAvgDNA_1_1


title: Picea_O1_P15_bark_phloem


title: Picea_O12_P11_bark_phloem

source_name: O12: 12th Offspring

source_name: P11: 11th Parent


title: S6_salt_r1

description: 251507210512_200907231219_S01_GE2_105_Dec08_RNAvgDNA_1_3

source_name: S6 High Salt

source_name: Progenitor DNA


title: S2_ypd_r2

description: 251507210511_200907231234_S01_GE2_105_Dec08_RNAvgDNA_1_4

source_name: S2 YPD


title: Progenitor_salt_r2

description: 251507210512_200907231219_S01_GE2_105_Dec08_RNAvgDNA_1_2

source_name: Progenitor High Salt


title: Picea_O4_P3_bark_phloem

source_name: O4: 4th Offspring

source_name: P3: 3rd Parent


title: BRCA2 Breast tumor 30184 1922058443_A DNA

source_name: kConFab


title: Picea_O15_P14_bark_phloem


title: Picea_P4_O4_bark_phloem

source_name: P4: 4th Parent


title: Progenitor_salt_r1

description: 251507210512_200907231219_S01_GE2_105_Dec08_RNAvgDNA_1_1


title: BRCAx Breast tumor 20021 1922058337_A DNA


title: M8_ypd_r2

description: 251507210511_200907231234_S01_GE2_105_Dec08_RNAvgDNA_1_2

source_name: M8 YPD


title: BRCA2 Breast tumor 20447 1922058188_A DNA


title: M8_ypd_r1

description: 251507210511_200907231234_S01_GE2_105_Dec08_RNAvgDNA_1_1


title: S6_ypd_r2

description: 251507210510_200907231203_S01_GE2_105_Dec08_RNAvgDNA_1_4

source_name: S6 YPD


title: Picea_P4_P3_bark_phloem


title: S2_ypd_r1

description: 251507210511_200907231234_S01_GE2_105_Dec08_RNAvgDNA_1_3


title: Picea_O14_P13_bark_phloem

source_name: P13: 13th Parent


title: S6_ypd_r1

description: 251507210510_200907231203_S01_GE2_105_Dec08_RNAvgDNA_1_3


title: Progenitor_ypd_r2

description: 251507210510_200907231203_S01_GE2_105_Dec08_RNAvgDNA_1_2

source_name: Progenitor YPD


title: Picea_O7_P6_bark_phloem

source_name: O7: 7th Offspring

source_name: P6: 6th Parent


title: BRCA2 Breast tumor 50018 1922058349_A DNA


title: Progenitor_ypd_r1

description: 251507210510_200907231203_S01_GE2_105_Dec08_RNAvgDNA_1_1


title: Dreducens_fermentation_T1_R1

description: This sample is of Desulftomaculum reducens MI-1 growing by fermentation of pyruvate. It is the first of four biological replicates used in this experiment, each from separate cultures. RNA extracted in mid-exponential phase (T1= 26 hours)

source_name: Desulfotomaculum reducens MI-1


title: Picea_O5_P4_bark_phloem

description: Interior spruce Bark and the attached phloem tissues were separated from the inner layers of the shoots, sampled from mature trees grown under the same environment at the Tree Breeding and Improvement Station, Prince George, BC.

source_name: O5: 5th Offspring


title: S2_ymm_r2

description: 251507210427_200907231242_S01_GE2_105_Dec08_RNAvgDNA_1_4

source_name: S2 Low Glucose


title: Picea_P14_P13_bark_phloem

source_name: P14: 14th Parent


title: S2_ymm_r1

description: 251507210427_200907231242_S01_GE2_105_Dec08_RNAvgDNA_1_3

source_name: Progenitor DNA


title: M8_ymm_r2

description: 251507210427_200907231242_S01_GE2_105_Dec08_RNAvgDNA_1_2

source_name: M8 Low Glucose


title: M8_ymm_r1

description: 251507210427_200907231242_S01_GE2_105_Dec08_RNAvgDNA_1_1


title: Picea_P6_O6_bark_phloem

source_name: O6: 6th Offspring


title: S6_ymm_r1

description: 251507210426_200907231227_S01_GE2_105_Dec08_RNAvgDNA_1_3

source_name: S6 Low Glucose


title: Picea_P6_P5_bark_phloem

source_name: P5: 5th Parent


title: Picea_P8_O8_bark_phloem

source_name: P8: 8th Parent

source_name: O8: 8th Offspring


title: Picea_P15_P14_bark_phloem

source_name: P15: 15th Parent


title: Picea_P11_P10_bark_phloem

source_name: P11: 11th Parent

source_name: P10: 10th Parent


title: Picea_O11_P10_bark_phloem

source_name: O11: 11th Offspring


title: Progenitor_ymm_r2

description: 251507210426_200907231227_S01_GE2_105_Dec08_RNAvgDNA_1_2

source_name: Progenitor Low Glucose


title: S6_ymm_r2

description: 251507210426_200907231227_S01_GE2_105_Dec08_RNAvgDNA_1_4


title: Progenitor_ymm_r1

description: 251507210426_200907231227_S01_GE2_105_Dec08_RNAvgDNA_1_1


title: BRCA2 Breast tumor 62018 1922058329_A DNA

source_name: kConFab


title: S2_salt_r2

description: 251507210425_200907231211_S01_GE2_105_Dec08_RNAvgDNA_1_4

source_name: S2 High Salt


title: Picea_O8_P7_bark_phloem

source_name: P7: 7th Parent


title: Picea_P8_P7_bark_phloem


title: M8_salt_r2

description: 251507210425_200907231211_S01_GE2_105_Dec08_RNAvgDNA_1_2

source_name: M8 High Salt


title: S2_salt_r1

description: 251507210425_200907231211_S01_GE2_105_Dec08_RNAvgDNA_1_3


title: Picea_O10_P9_bark_phloem

source_name: O10: 10th Offspring

source_name: P9: 9th Parent


title: M8_salt_r1

description: 251507210425_200907231211_S01_GE2_105_Dec08_RNAvgDNA_1_1

source_name: Progenitor DNA


title: Picea_P7_O7_bark_phloem

source_name: O7: 7th Offspring


title: Picea_O9_P8_bark_phloem

source_name: O9: 9th Offspring


title: Picea_P9_P8_bark_phloem


title: Extended-2

city: Jupiter

first: Paul

middle: J.

last: Kenny

state: FL

address: 130 Scripps Way

department: Molecular Therapeutics

institute: The Scripps Research Institute - Florida

description: MicroRNA expression from extended access rats

hyb_protocol: Labelled RNA was hybridized overnight to epoxide glass slides spotted with the Ncode version 2 Probe set. The probe set was spotted in duplicate, so wach miRNA is detected in duplicate (REF_IDs for each miRNA in Matrix sheet given as x1 and x2).

scan_protocol: Microarrays were scanned on an Axon Genepix 4000B scanner and data extracted using GenePix GX V4.1 software.

data_processing:
After scanning and feature extraction, background-subtracted data were log base 2 transformed, then normalized and scaled on the basis of the median rat miRNA probe intensity for each probe. Because the probe set was spotted in duplicate, each miRNA was detected in duplicate (therefore, ID_REFs for each in Matrix sheet given as x1 and x2).
There was a total of n=6 rats per access condition. RNA from 2 rats per access condition were pooled on to arrays, for a total of 3 arrays per access condition, and 9 arrays in total.
Each GPR file contains data for 6 arrays (1 slide). Three are filled with samples, and three were left blank. Control samples are on GPR File-1 (blocks 1, 7 and 13), restricted access samples are on GPR File-2 (blocks 1, 7 and 13) and extended access are on GPR File-3 (blocks 4, 10 and 16).
The data shown in the non-normalized data sheet on the Series record are the raw, background-subtracted, data extracted from the GPR files.

label: Oyster-550 Fluorescent dye

organism: Rattus norvegicus

source_name: Rats dorsal striatum

label_protocol: Small RNAs were 3'-end labelled with Oyster-550 fluorescent dye using Flash-Tag kit (Genisphere).

extract_protocol: Total RNA was extracted from striatal tissues using phenol and chloroform. The upper aqueous RNA-containing layer was subjected to an additional extraction using RNASTAT60/chloroform.

treatment_protocol: Rats that had extended cocaine access

value: rat dorsal striatum

value: Wistar

tag: gender

value: male


title: Picea_O13_P12_bark_phloem

source_name: O13: 13th Offspring

source_name: P12: 12th Parent


title: Picea_P10_P9_bark_phloem


title: Restricted-2

description: MicroRNA expression from restricted access rats

treatment_protocol: Rats that had restricted cocaine access


title: Extended-1


title: Restricted-3


title: Extended-3


title: Picea_P10_O10_bark_phloem


title: Picea_P3_O3_bark_phloem

source_name: P3: 3rd Parent

source_name: O3: 3rd Offspring


title: Picea_P2_P1_bark_phloem

source_name: P2: 2nd Parent

source_name: P1: 1st Parent


title: Restricted-1


title: Control-2

description: MicroRNA expression from control rats

treatment_protocol: Rats that were cocaine-naive


title: Picea_P13_O13_bark_phloem

source_name: P13: 13th Parent


title: Control-1

description: MicroRNA expression from control rats


title: Control-3

description: MicroRNA expression from control rats


title: Picea_P13_P12_bark_phloem


title: Picea_P12_O12_bark_phloem

source_name: O12: 12th Offspring


title: Picea_P12_P11_bark_phloem

source_name: P12:12th Parent

source_name: P11: 11th Parent


title: Sternohyoid 5

city: Cleveland

first: Erik

last: van Lunteren

state: OH

address: 10701 East Boulevard

department: Pulmonary 111J(W)

institute: Cleveland VA Medical Center

description: Sternohyoid 5

hyb_protocol: Standard Affy

scan_protocol: Standard Affy

data_processing: GCOS

label: biotin

source_name: Sternohyoid muscle

label_protocol: Standard Affy

extract_protocol: Standard Affy

tag: Normal


title: liver, control, biological rep2

city: Jena

first: Steffen

last: Priebe

address: Beutenbergstr. 11a

department: Systems Biology / Bioinformatics

country: Germany

institute: Hans-Knöll-Institute (HKI)

description: Gene expression data from 4 male crossbred pig livers treated without carnitine

hyb_protocol: cRNA was fractionated and hybridized with the Affymetrix GeneChip porcine genome arrays. GeneChips were washed and stained with the Affymetrix GeneChip Fluidics station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip scanner 3000.

data_processing: After scanning the arrays, cell intensity files containing a single intensity value for each probe cell were computed from the image data with the Affymetrix GeneChip Operating Software (GCOS ver 1.1.2). Probe cell intensity data were further analyzed in the Affymetrix Expression Console 1.1 software using the Affymetrix Microarray Suite Version 5.0 (MAS 5.0) algorithm to create chip files.

organism: Sus scrofa

source_name: pig liver at 7 weeks treated without carnitine

label_protocol: cRNA was labeled with biotin using the Affymetrix GeneChip labeling kit.

growth_protocol: Sixteen male pigs with an average body weight of 10(±1) kg at four weeks of age received a basal diet for 21 days. The diet for the 8 pigs of both carnitine groups was supplemented with 500 mg L-carnitine per kg.

extract_protocol: Total RNA was isolated from liver samples using the RNeasy Minikit according to the manufacturer's instructions.

treatment_protocol: The animals were anaesthesised and exsanguinated 2.5 h after their last meal. Liver was excised and samples were stored at -80°C pending further analysis.

value: (German Landrace x Large White) x Pietrain

tag: age

value: 7 weeks

value: liver


title: Sternohyoid 6

description: Sternohyoid 6


title: liver, carnitine, biological rep1

description: Gene expression data from 4 male crossbred pig livers treated with carnitine

source_name: pig liver at 7 weeks treated with carnitine


title: Sternohyoid 4

description: Sternohyoid 4


title: Donor 3 human lung fibroblast on 25600 Pa stiffness gel

city: Boston

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

hyb_protocol: Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.  Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.

scan_protocol: Scanning is carried out on a Affymetrix GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.

data_processing: All 15 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.

label: Biotin

source_name: normal human lung fibroblast

label_protocol: In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.

growth_protocol: Normal human lung fibroblast from (Lonza) from 3 independent human subjects were seeded at a density of 50 cells per square millimeter in 96-well plates containing gels with 5 individual discrete stiffness: 100, 400, 1600, 6400, 25600 Pascals.

extract_protocol: For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. Concentrations may also be determined using a NanoDrop 1000 spectrophotometer. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).

treatment_protocol: Cells were allowed to attach to the gels in serum-free F12K media for 4 hours and incubated at 37 Celsius and 5% carbon dioxide. Media was then replaced with F12K containing 0.1% FBS for 48 hours after which cells were harvested for RNA extraction.

tag: sex

value: unknown

tag: race

tag: expt date

tag: cell type

value: normal human lung fibroblast


title: Donor 3 human lung fibroblast on 400 Pa stiffness gel


title: BRCAx Breast tumor 60450 1922058336_A DNA

source_name: kConFab


title: Sternohyoid 2

description: Sternohyoid 2


title: Donor 2 human lung fibroblast on 400 Pa stiffness gel


title: liver, carnitine, biological rep2


title: Donor 2 human lung fibroblast on 1600 Pa stiffness gel


title: Donor 3 human lung fibroblast on 100 Pa stiffness gel


title: Donor 3 human lung fibroblast on 1600 Pa stiffness gel


title: Donor 1 human lung fibroblast on 25600 Pa stiffness gel


title: Sternohyoid 3

description: Sternohyoid 3


title: Donor 3 human lung fibroblast on 6400 Pa stiffness gel


title: Donor 2 human lung fibroblast on 100 Pa stiffness gel


title: Donor 2 human lung fibroblast on 25600 Pa stiffness gel


title: Sternohyoid 1

description: Sternohyoid 1


title: Donor 1 human lung fibroblast on 100 Pa stiffness gel


title: Donor 2 human lung fibroblast on 6400 Pa stiffness gel


title: Donor 1 human lung fibroblast on 400 Pa stiffness gel


title: liver, control, biological rep1


title: Picea_P5_O5_bark_phloem

description: Interior spruce Bark and the attached phloem tissues were separated from the inner layers of the shoots, sampled from mature trees grown under the same environment at the Tree Breeding and Improvement Station, Prince George, BC.

source_name: P5: 5th Parent

source_name: O5: 5th Offspring


title: CD34+hUCBH07112

city: Tokyo

first: Jun

last: Yasuda

address: 3-8-31, Ariake, Koto-ku

department: Cell Biology

country: Japan

institute: The JFCR-Cancer Institute

description: Gene expression before transplantation

hyb_protocol: Based on standard Agilent protocol (Gene Expression Hybridization kit)

scan_protocol: Agilent Technologies Scanner G2505C US84100219

data_processing: Feature Extraction Ver. 9.5.3. The normalization and filtering steps were based on the Agi4x44PreProcess reference manual. I have utilized the parameters in the manual automatically as default. Probes before filtering 45015. Probes after filtering for controls, flags, above background, ect. 23807.

source_name: cryopreserved CD40+ human UCB

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 250 ng RNA using the One-Color Low RNA Fluorescent Linear Amplification PLUS kit (Agilent)

extract_protocol: Qiagen RNA easy mini kit

tag: engraftment

value: failed


title: Donor 1 human lung fibroblast on 6400 Pa stiffness gel


title: CD34+hUCBH07105

description: Gene expression before transplantation

source_name: cryopreserved CD39+ human UCB

value: successful

value: CD34+ UCB


title: CD34+hUCBH07093

description: Gene expression before transplantation

source_name: cryopreserved CD38+ human UCB


title: Donor 1 human lung fibroblast on 1600 Pa stiffness gel


title: CD34+hUCBH07088

description: Gene expression before transplantation

source_name: cryopreserved CD44+ human UCB


title: CD34+hUCBH07133

description: Gene expression before transplantation

source_name: cryopreserved CD42+ human UCB


title: CD34+hUCBH07059

description: Gene expression before transplantation

source_name: cryopreserved CD45+ human UCB


title: CD34+hUCBH07056

description: Gene expression before transplantation

source_name: cryopreserved CD36+ human UCB


title: CD34+hUCBH07122

description: Gene expression before transplantation

source_name: cryopreserved CD41+ human UCB


title: CD34+hUCBH07030

description: Gene expression before transplantation

source_name: cryopreserved CD43+ human UCB


title: CD34+hUCBH07041

description: Gene expression before transplantation

source_name: cryopreserved CD35+ human UCB


title: Picea_P9_O9_bark_phloem

source_name: P9: 9th Parent

value: interior bark and phloem tissues

value: mature trees

source_name: O9: 9th Offspring


title: KO_493

city: Philadelphia

first: Duonan

last: Yu

state: PA

address: 3615 Civic center Blvd, ARC Rm315F

department: hematology

institute: The children's hospital of philadelphia

description: Gene expression data from miR-144/451-null primary Ter119+/CD71+/FSC-high bone marrow cells

hyb_protocol: According to the standard procesure from microarray core facility at the University of Pennsylvania (http://www.med.upenn.edu/microarr/Data%20Analysis/Affymetrix/methods.htm).

data_processing: Raw array data was processed by the R/Bioconductor implementation of Robust Multi-chip Average (RMA) method.

organism: Mus musculus

source_name: Ter119+/CD71+/FSC-high miR-144/451-null BM cells

growth_protocol: Bone marrow cells were freshly isolated from mice.

extract_protocol: According to the manufacture's instruction from Invitrogen.

treatment_protocol: Primary cells were stained with Ter119 and CD71 antibodies and double positive cells with large cell size (FSC high) were sorted directly to Trizol LS reagent for total RNA extraction.

value: primary bone marrow cell

tag: mirna construct

value: mir 493

tag: genotype/variation

value: miR-144/451 knockout


title: WT_497

description: Gene expression data from wide type primary Ter119+/CD71+/FSC-high bone marrow cells

scan_protocol: According to the standard procesure from microarray core facility at the University of Pennsylvania (http://www.med.upenn.edu/microarr/Data%20Analysis/Affymetrix/methods.htm).

source_name: Ter119+/CD71+/FSC-high WT BM cells

value: mir 497

value: wild type


title: KO_548

label_protocol: According to the standard procesure from microarray core facility at the University of Pennsylvania (http://www.med.upenn.edu/microarr/Data%20Analysis/Affymetrix/methods.htm).

value: mir 548


title: CD34+hUCBH07007

description: Gene expression before transplantation

source_name: cryopreserved CD34+ human UCB


title: KO_551

value: mir 551


title: WT_504

value: mir 504


title: WT_550

value: mir 550


title: CD34+hUCBH07089

description: Gene expression before transplantation

source_name: cryopreserved CD37+ human UCB


title: AICD/P19_differentiated

status: Public on Jul 14 2010

city: Matsumoto

first: Kohzo

last: Nakayama

address: Asahi

department: Anatomy

institute: Shinshu University

description: Gene expression of AICD/P19 cells in the differentiated state

hyb_protocol: Cy3-labeled cRNAs were hybridized to Whole Mouse Genome oligo-DNA microarray (Agilent) at 65°C for 17 hours using Gene Expression Hybridization Kit (Agilent) and washed using Gene Expression Wash Pack (Agilent).

scan_protocol: Intensities of Cy3-fluorescent signals were scanned by Agilent DNA microarray scanner.

data_processing: The raw data was converted into the quantitative data using Agilent Feature Extraction software version 10.1.1.1.  Data were further normalized using GeneSpringGX10 using Median shift normalization to the 75th percentile and baseline transformed to the median of all samples.

source_name: AICD/P19, differentiated state

label_protocol: Cy3-labeled cRNA probes were synthesized according to the manufacture’s instruction (Agilent, Quick Amp Labeling Kit). Briefly mentioned, 0.2μg of each total RNA was reverse transcribed to double-stranded cDNA using T7 promoter sequence adding to oligo dT nucleotide as a primer. cRNAs were transcribed from these double-stranded cDNAs by T7 RNA polymerase.

growth_protocol: P19 cells were cultured in alpha-modified Eagle’s essential medium (Sigma) containing 10% FCS and 2 mM L-glutamine.

extract_protocol: Total RNAs were prepared using ISOGENE (Nippon Gene, Toyama Japan) at each state of these cells according to the manufacture’s instruction. The qualities and integrities of these RNAs were verified by gel electrophoresis and by Agilent Bioanalyzer (Böblingen, Germany).

treatment_protocol: To induce neural differentiation of these P19 cell lines, cells were allowed to aggregate in culture medium with 5×10-7 M all-trans-retinoic acid (RA) for 4 days. After aggregation, cells were replated onto cell culture grade dishes or poly-L-Lysine coated cell-disks for two days.

value: embryonic carcinoma cell line

tag: cell line

value: expressing AICD


title: nusA11 mutant, replicate 2

first: Diogo

middle: M.

last: Camacho

address: 44 Cummington Street

department: Biomedical Engineering

institute: Howard Hughes Medical Institute

hyb_protocol: Following fragmentation, biotynilated cDNA was hybridized to Affymetrix E. coli Antisense Genome arrays for 16h at 45C and 60rpm.

scan_protocol: GeneChips were scanned at 532 nm using an Affymetrix Gene Scanner 3000.

data_processing: Data were normalized with RMA Express

organism: Escherichia coli

source_name: nusA11 mutant

label_protocol: Biotinylated cDNA was prepared using and Enzo BioArray Terminal Labeling Kit with Biotin-ddUTP.

extract_protocol: Total RNA was obtained using the Rneasy Protect Bateria Mini kit (Qiagen) according to manufacturer's instructions.


title: AICD/P19_undifferentiated

description: Gene expression of AICD/P19 cells in the undifferentiated state

source_name: AICD/P19, undifferentiated state


title: nusA11 mutant, replicate 1


title: MB10 (S14764)

city: Chiba

first: Takashi

last: Takabatake

state: Chiba

address: Anagawa 4-9-1, Inage-ku

institute: National Institute of Radiological Sciences

description:
Gene expression in medulloblastoma developed in mouse after 1.5 Gy irradiation.
R-type

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity > 10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters (protocol GE1-v1-v5_95_Feb07 and Grid: 014868_D_F_20080627) to obtain background-subtracted Processed Signal intensities. Data were analyzed with GeneSpring GX 10.0.2.
Expression data were normalized both “per chip” to the 75th percentile of all measurements in that sample and “per gene” to median expression levels of the gene across all samples (Median_all) or to mean expression levels of the gene of Sample 'MB1 (S14516)' (GSM480632) and Sample 'MB2 (S14610)' (GSM480633) (VALUE).

source_name: Medulloblastoma, 1.5 Gy irradiation

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.8 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All animals were bred under conventional conditions in our animal facility.  They were housed in an air-conditioned room (23 ± 3˚C) with a relative humidity of 40 ± 10% under an alternating 12-hour light/dark schedule (lights on at 7:00am).

extract_protocol: Total RNA were purified by using AllPrep DNA/RNA mini kit (Qiagen, Valencia, CA) and Trizol Reagent (Invitrogen, Carlsbad, CA).  Briefly, samples were homogenized in RLT plus buffer included in the kit. The homogenates were ten-fold diluted with Trizol Reagent and total RNA was subsequently purified according to manufacturer’s instructions for Trizol Reagent.  The quality of total RNA was assessed by using the QIAxcel system (Qiagen). RNA was quantified using a NanoDrop-1000.

treatment_protocol: Ptch1+/- mice (C3B6F1 background) were irradiated at postnatal day 1 using a Pantak HF-320 X-ray generator (Pantak Ltd., East Haven, CT, USA). Mice were observed daily until moribund and then were killed under ether anesthesia.

tag: genotype

tag: tissue

value: medulloblastoma

value: female

tag: irradiation


title: Wild type cells, replicate 1

source_name: wild type cells

tag: strain


title: MB12 (S14862)


title: MB11 (S14843)


title: MB9 (S14636)

description:
Gene expression in medulloblastoma developed in mouse after 0.2 Gy irradiation.
R-type

source_name: Medulloblastoma, 0.2 Gy irradiation


title: pCDNA/P19_aggregated

description: Gene expression of pCDNA/P19 cells in the aggregated state

source_name: pCDNA/P19, aggregated state

value: carrying an empty vector


title: pCDNA/P19_undifferentiated

description: Gene expression of pCDNA/P19 cells in the undifferentiated state

source_name: pCDNA/P19, undifferentiated state


title: Wild type cells, replicate 3


title: pCDNA/P19_differentiated

description: Gene expression of pCDNA/P19 cells in the differentiated state

source_name: pCDNA/P19, differentiated state


title: nusA11 mutant, replicate 3


title: AICD/P19_aggregated

description: Gene expression of AICD/P19 cells in the aggregated state

source_name: AICD/P19, aggregated state


title: MB8 (S14586)


title: PHRI2347

type: protein

city: Bronx

first: Shajo

last: Kunnath-Velayudhan

state: NY

address: 1300 Morris Park Ave

department: Microbiology and Immunology

institute: Albert Einstein College of Medicine

hyb_protocol: Sera were pre-absorbed with E. coli-lysate for 30 minutes.  Prior to incubating with serum, slides were blocked for 30 minutes with Blocking Solution (Candor Bioscience, Germany).  Slides were incubated with sera diluted with LowCross Buffer (Candor Bioscience, Germany) at 40C overnight with gentle shaking.  After washing the slides, the arrays were incubated with biotinylated secondary antibody (Jackson Immunoresearch, USA) for one hour.  After washing, the arrays were incubated with streptavidin SureLightP-3 (Columbia Biosciences, USA) for one hour.  The slides were washed and dried by centrifugation before scanning.

scan_protocol: The slides were scanned with a Genepix 4200AL microarray scanner (Molecular Devices, USA). The scanner’s laser power and PMT gain were calibrated daily to intensities obtained with two reference sera to control for day-to-day variation.  Fluorescence intensities were quantified by using Genepix Pro 6.0 (Molecular Devices, USA).

data_processing: log transformed raw data were used for analysis without normalization.

label: biotin/streptavidin SureLightP-3

molecule: protein

label_protocol: See hyb protocol for detection method using biotinylated secondary antibody.

growth_protocol: not applicable

extract_protocol: Used fresh serum.

treatment_protocol: not applicable

tag: final diagnosis

value: Smear neg Culture pos TB HIV neg

tag: age in years

value: F

tag: country of serum collection

value: GAMBIA

tag: m. tuberculosis culture

value: POS

tag: acid fast bacilli (afb) smear microscopy

value: NEG

tag: afb smear grade

value: not applicable

tag: chest x-ray

value: ABNORMAL

tag: chest x-ray description

value: NONCAVITARY

tag: previous history of active tb

value: NO

tag: hiv status

tag: bcg scar or history

tag: tuberculin skin test

tag: quantiferon test

value: NOT DONE

tag: t-spot. tb test


title: PHRI2340

value: Smear pos Culture pos TB HIV neg

tag: sex

value: M

value: Kenya

value: CAVITARY

value: YES

value: UNKNOWN


title: PHRI2343

value: Brazil


title: MB6 (S14815)

description:
Gene expression in medulloblastoma developed in mouse after 0.2 Gy irradiation.
S-type

tag: genotype

tag: tissue

value: medulloblastoma

tag: gender

value: male

tag: age

tag: irradiation


title: MB7 (S14360)

tag: strain

value: female


title: PHRI2336

source_name: serum_nonTB disease

tag: final diagnosis

value: NonTB HIVneg

tag: age in years

tag: country of serum collection

value: Spain

tag: m. tuberculosis culture

tag: acid fast bacilli (afb) smear microscopy

value: NORMAL


title: PHRI2337

value: POS

tag: afb smear grade

tag: chest x-ray

value: ABNORMAL

tag: chest x-ray description

tag: previous history of active tb

tag: hiv status

value: NEG


title: PHRI2344

tag: sex

value: Bangladesh

value: not applicable

value: NONCAVITARY

value: NO

tag: bcg scar or history

tag: tuberculin skin test

tag: quantiferon test

value: NOT DONE

tag: t-spot. tb test


title: MB4 (S14762)

tag: genotype

tag: tissue

tag: gender

tag: age

tag: irradiation


title: MB5 (S14789)

tag: strain


title: Normal cerebellum 3 (S15560)

description: Gene expression in normal cerebellum.

source_name: Normal cerebellum

value: cerebellum


title: MB2 (S14610)

description:
Gene expression in medulloblastoma developed in nonirradiated mouse.
S-type

source_name: Medulloblastoma, nonirradiated


title: PHRI2335

tag: final diagnosis

value: Smear pos Culture pos TB HIV neg

tag: age in years

value: M

tag: country of serum collection

value: Peru

tag: m. tuberculosis culture

tag: acid fast bacilli (afb) smear microscopy

value: UNKNOWN

value: YES


title: PHRI2339

value: NonTB HIVneg

value: GAMBIA

tag: afb smear grade

tag: chest x-ray

tag: chest x-ray description

tag: previous history of active tb

tag: hiv status


title: PHRI2324

tag: sex

value: Colombia

tag: bcg scar or history

tag: tuberculin skin test

tag: quantiferon test

tag: t-spot. tb test


title: PHRI2322

value: POS


title: PHRI2331

value: ABNORMAL

value: CAVITARY


title: PHRI2323

value: Smear neg Culture pos TB HIV neg

value: F

value: NEG


title: PHRI2319

value: not applicable

value: NONCAVITARY

value: NO


title: Normal cerebellum 2 (S15409)

description: Gene expression in normal cerebellum.

tag: tissue

value: cerebellum

tag: gender

value: female

tag: age

tag: irradiation


title: MB3 (S14611)

tag: strain

tag: genotype

value: medulloblastoma


title: MB1 (S14516)


title: Normal cerebellum 1 (S15407)

description: Gene expression in normal cerebellum.


title: PHRI2315

tag: final diagnosis

tag: age in years

tag: country of serum collection

tag: m. tuberculosis culture

tag: acid fast bacilli (afb) smear microscopy

value: NOT DONE


title: PHRI2318

value: Bangladesh

tag: afb smear grade

tag: chest x-ray

tag: chest x-ray description

tag: previous history of active tb

tag: hiv status

value: YES

value: UNKNOWN


title: PHRI2313

value: Smear pos Culture pos TB HIV neg

tag: sex

value: M

value: Colombia

tag: bcg scar or history

tag: tuberculin skin test

tag: quantiferon test

tag: t-spot. tb test


title: PHRI2314

value: NonTB HIVneg

value: Spain

value: ABNORMAL

value: POS


title: PHRI2321

value: South Africa

value: CAVITARY

value: NEG


title: PHRI2307

value: F

value: NONCAVITARY

value: NO


title: PHRI2311

value: Tanzania

value: not applicable

value: NORMAL

value: NOT DONE


title: PHRI2310

value: Smear neg Culture pos TB HIV neg

value: UNKNOWN


title: PHRI2305

value: YES


title: PHRI2309

source_name: serum_LTBI neg

value: Asymptomatic LTBI neg nonendemic

value: M

value: ITALY


title: PHRI2306

value: NonTB HIVneg


title: Wild type cells, replicate 2

tag: strain


title: PHRI2308

value: Smear pos Culture pos TB HIV neg

value: Kenya

value: POS

value: ABNORMAL


title: PHRI2295

value: Spain

value: NEG


title: PHRI2297

value: NONCAVITARY

value: NO


title: PHRI2282

value: F

value: not applicable

value: CAVITARY


title: PHRI2279

value: Peru

value: UNKNOWN

value: NOT DONE


title: PHRI2294

value: M

value: Colombia

value: NORMAL

value: YES


title: PHRI2289

value: Smear pos Culture pos TB HIV neg


title: PHRI2287

value: NonTB HIVneg


title: PHRI2284

value: GAMBIA

value: ABNORMAL

value: POS


title: PHRI2275

value: Spain

value: NEG


title: PHRI2291

value: F

value: NONCAVITARY

value: NO


title: PHRI2271

value: Smear neg Culture pos TB HIV neg

value: not applicable


title: PHRI2272

value: Vietnam

value: UNKNOWN

value: NOT DONE


title: PHRI2276

value: Asymptomatic LTBI neg nonendemic

value: M

value: ITALY


title: PHRI2293

value: NonTB HIVneg

value: Tanzania

value: YES


title: PHRI2252

value: Smear pos Culture pos TB HIV neg

value: Kenya

value: POS

value: ABNORMAL


title: PHRI2270

value: F

value: NONCAVITARY

value: NEG


title: PHRI2250

value: Spain

value: not applicable

value: NO


title: PHRI2243

value: Bangladesh

value: CAVITARY

value: UNKNOWN

value: NOT DONE


title: PHRI2263

value: M


title: PHRI2254

value: Smear neg Culture pos TB HIV neg

value: Vietnam


title: PHRI2269

value: GAMBIA


title: PHRI2257

value: Smear pos Culture pos TB HIV neg

value: South Africa

value: YES


title: PHRI2262

value: NonTB HIVneg

value: F

value: NORMAL


title: PHRI2240

value: Colombia

value: NEG


title: PHRI2247

value: Spain

value: not applicable

value: ABNORMAL

value: NONCAVITARY

value: NO


title: PHRI2249

value: M

value: POS

value: CAVITARY

value: NOT DONE


title: PHRI2248

value: Smear neg Culture pos TB HIV neg

value: Kenya

value: UNKNOWN


title: PHRI2303

value: Smear pos Culture pos TB HIV neg

value: Brazil


title: PHRI2241

value: Asymptomatic LTBI neg nonendemic

value: F

value: ITALY


title: PHRI2236

value: NonTB HIVneg

value: Tanzania

value: NEG

value: NORMAL

value: YES


title: PHRI2237

value: M

value: South Africa

value: ABNORMAL

value: NO


title: PHRI2242

value: POS

value: CAVITARY

value: NOT DONE


title: PHRI2211

value: Smear pos Culture pos TB HIV neg

value: Vietnam

value: UNKNOWN


title: PHRI2208

value: Asymptomatic LTBI neg nonendemic

value: F

value: not applicable


title: PHRI2232

value: NonTB HIVneg

value: Spain


title: PHRI2229

value: NEG


title: PHRI2209

value: NORMAL

value: YES


title: PHRI2238

value: M

value: Colombia


title: PHRI2233

value: GAMBIA

value: ABNORMAL

value: NONCAVITARY

value: NO


title: PHRI2213

value: Smear pos Culture pos TB HIV neg

value: Bangladesh

value: POS

value: NOT DONE


title: PHRI2217

value: Smear neg Culture pos TB HIV neg

value: UNKNOWN


title: PHRI2207

value: NonTB HIVneg

value: Tanzania

value: not applicable


title: PHRI2223

value: CAVITARY

value: NEG


title: PHRI2204

value: M

value: Brazil


title: PHRI2199

value: F

value: South Africa

value: YES


title: PHRI2200

value: Vietnam

value: ABNORMAL

value: NONCAVITARY

value: NO


title: PHRI2198

value: Bangladesh

value: POS

value: NOT DONE


title: PHRI2175

value: NonTB HIVneg

value: Spain

value: UNKNOWN


title: PHRI2181

value: Smear neg Culture pos TB HIV neg

value: not applicable


title: PHRI2178

value: Colombia

value: NEG


title: PHRI2184

value: F

value: NORMAL


title: PHRI2162

value: Tanzania


title: PHRI2194


title: PHRI2172

value: Smear pos Culture pos TB HIV neg

value: Peru

value: YES


title: PHRI2196

value: ABNORMAL

value: NONCAVITARY

value: NO


title: PHRI2197

value: M

value: NOT DONE


title: PHRI2163

value: Spain

value: POS


title: PHRI2160

value: Smear neg Culture pos TB HIV neg

value: GAMBIA


title: PHRI2146

value: UNKNOWN

value: Bangladesh

value: not applicable


title: PHRI2135

value: NonTB HIVneg

value: F

value: Colombia

value: NEG


title: PHRI2142

value: NORMAL

value: YES


title: PHRI2148

value: ABNORMAL

value: NONCAVITARY


title: PHRI2145

value: Asymptomatic LTBI neg nonendemic

value: ITALY


title: PHRI2132

value: Tanzania

value: NO

value: NOT DONE


title: PHRI2153

value: M

value: GAMBIA


title: PHRI2158

value: Smear neg Culture pos TB HIV neg

value: Vietnam

value: POS

value: UNKNOWN


title: PHRI2143

value: NonTB HIVneg

value: F

value: not applicable


title: PHRI2159

value: Colombia

value: NEG

value: NORMAL

value: YES


title: PHRI2128

value: Spain


title: PHRI2127

value: ABNORMAL

value: NONCAVITARY


title: PHRI2125

value: Asymptomatic LTBI neg nonendemic

value: ITALY


title: PHRI2131


title: PHRI2183

value: NO

value: NOT DONE


title: PHRI2182

value: Smear pos Culture pos TB HIV neg

value: M

value: Bangladesh


title: PHRI2134

value: NonTB HIVneg

value: Tanzania

value: UNKNOWN


title: PHRI2124

value: F

value: not applicable


title: PHRI2116

value: NEG


title: PHRI2120

value: Kenya

value: POS

value: CAVITARY

value: YES


title: PHRI2119

value: GAMBIA

value: NORMAL


title: PHRI2117

value: Vietnam

value: ABNORMAL

value: NONCAVITARY

value: NO


title: PHRI2109

value: Asymptomatic LTBI neg nonendemic

value: ITALY


title: PHRI2118

value: NonTB HIVneg

value: M

value: Colombia

value: NOT DONE


title: PHRI2115

value: Tanzania

value: NEG

value: not applicable

value: UNKNOWN


title: PHRI2111

value: F


title: PHRI2113

value: GAMBIA


title: PHRI2106

value: Smear neg Culture pos TB HIV neg

value: POS


title: PHRI2114

value: Smear pos Culture pos TB HIV neg

value: Kenya

value: ABNORMAL

value: CAVITARY

value: YES


title: PHRI2101

value: Bangladesh

value: NONCAVITARY

value: NO


title: PHRI2092

value: Colombia

value: NOT DONE


title: PHRI2093

value: NonTB HIVneg

value: M

value: NEG


title: PHRI2105

value: F

value: not applicable

value: UNKNOWN


title: PHRI2103

value: GAMBIA


title: PHRI2088

value: Asymptomatic LTBI neg nonendemic

value: ITALY


title: PHRI2087

value: Smear pos Culture pos TB HIV neg

value: Peru

value: POS


title: PHRI2074

value: Tanzania

value: NORMAL

value: YES


title: PHRI2084

value: Smear neg Culture pos TB HIV neg

value: ABNORMAL

value: NONCAVITARY

value: NO


title: PHRI2077

value: NonTB HIVneg

value: M

value: Colombia

value: NEG

value: NOT DONE


title: PHRI2075

value: not applicable

value: UNKNOWN


title: PHRI2086

value: F

value: Vietnam


title: PHRI2076


title: PHRI2070

value: Smear pos Culture pos TB HIV neg

value: Brazil

value: POS


title: PHRI2067

value: Tanzania

value: NORMAL


title: PHRI2058

value: ABNORMAL

value: CAVITARY

value: YES


title: PHRI2091

value: NONCAVITARY

value: NO


title: PHRI2061

value: NonTB HIVneg

value: Colombia


title: PHRI2063

value: Bangladesh

value: NEG

value: NOT DONE


title: PHRI2064

value: F

value: GAMBIA

value: not applicable


title: PHRI2046

value: M

value: UNKNOWN


title: PHRI2045


title: PHRI2048


title: PHRI2042

value: Spain


title: PHRI2112

value: Smear pos Culture pos TB HIV neg

value: Peru

value: POS


title: PHRI2039

value: ABNORMAL

value: CAVITARY

value: YES


title: PHRI2056

value: NO


title: PHRI2032

value: NonTB HIVneg

value: NONCAVITARY


title: PHRI2060

value: NEG


title: PHRI2052

value: NORMAL

value: NOT DONE


title: PHRI2035

value: Kenya


title: PHRI2012

value: Smear neg Culture pos TB HIV neg

value: South Africa

value: not applicable


title: PHRI2013

value: M

value: Colombia

value: UNKNOWN


title: PHRI2026

value: Spain


title: PHRI2020

value: Smear pos Culture pos TB HIV neg

value: POS

value: ABNORMAL


title: PHRI2007

value: F

value: NO

value: YES


title: PHRI2019

value: Brazil

value: CAVITARY

value: NEG


title: PHRI2006

value: NonTB HIVneg

value: NORMAL

value: NOT DONE


title: PHRI2016

value: not applicable


title: PHRI2011

value: GAMBIA


title: PHRI2018

value: NONCAVITARY


title: PHRI2017

value: M

value: Vietnam

value: UNKNOWN


title: PHRI2022

value: Bangladesh


title: PHRI2005

value: Smear pos Culture pos TB HIV neg

value: South Africa

value: POS

value: ABNORMAL


title: PHRI1996

value: F

value: Tanzania

value: NO


title: PHRI2033

value: NonTB HIVneg

value: NEG

value: YES


title: PHRI1999

value: NOT DONE


title: PHRI1997

value: Canada

value: not applicable


title: PHRI2001

value: Smear neg Culture pos TB HIV neg

value: M

value: GAMBIA

value: CAVITARY


title: PHRI1992

value: Smear pos Culture pos TB HIV neg

value: Brazil

value: NONCAVITARY

value: UNKNOWN


title: PHRI1995

value: F

value: Colombia

value: NORMAL


title: PHRI1986

value: Bangladesh

value: POS

value: ABNORMAL

value: NO


title: PHRI1976

value: NonTB HIVneg

value: Spain

value: NEG

value: NOT DONE


title: PHRI1980

value: M

value: GAMBIA

value: not applicable

value: YES


title: PHRI1977

value: Smear pos Culture pos TB HIV neg

value: Brazil

value: NONCAVITARY


title: PHRI1994

value: F

value: Peru

value: UNKNOWN


title: PHRI1979

value: Tanzania

value: NORMAL


title: PHRI1974

value: ABNORMAL

value: NO

value: POS


title: PHRI1975

value: Smear neg Culture pos TB HIV neg

value: Vietnam

value: NEG


title: PHRI1973

value: NonTB HIVneg

value: Bangladesh

value: NOT DONE


title: PHRI1990

value: Smear pos Culture pos TB HIV neg

value: M

value: South Africa

value: CAVITARY


title: PHRI1968

value: Spain

value: not applicable

value: NONCAVITARY

value: YES


title: PHRI1955

value: Colombia

value: NORMAL

value: UNKNOWN


title: PHRI1944

value: Asymptomatic LTBI neg nonendemic

value: ITALY

value: INDET


title: PHRI1952

value: NEG


title: PHRI1962

value: NonTB HIVneg

value: F

value: NO


title: PHRI1965

value: NOT DONE


title: PHRI1964

value: Smear pos Culture pos TB HIV neg

value: M

value: Vietnam

value: POS

value: ABNORMAL


title: PHRI1942

value: Smear neg Culture pos TB HIV neg

value: Kenya

value: not applicable

value: NONCAVITARY

value: YES


title: PHRI1939

value: Spain

value: UNKNOWN


title: PHRI1961

value: Colombia

value: NEG


title: PHRI1957

value: NonTB HIVneg

value: NORMAL


title: PHRI1945

value: F

value: GAMBIA

value: NO

value: NOT DONE


title: PHRI1949

value: Smear pos Culture pos TB HIV neg

value: M

value: Vietnam

value: POS


title: PHRI1963

value: South Africa

value: ABNORMAL

value: CAVITARY


title: PHRI1948

value: YES


title: PHRI1983

value: Bangladesh

value: NONCAVITARY

value: UNKNOWN


title: PHRI1937

value: NonTB HIVneg

value: Tanzania

value: NEG

value: not applicable


title: PHRI1967

value: F

value: NORMAL

value: NO


title: PHRI1950

value: Smear neg Culture pos TB HIV neg

value: M

value: NOT DONE


title: PHRI1935


title: PHRI1934

value: Smear pos Culture pos TB HIV neg

value: Brazil

value: POS


title: PHRI1930

value: YES


title: PHRI1929

value: Colombia


title: PHRI1931

value: Bangladesh

value: ABNORMAL

value: NONCAVITARY


title: PHRI1928

value: Asymptomatic LTBI neg nonendemic

value: ITALY

value: UNKNOWN


title: PHRI1924

value: NonTB HIVneg

value: F

value: Canada

value: NEG

value: not applicable


title: PHRI1926

value: M

value: GAMBIA

value: NO

value: NOT DONE


title: PHRI1920

value: Smear neg Culture pos TB HIV neg

value: Brazil

value: POS


title: PHRI1906

value: Bangladesh

value: ABNORMAL


title: PHRI1904

value: Spain

value: NONCAVITARY


title: PHRI1899

value: Asymptomatic LTBI neg nonendemic

value: ITALY

value: UNKNOWN


title: PHRI1884

value: Smear pos Culture pos TB HIV neg

value: Colombia

value: YES


title: PHRI1912

value: M

value: South Africa

value: CAVITARY

value: NEG


title: PHRI1913

value: NonTB HIVneg

value: F

value: Tanzania

value: not applicable

value: NORMAL

value: NO

value: NOT DONE


title: PHRI1909

value: GAMBIA

value: ABNORMAL

value: NONCAVITARY


title: PHRI1925

value: Smear pos Culture pos TB HIV neg

value: Peru

value: POS

value: UNKNOWN


title: PHRI1888

value: M

value: Brazil


title: PHRI1918

value: NEG


title: PHRI1873

value: NonTB HIVneg

value: Colombia

value: YES


title: PHRI1891

value: Asymptomatic LTBI neg nonendemic

value: ITALY

value: not applicable


title: PHRI1890

value: F

value: NO


title: PHRI1878

value: Vietnam

value: ABNORMAL

value: NOT DONE


title: PHRI1895

value: Smear pos Culture pos TB HIV neg

value: NONCAVITARY


title: PHRI1889

value: Smear neg Culture pos TB HIV neg

value: Spain

value: POS


title: PHRI1877

value: NEG

value: UNKNOWN


title: PHRI1875

value: M

value: Kenya


title: PHRI1868

value: GAMBIA

value: YES


title: PHRI1869

value: CAVITARY


title: PHRI1893

value: Peru


title: PHRI1867

value: Asymptomatic LTBI neg nonendemic

value: F

value: ITALY

value: not applicable


title: PHRI1874

value: NonTB HIVneg

value: Tanzania

value: NORMAL

value: NO

value: NOT DONE


title: PHRI1857

value: Smear pos Culture pos TB HIV neg

value: POS

value: ABNORMAL

value: NEG


title: PHRI1862

value: Smear neg Culture pos TB HIV neg

value: M

value: Vietnam

value: NONCAVITARY

value: UNKNOWN


title: PHRI1859

value: F

value: YES


title: PHRI1850

value: GAMBIA

value: not applicable


title: PHRI1838

value: NonTB HIVneg

value: Spain


title: PHRI1856

value: NO


title: PHRI1839

value: Tanzania

value: NORMAL

value: NOT DONE


title: PHRI1812

value: Smear pos Culture pos TB HIV neg

value: Peru

value: POS


title: PHRI1815

value: Colombia

value: NEG


title: PHRI1840

value: Smear neg Culture pos TB HIV neg

value: ABNORMAL

value: NONCAVITARY


title: PHRI1842

value: M

value: Vietnam

value: YES

value: UNKNOWN


title: PHRI1865

value: Kenya

value: CAVITARY


title: PHRI1814

value: NonTB HIVneg

value: F

value: not applicable

value: NO


title: PHRI1846

value: GAMBIA

value: NOT DONE


title: PHRI1849

value: POS


title: PHRI1835

value: Smear pos Culture pos TB HIV neg

value: South Africa

value: NEG


title: PHRI1819

value: Smear neg Culture pos TB HIV neg

value: ABNORMAL

value: NONCAVITARY


title: PHRI1847

value: M

value: Brazil


title: PHRI1822

value: Asymptomatic LTBI neg nonendemic

value: UNKNOWN

value: ITALY


title: PHRI1825


title: PHRI1818


title: PHRI1855


title: PHRI1854

value: NonTB HIVneg

value: F

value: Colombia

value: YES


title: PHRI1852

value: not applicable

value: NOT DONE


title: PHRI1820

value: GAMBIA

value: NO


title: PHRI1824

value: Smear pos Culture pos TB HIV neg

value: Bangladesh

value: POS

value: NEG


title: PHRI1837

value: M

value: Spain

value: NORMAL


title: PHRI1829

value: ABNORMAL

value: NONCAVITARY


title: PHRI1802

value: NonTB HIVneg

value: UNKNOWN


title: PHRI1809

value: Peru


title: PHRI1807

value: South Africa

value: YES


title: PHRI1794

value: Brazil

value: CAVITARY

value: NOT DONE


title: PHRI1792

value: Smear pos Culture pos TB HIV neg

value: F

value: NO


title: PHRI1787

value: Colombia

value: NEG

value: not applicable


title: PHRI1801

value: POS


title: PHRI1790

value: M

value: ABNORMAL


title: PHRI1793

value: GAMBIA


title: PHRI1789

value: NONCAVITARY

value: UNKNOWN


title: PHRI1758

value: Peru


title: PHRI1756

value: NonTB HIVneg

value: Tanzania

value: NORMAL

value: YES


title: PHRI1739

value: NOT DONE


title: PHRI1769


title: PHRI1759

value: Spain


title: PHRI1740

value: Smear neg Culture pos TB HIV neg

value: CAVITARY

value: NO


title: PHRI1782

value: Vietnam

value: NEG

value: not applicable


title: PHRI1755

value: M

value: ABNORMAL


title: PHRI1760


title: PHRI1772

value: F

value: GAMBIA

value: NONCAVITARY


title: PHRI1738

value: NonTB HIVneg

value: UNKNOWN


title: PHRI1761

value: Smear pos Culture pos TB HIV neg

value: Bangladesh

value: POS


title: PHRI1735

value: Brazil

value: NOT DONE


title: PHRI1770

value: Spain


title: PHRI1736

value: Peru

value: NO

value: YES


title: PHRI1779

value: NEG

value: not applicable

value: NORMAL


title: PHRI1734

value: Asymptomatic LTBI neg nonendemic

value: F

value: ITALY

value: INDET


title: PHRI1733

value: NonTB HIVneg

value: M

value: Colombia

value: UNKNOWN


title: PHRI1767

value: Smear neg Culture pos TB HIV neg

value: GAMBIA

value: POS

value: ABNORMAL

value: NONCAVITARY


title: PHRI1731

value: Spain

value: NO

value: NOT DONE


title: PHRI1730

value: Bangladesh

value: NEG

value: not applicable

value: YES


title: PHRI1741

value: F

value: Brazil


title: PHRI1749

value: Smear pos Culture pos TB HIV neg

value: M

value: Kenya

value: CAVITARY


title: PHRI1751

value: NonTB HIVneg

value: Tanzania

value: NORMAL

value: UNKNOWN


title: PHRI1799


title: PHRI1719

value: Smear neg Culture pos TB HIV neg

value: POS


title: PHRI1717

value: GAMBIA

value: NO

value: NOT DONE


title: PHRI1724

value: Spain

value: NEG

value: not applicable

value: ABNORMAL

value: NONCAVITARY


title: PHRI1723

value: F


title: PHRI1721

value: M


title: PHRI1685

value: Vietnam


title: PHRI1716


title: PHRI1699

value: NonTB HIVneg


title: PHRI1696

value: Smear pos Culture pos TB HIV neg

value: South Africa

value: CAVITARY


title: PHRI1679

value: Peru

value: UNKNOWN

value: YES


title: PHRI1697

value: Colombia

value: NO


title: PHRI1702

value: Tanzania

value: NOT DONE


title: PHRI1695

value: Brazil

value: POS

value: NEG


title: PHRI1705

value: Asymptomatic LTBI neg nonendemic

value: ITALY

value: not applicable


title: PHRI1714

value: F

value: ABNORMAL


title: PHRI1692

value: Smear neg Culture pos TB HIV neg

value: Bangladesh

value: NONCAVITARY


title: PHRI1709

value: NonTB HIVneg

value: NORMAL

value: UNKNOWN


title: PHRI1710

value: GAMBIA

value: NO


title: PHRI1711

value: M

value: CAVITARY

value: YES

value: NOT DONE


title: PHRI1680

value: Asymptomatic LTBI neg nonendemic

value: NEG


title: PHRI1678

value: not applicable

value: POS


title: PHRI1691

value: ITALY


title: PHRI1689

value: Tanzania

value: ABNORMAL


title: PHRI1688

value: Smear pos Culture pos TB HIV neg

value: F

value: Vietnam

value: NONCAVITARY


title: PHRI1674

value: NonTB HIVneg

value: Bangladesh

value: UNKNOWN


title: PHRI1663

value: M

value: Spain

value: NORMAL

value: NO


title: PHRI1670

value: GAMBIA

value: NEG

value: YES

value: NOT DONE


title: PHRI1675

value: Tanzania

value: not applicable


title: PHRI1676

value: Colombia


title: PHRI1644

value: F

value: ABNORMAL

value: POS


title: PHRI1654

value: NonTB HIVneg


title: PHRI1647

value: Asymptomatic LTBI neg nonendemic

value: ITALY

value: INDET


title: PHRI1651

value: Smear pos Culture pos TB HIV neg

value: Brazil

value: NONCAVITARY

value: UNKNOWN


title: PHRI1652

value: M

value: Kenya

value: CAVITARY

value: NO

value: NEG


title: PHRI1643

value: Tanzania

value: not applicable

value: NORMAL

value: NOT DONE


title: PHRI1641

value: Bangladesh

value: POS

value: ABNORMAL

value: YES


title: PHRI1639

value: NonTB HIVneg

value: F

value: Colombia


title: PHRI1640

value: NONCAVITARY

value: UNKNOWN


title: PHRI1611

value: M

value: Spain


title: PHRI1638

value: NO


title: PHRI1620

value: Smear pos Culture pos TB HIV neg

value: GAMBIA

value: NEG


title: PHRI1621

value: Asymptomatic LTBI neg nonendemic

value: ITALY

value: not applicable


title: PHRI1618

value: INDET


title: PHRI1625

value: POS

value: ABNORMAL

value: NOT DONE


title: PHRI1617

value: NonTB HIVneg

value: Canada


title: PHRI1626

value: CAVITARY


title: PHRI1615

value: Vietnam

value: NONCAVITARY

value: YES

value: UNKNOWN


title: PHRI1603

value: Smear pos Culture pos TB HIV neg

value: F

value: Kenya

value: NO


title: PHRI1635

value: M

value: Spain

value: NEG

value: NORMAL


title: PHRI1629

value: Tanzania

value: not applicable


title: PHRI1592

value: NonTB HIVneg

value: GAMBIA

value: ABNORMAL

value: NOT DONE


title: PHRI1596

value: Asymptomatic LTBI neg nonendemic

value: ITALY


title: PHRI1631

value: Smear neg Culture pos TB HIV neg

value: Brazil

value: POS

value: NONCAVITARY

value: UNKNOWN


title: PHRI1604

value: F

value: NO


title: PHRI1599

value: Smear pos Culture pos TB HIV neg

value: NEG


title: PHRI1598

value: Tanzania

value: NORMAL


title: PHRI1594

value: NonTB HIVneg

value: M

value: Colombia

value: not applicable


title: PHRI1605

value: Asymptomatic LTBI neg nonendemic


title: PHRI1607

value: Vietnam

value: ABNORMAL

value: NOT DONE


title: PHRI1636

value: Smear neg Culture pos TB HIV neg

value: POS

value: YES


title: PHRI1609

value: Spain


title: PHRI1591

value: NONCAVITARY

value: NO


title: PHRI1608

value: NEG


title: PHRI1628

value: UNKNOWN


title: PHRI1649

value: GAMBIA


title: PHRI1589

value: F

value: ITALY


title: PHRI1587

value: NonTB HIVneg

value: Tanzania

value: NORMAL


title: PHRI1585

value: Asymptomatic LTBI neg nonendemic

value: not applicable


title: PHRI1590

value: Smear pos Culture pos TB HIV neg

value: M

value: Peru

value: NOT DONE


title: PHRI1572

value: Kenya

value: POS

value: ABNORMAL

value: CAVITARY

value: YES


title: PHRI1573

value: Smear neg Culture pos TB HIV neg

value: Colombia

value: NEG

value: NONCAVITARY

value: NO

value: UNKNOWN


title: PHRI1570

value: NonTB HIVneg

value: Spain


title: PHRI1566

value: not applicable

value: NORMAL


title: PHRI1581

value: Smear pos Culture pos TB HIV neg

value: M

value: South Africa


title: PHRI1567

value: Asymptomatic LTBI neg nonendemic

value: F

value: ITALY


title: PHRI1537

value: NOT DONE


title: PHRI1582

value: Canada

value: ABNORMAL


title: PHRI1583

value: Colombia

value: NEG

value: YES


title: PHRI1539

value: Kenya

value: POS

value: CAVITARY

value: NO

value: UNKNOWN


title: PHRI1556

value: NonTB HIVneg

value: not applicable

value: NORMAL


title: PHRI1551

value: M

value: Spain

value: NONCAVITARY


title: PHRI1553

value: Asymptomatic LTBI neg nonendemic

value: ITALY

value: INDET


title: PHRI1557

value: F


title: PHRI1562

value: Smear pos Culture pos TB HIV neg

value: Colombia

value: ABNORMAL

value: NEG

value: NOT DONE


title: PHRI1550

value: Kenya

value: POS

value: CAVITARY

value: NO

value: YES


title: PHRI1548

value: M

value: South Africa

value: UNKNOWN


title: PHRI1563

value: Vietnam

value: NONCAVITARY


title: PHRI1544

value: NonTB HIVneg

value: GAMBIA

value: not applicable


title: PHRI1558

value: Asymptomatic LTBI neg nonendemic

value: F

value: ITALY


title: PHRI1541

value: NEG


title: PHRI1540

value: NORMAL

value: NOT DONE


title: PHRI1524

value: Smear pos Culture pos TB HIV neg

value: Kenya

value: POS

value: ABNORMAL

value: CAVITARY


title: PHRI1522

value: M

value: NO

value: YES


title: PHRI1528

value: Brazil

value: UNKNOWN


title: PHRI1584

value: NonTB HIVneg

value: Spain

value: not applicable

value: NONCAVITARY


title: PHRI1534

value: NEG


title: PHRI1520

value: F

value: Peru


title: PHRI1519

value: NOT DONE


title: PHRI1516

value: Smear pos Culture pos TB HIV neg

value: Vietnam


title: PHRI1514

value: GAMBIA

value: NORMAL


title: PHRI1513

value: Tanzania


title: PHRI1511

value: Bangladesh

value: POS

value: ABNORMAL

value: NO


title: PHRI1497

value: NonTB HIVneg


title: PHRI1495

value: Asymptomatic LTBI neg nonendemic

value: ITALY

value: UNKNOWN


title: PHRI1500

value: M

value: not applicable

value: NEG

value: YES


title: PHRI1509

value: Smear neg Culture pos TB HIV neg

value: Colombia

value: NONCAVITARY

value: NOT DONE


title: PHRI1504

value: Smear pos Culture pos TB HIV neg

value: South Africa

value: CAVITARY


title: PHRI1503

value: F

value: Bangladesh

value: POS

value: ABNORMAL


title: PHRI1475

value: Asymptomatic LTBI neg nonendemic

value: ITALY


title: PHRI1488

value: M

value: Vietnam

value: NO

value: UNKNOWN


title: PHRI1493

value: not applicable

value: NEG


title: PHRI1480

value: NonTB HIVneg

value: GAMBIA

value: NORMAL


title: PHRI1491

value: Smear pos Culture pos TB HIV neg

value: NONCAVITARY

value: YES

value: NOT DONE


title: PHRI1457

value: F

value: Tanzania


title: PHRI1476

value: ABNORMAL


title: PHRI1452

value: Smear neg Culture pos TB HIV neg

value: POS


title: PHRI1510

value: M

value: Bangladesh


title: PHRI1454

value: Vietnam

value: NO

value: UNKNOWN


title: PHRI1468

value: NEG

value: not applicable


title: PHRI1461

value: Asymptomatic LTBI neg nonendemic

value: ITALY


title: PHRI1487

value: NonTB HIVneg

value: Spain

value: NONCAVITARY


title: PHRI1445

value: Smear pos Culture pos TB HIV neg

value: F

value: Peru

value: YES

value: NOT DONE


title: PHRI1450

value: M

value: Kenya

value: POS

value: ABNORMAL

value: CAVITARY


title: PHRI1502

value: NO

value: NEG


title: PHRI1470

value: not applicable

value: UNKNOWN


title: PHRI1447

value: NonTB HIVneg


title: PHRI1443

value: Spain

value: NORMAL


title: PHRI1459

value: Asymptomatic LTBI neg nonendemic

value: ITALY


title: PHRI1462

value: NONCAVITARY


title: PHRI1439

value: Smear pos Culture pos TB HIV neg

value: South Africa


title: PHRI1441

value: F

value: Vietnam

value: NOT DONE


title: PHRI1422

value: M

value: YES


title: PHRI1421


title: PHRI1425

value: Tanzania

value: ABNORMAL

value: NO


title: PHRI1413

value: not applicable

value: UNKNOWN

value: NEG


title: PHRI1436

value: Colombia

value: POS

value: CAVITARY


title: PHRI1438

value: NonTB HIVneg

value: GAMBIA

value: NORMAL


title: PHRI1408

value: NONCAVITARY


title: PHRI1406

value: F

value: Spain


title: PHRI1435

value: Smear pos Culture pos TB HIV neg

value: Peru

value: NOT DONE


title: PHRI1428

value: Asymptomatic LTBI neg nonendemic

value: ITALY


title: PHRI1399

value: Bangladesh

value: ABNORMAL

value: NO

value: YES


title: PHRI1440

value: M

value: POS

value: UNKNOWN

value: NEG


title: PHRI1405

value: Smear neg Culture pos TB HIV neg

value: GAMBIA

value: not applicable


title: PHRI1402

value: NonTB HIVneg

value: F

value: Tanzania

value: NONCAVITARY


title: PHRI1400

value: Spain

value: NORMAL

value: NOT DONE


title: PHRI1409

value: Vietnam

value: ABNORMAL


title: PHRI1395

value: Kenya

value: NO

value: YES


title: PHRI1396

value: Smear pos Culture pos TB HIV neg

value: South Africa

value: POS

value: UNKNOWN


title: PHRI1393

value: Smear neg Culture pos TB HIV neg

value: M

value: NEG

value: not applicable


title: PHRI1381

value: NonTB HIVneg

value: F

value: Colombia


title: PHRI1392

value: Tanzania

value: NORMAL

value: NOT DONE


title: PHRI1389

value: Vietnam

value: ABNORMAL

value: NONCAVITARY


title: PHRI1377

value: Smear pos Culture pos TB HIV neg

value: Kenya

value: CAVITARY

value: NO

value: YES


title: PHRI1385

value: Smear neg Culture pos TB HIV neg

value: M

value: POS

value: UNKNOWN


title: PHRI1387

value: NonTB HIVneg

value: F

value: NEG

value: not applicable


title: PHRI1374

value: Colombia

value: NORMAL

value: NOT DONE


title: PHRI1394

value: Tanzania

value: ABNORMAL

value: NONCAVITARY


title: PHRI1386

value: Asymptomatic LTBI neg nonendemic

value: ITALY

value: INDET


title: PHRI1384

value: Vietnam

value: NO

value: YES


title: PHRI1372

value: Smear pos Culture pos TB HIV neg

value: M

value: South Africa

value: POS

value: CAVITARY

value: UNKNOWN


title: PHRI1370

value: Bangladesh

value: NEG


title: PHRI1383

value: Kenya

value: NOT DONE


title: PHRI1365

value: NonTB HIVneg

value: Colombia

value: not applicable

value: NORMAL


title: PHRI1343

value: F

value: Spain

value: ABNORMAL

value: NONCAVITARY


title: PHRI1341

value: NO


title: PHRI1369

value: Vietnam


title: PHRI1347

value: M

value: GAMBIA


title: PHRI1345

value: Smear pos Culture pos TB HIV neg

value: POS

value: CAVITARY


title: PHRI1342

value: Smear neg Culture pos TB HIV neg

value: Kenya

value: NEG

value: YES

value: UNKNOWN


title: PHRI1350

value: NonTB HIVneg

value: Colombia

value: not applicable

value: NORMAL

value: NOT DONE


title: PHRI1362

value: ABNORMAL

value: NONCAVITARY

value: NO


title: PHRI1358

value: M

value: South Africa


title: PHRI1371

value: Smear pos Culture pos TB HIV neg

value: F

value: Vietnam

value: POS


title: PHRI1366

value: Spain

value: NEG


title: PHRI1360

value: GAMBIA

value: YES


title: PHRI1320

value: Smear neg Culture pos TB HIV neg

value: Bangladesh

value: UNKNOWN


title: PHRI1319

value: Brazil

value: CAVITARY

value: NOT DONE


title: PHRI1326

value: NonTB HIVneg

value: not applicable

value: ABNORMAL

value: NONCAVITARY


title: PHRI1338

value: F

value: Colombia

value: NORMAL

value: NO


title: PHRI1332

value: POS

value: NEG


title: PHRI1335

value: Tanzania


title: PHRI1330

value: Asymptomatic LTBI neg nonendemic

value: M

value: ITALY


title: PHRI1314

value: Smear pos Culture pos TB HIV neg

value: Bangladesh

value: YES

value: UNKNOWN


title: PHRI1315

value: NonTB HIVneg

value: GAMBIA

value: not applicable

value: NOT DONE


title: PHRI1316

value: F

value: Peru


title: PHRI1312

value: ABNORMAL

value: CAVITARY

value: NO


title: PHRI1310

value: Vietnam

value: POS

value: NONCAVITARY

value: NEG


title: PHRI1318

value: Smear pos Culture pos TB HIV neg

value: M

value: Kenya


title: PHRI1337

value: Tanzania

value: UNKNOWN


title: PHRI1327

value: NonTB HIVneg

value: Spain


title: PHRI1311

value: Colombia

value: not applicable

value: YES

value: NOT DONE


title: PHRI1323

value: GAMBIA

value: ABNORMAL


title: PHRI1297

value: CAVITARY

value: NO


title: PHRI1303

value: NORMAL


title: PHRI1298

value: Asymptomatic LTBI neg nonendemic

value: F

value: ITALY

value: NEG


title: PHRI1308


title: PHRI1304

value: Tanzania


title: PHRI1299

value: UNKNOWN


title: PHRI1289


title: PHRI1288

value: Smear pos Culture pos TB HIV neg

value: POS


title: PHRI1285

value: NonTB HIVneg

value: M

value: Canada

value: NONCAVITARY


title: PHRI1307

value: not applicable


title: PHRI1281

value: GAMBIA

value: ABNORMAL

value: NOT DONE


title: PHRI1250

value: NO


title: PHRI1295

value: Vietnam


title: PHRI1251

value: F

value: Bangladesh

value: YES


title: PHRI1262

value: Spain

value: NEG

value: NORMAL


title: PHRI1263

value: POS


title: PHRI1260

value: Smear pos Culture pos TB HIV neg

value: Brazil

value: UNKNOWN


title: PHRI1256

value: NonTB HIVneg

value: M


title: PHRI1257

value: GAMBIA

value: not applicable

value: NONCAVITARY


title: PHRI1249

value: Asymptomatic LTBI neg nonendemic

value: ITALY

value: NO


title: PHRI1269

value: ABNORMAL

value: NOT DONE


title: PHRI1265

value: F

value: Colombia

value: YES


title: PHRI1272

value: NEG

value: POS


title: PHRI1247


title: PHRI1275

value: Tanzania

value: NORMAL


title: PHRI1290

value: UNKNOWN


title: PHRI1276

value: Smear neg Culture pos TB HIV neg

value: Bangladesh


title: PHRI1246

value: NonTB HIVneg

value: M

value: not applicable


title: PHRI1245

value: Smear pos Culture pos TB HIV neg

value: NONCAVITARY


title: PHRI1244

value: Vietnam

value: ABNORMAL

value: NO


title: PHRI1234

value: Peru

value: NOT DONE


title: PHRI1230

value: F

value: NEG

value: YES


title: PHRI1229

value: POS


title: PHRI1233

value: Spain

value: NORMAL


title: PHRI1241

value: Smear neg Culture pos TB HIV neg

value: Colombia

value: UNKNOWN


title: PHRI1220

value: NonTB HIVneg

value: not applicable


title: PHRI1214

value: Smear pos Culture pos TB HIV neg

value: M

value: South Africa

value: CAVITARY


title: PHRI1235

value: GAMBIA

value: NO


title: PHRI1225

value: Asymptomatic LTBI neg nonendemic

value: ITALY


title: PHRI1243

value: F

value: NEG

value: YES

value: NOT DONE


title: PHRI1207

value: ABNORMAL

value: NONCAVITARY

value: POS


title: PHRI1183

value: UNKNOWN


title: PHRI1208

value: NonTB HIVneg

value: not applicable


title: PHRI1192

value: Tanzania

value: NORMAL


title: PHRI1180

value: M

value: Colombia


title: PHRI1224

value: NO


title: PHRI1178

value: Smear pos Culture pos TB HIV neg

value: Vietnam

value: CAVITARY


title: PHRI1185

value: F

value: Kenya

value: NEG


title: PHRI1191

value: GAMBIA

value: YES

value: NOT DONE


title: PHRI1200

value: ABNORMAL

value: NONCAVITARY

value: UNKNOWN


title: PHRI1188

value: POS


title: PHRI1199

value: Smear neg Culture pos TB HIV neg

value: Brazil

value: not applicable


title: PHRI1184

value: NonTB HIVneg

value: Bangladesh

value: NORMAL

value: NO


title: PHRI1205

value: Smear pos Culture pos TB HIV neg

value: F


title: PHRI1202

value: Spain

value: NEG


title: PHRI1194

value: Tanzania

value: YES


title: PHRI1209

value: Kenya

value: ABNORMAL

value: CAVITARY

value: NOT DONE


title: PHRI1206

value: Smear neg Culture pos TB HIV neg

value: M

value: POS

value: UNKNOWN


title: PHRI1181

value: NonTB HIVneg

value: GAMBIA

value: not applicable

value: NONCAVITARY


title: PHRI1175

value: NO


title: PHRI1170

value: Smear pos Culture pos TB HIV neg

value: Vietnam


title: PHRI1171

value: F

value: Colombia

value: NEG


title: PHRI1173

value: Spain

value: NORMAL


title: PHRI1164

value: YES

value: NOT DONE


title: PHRI1166

value: Smear neg Culture pos TB HIV neg

value: M

value: Kenya


title: PHRI1161

value: Bangladesh

value: POS

value: ABNORMAL

value: CAVITARY

value: UNKNOWN


title: PHRI1163

value: NonTB HIVneg

value: Tanzania

value: not applicable

value: NONCAVITARY

value: NO


title: PHRI1162

value: Asymptomatic LTBI neg nonendemic

value: ITALY

value: NEG


title: PHRI1136

value: F

value: Colombia

value: YES

value: NOT DONE


title: PHRI1144


title: PHRI1167

value: M


title: PHRI1149


title: PHRI1137

value: Spain


title: PHRI1154

value: GAMBIA

value: NORMAL

value: POS


title: PHRI1155

value: NonTB HIVneg

value: ABNORMAL


title: PHRI1156

value: Smear pos Culture pos TB HIV neg

value: South Africa

value: CAVITARY

value: UNKNOWN


title: PHRI1158

value: not applicable

value: NONCAVITARY

value: NO


title: PHRI1121

value: F

value: Colombia

value: NEG


title: PHRI1165

value: M

value: Bangladesh

value: NOT DONE


title: PHRI1117

value: Brazil


title: PHRI1115

value: Smear neg Culture pos TB HIV neg

value: POS


title: PHRI1122

value: ABNORMAL

value: YES


title: PHRI1128

value: Asymptomatic LTBI neg nonendemic

value: ITALY


title: PHRI1126

value: NonTB HIVneg

value: NORMAL

value: UNKNOWN


title: PHRI1127

value: not applicable

value: NO


title: PHRI1113

value: F

value: Tanzania


title: PHRI1131

value: Spain

value: NEG


title: PHRI1129

value: Smear pos Culture pos TB HIV neg

value: M

value: Kenya

value: CAVITARY

value: NOT DONE


title: PHRI1120


title: PHRI1159

value: GAMBIA

value: ABNORMAL

value: NONCAVITARY


title: PHRI1111

value: NonTB HIVneg

value: Colombia

value: YES


title: PHRI1110

value: not applicable


title: PHRI1106

value: UNKNOWN

value: NO


title: PHRI1103

value: Asymptomatic LTBI neg nonendemic

value: F

value: ITALY


title: PHRI1104

value: Smear neg Culture pos TB HIV neg

value: POS

value: NEG


title: PHF8 RNAi1-6

first: Hank

middle: heng

last: qi

address: NRB 854, 77 Ave. Louis Pasteur

department: Pathology

institute: Harvard Medical School

description:
Biological replicate 3 of 3. Technical replicate 2 of 2.

H008-0606043576

hyb_protocol: Hybridization was carried out to a human Oligo Microarray (Phalanx Human Whole Genome OneArray, Phalanx Biotech) according to the manufacturer's protocol. Technical duplicates were performed.

scan_protocol: After hybridization, arrays were scanned using a Molecular Dynamics™ Axon 4100A scanner. Raw intensity signals for each microarray were measured using GenePix Pro™ 6.0 software (Molecular Devices) and stored in GPR format.

data_processing:
The data from all microarrays in each experimental set were passed to Omicsoft Array Studio software, control and missing features were removed, and the remaining signals were quantile normalized and transformed to log2 values.
Testing was performed by combining technical replicates and performing a standard student's T-test to calculate P-values. Adjusted P-values were calculated using the Benjamini and Hochberg method with a false discovery rate a-value of 0.05. Fold changes were calculated based on the mean values of the technical replicates for each probe.

source_name: HeLa cells, PHF8 RNAi

label_protocol: RNAs were labeled with Cy5. The reactive amino group of 5-(3-aminoallyl)-UTP/5-(3-aminoallyl)-dUTP was used to conjugate the purified aRNA/cDNA with the NHS-CyDye.

growth_protocol: HeLa cells were cultured in DMEM medium with 10% FBS.

extract_protocol: RNAs were isolated by Trizol lysis, chloroform separation and isopropanol precipitation. Obtained RNAs were further cleaned with Qiagen RNeasy Mini Kit (Cat. No.: 74104). Total RNA was isolated from triplicate cell cultures.

treatment_protocol: HeLa cells were transfected with pBabe control or PHF8 shRNA and puromycin-selected for more than 6 days. The stable cell lines of control and PHF8 RNAi were retransfected with the corresponding shRNA for an additional three days.

tag: cell line

value: HeLa

tag: cell type

value: human cervical cancer cells

tag: rnai


title: PHRI1091

tag: final diagnosis

value: Smear pos Culture pos TB HIV neg

tag: age in years

value: M

tag: country of serum collection

value: South Africa

value: NOT DONE


title: PHRI1092

value: NonTB HIVneg

value: Colombia

tag: m. tuberculosis culture

tag: acid fast bacilli (afb) smear microscopy

tag: afb smear grade

value: NORMAL


title: PHRI1107

value: Vietnam

value: not applicable

tag: chest x-ray

value: ABNORMAL

tag: chest x-ray description

value: CAVITARY

tag: previous history of active tb

value: YES

value: UNKNOWN


title: PHRI1093

tag: sex

value: F

value: NO

tag: hiv status

tag: bcg scar or history


title: PHRI1084

value: NEG

value: NONCAVITARY

tag: tuberculin skin test

tag: quantiferon test

tag: t-spot. tb test


title: PHRI1086

value: GAMBIA

value: POS


title: PHRI1083


title: PHRI1105

value: Smear pos Culture pos TB HIV neg


title: PHRI1082

value: M

value: Kenya

value: NOT DONE


title: PHRI1101

value: NonTB HIVneg

value: Spain


title: PHRI1096

value: Smear neg Culture pos TB HIV neg

value: not applicable


title: PHF8 RNAi1-5

description:
Biological replicate 3 of 3. Technical replicate 1 of 2.

H007-0606043575

tag: cell line

value: HeLa

tag: cell type

value: human cervical cancer cells


title: PHF8 RNAi1-3

description:
Biological replicate 2 of 3. Technical replicate 1 of 2.

H003-0606043585

tag: rnai


title: MyD88-/-_macrophage_48h_rep3

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the Mouse Genome 430 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: macrophage MyD88 -/- 48h

label_protocol: Biotinylated cRNA were prepared according to the standard one-cycle eukaryote target Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Bone marrow derived macrophages (BMDMs) were prepared from 3 individual Myd88+/+ and Myd88-/- (C57Bl/6 background) female mice.  Bone marrow cells were grown in L-cell conditioned media for 5 days.  10cm cell culture plates were prepared with 5e6 cells per plate.

extract_protocol: RNA was collected from TRIZOL lysates (2mL per 10 cm plate) according to the manufacturer's protocol.

treatment_protocol: BMDMs were infected with M.bovis BCG (MOI ~ 10:1) for 12, 24, and 48 hrs in DMEM without antibiotics and containing 10% FCS.

tag: gender

value: female

tag: strain

value: Bone marrow derived macrophage (BMDM)

tag: genotype/variation

tag: infection

value: M.bovis BCG

tag: time


title: Control RNAi1-2

description:
Biological replicate 1 of 3. Technical replicate 2 of 2.

H02-0607003389

source_name: HeLa cells, control RNAi

value: control


title: Control RNAi1-6

description:
Biological replicate 3 of 3. Technical replicate 2 of 2.

H006-0606043574


title: PHF8 RNAi1-4

description:
Biological replicate 2 of 3. Technical replicate 2 of 2.

H004-0606043586


title: MyD88-/-_macrophage_48h_rep1


title: Control RNAi1-4

description:
Biological replicate 2 of 3. Technical replicate 2 of 2.

H002-0606043582


title: Control RNAi1-5

description:
Biological replicate 3 of 3. Technical replicate 1 of 2.

H005-0606043573


title: PHF8 RNAi1-1

description:
Biological replicate 1 of 3. Technical replicate 1 of 2.

H03-0607003390


title: PHRI1079

tag: final diagnosis

tag: age in years

tag: country of serum collection

value: Bangladesh

tag: m. tuberculosis culture

tag: acid fast bacilli (afb) smear microscopy

tag: afb smear grade

tag: chest x-ray

value: ABNORMAL

value: CAVITARY

value: NO

value: NEG

value: UNKNOWN


title: PHRI1080

tag: sex

value: M

value: POS

tag: chest x-ray description

value: NONCAVITARY

tag: previous history of active tb

tag: hiv status

tag: bcg scar or history

tag: tuberculin skin test

tag: quantiferon test

value: NOT DONE


title: Control RNAi1-3

description:
Biological replicate 2 of 3. Technical replicate 1 of 2.

H001-0606043581

tag: cell line

tag: cell type

tag: rnai


title: Control RNAi1-1

description:
Biological replicate 1 of 3. Technical replicate 1 of 2.

H01-0607003388


title: PHRI1074

tag: final diagnosis

value: NonTB HIVneg

value: F

value: Colombia

value: not applicable

value: NORMAL

tag: t-spot. tb test


title: PHF8 RNAi1-2

description:
Biological replicate 1 of 3. Technical replicate 2 of 2.

H04-0607003391

value: HeLa

value: human cervical cancer cells


title: wild-type_macrophage_48h_rep3

source_name: macrophage wild-type 48h

tag: gender

value: female

tag: strain

value: Bone marrow derived macrophage (BMDM)

tag: genotype/variation

tag: infection

value: M.bovis BCG

tag: time


title: MyD88-/-_macrophage_48h_rep2


title: MCF7 treated with SN38, rep2

city: Nerviano

first: Roberta

last: Bosotti

state: MI

address: viale Pasteur,10

department: Biotechnology

country: Italy

institute: Nerviano Medical Sciences srl

description: Gene expression data from MCF7 treated with SN38.

hyb_protocol: Samples were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays and processed as per manufacturer’s instructions using ‘GeneChip® Hybridization, Wash, and Stain Kit’ components (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: Scanned images were first inspected for quality control (QC) using a variety of built-in QC tools from the Bioconductor package [www.bioconductor.org] of R, the open source environment for statistical analysis. Feature intensity values from scanned arrays were normalised and reduced to expression summaries using MAS5 implemented in the R statistical environment.

source_name: MCF7, SN38

label_protocol: Biotin-labeled, fragmented cRNA probes were prepared starting from 1.5 µg of total RNA per replicate sample, using the ‘One-Cycle Target Labeling and Control Reagents’ (Affymetrix, Santa Clara, CA) according to the protocols included in the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).

growth_protocol: MCF7 (human adenocarcinoma mammary) from ECACC were seeded in T-75 tissue culture flasks (Corning), 25.000 cells/cm2 in RPMI 1640 (Gibco), pH 7.4, 10% FBS (EUROCLONE Australia-USDA approved, cat. ECSO170D, lot.EUS003383), 2mM L-Glutamine (Gibco), 1x Penicillin-Streptomycin (Gibco) and maintained in 5% CO2 at 37°C with 96% relative humidity.

extract_protocol: Total RNA was extracted using Qiagen Rneasy kit (Qiagen  cat. no. 74104), starting from total cell lysates.

treatment_protocol: After 24 hours, cells were treated with the different compounds at a dose equal to 5 times the IC50 for 6 hours and collected using Qiagen lysis buffer RLT (Qiagen cat no. 79216).

value: adenocarcinoma mammary cells

tag: treatment


title: wild-type_macrophage_48h_rep2


title: MCF7 treated with SN38, rep1


title: PHRI1068

value: Smear pos Culture pos TB HIV neg

tag: age in years

tag: sex

tag: country of serum collection

value: Brazil

tag: m. tuberculosis culture

tag: acid fast bacilli (afb) smear microscopy

tag: afb smear grade

tag: chest x-ray

value: ABNORMAL

tag: chest x-ray description

value: NEG


title: PHRI1073

value: Spain

value: POS

value: CAVITARY

tag: previous history of active tb

value: NO

tag: hiv status

tag: bcg scar or history

tag: tuberculin skin test

tag: quantiferon test


title: PHRI1070

tag: final diagnosis

value: NonTB HIVneg

value: M

value: Tanzania

value: YES

value: UNKNOWN

value: NOT DONE

tag: t-spot. tb test


title: PHRI1076

value: F

value: GAMBIA

value: not applicable

value: NORMAL


title: PHRI1075

value: Smear neg Culture pos TB HIV neg

value: Bangladesh

value: NONCAVITARY


title: PHRI1078

value: Spain

value: NEG


title: PHRI1067

value: Smear pos Culture pos TB HIV neg

value: POS

value: ABNORMAL


title: MyD88-/-_macrophage_24h_rep3

source_name: macrophage MyD88 -/- 24h

tag: gender

value: female

tag: strain

tag: cell type

value: Bone marrow derived macrophage (BMDM)

tag: genotype/variation

tag: infection

value: M.bovis BCG

tag: time


title: wild-type_macrophage_48h_rep1


title: MCF7 treated with E973, rep2

description: Gene expression data from MCF7 treated with E973.

tag: cell line

value: adenocarcinoma mammary cells

tag: treatment


title: MyD88-/-_macrophage_24h_rep2


title: PHRI1066

value: NonTB HIVneg

tag: age in years

tag: sex

value: M

tag: country of serum collection

value: Colombia

tag: m. tuberculosis culture

tag: acid fast bacilli (afb) smear microscopy

tag: afb smear grade

tag: chest x-ray

value: YES

value: UNKNOWN

value: NOT DONE


title: PHRI1072

tag: final diagnosis

value: not applicable

tag: chest x-ray description

tag: previous history of active tb

tag: hiv status

tag: bcg scar or history

value: NO

tag: tuberculin skin test

tag: quantiferon test


title: PHRI1065

value: F

value: NONCAVITARY

tag: t-spot. tb test


title: MyD88-/-_macrophage_24h_rep1

tag: gender

tag: strain

tag: cell type

tag: genotype/variation

tag: infection

tag: time


title: PHRI1064

tag: age in years

tag: sex

tag: country of serum collection

tag: m. tuberculosis culture

value: NEG

tag: acid fast bacilli (afb) smear microscopy


title: wild-type_macrophage_24h_rep1

source_name: macrophage wild-type 24h


title: MCF7 treated with doxo, rep2

description: Gene expression data from MCF7 treated with doxo.

source_name: MCF7, doxo

tag: cell line

tag: treatment

value: doxorubicin


title: MCF7 treated with doxo, rep1


title: MCF7 treated with CDK-887, rep1

description: Gene expression data from MCF7 treated with CDK-887.

source_name: MCF7, CDK-887


title: MCF7 treated with E973, rep1


title: MCF7 treated with AUY922, rep2

description: Gene expression data from MCF7 treated with AUY922.

source_name: MCF7, AUY922


title: PHRI1060

tag: final diagnosis

value: GAMBIA

tag: afb smear grade

tag: chest x-ray

value: ABNORMAL

tag: chest x-ray description

value: CAVITARY

tag: previous history of active tb

tag: hiv status

tag: bcg scar or history


title: PHRI1063

tag: tuberculin skin test

value: POS

tag: quantiferon test

tag: t-spot. tb test


title: MCF7 treated with CDK-887, rep2

tag: cell type

value: adenocarcinoma mammary cells


title: wild-type_macrophage_24h_rep2

tag: gender

value: female

tag: strain

value: Bone marrow derived macrophage (BMDM)

tag: genotype/variation

tag: infection

value: M.bovis BCG

tag: time


title: PHRI1057

value: Smear pos Culture pos TB HIV neg

tag: age in years

tag: sex

value: M

tag: country of serum collection

value: Bangladesh

tag: m. tuberculosis culture

tag: acid fast bacilli (afb) smear microscopy


title: PHRI1050

tag: final diagnosis

value: NonTB HIVneg

value: South Africa

tag: afb smear grade

value: not applicable

tag: chest x-ray

tag: chest x-ray description

tag: previous history of active tb

value: UNKNOWN

value: NOT DONE


title: MCF7 treated with 17AAG, rep1

description: Gene expression data from MCF7 treated with 17AAG.

source_name: MCF7, 17AAG

tag: cell line

tag: treatment


title: MCF7 treated with AUY922, rep1

tag: cell type


title: wild-type_macrophage_24h_rep3

tag: gender

tag: strain


title: MCF7 treated with 17AAG, rep2


title: MyD88-/-_macrophage_12h_rep3

source_name: macrophage MyD88 -/- 12h

tag: genotype/variation

tag: infection


title: PHRI1051

tag: age in years

value: Peru

value: YES

tag: hiv status

value: NEG

tag: bcg scar or history

tag: tuberculin skin test

tag: quantiferon test

tag: t-spot. tb test


title: MyD88-/-_macrophage_12h_rep1

tag: time


title: MCF7 untreated cells, rep1

description: Gene expression data from MCF7 untreated.

source_name: MCF7, untreated

value: untreated


title: PHRI1048

source_name: serum_nonTB disease

tag: final diagnosis

tag: sex

tag: country of serum collection

value: Spain

tag: m. tuberculosis culture

tag: acid fast bacilli (afb) smear microscopy

tag: afb smear grade

tag: chest x-ray

value: NORMAL

value: NO

value: POS


title: MCF7 untreated cells, rep2

tag: cell line

tag: cell type

value: adenocarcinoma mammary cells

tag: treatment


title: MyD88-/-_macrophage_12h_rep2

tag: gender

value: female

tag: strain

value: Bone marrow derived macrophage (BMDM)

tag: genotype/variation

tag: infection

value: M.bovis BCG


title: PHRI1044

value: Asymptomatic LTBI neg nonendemic

tag: age in years

value: M

value: ITALY

tag: chest x-ray description

tag: previous history of active tb

tag: hiv status

tag: bcg scar or history

tag: tuberculin skin test

tag: quantiferon test


title: PHRI1043

tag: final diagnosis

value: NonTB HIVneg

tag: sex

tag: country of serum collection

value: Kenya

tag: m. tuberculosis culture

tag: acid fast bacilli (afb) smear microscopy

value: not applicable

value: ABNORMAL

value: NONCAVITARY

value: UNKNOWN

tag: t-spot. tb test


title: A2780 treated with Flavo, rep2

description: Gene expression data from A2780 treated with Flavopiridol.

source_name: A2780, Flavopiridol

growth_protocol: A2780 (human adenocarcinoma ovary) from ECACC were seeded in T-75 tissue culture flasks (Corning), 25.000 cells/cm2 in RPMI 1640 (Gibco), pH 7.4, 10% FBS (EUROCLONE Australia-USDA approved, cat. ECSO170D, lot.EUS003383), 2mM L-Glutamine (Gibco), 1x Penicillin-Streptomycin (Gibco) and maintained in 5% CO2 at 37°C with 96% relative humidity.

treatment_protocol: After 24 hours, cells were treated with the compound at a dose equal to 5 times the IC50 for 6 hours and collected using Qiagen lysis buffer RLT (Qiagen cat no. 79216).

tag: cell line

tag: cell type

value: adenocarcinoma ovary

tag: treatment

value: Flavopiridol


title: wild-type_macrophage_12h_rep2

source_name: macrophage wild-type 12h

tag: gender

tag: strain

tag: genotype/variation

tag: infection

tag: time


title: MyD88-/-_macrophage_0h_rep3

source_name: macrophage MyD88 -/- 0h

value: uninfected