title: 11469_Fa

status: Public on Apr 30 2011

type: genomic

city: Houston

first: Patricia

middle: Borges

last: Celestino

state: TX

address: One Baylor Plaza, T613

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

description: Rutgers ID: 11469_Fa

hyb_protocol: The nanodrop fluorospectrometer was used to measure DNA concentrantion and Dye incorporation in order to pair subjects with controls according to the following criteria: pmoles of dye were required to be within 3 units and DNA concentration within 100ng/uL. For each hybridization, the labeled experimental and reference DNAs were boiled for 3 minuted and incubated at 37°C for 30-90 minutes with human Cot-1 DNA (Invitrogen, Carlsbad, CA), blocking agent and hybridization buffer (Agilent Technologies, Santa Clara, CA).  The samples were then added to an array, which was placed inside a microarray hybridization chamber (Agilent Technologies, Santa Clara, CA), and allowed to hybridize at 65°C for 35-68 hours in a rotating hybridization oven (Agilent Technologies, Santa Clara, CA).  Following hybridization, slides were washed following the manufacturer’s protocol (Agilent Technologies).

scan_protocol: Agilent G2565 DNA Microarray Scanner (Agilent Technologies, Santa Clara, CA) with 3 um resolution.

data_processing: scanned images were quantified using the Agilent Feature Extraction (FE) software (version 10.7.3.1, Agilent Technologies) and analyzed using an in-house analysis program

molecule: genomic DNA

organism: Homo sapiens

source_name: lymphobast cell lines

label_protocol: The digested DNA was labeled with Bioprime Array CGH Genomic Labeling System following the manufacturer’s recommended protocol with minor additions (Invitrogen, Carlsbad, CA). Following the addition of random primers to the digested DNA, the mixture was boiled for 5 minutes then cooled on ice for 5 minutes. Cyanine 5-dCTP (for the experimental sample), cyanine 3-dCTP (for the reference sample) (PerkinElmer, Boston, MA), dCTP nucleotide mix, and exo-Klenow fragment (40 units/µL) were added and the reaction was incubated at 37°C for 2 hours.  The labeled product was purified from unincorporated nucleotides using Millipore columns or plate (Millipore, Billerica, MA, USA)

growth_protocol: Lymphoblastoid cell lines were establihsed and maintained by Rutgers University for the NIMH

extract_protocol: DNA was isolated from lymphoblastoid cell lines by Rutgers University by desalting using the Autopure LS robotic workstation with Autopure reagents (Qiagen, Inc., Valencia, CA)

treatment_protocol: no treatment given

tag: sex

value: M

tag: tissue

value: lymphobast cell lines

value: blood


title: 11455_Mo

description: Rutgers ID: 11455_Mo

value: F


title: 11455_P1

description: Rutgers ID: 11455_P1


title: 11452_Fa

description: Rutgers ID: 11452_Fa


title: 11466_Fa

description: Rutgers ID: 11466_Fa


title: 11469_P1

description: Rutgers ID: 11469_P1


title: 11442_Mo

description: Rutgers ID: 11442_Mo


title: 11452_P1

description: Rutgers ID: 11452_P1


title: 11461_Mo

description: Rutgers ID: 11461_Mo


title: 11455_Fa

description: Rutgers ID: 11455_Fa


title: 11450_P1

description: Rutgers ID: 11450_P1


title: 11450_Mo

description: Rutgers ID: 11450_Mo


title: 11459_Fa

description: Rutgers ID: 11459_Fa


title: 11443_P1

description: Rutgers ID: 11443_P1


title: 11458_Fa

description: Rutgers ID: 11458_Fa


title: 11443_Fa

description: Rutgers ID: 11443_Fa


title: 11459_P1

description: Rutgers ID: 11459_P1


title: 11443_Mo

description: Rutgers ID: 11443_Mo


title: 11466_P1

description: Rutgers ID: 11466_P1


title: 11461_Fa

description: Rutgers ID: 11461_Fa


title: 11442_Fa

description: Rutgers ID: 11442_Fa


title: 11466_Mo

description: Rutgers ID: 11466_Mo


title: 11452_Mo

description: Rutgers ID: 11452_Mo


title: 11458_P1

description: Rutgers ID: 11458_P1


title: 11459_Mo

description: Rutgers ID: 11459_Mo


title: 11450_Fa

description: Rutgers ID: 11450_Fa


title: 11458_Mo

description: Rutgers ID: 11458_Mo


title: 11461_P1

description: Rutgers ID: 11461_P1


title: 11469_Mo

description: Rutgers ID: 11469_Mo


title: 11442_P1

description: Rutgers ID: 11442_P1


title: 11429_Mo

description: Rutgers ID: 11429_Mo


title: 11429_Fa

description: Rutgers ID: 11429_Fa


title: 11428_Mo

description: Rutgers ID: 11428_Mo


title: 11426_Fa

description: Rutgers ID: 11426_Fa


title: 11429_P1

description: Rutgers ID: 11429_P1


title: 11428_Fa

description: Rutgers ID: 11428_Fa


title: 11426_P1

description: Rutgers ID: 11426_P1


title: 11424_Mo

description: Rutgers ID: 11424_Mo


title: 11425_P1

description: Rutgers ID: 11425_P1


title: 11425_Fa

description: Rutgers ID: 11425_Fa


title: 11417_Fa

description: Rutgers ID: 11417_Fa


title: 11424_P1

description: Rutgers ID: 11424_P1


title: 11420_P1

description: Rutgers ID: 11420_P1


title: 11418_P1

description: Rutgers ID: 11418_P1


title: 11424_Fa

description: Rutgers ID: 11424_Fa


title: 11417_P1

description: Rutgers ID: 11417_P1


title: 11418_Mo

description: Rutgers ID: 11418_Mo


title: 11415_Fa

description: Rutgers ID: 11415_Fa


title: 11420_Fa

description: Rutgers ID: 11420_Fa


title: 11425_Mo

description: Rutgers ID: 11425_Mo


title: 11428_P1

description: Rutgers ID: 11428_P1


title: 11418_Fa

description: Rutgers ID: 11418_Fa


title: 11417_Mo

description: Rutgers ID: 11417_Mo


title: 11415_Mo

description: Rutgers ID: 11415_Mo


title: 11420_Mo

description: Rutgers ID: 11420_Mo


title: 11415_P1

description: Rutgers ID: 11415_P1


title: 11413_Fa

description: Rutgers ID: 11413_Fa


title: 11413_P1

description: Rutgers ID: 11413_P1


title: 11413_Mo

description: Rutgers ID: 11413_Mo


title: 11426_Mo

description: Rutgers ID: 11426_Mo

source_name: blood


title: 11412_Fa

description: Rutgers ID: 11412_Fa


title: 11412_P1

description: Rutgers ID: 11412_P1


title: 11412_Mo

description: Rutgers ID: 11412_Mo


title: 11411_Mo

description: Rutgers ID: 11411_Mo


title: 11411_Fa

description: Rutgers ID: 11411_Fa


title: 11406_Fa

description: Rutgers ID: 11406_Fa


title: 11378_P1

description: Rutgers ID: 11378_P1


title: 11379_P1

description: Rutgers ID: 11379_P1


title: 11364_Fa

description: Rutgers ID: 11364_Fa


title: 11378_Fa

description: Rutgers ID: 11378_Fa


title: 11411_P1

description: Rutgers ID: 11411_P1


title: 11406_Mo

description: Rutgers ID: 11406_Mo


title: 11376_Fa

description: Rutgers ID: 11376_Fa


title: 11376_Mo

description: Rutgers ID: 11376_Mo


title: 11406_P1

description: Rutgers ID: 11406_P1


title: 11379_Mo

description: Rutgers ID: 11379_Mo


title: 11399_Mo

description: Rutgers ID: 11399_Mo


title: 11399_Fa

description: Rutgers ID: 11399_Fa


title: 11353_Fa

description: Rutgers ID: 11353_Fa


title: 11364_P1

description: Rutgers ID: 11364_P1


title: 11353_P1

description: Rutgers ID: 11353_P1


title: 11379_Fa

description: Rutgers ID: 11379_Fa


title: 11399_P1

description: Rutgers ID: 11399_P1


title: 11348_Fa

description: Rutgers ID: 11348_Fa


title: 11376_P1

description: Rutgers ID: 11376_P1


title: 11364_Mo

description: Rutgers ID: 11364_Mo


title: 11378_Mo

description: Rutgers ID: 11378_Mo


title: 11353_Mo

description: Rutgers ID: 11353_Mo


title: 11345_Fa

description: Rutgers ID: 11345_Fa


title: 11348_Mo

description: Rutgers ID: 11348_Mo


title: 11345_Mo

description: Rutgers ID: 11345_Mo


title: 11348_P1

description: Rutgers ID: 11348_P1


title: 11345_P1

description: Rutgers ID: 11345_P1


title: 11335_Mo

description: Rutgers ID: 11335_Mo


title: 11335_P1

description: Rutgers ID: 11335_P1


title: 11337_P1

description: Rutgers ID: 11337_P1


title: 11335_Fa

description: Rutgers ID: 11335_Fa


title: 11338_Mo

description: Rutgers ID: 11338_Mo


title: 11327_Mo

description: Rutgers ID: 11327_Mo


title: 11337_Mo

description: Rutgers ID: 11337_Mo


title: 11338_Fa

description: Rutgers ID: 11338_Fa


title: 11293_Fa

description: Rutgers ID: 11293_Fa


title: 11337_Fa

description: Rutgers ID: 11337_Fa


title: 11316_Mo

description: Rutgers ID: 11316_Mo


title: 11303_P1

description: Rutgers ID: 11303_P1


title: 11316_Fa

description: Rutgers ID: 11316_Fa


title: 11303_Mo

description: Rutgers ID: 11303_Mo


title: 11291_Fa

description: Rutgers ID: 11291_Fa


title: 11338_P1

description: Rutgers ID: 11338_P1


title: 11316_P1

description: Rutgers ID: 11316_P1


title: 11303_Fa

description: Rutgers ID: 11303_Fa


title: 11327_P1

description: Rutgers ID: 11327_P1


title: 11300_P1

description: Rutgers ID: 11300_P1


title: 11291_Mo

description: Rutgers ID: 11291_Mo


title: 11327_Fa

description: Rutgers ID: 11327_Fa


title: 11293_Mo

description: Rutgers ID: 11293_Mo


title: 11291_P1

description: Rutgers ID: 11291_P1


title: 11300_Mo

description: Rutgers ID: 11300_Mo


title: 11300_Fa

description: Rutgers ID: 11300_Fa


title: 11293_P1

description: Rutgers ID: 11293_P1


title: 11284_Fa

description: Rutgers ID: 11284_Fa


title: 11284_Mo

description: Rutgers ID: 11284_Mo


title: 11271_Fa

description: Rutgers ID: 11271_Fa


title: 11265_P1

description: Rutgers ID: 11265_P1


title: 11265_Fa

description: Rutgers ID: 11265_Fa


title: 11271_Mo

description: Rutgers ID: 11271_Mo


title: 11242_P1

description: Rutgers ID: 11242_P1


title: 11271_P1

description: Rutgers ID: 11271_P1


title: 11265_Mo

description: Rutgers ID: 11265_Mo


title: 11208_Mo

description: Rutgers ID: 11208_Mo


title: 11197_P1

description: Rutgers ID: 11197_P1


title: 11216_Fa

description: Rutgers ID: 11216_Fa


title: 11216_P1

description: Rutgers ID: 11216_P1


title: 11220_P1

description: Rutgers ID: 11220_P1


title: 11197_Mo

description: Rutgers ID: 11197_Mo


title: 11242_Fa

description: Rutgers ID: 11242_Fa


title: 11189_Mo

description: Rutgers ID: 11189_Mo


title: 11220_Fa

description: Rutgers ID: 11220_Fa


title: 11197_Fa

description: Rutgers ID: 11197_Fa


title: 11208_P1

description: Rutgers ID: 11208_P1


title: 11220_Mo

description: Rutgers ID: 11220_Mo


title: 11186_Mo

description: Rutgers ID: 11186_Mo


title: 11189_Fa

description: Rutgers ID: 11189_Fa


title: 11189_P1

description: Rutgers ID: 11189_P1


title: 11284_P1

description: Rutgers ID: 11284_P1


title: 11242_Mo

description: Rutgers ID: 11242_Mo


title: 11178_Fa

description: Rutgers ID: 11178_Fa


title: 11178_Mo

description: Rutgers ID: 11178_Mo


title: 11208_Fa

description: Rutgers ID: 11208_Fa


title: 11186_Fa

description: Rutgers ID: 11186_Fa


title: 11216_Mo

description: Rutgers ID: 11216_Mo


title: 11186_P1

description: Rutgers ID: 11186_P1


title: 11168_Mo

description: Rutgers ID: 11168_Mo


title: 11168_P1

description: Rutgers ID: 11168_P1


title: 11156_Fa

description: Rutgers ID: 11156_Fa


title: 11154_Mo

description: Rutgers ID: 11154_Mo

data_processing:
scanned images were quantified using the Agilent Feature Extraction (FE) software (version 10.7.3.1, Agilent Technologies) and analyzed using an in-house analysis program

This sample was removed from the final analysis for quality control.


title: 11168_Fa

description: Rutgers ID: 11168_Fa


title: 11156_P1

description: Rutgers ID: 11156_P1


title: 11152_Mo

description: Rutgers ID: 11152_Mo


title: 11152_Fa

description: Rutgers ID: 11152_Fa


title: 11178_P1

description: Rutgers ID: 11178_P1


title: 11113_Fa

description: Rutgers ID: 11113_Fa


title: 11156_Mo

description: Rutgers ID: 11156_Mo


title: 11154_Fa

description: Rutgers ID: 11154_Fa


title: 11152_P1

description: Rutgers ID: 11152_P1


title: 11114_Mo

description: Rutgers ID: 11114_Mo


title: 11114_P1

description: Rutgers ID: 11114_P1


title: 11146_Mo

description: Rutgers ID: 11146_Mo


title: 11114_Fa

description: Rutgers ID: 11114_Fa


title: 11149_Fa

description: Rutgers ID: 11149_Fa


title: 11149_Mo

description: Rutgers ID: 11149_Mo


title: 11149_P1

description: Rutgers ID: 11149_P1


title: 11102_Fa

description: Rutgers ID: 11102_Fa


title: 11102_Mo

description: Rutgers ID: 11102_Mo


title: 11098_Fa

description: Rutgers ID: 11098_Fa


title: 11098_Mo

description: Rutgers ID: 11098_Mo


title: 11146_Fa

description: Rutgers ID: 11146_Fa


title: 11102_P1

description: Rutgers ID: 11102_P1


title: 11113_Mo

description: Rutgers ID: 11113_Mo


title: 11098_P1

description: Rutgers ID: 11098_P1


title: 11091_P1

description: Rutgers ID: 11091_P1


title: 11091_Fa

description: Rutgers ID: 11091_Fa


title: 11089_P1

description: Rutgers ID: 11089_P1


title: 11146_P1

description: Rutgers ID: 11146_P1


title: 11089_Fa

description: Rutgers ID: 11089_Fa


title: 11154_P1

description: Rutgers ID: 11154_P1


title: 11091_Mo

description: Rutgers ID: 11091_Mo


title: 11076_Fa

description: Rutgers ID: 11076_Fa


title: 11089_Mo

description: Rutgers ID: 11089_Mo


title: 11076_Mo

description: Rutgers ID: 11076_Mo


title: 11075_Mo

description: Rutgers ID: 11075_Mo


title: 11083_Mo

description: Rutgers ID: 11083_Mo


title: 11071_Fa

description: Rutgers ID: 11071_Fa


title: 11076_P1

description: Rutgers ID: 11076_P1


title: 11083_Fa

description: Rutgers ID: 11083_Fa


title: 11059_Fa

description: Rutgers ID: 11059_Fa


title: 11063_Fa

description: Rutgers ID: 11063_Fa


title: 11063_P1

description: Rutgers ID: 11063_P1


title: 11062_P1

description: Rutgers ID: 11062_P1


title: 11071_Mo

description: Rutgers ID: 11071_Mo


title: 11075_Fa

description: Rutgers ID: 11075_Fa


title: 11063_Mo

description: Rutgers ID: 11063_Mo


title: 11062_Fa

description: Rutgers ID: 11062_Fa


title: 11059_Mo

description: Rutgers ID: 11059_Mo


title: 11046_Fa

description: Rutgers ID: 11046_Fa


title: 11046_P1

description: Rutgers ID: 11046_P1


title: 11030_Mo

description: Rutgers ID: 11030_Mo


title: 11030_Fa

description: Rutgers ID: 11030_Fa


title: 11030_P1

description: Rutgers ID: 11030_P1


title: 11113_P1

description: Rutgers ID: 11113_P1


title: 11059_P1

description: Rutgers ID: 11059_P1


title: 11007_Mo

description: Rutgers ID: 11007_Mo


title: 11007_P1

description: Rutgers ID: 11007_P1


title: 11014_P1

description: Rutgers ID: 11014_P1


title: 11083_P1

description: Rutgers ID: 11083_P1


title: 11007_Fa

description: Rutgers ID: 11007_Fa


title: 11014_Fa

description: Rutgers ID: 11014_Fa


title: 11006_Fa

description: Rutgers ID: 11006_Fa


title: 11075_P1

description: Rutgers ID: 11075_P1


title: 11046_Mo

description: Rutgers ID: 11046_Mo


title: 11000_P1

description: Rutgers ID: 11000_P1


title: 11014_Mo

description: Rutgers ID: 11014_Mo


title: 11000_Mo

description: Rutgers ID: 11000_Mo


title: 11071_P1

description: Rutgers ID: 11071_P1


title: 11581_Fa

description: Rutgers ID: 11581_Fa


title: 11587_Fa

description: Rutgers ID: 11587_Fa


title: 11000_Fa

description: Rutgers ID: 11000_Fa


title: 11006_P1

description: Rutgers ID: 11006_P1


title: 11581_Mo

description: Rutgers ID: 11581_Mo


title: 11587_P1

description: Rutgers ID: 11587_P1


title: 11578_P1

description: Rutgers ID: 11578_P1


title: 11578_Mo

description: Rutgers ID: 11578_Mo


title: 11587_Mo

description: Rutgers ID: 11587_Mo


title: 11563_Fa

description: Rutgers ID: 11563_Fa


title: 11578_Fa

description: Rutgers ID: 11578_Fa


title: 11581_P1

description: Rutgers ID: 11581_P1


title: 11579_Mo

description: Rutgers ID: 11579_Mo


title: 11579_P1

description: Rutgers ID: 11579_P1


title: 11577_Fa

description: Rutgers ID: 11577_Fa


title: 11579_Fa

description: Rutgers ID: 11579_Fa


title: 11563_Mo

description: Rutgers ID: 11563_Mo


title: 11563_P1

description: Rutgers ID: 11563_P1


title: 11006_Mo

description: Rutgers ID: 11006_Mo


title: 11577_Mo

description: Rutgers ID: 11577_Mo


title: 11554_Mo

description: Rutgers ID: 11554_Mo


title: 11555_P1

description: Rutgers ID: 11555_P1


title: 11555_Mo

description: Rutgers ID: 11555_Mo


title: 11554_Fa

description: Rutgers ID: 11554_Fa


title: 11554_P1

description: Rutgers ID: 11554_P1


title: 11550_P1

description: Rutgers ID: 11550_P1


title: 11550_Fa

description: Rutgers ID: 11550_Fa


title: 11550_Mo

description: Rutgers ID: 11550_Mo


title: 11533_Mo

description: Rutgers ID: 11533_Mo


title: 11555_Fa

description: Rutgers ID: 11555_Fa


title: 11537_Fa

description: Rutgers ID: 11537_Fa


title: 11533_P1

description: Rutgers ID: 11533_P1


title: 11062_Mo

description: Rutgers ID: 11062_Mo


title: 11533_Fa

description: Rutgers ID: 11533_Fa


title: 11524_Mo

description: Rutgers ID: 11524_Mo


title: 11523_Mo

description: Rutgers ID: 11523_Mo


title: 11524_Fa

description: Rutgers ID: 11524_Fa


title: 11520_P1

description: Rutgers ID: 11520_P1


title: 11520_Mo

description: Rutgers ID: 11520_Mo


title: 11537_P1

description: Rutgers ID: 11537_P1


title: 11523_P1

description: Rutgers ID: 11523_P1


title: 11511_P1

description: Rutgers ID: 11511_P1


title: Non-Exposed_SCLC_Normal

type: RNA

city: Helsinki

first: Mohamed

last: Guled

address: Haarmaninkatu 3

department: Department of Pathology

country: Finland

institute: Haartman Institute, University of Helsinki

description: asbestos-fiber count: 0.0

hyb_protocol: Agilent’s miRNA Complete Labeling and Hybridization Kit V2 (Protocol Version 2.1, Agilent Technologies, Palo Alto, CA, USA) was utilized for processing the samples.

scan_protocol: High-resolution Microarray Scanner (G2565CA, Agilent Technologies, Palo Alto, CA, USA) was used to scan the microarrays and the images were processed with Agilent Feature Extraction Software v. 9.5.

data_processing: The data was analyzed using Chipster version 1.4.2 (http://chipster.csc.fi/).

molecule: total RNA

source_name: Lung Tissue

growth_protocol: The tissues were maintained at -70°C prior to extraction

extract_protocol: Total RNA extraction was performed by using the miRNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer's protocol.

tag: gender

value: Male

tag: disease state

value: SCLC

value: normal lung


title: 11524_P1

description: Rutgers ID: 11524_P1


title: 11511_Mo

description: Rutgers ID: 11511_Mo


title: 11511_Fa

description: Rutgers ID: 11511_Fa


title: Non-Exposed_AC/SCC_Normal

description: asbestos-fiber count: 0.0

label_protocol: Agilent’s miRNA Complete Labeling and Hybridization Kit V2 (Protocol Version 2.1, Agilent Technologies, Palo Alto, CA, USA) was utilized for processing the samples.

value: AC/SCC


title: 11537_Mo

description: Rutgers ID: 11537_Mo


title: Non-Exposed_LCLC_Normal

description: asbestos-fiber count: 0.5

value: LCLC


title: 11523_Fa

description: Rutgers ID: 11523_Fa


title: 11510_Fa

description: Rutgers ID: 11510_Fa


title: Non-Exposed_SCC_Normal 4

description: asbestos-fiber count: 0.0

value: SCC


title: Non-Exposed_SCC_Normal 2

description: asbestos-fiber count: 0.0


title: 11510_P1

description: Rutgers ID: 11510_P1


title: 11520_Fa

description: Rutgers ID: 11520_Fa


title: Non-Exposed_AC_Normal 5

description: asbestos-fiber count: 0.0

value: AC


title: Non-Exposed_SCC_Normal 3

description: asbestos-fiber count: 0.0


title: Non-Exposed_SCC_Normal 5

description: asbestos-fiber count: 0.0


title: 11502_Mo

description: Rutgers ID: 11502_Mo


title: 11577_P1

description: Rutgers ID: 11577_P1


title: Non-Exposed_AC_Normal 3

description: asbestos-fiber count: 0.0


title: 11501_Mo

description: Rutgers ID: 11501_Mo


title: qRT-PCR of F. tularensis strain LVS at 45min after infection

city: Rockville

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

hyb_protocol: RNA samples were reverse transcribed to produce cDNA using SuperScript III (Invitrogen) and then subjected to qRT-PCR using Roche Sybr Green 2x matermix on the Roche 480 Light Cycler in 384-well format.  Genes for each sample were represented in duplicates.  Reactions were carried out at 10ul final volume. Each reaction contained 10ng of total RNA.  PCR activation at 95°C for 10 min was followed by 70 cycles of 15 s at 95°C, 10 s at 55°C and 10 s at 70°C. Sybr green fluorescence was captured in each cycle following 70°C extension.

scan_protocol: Expression levels were reported in Cp values.

data_processing: We found the average of all Cp values for the strain/timepoint and used it as internal control. We extracted this average Cp value from each individual Cp value for that strain/timepoint and that gave us the notmalized Cp value.

label: Sybr Green

organism: Francisella tularensis

source_name: F. tularensis strain LVS at 45min after infection dendritic cell model

extract_protocol: Ambion mirVana RNA extraction

treatment_protocol: Infection of human monocyte derived macrophage with F. tularensis. hMDM were isolated by the fractionation of human blood to obtain a pure population of monocytes, with subsequent differentiation into adherent macrophage using macrophage colony stimulating factor (MCSF).  Five F. tularensis strains were  grown to mid-log phase in a modified Brain Heart Infusion (BHI) broth and diluted to give an OD600=0.1. Based on previous experiments, this corresponds to ~7.2 x 108 cfu mL-1. Bacteria were centrifuged and resuspended in culture medium to the appropriate concentration. As the Time 0 control, a 4 mL aliquot of resuspended F. tularensis were removed prior to infection, treated with RNA Protect (Qiagen, CA, USA) to stabilize and preserve RNA, centrifuged and the resulting pellet stored at -80oC. Adherent macrophage were infected with a Multiplicity of Infection (MOI) of 100:1 using all seven strains, and bacteria were allowed to attach and invade for 90 minutes. Extracellular bacteria were eliminated using gentamycin at a concentration of 50 µg/mL for 30 minutes. After thorough washing, infected cells were incubated at 37oC/5% CO2 and cells harvested at 2, 4 and 8 hours post-gentamycin treatment. Infected cells were immediately resuspended in RNA Protect (Qiagen, CA, USA) to stabilize and preserve RNA, centrifuged, and the resulting pellet stored at -80oC for no longer than 24 hours before RNA extraction. To ensure adequate controls and replicates, all experiments were performed in triplicate and included uninfected hMDM as controls.

tag: time

value: 45min after infection

tag: strain

value: LVS


title: 11502_Fa

description: Rutgers ID: 11502_Fa


title: Non-Exposed_AC_Normal 2

description: asbestos-fiber count: 0.0


title: Non-Exposed_AC_Normal 4

description: asbestos-fiber count: 0.0


title: 11502_P1

description: Rutgers ID: 11502_P1


title: qRT-PCR of F. tularensis strain LVS at 8 hours after infection

source_name: F. tularensis strain LVS at 8 hours after infection dendritic cell model

value: 8 hours after infection


title: 11490_P1

description: Rutgers ID: 11490_P1


title: 11501_P1

description: Rutgers ID: 11501_P1


title: 11499_P1

description: Rutgers ID: 11499_P1


title: 11499_Fa

description: Rutgers ID: 11499_Fa


title: 11482_Fa

description: Rutgers ID: 11482_Fa


title: 11489_Fa

description: Rutgers ID: 11489_Fa


title: qRT-PCR of F. tularensis strain LVS at 0 hours after infection

source_name: F. tularensis strain LVS at 0 hours after infection dendritic cell model

value: 0 hours after infection


title: qRT-PCR of F. tularensis strain FRAN050 at 8 hours after infection

source_name: F. tularensis strain FRAN050 at 8 hours after infection dendritic cell model


title: qRT-PCR of F. tularensis strain LVS at 4 hours after infection

source_name: F. tularensis strain LVS at 4 hours after infection dendritic cell model

value: 4 hours after infection


title: Exposed_LCLC_Normal 1

description: asbestos-fiber count: 8.4

tag: agent

value: asbestos


title: Exposed_LCLC_Normal 2

description: asbestos-fiber count: 19.0


title: 11499_Mo

description: Rutgers ID: 11499_Mo

value: M


title: Exposed_AC/SCC_Normal

description: asbestos-fiber count: 145


title: Non-Exposed_AC_Normal 1

description: asbestos-fiber count: 0.0


title: qRT-PCR of F. tularensis strain FRAN050 at 4 hours after infection

source_name: F. tularensis strain FRAN050 at 4 hours after infection dendritic cell model


title: Exposed_SCC_Normal 3

description: asbestos-fiber count: 6.6


title: 11490_Fa

description: Rutgers ID: 11490_Fa

value: lymphobast cell lines


title: qRT-PCR of F. tularensis strain LVS at 2 hours after infection

source_name: F. tularensis strain LVS at 2 hours after infection dendritic cell model

value: 2 hours after infection


title: 11482_Mo

description: Rutgers ID: 11482_Mo

value: F

value: blood


title: 11479_Mo

description: Rutgers ID: 11479_Mo


title: qRT-PCR of F. tularensis strain FRAN050 at 2 hours after infection

source_name: F. tularensis strain FRAN050 at 2 hours after infection dendritic cell model


title: qRT-PCR of F. tularensis strain FRAN050 at 0 hours after infection

source_name: F. tularensis strain FRAN050 at 0 hours after infection dendritic cell model


title: Exposed_SCC_Normal 1

description: asbestos-fiber count: 6.0

value: Male


title: Non-Exposed_SCC_Normal 1

description: asbestos-fiber count: 0.0

value: normal lung


title: Exposed_LCLC_Normal 3

description: asbestos-fiber count: 90


title: 11490_Mo

description: Rutgers ID: 11490_Mo


title: 11489_Mo

description: Rutgers ID: 11489_Mo


title: 11489_P1

description: Rutgers ID: 11489_P1


title: Exposed_AC_Normal 5

description: asbestos-fiber count: 10.8


title: qRT-PCR of F. tularensis strain WY 96 at 8 hours after infection

source_name: F. tularensis strain WY 96  at 8 hours after infection dendritic cell model

value: WY 96


title: qRT-PCR of F. tularensis strain WY 96 at 4 hours after infection

source_name: F. tularensis strain WY 96  at 4 hours after infection dendritic cell model


title: Exposed_SCLC_Normal

description: asbestos-fiber count: 12.8

value: SCLC


title: Exposed_AC_Normal 4

description: asbestos-fiber count: 9.4


title: qRT-PCR of F. tularensis strain WY 96 at 2 hours after infection

source_name: F. tularensis strain WY 96  at 2 hours after infection dendritic cell model


title: 11479_P1

description: Rutgers ID: 11479_P1


title: Exposed_SCC_Normal 2

description: asbestos-fiber count: 5.9

value: SCC


title: Exposed_AC_Norma 3

description: asbestos-fiber count: 35.0

value: AC


title: qRT-PCR of F. tularensis strain Schu S4 at 45 min after infection

source_name: F. tularensis strain Schu S4 at 45min after infection dendritic cell model

value: 45min after infection

value: Schu S4


title: Inflammatory pseudotumour

description: asbestos-fiber_count  2.8

data_processing: Images were processed with Agilent Feature Extraction Software v. 9.5.  The data was analyzed using Chipster version 1.4.2 (http://chipster.csc.fi/).

value: Inflammatory pseudotumour

value: lung

tag: asbestos-fiber count


title: Exposed_AC_Normal 1

description: asbestos-fiber count: 72.9


title: Lung abscess

description: asbestos-fiber_count  3.0

value: Lung abscess


title: 11473_P1

description: Rutgers ID: 11473_P1


title: qRT-PCR of F. tularensis strain Schu S4 at 8 hours after infection

source_name: F. tularensis strain Schu S4 at 8 hours after infection dendritic cell model

value: 8 hours after infection


title: 11473_Mo

description: Rutgers ID: 11473_Mo

source_name: lymphobast cell lines

value: M


title: Tuberculosis

description: asbestos-fiber_count  0.9

value: Tuberculosis


title: L1_EcR_with_ecdysone

city: Athens

first: Melissa

last: Davis

state: GA

address: 500 DW Brooks Dr S 270C

department: Genetics  and MCG/UGA Medical Partnership

institute: University of Georgia

description:
EcR binding in response to hormone in L1 imaginal disc cell lines:
replicate: L1Ee1
replicate: L1Ee2
replicate: L1Ee3

test CEL: L1EcRe1.CEL
test CEL: L1EcRe2.CEL
test CEL: L1EcRe3.CEL
control CEL: L1DOe1.CEL
control CEL: L1DOe2.CEL
control CEL: L1DOe3.CEL

hyb_protocol: Arrays were hybridized using standard operating procedures for the Affymetrix system utilized at the Yale Unviersity and University of Chicago Functional genomics facilites

scan_protocol: Arrays were scanned on an Affymetrix 6000 Scanner

data_processing:
Data was quantile normalized using the TAS software
BAR files were generated with TAS software and the BED files included in this submission were generated with MAT software or TAS software. BED files generated with the MAT algorithm, (including variation control) have the letters MAT in the file name.

label: biotin

organism: Drosophila melanogaster

source_name: EcR-DAM fusion construct, Ecdysone Receptor DAM-ID from L1 cell lines, restriction enzyme treated methylated genomic DNA

label_protocol: enzymatically processed DNA was nick' end labeled with an SA- bioscience end labelling kit, following the manufacturer's instructions

growth_protocol: cells were grown at normal conditions (25C with no CO2) following the Drosophila Genome Center's instructions for each cell type.

extract_protocol: cells were harvested after transfection and hormone treatment. DNA was extracted by DNAzol protocol using manufacturer's protocol.

treatment_protocol: cells that were hormone treated were treated with either 3ug of 20-hydroxyecdysone in an isopropanol carrier

tag: hormone

tag: cell line

tag: cell type

value: imaginal disc

tag: transfection construct

source_name: DAM-only construct, Ecdysone Receptor DAM-ID from L1 cell lines, restriction enzyme treated methylated genomic DNA


title: qRT-PCR of F. tularensis strain WY 96 at 45min after infection

source_name: F. tularensis strain WY 96  at 45min after infection dendritic cell model


title: Lymphoid hyperplasia

description: asbestos-fiber_count  <0.3

source_name: Lung Tissue

value: Lymphoid hyperplasia


title: 11479_Fa

description: Rutgers ID: 11479_Fa

value: lymphobast cell lines

value: blood


title: qRT-PCR of F. tularensis strain Schu S4 at 4 hours after infection

source_name: F. tularensis strain Schu S4 at 4 hours after infection dendritic cell model

value: 4 hours after infection


title: Kc_EcR_no_ecdysone

description:
EcR binding without hormone in Kc embryonic cell lines:
replicate: KcEno1
replicate: KcEno2
replicate: KcEno3

test CEL: KcEcRno1.CEL
test CEL: KCEcRno2.CEL
test CEL: KcEcRno3.CEL
control CEL: KcDOno1.CEL
control CEL: KcDOno2.CEL
control CEL: KcDOno3.CEL

source_name: EcR-DAM fusion construct, Ecdysone Receptor DAM-ID from Kc cell lines, restriction enzyme treated methylated genomic DNA

value: Kc

value: embryonic

source_name: DAM-only construct, Ecdysone Receptor DAM-ID from Kc cell lines, restriction enzyme treated methylated genomic DNA


title: 11473_Fa

description: Rutgers ID: 11473_Fa


title: qRT-PCR of F. tularensis strain Schu S4 at 2 hours after infection

source_name: F. tularensis strain Schu S4 at 0 hours after infection dendritic cell model

value: 0 hours after infection


title: Intrapulmonary lymph node

description: asbestos-fiber_count  0.0

value: Male

value: Intrapulmonary lymph node


title: Hamartoma 1

description: asbestos-fiber_count  0.0

value: Hamartoma


title: Hamartoma 2

description: asbestos-fiber_count  0.0


title: Commercial lung RNA

description: asbestos-fiber_count  -

tag: sample type

value: Commercial lung RNA


title: 11501_Fa

description: Rutgers ID: 11501_Fa


title: Non-Exposed_SCLC

description: asbestos-fiber_count  0.0

value: SCLC

value: lung tumor


title: qRT-PCR of F. tularensis strain Schu S4 at 0 hours after infection

value: Schu S4


title: qRT-PCR of F. tularensis strain 2827G at 8 hours after infection

source_name: F. tularensis strain 2827G at 8 hours after infection dendritic cell model

value: 8 hours after infection


title: Non-Exposed_AC/SCC

description: asbestos-fiber_count  0.0

value: AC/SCC


title: D20_EcR_no_ecdysone

description:
EcR binding without hormone in D20 imaginal disc cell lines:
replicate: D20Eno1
replicate: D20Eno2
replicate: D20Eno3

test CEL: D20EcRno1.CEL
test CEL: D20EcRno2.CEL
test CEL: D20EcRno3.CEL
control CEL: D20DOno1.CEL
control CEL: D20DOno3.CEL

source_name: EcR-DAM fusion construct, Ecdysone Receptor DAM-ID from D20 cell lines, restriction enzyme treated methylated genomic DNA

value: imaginal disc

source_name: DAM-only construct, Ecdysone Receptor DAM-ID from D20 cell lines, restriction enzyme treated methylated genomic DNA


title: Kc_EcR_with_ecdysone

description:
EcR binding in response to hormone in Kc embryonic cell lines:
replicate: KcEe1
replicate: KcEe2
replicate: KcEe3

test CEL: KCEcRe1.CEL
test CEL: KcEcRe2.CEL
test CEL: KcEcRe3.CEL
control CEL: KcDOe1.CEL
control CEL: KcDOe2.CEL [corresponds to GPL5919, Dm35b_MR]
control CEL: KCDOe3.CEL


title: S2_EcR_no_ecdysone

description:
EcR binding without hormone in S2 embryonic cell lines:
replicate: S2Eno1
replicate: S2Eno2

test CEL: S2EcRno1.CEL
test CEL: S2EcRno2.CEL
control CEL: S2DOno1.CEL
control CEL: S2DOno2.CEL

source_name: EcR-DAM fusion construct, Ecdysone Receptor DAM-ID from S2 cell lines, restriction enzyme treated methylated genomic DNA

source_name: DAM-only construct, Ecdysone Receptor DAM-ID from S2 cell lines, restriction enzyme treated methylated genomic DNA


title: 11482_P1

description: Rutgers ID: 11482_P1

value: F

value: M


title: S2_EcR_with_ecdysone

description:
EcR binding in response to hormone in S2 embryonic cell lines:
replicate: S2Ee1
replicate: S2Ee2
replicate: S2Ee3

test CEL: S2EcRe1.CEL
test CEL: S2EcRe2.CEL
test CEL: S2EcRe3.CEL
control CEL: S2DOe1.CEL
control CEL: S2DOe2.CEL [corresponds to GPL5919, Dm35b_MR]


title: qRT-PCR of F. tularensis strain 2827G at 4 hours after infection

source_name: F. tularensis strain 2827G at 4 hours after infection dendritic cell model


title: Non-Exposed_SCC 5

description: asbestos-fiber_count  0.0

value: SCC


title: Non-Exposed_LCLC

description: asbestos-fiber_count  0.5

value: LCLC


title: qRT-PCR of F. tularensis strain 2827G at 2 hours after infection

source_name: F. tularensis strain 2827G at 2 hours after infection dendritic cell model

value: 2 hours after infection


title: qRT-PCR of F. tularensis strain 2827G at 45 min after infection

source_name: F. tularensis strain 2827G at 45 min after infection dendritic cell model

value: 45 min after infection


title: qRT-PCR of F. tularensis strain 2827G at 0 hours after infection (control)

source_name: F. tularensis strain 2827G at 0 hours after infection dendritic cell model

value: 0 hours after infection


title: 11510_Mo

description: Rutgers ID: 11510_Mo

source_name: lymphobast cell lines

value: lymphobast cell lines

value: blood


title: Non-Exposed_SCC 1

description: asbestos-fiber_count  0.0

value: Male


title: Non-Exposed_SCC 3

description: asbestos-fiber_count  0.0


title: Non-Exposed_SCC 4

description: asbestos-fiber_count  0.0


title: Non-Exposed_SCC 2

description: asbestos-fiber_count  0.0


title: Non-Exposed_AC 4

description: asbestos-fiber_count  0.0

value: AC


title: Non-Exposed_AC 5

description: asbestos-fiber_count  0.0


title: Non-Exposed_AC 2

description: asbestos-fiber_count  0.0


title: Non-Exposed_AC 3

description: asbestos-fiber_count  0.0


title: Exposed_SCLC

description: asbestos-fiber_count  12.8

value: asbestos

value: SCLC


title: Exposed_AC_Normal 2

description: asbestos-fiber count: 12.6

value: normal lung


title: Exposed_LCLC 2

description: asbestos-fiber_count  19.0

value: lung tumor


title: Exposed_AC/SCC

description: asbestos-fiber_count  145

value: AC/SCC


title: Exposed_LCLC 3

description: asbestos-fiber_count  90


title: 7-days-old Schistosomulum vs. Adult worm Rep. 8

city: São Paulo

first: Katia

middle: Cristina Pereira

last: Oliveira

state: O

address: Av Prof lineu prestes 748

department: Centro de Parasitologia e Micologia

country: Brazil

institute: Instituto Adolfo Lutz

description: Biological replica 2 technical replica 4 of 4

hyb_protocol: The hybridization and washing steps were performed using ASP equipament (Armershan Pharmacia biotech) according to the protocol described in  DeMarco R, et al. (2006). Mol Biochem Parasitol 150: 123-131.

scan_protocol: The slides were scanned using the same method described in DeMarco R, et al. (2006). Mol Biochem Parasitol 150: 123-131.

data_processing: The intensities of cy3 and cy5 channels were normalized using LOWESS method and we compute the log2 ratio from the MTM intensities (total intensity - background intensity)

organism: Schistosoma mansoni

source_name: Adult worm biol. Rep. 2

label_protocol: 1 ug of total RNA were linearly amplified and labeled with Cy3 or Cy5 according to described method in Wang E, et. al (2000). Nat Biotechnol 18: 457-459.

growth_protocol: all stages were obtained according to the described methods in Verjovski-Almeida, S. et al. (2003). Nature genetics 35(2):148-57.

extract_protocol: RNA from samples were extract using Trizol reagent (Invitrogen) according to manufacturer's instructions

tag: developmental stage

value: Adult worm obtained by portal perfusion of 42 days infected hamster

source_name: 7-days-old Schistosomulum biol. Replica 2

value: Mecanically transformed schistosomulum kept in culture during 7 days


title: 7-days-old Schistosomulum vs. Adult worm Rep. 7

description: Biological replica 2 technical replica 3 of 4


title: 7-days-old Schistosomulum vs. Adult worm Rep. 6

description: Biological replica 2 technical replica 2 of 4


title: Exposed_LCLC 1

description: asbestos-fiber_count  8.4

source_name: Lung Tissue


title: 7-days-old Schistosomulum vs. Adult worm Rep. 5

description: Biological replica 2 technical replica 1 of 4


title: Exposed_SCC 2

description: asbestos-fiber_count  5.9


title: Exposed_SCC 1

description: asbestos-fiber_count  6.0


title: qRT-PCR of F. tularensis strain FRAN050 at 45min after infection

source_name: F. tularensis strain FRAN050 at 45min after infection dendritic cell model

value: 45min after infection


title: Exposed_AC 5

description: asbestos-fiber_count  10.8


title: Exposed_AC 4

description: asbestos-fiber_count  9.4


title: 7-days-old Schistosomulum vs. Adult worm Rep. 4

description: Biological replica 1 technical replica 4 of 4

source_name: 7-days-old Schistosomulum biol. Replica 1

source_name: Adult worm biol. Rep. 1


title: 7-days-old Schistosomulum vs. Adult worm Rep. 3

description: Biological replica 1 technical replica 3 of 4


title: Rh36 spheres late replicate2

city: Zurich

first: Dagmar

last: Walter

address: August-Forel Str 1

department: Oncology

country: Switzerland

institute: University Children's Hospital

description: Rh36 spheres passage10

hyb_protocol: Biotin-labeled single-stranded cDNA targets (5ug) were mixed in 220ul of Hybridization Mix (Affymetrix Inc., P/N 900720) containing a Hybridization Controls and Control Oligonucleotide B2 (Affymetrix Inc., P/N 900454)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using Affymetrix Power Tools and using the CDF File  HuEx10stv2_Hs_ENSG.cdf from BrainArray [version 11.0.1].

source_name: Rh36 spheres passage10

label_protocol: Single-stranded cDNA (3ug) was converted into sense target cDNA (ST-cDNA) using WT-OvationT Exon (Cat # 2000-12). Fragmented and biotin-labeled ST-cDNA targets were generated with the FL-Ovation cDNA Biotin Module V2 (NuGEN, 4200-12)

growth_protocol: Adherent cells were cultured in DMEM medium containing 10%FCS. Sphere cultures were obtained by cultivating them in Neurobasal medium supplemented with EGF and b-FGF and no FCS.

extract_protocol: RNA was extracted according to manusfactor instruction of RNAeasy MiniKIT

treatment_protocol: not applicable

value: rhabdomyosarcoma

value: spheres


title: 7-days-old Schistosomulum vs. Adult worm Rep. 2

description: Biological replica 1 technical replica 2 of 4


title: Rh36 spheres late replicate1

description: Rh36 spheres passage10


title: D20_EcR_with_ecdysone

description:
EcR binding in response to hormone in D20 imaginal disc cell lines:
replicate: D20Ee1
replicate: D20Ee2
replicate: D20Ee3

test CEL: D20EcRe1.CEL
test CEL: D20EcRe2.CEL
test CEL: D20EcRe3.CEL
control CEL: D20DOe1.CEL
control CEL: D20DOe2.CEL
control CEL: D20DOe3.CEL

value: imaginal disc


title: Exposed_SCC 3

description: asbestos-fiber_count  6.6

value: SCC


title: Exposed_AC 3

description: asbestos-fiber_count  35.0


title: Exposed_AC 1

description: asbestos-fiber_count  72.9


title: Exposed_AC 2

description: asbestos-fiber_count  12.6


title: 7-days-old Schistosomulum vs. Adult worm Rep. 1

description: Biological replica 1 technical replica 1 of 4


title: Cercaria vs. 7-days-old Schistosomulum Rep. 8

source_name: Cercaria biol. Rep 2

value: Cercaria (obtained by exposition of infected snails under the light)


title: Cercaria vs. 7-days-old Schistosomulum Rep. 7


title: Non-Exposed_AC 1

description: asbestos-fiber_count  0.0


title: Rh36 spheres intermediate replicate1

description: Rh36 spheres passage7

source_name: Rh36 spheres passage7


title: Cercaria vs. 7-days-old Schistosomulum Rep. 6


title: Rh36 spheres early replicate2

description: Rh36 spheres passage3

source_name: Rh36 spheres passage3


title: Rh36 spheres early replicate1

description: Rh36 spheres passage3


title: Rh36 spheres intermediate replicate2

description: Rh36 spheres passage7


title: Cercaria vs. 7-days-old Schistosomulum Rep. 4

source_name: Cercaria biol. Rep 1


title: Cercaria vs. 7-days-old Schistosomulum Rep. 5


title: Rh36 cells replicate1

description: Rh36 adherent cells

source_name: Rh36 adherent cells

value: adherent


title: Cercaria vs. 7-days-old Schistosomulum Rep. 3


title: Rh36 cells replicate2

description: Rh36 adherent cells


title: Cercaria vs. 7-days-old Schistosomulum Rep. 2


title: Cercaria vs. 7-days-old Schistosomulum Rep. 1


title: Egg vs. Miracidium Rep.8

source_name: Miracidium biol. Rep 2

value: Miracidium (obtained by eclosion of eggs)

source_name: Egg biol. Rep.2

value: Egg extracted from livers of infected hamsters


title: RD spheres late replicate1

description: RD spheres passage10

source_name: RD spheres passage10

value: RD


title: RD spheres late replicate2

description: RD spheres passage10


title: RD spheres intermediate replicate2

description: RD spheres passage5

source_name: RD spheres passage5


title: RD spheres intermediate replicate1

description: RD spheres passage7

source_name: RD spheres passage7


title: qRT-PCR of F. tularensis strain WY 96 at 0 hours after infection

source_name: F. tularensis strain WY 96  at 0 hours after infection dendritic cell model

value: 0 hours after infection

value: WY 96


title: Egg vs. Miracidium Rep.7


title: Egg vs. Miracidium Rep.6


title: RD spheres early replicate1

description: RD spheres passage3

source_name: RD spheres passage3


title: RD spheres early replicate2

description: RD spheres passage3


title: L1_EcR_no_ecdysone

description:
EcR binding without hormone in L1 imaginal disc cell lines:
replicate: L1Eno1
replicate: L1Eno2
replicate: L1Eno3

test CEL: L1EcRno1.CEL
test CEL: L1EcRno2.CEL
test CEL: L1EcRno3.CEL
control CEL: L1DOno1.CEL
control CEL: L1DOno2.CEL
control CEL: L1DOno3.CEL

source_name: EcR-DAM fusion construct, Ecdysone Receptor DAM-ID from L1 cell lines, restriction enzyme treated methylated genomic DNA

source_name: DAM-only construct, Ecdysone Receptor DAM-ID from L1 cell lines, restriction enzyme treated methylated genomic DNA


title: Egg vs. Miracidium Rep.5


title: RD cells replicate2

description: RD aderent cells

source_name: RD aderent cells


title: Egg vs. Miracidium Rep.3

source_name: Egg biol. Rep.1

source_name: Miracidium biol. Rep 1


title: Egg vs. Miracidium Rep.2


title: RD cells replicate1

description: RD aderent cells


title: Egg vs. Miracidium Rep.1


title: Egg vs. Miracidium Rep.4


title: SU-DHL-4

city: Aalborg

first: Martin

last: Boegsted

address: Sdr. Skovvej 15

department: Department of Haematology

country: Denmark

institute: Aalborg Hospital, Aarhus University Hospital

description: Gene expression data from the diffuse large B-cell lymphoma cell line cell line SU-DHL-4

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 -18 hr at 45˚ C on GeneChip HG U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: .CEL files were background corrected and normalized by the just.rma function in the Bioconductor package affy

source_name: Diffuse large B-cell lymphoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, P/N 702232 Rev. 2, Affymetrix).

growth_protocol: The cell lines were subcultured 2 times per week. Subcultured 24 hours before harvest for RNA extraction.

extract_protocol: Total RNA was extracted using Invitrogen TRIzol Reagent combined with Qiagen RNeasy Mini kit. RNA quality was assessed using the Bioanalyser

treatment_protocol: Untreated. The density of the culture was determined and 5 million cells were harvested and stored in 1 ml Trizol until RNA extraction.

tag: culturing medium


title: MIA on day 21, biological rep1

city: Columbus

first: Jin

last: Nam

state: OH

address: 305 W. 12th Ave., 4010 Postle Hall

institute: The Ohio State University

description:
JN-4.CEL
Gene expression data from articular cartilage in the distal end of femur from MIA-induced arthritic knees on day 21 post-injection

hyb_protocol: 2ug of labeled and fragmented DNA was hybridized at 45C for 17 hours at 60rpm. GeneChips were washed and stained on the Affymetrix Fluidics Station 450 according to the manufacturers protocol.

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

data_processing: The data were analyzed by Partek Genomics Suite version 17 using GC-RMA normalization.

organism: Rattus norvegicus

source_name: monoiodoacetate induced arthritis on day 21 post-injection, biological rep1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng of total RNA according to Affymetrix's protocols.

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

treatment_protocol: Monoiodoacetate (MIA, 2 mg) dissolved in 50 ul of saline was intra-articularly injected into a knee of hinder limbs. Articular cartilage in the distal end of femur was exercised after 5, 9 or 21 days post-injection. Saline injected rats were used as sham controls.

value: Sprague-Dawley

tag: age

value: 12 ~ 14 weeks

value: articular cartilage

value: monoiodoacetate

value: day 21 post-injection


title: IV SCGB3A2 vs IV PBS treated rep 4

city: Yokohama

first: Reiko

last: Kurotani

state: Kanagawa

country: Japan

institute: Yokohama City University School of Medicine

description: Gene regulation by administration of PBS or SCGB3A2

hyb_protocol: According to FairPlay Kit (Catalog #252002, Stratagene, La Jolla, CA) instructions.

scan_protocol: Scanned on a GenePix 4000A.According to GenePix protocol.

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

organism: Mus musculus

source_name: intravenous administration of PBS

label_protocol: Total RNA were reverse-transcribed to label with Cy3 and Cy5 (GE Healthcare Life Sciences, Piscataway, NJ) using FairPlay Microarray Labeling Kit (Stratagene, La Jolla, CA) or SuperScriptTM Indirect cDNA Labeling Core Kit (Invitrogen), respectively.

growth_protocol: C57BL/6N mice (NCI-Frederick) were maintained under a standard 12-hrs light/12-hrs dark cycle with water and chow provided ad libitum.  At least ten 7-8-week-old C57BL/6N mice were prepared for each group.

extract_protocol: Total RNAs were purified using TRIzol (Invitrogen, Carlsbad, CA) and RNAeasy (QIAGEN, Valencia, CA) from lungs of mice treated with SCGB3A2/PBS 21 days after initial administraion of BLM/PBS or mice 12 hrs after SCGB3A2 treatment.

treatment_protocol: Eight unit/kg of bleomycin (BLM) (Sigma-Aldrich, St. Louis, MO) or PBS was directly administered once by intratracheal intubation into C57BL/6N mice using the BioLITE system (BioTex, Inc., Houston, TX).  Recombinant mouse (rm) SCGB3A2 (1.5 mg/kg/day) was intravenously administered.

value: lung

source_name: intravenous administration of SCGB3A2


title: MIA on day 9, biological rep2

description:
JN-16_9-8-09.CEL
Gene expression data from articular cartilage in the distal end of femur from MIA-induced arthritic knees on day 9 post-injection

source_name: monoiodoacetate induced arthritis on day 9 post-injection, biological rep2

value: day 9 post-injection


title: MIA on day 21, biological rep2

description:
JN-5.CEL
Gene expression data from articular cartilage in the distal end of femur from MIA-induced arthritic knees on day 21 post-injection

source_name: monoiodoacetate induced arthritis on day 21 post-injection, biological rep2


title: MIA on day 21, biological rep3

description:
JN-6.CEL
Gene expression data from articular cartilage in the distal end of femur from MIA-induced arthritic knees on day 21 post-injection

source_name: monoiodoacetate induced arthritis on day 21 post-injection, biological rep3


title: IV SCGB3A2 vs IV PBS treated rep 5


title: IV SCGB3A2 vs IV PBS treated rep 6


title: MIA on day 9, biological rep1

description:
JN-14_9-8-09.CEL
Gene expression data from articular cartilage in the distal end of femur from MIA-induced arthritic knees on day 9 post-injection

source_name: monoiodoacetate induced arthritis on day 9 post-injection, biological rep1


title: HT

description: Gene expression data from the diffuse large B-cell lymphoma cell line cell line HT

value: HT


title: RPMI-8226 LR5

description: Gene expression data from the multiple myeloma cell line RPMI-8226 LR5

source_name: Multiple myeloma cell line

value: RPMI-8226 LR5

value: RPMI-1640, 10% FBS, 5 μM melphalan was added once a week


title: MIA on day 9, biological rep3

description:
JL-1.CEL
Gene expression data from articular cartilage in the distal end of femur from MIA-induced arthritic knees on day 9 post-injection

source_name: monoiodoacetate induced arthritis on day 9 post-injection, biological rep3


title: IV SCGB3A2 vs IV PBS treated rep 3


title: MIA on day 5, biological rep2

description:
JN-2_7-31-09.CEL
Gene expression data from articular cartilage in the distal end of femur from MIA-induced arthritic knees on day 5 post-injection

source_name: monoiodoacetate induced arthritis on day 5 post-injection, biological rep2

value: day 5 post-injection


title: IV SCGB3A2 vs IV PBS treated rep 2


title: MIA on day 5, biological rep3

description:
JN-3_7-31-09.CEL
Gene expression data from articular cartilage in the distal end of femur from MIA-induced arthritic knees on day 5 post-injection

source_name: monoiodoacetate induced arthritis on day 5 post-injection, biological rep3


title: IV SCGB3A2 vs IV PBS treated rep 1


title: Embryonic age 17.5 mutant rep4 (PKD1_40)

city: Boston

first: Priyanka

last: Pandey

state: MA

address: Children's Hospital Boston, 300 Longwood avenue

department: Medicine/Nephrology

institute: Children's Hospital Boston

description:
PKD1_40
replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Beadarray and analyzed with Limma package in R

source_name: Mouse embryonic kidney

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: genotype/variation

value: Pkd1null/null mutant

value: embryo

value: kidney


title: U-266

description: Gene expression data from the multiple myeloma cell line U-266


title: BLM and SCGB3A2 vs BLM treated rep 5

description: Gene regulation by administration of BLM followed by intravenous injection of SCGB3A2 or PBS

source_name: administration of BLM followed by intravenous injection of PBS


title: Sham control, biological rep3

description:
JN-3.CEL
Gene expression data from articular cartilage in the distal end of femur from sham control

source_name: Saline-injected sham control, biological rep3

value: control


title: MIA on day 5, biological rep1

description:
JN-1_7-31-09.CEL
Gene expression data from articular cartilage in the distal end of femur from MIA-induced arthritic knees on day 5 post-injection

source_name: monoiodoacetate induced arthritis on day 5 post-injection, biological rep1


title: Embryonic age 17.5 mutant rep4 (PKD1_12)

description:
PKD1_12
replicate 4


title: BLM and SCGB3A2 vs BLM treated rep 4

source_name: administration of BLM followed by intravenous injection of SCGB3A2


title: NCI-H929

description: Gene expression data from the multiple myeloma cell line NCI-H929

value: RPMI-1640, 20% FBS, 2 mM L-glutamine, 1 mM sodium-pyrovate


title: Embryonic age 17.5 mutant rep4 (PKD1_42)

description:
PKD1_42
replicate 4


title: Sham control, biological rep2

description:
JN-2.CEL
Gene expression data from articular cartilage in the distal end of femur from sham control

source_name: Saline-injected sham control, biological rep2


title: Pre-miR-125b rep 2

city: Liege

first: Ingrid

last: Struman

address: Avenue de l'Hôpital, 1

department: BMGG

country: Belgium

institute: GIGA-R

hyb_protocol: 750 ng of biotinylated aRNA probe was hybridized to the Human Ref-8 BeadChip array (Illumina). Wash and scan were performed according to the manufacturer's instructions.

scan_protocol: the arrays were scanned using a BeadArray reader (Illumina). The images were registered and extracted automatically during the scan according to the manufacturer's settings

data_processing:
raw microarray intensity datat were analysed with GenomeStudio software normalized using the quantile normalization method according to the manufacturer's recommendation
differential analysis are performed for each group and the data were filtered on Differential Score. Probes are considered as expressed by filtering data on detection p-value lower than 0.01

source_name: HUVEC transf. Pre-miR-125b rep 2

label_protocol: 250 ng total RNA was labeled using the Illumina TotalPrep RNA amplification kit (Ambion, TX) according the manufacturer's instructions.

growth_protocol: HUVEC were grown on gelatin-coated plates with EGM-2 bullet kit medium (Lonza, Belgium)+ 5% FBS

extract_protocol: after 96h, total RNA was isolated using the miRNeasy kit (Qiagen). Purity and quality of extracted RNA was evaluated using the Experion RNA StdSens Analysis kit (Bio-Rad Laboratories CA). High quality RNA with RNA Quality Indicator (RQI) score ≥ 9.5 was used for hybridization

treatment_protocol: HUVEC were transfected with 25 nM of pre-miR molecules at passage 6 using Dharmafect-4 reagent according to the manufacturer's instructions (Dharmacon, C0)

value: Human vein umbilical endothelial cells (HUVEC)

tag: cell pool

value: HUVEC pool p6

tag: transfectant


title: Embryonic age 17.5 wild-type rep3 (PKD1_2)

description:
PKD1_2
replicate 3

value: wild-type

tag: tissue


title: BLM and SCGB3A2 vs BLM treated rep 1


title: Embryonic age 14.5 mutant rep2 (PKD1_65)

description:
PKD1_65
replicate 2


title: BLM and SCGB3A2 vs BLM treated rep 3


title: Embryonic age 17.5 wild-type rep3 (PKD1_41)

description:
PKD1_41
replicate 3


title: Sham control, biological rep1

description:
JN-1_9-8-09.CEL
Gene expression data from articular cartilage in the distal end of femur from sham control

source_name: Saline-injected sham control, biological rep1

value: Sprague-Dawley

value: 12 ~ 14 weeks

value: articular cartilage


title: BLM and SCGB3A2 vs BLM treated rep 2

value: lung


title: MOLP-2

description: Gene expression data from the multiple myeloma cell line MOLP-2


title: Pre-miR-125b rep 3

source_name: HUVEC transf. Pre-miR-125b rep 3


title: Pre-miR-125b rep 1

source_name: HUVEC transf. Pre-miR-125b rep 1


title: BLM treated vs PBS rep 4

description: Gene regulation by administration of BLM or PBS

source_name: administration of PBS followed by intravenous injection of PBS


title: BLM treated vs PBS rep 3


title: BLM treated vs PBS rep 5


title: Embryonic age 14.5 wild-type rep1 (PKD1_58)

description:
PKD1_58
replicate 1


title: Pre-miR-control rep 1

source_name: HUVEC transf. Pre-miR-control rep 1

value: Pre-miR-control


title: Embryonic age 14.5 wild-type rep1 (PKD1_57)

description:
PKD1_57
replicate 1


title: Pre-miR-control rep 2

source_name: HUVEC transf. Pre-miR-control rep 2


title: BLM treated vs PBS rep 2


title: BLM treated vs PBS rep 1


title: Embryonic age 14.5 mutant rep2 (PKD1_59)

description:
PKD1_59
replicate 2


title: Embryonic age 14.5 mutant rep2 (PKD1_35)

description:
PKD1_35
replicate 2


title: KMS-12-PE

description: Gene expression data from the multiple myeloma cell line KMS-12-PE

source_name: Multiple myeloma cell line


title: Embryonic age 17.5 wild-type rep3 (PKD1_38)

description:
PKD1_38
replicate 3


title: Embryonic age 14.5 wild-type rep1 (PKD1_34)

description:
PKD1_34
replicate 1


title: FastedHeart_rep4

status: Public on Apr 29 2011

city: Shinjuku

first: Isao

last: Ishii

state: Tokyo

address: 35 Shinanomachi

department: Biochemistry

institute: Keio Univ School of Medicine

description:
Heart (No.60)_008
Gene expression in the heart of fasted mice.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Heart of fasted mouse

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

growth_protocol: Mice were fed a standard rodent dry pellet diet (CE-2; Japan CLEA, Tokyo, Japan).

extract_protocol: RNA was prepared using the Trizol reagent (Invitrogen, Carlsbad, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer, and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Nine-week-old male mice were fasted (water with ad libitum) for 2 days.

value: heart

tag: gender

value: male

value: 9 weeks

tag: treatment

value: fasting

tag: treatment duration

value: 2 days


title: SatiatedHeart_rep4

description:
Heart (No.57)_006
Gene expression in the heart of satiated mice.

source_name: Heart of satiated mouse

tag: strain


title: 2TuR: tunicamycin and RANKL, mouse osteoclast cells, replicate #2

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the v3 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with RMA Express using the default settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

source_name: tunicamycin and RANKL treated, mouse osteoclast cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA using MessageAmp™ II aRNA Kit from Ambion

value: osteoclast

tag: disease state


title: 3Tu: tunicamycin, mouse osteoclast cells, replicate #3

source_name: tunicamycin treated, mouse osteoclast cells


title: 1TuR: tunicamycin and RANKL, mouse osteoclast cells, replicate #1


title: 2R: RANKL, mouse osteoclast cells, replicate #2

source_name: RANKL treated, mouse osteoclast cells


title: 3R: RANKL, mouse osteoclast cells, replicate #3


title: 1C: Control , mouse osteoclast cells, replicate #1

source_name: Control, mouse osteoclast cells


title: Pre-miR-control rep 3

source_name: HUVEC transf. Pre-miR-control rep 3


title: 3TuR: tunicamycin and RANKL, mouse osteoclast cells, replicate #3


title: FastedHeart_rep3

description:
Heart (No.47)_007
Gene expression in the heart of fasted mice.


title: SatiatedHeart_rep3

description:
Heart (No.56)_005
Gene expression in the heart of satiated mice.


title: 2C: Control , mouse osteoclast cells, replicate #2


title: 1R: RANKL, mouse osteoclast cells, replicate #1


title: 3C: Control , mouse osteoclast cells, replicate #3


title: FastedHeart_rep2

description:
Heart (No.63)_004
Gene expression in the heart of fasted mice.


title: SatiatedHeart_rep2

description:
Heart (No.45)_002
Gene expression in the heart of satiated mice.


title: SatiatedHeart_rep1

description:
Heart (No.31)_001
Gene expression in the heart of satiated mice.


title: FastedHeart_rep1

description:
Heart (No.48)_003
Gene expression in the heart of fasted mice.


title: 1Tu: tunicamycin, mouse osteoclast cells, replicate #1


title: 2Tu: tunicamycin, mouse osteoclast cells, replicate #2


title: Breast cancer cell line HCC70

city: Detroit

first: Zeng-Quan

last: Yang

state: MI

address: 4100 John R HWCRC 815

institute: Karmanos Cancer Institute

hyb_protocol: Differentially labeled experimental and reference DNAs were combined and hybridized to Agilent Human Genome CGH 244A microarrays at 65°C for 40 hr.  After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization.

source_name: Breast cancer cell line HCC70

label_protocol: Same amounts (1.5 μg) of experimental DNA and female reference DNA were digested. The digested DNAs were labeled by random priming with Cy3-dUTP (reference DNA) and Cy5-dUTP (experimental DNA) using Agilent Labeling Kit. The labeled DNAs were purified.

growth_protocol: Colo824 cells were cultured in 15% fetal bovine serum (FBS) RPMI-1640. HCC70 and HCC1954 cells were cultured in 10% FBS RPMI-1640.  KYSE 150 cells were cultured in 49% RPMI-1640 + 49% Ham's F12 + 2% FBS.

extract_protocol: DNA extracted using QIAGEN DNeasy Tissue kit following manufacturer's instructions

value: Breast cancer cell line HCC70

source_name: female DNA (Promega)

tag: reference

value: female reference DNA (Promega, Madison, WI)


title: Breast cancer cell line Colo824

source_name: Breast cancer cell line Colo824

tag: cell line

value: Breast cancer cell line Colo824


title: Breast cancer cell line HCC1954

source_name: Breast cancer cell line HCC1954

value: Breast cancer cell line HCC1954


title: SAMP22: Splenocytes treated with IFN-gamma, replicated #2

source_name: Splenocytes treated with IFN-gamma

tag: cell type

value: splenocyte

tag: Sex

value: female

tag: genotype

value: BALB/c


title: SAMP12: Splenocytes, replicate #2

source_name: Splenocytes obtained from BALB/C mice


title: SAMP11: Splenocytes, replicate #1


title: SAMP13: Splenocytes, replicate #3


title: SAMP23: Splenocytes treated with IFN-gamma, replicated #3


title: SAMP32: Splenocytes treated with IFN-gamma, replicate #2


title: SAMP31: Splenocytes treated with IFN-gamma, replicate #1


title: PF11: phenotypically normal db/m mice, replicate #3

source_name: liver from phenotypically normal db/m mice.

value: liver


title: dbM2: phenotypically normal db/m mice, replicate #2


title: MG4:  Mouse bone marrow, mature osteoclasts. replicate 2

source_name: Mouse bone marrow, mature osteoclasts

value: bone marrow

value: mature osteoclast


title: MG3: Mouse bone marrow, control osteoclast precursors. replicate 2

value: osteoclast precursor


title: AL3: db/db mice, replicate #3

source_name: Liver from ad-lib-fed type 2 diabetic mice (db/db mice).


title: PF1: db/db mice that were pair-fed, replicate #1

source_name: Liver from db/db mice that were pair-fed.


title: AL1: db/db mice, replicate #1


title: MG6:  Mouse bone marrow, mature osteoclasts. replicate 3


title: PF2: db/db mice that were pair-fed, replicate #2


title: PF3: db/db mice that were pair-fed, replicate #3


title: MG1:  Mouse bone marrow, control osteoclast precursors. replicate 1


title: MG2: Mouse bone marrow, mature osteoclasts. replicate 1


title: SAMP33: Splenocytes treated with IFN-gamma, replicate #3


title: esophageal cancer cell line KYSE150

source_name: esophageal cancer cell line KYSE150

value: esophageal cancer cell line KYSE150


title: AL2: db/db mice, replicate #2


title: F2329

description: F2329: CD4+CD8+ double positive (DP) T cells from mouse thymus, control, replicate #2.

value: thymus

value: CD4+CD8+ double positive (DP) T cells


title: MG5:  Mouse bone marrow, control osteoclast precursors. replicate 3


title: F2324

description: F2324: CD4+CD8+ double positive (DP) T cells from mouse thymus, control, replicate #2.


title: FF2333

description: FF2333: CD4+CD8+ double positive (DP) T cells from mouse thymus, Notch1 with a point mutation to prevent fucosylation in EGF12, replicate #3.


title: FF2332

description: FF2332: CD4+CD8+ double positive (DP) T cells from mouse thymus, Notch1 with a point mutation to prevent fucosylation in EGF12, replicate #2.


title: dbM1:  phenotypically normal db/m mice, replicate #1


title: F2323

description: F2323: CD4+CD8+ double positive (DP) T cells from mouse thymus, control, replicate #1.


title: FF2330

description: FF2330: CD4+CD8+ double positive (DP) T cells from mouse thymus, Notch1 with a point mutation to prevent fucosylation in EGF12, replicate #1.


title: SAMP21: Splenocytes treated with IFN-gamma, replicated #1


title: 12: Prion Protein knockout mouse brain at age 82 weeks, replicate #3

source_name: Mouse Brain, Prion Protein knockout mouse at age 82 weeks

value: brain

value: prion protein KO


title: 11: Prion Protein knockout mouse brain at age 82 weeks, replicate #2


title: 5: Prion Protein knockout mouse brain at age 2 weeks, replicate #2

source_name: Mouse Brain, Prion Protein knockout mouse at age 2 weeks


title: 6: Prion Protein knockout mouse brain at age 2 weeks, replicate #3


title: 2: Mouse Brain age 2 weeks, control, replicate #2

source_name: Mouse Brain age 2 weeks, control

value: WT


title: 1: Mouse Brain age 2 weeks, control, replicate #1


title: 3: Control, mutated construct that has no activity injected mice, replicate #3.

source_name: Control mouse leg muscle, mutated construct that has no activity injected

value: muscle


title: 2: Control, mutated construct that has no activity injected mice, replicate #2.


title: 1: Control, mutated construct that has no activity injected mice, replicate #1.


title: 4: Wild type construct injected mice, replicate #1.

source_name: Mouse leg muscle, overexpression of the glycosyltransferase LARGE construct injected


title: 4SCR8: 8 hours post-wounding, replicate 1

source_name: Epithelial cells of mouse corneas; 8 hours post-wounding

value: cornea

value: epithelial


title: 3: Mouse Brain age 2 weeks, control, replicate #3


title: 5SCR8: 8 hours post-wounding, replicate 2


title: 2CON8: Control, replicate 2

source_name: Epithelial cells of mouse corneas; Control 8 hours


title: 3CON8: Control, replicate 3


title: 6SCR8: 8 hours post-wounding, replicate 3


title: 9CON24: Control, replicate 3

source_name: Epithelial cells of mouse corneas; Control 24 hours


title: 10SCR24: 24 hours post-wounding, replicate 1

source_name: Epithelial cells of mouse corneas; 24 hours post-wounding


title: 7: Mouse Brain age 82 weeks, control, replicate #1

source_name: Mouse Brain age 82 weeks, control


title: 9: Mouse Brain age 82 weeks, control, replicate #3


title: 10: Prion Protein knockout mouse brain at age 82 weeks, replicate #1


title: 8: Mouse Brain age 82 weeks, control, replicate #2


title: 6: Wild type construct injected mice, replicate #3.


title: 11SCR24: 24 hours post-wounding, replicate 2


title: 5: Wild type construct injected mice, replicate #2.


title: 1CON8: Control, replicate 1


title: 12SCR24: 24 hours post-wounding, replicate 3


title: Mouse muscle with tumor, 12 days Replicate 3

source_name: Mouse muscle with tumor, 12 days

value: male

value: Tumor Bearing


title: Mouse muscle with tumor, 12 days Replicate 2


title: 4: Prion Protein knockout mouse brain at age 2 weeks, replicate #1


title: Mouse muscle tissue, PBS treated. No tumor (control) Replicate 2

source_name: Mouse muscle tissue, PBS treated. No tumor (control).

value: healthy


title: Mouse muscle tissue, PBS treated. No tumor (control) Replicate 3


title: IL43:  Mouse peritoneal macrophage, treated with IL-4, Replicate #3.

source_name: Mouse peritoneal macrophage, treated with IL-6

value: peritoneal macrophage


title: IL42:  Mouse peritoneal macrophage, treated with IL-4, Replicate #2.

source_name: Mouse peritoneal macrophage, treated with IL-5


title: IL41:  Mouse peritoneal macrophage, treated with IL-4, Replicate #1.


title: Mouse muscle with tumor, 12 days Replicate 1


title: 03: Mouse peritoneal macrophage, Control, Replicate #3.

source_name: Mouse peritoneal macrophage, Control


title: Mouse muscle with tumor, 22 days Replicate 2

source_name: Mouse muscle with tumor, 22 days


title: Mouse muscle with tumor, 22 days Replicate 3


title: 01: Mouse peritoneal macrophage, Control, Replicate #1.


title: Wild Type 2

source_name: Wild Type mouse olfactory epithelium

value: olfactory epithelium

value: 129Ola and C567BL/6

value: 50 days


title: 7CON24: Control, replicate 1


title: Wild Type 1


title: Beta3GnT1 KO 2

source_name: Beta3GnT1 KO mouse olfactory epithelium


title: Wild Type 3


title: Beta3GnT1 KO 1


title: Beta3GnT1 KO 3


title: 02: Mouse peritoneal macrophage, Control, replicate #2.


title: Mouse muscle tissue, PBS treated. No tumor (control) Replicate 1


title: Mouse muscle with tumor, 22 days Replicate 1


title: Spleen, BALB/C, day 14

source_name: Spleen, BALB/C, day 14

value: spleen

value: BALB/C

value: infected with 1000 trypomastigotes of T. cruzi strain Y i.p.


title: Spleen, BALB/C, day 28

source_name: Spleen, BALB/C, day 28


title: Spleen, BALB/C, day 21

source_name: Spleen, BALB/C, day 21


title: mouse eosinophils replicate 1

source_name: mouse eosinophiles

value: female

value: IL-5 transgenic

value: eosinophil


title: mouse eosinophils replicate 2


title: mouse eosinophils replicate 3


title: Spleen, BALB/C, day 7

source_name: Spleen, BALB/C, day 7


title: Spleen, BALB/C, control replicate 2

source_name: Spleen, BALB/C, control


title: Spleen, BALB/C, control replicate 1


title: Thymus, C57BL6, day 14

source_name: Thymus, C57BL6, day 14

value: thymus


title: Thymus, C57BL6, control

source_name: Thymus, C57BL6, control


title: Thymus, BALB/C, day 14

source_name: Thymus, BALB/C, day 14


title: Thymus, BALB/C, control

source_name: Thymus, BALB/C, control


title: Spleen, C57BL6, day 28

source_name: Spleen, C57BL6, day 28


title: Spleen, C57BL6, day 21

source_name: Spleen, C57BL6, day 21


title: Spleen, C57BL6, day 14

source_name: Spleen, C57BL6, day 14


title: NaCl stressed, Replicate #3

source_name: Mouse NS0 myeloma cells grown in culture: NaCL stressed

value: NS0 myeloma cells


title: NaCL stressed, Replicate #1


title: NaCl stressed, Replicate #2


title: Proline stressed, Replicate #2

source_name: Mouse NS0 myeloma cells grown in culture: Proline stressed


title: Control, Replicate #3

source_name: Mouse NS0 myeloma cells grown in culture: Control


title: Control, Replicate #1


title: Control, Replicate #2


title: Proline stressed, Replicate #3


title: Ammonia stressed, replicate #4

source_name: Mouse NS0 myeloma cells grown in culture: Ammonia stressed


title: Proline stressed, replicate #1


title: Ammonia stressed, Replicate #2


title: 4A: Normal myometrium from human uterus, replicate #4

source_name: Normal myometrium from human uterus.

tag: tissue type

value: healthy myometrium


title: 3A: Normal myometrium from human uterus, replicate #3


title: 6A: Normal myometrium from human uterus, replicate #6


title: 2A: Normal myometrium from human uterus, replicate #2


title: 7A: Normal myometrium from human uterus, replicate #7


title: Human immature monocyte-derived dendritic cells

value: Healthy


title: 8A: Normal myometrium from human uterus, replicate #8


title: Human mature monocyte-derived dendritic cells

value: mature monocyte-derived dendritic cells


title: 5A: Normal myometrium from human uterus, replicate #5


title: Spleen, C57BL6, control

source_name: Spleen, C57BL6, control


title: Spleen, C57BL6, day 7

source_name: Spleen, C57BL6, day 7


title: 9A: Normal myometrium from human uterus, replicate #9


title: 1B: Leiomyoma tumors, replicate #1

source_name: leiomyoma tumors.

value: leiomyoma tumor


title: Ammonia stressed, Replicate #1


title: 3B: Leiomyoma tumors, replicate #3


title: 2B: Leiomyoma tumors, replicate #2


title: 1A: Normal myometrium from human uterus, replicate #1


title: 7B: Leiomyoma tumors, replicate #17


title: 8B: Leiomyoma tumors, replicate #18


title: 9B: Leiomyoma tumors, replicate #19


title: 10B: Leiomyoma tumors, replicate #20


title: 10A: Normal myometrium from human uterus, replicate #10


title: F26: bFGF 6 hours, replicate #2

source_name: HUVEC bFGF treated 6 hours.

value: human umbilical vein endothelial cell (HUVEC)


title: F36: bFGF 6 hours, replicate #3


title: C10: Control, 0 hours, replicate#1

source_name: HUVEC untreated Control, 0 hours.


title: C36: Control, 6 hours, replicate #3

source_name: HUVEC untreated Control, 6 hours.


title: C16: Control, 6 hours, replicate #1


title: C26: Control, 6 hours, replicate #2


title: C20: Control, 0 hours, replicate#2


title: F16: bFGF 6 hours, replicate #1


title: C30: Control, 0 hours, replicate#3


title: 6B: Leiomyoma tumors, replicate #16


title: G16: Galectin-3, 6 hours, replicate #1

source_name: HUVEC Galectin-3 treated, 6 hours.


title: Macrophage Day 10 Uninfected with HIV

source_name: Macrophage Day 10 uninfected control

value: macrophage

value: Uninfected


title: Macrophage Day 7 Infected with HIV, replicate #3.

source_name: Macrophage 7 days post infection with HIV

value: Infected


title: Macrophage Day 10 Infected with HIV, replicate #3.

source_name: Macrophage 10 days post infection with HIV


title: Macrophage Day 5 Infected with HIV, replicate #3.

source_name: Macrophage 5 days post infection with HIV


title: Macrophage Day 7 Uninfected with HIV

source_name: Macrophage Day 7 uninfected control


title: 5B: Leiomyoma tumors, replicate #5


title: 4B: Leiomyoma tumors, replicate #4


title: 8CON24: Control, replicate 2

source_name: Epithelial cells of mouse corneas; Control 24 hours

value: cornea

value: epithelial


title: G36: Galectin-3, 6 hours, replicate #3


title: Macrophage Day 5 Uninfected with HIV

source_name: Macrophage Day 5 uninfected control


title: V16: VEGF 6 hours, replicate #1

source_name: HUVEC VEGF treated 6 hours.


title: G26: Galectin-3, 6 hours, replicate #2


title: V26: VEGF 6 hours, replicate #2


title: Serum 3

description: RNA from human corneal epithelial cells under normal culture condition, replicate 3

value: corneal epithelial


title: V36: VEGF 6 hours, replicate #3


title: Serum 2

description: RNA from human corneal epithelial cells under normal culture condition, replicate 2


title: Serum 1

description: RNA from human corneal epithelial cells under normal culture condition, replicate 1


title: Serum Free 3

description: RNA from the human corneal epithelial cells under induced serum free condition for keratan sulfate production, replicate 3

source_name: RNA from the cells under induced condition for keratan sulfate production (serum free)


title: Serum Free 2

description: RNA from the human corneal epithelial cells under induced serum free condition for keratan sulfate production, replicate 2


title: D1:  Dry eye disease, replicate 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the v2 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

source_name: conjunctival epithelium of patients with severe dry eye disease

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

value: conjunctival epithelium

value: Dry Eye Disease


title: D2: Dry eye disease, replicate 2


title: N2:  Normal, replicate 2

source_name: conjunctival epithelium of normal donor patients without severe dry eye disease


title: N1:  Normal, replicate 1


title: Serum Free 1

description: RNA from the human corneal epithelial cells under induced serum free condition for keratan sulfate production, replicate 1


title: N6: Normal, replicate 3


title: 100A2:  Human breast cancer cells treated with 100 uM Ac4ManNAc, replicate #2

value: female

value: WT

value: breast cancer


title: 100L3: Human breast cancer cells treated with 100 uM Ac4ManNLev, replicate 3


title: 0CON3:  Human breast cancer cells (control), replicate #3

source_name: Human breast cancer cells (control)


title: 0CON1:  Human breast cancer cells (control), replicate #1


title: 100L2: Human breast cancer cells treated with 100 uM Ac4ManNLev, replicate 2


title: MDCLPSB: LPS-matured dendritic cells, donor B, Replicate #2

source_name: LPS-matured dendritic cells

value: mature dendritic cells


title: MDCLPSA: LPS-matured dendritic cells, donor A, replicate #1


title: 100L1: Human breast cancer cells treated with 100 uM Ac4ManNLev, replicate 1


title: D3: Dry eye disease, replicate 3


title: 100A3:  Human breast cancer cells treated with 100 uM Ac4ManNAc, replicate #3


title: MACROA: Resting macrophage, donor A, replicate #1

source_name: Resting macrophage


title: MACROB: Resting macrophage, donor B, replicate #2


title: IDCB: Immature dendritic cells, donor B, replicate #2

source_name: Immature dendritic cells

value: immature dendritic cells


title: IL15DCB: Il-15 Immature dendritic cells, donor B, Replicate #2

source_name: IL-15 immature dendritic cells


title: IL15DCB: Il-15 Immature dendritic cells, donor B, Replicate #1


title: IL15DCA: IL-15 immature dendritic cells, donor A, replicate #1


title: IDCA: Immature dendritic cells, donor A, replicate #2


title: 0CON2:  Human breast cancer cells (control), replicate #2


title: IDCA: Immature dendritic cells, donor A, replicate #1


title: DxMDCB: Dexamethasone immature dendritic cells, donor B, replicate #2

source_name: Dexamethasone immature dendritic cells


title: DxMDCA: Dexamethasone immature dendritic cells, donor A, replicate #1


title: C: Monocytes (donor C), replicate #1.

source_name: Monocytes

value: Monocytes


title: Activated T-cells Replicate 2

source_name: Activated T-cells

value: 49 yr

value: healthy

tag: ethnicity

value: asian

value: T-cell


title: Bm:  Mature dendritic cells (donor B), replicate #2.

source_name: Mature dendritic cells

value: Mature dendritic cells


title: Activated T-cells Replicate 1

tag: age

value: 51 yr

value: caucasian, non-hispanic


title: Activated Macrophage Replicate 3

source_name: Activated Macrophage

value: male

value: 56 yr

value: caucasian

value: macrophage


title: Activated Macrophage Replicate 1

value: female


title: Activated Macrophage Replicate 2


title: Am:  Mature dendritic cells (donor A), replicate #1.


title: Ai:  Immature dendritic cells (donor A), replicate #1.

value: Immature dendritic cells


title: Bi: Immature dendritic cells (donor B), replicate #2.


title: Intermediate passage replicate 2

source_name: Intermediate passage human prostate LNCaP cells

value: prostate cancer

value: human prostate LNCaP


title: Activated T-cells Replicate 3


title: Low passage replicate 1

source_name: Low passage human prostate LNCaP cells


title: Low passage replicate 3


title: Low passage replicate 2


title: High passage replicate 3

source_name: High passage human prostate LNCaP cells


title: Intermediate passage replicate 3


title: Intermediate passage replicate 1


title: High passage replicate 1


title: Ishikawa cells replicate 3

source_name: Endometrial adenocarcinoma cell line (Ishikawa cells)

value: Ishikawa (human endometrial)

value: endometrial adenocarcinoma


title: Ishikawa cells replicate 2


title: Ishikawa cells replicate 1


title: High passage replicate 2


title: Monocyte, control replicate 3

source_name: Monocyte, control

value: monocyte


title: Patient 8, intact skin sample

first: Kristo

middle: Juhana

last: Nuutila

address: Haartmaninkatu 8, Biomedicum 1

department: Institute of Biomedicine

institute: University of Helsinki

description: Skin from split thickness skin grafting

hyb_protocol: According to Affymetrix GeneChip Hybridization, Wash and Stain Kit

scan_protocol: Chip scanning was performed with a GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Data analysis was performed with GeneSpring GX software, version 11.0.1 (Agilent Technologies), normalized to the median, filtered by expression, and presented as gene expression-fold changes.The results are expressed as means ± SEM. Statistical analysis was performed, using GeneSpring GX software, version 11.0.1 (Agilent Technologies).  Differences between the groups were compared using one-way analysis of variance (ANOVA) with Benjamini-Hochberg posttesting.

source_name: intact skin sample

label_protocol: According to Affymetrix GeneChip 3' IVT Express Kit

growth_protocol: No treatment, clinical patient samples from normal wound healing process.

extract_protocol: The skin samples were homogenized using the Precellys 24 tissue homogenizer with a Cryolys temperature controller unit (Bertin Technologies SA, Montigny-le-Bretonneux, France).Total RNA was extracted from the homogenized tissue samples with an RNeasy® mini kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: The skin biopsies were immediately immersed in RNAlater® (Qiagen) buffer, were incubated at +4°C for one day, and stored thereafter at -80°C until RNA isolation.

value: skin


title: Patient 7, 3rd post-operative day sample

description: Skin from split thickness skin grafting

source_name: 3rd post-operative day sample


title: Bmi1 embryonic stem cells sample_2 (Bmi1_ESC_2)

city: Aachen

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

country: Germany

institute: Institute for Biomedical Engineering

hyb_protocol: Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

source_name: Bmi1 transduced embryonic stem cells (Bmi1 ES cells).

label_protocol: Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 94°C for 35 minutes in Fragmentatin buffer of the compnay.

growth_protocol: Bmi1 transduced embryonic stem cells were cultured on gelatin coated dish in DMEM medium with 15% FSC and leukemia inhibitory factor (LIF). Lentivirus containing mouse BMI1 cDNA was used to infect CCE ES cells in the presence of 8 microgram polybrene. Empty vector served as control. After two passages eGFP positive CCE ES cells were sorted by flow cytometry and cells were further grown in culture medium as above.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.


title: Patient 7, acute wound sample

description: Skin from split thickness skin grafting

source_name: acute wound sample


title: Empty vector control embryoid body sample_2 (Vector_EB_2)

description: BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).

source_name: Embryoid body formation (10 days) of empty vector transduced embryonic stem cells (CCE ES cells).

growth_protocol: CCE ES cells were cultured on gelatin coated dish in DMEM medium with 15% FSC and leukemia inhibitory factor (LIF). Lentivirus containing mouse BMI1 cDNA was used to infect CCE ES cells in the presence of 8 microgram polybrene. Empty vector served as control. After two passages eGFP positive CCE ES cells were sorted by flow cytometry and cells were further grown in culture medium as above. For differentiation CCE ES cells were subjected to EB assay (10 days).

treatment_protocol: CCE ES cells were trypsinized and subjected to embryoid body (EB) assay in bacterial Petri dish. At day 10 EBs were harvested and total RNA was isolated.


title: Empty vector control embryoid body sample_1 (Vector_EB_1)


title: Bmi1 embryoid body sample_2 (Bmi1_EB_2)

source_name: Embryoid body formation (10 days) of Bmi1 transduced embryonic stem cells (CCE ES cells).


title: Patient 8, acute wound sample

description: Skin from split thickness skin grafting


title: Patient 7, 7th post-operative day sample

description: Skin from split thickness skin grafting

source_name: 7th post-operative day sample


title: Monocyte, control replicate 2

value: healthy


title: Patient 8, 3rd post-operative day sample

description: Skin from split thickness skin grafting


title: Monocyte, control replicate 1


title: Macrophage, stimulated with LPS for 18 hours, replicate 2


title: Macrophage, stimulated with LPS for 18 hours, replicate 1


title: Macrophage, stimulated with LPS for 4 hours, replicate 3


title: Macrophage, stimulated with LPS for 18 hours, replicate 3


title: Macrophage, stimulated with LPS for 4 hours, replicate 2


title: Bmi1 embryoid body sample_1 (Bmi1_EB_1)


title: Empty vector CCE embryonic stem cells (CCE_ESC_Vector)

source_name: Empty vector transduced CCE embryonic stem cells (empty vector CCE ES cells)

growth_protocol: Empty vector transduced CCE embryonic stem cells were cultured on gelatin coated dish in DMEM medium with 15% FSC and leukemia inhibitory factor (LIF). Lentivirus containing mouse BMI1 cDNA was used to infect CCE ES cells in the presence of 8 microgram polybrene. Empty vector served as control. After two passages eGFP positive CCE ES cells were sorted by flow cytometry and cells were further grown in culture medium as above.


title: Macrophage, stimulated with LPS for 4 hours, replicate 1


title: Patient 8, 7th post-operative day sample

description: Skin from split thickness skin grafting


title: Untreated CCE embryonic stem cells (CCE_ESC_Control)

source_name: CCE embryonic stem cells (CCE ES cells).

growth_protocol: CCE embryonic stem cells were cultured on gelatin coated dish in DMEM medium with 15% FSC and leukemia inhibitory factor (LIF). Lentivirus containing mouse BMI1 cDNA was used to infect CCE ES cells in the presence of 8 microgram polybrene. Empty vector served as control. After two passages eGFP positive CCE ES cells were sorted by flow cytometry and cells were further grown in culture medium as above.


title: Bmi1 embryonic stem cells sample_1 (Bmi1_ESC_1)

treatment_protocol: Bmi1 transduced embryonic stem cells were cultured on gelatin coated dish in DMEM medium with 15% FSC and leukemia inhibitory factor (LIF).


title: wt3

city: Bethesda

first: Jennifer

last: Barb

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

description: age-matched (6 months) C57Bl/6J WT controls

hyb_protocol: Biotin-labeled cRNA was then fragmented at 94°C for 35 min with 5X fragmentation buffer  (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45°C.

scan_protocol: Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400.  Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).

data_processing: Affymetrix Microarray Suite version 5.0

source_name: wild type control

label_protocol: Biotin-labeled cRNA was prepared from 1 ug of cDNA using the High Yield RNA Transcript Labeling kit from Enzo Diagnostics (Farmingdale NY).

extract_protocol: Mice were sacrificed between 7 and 8 AM, the hearts quickly removed, weighed, minced, and placed in RNALater solution (Qiagen).  Total RNA was isolated from 45 to 60 mg of heart tissue using the RNeasy Mini kit from Qiagen.  Integrity of total RNA was determined using a 1.2% formaldehyde agarose gel (Ambion, Austin TX).  Double-stranded cDNA was synthesized from total RNA (5-10 ug) using SuperScript Double-Stranded cDNA Synthesis kit.  cDNA was purified via phase lock gel-phenol/chloroform extraction followed by ethanol precipitation.

treatment_protocol: ob/ob mice were fed ad lib and aged to 6 months, at which time they were divided into groups that were leptin repleted, calorie restricted, or continued to be fed ad lib for 1 month

value: ventricular myocardium


title: Dendritic cell, Stimulated with LPS for 18 hours, replicate 1

value: dendritic


title: Dendritic cell, stimulated with LPS for 4 hours, replicate 3


title: Patient 7, intact skin sample

description: Skin from split thickness skin grafting


title: Macrophage, Control (non-stimulated), replicate 1

source_name: Macrophage, Control (non-stimulated)


title: Macrophage, Control (non-stimulated), replicate 2


title: wt1


title: Dendritic cell, Stimulated with LPS for 18 hours, replicate 2


title: Macrophage, Control (non-stimulated), replicate 3


title: Patient 6, 3rd post-operative day sample

description: Skin from split thickness skin grafting


title: Patient 5, 7th post-operative day sample

description: Skin from split thickness skin grafting


title: wt4


title: Dendritic cell, stimulated with LPS for 4 hours, replicate 1


title: oboblep3

description: 1 month of recombinant mouse leptin repletion via osmotic mini-pump in ob/ob mice aged to 6 months

value: C57Bl/6J ob/ob


title: Patient 5, intact skin sample

description: Skin from split thickness skin grafting


title: Patient 5, acute wound sample

description: Skin from split thickness skin grafting


title: Dendritic cell, Stimulated with LPS for 18 hours, replicate 3


title: Patient 4, 7th post-operative day sample

description: Skin from split thickness skin grafting


title: wt2


title: Patient 6, intact skin sample

description: Skin from split thickness skin grafting


title: oboblep4


title: obobcr5

description: 1 month Caloric restriction (imposing pair feeding to leptin repletion) in ob/ob mice aged to 6 months


title: oboblep1


title: Patient 6, 7th post-operative day sample

description: Skin from split thickness skin grafting


title: oboblep5


title: oboblep2


title: Dendritic, control (non-stimulated), replicate 1

source_name: Dendritic, control (non-stimulated)


title: Dendritic cell, stimulated with LPS for 4 hours, replicate 2


title: Control mouse NK cells, isolated from spleen: Replicate 3

tag: isolation source

value: spleen

value: natural killer (NK)

value: Rag1 deficient

value: 6 months


title: Control mouse NK cells, isolated from spleen: Replicate 2


title: Control mouse NK cells, isolated from spleen: Replicate 4


title: Control mouse NK cells, isolated from spleen: Replicate 5


title: Control mouse NK cells, isolated from spleen: Replicate 1


title: obobcr3


title: Patient 4, intact skin sample

description: Skin from split thickness skin grafting


title: Mouse NK cells isolated from B16 melanoma-bearing lymph nodes: Replicate 4

value: B16 melanoma-bearing lymph nodes


title: Mouse NK cells isolated from B16 melanoma-bearing lymph nodes: Replicate 3


title: Mouse NK cells isolated from B16 melanoma-bearing lymph nodes: Replicate 2


title: Patient 3, intact skin sample

description: Skin from split thickness skin grafting


title: Mouse NK cells isolated from B16 melanoma-bearing lymph nodes: Replicate 5


title: Patient 3, 3rd post-operative day sample

description: Skin from split thickness skin grafting


title: polyploidy sample1

city: Cincinnati

first: xinghong

last: ma

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: Biotin-labeled cRNAs were hybridized to GeneChip® mouse gene 1.0 ST array (Affymetrix Inc.).

scan_protocol: Affymetrix GeneChip Scanner 3000 7G used to scan and quantitate the gene chips using default scan settings

data_processing: Differentially expressed genes were selected based on the GeneSpring GX10 program, with a threshold of unpaired t-test (P-value < 0.05), false discovery rate (FDR) < 5%, and a fold change cut off = 2.0.

source_name: pregnancy Day 7 decidual cells

label_protocol: Biotin-labeled cRNAs were generated using the Affymetrix Whole Transcript Sense Target Labeling Assay (Affymetrix)

extract_protocol: RNAs were extracted from polyploid and non-polyploid decidual cell populations using RNeasy Mini Kit according to the manufacturer’s instructions (QIAGEN, Valencia, CA).

treatment_protocol: Deciduomal tissues were separated from the muscle and minced by scalpel blade, and then placed in HBSS containing 0.25 % collagenase, 0.1 % DNase I, and 0.1 % hyaluronidase for 45 min. at 37o C. The enzyme digested tissues were then serially passed through 18, 22, and 25 gauge needles to make a single cell suspension.

value: uterus

value: polyploid

value: female


title: obobcr1


title: obobcr4


title: non-polyploidy sample3

value: non-polyploid


title: polyploidy sample3


title: obobad2

description: 6-month-old ob/ob mice with C57Bl/6J background


title: obobad4


title: Patient 3, acute wound sample

description: Skin from split thickness skin grafting


title: Patient 2, intact skin sample

description: Skin from split thickness skin grafting


title: Patient 2, 3rd post-operative day sample

description: Skin from split thickness skin grafting


title: obobcr2


title: Patient 4, acute wound sample

description: Skin from split thickness skin grafting


title: Mouse NK cells isolated from B16 melanoma-bearing lymph nodes: Replicate 1


title: polyploidy sample2


title: Patient 1, 3rd post-operative day sample

description: Skin from split thickness skin grafting


title: obobad1


title: non-polyploidy sample2


title: non-polyploidy sample1


title: obobad3


title: Patient 1, intact skin sample

description: Skin from split thickness skin grafting