title: 101777-187

city: Amsterdam

first: Michiel

middle: Emanuel

last: Adriaens

address: Meibergdreef 15

department: Experimental Cardiology

country: Netherlands

institute: AMC

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
14

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48 degrees C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadChip Reader (Illumina).

data_processing:
Genomic DNA extracted from left ventricular myocardium was genotyped using HumanOmniExpress BeadChips (Illumina).
Genotype: AA, AB, BB, or empty (no call); Nucleotide coded genotypes are provided according to Illumina's top-strand definition

label: C-Bio and A-DNP

source_name: heart, left ventricle

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37 degrees C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

value: Male

value: left ventricular myocardium

tag: center


title: 101777-162

status: Public on May 21 2014

type: genomic

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
3083

molecule: genomic DNA

organism: Homo sapiens

tag: gender

value: Female

tag: tissue

tag: age


title: RPE1-BAZ1B-F3-3

type: RNA

city: Tallahassee

first: Brian

middle: P

last: Chadwick

state: FL

address: 319 Stadium Drive, King 3076

department: Biological Science

country: USA

institute: Florida State University

description: RPE1 BAZ1B homozygous mutant.

hyb_protocol: Hybridization was performed at a NimbleGen Systems certified core facility at FSU, FL, USA, following the NimbleGen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed at a NimbleGen Systems certified core facilty at FSU, FL, USA, following the NimbleGen standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

molecule: total RNA

source_name: hTERT-RPE1 (retinal pigment epithelial cells), BAZ1B knockout

label_protocol: Labeling was performed at a NimbleGen Systems certified core facility at FSU, FL, USA, following the NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: Cells were grown in DMEM/F12, supplemented with 10% FBS, Pen/Strep, 2mM L-Glutamine, 0.348% NaBicarbonate. Cells were maintained at 37C in 5% CO2, humidified.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Spin Kit. RNA was treated with DNaseI, before cleaning on an RNeasy spin column. Confirmation of DNA absence was performed by PCR to the repeat element DXZ4, and RNA quality was determined by agarose gel electrophoresis.

treatment_protocol: The BAZ1B gene was knocked out by targeting both copies of exon-7 using zinc finger nucleases (D5, F3 and M1 - all independent clones). Clone A6 is targeted at one allele only and is a heterozygous mutant clone.

tag: cell line

tag: genotype/variation

value: BAZ1B knockout

value: female

tag: clone


title: 101777-57

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
31


title: WTC 157 PBS treated

status: Public on May 22 2014

city: Chicago

first: Rajasekaran

last: Subbiah

state: IL

address: 909, South Wolcott Ave, Room # 7160

department: Pediatrics

institute: University of Illinois at Chicago

hyb_protocol: Following fragmentation, 80 µl of hybridization cocktail containing 2.75 ug of fragmented cRNA placed on chip - Hybridized for overnight. The whole hybridization was performed according to Gene Chip Hybridization, Wash and Stain Kit.

scan_protocol: Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.

data_processing: Data extraction was processed by Affymetrix MoGene 1.0ST v1 Array. The raw probe signal intensities were quantile normalized over all samples, summarized with the robust multi-array average (RMA) algorithm and log2 transformed with a median polish, using the Affymetrix Power Tools. We considered a transcript cluster (gene-level) to be reliably expressed in a sample if the Affymetrix implemented DABG (detection above ground) p-value was less than 0.05. We used local-pooled-error (LPE) estimates and robust statistical tests for evaluating significance of each gene's differential expression in a comparison.

label: biotin

organism: Mus musculus

label_protocol: First strand cDNA synthesis, 2nd strand cDNA, IVT, 2nd cycle cDNA synthesis, hydrolysis of cRNA, clean up of the 2nd cycle cDNA, fragmentation of cDNA, and labeling of fragmented single strand cDNA.

extract_protocol: Total RNA extraction was performed using Qiagen Rneasy micro kit according to the manufacturer's protocol.

treatment_protocol: 30 µl of PBS or PBS containing bleomycin (0.075U/mouse) instilled intratracheally for 5 days

tag: strain background

value: Fra-1+/+; wild type

value: 2 months

tag: treated with

value: 30 µl of PBS for 5 days

value: lung


title: 101777-64

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
7024


title: RPE1-BAZ1B-D5-1

description: RPE1 BAZ1B homozygous mutant.


title: 101777-109

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
7054


title: 101777-29

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
4062


title: RPE1-Parental-3

description: Parental RPE1 cells.

source_name: hTERT-RPE1 (retinal pigment epithelial cells), parental

value: parental


title: 101777-179

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
5138


title: RPE1-BAZ1B-D5-2

description: RPE1 BAZ1B homozygous mutant.


title: RPE1-Parental-2

description: Parental RPE1 cells.


title: 101777-01

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
573M


title: 101777-63

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
5033


title: MLL#5pn

city: Ulm

first: Michael

last: Kuehn

address: Albert-Einstein-Allee 23

country: Germany

institute: University Hospital of Ulm

description: DNA extracted from tumor cells obtained at remission

hyb_protocol: 200-270 micrograms of amplified and biotinylated DNA were hybridized for 16-18 hr at 50C on a GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Genotyping Console/birdseed-v2

source_name: Leukemic cells obtained from bone marrow or blood at remission

label_protocol: 250 nanograms of genomic DNA were digested to completion with NspI or StyI, ligated to adapaters and amplified by PCR. 200-270 micrograms of pooled amplified DNA were fragmented and end-labeled with a biotinylated nucleotide according to the Genome-Wide Human SNP Nsp/Sty 6.0 User Guide 702504 Rev 3, 2008, Affymetrix)

growth_protocol: DNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from AML cases with t(9;11)

extract_protocol: AllPrep DNA/RNA Mini Kit (Qiagen)

tag: disease

value: leukemia (remission)

tag: cell type

value: t-AML


title: MLL#11

description: DNA extracted from tumor cells obtained at diagnosis

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis

value: leukemia

value: de novo AML


title: 101777-39

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
6092


title: RPE1-BAZ1B-M1-1

description: RPE1 BAZ1B homozygous mutant.


title: 101777-104

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
643M


title: MLL#5


title: 101777-165

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
503M


title: 101777-188

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H3


title: MLL#8


title: 101777-60

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
461M


title: 101777-34

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H37


title: 101777-95

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H38


title: 101777-30

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H39


title: 101777-182

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H40


title: 101777-120

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H4


title: 101777-96

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H42


title: 101777-46

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H45


title: 101777-58

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H47


title: 101777-158

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H48


title: 101777-90

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H5


title: 101777-127

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H50


title: 101777-103

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H59


title: 101777-21

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H6


title: MLL#3pn

description: DNA extracted from tumor cells obtained at remission


title: 101777-85

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H64


title: 101777-88

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H65


title: 101777-61

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H46


title: 101777-146

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H70


title: 101777-66

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H71


title: 101777-09

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H76


title: 101777-186

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
6028


title: 101777-107

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H78


title: 101777-78

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H77


title: 101777-100

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H82


title: 101777-76

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H81


title: 101777-70

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H80


title: 101777-35

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H85


title: 101777-83

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H9


title: 101777-185

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H86


title: 101777-92

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N1877


title: 101777-125

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N2658


title: 101777-77

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N3060


title: 101777-48

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N3064


title: 101777-54

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H8


title: 101777-178

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N3878


title: 101777-151

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H79


title: 101777-36

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N5713


title: 101777-59

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H54


title: 101777-142

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
3112


title: 101777-89

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N1754


title: 101777-116

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
259M


title: 101777-49

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
843M


title: MLL#2pn

description: DNA extracted from tumor cells obtained at remission


title: 101777-74

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
669M


title: MLL#2

description: DNA extracted from tumor cells obtained at diagnosis


title: 101777-97

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H66


title: MLL#1


title: 101777-47

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H33


title: 101777-122

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H84


title: MLL#7


title: 101777-38

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N0762


title: 101777-13

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N9511


title: 101777-115

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H20


title: 101777-153

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
827M


title: 101777-143

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
23


title: 101777-141

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
475M


title: 101777-110

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H36


title: 101777-04

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H30


title: 101777-108

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H17


title: 101777-172

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
29


title: 101777-84

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H49


title: 101777-06

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H27


title: 101777-112

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H10


title: 101777-159

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
455M


title: 101777-119

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H13


title: 101777-133

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H31


title: 101777-154

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
5126


title: 101777-91

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H29


title: 101777-161

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H25


title: 101777-56

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
4049


title: 101777-193

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H28


title: 101777-176

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H15


title: 101777-18

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H23


title: 101777-44

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
7040


title: 101777-32

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
5140


title: 101777-17

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
5048


title: 101777-183

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H24


title: MLL#3

description: DNA extracted from tumor cells obtained at diagnosis


title: 101777-67

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
711M


title: 101777-40

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H22


title: 101777-174

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
3091


title: 101777-138

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
16


title: 101777-24

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
608M


title: 101777-22

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H43


title: 101777-117

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
039M


title: 101777-71

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H19


title: 101777-62

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
238M


title: MLL#1pn

description: DNA extracted from tumor cells obtained at remission


title: 101777-23

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
916M


title: 101777-111

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N3077


title: 101777-26

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N2765


title: 101777-129

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N8073


title: 101777-137

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
429M


title: 101777-07

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
4043


title: 101777-11

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N7990


title: 101777-101

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
713M


title: 101777-55

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N2917


title: 101777-73

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H44


title: 101777-190

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N3145


title: 101777-02

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
LV4


title: 101777-43

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N9303


title: 101777-14

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
4184


title: 101777-51

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
7060


title: 101777-149

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H26


title: 101777-135

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N3736


title: 101777-50

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N4856


title: 101777-31

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N9365


title: 101777-113

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N5288


title: 101777-42

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H12


title: 101777-52

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H68


title: 101777-147

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N3683


title: 101777-33

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
10


title: 101777-12

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
N1212


title: 101777-10

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H61


title: Tbx1+/+, replica2

city: Bronx

first: Tingwei

last: Guo

state: NY

address: 1301 Morris Park Avenue, Room 408

department: Genetics

institute: Albert Einstein College of Medicine

hyb_protocol: 10ug of cRNA was hybridized for 16hrs at 45C on Affymetrix Mouse Gene ST 1.0 arrays.

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

data_processing: Data was analyzed by RMA using Affymetrix Expression Console software version 1.1 using Affymetrix default protocols.

source_name: E9.5 mandibular arches (MdPA1), Tbx1+/+

label_protocol: Biotinylated cRNA was prepared from 300ng of total RNA according to Affymetrix protocols.

extract_protocol: Qiagen RNeasy Micro kit according to the manufacturer's protocol.

tag: strain

tag: genotype

tag: developmental stage

value: embryonic

value: mandibular arches


title: 101777-170

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H2


title: Tbx1-/-, replica2

source_name: E9.5 mandibular arches (MdPA1), Tbx1-/-


title: Tbx1-/-, replica3


title: brains 10-12 wks pool 4

city: madison

first: jesus

last: Iruretagoyena

address: 1010 Mound street

institute: University of wisconsin

hyb_protocol: cDNA was synthesized from extracted RNA (300 ng) using the Ambion WT Expression Kit (Expression Kit Manual P/N 4425209 Rev. C). cDNA yield quantity and quality were assessed using NanoDrop Spectrophotometer (NanoDrop Products, Thermo Fisher Scientific Inc., Wilmington, DE, USA) and Agilent Bioanalyzer (Agilent Technology, Santa Clara, CA, USA). Extraction RNA samples with an A260/280 ratio of 1.7 to 2.1 were further analyzed by gel electrophoresis at the Biotech Center. Samples were considered acceptable for testing when 28S and 18S rRNA bands resolved into two discrete bands that had no significant smearing below each band. The 28S rRNA band had intensity approximately twice that of the 18S rRNA band. These samples were then further tested by cDNA generation for hybridization. cDNA was checked for yield and size distribution using NanoDrop Spectrophotometer (NanoDrop Products, Thermo Fisher Scientific Inc., Wilmington, DE, USA) and Agilent profile (Agilent Bioanalyzer, Agilent Technology, Santa Clara, CA, USA). Fragmentation check revealed a cDNA <500 bp reliable for hybridization to Human Gene 1.0 ST arrays. All subsequent experiments were then undertaken using RNA samples matching these requirements.  Fragmentation and end-terminus labeling of cDNAs were done at the Biotechnology Center  of the University of Wisconsin, Madison, using the Affymetrix WT Terminal Labeling Kit (see GeneChip® WT Terminal Labeling and Hybridization User Manual [P/N 702808 Rev. 4]). The samples were then hybridized to Human Gene 1.0 ST arrays at 45 degrees Celsius for 16 hours O/N, following all procedures outlined in the GeneChip® WT Terminal Labeling and Hybridization User Manual (P/N 702808 Rev. 4) for Human Gene 1.0 ST Arrays. GeneChips post-processed were done on the AFX Fluidics 450 Station, according to all AFX protocols and procedures defined for the Human Gene 1.0 ST Array (FS450 _0007), as outlined in the GeneChip Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3). GeneChips were scanned on the GC3000 G7 Scanner. Data was extracted and processed using Affymetrix Command Console version 3.1.1.1229.

scan_protocol: standard Affymetrix protocol

data_processing: All analyses of GeneChip data was carried out in R (R Development Core Team, 2007), a publicly available statistical analysis environment (available at www.r-project.org). Specific software packages (affy, EBarrays, allez) are available at Bioconductor (http://bioconductor.org/), an on-line suite of tools for the analysis of genomic data (Huber et al. 2004). The Affymetrix probe level data was processed using Robust Multi-Array Analysis (RMA) as implemented in the affy package, in order to obtain normalized summary expression scores for each probe set on each array (Irizarry et al. 2003). Cutoffs for sensitivity, ensuring a reliable positive detection result, were 0.95. Cutoffs for a significant change in expression were initially set at two-fold.In order to draw any conclusion, parameters had to first be established as to how the output chips would be analyzed. In this presentation, the probe sets are referred to as genes. RMA fits a linear model to the log probe intensities for each probe set. The linear model includes a sample effect (the parameter of interest), a probe effect and an error term. The standard errors are normalized so that each probe set has the same median standard error across arrays.  EBarrays was used to identify differentially expressed (DE) genes(Newton et al. 2001; Kendziorski et al. 2003). EBarrays is an empirical Bayes approach which models the probability distribution of a set of expression measurements. It accounts generally for differences in specific genes with regard to their true underlying expression levels, measurement fluctuations and distinct expression patterns for a given gene among conditions (Kendziorski et al. 2003). An expression pattern is an arrangement of the true underlying intensities (μ) in each condition. The number of patterns possible depends on the number of conditions from which the expression measurements were obtained. For example, when measurements are taken from two conditions, two patterns of expression are possible; equivalent expression (!μ1 = μ2) and differential expression (!μ1 ≠ μ2). Since there is no priori stating which genes are in which patterns, the marginal distribution of the data is a mixture of all possible patterns with model parameters being determined by the full set of array data. This approach utilizes information across a set of arrays optimizing model fit and is, therefore, more efficient than a number of methods that make gene inferences one gene at a time (Kendziorski et al. 2003). Fitted model parameters provide information on the number of genes expected in each expression pattern. Furthermore, the fitted model is used to assign probability distributions to every gene. Each gene-specific distribution gives the posterior probability of that gene's individual expression pattern. Thresholds were chosen to target an FDR of 5% when more than one sample was available within the condition (e.g. heart versus brain), the lognormal normal with moderated variance (LNNMV) model was used in EBarrays; otherwise, a lognormal normal model was used. EBarrays then provides the posterior probability of differential expression (DE) as well as equivalent expression (EE) for every gene (Table 1). A gene was defined as DE if its posterior probability of DE exceeded 0.95. This is analogous to its posterior probability of EE being less than or equal to 0.05. This threshold targets an overall false discovery rate (FDR) of 5%. In some cases (specified in the text), a second fold-change based filter was applied to the list of DE genes obtained from EBarrays. Tests for enrichment of common function among sets of differentially expressed genes were carried out using data from the Gene Ontology (GO) annotations and the Kyoto Encyclopedia of Genes and Genomes (KEGG). In GO, transcripts genes are categorized at varying levels of biological detail. The three broadest levels are molecular function, cellular component and biological process. There are many subcategories within each detail. The R package allez was used to perform tests of enrichment for each GO category and KEGG pathway (Newton et al. 2001). In general, the interpretation of p-values resulting from enrichment tests is not straightforward due to the many dependent hypotheses tested. Furthermore, the enrichment test tends to result in small p-values when groups with few transcripts are considered. The statistical methods underlying allez adjust for these factors, allowing increased power and sensitivity for identifying sets that are biologically meaningful.

source_name: fetal brain

label_protocol: standard Affymetrix protocol

extract_protocol: Tissue RNA was extracted using RNA STAT-60 reagents, as recommended by the manufacturer (Tel-Test, Inc., Friendswood, TX, USA). All procedures were run on ice. A starting ratio of 1 ml reagent/100 mg tissue was used to ensure efficient, intact RNA recovery.

tag: gestational age

value: brain


title: Tbx1-/-, replica1


title: 101777-171

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H35


title: Tbx1+/+, replica1


title: brains 13/15 wks pool 5


title: brains 16-18 weeks pool 6


title: hearts 13/15 wks pool 2

source_name: fetal heart

value: heart


title: Tbx1+/+, replica3


title: 101777-105

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
3108

value: left ventricular myocardium


title: hearts 10-12 wks pool 1


title: hearts 16-18 weeks pool 3


title: 101777-144

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H69

value: Male


title: 101777-163

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H73


title: 101777-05

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
3160


title: RPE1-Parental-1

description: Parental RPE1 cells.


title: C57 wild type dexamethasone treatment, biological rep5

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

description: Gene expression data from wild type C57Bl/6 mice embryonic neural progenitor/stem cells treated with dexamethasone.

hyb_protocol: Affy Mouse 430A 2.0 Script FS450_0002

data_processing: The data is RMA normalized using BRB Array-Tools Software

label: streptavidin phycoerythrin

source_name: Neurospheres prepared from embryonic day 14.5 mouse cerebral cortex

label_protocol: Ambion MessageAmp Premier Enhanced Assay

growth_protocol: Cerebral cortex dissected from embryonic day 14.5 fetal mice were dissociated into single cells and then cultured as neurospheres

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

treatment_protocol: Neurospheres at third passage were treated with 100 nM dexamethasone or equivalent volumes of ethanol vehicle for 4 hours

value: embryonic day E14.5 cerebral cortex

value: C57 Bl/6 wild type

value: embryonic day E14.5

tag: treatment

value: 100 nM dexamethasone


title: ThERF1-overexpression-Nacl 12

city: Harbin

first: Liuqiang

last: Wang

address: 26 Hexing Road

country: China

institute: Northeast Forestry University

description: Gene expression after 6 h of salt stress

hyb_protocol: 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1× Agilent fragmentation buffer and 2× Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 µl of 2× Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4×44k array slides (Scan resolution 10 µm, Dye channel is set to Green and Green PMT is set to 100%).

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

organism: Arabidopsis thaliana

source_name: Arabidopsis, NaCl, 6 h, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 µg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was isolated with an RNeasy® Plant Mini kit (Qiagen, German) according to the manufacture's instructions and treated with DNaseI to remove any genomic DNA contamination.

treatment_protocol: One-week-old seedlings were transferred from the plates to pots containing a mixture of perlite/soil and grown in a greenhouse (16 h light/8 h dark photocycle; 70–75% relative humidity; 22°C). Four-week-old seedlings treated with 120 mM NaCl for 6 h were immediately harvested for RNA isolation.

value: whole plants

value: Four-week-old

value: seedling

value: ThERF1 overexpression

tag: stress

value: salt


title: WT-Nacl 7

growth_protocol: 16 h light/8 h dark photocycle; 70–75% relative humidity; 22°C

value: wild type


title: Caveolin-1 knockout dexamethasone treatment, biological rep4

description: Gene expression data from caveolin-1 knockout mice embryonic neural progenitor/stem cells treated with dexamethasone.

value: Caveolin-1 knockout


title: Caveolin-1 knockout vehicle treatment, biological rep4

description: Gene expression data from caveolin-1 knockout mice embryonic neural progenitor/stem cells treated with ethanol vehicle.

value: ethanol vehicle


title: ThERF1-overexpression-Nacl 10


title: Caveolin-1 knockout dexamethasone treatment, biological rep5


title: Caveolin-1 knockout vehicle treatment, biological rep5


title: ThERF1-overexpression-Nacl 11


title: C57 wild type dexamethasone treatment, biological rep2


title: C57 wild type vehicle treatment, biological rep1

description: Gene expression data from wild type C57Bl/6 mice embryonic neural progenitor/stem cells treated with ethanol vehicle.


title: C57 wild type dexamethasone treatment, biological rep4


title: Caveolin-1 knockout dexamethasone treatment, biological rep1


title: Caveolin-1 knockout dexamethasone treatment, biological rep2


title: WT-Nacl 9


title: WT-Nacl 8


title: C57 wild type vehicle treatment, biological rep5


title: Caveolin-1 knockout vehicle treatment, biological rep3


title: Caveolin-1 knockout vehicle treatment, biological rep1


title: C57 wild type dexamethasone treatment, biological rep1


title: C57 wild type vehicle treatment, biological rep3


title: C57 wild type dexamethasone treatment, biological rep3


title: C57 wild type vehicle treatment, biological rep4


title: Caveolin-1 knockout vehicle treatment biological rep2


title: C57 wild type vehicle treatment biological rep2


title: Caveolin-1 knockout dexamethasone treatment, biological rep3


title: 101777-139

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
H14

tag: center


title: 101777-150

description:
Genomic DNA extracted from left ventricular myocardium was genotyped using Illumina HumanOmniExpress Genotyping BeadChips (Illumina).
6008

tag: gender


title: [genomic DNA]-[normal breast biopsy] MDG_172

city: Oslo

first: Miriam

middle: Ragle

last: Aure

address: Ullernchauséen 70

department: Dept. of Cancer Genetics

country: Norway

institute: Oslo University Hospital Radiumhospitalet

description: [genomic DNA]-[normal breast biopsy]

hyb_protocol: Cot-1 DNA, Agilent blocking agent and Hybridization buffer were added to the Cy3 and Cy5 labeled gDNA mixture. Sample mixture was added to the microarrays and arrays were incubated in in a hybridization oven at 65ºC for 40 hrs with rotary motion.

scan_protocol: Microarrays were manually washed using Agilent wash buffer 1 and 2, followed by acetonitrile and Agilent Stabilization and Drying Solution. Images were scanned using an Agilent Microarray Scanner, G2565CA.

data_processing: Data were preprocessed using Agilent Feature Extraction v10.1.1 with default settings (protocol CGH-v4_95_Feb07 and CGH-v4_10_Apr08).

source_name: Normal breast tissue

label_protocol: 1ug of genomic DNA from tumor and reference was digested using AluI and RsaI for 2 hrs on 37ºC folowed by a 20 min incubation on 65ºC for inactivation of enzymes. The samples were labeled using Agilent DNA Labeling Kit PLUS (containing random primers, 10X dNTPs, exo-Klenow-polymerase, buffer and Cy3- and Cy5-dUTPs). Samples were labeled with Cy5 and reference DNA with Cy3. Standard protocol provided by manufacturer was followed.

extract_protocol: DNA was isolated from snap frozen tumor tissue using chloroform/phenol extraction followed by ethanol precipitation (Nucler Acid Extractor 340A; Applied Biosystems, Foster City, CA, USA). Some of the normal breast tissue samples were preserved in ethanol prior to extraction.

value: Female

tag: age at onset

tag: histology

value: Normal

tag: histologic grade

tag: histologic grade and genomic grade combined

tag: tumor size

tag: lymph node status

tag: estrogen receptor status

tag: gene expression subtype

tag: tp53 mutation status

value: wild-type

source_name: Reference genomic DNA, Promega


title: [genomic DNA]-[normal breast biopsy] MDG_124

description: [genomic DNA]-[normal breast biopsy]


title: [genomic DNA]-[normal breast biopsy] MDG_160

description: [genomic DNA]-[normal breast biopsy]


title: [genomic DNA]-[normal breast biopsy] MDG_114

description: [genomic DNA]-[normal breast biopsy]


title: [genomic DNA]-[normal breast biopsy] MDG_110

description: [genomic DNA]-[normal breast biopsy]


title: [genomic DNA]-[normal breast biopsy] MDG_113

description: [genomic DNA]-[normal breast biopsy]


title: [genomic DNA]-[normal breast biopsy] MDG_158

description: [genomic DNA]-[normal breast biopsy]


title: [genomic DNA]-[normal breast biopsy] MDG_127

description: [genomic DNA]-[normal breast biopsy]


title: [genomic DNA]-[normal breast biopsy] MDG_095

description: [genomic DNA]-[normal breast biopsy]


title: [genomic DNA]-[normal breast biopsy] MDG_048

description: [genomic DNA]-[normal breast biopsy]


title: [genomic DNA]-[normal breast biopsy] MDG_052

description: [genomic DNA]-[normal breast biopsy]


title: [genomic DNA]-[normal breast biopsy] MDG_051

description: [genomic DNA]-[normal breast biopsy]


title: [genomic DNA]-[normal breast biopsy] MDG_047

description: [genomic DNA]-[normal breast biopsy]


title: [genomic DNA]-[normal breast biopsy] MDG_099

description: [genomic DNA]-[normal breast biopsy]


title: [genomic DNA]-[normal breast biopsy] MDG_062

description: [genomic DNA]-[normal breast biopsy]


title: [genomic DNA]-[normal breast biopsy] MDG_081

description: [genomic DNA]-[normal breast biopsy]


title: [genomic DNA]-[primary breast tumor] ULL_279

description: [genomic DNA]-[primary breast tumor]

source_name: Tumor (primary invasive ductal breast carcinoma)

value: IDC

value: positive


title: [genomic DNA]-[primary breast tumor] ULL_270

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_271

description: [genomic DNA]-[primary breast tumor]

value: mutated


title: [genomic DNA]-[normal breast biopsy] MDG_009

description: [genomic DNA]-[normal breast biopsy]


title: [genomic DNA]-[primary breast tumor] ULL_268

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[normal breast biopsy] MDG_084

description: [genomic DNA]-[normal breast biopsy]


title: [genomic DNA]-[primary breast tumor] ULL_263

description: [genomic DNA]-[primary breast tumor]

value: negative


title: [genomic DNA]-[primary breast tumor] ULL_264

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[normal breast biopsy] MDG_008

description: [genomic DNA]-[normal breast biopsy]


title: [genomic DNA]-[primary breast tumor] ULL_259

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_277

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_267

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_276

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_273

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_254

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_249

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_251

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_242

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_246

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_243

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_241

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_238

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[normal breast biopsy] MDG_071

description: [genomic DNA]-[normal breast biopsy]


title: [genomic DNA]-[primary breast tumor] ULL_244

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_226

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_230

description: [genomic DNA]-[primary breast tumor]

value: Lumil A


title: [genomic DNA]-[primary breast tumor] ULL_232

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_216

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_214

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_212

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_272

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_211

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_198

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_188

description: [genomic DNA]-[primary breast tumor]

value: Basal-like


title: [genomic DNA]-[primary breast tumor] ULL_203

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_180

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_202

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_207

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_186

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_201

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_209

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_185

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_183

description: [genomic DNA]-[primary breast tumor]

value: Lumil B


title: [genomic DNA]-[primary breast tumor] ULL_177

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_173

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_171

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_172

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_210

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_167

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_179

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_161

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_165

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_163

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_237

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_160

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_169

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_144

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_139

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_143

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_134

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_150

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_184

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_142

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_135

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_156

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_125

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_101

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_113

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_122

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_096

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_108

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_098

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_099

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_131

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_085

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_120

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_094

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_084

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_075

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_093

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_080

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_082

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_083

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_118

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_074

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_068

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_090

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_064

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_067

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_066

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_071

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_070

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_087

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_057

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_065

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_056

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_048

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_040

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_051

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_044

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_053

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_058

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_038

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_027

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_011

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_026

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_013

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_009

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] MicMa_722

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_016

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_008

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_002

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_005

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_004

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_015

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] MicMa_627

description: [genomic DNA]-[primary breast tumor]

value: Normal-like


title: [genomic DNA]-[primary breast tumor] ULL_022

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] MicMa_630

description: [genomic DNA]-[primary breast tumor]


title: R500, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 2

city: Loughborough

first: Neil

last: Graham

state: Leicestershire

address: Sutton Bonington Campus

department: Plant and Crop Sciences

country: United Kingdom

institute: University of Nottingham

hyb_protocol: Samples were hybridized to Affymetrix Brassica Exon 1.0 ST Arrays (Affymetrix) and scanned at the NASC (Nottingham Arabidopsis Stcok centre) Microarray Core Facility or at SourceBioScience (SOURCE) according to manufacturer's instructions.

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

data_processing:
Data analysis and statistical analysis was performed using the GeneSpring GX 11 programme (Agilent Technologies). Raw data was pre-normalised using the RMA algorithm and each gene signal was normalised to the median of the gene signal across all samples.
probe group file: BrasEX1S_gene.cdf

label: Biotin

organism: Brassica rapa

label_protocol: RNA was amplified, fragmented and labelled using the Ambion WT expression kit.

growth_protocol: The plants were grown in a compost substrate comprising of Shamrock Professional Range medium peat (pHwater 3.8-4.4) mixed with horticultural grade silver sand (particle size <1 mm; J. Arthur Bowers, Lincoln, UK) at a ratio of 3:1 (v:v). Nutrients were added as follows per volume of substrate: 0.629 g L-1 NH4NO3 (Nitram, GrowHow, Ince, UK), 0.184 g L-1 NH4H2PO4 (Krista MAP, Yara UK, Immingham, UK), 0.03 g L-1 Na2SO4, 2 mL L-1 44 mM FeNaEDTA,  and 4 mL L-1 of a micronutrient solution comprising 30 mM H3BO3, 10 mM MnSO4.H2O, 3 mM CuSO4.5H2O, 1 mM ZnSO4.7H2O, 0.5 mM Na2MoO4.2H2O. All chemicals were supplied by VWR (Lutterworth, UK), unless otherwise stated. Seeds were sown directly into the compost contained in in 9cm x 9cm x 8cm pots (Desch Plantpak B.V., Waalwijk, NL) and grown in a controlled environment (CE). The CE was a walk-in high-specification growth room (Weiss-Gallenkamp) at Wellesbourne, UK, set to a 16-h photoperiod using metal halide lamps, giving a photon flux density between 400 and 700 nm (photosynthetically active radiation) of 250 µmol photons m-2 s-1 at plant height. The day/night settings for temperature were 18°C/15°C and for relative humidity were 76%/71%.

extract_protocol: RNA was isolated using a modified TRIzol protocol. To each sample, 1ml of TRIzol was added and total RNA extracted according to the manufacturer's instructions, with the following modifications: (i) after homogenisation the samples were centrifuged and supernatant transferred to a clean Eppendorf tube, and (ii) to aid precipitation of RNA from the aqueous phase, 0.25ml of isopropanol and 0.25ml 1.2M NaCl solution containing 0.8M sodium citrate. Extracted total RNA was then purified using the 'RNA Cleanup' protocol for Qiagen RNeasy columns.

treatment_protocol: A 2x2 combination of external calcium and magnesium concentrations were imposed to give four treatments (LL, HL, LH, HH) as follows: the high (H) concentrations were 3.5 g L-1 (24 mM) CaCl2 and 3.04 g L-1 (15 mM) MgCl2 and the low (L) concentrations were 0.44 g L-1 (3 mM) CaCl2 and 0.2 g L-1 (1 mM) MgCl2

tag: line

tag: tissue

value: 10 day-old leaf

tag: external calcium concentration

value: 3 mM

tag: external magnesium concentration

value: 1 mM

tag: biological replicate

tag: technical replicate

tag: array processed by

value: SOURCE


title: [genomic DNA]-[primary breast tumor] ULL_017

description: [genomic DNA]-[primary breast tumor]

tag: gender


title: [genomic DNA]-[primary breast tumor] MicMa_334

description: [genomic DNA]-[primary breast tumor]

tag: age at onset


title: [genomic DNA]-[primary breast tumor] MicMa_357

description: [genomic DNA]-[primary breast tumor]

tag: histology


title: [genomic DNA]-[primary breast tumor] MicMa_277

description: [genomic DNA]-[primary breast tumor]

tag: histologic grade


title: [genomic DNA]-[primary breast tumor] MicMa_406

description: [genomic DNA]-[primary breast tumor]

tag: histologic grade and genomic grade combined


title: [genomic DNA]-[primary breast tumor] MicMa_632

description: [genomic DNA]-[primary breast tumor]

tag: tumor size


title: BralRRl146, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl146_3 mM [Ca]_15 mM [Mg]

value: 15 mM


title: BralRRl259, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 2

source_name: BralRRl259_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] ULL_023

description: [genomic DNA]-[primary breast tumor]

tag: lymph node status


title: [genomic DNA]-[primary breast tumor] MicMa_275

description: [genomic DNA]-[primary breast tumor]

tag: estrogen receptor status


title: [genomic DNA]-[primary breast tumor] MicMa_341

description: [genomic DNA]-[primary breast tumor]

tag: gene expression subtype


title: [genomic DNA]-[primary breast tumor] MicMa_470

description: [genomic DNA]-[primary breast tumor]

tag: tp53 mutation status


title: BralRRl002, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl002_3 mM [Ca]_1 mM [Mg]

tag: line


title: BralRRl301, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl301_3 mM [Ca]_1 mM [Mg]

tag: tissue


title: [genomic DNA]-[primary breast tumor] MicMa_363

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] MicMa_267

description: [genomic DNA]-[primary breast tumor]


title: BralRRl150, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl150_3 mM [Ca]_1 mM [Mg]

tag: external calcium concentration


title: [genomic DNA]-[primary breast tumor] MicMa_263

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_030

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] ULL_037

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] MicMa_232

description: [genomic DNA]-[primary breast tumor]


title: BralRRl021, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 2

source_name: BralRRl021_3 mM [Ca]_1 mM [Mg]

tag: external magnesium concentration


title: [genomic DNA]-[primary breast tumor] MicMa_223

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] MicMa_222

description: [genomic DNA]-[primary breast tumor]


title: BralRRl259, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl259_3 mM [Ca]_15 mM [Mg]

tag: biological replicate

value: NASC


title: BralRRl002, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl002_3 mM [Ca]_15 mM [Mg]

tag: technical replicate


title: BralRRl229, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 2

source_name: BralRRl229_3 mM [Ca]_1 mM [Mg]

tag: array processed by


title: [genomic DNA]-[primary breast tumor] MicMa_221

description: [genomic DNA]-[primary breast tumor]

tag: gender

value: Female


title: BralRRl329, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl329_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] MicMa_167

description: [genomic DNA]-[primary breast tumor]

tag: age at onset


title: [genomic DNA]-[primary breast tumor] MicMa_165

description: [genomic DNA]-[primary breast tumor]

tag: histology


title: BralRRl290, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl290_24 mM [Ca]_1 mM [Mg]

value: 24 mM


title: [genomic DNA]-[primary breast tumor] MicMa_119

description: [genomic DNA]-[primary breast tumor]

tag: histologic grade

value: wild-type


title: BralRRl235, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl235_3 mM [Ca]_15 mM [Mg]


title: BralRRl201, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl201_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] MicMa_088

description: [genomic DNA]-[primary breast tumor]

value: IDC

tag: histologic grade and genomic grade combined


title: BralRRl284, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl284_24 mM [Ca]_1 mM [Mg]


title: BralRRl198, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl198_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] MicMa_197

description: [genomic DNA]-[primary breast tumor]

tag: tumor size

source_name: Reference genomic DNA, Promega


title: BralRRl337, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl337_3 mM [Ca]_1 mM [Mg]


title: BralRRl329, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl329_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] MicMa_087

description: [genomic DNA]-[primary breast tumor]

source_name: Tumor (primary invasive ductal breast carcinoma)

tag: lymph node status

value: positive


title: [genomic DNA]-[primary breast tumor] MicMa_101

description: [genomic DNA]-[primary breast tumor]

tag: estrogen receptor status


title: [genomic DNA]-[primary breast tumor] MicMa_100

description: [genomic DNA]-[primary breast tumor]

tag: gene expression subtype


title: BralRRl021, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl021_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] MicMa_089

description: [genomic DNA]-[primary breast tumor]

tag: tp53 mutation status


title: [genomic DNA]-[primary breast tumor] MicMa_132

description: [genomic DNA]-[primary breast tumor]


title: BralRRl229, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl229_3 mM [Ca]_15 mM [Mg]

tag: line


title: BralRRl380, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl380_24 mM [Ca]_1 mM [Mg]

tag: tissue


title: BralRRl300, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl300_3 mM [Ca]_15 mM [Mg]

tag: external calcium concentration


title: BralRRl104, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl104_24 mM [Ca]_1 mM [Mg]

tag: external magnesium concentration


title: [genomic DNA]-[primary breast tumor] MicMa_201

description: [genomic DNA]-[primary breast tumor]


title: BralRRl204, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl204_3 mM [Ca]_1 mM [Mg]

tag: biological replicate


title: [genomic DNA]-[primary breast tumor] MicMa_079

description: [genomic DNA]-[primary breast tumor]

value: mutated


title: BralRRl124, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl124_24 mM [Ca]_1 mM [Mg]

tag: technical replicate


title: IMB211, 3 mM external [Ca], 1 mM external [Mg], bio rep 3, tech rep 1

source_name: IMB211_3 mM [Ca]_1 mM [Mg]

tag: array processed by


title: BralRRl136, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl136_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] MicMa_085

description: [genomic DNA]-[primary breast tumor]

tag: gender


title: BralRRl021, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl021_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] MicMa_023

description: [genomic DNA]-[primary breast tumor]

tag: age at onset


title: [genomic DNA]-[primary breast tumor] MicMa_022

description: [genomic DNA]-[primary breast tumor]

tag: histology


title: BralRRl184, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl184_3 mM [Ca]_1 mM [Mg]


title: BralRRl248, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl248_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] MicMa_066

description: [genomic DNA]-[primary breast tumor]

tag: histologic grade


title: BralRRl259, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl259_3 mM [Ca]_1 mM [Mg]


title: R500, 24 mM external [Ca], 1 mM external [Mg], bio rep 3, tech rep 1


title: [genomic DNA]-[primary breast tumor] MicMa_053

description: [genomic DNA]-[primary breast tumor]

tag: histologic grade and genomic grade combined

value: negative

source_name: Reference genomic DNA, Promega


title: BralRRl337, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl337_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] MicMa_044

description: [genomic DNA]-[primary breast tumor]

tag: tumor size


title: [genomic DNA]-[primary breast tumor] MicMa_052

description: [genomic DNA]-[primary breast tumor]

tag: lymph node status

value: Lumil A


title: BralRRl337, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl337_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] MicMa_014

description: [genomic DNA]-[primary breast tumor]

source_name: Tumor (primary invasive ductal breast carcinoma)

tag: estrogen receptor status


title: BralRRl229, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl229_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] MDG_91

description: [genomic DNA]-[primary breast tumor]

tag: gene expression subtype


title: [genomic DNA]-[primary breast tumor] MicMa_019

description: [genomic DNA]-[primary breast tumor]

tag: tp53 mutation status


title: [genomic DNA]-[primary breast tumor] MDG_73

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] MDG_88

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] MDG_90

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] MDG_6

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] MDG_56

description: [genomic DNA]-[primary breast tumor]


title: R500, 3 mM external [Ca], 15 mM external [Mg], bio rep 3, tech rep 1

tag: line


title: R500, 24 mM external [Ca], 15 mM external [Mg], bio rep 3, tech rep 1

tag: tissue


title: R500, 3 mM external [Ca], 1 mM external [Mg], bio rep 3, tech rep 1

tag: external calcium concentration


title: [genomic DNA]-[primary breast tumor] MDG_69

description: [genomic DNA]-[primary breast tumor]


title: R500, 3 mM external [Ca], 15 mM external [Mg], bio rep 2, tech rep 1

tag: external magnesium concentration


title: R500, 24 mM external [Ca], 1 mM external [Mg], bio rep 2, tech rep 1

tag: biological replicate


title: R500, 24 mM external [Ca], 15 mM external [Mg], bio rep 2, tech rep 1

tag: technical replicate


title: [genomic DNA]-[primary breast tumor] MDG_83

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] MDG_55

description: [genomic DNA]-[primary breast tumor]


title: R500, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

tag: array processed by


title: [genomic DNA]-[primary breast tumor] MDG_174

description: [genomic DNA]-[primary breast tumor]

tag: gender


title: R500, 3 mM external [Ca], 1 mM external [Mg], bio rep 2, tech rep 1


title: R500, 24 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1


title: R500, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1


title: R500, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1


title: [genomic DNA]-[primary breast tumor] MDG_171

description: [genomic DNA]-[primary breast tumor]

tag: age at onset


title: IMB211, 24 mM external [Ca], 15 mM external [Mg], bio rep 3, tech rep 1


title: IMB211, 24 mM external [Ca], 1 mM external [Mg], bio rep 3, tech rep 1


title: [genomic DNA]-[primary breast tumor] MDG_173

description: [genomic DNA]-[primary breast tumor]

tag: histology


title: IMB211, 3 mM external [Ca], 15 mM external [Mg], bio rep 3, tech rep 1


title: [genomic DNA]-[primary breast tumor] MDG_167

description: [genomic DNA]-[primary breast tumor]

tag: histologic grade


title: [genomic DNA]-[primary breast tumor] MDG_169

description: [genomic DNA]-[primary breast tumor]

tag: histologic grade and genomic grade combined


title: IMB211, 24 mM external [Ca], 15 mM external [Mg], bio rep 2, tech rep 1


title: [genomic DNA]-[primary breast tumor] MDG_2

description: [genomic DNA]-[primary breast tumor]

tag: tumor size


title: IMB211, 3 mM external [Ca], 15 mM external [Mg], bio rep 2, tech rep 1


title: IMB211, 3 mM external [Ca], 1 mM external [Mg], bio rep 2, tech rep 1


title: [genomic DNA]-[primary breast tumor] MDG_161

description: [genomic DNA]-[primary breast tumor]

tag: lymph node status


title: IMB211, 24 mM external [Ca], 1 mM external [Mg], bio rep 2, tech rep 1


title: IMB211, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1


title: [genomic DNA]-[primary breast tumor] MDG_154

description: [genomic DNA]-[primary breast tumor]

tag: estrogen receptor status


title: [genomic DNA]-[primary breast tumor] MDG_153

description: [genomic DNA]-[primary breast tumor]

tag: gene expression subtype


title: IMB211, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1


title: [genomic DNA]-[primary breast tumor] MDG_134

description: [genomic DNA]-[primary breast tumor]

tag: tp53 mutation status


title: [genomic DNA]-[primary breast tumor] MDG_155

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] MDG_151

description: [genomic DNA]-[primary breast tumor]

value: Basal-like


title: [genomic DNA]-[primary breast tumor] MDG_142

description: [genomic DNA]-[primary breast tumor]

value: Lumil B


title: IMB211, 24 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

tag: line


title: [genomic DNA]-[primary breast tumor] MDG_170

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] MDG_144

description: [genomic DNA]-[primary breast tumor]


title: BralRRl328, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl328_24 mM [Ca]_1 mM [Mg]

tag: tissue


title: [genomic DNA]-[primary breast tumor] MDG_168

description: [genomic DNA]-[primary breast tumor]


title: BralRRl373, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl373_24 mM [Ca]_1 mM [Mg]

tag: external calcium concentration


title: IMB211, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

tag: external magnesium concentration


title: [genomic DNA]-[primary breast tumor] MDG_129

description: [genomic DNA]-[primary breast tumor]


title: BralRRl136, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl136_24 mM [Ca]_1 mM [Mg]

tag: biological replicate


title: [genomic DNA]-[primary breast tumor] MDG_137

description: [genomic DNA]-[primary breast tumor]


title: BralRRl204, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl204_24 mM [Ca]_1 mM [Mg]

tag: technical replicate


title: [genomic DNA]-[primary breast tumor] MDG_128

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] MDG_132

description: [genomic DNA]-[primary breast tumor]


title: BralRRl229, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl229_24 mM [Ca]_1 mM [Mg]

tag: array processed by


title: [genomic DNA]-[primary breast tumor] MDG_122

description: [genomic DNA]-[primary breast tumor]

tag: gender


title: BralRRl016, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl016_24 mM [Ca]_1 mM [Mg]


title: BralRRl150, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl150_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] MDG_126

description: [genomic DNA]-[primary breast tumor]

tag: age at onset


title: BralRRl070, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl070_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] MDG_123

description: [genomic DNA]-[primary breast tumor]

tag: histology


title: [genomic DNA]-[primary breast tumor] MDG_100

description: [genomic DNA]-[primary breast tumor]

tag: histologic grade


title: [genomic DNA]-[primary breast tumor] MDG_1

description: [genomic DNA]-[primary breast tumor]

tag: histologic grade and genomic grade combined


title: BralRRl184, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl184_24 mM [Ca]_1 mM [Mg]


title: BralRRl001, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl001_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] MDG_104

description: [genomic DNA]-[primary breast tumor]

tag: tumor size


title: [genomic DNA]-[primary breast tumor] MDG_106

description: [genomic DNA]-[primary breast tumor]

tag: lymph node status


title: BralRRl143, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl143_3 mM [Ca]_15 mM [Mg]


title: BralRRl250, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl250_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] MDG_121

description: [genomic DNA]-[primary breast tumor]

tag: estrogen receptor status

source_name: Reference genomic DNA, Promega


title: BralRRl301, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl301_3 mM [Ca]_15 mM [Mg]


title: BralRRl259, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl259_24 mM [Ca]_1 mM [Mg]


title: BralRRl021, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl021_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] FW_9

description: [genomic DNA]-[primary breast tumor]

source_name: Tumor (primary invasive ductal breast carcinoma)

tag: gene expression subtype

value: Normal-like


title: [genomic DNA]-[primary breast tumor] MDG_133

description: [genomic DNA]-[primary breast tumor]

tag: tp53 mutation status


title: [genomic DNA]-[primary breast tumor] MDG_105

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] FW_87

description: [genomic DNA]-[primary breast tumor]


title: BralRRl143, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl143_3 mM [Ca]_1 mM [Mg]

tag: line

value: 10 day-old leaf


title: [genomic DNA]-[primary breast tumor] MDG_115

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] FW_86

description: [genomic DNA]-[primary breast tumor]


title: BralRRl235, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl235_3 mM [Ca]_1 mM [Mg]

tag: tissue

value: 3 mM


title: BralRRl277, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl277_3 mM [Ca]_15 mM [Mg]

tag: external calcium concentration


title: [genomic DNA]-[primary breast tumor] FW_89

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] FW_68

description: [genomic DNA]-[primary breast tumor]


title: IMB211, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 2

tag: external magnesium concentration


title: BralRRl025, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl025_3 mM [Ca]_15 mM [Mg]

tag: biological replicate


title: [genomic DNA]-[primary breast tumor] FW_78

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] FW_74

description: [genomic DNA]-[primary breast tumor]


title: BralRRl255, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl255_3 mM [Ca]_15 mM [Mg]

tag: technical replicate


title: [genomic DNA]-[primary breast tumor] FW_69

description: [genomic DNA]-[primary breast tumor]


title: BralRRl300, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl300_3 mM [Ca]_1 mM [Mg]

value: 1 mM

tag: array processed by


title: [genomic DNA]-[primary breast tumor] FW_59

description: [genomic DNA]-[primary breast tumor]

tag: gender


title: [genomic DNA]-[primary breast tumor] FW_65

description: [genomic DNA]-[primary breast tumor]

tag: age at onset


title: [genomic DNA]-[primary breast tumor] FW_53

description: [genomic DNA]-[primary breast tumor]

tag: histology


title: BralRRl277, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl277_3 mM [Ca]_1 mM [Mg]

value: SOURCE


title: BralRRl265, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl265_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] FW_51

description: [genomic DNA]-[primary breast tumor]

tag: histologic grade


title: BralRRl255, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl255_3 mM [Ca]_1 mM [Mg]


title: BralRRl215, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl215_3 mM [Ca]_1 mM [Mg]


title: BralRRl332, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl332_3 mM [Ca]_1 mM [Mg]


title: BralRRl042, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl042_3 mM [Ca]_15 mM [Mg]

value: 15 mM


title: IMB211, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 2

source_name: IMB211_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] FW_56

description: [genomic DNA]-[primary breast tumor]

tag: histologic grade and genomic grade combined

source_name: Reference genomic DNA, Promega


title: BralRRl042, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl042_3 mM [Ca]_1 mM [Mg]


title: BralRRl053, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl053_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] FW_49

description: [genomic DNA]-[primary breast tumor]

source_name: Tumor (primary invasive ductal breast carcinoma)

tag: tumor size


title: BralRRl155, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl155_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] FW_46

description: [genomic DNA]-[primary breast tumor]

tag: lymph node status


title: BralRRl147, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl147_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] FW_45

description: [genomic DNA]-[primary breast tumor]

tag: estrogen receptor status


title: [genomic DNA]-[primary breast tumor] FW_43

description: [genomic DNA]-[primary breast tumor]

tag: gene expression subtype


title: [genomic DNA]-[primary breast tumor] FW_48

description: [genomic DNA]-[primary breast tumor]

tag: tp53 mutation status


title: [genomic DNA]-[primary breast tumor] FW_44

description: [genomic DNA]-[primary breast tumor]


title: BralRRl318, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl318_3 mM [Ca]_1 mM [Mg]

tag: line


title: BralRRl174, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl174_3 mM [Ca]_1 mM [Mg]

tag: tissue


title: BralRRl147, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl147_3 mM [Ca]_15 mM [Mg]

tag: external calcium concentration


title: [genomic DNA]-[primary breast tumor] FW_57

description: [genomic DNA]-[primary breast tumor]


title: BralRRl103, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl103_3 mM [Ca]_15 mM [Mg]

tag: external magnesium concentration


title: [genomic DNA]-[primary breast tumor] FW_39

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] FW_36

description: [genomic DNA]-[primary breast tumor]


title: BralRRl053, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl053_3 mM [Ca]_15 mM [Mg]

tag: biological replicate


title: IMB211, 3 mM external [Ca], 1 mM external [Mg], bio rep 2, tech rep 2

tag: technical replicate


title: BralRRl041, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl041_3 mM [Ca]_1 mM [Mg]

tag: array processed by


title: BralRRl199, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl199_3 mM [Ca]_1 mM [Mg]


title: BralRRl076, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl076_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] FW_30

description: [genomic DNA]-[primary breast tumor]

tag: gender


title: [genomic DNA]-[primary breast tumor] FW_29

description: [genomic DNA]-[primary breast tumor]

tag: age at onset


title: [genomic DNA]-[primary breast tumor] FW_247

description: [genomic DNA]-[primary breast tumor]

tag: histology


title: [genomic DNA]-[primary breast tumor] FW_33

description: [genomic DNA]-[primary breast tumor]

tag: histologic grade


title: [genomic DNA]-[primary breast tumor] FW_25

description: [genomic DNA]-[primary breast tumor]

tag: histologic grade and genomic grade combined


title: [genomic DNA]-[primary breast tumor] FW_26

description: [genomic DNA]-[primary breast tumor]

tag: tumor size


title: BralRRl213, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl213_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] FW_238

description: [genomic DNA]-[primary breast tumor]

tag: lymph node status


title: BralRRl318, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl318_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] FW_229

description: [genomic DNA]-[primary breast tumor]

tag: estrogen receptor status


title: [genomic DNA]-[primary breast tumor] FW_241

description: [genomic DNA]-[primary breast tumor]

tag: gene expression subtype


title: [genomic DNA]-[primary breast tumor] FW_236

description: [genomic DNA]-[primary breast tumor]

tag: tp53 mutation status


title: [genomic DNA]-[primary breast tumor] FW_232

description: [genomic DNA]-[primary breast tumor]


title: IMB211, 3 mM external [Ca], 15 mM external [Mg], bio rep 2, tech rep 2

tag: line


title: BralRRl232, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl232_3 mM [Ca]_1 mM [Mg]

tag: tissue


title: BralRRl001, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl001_3 mM [Ca]_15 mM [Mg]

tag: external calcium concentration


title: BralRRl041, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl041_3 mM [Ca]_15 mM [Mg]

tag: external magnesium concentration


title: BralRRl174, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl174_3 mM [Ca]_15 mM [Mg]

tag: biological replicate


title: BralRRl303, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl303_3 mM [Ca]_1 mM [Mg]

tag: technical replicate


title: BralRRl232, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl232_3 mM [Ca]_15 mM [Mg]

tag: array processed by


title: BralRRl256, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl256_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] FW_219

description: [genomic DNA]-[primary breast tumor]

source_name: Tumor (primary invasive ductal breast carcinoma)

tag: gender

source_name: Reference genomic DNA, Promega


title: [genomic DNA]-[primary breast tumor] FW_218

description: [genomic DNA]-[primary breast tumor]

tag: age at onset


title: R500, 3 mM external [Ca], 15 mM external [Mg], bio rep 2, tech rep 2


title: [genomic DNA]-[primary breast tumor] FW_214

description: [genomic DNA]-[primary breast tumor]

tag: histology


title: [genomic DNA]-[primary breast tumor] FW_211

description: [genomic DNA]-[primary breast tumor]

tag: histologic grade


title: [genomic DNA]-[primary breast tumor] FW_209

description: [genomic DNA]-[primary breast tumor]

tag: histologic grade and genomic grade combined


title: [genomic DNA]-[primary breast tumor] FW_208

description: [genomic DNA]-[primary breast tumor]

tag: tumor size


title: BralRRl093, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl093_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] FW_198

description: [genomic DNA]-[primary breast tumor]

tag: lymph node status


title: [genomic DNA]-[primary breast tumor] FW_188

description: [genomic DNA]-[primary breast tumor]

tag: estrogen receptor status


title: [genomic DNA]-[primary breast tumor] FW_190

description: [genomic DNA]-[primary breast tumor]

tag: gene expression subtype


title: BralRRl289, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl289_3 mM [Ca]_15 mM [Mg]


title: BralRRl166, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl166_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] FW_174

description: [genomic DNA]-[primary breast tumor]

tag: tp53 mutation status


title: [genomic DNA]-[primary breast tumor] FW_162

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] FW_151

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] FW_141

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] FW_164

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] FW_145

description: [genomic DNA]-[primary breast tumor]


title: BralRRl069, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl069_3 mM [Ca]_15 mM [Mg]

tag: line


title: BralRRl231, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl231_3 mM [Ca]_1 mM [Mg]

tag: tissue


title: BralRRl205, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl205_3 mM [Ca]_15 mM [Mg]

tag: external calcium concentration


title: BralRRl215, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl215_3 mM [Ca]_15 mM [Mg]

tag: external magnesium concentration


title: BralRRl222, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl222_3 mM [Ca]_15 mM [Mg]

tag: biological replicate


title: BralRRl265, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl265_3 mM [Ca]_15 mM [Mg]

tag: technical replicate


title: [genomic DNA]-[primary breast tumor] FW_137

description: [genomic DNA]-[primary breast tumor]


title: BralRRl222, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl222_3 mM [Ca]_1 mM [Mg]

tag: array processed by


title: BralRRl341, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl341_3 mM [Ca]_1 mM [Mg]


title: BralRRl155, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl155_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] FW_13

description: [genomic DNA]-[primary breast tumor]

tag: gender


title: [genomic DNA]-[primary breast tumor] FW_136

description: [genomic DNA]-[primary breast tumor]

tag: age at onset


title: [genomic DNA]-[primary breast tumor] FW_17

description: [genomic DNA]-[primary breast tumor]

tag: histology


title: BralRRl187, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl187_3 mM [Ca]_1 mM [Mg]


title: BralRRl325, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl325_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] FW_135

description: [genomic DNA]-[primary breast tumor]

tag: histologic grade


title: BralRRl332, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl332_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] FW_112

description: [genomic DNA]-[primary breast tumor]

source_name: Tumor (primary invasive ductal breast carcinoma)

tag: histologic grade and genomic grade combined


title: [genomic DNA]-[primary breast tumor] FW_129

description: [genomic DNA]-[primary breast tumor]

tag: tumor size

source_name: Reference genomic DNA, Promega


title: BralRRl069, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl069_3 mM [Ca]_1 mM [Mg]


title: BralRRl261, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl261_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] FW_117

description: [genomic DNA]-[primary breast tumor]

tag: lymph node status


title: [genomic DNA]-[primary breast tumor] DBCG_9965

description: [genomic DNA]-[primary breast tumor]

tag: estrogen receptor status


title: BralRRl363, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl363_3 mM [Ca]_15 mM [Mg]


title: BralRRl264, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl264_3 mM [Ca]_1 mM [Mg]


title: BralRRl190, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl190_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_9904

description: [genomic DNA]-[primary breast tumor]

tag: gene expression subtype


title: [genomic DNA]-[primary breast tumor] DBCG_9842

description: [genomic DNA]-[primary breast tumor]

tag: tp53 mutation status


title: BralRRl256, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl256_3 mM [Ca]_15 mM [Mg]

tag: line


title: [genomic DNA]-[primary breast tumor] DBCG_9877

description: [genomic DNA]-[primary breast tumor]


title: BralRRl261, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl261_3 mM [Ca]_1 mM [Mg]

tag: tissue


title: [genomic DNA]-[primary breast tumor] DBCG_9817

description: [genomic DNA]-[primary breast tumor]


title: R500, 3 mM external [Ca], 1 mM external [Mg], bio rep 2, tech rep 2

tag: external calcium concentration


title: [genomic DNA]-[primary breast tumor] DBCG_9805

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] DBCG_9781

description: [genomic DNA]-[primary breast tumor]


title: [genomic DNA]-[primary breast tumor] DBCG_9880

description: [genomic DNA]-[primary breast tumor]


title: BralRRl363, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl363_3 mM [Ca]_1 mM [Mg]

tag: external magnesium concentration


title: BralRRl007, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl007_3 mM [Ca]_1 mM [Mg]

tag: biological replicate


title: BralRRl204, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 2

source_name: BralRRl204_3 mM [Ca]_1 mM [Mg]

tag: technical replicate


title: [genomic DNA]-[primary breast tumor] DBCG_9726

description: [genomic DNA]-[primary breast tumor]