title: Prostate_Tumor_HSPH0222


title: Prostate_Tumor_HSPH0215

status: Public on Dec 01 2014

type: RNA

city: Boston

first: Kathryn

last: Penney

address: 181 Longwood Ave

department: Medicine

country: USA

institute: Brigham and Women's Hospital

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: For the expression profiles generated, we regressed out technical variables including mRNA concentration, age of the block, batch (96-well plate), percent of the probes on the array detectable above the background, log transformed average background signal, and the median of the perfect match probes for each probe intensity of the raw data. The residuals were then shifted to have the original mean expression values and normalized using the RMA method. We mapped gene names to Affymetrix transcript cluster IDs using the NetAffx annotations as implemented in Bioconductor annotation package pd.hugene.1.0.st.v1; this resulted in 20,254 unique named genes.  As gene names were used in the final analysis, this is what we have included in the sample tables.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: FFPE prostate tumor

label_protocol: Not provided

extract_protocol: Not provided


title: Prostate_Tumor_HSPH0212


title: Prostate_Tumor_HSPH0210


title: Prostate_Tumor_HSPH0217


title: Prostate_Tumor_HSPH0214


title: Prostate_Tumor_HSPH0220


title: Prostate_Tumor_HSPH0213


title: Prostate_Tumor_HSPH0209


title: Prostate_Tumor_HSPH0208


title: Prostate_Tumor_HSPH0216


title: Prostate_Tumor_HSPH0207


title: Prostate_Tumor_HSPH0218


title: Prostate_Tumor_HSPH0205


title: Prostate_Tumor_HSPH0204


title: Prostate_Tumor_HSPH0206


title: Prostate_Tumor_HSPH0211


title: Prostate_Tumor_HSPH0203


title: Prostate_Tumor_HSPH0202


title: Prostate_Tumor_HSPH0200


title: Prostate_Tumor_HSPH0194


title: Prostate_Tumor_HSPH0201


title: Prostate_Tumor_HSPH0185


title: Prostate_Tumor_HSPH0192


title: Prostate_Tumor_HSPH0198


title: Prostate_Tumor_HSPH0186


title: Prostate_Tumor_HSPH0196


title: Prostate_Tumor_HSPH0179


title: Prostate_Tumor_HSPH0197


title: Prostate_Tumor_HSPH0187


title: Prostate_Tumor_HSPH0175


title: Prostate_Tumor_HSPH0182


title: Prostate_Tumor_HSPH0184


title: Prostate_Tumor_HSPH0193


title: Prostate_Tumor_HSPH0183


title: Prostate_Tumor_HSPH0177


title: Prostate_Tumor_HSPH0178


title: Prostate_Tumor_HSPH0199


title: Prostate_Tumor_HSPH0174


title: Prostate_Tumor_HSPH0191


title: Prostate_Tumor_HSPH0173


title: Prostate_Tumor_HSPH0176


title: Prostate_Tumor_HSPH0188


title: Prostate_Tumor_HSPH0181


title: Prostate_Tumor_HSPH0190


title: Prostate_Tumor_HSPH0180


title: Prostate_Tumor_HSPH0172


title: Prostate_Tumor_HSPH0171


title: Prostate_Tumor_HSPH0168


title: Prostate_Tumor_HSPH0170


title: Prostate_Tumor_HSPH0169


title: Prostate_Tumor_HSPH0189


title: Prostate_Tumor_HSPH0163


title: Prostate_Tumor_HSPH0164


title: Prostate_Tumor_HSPH0161


title: Prostate_Tumor_HSPH0166


title: Prostate_Tumor_HSPH0165


title: Prostate_Tumor_HSPH0154


title: Prostate_Tumor_HSPH0157


title: Prostate_Tumor_HSPH0146


title: Prostate_Tumor_HSPH0156


title: Prostate_Tumor_HSPH0155


title: Prostate_Tumor_HSPH0167


title: Prostate_Tumor_HSPH0153


title: Prostate_Tumor_HSPH0148


title: Prostate_Tumor_HSPH0160


title: Prostate_Tumor_HSPH0159


title: Prostate_Tumor_HSPH0152


title: Prostate_Tumor_HSPH0150


title: Prostate_Tumor_HSPH0158


title: Prostate_Tumor_HSPH0141


title: Prostate_Tumor_HSPH0149


title: Prostate_Tumor_HSPH0151


title: Prostate_Tumor_HSPH0144


title: Prostate_Tumor_HSPH0142


title: Prostate_Tumor_HSPH0137


title: Prostate_Tumor_HSPH0143


title: Prostate_Tumor_HSPH0139


title: Prostate_Tumor_HSPH0136


title: Prostate_Tumor_HSPH0138


title: Prostate_Tumor_HSPH0122


title: Prostate_Tumor_HSPH0131


title: Prostate_Tumor_HSPH0132


title: Prostate_Tumor_HSPH0140


title: Prostate_Tumor_HSPH0134


title: Prostate_Tumor_HSPH0124


title: Prostate_Tumor_HSPH0133


title: Prostate_Tumor_HSPH0128


title: Prostate_Tumor_HSPH0135


title: Prostate_Tumor_HSPH0126


title: Prostate_Tumor_HSPH0114


title: Prostate_Tumor_HSPH0118


title: Prostate_Tumor_HSPH0115


title: Prostate_Tumor_HSPH0121


title: Prostate_Tumor_HSPH0125


title: Prostate_Tumor_HSPH0120


title: Prostate_Tumor_HSPH0117


title: Prostate_Tumor_HSPH0112


title: Prostate_Tumor_HSPH0129


title: Prostate_Tumor_HSPH0111


title: Prostate_Tumor_HSPH0130


title: Prostate_Tumor_HSPH0113


title: Prostate_Tumor_HSPH0109


title: Prostate_Tumor_HSPH0107


title: Prostate_Tumor_HSPH0108


title: Prostate_Tumor_HSPH0119


title: Prostate_Tumor_HSPH0110


title: Prostate_Tumor_HSPH0116


title: Prostate_Tumor_HSPH0106


title: Prostate_Tumor_HSPH0105


title: Prostate_Tumor_HSPH0098


title: Prostate_Tumor_HSPH0099


title: Prostate_Tumor_HSPH0097


title: Prostate_Tumor_HSPH0094


title: Prostate_Tumor_HSPH0102


title: Prostate_Tumor_HSPH0101


title: Prostate_Tumor_HSPH0093


title: Prostate_Tumor_HSPH0092


title: Prostate_Tumor_HSPH0088


title: Prostate_Tumor_HSPH0083


title: Prostate_Tumor_HSPH0082


title: Prostate_Tumor_HSPH0091


title: Prostate_Tumor_HSPH0095


title: Prostate_Tumor_HSPH0104


title: Prostate_Tumor_HSPH0077


title: Prostate_Tumor_HSPH0100


title: Prostate_Tumor_HSPH0086


title: Prostate_Tumor_HSPH0081


title: Prostate_Tumor_HSPH0096


title: Prostate_Tumor_HSPH0087


title: Prostate_Tumor_HSPH0075


title: Prostate_Tumor_HSPH0074


title: Prostate_Tumor_HSPH0078


title: Prostate_Tumor_HSPH0073


title: Prostate_Tumor_HSPH0084


title: Prostate_Tumor_HSPH0103


title: Prostate_Tumor_HSPH0080


title: Prostate_Tumor_HSPH0076


title: Prostate_Tumor_HSPH0072


title: Prostate_Tumor_HSPH0079


title: Prostate_Tumor_HSPH0067


title: Prostate_Tumor_HSPH0065


title: Prostate_Tumor_HSPH0085


title: Prostate_Tumor_HSPH0069


title: Prostate_Tumor_HSPH0064


title: Prostate_Tumor_HSPH0066


title: Prostate_Tumor_HSPH0071


title: Prostate_Tumor_HSPH0070


title: Prostate_Tumor_HSPH0062


title: Prostate_Tumor_HSPH0068


title: Prostate_Tumor_HSPH0057


title: Prostate_Tumor_HSPH0060


title: Prostate_Tumor_HSPH0058


title: Prostate_Tumor_HSPH0055


title: Prostate_Tumor_HSPH0054


title: Prostate_Tumor_HSPH0056


title: Prostate_Tumor_HSPH0059


title: Prostate_Tumor_HSPH0046


title: Prostate_Tumor_HSPH0048


title: Prostate_Tumor_HSPH0047


title: Prostate_Tumor_HSPH0045


title: Prostate_Tumor_HSPH0053


title: Prostate_Tumor_HSPH0052


title: Prostate_Tumor_HSPH0051


title: Prostate_Tumor_HSPH0061


title: Prostate_Tumor_HSPH0049


title: Prostate_Tumor_HSPH0043


title: Prostate_Tumor_HSPH0044


title: Prostate_Tumor_HSPH0036


title: Prostate_Tumor_HSPH0050


title: Prostate_Tumor_HSPH0042


title: Prostate_Tumor_HSPH0040


title: Prostate_Tumor_HSPH0037


title: Prostate_Tumor_HSPH0033


title: Prostate_Tumor_HSPH0038


title: Prostate_Tumor_HSPH0019


title: Prostate_Tumor_HSPH0026


title: Prostate_Tumor_HSPH0031


title: Prostate_Tumor_HSPH0023


title: Prostate_Tumor_HSPH0022


title: Prostate_Tumor_HSPH0028


title: Prostate_Tumor_HSPH0024


title: Prostate_Tumor_HSPH0029


title: Prostate_Tumor_HSPH0035


title: Prostate_Tumor_HSPH0018


title: Prostate_Tumor_HSPH0032


title: Prostate_Tumor_HSPH0034


title: Prostate_Tumor_HSPH0020


title: Prostate_Tumor_HSPH0014


title: Prostate_Tumor_HSPH0039


title: Prostate_Tumor_HSPH0021


title: Prostate_Tumor_HSPH0030


title: Prostate_Tumor_HSPH0016


title: Prostate_Tumor_HSPH0025


title: Prostate_Tumor_HSPH0017


title: Prostate_Tumor_HSPH0013


title: Prostate_Tumor_HSPH0011


title: Prostate_Tumor_HSPH0015


title: Prostate_Tumor_HSPH0012


title: Prostate_Tumor_HSPH0007


title: WT Neurons 94 [miRNA]

status: Public on Oct 28 2014

city: Jerusalem

first: Nissim

last: Benvenisty

state: Israel

address: Edmond Safra Campus Givat Ram

department: Genetics

country: Israel

institute: Hebrew University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

source_name: iPS cells-derived neurons using RA, WT clone 94

label_protocol: 200 ng total RNA, Affymetrix protocol

extract_protocol: Total RNA

tag: material

value: Cell line

tag: gender

value: Male

tag: cell type


title: FXS Neurons 55 [miRNA]

source_name: iPS cells-derived neurons using RA, FXS clone 55


title: Prostate_Tumor_HSPH0009


title: Prostate_Tumor_HSPH0006


title: Prostate_Tumor_HSPH0004


title: Prostate_Tumor_HSPH0005


title: Prostate_Tumor_HSPH0008


title: Prostate_Tumor_HSPH0001


title: Prostate_Tumor_HSPH0002


title: Psc3-GFP_G1_cells-v50_2007

status: Public on Oct 22 2014

type: genomic

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2600D scanner.

data_processing:
Data were extracted using Agilent Feature Extraction Software. Signal was normalized by combined rank consistency filtering with LOWES intensity normalization. Background signal was estimated as a median processed signal of 152 oligonucleotides with no homology to S. pombe genome.
Enrichment values were calculated as a log 2 ratio of Cy5 processed signal/ Cy3 processed signal.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: input DNA

label_protocol: ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol: Wild type and clr4d were cultured in rich media at 30˚C. cdc10-v50 was initially cultured at 26˚C then shifted to 35˚C for 4 hours for G1 arrest.

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication and immunoprecipitated by anti-GFP (ab290; Abcam) antibody. Immunoprecipitated DNA was recovered by incubation with protein A slurry and reversed-crosslinked at 65˚C. After reverse cross-linked and digested with Rnase A and proteinase K, DNA was recovered by Qiagen QIAquick PCR column.

treatment_protocol: Exponentially growing cells were cross-linked with paraformadehyde at 18˚C for 30 minutes, followed by dimethyl adipimidate crosslinking at room temperature for 45 min.

tag: genotype/variation

tag: antibody

value: None (whole cell extract)

source_name: Psc3 ChIP in cdc10-v50 cells

tag: chip antibody

value: anti-GFP (Rb pAb to GFP)

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: WT Neurons 28 [miRNA]

source_name: iPS cells-derived neurons using RA, WT clone 28


title: Psc3-GFP_clr4d_2007

source_name: Psc3 ChIP in clr4d cells


title: FXS Neurons 52 [miRNA]

source_name: iPS cells-derived neurons using RA, FXS clone 52


title: CGH_h+WT_Msmt0WT_2007

hyb_protocol: Equal amounts of Cy5-labeled DNA and Cy3-labeled DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

data_processing:
Data were extracted using Agilent Feature Extraction Software. Signal was normalized by combined rank consistency filtering with LOWES intensity normalization. Background signal was estimated as a median processed signal of 152 oligonucleotides with no homology to S. pombe genome.
relative copy numbr values were calculated as a log 2 ratio of Cy5 processed signal/ Cy3 processed signal.

source_name: h+ wild-type

label_protocol: Digested DNA was used as template for a genomic DNA labelling reaction using the BioPrime® Array CGH Genomic Labeling kit (Invitrogen) according to the manufacturer's protocol.

growth_protocol: To detect rearrangements in rad21-K1, wild type and mutant cells cultured in YEA at 26°C were shifted to 32°C and grown overnight before DNA extraction.

extract_protocol: Grow 20 ml cells to OD595 of 1.0. After cell wall digestion using Zymolyase 100T, cells were resuspended in 0.55 ml TE, 1% SDS, 100ug of proteinase K and incubated at 65°C for 30 min. Add 175 µl 5M potassium acetate. Keep on ice for 5 minutes. Lysate was centrifuged for 15 min at maximum speed for removing the cell debris. Genomic DNA was precipitated with isopropanol. After RNaseA treatment, genomic DNA was purified by phenol/chloroform/isoamyl alcohol (PCI) extraction twice and precipitated with ethanol.

value: wild-type

source_name: Msmt0 wild-type


title: Prostate_Tumor_HSPH0003


title: CGH_rad21-K1_WT_2007

source_name: wild-type

value: mat1Msmto leu1-32 ade6-216 Psc3-GFP::kanMX


title: Expression_rad21-K1

hyb_protocol: Equal amounts of Cy5-labeled mutant cDNA and Cy3-labeled wild-type cDNA were mixed and combined with human Cot1DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (GE2-v5_95_Feb07 protocol) and subjected to combined rank consistency filtering with LOWES intensity normalization. Background signal was estimated as a median processed signal of 152 oligonucleotides with no homology to S. pombe genome.

source_name: log. growing cells

label_protocol: Ribosomal RNA was depleted with RiboMinus kit (Invitrogen) and total RNA reverse-transcribed and labeled using SuperScript Indirect cDNA labeling kit (Invitrogen).

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA) at 30˚C or 37˚C.

extract_protocol: Total RNA was extracted using Master Pure Yeast RNA purification kit (Epicenter) according manufacturer's instructions.

value: WT; mat1Msmto leu1-32 ade6-216 Psc3-GFP::kanMX


title: Expression_pht1D


title: Expression_pht1D.rad21-K1


title: Psc3-GFP_WT_2007

source_name: Psc3 ChIP in wild-type cells


title: breast_invasive ductal carcinoma_8055

status: Public on Dec 05 2013

city: Amsterdam

first: Paul

last: Roepman

address: Science Park 406

country: Netherlands

institute: Agendia

hyb_protocol: Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0 Last Updated: 2/2006 Number of Pages: 70

scan_protocol: Scanned on an Agilent G2565AA scanner

data_processing: Raw Green (ch1, sample) and Red (ch2, reference) expression levels were quantified using Agilent Feature Extraction software (version 9.5) based on MedianSignal output.  Expression levels were normalized by lowess normalization using standard Feature expression software settings (see manual for details at http://www.chem.agilent.com/Library/usermanuals/Public/ReferenceGuide_050416.pdf).

source_name: breast_invasive ductal carcinoma_8055

label_protocol: Low Input RNA Fluorescent Linear Amplification. Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis 1). Convert mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT. 2) amplify sample using T7 RNA Polymerase [http://www.chem.agilent.com/temp/rad6D82C/00056953.pdf]

extract_protocol:
RNA isolation. We used 2-5 sections of 20-µm thickness for total RNA isolation. Total RNA was isolated with Trizol, and finally dissolved in RNase-free H2O and treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns.
A reference sample was made by processing of a breast cancer reference pool (BRP) (previously generated by pooling breast tumor RNAs [Glas et al, BMC Genomics 2006]) similarly as the testsamples.

value: female

tag: age at diagnosis

tag: treatment type

value: exemestane

tag: age at start therapy

tag: menopausal status at start therapy

value: post

tag: tissue

value: breast

tag: tumor type

value: invasive ductal carcinoma

tag: location

tag: grade

tag: er status

value: positive

tag: pr status

tag: pik3ca status

tag: disease-free interval (months)

tag: disease relapse (event)

tag: time-to-progession (months)

tag: disease progression (event)

source_name: common breast cancer reference pool (BRP)

tag: sample type

value: reference


title: breast_invasive ductal carcinoma_8052

source_name: breast_invasive ductal carcinoma_8052

tag: gender

tag: her2 status

value: negative


title: Expression_WT

tag: genotype/variation


title: breast_invasive ductal carcinoma_8057

source_name: breast_invasive ductal carcinoma_8057

tag: age at diagnosis

tag: treatment type

value: anastrozole

tag: age at start therapy

value: wildtype


title: breast_invasive ductal carcinoma_8041

source_name: breast_invasive ductal carcinoma_8041

tag: menopausal status at start therapy

tag: tissue

tag: tumor type


title: breast_invasive ductal carcinoma_8047

source_name: breast_invasive ductal carcinoma_8047

tag: location

tag: er status


title: breast_invasive ductal carcinoma_8048

source_name: breast_invasive ductal carcinoma_8048

tag: grade

tag: pr status

tag: pik3ca status


title: breast_invasive ductal carcinoma_8039

source_name: breast_invasive ductal carcinoma_8039

tag: disease-free interval (months)

tag: disease relapse (event)

tag: time-to-progession (months)


title: breast_invasive ductal carcinoma_8045

source_name: breast_invasive ductal carcinoma_8045

tag: gender

tag: disease progression (event)

tag: sample type


title: breast_invasive ductal carcinoma_8053

source_name: breast_invasive ductal carcinoma_8053

tag: age at diagnosis

tag: her2 status


title: breast_invasive ductal carcinoma_8044

source_name: breast_invasive ductal carcinoma_8044

tag: treatment type

tag: age at start therapy


title: breast_invasive ductal carcinoma_8054

source_name: breast_invasive ductal carcinoma_8054

tag: menopausal status at start therapy

value: pre

tag: tissue


title: breast_invasive ductal carcinoma_8049

source_name: breast_invasive ductal carcinoma_8049

tag: tumor type

tag: location


title: breast_invasive ductal carcinoma_8040

source_name: breast_invasive ductal carcinoma_8040

tag: grade

tag: er status


title: breast_invasive ductal carcinoma_8043

source_name: breast_invasive ductal carcinoma_8043

tag: pr status

tag: pik3ca status


title: breast_invasive ductal carcinoma_8033

source_name: breast_invasive ductal carcinoma_8033

value: letrozole

tag: disease-free interval (months)

tag: disease relapse (event)


title: breast_invasive ductal carcinoma_8037

source_name: breast_invasive ductal carcinoma_8037

tag: gender

value: tamoxifen

tag: time-to-progession (months)


title: breast_invasive ductal carcinoma_8051

source_name: breast_invasive ductal carcinoma_8051

tag: disease progression (event)

tag: sample type


title: Prostate_Tumor_HSPH0063

source_name: FFPE prostate tumor


title: breast_invasive ductal carcinoma_8034

source_name: breast_invasive ductal carcinoma_8034

tag: age at diagnosis

tag: her2 status

source_name: common breast cancer reference pool (BRP)


title: breast_invasive ductal carcinoma_8038

source_name: breast_invasive ductal carcinoma_8038

tag: treatment type

tag: age at start therapy


title: breast_invasive ductal carcinoma_8026

source_name: breast_invasive ductal carcinoma_8026

tag: menopausal status at start therapy

tag: tissue


title: breast_invasive ductal carcinoma_8031

source_name: breast_invasive ductal carcinoma_8031

tag: tumor type

tag: location


title: breast_invasive ductal carcinoma_8032

source_name: breast_invasive ductal carcinoma_8032

tag: grade

tag: er status


title: breast_invasive ductal carcinoma_8024

source_name: breast_invasive ductal carcinoma_8024

tag: pr status

tag: pik3ca status


title: breast_invasive ductal carcinoma_8030

source_name: breast_invasive ductal carcinoma_8030

tag: disease-free interval (months)

tag: disease relapse (event)


title: breast_invasive ductal carcinoma_8022

source_name: breast_invasive ductal carcinoma_8022

tag: gender

tag: time-to-progession (months)


title: breast_invasive ductal carcinoma_8015

source_name: breast_invasive ductal carcinoma_8015

tag: disease progression (event)

tag: sample type


title: breast_invasive ductal carcinoma_4562

source_name: breast_invasive ductal carcinoma_4562

tag: age at diagnosis


title: breast_invasive ductal carcinoma_8014

source_name: breast_invasive ductal carcinoma_8014

tag: treatment type

tag: her2 status


title: breast_invasive ductal carcinoma_8005

source_name: breast_invasive ductal carcinoma_8005

tag: age at start therapy

tag: menopausal status at start therapy


title: breast_invasive ductal carcinoma_8018

source_name: breast_invasive ductal carcinoma_8018

tag: tissue

tag: tumor type


title: breast_invasive ductal carcinoma_4561

source_name: breast_invasive ductal carcinoma_4561

tag: location

tag: grade


title: breast_invasive ductal carcinoma_8013

source_name: breast_invasive ductal carcinoma_8013

tag: er status

tag: pr status


title: breast_invasive ductal carcinoma_8004

source_name: breast_invasive ductal carcinoma_8004

tag: pik3ca status

tag: disease-free interval (months)


title: breast_invasive ductal carcinoma_4558

source_name: breast_invasive ductal carcinoma_4558

tag: gender

tag: disease relapse (event)


title: breast_invasive ductal carcinoma_4555

source_name: breast_invasive ductal carcinoma_4555

tag: time-to-progession (months)

tag: disease progression (event)

source_name: common breast cancer reference pool (BRP)


title: breast_invasive ductal carcinoma_4559

source_name: breast_invasive ductal carcinoma_4559

tag: age at diagnosis

tag: sample type


title: breast_invasive ductal carcinoma_8001

source_name: breast_invasive ductal carcinoma_8001

tag: treatment type

tag: her2 status


title: breast_invasive ductal carcinoma_4554

source_name: breast_invasive ductal carcinoma_4554

tag: age at start therapy

tag: menopausal status at start therapy


title: breast_invasive ductal carcinoma_8006

source_name: breast_invasive ductal carcinoma_8006

tag: tissue

tag: tumor type


title: breast_invasive ductal carcinoma_8019

source_name: breast_invasive ductal carcinoma_8019

tag: location

tag: grade


title: breast_invasive ductal carcinoma_4557

source_name: breast_invasive ductal carcinoma_4557

tag: er status

tag: pr status


title: breast_invasive ductal carcinoma_4553

source_name: breast_invasive ductal carcinoma_4553

tag: pik3ca status

tag: disease-free interval (months)


title: breast_invasive ductal carcinoma_8007

source_name: breast_invasive ductal carcinoma_8007

tag: gender

tag: disease relapse (event)


title: breast_invasive ductal carcinoma_4549

source_name: breast_invasive ductal carcinoma_4549

tag: time-to-progession (months)

tag: disease progression (event)


title: breast_invasive ductal carcinoma_8012

source_name: breast_invasive ductal carcinoma_8012

tag: age at diagnosis

tag: sample type


title: breast_invasive ductal carcinoma_4548

source_name: breast_invasive ductal carcinoma_4548

tag: treatment type

tag: her2 status


title: breast_invasive ductal carcinoma_4552

source_name: breast_invasive ductal carcinoma_4552

tag: age at start therapy


title: breast_invasive ductal carcinoma_4550

source_name: breast_invasive ductal carcinoma_4550

tag: menopausal status at start therapy

tag: tissue


title: breast_invasive ductal carcinoma_4556

source_name: breast_invasive ductal carcinoma_4556

tag: tumor type

tag: location


title: breast_invasive ductal carcinoma_8003

source_name: breast_invasive ductal carcinoma_8003

tag: grade

tag: er status


title: breast_invasive ductal carcinoma_4560

source_name: breast_invasive ductal carcinoma_4560

tag: pr status

tag: pik3ca status


title: breast_invasive ductal carcinoma_4546

source_name: breast_invasive ductal carcinoma_4546

tag: gender

tag: disease-free interval (months)

source_name: common breast cancer reference pool (BRP)


title: breast_invasive ductal carcinoma_4547

source_name: breast_invasive ductal carcinoma_4547

tag: disease relapse (event)

tag: time-to-progession (months)


title: breast_invasive ductal carcinoma_4544

source_name: breast_invasive ductal carcinoma_4544

tag: age at diagnosis

tag: disease progression (event)


title: breast_invasive ductal carcinoma_4545

source_name: breast_invasive ductal carcinoma_4545

tag: treatment type

tag: sample type


title: breast_invasive ductal carcinoma_4543

source_name: breast_invasive ductal carcinoma_4543

tag: age at start therapy

tag: her2 status


title: breast_invasive ductal carcinoma_4538

source_name: breast_invasive ductal carcinoma_4538

tag: menopausal status at start therapy

tag: tissue


title: breast_invasive ductal carcinoma_4541

source_name: breast_invasive ductal carcinoma_4541

tag: tumor type

tag: location


title: breast_invasive ductal carcinoma_4528

source_name: breast_invasive ductal carcinoma_4528

tag: grade

tag: er status


title: breast_invasive ductal carcinoma_4542

source_name: breast_invasive ductal carcinoma_4542

tag: pr status

tag: pik3ca status


title: breast_invasive ductal carcinoma_4529

source_name: breast_invasive ductal carcinoma_4529

tag: gender

tag: disease-free interval (months)


title: breast_invasive ductal carcinoma_4537

source_name: breast_invasive ductal carcinoma_4537

tag: disease relapse (event)

tag: time-to-progession (months)


title: breast_invasive ductal carcinoma_4527

source_name: breast_invasive ductal carcinoma_4527

tag: age at diagnosis

tag: disease progression (event)


title: breast_invasive ductal carcinoma_4533

source_name: breast_invasive ductal carcinoma_4533

tag: treatment type

tag: sample type


title: breast_invasive ductal carcinoma_4535

source_name: breast_invasive ductal carcinoma_4535

tag: age at start therapy

tag: her2 status


title: breast_invasive ductal carcinoma_4534

source_name: breast_invasive ductal carcinoma_4534

tag: menopausal status at start therapy

tag: tissue


title: breast_invasive ductal carcinoma_4532

source_name: breast_invasive ductal carcinoma_4532

tag: tumor type

tag: location


title: breast_invasive ductal carcinoma_4520

source_name: breast_invasive ductal carcinoma_4520

tag: grade

tag: er status


title: breast_invasive ductal carcinoma_4540

source_name: breast_invasive ductal carcinoma_4540

tag: pik3ca status

source_name: common breast cancer reference pool (BRP)


title: breast_invasive ductal carcinoma_4523

source_name: breast_invasive ductal carcinoma_4523

tag: gender

tag: pr status


title: breast_invasive ductal carcinoma_4519

source_name: breast_invasive ductal carcinoma_4519

tag: disease-free interval (months)

tag: disease relapse (event)


title: breast_invasive ductal carcinoma_4539

source_name: breast_invasive ductal carcinoma_4539

tag: age at diagnosis

tag: time-to-progession (months)


title: breast_invasive ductal carcinoma_4524

source_name: breast_invasive ductal carcinoma_4524

tag: treatment type

tag: disease progression (event)


title: breast_invasive ductal carcinoma_4514

source_name: breast_invasive ductal carcinoma_4514

tag: age at start therapy

tag: sample type


title: breast_invasive ductal carcinoma_4513

source_name: breast_invasive ductal carcinoma_4513

tag: menopausal status at start therapy


title: breast_invasive ductal carcinoma_4522

source_name: breast_invasive ductal carcinoma_4522

tag: tissue

tag: her2 status


title: breast_invasive ductal carcinoma_4517

source_name: breast_invasive ductal carcinoma_4517

tag: tumor type

tag: location


title: breast_invasive ductal carcinoma_4526

source_name: breast_invasive ductal carcinoma_4526

tag: grade

tag: er status


title: breast_invasive ductal carcinoma_4521

source_name: breast_invasive ductal carcinoma_4521

tag: gender

tag: pik3ca status


title: breast_invasive ductal carcinoma_4531

source_name: breast_invasive ductal carcinoma_4531

tag: pr status

tag: disease-free interval (months)


title: breast_invasive ductal carcinoma_4510

source_name: breast_invasive ductal carcinoma_4510

tag: age at diagnosis

tag: disease relapse (event)


title: breast_invasive ductal carcinoma_4518

source_name: breast_invasive ductal carcinoma_4518

tag: treatment type

tag: time-to-progession (months)


title: breast_invasive ductal carcinoma_4511

source_name: breast_invasive ductal carcinoma_4511

tag: age at start therapy

tag: disease progression (event)


title: breast_invasive ductal carcinoma_4512

source_name: breast_invasive ductal carcinoma_4512

tag: menopausal status at start therapy

tag: sample type


title: breast_invasive ductal carcinoma_4504

source_name: breast_invasive ductal carcinoma_4504

tag: tissue

tag: her2 status


title: breast_invasive ductal carcinoma_4509

source_name: breast_invasive ductal carcinoma_4509

tag: tumor type

tag: location

source_name: common breast cancer reference pool (BRP)


title: breast_invasive ductal carcinoma_8065

source_name: breast_invasive ductal carcinoma_8065

tag: grade

tag: er status


title: breast_invasive ductal carcinoma_8066

source_name: breast_invasive ductal carcinoma_8066

tag: gender

tag: pik3ca status


title: breast_invasive ductal carcinoma_4505

source_name: breast_invasive ductal carcinoma_4505

tag: pr status

tag: disease-free interval (months)


title: breast_invasive ductal carcinoma_8046

source_name: breast_invasive ductal carcinoma_8046

tag: age at diagnosis

tag: disease relapse (event)


title: breast_invasive ductal carcinoma_4508

source_name: breast_invasive ductal carcinoma_4508

tag: treatment type

tag: time-to-progession (months)


title: breast_invasive ductal carcinoma_8073

source_name: breast_invasive ductal carcinoma_8073

tag: age at start therapy

tag: disease progression (event)


title: breast_invasive ductal carcinoma_4503

source_name: breast_invasive ductal carcinoma_4503

tag: menopausal status at start therapy

tag: sample type


title: breast_invasive ductal carcinoma_8071

source_name: breast_invasive ductal carcinoma_8071

tag: tissue

tag: her2 status


title: breast_invasive ductal carcinoma_8064

source_name: breast_invasive ductal carcinoma_8064

tag: tumor type

tag: location


title: breast_invasive ductal carcinoma_8062

source_name: breast_invasive ductal carcinoma_8062

tag: grade

tag: er status


title: breast_invasive ductal carcinoma_8068

source_name: breast_invasive ductal carcinoma_8068

tag: gender

tag: pik3ca status


title: breast_invasive ductal carcinoma_8061

source_name: breast_invasive ductal carcinoma_8061

tag: pr status

tag: disease-free interval (months)


title: breast_invasive ductal carcinoma_4501

source_name: breast_invasive ductal carcinoma_4501

tag: age at diagnosis

tag: disease relapse (event)


title: breast_invasive ductal carcinoma_8059

source_name: breast_invasive ductal carcinoma_8059

tag: treatment type

tag: time-to-progession (months)


title: breast_invasive ductal carcinoma_8060

source_name: breast_invasive ductal carcinoma_8060

tag: age at start therapy

tag: disease progression (event)


title: breast_invasive ductal carcinoma_4502

source_name: breast_invasive ductal carcinoma_4502

tag: menopausal status at start therapy

tag: sample type


title: breast_invasive ductal carcinoma_8023

source_name: breast_invasive ductal carcinoma_8023

tag: tissue

tag: her2 status

source_name: common breast cancer reference pool (BRP)


title: breast_invasive ductal carcinoma_8058

source_name: breast_invasive ductal carcinoma_8058

tag: tumor type

tag: location


title: breast_invasive ductal carcinoma_8069

source_name: breast_invasive ductal carcinoma_8069

tag: grade

tag: er status


title: spontaneous induced mammary carcinoma M1643-2

status: Public on Aug 09 2010

city: Chiba

first: Daisuke

last: IIZUKA

address: 4-9-1, Anagawa, Inage-ku

country: Japan

institute: Research Institutes for Quantum Science and Technology

hyb_protocol: Hybridization and post hybridization wash were carried out essentially according to the manufacturers’ protocol (version 4) for oligonucleotide array-based CGH for genomic DNA analysis (Agilent).

scan_protocol: Microarray slides were scanned immediately using an Agilent microarray scanner.

data_processing: Data for individual features on the microarray were extracted from the scan image using Agilent’s Feature Extraction (FE) Software. Output files from FE were subsequently imported into Agilent’s CGH data analysis software, CGH Analytics, for DNA copy number analysis.

organism: Rattus norvegicus

source_name: mammary carcinoma No. M1643-Mt2 genomic DNA

label_protocol: In brief, 1 ug of genomic DNA was digested with AluI and RsaI. Digested DNA was labeled using an Agilent Genomic DNA Labeling Kit. Test and reference DNA samples were labeled with either cyanine 5- or cyanine 3-dUTP, according to the manufacturer’s protocol. Labeled DNA products were purified using Microcon YM-30 filtration units (Millipore), and DNA yield and dye incorporation were determined using an ND-1000 spectrophotometer (NanoDrop).

extract_protocol: Genomic DNA was isolated according to standard procedures using proteinase K and phenol-chloroform extraction.

value: mammary carcinoma

tag: strain

value: Sprague-Dawley

tag: gender

source_name: reference genomic DNA

value: ear


title: spontaneous induced mammary carcinoma M1699-1

source_name: mammary carcinoma No. M1699-Mt1 genomic DNA


title: spontaneous induced mammary carcinoma M1592-2

source_name: mammary carcinoma No. M1592-Mt2 genomic DNA


title: Radiation-induced mammary carcinoma exposed to 2 Gy of gamma ray at 7 weeks of age rep7

source_name: mammary carcinoma No. M1148-Mt4 genomic DNA


title: Radiation-induced mammary carcinoma exposed to 2 Gy of gamma ray at 3 weeks of age rep3

source_name: mammary carcinoma No. M1495-Mt1 genomic DNA


title: Radiation-induced mammary carcinoma exposed to 2 Gy of gamma ray at 7 weeks of age rep6

source_name: mammary carcinoma No. M1222-Mt4 genomic DNA


title: Spontaneous induced mammary carcinoma rep1

source_name: mammary carcinoma No. M1298-Mt1 genomic DNA


title: Radiation-induced mammary carcinoma exposed to 2 Gy of gamma ray at 3 weeks of age rep5

source_name: mammary carcinoma No. M1496-Mt4 genomic DNA


title: Radiation-induced mammary carcinoma exposed to 2 Gy of gamma ray at 7 weeks of age rep5

source_name: mammary carcinoma No. M1197-Mt2 genomic DNA


title: Spontaneous induced mammary carcinoma rep2

source_name: mammary carcinoma No. M1299-Mt2 genomic DNA


title: Radiation-induced mammary carcinoma exposed to 2 Gy of gamma ray at 7 weeks of age rep2

source_name: mammary carcinoma No. M1113-Mt3 genomic DNA


title: Radiation-induced mammary carcinoma exposed to 2 Gy of gamma ray at 3 weeks of age rep7

source_name: mammary carcinoma No. M1501-Mt4 genomic DNA


title: Radiation-induced mammary carcinoma exposed to 2 Gy of gamma ray at 3 weeks of age rep4

source_name: mammary carcinoma No. M1501-Mt2 genomic DNA


title: Radiation-induced mammary carcinoma exposed to 2 Gy of gamma ray at 3 weeks of age rep1

source_name: mammary carcinoma No. M1493-Mt1 genomic DNA


title: Fusion: No, Deletion: No (prostate_1180)

status: Public on May 28 2008

city: New York

first: Mark

middle: A.

last: Rubin

state: NY

address: 1300 York Avenue Room C 410-A

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medical Center

description: no additional information

hyb_protocol: Refer to the Illumina DASL Assay System Manual. Hybridization was performed for 4 DASL assay oligo pool (DAP)s, DAP1~4, including 1536 probes each on 4 separate microarrays.

data_processing: For each probe, Red and Green intensities are computed as average of single bead values. The final signal is the sum of the Red and Green intensities. Data were median-centered by subtraction of median (log2 scale) within sample and within DAP, and median set to a target value computed as the overall within DAP median. Data were then normalized using the qspline algorithm (on the log2 intensity scale) with reference distribution computed as the marginal (always within DAP) mean of every gene.

label: Cy3 and Cy5

source_name: primary prostate cancer

extract_protocol: Using 3 biopsy cores (0.6µm each) taken from formalin-fixed paraffin-embeded tissue blocks, total RNA was extracted using Trizol LS reagent (Invitrogen).

tag: FUSION

value: NO

tag: DELETION


title: Spontaneous induced mammary carcinoma rep3

source_name: mammary carcinoma No. M1622-Mt1 genomic DNA

value: female


title: Radiation-induced mammary carcinoma exposed to 2 Gy of gamma ray at 7 weeks of age rep3

source_name: mammary carcinoma No. M1113-Mt2 genomic DNA


title: Radiation-induced mammary carcinoma exposed to 2 Gy of gamma ray at 7 weeks of age rep1

source_name: mammary carcinoma No. M1182-Mt1 genomic DNA

source_name: reference genomic DNA


title: Radiation-induced mammary carcinoma exposed to 2 Gy of gamma ray at 7 weeks of age rep4

source_name: mammary carcinoma No. M1192-Mt1 genomic DNA


title: Spontaneous induced mammary carcinoma rep4

source_name: mammary carcinoma No. M1212-Mt1 genomic DNA


title: Radiation-induced mammary carcinoma exposed to 2 Gy of gamma ray at 3 weeks of age rep6

source_name: mammary carcinoma No. M1499-Mt2 genomic DNA


title: Radiation-induced mammary carcinoma exposed to 2 Gy of gamma ray at 3 weeks of age rep2

source_name: mammary carcinoma No. M1180-Mt1 genomic DNA