title: neuron-differentiated hMSCs (2 of 2)

description: Chip-chip neuron-differentiated 3A6 cells EZH2

hyb_protocol: standard Nimblegen hybridization kits and protocols were used

scan_protocol: arrays were scanned with Axon scanner at 5 um resolution according to standard Nimblegen protocols

source_name: EZH2 ChIP DNA from neuron-differentiated 3A6 cells

label_protocol: standard Nimblegen ChIP labeling protocol (1 ug of Amplified ChIP DNA, direct incorporation of cy labeled primers with klenow extension

treatment_protocol: The 3A6 were treated with DMEM-HG neuronal induction medium (NIM) containing 10-7 M dexamethasone, 50 μg/ml  ascorbic acid-2-phosphate, 50 μM indomethacin, 10 μg/ml insulin, and 0.45 mM 3-isobutyl-1-methyl-xanthine for 5 days.

value: neuron-differentiated hMSCs

tag: chip antibody

value: anti-EZH2 mouse antibody

tag: chip antibody vendor

value: Cell Signaling

tag: chip antibody cat. #

tag: chip antibody lot #

source_name: Input DNA from neuron-differentiated 3A6 cells

tag: sample type

value: Input DNA


title: 786_O_pGIPZ_3

status: Public on Dec 05 2012

type: RNA

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

description: 786-O cells transduced with pGIPZ control vector

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: GCRMA as implemented in the R-package gcrma using the default settings and the custom Brain Array CDF-file hs133phsentrezgcdf version 10 (http://brainarray.mbni.med.umich.edu/).

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Standard Affymetrix protocol

growth_protocol: Standard tissue culture conditions.

extract_protocol: PrepEase RNA spin kit (USB)

tag: cell line

value: 786-O renal cell carcinoma cell line

tag: tranduced with

value: pGIPZ control vector


title: cellline1_rep1

city: Princeton

first: Eric

middle: Jungwoo

last: Suh

state: NJ

address: 14 Washington Rd

department: Molecular Biology

country: USA

institute: Princeton University

hyb_protocol: Labeled cRNA were hybridized to arrays according to Agilent's manufacturer's protocol

scan_protocol: Scanned using Agilent G2505B array scanner according to manufacturer's protocol.

data_processing: Probes were filtered to eliminate those with either a signal intensity below 350 or flagged by Feature Extractor for saturation or no signal above background in any hybridization. Replicated signals from identical sequence-probes were averaged. For each array, the ratio of Cy5 to Cy3 (red to green) was log2 transformed and zero-centered.

source_name: miR-29b transfected cell line 1

label_protocol: Total RNA extracts were cRNA labeled using the Agilent Low RNA Input Fluorescent Labeling Kit according to the manufacturer's protocol

extract_protocol: Total RNA isolated from fibroblasts 48 hours post-transfection using mirVana total RNA isolation kit and procedure.

treatment_protocol: Asynchronously proliferating fibroblasts were reverse transfected with either miR-29b or a microRNA negative control Pre-miR from Ambion.

tag: gender

value: Male

tag: cell type

value: Fibroblast

source_name: Negative control transfected cell line 1


title: early spring b02

city: Wuerzburg

first: Peter

last: Ache

address: Julius von Sachs Platz 2

country: Germany

institute: Julius von Sachs Institut

scan_protocol: Microarrays were scanned using the GCS3000 GeneChip scanner (Affymetrix) and GCOS software, version 1.4.

data_processing: Scanned images were subjected to visual inspection to control for hybridation artifacts and proper grind alignment. Files of quality control were generated using the program “Expression Console” (Affymetrix).

organism: Populus tremula x Populus alba

source_name: rays, enriched

label_protocol: All samples were amplified using the “One-Cycle Target Labellig Assay” (Affymetrix) according to the manufacture’s protocol and hybridized to the Gene Chip Poplar Genome (Affymetrix)

extract_protocol: Total RNA of LMPC-enriched ray cells was extracted using the RNeasy MicroKit (Qiagen,) according to the manufacturer’s protocols with minor modifications. The binding buffers were supplemented with 0,1% β- Mercaptoethanol. After incubation at room temperature for 30 min in a rotary mixer the sample were briefly centrifuged before transfer to the individual homogenation columns.

treatment_protocol: Wood samples were fixed using a modified Farmer's fixative, paraffin-embedded and stored at -80 °C until further processing. Cross-sections were prepared and used for LMPC.

tag: season

value: early spring


title: 786_O_DMSO_3

description:
786-O Cells treated with vehicle
786_O_DMSO_3_HG-U133_Plus_2.CEL

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: GCRMA as implemented in the R-package gcrma using the default settings and the custom CDF-file hs133phsentrezgcdf version 10.

source_name: 786-O cells

label_protocol: Standard Affymetrix protocol.

tag: cell  ine

tag: agent

value: control


title: 786_O_pGIPZ_1


title: early spring b01


title: 786_O_DMSO_2

description:
786-O Cells treated with vehicle
786_O_DMSO_2_HG-U133_Plus_2.CEL


title: 786_O_pGIPZ_2


title: summer a04

value: summer


title: 786_O_DMSO_1

description:
786-O Cells treated with vehicle
786_O_DMSO_1_HG-U133_Plus_2.CEL


title: summer a03


title: early spring b04


title: early spring b03


title: summer a01


title: T1_H04

city: Taichung

first: chanshiou

last: Wu

address: No6,Hsueh-shih road

country: Taiwan

institute: china medical university

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1080 control probes, spotted onto glass slides using a proprietary non-contact printing method.

hyb_protocol: HOA v4.3 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on HOA in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 600~630 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing: Raw data was calculated using F635 median minus B635 Median. The raw data were further adjust by Rosetta Resolver® (Ver 7.2 Build 7.2.2.0.0) error model calculation. The statistic values were calculated after the replicated probes squeezing and median scaling normalization (excluding flagged and control data). Please note that the raw data of gpr files contains two channels of data (i.e. F635 and F532) and only F635 relevant data were used for data processing.

source_name: 3A6_EZH2 KO

label_protocol: 2.5 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Cy3; Amershan).

growth_protocol: The 3A6 cells were grown in Dulbecco’s modified Eagle’s medium-low glucose (DMEM-LG) (HyClone, MA, USA) with 10% fetal bovine serum (FBS), 100 U/ml penicillin, and 100 μg/ml streptomycin in a humidified incubator with 5% CO2 at 37 °C.

extract_protocol: RNA extraction by TRIZOL reagent RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

treatment_protocol: Knockdown of genes were performed with the specific shRNAs delivered by the lentiviral  system from National RNAi Core Facility (Academia Sinica, Taipei, TW) according to the  instruction manual.

value: human mesenchymal stem cells (hMSCs)

tag: genotype/variation

value: knockdown EZH2


title: summer a02


title: WT  incubated with 1mM copper sulfate, biological rep1

city: Nagoya

first: Ayuna

last: Hattori

state: Aichi

address: Chikusa

department: Department of Molecular Biology

country: Japan

institute: Nagoya University

description: Gene expression data from WT adult worm incubated with copper sulfate for 1 hr.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip C.elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Caenorhabditis elegans

source_name: C. elegans WT animal incubated with copper sulfate for 1 hour

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3’ IVT Express Kit User Manual, Affymetrix).

growth_protocol: WT and kgb-1 mutant were maintained on nematode growth medium (NGM) plates at 20°C and fed with bacteria of the OP50 strain. Adult worms of each strain were incubated with H2O or 1 mM copper sulfate for 1 hour.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Worms were collected with H2O and incubated with H2O or 1mM copper sulfate for 1 hour at room temperature. Then Worms were washed by H2O and crushed in the Trizol solution (invitrogen) with beads.

tag: strain

value: N2 Bristol

tag: genotype

value: wildtype

tag: age

value: 1 day adult


title: kgb-1 incubated with H2O, biological rep1

description: Gene expression data from kgb-1 mutant adult worm incubated with H2O for 1 hr.

source_name: C. elegans kgb-1 mutant animal incubated with H2O for 1 hour


title: T1_H03


title: kgb-1 incubated with 1mM copper sulfate, biological rep1

description: Gene expression data from kgb-1 mutant adult worm incubated with copper sulfate for 1 hr.

source_name: C. elegans kgb-1 mutant animal incubated with copper sulfate for 1 hour


title: undifferentiated hMSCs (2 of 2)

type: genomic

description: Chip-chip undifferentiated 3A6 cells EZH2

data_processing: Signal intensity data is extracted from the scanned images of each array using NimbleScan (version 2.3.78), a NimbleGen's data extraction software. Arrays were scanned with Axon scanner at 5 um resolution according to standard NimbleGen protocols.Log2 ChIP/input ratios were created from the two raw pair files. Each feature on the array has a corresponding scaled log2-ratio. This is the ratio of the input signals for the experimental and test samples that were co-hybridized to the array. The log2-ratio is computed and scaled to center the ratio data around zero. Using NimbleScan, peak data files are generated from the scaled log2-ratio data. The ratio data is then randomized 20 times to evaluate the probability of false positives. Each peak is then assigned a false discovery rate (FDR) score based on the randomization. NimbleScan searches for peaks that appear in a specified promoter region around the transcription start site (TSS). Lists all peaks with an FDR 0.2 and maps them to promoter regions. Each row in the report lists a peak-transcript pair. For each transcript, if more than one peak lies within the promoter region, there will be multiple rows for that transcript.

molecule: genomic DNA

source_name: EZH2 ChIP DNA from 3A6 cells

growth_protocol: The 3A6 cells were grown in Dulbecco’s modified Eagle’s medium-low glucose (DMEM-LG) with 10% fetal bovine serum (FBS).

extract_protocol: cell lines were cross-linked with formaldehyde and the chromatin extracts were sonicated (Misonix Sonicater 3000). Following immunoprecipitation with anti-mouse EZH2 antibody (Cell Signaling, #3147, lot 4), DNAs were purified from ChIP samples and input control samples. Purified DNAs were blunt ended, ligated with linkers and amplified by PCR.

value: undifferentiated hMSCs

source_name: Input DNA from undifferentiated 3A6 cells

treatment_protocol: no special treatment


title: 786_O_5DC_2

description:
786-O Cells treated with 5DC
786_O_5DC_2_HG-U133_Plus_2.CEL

value: 5’-aza-deoxycytidine (5DC)


title: 786_O_5DC_3

description:
786-O Cells treated with 5DC
786_O_5DC_3_HG-U133_Plus_2.CEL


title: C_H02

value: control wild type


title: 786M1A-pBABE-3

description:
786-M1A cells with control plasmid pBabe-puro
786M1A_pBABE_3_HG-U133_Plus_2.CEL

value: 786-M1A cell line (metastatic)

tag: protocol


title: C_H01


title: WT incubated with H2O, biological rep1

description: Gene expression data from WT adult worm incubated with H2O for 1 hr.

source_name: C. elegans WT animal incubated with H2O for 1 hour


title: 786M1A-pBABE-2

description:
786-M1A cells with control plasmid pBabe-puro
786M1A_pBABE_2_HG-U133_Plus_2.CEL


title: 786_O_5DC_1

description:
786-O Cells treated with 5DC
786_O_5DC_1_HG-U133_Plus_2.CEL


title: 786M1A-pBABE-1

description:
786-M1A cells with control plasmid pBabe-puro
786M1A_pBABE_1_HG-U133_Plus_2.CEL


title: PV 7

city: Bronx

first: Yiting

last: Yu

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ,Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details.

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background.PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167.)

source_name: Neutrophil samples from polycythemia vera

label_protocol: Random 9-mers pre-labeled with either Cy5 or Cy3

extract_protocol: Genomic DNA from neutrophils isolated from peripheral blood via Ficoll-gradient density separation was prepared using Qiagen reagents.

tag: restriction enzyme

value: MspI representation of genomic DNA

value: neutrophil

tag: disease state

value: polycythemia vera

value: HpaII representation of genomic DNA


title: PV 8


title: 786M1A-HA-VHL-2

description:
786-M1A cells expressing HA-VHL
786M1A_HA_VHL_2_HG-U133_Plus_2.CEL

value: HA-VHL reintroduced


title: PV 1


title: PV 2


title: PV 3


title: LEC2_S3_rep3

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

description: Leaf at the onset of S3 stage of senescence-inducible LEC2 transgenic, biological replicate 3

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: Arabidopsis thaliana

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

growth_protocol: Arabidopsis thaliana (ecotype Columbia-0) and its transgenic plants were grown in potting soil in a controlled growth chambers at 22oC under a 16 h light/ 8h dark photoperiod.

extract_protocol: Total RNAs were extracted using TriReagent (Molecular Research Center, Inc.).

treatment_protocol: Transgenic plant lines transformed with a vector containing Arabidopsis LEC2 gene controlled by a senescence promoter, AtNAP were selected resistant plants to BASTA spray.

tag: ecotype

tag: self-fertile and virulent on host plants

value: S3 stage leaf (more than 50% yellow leaf)

value: senescence-inducible LEC2 transgenic


title: 786M1A-HA-VHL-3

description:
786-M1A cells expressing HA-VHL
786M1A_HA_VHL_3_HG-U133_Plus_2.CEL


title: PV 4


title: PV 6


title: LEC2_S3_rep2

description: Leaf at the onset of S3 stage of senescence-inducible LEC2 transgenic, biological replicate 2


title: ET 6

source_name: Neutrophil samples from essential thrombocytosis

value: essential thrombocytosis


title: LEC2_S1_rep3

description: Leaf at the onset of S1 stage of senescence-inducible LEC2 transgenic, biological replicate 3

value: S1 stage leaf (40 days plant, 100% green leaf)


title: LEC2_S1_rep1

description: Leaf at the onset of S1 stage of senescence-inducible LEC2 transgenic, biological replicate 1


title: PV 5


title: ET 5


title: LEC2_S3_rep1

description: Leaf at the onset of S3 stage of senescence-inducible LEC2 transgenic, biological replicate 1


title: 786M1A-HA-VHL-1

description:
786-M1A cells expressing HA-VHL
786M1A_HA_VHL_1_HG-U133_Plus_2.CEL


title: ET 4


title: LEC2_S1_rep2

description: Leaf at the onset of S1 stage of senescence-inducible LEC2 transgenic, biological replicate 2


title: WT_S1_rep3

description: Leaf at the onset of S1 stage of wild-type, biological replicate 3

value: wild-type


title: ET 3


title: 786-M2A

description:
Second generation metastatic derivative
786M2A_HG-U133A_2.CEL

data_processing: GCRMA as implemented in the R-package gcrma using the default settings and custom CDF-file hs133av2hsentrezgcdf version 10.

value: 2nd generation metastatic derivative of 786-O renal cell carcinoma cell line


title: 786-M2B

description:
Second generation metastatic derivative
786M2B_HG-U133A_2.CEL

value: 3rd generation metastatic derivative of 786-O renal cell carcinoma cell line


title: 786-M1B

description:
First generation metastatic derivative
786M1B_HG-U133A_2.CEL

value: 1st generation metastatic derivative of 786-O renal cell carcinoma cell line


title: 786-M1A

description:
First generation metastatic derivative
786M1A_HG-U133A_2.CEL


title: ET 2


title: ET 1


title: WT_S1_rep1

description: Leaf at the onset of S1 stage of wild-type, biological replicate 1


title: 786-O_B

description:
Parental 786-O
786O_B_HG-U133A_2.CEL

value: 786-O renal cell carcinoma cell line


title: PMF 12

source_name: Neutrophil samples from primary myelofibrosis

value: primary myelofibrosis


title: WT_S1_rep2

description: Leaf at the onset of S1 stage of wild-type, biological replicate 2


title: PSG at W, biological rep1

city: Hangzhou

first: Bo-xiong

last: Zhong

address: 268 Kaixuan Road

country: China

institute: College of Animal Sciences, Zhejiang University

description: The test samples and CKA were labeled with Cy3 and Cy5, respectively.

hyb_protocol: The labeled cDNA were hybridized with the hybridization solution (3×SSC, 0.2%SDS, 5×Denhart’s, 25% methanamide) for 16 hr at 42 °C on the 23K Silkworm Genome Arrays (CapitalBio Corp., Beijing, China). The arrays were washed with 0.2% SDS，2×SSC at 42 °C for 5 min followed by another 5 min washing with 0.2×SSC at room temperature.

scan_protocol: Array signals were scanned with a LuxScanTM 10K/A dual channels laser scanner and the images obtained were then analyzed using LuxScan™ 3.0 software (both from CapitalBio Corp.).

data_processing:
The data were analyzed with LuxScanTM 3.0 software (CapitalBio Corp.). The extracted signal data was filtered by removing faint spots, saturated spots (intensity >60,000), and signal intensities below 800 units after subtracting the background from both channels (Cy3 and Cy5). The prevalent LOWESS normalization method was applied for the checked signal intensity data.
After discarding the five housekeeping genes (including sw22934, sw13956, sw15061, sw01783, sw08699), exogenous controls (including Y1, Y2, Y3, Y4, Y5, Y6, Y7, Y8), immobilized control (Hex), and negative control (50%DMSO), the extracted signal data was filtered by removing faint spots, saturated spots (intensity >60,000), and signal intensities below 800 units after subtracting the background from both channels (Cy3 and Cy5). The prevalent LOWESS normalization method was applied for the checked signal intensity data. The active transcript is defined as that the signal intensities of at least two biological replicates at one stage have to pass the thresholds.

organism: Bombyx mori

source_name: silkworm PSG at W

label_protocol: Two micrograms of total RNA were used to prepare the fluorescent dye-labeled cDNA using the linear mRNA amplification procedure and a further Klenow enzyme labeling method. Dual-dye experiments were performed to analyze the gene expression patterns of PSG at M4, V1, V3, V5, and W; a total of 15 samples were tested including three biological replicates at each time point. An aliquot of the test samples were pooled as a common reference sample (CKA). The test samples and CKA were labeled with Cy3, Cy5, respectively. Cy5-dCTP, Cy3-dCTP (GE Healthcare Cat. No. PA 55021/ PA 53021).

growth_protocol: Silkworm strain p50 was reared on the fresh mulberry leaves under a 12 h light/12 h dark photoperiod at 26 ± 1 °C with 70–85% relative humidity.The developmental stages were synchronized after fourth molt by collecting new larvae.

treatment_protocol: The dissected PSGs were rinsed thrice in ice-cold RNase-free physiological saline, and then immediately froze with liquid nitrogen and stored at -80 °C.

tag: tissue

value: posterior silk gland (PSG)

tag: Stage

value: W

source_name: common refference (CKA)

value: Aliquots of each test sample were pooled as a common reference sample (CKA)


title: PSG at W, biological rep3


title: PSG at W, biological rep2


title: 786-O_A

description:
Parental 786-O
786O_A_HG-U133A_2.CEL

tag: cell line


title: PSG at V5, biological rep3

source_name: silkworm PSG at V5


title: PSG at V5, biological rep2


title: late28Cday7||log2ratioOfMediansBartonellaAgilent-15

city: San Francisco

first: Christopher

middle: S

last: Nelson

institute: UCSF

description: Biological replicate. 28C timepoint day 7

hyb_protocol: Hybridization mix was comprised of 10 ml of Cy5 labeled sample, 10 ml of Cy3 labeled pooled reference sample, 5 ml blocking buffer, and 25 ml of Agilent Gene Expression Buffer.  Hybridizations were carried out at 65°C for 16-19 h in Agilent hybridization chambers rotating at 10 rpm in a convection oven

scan_protocol: scanned on a Genepix 4000B scanner, adjusting PMT gains to balance the global dye signal balance ratio to 1.0 +/- 0.1

data_processing: gridded using Genepix6.0 software, background subtracted Cy5/Cy3 ratios were log2 transformed and zero centered

organism: Bartonella quintana

source_name: Bartonella quintana culture from blood agar

label_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

growth_protocol: Bartonella quintana cultures were passaged from thawed stocks on blood agar plates

extract_protocol: cDNA was generated from 0.5 mg of total RNA using random hexamer primers (Invitrogen) and SuperScriptä III (Invitrogen) following the manufacturer’s instructions

treatment_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: temperature

tag: day

source_name: pooled samples

tag: sample type

value: pooled from all samples


title: late37Cday7||log2ratioOfMediansBartonellaAgilent-12

description: Biological replicate. 37C timepoint day 7


title: PMF 9

value: MspI representation of genomic DNA

tag: cell type

value: neutrophil


title: late37Cday5||log2ratioOfMediansBartonellaAgilent-11

description: Biological replicate. 28C timepoint day 5


title: PMF 10

value: HpaII representation of genomic DNA


title: earlyJK31_28_D5


title: late28Cday9||log2ratioOfMediansBartonellaAgilent-16

description: Biological replicate. 28C timepoint day 9


title: 786-O_C

description:
Parental 786-O
786O_C_HG-U133A_2.CEL


title: PSG at V5, biological rep1


title: PSG at V3, biological rep3

source_name: silkworm PSG at V3


title: PMF 11


title: early28Cday5||log2ratioOfMediansBartonellaAgilent-14


title: TimKO rep2

city: Beijing

first: Gencheng

last: HAN

address: 27 Taiping Road, Haidian District

department: Department of Immunology

institute: Beijing Institute of Basic Medical Sciences

description: This sample is of Tim-3-siRNA transfected RAW264.7 cells. It is the second of three Tim-3 knockdown biological replicates used in this experiment, each from separate cultures.

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 2.5 (Roche NimbleGen, Inc.). All gene level files were imported into Agilent GeneSpring GX software(version 11.5.1) for further analysis. Genes that at least 3 out of 6 samples have values greater than or equal to lower cut-off: 100.0 were chosen for differentially expressed gene screening.

organism: Mus musculus

source_name: Tim-3 knockdown

growth_protocol: Tim-3 knockdown and control RAW264.7 cells were maintained in DMEM supplemented with 10% heat-inactivated FBS, 100 units/ml of penicillin, and 100 units/ml of streptomycin in a humidified 5% CO2 atmosphere at 37 °C.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: RAW264.7 cells were transfected with pRNAi-U6H1vector containing Tim-3 siRNA or control siRNA. The siRNA duplex giving maximal knockdown was selected. Raw264.7 cell clones stably express Tim-3 SiRNA were selected after continued culture with selecting drugs (G418, Sigma-Aldrich), and were analyzed for Tim-3 expression.

tag: treatment

value: Tim-3 knockdown


title: PMF 7


title: PSG at V3, biological rep2


title: earlyJK31_28_D4

description: Biological replicate. 28C timepoint day 4


title: PMF 6


title: earlyJK31_37_D4


title: PMF 8


title: CordBlood_CD4+_PIM123_siRNA_Act+IL4_6h__rep3

city: Turku

first: Kartiek

last: Kanduri

address: Tykistokatu 6

institute: Turku Centre for Biotechnology

description: CD4+ cell culture from cord blood of human neonates

hyb_protocol: Samples were hybridized to GeneChip Human Genome U219 array plate wit specific protocold for using the GeneTitan Hybridization, Wash and Stain Kit for 3_IVT Array Plates (P/N 901530).

scan_protocol: GeneTitan Instrument was used to scan the arrays. Affymetrix GeneChip Command Console (AGCC) 3.1 was used to control the GeneTitan hybridization process and in summarizing probe cell intensity data.

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

label: Biotin

source_name: human cord blood CD4+ cells, PIM123 siRNA treated, Act+IL4

label_protocol: Amplification was started from 250 ng of total RNA using the Affymetrix GeneChip 3_IVT Express Kit (P/N 901229), and cDNA/cRNA synthesis reactions and sample cleanup steps were performed according to manufacturer's protocol.

extract_protocol: Total RNA was extracted with RNeasy mini kit (Qiagen) according to manufacturers instructions. In-column DNase (RNase-Free Dnase Set, Qiagen) treatment was performed for 15 minutes. RNA was eluted in dH2O.

tag: genotype/variation

value: PIM kinase (PIM1+PIM2+PIM3) knockdown

value: cord blood

value: CD4+ T cells


title: CordBlood_CD4+_PIM123_siRNA_Act+IL4_6h__rep1


title: early37Cday4||log2ratioOfMediansBartonellaAgilent-10


title: CordBlood_CD4+_PIM123_siRNA_Act+IL4_6h__rep2


title: CordBlood_CD4+_control_siRNA_Act+IL4_6h__rep3

source_name: human cord blood CD4+ cells, control siRNA treated, Act+IL4

value: control


title: CordBlood_CD4+_control_siRNA_Act+IL4_6h__rep2


title: PSG at V1, biological rep3

source_name: silkworm PSG at V1

tag: strain


title: PMF 4


title: BMDC_CT-26

city: Tianjin, P.R.China

first: Yang

last: Rongcun

address: 94 Weijin Road, Nankai District

department: School of medicine

institute: Nankai University

hyb_protocol: The labeled samples were hybridized on the miRCURY LNA™ microRNA Array V11.0.

scan_protocol: Hybridization signals were detected by fluorescence using an GenePix 4000B scanner (Molecular Devices). Scanner images were quantified by GenePix Pro 6 (Molecular Devices).

data_processing: For each spot, verify the signal by subtracting background intensity (B) from foreground intensity (F). Verified signal value= F - B. The spots, of which verified signal values are less than 50, and the control spots are filtered. For verified signal values of the left spots, perform median normalization.

source_name: BMDC_tumor cells

label_protocol: The samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit (Cat #208032-A, Exiqon) according to manufacturer's instructions.

extract_protocol: Total RNAs were isolated using the TRIZOL® Reagent(Invitrogen) according to manufacturer’s instructions.

value: Bone Marrow-derived Dendritic Cells (BMDCs)

tag: co-cultured with

value: CT-26 tumor cells


title: early37Cday3||log2ratioOfMediansBartonellaAgilent-9

description: Biological replicate. 37C timepoint day 3


title: PSG at V3, biological rep1


title: PSG at M41, biological rep3

source_name: silkworm PSG at M4


title: PSG at V1, biological rep2


title: PMF 2


title: control 3

source_name: Neutrophil samples from healthy control

value: healthy control


title: BMDC_Control


title: earlyJK31_37_D3


title: PMF 1


title: PMF 5


title: PMF 3


title: PSG at M4, biological rep2


title: CordBlood_CD4+_PIM123_siRNA_Act+IL12_6h__rep2

hyb_protocol: Samples were hybridized to GeneChip Human Genome U219 array plate wit specific protocold for using the GeneTitan Hybridization, Wash and Stain Kit for 3‰IVT Array Plates (P/N 901530).

source_name: human cord blood CD4+ cells, PIM123 siRNA treated, Act+IL12

label_protocol: Amplification was started from 250 ng of total RNA using the Affymetrix GeneChip 3‰IVT Express Kit (P/N 901229), and cDNA/cRNA synthesis reactions and sample cleanup steps were performed according to manufacturer's protocol.


title: US50

status: Public on Dec 04 2012

type: protein

city: Irvine

first: Carolina

last: Lessa Aquino

address: 302 MedSurge II

institute: University of California Irvine

description:
Sample_274
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray

hyb_protocol: Human sera were used at 1/100 dilution in protein array blocking buffer (Whatman) containing E. coli lysate (Antigen Discovery Inc, Irvine CA) to a final concentration of 10% to block anti-E. coli antibodies. Sera were preincubated at RT for 30 minutes with constant mixing prior to applying to the arrays and incubated overnight at 4oC with gentle agitation. After washing three times in TBS + 0.05% Tween 20% (TTBS), biotinylated anti-human IgG (JacksonImmunoResearch) was used at 1/2000 as secondary antibody followed after washing another 3 times in TTBS by streptavidin-PBXL3 conjugate (Columbia Biosciences) at 1/200 in blocking buffer.

scan_protocol: After washing six times in TTBS and one time in DDI water, slides were air dried by brief centrifugation and then scanned and analyzed using a Perkin Elmer ScanArray Express HT microarray scanner (PerkinElmer). Fluorescence intensities were quantified from tiff images by using ProScanArray Express software (PerkinElmer).

data_processing:
Data analysis was performed using the R (http://www.r-project.org) statistical software.
In order to stabilize the variance observed in microarray signals, the vsn normalization was implemented as part of the Bioconductor suite (www.bioconductor.org) to the quantified array intensities using the 'no DNA' spots (IVTT reactions lacking the template DNA) as normalization controls.
Inter-group comparisons were performed using a Bayes regularized t-test adapted from Cyber-T for protein arrays (Baldi and Hatfield, 2002; Baldi and Long, 2001).
To account for multiple comparison conditions, p-values were corrected by the Benjamini and Hochberg (pBH) method  to control the false discovery rate (Benjamini and Hochberg, 1995).
After correction, p-values < 0.05 were considered significant and the corresponding protein was considered differentially reactive.
References:
Baldi, P., and Hatfield, G.W. (2002). DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling. Cambridge University Press
Baldi, P., and Long, A.D. (2001). A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. Bioinformatics 17, 509-519.
Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 57, 289--300.
Long, A.D., Mangalam, H.J., Chan, B.Y., Tolleri, L., Hatfield, G.W., and Baldi, P. (2001). Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem 276, 19937-19944.

molecule: protein

source_name: serum

tag: serum type

value: US naïve

tag: country

value: UNITED STATES

tag: date of patient identification

tag: date of sample collection

tag: days of symptoms before patient identification

tag: gender

value: Unknown

tag: mat titer acute sample

tag: mat titer convalescent sample


title: US30

description:
Sample_273
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: PSG at V1, biological rep1

tag: tissue

value: posterior silk gland (PSG)

tag: Stage


title: CordBlood_CD4+_control_siRNA_Act+IL12_6h__rep3

source_name: human cord blood CD4+ cells, control siRNA treated, Act+IL12


title: BMDC_ID8

value: ID8 tumor cells


title: control 2

tag: restriction enzyme

tag: disease state


title: US29

description:
Sample_272
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CordBlood_CD4+_PIM123_siRNA_Act+IL12_6h__rep1

tag: cell type


title: PSG at M4, biological rep1

value: Aliquots of each test sample were pooled as a common reference sample (CKA)


title: CordBlood_CD4+_control_siRNA_Act+IL4_6h__rep1


title: control 1

value: MspI representation of genomic DNA


title: US28

description:
Sample_271
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CordBlood_CD4+_PIM123_siRNA_Act+IL12_6h__rep3


title: early28Cday3||log2ratioOfMediansBartonellaAgilent-13

description: Biological replicate. 28C timepoint day 3

tag: temperature

tag: day

tag: sample type

value: pooled from all samples


title: CordBlood_CD4+_control_siRNA_Act+IL12_6h__rep1

tag: genotype/variation


title: CordBlood_CD4+_control_siRNA_Act+IL12_6h__rep2


title: US25

description:
Sample_268
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray

tag: serum type


title: US26

description:
Sample_269
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray

tag: country


title: US27

description:
Sample_270
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray

tag: date of patient identification


title: US23

description:
Sample_266
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray

tag: date of sample collection


title: US24

description:
Sample_267
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray

tag: days of symptoms before patient identification


title: US20

description:
Sample_263
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray

tag: gender


title: US22

description:
Sample_265
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray

tag: mat titer acute sample


title: US18

description:
Sample_261
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray

tag: mat titer convalescent sample


title: US16

description:
Sample_259
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: US17

description:
Sample_260
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: US21

description:
Sample_264
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: US14

description:
Sample_257
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: US10

description:
Sample_254
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: US7

description:
Sample_252
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: US9

description:
Sample_253
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: US6

description:
Sample_251
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: US11

description:
Sample_255
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: US4

description:
Sample_249
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: US2

description:
Sample_247
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD274

description:
Sample_244
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray

value: Blood donor

value: Brazil


title: BD273

description:
Sample_243
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD272

description:
Sample_242
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: US19

description:
Sample_262
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD271

description:
Sample_241
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD270

description:
Sample_240
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD269

description:
Sample_239
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD268

description:
Sample_238
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: US15

description:
Sample_258
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: US13

description:
Sample_256
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD267

description:
Sample_237
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: US5

description:
Sample_250
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD266

description:
Sample_236
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD264

description:
Sample_234
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD265

description:
Sample_235
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD262

description:
Sample_232
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: US3

description:
Sample_248
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: US1

description:
Sample_246
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD263

description:
Sample_233
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD255

description:
Sample_225
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD257

description:
Sample_227
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD259

description:
Sample_229
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD261

description:
Sample_231
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD275

description:
Sample_245
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD258

description:
Sample_228
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD260

description:
Sample_230
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD252

description:
Sample_222
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD253

description:
Sample_223
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD251

description:
Sample_221
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD250

description:
Sample_220
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD249

description:
Sample_219
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD248

description:
Sample_218
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD246

description:
Sample_216
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD245

description:
Sample_215
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD247

description:
Sample_217
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD244

description:
Sample_214
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD242

description:
Sample_212
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD256

description:
Sample_226
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD243

description:
Sample_213
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD254

description:
Sample_224
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND209

description:
Sample_209
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray

value: Healthy individual from high endemic area

value: F


title: HEND210

description:
Sample_210
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND208

description:
Sample_208
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND205

description:
Sample_205
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND206

description:
Sample_206
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND207

description:
Sample_207
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray

value: M


title: HEND204

description:
Sample_204
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND198

description:
Sample_198
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND200

description:
Sample_200
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND196

description:
Sample_196
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND201

description:
Sample_201
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND199

description:
Sample_199
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND197

description:
Sample_197
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND195

description:
Sample_195
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND192

description:
Sample_192
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND194

description:
Sample_194
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND193

description:
Sample_193
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: BD241

description:
Sample_211
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND190

description:
Sample_190
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND189

description:
Sample_189
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND187

description:
Sample_187
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND188

description:
Sample_188
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND185

description:
Sample_185
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND191

description:
Sample_191
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND183

description:
Sample_183
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND184

description:
Sample_184
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND181

description:
Sample_181
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND180

description:
Sample_180
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND182

description:
Sample_182
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND178

description:
Sample_178
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND202

description:
Sample_202
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND203

description:
Sample_203
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND177

description:
Sample_177
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND179

description:
Sample_179
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND176

description:
Sample_176
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND175

description:
Sample_175
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND173

description:
Sample_173
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND174

description:
Sample_174
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND172

description:
Sample_172
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND186

description:
Sample_186
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND169

description:
Sample_169
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND168

description:
Sample_168
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND171

description:
Sample_171
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND170

description:
Sample_170
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND167

description:
Sample_167
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND166

description:
Sample_166
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON160

description:
Sample_160
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray

value: Convalescent


title: CON159

description:
Sample_159
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND161

description:
Sample_161
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND163

description:
Sample_163
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND164

description:
Sample_164
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON158

description:
Sample_158
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND162

description:
Sample_162
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: HEND165

description:
Sample_165
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON157

description:
Sample_157
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON154

description:
Sample_154
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON152

description:
Sample_152
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON153

description:
Sample_153
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON151

description:
Sample_151
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON156

description:
Sample_156
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON149

description:
Sample_149
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON150

description:
Sample_150
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON155

description:
Sample_155
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON147

description:
Sample_147
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON146

description:
Sample_146
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON148

description:
Sample_148
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON144

description:
Sample_144
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON145

description:
Sample_145
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON143

description:
Sample_143
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON142

description:
Sample_142
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON141

description:
Sample_141
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON138

description:
Sample_138
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON137

description:
Sample_137
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON139

description:
Sample_139
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON136

description:
Sample_136
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON135

description:
Sample_135
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON140

description:
Sample_140
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON130

description:
Sample_130
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON134

description:
Sample_134
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON131

description:
Sample_131
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON132

description:
Sample_132
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON128

description:
Sample_128
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON129

description:
Sample_129
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON127

description:
Sample_127
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON133

description:
Sample_133
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON124

description:
Sample_124
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON126

description:
Sample_126
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON122

description:
Sample_122
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON123

description:
Sample_123
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON119

description:
Sample_119
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON125

description:
Sample_125
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON120

description:
Sample_120
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON118

description:
Sample_118
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON117

description:
Sample_117
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON116

description:
Sample_116
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON114

description:
Sample_114
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON113

description:
Sample_113
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON115

description:
Sample_115
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON112

description:
Sample_112
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON110

description:
Sample_110
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON111

description:
Sample_111
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON109

description:
Sample_109
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON106

description:
Sample_106
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON121

description:
Sample_121
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON102

description:
Sample_102
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON105

description:
Sample_105
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON104

description:
Sample_104
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON108

description:
Sample_108
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON101

description:
Sample_101
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON98

description:
Sample_98
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON103

description:
Sample_103
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON99

description:
Sample_99
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON97

description:
Sample_97
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON94

description:
Sample_94
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON93

description:
Sample_93
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON100

description:
Sample_100
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON107

description:
Sample_107
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON95

description:
Sample_95
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON90

description:
Sample_90
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON91

description:
Sample_91
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON92

description:
Sample_92
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON96

description:
Sample_96
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON85

description:
Sample_85
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU64

description:
Sample_64
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray

value: Acute


title: ACU61

description:
Sample_61
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON89

description:
Sample_89
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU72

description:
Sample_72
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU74

description:
Sample_74
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU73

description:
Sample_73
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON88

description:
Sample_88
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON82

description:
Sample_82
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU62

description:
Sample_62
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON87

description:
Sample_87
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU80

description:
Sample_80
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU63

description:
Sample_63
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON81

description:
Sample_81
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON84

description:
Sample_84
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU68

description:
Sample_68
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU66

description:
Sample_66
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU67

description:
Sample_67
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU65

description:
Sample_65
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU69

description:
Sample_69
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU75

description:
Sample_75
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU78

description:
Sample_78
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU77

description:
Sample_77
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU76

description:
Sample_76
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON86

description:
Sample_86
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU70

description:
Sample_70
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU71

description:
Sample_71
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: CON83

description:
Sample_83
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU79

description:
Sample_79
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU60

description:
Sample_60
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU54

description:
Sample_54
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU48

description:
Sample_48
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU57

description:
Sample_57
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU43

description:
Sample_43
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU47

description:
Sample_47
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU38

description:
Sample_38
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU52

description:
Sample_52
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU37

description:
Sample_37
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU58

description:
Sample_58
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU55

description:
Sample_55
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU56

description:
Sample_56
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU46

description:
Sample_46
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU53

description:
Sample_53
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU44

description:
Sample_44
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU35

description:
Sample_35
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU42

description:
Sample_42
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU36

description:
Sample_36
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU41

description:
Sample_41
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU51

description:
Sample_51
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU31

description:
Sample_31
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU45

description:
Sample_45
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU32

description:
Sample_32
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU49

description:
Sample_49
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU50

description:
Sample_50
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU33

description:
Sample_33
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU59

description:
Sample_59
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU34

description:
Sample_34
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU40

description:
Sample_40
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU30

description:
Sample_30
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU39

description:
Sample_39
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU23

description:
Sample_23
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU29

description:
Sample_29
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU28

description:
Sample_28
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU22

description:
Sample_22
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU25

description:
Sample_25
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU18

description:
Sample_18
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU21

description:
Sample_21
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU20

description:
Sample_20
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU26

description:
Sample_26
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU17

description:
Sample_17
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU15

description:
Sample_15
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU24

description:
Sample_24
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU12

description:
Sample_12
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU14

description:
Sample_14
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU16

description:
Sample_16
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU13

description:
Sample_13
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU19

description:
Sample_19
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU9

description:
Sample_9
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU8

description:
Sample_8
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU6

description:
Sample_6
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU10

description:
Sample_10
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU3

description:
Sample_3
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU5

description:
Sample_5
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU2

description:
Sample_2
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU27

description:
Sample_27
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: PAEC APJ APEL SIRNA3

city: New Haven

first: hyung

last: chun

state: CT

address: 300 George St Room 770H

department: Internal Medicine

institute: Yale University

hyb_protocol: Samples were hybridized onto beadchips according to microRNA expression profiling protocol from Illumina.

scan_protocol: The Illumina BeadArray Reader and BeadScan software were used to scan and extract raw intensity values.

data_processing: Background subtraction and quantile normalization were performed using the Illumina GenomeStudio package.

source_name: PAEC

label_protocol: Samples were labeled according to microRNA expression profiling protocol from Illumina.

growth_protocol: PAECs grown in EGM-2 (Lonza)

extract_protocol: Qiagen miRNeasy per manufacturer's protocol

treatment_protocol: Transfected with siRNAs (Stealth siRNA, invitrogen) for 72 hours

tag: cells

value: PAEC

tag: knockdown

value: APELIN + APJ


title: ACU1

description:
Sample_1
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU11

description:
Sample_11
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU7

description:
Sample_7
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: ACU4

description:
Sample_4
IgG antibody profiling of Leptospira interrogans serovar Copenhageni in infected and non-infected subjects using protein microarray


title: PAEC APJ APEL SIRNA2


title: PAEC HIGH GC CONTROL2

value: CONTROL


title: PAEC APEL 87 SIRNA1

value: APELIN


title: PAEC APJ SIRNA1

value: APJ


title: PAEC APEL 87 SIRNA2


title: PAEC HIGH GC CONTROL3


title: PAEC APJ SIRNA2


title: PAEC APJ APEL SIRNA1


title: PAEC APJ SIRNA3


title: PAEC HIGH GC CONTROL1


title: PAEC APEL 87 SIRNA3


title: LPA_M_1134

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

description:
trait 1: Fat area [cm2]: fat area on M. longissimus dorsi at 13th/14th rib
trait 2: Drip loss (%): percentage of weight loss of M. longissimus dorsi samples collected at 24 hours post mortem that was weighted, suspended in a plastic bag, held at 4 °C for 48 h, and thereafter re-weighed

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500. Affymetrix 'ExpressionConsole' was used to generate the PLIER data.

organism: Sus scrofa

source_name: muscle taken at slaughter, mean end weight of 110 kg

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer's protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: herd

value: commercial pig of crosbred Pix(DLxDE)

tag: trait 1 (see description below)

tag: trait 2 (see description below)

tag: tissue

value: muscle


title: LPA_M_1130


title: LPA_M_1105


title: LPA_M_1135


title: LPA_M_1109


title: LPA_M_1123


title: LPA_M_1125


title: LPA_M_1120


title: LPA_M_1115


title: LPA_M_1131


title: LPA_M_1106


title: LPA_M_1117


title: LPA_M_1138


title: LPA_M_1114


title: LPA_M_1112


title: LPA_M_1088


title: LPA_M_1092


title: LPA_M_1126


title: LPA_M_1086


title: LPA_M_1082


title: LPA_M_1083


title: LPA_M_1074


title: LPA_M_1079


title: LPA_M_1070


title: LPA_M_1071


title: LPA_M_1080


title: LPA_M_1073


title: LPA_M_1075


title: LPA_M_1072


title: LPA_M_710


title: LPA_M_759


title: LPA_M_706


title: LPA_M_704


title: LPA_M_659


title: LPA_M_705


title: LPA_M_728


title: LPA_M_726


title: LPA_M_725


title: LPA_M_708


title: LPA_M_629


title: LPA_M_675


title: LPA_M_695


title: LPA_M_1063


title: LPA_M_1066


title: LPA_M_693


title: LPA_M_711


title: LPA_M_635


title: LPA_M_624


title: LPA_M_614


title: LPA_M_600


title: LPA_M_622


title: LPA_M_627


title: LPA_M_587


title: LPA_M_604


title: LPA_M_575


title: LPA_M_592


title: LPA_M_594


title: LPA_M_573


title: LPA_M_598


title: LPA_M_568


title: LPA_M_551


title: LPA_M_559


title: LPA_M_541


title: LPA_M_543


title: LPA_M_579


title: LPA_M_571


title: LPA_M_580


title: LPA_M_586


title: LPA_M_596


title: LPA_M_557


title: LPA_M_545


title: LPA_M_615


title: LPA_M_560


title: LPA_M_542


title: LPA_M_530


title: LPA_M_538


title: LPA_M_497


title: LPA_M_536


title: LPA_M_510


title: LPA_M_499


title: LPA_M_482


title: LPA_M_489


title: LPA_M_478


title: LPA_M_532


title: LPA_M_484


title: LPA_M_474


title: LPA_M_485


title: LPA_M_424


title: LPA_M_428


title: LPA_M_438


title: LPA_M_1099


title: LPA_M_423


title: LPA_M_443


title: LPA_M_447


title: LPA_M_415


title: LPA_M_419


title: LPA_M_425


title: LPA_M_426


title: LPA_M_475


title: LPA_M_421


title: LPA_M_476


title: LPA_M_418


title: LPA_M_1068


title: LPA_M_403


title: LPA_M_393


title: LPA_M_375


title: LPA_M_391


title: LPA_M_388


title: LPA_M_378


title: LPA_M_386


title: LPA_M_409


title: LPA_M_392


title: LPA_M_413


title: LPA_M_405


title: LPA_M_368


title: LPA_M_380


title: LPA_M_376


title: LPA_M_367


title: LPA_M_346


title: LPA_M_364


title: LPA_M_335


title: LPA_M_328


title: LPA_M_343


title: LPA_M_326


title: LPA_M_358


title: LPA_M_333


title: LPA_M_354


title: LPA_M_360


title: LPA_M_353


title: LPA_M_324


title: LPA_M_361


title: LPA_M_325


title: LPA_M_322


title: LPA_M_321


title: LPA_M_305


title: LPA_M_311


title: LPA_M_307


title: LPA_M_303


title: LPA_M_319


title: LPA_M_294


title: LPA_M_229


title: LPA_M_306


title: LPA_M_232


title: LPA_M_261


title: LPA_M_309


title: LPA_M_247


title: LPA_M_259


title: LPA_M_262


title: LPA_M_315


title: LPA_M_240


title: LPA_M_218


title: LPA_M_241


title: LPA_M_214


title: LPA_M_206


title: LPA_M_288


title: LPA_M_245


title: LPA_M_216


title: LPA_M_215


title: LPA_M_204


title: LPA_M_208


title: LPA_M_198


title: LPA_M_193


title: LPA_M_200


title: LPA_M_194


title: LPA_M_191


title: LPA_M_195


title: LPA_M_184


title: LPA_M_185


title: LPA_M_221


title: LPA_M_188


title: LPA_M_186


title: LPA_M_180


title: LPA_M_171


title: BJV+inf.2 - BJ cells with empty vector, treated with IFNb, rep 2

city: Philadelphia

first: Louise

middle: C

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

hyb_protocol: Hyb on Illumina Human-6 v2 Expression BeadChip Kit (catolog #BD-25-112) using Illumina whole-Genome Gene Exprssion with Intellihyb Seal system which detect signal with streptavidin-Cy3.

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Illumina BeadStudio v.3.0 software was used to export expression levels and detection p-values for each probe of each sample. Arrays were quantile normalized between each other and filtered to remove non-informative probes. A probe was called non-informative if it had detection p-value>0.05 in all samples or if maximum ratio between expression values was not at least 1.2 between at least two samples.

source_name: BJ cells, transduced with empty vector

label_protocol: Biotin Labeling of RNA at 250ng with Ambion Illumina® TotalPrep RNA Amplification Kit(Cat #AMIL1791)

extract_protocol: total RNA

tag: cell passage

tag: cell line

value: BJ cells

tag: genome/variation

value: transduced with empty vector

tag: treatment group

value: treated with IFNb


title: BJV+inf.3 - BJ cells with empty vector, treated with IFNb, rep 3


title: LPA_M_109


title: BJ-S+inf.1 - BJ cells with Sp100 knock out, treated with IFNb, rep 1

source_name: BJ cells transduced with the vector reducing all Sp100 isoforms

value: Sp100 knock out


title: LPA_M_93


title: BJ-S.1 - BJ cells with Sp100 knock out, rep 1

label_protocol: Biotin Labeling of RNA at 250ng  with Ambion Illumina® TotalPrep RNA Amplification Kit(Cat #AMIL1791)


title: BJV.2 - BJ cells with empty vector, rep 2


title: BJ-S+inf.2 - BJ cells with Sp100 knock out, treated with IFNb, rep 2


title: BJ-S.2 - BJ cells with Sp100 knock out, rep 2


title: LPA_M_82


title: BJV.3 - BJ cells with empty vector, rep 3


title: LPA_M_108


title: BJ-S+inf.3 - BJ cells with Sp100 knock out, treated with IFNb, rep 3


title: LPA_M_104


title: LPA_M_86


title: BJ-S.3 - BJ cells with Sp100 knock out, rep 3


title: LPA_M_83


title: LPA_M_227


title: LPA_M_115


title: LPA_M_81


title: LPA_M_80


title: Vs008 LC + L3

city: Bethesda

first: Roshanak

middle: T

last: Semnani

state: MD

address: Center Drive

department: LPD

institute: NIAID

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol and scanned with Illumina Beadstation 500 bead array reader.

data_processing: The data were background subtracted and average normalized using Illumina Genome Studio.

label_protocol: Biotynlated cDNA were generated following manufacturer protocols using WT-Ovation pico RNA amplification system (NuGen).

extract_protocol: RNA was extracted with Ambion's RNAqueous-Micro Kit (Life Technologies)  according to the manufacture's instructions. Quality control was performed with Agilent Bioanalyser.

tag: culture condition

tag: donor id

tag: infection

value: Filarial infection by mosquito-derived, third-stage larvae (L3)

tag: cell type

value: skin


title: Vs007 LC + L3


title: BJV.1 - BJ cells with empty vector, rep 1


title: BJV+inf.1 - BJ cells with empty vector, treated with IFNb, rep 1


title: Vs008 LC

source_name: LC

value: LC

value: control


title: Vs004 LC + L3


title: LPA_M_88


title: LPA_M_77


title: LPA_M_71


title: LPA_M_73


title: LPA_M_52


title: Vs007 LC


title: LPA_M_50


title: LPA_M_63


title: Vs005a LC


title: LPA_M_72


title: LPA_M_70


title: LPA_M_45


title: Vs005b LC


title: Vs006 LC


title: Vs005b LC + L3


title: LPA_M_51


title: Vs005a LC + L3


title: LPA_M_48


title: Vs006 LC + L3


title: Vs004 LC


title: LPA_M_42


title: LPA_M_176


title: LPA_M_49


title: HTEC-d21_IL13-36

city: St. Louis

first: Anand

middle: Champak

last: Patel

state: MO

address: Campus Box 8116, 660 S. Euclid Ave.

department: Pulmonary/Critical Care Medicine

description:
d21 IL-13 rep 4
IL13_504_36

hyb_protocol: Hybridization was performed according to the manufacturer’s instructions at the Washington University School of Medicine Genome Sequencing Center Microarray Core Facility.

scan_protocol: Scanning, including background correction, was performed per manufacturer's instructions using BeadStudio 3.0 software (Illumina) at the Washington University School of Medicine Genome Sequencing Center Microarray Core Facility.

data_processing: Microarray normalization and statistical analysis was performed using packages from the Bioconductor project executed in the R programming environment. Raw image data were imported into Bioconductor using readIllumina as implemented in the beadarray package with background subtraction and image sharpening. The resulting bead-level data was then normalized for intensity at the bead level using the HULK algorithm, to adjust for local spatial effects (i.e. cross-array gradients). The data were then summarized for each bead type. A model-based variance stabilizing transformation was applied to the bead-type summaries, followed by quantile normalization across the experiment using functions in the beadarray package. Bead-types not detected on at least 1 array (detection p<0.01) were then filtered to improve power to detect differentially expressed genes. We assessed differential expression after 21 days of IL-13 treatment (IL-13 versus control) using linear models and empirical Bayes moderated F statistics as implemented in the LIMMA package. We considered differences in gene expression significant if P values were <0.05 after adjustment for multiple testing, so that false discovery rate was <5%. Bead-types were annotated to genes using a combination of the manufacturer’s annotation, transcript level annotations obtained from AceView, and annotations from the University of Cambridge Computational Biology Group in order to optimize interpretation of the gene expression data.

source_name: primary culture airway epithelial cells d21, with IL-13 rep 4

label_protocol: RNA was amplified and biotinylated using the Ambion Illumina TotalPrep Kit.

growth_protocol: Human tracheal epithelial cells (hTECs) were isolated and placed into culture in growth factor enriched medium as described previously. For the present experiments, cells were seeded at 2 x 105 cells per well (24-well Transwell, Corning, Corning, NY) and cultured under submerged conditions until confluence. Cultures were then maintained in DMEM-Ham’s F12 medium with 2% NuSerum (BD, Franklin, NJ), Primocin (100 µg/ml, InvivoGen, San Diego, CA), and retinoic acid (1 x 10–8 M, Sigma), and were switched to air-liquid interface conditions for 3 weeks.  Media was changed twice weekly, cells were fed from the bottom reservoir.

extract_protocol: Total RNA was isolated from hTECs using the Qiagen RNEasy kit (Qiagen)

treatment_protocol: IL-13 (50 ng/ml) was added starting day -2 (two days before ALI), and twice weekly for 21 days thereafter.

tag: day

tag: agent

value: primary culture airway epithelial cell, tracheal


title: HTEC-d21_IL13-35

institute: Washington University School of Medicine

description:
d21 IL-13 rep 3
IL13_504_35

source_name: primary culture airway epithelial cells d21, with IL-13 rep 3


title: HTEC-d21_IL13-33

description:
d21 IL-13 rep 1
IL13_504_33

source_name: primary culture airway epithelial cells d21, with IL-13 rep 1


title: HTEC-d21_NT-32

description:
d21 NT rep 4
NT_504_32

source_name: primary culture airway epithelial cells d21, no IL-13 rep 4

value: No Treatment


title: LPA_M_39


title: HTEC-d21_IL13-34

description:
d21 IL-13 rep 2
IL13_504_34

source_name: primary culture airway epithelial cells d21, with IL-13 rep 2


title: HTEC-d21_NT-31

description:
d21 NT rep 3
NT_504_31

source_name: primary culture airway epithelial cells d21, no IL-13 rep 3


title: LPA_M_20


title: HTEC-d21_NT-29

description:
d21 NT rep 1
NT_504_29

source_name: primary culture airway epithelial cells d21, no IL-13 rep 1


title: LPA_M_29


title: LPA_M_38