title: BralRRl251, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl251_3 mM [Ca]_1 mM [Mg]

tag: array processed by


title: [genomic DNA]-[primary breast tumor] DBCG_9687

status: Public on May 21 2014

type: genomic

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]-[primary breast tumor]

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).

molecule: genomic DNA

organism: Homo sapiens

source_name: Tumor (primary invasive ductal breast carcinoma)

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.

tag: gender

value: Female

tag: age at onset

tag: histology

value: IDC

tag: histologic grade

tag: histologic grade and genomic grade combined

tag: tumor size

tag: lymph node status

tag: estrogen receptor status

value: positive

tag: gene expression subtype

value: Lumil A

tag: tp53 mutation status

value: wild-type

source_name: Reference genomic DNA, Promega


title: BralRRl346, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

type: RNA

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

molecule: total RNA

organism: Brassica rapa

source_name: BralRRl346_3 mM [Ca]_1 mM [Mg]

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

value: SOURCE


title: [genomic DNA]-[primary breast tumor] FW_111

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

value: negative

value: Lumil B


title: [genomic DNA]-[primary breast tumor] DBCG_9759

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

value: mutated


title: BralRRl225, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl225_3 mM [Ca]_1 mM [Mg]

tag: array processed by


title: [genomic DNA]-[primary breast tumor] DBCG_9778

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

tag: gender

value: Normal-like


title: BralRRl223, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl223_3 mM [Ca]_1 mM [Mg]


title: BralRRl009, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl009_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_9654

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

tag: age at onset


title: BralRRl115, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl115_3 mM [Ca]_1 mM [Mg]


title: BralRRl346, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl346_3 mM [Ca]_15 mM [Mg]

value: 15 mM


title: BralRRl251, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl251_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_9544

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

tag: histology


title: [genomic DNA]-[primary breast tumor] DBCG_9571

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

tag: histologic grade


title: BralRRl093, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl093_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_9490

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

tag: histologic grade and genomic grade combined


title: [genomic DNA]-[primary breast tumor] DBCG_9645

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

tag: tumor size


title: [genomic DNA]-[primary breast tumor] DBCG_9493

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

tag: lymph node status


title: [genomic DNA]-[primary breast tumor] DBCG_8919

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

tag: estrogen receptor status


title: [genomic DNA]-[primary breast tumor] DBCG_8900

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

tag: gene expression subtype

value: Basal-like


title: BralRRl115, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl115_3 mM [Ca]_15 mM [Mg]


title: BralRRl009, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl009_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_8875

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

tag: tp53 mutation status


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

tag: line


title: BralRRl373, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl373_3 mM [Ca]_1 mM [Mg]

tag: tissue


title: [genomic DNA]-[primary breast tumor] DBCG_8807

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


title: BralRRl223, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl223_3 mM [Ca]_15 mM [Mg]

tag: external calcium concentration


title: BralRRl184, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl184_3 mM [Ca]_15 mM [Mg]

tag: external magnesium concentration


title: [genomic DNA]-[primary breast tumor] DBCG_8706

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


title: BralRRl136, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl136_3 mM [Ca]_15 mM [Mg]

tag: biological replicate


title: BralRRl089, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl089_3 mM [Ca]_15 mM [Mg]

tag: technical replicate


title: [genomic DNA]-[primary breast tumor] DBCG_8655

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

source_name: Tumor (primary invasive ductal breast carcinoma)


title: BralRRl065, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl065_3 mM [Ca]_1 mM [Mg]

tag: array processed by


title: BralRRl231, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl231_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_8701

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

tag: gender

source_name: Reference genomic DNA, Promega


title: BralRRl373, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl373_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_8590

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

tag: age at onset


title: BralRRl046, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl046_3 mM [Ca]_1 mM [Mg]


title: BralRRl328, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl328_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_8645

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

tag: histology


title: [genomic DNA]-[primary breast tumor] DBCG_8526

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

tag: histologic grade


title: BralRRl250, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl250_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_8670

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

tag: histologic grade and genomic grade combined


title: [genomic DNA]-[primary breast tumor] DBCG_8510

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

tag: tumor size


title: BralRRl016, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl016_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_8779

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

tag: lymph node status


title: [genomic DNA]-[primary breast tumor] DBCG_8493

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

tag: estrogen receptor status


title: [genomic DNA]-[primary breast tumor] DBCG_8455

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

tag: gene expression subtype


title: [genomic DNA]-[primary breast tumor] DBCG_8443

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

tag: tp53 mutation status


title: [genomic DNA]-[primary breast tumor] DBCG_8445

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


title: BralRRl070, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl070_3 mM [Ca]_1 mM [Mg]

tag: line


title: [genomic DNA]-[primary breast tumor] DBCG_8418

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


title: BralRRl284, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl284_3 mM [Ca]_1 mM [Mg]

tag: tissue


title: BralRRl124, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl124_3 mM [Ca]_1 mM [Mg]

tag: external calcium concentration


title: BralRRl380, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl380_3 mM [Ca]_1 mM [Mg]

tag: external magnesium concentration


title: BralRRl104, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl104_3 mM [Ca]_1 mM [Mg]

tag: biological replicate


title: BralRRl284, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl284_3 mM [Ca]_15 mM [Mg]

tag: technical replicate


title: BralRRl198, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl198_3 mM [Ca]_15 mM [Mg]

tag: array processed by


title: BralRRl380, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl380_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_8372

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

source_name: Tumor (primary invasive ductal breast carcinoma)

tag: gender


title: [genomic DNA]-[primary breast tumor] DBCG_8380

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

tag: age at onset


title: BralRRl253, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl253_24 mM [Ca]_1 mM [Mg]

value: 24 mM

value: NASC


title: BralRRl360, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl360_3 mM [Ca]_15 mM [Mg]


title: BralRRl205, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl205_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_8371

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

value: Female

tag: histology

source_name: Reference genomic DNA, Promega


title: BralRRl060, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl060_24 mM [Ca]_1 mM [Mg]


title: BralRRl065, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl065_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_8360

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

value: IDC

tag: histologic grade


title: [genomic DNA]-[primary breast tumor] DBCG_7717B

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

tag: histologic grade and genomic grade combined

value: positive


title: [genomic DNA]-[primary breast tumor] DBCG_7797A

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

tag: tumor size


title: BralRRl089, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl089_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_7722

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

tag: lymph node status

value: Lumil A


title: [genomic DNA]-[primary breast tumor] DBCG_8100

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

tag: estrogen receptor status

value: wild-type


title: BralRRl290, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl290_3 mM [Ca]_15 mM [Mg]

value: 10 day-old leaf


title: [genomic DNA]-[primary breast tumor] DBCG_7862c

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

tag: gene expression subtype


title: BralRRl376, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl376_24 mM [Ca]_1 mM [Mg]


title: BralRRl031, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl031_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_7434A

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

tag: tp53 mutation status


title: [genomic DNA]-[primary breast tumor] DBCG_7751

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


title: [genomic DNA]-[primary breast tumor] DBCG_7522C

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


title: [genomic DNA]-[primary breast tumor] DBCG_7234

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


title: [genomic DNA]-[primary breast tumor] DBCG_7366

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


title: [genomic DNA]-[primary breast tumor] DBCG_7690D

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


title: BralRRl223, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl223_24 mM [Ca]_1 mM [Mg]

tag: line


title: BralRRl093, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl093_24 mM [Ca]_1 mM [Mg]

tag: tissue


title: BralRRl115, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl115_24 mM [Ca]_1 mM [Mg]

tag: external calcium concentration


title: [genomic DNA]-[primary breast tumor] DBCG_7102C

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


title: [genomic DNA]-[primary breast tumor] DBCG_8323

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


title: [genomic DNA]-[primary breast tumor] DBCG_6599

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


title: [genomic DNA]-[primary breast tumor] DBCG_6932

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


title: [genomic DNA]-[primary breast tumor] DBCG_6962

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


title: BralRRl251, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl251_24 mM [Ca]_1 mM [Mg]

tag: external magnesium concentration


title: BralRRl001, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl001_24 mM [Ca]_1 mM [Mg]

tag: biological replicate


title: [genomic DNA]-[primary breast tumor] DBCG_6692

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


title: BralRRl009, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl009_24 mM [Ca]_1 mM [Mg]

tag: technical replicate


title: [genomic DNA]-[primary breast tumor] DBCG_6412

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

source_name: Tumor (primary invasive ductal breast carcinoma)


title: BralRRl281, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl281_24 mM [Ca]_1 mM [Mg]

tag: array processed by


title: BralRRl041, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl041_24 mM [Ca]_1 mM [Mg]


title: BralRRl264, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl264_24 mM [Ca]_1 mM [Mg]


title: BralRRl213, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl213_24 mM [Ca]_1 mM [Mg]


title: BralRRl231, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl231_24 mM [Ca]_1 mM [Mg]


title: BralRRl303, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl303_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_6014

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

tag: gender

source_name: Reference genomic DNA, Promega


title: [genomic DNA]-[primary breast tumor] DBCG_6186

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

tag: age at onset


title: BralRRl190, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl190_24 mM [Ca]_1 mM [Mg]


title: BralRRl346, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl346_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_5705

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

tag: histology


title: [genomic DNA]-[primary breast tumor] DBCG_6198

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

tag: histologic grade


title: [genomic DNA]-[primary breast tumor] DBCG_6332

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

tag: histologic grade and genomic grade combined


title: [genomic DNA]-[primary breast tumor] DBCG_5775

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

tag: tumor size


title: BralRRl256, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl256_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_5911

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

tag: lymph node status


title: [genomic DNA]-[primary breast tumor] DBCG_5960

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

tag: estrogen receptor status


title: BralRRl076, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl076_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_5781

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

tag: gene expression subtype


title: BralRRl103, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl103_24 mM [Ca]_1 mM [Mg]


title: BralRRl232, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl232_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_6351

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

tag: tp53 mutation status


title: BralRRl174, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl174_24 mM [Ca]_1 mM [Mg]

tag: line


title: [genomic DNA]-[primary breast tumor] DBCG_5653

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


title: [genomic DNA]-[primary breast tumor] DBCG_5695

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


title: BralRRl318, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl318_24 mM [Ca]_1 mM [Mg]

tag: tissue


title: BralRRl147, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl147_24 mM [Ca]_1 mM [Mg]

tag: external calcium concentration


title: [genomic DNA]-[primary breast tumor] DBCG_5335

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

source_name: Tumor (primary invasive ductal breast carcinoma)


title: BralRRl277, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl277_24 mM [Ca]_1 mM [Mg]

tag: external magnesium concentration


title: [genomic DNA]-[primary breast tumor] DBCG_5704

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


title: BralRRl053, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl053_24 mM [Ca]_1 mM [Mg]

tag: biological replicate


title: [genomic DNA]-[primary breast tumor] DBCG_5276

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


title: BralRRl155, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl155_24 mM [Ca]_1 mM [Mg]

tag: technical replicate


title: BralRRl069, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl069_24 mM [Ca]_1 mM [Mg]

tag: array processed by


title: [genomic DNA]-[primary breast tumor] DBCG_4988

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

tag: gender


title: BralRRl332, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl332_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_4959

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

tag: age at onset


title: [genomic DNA]-[primary breast tumor] DBCG_5509

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

tag: histology


title: BralRRl025, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl025_24 mM [Ca]_1 mM [Mg]


title: BralRRl146, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl146_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_5422

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

tag: histologic grade

source_name: Reference genomic DNA, Promega


title: BralRRl042, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl042_24 mM [Ca]_1 mM [Mg]


title: BralRRl265, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl265_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_3301

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

tag: histologic grade and genomic grade combined


title: BralRRl211, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl211_24 mM [Ca]_1 mM [Mg]


title: BralRRl341, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl341_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_5052

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

tag: tumor size


title: [genomic DNA]-[primary breast tumor] DBCG_4976

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

tag: lymph node status


title: BralRRl300, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl300_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_5200

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

tag: estrogen receptor status


title: [genomic DNA]-[primary breast tumor] DBCG_4867

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

tag: gene expression subtype


title: BralRRl002, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl002_24 mM [Ca]_1 mM [Mg]


title: BralRRl143, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl143_24 mM [Ca]_1 mM [Mg]


title: BralRRl235, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl235_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_3174

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

source_name: Tumor (primary invasive ductal breast carcinoma)

tag: tp53 mutation status


title: BralRRl289, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl289_24 mM [Ca]_1 mM [Mg]

tag: line


title: [genomic DNA]-[primary breast tumor] DBCG_3172

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


title: [genomic DNA]-[primary breast tumor] DBCG_2829

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


title: [genomic DNA]-[primary breast tumor] DBCG_2625

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


title: [genomic DNA]-[primary breast tumor] DBCG_5598

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


title: [genomic DNA]-[primary breast tumor] DBCG_2653

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


title: BralRRl222, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl222_24 mM [Ca]_1 mM [Mg]

tag: tissue


title: BralRRl301, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl301_24 mM [Ca]_1 mM [Mg]

tag: external calcium concentration


title: BralRRl060, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl060_3 mM [Ca]_1 mM [Mg]

value: 3 mM

tag: external magnesium concentration


title: BralRRl089, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl089_3 mM [Ca]_1 mM [Mg]

value: 1 mM

tag: biological replicate


title: [genomic DNA]-[primary breast tumor] DBCG_2392

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


title: BralRRl337, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 2

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

tag: technical replicate

value: SOURCE


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

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

tag: array processed by


title: BralRRl328, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl328_3 mM [Ca]_1 mM [Mg]


title: BralRRl021, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 2

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


title: BralRRl242, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl242_3 mM [Ca]_1 mM [Mg]


title: BralRRl031, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl031_3 mM [Ca]_1 mM [Mg]


title: BralRRl337, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 2

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


title: [genomic DNA]-[primary breast tumor] DBCG_2253

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

tag: gender

source_name: Reference genomic DNA, Promega


title: [genomic DNA]-[primary breast tumor] DBCG_1962

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

tag: age at onset


title: [genomic DNA]-[primary breast tumor] DBCG_15882

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

tag: histology


title: [genomic DNA]-[primary breast tumor] DBCG_1860

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

tag: histologic grade

value: negative


title: [genomic DNA]-[primary breast tumor] DBCG_2256

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

tag: histologic grade and genomic grade combined


title: BralRRl242, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl242_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_13760

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

tag: tumor size


title: BralRRl060, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl060_3 mM [Ca]_15 mM [Mg]


title: BralRRl329, 24 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl329_24 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_14587

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

source_name: Tumor (primary invasive ductal breast carcinoma)

tag: lymph node status


title: [genomic DNA]-[primary breast tumor] DBCG_13148

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

tag: estrogen receptor status


title: [genomic DNA]-[primary breast tumor] DBCG_12617

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

tag: gene expression subtype


title: [genomic DNA]-[primary breast tumor] DBCG_2034

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

value: Lumil B

tag: tp53 mutation status


title: BralRRl376, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl376_3 mM [Ca]_15 mM [Mg]

tag: line


title: [genomic DNA]-[primary breast tumor] DBCG_2509

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

value: mutated


title: BralRRl183, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl183_3 mM [Ca]_15 mM [Mg]

tag: tissue


title: BralRRl031, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl031_3 mM [Ca]_15 mM [Mg]

tag: external calcium concentration


title: [genomic DNA]-[primary breast tumor] DBCG_13722

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


title: BralRRl136, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 2

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

tag: external magnesium concentration


title: BralRRl065, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl065_3 mM [Ca]_15 mM [Mg]

tag: biological replicate


title: [genomic DNA]-[primary breast tumor] DBCG_12185

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


title: [genomic DNA]-[primary breast tumor] DBCG_12171

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


title: [genomic DNA]-[primary breast tumor] DBCG_11884

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


title: [genomic DNA]-[primary breast tumor] DBCG_11989

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


title: TMD8 shTLR7 - day 1 - mAdbID:123812

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

country: USA

institute: National Cancer Institute

description: mAdb experiment ID: 123812

hyb_protocol: Agilent Hybridization Protocol Other: According to the manufacturer's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

source_name: TMD8, shTLR7, 24 hr

label_protocol: 100 ng of total RNA was labeled with Cy5.

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA).

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hours
In-vitro treatment: Cells were transduced with retroviruses carrying TLR-specific (shTLR7) shRNA. shRNA expression was induced with doxycycline for 24 hours.

value: blood

tag: cell line

tag: disease state

value: B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

tag: shRNA

tag: time point

value: day 1

source_name: TMD8, shControl, 24 hr

label_protocol: 100 ng of total RNA was labeled with Cy3.

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hours
In-vitro treatment: Cells were transduced with retroviruses carrying control (shSC4) shRNA. shRNA expression was induced with doxycycline for 24 hours.

value: shControl


title: [genomic DNA]-[primary breast tumor] DBCG_11948

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

tag: gender

tag: age at onset

tag: histology


title: [genomic DNA]-[primary breast tumor] DBCG_12135

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

tag: histologic grade

tag: histologic grade and genomic grade combined

tag: tumor size


title: [genomic DNA]-[primary breast tumor] DBCG_12007

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

tag: lymph node status

tag: estrogen receptor status

tag: gene expression subtype


title: BralRRl213, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl213_3 mM [Ca]_1 mM [Mg]

tag: line

tag: tissue

tag: technical replicate

tag: array processed by


title: BI-3

city: Hangzhou

first: Yun

last: Xiao

address: Yuhangtang Road

country: China

institute: Zhejiang University

description: Type 2 diabetes

hyb_protocol: Labeled cDNA was hybridized to the GeneChip Mouse Genome 430A 2.0 array (Affymetrix, Santa Clara, CA) at 45°C for 16 h. The arrays were washed and stained in the Affymetrix GeneChip Fluidics Station 450 using the supplier’s reagents.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000.

data_processing: Slides were scanned by GeneChip® Scanner 3000 and Command Console Software 3.1 with default settings. Spike-in control transcripts were monitored to verify hybridization integrity.

label: biotin

organism: Mus musculus

source_name: KKAy mouse

label_protocol: Total RNA were amplified, labeled, and purified using GeneChip® 3’IVT Express Kit (Affymetrix) according to the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol:
The mice were fed with powdered chow consisting of 48% carbohydrates, 17% protein, 34% fat, 1% fiber, minerals, and vitamins (HFK Biosciencem, China), and water was given ad lib.
The mice were fed with powdered chow consisting of 48% carbohydrates, 17% protein, 34% fat, 1% fiber, minerals, and vitamins (HFK Biosciencem, China), and water was given ad lib.

extract_protocol: Total RNA was extracted using TRIZol Reagent (Life technologies) and purified using RNeasy Mini kit (QIAGEN), following manufacturers’ protocols.

treatment_protocol: The mice were divided randomly into three groups of eight to 12 mice each. The animals in the control group were intraperitoneally injected with 100 µL DMEM, whereas the two treated groups were intraperitoneally injected with 100 µL of DMEM solution containing insulin (40 µg/mL) or in situ biomineralization modified insulin (total insulin concentration was 40 µg/mL, in which 11% was in BI form).

value: liver

tag: treatment

value: Biomineralized insulin

tag: age

value: 8 weeks


title: [genomic DNA]-[primary breast tumor] DBCG_11801

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

value: Female

value: IDC

value: positive

tag: tp53 mutation status


title: TMD8 shTLR9 - day 1 - mAdbID:123814

description: mAdb experiment ID: 123814

source_name: TMD8, shTLR9, 24 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hours
In-vitro treatment: Cells were transduced with retroviruses carrying TLR-specific (shTLR9) shRNA. shRNA expression was induced with doxycycline for 24 hours.

tag: cell line

tag: disease state

tag: shRNA

tag: time point


title: [genomic DNA]-[primary breast tumor] DBCG_11798

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

tag: gender

tag: age at onset

tag: histology

tag: histologic grade


title: [genomic DNA]-[primary breast tumor] DBCG_11873

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

tag: histologic grade and genomic grade combined

tag: tumor size

tag: lymph node status

tag: estrogen receptor status

value: Basal-like


title: BralRRl211, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl211_3 mM [Ca]_15 mM [Mg]

tag: line

tag: tissue

value: 10 day-old leaf

tag: external calcium concentration

value: 3 mM

tag: external magnesium concentration

value: 15 mM

tag: biological replicate

tag: technical replicate


title: Insulin-3

description: Type 2 diabetes

growth_protocol: The mice were fed with powdered chow consisting of 48% carbohydrates, 17% protein, 34% fat, 1% fiber, minerals, and vitamins (HFK Biosciencem, China), and water was given ad lib.

tag: treatment

value: Insulin

tag: age


title: BI-1

description: Type 2 diabetes


title: TMD8 shTLR7 - day 2 - mAdbID:123813

description: mAdb experiment ID: 123813

source_name: TMD8, shTLR7, 48 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hours
In-vitro treatment: Cells were transduced with retroviruses carrying TLR-specific (shTLR7) shRNA. shRNA expression was induced with doxycycline for 48 hours.

tag: cell line

tag: disease state

tag: shRNA

tag: time point

value: day 2

source_name: TMD8, shControl, 48 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hours
In-vitro treatment: Cells were transduced with retroviruses carrying control (shSC4) shRNA. shRNA expression was induced with doxycycline for 48 hours.


title: BralRRl103, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl103_3 mM [Ca]_1 mM [Mg]

value: 1 mM

tag: array processed by

value: SOURCE


title: Insulin-2

description: Type 2 diabetes


title: BralRRl076, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl076_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_11716

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

tag: gender

tag: age at onset

tag: histology

tag: histologic grade

tag: histologic grade and genomic grade combined

tag: gene expression subtype

tag: tp53 mutation status

value: wild-type

source_name: Reference genomic DNA, Promega


title: BralRRl199, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl199_3 mM [Ca]_15 mM [Mg]

tag: line

tag: tissue

tag: external calcium concentration

tag: external magnesium concentration


title: BralRRl325, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl325_3 mM [Ca]_1 mM [Mg]

tag: biological replicate

tag: technical replicate


title: BralRRl341, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl341_3 mM [Ca]_15 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_11740

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

source_name: Tumor (primary invasive ductal breast carcinoma)

tag: tumor size

tag: lymph node status

tag: estrogen receptor status

value: Normal-like


title: KKAy-3

description: Type 2 diabetes

tag: treatment

tag: age


title: TMD8 shTLR9 - day 2 - mAdbID:123815

description: mAdb experiment ID: 123815

source_name: TMD8, shTLR9, 48 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hours
In-vitro treatment: Cells were transduced with retroviruses carrying TLR-specific (shTLR9) shRNA. shRNA expression was induced with doxycycline for 48 hours.

value: blood

tag: cell line

tag: disease state

value: B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

tag: shRNA

tag: time point

value: shControl


title: BralRRl211, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl211_3 mM [Ca]_1 mM [Mg]

tag: array processed by


title: [genomic DNA]-[primary breast tumor] DBCG_11514

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

tag: gender

tag: age at onset

tag: histology

tag: histologic grade

tag: histologic grade and genomic grade combined

tag: gene expression subtype

tag: tp53 mutation status


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

tag: line

tag: tissue

tag: external calcium concentration

tag: external magnesium concentration

tag: biological replicate

tag: technical replicate


title: Tbx1+/+, replica 3

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: A total of 3.75 μg cDNA from the last step was hybridized to the GeneChip Test3 array (Affymetrix) to test the quality of the labeled target. Nucleic acid samples that passed quality control were then hybridized to the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix).

scan_protocol: Hybridization, washing, staining and scanning were performed in the Genomics Core at Einstein (http://www.einstein.yu.edu/genetics/CoreFacilities.aspx?id=23934) according to the Affymetrix manual.

data_processing: GeneChip data were analyzed with ArrayAssist (Stratagene). Briefly, the original Affymetrix GeneChip CEL files generated by the Genomics Core were imported into ArrayAssist Lite and a master data table was created based on them by GC-RMA. Then the data was converted to logarithmic scale and the significance analysis was performed using two classes, unpaired t-test with a cut-off of fold change >1.5 and p-value <0.05.

source_name: mandibular arches (MdPA1), Tbx1+/+

label_protocol: Biotinylated single-stranded cDNA targets were amplified from 100 nanograms (ng) starting total RNA using the Ovation RNA Amplification System V2 and FL- Ovation cDNA Biotin Module V2 (NuGEN).

extract_protocol: The tissue was homogenized in Buffer RLT (QIAGEN). Total RNA was isolated with the RNeasy Micro Kit according to the manufacturer’s protocol. Quality and quantity of total RNA was determined using an Agilent 2100 Bioanalyzer (Agilent) and a ND-1000 Spectrophotometer (NanoDrop), respectively.

tag: strain

tag: genotype

tag: developmental stage

value: embryonic

tag: age

value: mandibular arches


title: KKAy-2

description: Type 2 diabetes

value: liver

tag: treatment

value: 8 weeks


title: Insulin-1

description: Type 2 diabetes


title: EA07047_56017_H133+_8

city: Rockville

first: Radu

last: Cojocaru

address: 5635 Fishers Lane, Suite 510

institute: Elsevier

description: Cells were treated with doxycycline to induce myocilin expression

hyb_protocol: Not provided.

scan_protocol: Not provided.

data_processing: Data was analyzed using GeneSpring software including QC analysis.

source_name: Stable Cell line transfected with myocilin expressing vector

label_protocol: Not provided.

growth_protocol: Tet-on stably transfected cells were maintained in Dulbecco modified Eagle medium (DMEM) supplemented with 10% Tet system proved fetal bovine serum, penicillin (100 U/ml), streptomycin (100 µg/ml), hygromycin B (200 µg/ml) and G418 (100 µg/ml) at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol: RNA was extracted from control and myocilin expressing cells after induction with selected concentrations of doxycycline using a Trizol reagent. The extracted RNA was used for each microarray study.

treatment_protocol: Tet-on stably transfected cells were treated with 0.2 or 1 μg/ ml of doxycycline for 48 hr to induce myocilin expression.

tag: cell line


title: [genomic DNA]-[primary breast tumor] DBCG_11486

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

tag: gender

value: Female

tag: age at onset

tag: histology

value: IDC

tag: tumor size

tag: lymph node status

tag: estrogen receptor status

value: positive


title: EA07047_56016_H133+_7


title: BralRRl303, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl303_3 mM [Ca]_15 mM [Mg]

tag: line

tag: tissue

value: 10 day-old leaf

value: 3 mM

value: 15 mM

tag: array processed by


title: EA07047_56018_H133+_9


title: Tbx1-/-, replica 3

source_name: mandibular arches (MdPA1), Tbx1-/-


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

tag: external calcium concentration

tag: external magnesium concentration

tag: biological replicate


title: BralRRl253, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl253_3 mM [Ca]_1 mM [Mg]

value: 1 mM

tag: technical replicate


title: KKAy-1

description: Type 2 diabetes

source_name: KKAy mouse


title: Tbx1+/+, replica 2

tag: strain

tag: genotype

tag: developmental stage


title: BralRRl376, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl376_3 mM [Ca]_1 mM [Mg]

value: SOURCE


title: Tbx1-/-, replica 2

tag: age


title: [genomic DNA]-[primary breast tumor] DBCG_11436

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

tag: gender

tag: histologic grade

tag: histologic grade and genomic grade combined

tag: gene expression subtype

value: Lumil A

tag: tp53 mutation status

value: wild-type


title: Tbx1-/-, replica 1


title: Yorkshire endometrium 03

city: Wuhan

first: Ting

last: Gu

state: Hubei

address: Shizi shan road

department: Animal Science

institute: Huazhong Agricultrural University

hyb_protocol: The biotinylated cRNA were hybridized to the Affymetrix array(cat. No.900623, santa clara,CA) following the manufacture's protocol, . Genechips were washed and stained in Genechip fluidics station 450

scan_protocol: Affymetrix Genechip scanner 3000

data_processing: Data from cel files were converted to gene signal files by GCOS 1.2. Natural log was taken for all the raw gene signals for normalization. The SAS ANOVA analysis was used to identify differential gene expression.

organism: Sus scrofa

source_name: Yorkshire

label_protocol: biotinylated cRNA were prepared by genechip one-cycle cDNA synthesis following the standard protocol

growth_protocol: heat-check positive Yorkshire and meishan gilts were bred twice, natually at their second or third estrus

extract_protocol: total RNA was isolated from 200mg of tissues using Qiagen Rneasy kit

treatment_protocol: reproductive tracts were recovered immediately after slaughter

value: endometrium

tag: breed

value: Yorkshire


title: [genomic DNA]-[primary breast tumor] DBCG_11435

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

tag: age at onset

tag: histology

tag: tumor size

tag: lymph node status

tag: estrogen receptor status


title: Yorkshire endometrium 04

tag: tissue


title: Yorkshire endometrium 01


title: [genomic DNA]-[primary breast tumor] DBCG_11434

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

value: Normal-like


title: BralRRl281, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl281_3 mM [Ca]_1 mM [Mg]

tag: line

tag: external calcium concentration

tag: external magnesium concentration

tag: biological replicate

tag: technical replicate

tag: array processed by


title: BI-2

description: Type 2 diabetes

growth_protocol: The rats were maintained in air-conditioned rooms (temperature, 22-26 ºC; humidity, 40%-70%) with a 12-h light-dark cycle, and were acclimatized to the setting for 1 week.To provide comfortable conditions for rats, each cage contained 5 rats, and the sawdust in the bottom of the cage were renewed every 2 days. Rats were free to get fresh foods and water, and the water was renewed everyday.

tag: treatment

value: Biomineralized insulin

tag: age


title: [genomic DNA]-[primary breast tumor] DBCG_11376

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

tag: gender

tag: histologic grade

tag: histologic grade and genomic grade combined

tag: gene expression subtype


title: Yorkshire endometrium 02

tag: breed


title: 154 LPS replicate 1

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
12139_154_L_Rep_1_(HG-U133_Plus_2)
Gene expression from LPS-treated macrophages.

hyb_protocol: 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files.

source_name: macrophages, LPS

label_protocol: One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.

extract_protocol: Monocyte-derived macrophages were obtained as previously described in: Hiebl B, Fuhrmann R, Franke RP (2008) Characterization of cryopreserved CD14+-human monocytes after differentiation towards macrophages and stimulation with VEGF-A(165). Clin Hemorheol Microcirc 39: 221-228 (PMID 18503129).

treatment_protocol: Macrophages were differentiated x-vivo from monocytes obtained from healthy volunteers either left untreated or treated for 2 hours with 100 ng/mL of LPS, 0.1%v/v of DMSO (vehicle control for Nutlin-3) or 10 micromolar Nutlin-3.

tag: disease status

value: healthy

tag: cell type

value: macrophages

value: male

tag: race

value: African American

value: LPS

tag: individual identifier


title: 154 LPS replicate 3

description:
12141_154_L_Rep_3_(HG-U133_Plus_2)
Gene expression from LPS-treated macrophages.


title: EA07047_56011_H133+_2

source_name: Stable Cell line transfected with control vector

tag: cell line


title: BralRRl007, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl007_3 mM [Ca]_15 mM [Mg]

tag: line

tag: tissue

tag: external calcium concentration


title: Tbx1+/+, replica 1

tag: strain

tag: genotype

tag: developmental stage

value: embryonic

value: mandibular arches


title: BralRRl080, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl080_3 mM [Ca]_1 mM [Mg]

value: 10 day-old leaf

value: 3 mM

tag: external magnesium concentration

tag: biological replicate

tag: technical replicate

tag: array processed by


title: EA07047_56012_H133+_3


title: EA07047_56010_H133+_1


title: BralRRl225, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl225_3 mM [Ca]_15 mM [Mg]

value: 15 mM


title: BralRRl190, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl190_3 mM [Ca]_15 mM [Mg]

value: SOURCE


title: Meishan endometrium 03

source_name: Meishan

value: Meishan


title: BralRRl281, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl281_3 mM [Ca]_15 mM [Mg]


title: BralRRl080, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl080_3 mM [Ca]_15 mM [Mg]


title: Meishan endometrium 04


title: 154 LPS replicate 2

description:
12140_154_L_Rep_2_(HG-U133_Plus_2)
Gene expression from LPS-treated macrophages.

tag: age

tag: gender

tag: treatment


title: Meishan endometrium 02

tag: breed


title: BralRRl183, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl183_3 mM [Ca]_1 mM [Mg]

value: 1 mM


title: 154 no treatment replicate 3

description:
12138_154_NT_Rep_3_(HG-U133_Plus_2)
Gene expression from untreated macrophages.

source_name: macrophages, untreated

tag: disease status

tag: cell type

tag: race


title: BralRRl264, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl264_3 mM [Ca]_15 mM [Mg]

tag: line


title: Meishan endometrium 01

tag: tissue

value: endometrium


title: 154 no treatment replicate 1

description:
12136_154_NT_Rep_1_(HG-U133_Plus_2)
Gene expression from untreated macrophages.

tag: individual identifier


title: 154 no treatment replicate 2

description:
12137_154_NT_Rep_2_(HG-U133_Plus_2)
Gene expression from untreated macrophages.


title: BralRRl360, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl360_3 mM [Ca]_1 mM [Mg]

tag: external calcium concentration


title: BralRRl248, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 2

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


title: 154 Nutlin-3 replicate 3

description:
12135_154_Nut_Rep_3_(HG-U133_Plus_2)
Gene expression from Nutlin-3-treated macrophages.

source_name: macrophages, Nutlin-3


title: 154 Nutlin-3 replicate 2

description:
12134_154_Nut_Rep_2_(HG-U133_Plus_2)
Gene expression from Nutlin-3-treated macrophages.


title: BralRRl289, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl289_3 mM [Ca]_1 mM [Mg]


title: [genomic DNA]-[primary breast tumor] DBCG_11369

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

source_name: Tumor (primary invasive ductal breast carcinoma)

value: Female

tag: age at onset

tag: histology

value: IDC

tag: histologic grade

tag: histologic grade and genomic grade combined

tag: tumor size

tag: lymph node status

tag: estrogen receptor status

value: positive

tag: gene expression subtype

value: Lumil B

tag: tp53 mutation status

value: wild-type

source_name: Reference genomic DNA, Promega


title: [genomic DNA]-[primary breast tumor] DBCG_11359

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

tag: gender


title: [genomic DNA]-[primary breast tumor] DBCG_11228

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

value: Lumil A


title: 154 Nutlin-3 replicate 1

description:
12133_154_Nut_Rep_1_(HG-U133_Plus_2)
Gene expression from Nutlin-3-treated macrophages.

tag: disease status

value: healthy

value: macrophages

tag: age

value: male

value: African American

tag: treatment


title: 154 DMSO replicate 1

description:
12130_154_DM_Rep_1_(HG-U133_Plus_2)
Gene expression from DMSO-treated macrophages.

source_name: macrophages, DMSO

tag: cell type

tag: race

value: DMSO


title: 154 DMSO replicate 2

description:
12131_154_DM_Rep_2_(HG-U133_Plus_2)
Gene expression from DMSO-treated macrophages.

tag: individual identifier


title: 154 DMSO replicate 3

description:
12132_154_DM_Rep_3_(HG-U133_Plus_2)
Gene expression from DMSO-treated macrophages.


title: 155 LPS replicate 3

description:
12129_155_L_Rep_3_(HG-U133_Plus_2)
Gene expression from LPS-treated macrophages.

source_name: macrophages, LPS

value: LPS


title: [genomic DNA]-[primary breast tumor] DBCG_11619

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


title: BralRRl166, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl166_3 mM [Ca]_1 mM [Mg]

tag: line

tag: tissue

value: 10 day-old leaf

tag: external calcium concentration

value: 3 mM

tag: external magnesium concentration

tag: biological replicate

tag: technical replicate

tag: array processed by


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

value: 15 mM

value: SOURCE


title: [genomic DNA]-[primary breast tumor] DBCG_11204

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

tag: age at onset

tag: histology

tag: histologic grade

tag: histologic grade and genomic grade combined

tag: tumor size

tag: lymph node status

tag: estrogen receptor status

value: negative


title: [genomic DNA]-[primary breast tumor] DBCG_10728

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

tag: gender

value: Female

tag: gene expression subtype

value: Normal-like

tag: tp53 mutation status


title: BralRRl259, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 2

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

tag: line


title: [genomic DNA]-[primary breast tumor] DBCG_11280

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

value: IDC

value: positive


title: [genomic DNA]-[primary breast tumor] DBCG_11282

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

value: wild-type


title: BralRRl201, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl201_3 mM [Ca]_15 mM [Mg]

tag: tissue


title: [genomic DNA]-[primary breast tumor] DBCG_10438

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


title: [genomic DNA]-[primary breast tumor] DBCG_11177

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

value: Lumil A


title: [genomic DNA]-[primary breast tumor] DBCG_11171

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

value: mutated


title: BralRRl290, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl290_3 mM [Ca]_1 mM [Mg]

tag: external calcium concentration

value: 1 mM


title: [genomic DNA]-[primary breast tumor] DBCG_10557

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


title: [genomic DNA]-[primary breast tumor] DBCG_10446

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


title: [genomic DNA]-[primary breast tumor] DBCG_10826

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


title: [genomic DNA]-[primary breast tumor] DBCG_11071

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

value: Basal-like


title: [genomic DNA]-[primary breast tumor] DBCG_10669

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


title: [genomic DNA]-[primary breast tumor] DBCG_10457

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


title: BralRRl201, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl201_3 mM [Ca]_1 mM [Mg]

tag: external magnesium concentration


title: 155 LPS replicate 1

description:
12127_155_L_Rep_1_(HG-U133_Plus_2)
Gene expression from LPS-treated macrophages.

tag: disease status

value: healthy

tag: cell type

value: macrophages

tag: age

value: male

tag: race

value: African American

tag: treatment

tag: individual identifier


title: [genomic DNA]-[primary breast tumor] DBCG_10386

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

tag: age at onset

tag: histology

tag: histologic grade

tag: histologic grade and genomic grade combined


title: [genomic DNA]-[primary breast tumor] DBCG_10332

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

tag: gender

tag: tumor size

tag: lymph node status

tag: estrogen receptor status


title: BralRRl198, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl198_3 mM [Ca]_1 mM [Mg]

tag: line

tag: tissue

value: 10 day-old leaf

value: 3 mM

tag: biological replicate

tag: technical replicate

tag: array processed by


title: 155 no treatment replicate 2

description:
12125_155_NT_Rep_2_(HG-U133_Plus_2)
Gene expression from untreated macrophages.

tag: disease status

tag: cell type

tag: age


title: 155 no treatment replicate 3

description:
12126_155_NT_Rep_3_(HG-U133_Plus_2)
Gene expression from untreated macrophages.

tag: race

tag: treatment

tag: individual identifier


title: 155 Nutlin-3 replicate 2

description:
12122_155_Nut_Rep_2_(HG-U133_Plus_2)
Gene expression from Nutlin-3-treated macrophages.


title: 155 Nutlin-3 replicate 1

description:
12121_155_Nut_Rep_1_(HG-U133_Plus_2)
Gene expression from Nutlin-3-treated macrophages.


title: brain Tardbp rep4

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalised using cubic spline normalisation with Illumina Genomestudio 2011.1

source_name: brain

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

value: brain

tag: genetic background

tag: genotype

value: heterozygote transgenic human mutant TDP-43

value: 17 weeks

tag: mouse id


title: 155 DMSO replicate 2

description:
12119_155_DM_Rep_2_(HG-U133_Plus_2)
Gene expression from DMSO-treated macrophages.

tag: gender

value: DMSO


title: 155 no treatment replicate 1

description:
12124_155_NT_Rep_1_(HG-U133_Plus_2)
Gene expression from untreated macrophages.

source_name: macrophages, untreated


title: BralRRl104, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl104_3 mM [Ca]_15 mM [Mg]

tag: external calcium concentration

tag: external magnesium concentration

value: 15 mM

value: SOURCE


title: 155 DMSO replicate 3

description:
12120_155_DM_Rep_3_(HG-U133_Plus_2)
Gene expression from DMSO-treated macrophages.


title: 155 Nutlin-3 replicate 3

description:
12123_155_Nut_Rep_3_(HG-U133_Plus_2)
Gene expression from Nutlin-3-treated macrophages.


title: BralRRl016, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl016_3 mM [Ca]_15 mM [Mg]

tag: line


title: BralRRl046, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl046_3 mM [Ca]_15 mM [Mg]

tag: tissue


title: brain Tardbp rep3

description: replicate 3


title: brain Tardbp rep6

description: replicate 6


title: brain Tardbp rep5

description: replicate 5


title: BralRRl124, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl124_3 mM [Ca]_15 mM [Mg]

tag: biological replicate


title: BralRRl182, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl182_3 mM [Ca]_15 mM [Mg]

tag: technical replicate


title: [genomic DNA]-[primary breast tumor] DBCG_11138

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

source_name: Tumor (primary invasive ductal breast carcinoma)

value: Female

tag: age at onset

tag: histology

value: IDC

tag: histologic grade

tag: histologic grade and genomic grade combined

tag: tumor size

tag: lymph node status

tag: estrogen receptor status

value: positive

tag: gene expression subtype

tag: tp53 mutation status

value: wild-type


title: BralRRl070, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl070_3 mM [Ca]_15 mM [Mg]

tag: array processed by


title: BralRRl229, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 2

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


title: [genomic DNA]-[primary breast tumor] DBCG_10211

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

tag: gender

value: negative

value: Normal-like

source_name: Reference genomic DNA, Promega


title: brain Tardbp rep2

description: replicate 2

tag: genetic background

tag: genotype

tag: age

tag: mouse id


title: brain wt rep6

description: replicate 6

tag: tissue

value: heterozygote wt


title: BralRRl311, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl311_3 mM [Ca]_1 mM [Mg]

tag: line

tag: external calcium concentration

tag: external magnesium concentration

value: 1 mM

tag: biological replicate

tag: technical replicate


title: brain Tardbp rep1

description: replicate 1


title: [genomic DNA]-[primary breast tumor] DBCG_10070

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

tag: age at onset

tag: histology

tag: histologic grade

tag: histologic grade and genomic grade combined

tag: tumor size

value: Lumil B

value: mutated


title: [genomic DNA]-[primary breast tumor] DBCG_10176

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

tag: lymph node status

tag: estrogen receptor status

tag: gene expression subtype

tag: tp53 mutation status


title: brain wt rep4

description: replicate 4

tag: genetic background

tag: genotype

tag: age


title: BralRRl204, 3 mM external [Ca], 15 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl204_3 mM [Ca]_15 mM [Mg]

tag: line

tag: tissue

value: 10 day-old leaf

value: 3 mM

tag: array processed by


title: brain wt rep2

description: replicate 2

value: brain

tag: mouse id


title: B.anthracis_ΔsaiR/ΔspxA1_1_versus_B.anthracis_ΔspxA1_1

first: Bryan

last: Frank

address: 9704 Medical Center Drive

department: Dept of Infectious Diseases

institute: The J. Craig Venter Institute

hyb_protocol: Aminosilane-coated slides representing a set of B. anthracis unique open reading frame sequences derived from seven reference genomes (www.jcvi.org) were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42°C for 60 min.  The slides were then washed at room temperature with distilled water, and allowed to dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were heated to 95ºC prior to hybridization.  The probe mixture was then added to the microarray slide and allowed to hybridize overnight at 42°C.

scan_protocol: Hybridizations were scanned on the Axon 4000B scanner with GenePix Pro software.

data_processing: Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at http://www.jcvi.org/software/tm4).  Microarray data were normalized by LOWESS in TIGR MIDAS software (available at http://www.jcvi.org/software/tm4). The 'IA' and 'IB' channels in the *.mev files correspond to Cy3 (Ch2) and Cy5 (Ch1).

organism: Bacillus anthracis

source_name: ΔsaiR/ΔspxA1 knockout cells

label_protocol: A total of 2 ug of RNA in a mixture containing 6 ug of random hexamers, 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amini-allyl dUTP (aa-dUTP), reaction buffer, and 400 units of SuperScript III reverse transcriptase at 42C overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubated at 65C for 15 min. Unincorporated aa-UTP was removed with a MinElute column. The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried and resuspended in 0.1 M sodium carbonate buffer (ph 9.0). To couple the amino-allyl cDNA with fluorescent labels, Cy3 or Cy5 mono-reactive dye (Amersham) was added for 1h. Uncoupled label was removed using the Qiagen QIAquick PCR purification kit (Valencia, CA).

growth_protocol: B.anthracis cells were grown in suspended culture in LB media into a logarithmic growth phase reaching an optical density of 0.4 to 0.5.

extract_protocol: Total RNA was extracted using the Ambion mirVana RNA extraction kit according to the manufacturer's protocol

tag: genotype/variation

value: ΔsaiR/ΔspxA1 knockout

tag: growth phase

value: logarithmic phase reaching OD= 0.4 to 0.5

source_name: ΔspxA1 knockout cells

value: ΔspxA1 knockout


title: B.anthracis_ΔsaiR_3_versus_B.anthracis_wildtype_3

source_name: ΔsaiR knockout cells

value: ΔsaiR knockout

source_name: wild type cells

value: wild type


title: B.anthracis_ΔsaiR_2_versus_B.anthracis_wildtype_2


title: muscle Tardbp rep2

description: replicate 2

source_name: muscle

value: muscle

value: heterozygote transgenic human mutant TDP-43

value: 17 weeks


title: B.anthracis_ΔsaiR/ΔspxA1_2_versus_B.anthracis_ΔspxA1_2


title: B.anthracis_ΔsaiR_1_versus_B.anthracis_wildtype_1


title: 155 LPS replicate 2

description:
12128_155_L_Rep_2_(HG-U133_Plus_2)
Gene expression from LPS-treated macrophages.

source_name: macrophages, LPS

tag: disease status

value: healthy

tag: cell type

value: macrophages

tag: gender

value: male

tag: race

value: African American

tag: treatment

value: LPS

tag: individual identifier


title: muscle Tardbp rep4

description: replicate 4


title: B.anthracis_ΔsaiR/ΔspxA1_3_versus_B.anthracis_ΔspxA1_3


title: [genomic DNA]-[primary breast tumor] DBCG_10207

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

value: Female

tag: age at onset

tag: histology

value: IDC

tag: histologic grade

tag: histologic grade and genomic grade combined

tag: tumor size

tag: lymph node status

tag: estrogen receptor status

value: positive

tag: gene expression subtype

value: Lumil A

value: wild-type


title: muscle wt rep4

description: replicate 4

tag: tissue

tag: genetic background

tag: genotype

value: heterozygote wt

tag: age

tag: mouse id


title: 155 DMSO replicate 1

description:
12118_155_DM_Rep_1_(HG-U133_Plus_2)
Gene expression from DMSO-treated macrophages.

source_name: macrophages, DMSO

tag: disease status

tag: cell type

tag: gender

value: DMSO


title: muscle Tardbp rep3

description: replicate 3


title: muscle wt rep2

description: replicate 2


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

source_name: BralRRl025_3 mM [Ca]_1 mM [Mg]

tag: line

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: brain wt rep3

description: replicate 3

source_name: brain

value: brain

value: 17 weeks


title: brain wt rep1

description: replicate 1


title: muscle Tardbp rep1

description: replicate 1

value: muscle

value: heterozygote transgenic human mutant TDP-43


title: brain wt rep5

description: replicate 5


title: muscle wt rep3

description: replicate 3


title: muscle wt rep1

description: replicate 1


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

source_name: BralRRl146_3 mM [Ca]_1 mM [Mg]


title: BralRRl250, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl250_3 mM [Ca]_1 mM [Mg]


title: BralRRl184, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 2

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


title: ALL-57 Control sample 1

status: Public on May 20 2014

city: Randwick

first: Duohui

last: Jing

state: NSW

address: Lowy Cancer Research Centre, UNSW

department: Leukaemia Biology

country: Australia

institute: Children’s Cancer Institute Australia

description:
control_1
patient-derived xenograft cells

scan_protocol: Standard Illumina scanning protocol

data_processing: The non-normalized matrix was generated using IlluminaExpressionFileCreator module in GenePattern. The data were then normalized using quantile normalization with NormalizeColumns module in Genepattern

source_name: Patient-derived xenograft cells

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA kit for Illumina arrays

growth_protocol: ALL xenograft cells were inoculated by tail-vein injection into NOD/SCID mice, and engraftment was monitored weekly.

extract_protocol: RNA was extracted with a combination of Trizol reagent and QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: When >70% %huCD45+ engraftment in the peripheral blood was apparent, which occurred 8-10 weeks post-transplantation, mice were treated with either dexamethasone (15 mg/kg) or vehicle control by intra-peritoneal (IP) injection, and culled at 8 hours following the treatment.

tag: strain

value: NOD/SCID

tag: injection

value: ALL patient-derived xenograft cells were inoculated by tail-vein injection

tag: age (mouse)

value: xenograft cells injected at 6-10 weeks

tag: treatment

value: control

value: xenograft cells (>95% hCD45+ cells) from mouse spleens

tag: dexamethasone response

value: Resistant patient


title: ALL-56 8h Dex treatment sample 2

description:
ALL-56_8hDex_2
patient-derived xenograft cells

value: 8h dexamethasone

tag: tissue


title: ALL-56 Control sample 3

description:
control_3
patient-derived xenograft cells


title: ALL-57 8h Dex treatment sample 3

description:
ALL-57_8hDex_3
patient-derived xenograft cells


title: ALL-57 8h Dex treatment sample 2

description:
ALL-57_8hDex_2
patient-derived xenograft cells


title: ALL-56 8h Dex treatment sample 3

description:
ALL-56_8hDex_3
patient-derived xenograft cells


title: ALL-57 Control sample 2

description:
control_2
patient-derived xenograft cells


title: ALL-55 8h Dex treatment sample 3

description:
ALL-55_8hDex_3
patient-derived xenograft cells


title: ALL-57 8h Dex treatment sample 1

description:
ALL-57_8hDex_1
patient-derived xenograft cells


title: ALL-55 Control sample 1


title: ALL-55 Control sample 3


title: ALL-55 Control sample 2


title: ALL-56 8h Dex treatment sample 1

description:
ALL-56_8hDex_1
patient-derived xenograft cells


title: ALL-56 Control sample 2


title: ALL-56 Control sample 1


title: BralRRl182, 3 mM external [Ca], 1 mM external [Mg], bio rep 1, tech rep 1

source_name: BralRRl182_3 mM [Ca]_1 mM [Mg]


title: ALL-54 Control sample 3

value: Sensitive patient


title: ALL-55 8h Dex treatment sample 2

description:
ALL-55_8hDex_2
patient-derived xenograft cells


title: ALL-55 8h Dex treatment sample 1

description:
ALL-55_8hDex_1
patient-derived xenograft cells


title: ALL-54 8h Dex treatment sample 1

description:
ALL-54_8hDex_1
patient-derived xenograft cells


title: ALL-54 8h Dex treatment sample 2

description:
ALL-54_8hDex_2
patient-derived xenograft cells


title: ALL-53 8h Dex treatment sample 2

description:
ALL-53_8hDex_2
patient-derived xenograft cells


title: ALL-54 8h Dex treatment sample 3

description:
ALL-54_8hDex_3
patient-derived xenograft cells


title: ALL-54 Control sample 2


title: ALL-52 8h Dex treatment sample 3

description:
ALL-52_8hDex_3
patient-derived xenograft cells


title: ALL-52 Control sample 1

description:
control_1
patient-derived xenograft cells


title: ALL-54 Control sample 1


title: ALL-53 Control sample 2


title: ALL-53 8h Dex treatment sample 3

description:
ALL-53_8hDex_3
patient-derived xenograft cells


title: ALL-53 Control sample 1


title: ALL-52 Control sample 2


title: ALL-51 8h Dex treatment sample 1

description:
ALL-51_8hDex_1
patient-derived xenograft cells


title: ALL-51 Control sample 3

description:
control_3
patient-derived xenograft cells


title: ALL-53 Control sample 3


title: ALL-51 Control sample 2


title: ALL-51 8h Dex treatment sample 2

description:
ALL-51_8hDex_2
patient-derived xenograft cells


title: ALL-50 8h Dex treatment sample 3

description:
ALL-50_8hDex_3
patient-derived xenograft cells


title: ALL-52 8h Dex treatment sample 1

description:
ALL-52_8hDex_1
patient-derived xenograft cells


title: ALL-50 8h Dex treatment sample 1

description:
ALL-50_8hDex_1
patient-derived xenograft cells


title: ALL-52 Control sample 3


title: ALL-50 Control sample 1


title: ALL-50 8h Dex treatment sample 2

description:
ALL-50_8hDex_2
patient-derived xenograft cells


title: ALL-53 8h Dex treatment sample 1

description:
ALL-53_8hDex_1
patient-derived xenograft cells


title: ALL-50 Control sample 3


title: ALL-52 8h Dex treatment sample 2

description:
ALL-52_8hDex_2
patient-derived xenograft cells


title: ALL-51 Control sample 1


title: ALL-28 8h Dex treatment sample 1

description:
ALL-28_8hDex_1
patient-derived xenograft cells


title: ALL-28 8h Dex treatment sample 3

description:
ALL-28_8hDex_3
patient-derived xenograft cells


title: ALL-26 8h Dex treatment sample 2

description:
ALL-26_8hDex_2
patient-derived xenograft cells


title: ALL-28 8h Dex treatment sample 2

description:
ALL-28_8hDex_2
patient-derived xenograft cells


title: ALL-26 8h Dex treatment sample 3

description:
ALL-26_8hDex_3
patient-derived xenograft cells


title: ALL-50 Control sample 2

description:
control_2
patient-derived xenograft cells


title: ALL-28 Control sample 2


title: ALL-51 8h Dex treatment sample 3

description:
ALL-51_8hDex_3
patient-derived xenograft cells


title: ALL-26 control sample 2


title: E14.5 mouse liver rep2

city: shanghai

first: shu-han

last: sun

address: 800 Xiang-Yin Road

institute: Second Military Medical University

hyb_protocol: 1 μg of each labeled cRNA was  fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Raw signal intensities were normalized in quantile method by GeneSpring GX v12.1, and low intensity LncRNAs/mRNAs were filtered (LncRNAs/mRNAs that at least 12 out of 15 samples have flags in Present or Marginal were chosen for further analysis.

source_name: E14.5 mouse fetal liver rep2

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method.

extract_protocol: The total RNA was extracted from the mouse livers in different developmental stages using TRIzol reagent (ambion),and then Mrna was purified from 1 μg total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

tag: developmental stage

value: liver


title: ALL-26 control sample 1

description:
control_1
patient-derived xenograft cells


title: E12.5 mouse liver rep3

source_name: E12.5 mouse fetal liver rep3


title: E17.5 mouse liver rep1

source_name: E17.5 mouse fetal liver rep1


title: ALL-26 8h Dex treatment sample 1

description:
ALL-26_8hDex_1
patient-derived xenograft cells


title: E12.5 mouse liver rep1

source_name: E12.5 mouse fetal liver rep1


title: E12.5 mouse liver rep2

source_name: E12.5 mouse fetal liver rep2


title: ALL-28 Control sample 3

description:
control_3
patient-derived xenograft cells


title: E14.5 mouse liver rep1

source_name: E14.5 mouse fetal liver rep1


title: Adult mouse liver  rep1

source_name: Adult mouse liver  rep1

value: Adult


title: E14.5 mouse liver rep3

source_name: E14.5 mouse fetal liver rep3


title: Neonatal mouse liver rep3

source_name: Neonatal mouse liver rep3

value: Neonatal


title: Adult mouse liver  rep3

source_name: Adult mouse liver  rep3


title: Neonatal mouse liver rep2

source_name: Neonatal mouse liver rep2


title: E17.5 mouse liver rep2

source_name: E17.5 mouse fetal liver rep2


title: Adult mouse liver  rep2

source_name: Adult mouse liver  rep2


title: Neonatal mouse liver rep1

source_name: Neonatal mouse liver rep1


title: E17.5 mouse liver rep3

source_name: E17.5 mouse fetal liver rep3


title: genomic DNA from placenta 2063

city: Philadelphia

first: Lauren

last: Anton

state: PA

address: 421 Curie Blvd, 1349 BRB II/III

department: Obstetrics and Gynecology

institute: University of Pennsylvania

description: preeclamptic placenta sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: 2063 placenta

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from placenta samples using Qiagen DNeasy Kit according to standard instructions

value: placenta

tag: disease state

value: preeclampsia

tag: gestational classification

value: Preterm


title: genomic DNA from placenta 2043

description: preeclamptic placenta sample

source_name: 2043 placenta

value: Term


title: genomic DNA from placenta 2055

description: preeclamptic placenta sample

source_name: 2055 placenta


title: genomic DNA from placenta 2048

description: preeclamptic placenta sample

source_name: 2048 placenta


title: ALL-28 Control sample 1

source_name: Patient-derived xenograft cells


title: genomic DNA from placenta 2029

description: preeclamptic placenta sample

source_name: 2029 placenta


title: genomic DNA from placenta 2042

description: preeclamptic placenta sample

source_name: 2042 placenta


title: Pedicel_Lateral1_X3177_12DAP_replicate 2

city: Beaucouzé

first: Jean-Marc

last: Celton

address: 42 rue Georges Morel

country: France

institute: INRA-IRHS

hyb_protocol: The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. NimbleScan Software v2.4 was used to extract pair-data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA.

organism: Malus domestica

source_name: Wild type X3177 Whole Lateral1 pedicel, no abscission zone

label_protocol: 400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1,5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized to the Medtr_v1 12x135K arrays.

growth_protocol:
orchard conditions
Trees were grown in orchard at the INRA experimental station ' la Rétuzière', Champigné, France

extract_protocol:
Macherey-Nagel NucleoSpin RNA Plant
RNA was purified using NucleoSpin RNA Plant extraction kit (Macherey-Nagel) according to the manufacturer specifications

treatment_protocol: Trees were trained according to horticultural practices. No thinning reagent was applied

tag: tissus

value: whole lateral1 pedicel, no abscission zone

tag: genetic background

value: Hybrid X3177

tag: genotype

value: Wild-type

tag: phenotype

tag: age

value: 12 days after pollination (DAP)


title: genomic DNA from placenta 2039

description: preeclamptic placenta sample

source_name: 2039 placenta


title: genomic DNA from placenta 2052

description: preeclamptic placenta sample

source_name: 2052 placenta


title: genomic DNA from placenta 2049

description: preeclamptic placenta sample

source_name: 2049 placenta


title: genomic DNA from placenta 2026

description: preeclamptic placenta sample

source_name: 2026 placenta


title: genomic DNA from placenta 2030

description: preeclamptic placenta sample

source_name: 2030 placenta


title: genomic DNA from placenta 2016

description: preeclamptic placenta sample

source_name: 2016 placenta


title: genomic DNA from placenta 2004

description: preeclamptic placenta sample

source_name: 2004 placenta


title: genomic DNA from placenta 2028

description: preeclamptic placenta sample

source_name: 2028 placenta


title: genomic DNA from placenta 2019

description: preeclamptic placenta sample

source_name: 2019 placenta


title: genomic DNA from placenta 2005

description: preeclamptic placenta sample

source_name: 2005 placenta


title: genomic DNA from placenta 2020

description: preeclamptic placenta sample

source_name: 2020 placenta


title: Pedicel_Lateral1_X3177_12DAP_replicate 1


title: genomic DNA from placenta 2025

description: preeclamptic placenta sample

source_name: 2025 placenta


title: genomic DNA from placenta 2047

description: preeclamptic placenta sample

source_name: 2047 placenta


title: genomic DNA from placenta 2007

description: preeclamptic placenta sample

source_name: 2007 placenta


title: genomic DNA from placenta 2017

description: preeclamptic placenta sample

source_name: 2017 placenta


title: genomic DNA from placenta 2034

description: preeclamptic placenta sample

source_name: 2034 placenta


title: Pedicel_Central_X3177_12DAP_replicate 1

source_name: Wild type X3177 Whole central pedicel, no abscission zone

value: whole central pedicel, no abscission zone


title: genomic DNA from placenta 2012

description: preeclamptic placenta sample

source_name: 2012 placenta


title: genomic DNA from placenta 2008

description: preeclamptic placenta sample

source_name: 2008 placenta


title: genomic DNA from placenta 2014

description: preeclamptic placenta sample

source_name: 2014 placenta


title: genomic DNA from placenta 2006

description: preeclamptic placenta sample

source_name: 2006 placenta


title: genomic DNA from placenta 2009

description: preeclamptic placenta sample

source_name: 2009 placenta


title: genomic DNA from placenta 2013

description: preeclamptic placenta sample

source_name: 2013 placenta


title: genomic DNA from placenta 2002

description: preeclamptic placenta sample

source_name: 2002 placenta


title: Pedicel_Central_X3177_12DAP_replicate 2


title: genomic DNA from placenta 2000

description: preeclamptic placenta sample

source_name: 2000 placenta


title: Pedicel_Central_X3177_stageF1_replicate 2

value: stage F1


title: Pedicel_Lateral1_X3177_stageF1_replicate 2

source_name: Wild type X3177 Whole Lateral1 pedicel, no abscission zone


title: Pedicel_Central_X3177_6DAP_replicate 1

value: 6 days after pollination (DAP)


title: Pedicel_Lateral1_X3177_6DAP_replicate 2


title: Pedicel_Lateral1_X3177_stageF1_replicate 1


title: genomic DNA from placenta 4031

description: normal placenta sample

source_name: 4031 placenta

value: normal


title: Pedicel_Central_X3177_stageF1_replicate 1


title: Pedicel_Lateral1_X3177_stageE2_replicate 2

value: stage E2


title: Pedicel_Central_X3177_stageE2_replicate 2


title: Normal symmetry, class III, open bite, rep 1

city: philadelphia

first: michael

middle: joseph

last: horton

state: pennsylvania

address: 3223 n broad st

department: orthodontics

institute: temple university school of dentistry

hyb_protocol: Labeled cDNA (5.5g) were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Transcriptome 2.0 GeneChips. Following low and high stringency washes, chips were stained with streptavidin-phycoerythrin.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Affymetrix Command Console was used with default settings to generate .cel files. Cel files were RMA normalized using Partek Genomics Suite, v6.6.

source_name: subject 6_left_normal facial symmetry; J CRANIOFAC SURG_4

label_protocol: Total RNA (250ng) was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers. Second-strand cDNA was in vitro transcribed with T7 RNA polymerase. Resulting cRNA was converted to cDNA, fragmented, and biotinylated by terminal transferase end labeling according to the Ambion WT Expression Manual.

extract_protocol: Muscle was homogenized in QIAzol Lysis Reagent and total RNA was isolated using a Qiagen miRNeasy Mini Kit according to the manufacturer’s instructions. Quantity and quality of total RNA sampleswere evaluated by Agilent Bioanalyzer and Nanodrop spectrophotometry.

treatment_protocol: Specimens of the deep portion of masseter muscles were collected from patients at orthognathic surgery for correction of malocclusion with jaw discrepancies. Muscles were positioned vertically with mounting medium and snap frozen in the operating room before transfer and storage at -80C. Muscle sections were taken for immunohistochemistry.  RNA was isolated from remaining muscle.

tag: subject id

value: Orthognathic surgical subject 6

tag: race/ethnicity

value: North African

tag: gender

value: Female

tag: facial symmetry

value: normal facial symmetry

tag: malocclusion classification

value: class III open bite

value: masseter muscle


title: Posterior facial asymmetry, class II, open bite

source_name: subject 38_right_posterior facial asymmetry; J CRANIOFAC SURG_1

value: Orthognathic surgical subject 38

value: French caucasian

value: posterior facial asymmetry

value: class II open bite


title: Pedicel_AZ_Central_X3177_Hybrid2_21DAP_replicate 2

source_name: Wild type X3177 central pedicel abscission zone

value: Abscission zone

value: Hybrid X3177

value: Wild-type

value: no abscission

value: 21 days after flower pollination


title: Pedicel_Lateral1_X3177_stageE2_replicate 1

value: whole lateral1 pedicel, no abscission zone


title: genomic DNA from placenta 2001

description: preeclamptic placenta sample

source_name: 2001 placenta

value: placenta

value: preeclampsia

value: Preterm


title: genomic DNA from placenta 4011

description: normal placenta sample

source_name: 4011 placenta

value: normal

value: Term


title: Pedicel_Central_X3177_stageE2_replicate 1

value: whole central pedicel, no abscission zone

value: stage E2


title: Posterior facial asymmetry, class III, open bite

source_name: subject 5_left_posterior facial asymmetry; J CRANIOFAC SURG_2

value: Orthognathic surgical subject 5

value: Female

value: class III open bite

value: masseter muscle


title: Pedicel_Lateral1_X3177_6DAP_replicate 1

value: 6 days after pollination (DAP)


title: Normal symmetry, class II, deep bite, rep 3

source_name: subject 12_left_normal facial symmetry; J CRANIOFAC SURG_9

value: Orthognathic surgical subject 12

value: French caucasian

value: Male

value: normal facial symmetry

value: class II deep bite


title: Pedicel_AZ_Lateral1_X3177_Hybrid2_21DAP_replicate2

source_name: Wild type X3177 lateral1 pedicel abscission zone

value: Abscission zone

value: Hybrid X3177

value: Wild-type

value: abscission

value: 21 days after flower pollination


title: Pedicel_Central_X3177_6DAP_replicate 2

source_name: Wild type X3177 Whole central pedicel, no abscission zone

value: whole central pedicel, no abscission zone


title: Normal symmetry, class II, deep bite, rep 1

source_name: subject 19_right_normal facial symmetry; J CRANIOFAC SURG_3

value: Orthognathic surgical subject 19


title: Normal symmetry, class III, open bite, rep 2

source_name: subject 36_right_normal facial symmetry; J CRANIOFAC SURG_6

value: Orthognathic surgical subject 36


title: Normal symmetry, class II, deep bite, rep 4

source_name: subject 10_left_normal facial symmetry; J CRANIOFAC SURG_10

value: Orthognathic surgical subject 10

value: Female


title: genomic DNA from placenta 4023

description: normal placenta sample

source_name: 4023 placenta

value: placenta

value: normal

value: Term


title: genomic DNA from placenta 4028

description: normal placenta sample

source_name: 4028 placenta


title: genomic DNA from placenta 4024

description: normal placenta sample

source_name: 4024 placenta


title: genomic DNA from placenta 4027

description: normal placenta sample

source_name: 4027 placenta


title: Normal symmetry, sleep apnea, class II, open bite

source_name: subject 4_left_normal facial symmetry_sleep apnea

value: Orthognathic surgical subject 4

value: French caucasian

value: class II open bite

value: masseter muscle


title: genomic DNA from placenta 4018

description: normal placenta sample

source_name: 4018 placenta


title: genomic DNA from placenta 4007

description: normal placenta sample

source_name: 4007 placenta


title: genomic DNA from placenta 4029

description: normal placenta sample

source_name: 4029 placenta


title: Normal symmetry, class II, deep bite, rep 2

source_name: subject 11_left_normal facial symmetry; J CRANIOFAC SURG_5

value: Orthognathic surgical subject 11

value: normal facial symmetry

value: class II deep bite


title: genomic DNA from placenta 4002

description: normal placenta sample

source_name: 4002 placenta


title: genomic DNA from placenta 4003

description: normal placenta sample

source_name: 4003 placenta


title: genomic DNA from placenta 4006

description: normal placenta sample

source_name: 4006 placenta


title: Pedicel_AZ_Lateral1_X3177_Hybrid2_21DAP_replicate1

source_name: Wild type X3177 lateral1 pedicel abscission zone

value: Abscission zone

value: Hybrid X3177

value: Wild-type

value: abscission


title: Pedicel_AZ_Central_X3177_Hybrid2_21DAP_replicate 1

source_name: Wild type X3177 central pedicel abscission zone

value: no abscission

value: 21 days after flower pollination


title: genomic DNA from placenta 4001

description: normal placenta sample

source_name: 4001 placenta


title: Normal symmetry, class II , open bite, rep 2

source_name: subject 3_right_normal facial symmetry; J CRANIOFAC SURG_8

value: Orthognathic surgical subject 3

value: Female

value: class II  open bite


title: Normal symmetry, class II, open bite, rep 1

source_name: subject 35_right_ normal facial symmetry; J CRANIOFAC SURG_7

value: Orthognathic surgical subject 35


title: Tail fibroblast 1

city: Melbourne

first: Milena

middle: B

last: Furtado

state: VIC

address: Wellington Road, Building 75, Level 1

institute: Monash University-Australian Regenerative Medicine Institute

hyb_protocol: 600ng of Cy3 labeled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60oC for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion 25ul of 2x Agilent gene expression hybridisation buffer was added and 40ul of sample hybridised for 17 hours at 65oC in a rotating Agilent hybridisation oven. After hybridisation, microarrays were washed 1 minute at room temperature with GE wash buffer 1(Agilent) and 1 minute with 37oC GE wash buffer 2(Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent C, DNA microarray scanner using one color scan settings for 8x60k array slides; scan area 61x21.6mm, scan resolution 3um, dye channel is set to Green and 20 bit Tiff.

data_processing: The scanned images were analysed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1-1100_Jul11 and Grid: (028005_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities. Agilent.SingleColor.28005 microarray, Software GeneSpring 12.6; Threshold: 1.0, Logbase: 2; Normalization: Quantile; Baseline Transformation: None; Filtered on Expression (20.0-100.0); Filtered on Flags (Detected, Not Detected); T test unpaired , P<=:0.05, FC>=2.0 Benjamini-Hochberg

source_name: tail fibroblast

label_protocol: Cyanine-3 (Cy3) labelled cRNA was prepared from 0.1ug total RNA using the One-Color Low input Quick Amp labelling Kit (Agilent) according to the manufacturer’s instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was prepared using the mirVana kit (Invitrogen) folowed by DNAseI digestion following the manufacturer's recommendations. RNA was quantified  and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 8-10week old mouse hearts were finely chopped with surgical scissors and whole tails were skinned and cut into 2-3mm pieces. Both tissues were subjected to enzymatic digestion [0.05% trypsin/EDTA (Gibco) or 0.5mg/mL collagenase type II (Worthington)] at 37oC under agitation for 40 minutes, washed in HBSS and plated on 10cm dishes in DMEM high glucose supplemented with 10% FBS, 1x pen/strep and sodium pyruvate for 5 days at 37 ºC in a humidified incubator with 5% CO2

value: male

tag: strain

value: 8 weeks adult

value: tail

tag: cell type

value: fibroblast


title: genomic DNA from placenta 4015

description: normal placenta sample

source_name: 4015 placenta

value: placenta

value: normal

value: Term


title: Pedicel_AZ_Lateral1_X3177_Hybrid2_17DAP_replicate2

value: Abscission zone

tag: treatment

value: 17 days after flower pollination


title: Tail fibroblast 3

tag: tissue


title: Pedicel_AZ_Lateral1_X3177_Hybrid1_21DAP_replicate2

value: Hybrid X3177

value: Wild-type


title: Heart fibroblast 1

source_name: heart fibroblast

value: heart