title: A_2253742

first: Bea

last: Wisman

address: PObox 30001

department: Gynecologic Oncology

institute: University Medical Center Groningen

hyb_protocol: Hybridisation was performed according to NimbleGen by ImaGenes service (www.imagenes-bio.de, Berlin, Germany).

scan_protocol: Scanning was performed according to NimbleGen by ImaGenes service (www.imagenes-bio.de, Berlin, Germany).

data_processing: The array signals were expressed as log2 (enriched/input) ratios. The signal distributions within patient groups were quantile normalised and mean-adjusted across groups.

source_name: MeDIP enriched DNA from normal cervix

label_protocol: Fluorescent labelling,was performed according to NimbleGen by ImaGenes service (www.imagenes-bio.de, Berlin, Germany). The input samples were labelled with Cy3 and enriched samples were labelled with Cy5.

extract_protocol: MeDIP assay was performed as described previously (Weber et al, Nat Genet 2005) with the following modifications. DNA samples (5 µg) were sheared to a  size range of 300-1000 bps using a Bioruptor™ UCD-200 (Diagenode). Random fragmented DNA was denaturated at 95°C for 10 min and snapped-cooled on ice for at least 5 min. 4 µg of DNA was immunoprecipitated as described previously (Chavez et al, Genome Res 2010)) using 50 µl  Dynabeads (M-280 sheep anti-mouse IgG, Dynal Biotech) Grimm et al,. In: Turksen K, editor. Human Embryonic Stem Cell Handbook: Methods and Protocols: Springer Protocols Humana Press.)

tag: tissue

value: normal cervix

tag: chip antibody

tag: vendor

value: Eurogentec

tag: catalog/lot#

source_name: input DNA from normal cervix

value: input DNA


title: A_2229132

status: Public on Nov 01 2012

type: genomic

city: Groningen

country: Netherlands

molecule: genomic DNA

organism: Homo sapiens

source_name: MeDIP enriched DNA from CIN3

tag: gender

value: female

tag: age

source_name: input DNA from CIN3


title: genomic DNA from whole blood_1848345023_72970

city: Detroit

first: Michael

middle: A.

last: Tainsky

state: MI

address: 110 E. Warren

department: Department of Oncology, Molecular Biology and Genetics

country: USA

institute: Wayne State University School Of Medicine

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software V3.1.0  (Illumina)

label: Biotin

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA samples were extracted from blood specimens and  bisulfite treated with EZ DNA Methylation Kit (Zymo Research)

tag: study id number

tag: classification for analysis

value: Case_Mutation Neg

value: Female

tag: race

value: White

tag: age at blood sample collection

tag: 1st diagnosis

value: Breast

tag: age at 1st diagnosis

tag: 2nd diagnosis

value: Skin

tag: age at 2nd diagnosis

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).

tag: number of relatives in the family dignosed with breast cancers before age 50


title: genomic DNA from whole blood_1848345023_72925

value: Case_Mutation Pos


title: genomic DNA from whole blood_1848345023_72906

value: Black, African American

value: Ovary

tag: breast and ovarian cancer in same person in the family

value: yes


title: Colorectal carcinoma CRC18 [MCIp]

city: Regensburg

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

country: Germany

institute: University Hospital Regensburg

description: Comparative MCIp-on-Chip for colorectal carcinoma and normal human colon

hyb_protocol: Comparative MCIp hybridizations on CpG island oligonucleotide microarrays (Agilent) were performed using the recommended, stringent protocol (Agilent).

scan_protocol: Scanned on an Agilent scanner at 5 µm resolution. Images were analysed and data extracted using Agilent Feature Extraction Software (version 9.5.1).

data_processing: Linear normalized, background subtracted VALUE data were obtained from log10 transformed, processed Red signal/processed Green signal values derived from image analysis with Agilent Feature Extraction Software (version 9.5.1).  Processed signal intensities were further normalized using GC-dependent regression and imported into Microsoft Office Excel 2007 for further analysis.

label: Alexa Fluor 5–dCTP

source_name: colorectal carcinoma

label_protocol: Enriched methylated DNA fragments of the high-salt MCIp fractions were labeled with Alexa Fluor 5–dCTP (cancer cells) and Alexa Fluor 3–dCTP (normal cells) using the BioPrime Total Genomic Labeling System (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

growth_protocol: Colorectal cancer samples were collected from 9 patients who underwent colon resection for biopsy-proven invasive colorectal adenocarcinoma at the University of Regensburg. The study was performed in agreement with the Institutional ethical review board of the University of Regensburg (05/003). DNA from frozen colon tissues was isolated using the PUREGENE™ DNA Purification Kit (Gentra, Minneapolis, USA) according to the supplier’s recommendation. Three normal colon DNAs (male, age 50-63) were purchased from BioChain Institute Inc. (Hayward, CA)

extract_protocol: MCIp enrichment of methylated DNA was performed essentially as described (Gebhard et al. 2006, Cancer Research). In brief, genomic DNA was sonicated to a mean fragment size of 350-400 bp. Two µg of each sample were incubated with 150 µl Protein A-Sepharose 4 Fast Flow beads (GE Healthcare) coated with 60 µg purified MBD-Fc protein in 2 ml Ultrafree-MC centrifugal filter devices (Amicon/Millipore) for 3 h at 4°C in buffer containing 300 mM NaCl. Beads were centrifuged to recover unbound DNA fragments (300 mM fraction) and subsequently washed with buffers containing increasing NaCl concentrations (400, 500, 550 mM). Densely CpG-methylated DNA was eluted with a high-salt buffer (1000 mM NaCl) and all fractions were desalted using the MinElute PCR purification kit (Qiagen). The separation of CpG methylation densities of individual MCIp fractions was controlled by qPCR using primers covering the imprinted SNRPN

tag: crc location

value: Colon-Ca

tag: ms status

value: microsatellite stable (MSS)

tag: kras- and braf mutational status

value: KRAS-wt; BRAF-wt

label: Alexa Fluor 3–dCTP

source_name: normal colon

value: male

tag: sample

value: normal colon; mixture of three samples (age 50-63)


title: Colorectal carcinoma CRC16 [MCIp]

tag: gender

tag: age

value: Rectum-Ca


title: genomic DNA from whole blood_1848345023_72920

tag: study id number

tag: classification for analysis

tag: race

tag: age at blood sample collection


title: genomic DNA from whole blood_1848345023_72895

tag: 1st diagnosis

tag: age at 1st diagnosis

tag: 2nd diagnosis

tag: age at 2nd diagnosis


title: A_2252892

tag: tissue

value: normal cervix

tag: chip antibody

tag: vendor

value: Eurogentec

tag: catalog/lot#

value: input DNA


title: genomic DNA from whole blood_1848345023_72980

value: Case_Mutation Neg

value: Female

value: DCIS

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).

tag: number of relatives in the family dignosed with breast cancers before age 50

tag: number of the members of the same family (1st degree relatives) on the arrays.

tag: relatives on the array.


title: A_2284682

tag: gender

value: female

tag: age


title: Colorectal carcinoma CRC20 [MCIp]

tag: crc location

value: Sigma-Ca

tag: ms status

tag: kras- and braf mutational status

value: KRAS-mut; BRAF-wt

tag: sample


title: Colorectal carcinoma CRC13 [MCIp]


title: A_2251812

tag: tissue


title: genomic DNA from whole blood_1848345023_72863

tag: study id number

tag: classification for analysis

value: Control_Mutation Neg

tag: race

value: White

tag: age at blood sample collection


title: A_231353

tag: chip antibody

tag: vendor

tag: catalog/lot#


title: genomic DNA from whole blood_1848345023_72862

tag: 1st diagnosis

value: Ovary

tag: age at 1st diagnosis

tag: 2nd diagnosis

value: colon

tag: age at 2nd diagnosis

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).

tag: number of relatives in the family dignosed with breast cancers before age 50


title: A_2281163

tag: gender

tag: tissue

tag: age


title: Colorectal carcinoma CRC12 [MCIp]

tag: crc location

value: Colon-Ca

tag: ms status

value: microsatellite stable (MSS)

tag: kras- and braf mutational status

tag: sample


title: genomic DNA from whole blood_1848345023_72828

tag: study id number

tag: classification for analysis

value: Case_Mutation Pos

tag: race

tag: age at blood sample collection

value: Breast

value: Spindle Cell Sarcoma

tag: number of the members of the same family (1st degree relatives) on the arrays.

tag: relatives on the array.


title: genomic DNA from whole blood_1848345023_72923

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).


title: A_2280622

tag: chip antibody

tag: vendor

value: Eurogentec

tag: catalog/lot#


title: genomic DNA from whole blood_1848345023_72881

value: Control_Mutation Pos

tag: gender

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).

tag: number of relatives in the family dignosed with breast cancers before age 50


title: A_2276712

tag: tissue

tag: age

value: input DNA


title: genomic DNA from whole blood_1848345023_72816

tag: study id number

value: Female


title: A_2313532

value: normal cervix


title: A_230916

value: female


title: genomic DNA from whole blood_1848345023_72806

tag: classification for analysis

value: Case_Mutation Neg

tag: 1st diagnosis

tag: age at 1st diagnosis


title: A_252435


title: A_2283872


title: genomic DNA from whole blood_1848345023_2347

tag: race

tag: age at blood sample collection

tag: 2nd diagnosis

tag: age at 2nd diagnosis

tag: number of the members of the same family (1st degree relatives) on the arrays.


title: A_222904

tag: chip antibody

tag: vendor


title: A_2280672

tag: gender

tag: catalog/lot#


title: A_2524352


title: genomic DNA from whole blood_1848345023_72594

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).

tag: relatives on the array.


title: genomic DNA from whole blood_1848345023_2216

tag: study id number

tag: classification for analysis

tag: number of relatives in the family dignosed with breast cancers before age 50


title: genomic DNA from whole blood_1848345023_3460

tag: race

tag: 1st diagnosis

tag: age at 1st diagnosis


title: A_228388

tag: tissue

tag: age


title: genomic DNA from whole blood_1848345023_72601

tag: age at blood sample collection

tag: 2nd diagnosis

tag: age at 2nd diagnosis

tag: number of the members of the same family (1st degree relatives) on the arrays.


title: genomic DNA from whole blood_1848345023_72565

tag: gender

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).


title: genomic DNA from whole blood_1848345023_72582

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)


title: A_224893

tag: chip antibody

tag: vendor

tag: catalog/lot#


title: genomic DNA from whole blood_1848345023_72902

tag: study id number

tag: classification for analysis

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).

tag: number of relatives in the family dignosed with breast cancers before age 50

tag: relatives on the array.


title: A_227671

tag: tissue

tag: age


title: A_222909


title: Colorectal cancer CRC19 [aCGH]

description: Comparative genomic hybridization of CRC DNA samples against a common reference

hyb_protocol: Labelled samples were hybridized on Human 4x180K CGH SurePrint G3 Microarrays (Agilent, GPL10123) according to the manufacturer’s instructions.

scan_protocol: Images were scanned after washing using a DNA microarray scanner (Agilent)

data_processing: Image data was processed using Feature Extraction Software 10 (Agilent) and analyzed using Agilent Genomic Workbench

label: Cy 5–dUTP

label_protocol: Genome-wide analysis of unbalanced chromosomal changes was done by microarray-based Comparative Genomic Hybridization (aCGH). CRC DNA (1 µg) as well as normal reference DNA (mixed normal human monocytes, 1 µg) were labelled using the Genomic DNA Enzymatic Labeling Kit (Agilent)

extract_protocol:
Colorectal cancer samples were collected from 17 patients who underwent colon resection for biopsy-proven invasive colorectal adenocarcinoma at the University of Regensburg. The study was performed in agreement with the Institutional ethical review board of the University of Regensburg (05/003). DNA from frozen colon tissues was isolated using the PUREGENE™ DNA Purification Kit (Gentra, Minneapolis, USA) according to the supplier’s recommendation.
Human peripheral blood monocytes were separated by leukapheresis of healthy donors followed by density gradient centrifugation over Ficoll/Hypaque and subsequent counter current centrifugal elutriation in a J6M-E centrifuge (Beckman Instruments) or by magnetic bead separation from buffy coats of healthy donors using CD14 antibodies. DNA from monocytes was prepared using Qiagen Blood & Cell Culture DNA Kit. Leukapharesis was performed in agreement with the Institutional ethical review board of the University of Regensburg.

tag: crc location

value: Sigma-Ca

tag: ms status

tag: kras- and braf mutational status

value: KRAS-wt; BRAF-wt

label: Cy 3–dUTP

source_name: normal monocyte

value: male

tag: sample

value: normal monocytes; mixture of six donors


title: genomic DNA from whole blood_1848345023_72569

value: Control_Mutation Neg

tag: gender

tag: race

value: White

tag: age at blood sample collection

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).

tag: number of the members of the same family (1st degree relatives) on the arrays.


title: A_225289

tag: chip antibody

tag: vendor

tag: catalog/lot#


title: Colorectal cancer CRC21 [aCGH]

value: Colon-Ca

value: not available


title: Colorectal cancer CRC16 [aCGH]

value: Rectum-Ca

value: microsatellite stable (MSS)


title: A_225374

value: Eurogentec


title: Colorectal cancer CRC11 [aCGH]


title: genomic DNA from whole blood_1848345023_72568

tag: study id number

tag: classification for analysis

value: Control_Mutation Pos

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).


title: genomic DNA from whole blood_1848345023_3514

tag: number of relatives in the family dignosed with breast cancers before age 50

tag: relatives on the array.


title: Colorectal cancer CRC09 [aCGH]

tag: age

tag: crc location

tag: ms status

tag: kras- and braf mutational status


title: Colorectal cancer CRC12 [aCGH]

tag: gender

value: KRAS-mut; BRAF-wt

tag: sample


title: genomic DNA from whole blood_1848345023_1838

value: Female

tag: race

tag: age at blood sample collection

tag: 1st diagnosis

value: breast

tag: age at 1st diagnosis

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).

tag: number of the members of the same family (1st degree relatives) on the arrays.


title: Colorectal cancer CRC10 [aCGH]

value: female


title: genomic DNA from whole blood_1848345023_3495

tag: study id number

tag: classification for analysis

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).


title: Colorectal cancer CRC20 [aCGH]


title: Colorectal cancer CRC07 [aCGH]


title: Colorectal cancer CRC17 [aCGH]


title: A_228062

tag: tissue

tag: chip antibody

tag: vendor

tag: catalog/lot#

value: input DNA


title: A_228116

value: normal cervix

tag: age


title: genomic DNA from whole blood_1848345023_72364

value: Case_Mutation Neg

value: Ovary

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).

tag: number of relatives in the family dignosed with breast cancers before age 50


title: genomic DNA from whole blood_1848345023_3512

tag: gender

tag: race

value: Head/Face/Neck

tag: 2nd diagnosis

value: Breast, Breast

tag: age at 2nd diagnosis

tag: relatives on the array.


title: Colorectal cancer CRC15 [aCGH]

value: male

tag: crc location

value: Sigma-Ca

tag: ms status

tag: kras- and braf mutational status

tag: sample

value: normal monocytes; mixture of six donors


title: genomic DNA from whole blood_1848345023_170

tag: study id number

tag: classification for analysis

value: Case_Mutation Pos

value: White

tag: age at blood sample collection

tag: 1st diagnosis

value: Breast

tag: age at 1st diagnosis

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).

tag: breast and ovarian cancer in same person in the family

value: yes


title: genomic DNA from whole blood_1848345023_3493

tag: gender

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).

tag: number of relatives in the family dignosed with breast cancers before age 50

tag: number of the members of the same family (1st degree relatives) on the arrays.


title: Colorectal cancer CRC05 [aCGH]

tag: age

tag: crc location

value: Colon-Ca

value: microsatellite stable (MSS)

value: KRAS-wt; BRAF-wt


title: genomic DNA from whole blood_1848345023_2940

value: Female

tag: race


title: A_228067

value: female

tag: tissue

tag: chip antibody

tag: vendor

value: Eurogentec

tag: catalog/lot#

value: input DNA


title: Colorectal cancer CRC06 [aCGH]

tag: ms status

tag: kras- and braf mutational status

value: KRAS-mut; BRAF-wt

tag: sample


title: genomic DNA from whole blood_1848345023_72739

tag: study id number

tag: classification for analysis

value: Case_Mutation Neg

tag: age at blood sample collection

tag: 1st diagnosis

tag: age at 1st diagnosis

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).

tag: relatives on the array.


title: CD14dimCD16+ monocytes donor4

type: RNA

city: PAris

first: Maxime

last: Touzot

address: 26 rue d'ULM

country: France

institute: Institut Curie

description: RMA expression value derived from Genesprings GX 7.3 (Agilent)

hyb_protocol: Labelled DNA was hybrized on the Affymetrix Human Gene 1.1 ST processed on an Affymetrix GeneTitan device.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Statistical analysis were performed using GenSpring GX 7.3 (Agilent). Expression data was normalized using the RMA algorithm. Probes with an expression lower than 25 Units were filtered out.

label: biotin

molecule: total RNA

source_name: Healthy donor4

label_protocol: 100 ng of polysomal-bound RNA were employed to synthesize double-stranded cDNA using 2 successive reverse-transcription reactions according to the std affymetrix protocol

extract_protocol: RNA was extracted using Rneasy Microquit (Qiagen).

tag: cell

value: primary cells

tag: cell population

value: CD14dimCD16+ monocytes


title: genomic DNA from whole blood_1848345023_2730

tag: gender

tag: race

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).

tag: number of relatives in the family dignosed with breast cancers before age 50

tag: number of the members of the same family (1st degree relatives) on the arrays.


title: genomic DNA from whole blood_1848345023_2717


title: genomic DNA from whole blood_1848345023_2716


title: genomic DNA from whole blood_1848345023_2926

value: Control_Mutation Neg


title: genomic DNA from whole blood_848345069_72828

tag: 2nd diagnosis

value: Spindle Cell Sarcoma

tag: age at 2nd diagnosis


title: genomic DNA from whole blood_1848345069_72186

tag: study id number

tag: classification for analysis

value: Case_Mutation Pos

value: BREAST


title: genomic DNA from whole blood_1848345069_72601

value: White

tag: age at blood sample collection

tag: 1st diagnosis

value: Breast


title: Dendritic cells BDCA1 donor4

value: Dendritic cells BDCA1


title: CD14dimCD16+ monocytes donor3

source_name: Healthy donor3


title: CD14+CD16- monocytes donor3

value: CD14+CD16- monocytes


title: CD14+CD16- monocytes donor4


title: Dendritic cells BDCA1 donor3


title: Inflammatory macrophages donor4

source_name: Ovarian cancer donor 4

value: cells isolated from ascites

value: inflammatory macrophages


title: Colorectal cancer CRC02 [aCGH]

value: male

tag: age

tag: crc location

value: Sigma-Ca

tag: ms status

value: microsatellite stable (MSS)

tag: kras- and braf mutational status

tag: sample

value: normal monocytes; mixture of six donors


title: Inflammatory macrophages donor5

source_name: Ovarian cancer donor 5

tag: cell

tag: cell population


title: genomic DNA from whole blood_1848345069_73153

value: Case_Mutation Neg

tag: gender

value: Female

tag: race

tag: age at 1st diagnosis

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)


title: genomic DNA from whole blood_1848345069_73166

tag: study id number

value: Control_Mutation Pos

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).

tag: number of relatives in the family dignosed with breast cancers before age 50


title: Colorectal cancer CRC03 [aCGH]

value: Rectum-Ca

value: KRAS-wt; BRAF-wt


title: Colorectal cancer CRC01 [aCGH]


title: genomic DNA from whole blood_1848345069_73146

tag: classification for analysis

tag: age at blood sample collection

tag: 1st diagnosis

value: breast


title: genomic DNA from whole blood_1848345069_73145

value: Ovary


title: Colorectal cancer CRC04 [aCGH]

tag: age

tag: crc location

tag: ms status

value: KRAS-mut; BRAF-wt


title: Inflammatory Dendritic cells donor5

tag: cell

value: inflammatory Dendritic cells


title: Inflammatory macrophages donor3

source_name: Ovarian cancer donor 3

tag: cell population


title: genomic DNA from whole blood_1848345069_73131

tag: gender

value: White


title: genomic DNA from whole blood_1848345069_73155

tag: race

tag: number of the members of the same family (1st degree relatives) on the arrays.

tag: relatives on the array.


title: genomic DNA from whole blood_1848345069_73138

tag: age at 1st diagnosis

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).


title: genomic DNA from whole blood_1848345069_73130

tag: study id number

value: Case_Mutation Pos

value: Breast

tag: 2nd diagnosis

value: Bone

tag: age at 2nd diagnosis

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).


title: genomic DNA from whole blood_1848345069_73129

tag: classification for analysis

tag: age at blood sample collection

tag: breast and ovarian cancer in same person in the family

value: yes

tag: number of relatives in the family dignosed with breast cancers before age 50


title: Inflammatory Dendritic cells donor3

tag: cell

value: cells isolated from ascites

tag: cell population


title: Inflammatory macrophages donor2

source_name: Ovarian cancer donor 2

value: inflammatory macrophages


title: CD14+CD16- monocytes donor2

source_name: Healthy donor2

value: primary cells

value: CD14+CD16- monocytes


title: genomic DNA from whole blood_1848345069_73125

value: Case_Mutation Neg

tag: gender

value: Female

tag: race

tag: 1st diagnosis


title: genomic DNA from whole blood_1848345069_73124

tag: age at 1st diagnosis


title: Dendritic cells BDCA1 donor2

value: Dendritic cells BDCA1


title: Inflammatory macrophages donor1

source_name: Ovarian cancer donor 1


title: Inflammatory Dendritic cells donor4


title: Inflammatory Dendritic cells donor1


title: CD14dimCD16+ monocytes donor1

source_name: Healthy donor1

value: CD14dimCD16+ monocytes


title: genomic DNA from whole blood_1848345069_73121

value: breast

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).


title: CD14dimCD16+ monocytes donor2


title: genomic DNA from whole blood_1848345069_73113

value: Native American/African American

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).

tag: number of the members of the same family (1st degree relatives) on the arrays.

tag: relatives on the array.


title: genomic DNA from whole blood_1848345069_73112

tag: study id number

value: Control_Mutation Pos


title: Dendritic cells BDCA1 donor1


title: genomic DNA from whole blood_1848345069_73106

value: Black, African American

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)


title: genomic DNA from whole blood_1848345069_73103

value: Control_Mutation Neg

value: White

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).


title: genomic DNA from whole blood_1848345069_73102

tag: classification for analysis

value: breast (DCIS)


title: CD14+CD16- monocytes donor1


title: genomic DNA from whole blood_1848345069_73095

tag: age at blood sample collection

value: Ovary


title: Wildtype_Et_3

city: Leiden

first: Michiel

last: van der Vaart

address: Einsteinweg 55

department: IBL

institute: University of Leiden

description:
Biological replicate 3 of 3: control embryos E. tarda infected
252162610080_S01_GE2_107_Sep09_1_2.txt

hyb_protocol: The dual colour hybridization of the microarray chips was performed at the Microarray Department (MAD) of the University of Amsterdam (Amsterdam, The Netherlands) using the standard Agilent protocol.

scan_protocol: The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies. The arrays were scanned twice with 10% PMT and 100% PMT laser power.

data_processing: Microarray data was processed from raw data image files with Feature Extraction Software 9.5.3.1 (Agilent Technologies). The XDR function was used to extend the dynamic range. Processed data were subsequently imported into Rosetta Resolver 7.0 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. The Agilent Feature Extraction files contain the final log ratio data. The algorithms that were used to normalize the feature signal and calculate the log ratios are described in the Reference Guide for Agilent Feature Extraction Software v9.5. The standard settings as described for the GE2-v5_95 protocol in the Reference Guide were used. In order to calculate the normalized signal, the Rank Consistency Probes method was used and the Linear&LOWESSDyeNormFactor (= DyeNormalSignal/(BGSubSignal x LinearDyeNormFactor) was calculated as described on page 231 of the Reference Guide. The dye normalized signal was calculated as follows (page 232): DyeNormSignal = BGSubSignal x DyeNormFactor. The log10 ratio was subsequently calculated as follows (page 232): LogRatio = Log(rProcessedSignal/gProcessedSignal), where rProcessedSignal and gProcessedSignal are signals post dye normalization and post surrogate processing in the red and green channels, respectively. The surrogate values are calculated and used as the lowest limit of detection to replace the dye normalized signal when either the mean feature signal is less than the background signal or not significant when compared to the background signal, or when the mean signal is less than its background standard deviation (page 226).

organism: Danio rerio

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 ug of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 or Cy5 dye (GE Healthcare) and column purified.

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: Single embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro-injected into the caudal vein with (1) 200 CFU of S. typhimurium SL1027 bacteria suspended in PBS (phosphate-buffered saline), (2)  mock-injected with PBS as a control for S. typhimurium infection, (3) 200 CFU of M. marinum Mma20 bacteria suspended in PBS/2%PVP (polyvinylpyrrolidone), (4) mock-injected with PBS/2%PVP as a control for M. marinum infection, (5) 200 CFU of E. tarda bacteria suspended in PBS/2%PVP, (6) mock-injected with PBS/2%PVP as a control for E. tarda . At 36 hpf (8 h post infection)  three single embryos per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.Additionally, for the M. marinum infection and its control group samples were also taken at 5 dpf (4 d post infection)

tag: common reference

value: The CR was a mixture of all RNA samples from  the E. tarda infection experiment

tag: injection

value: E. tarda

tag: injection site

value: caudal vein

tag: developmental stage

value: 28 hpf

tag: time

value: 8 h post injection


title: genomic DNA from whole blood_1848345069_73099

value: Case_Mutation Neg

tag: gender

tag: race

value: Breast

tag: 2nd diagnosis

value: Skin

tag: age at 2nd diagnosis

tag: number of relatives in the family dignosed with breast cancers before age 50


title: genomic DNA from whole blood_1848345069_73080

value: Female

tag: 1st diagnosis

tag: age at 1st diagnosis

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).

tag: number of the members of the same family (1st degree relatives) on the arrays.


title: genomic DNA from whole blood_1848345069_73074

tag: study id number

tag: classification for analysis

value: Case_Mutation Pos

value: breast

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).


title: Wildtype_Et_2

description:
Biological replicate 2 of 3: control embryos E. tarda infected
252162610079_S01_GE2_107_Sep09_1_4.txt

tag: common reference

tag: injection

tag: injection site


title: genomic DNA from whole blood_1848345069_73115

tag: gender

tag: age at blood sample collection

tag: relatives on the array.


title: genomic DNA from whole blood_1848345069_73083

tag: race


title: Wildtype_Et_1

description:
Biological replicate 1 of 3: control embryos E. tarda infected
252162610078_S01_GE2_107_Sep09_1_1.txt

tag: developmental stage

tag: time


title: Wildtype_PBS-PVP-Et_1

description:
Biological replicate 1 of 3: control embryos PBS/PVP control
252162610078_S01_GE2_107_Sep09_1_4.txt

value: PBS buffer (mock-injected)_control for E. tarda


title: Wildtype_PBS-PVP-Et_3

description:
Biological replicate 3 of 3: control embryos PBS/PVP control
252162610080_S01_GE2_107_Sep09_1_1.txt


title: Wildtype_PBS-PVP-Et_2

description:
Biological replicate 2 of 3: control embryos PBS/PVP control
252162610079_S01_GE2_107_Sep09_1_1.txt


title: genomic DNA from whole blood_1848345069_73090

tag: 1st diagnosis

tag: age at 1st diagnosis

tag: number of relatives in the family dignosed with breast cancers before age 50


title: genomic DNA from whole blood_1848345069_73072

value: Control_Mutation Pos

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).

tag: breast and ovarian cancer in same person in the family

value: yes


title: genomic DNA from whole blood_1848345069_73056

tag: study id number

tag: classification for analysis

value: Black, African American

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)


title: genomic DNA from whole blood_1848345069_73054

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).


title: Inflammatory Dendritic cells donor2

tag: cell

value: cells isolated from ascites

tag: cell population

value: inflammatory Dendritic cells


title: BY4741/pBY_MIG3 rep 1

city: Fayetteville

first: Jeffrey

last: Lewis

state: AR

address: 850 W. Dickson St.

department: Biological Sciences

institute: University of Arkansas

description: BY4741/pBY_MIG3-1 log2 650/550

hyb_protocol: Hybridized for 16 hours on a Maui hybridization machine as per Nimblegen protocol.

scan_protocol: Arrays were scanned using GenePix (4000B from Axon Instruments)

data_processing:
Data were extracted using Nimblescan version 2.6.0.0.  Probes were removed if they fell within 2 standard deviations of the median empty spot value, and background subtraction was performed by subtracting the median empty spot value from remaining probes.  Probe data for each experimental set (YPS163 vs. YPS163mig3∆, BY4741 vs. BY4741mig3∆, BY4741/pBY_MIG3, and YPS163/BY4741mig3∆ vs YPS163mig3∆/BY4742) were quantile normalized together using the bioconductor affy package.  Gene expression change was calculated as the median log2 ratio for all probes completely encompassed by the open reading frame of interest.  For YPS163 arrays, probes with mismatches against the YPS163 genome sequence were excluded.
normalized log2 ratio Cy5/Cy3 or Cy3/Cy5 as noted for dye-swapped samples in the 'description' above.

label: Oyster 550 cyanine dye

organism: Saccharomyces cerevisiae

source_name: BY4741/pEGH grown 8 generations in 2% galactose

label_protocol: Cyanine dyes (Flownamics, Madison, WI) were used; otherwise, as in Gasch, Methods in Enzymology, 2002

growth_protocol: For over-expression in galactose, cells were grown seven doublings in SC (synthetic complete) minus uracil plus 2% galactose to an OD600 of 0.3.

extract_protocol: Hot phenol extraction as in Gasch, Methods in Enzymology, 2002

tag: strain

value: BY4741/pEGH (cloning vector from Open Biosystems Yeast GST-Tagged Collection)

label: Oyster cyanine 650 dye

source_name: BY4741/pBY_MIG3 grown 8 generations in 2% galactose

value: BY4741/pBY_MIG3 (galactose-inducible BY allele of MIG3 from Open Biosystems Yeast GST-Tagged Collection)


title: Wildtype_St_2

description:
Biological replicate 2 of 3: control embryos S.typhimurium infected
252162610085_5u20b_S01_GE2_107_Sep09_1_3.txt

tag: common reference

value: The CR was a mixture of all RNA samples from  the S. typhimurium infection experiment

tag: injection

value: S. typhimurium

tag: injection site

value: caudal vein


title: BY4741/pBY_MIG3 rep 2

description: BY4741/pBY_MIG3-2 log2 550/650


title: YPS163mig3∆/BY4742 rep 2

description: YPS163mig3d/BY4742-2 log2 550/650

source_name: YPS163 grown 4 generations and collected

growth_protocol: Cells were grown in YPD (2% peptone, 2% dextrose, 1% yeast extract) for 4 generations to an OD600 of 0.3.

value: YPS163 (MATa ho::Hyg)

source_name: YPS163mig3∆/BY4742 grown 4 generations

value: YPS163mig3∆/BY4742 hybrid


title: genomic DNA from whole blood_1848345069_73030

source_name: whole blood

tag: gender

tag: race

value: White

tag: age at blood sample collection

value: Melanoma

tag: 2nd diagnosis

value: Breast

tag: age at 2nd diagnosis


title: BY4741/pBY_MIG3 rep 3

description: BY4741/pBY_MIG3-3 log2 650/550


title: Wildtype_St_3

description:
Biological replicate 3 of 3: control embryos S.typhimurium infected
252162610084_5u20b_S01_GE2_107_Sep09_1_1.txt

tag: developmental stage

value: 28 hpf

tag: time

value: 8 h post injection


title: Wildtype_PBS-St_3

description:
Biological replicate 3 of 3: control embryos PBS control
252162610084_5u20b_S01_GE2_107_Sep09_1_2.txt

value: PBS buffer (mock-injected)_control for S. typhimurium


title: Wildtype_PBS-St_2

description:
Biological replicate 2 of 3: control embryos PBS control
252162610086_5u20b_S01_GE2_107_Sep09_1_2.txt


title: Wildtype_PBS-St_1

description:
Biological replicate 1 of 3: control embryos PBS control
252162610085_5u20b_S01_GE2_107_Sep09_1_4.txt


title: genomic DNA from whole blood_1848345069_73025

tag: study id number

value: Case_Mutation Neg

value: Female

tag: 1st diagnosis

value: breast

tag: age at 1st diagnosis

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).

tag: number of relatives in the family dignosed with breast cancers before age 50


title: genomic DNA from whole blood_1848345069_73020

tag: classification for analysis

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).


title: genomic DNA from whole blood_1848345069_73035

value: Case_Mutation Pos

value: Ovary

tag: breast and ovarian cancer in same person in the family

value: yes


title: genomic DNA from whole blood_1848345069_1049

tag: gender


title: genomic DNA from whole blood_1848345069_72082

tag: race

value: DCIS


title: genomic DNA from whole blood_1848345069_73026

tag: age at blood sample collection


title: genomic DNA from whole blood_1848345069_73038


title: genomic DNA from whole blood_1848345069_73021


title: genomic DNA from whole blood_1848345069_73039

value: Control_Mutation Neg


title: genomic DNA from whole blood_1848345069_72975


title: YPS163/BY4741mig3∆ rep 2

description: YPS163/BY4741mig3d-2 log2 550/650

tag: strain

source_name: YPS163/BY4741mig3∆ grown 4 generations and collected

value: YPS163/BY4741mig3∆ hybrid


title: BY4741mig3∆ EtOH 30 min rep3

description: BY4741mig3d-3 log2 650/550

source_name: BY4741mig3∆ grown 4 generations and collected

growth_protocol: Cells were grown in YPD (2% peptone, 2% dextrose, 1% yeast extract) for 4 generations to an OD600 of 0.3.  A sample of unstressed cells was collected directly prior to ethanol treatment.

treatment_protocol: Ethanol was added to a final concentration of 5% (v/v) for 30 min

value: BY4741 (MATa his3∆1 leu2∆0 met15∆0 ura3∆0 mig3∆::Kan)

source_name: BY4741mig3∆ grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected


title: YPS163mig3∆/BY4742 rep 1

description: YPS163mig3d/BY4742-1 log2 650/550

value: YPS163mig3∆/BY4742 hybrid

value: YPS163 (MATa ho::Hyg)


title: genomic DNA from whole blood_1848345069_73009

value: Black, African American


title: BY4741mig3∆ EtOH 30 min rep2

description: BY4741mig3d-2 log2 550/650


title: BY4741mig3∆ EtOH 30 min rep1

description: BY4741mig3d-1 log2 650/550


title: YPS163/BY4741mig3∆ rep 1

description: YPS163/BY4741mig3d-1 log2 650/550


title: BY4741 EtOH 30 min rep1

description: BY4741-1 log2 650/550

source_name: BY4741 grown 4 generations and collected

value: BY4741 (MATa his3∆1 leu2∆0 met15∆0 ura3∆0)

source_name: BY4741 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected


title: BY4741 EtOH 30 min rep2

description: BY4741-2 log2 550/650


title: Wildtype_St_1

description:
Biological replicate 1 of 3: control embryos S.typhimurium infected
252162610086_5u20b_S01_GE2_107_Sep09_1_3.txt

tag: common reference

value: The CR was a mixture of all RNA samples from  the S. typhimurium infection experiment

tag: injection

value: S. typhimurium

tag: injection site

value: caudal vein

value: 28 hpf


title: YPS163mig3∆ EtOH 30 min rep 3

description: YPS163mig3d-3 log2 650/550

source_name: YPS163mig3∆ grown 4 generations and collected

value: YPS163 (MATa ho::Hyg mig3∆::Kan)

source_name: YPS163mig3∆ grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected


title: genomic DNA from whole blood_1848345069_72979

tag: study id number

value: Female

value: White


title: genomic DNA from whole blood_1848345069_612

value: Case_Mutation Pos

tag: 1st diagnosis

value: Melanoma

tag: 2nd diagnosis

value: Breast

tag: age at 2nd diagnosis

tag: number of the members of the same family (1st degree relatives) on the arrays.

tag: relatives on the array.


title: genomic DNA from whole blood_1848345069_72976

tag: classification for analysis

tag: age at 1st diagnosis

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).

tag: number of relatives in the family dignosed with breast cancers before age 50


title: YPS163mig3∆ EtOH 30 min rep 2

description: YPS163mig3d-2log2 550/650


title: genomic DNA from whole blood_1848345069_72970

value: Case_Mutation Neg

tag: gender

tag: race

value: Skin

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).


title: YPS163mig3∆ EtOH 30 min rep 1

description: YPS163mig3d-1 log2 650/550

tag: strain


title: genomic DNA from whole blood_1848345069_2213

tag: age at blood sample collection

tag: breast and ovarian cancer in same person in the family

value: yes


title: BY4741 EtOH 30 min rep3

description: BY4743-3 log2 650/550


title: genomic DNA from whole blood_1848345069_72925

tag: study id number

tag: 1st diagnosis


title: genomic DNA from whole blood_1848345069_72666

value: breast

tag: 2nd diagnosis

tag: age at 2nd diagnosis


title: YPS163 EtOH 30 min rep 1

description: YPS163-1 log2 650/550

value: YPS163 (MATa ho::Hyg)

source_name: YPS163 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected


title: genomic DNA from whole blood_1848345069_72906

value: Black, African American

value: Ovary


title: YPS163 EtOH 30 min rep 3

description: YPS163-3 log2 650/550


title: genomic DNA from whole blood_1848345069_72920


title: (p)ppGpp0 Cells Replicate 3

city: Houston

first: Jue

middle: D.

last: Wang

state: TX

address: 1 Baylor Plaza, Rm T932

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Biological replicate 3 of 3.(p)ppGpp0 cells untreated

hyb_protocol: The procedure for hybridization was performed as described previously (Britton et al., 2002).

scan_protocol: Scanned on a GenePix 4000B Scanner (Axon Instruments).

data_processing: GenePix Pro (v 6.1) was used for background subtraction and normalization.

organism: Bacillus subtilis

source_name: SMY delta yjbM delta ywaC delta relA

label_protocol: The procedures for reverse transcription and labeling were performed as described previously (Britton et al., 2002).

growth_protocol: Cells were grown in S7 defined medium (Vasantha and Freese, 1980); MOPS was used at 50 mM rather than 100 mM, supplemented with 0.1% glutamate, 1% glucose, and 0.5% casamino acids at 37°C with shaking.

extract_protocol: RNA was extracted using QIAGEN RNeasy Mini Kit following manufacturer's instructions.

treatment_protocol: At OD600~0.3, arginine hydroxamate was added to a final concentration of 0.5mg/ml, cells were collected 20 minutes later.

value: SMY delta yjbM delta ywaC delta relA

tag: treatment

value: No treatment

source_name: pooled reference RNA

tag: genotype

value: wild-type

tag: reference

value: Pooled RNA from mixture of the same amount of wt standards


title: (p)ppGpp0 Cells Replicate 2

description: Biological replicate 2 of 3. (p)ppGpp0 cells untreated


title: genomic DNA from whole blood_1848345069_72827

tag: classification for analysis

tag: age at 1st diagnosis

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).


title: RHX-treated (p)ppGpp0 Cells Replicate 1

description: Biological replicate 1 of 3. (p)ppGpp0 cells treated with RHX

value: 0.5mg/ml RHX for 20min


title: genomic DNA from whole blood_1848345069_948

tag: gender

value: Female

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).

tag: number of relatives in the family dignosed with breast cancers before age 50


title: genomic DNA from whole blood_1848345069_72895

tag: race

value: White

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).


title: RHX-treated (p)ppGpp0 Cells Replicate 3

description: Biological replicate 3 of 3. (p)ppGpp0 cells treated with RHX

tag: strain


title: genomic DNA from whole blood_1848345069_72887

tag: study id number

tag: age at blood sample collection

value: breast (DCIS)


title: YPS163 EtOH 30 min rep 2

description: YPS163-2 log2 550/650


title: genomic DNA from whole blood_1848345069_72935

value: Case_Mutation Pos

tag: 1st diagnosis


title: genomic DNA from whole blood_1848345069_116

value: Breast


title: RHX-treated Wild-type Cells Replicate 3

description: Biological replicate 3 of 3. WT cells treated with RHX

source_name: SMY

value: SMY wild-type


title: genomic DNA from whole blood_1848345069_72881

value: Control_Mutation Pos

tag: number of the members of the same family (1st degree relatives) on the arrays.

tag: relatives on the array.


title: RHX-treated Wild-type Cells Replicate 1

description: Biological replicate 1 of 3. WT cells treated with RHX

tag: treatment

tag: genotype


title: RHX-treated (p)ppGpp0 Cells Replicate 2

description: Biological replicate 2 of 3. (p)ppGpp0 cells treated with RHX

tag: reference


title: (p)ppGpp0 Cells Replicate 1

description: Biological replicate 1 of 3. (p)ppGpp0 cells untreated


title: Wild-type Cells Replicate 3

description: Biological replicate 3 of 3.WT cells untreated


title: genomic DNA from whole blood_1848345069_72806

tag: classification for analysis

value: Case_Mutation Neg

tag: age at 1st diagnosis


title: Wild-type Cells Replicate 2

description: Biological replicate 2 of 3. WT cells untreated


title: genomic DNA from whole blood_1848345069_72820

tag: gender

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).


title: genomic DNA from whole blood_1848345069_72729

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).

tag: number of relatives in the family dignosed with breast cancers before age 50


title: genomic DNA from whole blood_1848345069_72730

tag: race

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)


title: Wild-type Cells Replicate 1

description: Biological replicate 1 of 3. WT cells untreated

tag: strain


title: genomic DNA from whole blood_1848345069_2089

tag: study id number

value: breast

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).


title: genomic DNA from whole blood_1848345069_72773

tag: age at blood sample collection


title: genomic DNA from whole blood_1848345069_2216

tag: 1st diagnosis

tag: 2nd diagnosis

tag: age at 2nd diagnosis


title: RHX-treated Wild-type Cells Replicate 2

description: Biological replicate 2 of 3. WT cells treated with RHX

tag: treatment

tag: genotype


title: genomic DNA from whole blood_1848345069_72708

tag: classification for analysis


title: genomic DNA from whole blood_1848345069_72722

value: Control_Mutation Neg


title: genomic DNA from whole blood_1848345069_72902

tag: number of the members of the same family (1st degree relatives) on the arrays.

tag: relatives on the array.


title: genomic DNA from whole blood_1848345069_2940

tag: gender

tag: age at 1st diagnosis

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).


title: genomic DNA from whole blood_1848345069_72290

tag: race

value: ovary

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).

tag: breast and ovarian cancer in same person in the family

value: yes

tag: number of relatives in the family dignosed with breast cancers before age 50


title: genomic DNA from whole blood_1848345069_2730

tag: study id number

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).


title: skeletal muscle, NM 5

city: Gaithersburg

first: Wei

last: Zhu

state: Md

address: One MedImmune Way

department: Translational Sciences

institute: MedImmune

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HGU133 Plus 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed using fRMA normalization.

source_name: Quadriceps

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Open muscle biopsies was performed at the time of a diagnostic biopsy  and immediately frozen in liquid nitrogen.  RNA was extracted from muscle biopsies using the mirVana miRNA Isolation kit (Applied Biosystems/Ambion, Austin, TX).

tag: age (y)

value: M

tag: disease state

value: necrotizing myopathy NM

tag: tissue

value: Quadriceps


title: genomic DNA from whole blood_1848345069_2717

tag: age at blood sample collection

tag: 1st diagnosis


title: skeletal muscle, IBM 9

value: Inclusion body myositis IBM


title: skeletal muscle, PM 8

source_name: Biceps

value: F

value: Polymyositis PM

value: Biceps


title: skeletal muscle, IBM 10


title: genomic DNA from whole blood_1848345069_2928

tag: classification for analysis

value: Female

value: White


title: genomic DNA from whole blood_1848345069_2719

value: Case_Mutation Pos

value: Breast


title: skeletal muscle, DM 8

value: Dermatomyositis DM (with PFA)


title: skeletal muscle, DM 5

source_name: Deltoid

value: Dermatomyositis DM

value: Deltoid


title: skeletal muscle, DM 6


title: skeletal muscle, IBM 6


title: skeletal muscle, NM 4


title: skeletal muscle, IBM 8


title: skeletal muscle, DM 7


title: skeletal muscle, IBM 7


title: skeletal muscle, IBM 5


title: skeletal muscle, DM 4


title: skeletal muscle, IBM 3


title: skeletal muscle, IBM 2


title: skeletal muscle, PM 5


title: skeletal muscle, PM 7


title: skeletal muscle, PM 6


title: skeletal muscle, DM 3


title: skeletal muscle, DM 2


title: skeletal muscle, PM 4


title: skeletal muscle, NM 2


title: skeletal muscle, IBM 1


title: 32D-miR-9/9* IL-3 #3

city: Rotterdam

first: Su Ming

last: Sun

address: Dr. Molewaterplein 50

department: Hematology

institute: Erasmus University Medical Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Mus musculus

source_name: Myeloid murine cell line, 32D

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

growth_protocol: Cells were grown with density between 1E5/ml and 1E6/ml in RPMI supplemented with 10% FCS, Pen/Strep (100 IU/ml; 100 µg/ml) and murine IL-3 (10 ng/ml).

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

treatment_protocol: Not applicable

tag: cell line

tag: expression construct


title: 32D-miR-9/9* IL-3 #1


title: 32D-miR-9/9* IL-3 #2


title: skeletal muscle, NM 3

tag: gender


title: skeletal muscle, IBM 4


title: skeletal muscle, PM 3


title: skeletal muscle, PM 2


title: 32D-EV IL-3 #2


title: Bd-Tryp5

city: Berkeley

first: Thomas

last: Poorten

state: CA

address: 54 Mulford Hall

department: Environmental Science, Policy, and Management

institute: UC Berkeley

hyb_protocol: All samples were hybridized to a single 12-plex chip to reduce technical noise. An 18-hour hybridization was conducted at 42 degrees in a NimbleGen Hybridization System 4 chamber (NimbleGen, Madison, WI). The chip was washed in an automated MAUI Wash System (BioMicro Systems, Salt Lake City, UT)

scan_protocol: The chip was scanned on an Axon GenePix 4000B Scanner (Molecular Devices, Sunnyvale, CA) using GenePix Pro v6.1 software (Molecular Devices, Sunnyvale, CA).

data_processing: NimbleScan v2.5 software (NimbleGen. Madison, WI) was used to align a chip-specific grid to control features and extract raw intensity data for each probe and each array. Chip images were then visually checked for each array and verified not to contain any significant spatial artifacts. Raw intensity data was then read into the R statistical computing environment (www.R-project.org) and checked for quality. Further, chip intensity distributions, boxplots, and hierarchical clusters were compared and checked for any unusual global patterns. Each array was then background corrected and normalized using the quantile normalization procedure. Finally each probe set was summarized using the median polish procedure as described with the robust multichip average (RMA) procedure (Bolstad et al 2003, Irizarry et al 2003). The median polish procedure is a robust method for summarizing all probes contained within each probe set to a single expression value for each gene taking into account individual probe effects. Probe sets with particularly low (IQR < 0.5) or particularly high (IQR>1.0) levels of expression variation across all samples were removed from further analysis, reducing the overall number of statistical tests to be performed.

organism: Batrachochytrium dendrobatidis JAM81

label_protocol: Double-stranded cDNAs were synthesized using Invitrogen’s SuperScript cDNA Synthesis Kit with the standard protocol using oligo dT primers (Invitrogen, Carlsbad, CA). cDNAs were fluorescently labeled with Cy5 from TRILink BioTechnologies (TRILink BioTechnologies, San Diego, CA) using the standard NimbleGen Gene Expression Analysis v3.2 protocol.

growth_protocol: We used a 250mL flask containing 100mL nutrient broth for each replicate. Each flask was inoculated with approximately 5 x 106 zoospores. Flasks were incubated for 2 weeks at room temperature under agitation. At the end of the experimental period, a sample from each flask was checked for live Bd under magnification. Samples were then washed 3 times with sterile DI water, pelleted, frozen in RNAlater buffer (Ambion, Life Technologies, Grand Island, NY), and stored at -80C.

extract_protocol: RNA was isolated with Trizol/Chloroform (Invitrogen, Carlsbad, CA) with a standard protocol and DNase digestion (Ambion Turbo DNA-free DNase, Austin, TX).

treatment_protocol: Each Bd isolate was then grown under two nutrient conditions: 1% liquid tryptone and 1% pulverized frog skin. The 1% tryptone broth was prepared with DI water, aliquoted, and autoclaved before inoculation with Bd. The preparation of the 1% frog skin broth was more involved to ensure that frog skin proteins remained intact and to eliminate microbial contaminants. We ground cane-toad (Bufo marinus) skin in liquid nitrogen with a mortar and pestle. We did not autoclave the skin so as not to denature host proteins. Instead we sterilized the skin by submerging in 95% ethanol for 10 minutes, washed the skin 5 times in sterile DI water, submerged skin in 10% hydrogen peroxide, and washed the skin 5 more times in sterile DI water. We then made our final 1% solution of frog skin in DI water and subjected the solution to UV radiation for 1 hour.

tag: strain

tag: subarray


title: skeletal muscle, NM 1


title: Bd-Tryp4

organism: Batrachochytrium dendrobatidis


title: Bd-Tryp6


title: Bd-Frog6


title: 32D-EV IL-3 #1


title: DNA11091-067A Whole blood sample, SLE patient 26

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

country: Belgium

institute: Université catholique de Louvain

description:
Whole blood sample, SLE patient
DNA11091-067A

hyb_protocol: Labeled RNA was hybridized to GeneChip® HumanGenome U133 Plus 2.0 Arrays (Affymetrix).

scan_protocol: The slides were washed and stained on a GeneChip® Fluidics Station (Affymetrix) and scanned using a GeneChip® Scanner 3000 (Affymetrix).

data_processing:
One SLE patient was excluded from gene expression analysis because of a missing baseline sample. All the analyses displayed in the manuscript were repeated using extrapolated baseline data for this patient (based on expression data of a day 38 whole blood sample), and delivered the same results. Also, a SLE patient who had a disease flare before receiving a second dose of IFN-K was excluded from the analysis at days 84, 112, and 168. One placebo-treated patient received high-dose oral and intravenous steroids between days 112 and 168, so her day 168 samples were excluded from the analysis. Thus, valid gene expression profiles were obtained for 26 SLE patients at baseline, 26 at day 112, and 26 at day 168. Valid gene expression profiles were also obtained for 46 of the 50 healthy volunteers (4 with a RNA integrity number < 6 were excluded) and for all 18 IFNalpha-stimulated healthy volunteer samples.
Fluorescence intensity data were normalized by robust multiarray analysis (RMA) using GeneSpring® (Agilent Technologies, Santa Clara, CA).

source_name: SLE Patient, IFN-K 240 microgram, 4 injections, baseline

label_protocol: RNA was labeled using a One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA)

extract_protocol: RNA was extracted from blood samples (controls, IFN-stimulated controls and SLE patients at days 0, 112 and 168) using a Paxgene Blood RNA kit (Qiagen) according to the manufacturer's instructions. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies, Santa Clara, CA). Samples with a RNA integrity number < 6 were discarded.

treatment_protocol: SLE patients were treated with IFN K or an equivalent volume of 0.9% NaCl (placebo), both mixed with an equal volume of ISA-51vg adjuvant (Seppic, Paris, France). IFN-K was prepared by crosslinking recombinant human IFNalpha2b with KLH. Subjects were randomized to treatments using an interactive web response system, and both subjects and investigators were blinded to the treatment type. All treatments were delivered by intramuscular injection. A first group of four subjects was randomized 3:1 to receive 30 microgram IFN K or placebo in a volume of 0.15 ml. The second, third, and fourth groups each included eight subjects each who were randomized 3:1 to receive, respectively, 60 microgram IFN K or placebo in 0.3 ml, 120 microgram IFN K or placebo in 0.6 ml, and 240 microgram IFN K or placebo in two injections of 0.6 ml. Safety data were reviewed by an independent medical safety board after 48 hours and before administering the first dose to the next group. All groups received a second dose of IFN K or placebo on day 7 and a third dose of IFN K or placebo on day 28. On day 84, four subjects in each of the 60-, 120-, or 240- microgram IFN K groups received a fourth dose of IFN K or placebo if the independent medical safety board decided there were no safety issues from the previous dose of IFN K and if human IFNalpha-neutralizing antibodies were not detected at day 56 in at least two of the first four subjects at the specific dose.

value: SLE

tag: treatment

value: IFN-K 240 microgram, 4 injections

tag: day

value: Whole blood

tag: ethnicity

value: Caucasian

tag: age


title: DNA11091-137A Whole blood sample, SLE patient 26

description:
Whole blood sample, SLE patient
DNA11091-137A

source_name: SLE Patient, IFN-K 240 microgram, 4 injections, day 112


title: Bd-Frog5


title: Bd-Frog2


title: DNA11159-012A Whole blood sample, SLE patient 26

description:
Whole blood sample, SLE patient
DNA11159-012A

source_name: SLE Patient, IFN-K 240 microgram, 4 injections, day 168


title: Bd-Frog4


title: skeletal muscle, PM 1

value: M


title: Bd-Tryp2


title: DNA11159-018A Whole blood sample, SLE patient 25

description:
Whole blood sample, SLE patient
DNA11159-018A


title: Bd-Frog3


title: Bd-Frog1

value: SWII


title: Bd-Tryp1


title: DNA11091-147A Whole blood sample, SLE patient 25

description:
Whole blood sample, SLE patient
DNA11091-147A


title: P47KO hfd pool3

city: Little Rock

first: Horacio

last: Gomez-Acevedo

state: Arkansas

address: 4301 W. Markham St

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

description:
abdominal fat gene expression
Groups of C57BL/6 and P47KO  female mice were fed casein or high fat diet starting at post-natal day (PND) 28. After 13 weeks the mice were sacrifized and abdominal fat pads were collected and fresh frozen in liquid nitrogen.
Abdominal fat pads were collected and fresh frozen in liquid nitrogen

hyb_protocol: Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N = 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.

scan_protocol: The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.

data_processing:
Cel files were generated using GCOS and utilized for analysis using GeneSpring  v 11.5.1
RMA normalization was utilized to generated values using GeneSpring v 11.5.1

source_name: abdominal fat pads

label_protocol: First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA  reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions

extract_protocol: Total fat pads RNA was isolated from the rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion

value: High fat diet

value: female

value: abdominal fat pads

tag: genetic background

tag: genotype

value: p47phox null


title: proB wt rep2

city: Lund

first: Robert

last: Månsson

address: Klinikgatan 26, BMC B12

department: Hemapotoietic stem cell biology

country: Sweden

institute: Lund University

description: Expression profiling of proB cells derived from wild-type mice.

hyb_protocol: cRNA fragments hybridized against MOE430 2.0 Affymetrix gene expression arrays chip according to manufacturer instructions

scan_protocol: Chips were scanned using a GeneChip TM Scanner 3000

data_processing: Expression values were acquired using RMA and custom CDF files (Brainarray, ENTREZG_14.1.0).

source_name: proB wt

label_protocol: RNA was labelled and amplified according to Affymetrix TM GeneChip Expression Analysis Technical Manual 2011

growth_protocol: Cells obtained fresh from the bone marrow of mice.

extract_protocol: RNeasy Micro kit (Qiagen) has been used to extract RNA according to manufacturer instruction

treatment_protocol: No treatment has been used.

tag: tissue type

value: bone marrow

tag: genotype/variation

value: wild-type

tag: facs-sorting


title: P47KO hfd pool1

tag: tissue


title: proB wt rep1


title: P47KO hfd pool2


title: DNA11091-079A Whole blood sample, SLE patient 25

description:
Whole blood sample, SLE patient
DNA11091-079A

tag: disease state

value: Female


title: DNA11091-140A Whole blood sample, SLE patient 24

description:
Whole blood sample, SLE patient
DNA11091-140A


title: CLP LY6D+ FOXO1wt rep2

description: Expression profiling of LY6D- CLPs derived from Foxo1 wild-type mice.

source_name: CLP LY6D+ FOXO1 wt


title: Wild type hfd pool2

value: wild type


title: DNA11159-010A Whole blood sample, SLE patient 24

description:
Whole blood sample, SLE patient
DNA11159-010A


title: Wild type hfd pool1


title: Bd-Tryp3


title: 32D-EV IL-3 #3


title: CLP LY6D+ FOXO1wt rep1


title: P47KO casein pool3

value: Casein


title: CLP LY6D+ FOXO1ko rep2

description: Expression profiling of LY6D- CLPs derived from Foxo1 deficient mice.

source_name: CLP LY6D+ FOXO1 ko

value: Foxo1 knock-out


title: CLP LY6D+ FOXO1ko rep1


title: CLP LY6D+ EBF1wt rep2

description: Expression profiling of LY6D- CLPs derived from Ebf1 wild-type mice.

source_name: CLP LY6D+ EBF1 wt


title: P47KO casein pool2


title: DNA11091-071A Whole blood sample, SLE patient 24

description:
Whole blood sample, SLE patient
DNA11091-071A


title: DNA11091-168A Whole blood sample, SLE patient 23

description:
Whole blood sample, SLE patient
DNA11091-168A

source_name: SLE Patient, IFN-K 240 microgram, 3 injections, day 168

value: IFN-K 240 microgram, 3 injections


title: CLP LY6D+ EBF1wt rep1


title: P47KO casein pool1


title: mouse_14m_Heart

city: Kodaira

first: Hirohiko

last: Hohjoh

state: Tokyo

address: 4-1-1 Ogawahigashi

country: Japan

institute: National Institute of Neuroscience, NCNP

hyb_protocol: Hybridization was carried out with the Genopal®-MICM DNA chips (Mitsubishi Rayon) for detection of mouse miRNAs in 100 µl of hybridization buffer [6 x SSC, 0.2% SDS and 1 µg of heat-denatured labeled RNAs] at 42℃ overnight using a hybridization chamber specific for the Genopal®-DNA chip (Mitsubishi Rayon).

scan_protocol: After hybridization, the DNA chips were washed twice in 2xSSC containing 0.2% SDS at 50℃ for 20 min followed by washing in 2xSSC at 50℃ for 10 min, and then hybridization signals were examined by means of a DNA chip reader adopting multi-beam excitation technology according to the manufacturer’s instructions (Yokogawa Electric Corporation).

data_processing: Hybridization signal intensity of each miRNA was normalized to that of the external control oligonucleotides provided by Mitsubishi Rayon.

source_name: ICR mouse Heart

label_protocol: Isolated small-sized RNAs (~1 µg) were subjected to direct labeling with a fluorescent dye using a PlatinumBright 647 Infrared nucleic acid labeling kit (KREATECH), according to the manufacturer’s instructions. After fluorescent labeling, the labeled RNAs were purified from free fluorescent substrates by the KREApure columns (KREATECH) and used in hybridization.

extract_protocol: Total RNAs were extracted from various tissues using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. For preparation of cellular miRNAs, 20 µg of each isolated total RNA was mixed with 5 µl of the external control oligonucleotides provided by Mitsubishi Rayon, and subjected to isolation of small-sized RNAs containing miRNAs using an RNeasy MinElute Cleanup kit (Qiagen).

tag: background strain

value: ICR

tag: Sex

value: male

value: Heart


title: mouse_14m_Kidney

source_name: ICR mouse Kidney

value: Kidney


title: CLP LY6D+ EBF1ko rep2

description: Expression profiling of LY6D- CLPs derived from Ebf1 deficient mice.

source_name: CLP LY6D+ EBF1 ko

value: Ebf1 knock-out


title: mouse_1m_Kidney


title: CLP LY6D+ EBF1ko rep1


title: mouse_14m_Liver

source_name: ICR mouse Liver

value: Liver


title: mouse_1m_Heart


title: Wild type casein pool2


title: DNA11091-166A Whole blood sample, SLE patient 22

description:
Whole blood sample, SLE patient
DNA11091-166A

source_name: SLE Patient, IFN-K 240 microgram, 3 injections, day 112

value: SLE

value: Whole blood

value: Caucasian


title: DNA11091-061A Whole blood sample, SLE patient 22

description:
Whole blood sample, SLE patient
DNA11091-061A

source_name: SLE Patient, IFN-K 240 microgram, 3 injections, baseline


title: DNA11091-161A Whole blood sample, SLE patient 23

description:
Whole blood sample, SLE patient
DNA11091-161A


title: mouse_1m_Liver


title: DNA11091-052A Whole blood sample, SLE patient 23

description:
Whole blood sample, SLE patient
DNA11091-052A


title: CLP LY6D- FOXO1wt rep1

source_name: CLP LY6D- FOXO1 wt


title: mouse_1m_Lung

source_name: ICR mouse Lung

value: Lung


title: mouse_14m_Lung


title: CLP LY6D- FOXO1wt rep2

value: bone marrow


title: DNA11091-152A Whole blood sample, SLE patient 22

description:
Whole blood sample, SLE patient
DNA11091-152A


title: Wild type casein pool3

value: female

value: abdominal fat pads


title: Wild type casein pool1

value: wild type


title: 5W_wild-type_Spleen_2

hyb_protocol: Hybridization was carried out with Genopal®-MICM DNA chips (Mitsubishi Rayon) for detection of mouse miRNAs in 100 µl of hybridization buffer [6 x SSC, 0.2% SDS and 1 µg of heat-denatured labeled RNAs] at 42℃ overnight using a hybridization chamber specific for the Genopal®-DNA chip (Mitsubishi Rayon).

source_name: wild-type Spleen

value: wild-type

value: Spleen


title: DNA10204-307A Whole blood sample, SLE patient 21

description:
Whole blood sample, SLE patient
DNA10204-307A

source_name: SLE Patient, IFN-K 120 microgram, 4 injections, baseline

value: IFN-K 120 microgram, 4 injections

value: Female


title: Joint tissue-time 16 weeks-DMM-replicate 1

city: Winston-Salem

first: Richard

middle: F.

last: Loeser

state: NC

address: Medical Center Blvd.

department: Molecular Medicine

institute: Wake Forest School of Medicine

description:
Gene expression data from DMM joints 16 weeks after surgery
DMM16_pool1

hyb_protocol: Following fragmentation, 10 ug of labeled cRNA was hybridized for 16 hr at 45oC on the Affymetrix GeneChips. GeneChips were washed and stained using the GeneChip 450 Fluidics Station according to standard Affymetrix operating procedures (GeneChip Expression Analysis Technical Manual, v.3, 2005, Affymetrix)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G system according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, v.3, 2005, Affymetrix)

data_processing: The data were normalized using the Systematic Variation Normalization method (PMID 15852502; http://www.niehs.nih.gov/research/resources/software/biostatistics/svn/index.cfm).

source_name: Joint tissue-16 weeks after DMM surgery

label_protocol: Approximately 5ug of purified total RNA was processed to produce biotinylated cRNA targets according to the standard Affymetrix 3’-IVT labeling protocol (GeneChip Expression Analysis Technical Manual, v.3, 2005, Affymetrix)

extract_protocol: RNA was extracted from the tissue by homogenization in RNA extraction solution (UltraClean®Tissues and Cells RNA isolation kit from MO BIO Laboratories, Carlsbad, CA) using the Precellys 24 tissue homogenizer (Bertin Technologies purchased from MO BIO) and 1.4mm ceramic beads. The amount and quality of the RNA was determined using an Agilent 2100 Bioanalyzer. Only samples with an RIN ≥ 8 were used for analysis.

treatment_protocol: Mice were sacrificed at the given time points, the medial side of the knee joint was opened under sterile conditions, skin, muscle and other soft tissues outside of the knee joint were removed, and a block of tissue was dissected out from the knee that include the medial tibial plateau (cartilage and subcondral bone), medial femoral condyle (cartilage and subchondral bone, medial synovium, joint capsule, and ligaments. Tissue was immediately placed in RNAlater® (Invitrogen) and stored overnight at 40 C. The next day the RNAlater® solution was removed and the tissue frozen at -80 C until RNA isolation.

value: male

tag: protocol

value: DMM surgery

tag: time (post-protocol)

value: 16 weeks

value: 28 weeks

value: Joint tissue


title: Wild type hfd pool3

description:
abdominal fat gene expression
Groups of C57BL/6 and P47KO  female mice were fed casein or high fat diet starting at post-natal day (PND) 28. After 13 weeks the mice were sacrifized and abdominal fat pads were collected and fresh frozen in liquid nitrogen.
Abdominal fat pads were collected and fresh frozen in liquid nitrogen

source_name: abdominal fat pads

value: High fat diet

tag: gender


title: DNA11091-098A Whole blood sample, SLE patient 21

description:
Whole blood sample, SLE patient
DNA11091-098A

source_name: SLE Patient, IFN-K 120 microgram, 4 injections, day 168

value: SLE

value: Whole blood


title: Joint tissue-time 16 weeks-DMM-replicate 3

description:
Gene expression data from DMM joints 16 weeks after surgery
DMM16_pool3

tag: strain


title: DNA11091-045A Whole blood sample, SLE patient 20

description:
Whole blood sample, SLE patient
DNA11091-045A

tag: treatment

value: Caucasian


title: Joint tissue-time 16 weeks-DMM-replicate 2

description:
Gene expression data from DMM joints 16 weeks after surgery
DMM16_pool2


title: DNA11091-113A Whole blood sample, SLE patient 21

description:
Whole blood sample, SLE patient
DNA11091-113A

source_name: SLE Patient, IFN-K 120 microgram, 4 injections, day 112

tag: day


title: 5W_wild-type_Heart_2

source_name: wild-type Heart

value: Heart


title: Joint tissue-time 8 weeks-DMM-replicate 3

description:
Gene expression data from DMM joints 8 weeks after surgery
DMM8_pool3

source_name: Joint tissue-8 weeks after DMM surgery

value: 8 weeks

value: 20 weeks


title: 5W_wild-type_Heart_1


title: 5W_wild-type_Spleen_1


title: DNA11091-042A Whole blood sample, SLE patient 20

description:
Whole blood sample, SLE patient
DNA11091-042A

tag: ethnicity


title: 5W_wild-type_Kidney_2

source_name: wild-type Kidney

tag: age

value: Kidney


title: Joint tissue-time 8 weeks-DMM-replicate 2

description:
Gene expression data from DMM joints 8 weeks after surgery
DMM8_pool2


title: Joint tissue-time 4 weeks-DMM-replicate 3

description:
Gene expression data from DMM joints 4 weeks after surgery
DMM4_pool3

source_name: Joint tissue-4 weeks after DMM surgery

value: 4 weeks


title: 5W_wild-type_Kidney_1

value: wild-type


title: Joint tissue-time 8 weeks-DMM-replicate 1

description:
Gene expression data from DMM joints 8 weeks after surgery
DMM8_pool1


title: DNA11091-039A Whole blood sample, SLE patient 19

description:
Whole blood sample, SLE patient
DNA11091-039A

value: IFN-K 120 microgram, 4 injections


title: Joint tissue-time 4 weeks-DMM-replicate 1

description:
Gene expression data from DMM joints 4 weeks after surgery
DMM4_pool1


title: DNA11091-048A Whole blood sample, SLE patient 19

description:
Whole blood sample, SLE patient
DNA11091-048A

value: Female


title: 5W_wild-type_Liver_1

source_name: wild-type Liver

value: male

value: Liver


title: 5W_wild-type_Lung_2

source_name: wild-type Lung

value: Lung


title: 5W_wild-type_Liver_2


title: DNA10204-301A Whole blood sample, SLE patient 20

description:
Whole blood sample, SLE patient
DNA10204-301A


title: DNA11091-059A Whole blood sample, SLE patient 18

description:
Whole blood sample, SLE patient
DNA11091-059A

source_name: SLE Patient, IFN-K 120 microgram, 3 injections, day 168

value: IFN-K 120 microgram, 3 injections


title: skeletal muscle, DM 1

source_name: Biceps

tag: age (y)

value: F

value: Dermatomyositis DM

value: Biceps


title: 5W_kl(-/-)_Spleen_2

source_name: klotho(-/-) Spleen

value: klotho(-/-)

value: Spleen


title: 5W_wild-type_Lung_1


title: Joint tissue-time 4 weeks-DMM-replicate 2

description:
Gene expression data from DMM joints 4 weeks after surgery
DMM4_pool2

value: DMM surgery

value: 16 weeks

value: Joint tissue


title: DNA10204-299A Whole blood sample, SLE patient 19

description:
Whole blood sample, SLE patient
DNA10204-299A

value: SLE

value: Whole blood

value: Caucasian


title: Joint tissue-time 2 weeks-DMM-replicate 3

description:
Gene expression data from DMM joints 2 weeks after surgery
DMM2_pool3

source_name: Joint tissue-2 weeks after DMM surgery

value: 2 weeks

value: 14 weeks


title: Nonylphenol 18ug/L rep 8

city: Nanaimo

first: Shaorong

last: Li

state: British Columbia

address: 3190 Hammond Bay Road

department: Salmon and Freshwater Ecosystems Division

country: Canada

institute: Fisheries and Oceans Canada

description: biological replicate 8 of 8 (nonylphenol)

hyb_protocol: As reported in Miller et al., (2009, Comp. Biochem. Physiol. D., 4:75-89).  Samples were cleaned up by addition of 150 uL of DNA binding buffer.  Each experimental sampled was then combined with the pooled reference sample and passed through Zymo-25 Clean-up columns.  Unbound portion of labeled cDNA was removed by centrifuging at 12000 x g.  Labeled cDNA was washed 3x with DNA wash buffer (Zymo), eluted into 9 uL of 1 x TE buffer and 2 uL of poly dA was added.  Samples were denatured for 10 min at 80C, 125 uL of pre-warmed SlideHybe3 buffer (Ambion) was added and samples loaded into hybridization champber of Tecan-HS4800 Pro Hybridization Station.

scan_protocol: A Tecan LSReloaded was used to collect fluorescent images, with Automatic Gain Control (AGC) setting adjusted to optimize the visualization of each image.  Images were quantified with Imagene (Biodiscovery) and spots with poor quality or no signal were flagged.

data_processing: As reported in Miller et al., (2009, Comp. Biochem. Physiol. D., 4:75-89).  GeneSight (Biodiscovery) was used to normalize intensity data (loess normalzation), flagged spots were replaced with the experimental means for each gene, data was log transformed (base 2), and an intesity ratio was computed taking the difference in log transformed intensity between the experimental sample and pooled reference sample.

label: Alexa 555

organism: Oncorhynchus mykiss

source_name: liver, nonylphenol group fish

label_protocol: As reported in Miller et al., (2009, Comp. Biochem. Physiol. D., 4:75-89).  RNA was first amplified (using MessageAMP II-96 kits, Ambion, as per manufacturer instructions) and then reverse transcribed and labeled using a SuperScript Plus Indirect Labeling Kit (Invitrogen) as per manufacturer instructions.  The pooled reference sample was labeled with Alexa 647, experimental samples were labeled with Alexa 555.

growth_protocol: Fish were maintained in 125L tanks with continuously flowing dechlorinated municipal water.

extract_protocol: As reported in Miller et al., (2009, Comp. Biochem. Physiol. D., 4:75-89).  Approximately 10 mg of liver was homogenized in TRI reagent using a MM301 tissue homogenizer, extractions of total RNA were done using an automated liquid handling instrument and Magmax-96 for Microarray Kits (Ambion) as per manufacturer instructions

treatment_protocol: Fish were exposed to experimental treatments (control, 555 ug/L atrazine or 18 ug/L nonylphenol, measured concentrations) under flow-through conditions for a period of 4 days and were sampled at the end of the exposure period

tag: plasma cortisol

tag: proportion of lymphocytes

tag: proportion of granulocytes

tag: proportion of monocytes

value: Nonylphenol 18ug/L

value: liver

label: Alexa 647

source_name: liver, pooled reference sample

value: pooled reference


title: Joint tissue-time 2 weeks-DMM-replicate 2

description:
Gene expression data from DMM joints 2 weeks after surgery
DMM2_pool2

value: male

tag: tissue


title: Nonylphenol 18ug/L rep 6

description: biological replicate 6 of 8 (nonylphenol)


title: Joint tissue-time 16 weeks-sham-replicate 1

description:
Gene expression data from sham controls 16 weeks after surgery
Con16_pool1

source_name: Joint tissue-16 weeks after sham control surgery

value: sham control surgery

value: 28 weeks


title: Joint tissue-time 16 weeks-sham-replicate 3

description:
Gene expression data from sham controls 16 weeks after surgery
Con16_pool3


title: Joint tissue-time 16 weeks-sham-replicate 2

description:
Gene expression data from sham controls 16 weeks after surgery
Con16_pool2


title: DNA11091-044A Whole blood sample, SLE patient 17

description:
Whole blood sample, SLE patient
DNA11091-044A

tag: disease state

value: IFN-K 120 microgram, 3 injections

value: Female


title: Nonylphenol 18ug/L rep 7

description: biological replicate 7 of 8 (nonylphenol)


title: Nonylphenol 18ug/L rep 5

description: biological replicate 5 of 8 (nonylphenol)


title: 5W_kl(-/-)_Spleen_1

tag: genotype/variation

value: klotho(-/-)

value: Spleen


title: DNA10204-291A Whole blood sample, SLE patient 18

description:
Whole blood sample, SLE patient
DNA10204-291A

source_name: SLE Patient, IFN-K 120 microgram, 3 injections, baseline


title: DNA11091-031A Whole blood sample, SLE patient 18

description:
Whole blood sample, SLE patient
DNA11091-031A

source_name: SLE Patient, IFN-K 120 microgram, 3 injections, day 112


title: Joint tissue-time 8 weeks-sham-replicate 3

description:
Gene expression data from sham controls 8 weeks after surgery
Con8_pool3

source_name: Joint tissue-8 weeks after sham control surgery

value: 8 weeks

value: 20 weeks


title: DNA11091-035A Whole blood sample, SLE patient 17

description:
Whole blood sample, SLE patient
DNA11091-035A

value: SLE


title: Joint tissue-time 8 weeks-sham-replicate 2

description:
Gene expression data from sham controls 8 weeks after surgery
Con8_pool2

value: Joint tissue


title: Nonylphenol 18ug/L rep 4

description: biological replicate 4 of 8 (nonylphenol)


title: 5W_kl(-/-)_Heart_1

source_name: klotho(-/-) Heart

tag: Sex

value: Heart


title: Nonylphenol 18ug/L rep 2

description: biological replicate 2 of 8 (nonylphenol)


title: 5W_kl(-/-)_Heart_2


title: Nonylphenol 18ug/L rep 3

description: biological replicate 3 of 8 (nonylphenol)


title: DNA10204-305A Whole blood sample, SLE patient 17

description:
Whole blood sample, SLE patient
DNA10204-305A

value: Whole blood

value: Caucasian


title: Joint tissue-time 8 weeks-sham-replicate 1

description:
Gene expression data from sham controls 8 weeks after surgery
Con8_pool1

tag: protocol


title: DNA11091-093A Whole blood sample, SLE patient 16

description:
Whole blood sample, SLE patient
DNA11091-093A


title: Nonylphenol 18ug/L rep 1

description: biological replicate 1 of 8 (nonylphenol)

value: Nonylphenol 18ug/L


title: Atrazine 555ug/L rep 8

description: biological replicate 8 of 8 (atrazine)

source_name: liver, atrazine group fish

value: Atrazine 555ug/L

value: liver


title: DNA10204-283A Whole blood sample, SLE patient 16

description:
Whole blood sample, SLE patient
DNA10204-283A


title: Joint tissue-time 4 weeks-sham-replicate 3

description:
Gene expression data from sham controls 4 weeks after surgery
Con4_pool3

source_name: Joint tissue-4 weeks after sham control surgery

value: male

tag: time (post-protocol)

value: 4 weeks

value: 16 weeks


title: DNA11091-069A Whole blood sample, SLE patient 16

description:
Whole blood sample, SLE patient
DNA11091-069A

value: IFN-K 120 microgram, 3 injections

tag: gender


title: Joint tissue-time 4 weeks-sham-replicate 2

description:
Gene expression data from sham controls 4 weeks after surgery
Con4_pool2

tag: strain

value: sham control surgery


title: 5W_kl(-/-)_Kidney_2

source_name: klotho(-/-) Kidney

value: klotho(-/-)

value: Kidney


title: 5W_kl(-/-)_Kidney_1


title: Atrazine 555ug/L rep 7

description: biological replicate 7 of 8 (atrazine)

tag: treatment

value: pooled reference


title: 5W_kl(-/-)_Liver_1

source_name: klotho(-/-) Liver

value: Liver


title: Joint tissue-time 4 weeks-sham-replicate 1

description:
Gene expression data from sham controls 4 weeks after surgery
Con4_pool1


title: 5W_kl(-/-)_Lung_2

source_name: klotho(-/-) Lung

value: Lung


title: DNA11091-120A Whole blood sample, SLE patient 15

description:
Whole blood sample, SLE patient
DNA11091-120A

source_name: SLE Patient, IFN-K 60 microgram, 4 injections, day 112

value: SLE

value: IFN-K 60 microgram, 4 injections

tag: day

value: Female


title: DNA10204-285A Whole blood sample, SLE patient 15

description:
Whole blood sample, SLE patient
DNA10204-285A

source_name: SLE Patient, IFN-K 60 microgram, 4 injections, baseline

value: Whole blood

tag: ethnicity

value: Caucasian


title: Joint tissue-time 2 weeks-sham-replicate 3

description:
Gene expression data from sham controls 2 weeks after surgery
Con2_pool3

source_name: Joint tissue-2 weeks after sham control surgery

value: 2 weeks

tag: age

value: 14 weeks

value: Joint tissue


title: Joint tissue-time 2 weeks-sham-replicate 2

description:
Gene expression data from sham controls 2 weeks after surgery
Con2_pool2

value: male


title: Atrazine 555ug/L rep 6

description: biological replicate 6 of 8 (atrazine)

value: Atrazine 555ug/L

value: liver


title: 5W_kl(-/-)_Lung_1


title: Atrazine 555ug/L rep 4

description: biological replicate 4 of 8 (atrazine)


title: DNA11091-130A Whole blood sample, SLE patient 14

description:
Whole blood sample, SLE patient
DNA11091-130A

source_name: SLE Patient, IFN-K 60 microgram, 4 injections, day 168


title: Atrazine 555ug/L rep 5

description: biological replicate 5 of 8 (atrazine)


title: DNA11091-091A Whole blood sample, SLE patient 15

description:
Whole blood sample, SLE patient
DNA11091-091A


title: Joint tissue-time 0-replicate 2

description:
Gene expression data from baseline unoperated joints
Con0_pool2

source_name: Joint tissue-baseline, no surgery

value: no surgery

value: baseline

value: 12 weeks


title: DNA10204-281A Whole blood sample, SLE patient 14

description:
Whole blood sample, SLE patient
DNA10204-281A


title: Joint tissue-time 2 weeks-sham-replicate 1

description:
Gene expression data from sham controls 2 weeks after surgery
Con2_pool1

value: sham control surgery


title: Atrazine 555ug/L rep 3

description: biological replicate 3 of 8 (atrazine)

value: pooled reference


title: DNA11091-027A Whole blood sample, SLE patient 14

description:
Whole blood sample, SLE patient
DNA11091-027A


title: Atrazine 555ug/L rep 1

description: biological replicate 1 of 8 (atrazine)


title: Joint tissue-time 0-replicate 3

description:
Gene expression data from baseline unoperated joints
Con0_pool3


title: Joint tissue-time 0-replicate 1

description:
Gene expression data from baseline unoperated joints
Con0_pool1


title: DNA11091-038A Whole blood sample, SLE patient 13

description:
Whole blood sample, SLE patient
DNA11091-038A


title: DNA11091-107A Whole blood sample, SLE patient 13

description:
Whole blood sample, SLE patient
DNA11091-107A


title: breast tumor part_IDC_rep1_8575

city: Taipei

first: King-Jen

last: Chang

address: No.1, Changde St., Zhongzheng Dist.

department: Department of Surgery

country: Taiwan

institute: National Taiwan University Hospital

hyb_protocol: Agilent Oligo Microarray Kit, hybridization protocol version 5.0

scan_protocol: Agilent scanner and Feature Extraction 6.0.

data_processing: The log2-ratio gene expression data in the microarray dataset were normalized by quantile normalization.

source_name: Infiltrating Ductal Carcinoma (IDC), Buffer 1, ER(-), PR(-), HER2(-).

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit, protocol version 2.0

growth_protocol: The breast tumor samples were immediately frozen by liquid nitrogen without any additional growth procedure before RNA extraction.

extract_protocol: Trizol reagent combined with RNAeasy mini kit

treatment_protocol: The breast tumor samples were excised, collected, and snap-frozen in liquid nitrogen immediately before RNA extraction.

tag: tissue type

value: breast tumor

tag: cell type

value: Infiltrating Ductal Carcinoma (IDC)

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: ajcc stage

value: IV

tag: lymph node metastasis

tag: lymphovascular invasion

tag: grade

tag: mitotic count

tag: nuclear pleomorphism

tag: tubule formation

tag: tumor size

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

source_name: Stratagene's human common reference RNA

tag: sample type

value: Commercially-available reference


title: breast tumor part_IDC_rep1_8573

tag: tissue type

tag: cell type

tag: age


title: Control rep 8

description: biological replicate 8 of 8 (control)

source_name: liver, control group fish

tag: plasma cortisol

tag: proportion of lymphocytes

tag: proportion of granulocytes

tag: proportion of monocytes

tag: treatment

value: Control

tag: tissue

source_name: liver, pooled reference sample


title: breast tumor part_IDC_rep1_8577

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: ajcc stage

tag: lymph node metastasis

tag: lymphovascular invasion

tag: grade

tag: mitotic count


title: Control rep 6

description: biological replicate 6 of 8 (control)


title: DNA10204-303A Whole blood sample, SLE patient 13

description:
Whole blood sample, SLE patient
DNA10204-303A

tag: disease state

value: SLE

value: IFN-K 60 microgram, 4 injections

tag: day

value: Whole blood

tag: ethnicity

value: Caucasian

tag: gender

value: Female


title: DNA11091-022A Whole blood sample, SLE patient 12

description:
Whole blood sample, SLE patient
DNA11091-022A

source_name: SLE Patient, IFN-K 60 microgram, 3 injections, day 168

value: IFN-K 60 microgram, 3 injections

tag: age


title: Control rep 7

description: biological replicate 7 of 8 (control)

tag: plasma cortisol

tag: proportion of lymphocytes

tag: proportion of granulocytes

tag: proportion of monocytes

value: liver


title: DNA11091-124A Whole blood sample, SLE patient 12

description:
Whole blood sample, SLE patient
DNA11091-124A

source_name: SLE Patient, IFN-K 60 microgram, 3 injections, day 112

tag: treatment

tag: tissue


title: breast tumor part_IDC_rep1_5399

tag: tissue type

tag: cell type

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

value: IIIC

tag: nuclear pleomorphism

tag: tubule formation

tag: tumor size

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

tag: sample type


title: breast tumor part_IDC_rep1_8571

tag: age

tag: ajcc stage

value: IIA

tag: lymph node metastasis

tag: lymphovascular invasion

tag: grade

tag: mitotic count


title: breast tumor part_IDC_rep1_5393

tag: tissue type

tag: cell type

tag: array id


title: DNA10204-343A Whole blood sample, SLE patient 12

description:
Whole blood sample, SLE patient
DNA10204-343A

source_name: SLE Patient, IFN-K 60 microgram, 3 injections, baseline

tag: disease state

tag: treatment

tag: day

tag: tissue

tag: ethnicity

tag: gender


title: DNA11091-108A Whole blood sample, SLE patient 11

description:
Whole blood sample, SLE patient
DNA11091-108A


title: DNA10204-333A Whole blood sample, SLE patient 11

description:
Whole blood sample, SLE patient
DNA10204-333A


title: Control rep 4

description: biological replicate 4 of 8 (control)

tag: plasma cortisol

tag: proportion of lymphocytes

tag: proportion of granulocytes

tag: proportion of monocytes


title: Control rep 5

description: biological replicate 5 of 8 (control)


title: DNA11091-136A Whole blood sample, SLE patient 10

description:
Whole blood sample, SLE patient
DNA11091-136A

source_name: SLE Patient, IFN-K 30 microgram, 3 injections, day 168

value: IFN-K 30 micrograms, 3 injections

tag: age


title: Control rep 2

description: biological replicate 2 of 8 (control)


title: Control rep 1

description: biological replicate 1 of 8 (control)


title: Control rep 3

description: biological replicate 3 of 8 (control)


title: DNA11091-050A Whole blood sample, SLE patient 10

description:
Whole blood sample, SLE patient
DNA11091-050A

source_name: SLE Patient, IFN-K 30 microgram, 3 injections, day 112


title: breast tumor part_IDC_rep1_5345

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: ajcc stage

value: I

tag: lymph node metastasis

tag: lymphovascular invasion

tag: nuclear pleomorphism

tag: tubule formation

tag: tumor size

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

tag: sample type


title: breast tumor part_IDC_rep1_5357

tag: tissue type

tag: cell type

tag: array id

tag: grade

tag: mitotic count


title: Atrazine 555ug/L rep 2

description: biological replicate 2 of 8 (atrazine)

source_name: liver, atrazine group fish

tag: plasma cortisol

tag: proportion of lymphocytes

tag: proportion of granulocytes

tag: proportion of monocytes

tag: treatment

value: Atrazine 555ug/L

tag: tissue

value: pooled reference


title: breast tumor part_IDC_rep1_5347

value: breast tumor

value: Infiltrating Ductal Carcinoma (IDC)

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: age

tag: ajcc stage

value: IIB

tag: lymph node metastasis

tag: lymphovascular invasion

tag: nuclear pleomorphism

tag: tubule formation


title: breast tumor part_IDC_rep1_5307

tag: tissue type

tag: cell type

tag: array id

value: IIIB

tag: grade

tag: tumor size

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

tag: sample type

value: Commercially-available reference


title: breast tumor part_IDC_rep1_5317

tag: er ihc

tag: pr ihc

tag: mitotic count


title: breast tumor part_IDC_rep1_5323

tag: her-2/neu ihc

tag: age

tag: ajcc stage


title: breast tumor part_IDC_rep1_4413

tag: lymph node metastasis

tag: lymphovascular invasion

tag: nuclear pleomorphism


title: DFM Replicate 1

city: Beltsville

first: Duk Kyung

last: Kim

state: MD

address: Bldg. 1043, BARC-East

institute: USDA, ARS

description: Biological replicate 1 of 2

hyb_protocol: With the use of Agilent’s Gene Expression Hybridization Kit (Cat# 5188-5242), 825ng of cyanine 3-labeled and cyanine 5-labeled linearly amplified cRNA was added to individual hybridization cocktails and then fragmented. At hybridization each well contained one cy3 and one cy5 labeled sample and control per pair.  The hybridization cocktail is then dispensed into the wells of gasket slides (4 samples/slide: Cat# G2534-60012) on top of which a Chicken 4x44K Gene Expression Microarray, (Cat# G2519F, AMADID 015068) was placed.  This microarray “sandwich” was then sealed in a hybridization chamber.  The microarrays were hybridized at 65°C rotating at 10 RPMs for 17 hours.  Slides were washed in Agilent’s Gene Expression Wash Buffers according to manufacturer recommendations.

scan_protocol: The microarrays were scanned on the Agilent Microarray Scanner.  Scanner data extraction and analysis was performed using Feature Extraction software version 10.7.3.1.

data_processing: Data quality was evaluated by reviewing ten standard QC metrics generated by the Agilent Technologies Feature Extraction Software version 10.7.3.1. Microarrays were determined to be free of any large artifacts (≥ 10% of total surface area) that could have affected the quality of the data.

organism: Gallus gallus

source_name: intraepithelial lymphocyte IEL DFM

label_protocol: Using Agilent’s 2-Color Quick Amp Labeling Kit, (Cat# 5190-0444), 0.5 to 1 ug of RNA (Agilent suggested: total RNA input range 50 ng - 2 μg) and Spike-In (2-Color RNA Spike-In Kit Cat# 5188-5279) were denatured in the presence of a T7 promoter primer.  Reverse Transcriptase was used to reverse-transcribe the mRNA.  cDNA was used as a template for in vitro transcription where a T7 RNA polymerase simultaneously amplified target material and incorporated cyanine 3- or cyanine 5-labeled CTP.  Labeled cRNA was purified using spin columns from the Qiagen RNeasy Mini Kit and the quantity and quality of the cRNA was determined by Nanodrop ND-1000 UV-VIS spectrophotometer.

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

tag: treatment

value: direct fed microbial

value: day 14

tag: cell type

value: Intestinal intraepithelial lymphocyte IEL

tag: strain

value: Broiler

source_name: intraepithelial lymphocyte IEL Control

value: control


title: DFM Replicate 2

description: Biological replicate 2 of 2 (Dye-exchange of Replicate 1)


title: DNA11091-087A Whole blood sample, SLE patient 9

description:
Whole blood sample, SLE patient
DNA11091-087A

tag: disease state

value: SLE

tag: day

tag: tissue

value: Whole blood

tag: ethnicity

value: Caucasian

tag: gender

value: Female


title: DNA10204-337A Whole blood sample, SLE patient 10

description:
Whole blood sample, SLE patient
DNA10204-337A

source_name: SLE Patient, IFN-K 30 microgram, 3 injections, baseline

value: IFN-K 30 micrograms, 3 injections


title: breast tumor part_IDC_rep1_5329

tag: tissue type

tag: array id

tag: er ihc

value: IIA

tag: grade

tag: tubule formation

tag: tumor size

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

tag: sample type


title: DNA10204-339A Whole blood sample, SLE patient 9

description:
Whole blood sample, SLE patient
DNA10204-339A

tag: treatment

tag: age


title: DNA11091-055A Whole blood sample, SLE patient 9

description:
Whole blood sample, SLE patient
DNA11091-055A

tag: disease state


title: DNA11091-058A Whole blood sample, SLE patient 8

description:
Whole blood sample, SLE patient
DNA11091-058A

tag: day