title: BHI_Enteritidis_chlorine_130ppm_rep2

description: This sample is of Salmonella enterica Enteritidis in BHI broth w/ 130ppm chlorine treatment for 30 minutes . It is the second of three biological replicates used in this experiment, each from separate cultures.

source_name: Salmonella enterica Enteritidis, chlorine, 130ppm 30min


title: SAE 13727666 GEO E1' t1 - cy5 vs S1' t1 - cy3

status: Public on Mar 10 2010

type: RNA

city: Cologne

first: Ludwig

last: Eichinger

address: Joseph-Stelzmann-Strasse 52

country: Germany

institute: Institute for Biochemistry 1

description: DNA microarrays cotainining 5,423 non-redundant ESTs from the D. discoideum cDNA project (Urushihara et al., 2004), partial sequences of 450 selected genes, probes of the SpotReport-10 Array Validation System (Stratagene, La Jolla, USA) and appropriate positive and negative controls were produced in-house using standard protocols (see also: http://www.uni-koeln.de/medfak/biochemie/transcriptomics/ production.e.shtml). Briefly, probes were amplified by two 100µl PCR reactions in 96-well microtiter plates using standard primers (M13F2: 5’-GTAAAACGACGGCCAGTG-3’, M13R2: 5’-C6-Aminolink-ACCATGATTACGCCAAGC-3’) for the cloned ESTs and gene-specific primers for the selected genes and the positive controls. After analysis by agarose gel electrophoresis (10µl of each reaction) the two reactions were combined, precipitated, solubilised in 11µl 25% DMSO, 1µl separated again by agarose gel electrophoresis and evaluated (Farbrother et al., 2002). Probes were transferred with the proteineer dp pipetting robot (Bruker, Germany) into 384-well microarray plates with cylindrical wells (Abgene, Hamburg, Germany) and printed onto UltraGaps slides (Corning, New York, USA) at 18°C and 45% humidity with a BioRobotics MicroGrid 600 microarray robot (Genomic Solutions, Huntingdon, UK) using MicroSpot 2500 microarraying pins. Each probe was spotted in duplicate, positive and negative controls were spotted 6, 24, 192 or 286 times and the SpotReport controls 96 times. The microarray is composed of three grids with 16 subarrays each and 14,620 spots in total. The complete microarray dataset is available at GEO, http://www.ncbi.nlm.nih.gov/geo; accession number GPL1972.

hyb_protocol: Cy3 and Cy5 labelled targets were mixed, ethanol precipitated and dissolved in 65 µl of hybridisation buffer (Noegel et al., 1985) with 500 µg/ml Fish sperm DNA (Roche, Mannheim, Germany) and 2 µM Oligo dA 18-mer. The hybridisation mix was heated to 80 °C for 10 min, applied to the microarray under a cover-slip and incubated in a hybridisation chamber (Corning, New York, USA) for 15 hours at 37°C. Post-hybridisation washes were performed twice with 2x SSC, 0.1% SDS and once with 0.1x SSC, 0.1% SDS for 5 min each, five times with 0.1x SSC and once with with 0.01x SSC for 5 sec each and dried by centrifugation at 235xg for 5 min. See also Farbrother et al., Cell. Microbiol., 3:438-456, 2006.

scan_protocol: Signal detection was performed with the ScanArray 4000XL confocal laser scanner (PerkinElmer Life Sciences, Wellesley, USA). Images for Cy3 and Cy5 were obtained, spots were detected and quantified with ScanArray Express v2.2 (PerkinElmer Life Sciences), then manually inspected and if necessary corrected. See also Farbrother et al., Cell. Microbiol., 3:438-456, 2006.

data_processing:
For each individual comparison four microarrays were hybridised and analysed. Two imagepairs were produced per microarray slide, one with high laser intensity so that signals for most probes and also some saturated signals were obtained and a second one with lower laser intensity so that none of the signals was saturated. This way the dynamic range of the measurement was expanded. To handle the import and export of microarray data to different analysis programs an Excel Add-In, Array tools (http://www.uni-koeln.de/med-fak/biochemie/ transcriptomics/tools-array.e.shtml), was programmed in Visual Basic. Upon import of two data files of the same microarray scanned with different laser powers the saturated spots of the high laser power scan were replaced by non-saturated spots from the low laser power scan. In addition the import also performed data filtering by flagging SpotReport controls, negative controls, empty spots, spots where only spotting solution was printed and spots whose intensities were below or equal to zero as "Bad". Fluorescence ratios were normalised by LOWESS-norma-lisation using R1.6.2 (BioConductor, http://www.bioconductor.org/). The normalized M values (M = log2 (Intensityexperiment/Intensitycontrol) were transferred into a new worksheet for significance analysis of microarrays (SAM) analysis (Tusher et al., 2001). At the transfer all probes spotted in higher replicates were reduced to double spots by averaging. Furthermore all probes that were flagged "Found" in less than half of the spots, were excluded from SAM analysis. Differentially regulated genes were identified using the one-class SAM method calculating 1000 permutations. The SAM program not only identifies the differentially regulated genes, but also predicts the number of false positives. These are the genes that are falsely reported as differentially expressed. This feature was used in all microarray experiments to set the significance level such, that the 90th percentile of the false discovery rate (FDR) was minimal.
See also Farbrother et al., Cell. Microbiol., 3:438-456, 2006.

molecule: total RNA

organism: Dictyostelium discoideum

label_protocol: Fairplay indirect labelling kit (Stratagene)

extract_protocol: RNA was isolated using TRIzol

tag: sample type

value: AX2 cells treated with S. typhimurium. Total RNA isolated at 1h time point.

tag: strain

value: AX2 cells treated with E. Coli B/r as control. Total RNA isolated at 1h time point.


title: SAE 13727669 GEO E2 t1 - cy3 vs S2 t1 - cy5

source_name: E2 t1 - cy3

source_name: S2 t1 - cy5


title: SAE 13513872 GEO E1 t1 - cy5 vs S3 t1 - cy3

source_name: S3 t1 - cy3

source_name: E1 t1 - cy5


title: BHI_Enteritidis_chlorine_130ppm_rep1

city: SUMMIT

first: SIYUN

last: WANG

state: IL

address: 6502 S ARCHER ROAD

country: USA

institute: ILLINOIS INSTITUTE OF TECHNOLOGY

description: This sample is of Salmonella enterica Enteritidis in BHI broth w/ 130ppm chlorine treatment for 30 minutes . It is the first of three biological replicates used in this experiment, each from separate cultures.

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 2.5 (Roche NimbleGen, Inc.).

organism: Salmonella enterica subsp. enterica serovar Enteritidis

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

growth_protocol: Salmonella Enteritidis and Typhimurium were grown to early-log phase at 37°C in BHI broth

extract_protocol: Total RNA was extracted using the RNeasy Midi kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.

treatment_protocol: Cells were washed and resuspended in (1) BHI broth, 30 min (2) chlorinated BHI broth, 130 ppm, 30 min (3) chlorinated BHI broth, 390 ppm, 10 min

tag: genotype

value: Wild-type

tag: accession


title: SAE 13731064 GEO E1' t0 - cy5 vs S2' t0 - cy3

value: AX2 cells treated with S. typhimurium. Total RNA isolated at 0h time point.

value: AX2 cells treated with E. Coli B/r as control. Total RNA isolated at 0h time point.


title: SAE 13727665 GEO E1' t1 - cy3 vs S1' t1 - cy5


title: BHI_Enteritidis_chlorine_390ppm_rep1

description: This sample is of Salmonella enterica Enteritidis in BHI broth w/ 390ppm chlorine treatment for 10 minutes . It is the first of three biological replicates used in this experiment, each from separate cultures.

source_name: Salmonella enterica Enteritidis, chlorine, 390ppm 10min


title: SAE 13727630 GEO E3' t0 - cy5 vs S3' t0 - cy3


title: BHI_Enteritidis_chlorine_control_rep3

description: This sample is of Salmonella enterica Enteritidis in BHI broth. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: Salmonella enterica Enteritidis, control


title: Control Thymus (AEM)-4

city: Tucson

first: Ty

middle: W

last: Lebsack

state: AZ

address: 1656 E Mabel

department: Immunobiology

institute: University of Arizona

hyb_protocol: Standard manufacturer's protocol (Affymetrix).

scan_protocol: Arrays were set to standard manufacturer's protocol (Affymetrix).

data_processing: Arrays were normalized using RMA (Robust Multichip Average methodology) from the Oligo library from BioConductor.  Analysis of variance was used to determine the statistical significance of the expression level changes between space and control conditions, using the affy and limma Bioconductor libraries.

label: biotin

organism: Mus musculus

source_name: Thymus mRNA extracted from ground-control mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Live Mus musculus (in vivo).

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

tag: tissue

value: thymus


title: SAE 13727464 GEO E2 t1 - cy5 vs S2 t1 - cy3

source_name: S2 t1 - cy3

source_name: E2 t1 - cy5


title: Control Thymus (AEM)-3


title: SAE 13727629 GEO E3' t0 - cy3 vs S3' t0 - cy5


title: BHI_Enteritidis_chlorine_130ppm_rep3

description: This sample is of Salmonella enterica Enteritidis in BHI broth w/ 130ppm chlorine treatment for 30 minutes . It is the third of three biological replicates used in this experiment, each from separate cultures.


title: BHI_Enteritidis_chlorine_control_rep2

description: This sample is of Salmonella enterica Enteritidis in BHI broth. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Control Thymus (AEM)-2


title: SAE 13731063 GEO E1' t0 - cy3 vs S2' t0 - cy5


title: BHI_Typhimurium_chlorine_130ppm_rep1

description: This sample is of Salmonella enterica Typhimurium in BHI broth w/ 130ppm chlorine treatment for 30 minutes . It is the first of three biological replicates used in this experiment, each from separate cultures.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: Salmonella enterica Typhimurium, chlorine, 130ppm 30min


title: microRNA Jurkat 24hr Ag ions exposure rep1

city: seoul

first: jinhee

last: choi

address: 90 Jeonnong-dong, Dongdaemun-gu

department: College of Urban Science

country: South Korea

institute: University of Seoul

description: replicate 1

hyb_protocol: Fluorescently labelled cDNA PCR products were hybridized to the Illumina Sentrix BeadChip U1536-16 according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader  Confocal  Scanner

data_processing: Array data export processing and analysis was performed using Illumina BeadStudio v3.1.3  (Gene Expression Module v3.3.8). The data were normalised using quantile normalisation with ArrayAssist® 5.5.1 (Stratagene, La Jolla, USA) and R statistical language v. 2.4.1

organism: Homo sapiens

source_name: mRNA isolated from Jurkat cells

label_protocol: Biotinylated cDNA were prepared from 0.2-1ug total RNA using the high-throughput Gene expression profiling, the DASL Assay (cDNA-mediated annealing, selection, extension and ligation)

growth_protocol: Human leukemia Jurkat cells were were maintained in RPMI 1640 (GIBCO BRL Life Technologies, Rockville, MD, USA) and supplemented with 10% (v/v) fetal bovine serum, at 37 ◦C in a humidified atmosphere of air and 5% CO2.

extract_protocol: The total RNA prepared from the exposed and control cells according to the standard protocol of the RNeasy Mini kit (Qiagen, Hilden, Germany).

treatment_protocol: From stock solutions, experimental concentration(0.2mg/L) of AgNPs and Ag ions was prepared in medium. For toxicity tests, cells were incubated for 24 hr at 37 ◦C in a humidified atmosphere of air and 5% CO2.

tag: celline

value: Human leukemia Jurkat cells


title: microRNA Jurkat 24hr AgNPs exposure rep1

description: replicate 1


title: BHI_Enteritidis_chlorine_control_rep1

description: This sample is of Salmonella enterica Enteritidis in BHI broth. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: microRNA Jurkat not exposed rep1

description: replicate 1


title: SAE 13727460 GEO E3 t0 - cy5 vs S1 t0 - cy3

source_name: S1 t0 - cy3

source_name: E3 t0 - cy5


title: Space-Flown Thymus (FLT)-4

source_name: Thymus mRNA extracted from space-flown mice


title: Space-Flown Thymus (FLT)-2


title: Control Thymus (AEM)-1


title: SAE 13727433 GEO E3 t0 - cy3 vs S1 t0 - cy5

source_name: E3 t0 - cy3

value: AX2 cells treated with E.Coli B/R used as control. Total RNA isolated at 0h time point.

source_name: S1 t0 - cy5


title: SAE 13513874 GEO E1 t0 - cy5 vs S3 t0 - cy3

source_name: S3 t0 - cy3

source_name: E1 t0 - cy5


title: Space-Flown Thymus (FLT)-3


title: Space-Flown Thymus (FLT)-1


title: EPS8 liver_rep3

status: Public on Mar 09 2010

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.0: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: male, age

value: 17 weeks

source_name: Wt RNA pool liver

tag: RNA pool; male, age


title: EPS8 liver_rep5


title: EPS8 liver_rep8


title: EPS8 liver_rep7


title: EPS8 liver_rep6


title: EPS8 liver_rep4


title: EPS8 liver_rep1


title: SAE 13513874 GEO E1 t0 - cy3 vs S3 t0 - cy5

source_name: E1 t0 - cy3

value: AX2 cells treated with E.Coli B/R used as Control. Total RNA isolated at 0h time point.

source_name: S3 t0 - cy5


title: SAE 13513778 GEO E1 t1 - cy3 vs S3 t1 - cy5

source_name: E1 t1 - cy3

value: AX2 cells treated with E.Coli B/R used as Control. Total RNA isolated at 1h time point.

label: Cy 5

source_name: S3 t1 - cy5


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Verification set_rep1_RI17

city: Yokohama

first: Motohiko

last: Tanino

state: Kanagawa

address: 1-1-43, Suehirocho, Tsurumi-ku

country: Japan

institute: DNA Chip Research Inc.

description: Gene expression of whole blood cells from Rheumatoid Arthritis patients before infliximab treatment

hyb_protocol: Hybridization was performed for 17 hrs at 65°C.

scan_protocol: Arrays were scanned on an Agilent DNA microarray scanner.

data_processing: Image analyses, data extraction, and background subtraction were done with the standard procedures of Agilent Feature Extraction Software Ver.9.1.

source_name: Peripheral Blood, sampling at pre treatment with infliximab infusion, residual inflammation at 14 weeks after the treatment

label_protocol: Sample RNA was amplified and 250 ng of total RNA was labeled using Cy3.

growth_protocol: RA patients who were resistant to standard MTX treatment.

extract_protocol: Blood (2.5ml) was collected from the patient into PAXgene Blood RNA Kit (QIAGEN, Valencia, CA). Total RNA was extracted according to the manufacturer’s protocol

treatment_protocol: Right before the infusion of Infliximab.

value: whole blood

tag: gender

value: male

tag: age

tag: serum crp level at 14 weeks (mg/dl)


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Verification set_rep1_RI23

value: female


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Verification set_rep1_RI21


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Verification set_rep1_RI25


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Verification set_rep1_RI16


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Verification set_rep1_RI22


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Verification set_rep1_RI20


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Verification set_rep1_RI15


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Verification set_rep1_NI43

source_name: Peripheral Blood, sampling at pre treatment with infliximab infusion, no inflammation at 14 weeks after the treatment


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Verification set_rep1_RI19


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Verification set_rep1_RI24


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Verification set_rep1_NI40


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Verification set_rep1_RI18


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Verification set_rep1_NI41


title: Patient_7170_diagnosis

city: Wageningen

first: Dick

middle: de

last: de Ridder

address: Droevendaalsesteeg 1

department: Plant Sciences

country: Netherlands

institute: Wageningen University

hyb_protocol: Affymetrix standard 16 hours at 45 C Hybridization Oven 640

scan_protocol: GeneChip® Scanner 3000; GCOSv1

data_processing: Data were quantile normalized and RMA was used for probeset summarization; when subsets were analysed, these were individually normalized and summarized. Differential expression was assessed using SAM (Significance Analysis of Microarrays). All analyses were performed in Matlab; the code is available upon request.

source_name: leukemic cells, purified using CD19 beads on autoMACS

label_protocol: Afymetrix one cycle labeling kit

extract_protocol: Qiagen RNAesy plus shredder

tag: cell type

value: leukemic lymphoblasts

tag: disease status

value: Acute Lymphoblastic Leukemia (ALL)

tag: all type

value: Precursor-B-ALL

tag: all subtype

value: Common ALL

tag: relapse type

value: isolated bone marrow

tag: months to relapse

tag: conclusions ig/tcr

value: stable

tag: selected

value: no


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Verification set_rep1_NI39


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Verification set_rep1_NI32


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Training set_rep1_RI14


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Verification set_rep1_NI42


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Verification set_rep1_NI37


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Verification set_rep1_NI35


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Verification set_rep1_NI33


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Verification set_rep1_NI36


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Training set_rep1_RI12


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Verification set_rep1_NI31


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Training set_rep1_RI11


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Verification set_rep1_NI30


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Training set_rep1_RI13


title: Universal control_rep2

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

description: Gene expression of human universal reference RNA, biological replicate 2 of 2.

hyb_protocol: Array hybridization was performed in 100 ul of a hybridization mixture containing cRNA probes at 65℃ for 17 hrs.

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

data_processing: Fluorescence intensities of spots were quantified, background subtracted, and dye normalized by Feature Extraction software, version 8.1.1 (Agilent Technologies). The data were then imported and analyzed using GeneSpring GX (Agilent Technologies) to generate gene lists of differentially expressed (change in expression with fold change > 2).

source_name: ten kinds of tumors

label_protocol: The Agilent’s low RNA input linear amplification / one-color labeling kit were used for target preparation essentially followed the protocol recommended by Agilent Technologies. Briefly, 1000 ng of total RNA was reverse transcribed into cDNA using the T7 promoter primer. Cyanine 3-dCTP labeled cRNA was synthesized from the cDNA by using the T7 RNA polymerase. To remove unincorporated nucleotides, the labeled cRNA was purified using the RNeasy mini kit (Qiagen).

extract_protocol: Total RNAs were extracted with RNeasy mini kit (Qiagen) according to the manufacturer’s introduction. The integrity of the RNA samples was verified using the RNA 6000 Nano Assay (Agilent Technologies, Palo Alto, CA, USA).

value: mammary gland, liver, cervix, testis, brain

value: lipoblasts, macrophages, histocytes, lymphoblasts, B lymphocyte

tag: cell line

value: mammary gland adenocarcinoma, hepatoblastoma, embryonal carcinoma, cervix adenocarcinoma, brain glioblastoma, melanoma, liposarcoma, histiocytic lymphoma, lymphoblastic leukemia, plasmacytoma, myeloma

tag: disease state

value: control

tag: other

value: Cell lines derived from the various tissues and cell types


title: Universal control_rep1

description: Gene expression of human universal reference RNA, biological replicate 1 of 2.

tag: tissue


title: NP460hTert_rep2

description: Gene expression of NP460, biological replicate 2 of 2.

source_name: epithelial biopsies of nonmalignant tissue

growth_protocol: The TW01 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS). The HONE1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS. The NP460hTert cells were maintained in culture medium as previously described (H.M. Li et al., 2006).

value: nasopharynx

value: nonmalignant


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Verification set_rep1_NI34

value: whole blood


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Verification set_rep1_NI29


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Verification set_rep1_NI38


title: HONE1_rep2

description: Gene expression of HONE1, biological replicate 2 of 2.

source_name: epithelial biopsies of carcinoma

value: carcinoma


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Training set_rep1_RI4

value: male


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Training set_rep1_RI8

value: female


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Training set_rep1_RI10


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Training set_rep1_RI2


title: TW01_rep1

description: Gene expression of TW01, biological replicate 1 of 2.


title: NP460hTert_rep1

description: Gene expression of NP460, biological replicate 1 of 2.


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Training set_rep1_RI9


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Training set_rep1_RI3


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Training set_rep1_RI5


title: EPS8 liver_rep2

tag: male, age

value: 17 weeks


title: HONE1_rep1

description: Gene expression of HONE1, biological replicate 1 of 2.


type: genomic

city: Kyoto

first: Atsushi

last: Kubo

state: Kyoto

address: Sakyo-ku

department: Department of zoology, Graduate School of Science

institute: Kyoto University

description: Twist-like-1a/b ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 2, Array 1  GFP-tagged Twist-like-1a/b ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)

hyb_protocol: Hybridization and washing protocols were according to the manufacturer’s instructions (Agilent Technologies).

scan_protocol: The microarrays were scanned with an Agilent G2565BA Microarray Scanner (Agilent Technologies).

data_processing: The resulting fluorescence intensity for each spot was quantified using Agilent Feature Extraction Software ver. 9.1 (Agilent Technologies).

molecule: genomic DNA

organism: Ciona intestinalis

source_name: Whole Cell Extract (WCE) DNA

label_protocol: Amplified DNA was directly labeled by random-primed, Klenow-based extension protocol that is used with CGH Labeling kit (Invitrogen).

growth_protocol: C. intestinalis adults were obtained from the national bio-resource project for Ciona intestinalis and were maintained under constant light to induce oocyte maturation. Eggs and sperm were obtained surgically from the gonoduct. Following insemination, eggs were washed and maintained in seawater at 18˚C in Millipore-filtered seawater containing 50ug/ml streptomycin sulfate.

extract_protocol: The embryo were fixed with 1% formaldehyde for 15 min. Chromatin was sonicated to obtain DNA fragments with an average of size of 1kb.  After reversal of the fixation, the WCE DNA were amplified by LM-PCR.

treatment_protocol: Approximately 1.5 kb of the Twist-like-1a/b promoter and the coding region of Twist-like-1a/b were cloned into pDONR P4-P1R and pDONR221 (Invitrogen), respectively. cDNA encoding GFP was cloned into pDONR P2R-P3. Recombination of these three plasmids with Multisite Gateway technology (Invitrogen) resulted in a construct encoding GFP-tagged Twist-like-1a/b.  Fertilized eggs were electroporated with this DNA construct.

tag: fraction

value: input

tag: antibody

source_name: GFP-tagged Twist-like-1a/b ChIP in Ciona intestinalis embryo (early gastrula)

extract_protocol: The embryo were fixed with 1% formaldehyde for 15 min. Chromatin was sonicated to obtain DNA fragments with an average of size of 1kb. The DNA fragments were enriched by immunoprecipitation with an polyclonal antibody specific for GFP (Invitrogen). After reversal of the fixation, the immunoprecipitated DNA were amplified by LM-PCR.

value: IP

tag: embryo

value: earyl gastrula

tag: construct

value: GFP-tagged Twist-like-1a/b


title: TW01_rep2

description: Gene expression of TW01, biological replicate 2 of 2.


description: Twist-like-1a/b ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 1, Array 1  GFP-tagged Twist-like-1a/b ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)


description: Twist-like-1a/b ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 3, Array 1  GFP-tagged Twist-like-1a/b ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)


description: SoxC ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 2  GFP-tagged SoxC ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)

treatment_protocol: Approximately 3.0 kb of the SoxC promoter and the coding region of SoxC were cloned into pDONR P4-P1R and pDONR221 (Invitrogen), respectively. cDNA encoding GFP was cloned into pDONR P2R-P3. Recombination of these three plasmids with Multisite Gateway technology (Invitrogen) resulted in a construct encoding GFP-tagged SoxC.  Fertilized eggs were electroporated with this DNA construct.

source_name: GFP-tagged SoxC ChIP in Ciona intestinalis embryo (early gastrula)

value: GFP-tagged SoxC


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Training set_rep1_RI6

tag: gender

tag: age

tag: serum crp level at 14 weeks (mg/dl)


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI25


title: PAXgeneBlood_PreTreatment_Residual Inflammation (RI)_Training set_rep1_RI1


description: SoxC ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 1, Array 1  GFP-tagged SoxC ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI28


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI26


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI27


description: Tbx6b ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 2  GFP-tagged Tbx6b ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)

treatment_protocol: Approximately 3.1 kb of the Tbx6b promoter and the coding region of Tbx6b were cloned into pDONR P4-P1R and pDONR221 (Invitrogen), respectively. cDNA encoding GFP was cloned into pDONR P2R-P3. Recombination of these three plasmids with Multisite Gateway technology (Invitrogen) resulted in a construct encoding GFP-tagged Tbx6b.  Fertilized eggs were electroporated with this DNA construct.

source_name: GFP-tagged Tbx6b ChIP in Ciona intestinalis embryo (early gastrula)

value: GFP-tagged Tbx6b


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI22


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI24


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI23


description: Neurogenin ChIP-chip on Ciona intestinalis embryo (64-cell stage) Sample 1, Array 1  GFP-tagged Neurogenin ChIP-chip in Whole Genome region in Ciona intestinais embryo (64-cell stage) using polyclonal anti-GFP antibody (Invitrogen)

treatment_protocol: Approximately 3.1 kb of the Neurogenin promoter and the coding region of Neurogenin were cloned into pDONR P4-P1R and pDONR221 (Invitrogen), respectively. cDNA encoding GFP was cloned into pDONR P2R-P3. Recombination of these three plasmids with Multisite Gateway technology (Invitrogen) resulted in a construct encoding GFP-tagged Neurogenin.  Fertilized eggs were electroporated with this DNA construct.

source_name: GFP-tagged Neurogenin ChIP in Ciona intestinalis embryo (64-cell stage)

value: 64-cell stage

value: GFP-tagged Neurogenin


description: Snail ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 1, Array 1  GFP-tagged Snail ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)

treatment_protocol: Approximately 3.1 kb of the Snail promoter and the coding region of Snail were cloned into pDONR P4-P1R and pDONR221 (Invitrogen), respectively. cDNA encoding GFP was cloned into pDONR P2R-P3. Recombination of these three plasmids with Multisite Gateway technology (Invitrogen) resulted in a construct encoding GFP-tagged Snail.  Fertilized eggs were electroporated with this DNA construct.

source_name: GFP-tagged Snail ChIP in Ciona intestinalis embryo (early gastrula)

value: GFP-tagged Snail


description: FoxD-a/b ChIP-chip on Ciona intestinalis embryo (32-cell stage) Sample 1, Array 1  GFP-tagged FoxD-a/b ChIP-chip in Whole Genome region in Ciona intestinais embryo (32-cell stage) using polyclonal anti-GFP antibody (Invitrogen)

treatment_protocol: Approximately 3.1 kb of the FoxD-a/b promoter and the coding region of FoxD-a/b were cloned into pDONR P4-P1R and pDONR221 (Invitrogen), respectively. cDNA encoding GFP was cloned into pDONR P2R-P3. Recombination of these three plasmids with Multisite Gateway technology (Invitrogen) resulted in a construct encoding GFP-tagged FoxD-a/b.  Fertilized eggs were electroporated with this DNA construct.

source_name: GFP-tagged FoxD-a/b ChIP in Ciona intestinalis embryo (32-cell stage)

value: anti-GFP antibody

value: 32-cell stage

value: GFP-tagged FoxD-a/b


description: FoxA-a ChIP-chip on Ciona intestinalis embryo (64-cell stage) Sample 1, Array 1  GFP-tagged FoxA-a ChIP-chip in Whole Genome region in Ciona intestinais embryo (64-cell stage) using polyclonal anti-GFP antibody (Invitrogen)

treatment_protocol: Approximately 3.0 kb of the FoxA-a promoter region, the coding region of FoxA-a and GFP were cloned into pCS2 vector. So, this encodes GFP-tagged FoxA-a.  Fertilized eggs were electroporated with this DNA construct.

source_name: GFP-tagged FoxA-a ChIP in Ciona intestinalis embryo (64-cell stage)

value: GFP-tagged FoxA-a


description: Tbx6b ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 1, Array 1  GFP-tagged Tbx6b ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)


description: FoxD-a/b ChIP-chip on Ciona intestinalis embryo (64-cell stage) Sample 1, Array 1  GFP-tagged FoxD-a/b ChIP-chip in Whole Genome region in Ciona intestinais embryo (64-cell stage) using polyclonal anti-GFP antibody (Invitrogen)

source_name: GFP-tagged FoxD-a/b ChIP in Ciona intestinalis embryo (64-cell stage)


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI20

description: Gene expression of whole blood cells from Rheumatoid Arthritis patients before infliximab treatment

value: whole blood


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI21


description: Neurogenin ChIP-chip on Ciona intestinalis embryo (64-cell stage) Sample 2  GFP-tagged Neurogenin ChIP-chip in Whole Genome region in Ciona intestinais embryo (64-cell stage) using polyclonal anti-GFP antibody (Invitrogen)


description: FoxD-a/b ChIP-chip on Ciona intestinalis embryo (32-cell stage) Sample 2  GFP-tagged FoxD-a/b ChIP-chip in Whole Genome region in Ciona intestinais embryo (32-cell stage) using polyclonal anti-GFP antibody (Invitrogen)


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI18


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI19


title: M202(Sub1) vs M202_6d_2

city: Davis

first: Ki-hong

last: Jung

state: CA

address: one shields

department: Plant pathology

institute: UC DAVIS

description: Biological replicate 2 of 2. Comparison of M202(Sub1) vs M202 at 6 day after submergence using 2 weeks old seedlings

hyb_protocol: NSF45K oligo array and hybridization buffer (GeneFrames hybridization solution, MWG Biotech) were added, and dyes labeled control and target cDNAs were applied to microarrays enclosed in HS4800 Automated Slide Hybridization Station . After hybridization, slides were washed sequential

scan_protocol: Images were quantified using Genepix4000B and Genepix pro 4.0 software were used to do spot finding and generate gene pix result (gpr) data.

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Green signal (Cy3)/processed Red signal (Cy5). We used LMGene Package

label: cy 3

organism: Oryza sativa

source_name: M202(Sub1) after  6d submergence_biological replicate 2

label_protocol: We isolated 500 µg-1 mg total RNA using TRIZOL reagent and the total RNA was DNaseI-treated for 15 minutes then purified using the RNeasy Midi Kit (Qiagen, Germantown, MD). The total RNA was then enriched for poly-A RNA (1-2 µg) by using the Oligotex mRNA Kit (Qiagen). 0.5-1.0 µg of mRNAs were primed with 2 µl of 100 µM oligodT primer (20mer, invitrogen) at 70°C for 10 min, then reversed transcribed at 46°C for 2 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: The seeds of rice (Oryza sativa) cv M202 and the Sub1 introgression line M202(Sub1) were sterilized in 1%(v/v) sodium hypochlorite for 1 h and rinsed thoroughly with deionized water. Seeds were placed on wet filter paper for 3 d at 258C in the dark, and pregerminated seeds were transplanted into soil containing pots and grown for 14 d in a greenhouse (30°C day, 20°C night) under natural light conditions.

extract_protocol: 500ug total RNA extracted using Trizol following manufacturer's instructions. And then, 4-5ug mRNAs were isolated using Qiagen oligotex mRNA isolation midi kit. We used 0.5-1ug mRNAs for each hybridization

treatment_protocol: At least three replicates with two biological replicates were prepared for three time points (0 d, 1 d and 6 d submergence).

value: 2 weeks old

value: leaf

label: cy 5

source_name: M202 after  6d submergence_biological replicate 2


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI17

value: female


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI15


description: Snail ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 2  GFP-tagged Snail ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)

value: input


title: M202(Sub1) vs M202_6d_1_dye-swap

description: Dye-swap of biological replicate 1 of 2. Comparison of M202(Sub1) vs M202 at 6 day after submergence using 2 weeks old seedlings

source_name: M202 after  6d submergence_biological replicate 1

source_name: M202(Sub1) after  6d submergence_biological replicate 1


title: MyoD ChIP-chip on Ciona intestinalis embryo (early-mid gastrula) Sample 2, Array 1

description:
MyoD ChIP-chip on Ciona intestinalis embryo (early-mid gastrula) Sample 1, Array 2
GFP-tagged MyoD ChIP-chip in Whole Genome region in Ciona intestinalis embryo (early-mid gastrula) using polyclonal anti-GFP antibody (Invitrogen)

data_processing:
The resulting fluorescence intensity for each spot was quantified using Agilent Feature Extraction Software ver. 9.1 (Agilent Technologies).
value = log2(Signal for Cy5 / Signal for Cy3)

extract_protocol:
The embryos were fixed with 1% formaldehyde for 15 min. Chromatin was sonicated to obtain DNA fragments with an average of size of 1kb.
After reversal of the fixation, the WCE DNA were amplified by LM-PCR.

treatment_protocol:
Approximately 3 kb of the MyoD promoter and the coding region of MyoD were cloned into pDONR P4-P1R and pDONR221 (Invitrogen), respectively. cDNA encoding GFP was cloned into pDONR P2R-P3. Recombination of these three plasmids with Multisite Gateway technology (Invitrogen) resulted in a construct encoding GFP-tagged MyoD.
Fertilized eggs were electroporated with this DNA construct.

tag: Whole Cell Extract (WCE) DNA

source_name: GFP-tagged MyoD ChIP in Ciona intestinalis embryo (early-mid Gastrula)

extract_protocol: The embryos were fixed with 1% formaldehyde for 15 min. Chromatin was sonicated to obtain DNA fragments with an average of size of 1kb. The DNA fragments were enriched by immunoprecipitation with an polyclonal antibody specific for GFP (Invitrogen). After reversal of the fixation, the immunoprecipitated DNA were amplified by LM-PCR.


title: M202(Sub1) vs M202_6d_1

description: Biological replicate 1 of 2. Comparison of M202(Sub1) vs M202 at 6 day after submergence using 2 weeks old seedlings


title: M202(Sub1) vs M202_1d_2

description: Biological replicate 2 of 2. Comparison of M202(Sub1) vs M202 at 1 day after submergence using 2 weeks old seedlings

source_name: M202(Sub1) after 1d submergence_biological replicate 2

source_name: M202 after 1d submergence_biological replicate 2


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI14

source_name: Peripheral Blood, sampling at pre treatment with infliximab infusion, no inflammation at 14 weeks after the treatment


title: Brachyury ChIP-chip on Ciona intestinalis embryo (early-mid gastrula) Sample 2, Array 1

description:
Brachyury ChIP-chip on Ciona intestinalis embryo (early-mid gastrula) Sample 1, Array 1
GFP-tagged Brachyury ChIP-chip in Whole Genome region in Ciona intestinais embryo (early-mid gastrula) using polyclonal anti-GFP antibody (Invitrogen)

source_name: Whole Cell Extract (WCE) DNA

extract_protocol:
The embryo were fixed with 1% formaldehyde for 15 min. Chromatin was sonicated to obtain DNA fragments with an average of size of 1kb.
After reversal of the fixation, the WCE DNA were amplified by LM-PCR.

treatment_protocol:
Approximately 2.2 kb of the Brachyury promoter and the coding region of Brachyury were cloned into pDONR P4-P1R and pDONR221 (Invitrogen), respectively. cDNA encoding GFP was cloned into pDONR P2R-P3. Recombination of these three plasmids with Multisite Gateway technology (Invitrogen) resulted in a construct encoding GFP-tagged Brachyury.
Fertilized eggs were electroporated with this DNA construct.

source_name: GFP-tagged Brachyury ChIP in Ciona intestinalis embryo (early-mid Gastrula)


description: FoxA-a ChIP-chip on Ciona intestinalis embryo (64-cell stage) Sample 2  GFP-tagged FoxA-a ChIP-chip in Whole Genome region in Ciona intestinais embryo (64-cell stage) using polyclonal anti-GFP antibody (Invitrogen)

value: IP


description: Otx ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 2  GFP-tagged Otx ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)

treatment_protocol: Approximately 3.0 kb of the Otx promoter and the coding region of Otx were cloned into pDONR P4-P1R and pDONR221 (Invitrogen), respectively. cDNA encoding GFP was cloned into pDONR P2R-P3. Recombination of these three plasmids with Multisite Gateway technology (Invitrogen) resulted in a construct encoding GFP-tagged Otx.  Fertilized eggs were electroporated with this DNA construct.

source_name: GFP-tagged Otx ChIP in Ciona intestinalis embryo (early gastrula)

value: earyl gastrula

value: GFP-tagged Otx


description:
MyoD ChIP-chip on Ciona intestinalis embryo (early-mid gastrula) Sample 1, Array 1
GFP-tagged MyoD ChIP-chip in Whole Genome region in Ciona intestinalis embryo (early-mid gastrula) using polyclonal anti-GFP antibody (Invitrogen)

tag: GFP-tagged MyoD ChIP in Ciona intestinalis embryo (early-mid Gastrula)


title: M202(Sub1) vs M202_1d_1_dye-swap

description: Dye-swap of biological replicate 1 of 2. Comparison of M202(Sub1) vs M202 at 1 day after submergence using 2 weeks old seedlings

source_name: M202 after 1d submergence_biological replicate 1

source_name: M202(Sub1) after 1d submergence_biological replicate 1


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI13

value: male


description: FoxD-a/b ChIP-chip on Ciona intestinalis embryo (64-cell stage) Sample 2  GFP-tagged FoxD-a/b ChIP-chip in Whole Genome region in Ciona intestinais embryo (64-cell stage) using polyclonal anti-GFP antibody (Invitrogen)


description:
ZicL ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 1, Array 1
GFP-tagged ZicL ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)

data_processing:
The resulting fluorescence intensity for each spot was  quantified using Agilent Feature Extraction Software ver. 9.1 (Agilent Technologies).
value = log2(Signal for Cy5 / Signal for Cy3)

treatment_protocol:
Approximately 2.1 kb of the ZicL promoter and the coding region of ZicL were cloned into pDONR P4-P1R and pDONR221 (Invitrogen), respectively. cDNA encoding GFP was cloned into pDONR P2R-P3. Recombination of these three plasmids with Multisite Gateway technology (Invitrogen) resulted in a construct encoding GFP-tagged ZicL.
Fertilized eggs were electroporated with this DNA construct.

source_name: GFP-tagged ZicL ChIP in Ciona intestinalis embryo (early Gastrula)


description:
ZicL ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 2, Array 1
GFP-tagged ZicL ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)

tag: GFP-tagged ZicL ChIP in Ciona intestinalis embryo (early Gastrula)


title: Brachyury ChIP-chip on Ciona intestinalis embryo (early-mid gastrula) Sample 1, Array 1

tag: GFP-tagged Brachyury ChIP in Ciona intestinalis embryo (early-mid Gastrula)


title: M202(Sub1) vs M202_1d_1

description: Biological replicate 1 of 2. Comparison of M202(Sub1) vs M202 at 1 day after submergence using 2 weeks old seedlings


title: M202(Sub1) vs M202_0d_2_dye-swap

description: Dye-swap of Biological replicate 2 of 2. Comparison of M202(Sub1) vs M202 before submergence using 2 weeks old seedlings

source_name: M202 before submergence (0d) biological replicate 2

source_name: M202(Sub1) before submergence (0d) biological replicate 2


title: M202(Sub1) vs M202_0d_1_dye-swap

description: Dye-swap of Biological replicate 1 of 2. Comparison of M202(Sub1) vs M202 before submergence using 2 weeks old seedlings

source_name: M202 before submergence (0d) biological replicate 1

source_name: M202(Sub1) before submergence (0d) biological replicate 1


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI11

description: Gene expression of whole blood cells from Rheumatoid Arthritis patients before infliximab treatment


title: M202(Sub1) vs M202_0d_1

description: Biological replicate 1 of 2. Comparison of M202(Sub1) vs M202 before submergence using 2 weeks old seedlings


title: M202(Sub1) vs M202_0d_2

description: Biological replicate 2 of 2. Comparison of M202(Sub1) vs M202 before submergence using 2 weeks old seedlings


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI16


title: M202(Sub1) vs M202_1d_2


description: Otx ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 1, Array 1  GFP-tagged Otx ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI10


title: Adipose 23.75-2

city: Buffalo

first: Siddharth

last: Sukumaran

state: NY

address: 109 Cooke Hall, University at Buffalo, North/Amherst Campus

department: Dept of Biological Sciences

institute: State University of New York at Buffalo

description: Almon CF 53_1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChips Rat Genome 230-2. S450_001 Fluidics Script was used for Staining.

scan_protocol: The array chips were scanned using GeneChip scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using default settings

label: Biotin

organism: Rattus norvegicus

source_name: Wistar rat abdominal adipose tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from the purified total RNA

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and was further purified using RNeasy mini-column

tag: strain

value: Wistar

tag: sex

value: abdominal adipose tissue

tag: circadian time (hrs after lights on)


title: Adipose 23.75-3

description: Almon CF 54_1


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI9


title: Adipose 23.75-1

description: Almon CF 52_1


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI8


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI7


title: Adipose 23-3

description: Almon CF 51_2


title: Adipose 23-2

description: Almon CF 50_1


title: Adipose 23-1

description: Almon CF 49_1


title: M202(Sub1) vs M202_0d_2_dye-swap


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI6


title: Adipose 22-3

description: Almon CF 48_1


title: Adipose 22-1

description: Almon CF 46_1


title: Adipose 20-3

description: Almon CF 45_1


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI12


title: M202(Sub1) vs M202_0d_1


title: Adipose 18-3

description: Almon CF 42_1


title: Adipose 16-3

description: Almon CF 39_1


title: Adipose 20-1

description: Almon CF 43_1


title: Adipose 18-1

description: Almon CF 40_1


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI5


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI4


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI1


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI2


title: PAXgeneBlood_PreTreatment_No Inflammation (NI)_Training set_rep1_NI3


title: M202(Sub1) vs M202_0d_1_dye-swap


title: Adipose 16-2

description: Almon CF 38_1


title: Adipose 14-3

description: Almon CF 36_1


title: Adipose 16-1

description: Almon CF 37_1


title: Adipose 13-3

description: Almon CF 33_1


title: Adipose 14-1

description: Almon CF 34_1


title: Adipose 22-2

description: Almon CF 47_1


title: Adipose 13-1

description: Almon CF 31_1


title: Adipose 18-2

description: Almon CF 41_1


description: Twist-like-1a/b ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 3, Array 2  GFP-tagged Twist-like-1a/b ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)

source_name: GFP-tagged Twist-like-1a/b ChIP in Ciona intestinalis embryo (early gastrula)

value: GFP-tagged Twist-like-1a/b


title: Adipose 14-2

description: Almon CF 35_1


description: Twist-like-1a/b ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 1, Array 2  GFP-tagged Twist-like-1a/b ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)


title: Adipose 20-2

description: Almon CF 44_1


title: Adipose 13-2

description: Almon CF 32_1


description: Snail ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 1, Array 2  GFP-tagged Snail ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)

source_name: GFP-tagged Snail ChIP in Ciona intestinalis embryo (early gastrula)

value: GFP-tagged Snail


description: Tbx6b ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 1, Array 2  GFP-tagged Tbx6b ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)

source_name: GFP-tagged Tbx6b ChIP in Ciona intestinalis embryo (early gastrula)

value: GFP-tagged Tbx6b


description: SoxC ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 1, Array 2  GFP-tagged SoxC ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)

source_name: GFP-tagged SoxC ChIP in Ciona intestinalis embryo (early gastrula)

value: GFP-tagged SoxC


description: Otx ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 1, Array 2  GFP-tagged Otx ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)


description: Neurogenin ChIP-chip on Ciona intestinalis embryo (64-cell stage) Sample 1, Array 2  GFP-tagged Neurogenin ChIP-chip in Whole Genome region in Ciona intestinais embryo (64-cell stage) using polyclonal anti-GFP antibody (Invitrogen)

source_name: GFP-tagged Neurogenin ChIP in Ciona intestinalis embryo (64-cell stage)

value: 64-cell stage

value: GFP-tagged Neurogenin


description: FoxD-a/b ChIP-chip on Ciona intestinalis embryo (64-cell stage) Sample 1, Array 2  GFP-tagged FoxD-a/b ChIP-chip in Whole Genome region in Ciona intestinais embryo (64-cell stage) using polyclonal anti-GFP antibody (Invitrogen)

source_name: GFP-tagged FoxD-a/b ChIP in Ciona intestinalis embryo (64-cell stage)

value: GFP-tagged FoxD-a/b


description: FoxA-a ChIP-chip on Ciona intestinalis embryo (64-cell stage) Sample 1, Array 2  GFP-tagged FoxA-a ChIP-chip in Whole Genome region in Ciona intestinais embryo (64-cell stage) using polyclonal anti-GFP antibody (Invitrogen)

source_name: Whole Cell Extract (WCE) DNA

source_name: GFP-tagged FoxA-a ChIP in Ciona intestinalis embryo (64-cell stage)

value: GFP-tagged FoxA-a


title: Adipose 12.25-2

description: Almon CF 29_1


description: Twist-like-1a/b ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 2, Array 2  GFP-tagged Twist-like-1a/b ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)


title: Adipose 11.75-3

description: Almon CF 27_1


title: Adipose 12.25-3

description: Almon CF 30_1


title: Adipose 11-3

description: Almon CF 24_1_2


title: MT1 Bio rep 3

city: London

first: Ann

last: Chambers

state: Ontario

address: 790 Commissioner's Road E

department: Victoria research labs

country: Canada

institute: London Regional Cancer program

description: cell line MT1, Third Biological replicate. represents IDC

hyb_protocol: cRNA was synthesized and Biotin labeled as per the array manufacturer's instructions (www.affymetrix.com).  Arrays were washed, stained with Streptavidin-phycoerythrin, washed again, and scanned

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Washing, scanning and probe quantification were carried out according to the manufacturer's instructions, using GeneChip Operating Software (GCOS, www.affymetrix.com), with target intensity set to 150.  For each array, GCOS output was imported as .txt files into Genespring GX 7.3 software (Agilent), and data were normalized as follows: Values <0.01 were set to 0.01 and the median intensity of each array was normalized to the 50th percentile of all arrays.  Finally, the intensity of each probe set in each of the three 21NTci or 21MT-1 arrays was divided by the normalized mean intensity of that probe set in the control arrays.

label: Biotin/SAPE

source_name: IDC

label_protocol: Ligation mediated PCR amplified genomic DNA, after restriction with HhaI, was labeled as per Affymetrix standard protocol for Human Promoter 1.0R arrays

growth_protocol: For all 3D cultures, 21PTci, 21NTci and 21MT-1 cells were grown in Matrigel Basement Membrane Matrix (BD Biosciences, Mississauga, ON) for 9 days.  Cultures were created in 24-well plates (Nunc, VWR International, Mississauga, ON) with three distinct layers.  The bottom layer consisted of undiluted Matrigel for a solid base.  The middle layer contained a 1:1 mix of Matrigel and 2 x 105 cells in media supplemented with 0.1% BSA, instead of FBS.  These two layers were topped with growth media supplemented with 0.1% BSA (without FBS)

extract_protocol: Three wells per cell line, representing 3 biological replicates, were grown.  Total RNA from each biological replicate was isolated using Cell Recovery Solution (BD Biosciences, Mississauga, ON) to non-enzymatically dissociate the Matrigel, followed by TRIzol (Invitrogen), as per the manufacturer's instructions

treatment_protocol: No treatment

tag: cell ine


description: FoxD-a/b ChIP-chip on Ciona intestinalis embryo (32-cell stage) Sample 1, Array 2  GFP-tagged FoxD-a/b ChIP-chip in Whole Genome region in Ciona intestinais embryo (32-cell stage) using polyclonal anti-GFP antibody (Invitrogen)

source_name: GFP-tagged FoxD-a/b ChIP in Ciona intestinalis embryo (32-cell stage)

value: anti-GFP antibody

value: 32-cell stage


title: M202(Sub1) vs M202_6d_2

description: Biological replicate 2 of 2. Comparison of M202(Sub1) vs M202 at 6 day after submergence using 2 weeks old seedlings

source_name: M202 after  6d submergence_biological replicate 2

value: 2 weeks old

tag: tissue

value: leaf

source_name: M202(Sub1) after  6d submergence_biological replicate 2


title: Adipose 8-1

description: Almon CF 16_1


title: Adipose 8-2

description: Almon CF 17_1


title: Adipose 6-1

description: Almon CF 13_1


title: Adipose 10-2

description: Almon CF 20_1


title: Adipose 6-2

description: Almon CF 14_1


title: MyoD ChIP-chip on Ciona intestinalis embryo (early-mid gastrula) Sample 2, Array 2

description:
MyoD ChIP-chip on Ciona intestinalis embryo (early-mid gastrula) Sample 1, Array 2
GFP-tagged MyoD ChIP-chip in Whole Genome region in Ciona intestinalis embryo (early-mid gastrula) using polyclonal anti-GFP antibody (Invitrogen)

source_name: GFP-tagged MyoD ChIP in Ciona intestinalis embryo (early-mid Gastrula)


title: Adipose 12.25-1

description: Almon CF 28_1


title: Adipose 11.75-1

description: Almon CF 25_1


title: Adipose 10-3

description: Almon CF 21_1


title: MT1 Bio rep 2

description: cell line MT1, Second Biological replicate. represents IDC


title: Adipose 4-2

description: Almon CF 11_1


title: Adipose 8-3

description: Almon CF 18_1


title: Adipose 6-3

description: Almon CF 15_1


title: Adipose 10-1

description: Almon CF 19_1


title: Adipose 11-1

description: Almon CF 22_1


title: Adipose 11.75-2

description: Almon CF 26_1_2


title: MyoD ChIP-chip on Ciona intestinalis embryo (early-mid gastrula) Sample 1, Array 2


title: Adipose 4-3

description: Almon CF 12_1


title: NTci bio rep 3

description: cell line NTci, Third Biological replicate. represents DCIS

source_name: DCIS

value: NTci


title: Adipose 4-1

description: Almon CF 10_1


title: MT1 Bio rep 1

description: cell line MT1, First Biological replicate. represents IDC


title: Brachyury ChIP-chip on Ciona intestinalis embryo (early-mid gastrula) Sample 2, Array 2

description:
Brachyury ChIP-chip on Ciona intestinalis embryo (early-mid gastrula) Sample 1, Array 1
GFP-tagged Brachyury ChIP-chip in Whole Genome region in Ciona intestinais embryo (early-mid gastrula) using polyclonal anti-GFP antibody (Invitrogen)

source_name: GFP-tagged Brachyury ChIP in Ciona intestinalis embryo (early-mid Gastrula)


title: PTci bio rep 2

description: cell line PTci, Second Biological replicate. represents ADH

source_name: ADH

value: PTci


title: Adipose 2-3

description: Almon CF 9_1

source_name: Wistar rat abdominal adipose tissue

value: male


title: PTci bio rep 3

description: cell line PTci, Third Biological replicate. represents ADH


title: Adipose 2-1

description: Almon CF 7_1

value: Wistar


title: NTci bio rep 2

description: cell line NTci, Second Biological replicate. represents DCIS


title: Adipose 2-2

description: Almon CF 8_1

value: abdominal adipose tissue


title: Bbreve_kal

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

description: All the procedures provided were performed as indicated by Combimatrix protocols available at Combimatrix website (www.combimatrix.com)

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C. 5 ug of Labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20' at 95 °C Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS). Hybridization washings were performed as following: - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20). - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20). - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20). - wash with PBST was solution (2X PBS, 0.1% Tween-20). - 2 washes with 2X PBS

scan_protocol: Scanning was performed on a GenePix 4000B scanner. Laser was set at 33% power and PMT at 650.

data_processing:
Original .gpr raw file for Sample GSM518038 (subarray 1) linked below as supplementary file.
Data extraction was carried out using CombiMatrix Microarray Imager software and a quantile normalization of data was performed using Combimatrix Blist v0.6 software

organism: Bifidobacterium breve

source_name: Bifidobacterium breve grown anaerobically in the Man-Rogosa-Sharp (MRS) kallikrein added

label_protocol: Five µg of the same pool of total RNA were labeled using RNA Ampulse amplification and labeling kit with Cy5 for Combimatrix arrays (Kreatech Diagnostics, The Netherlands) according to manufacturer instructions.

growth_protocol: B. breve 210B was grown anaerobically in the Man-Rogosa-Sharp (MRS) supplemented with 0.05% (w/v) L-cysteine hydrochloride and incubated at 37°C.

extract_protocol: Total RNA was isolated using the macaloid acid method  and then treated with DNase. Briefly, cell pellets were resuspended in 1 ml of QUIAZOL and placed in a tube containing 0.8 g of glass beads (diameter, 106 μm). The cells were lysed by shaking the mix on a BioSpec homogenizer at 4°C for 2 min (maximum setting). The mixture was then centrifuged at 12,000 rpm for 15 min, and the upper phase containing the RNA-containing sample was recovered. The RNA sample was further purified by phenol extraction and ethanol precipitation according to a previously described method (Sambrook et al., 1989).

treatment_protocol: B. breve 210B cultures were grown at 37°C in MRS to an OD600 of 0.6, after which enzyme treatment was initiated by the addition of kallikrein (0.55 mg/ml). Cultures were left at 37°C for various times of exposure (90 and 180 min), after which samples (30 ml) were collected, briefly centrifuged to harvest cells and submitted to total RNA extraction.

tag: b.breve strain

tag: agent

value: kallikrein


description:
ZicL ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 2, Array 2
GFP-tagged ZicL ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)

source_name: GFP-tagged ZicL ChIP in Ciona intestinalis embryo (early Gastrula)


title: PTci bio rep 1

description: cell line PTci, First Biological replicate. represents ADH


description:
ZicL ChIP-chip on Ciona intestinalis embryo (early gastrula) Sample 1, Array 2
GFP-tagged ZicL ChIP-chip in Whole Genome region in Ciona intestinais embryo (early gastrula) using polyclonal anti-GFP antibody (Invitrogen)


title: Adipose 1-1

description: Almon CF 4_1


title: 3rd_generation_grandson (proband)

city: Seoul

first: Woong Yang

last: Park

address: 28 Yongondong, Chongnogu

department: Biochemistry and Molecular Biology

institute: Seoul National University

hyb_protocol: Hybridization was performed with the Agilent Oligo aCGH hybridiaztion kit according to the manufacturer’s instructions.

scan_protocol: Slides were scanned on an Agilent Microarray Scanner and captured images were analysed with Feature Extraction Software v 10.5.

data_processing: Feature Extraction Software v 10.5 was used for background subtraction and LOWESS normalization.

source_name: whole blood

label_protocol: Samples (1.5 μg of DNA) were labeled with  the Agilent labelling kit according to the manufacturer’s instructions.

extract_protocol: Genomic DNA was prepared using the QIAamp DNA blood Midi Kit (Qiagen, Valencia, CA, US)

tag: sample type

value: test

tag: generation

tag: disease state (mesomelic dysplasia kantaputra)

value: affected

source_name: Promega, Human Genomic DNA, Male (G1471)

value: reference


title: Brachyury ChIP-chip on Ciona intestinalis embryo (early-mid gastrula) Sample 1, Array 2


title: Bbreve_papain

data_processing:
Original .gpr raw file for Sample GSM517972 (subarray 2) linked below as supplementary file.
Data extraction was carried out using CombiMatrix Microarray Imager software and a quantile normalization of data was performed using Combimatrix Blist v0.6 software

source_name: Bifidobacterium breve grown anaerobically in the Man-Rogosa-Sharp (MRS) papain added

treatment_protocol: B. breve 210B cultures were grown at 37°C in MRS to an OD600 of 0.6, after which enzyme treatment was initiated by the addition of papain (0.5 mg/ml). Cultures were left at 37°C for various times of exposure (90 and 180 min), after which samples (30 ml) were collected, briefly centrifuged to harvest cells and submitted to total RNA extraction.

value: papain


title: 3rd_generation_granddaugther

source_name: sputum

tag: gender

value: female


title: Adipose .25-3

description: Almon CF 3_1


title: HONE1 cell line replicate 2

description: Biological replicate 2 of 2. genomic DNA of NPC cell lines vs. pool of normal male genome .

hyb_protocol: Array hybridizations were carried out with 490μl of hybridization mixtures for 40 h at 65℃, then washed for 5 min at room temperature in Oligo aCGH Wash Buffer 1 (Agilent), followed by 1 min at 37℃ in Oligo aCGH Wash Buffer 2 (Agilent).

scan_protocol: The hybridized arrays were scanned using an Agilent G2565BA DNA microarray scanner (Agilent Technologies). The ScanControl Software (Agilent Technologies) was used for image acquisition. In brief, the arrays were imaged at a resolution of 5 μm. Excitation of Cy3 and Cy5 was performed at a wavelength of 532 and 635 nm, respectively. A laser power of 100% was used. Each array was subjected to a series of scans. The signals were digitized into 16 bit/pixel, yielding a maximum detection range from 1 to 65536; i.e., almost five orders of magnitude.

data_processing: After image acquisition, data extraction, normalization and transformation were carried out by using Agilent Feature Extraction Software, version 8.1.1 (Agilent Technologies), procedures listed as follow:  (1) Place Grid, find and measure spots  -define what is the array format of the image to be processed.  (2) Flag outliers  a. Compute population outliers- flag features and local backgrounds as population outliers if the minimum number of replicates is met and the mean signals varies significantly from the distribution.  b. Compute NonUniform outliers- flag features and local backgrounds as NonUniform if the pixel distribution is outside the boundary defined by the three-parameter noise model.  (3)   Compute Background, bias and error              Background subtraction→ signal correction → choose error model   (4) Dye normalization –   a. Use rank consistent probes.  b. Normalization correction methods: Linear method  (5) Compute ratios- the log ratio values are capped to 4 with appropriate signs in positive and negative directions.  Subsequent data analysis was performed with the other custom analytical software, CGH Analytics (version 3.5.14, Agilent Technologies). The Linear smoothing algorithm is used in the Moving Average approach to smooth the data sets with window size of 5 Mb.

source_name: epithelial biopsies of carcinoma

label_protocol: Genomic DNA was completely fragmented with AluI and RsaI (Promega, Madison, WI, USA ), followed by purification with QIAprep Spin Miniprep Kit (Qiagen). All of the digested DNAs were subjected to labeling reactions using Agilent’s Genomic DNA Labeling Kit PLUS per manufacturer’s instructions. For each array-CGH experiment, we used DNA isolated from NPC cell line as experimental genome (cyanine 5 UTP-labeled) and the commercial healthy Caucasian male genome (Promega) as reference (cyanine 3 UTP-labeled).

growth_protocol: The TW01 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS). The HONE1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS.

extract_protocol: Genomic DNA were isolated by using DNeasy Tissue Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Both cell lines were without any treatment before extraction of genomic DNA.

value: nasopharynx

tag: cell line

tag: disease state

value: carcinoma

source_name: peripheral lymphocytes

value: normal male reference


title: 2nd_generation_son_in_law

value: unaffected


title: Adipose 1-3

description: Almon CF 6_1


title: 2nd_generation_son


title: Bbreve_MRS

data_processing:
Original .gpr raw file for Sample GSM517943 (subarray 1) linked below as supplementary file.
Data extraction was carried out using CombiMatrix Microarray Imager software and a quantile normalization of data was performed using Combimatrix Blist v0.6 software

source_name: Bifidobacterium breve grown anaerobically in the Man-Rogosa-Sharp (MRS)

treatment_protocol: B. breve 210B cultures were grown at 37°C in MRS to an OD600 of 0.6. Cultures were left at 37°C for various times of exposure (90 and 180 min), after which samples (30 ml) were collected, briefly centrifuged to harvest cells and submitted to total RNA extraction.

value: control


title: NTci bio rep 1

description: cell line NTci, First Biological replicate. represents DCIS


title: Adipose .25-2

description: Almon CF 2_1


title: TW01 cell line replicate 2


title: Bbreve_chymo

data_processing:
Original .gpr raw file for Sample GSM518025 (subarray 2) linked below as supplementary file.
Data extraction was carried out using CombiMatrix Microarray Imager software and a quantile normalization of data was performed using Combimatrix Blist v0.6 software

source_name: Bifidobacterium breve grown anaerobically in the Man-Rogosa-Sharp (MRS) chymotrypsin added

treatment_protocol: B. breve 210B cultures were grown at 37°C in MRS to an OD600 of 0.6, after which enzyme treatment was initiated by the addition of chymotrypsin (0.16 mg/ml). Cultures were left at 37°C for various times of exposure (90 and 180 min), after which samples (30 ml) were collected, briefly centrifuged to harvest cells and submitted to total RNA extraction.

value: chymotrypsin


title: 2nd_generation_daughter


title: Human hepatitis C virus liver biopsy sample 2 Replicate 4

status: Public on Mar 08 2010

city: Seattle

first: Xinxia

last: Peng

state: WA

address: Rosen Building, 960 Republican St.

department: Microbiology

institute: University of Washington

description: Hepatitis C virus positive (HCV+) and negative (HCV-) tissue samples from percutaneous core needle biopsy specimens from liver transplantation patients were obtained according to clinical protocols at the University of Washington Medical Center.

hyb_protocol: A single experiment comparing two mRNA samples was done with four replicate Human 1A (V2)22K oligonucleotide expression arrays (Agilent Technologies) using the dye label reverse technique (Agilent Microarray protocol, version 2). The common reference sample was pooled RNA obtained from normal donor livers.

scan_protocol: Scanned on an Agilent G2505B Scanner

data_processing: Agilent Feature Extraction v9.5.3, default mRNA parameters. For a complete description of the columns in the supplemental array data files, see Agilent's Reference Guide for Feature Extraction Software v9.5, http://www.chem.agilent.com/en-US/Search/Library/_layouts/Agilent/PublicationSummary.aspx?whid=50416&liid=1568

source_name: common reference sample

label_protocol: Probe labeling was performed using Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies, Santa Clara, CA). Total input RNA was 200-400ng per reaction.

extract_protocol: Frozen liver tissues were disrupted in Trizol Reagent (Invitrogen, Carlsbad, CA) using a Polytron homogenizer (PowerGene 700, Fisher Scientific), and total RNA was isolated according to the Trizol protocol. The quality of amplified RNA was evaluated by capillary electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA)

tag: sample

value: Reference

source_name: human hepatitis C virus liver biopsy sample

value: HCV negative


title: Human hepatitis C virus liver biopsy sample 2 Replicate 1


title: Human hepatitis C virus liver biopsy sample 2 Replicate 2


title: Human hepatitis C virus liver biopsy sample 6 Replicate 1


title: Human hepatitis C virus liver biopsy sample 2 Replicate 3


title: Human hepatitis C virus liver biopsy sample 6 Replicate 3


title: Human hepatitis C virus liver biopsy sample 6 Replicate 4


title: 1st_generation_grandmother (founder)

value: male


title: IUGR islets #4

city: Bronx

first: Reid

middle: F

last: Thompson

address: 1301 Morris Park Avenue

department: Molecular Genetics

institute: Albert Einstein College of Medicine

description: IUGR islets #4

hyb_protocol: See Roche NimbleGen website and R.R. Selzer et al., PMID: 16075461, for details.

scan_protocol: Scanned using a GenePix 4000B scanner (Axon Instruments) (See R.R. Selzer et al., PMID: 16075461)

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 (See R.F. Thompson et al., PMID: 18353789, for more details).

source_name: pancreatic islets (IUGR)

label_protocol: Random 9-mers pre-labeled with Cy3 or Cy5, for MspI or HpaII, respectively

extract_protocol: Representation of the genome generated by digestion with either HpaII or MspI and amplification by ligation-mediated PCR according to the revised HELP protocol (See M. Oda, et al., PMID:19386619)

treatment_protocol: maternal bilateral uterine artery ligation

value: Sprague-Dawley

tag: age

value: 7 weeks

value: purified pancreatic islets (pooled)

tag: restriction enzyme

value: MspI

value: HpaII


title: Human hepatitis C virus liver biopsy sample 22 Replicate 4

value: HCV positive


title: TW01 cell line replicate 1

description: Biological replicate 1 of 2. genomic DNA of NPC cell lines vs. pool of normal male genome .


title: Human hepatitis C virus liver biopsy sample 21 Replicate 2


title: Human hepatitis C virus liver biopsy sample 21 Replicate 4


title: Human hepatitis C virus liver biopsy sample 21 Replicate 3


title: Human hepatitis C virus liver biopsy sample 32 Replicate 2


title: Human hepatitis C virus liver biopsy sample 30 Replicate 2


title: Human hepatitis C virus liver biopsy sample 32 Replicate 4


title: Human hepatitis C virus liver biopsy sample 32 Replicate 3


title: Human hepatitis C virus liver biopsy sample 30 Replicate 1


title: Human hepatitis C virus liver biopsy sample 32 Replicate 1


title: Human hepatitis C virus liver biopsy sample 30 Replicate 4


title: Human hepatitis C virus liver biopsy sample 31 Replicate 4


title: Human hepatitis C virus liver biopsy sample 24 Replicate 2


title: IUGR islets #3

description: IUGR islets #3


title: Human hepatitis C virus liver biopsy sample 31 Replicate 3


title: Human hepatitis C virus liver biopsy sample 6 Replicate 2


title: Adipose 1-2

description: Almon CF 5_1

value: Wistar

value: abdominal adipose tissue


title: Human hepatitis C virus liver biopsy sample 3 Replicate 2


title: Human hepatitis C virus liver biopsy sample 4 Replicate 2


title: Human hepatitis C virus liver biopsy sample 29 Replicate 4


title: Control islets #3

description: Control islets #3

source_name: pancreatic islets (Control)

treatment_protocol: sham operation


title: Human hepatitis C virus liver biopsy sample 26 Replicate 2


title: IUGR islets #1

description: IUGR islets #1


title: Human hepatitis C virus liver biopsy sample 24 Replicate 4


title: Human hepatitis C virus liver biopsy sample 4 Replicate 1


title: Human hepatitis C virus liver biopsy sample 1 Replicate 2


title: Human hepatitis C virus liver biopsy sample 5 Replicate 4


title: Human hepatitis C virus liver biopsy sample 24 Replicate 1


title: Human hepatitis C virus liver biopsy sample 5 Replicate 2


title: Human hepatitis C virus liver biopsy sample 5 Replicate 3


title: Control islets #4

description: Control islets #4


title: Control islets #2

description: Control islets #2


title: Human hepatitis C virus liver biopsy sample 26 Replicate 4


title: HONE1 cell line replicate 1

value: nasopharynx


title: Human hepatitis C virus liver biopsy sample 26 Replicate 1


title: Human hepatitis C virus liver biopsy sample 21 Replicate 1


title: Human hepatitis C virus liver biopsy sample 26 Replicate 3


title: Human hepatitis C virus liver biopsy sample 22 Replicate 2


title: Human hepatitis C virus liver biopsy sample 22 Replicate 3


title: IUGR islets #2

description: IUGR islets #2


title: Human hepatitis C virus liver biopsy sample 31 Replicate 2


title: Human hepatitis C virus liver biopsy sample 1 Replicate 3


title: Human hepatitis C virus liver biopsy sample 27 Replicate 2


title: Human hepatitis C virus liver biopsy sample 22 Replicate 1


title: Human hepatitis C virus liver biopsy sample 20 Replicate 4


title: Human hepatitis C virus liver biopsy sample 24 Replicate 3


title: Human hepatitis C virus liver biopsy sample 31 Replicate 1


title: Human hepatitis C virus liver biopsy sample 4 Replicate 3


title: Human hepatitis C virus liver biopsy sample 18 Replicate 2


title: Human hepatitis C virus liver biopsy sample 20 Replicate 3


title: Human hepatitis C virus liver biopsy sample 18 Replicate 4


title: Human hepatitis C virus liver biopsy sample 1 Replicate 4


title: Human hepatitis C virus liver biopsy sample 18 Replicate 3


title: Human hepatitis C virus liver biopsy sample 28 Replicate 3


title: Human hepatitis C virus liver biopsy sample 15 Replicate 4


title: Human hepatitis C virus liver biopsy sample 4 Replicate 4


title: Human hepatitis C virus liver biopsy sample 16 Replicate 4


title: Human hepatitis C virus liver biopsy sample 15 Replicate 3


title: Human hepatitis C virus liver biopsy sample 20 Replicate 2


title: Human hepatitis C virus liver biopsy sample 15 Replicate 1


title: Human hepatitis C virus liver biopsy sample 35 Replicate 2


title: Human hepatitis C virus liver biopsy sample 34 Replicate 2


title: Human hepatitis C virus liver biopsy sample 14 Replicate 4


title: Human hepatitis C virus liver biopsy sample 16 Replicate 1


title: Human hepatitis C virus liver biopsy sample 14 Replicate 3


title: Human hepatitis C virus liver biopsy sample 14 Replicate 2


title: Sample Polygons

city: Montreal

first: Etienne

last: Yergeau

state: Qc

address: 6100 Royalmount Ave

department: Environmental Microbiology

institute: NRC-BRI

hyb_protocol: Slides were pre-hybridized for 1 h at 37°C with a DIG easy hybridization solution (Roche Applied Science, Laval, QC, Canada) containing 5% BSA. Samples were then assigned randomly to a sub-array and hybridization was carried out for approximately 20 h at 37°C on a Slide Booster apparatus (Implen, Calabasas, CA). Slides were washed three times for 5 minutes at 37°C in 0.1X SSC / 0.1% SDS followed by a single wash for 5 minutes at 37°C in 0.1X SSC.

scan_protocol: Slides were scanned in a ScanArray GX PLUS Microarray Scanner (Perkin-Elmer, Boston, MA) at a resolution of 10µm

data_processing: Spot presence-absence was scored by visual examination of the gridded microarray images. If a spot was visible by eye, it was scored as present (1), if not it was scored as absent (0). For a taxon to be scored as present, all of its triplicate spots had to be scored as present. The results from the 16S rRNA gene microarray were only used in the binary form (presence/absence of taxa).

organism: environmental samples

source_name: Alert

label_protocol: Total DNA extracted from all soil samples was submitted to a PCR procedure with eubacterial 16S rRNA gene primers F1-R13, with an annealing temperature of 50°C. RT-PCR products were then chemically labelled using the Label IT nucleic acid labelling kit (Mirus Bio, Madison, WI).

extract_protocol: Soil DNA was extracted from a 10 g soil sub-sample using the MoBio PowerMax Soil DNA Isolation kit (MoBio Laboratories, Carlsbad, CA).

tag: year

value: Pristine

tag: sample name

value: Polygons

tag: source

value: Pristine active layer soil from a frost-sorted polygon nearby Canadian Forces Station Alert


title: Human hepatitis C virus liver biopsy sample 34 Replicate 1


title: Human hepatitis C virus liver biopsy sample 15 Replicate 2


title: Sample Vegetated

value: Vegetated

value: Pristine active layer soil from a vegetated area nearby Canadian Forces Station Alert


title: Human hepatitis C virus liver biopsy sample 35 Replicate 3

value: Reference


title: Human hepatitis C virus liver biopsy sample 30 Replicate 3


title: Human hepatitis C virus liver biopsy sample 35 Replicate 1


title: Human hepatitis C virus liver biopsy sample 16 Replicate 3


title: Human hepatitis C virus liver biopsy sample 34 Replicate 4


title: Human hepatitis C virus liver biopsy sample 13 Replicate 4


title: Sample Biopile control

value: Biopile control

value: Pristine active layer soil from a control biopile nearby Canadian Forces Station Alert


title: Human hepatitis C virus liver biopsy sample 13 Replicate 2


title: Human hepatitis C virus liver biopsy sample 14 Replicate 1


title: Human hepatitis C virus liver biopsy sample 20 Replicate 1


title: Sample NC

value: NC

value: Pristine active layer soil samples from nearby Canadian Forces Station Alert


title: Sample 33D

source_name: Eureka

value: Pristine active layer soil from a ditch nearby Eureka weather station


title: Sample 32D


title: Sample 35B

value: Pristine active layer soil from a beach nearby Eureka weather station


title: Human hepatitis C virus liver biopsy sample 17 Replicate 2


title: Human hepatitis C virus liver biopsy sample 13 Replicate 3


title: Human hepatitis C virus liver biopsy sample 17 Replicate 3


title: Sample 23S

value: Pristine active layer soil nearby Eureka weather station


title: Human hepatitis C virus liver biopsy sample 17 Replicate 1

value: HCV positive


title: Human hepatitis C virus liver biopsy sample 33 Replicate 3


title: Active layer

value: Active layer soil

value: A

value: overlying active layer soil of 2M


title: 2m permafrost

value: 2m permafrost soil

value: 2 m deep permafrost


title: Human hepatitis C virus liver biopsy sample 18 Replicate 1


title: Human hepatitis C virus liver biopsy sample 33 Replicate 2


title: Human hepatitis C virus liver biopsy sample 28 Replicate 1


title: Human hepatitis C virus liver biopsy sample 28 Replicate 2


title: Human hepatitis C virus liver biopsy sample 17 Replicate 4


title: Macaca mulatta 14 dpi SIVmac239 LN-R98032-replicate-1

city: minneapolis

first: qingsheng

last: li

state: MN

address: Box 196, 420 Delaware ST SE

institute: University of Minnesota

hyb_protocol: Li et al., The Journal of infectious diseases 2004, 189, 572-582; Li et al., J Immunol 2009, 2009, 183: 1975–1982

scan_protocol: standard Affymetrix protocol

data_processing: Cel. files were uploaded into the Expressionist program (Genedata, Pro version 5.1) and the expression level for each of the 47,000 transcripts in the arrays were analyzed using the RMA algorithm

organism: Macaca mulatta

source_name: Lymph node snap-fronzen in liquid nitrogen

value: Lmyph node

tag: siv infection

value: 14 dpi

tag: siv type


title: Human hepatitis C virus liver biopsy sample 33 Replicate 1


title: Human hepatitis C virus liver biopsy sample 27 Replicate 3


title: Macaca mulatta 14 dpi SIVmac239 LN-R98032-replicate-2

label_protocol: Li et al., The Journal of infectious diseases 2004, 189, 572-582; Li et al., J Immunol 2009, 2009, 183: 1975–1982

tag: tissue


title: Human hepatitis C virus liver biopsy sample 3 Replicate 1

value: HCV negative


title: Human hepatitis C virus liver biopsy sample 13 Replicate 1

value: Reference


title: Human hepatitis C virus liver biopsy sample 27 Replicate 1


title: Macaca mulatta 14 dpi SIVmac239 LN-R93047-replicate-2

extract_protocol: Li et al., The Journal of infectious diseases 2004, 189, 572-582; Li et al., J Immunol 2009, 2009, 183: 1975–1982


title: Human hepatitis C virus liver biopsy sample 3 Replicate 4


title: Macaca mulatta 14 dpi SIVmac239 LN-R93047-replicate-1


title: Human hepatitis C virus liver biopsy sample 27 Replicate 4


title: Macaca mulatta 14 dpi SIVmac239 LN-24037-replicate-1


title: Human hepatitis C virus liver biopsy sample 19 Replicate 4


title: Human hepatitis C virus liver biopsy sample 3 Replicate 3


title: Macaca mulatta 14 dpi SIVmac239 LN-24037-replicate-2


title: Human hepatitis C virus liver biopsy sample 19 Replicate 3


title: Macaca mulatta 14 dpi SIVmac239 LN-R00034-replicate-2


title: Macaca mulatta 14 dpi SIVmac239 LN-R00034-replicate-1


title: Macaca mulatta uninfected LN-31391-replicate-2

value: uninfected


title: Macaca mulatta uninfected LN-31391-replicate-1


title: Macaca mulatta uninfected LN-34550-replicate-2


title: Human hepatitis C virus liver biopsy sample 19 Replicate 2


title: Human hepatitis C virus liver biopsy sample 19 Replicate 1


title: Macaca mulatta uninfected LN-34550-replicate-1


title: Macaca mulatta uninfected LN-RYe8-replicate-2


title: Human hepatitis C virus liver biopsy sample 25 Replicate 4


title: Human hepatitis C virus liver biopsy sample 36 Replicate 4


title: Human hepatitis C virus liver biopsy sample 36 Replicate 3


title: Human hepatitis C virus liver biopsy sample 5 Replicate 1


title: Cercocebus atys 30 dpi SIVsmm LN-FWv-replicate-2

description: FWv

organism: Cercocebus atys

value: 30 dpi

value: SIVsmm


title: Human hepatitis C virus liver biopsy sample 23 Replicate 2


title: Macaca mulatta uninfected LN-RF8-replicate-1


title: Macaca mulatta uninfected LN-RF8-replicate-2


title: Human hepatitis C virus liver biopsy sample 29 Replicate 2


title: Macaca mulatta uninfected LN-RYe8-replicate-1


title: Cercocebus atys 30 dpi SIVsmm LN-FWv-replicate-1

description: FWv


title: Human hepatitis C virus liver biopsy sample 23 Replicate 1


title: Cercocebus atys 30 dpi SIVsmm LN-Fuv-replicate-2

description: Fuv


title: Human hepatitis C virus liver biopsy sample 23 Replicate 3


title: Cercocebus atys 14 dpi SIVsmm LN-FWv-replicate-2

description: FWv


title: Human hepatitis C virus liver biopsy sample 25 Replicate 2


title: Human hepatitis C virus liver biopsy sample 23 Replicate 4


title: Human hepatitis C virus liver biopsy sample 25 Replicate 1


title: Cercocebus atys 14 dpi SIVsmm LN-FWv-replicate-1

description: FWv


title: Cercocebus atys 30 dpi SIVsmm LN-Fuv-replicate-1

description: Fuv


title: Cercocebus atys 14 dpi SIVsmm LN-FRs-replicate-1

description: FRs


title: Cercocebus atys 14 dpi SIVsmm LN-FRs-replicate-2

description: FRs


title: Human hepatitis C virus liver biopsy sample 29 Replicate 1


title: Human hepatitis C virus liver biopsy sample 25 Replicate 3


title: Human hepatitis C virus liver biopsy sample 36 Replicate 2


title: BRZ-CD99-shRNA#2, replicate 1

city: Bologna

first: Katia

last: Scotlandi

address: Via di Barbiano 1/10

institute: Istituto Ortopedico Rizzoli

description: Biological replicate 1 of 2. CD99 shRNA transfected cell line vs untrasfected cell line, harvested after 7 passages.

hyb_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

scan_protocol: Hybridized slides were scanned using GenePix 4000B microarray scanner (Axon Instruments) that acquires data at two wavelenghts simultaneously  [532nm (green) and 635nm (red)]. Signal and background intensities for both channels were calculated with GenePix 3.0 (Axon Instruments).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. (BRB-ArrayTools http://linus.nci.nih.gov/BRB-ArrayTools.html).

label_protocol: Total RNA was used to obtain labeled cRNA, according to the manufacturer's instructions (Low RNA Input Fluorescent Linear Amplification Kit-Agilent Technologies).

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

tag: IOR-BRZ Ewing Sarcoma trasfected cell line

tag: Transfected with CD99 shRNA plasmid.

source_name: Total RNA from IOR-BRZ Ewing Sarcoma cell line

tag: IOR-BRZ Ewing Sarcoma cell line


title: BRZ-CD99-shRNA#2, replicate 2

description: Biological replicate 2 of 2. CD99 shRNA transfected cell line vs untrasfected cell line, harvested after 7 passages.


title: BRZ-CD99-shRNA#1, replicate 2


title: Cercocebus atys uninfected LN-Fuv-replicate-1

description: Fuv


title: Cercocebus atys uninfected LN-Fuv-replicate-2

description: Fuv


title: BRZ-CTR-shRNA, replicate 2

description: Biological replicate 2 of 2. Control shRNA transfected cell line vs untrasfected cell line, harvested after 7 passages.

source_name: BRZ-CTR-shRNA

tag: Transfected with control shRNA plasmid.


title: Cercocebus atys uninfected LN-FRs-replicate-2

description: FRs


title: blood_RM_RWf7_SIVmac239_day224

city: Philadelphia

first: Steven

middle: E

last: Bosinger

state: PA

address: room 702 Stellar-Chance Laboratories, 422 Curie Blvd

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

description:
Animals had previous treatment with OKT8 antibody to deplete CD8+ T cells, and the antiretroviral drugs PMPA (tenofovir) and FTC (Emtricitabine), but were removed from treatment for >30 days prior to sampling.
GS-284

hyb_protocol: Following fragmentation, 20 micrograms of cRNA were diluted into 300 microlitres of hybridization cocktail, with 200 microlitres hybridized for 16 hr at 45 C on GeneChip Rhesus Macaque Genome Array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data from .CEL files were analyzed using Partek Genomics Suite with RMA normalization (quantile normalization, probeset summarization, RMA background subtraction).

source_name: blood, SIVmac239 infected, chronic (180+ days)

label_protocol: Biotinylated cRNAs were prepared using a modified version of the 2-cycle Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). 5 peptide-nucleic acid (PNA) blocking oligonucleotides directed against consensus sequences in the macaque and mangabey hemoglobin I and II genes were added into the initial reverse-transcription reaction.

growth_protocol: All animals used in this study were housed at the Yerkes National Primate Research Center (Atlanta, GA) in accordance with the regulations of the American Association of Accreditation of Laboratory Animal Care standards. This study was approved by the Institutional Animal Care and Usage Committees (IACUC) of Emory University and the University of Pennsylvania.

extract_protocol: RNA was extracted using the PAXgene RNA Isolation Kit according to manufacturer's instructions.

treatment_protocol: 5 sooty mangabeys and 4 rhesus macaques were inoculated intravenously with 1 ml of an uncloned strain of simian immunodeficiency virus, SIVsmm, derived from an experimentally infected SM at 11 days post-infection (1 ml of 29 plasma) as described  (Gordon et al., J Immunol. 2007 Sep 1;179(5):3026-34.; Estes et al., J Immunol. 2008 May 15;180(10):6798-807.).  8 rhesus macaques were inoculated i.v. with 3000 TCID50 of SIVmac239. Blood was drawn into PaxGene RNA tubes prior to SIV infection and at post-infection times indicated.

value: female

tag: age at infection

tag: weight at infection (kg)

tag: animal id

tag: siv strain

value: blood

tag: day after infection

tag: institution

value: University of Pennsylvania

tag: infection group

value: D

tag: bleed date

tag: rna purification date

tag: rna purification batch

tag: hybridization batch

tag: chamber batch

tag: acquisition date


title: blood_RM_RUe7_SIVmac239_day224

description:
Animals had previous treatment with OKT8 antibody to deplete CD8+ T cells, and the antiretroviral drugs PMPA (tenofovir) and FTC (Emtricitabine), but were removed from treatment for >30 days prior to sampling.
GS-266

tag: gender

tag: tissue


title: blood_RM_RRf6_SIVmac239_day217

description:
Animals had previous treatment with OKT8 antibody to deplete CD8+ T cells, and the antiretroviral drugs PMPA (tenofovir) and FTC (Emtricitabine), but were removed from treatment for >30 days prior to sampling.
GS-275

value: C


title: TC-CD99-shRNA#2, replicate 2

tag: TC-71 Ewing Sarcoma trasfected cell line

tag: Transfected with CD99 shRNA plasmid.

source_name: Total RNA from TC-71 Ewing Sarcoma cell line

tag: TC-71 Ewing Sarcoma cell line


title: BRZ-CTR-shRNA, replicate 1

description: Biological replicate 1 of 2. Control shRNA transfected cell line vs untrasfected cell line, harvested after 7 passages.

tag: IOR-BRZ Ewing Sarcoma trasfected cell line

tag: Transfected with control shRNA plasmid.

tag: IOR-BRZ Ewing Sarcoma cell line


title: TC-CD99-shRNA#2, replicate 1


title: Human hepatitis C virus liver biopsy sample 34 Replicate 3

tag: sample

value: HCV positive


title: TC-CTR-shRNA, replicate 2

source_name: TC-CTR-shRNA


title: blood_RM_RPp6_SIVmac239_day31

description:
No additional manipulation.
GS-255

source_name: blood, SIVmac239 infected, 30 days

tag: age at infection

tag: weight at infection (kg)

tag: animal id

tag: siv strain

tag: day after infection

tag: institution


title: blood_RM_XHB_SIVmac239_day189

description:
Animals had previous treatment with OKT8 antibody to deplete CD8+ T cells, and the antiretroviral drugs PMPA (tenofovir) and FTC (Emtricitabine), but were removed from treatment for >30 days prior to sampling.
GS-237

value: XHB

tag: infection group

tag: bleed date

tag: rna purification date

tag: rna purification batch

tag: hybridization batch

tag: chamber batch


title: blood_RM_XHB_SIVmac239_day31

description:
No additional manipulation.
GS-233

tag: gender

tag: tissue

tag: acquisition date


title: Human hepatitis C virus liver biopsy sample 1 Replicate 1


title: blood_RM_RUe7_SIVmac239_day31

description:
No additional manipulation.
GS-261


title: blood_RM_RZl5_SIVmac239_day31

description:
No additional manipulation.
GS-305


title: Control islets #1

description: Control islets #1

tag: strain

value: Sprague-Dawley

value: male

tag: age

value: 7 weeks

value: purified pancreatic islets (pooled)

tag: restriction enzyme

value: MspI

value: HpaII


title: blood_RM_RLi6_SIVmac239_day217

description:
Animals had previous treatment with OKT8 antibody to deplete CD8+ T cells, and the antiretroviral drugs PMPA (tenofovir) and FTC (Emtricitabine), but were removed from treatment for >30 days prior to sampling.
GS-292

tag: age at infection

tag: weight at infection (kg)


title: blood_RM_RSq8_SIVmac239_day224

description:
Animals had previous treatment with OKT8 antibody to deplete CD8+ T cells, and the antiretroviral drugs PMPA (tenofovir) and FTC (Emtricitabine), but were removed from treatment for >30 days prior to sampling
GS-301

tag: animal id

tag: siv strain


title: TC-CTR-shRNA, replicate 1

tag: TC-71 Ewing Sarcoma trasfected cell line

tag: Transfected with control shRNA plasmid.

tag: TC-71 Ewing Sarcoma cell line


title: Human hepatitis C virus liver biopsy sample 29 Replicate 3

tag: sample

value: Reference


title: Human hepatitis C virus liver biopsy sample 16 Replicate 2


title: TC-CD99-shRNA#1, replicate 2

tag: Transfected with CD99 shRNA plasmid.