title: TAUmn biological replicate 4

city: Torrance

first: Stanislav

middle: L

last: Karsten

address: 1124 West Carson Street

department: Neurology

institute: UCLA School of Medicine

description: TAU-P301L motor neurons (TAUmn) (experiment) vs. littermate nontransgenic control motor neurons. Biological replicate 4 of 4

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

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and global LOWESS normalization.

label_protocol: Amplification and labeling of the RNA samples were performed using the Agilent Low RNA Input Linear Amplification Kit PLUS, and the quality of the labeled cRNA was checked using the Agilent 2100 Bioanalyzer.

extract_protocol:
Mice were killed with excess pentobarbital, decapitated, and the spinal cord removed as rapidly as possible. Spinal cords were briefly frozen in 2-methylbutane at -10 °C and stored at -80 °C until use. They were then cut on a cryostat to 12 um thickness onto noncharged slides. The slides were stored at -80 °C.
Immediately before use of the LCM, the slides were put through a series of washes in the following order: 75% ethanol, H2O, cresyl violet, a series of ethanol dehydration steps followed by xylene. Identification of motor neurons on the cresyl violet (Nissl)-stained slides was accomplished with the guidance of an anatomical atlas. Harvesting of motor neurons or surrounding glial cells was performed using optimized parameters for the PixCell IIe LCM System. 500 motor neurons or surrounding glial cells were collected from each mouse.
Total RNA isolation for the LCM cells was performed using Qiagen RNeasy Micro kit with a slight modification of the manufacturer’s protocol for optimal yield. Up to 3 cap linings containing the cells were removed and placed in 75uL of RNALysis Tissue buffer (RLT, Qiagen) on ice until all cells were collected. Subsequently, 75 uL of RLT containing beta-mercaptoethanol were added before proceeding with the Qiagen protocol.

tag: gender

value: female

value: 16 weeks

value: Lumbar spinal cord anterior horn motor neurons

tag: strain


title: TAUgl biological replicate 3 dye-switch

status: Public on Jun 24 2010

type: RNA

state: CA

country: USA

description: TAU-P301L glia (TAUgl) (experiment) vs. littermate nontransgenic control glia. Biological replicate 3 of 4

molecule: total RNA

organism: Mus musculus

tag: age

tag: tissue

value: Cells surrounding lumbar spinal cord anterior horn motor neurons


title: TAUgl biological replicate 4 dye-switch

description: TAU-P301L glia (TAUgl) (experiment) vs. littermate nontransgenic control glia. Biological replicate 4 of 4


title: SODgl biological replicate 4 dye-switch

description: SOD1-G93A glia (SODgl) (experiment) vs. littermate nontransgenic control glia. Biological replicate 4 of 4

value: 8 weeks


title: TAUgl biological replicate 1

description: TAU-P301L glia (TAUgl) (experiment) vs. littermate nontransgenic control glia. Biological replicate 1 of 4


title: Prostate tumor PCA0074 miRNA

city: New York

first: Barry

middle: Stephen

last: Taylor

state: NY

address: 1275 York Avenue, Box #460

institute: Memorial Sloan-Kettering Cancer Center

description: microRNA expression profiling

hyb_protocol: Per manufacturer's instructions

scan_protocol: Per manufacturer's instructions

data_processing: Images were quantified using Agilent Feature Extraction version 9.5 and data was normalized with between-array variance stabilization normalization (VSN) after excluding any microRNA not present in >80% of the samples profiled

organism: Homo sapiens

source_name: human prostate

label_protocol: 200ng of total RNA was labeled using the miRNA Complete Labeling and Hybridization Kit (Agilent)

extract_protocol: Total RNA was isolaged using TRIzol@Reagent Total RNA Isoloation (Invitrogen), quantified with Thermo Scientific NanoDrop 1000 Spectrophotometer, and quality controlled with RNA 6000 picoAssay and Bioanalyzer 2100 (Agilent).

tag: sample id

value: Prostate

tag: disease status

value: prostate cancer

tag: tumor type

value: Primary tumor


title: TAUmn biological replicate 4 dye-switch


title: Prostate tumor PCA0066 miRNA

description: microRNA expression profiling


title: TAX577488

type: genomic

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

description:
raw data file TAX577488_Cy5_1.gpr is labeled as follows: ch1 = Cy5, ch2 = Cy3
raw data file TAX577488_Cy3_1.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5
raw data file TAX577488_Cy3_2.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5

hyb_protocol: BAC aCGH microarrays were hybridized as described (PMID: 17334996)

scan_protocol: Arrays were washed as described (PMID: 17334996) and fluorescence was recorded using an Agilent G2565AA microarray scanner (Agilent Technologies).

data_processing: TIFF images were analyzed using the Gene Pix Pro software (Axon Instruments, Foster City, CA), and the quantified data matrix was loaded into a local installation of BioArray Software Environment (BASE) (http://base.thep.lu.se). Quantified intensities for tumor sample were stored as channel 1 (ch1) whereas quantified intensities for reference sample were stored as channel 2 (ch2). Median spot pixel values were used to calculate background corrected intensities (Int1 and Int2). Spots were removed and regarded as missing values if either: (1) flagged during image-analysis, (2) background corrected intensity value >64999 signal units, (3) background corrected intensity value <0 signal units, or (4) Signal to noise ratio <5 in either Int1 or Int2 channel. For spots, log ratio (M) was calculated as log2(Int1/Int2) and average intensity (A) was calculated as log10(Int1*Int2)/2. Normalization was performed by applying popLowess (PMID: 17953745). Spots from dye-swap hybridization were merged using geometric mean of ratios after normalization.

molecule: genomic DNA

source_name: Breast tumor

label_protocol: Fluorescently labeled DNA targets for hybridization were prepared according to manufacturers' instructions using the Invitrogen Bioprime aCGH Genomic Labeling Module as described (PMID:17334996).

extract_protocol: Genomic DNA from fresh frozen breast tumor tissue was extracted using overnight digestion with proteinase K at 55C, followed by repeated phenol-chloroform purification steps. DNA concentrations were measured using a Nanodrop.

value: Breast tumor

tag: hu subtype

value: Basal

tag: familial status

value: familial

tag: er

tag: osbin

tag: os

tag: pgr

tag: grade

tag: genomic subtype

value: Luminal-complex

source_name: promega male reference

tag: reference

value: promega male reference


title: TAUmn biological replicate 1 dye-switch

description: TAU-P301L motor neurons (TAUmn) (experiment) vs. littermate nontransgenic control motor neurons. Biological replicate 1 of 4


title: TAUgl biological replicate 1 dye-switch


title: TAUmn biological replicate 2

description: TAU-P301L motor neurons (TAUmn) (experiment) vs. littermate nontransgenic control motor neurons. Biological replicate 2 of 4


title: TAX577320

value: Normal

value: mixed


title: Prostate tumor PCA0065 miRNA

description: microRNA expression profiling


title: TAUgl biological replicate 4


title: TAUgl biological replicate 2

description: TAU-P301L glia (TAUgl) (experiment) vs. littermate nontransgenic control glia. Biological replicate 2 of 4


title: TAUmn biological replicate 3

description: TAU-P301L motor neurons (TAUmn) (experiment) vs. littermate nontransgenic control motor neurons. Biological replicate 3 of 4


title: Prostate tumor PCA0064 miRNA

description: microRNA expression profiling


title: TAUmn biological replicate 2 dye-switch


title: TAUmn biological replicate 1


title: TAX577404

value: Basal-complex


title: TAX577476

value: LumB

value: Luminal-simple


title: TAUgl biological replicate 2 dye-switch

value: female

value: 16 weeks


title: SODgl biological replicate 1

description: SOD1-G93A glia (SODgl) (experiment) vs. littermate nontransgenic control glia. Biological replicate 1 of 4

value: Cells surrounding lumbar spinal cord anterior horn motor neurons


title: SODgl biological replicate 2 dye-switch

description: SOD1-G93A glia (SODgl) (experiment) vs. littermate nontransgenic control glia. Biological replicate 2 of 4

value: 8 weeks


title: TAX577331

value: sporadic


title: TAX577093

value: LumA


title: SODgl biological replicate 2


title: SODgl biological replicate 3

description: SOD1-G93A glia (SODgl) (experiment) vs. littermate nontransgenic control glia. Biological replicate 3 of 4


title: SODgl biological replicate 3 dye-switch


title: Prostate tumor PCA0063 miRNA

description: microRNA expression profiling

value: Prostate

value: prostate cancer

value: Primary tumor


title: TAX577475

value: Breast tumor

value: nonClassified


title: SODgl biological replicate 1 dye-switch


title: TAUgl biological replicate 3


title: TAX577452

value: promega male reference


title: SODgl biological replicate 4


title: TAUmn biological replicate 3 dye-switch

value: Lumbar spinal cord anterior horn motor neurons


title: SODmn biological replicate 3

description: SOD1-G93A motor neurons (SODmn) (experiment) vs. littermate nontransgenic control motor neurons. Biological replicate 3 of 4


title: SODmn biological replicate 4 dye-switch

description: SOD1-G93A motor neurons (SODmn) (experiment) vs. littermate nontransgenic control motor neurons. Biological replicate 4 of 4


title: SODmn biological replicate 2 dye-switch

description: SOD1-G93A motor neurons (SODmn) (experiment) vs. littermate nontransgenic control motor neurons. Biological replicate 2 of 4


title: SODmn biological replicate 4


title: TAX577354

value: Basal

value: familial


title: Prostate tumor PCA0054 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0056 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0057 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0062 miRNA

description: microRNA expression profiling


title: TAX577067

value: mixed


title: SODmn biological replicate 3 dye-switch


title: Prostate tumor PCA0040 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0050 miRNA

description: microRNA expression profiling


title: SODmn biological replicate 2


title: TAX577466

value: Luminal-complex


title: SODmn biological replicate 1 dye-switch

description: SOD1-G93A motor neurons (SODmn) (experiment) vs. littermate nontransgenic control motor neurons. Biological replicate 1 of 4

value: female


title: TAX577470


title: Prostate tumor PCA0033 miRNA

description: microRNA expression profiling


title: TAX577486


title: TAX577435


title: SODmn biological replicate 1


title: Prostate tumor PCA0029 miRNA

description: microRNA expression profiling


title: TAX577361

value: Basal-complex


title: Prostate tumor PCA0027 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0024 miRNA

description: microRNA expression profiling


title: TAX577483


title: TAX577260

value: LumB


title: Cell line LNCaP (aCGH)

description: DNA copy number

data_processing: Images quantified with Agilent Feature Extraction ver9.1. Probe sequences were re-mapped to the hg18 build of the human genome and merged. Probe-level data was subsequently normalized for local GC content with a two-stage LOESS fit. Probe-level data is the log2 ratio of tumor-to-normal.

source_name: tumor DNA

label_protocol: Bioprime Array CHG labeling kit (Invitrogen) using Cy3/Cy5

extract_protocol: Genome DNA was extracted from all samples with standard proteinase K digestion and phenol/chloroform extraction.

value: LNCaP

value: prostate

tag: cell line

value: Cell line

source_name: Promega reference DNA

tag: sample source

value: Promega reference DNA

value: normal


title: Xenograft LAPC4-1 (aCGH)

description: DNA copy number

tag: cell type

value: Xenograft LAPC4-1

value: prostate cancer

value: Xenograft


title: TAX577554

value: Breast tumor

value: LumA

value: sporadic

value: Luminal-simple

value: promega male reference


title: TAX577323

value: Normal

value: familial

value: amplifier


title: Prostate tumor PCA0023 miRNA

description: microRNA expression profiling

value: Prostate

value: Primary tumor


title: Xenograft LAPC9 (aCGH)

description: DNA copy number

value: prostate

value: Xenograft LAPC9


title: Xenograft LAPC4-2 (aCGH)

description: DNA copy number

value: Xenograft LAPC4-2

value: Promega reference DNA


title: Cell line Vcap (aCGH)

description: DNA copy number

value: Vcap

value: Cell line

value: normal


title: Xenograft LNM971 (aCGH)

description: DNA copy number

value: Xenograft LNM971

value: prostate cancer

value: Xenograft


title: Cell line PC3 (aCGH)

description: DNA copy number


title: TAX577036

value: Breast tumor

value: nonClassified


title: Xenograft LAPC3-2 (aCGH)

description: DNA copy number

value: Xenograft LAPC3-2


title: Prostate tumor PCA0017 miRNA

description: microRNA expression profiling


title: Cell line LNCaP104S (aCGH)

description: DNA copy number


title: Cell line DU145 (aCGH)

description: DNA copy number


title: TAX577547

value: Normal

value: sporadic

value: Luminal-simple

value: promega male reference


title: TAX577396

description:
raw data file TAX577396_Cy3_1.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5
raw data file TAX577396_Cy5_1.gpr is labeled as follows: ch1 = Cy5, ch2 = Cy3

value: Basal

value: Basal-complex


title: TAX577387

value: amplifier


title: Prostate tumor PCA0009 miRNA

description: microRNA expression profiling

value: Prostate

value: Primary tumor


title: Prostate tumor PCA0216 (aCGH)

description: DNA copy number

value: prostate

value: Metastasis

source_name: normal bladder DNA

value: bladder


title: Xenograft LAPC3-1 (aCGH)

description: DNA copy number

value: Xenograft LAPC3-1

value: prostate cancer

value: Promega reference DNA

value: normal


title: Prostate tumor PCA0214 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0215 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0007 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0012 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0217 (aCGH)

description: DNA copy number

source_name: normal bone DNA

value: bone


title: Cell line CWR22Rv1 (aCGH)

description: DNA copy number

value: Cell line


title: Prostate tumor PCA0218 (aCGH)

description: DNA copy number

source_name: normal lung DNA

value: lung


title: Xenograft LuCAP35 (aCGH)

description: DNA copy number

value: Xenograft LuCAP35

value: Xenograft


title: Prostate tumor PCA0213 (aCGH)

description: DNA copy number

source_name: normal colon DNA

value: colon


title: Prostate tumor PCA0212 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0209 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0005 miRNA

description: microRNA expression profiling


title: TAX577471

value: Breast tumor

value: nonClassified

value: sporadic

value: promega male reference


title: Prostate tumor PCA0003 miRNA

description: microRNA expression profiling

value: Prostate

value: Primary tumor


title: Prostate tumor PCA0001 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0211 (aCGH)

description: DNA copy number

value: prostate

value: Metastasis


title: Prostate tumor PCA0210 (aCGH)

description: DNA copy number

value: prostate cancer


title: TAX577161

value: LumB

value: familial

value: Luminal-complex


title: Prostate tumor PCA0208 (aCGH)

description: DNA copy number

value: Promega reference DNA

value: normal


title: TAX577535

value: Luminal-simple


title: Prostate tumor PCA0207 (aCGH)

description: DNA copy number

source_name: normal lymph node DNA

value: lymph node


title: TAX577159

value: LumA


title: TAX577375

value: Breast tumor

value: Basal

value: Basal-complex


title: TAX577462

value: promega male reference


title: TAX577388

value: sporadic

value: mixed


title: Prostate tumor PCA0206 (aCGH)

description: DNA copy number

value: prostate


title: TAX577365


title: Prostate tumor PCA0203 (aCGH)

description: DNA copy number

value: Metastasis


title: Prostate tumor PCA0205 (aCGH)

description: DNA copy number

value: prostate cancer


title: TAX577210

value: LumB


title: Prostate tumor PCA0204 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0202 (aCGH)

description: DNA copy number


title: TAX577421


title: Prostate tumor PCA0192 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0195 (aCGH)

description: DNA copy number


title: TAX577446


title: Prostate tumor PCA0200 (aCGH)

description: DNA copy number


title: TAX577458

value: nonClassified


title: Prostate tumor PCA0198 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0199 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0196 (aCGH)

description: DNA copy number


title: TAX577465

value: Luminal-complex


title: Prostate tumor PCA0201 (aCGH)

description: DNA copy number

value: Promega reference DNA


title: Prostate tumor PCA0193 (aCGH)

description: DNA copy number

value: normal


title: Prostate tumor PCA0194 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0187 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0197 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0190 (aCGH)

description: DNA copy number

source_name: adjacent normal prostate DNA


title: Prostate tumor PCA0184 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0186 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0183 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0185 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0189 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0191 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0188 (aCGH)

description: DNA copy number


title: TAX577484

value: amplifier


title: Prostate tumor PCA0182 (aCGH)

description: DNA copy number


title: TAX577357


title: TAX577457


title: TAX577411


title: TAX577455


title: Prostate tumor PCA0180 (aCGH)

description: DNA copy number

value: Primary tumor


title: Prostate tumor PCA0181 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0179 (aCGH)

description: DNA copy number


title: TAX577259

value: LumA


title: Prostate tumor PCA0178 (aCGH)

description: DNA copy number


title: TAX577546

value: Breast tumor

value: Luminal-simple


title: Prostate tumor PCA0171 (aCGH)

description: DNA copy number


title: TAX577508


title: Prostate tumor PCA0172 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0168 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0170 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0165 (aCGH)

description: DNA copy number


title: TAX577545


title: Prostate tumor PCA0167 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0166 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0173 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0169 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0177 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0176 (aCGH)

description: DNA copy number


title: TAX577249

value: familial


title: Prostate tumor PCA0174 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0164 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0161 (aCGH)

description: DNA copy number


title: TAX577548

value: Normal

value: promega male reference


title: Prostate tumor PCA0162 (aCGH)

description: DNA copy number


title: TAX577114

value: sporadic


title: TAX577536

value: Basal


title: Prostate tumor PCA0163 (aCGH)

description: DNA copy number

value: prostate


title: Prostate tumor PCA0160 (aCGH)

description: DNA copy number

value: prostate cancer


title: TAX577527


title: Prostate tumor PCA0175 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0159 (aCGH)

description: DNA copy number


title: TAX577531


title: TAX577002


title: Prostate tumor PCA0158 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0157 (aCGH)

description: DNA copy number


title: TAX577143


title: Prostate tumor PCA0155 (aCGH)

description: DNA copy number


title: TAX577343

value: Basal-complex


title: Prostate tumor PCA0154 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0156 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0149 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0148 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0144 (aCGH)

description: DNA copy number


title: TAX577188

value: LumB


title: TAX577473


title: Prostate tumor PCA0150 (aCGH)

description: DNA copy number


title: TAX577233

value: Luminal-complex


title: Prostate tumor PCA0151 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0145 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0146 (aCGH)

description: DNA copy number


title: TAX577298

value: mixed


title: Prostate tumor PCA0152 (aCGH)

description: DNA copy number

value: normal


title: Prostate tumor PCA0147 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0137 (aCGH)

description: DNA copy number


title: TAX577499


title: TAX577409


title: TAX577175


title: Prostate tumor PCA0141 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0142 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0153 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0143 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0140 (aCGH)

description: DNA copy number


title: TAX577522

description:
raw data file TAX577522_Cy5_1.gpr is labeled as follows: ch1 = Cy5, ch2 = Cy3
raw data file TAX577522_Cy3_1.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5


title: Prostate tumor PCA0138 (aCGH)

description: DNA copy number


title: TAX577108


title: Prostate tumor PCA0135 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0139 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0136 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0134 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0133 (aCGH)

description: DNA copy number

value: Promega reference DNA


title: TAX577256


title: Prostate tumor PCA0129 (aCGH)

description: DNA copy number

value: Primary tumor


title: Prostate tumor PCA0131 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0128 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0132 (aCGH)

description: DNA copy number


title: TAX577450


title: Prostate tumor PCA0130 (aCGH)

description: DNA copy number


title: TAX577149

value: LumA

value: amplifier


title: TAX577549

value: Breast tumor


title: TAX577178

value: familial

value: Luminal-simple


title: TAX577492

value: promega male reference


title: Prostate tumor PCA0127 (aCGH)

description: DNA copy number


title: TAX577496

value: sporadic


title: Prostate tumor PCA0126 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0120 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0121 (aCGH)

description: DNA copy number


title: TAX577369

value: Basal


title: TAX577564

value: Normal


title: TAX577098


title: Prostate tumor PCA0119 (aCGH)

description: DNA copy number

value: prostate

value: prostate cancer


title: Prostate tumor PCA0124 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0118 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0122 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0117 (aCGH)

description: DNA copy number


title: TAX577427


title: Prostate tumor PCA0125 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0116 (aCGH)

description: DNA copy number


title: TAX577560


title: Prostate tumor PCA0114 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0110 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0123 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0115 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0113 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0107 (aCGH)

description: DNA copy number


title: TAX577137


title: Prostate tumor PCA0108 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0109 (aCGH)

description: DNA copy number


title: TAX577566

value: LumB


title: TAX577204

value: Luminal-complex


title: TAX577347

value: Basal-complex


title: Prostate tumor PCA0105 (aCGH)

description: DNA copy number

value: normal


title: Prostate tumor PCA0112 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0111 (aCGH)

description: DNA copy number


title: TAX577032


title: Prostate tumor PCA0106 (aCGH)

description: DNA copy number


title: TAX577426


title: Prostate tumor PCA0104 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0094 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0103 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0102 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0100 (aCGH)

description: DNA copy number

value: Promega reference DNA


title: TAX577420


title: TAX577091


title: TAX577257

value: nonClassified


title: Prostate tumor PCA0092 (aCGH)

description: DNA copy number

value: Primary tumor


title: Prostate tumor PCA0101 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0091 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0099 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0096 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0098 (aCGH)

description: DNA copy number


title: TAX577327

value: mixed


title: TAX577150

value: Breast tumor

value: LumA


title: TAX577316


title: TAX577469


title: Prostate tumor PCA0097 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0090 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0083 (aCGH)

description: DNA copy number


title: TAX577515

value: familial


title: Prostate tumor PCA0081 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0082 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0085 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0095 (aCGH)

description: DNA copy number


title: TAX577485

value: promega male reference


title: Prostate tumor PCA0093 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0089 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0084 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0086 (aCGH)

description: DNA copy number


title: TAX577211


title: Prostate tumor PCA0087 (aCGH)

description: DNA copy number


title: TAX577407

value: sporadic


title: Prostate tumor PCA0077 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0079 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0080 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0078 (aCGH)

description: DNA copy number


title: TAX577155


title: TAX577313


title: Prostate tumor PCA0075 (aCGH)

description: DNA copy number


title: TAX577346

value: Basal


title: Prostate tumor PCA0074 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0069 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0088 (aCGH)

description: DNA copy number


title: TAX577530


title: TAX577441


title: Prostate tumor PCA0070 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0072 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0071 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0067 (aCGH)

description: DNA copy number


title: TAX577059


title: Prostate tumor PCA0066 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0076 (aCGH)

description: DNA copy number


title: TAX577069


title: Prostate tumor PCA0064 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0063 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0073 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0059 (aCGH)

description: DNA copy number


title: TAX577200


title: TAX577276


title: Prostate tumor PCA0065 (aCGH)

description: DNA copy number


title: TAX577240

value: Luminal-simple


title: Prostate tumor PCA0062 (aCGH)

description: DNA copy number

value: prostate


title: TAX577567


title: Prostate tumor PCA0068 (aCGH)

description: DNA copy number

value: prostate cancer


title: Prostate tumor PCA0058 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0061 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0055 (aCGH)

description: DNA copy number


title: TAX577477


title: Prostate tumor PCA0054 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0050 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0056 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0051 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0047 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0049 (aCGH)

description: DNA copy number


title: 24-JA-CGH

first: Anna

middle: Isinger

last: Ekstrand

address: Barngatan 2b

department: Oncology

institute: Clinical Sciences

description: Junctional adenocarcinoma

hyb_protocol: Hybridizations were performed in 100 µg Cot-1 DNA, 2 x SSC, 2% SDS, deionized formamide, yeast tRNA and water at 37degC in 48 hours. Arrays were washed 2X SSC, 0.1 % SDS 15 min RT, 2X SSC, 50% formamide  pH 7.0 at 45degC, 2X SSC, 0.1% SDS 30 min at 45degC and 0.2X SSC15 min in RT.

scan_protocol: Arrays were scanned in Agilent scanner (Agilent Technologies)

data_processing: Image analysis was performed using Genepix v4.0. Result files were uploaded into BASE where they were filtered and normalized.

source_name: Gastroesophageal adenocarcinoma (type II), fresh frozen

label_protocol: 2 μg of tumor DNA and 1.5 μg of a pool of male reference DNA (Promega, Madison, WI, USA), were differentially labeled with Cy3-dCTP and Cy5-dCTP (Amersham Biosciences, UK) using the Bioprime Genomic labeling system (Invitrogen Life Technologies, Carlsbad, CA, USA).

extract_protocol: Genomic DNA was extracted using Proteinase K treatment followed by phenol-chloroform purification. Ext5racted DNA was eluted in 100 ul milli-Q water.

tag: biomaterial

value: Fresh frozen tissue

tag: gender

value: Male

tag: tumor stage

value: II

source_name: Male pool of DNA (Promega)

value: Pool of male DNA derived from blood


title: 26-EA-CGH

description: Distal esophageal adenocarcinoma

source_name: Esophageal adenocarcinoma (type I), fresh frozen tissue

value: III


title: 25-JA-CGH

description: Junctional adenocarcinoma

value: Female

value: IV


title: Prostate tumor PCA0060 (aCGH)

description: DNA copy number

tag: sample id

tag: tissue

tag: disease status

value: Primary tumor

value: normal


title: Prostate tumor PCA0048 (aCGH)

description: DNA copy number

tag: tumor type


title: TAX577500

value: Breast tumor

tag: hu subtype

value: LumB

tag: familial status

tag: er

value: Luminal-complex


title: Prostate tumor PCA0046 (aCGH)

description: DNA copy number


title: 27-JA-CGH

description: Junctional adenocarcinoma


title: Prostate tumor PCA0053 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0040 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0045 (aCGH)

description: DNA copy number

value: Promega reference DNA


title: Prostate tumor PCA0044 (aCGH)

description: DNA copy number


title: 23-GA-CGH

description: Proximal stomach adenocarcinoma

source_name: Gastric adenocarcinoma, fresh frozen tissue


title: 21-GA-CGH

description: Proximal stomach adenocarcinoma


title: Prostate tumor PCA0042 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0037 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0038 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0043 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0041 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0057 (aCGH)

description: DNA copy number


title: 20-GA-CGH

description: Proximal stomach adenocarcinoma


title: Prostate tumor PCA0039 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0052 (aCGH)

description: DNA copy number


title: 22-JA-CGH

description: Junctional adenocarcinoma


title: Prostate tumor PCA0032 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0031 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0036 (aCGH)

description: DNA copy number


title: 18-EA-CGH-2

description: Distal esophageal adenocarcinoma replicate 2


title: 19-JA-CGH

description: Junctional adenocarcinoma


title: 18-EA-CGH

description: Distal esophageal adenocarcinoma


title: Prostate tumor PCA0033 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0035 (aCGH)

description: DNA copy number


title: 16-JA-CGH

description: Junctional adenocarcinoma

value: I


title: Prostate tumor PCA0034 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0025 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0023 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0027 (aCGH)

description: DNA copy number


title: 12-EA_CGH-2


title: 15-GA-CGH

description: Proximal stomach adenocarcinoma


title: Prostate tumor PCA0021 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0022 (aCGH)

description: DNA copy number


title: 11-JA-CGH

description: Junctional adenocarcinoma


title: Prostate tumor PCA0024 (aCGH)

description: DNA copy number


title: 12-EA_CGH

description: Distal esophageal adenocarcinoma


title: Prostate tumor PCA0017 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0020 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0026 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0016 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0029 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0015 (aCGH)

description: DNA copy number


title: 9-GA-CGH

description: Proximal stomach adenocarcinoma


title: Prostate tumor PCA0014 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0012 (aCGH)

description: DNA copy number


title: 8-JA_CGH

description: Junctional adenocarcinoma


title: Prostate tumor PCA0018 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0028 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0019 (aCGH)

description: DNA copy number


title: Fr.A Ebf1 -/- : pMYs Ebf1beta 3

city: Freiburg

first: Rudolf

last: Grosschedl

address: Stuebeweg 51

department: Cellular and Molecular Immunology

country: Germany

institute: Max Planck Institute of Immunobiology

description: Gene expression profile after infection of Ebf1-deficient pre-pro-B cells with an Ebf1 expressing retroviral vector

hyb_protocol: Samples were hybridized to Agilent technologies Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F by Imagenes (Berlin, Germany)

scan_protocol: Arrays were scanned with an Agilent Technologies Scanner G2505B using one color scan setting for 4x44k array slides.

data_processing: default Agilent Feature Extraction procedure

source_name: Ebf1 deficient preproB-cells, transduced with Ebf1

label_protocol: c-RNA was prepared from 0.2ug of total RNA using oligo dT as primer for the first strand synthesis reaction. During the synthesis, Cy3-labeled nucelotides were incorporated to an incorporation rate of 8.5-11pmol/ug.

growth_protocol: Ebf1 deficient pre-pro B cells were grown in Opti-MEM medium (Invitrogen) supplemented with 4% fetal bovine serum, 10ng/ml Interleukin 7, 10ng/ml stem cell factor and 10ng/ml Flt3-ligand on a feeder layer of OP9 stromal cells.

extract_protocol: Total RNA was prepared using the Rneasy mini kit (Qiagen) according to the manufacturers protocol including an on-column DNAse digest.

treatment_protocol: Retrovirus was produced by transient transfection of Plat-E cells with retroviral constructs encoding Ebf1-EGFP (pMYs-Ebf1-IRES-EGFP) or EGFP alone (pMYs-IRES-EGFP). The supernatant was collected 24h and 48h after transfection and supplemented with 10 μg/ml polybrene.  For spin infection, the target cells were resuspended in retroviral supernatant at 0.7x106 cells/ml.  Cells were spun for 2.5 h at 2600 rpm in 24-well plates.  Following infection, the cells were re-suspended in fresh media and cultured for 24hrs. Cells were sorted for EGFP expression prior to analysis.

tag: genotype

value: Ebf -/-

tag: transfection

value: pre-pro-B


title: 7-EA_CGH

description: Distal esophageal adenocarcinoma


title: Fr.A Ebf1 -/- : pMYs Ebf1beta 2


title: Prostate tumor PCA0010 (aCGH)

description: DNA copy number

value: prostate

value: prostate cancer


title: Fr.A Ebf1 -/- : pMYs Ebf1beta 1


title: 6-JA-CGH

description: Junctional adenocarcinoma

value: Fresh frozen tissue

value: Male


title: Prostate tumor PCA0030 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0009 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0011 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0006 (aCGH)

description: DNA copy number


title: Fr.A Ebf1 -/- : pMYs 3

description: Gene expression profile after control infection of Ebf1-deficient pre-pro-B cells with a retroviral vector

source_name: Ebf1 deficient preproB-cells, control-virus infected

value: pMYs-IRES-EGFP


title: 3-GA-CGH

description: Proximal stomach adenocarcinoma

value: III

value: Pool of male DNA derived from blood


title: Prostate tumor PCA0013 (aCGH)

description: DNA copy number


title: 5-EA-CGH

description: Distal esophageal adenocarcinoma

value: II


title: Prostate tumor PCA0008 (aCGH)

description: DNA copy number

value: Primary tumor


title: 4-EA-CGH

description: Distal esophageal adenocarcinoma

value: IV


title: Fr.A Ebf1 -/- : pMYs 2


title: Ebf fl/fl, FL 93/7

description: Gene expression profile after conditional deletion of both Ebf1 alleles in pro-B cells

source_name: cultured pro-B cells, treated with 4OHT for 24h

label_protocol: c-RNA was prepared from 0.2ug of total RNA using oligo dT as primer for the first strand synthesis reaction. During the synthesis, Cy3-labeled nucelotides were incorporated to an incorporation rate of 10-13pmol/ug.

growth_protocol: Total cell preparations from livers of 16.5 dpc. embryos were cultured in the presence of OP-9 bone marrow stromal cells in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum and Interleukin-7 until a pure pro-B cell population was obtained.

treatment_protocol: For deletion of Ebf1, the B cells were treated with 2 mM 4-hydroxy-tamoxifen for 24 hours, washed and cultured for an additional four days.

value: Ebf fl/fl

value: fetal liver pro-B


title: Prostate tumor PCA0007 (aCGH)

description: DNA copy number

value: normal


title: Prostate tumor PCA0003 (aCGH)

description: DNA copy number


title: Prostate tumor PCA0005 (aCGH)

description: DNA copy number

value: Promega reference DNA


title: 2-GA-CGH

description: Proximal stomach adenocarcinoma

value: Female


title: 1-EA-CGH

description: Distal esophageal adenocarcinoma


title: Prostate tumor PCA0004 (aCGH)

description: DNA copy number


title: Fr.A Ebf1 -/- : pMYs 1

value: Ebf -/-


title: Ebf fl/fl, FL 93/5


title: Ebf fl/fl, FL 93/4


title: TAX577565

source_name: Breast tumor

value: Breast tumor

value: Normal

value: familial

tag: osbin

tag: os

tag: pgr

tag: grade

tag: genomic subtype

value: amplifier

value: promega male reference


title: TAX577224

value: LumA

value: Luminal-simple

source_name: promega male reference

tag: reference


title: Ebf+/fl, FL 111/3

description: Gene expression profile after conditional deletion of one Ebf1 allele in pro-B cells

value: Ebf+/fl

tag: cell type


title: Prostate tumor PCA0001 (aCGH)

description: DNA copy number

source_name: tumor DNA

value: prostate

value: prostate cancer

tag: sample source


title: TAX577544

description:
raw data file TAX577544_Cy3_1.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5
raw data file TAX577544_Cy3_2.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5

value: sporadic


title: Prostate tumor PCA0002 (aCGH)

description: DNA copy number

tag: sample id

value: Primary tumor

source_name: Promega reference DNA


title: TAX577215

tag: tissue


title: TAX577227


title: TAX577097


title: Patient 20, IDC

city: Augusta

first: Lesleyann

last: Hawthorn

state: GA

department: Molecular Oncology

institute: Medical College of Georgia Cancer Center

hyb_protocol: 16 hours in Affymetrix hyb oven.

scan_protocol: Scanned on an Affymetrix 7G-Plus scanner.

data_processing: GC-RMA Partek 6.0.

label: biotin

source_name: Breast, IDC

label_protocol: cDNA was made from RNA using Superscript. First strand was synthesized by 3' dt24 primer, followed by IVT and labelling with biotinylated 11-CTP and 16 UTP.

growth_protocol: N/A.

extract_protocol: Tissues microdissected for 80% tumor, total RNA extracted with TRIzol, quality assessed on Bioanalyzer.

treatment_protocol: N/A.

value: breast cancer

tag: tissue type

value: infiltrating ductal carcinoma (IDC)

tag: patient


title: Patient 22, IDC


title: 1-EA-CGH-2

tag: biomaterial

value: Fresh frozen tissue

tag: gender

value: Male

tag: tumor stage

value: III

value: Pool of male DNA derived from blood


title: Patient 24, IDC


title: Patient 26, IDC


title: Patient 27, IDC


title: Patient 15, IDC

description: 13201-1P 10-23-07


title: Patient 25, IDC


title: Patient 14, IDC

description: 13153-1P 10-23-07


title: Patient 15, normal

description: 13201-4br 1-11-08

source_name: Breast, normal

value: breast

value: normal


title: Patient 18, node metastasis

description: 13617-1M 10-23-07

source_name: Breast, node metastasis

value: node metastasis


title: Patient 15, IDC, biological replicate

description: 13201-1P 10-17-07


title: Patient 28, normal

description: 13080 2br 1-11-08


title: Patient 29, normal

description: 13108 3br 1-11-08


title: Patient 7, IDC

description: 13038-1P 10-17-07


title: Patient 5, IDC

description: 12866-1P 10-17-07


title: Patient 4, normal

description: 12838-6br 1-11-08


title: Patient 6, node metastasis

description: 12955-1M 10-23-07


title: Ebf+/fl, FL 111/6

tag: genotype

value: fetal liver pro-B


title: Patient 1, IDC

description: 12605-1P 10-17-07


title: Patient 4, IDC

description: 12838-1P 10-23-07


title: Prostate normal PAN0157 exon

description: exon and whole-transcript expression profiling

scan_protocol: Affymetrix high-numeric aperture and flying objective lens (FOL) GS3000 scanner

data_processing: Images were quantified using the GeneChip Operating Software (GCOS) version 1.4. Data were processed with Aroma Affymetrix using standard RMA background adjustment and quantile normalization

source_name: human adjacent normal prostate

label_protocol: Per manufacturer's instructions with the Affymetrix WT Sense Target Labeling Assay

value: Prostate

tag: disease status

value: normal adjacent benign prostate


title: Prostate normal PAN0134 exon


title: Prostate normal PAN0174 exon


title: Prostate normal PAN0167 exon


title: Prostate normal PAN0172 exon


title: Prostate normal PAN0171 exon


title: Patient 2, IDC

description: 12738-1P 10-17-07


title: Prostate normal PAN0135 exon


title: Prostate normal PAN0162 exon


title: Prostate normal PAN0136 exon


title: Prostate normal PAN0147 exon


title: Prostate normal PAN0115 exon


title: Prostate normal PAN0129 exon


title: Prostate normal PAN0144 exon


title: Prostate normal PAN0172 transcript


title: Prostate normal PAN0174 transcript


title: Prostate normal PAN0128 exon


title: Prostate normal PAN0164 exon


title: Prostate normal PAN0120 exon


title: Prostate normal PAN0151 exon


title: Prostate normal PAN0171 transcript


title: Prostate normal PAN0113 exon


title: Prostate normal PAN0122 exon


title: Prostate normal PAN0125 exon


title: Prostate normal PAN0167 transcript


title: Prostate normal PAN0164 transcript


title: Prostate normal PAN0162 transcript


title: Prostate normal PAN0114 exon


title: Prostate normal PAN0157 transcript


title: Prostate normal PAN0169 transcript


title: Prostate normal PAN0151 transcript


title: Prostate normal PAN0147 transcript


title: Prostate normal PAN0144 transcript


title: Prostate normal PAN0109 exon


title: Prostate normal PAN0127 exon


title: Prostate normal PAN0110 exon


title: Xenograft LNCaP104S exon

source_name: human prostate xenograft

value: Xenograft LNCaP104S


title: Prostate normal PAN0129 transcript


title: Prostate normal PAN0134 transcript


title: Prostate normal PAN0135 transcript


title: Prostate normal PAN0117 exon


title: Prostate normal PAN0136 transcript


title: Prostate normal PAN0107 exon


title: Prostate normal PAN0128 transcript


title: Cell line PC3 exon

source_name: human prostate cancer cell line

tag: cell line


title: Prostate normal PAN0095 exon


title: Prostate normal PAN0112 exon


title: Xenograft LNCaP104R exon

value: Xenograft LNCaP104R


title: Prostate normal PAN0125 transcript


title: Prostate normal PAN0169 exon


title: Prostate normal PAN0127 transcript


title: Prostate normal PAN0122 transcript


title: Cell line Vcap exon

value: Vcap


title: Prostate tumor PCA0208 exon

source_name: human prostate

value: prostate cancer

tag: tumor type

value: Metastasis


title: Prostate normal PAN0117 transcript


title: Cell line DU145 exon


title: Prostate tumor PCA0215 exon


title: Prostate tumor PCA0211 exon


title: Cell line LNCaP exon

value: LNCaP


title: Prostate tumor PCA0213 exon


title: Prostate normal PAN0114 transcript


title: Prostate tumor PCA0206 exon


title: Prostate normal PAN0115 transcript


title: Prostate normal PAN0113 transcript


title: Prostate normal PAN0110 transcript


title: Prostate normal PAN0109 transcript


title: Prostate tumor PCA0209 exon


title: Prostate tumor PCA0210 exon


title: Prostate tumor PCA0200 exon


title: Prostate tumor PCA0201 exon


title: Prostate normal PAN0112 transcript


title: Prostate tumor PCA0199 exon


title: Prostate normal PAN0120 transcript


title: Cell line PC3 transcript


title: Cell line Vcap transcript


title: Prostate tumor PCA0207 exon


title: Prostate tumor PCA0194 exon


title: Prostate normal PAN0095 transcript


title: Prostate normal PAN0107 transcript


title: Xenograft LNCaP104S transcript


title: Cell line LNCaP transcript


title: Cell line DU145 transcript


title: Xenograft LNCaP104R transcript


title: Prostate tumor PCA0190 exon


title: Prostate tumor PCA0189 exon


title: Prostate tumor PCA0193 exon


title: Prostate tumor PCA0188 exon


title: Prostate tumor PCA0184 exon


title: Prostate tumor PCA0211 transcript


title: Prostate tumor PCA0213 transcript


title: Prostate tumor PCA0215 transcript


title: Prostate tumor PCA0210 transcript


title: Prostate tumor PCA0209 transcript


title: Prostate tumor PCA0208 transcript


title: Prostate tumor PCA0207 transcript


title: Prostate tumor PCA0187 exon


title: Prostate tumor PCA0182 exon


title: Prostate tumor PCA0181 exon

value: Primary tumor


title: Prostate tumor PCA0180 exon


title: Prostate tumor PCA0206 transcript


title: Prostate tumor PCA0170 exon


title: Prostate tumor PCA0179 exon


title: Prostate tumor PCA0193 transcript


title: Prostate tumor PCA0200 transcript


title: Prostate tumor PCA0199 transcript


title: Prostate tumor PCA0201 transcript


title: Prostate tumor PCA0175 exon


title: Prostate tumor PCA0194 transcript


title: Prostate tumor PCA0174 exon


title: Prostate tumor PCA0189 transcript


title: Prostate tumor PCA0190 transcript


title: Prostate tumor PCA0171 exon


title: Prostate tumor PCA0165 exon


title: Prostate tumor PCA0172 exon


title: Prostate tumor PCA0188 transcript


title: Prostate tumor PCA0169 exon


title: Prostate tumor PCA0162 exon


title: Prostate tumor PCA0184 transcript


title: Prostate tumor PCA0173 exon


title: Prostate tumor PCA0168 exon


title: Prostate tumor PCA0164 exon


title: Prostate tumor PCA0176 exon


title: Prostate tumor PCA0167 exon


title: Prostate tumor PCA0187 transcript


title: Prostate tumor PCA0180 transcript


title: Prostate tumor PCA0181 transcript


title: Prostate tumor PCA0163 exon


title: Prostate tumor PCA0178 transcript


title: Prostate tumor PCA0179 transcript


title: Prostate tumor PCA0178 exon


title: Prostate tumor PCA0157 exon


title: Prostate tumor PCA0174 transcript


title: Prostate tumor PCA0160 exon


title: Prostate tumor PCA0161 exon


title: Prostate tumor PCA0175 transcript


title: Prostate tumor PCA0182 transcript


title: Prostate tumor PCA0172 transcript


title: Prostate tumor PCA0173 transcript


title: Prostate tumor PCA0159 exon


title: Prostate tumor PCA0171 transcript


title: Prostate tumor PCA0151 exon


title: Prostate tumor PCA0170 transcript


title: Prostate tumor PCA0156 exon


title: Prostate tumor PCA0169 transcript


title: Prostate tumor PCA0155 exon


title: Prostate tumor PCA0167 transcript


title: Prostate tumor PCA0150 exon


title: Prostate tumor PCA0168 transcript


title: Prostate tumor PCA0165 transcript


title: Prostate tumor PCA0176 transcript


title: Prostate tumor PCA0158 exon


title: Prostate tumor PCA0146 exon


title: Prostate tumor PCA0163 transcript


title: Prostate tumor PCA0164 transcript


title: Prostate tumor PCA0149 exon


title: Prostate tumor PCA0135 exon


title: Prostate tumor PCA0145 exon


title: Prostate tumor PCA0141 exon


title: Prostate tumor PCA0136 exon


title: Prostate tumor PCA0133 exon


title: Prostate tumor PCA0130 exon


title: Prostate tumor PCA0147 exon


title: Prostate tumor PCA0129 exon


title: Prostate tumor PCA0144 exon


title: Prostate tumor PCA0132 exon


title: Prostate tumor PCA0134 exon


title: Prostate tumor PCA0160 transcript


title: Prostate tumor PCA0159 transcript


title: Prostate tumor PCA0127 exon


title: Prostate tumor PCA0156 transcript


title: Prostate tumor PCA0161 transcript


title: Prostate tumor PCA0162 transcript


title: Prostate tumor PCA0158 transcript


title: Prostate tumor PCA0157 transcript


title: Prostate tumor PCA0151 transcript


title: Prostate tumor PCA0150 transcript


title: Prostate tumor PCA0126 exon


title: Prostate tumor PCA0124 exon


title: Prostate tumor PCA0128 exon


title: Prostate tumor PCA0149 transcript


title: Prostate tumor PCA0146 transcript


title: Prostate tumor PCA0147 transcript


title: Prostate tumor PCA0145 transcript


title: Prostate tumor PCA0125 exon


title: Prostate tumor PCA0120 exon


title: Prostate tumor PCA0144 transcript


title: Prostate tumor PCA0122 exon


title: Prostate tumor PCA0141 transcript


title: Prostate tumor PCA0136 transcript


title: Prostate tumor PCA0155 transcript


title: Prostate tumor PCA0134 transcript


title: Prostate tumor PCA0132 transcript


title: Prostate tumor PCA0135 transcript


title: Prostate tumor PCA0123 exon


title: Prostate tumor PCA0133 transcript


title: Prostate tumor PCA0130 transcript


title: Prostate tumor PCA0119 exon


title: Prostate tumor PCA0129 transcript


title: Prostate tumor PCA0110 exon


title: Prostate tumor PCA0126 transcript


title: Prostate tumor PCA0125 transcript


title: Prostate tumor PCA0113 exon


title: Prostate tumor PCA0111 exon


title: Prostate tumor PCA0115 exon


title: Prostate tumor PCA0127 transcript


title: Prostate tumor PCA0117 exon


title: Prostate tumor PCA0112 exon


title: Prostate tumor PCA0109 exon


title: Prostate tumor PCA0118 exon


title: Prostate tumor PCA0104 exon


title: Prostate tumor PCA0114 exon


title: Prostate tumor PCA0107 exon


title: Patient 07_Frozen_mirVana

city: Toronto

first: Patricia

last: Reis

state: Ontario

address: 610 University Avenue

department: Applied Molecular Oncology

country: Canada

institute: University Health Network

description: Total RNA was amplified using a quantitative PCR-based approach (TaqMan Low Density Array platform containing 365 microRNA sequences).

data_processing: Mixed model regression analysis was used to adjust for repeated measures of the same sample and the potential dilution effects.  This, as well as bar plots, were generated using SAS software, Version 9.1 of the SAS System, Copyright ©2009 SAS Institute Inc. SAS and all other SAS Institute Inc. product or service names are registered trademarks or trademarks of SAS Institute Inc., Cary, NC, USA.  3-D principal component analysis (PCA) was performed using Partek® software, version 6.4 Copyright © 2009 Partek Inc., St. Louis, MO, USA.  All other statistical analysis and plotting were performed using the R statistical environment (R Development Core Team, 2008, v2.8.1), on the IBM HS21XM BladeCentre cluster running CentOS 5.1.  Additional plotting functions were used from the fields (Furrer et al. 2009, v.5.0.2) and RColorBrewer (Neuwirth 2007, v1.0-2) R packages.

source_name: Lymph node

extract_protocol: RNA from FFPE samples was extracted using the RecoverAll Total Nucleic Acid Isolation Kit (Ambion). RNA from the fresh-frozen samples was obtained using two different extraction methods: mirVana Total RNA Isolation Kit (Ambion) and TRIzol (invitrogen), according to the manufactirer's instructions.

tag: histological diagnosis

value: Mantle cell lymphoma

tag: method of preservation

value: Fresh frozen


title: Prostate tumor PCA0124 transcript


title: Prostate tumor PCA0108 exon


title: Prostate tumor PCA0105 exon


title: Patient 07_FFPE

value: FFPE


title: Prostate tumor PCA0100 exon


title: Prostate tumor PCA0101 exon


title: Patient 06_Frozen_mirVana

source_name: Gastrointestinal tract

value: Mantle cell lymphoma; multiple lymphomatous polyposis


title: Patient 06_Frozen_TRIzol


title: Prostate tumor PCA0103 exon


title: Prostate tumor PCA0097 exon


title: Patient 07_Frozen_TRIzol


title: Prostate tumor PCA0122 transcript


title: Prostate tumor PCA0128 transcript


title: Patient 05_Frozen_TRIzol


title: Prostate tumor PCA0119 transcript


title: Prostate tumor PCA0094 exon


title: Prostate tumor PCA0120 transcript


title: Prostate tumor PCA0096 exon


title: Prostate tumor PCA0118 transcript


title: Prostate tumor PCA0089 exon


title: Patient 05_Frozen_mirVana


title: Patient 05_FFPE


title: Prostate tumor PCA0123 transcript


title: Prostate tumor PCA0099 exon


title: Prostate tumor PCA0092 exon


title: Patient 04_Frozen_TRIzol

value: Moderate reactive hyperplasia


title: Patient 04_Frozen_mirVana


title: Prostate tumor PCA0114 transcript


title: Patient 06_FFPE


title: Patient 03_Frozen_TRIzol

value: Florid hyperplasia


title: Prostate tumor PCA0093 exon


title: Prostate tumor PCA0090 exon


title: Prostate tumor PCA0112 transcript


title: Prostate tumor PCA0113 transcript


title: Prostate tumor PCA0095 exon


title: Patient 03_Frozen_mirVana


title: Patient 03_FFPE


title: Prostate tumor PCA0110 transcript


title: Prostate tumor PCA0086 exon


title: Prostate tumor PCA0087 exon


title: Prostate tumor PCA0109 transcript


title: Patient 02_Frozen_mirVana

value: Mild reactive hyperplasia


title: Prostate tumor PCA0108 transcript


title: Patient 02_Frozen_TRIzol


title: Patient 02_FFPE


title: Prostate tumor PCA0111 transcript


title: Prostate tumor PCA0107 transcript


title: Prostate tumor PCA0117 transcript


title: Patient 04_FFPE


title: Prostate tumor PCA0115 transcript


title: Prostate tumor PCA0080 exon


title: Prostate tumor PCA0084 exon


title: Patient 01_FFPE_100ng(62.5Xdil)


title: Patient 01_FFPE_100ng(7.5Xdil)


title: Patient 01_FFPE_66.7ng(5Xdil)


title: Patient 01_FFPE_100ng(30Xdil)


title: Prostate tumor PCA0075 exon


title: Prostate tumor PCA0104 transcript


title: Prostate tumor PCA0074 exon


title: Patient 01_FFPE_200ng(62.5xdil)


title: Prostate tumor PCA0105 transcript


title: Patient 01_FFPE_200ng(30xdil)


title: Prostate tumor PCA0103 transcript


title: Prostate tumor PCA0100 transcript


title: Prostate tumor PCA0101 transcript


title: Prostate tumor PCA0065 exon


title: Prostate tumor PCA0081 exon


title: Prostate tumor PCA0099 transcript


title: Prostate tumor PCA0066 exon


title: Prostate tumor PCA0097 transcript


title: Prostate tumor PCA0083 exon


title: Prostate tumor PCA0077 exon


title: Patient 01-FFPE_100ng dupl


title: Prostate tumor PCA0096 transcript


title: Prostate tumor PCA0068 exon


title: Prostate tumor PCA0082 exon


title: Prostate tumor PCA0064 exon


title: Prostate tumor PCA0094 transcript


title: Patient 01_FFPE_100ng


title: Prostate tumor PCA0062 exon


title: Prostate tumor PCA0095 transcript


title: Prostate tumor PCA0063 exon


title: Patient 01_FFPE_200ng


title: Prostate tumor PCA0092 transcript


title: Prostate tumor PCA0073 exon


title: Patient 01-FFPE_25ng dupl


title: Patient 01-FFPE_50ng dupl


title: Prostate tumor PCA0093 transcript


title: Patient 01_FFPE_50ng


title: Patient 01_FFPE_25ng


title: Prostate tumor PCA0058 exon


title: Patient 01-FFPE_10ng dupl


title: Prostate tumor PCA0087 transcript


title: Patient 01-FFPE_200ng dupl


title: Prostate tumor PCA0090 transcript


title: Prostate tumor PCA0089 transcript


title: Prostate tumor PCA0086 transcript


title: Prostate tumor PCA0054 exon


title: Prostate tumor PCA0056 exon


title: Prostate tumor PCA0084 transcript


title: Patient 01_FFPE_10ng


title: Sirt1KO#1

city: cambridge

first: wenyuan

last: wang

state: MA

address: 43 vassar st

department: BCS

institute: MIT

hyb_protocol: Labeled RNA samples were hybridized on the miRCURY LNA Array (v11.0) along with a Hy5-labeled common reference, composed of a pool of equal quantities of all 4 samples.

scan_protocol: Scans were performed and quantified by Exiqon A/S using GenePix software (Molecular Devices).

data_processing: The data were exported to Microsoft Excel worksheets, log2-transformed, and analyzed. The normalization involved normalization with a global Lowess algorithm.

label_protocol: RNA samples were sent to Exiqon A/S (Vedbaek, Denmark) where they were labeled using the miRCURY Hy3/Hy5 labeling kit.

extract_protocol: Total hippocampul RNA was isolated using TRIzol (Invitrogen) followed by purification over a glass fiber filter column (mirVana; Ambion), according to manufacturers' instructions. RNA quality was assessed using an Agilent BioAnalyzer 2100.

tag: strain

value: Male

value: hippocampus

source_name: common reference (comprised of an equal mixture of all 4 experimental samples)


title: Ctrl#1

source_name: wild-type


title: Ctrl#2


title: Prostate tumor PCA0082 transcript

value: Prostate


title: Prostate tumor PCA0080 transcript


title: Prostate tumor PCA0057 exon


title: Prostate tumor PCA0050 exon


title: Prostate tumor PCA0081 transcript


title: Prostate tumor PCA0083 transcript


title: Prostate tumor PCA0040 exon


title: Prostate tumor PCA0077 transcript


title: Prostate tumor PCA0052 exon


title: Sirt1KO#2


title: Prostate tumor PCA0075 transcript


title: Prostate tumor PCA0036 exon


title: Prostate tumor PCA0037 exon


title: Prostate tumor PCA0074 transcript


title: Prostate tumor PCA0038 exon


title: Control 48h rep 3

first: Allen

last: Volchuk

address: 101 College Street

department: Cellular & Molecular Biology

institute: Toronto General Research Inst.

description: Stable Insulinoma cell line (clone #4S2) expressing doxycycline-inducible proinsulin C96Y-GFP

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 17 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data sets were analyzed using GeneSpring software (Version 7.1) (Agilent Technologies) and statistical analysis was performed using GeneSpring software according to the manufacturer's specifications. Raw data is filtered on expression and this data was used for downstream analysis. Quality control reports were generated using R and Bioconductor. Significance analysis was done as there were no replicates done per experiment (data sets). GeneSpring-normalized signal intensities were unavailable for the GEO submission.

organism: Rattus norvegicus

source_name: Control 48h

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: Stable proinsulin 96Y-GFP expressing INS-1 insulinoma cell line was grown under standard growth conditions in RPMI media

extract_protocol: Total RNA was isolated by Trizol Reagent (Invitrogen) followed by Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Cells were seeded the day before the experimental procedure then treated or not with doxycyline (2 ug/ml) for 24h, 48h or days


title: Prostate tumor PCA0035 exon


title: Doxycyline-treated 48h rep 3

source_name: Doxycyline-treated 48h

value: Stable Insulinoma cell line (clone #4S2) expressing doxycycline-inducible proinsulin C96Y-GFP


title: Prostate tumor PCA0073 transcript


title: Prostate tumor PCA0034 exon


title: Control 5 day rep 3

source_name: Control 5 day


title: Prostate tumor PCA0068 transcript


title: Prostate tumor PCA0066 transcript


title: Doxycyline-treated 48h rep 2


title: Doxycyline-treated 24h rep 3

source_name: Doxycyline-treated 24h


title: Control 48h rep 2


title: Doxycyline-treated 5 day rep 3

source_name: Doxycyline-treated 5 day


title: Prostate tumor PCA0032 exon


title: Prostate tumor PCA0065 transcript


title: Prostate tumor PCA0033 exon


title: Prostate tumor PCA0064 transcript


title: Prostate tumor PCA0031 exon


title: Prostate tumor PCA0063 transcript


title: Prostate tumor PCA0029 exon


title: Doxycyline-treated 48h rep 1


title: Prostate tumor PCA0058 transcript


title: Doxycyline-treated 5 day rep 2


title: Prostate tumor PCA0028 exon


title: Control 5 day rep 2


title: Prostate tumor PCA0027 exon


title: Prostate tumor PCA0025 exon


title: Prostate tumor PCA0026 exon


title: Prostate tumor PCA0057 transcript


title: Prostate tumor PCA0056 transcript


title: Control 24h rep 3

source_name: Control 24h


title: Control 48h rep 1


title: Prostate tumor PCA0024 exon


title: Doxycyline-treated 24h rep 2


title: Prostate tumor PCA0054 transcript


title: Prostate tumor PCA0022 exon


title: Control 24h rep 2


title: Prostate tumor PCA0052 transcript


title: Doxycyline-treated 5 day rep 1


title: Control 5 day rep 1


title: Prostate tumor PCA0050 transcript


title: Prostate tumor PCA0020 exon


title: Doxycyline-treated 24h rep 1


title: Prostate tumor PCA0018 exon


title: Prostate tumor PCA0021 exon


title: Prostate tumor PCA0030 exon


title: Control 24h rep 1


title: Prostate tumor PCA0062 transcript


title: Prostate tumor PCA0017 exon


title: Prostate tumor PCA0015 exon


title: Prostate tumor PCA0037 transcript


title: SV40-immortalized_human_corneal_epithelial_cells_rep3

city: Helsinki

first: Kati-Sisko

last: Vellonen

address: Viikinkaari 5 E (P.O.Box 56)

department: Centre for Drug Research

country: Finland

institute: University of Helsinki, Faculty of Pharmacy

description: Sample comprises of RNA isolated from immortalized human corneal epithelial cells cultured on the collagen coated permeable support at the air-liquid interface.

hyb_protocol: The hybridization cocktail was made according to Affymetrix protocols. The cocktail was heated to 99°C and then kept on heat block for 5 mins at 45°C. The probe array was incubated with 1X hybridization buffer (MES, 1M [Na], 20mM EDTA, 0.01% Tween) for 10 mins at 45°C. Samples were hybridized for 16 h at 45°C using a final volume of 200 µl. GeneChip Fluidics Station 450 using fluidics protocol EukGE-WS2v4 was utilized for washing. Hybridized microarrays were stained with a streptavidin-phycoerythrin (SAPE) reagent.

scan_protocol: Hybridized microarrays were stained with a streptavidin-phycoerythrin (SAPE) reagent and fluorescence images were captured using an Agilent G2500A laser scanner.

data_processing: The data were analyzed with R v. 2.8.0 Bioconductor. Probes present in HGU133A were re-annotated according to Entrez Gene database using custom CDF v. 10. RMA algorithm was used to calculate relative gene expression values.

source_name: SV40-immortalized human corneal epithelial cell line

label_protocol: Biotin labeling of cRNA was performed using the ENZO RNA transcript labeling Kit 9 (BioArray High Yeald Labeling Kit, P/N 900182). IVT cRNA cleanup and quantitation, cRNA fragmentation, control targets were performed according to Affymetrix protocols. cDNA was synthesized using T7-(dT)24 Primer (Genset Corp) and Superscript Choice System (Gibco BRL Life technologies).

growth_protocol: iHCE cells (passages of 22–23) were cultured in DMEM/Ham’s F12 (1:1) (Gibco, Invitrogen, Paisley, U.K.), 15% FBS (Gibco, Invitrogen), 0.3 mg/ml L-glutamine (Gibco, Invitrogen), 5 µg/ml insulin (Gibco, Invitrogen), 0.1 µg/ml cholera toxin (Calbiochem, La Jolla, CA), 10 ng/ml EGF (Invitrogen, Carlsbad, CA), 0.5% dimethylsulfoxide (DMSO; Sigma, St. Louis, MO), 0.1 mg/ml streptomycin and 1000 IU/ml penicillin (Gibco, Invitrogen). Cells were seeded on collagen coated permeable inserts (Transwell® Polyester Membrane Insert, Costar, Cambridge, MA) and maintained submerged into medium. After one week in culture the medium was supplemented with 40 µg/ml L(+)-ascorbic acid (Sigma, St. Louis, MO) and cells were changed to grow at the air-liquid interface (medium in the apical side was removed). Trans-epithelial electrical resistance (TEER) was followed with an EVOM resistance meter in Endohm chambers (World Precision Instruments, Sarasota, FL).

extract_protocol: Total RNA was isolated using TriReagent (Sigma, St. Louis, MO) and RNA samples were further purified using RNAeasy spin columns (Qiagen, Valencia, CA). RNA concentration and purity were determined by measuring absorbances (260 nm and 280 nm) and integrity was determined using the Agilent 2100 BioChip (Agilent Technologies., Palo Alto, CA).

treatment_protocol: Standard culture protocol

tag: teer

value: 468 Ω x cm2


title: SV40-immortalized_human_corneal_epithelial_cells_rep1

value: 489 Ω x cm2


title: Prostate tumor PCA0036 transcript

value: prostate cancer


title: SV40-immortalized_human_corneal_epithelial_cells_rep2

value: 439 Ω x cm2


title: Untreated Myd88 knockout - repeat 5 - mAdbID:102775

city: Frederick

first: Rosalba

last: Salcedo

state: MD

address: 1050 Boyles Street, Bldg. 567

institute: SAIC-NCI

description: mAdb experiment ID: 102775

hyb_protocol: Hybridization Protocol Other: Test aRNA was loaded into Affymetrix whole genome mouse arrays 430 2.0 and hybridized overnight in a hybridization oven.

scan_protocol: Affy Scanning Protocol Other: Scanning was performed by the Affymetrix GeneChip Scanner 7G.

data_processing:
BRBArray Tools Data Processing Protocol
Calculation Method: Resulting data files analyzed using BRBArrayTools, developed by the Biometric Research Branch, National Cancer Institute (Rubinfeld et al., 1997) (http//:linus.nci.nih.gov/BRB-ArrayTools.html. Data were normalized using median over the entire array as the reference because single color labeling technology was used. Gene ratios were average corrected across experimental samples and displayed according to an uncentered correlation algorithm (Ross et al., 2000).

source_name: Untreated Myd88 knockout

label_protocol:
Labeling Protocol
Other: Post-hybridization arrays were labeled using an Affymetrix fluidics wash and stain station.

extract_protocol:
Extraction Protocol
Other: Total RNA was extracted using Qiagen reagent according to the manufacturer’s instructions. RNA was digested using the RNase-Free Dnase Set and amplified into anti-sense RNA (aRNA) according to the Affymetrix gene expression protocol. The quality of both, total RNA and secondarily amplified RNA was tested using an Agilent Bioanalyzer 2000 (Agilent Technologies, Palo Alto, CA).

value: C57 BL6NCr

value: Distal colon


title: Prostate tumor PCA0035 transcript

value: Primary tumor


title: Prostate tumor PCA0040 transcript


title: Prostate tumor PCA0014 exon


title: Prostate tumor PCA0034 transcript


title: Untreated Myd88 knockout - repeat 2 - mAdbID:102772

description: mAdb experiment ID: 102772


title: Untreated Myd88 knockout - repeat 4 - mAdbID:102774

description: mAdb experiment ID: 102774


title: Prostate tumor PCA0032 transcript


title: Prostate tumor PCA0013 exon


title: Prostate tumor PCA0010 exon


title: Untreated Myd88 knockout - repeat 1 - mAdbID:102771

description: mAdb experiment ID: 102771


title: Prostate tumor PCA0038 transcript


title: Untreated Myd88 knockout - repeat 3 - mAdbID:102773

description: mAdb experiment ID: 102773


title: Prostate tumor PCA0033 transcript


title: Untreated WT - repeat 5 - mAdbID:102769

description: mAdb experiment ID: 102769

source_name: Untreated WT


title: Prostate tumor PCA0030 transcript


title: Prostate tumor PCA0012 exon


title: Untreated WT - repeat 6 - mAdbID:102770

description: mAdb experiment ID: 102770


title: Prostate tumor PCA0029 transcript


title: Untreated WT - repeat 4 - mAdbID:102768

description: mAdb experiment ID: 102768


title: Untreated WT - repeat 3 - mAdbID:102767

description: mAdb experiment ID: 102767


title: Untreated WT - repeat 2 - mAdbID:102766

description: mAdb experiment ID: 102766


title: Prostate tumor PCA0008 exon


title: Prostate tumor PCA0028 transcript


title: Prostate tumor PCA0026 transcript


title: Untreated Myd88 knockout - repeat 6 - mAdbID:102776

description: mAdb experiment ID: 102776


title: Prostate tumor PCA0009 exon


title: Prostate tumor PCA0027 transcript


title: Treated Myd88 knockout - repeat 10 - mAdbID:102764

description: mAdb experiment ID: 102764

source_name: Treated Myd88 knockout

treatment_protocol:
Treatment type: compound
Agent: Azoxymethane (AOM), Dextran Sodium Sulfate (DSS)
Treatment dose: AOM (10mg/kg), DSS (2%)
In-vivo treatment: Mice six to eight weeks of age were injected i.p. with AOM (10 mg/kg) in 0.2 ml saline. One week after AOM administration, DSS at 2% was administered in the drinking water for 3 consecutive days, thereafter mice were euthanized.

tag: disease state

value: colitis


title: Prostate tumor PCA0011 exon


title: Untreated WT - repeat 1 - mAdbID:102765

description: mAdb experiment ID: 102765


title: Prostate tumor PCA0025 transcript


title: Prostate tumor PCA0022 transcript


title: Prostate tumor PCA0024 transcript


title: Prostate tumor PCA0007 exon


title: Treated Myd88 knockout - repeat 9 - mAdbID:102763

description: mAdb experiment ID: 102763


title: Prostate tumor PCA0002 exon


title: Prostate tumor PCA0003 exon


title: Treated Myd88 knockout - repeat 7 - mAdbID:102761

description: mAdb experiment ID: 102761


title: Prostate tumor PCA0021 transcript


title: Prostate tumor PCA0020 transcript


title: Prostate tumor PCA0005 exon


title: Prostate tumor PCA0015 transcript


title: Prostate tumor PCA0018 transcript


title: Prostate tumor PCA0017 transcript


title: Treated Myd88 knockout - repeat 5 - mAdbID:102759

description: mAdb experiment ID: 102759


title: Prostate tumor PCA0014 transcript


title: Prostate tumor PCA0001 exon


title: Treated Myd88 knockout - repeat 3 - mAdbID:102757

description: mAdb experiment ID: 102757


title: Treated Myd88 knockout - repeat 2 - mAdbID:102756

description: mAdb experiment ID: 102756


title: Treated Myd88 knockout - repeat 4 - mAdbID:102758

description: mAdb experiment ID: 102758


title: Treated Myd88 knockout - repeat 8 - mAdbID:102762

description: mAdb experiment ID: 102762


title: 1218-6C

city: Oxford

first: Shoumo

last: Bhattacharya

address: Roosevelt Drive

department: RDM Cardiovascular Medicine

country: United Kingdom

institute: Wellcome Centre For Human Genetics, University of Oxford

description: Embryonic_Control maternal diet, wildtype_replicate3

hyb_protocol: Samples were hybridised for 16 hours to an Illumina Sentrix Mouse Whole Genome Ref 6 v2 chip.  Washing, staining and scanning was performed according to the manufacturer’s protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data generated from scanning was imported into Illumina BeadStudio version 3.2.6 to generate signal values for each bead type. These data were exported to the R statistical computing language where it was background corrected, and transformed and normalised using the BioConductor package, vsn2 (Huber et al. 2002).

label: Biotin

source_name: Control maternal diet, wildtype

label_protocol: Standard Illumina labelling protocol was used to prepare biotinylated cRNA

growth_protocol: Female Cited2+/— mice were fed with Beekay Rat and Mouse Diet (BK002P) between weaning and 6 weeks of age, and then were randomly assigned to specially formulated high-fat or control diets, which were provided ad libitum. At baseline and after 8 weeks on the diet, the mice were weighed and a 6-hour fasting blood sample was collected. Blood glucose and plasma insulin were measured. Following 8 weeks on diet, Cited2+/— female mice were mated with Cited2+/— males, and the diet continued through pregnancy.

extract_protocol: Qiagen Rneasy Micro Kit was used as per manufacturer's instructions.  Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Embryos were harvested at 8.5 dpc in chilled DEPC-PBS, dissected out of the yolk sac, the allantois was removed, somites counted for the purposes of stage-matching, then flash frozen in liquid nitrogen.

tag: maternal diet

value: Control

tag: genotype/variation

value: Wildtype

tag: developmental stage

value: Embryonic (8.5 days post coitum)


title: 1312-1HF

description: Embryonic_High fat maternal diet, wildtype_replicate3

source_name: High fat maternal diet, wildtype

value: High fat


title: Prostate tumor PCA0013 transcript

source_name: human prostate

tag: sample id

tag: tissue


title: Treated WT - repeat 10 - mAdbID:102754

description: mAdb experiment ID: 102754

source_name: Treated WT

value: wild-type


title: Prostate tumor PCA0012 transcript


title: Ebf1 ChIP-chip 1

hyb_protocol: Samples were hybridized to 2006-07-18-MM8-RefSeq_promoter tiling arrays (NimbleGen)

scan_protocol: Data was scanned using Nimblescan version 2.3.75

data_processing: Labeling, hybridization, scanning and data processing were performed by Imagenes (Berlin, Germany)

source_name: cultured primary bone marrow pro-B cells

label_protocol: ChIP DNA was labeled by random priming, between 8.7 and 10.5 pmol/ug Dye-incorporation rate was achieved.

growth_protocol: Cells were grown in RPMI1640 with 10% fetal bovine serum and 10ng/ml Interleukin 7 on a layer of OP9 stromal cells

extract_protocol: For ChIP, proteins were crosslinked to DNA in intact cells by addition of 0.9% (v/v) final concentration of formaldehyde to a cell suspension in growth medium (106 cells/ml) followed by an incubation for 5 minutes at 37°C. The crosslinking reaction was stopped by addition of 11% of the suspension volume of an ice cold 1M solution of glycine. The cells were spun down immediately (5min, 2000g) and washed three times with ice cold PBS. After the final wash the cells were lysed in 600µl L2-buffer (50mM Tris pH 8.0, 5mM EDTA, 1% (w/v) SDS) per 5x 106 cells. To shear the chromatin into pieces of a few hundred base pairs, the cell lysate was sonicated using a vibra cell sonifier (sonics) at an amplitude setting of 45%. Sonication was performed in 600µl aliquots applying 6 pulses of 10 seconds of ultrasound. Between the pulses the solution was cooled on ice for 40 seconds. 600µl of magnetic beads coated with sheep anti rabbit antibody (Dynabeads M-280 sheep anti-rabbit IgG, Dynal/Invitrogen) were washed three times with 10ml of a solution of 0.5% (w/v) BSA in PBS and then resuspended in 1ml of this blocking solution. 100µg of antibody were added to the suspension and the reaction was rotated over night at 4°C. To remove unbound antibody the beads were washed three times with PBS following the incubation. Finally the beads were resuspended in 600µl dilution buffer (50mM Tris pH 8.0, 5mM EDTA, 200mM NaCl, 0.5% (v/v) NP40). The IP reaction was set up by combining 150µl of cell lysate, 1350µl of dilution buffer, 100µl beads suspension and 10µl of a 100mM solution of PMSF in ethanol. This reaction was rotated over night at 4°C. To remove unbound proteins and DNA, the beads were washed five times with wash buffer (20mM Tris pH 8.0, 2mM EDTA, 0.1 (w/v) SDS, 1% (v/v) NP40, 500mM NaCl) and four times with TE-buffer using a magnetic particle concentrator (Dynal). The bound chromatin was eluted twice by addition of 50µl of ChIP elution buffer (10mM Tris pH 8.0, 1mM EDTA, 2% (w/v) SDS) to the beads followed by centrifugation (10000g, 1min). To reverse the crosslinking reaction, the eluted chromatin was incubated at 65°C over night. Finally, pure DNA was extracted from the ChIP samples using the Qiaquick PCR purification kit (Qiagen). For microarray analysis the DNA from ChIP experiments was amplified using the Whole Genome Amplification and Whole Genome Reamplification Kits (Sigma). For the first amplification, 10µl of ChIP sample were used. For reamplification the amplified material was diluted to 1ng/µl before using 10ml per PCR reaction.

treatment_protocol: after crosslinking and sonication (see below) an aliquot of the input material was decrosslinked and 10ng of this material was used in the amplification steps (see below)

tag: sample type

value: Input

tag: cell type

treatment_protocol: The full sample preparation and ChIP protocol (see below) was applied on these samples.

value: chromatin IP

tag: antibody

value: polyclonal Ebf1 Ab


title: 1214-5C

description: Embryonic_Control maternal diet, wildtype_replicate2


title: Treated Myd88 knockout - repeat 1 - mAdbID:102755

description: mAdb experiment ID: 102755

tag: genotype


title: Prostate tumor PCA0011 transcript

value: Prostate

tag: disease status


title: Treated WT - repeat 7 - mAdbID:102751

description: mAdb experiment ID: 102751


title: Prostate tumor PCA0008 transcript


title: Treated WT - repeat 9 - mAdbID:102753

description: mAdb experiment ID: 102753


title: Prostate tumor PCA0010 transcript


title: Treated WT - repeat 8 - mAdbID:102752

description: mAdb experiment ID: 102752


title: Treated WT - repeat 4 - mAdbID:102748

description: mAdb experiment ID: 102748


title: 1307-2HF

description: Embryonic_High fat maternal diet, wildtype_replicate2


title: Treated WT - repeat 6 - mAdbID:102750

description: mAdb experiment ID: 102750


title: 1214-3C

description: Embryonic_Control maternal diet, Cited2 -/-_replicate2

source_name: Control maternal diet, Cited2 -/-

value: Cited2 -/-


title: Prostate tumor PCA0007 transcript


title: 1216-4HF

description: Embryonic_High fat maternal diet, Cited2 -/-_replicate3

source_name: High fat maternal diet, Cited2 -/-


title: Treated WT - repeat 5 - mAdbID:102749

description: mAdb experiment ID: 102749


title: 1216-2HF

description: Embryonic_High fat maternal diet, wildtype_replicate1


title: 1295-2C

description: Embryonic_Control maternal diet, Cited2 -/-_replicate3


title: Prostate tumor PCA0005 transcript


title: 1295-1C

description: Embryonic_Control maternal diet, wildtype_replicate1


title: Prostate tumor PCA0009 transcript


title: Treated WT - repeat 2 - mAdbID:102746

description: mAdb experiment ID: 102746


title: Prostate tumor PCA0002 transcript


title: Prostate tumor PCA0031 transcript


title: Treated WT - repeat 1 - mAdbID:102745

description: mAdb experiment ID: 102745


title: Prostate tumor PCA0001 transcript


title: 1312-6HF

description: Embryonic_High fat maternal diet, Cited2 -/-_replicate2


title: Treated WT - repeat 3 - mAdbID:102747

description: mAdb experiment ID: 102747


title: Prostate tumor PCA0003 transcript


title: 1218-4C

description: Embryonic_Control maternal diet, Cited2 -/-_replicate1


title: Ebf1 ChIP-chip 2

value: cultured primary bone marrow pro-B cells


title: pCR breast biopsy, sample 19 rep 2

status: Public on Jun 23 2010

city: Nashville

first: Jennifer

last: Pietenpol

state: TN

address: 652 Preston Research Building, 23rd Avenue South at Pierce

institute: Vanderbilt University Medical Center

description: Gene expression data from pretreatment breast needle biopsies

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed for differentially expressed probes between responder and non-responder patient tumor samples. Data was RMA summarized, quantile normalized and baseline transformed to the median of all samples using GeneSpring GX Software (Agilent).

source_name: breast needle biopsy, pretreatment, sample 19 rep 2

label_protocol: standard Affymetrix protocol

growth_protocol: all samples are from frozen primary breast needle biopsies

extract_protocol: frozen biopsies were sectioned, laser capture microdissected for invasive tumor cells, and total RNA was isolated according to the manufacturer's instructions.

treatment_protocol: all samples are from pretreatment patients

tag: pathological complete response

value: yes

value: Breast tumor biopsy


title: pCR breast biopsy, sample 18 rep 1

source_name: breast needle biopsy, pretreatment, sample 18 rep 1


title: non-pCR breast biopsy, sample 13 rep 2

source_name: breast needle biopsy, pretreatment, sample 13 rep 2

value: no


title: pCR breast biopsy, sample 19 rep 1

source_name: breast needle biopsy, pretreatment, sample 19 rep 1


title: pCR breast biopsy, sample 15 rep 2

source_name: breast needle biopsy, pretreatment, sample 15 rep 2


title: pCR breast biopsy, sample 16 rep 1

source_name: breast needle biopsy, pretreatment, sample 16 rep 1


title: non-pCR breast biopsy, sample 10 rep 1

source_name: breast needle biopsy, pretreatment, sample 10 rep 1


title: non-pCR breast biopsy, sample 5 rep 2

source_name: breast needle biopsy, pretreatment, sample 5 rep 2


title: non-pCR breast biopsy, sample 8 rep 1

source_name: breast needle biopsy, pretreatment, sample 8 rep 1


title: Treated Myd88 knockout - repeat 6 - mAdbID:102760

description: mAdb experiment ID: 102760

source_name: Treated Myd88 knockout

value: C57 BL6NCr

value: Distal colon


title: non-pCR breast biopsy, sample 10 rep 2

source_name: breast needle biopsy, pretreatment, sample 10 rep 2


title: clone 14 control

city: Farmington

first: Richard

middle: E

last: Mains

state: CT

address: 263 Farmington Ave

department: Neuroscience

institute: University of Connecticut Health Center

description: clone 14 AtT-20 cells treated with control medium for 48 hrs

hyb_protocol: Labeled cRNA samples were hybridized to an Illumina MouseWG-6 v 2.0 Expression BeadChip for 16 h at 58°C, following the manufacturer's instructions. BeadChips were washed and stained with streptavidin-Cy3.

scan_protocol: BeadChips were scanned using an Illumina BeadArray Reader with confocal laser at 0.8 µm resolution creating one image file for the Cy3 channel.

data_processing: Microarray data were extracted, normalized and analyzed using Illumina GenomeStudio software(BeadStudio Gene Expression Analysis Module 3.2.7). Intensity data were normalized using the cubic spline algorithm.

label_protocol: 300 ng total RNA was reverse transcribed to cDNA using a T7 oligo(dT) primer.  Second-strand cDNA was synthesized, in vitro transcribed, and labeled by incorporation of biotin-16-UTP.

growth_protocol: AtT-20 mouse corticotrope tumor cells stably transfected with doxycycline-inducible rat PAM-1 (iPAM) were maintained in DMEM-F12, penicillin/streptomycin, net 25 mM HEPES, 10% tetracycline-free fetal bovine serum (Hyclone). Cells were passaged weekley using trypsin, split 1:50.

extract_protocol: The Trizol protocol (Invitrogen) was followed with minor modifications. Cells (~3 million) were scraped off the dish, pelleted, suspended in 1 ml Trizol, disrupted with a polytron, extracted with 0.25 ml chloroform, the aqueous phase was precipitated overnight with 1 ml isopropanol, washed in 1 ml 75% ethanol, and suspended in 20 ml DEPC water. The OD @ 260nm and 280 nm was determined for a 1:100 dilution, and 1 ml was analyzed on a MOPS-buffered formaldehyde-agarose gel. The typical ratio 260nm/280nm was 1.7; the ratio of 28S to 18S rRNA on the gel was 1.53 +/- 0.04.

treatment_protocol: Three clones of AtT-20 iPAM cells were examined.  Each clone was maintained in control medium or medium containing 4µg/ml of doxycycline for 48 h.

tag: gender

value: male

value: corticotrope tumor cells

tag: cell line

tag: treatment group

value: treated with control medium for 48 hrs


title: pCR breast biopsy, sample 18 rep 2

source_name: breast needle biopsy, pretreatment, sample 18 rep 2


title: clone 6_1 control

description: clone 6_1 AtT-20 cells treated with control medium for 48 hrs

source_name: AtT-20 mouse corticotrope tumor cells stably transfected with doxycycline-inducible rat PAM-1


title: clone 6_2 control

description: clone 6_2 AtT-20 cells treated with control medium for 48 hrs


title: pCR breast biopsy, sample 15 rep 1

source_name: breast needle biopsy, pretreatment, sample 15 rep 1


title: clone 6_1 + doxycycline

description: clone 6_1 AtT-20 cells treated with 4mg/ml of doxycycline for 48 hrs


title: non-pCR breast biopsy, sample 6 rep 2

source_name: breast needle biopsy, pretreatment, sample 6 rep 2


title: pCR breast biopsy, sample 16 rep 2

source_name: breast needle biopsy, pretreatment, sample 16 rep 2


title: non-pCR breast biopsy, sample 9 rep 1

source_name: breast needle biopsy, pretreatment, sample 9 rep 1


title: clone 6_2 + doxycycline

description: clone 6_2 AtT-20 cells treated with 4mg/ml of doxycycline for 48 hrs


title: non-pCR breast biopsy, sample 13 rep 1

source_name: breast needle biopsy, pretreatment, sample 13 rep 1


title: non-pCR breast biopsy, sample 9 rep 2

source_name: breast needle biopsy, pretreatment, sample 9 rep 2


title: non-pCR breast biopsy, sample 6 rep 1

source_name: breast needle biopsy, pretreatment, sample 6 rep 1


title: non-pCR breast biopsy, sample 8 rep 2

source_name: breast needle biopsy, pretreatment, sample 8 rep 2


title: BDC Treg #2

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Biotin-labeled cRNA was fragmented and hybridized to the array in a cocktail containing control oligos at 45°C for 16 hours, rotated at 60rpm, in the Affymetrix GeneChip Hybridization Oven 640. After hybridization, the arrays were automatically cycled through buffer washes and stained with streptavidin R-phycoerythrin conjugate (Invitrogen) in the Affymetrix GeneChip Fluidics Station 400 (EukGE-WS2v4 protocol).

scan_protocol: After staining and washing, the arrays were scanned in the Affymetrix GeneChip Scanner 3000 using the Affymetrix GCOS (GeneChip Operating Software) to automatically generate .CEL files.

data_processing: Raw data were preprocessed with the RMA algorithm in GenePattern, and averaged expression values were used for analysis.

source_name: T cells were sorted from the spleen of BDC2.5 RAG+/o NOD without treatment

label_protocol: Biotin

extract_protocol: RNA isolated with Trizol reagent and amplified twice with the MessageAmp aRNA Kit (Ambion)

treatment_protocol: Anti-CD3 treatment (37.5 ug of anti-CD3 mAb (clone:KT3) was iv injected for 5 consecutive days from 17 days of age) or no treatment.

tag: strain

value: NOD

value: BDC2.5 TCR tg RAG1+/o Foxp3GFP NOD

tag: age

value: 28 days old

tag: number of mice per chip

value: one

value: female

value: spleen

value: B220-, CD8a-, CD11b/c-, CD4+,GFP+ T cells

tag: protocol

value: no treatment


title: BDC Treg #1

tag: genotype/variation

value: 29 days old


title: BDC Treg #3


title: Mexico_48h_32C_rep3

city: University Park

first: Nicholas

last: Polato

state: PA

address: 208 Mueller Lab

department: Biology

institute: Penn State University

description: technical replicate

hyb_protocol: Dye coupled cDNAs were mixed together in a hybridization buffer consisting of 0.25% SDS, 25 mM HEPES, and 3× SSC. Hybridization mixtures were boiled at 99°C for 2 minutes then allowed to cool at room temperature for 5 minutes. Cooled hybridization mixtures were pipetted under an mSeries Lifterslip (Erie Scientific, NH) and slides were incubated overnight at 63°C in a custom hybridization chamber.  The hybridized microarray slides were washed twice in 0.6× SSC and 0.01% SDS, rinsed in 0.06× SSC, and dried via centrifugation.

scan_protocol: Slides were immediately scanned using an Axon 4000B slide scanner (MDS).

data_processing: Spot intensities were extracted and background was subtracted using GenePix Pro 6.0.  GPR files were read into the Bioconductor package LIMMA (Smyth 2005) for further analysis. Normalization was performed using print-tip specific LOWESS to normalize within arrays and the quantile normalization method (Yang and Thorne 2003) to normalize between arrays.

organism: Orbicella faveolata

source_name: common reference

label_protocol: 1 μg of total RNA was amplified with the MessageAmp II aRNA Kit (Ambion, TX). To prime the reverse transcription (RT) reaction 3 μg of aRNA was incubated with 2 μL of 5 μg/μL random nonamers for 10 minutes at 70°C. RT was carried out for 2 hours at 50°C using a master mix with a 4:1 ratio of aminoallyl-dUTP to TTP. Products of the RT reaction were hydrolyzed by incubating the cDNA in 10 μL of 0.5M EDTA and 10 μL of 1M NaOH for 15 minutes at 65°C. Following hydrolysis, RT products were purified using MinElute columns (Qiagen, CA). Dye coupling reactions were performed using Cy3 and Cy5 dyes (GE Healthcare, PA) diluted in 18 μL of dimethyl sulphoxide. The coupling reactions were run in the dark for 2 hours at room temperature. A final cleanup was performed using the MinElute Cleanup Kit, and dye coupling was confirmed on a NanoDrop spectrophotometer.

growth_protocol: Gametes from multiple parent colonies of M. faveolata were collected during mass spawning events in Puerto Morelos, Mexico (20°52’28.77”N, 86°51’04.53”W) and Key Largo, Florida  (25°6’42.66”N, 80°18’18.72”W). Sperm and eggs were pooled and incubated for two hours to allow for fertilization. Sperm concentration ranged from 2.3*10^11 to 6*10^11. Fertilized eggs were washed and transferred to temperature controlled aquaria consisting of small plastic containers suspended in polycarbonate bins containing filtered sea water. To prevent fouling, water was circulated with an aquarium pump and changed daily with filtered sea water pretreated to the target temperature.

extract_protocol: Total RNA of coral larvae was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. RNA pellets were cleaned further with RNeasy Mini columns (Qiagen).

treatment_protocol: Two treatment temperatures were chosen to reflect non-stressful and elevated temperatures for each sampling location; 27°C & 30°C in Florida, and 27.5°C & 31.5°C in Mexico.

value: pooled reference of coral larvae from Mexico raised at three temperatures (27.5°C, 29°C, 31.5°C) at 12, 24, 36, and 48 hours after fertilization

tag: developmental stage

value: coral larvae

tag: site

value: Mexico

tag: temperature

value: raised at 31.5°C

value: 48 hours after fertilization


title: non-pCR breast biopsy, sample 4 rep 1

source_name: breast needle biopsy, pretreatment, sample 4 rep 1

value: no

tag: tissue

value: Breast tumor biopsy


title: antiCD3_BDCRAGkoTreg #1

source_name: T cells were sorted from the spleen of BDC2.5 RAGo/o NOD after anti-CD3 treatment

value: BDC2.5 TCR tg RAG1o/o Foxp3GFP NOD

tag: cell type

value: anti-CD3 treatment

tag: time

value: 12 days (after treatment)


title: non-pCR breast biopsy, sample 4 rep 2

source_name: breast needle biopsy, pretreatment, sample 4 rep 2


title: antiCD3_BDCRAGkoTreg #3

value: NOD

value: 28 days old

value: 11 days (after treatment)


title: Mexico_24h_32C_rep3

description: technical replicate

tag: sample type

value: 24 hours after fertilization


title: non-pCR breast biopsy, sample 3 rep 2

source_name: breast needle biopsy, pretreatment, sample 3 rep 2


title: Mexico_48h_28C_rep1

description: technical replicate

value: raised at 27.5°C


title: Mexico_48h_28C_rep3

description: technical replicate


title: Mexico_48h_32C_rep2

description: technical replicate


title: Mexico_48h_32C_rep1

description: technical replicate


title: 1307-8HF

description: Embryonic_High fat maternal diet, Cited2 -/-_replicate1

source_name: High fat maternal diet, Cited2 -/-

tag: maternal diet

value: High fat

value: Cited2 -/-

value: Embryonic (8.5 days post coitum)


title: Mexico_48h_28C_rep2

description: technical replicate

value: pooled reference of coral larvae from Mexico raised at three temperatures (27.5°C, 29°C, 31.5°C) at 12, 24, 36, and 48 hours after fertilization

value: coral larvae


title: antiCD3_BDCRAGkoTreg #2

value: 29 days old

value: one

value: female

value: spleen

value: B220-, CD8a-, CD11b/c-, CD4+,GFP+ T cells


title: non-pCR breast biopsy, sample 3 rep 1

source_name: breast needle biopsy, pretreatment, sample 3 rep 1

tag: pathological complete response

value: no

value: Breast tumor biopsy


title: non-pCR breast biopsy, sample 5 rep 1

source_name: breast needle biopsy, pretreatment, sample 5 rep 1


title: Control TF

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

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

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

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

source_name: ten healthy women

label_protocol: Genomic DNA was completely fragmented with AluI and RsaI (Promega, Madison, WI, USA ), followed by purification with QIAprep Spin Miniprep Kit (Qiagen). All of the digested DNAs were subjected to labeling reactions using Agilent’s Genomic DNA Labeling Kit PLUS per manufacturer’s instructions.

extract_protocol: Genomic DNA was isolated from peripheral blood lymphocytes with the PureGene DNA Purification Kit (Gentra Systems, Minneapolis, MN, USA) according to the manufacturer’s instructions.

tag: gender

value: peripheral blood lymphocytes

tag: disease state

value: Healthy

source_name: commercialized normal Caucasian samples

extract_protocol: not applicable, commercialized normal Caucasian samples purchased from Promega, Madison, WI, USA.

tag: reference

value: commercialized normal Caucasian samples


title: non-pCR breast biopsy, sample 2 rep 1

source_name: breast needle biopsy, pretreatment, sample 2 rep 1


title: Control TM

source_name: ten healthy men

value: male


title: Mexico_24h_32C_rep2

description: technical replicate

value: Mexico

value: raised at 31.5°C

value: 24 hours after fertilization


title: clone 14 + doxycycline

description: clone 14 AtT-20 cells treated with 4mg/ml of doxycycline for 48 hrs

source_name: AtT-20 mouse corticotrope tumor cells stably transfected with doxycycline-inducible rat PAM-1

value: corticotrope tumor cells

tag: cell line

tag: treatment group


title: non-pCR breast biopsy, sample 2 rep 2

source_name: breast needle biopsy, pretreatment, sample 2 rep 2


title: Mexico_24h_32C_rep1

description: technical replicate

value: pooled reference of coral larvae from Mexico raised at three temperatures (27.5°C, 29°C, 31.5°C) at 12, 24, 36, and 48 hours after fertilization

tag: age


title: non-pCR breast biopsy, sample 1 rep 2

source_name: breast needle biopsy, pretreatment, sample 1 rep 2


title: non-pCR breast biopsy, sample 1 rep 1

source_name: breast needle biopsy, pretreatment, sample 1 rep 1


title: Mexico_24h_28C_rep3

description: technical replicate

value: coral larvae

value: raised at 27.5°C


title: Schiz J1

source_name: schizophrenia patient J1

value: Schizophrenia

source_name: equal amounts of DNA extracted from ten healthy men or ten healthy women who live in Taiwan