title: BreastTumor_OSL2R-3030T2

status: Public on Jan 31 2015

type: RNA

city: Oslo

first: Miriam

middle: Ragle

last: Aure

address: Ullernchauséen 70

department: Dept. of Cancer Genetics

country: Norway

institute: Oslo University Hospital Radiumhospitalet

hyb_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, v.6.5, May 2010

scan_protocol: Scanning on Agilent scanner G2565A and Feature Extraction (FE) v10.7.3.1 was used to extract signals

data_processing: Signals were extracted using FE v.10.7.3.1 and protocol GE1_107_Sep09 (Agilent Technologies). Arrays were log2-transformed, quantile normalized and hospital-adjusted by subtracting from each probe value the mean probe value among samples from the same hospital.

molecule: total RNA

organism: Homo sapiens

source_name: Breast primary tumor

growth_protocol: Human primary tumors

extract_protocol: TRIzol, following manufactors protocol

treatment_protocol: Fresh frozen in liquid nitrogen

tag: tissue

value: Breast tumor

tag: estrogen receptor (er) status

value: pos

tag: human epidermal growth factor receptor 2 (her2) status

value: neg

tag: histological grade

tag: pam50 subgroup

value: LumA

tag: rppa subgroup

value: Luminal


title: BreastTumor_OSL2U-0110T5

label_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, v.6.5, May 2010


title: BreastTumor_OSL2U-0523T1

value: Normal


title: BreastTumor_OSL2U-0437T1


title: BreastTumor_OSL2U-0016T1

value: ReacI


title: BreastTumor_OSL2U-0525T1

value: Basal


title: BreastTumor_OSL2U-0358T1

value: LumB


title: BreastTumor_OSL2U-0017T1


title: BreastTumor_OSL2U-0040T1


title: BreastTumor_OSL2U-0555T1


title: BreastTumor_OSL2U-0381T1


title: BreastTumor_OSL2U-0182T1


title: BreastTumor_OSL2U-0248T1


title: BreastTumor_OSL2U-0186T6


title: BreastTumor_OSL2R-3005T1


title: BreastTumor_OSL2U-0215T1


title: BreastTumor_OSL2U-0106T1


title: BreastTumor_OSL2U-0488T1


title: BreastTumor_OSL2U-0314T1


title: BreastTumor_OSL2U-0175T1


title: BreastTumor_OSL2U-0269T1


title: BreastTumor_OSL2U-0046T1


title: BreastTumor_OSL2U-0370T1


title: BreastTumor_OSL2U-0231T1


title: BreastTumor_OSL2U-0199T1


title: BreastTumor_OSL2U-0266T4


title: BreastTumor_OSL2U-0531T1


title: BreastTumor_OSL2U-0553T1


title: BreastTumor_OSL2U-0232T1


title: BreastTumor_OSL2U-0007T1


title: BreastTumor_OSL2U-0025T1


title: BreastTumor_OSL2U-0082T1


title: BreastTumor_OSL2U-0468T1


title: BreastTumor_OSL2U-0167T1


title: BreastTumor_OSL2U-0059T1


title: BreastTumor_OSL2U-0202T1


title: BreastTumor_OSL2U-0400T1


title: BreastTumor_OSL2U-0556T1


title: BreastTumor_OSL2U-0201T1


title: BreastTumor_OSL2U-0045T1


title: BreastTumor_OSL2U-0263T1


title: BreastTumor_OSL2U-0053T1


title: BreastTumor_OSL2U-0104T1


title: BreastTumor_OSL2U-0396T1


title: BreastTumor_OSL2U-0078T1


title: BreastTumor_OSL2U-0540T1


title: BreastTumor_OSL2U-0085T5


title: BreastTumor_OSL2U-0353T1

value: ReacII


title: BreastTumor_OSL2U-0280T1


title: BreastTumor_OSL2U-0043T1


title: BreastTumor_OSL2U-0337T1


title: BreastTumor_OSL2U-0325T1


title: BreastTumor_OSL2U-0152T8


title: BreastTumor_OSL2U-0411T1


title: BreastTumor_OSL2U-0288T1


title: BreastTumor_OSL2U-0279T4


title: BreastTumor_OSL2U-0519T1


title: BreastTumor_OSL2U-0211T6


title: BreastTumor_OSL2U-0391T1


title: BreastTumor_OSL2U-0030T1


title: BreastTumor_OSL2U-0249T1


title: BreastTumor_OSL2U-0491T1


title: BreastTumor_OSL2U-0393T1


title: BreastTumor_OSL2U-0024T1


title: BreastTumor_OSL2R-3002T4


title: BreastTumor_OSL2U-0205T5


title: BreastTumor_OSL2U-0536T1


title: BreastTumor_OSL2U-0422T1


title: BreastTumor_OSL2U-0023T4


title: BreastTumor_OSL2U-0080T6


title: BreastTumor_OSL2U-0324T1


title: BreastTumor_OSL2U-0557T1


title: BreastTumor_OSL2U-0123T8


title: BreastTumor_OSL2U-0218T1


title: BreastTumor_OSL2U-0406T1


title: BreastTumor_OSL2U-0076T1


title: BreastTumor_OSL2U-0028T4


title: BreastTumor_OSL2U-0159T7


title: BreastTumor_OSL2U-0267T1


title: BreastTumor_OSL2U-0149T1


title: BreastTumor_OSL2U-0103T1


title: BreastTumor_OSL2U-0209T1


title: BreastTumor_OSL2R-3057T3


title: BreastTumor_OSL2U-0197T1


title: BreastTumor_OSL2U-0486T1


title: BreastTumor_OSL2U-0462T1


title: BreastTumor_OSL2U-0544T1


title: BreastTumor_OSL2U-0112T4


title: BreastTumor_OSL2U-0489T1


title: BreastTumor_OSL2U-0347T1


title: BreastTumor_OSL2U-0430T1


title: BreastTumor_OSL2U-0214T1


title: BreastTumor_OSL2U-0037T1


title: BreastTumor_OSL2U-0463T1


title: BreastTumor_OSL2R-3044T4


title: BreastTumor_OSL2U-0382T1


title: BreastTumor_OSL2U-0198T1


title: BreastTumor_OSL2U-0436T1


title: BreastTumor_OSL2U-0484T1


title: BreastTumor_OSL2U-0130T1


title: BreastTumor_OSL2U-0225T5


title: BreastTumor_OSL2U-0487T1


title: BreastTumor_OSL2U-0362T1


title: BreastTumor_OSL2U-0472T1


title: BreastTumor_OSL2U-0221T1


title: BreastTumor_OSL2U-0352T1


title: BreastTumor_OSL2U-0079T1


title: BreastTumor_OSL2U-0485T1


title: BreastTumor_OSL2U-0042T1


title: BreastTumor_OSL2U-0020T1


title: BreastTumor_OSL2R-3059T2


title: BreastTumor_OSL2U-0452T1


title: BreastTumor_OSL2U-0334T1


title: BreastTumor_OSL2U-0174T1


title: BreastTumor_OSL2U-0220T1


title: BreastTumor_OSL2U-0423T1


title: BreastTumor_OSL2U-0311T1


title: BreastTumor_OSL2U-0216T4


title: BreastTumor_OSL2U-0029T1


title: BreastTumor_OSL2U-0243T4


title: BreastTumor_OSL2U-0367T1


title: BreastTumor_OSL2U-0215T9


title: BreastTumor_OSL2U-0289T1


title: BreastTumor_OSL2R-3053T1


title: BreastTumor_OSL2U-0212T5


title: BreastTumor_OSL2U-0113T1


title: BreastTumor_OSL2U-0236T1


title: BreastTumor_OSL2U-0223T1


title: BreastTumor_OSL2U-0368T1


title: BreastTumor_OSL2U-0276T1


title: BreastTumor_OSL2U-0135T1


title: BreastTumor_OSL2U-0429T1


title: BreastTumor_OSL2U-0291T1


title: BreastTumor_OSL2U-0120T1


title: BreastTumor_OSL2U-0075T1


title: BreastTumor_OSL2U-0210T1


title: BreastTumor_OSL2R-3001T1


title: BreastTumor_OSL2U-0101T1


title: BreastTumor_OSL2U-0379T1


title: BreastTumor_OSL2U-0319T1


title: BreastTumor_OSL2U-0105T1


title: BreastTumor_OSL2U-0323T1


title: BreastTumor_OSL2U-0413T1


title: BreastTumor_OSL2U-0127T1


title: BreastTumor_OSL2U-0433T1


title: BreastTumor_OSL2U-0365T1


title: BreastTumor_OSL2U-0342T1


title: BreastTumor_OSL2U-0265T1


title: BreastTumor_OSL2U-0034T1


title: BreastTumor_OSL2U-0117T1


title: BreastTumor_OSL2U-0121T1


title: BreastTumor_OSL2U-0109T1


title: BreastTumor_OSL2U-0056T4


title: BreastTumor_OSL2U-0395T1


title: BreastTumor_OSL2U-0015T1


title: BreastTumor_OSL2U-0328T1


title: BreastTumor_OSL2U-0448T1


title: BreastTumor_OSL2U-0145T4


title: BreastTumor_OSL2U-0226T1


title: BreastTumor_OSL2U-0438T1


title: BreastTumor_OSL2R-3043T1


title: BreastTumor_OSL2U-0447T1


title: BreastTumor_OSL2U-0070T1


title: BreastTumor_OSL2R-3052T3


title: BreastTumor_OSL2U-0096T1


title: BreastTumor_OSL2U-0299T1


title: BreastTumor_OSL2U-0445T1


title: BreastTumor_OSL2U-0181T4


title: BreastTumor_OSL2U-0064T1


title: BreastTumor_OSL2U-0305T1


title: BreastTumor_OSL2U-0107T1


title: BreastTumor_OSL2U-0207T4


title: BreastTumor_OSL2U-0340T1


title: BreastTumor_OSL2U-0417T1


title: BreastTumor_OSL2U-0529T1


title: BreastTumor_OSL2U-0128T1


title: BreastTumor_OSL2U-0313T1


title: BreastTumor_OSL2U-0550T1


title: BreastTumor_OSL2U-0383T1


title: BreastTumor_OSL2U-0420T1


title: BreastTumor_OSL2U-0392T1


title: BreastTumor_OSL2U-0227T1


title: BreastTumor_OSL2U-0242T4


title: BreastTumor_OSL2U-0262T4


title: BreastTumor_OSL2U-0219T1


title: BreastTumor_OSL2U-0171T1


title: BreastTumor_OSL2U-0090T1


title: BreastTumor_OSL2U-0390T1


title: BreastTumor_OSL2U-0250T1


title: BreastTumor_OSL2U-0384T1


title: BreastTumor_OSL2U-0083T1


title: BreastTumor_OSL2U-0172T1


title: BreastTumor_OSL2U-0093T6


title: BreastTumor_OSL2U-0143T1


title: BreastTumor_OSL2U-0385T1


title: BreastTumor_OSL2U-0194T1


title: BreastTumor_OSL2U-0094T4


title: BreastTumor_OSL2U-0052T1


title: BreastTumor_OSL2U-0097T1


title: BreastTumor_OSL2U-0132T4


title: BreastTumor_OSL2U-0547T1


title: BreastTumor_OSL2U-0208T1


title: BreastTumor_OSL2U-0260T1


title: BreastTumor_OSL2U-0074T1


title: BreastTumor_OSL2U-0255T1


title: BreastTumor_OSL2U-0065T4


title: BreastTumor_OSL2U-0278T1


title: BreastTumor_OSL2U-0290T1


title: BreastTumor_OSL2U-0153T4


title: BreastTumor_OSL2U-0026T1


title: BreastTumor_OSL2U-0431T1


title: BreastTumor_OSL2U-0360T1


title: BreastTumor_OSL2U-0219T8


title: BreastTumor_OSL2U-0086T1


title: BreastTumor_OSL2U-0285T1


title: BreastTumor_OSL2R-3045T5


title: BreastTumor_OSL2U-0524T1


title: BreastTumor_OSL2U-0530T1


title: BreastTumor_OSL2U-0261T1


title: BreastTumor_OSL2U-0450T1


title: BreastTumor_OSL2U-0169T1


title: BreastTumor_OSL2U-0373T1


title: BreastTumor_OSL2U-0329T1


title: BreastTumor_OSL2U-0515T1


title: BreastTumor_OSL2U-0166T1


title: BreastTumor_OSL2U-0183T6


title: BreastTumor_OSL2U-0251T1


title: BreastTumor_OSL2U-0457T1


title: BreastTumor_OSL2U-0129T1


title: BreastTumor_OSL2U-0213T1


title: BreastTumor_OSL2U-0552T1


title: BreastTumor_OSL2U-0514T1


title: BreastTumor_OSL2U-0441T1


title: BreastTumor_OSL2U-0268T1


title: BreastTumor_OSL2U-0512T1


title: BreastTumor_OSL2U-0257T1


title: BreastTumor_OSL2U-0080T1


title: BreastTumor_OSL2U-0193T5


title: BreastTumor_OSL2U-0274T1


title: BreastTumor_OSL2U-0142T1


title: BreastTumor_OSL2U-0364T1


title: BreastTumor_OSL2U-0069T1


title: BreastTumor_OSL2U-0275T1


title: BreastTumor_OSL2U-0009T1


title: BreastTumor_OSL2U-0173T5


title: BreastTumor_OSL2U-0513T1


title: BreastTumor_OSL2U-0320T1


title: BreastTumor_OSL2U-0157T1


title: BreastTumor_OSL2U-0439T1


title: BreastTumor_OSL2U-0479T1


title: BreastTumor_OSL2U-0073T1


title: BreastTumor_OSL2U-0464T1


title: BreastTumor_OSL2U-0229T4


title: BreastTumor_OSL2U-0454T1


title: BreastTumor_OSL2U-0217T1


title: BreastTumor_OSL2U-0011T1


title: BreastTumor_OSL2R-3037T4


title: BreastTumor_OSL2U-0407T1


title: BreastTumor_OSL2U-0179T4


title: BreastTumor_OSL2U-0318T1


title: BreastTumor_OSL2U-0548T1


title: BreastTumor_OSL2U-0471T1


title: BreastTumor_OSL2U-0148T1


title: BreastTumor_OSL2U-0126T1


title: BreastTumor_OSL2U-0222T1


title: BreastTumor_OSL2U-0237T1


title: BreastTumor_OSL2R-3013T1


title: BreastTumor_OSL2U-0461T1


title: BreastTumor_OSL2U-0296T1


title: BreastTumor_OSL2U-0170T1


title: BreastTumor_OSL2U-0388T1


title: BreastTumor_OSL2U-0310T1


title: BreastTumor_OSL2U-0114T1


title: BreastTumor_OSL2U-0542T1


title: BreastTumor_OSL2U-0537T1


title: BreastTumor_OSL2U-0545T1


title: BreastTumor_OSL2U-0027T5


title: BreastTumor_OSL2U-0496T1


title: BreastTumor_OSL2U-0177T1


title: BreastTumor_OSL2U-0351T1


title: BreastTumor_OSL2R-3045T5

hyb_protocol: Agilent miRNA Labeling Reagent and Hybridization Kit, Protocol v.2.3.

data_processing: Signals were extracted using Feature Extraction v10.7.3.1 and the subsequent data processing was performed using the GeneSpring software v11.0 (Agilent Technologies). In brief, the miRNA signal intensities were log2-transformed and normalized to the 90th percentile, and miRNAs that were detected in less than 10% of the samples were excluded. This resulted in 421 unique mature miRNAs.


title: BreastTumor_OSL2U-0442T1


title: BreastTumor_OSL2U-0285T1

label_protocol: Agilent miRNA Labeling Reagent and Hybridization Kit, Protocol v.2.3.


title: BreastTumor_OSL2U-0406T1


title: BreastTumor_OSL2U-0080T6


title: BreastTumor_OSL2U-0529T1


title: BreastTumor_OSL2U-0319T1


title: BreastTumor_OSL2U-0175T1


title: LN-308 shVEGFR-2 3

city: Heidelberg

first: Tobias

last: Kessler

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

source_name: glioma cell line

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

growth_protocol: LN-308 and U138MG glioma cell lines were cultured in Dulbecco´s ;odified Eagle´s Medium (DMEM) containing 10 % fetal bovine serum, 100 IU/ml penicillin and 100 mg/ml streptomycin.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: shRNA mediated knock-down of VEGFR-2 was done in LN-308 and U138MG glioma cells.

tag: treatment

tag: cell line


title: BreastTumor_OSL2U-0477T1


title: BreastTumor_OSL2U-0329T1


title: BreastTumor_OSL2U-0512T1


title: BreastTumor_OSL2U-0261T1


title: BreastTumor_OSL2U-0179T4


title: LN-308 shcontrol 3

value: shcontrol


title: LN-308 shVEGFR-2 1


title: LN-308 shcontrol 1


title: BreastTumor_OSL2U-0252T1


title: U138MG shVEGFR-2 3


title: BreastTumor_OSL2U-0097T1


title: U138MG shVEGFR-2 2


title: U138MG shcontrol 1


title: LN-308 shcontrol 2


title: U138MG shcontrol 2


title: U138MG shVEGFR-2 1


title: LN-308 shVEGFR-2 2


title: U138MG shcontrol 3


title: BreastTumor_OSL2U-0056T4


title: BreastTumor_OSL2U-0454T1


title: BreastTumor_OSL2U-0090T1


title: BreastTumor_OSL2U-0212T5


title: BreastTumor_OSL2U-0007T1


title: BreastTumor_OSL2U-0323T1


title: BreastTumor_OSL2U-0210T1


title: BreastTumor_OSL2U-0193T5


title: BreastTumor_OSL2U-0221T1


title: BreastTumor_OSL2U-0278T1


title: BreastTumor_OSL2U-0194T1


title: BreastTumor_OSL2U-0463T1


title: BreastTumor_OSL2U-0218T1


title: BreastTumor_OSL2U-0556T1


title: BreastTumor_OSL2U-0438T1


title: BreastTumor_OSL2U-0395T1


title: BreastTumor_OSL2U-0042T1


title: BreastTumor_OSL2R-3013T1


title: BreastTumor_OSL2U-0186T6


title: BreastTumor_OSL2U-0029T1


title: BreastTumor_OSL2U-0388T1


title: BreastTumor_OSL2U-0255T1


title: BreastTumor_OSL2U-0447T1


title: BreastTumor_OSL2U-0220T1


title: BreastTumor_OSL2U-0027T5


title: BreastTumor_OSL2U-0365T1


title: BreastTumor_OSL2U-0094T4


title: BreastTumor_OSL2U-0450T1


title: BreastTumor_OSL2U-0028T4


title: BreastTumor_OSL2U-0103T1


title: BreastTumor_OSL2U-0198T1


title: BreastTumor_OSL2U-0145T4


title: BreastTumor_OSL2U-0383T1


title: BreastTumor_OSL2U-0074T1


title: BreastTumor_OSL2U-0199T1


title: BreastTumor_OSL2R-3037T4


title: BreastTumor_OSL2U-0265T1


title: BreastTumor_OSL2U-0023T4


title: BreastTumor_OSL2U-0148T1


title: BreastTumor_OSL2U-0172T1


title: BreastTumor_OSL2U-0142T1


title: BreastTumor_OSL2U-0026T1


title: BreastTumor_OSL2U-0479T1


title: BreastTumor_OSL2U-0157T1


title: BreastTumor_OSL2U-0337T1


title: BreastTumor_OSL2U-0126T1


title: BreastTumor_OSL2U-0132T4


title: BreastTumor_OSL2U-0417T1


title: BreastTumor_OSL2U-0080T1


title: BreastTumor_OSL2U-0202T1


title: BreastTumor_OSL2U-0040T1


title: BreastTumor_OSL2R-3059T2


title: BreastTumor_OSL2U-0075T1


title: BreastTumor_OSL2U-0514T1


title: BreastTumor_OSL2U-0120T1


title: BreastTumor_OSL2U-0167T1


title: BreastTumor_OSL2U-0368T1


title: BreastTumor_OSL2U-0250T1


title: BreastTumor_OSL2U-0373T1


title: BreastTumor_OSL2U-0324T1


title: BreastTumor_OSL2U-0227T1


title: BreastTumor_OSL2U-0314T1


title: BreastTumor_OSL2U-0079T1


title: BreastTumor_OSL2U-0268T1


title: BreastTumor_OSL2U-0548T1


title: BreastTumor_OSL2U-0201T1


title: BreastTumor_OSL2U-0340T1


title: BreastTumor_OSL2U-0276T1


title: BreastTumor_OSL2U-0121T1


title: BreastTumor_OSL2U-0170T1


title: BreastTumor_OSL2U-0486T1


title: BreastTumor_OSL2U-0106T1


title: BreastTumor_OSL2U-0360T1


title: BreastTumor_OSL2U-0046T1


title: BreastTumor_OSL2U-0129T1


title: BreastTumor_OSL2U-0555T1


title: BreastTumor_OSL2U-0232T1


title: BreastTumor_OSL2U-0153T4


title: BreastTumor_OSL2U-0016T1


title: BreastTumor_OSL2U-0260T1


title: BreastTumor_OSL2U-0290T1


title: BreastTumor_OSL2U-0515T1


title: BreastTumor_OSL2U-0064T1


title: BreastTumor_OSL2U-0159T7


title: BreastTumor_OSL2U-0392T1


title: BreastTumor_OSL2U-0219T8


title: BreastTumor_OSL2U-0257T1


title: BreastTumor_OSL2U-0117T1


title: BreastTumor_OSL2R-3030T2


title: BreastTumor_OSL2U-0069T1


title: BreastTumor_OSL2U-0043T1


title: BreastTumor_OSL2U-0143T1


title: BreastTumor_OSL2U-0034T1


title: BreastTumor_OSL2U-0536T1


title: BreastTumor_OSL2R-3002T4


title: BreastTumor_OSL2U-0169T1


title: BreastTumor_OSL2U-0231T1


title: BreastTumor_OSL2U-0547T1


title: BreastTumor_OSL2R-3053T1


title: BreastTumor_OSL2U-0045T1


title: BreastTumor_OSL2U-0065T4


title: BreastTumor_OSL2U-0464T1


title: BreastTumor_OSL2U-0219T1


title: BreastTumor_OSL2U-0093T6


title: BreastTumor_OSL2U-0085T5


title: BreastTumor_OSL2U-0396T1


title: BreastTumor_OSL2U-0177T1


title: BreastTumor_OSL2U-0251T1


title: BreastTumor_OSL2U-0471T1


title: BreastTumor_OSL2U-0519T1


title: BreastTumor_OSL2U-0448T1


title: BreastTumor_OSL2U-0433T1


title: BreastTumor_OSL2U-0183T6


title: BreastTumor_OSL2R-3043T1


title: BreastTumor_OSL2U-0037T1


title: BreastTumor_OSL2U-0411T1


title: BreastTumor_OSL2U-0211T6


title: BreastTumor_OSL2U-0215T9


title: BreastTumor_OSL2U-0279T4


title: BreastTumor_OSL2U-0485T1


title: BreastTumor_OSL2U-0174T1


title: BreastTumor_OSL2U-0381T1


title: BreastTumor_OSL2U-0299T1


title: BreastTumor_OSL2U-0525T1


title: BreastTumor_OSL2U-0488T1


title: BreastTumor_OSL2U-0011T1


title: BreastTumor_OSL2U-0207T4


title: BreastTumor_OSL2U-0070T1


title: BreastTumor_OSL2U-0248T1


title: BreastTumor_OSL2U-0296T1


title: BreastTumor_OSL2U-0236T1


title: BreastTumor_OSL2R-3044T4


title: BreastTumor_OSL2U-0540T1


title: BreastTumor_OSL2U-0420T1


title: BreastTumor_OSL2U-0445T1


title: BreastTumor_OSL2U-0382T1


title: BreastTumor_OSL2U-0328T1


title: BreastTumor_OSL2U-0242T4


title: BreastTumor_OSL2U-0082T1


title: BreastTumor_OSL2U-0530T1


title: BreastTumor_OSL2U-0076T1


title: BreastTumor_OSL2U-0229T4


title: BreastTumor_OSL2U-0269T1


title: BreastTumor_OSL2U-0353T1


title: BreastTumor_OSL2U-0423T1


title: BreastTumor_OSL2U-0086T1


title: BreastTumor_OSL2R-3052T3


title: BreastTumor_OSL2R-3001T1


title: BreastTumor_OSL2U-0468T1


title: BreastTumor_OSL2U-0209T1


title: BreastTumor_OSL2U-0197T1


title: BreastTumor_OSL2U-0557T1


title: BreastTumor_OSL2U-0313T1


title: BreastTumor_OSL2U-0053T1


title: BreastTumor_OSL2U-0024T1


title: BreastTumor_OSL2U-0208T1


title: BreastTumor_OSL2U-0130T1


title: BreastTumor_OSL2U-0110T5


title: BreastTumor_OSL2R-3057T3


title: BreastTumor_OSL2U-0462T1


title: BreastTumor_OSL2R-3005T1


title: BreastTumor_OSL2U-0318T1


title: BreastTumor_OSL2U-0274T1


title: BreastTumor_OSL2U-0107T1


title: BreastTumor_OSL2U-0325T1


title: BreastTumor_OSL2U-0531T1


title: BreastTumor_OSL2U-0544T1


title: BreastTumor_OSL2U-0436T1


title: BreastTumor_OSL2U-0171T1


title: BreastTumor_OSL2U-0017T1


title: BreastTumor_OSL2U-0320T1


title: BreastTumor_OSL2U-0288T1


title: BreastTumor_OSL2U-0222T1


title: BreastTumor_OSL2U-0025T1


title: BreastTumor_OSL2U-0367T1


title: BreastTumor_OSL2U-0545T1


title: BreastTumor_OSL2U-0407T1


title: BreastTumor_OSL2U-0442T1


title: BreastTumor_OSL2U-0429T1


title: BreastTumor_OSL2U-0461T1


title: BreastTumor_OSL2U-0334T1


title: BreastTumor_OSL2U-0214T1


title: BreastTumor_OSL2U-0537T1


title: BreastTumor_OSL2U-0243T4


title: BreastTumor_OSL2U-0413T1


title: BreastTumor_OSL2U-0113T1


title: BreastTumor_OSL2U-0223T1


title: BreastTumor_OSL2U-0073T1


title: BreastTumor_OSL2U-0101T1


title: BreastTumor_OSL2U-0364T1


title: BreastTumor_OSL2U-0263T1


title: BreastTumor_OSL2U-0237T1


title: BreastTumor_OSL2U-0225T5


title: BreastTumor_OSL2U-0347T1


title: BreastTumor_OSL2U-0542T1


title: BreastTumor_OSL2U-0390T1


title: BreastTumor_OSL2U-0311T1


title: BreastTumor_OSL2U-0078T1


title: BreastTumor_OSL2U-0477T1


title: BreastTumor_OSL2U-0252T1


title: BreastTumor_OSL2U-0109T1


title: BreastTumor_OSL2U-0127T1


title: BreastTumor_OSL2U-0441T1


title: BreastTumor_OSL2U-0009T1


title: BreastTumor_OSL2U-0513T1


title: BreastTumor_OSL2U-0358T1


title: BreastTumor_OSL2U-0266T4


title: BreastTumor_OSL2U-0280T1


title: BreastTumor_OSL2U-0351T1


title: BreastTumor_OSL2U-0430T1


title: BreastTumor_OSL2U-0550T1


title: BreastTumor_OSL2U-0491T1


title: BreastTumor_OSL2U-0457T1


title: BreastTumor_OSL2U-0217T1


title: BreastTumor_OSL2U-0052T1


title: BreastTumor_OSL2U-0181T4


title: BreastTumor_OSL2U-0104T1


title: BreastTumor_OSL2U-0216T4


title: BreastTumor_OSL2U-0275T1


title: BreastTumor_OSL2U-0431T1


title: BreastTumor_OSL2U-0310T1


title: BreastTumor_OSL2U-0020T1


title: BreastTumor_OSL2U-0096T1


title: BreastTumor_OSL2U-0083T1


title: BreastTumor_OSL2U-0291T1


title: BreastTumor_OSL2U-0128T1


title: BreastTumor_OSL2U-0112T4


title: BreastTumor_OSL2U-0496T1


title: BreastTumor_OSL2U-0059T1


title: BreastTumor_OSL2U-0114T1


title: BreastTumor_OSL2U-0262T4


title: BreastTumor_OSL2U-0487T1


title: BreastTumor_OSL2U-0393T1


title: BreastTumor_OSL2U-0342T1


title: BreastTumor_OSL2U-0552T1


title: BreastTumor_OSL2U-0422T1


title: BreastTumor_OSL2U-0166T1


title: BreastTumor_OSL2U-0384T1


title: BreastTumor_OSL2U-0452T1


title: BreastTumor_OSL2U-0523T1


title: BreastTumor_OSL2U-0352T1


title: BreastTumor_OSL2U-0030T1


title: BreastTumor_OSL2U-0362T1


title: BreastTumor_OSL2U-0173T5


title: BreastTumor_OSL2U-0135T1


title: BreastTumor_OSL2U-0205T5


title: BreastTumor_OSL2U-0215T1


title: BreastTumor_OSL2U-0400T1


title: BreastTumor_OSL2U-0391T1


title: BreastTumor_OSL2U-0105T1


title: BreastTumor_OSL2U-0226T1


title: BreastTumor_OSL2U-0553T1


title: BreastTumor_OSL2U-0472T1


title: BreastTumor_OSL2U-0379T1


title: BreastTumor_OSL2U-0437T1


title: BreastTumor_OSL2U-0267T1


title: BreastTumor_OSL2U-0289T1


title: BreastTumor_OSL2U-0484T1


title: BreastTumor_OSL2U-0213T1


title: BreastTumor_OSL2U-0182T1


title: BreastTumor_OSL2U-0370T1


title: BreastTumor_OSL2U-0149T1


title: BreastTumor_OSL2U-0152T8


title: BreastTumor_OSL2U-0489T1


title: BreastTumor_OSL2U-0015T1


title: BreastTumor_OSL2U-0123T8


title: BreastTumor_OSL2U-0249T1


title: BreastTumor_OSL2U-0385T1


title: BreastTumor_OSL2U-0439T1


title: BreastTumor_OSL2U-0305T1


title: BreastTumor_OSL2U-0524T1


title: Day5_OTI_9H10+rapa_3

city: Cambridge

first: Martin

middle: L

last: Miller

address: Robinson Way

department: Cancer research UK, Cambridge Institute

country: United Kingdom

institute: University of Cambridge

description: Replicate 3

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina MouseWG-6 v2.0 expression beadchip. Slides were washed and stained in the Illumina instrument.

data_processing: BeadStudio version 3.3.7 Average Signal and Detection pvalue

organism: Mus musculus

source_name: FACS-sorted CD8+CD45.1+ OTI T cells

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

growth_protocol: OVA-specific T cells were activated by infecting mice with Listeria monocytogenes expressing OVA

extract_protocol: Cells were lysed and RNA extracted with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser and Nanodrop.

treatment_protocol: Mice were treated with control Ig or anti-CTLA-4 (9H10) just prior to infection and with daily rapamycin (rapa) day -1 thru 8 post-infection/immunization

tag: strain

value: C57BL/6J w/ AT of CD45.1+ OTI cells

tag: age

value: 8 weeks

tag: cell type

value: FACS-sorted CD8+CD45.1+ OTI T cells

value: pooled spleen & lymph nodes


title: Day5_OTI_hIg_1

description: Replicate 1


title: Day35_hIg-3

description: Replicate 3

source_name: FACS-sorted SIINFEKL tetramer+ T cells

value: FACS-sorted SIINFEKL tetramer+ T cells


title: SasaO

city: Tsukuba

first: Keita

last: Tsukahara

address: 2-1-12 Kannon-dai

country: Japan

institute: National Food Research Institute, NARO

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x hybridization buffer was added to the fragmentation mixture and hybridized to Agilent rice 4x44K custom oligo-DNA microarray chip for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried in air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan resolution 5 um).

data_processing: The scanned images were analyzed with Feature Extraction Software ver. 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 015241_D_F_20101006) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Oryza sativa

source_name: Sasanishiki, inflorescence meristem, elevated ozone condition, rep1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy mini spin columns (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seeds of two rice cultivars were sown in plastic boxes filled with seedbed soil, and the seedlings were grown in a glasshouse under ambient air condition. Six weeks after sowing, the seedlings were transplanted into pots (0.05 m2 surface area and 0.015 m3 volume; four plants per pot), and grown in glasshouses (five pots of each line per glasshouse) until harvest.

extract_protocol: RNA was prepared using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For the elevated ozone treatment, artificially generated ozone was added to ambient air via a mass flow controller. The mean ozone concentrations during the daytime (6:00 to 18:00) were 43.7 nL L−1 and 85.7 nL L−1.

tag: cultivar

value: Sasanishiki

value: inflorescence meristem

value: 23-day-before heading


title: HabaA

source_name: Habataki, inflorescence meristem, ambient air condition, rep1

value: Habataki


title: Day5_OTI_9H10+rapa_1

description: Replicate 1


title: WT3_TEN899liv-b_Signal

city: Cardiff

first: Karen

middle: Ruth

last: Reed

address: Maindy Road

institute: ECSCRI, Cardiff University

description: Day 4 WT liver

hyb_protocol: PICR Standard 11uM feature-1 protocol - carried out in the Affymetrix Hybridization Oven 640 according to the manufacturer’s instructions

scan_protocol: PICR Standard 11uM feature-1 protocol - using the Affymetrix GeneChip Scanner 3000 system with Autoloader

data_processing:
Raw signal intensities were initially screened by using the MaxD/View-Program to remove false positive and false negative signals (using a cut off of at least one P value for each transcript <0.2). The data were then normalized by using the global geometric mean (GGM) normalization option within the MaxD/View-Program
Pairwise comparisons of the GGM data were then performed by SAM analysis (Statistical Analysis of Microarray)

label: BITION

source_name: liver tissue

label_protocol: PICR Std Label v 2-0 - utalizing the Enzo BioArray High Yield Transcript Labelling Kit

extract_protocol: Trizol and RNeasy clean up

treatment_protocol: Mice treated with 3x 80mg/kg Beta-Napthoflavone in one day and samples collected 4 days post induction

tag: genotype/variation

value: AhCre-positive control (wild-type) mice


title: Day35_hIg-2

description: Replicate 2


title: HabaO

source_name: Habataki, inflorescence meristem, elevated ozone condition, rep1


title: Day35_9H10+rapa-2

description: Replicate 2


title: MA-349

city: Kyoto

first: Megumu

last: Saito

address: 53, Shogoin-Kawahara

institute: Kyoto University

hyb_protocol: Labelled cDNA was fragmented with Gene Expression Hybridization Kit (Agilent Technologies), followed by hybridization at 65˚C for 17 hrs.

scan_protocol: Images were acquired by DNA Microarray Scanner (Agilent Technologies)

data_processing: Raw data were processed with FeatureExtraction version 10.7.3.1. Normalization among samples were performed by GeneSpring GX 12.6.1.  Signal were normalized to 75% percentile.

source_name: fibroblast

label_protocol: 100 ng of total RNA was first amplified with WT-OvationTM Pico System (Nugen). The RNA was labelled with Cy3 using Genomic DNA Enzymatic Labeling Kit (Agilent Technologies).

growth_protocol: Episomal vectors encoding reprogramming factors (OCT3/4, SOX2, KLF4, L-MYC, LIN28 and p53 shRNA) were transduced into fibroblasts on day 0 as described previously (Okita et al., 2011). The transfected cells were reseeded onto feeder layers on day 7, and maintained in embryonic stem cell medium (ReproCELL). Around day 30, the iPSC colonies were picked up and expanded. Cell culture was performed under 37°C , with 5% CO2 and 21% O2.

extract_protocol: Total RNA was extracted and purified using RNA mini kit (QIAGEN) according to manufacturer’s instruction.

treatment_protocol: No treatment applied.

value: fibroblast


title: Day5_OTI_hIg_3

description: Replicate 3


title: Day5_9H10+rapa-3

description: Replicate 3


title: MA-348


title: WT2_TEN900liv_Signal

description: Day 4 WT liver


title: Day35_9H10+rapa-1

description: Replicate 1


title: Day5_9H10+rapa-2

description: Replicate 2


title: Day35_9H10+rapa-3

description: Replicate 3


title: Day5_OTI_9H10+rapa_2

description: Replicate 2


title: MA-347


title: Day35_hIg-1

description: Replicate 1


title: WT1_TEN460liv_Signal

description: Day 4 WT liver


title: Day5_9H10+rapa-1

description: Replicate 1


title: Day5_OTI_hIg_2

description: Replicate 2


title: 0805_OS9_uM_AM480-Myc_Signal

description: Day 4 Myc liver

value: AhCre-positive Cmyc flox hom mice


title: SasaA

source_name: Sasanishiki, inflorescence meristem, ambient air condition, rep1


title: 0805_OS11_uM_AM285-ApcMyc_Signal

description: Day 4 APC/Myc liver

value: AhCre-positive double APCflox homm Cmyc flox hom mice


title: 0805_OS12_uM_AM297-ApcMyc_Signal

description: Day 4 APC/Myc liver


title: Day5_hIg-1

description: Replicate 1


title: Apchom3_ACG293liv-b_Signal

description: Day 4 APCflox liver

value: AhCre-positive APCflox hom mice


title: 0805_OS7_uM_AM440-Myc_Signal

description: Day 4 Myc liver


title: 0805_OS10_uM_AM367-ApcMyc_Signal

description: Day 4 APC/Myc liver


title: 0805_OS8_uM_AM459-Myc_Signal

description: Day 4 Myc liver


title: Day5_hIg-2

description: Replicate 2


title: APchom2_ACG294liv_Signal

description: Day 4 APCflox liver


title: Asthmatic airway smooth muscle following treatment with TGFB (10ng/ml) for 8H, patient 1

city: Sydney

first: Alen

last: Faiz

state: NSW

address: 431 Glebe Point Rd

country: Australia

institute: Woolcock Institute of Medical Research

hyb_protocol: Following fragmentation, 2.5 ug of cRNA were hybridized for 17 hr at 45C on Affymetrix Human Gene 1.0ST. GeneChips were washed and stained in the Affymetrix FS540 fluidics station.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner

data_processing: The data were analyzed with using R/bioconductor, GCRMA was used and data was then log transformed

source_name: Asthmatic airway smooth muscle following treatment with TGFB (10ng/ml) for 24H

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

growth_protocol: Following isolation and initial culturing ASMC at passages 3-4 were seeded at 10,000 cell/cm2 and grown in growth media (Dulbecco's modification of Eagle's medium (DMEM) (Invitrogen), 5% fetal bovine serum (FBS) and 1% antibiotics (Invitrogen)) for 3-4 days.

extract_protocol: Total cellular mRNA was isolated using the Qiagen total RNA isolation kit (Qiagen)

treatment_protocol: Cells were then quiesced in 0.1% BSA and 1% antibiotics in DMEM (quiescing media) for 3 days and treated with IL1β (10 ng/ml), TGFβ (10 ng/ml) and 10% FBS. mRNA was collected at 0 hours for baseline and 8 hours for treatments

tag: gender

value: M

tag: disease

value: Asthmatic

value: TGFB 10ng/ml


title: Healthy airway smooth muscle following treatment with IL1B (10ng/ml) for 8H, patient 1

source_name: Healthy airway smooth muscle following treatment with IL1B (10ng/ml) for 24H

value: Healthy

value: IL1B 10ng/ml


title: Apchom1_PAF917liv-b_Signal

description: Day 4 APCflox liver


title: Day5_hIg-3

description: Replicate 3

value: 8 weeks


title: IL22KO5_ileum, 5 days post-infection with T. gondii

city: South San Francisco

first: Jason

middle: A

last: Hackney

state: CA

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

country: USA

institute: Genentech, Inc.

description: Gene expression data from IL-22 knockout mouse ileum after infection with T. gondii

hyb_protocol: The method for hybridization of the arrays was provided by Affymetrix. Twenty micrograms of cRNA was fragmented and then hybridized to the arrays at 45°C for 19 hours in a rotisserie oven set at 60 rpm.

scan_protocol: The method for array schanning was provided by Affymetrix. Arrays were washed and stained in Fluidics station and scanned on Affymterix scanner.

data_processing: Raw data were processed using the RMA algorithm using the affy Bioconductor package (affy_1.42.3).

label: Biotin

source_name: IL22KO_T. gondii-infected_5dpi_ileum

label_protocol: The method for prepartation of cRNA was provided by Affymetrix. Briefly, 5 ug of total RNA was converted into double-stranded cDNA using a cDNA synthesis kit SuperScript Choice and a T7-(dT)24 oligomer primer. Double-stranded cDNA was purified on an affinity resin and ethanol precipitation. Following second-strand cDNA synthesis, labeled cRNA was generated using a T7 RNA polymerase and biotin-labeled nucleotide in an in vitro transcription reaction (Enzo Diagnostics). The labeled cRNA was purified on an affinity resin.

extract_protocol: RNA was isolated using QIAGEN RNAeasy midi kit

treatment_protocol: WT C57BL/6 mice and IL-22 KO mice were infected with the ME49 strain of Toxoplasma gondii (100 cysts in 0.3ml of PBS by gavage). Ileum of these mice was harvested at day 5 post-infection

tag: strain background

tag: infected with

value: ME49 strain of T. gondii

tag: time point

value: at day 5 post-infection

value: ileum


title: IL22KO4_ileum, 5 days post-infection with T. gondii

tag: tissue


title: IL22KO3_ileum, 5 days post-infection with T. gondii


title: IL22KO2_ileum, 5 days post-infection with T. gondii


title: Healthy airway smooth muscle following treatment with 0.1% BSA for 0H, patient 3

source_name: Healthy airway smooth muscle following treatment with 0.1% BSA for 24H

value: F


title: IL22KO1_ileum, 5 days post-infection with T. gondii


title: Asthmatic airway smooth muscle following treatment with 10% FBS for 8H, patient 3

source_name: Asthmatic airway smooth muscle following treatment with 10% FBS for 24H

value: FBS 10%


title: WT5_ileum, 5 days post-infection with T. gondii

description: Gene expression data from wild type mouse ileum after infection with T. gondii

source_name: WT_T. gondii-infected_5dpi_ileum

value: WT


title: Asthmatic airway smooth muscle following treatment with 0.1% BSA for 0H, patient 1

source_name: Asthmatic airway smooth muscle following treatment with 0.1% BSA for 24H


title: Asthmatic airway smooth muscle following treatment with IL1B (10ng/ml) for 8H, patient 3

source_name: Asthmatic airway smooth muscle following treatment with IL1B (10ng/ml) for 24H


title: WT1_ileum, 5 days post-infection with T. gondii


title: 0404_AC(3)17_uM2_MAGIC67

source_name: colon - normal colonic mucosia collected from a APCmin mouse

extract_protocol: trizol phenol extraction followed by Rneasy clean up

treatment_protocol: samples 1 - 18: Mice treated with 3x 80mg/kg Beta-Napthoflavone in one day and culled and dissected at the desiganted day post induction., samples 20-24 collected from untreated mice.

tag: genotype

value: ApcMin mouse

tag: tissue type

value: colon


title: WT3_ileum, 5 days post-infection with T. gondii


title: WT2_ileum, 5 days post-infection with T. gondii


title: Healthy airway smooth muscle following treatment with 0.1% BSA for 0H, patient 1


title: 0704_AC(3)30_uM_MY395


title: WT4_ileum, 5 days post-infection with T. gondii


title: genomic DNA from human articular chondrocytes 11

type: genomic

city: Shenzhen

first: Li

last: Duan

state: Guangdong

address: Futian District, Sungang WestRoad 3002#

department: Department of Orthopedics

country: China

institute: Shenzhen Second People's Hospital

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K 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

molecule: genomic DNA

source_name: normal human articular chondroytes

label_protocol: Standard Illumina Protocol

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

value: articular chondroyte

tag: passage

value: DMSO


title: 0404_AC(3)15_uM2_MAGIC93


title: Healthy airway smooth muscle following treatment with 0.1% BSA for 0H, patient 2


title: Healthy airway smooth muscle following treatment with IL1B (10ng/ml) for 8H, patient 3


title: 0404_TH4_uM2_MA1228u

source_name: Polyp - pooled polyps from colon of a APCmin mouse

value: colonic polyps


title: genomic DNA from human articular chondrocytes 9


title: genomic DNA from human articular chondrocytes 12


title: genomic DNA from human articular chondrocytes 10


title: 0404_TH1_uM2_MY74u


title: 0404_TH2_uM2_MY77u


title: Asthmatic airway smooth muscle following treatment with TGFB (10ng/ml) for 8H, patient 3


title: d5wt_110u

source_name: Day 5 WT

value: AhCre-positive control (wild-type) mice

value: Small intestinal


title: d5wt_474u


title: d5wt_323u


title: genomic DNA from human articular chondrocytes 7


title: d4wt_Ras25

source_name: Day 4 WT


title: d4wt_Ras14


title: Asthmatic airway smooth muscle following treatment with 0.1% BSA for 0H, patient 3

value: Asthmatic


title: d3wt_CAB1009

source_name: Day 3 WT


title: d4wt_Ras27


title: Asthmatic airway smooth muscle following treatment with 10% FBS for 8H, patient 2

value: M


title: d3wt_CAB891


title: genomic DNA from human articular chondrocytes 3


title: genomic DNA from human articular chondrocytes 5


title: genomic DNA from human articular chondrocytes 8


title: Case_1_mothers_father

city: Utrecht

first: Wigard

last: Kloosterman

address: Universiteitsweg 100

country: Netherlands

institute: University Medical Center Utrecht

description:
Genomic DNA extracted from sample was genotyped using Illumina Infinium CytoSNP-850K beadchips
Mothers_father1

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

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

data_processing: Data processing was done using GenomeStudio (Illumina)

label: Biotin (C, G), DNP (A,T)

source_name: DNA from blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (MSM) and primer/neutralization mix (MA1-MA2-0.1N NaOH). After incubation the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol and PM1 and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using the Qiagen/Gentra systems DNA isolation robot according to the manufacturers protocol

value: Male

value: blood

tag: disease state

value: not applicable


title: genomic DNA from human articular chondrocytes 6

tag: treatment


title: Case_1_father

description:
Genomic DNA extracted from sample was genotyped using Illumina Infinium CytoSNP-850K beadchips
Father1


title: Asthmatic airway smooth muscle following treatment with IL1B (10ng/ml) for 8H, patient 2

value: IL1B 10ng/ml


title: Asthmatic airway smooth muscle following treatment with TGFB (10ng/ml) for 8H, patient 2

value: TGFB 10ng/ml


title: D5fl_331u

source_name: Day5 APC flox hom

value: AhCre-positive APCflox hom mice


title: genomic DNA from human articular chondrocytes 4


title: D4fl_APCfl_r1

source_name: Day4 APC flox hom


title: Healthy airway smooth muscle following treatment with TGFB (10ng/ml) for 8H, patient 3

source_name: Healthy airway smooth muscle following treatment with TGFB (10ng/ml) for 24H

value: F

value: Healthy


title: D4fl_APCfl_r2


title: D5fl_444t


title: Case_1_mother

description:
Genomic DNA extracted from sample was genotyped using Illumina Infinium CytoSNP-850K beadchips
Mother1

value: Female


title: D4fl_APCfl_r3


title: Case_1_mothers_mother

description:
Genomic DNA extracted from sample was genotyped using Illumina Infinium CytoSNP-850K beadchips
Mothers_mother1


title: D5fl_131u


title: genomic DNA from human articular chondrocytes 2


title: Asthmatic airway smooth muscle following treatment with 0.1% BSA for 0H, patient 2


title: d3fl_PAF776

source_name: Day3 APC flox hom


title: sperm genomic DNA from Donor T (0.35 subpopulatoin)

city: Salt Lake City

first: Douglas

last: Carrell

state: UT

address: 675 Arapeen Dr. Suite 201

institute: University of Utah

description: sperm subpopulation from the 0.35 layer of Donor T

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

source_name: Donor T

extract_protocol: genomic DNA was extracted following somatic cell lysis using a sperm specific modification to Qiagen DNeasy Kit

tag: gradient layer


title: genomic DNA from human articular chondrocytes 1


title: sperm genomic DNA from Donor S (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor S

source_name: Donor S


title: sperm genomic DNA from Donor T (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor T


title: sperm genomic DNA from Donor S (0.35 subpopulatoin)

description: sperm subpopulation from the 0.35 layer of Donor S


title: Case_1_child

description:
Genomic DNA extracted from sample was genotyped using Illumina Infinium CytoSNP-850K beadchips
Child1

value: multiple congenital abnormalities and mental retardation


title: Healthy airway smooth muscle following treatment with 10% FBS for 8H, patient 2

source_name: Healthy airway smooth muscle following treatment with 10% FBS for 24H

value: FBS 10%


title: d3fl_BCAB107


title: sperm genomic DNA from Donor R (0.35 subpopulatoin)

description: sperm subpopulation from the 0.35 layer of Donor R

source_name: Donor R


title: Asthmatic airway smooth muscle following treatment with IL1B (10ng/ml) for 8H, patient 1


title: Asthmatic airway smooth muscle following treatment with 10% FBS for 8H, patient 1

source_name: Asthmatic airway smooth muscle following treatment with 10% FBS for 24H


title: Healthy airway smooth muscle following treatment with TGFB (10ng/ml) for 8H, patient 2


title: Healthy airway smooth muscle following treatment with TGFB (10ng/ml) for 8H, patient 1


title: Healthy airway smooth muscle following treatment with IL1B (10ng/ml) for 8H,  patient 2

source_name: Healthy airway smooth muscle following treatment with IL1B (10ng/ml) for 24H


title: sperm genomic DNA from Donor R (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor R


title: Amplified DNA_AD14_rep3

city: Berkeley

first: Patrick

last: Lee

address: 209 O'Brien Hall

department: Civil and Environmental Engineering

institute: University of California, Berkeley

description: Amplified DNA

hyb_protocol: According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

data_processing: Data analysis was performed using Affymetrix GeneChip software and the MAS5 algorithm. Each microarray was normalized by scaling the signal intensities of the positive control spike-mix to a target signal intensity of 2500 to allow comparison between microarrays.

organism: Dehalococcoides mccartyi 195

source_name: 1 µg of DNA

label_protocol: One µg of gDNA was prepared for each microarray according to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

growth_protocol: Replicate 100 mL cultures were grown in parallel with chlorinated ethene, hydrogen and acetate.

extract_protocol: gDNA from cultures was extracted using the Qiagen (Valencia, CA) DNeasy Blood & Tissue kit according to the manufacturers’ recommendations.The DNA of sorted cells were amplifed by the Qiagen REPLI-g midi kit (Valencia, CA).

tag: bacteria

value: Enrichment culture

tag: sample type

value: Amplified DNA


title: Amplified DNA_AD14_rep2

description: Amplified DNA

scan_protocol: According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).


title: gDNA_AD14_rep2

description: Genomic DNA

value: Genomic DNA


title: gDNA_AD14_rep3

description: Genomic DNA


title: Amplified DNA_AD14_rep1

description: Amplified DNA


title: d3wt_CAB723

value: AhCre-positive control (wild-type) mice

value: Small intestinal


title: Healthy airway smooth muscle following treatment with 10% FBS for 8H, patient 1

value: M


title: Induced, technical rep2

city: New York

first: Le

last: Jiang

state: NY

address: 1130 St. Nicholas Ave

institute: Columbia University

description: expression after wtp53 induction

hyb_protocol: Following fragmentation, biotin labeled cDNA were hybridized for 16 hr on human gene ST 1.0 array.

scan_protocol: GeneChips were scanned using the Affymetrix genechip scanner.

data_processing: The data were analyzed with Affymetrix expression console default analysis settings and RMA as normalization method.

source_name: wtp53 stable line after induction

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Cells were maintained in DMEM media supplemented with 10% tet-free FBS.

extract_protocol: RNA was extracted by Tryzol according to manufacturer's instruction.

treatment_protocol: wtp53 inducible cells were treated by 0.5 ug/mL doxycycline for 24 hours to induce p53 expression.

tag: cell line


title: Amplified DNA_GW2_1e5 cells_rep1

description: Amplified DNA


title: Amplified DNA_GW2_1e5 cells_rep2

description: Amplified DNA


title: None-induced, technical rep2

description: expression before wtp53 induction

source_name: wtp53 stable line before induction


title: Amplified DNA_GW2_1e5 cells_rep3

description: Amplified DNA


title: Amplified DNA_GW2_1e6 cells_rep3

description: Amplified DNA


title: Induced, technical rep1

description: expression after wtp53 induction


title: sperm genomic DNA from Donor O (0.35 subpopulatoin)

description: sperm subpopulation from the 0.35 layer of Donor O

source_name: Donor O

value: Male


title: Healthy airway smooth muscle following treatment with 10% FBS for 8H, patient 3


title: sperm genomic DNA from Donor P (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor P

source_name: Donor P


title: Amplified DNA_GW2_1e6 cells_rep2

description: Amplified DNA


title: Amplified DNA_Strain 195 Combined 4_rep3

description: Amplified DNA

value: Pure culture


title: Amplified DNA_GW2_1e6 cells_rep1

description: Amplified DNA


title: sperm genomic DNA from Donor Q (0.35 subpopulatoin)

description: sperm subpopulation from the 0.35 layer of Donor Q

source_name: Donor Q


title: sperm genomic DNA from Donor P (0.35 subpopulatoin)

description: sperm subpopulation from the 0.35 layer of Donor P


title: Amplified DNA_Strain 195 Combined 4_rep2

description: Amplified DNA


title: None-induced, technical rep1

description: expression before wtp53 induction


title: Amplified DNA_Strain 195 Combined 4_rep1

description: Amplified DNA


title: Amplified DNA_Strain 195 Sample 2_rep3

description: Amplified DNA


title: MDA-MB-231/shDBC1, biological rep2

city: Seoul

first: Jeong

middle: Hoon

last: Kim

address: Irwon-dong Gangnam-gu

country: South Korea

institute: Sungkyunkwan University

description: Gene expression data from MDA-MB-231 cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Image analysis was performed by Affymetrix GCOS Software, and data was normalized by RMA.

source_name: MDA-MB-231 breast cancer cells

label_protocol: Total RNA was reverse-transcribed, and the double stranded cDNAs were used to generate biotin-labeled cRNA.

growth_protocol: MDA-MB-231 cells were grown in DMEM supplemented with 10% FBS.

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen)

treatment_protocol: No treatment

value: shRNA against DBC1 (shDBC1)


title: sperm genomic DNA from Donor O (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor O


title: Amplified DNA_Strain 195 Sample 2_rep1

description: Amplified DNA


title: Amplified DNA_Strain 195 Sample 1_rep3

description: Amplified DNA


title: d3fl_CAB1757


title: sperm genomic DNA from Donor Q (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor Q


title: Amplified DNA_Strain 195 Sample 1_rep2

description: Amplified DNA


title: gDNA_AD14_rep1

description: Genomic DNA


title: MDA-MB-231/shDBC1, biological rep1


title: Amplified DNA_Strain 195 Sample 1_rep1

description: Amplified DNA


title: sperm genomic DNA from Donor N (0.35 subpopulatoin)

description: sperm subpopulation from the 0.35 layer of Donor N

source_name: Donor N


title: Rhipicephalus microplus vs.  Rhipicephalus decoloratus biological replicate 1, Technical replicate

city: Pretoria

first: Christian

last: Stutzer

state: Gauteng

address: Lynnwood road

department: Biochemistry

country: South Africa

institute: University of Pretoria

description:
Technical replicate of biological replicate 1. Midguts, harvested after 20 days post infestation.
Rm1R vs Rd1R
Pair-wise comparisons for R. microplus (Rm) and R. decoloratus (Rd): midgut vs midgut with biological replicates (1-3) and a technical replicate (1R).

hyb_protocol: Hybridization was performed at 65oC for 17 hours. Prior to scanning, each slide was washed, rinsed and dried in Stabilization and Drying Solution (Agilent Technologies, USA). Following a drying step, slides were scanned with the GenePixTM 4000B microarray laser scanner (Molecular devices Inc., USA).Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on a 4000B microarray laser scanner (Molecular devices Inc., USA) Images were quantified using GenepixPro feature extraction software (v6.0, Axon Molecular Devices, USA).

data_processing:
Normalization within slides was performed using the Limma package in R (http://CRAN.R-project.org), employing the locally weighted scatterplot smoothing (LOWESS) technique, followed by Aquantile normalization between slides.
The Limma package was also used to calculate the fold change between the pair-wise comparison, to identify significantly differentially expressed transcripts with p-values adjusted for multiple comparisons false discovery rates.

organism: Rhipicephalus microplus

source_name: Midgut

label_protocol: 3 µg of high quality DNaseI-treated total RNA was used for cDNA synthesis using 500 U SuperscriptTM III (InvitrogenTM life technologies, USA), a poly-dT primer (250 pmol), random nanomers (775 pmol) and 5 mM each dATP, dTTP, dGTP, with 5 mM aminoallyl dUTP for Cyanine 3-dCTP/Cyanine 5-dCTP dye coupling.  DNA was primed at 70°C for 10 min, then reversed transcribed at 42°C for 16 h.

growth_protocol: R. microplus (Mozambique strain) larvae, hatched at 25oC (75-85% humidity), were allowed to feed on Holstein-Friesian cattle.

extract_protocol: Total RNA was isolated according to manufacturer’s guidelines for TRI REAGENT

tag: age

value: day 20

tag: strain

value: Mozambique

organism: Rhipicephalus decoloratus


title: sperm genomic DNA from Donor M  (0.35 subpopulatoin)

description: sperm subpopulation from the 0.35 layer of Donor M

source_name: Donor M

tag: gender


title: MDA-MB-231/shNS, biological rep2

value: Non-specific shRNA (shNS)


title: MDA-MB-231/shNS, biological rep1


title: sperm genomic DNA from Donor N (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor N


title: Rhipicephalus microplus vs.  Rhipicephalus decoloratus biological replicate 3

description:
Biological replicate 3 of 3. Midguts, harvested after 20 days post infestation.
Rm3 vs. Rd3
Pair-wise comparisons for R. microplus (Rm) and R. decoloratus (Rd): midgut vs midgut with biological replicates (1-3) and a technical replicate (1R).


title: Rhipicephalus microplus vs.  Rhipicephalus decoloratus biological replicate 2

description:
Biological replicate 2 of 3. Midguts, harvested after 20 days post infestation.
Rd2 vs. Rm2
Pair-wise comparisons for R. microplus (Rm) and R. decoloratus (Rd): midgut vs midgut with biological replicates (1-3) and a technical replicate (1R).


title: Rhipicephalus microplus vs.  Rhipicephalus decoloratus biological replicate 1

description:
Biological replicate 1 of 3. Midguts, harvested after 20 days post infestation.
Rd1 vs. Rm1
Pair-wise comparisons for R. microplus (Rm) and R. decoloratus (Rd): midgut vs midgut with biological replicates (1-3) and a technical replicate (1R).


title: 2day18hrs-Ozone4

city: Durham

first: William

last: Ward

state: NC

address: 109 TW Alexander Dr

department: NHEERL

institute: United States EPA

description: replicate 4

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were normalised using PLIER-PM-Only in Affymetrix Expression Console (Build 1.3.1.187).

organism: Rattus norvegicus

label_protocol: Biotinylated cRNA were prepared with the Affymetrix protocol for HT-Rat-230 PM arrays.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit with DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser and quantified by NanoDrop spectrophotometer.

value: Wistar Kyoto (WKY)

value: male

value: 10 week old

tag: weight

tag: exposed to

value: Ozone at 1 ppm

tag: exposure time

value: 6h/day for 2day

tag: harvest time point

value: 18 hours after the 6 hour exposure period on the 2nd day

value: liver


title: 2day18hrs-Ozone5

description: replicate 5

tag: tissue


title: sperm genomic DNA from Donor L (0.35 subpopulatoin)

description: sperm subpopulation from the 0.35 layer of Donor L

source_name: Donor L


title: sperm genomic DNA from Donor L (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor L


title: Case_3_mother

description:
profiling of germline copy number variations
Mother3

hyb_protocol: Labeled DNA was mixed with Hybridization buffer, Blocking Agent and Cot-1 DNA and heated for 3 minutes at 95 C followed by incubation at 37 C for 30 minutes. Hybridization was carried out in Agilent SureHyb chambers using microarray slides and gasket slides for 40 hours at 65 C followed by sequential washes according to the manufacturer's protocol.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Data processing was performed using Feature Extraction and DNA analytics software (Agilent)

source_name: whole blood sample

label_protocol: 1 microgram DNA was labeled with Cy5 (case) or Cy3 (controls) using Exo-Klenow enzyme according to the manufacturer's specifications (Agilent Array-Based CGH for Genomic DNA Analysis version 4.0, June 2006).

extract_protocol: DNA was extracted from whole blood using Qiagen genomic DNA extraction kit following manufacturer's specifications

value: female

value: whole blood

source_name: whole blood from 100 female controls

value: pool of DNA from whole blood samples of 100 female controls


title: Case_3_father

description:
profiling of germline copy number variations
Father3

source_name: whole blood from 100 male controls

value: pool of DNA from whole blood samples of 100 male controls


title: Case_3_child

description:
profiling of germline copy number variations
Child3


title: CD4_60hr_Ctrl

city: Boston

first: Vijay

middle: K

last: Kuchroo

state: MA

address: 77 Ave Louis Pasteur

department: Evergrande Center for Immunologic Diseases

institute: Brigham and Women's Hospital

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix microarray HT_MG-430A. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
Data were analyzed by GenePattern suite with RMA correction.
Data were processed using the RMA algorithum followed by quantile normalization.

source_name: Untreated CD4+ T cells

label_protocol: Biotinylated cRNA were prepared by following the standard Affymetrix protocol from 100 ng total RNA (3' IVT Express Kit, Affymetrix).

growth_protocol: Naïve CD4+ T cells from C57BL/6J mice were activated by plate-bound anti-CD3 and anti-CD28 antibodies for 60 hours.

extract_protocol: Total RNA were extracted from cultured cells 60 hours after activation according to the RNeasy Mini Kit (Qiagen) manufacturer's instructions..

treatment_protocol: Cells were treated either without or with the presence of 25 ng/ml of murine recombinant IL-27 (R&D systems).

value: peripheral lymphoid organs; spleen lymph nodes

tag: cell type

value: Naïve CD4+ T cells

tag: stimulated by

value: plate-bound anti-CD3 and anti-CD28 antibodies for 60 hrs


title: 2day18hrs-Ozone2

description: replicate 2


title: CD4_60hr_IL-27

source_name: IL-27-treated CD4+ T cells

value: plate-bound anti-CD3 and anti-CD28 antibodies for 60 hrs in the presence of IL-27


title: 2day18hrs-Ozone3

description: replicate 3


title: 2day18hrs-Ozone1

description: replicate 1


title: FD_RECTAS_rep3

city: Kyoto-shi, Sakyo-ku

first: Mayumi

last: Yoshida

state: Kyoto-fu

address: Yoshida-Konoe-cho

department: Anatomy and Developmental Biology

description: RNA expression value derived from Expression Console software; full-exon analysis

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned.

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

data_processing: Raw data were processed with the Expression Console 1.2.1.20 (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed according to the method descrived in a previous plublication (Yamashita et al. J. Hum. Genet. 57, 368-374).

source_name: fibroblast FD, RECTAS 2µM, rep3

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Expression Kit (Ambion) and then fragmented and labeled with the WT Terminal Labelingand and Controls Kit (Affymetrix).

growth_protocol: Fibroblast cells derived from FD patient were plated on 6-well plate at 1 x 10^5 cells/well in 2mL medium (DMEM supplimented with 15% fetal bovine serum).

extract_protocol: Total RNA from the fibroblast of control (DMSO) and treated (2 µM RECTAS) were extracted using TRIzol reagent according to the manufacturer’s instructions.

treatment_protocol: After 3 days from plating, cells were treated with 0.1% DMSO (for control) or 2 µM RECTAS (for treated) in fresh medium at 37ºC and 5% CO2 for 6 hours.

value: FD patient fibroblast

value: RECTAS


title: sperm genomic DNA from Donor M  (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor M

value: Male


title: 2day18hrs-Air5

description: replicate 5

value: Wistar Kyoto (WKY)

value: male

value: filtered air (FA)


title: sperm genomic DNA from Donor J (0.35 subpopulatoin)

description: sperm subpopulation from the 0.35 layer of Donor J

source_name: Donor J


title: sperm genomic DNA from Donor K (0.35 subpopulatoin)

description: sperm subpopulation from the 0.35 layer of Donor K

source_name: Donor K


title: FD_DMSO_rep2

source_name: fibroblast FD, DMSO, rep2

value: DMSO


title: 2day18hrs-Air4

description: replicate 4

value: 10 week old

value: 6h/day for 2day

value: 18 hours after the 6 hour exposure period on the 2nd day


title: 2day18hrs-Air3

description: replicate 3

value: liver


title: Twin 2_t

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

description: Testicular_Cancer_A12_AC_Camargo_Hospital

hyb_protocol: Hybridization was performed using Agilent Human CGH 44K Oligo Microarrays according to the manufacturer’s instructions.

scan_protocol: The array images were acquired using a DNA microarray scanner with Surescan High- Resolution Technology (Agilent Technologies, Santa Clara, CA) and Scan Control (version 8.1, Agilent Technologies) software programs. Images were quantified using Agilent Feature Extraction Software version v.10.1.1.1 (Agilent Technologies, CA, USA).

data_processing: Statistical analysis was performed using the Nexus Copy Number software (version 6.0, Biodiscovery Inc., El Segundo, CA, USA). The Fast Adaptive States Segmentation Technique 2 (FASST2) algorithm and Significance Testing for Aberrant Copy number (STAC) statistical methods were used to identify non-random genomic copy-number alterations [23]. According to these algorithms, DNA copy number alteration was defined as follows: exceeding the significance threshold of 1×10−5; containing at least three consecutive altered probes per segment; and specified 1000 kb as being the maximum spacing between adjacent probes. These parameters were used to define the values for copy number gains (log2≥ 0.2), high copy number gains (log2≥ 0.6), losses (log2≤ -0.2) and homozygous losses (log2≤ -1.0).

source_name: seminoma

label_protocol: The Peripheral blood samples, tumors and reference genomic DNA (Promega, G1471, male) were differentially labeled using a Genomic DNA Enzymatic Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: Not applicable

extract_protocol: Blood samples and formalin fixed paraffin-embedded tumors, one embryonal carcinoma (Twin-1t) and one seminoma (Twin-2t), were macro-dissected and genomic DNA extracted using a standard phenol/chloroform method.

value: tumor

source_name: Reference genomic DNA (Promega, G1471, male)


title: FD_RECTAS_rep1

source_name: fibroblast FD, RECTAS 2µM, rep1


title: 2day18hrs-Air2

description: replicate 2


title: 2day18hrs-Air1

description: replicate 1


title: sperm genomic DNA from Donor K (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor K


title: Amplified DNA_Strain 195 Sample 2_rep2

description: Amplified DNA

source_name: 1 µg of DNA

value: Pure culture

value: Amplified DNA


title: 2day0hrs-Ozone5

description: replicate 5

value: Ozone at 1 ppm

value: at the end of the of the 2nd day 6 hour exposure period


title: Twin 1_t

description: Testicular_Cancer_A10_AC_Camargo_Hospital

source_name: embryonal carcinoma


title: 2day0hrs-Ozone4

description: replicate 4


title: 2day0hrs-Ozone3

description: replicate 3


title: 2day0hrs-Ozone2

description: replicate 2


title: sperm genomic DNA from Donor J (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor J


title: sperm genomic DNA from Donor I (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor I

source_name: Donor I


title: Twin 2_b

source_name: blood sample

value: blood sample


title: 2day0hrs-Ozone1

description: replicate 1


title: sperm genomic DNA from Donor H (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor H

source_name: Donor H


title: sperm genomic DNA from Donor H (0.35 subpopulatoin)

description: sperm subpopulation from the 0.35 layer of Donor H


title: FD_DMSO_rep1

source_name: fibroblast FD, DMSO, rep1

value: FD patient fibroblast


title: sperm genomic DNA from Donor I (0.35 subpopulatoin)

description: sperm subpopulation from the 0.35 layer of Donor I


title: 2day0hrs-Air5

description: replicate 5


title: FD_DMSO_rep3

source_name: fibroblast FD, DMSO, rep3


title: Mother_b

value: female


title: Vpara_stationary_rep8

city: Berlin

first: Stephan

last: Huehn

address: Koenigsweg 69

institute: Freie Universität Berlin

description: bacterial cell culture incubated at 37°C for 7 h

hyb_protocol: Finally 600 ng of the labelled and linear amplified cRNA (specific activity 9,0 pmol Cy3/µg cRNA) was fragmented, added to 25 µl Agilent-hybridization buffer resulting in 480 ng loaded on a microarray in a hybridization chamber (following manufacturers instructions). The hybridization was performed at 65°C for 17 hours and 10 rpm.  Washing of the slides was performed using preheated washing buffer (Gene expression wash buffer kit, Agilent). First the chamber was rinsed with washing buffer. Then the slides were washed once followed by a second wash using washing buffer containing 0.01% Triton X-102 (Agilent). The slides were dried using acetonitrile.

scan_protocol: Scanning was carried out immediately after washing using the Agilent G2565CA scanner with a resolution of 5 µm.

data_processing: After scanning, tiff-files were analysed and raw data was extracted using Feature Extraction Software (Agilent). Data processing was performed using Bioconductor V 2.12 package of the software R. At first, filtering of bad quality spots was performed and the data was background corrected with normexp method using offset = 50.

organism: Vibrio parahaemolyticus RIMD 2210633

label_protocol: Reverse transcription of the RNA was performed. Briefly 200 ng of RNA were linear amplified using the full spectrum MultiStart primer (Biocat, Heidelberg, Germany) and Moloney murine leukemia virus (MMLV) reverse transcriptase (Agilent). The amplification was performed at 40°C for 2 hours followed by 65°C for 15 minutes and stored at 4°C. Labelling was performed using the Quick Amp Labeling Kit (Agilent). Briefly the amplified cDNA, the full spectrum MultiStart primer and T7 RNA polymerase were used along with Cyanine 3-CTP. Labeled cRNA was purified using the Qiagen RNeasy Mini Kit (Qiagen). A 3 µl-aliquot was used for quality control (NanoDrop 2000, Thermo Scientific).

growth_protocol: Prior use, the strain was stored in cryovials at -80°C (Cryobank; Mast Diagnostica, Bootle, England). For initial growth, cells were grown using a rotary shaker (Unimax 1010 and Incubator 1000; Heidolph, Schwabach, Germany) in alkaline peptone water (APW; 0.3% Yeast-Extract, 1% Peptone, 2% NaCl; pH 8.6) at 37°C overnight.A 50 μL aliquot of the resulting culture was then diluted into 50 mL APW and grown at 37 °C for 4 h and 7 h, respectively, in order to generate exponential phase and early stationary phase cultures.

extract_protocol: Total RNA was isolated using the peqGold Bacterial RNA Kit (Peqlab, Erlangen, Germany). Obtained RNA was eluted into 43 µl of DEPC-treated, DNase- and RNase-free water (Carl Roth, Karlsruhe, Germany). Samples were then treated by DNase I along with an RNase-A, -B and -C inhibitor (Fermentas, Vilnius, Lithuania). RNA quantity was measured by spectrophotometry (NanoDrop 2000, Thermo Scientific). RNA quality of each sample was monitored via gel electrophoresis. Additionally, the RNA quality was assessed using the Agilent RNA 6000 Nano Kit on a 2100 Bioanalyzer (Agilent, Santa Clara, US).

treatment_protocol: The cultures were centrifuged (2 minutes, 8000 x g) and the supernatant was discarded. The pellet was immediately resuspended in 1.5 ml RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany) to minimize RNA degradation.

tag: cell

value: whole cell

tag: growth phase

value: early stationary phase


title: 2day0hrs-Air1

description: replicate 1

value: Wistar Kyoto (WKY)

value: male


title: FD_RECTAS_rep2

source_name: fibroblast FD, RECTAS 2µM, rep2

tag: treatment

value: RECTAS


title: sperm genomic DNA from Donor G (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor G

source_name: Donor G

value: Male

tag: gradient layer


title: sperm genomic DNA from Donor G (0.35 subpopulatoin)

description: sperm subpopulation from the 0.35 layer of Donor G


title: Father_b


title: Vpara_stationary_rep7

source_name: bacterial cell culture incubated at 37°C


title: 1day0hrs-Ozone6

description: replicate 6

value: 10 week old

value: 6h/day for 1day

value: at the end of the 6 hour exposure period


title: 2day0hrs-Air4

description: replicate 4

value: filtered air (FA)

value: 6h/day for 2day

value: liver


title: 2day0hrs-Air2

description: replicate 2


title: sperm genomic DNA from Donor F (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor F

source_name: Donor F


title: sperm genomic DNA from Donor F (0.35 subpopulatoin)

description: sperm subpopulation from the 0.35 layer of Donor F


title: 2day0hrs-Air3

description: replicate 3


title: Vpara_stationary_rep5


title: Vpara_stationary_rep4


title: 1day0hrs-Ozone4

description: replicate 4

value: Ozone at 1 ppm


title: 1day0hrs-Ozone5

description: replicate 5


title: Vpara_stationary_rep3


title: 1day0hrs-Ozone3

description: replicate 3


title: Vpara_stationary_rep6


title: sperm genomic DNA from Donor D (0.35 subpopulatoin)

description: sperm subpopulation from the 0.35 layer of Donor D

source_name: Donor D


title: 1day0hrs-Ozone2

description: replicate 2


title: Vpara_stationary_rep2


title: 1day0hrs-Air6

description: replicate 6


title: sperm genomic DNA from Donor C (0.35 subpopulatoin)

description: sperm subpopulation from the 0.35 layer of Donor C

source_name: Donor C


title: sperm genomic DNA from Donor E (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor E

source_name: Donor E


title: sperm genomic DNA from Donor D (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor D


title: Vpara_exponential_rep6

description: bacterial cell culture incubated at 37°C for 4 h

value: exponential phase


title: Vpara_exponential_rep8


title: Vpara_stationary_rep1


title: Twin 1_b

value: blood sample


title: 1day0hrs-Air5

description: replicate 5


title: G2B2 - Condition: glucose, Biological Replicate: 2, Preparation: B, Chip 2

city: Princeton

first: David

middle: Garrett

last: Robinson

state: New Jersey

address: Washington Road

department: Lewis-Sigler Institute

institute: Princeton University

hyb_protocol: Each cRNA library was hybridized on two separate chips (Yeast Expression 8x15K arrays)

scan_protocol: Scanned on an Agilent G2505B Scanner

data_processing: Images were quantified using Agilent Feature Extraction Software. Probes were filtered for genes that also appeared in the RNA-Seq parallel experiment (PRJNA271248) and then quantile normalized using limma's normalizeBetweenArrays.

organism: Saccharomyces cerevisiae

source_name: yeast grown on glucose on chemostat

label_protocol: The 4 RNA samples were processed twice on different days using the Agilent Quick Amp Labeling kit (Part no. 5190-0424) to produce 8 cRNA libraries

growth_protocol: The experiment was performed using yeast haploid strain DBY 12000 FY, a S288C derivative containing the wild-type HAP1 allele.  A single colony was split into 2 overnight cultures, one containing ethanol limitation medium with 60 C-mM and the other containing glucose limitation medium with 27 C-mM Carbon as the carbon source. 1 mL of each culture was used to inoculate a chemostat. This was done in two separate batches for biological replicates

extract_protocol: After the chemostats reached stasis, 10 ml culture was collected and frozen at -80C as in http://dunham.gs.washington.edu/MDchemostat.pdf

tag: condition

value: glucose

tag: biological replicate

tag: preparation

value: B

tag: ChIP

source_name: Pooled samples

tag: reference

value: Pooled samples


title: Vpara_exponential_rep7

value: whole cell


title: G2B1 - Condition: glucose, Biological Replicate: 2, Preparation: B, Chip 1


title: 1day0hrs-Ozone1

description: replicate 1

tag: strain

value: Wistar Kyoto (WKY)

tag: gender

tag: age


title: G2A2 - Condition: glucose, Biological Replicate: 2, Preparation: A, Chip 2

value: A


title: 1day0hrs-Air4

description: replicate 4

value: male

tag: weight

tag: exposed to

tag: exposure time


title: Vpara_exponential_rep5


title: sperm genomic DNA from Donor C (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor C

value: Male


title: Fallopian tube exposed 2h (Eh_15o)

city: GÖTEBORG

first: Anna

last: Bylander

address: Guldhedsgatan 10A

department: Biomedicine

country: Sweden

institute: Göteborgsuniversitet

scan_protocol: Standard Illumina iScan N240 scanning protocol

data_processing: The data were normalized using quantile normalization with BASE

source_name: Fallopian tube

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevD, (Modification of Amplification kit v 2.2)

extract_protocol: Total RNA was extracted using the RNeasy Plus micro Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Mice fallopian tubes were exposed in vitro to prpgesterone fo 20 min or 2 h.

value: Female

tag: tissue

value: Fallopian tube

value: exposed in vitro to progesterone

tag: time


title: 1day0hrs-Air3

description: replicate 3

value: 10 week old

value: filtered air (FA)

value: 6h/day for 1day

tag: harvest time point

value: at the end of the 6 hour exposure period


title: sperm genomic DNA from Donor B (0.35 subpopulatoin)

description: sperm subpopulation from the 0.35 layer of Donor B

source_name: Donor B


title: sperm genomic DNA from Donor E (0.35 subpopulatoin)

description: sperm subpopulation from the 0.35 layer of Donor E


title: sperm genomic DNA from Donor A (0.35 subpopulatoin)

description: sperm subpopulation from the 0.35 layer of Donor A

source_name: Donor A


title: G1B1 - Condition: glucose, Biological Replicate: 1, Preparation: B, Chip 1


title: G1B2 - Condition: glucose, Biological Replicate: 1, Preparation: B, Chip 2


title: G1A1 - Condition: glucose, Biological Replicate: 1, Preparation: A, Chip 1


title: G1A2 - Condition: glucose, Biological Replicate: 1, Preparation: A, Chip 2


title: E2B1 - Condition: ethanol, Biological Replicate: 2, Preparation: B, Chip 1

source_name: yeast grown on ethanol on chemostat

value: ethanol


title: Vpara_exponential_rep2

tag: cell

tag: growth phase

value: exponential phase


title: Vpara_exponential_rep1


title: 1day0hrs-Air2

description: replicate 2

value: liver


title: Vpara_exponential_rep4


title: Vpara_exponential_rep3


title: 1day0hrs-Air1

description: replicate 1


title: Fallopian tube exposed 2h (Kh_15o)

tag: treatment

value: Control


title: G2A1 - Condition: glucose, Biological Replicate: 2, Preparation: A, Chip 1

tag: condition

value: glucose

value: Pooled samples


title: Fallopian tube exposed 2h (Kh_19n)


title: E2B2 - Condition: ethanol, Biological Replicate: 2, Preparation: B, Chip 2

tag: biological replicate

value: B


title: colon 4-13 (HPM)

city: Shanghai

first: Kai

last: Wei

address: 130 Dong'an Road, Xuhui District, Shanghai, China

institute: Shanghai Medical College of Fudan University

description: Experimental animals were male and commercially-available SD rats (SCXK, Shanghai, China).

hyb_protocol: The Hy3™-labeled samples were hybridized on the miRCURY™ LNA Array (v.18.0) (Exiqon) according to array manual.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities≥30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, the differences in miRNA expression were considered significant if 1) fold change > 2.0; and 2) analysis of variance or nonparametric test, P-value < 0.05.

source_name: Colon

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline, of which only Hy3 was used for miRNA labeling.

growth_protocol: All rats were raised in specific pathogen-free room and the room was maintained at a constant temperature of 23℃ with a 12 h light/dark cycle. Food and water were available ad libitum in the home cages.

extract_protocol: Total RNA including miRNA from the colon samples was extracted using TRIzol (Invitrogen) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-2000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: The CD models were prepared according to Morris’ method, and HPM treatment was performed one session a day for totally 7 days. After treatment, all rats were deeply anesthetized with pentobarbital sodium and then distal colons (6~8 cm) were rapidly dissected.

value: Colon

value: 8 weeks old

tag: group

value: herb-partitioned moxibustion


title: colon 4-11 (HPM)


title: Fallopian tube exposed 2h (Kh_6d)

value: Female


title: colon 4-9 (HPM)


title: E2A2 - Condition: ethanol, Biological Replicate: 2, Preparation: A, Chip 2

tag: preparation

value: A

tag: ChIP


title: Fallopian tube exposed 2h (Eh_19n)

tag: strain

value: Fallopian tube

value: exposed in vitro to progesterone


title: Fallopian tube exposed 20min (Em_22ob)

tag: gender


title: colon 2-10 (MC)

tag: age

value: model control


title: colon 4-10 (HPM)


title: E2A1 - Condition: ethanol, Biological Replicate: 2, Preparation: A, Chip 1

tag: reference


title: Partially reprogrammed cell line

city: Stanford

first: Marius

last: Wernig

address: 265 Campus Drive, 3rd Floor

department: Pathology

institute: Stanford University

hyb_protocol: Per Affymetric protocol (performed by Stanford PAN Facility)

data_processing:
Data was normalized and gene names were assigned by Partek Genomic Suite.  Preprocessing (floor = 100, ceiling = 20000) was generated by Gene Pattern (http://www.broadinstitute.org/cancer/software/genepattern/).
probe group file: MoGene-2_0-st.pgf
meta-probeset file: MoGene-2_0-st.mps

label_protocol: Affymetrix GeneChip WT Terminal Labeling kit (Performed by Stanford PAN Facility)

growth_protocol: MEFs were cultured in MEF medium which consisted of 10% cosmic calf serum (Thermo Scientific) in DMEM (Invitrogen) supplemented with non-essential amino acids (Invitrogen), penicillin-streptomycin (Invitrogen), sodium pyruvate (Invitrogen) and 2-mercaptoethanol (Invitrogen). Our partially reprogrammed line was grown in MEF medium supplemented with 15% cosmic calf serum. mouse ES cells were grown in mESC medium which consisted of 12% knockout replacement serum (Invitrogen), 3% cosmic calf serum and supplemented with non-essential amino acids, penicillin-streptomycin, sodium pyruvate, 2-mercaptoethanol and LIF.

extract_protocol: RNA of reprogramming populations for microarray analysis was prepared from Rosa-rtTA+/- day 6 and day 9 reprogramming cultures double sorted for CD73 or CD49d.  RNA of control populations for microarray analysis was prepared from Rosa-rtTA+/- MEFs (passage 4), partially reprogrammed cells (passage 10) and V6.5 mouse ESCs (passage 11).  RNA was prepared with RNeasy Mini Kit (Qiagen) and DNA was removed by on-column RNase-Free DNase treatment (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Reprogramming assays were conducted with passage 4 Rosa-rtTA+/- mouse embryonic fibroblasts.  Passage 3 MEFs s were split onto 10cm 0.2% gelatin coated plates at 250,000 cells per plate one day before infection.   Cells were infected with tetO-Klf4, tetO-Oct4, tetO-Myc and tetO-Sox2 in MEF medium supplemented with polybrene (8 μg/mL; Sigma).  One day after infection, MEF medium supplemented with doxycycline was added and this was considered to be day 0.  Media was replaced every 2 days.

tag: cell type

value: partially reprogrammed cells (SC4)

tag: cell subtype

value: control population

tag: reprogramming day


title: Fallopian tube exposed 20min (Km_22ob)

tag: tissue

tag: time


title: sperm genomic DNA from Donor B (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor B

value: Male

tag: gradient layer


title: sperm genomic DNA from Donor A (0.9 subpopulatoin)

description: sperm subpopulation from the 0.9 layer of Donor A


title: Mouse embryonic stem cells

description: mESC

scan_protocol: Per Affymetric protocol (performed by Stanford PAN Facility)

source_name: V6.5 mESCs

value: mouse embryonic stem cell (ESC)


title: Fallopian tube exposed 2h (Eh_30o)


title: E1B2 - Condition: ethanol, Biological Replicate: 1, Preparation: B, Chip 2

value: ethanol


title: E1B1 - Condition: ethanol, Biological Replicate: 1, Preparation: B, Chip 1


title: Fallopian tube exposed 2h (Eh_6d)


title: colon 2-8 (MC)


title: colon 2-3 (MC)


title: colon 2-1 (MC)


title: E1A2 - Condition: ethanol, Biological Replicate: 1, Preparation: A, Chip 2


title: Fallopian tube exposed 20min (Km_12n)

value: Control


title: colon 1-3-1 (NC)

value: normal control


title: E1A1 - Condition: ethanol, Biological Replicate: 1, Preparation: A, Chip 1

value: Pooled samples


title: Day 9 Total

description: Day 9 Total

source_name: Rosa-rtTA MEFs +/- infected with KOSM

value: Rosa-rtTA MEFs +/- infected with KOSM

value: unsorted total reprogramming sample

value: Day 9


title: Fallopian tube exposed 20min (Em_12n)


title: Fallopian tube exposed 20min (Km_26n)


title: Day 9 CD73+

description: Day 9 73+

value: double sorted, poised (CD73+) reprogramming samples


title: Fallopian tube exposed 20min (Em_27n)

value: Female


title: colon 1-4-1 (NC)

value: Colon

value: 8 weeks old


title: colon 1-5-1 (NC)


title: colon 1-8-1 (NC)


title: Mouse embryonic fibroblasts

description: MEF

source_name: Rosa-rtTA MEFs +/-

value: Rosa-rtTA MEFs +/-


title: Fallopian tube exposed 20min (Km_27n)

value: Fallopian tube


title: Day 6 Total

description: Day 6 Total

value: Day 6


title: Day 9 CD49d+

description: Day 9 49+

value: double sorted, poised (CD49d+) reprogramming sample


title: Day 6 CD73-

description: Day 6 73-

value: double sorted, non-poised (CD73-) reprogramming samples


title: 131I_thyroid_C

city: Göteborg

first: Nils

last: Rudqvist

state: VG

address: Gula stråket 2b

institute: Gothenburg university

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

source_name: Mouse thyroid, 17 Gy, 24h

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

value: Balb/c

value: thyroid

tag: absorbed dose

value: 17 Gy


title: Day 6 CD73+

description: Day 6 73+


title: 131I_thyroid_D

source_name: Mouse thyroid, 0 Gy, 24h

value: 0 Gy


title: Mirtazapine_rep1

status: Public on Jan 30 2015

city: Chuoshi

first: Kunio

last: Miyake

state: Yamanashi

address: 1110 Shimokato

institute: Yamanashi University

hyb_protocol: Following fragmentation, 7 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Expression Console Software, Genespring GX, RMA

source_name: Primary neuron, treatment of mirtazapine, 48 hr

label_protocol: cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA. Single-stranded DNA were labeled using the GeneChip® WT Terminal Labeling Kit

growth_protocol: Primary neuronal cultures were suspended in Neurobasal media (Life Technologies Ltd, Carlsbad, CA) supplemented with 1% L-glutamine, penicillin/streptomycin, and B27 serum-free supplement

extract_protocol: Total RNA was performed according to the manufacturer's instructions

treatment_protocol: cultured cells were used to evaluate 48 hour effects of antidepressants. Briefly, cultured neurons at day in vitro 3 (DIV3) were treated with 5µM imipramine, 10 µM citalopram, 0.1 µM duloxetine, 5 µM amitriptylline, 50 µM mirtazepine. These cultures were harvested after 48 hours (DIV5)

value: ICR (CD-1)

value: brain

tag: culture type

value: primary neuronal

tag: developmental stage

value: embryo


title: Day 9 CD73-

description: Day 9 73-

value: Rosa-rtTA MEFs +/- infected with KOSM

value: Day 9


title: 131I_thyroid_B

source_name: Mouse thyroid, 8.5 Gy, 24h


title: Imipramine_rep1

source_name: Primary neuron, treatment of imipramine, 48 hr


title: Day 6 CD49d+

description: Day 6 49+


title: Citalopram_rep2

source_name: Primary neuron, treatment of citalopram, 48 hr


title: Duloxetine_rep2

source_name: Primary neuron, treatment of duloxetine, 48 hr


title: Control_rep2

source_name: Primary neuron, treatment of control, 48 hr


title: Duloxetine_rep1


title: Case_2_sibling_1

city: Utrecht

first: Wigard

last: Kloosterman

address: Universiteitsweg 100

description:
Genomic DNA extracted from sample was genotyped using Illumina HumanCNV370-QuadV3 DNA Analysis BeadChip.
C2_Sibling1

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

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

source_name: DNA from blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (MSM) and primer/neutralization mix (MA1-MA2-0.1N NaOH). After incubation the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol and resuspended in hybridization buffer (RA1).

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

value: male

value: blood

tag: disease state

value: not applicable


title: Control_rep1


title: Amitriptyline_rep1

source_name: Primary neuron, treatment of amitriptyline, 48 hr


title: 131I_thyroid_A

source_name: Mouse thyroid, 0.85 Gy, 24h


title: Mirtazapine_rep2


title: Imipramine_rep2


title: Citalopram_rep1


title: Amitriptyline_rep2


title: Fallopian tube exposed 2h (Kh_30o)

source_name: Fallopian tube

value: Female

value: Fallopian tube

tag: treatment

value: Control


title: U251-shHOXA9_Replicate1

city: Braga

first: Bruno

middle: M.

last: Costa

address: Universidade do Minho, Campus de Gualtar

department: Life and Health Sciences Research Institute (ICVS)

country: Portugal

institute: University of Minho

description: Gene expression in U251-shHOXA9 silenced cells.

hyb_protocol: 1.65 µg cyanine 3-labeled and linearly amplified cRNA was fragmented for 30 minutes at 60ºC using the One-Color Microarray-Based Gene Expression Analysis Kit (Quick Amp Labeling; Agilent) according to manufacturer’s instructions for 44K microarrays. Fragmentation was stopped by addition of 2X Hybridization Buffer, and hybridized to an Agilent Microarray Hybridization Chamber Kit (G2534A) for 17 hours at 65ºC in a hybridization oven. Microarrays were then washed with Agilent wash buffers according to manufacturer’s instructions.

scan_protocol: Slides were scanned on the Agilent Technologies Scanner G2505B using one color settings for 44K slides. Dye channel was set to Green, and Green PMT at 100% for HOXA9 overexpression replicates 1, 3 and 4, and 40% for replicate 2, and 80% for all replicates in HOXA9-silenced cell lines.

data_processing: Data is processed using the limma package from Bioconductor: background correction (using the normexp method) is performed, normalisation between arrays is performed using quantile normalisation and the resulting data is transformed using log2. Probes representing control spots are filtered, keeping only the ones with status equal to “Gene”. Replicated probes (same ProbeName) are averaged.

source_name: U251, human glioblastoma cell line; HOXA9 silencing

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1000ng of total RNA using the One-Color Microarray-Based Gene Expression Analysis Kit (Quick Amp Labeling; Agilent) according to the manufacturer’s protocol. cRNA quantification and dye incorporation were checked using a NanoDrop ND-1000 Spectrophotometer and calculated according to the manufacturer’s instructions.

growth_protocol: Cell lines were grown in DMEM supplemented with 10% FBS and 1% Penicillin-Streptomycin, and continuously selected with 500µg/mL G418 (HOXA9-overexpressing cell lines) or 0.5μg/mL puromycin (HOXA9-silenced cell lines).

extract_protocol: Total RNA extracted with RNeasy Total RNA Isolation kit (Qiagen) according to manufacturer's protocol. RNA was quantified by a NanoDrop-1000 spectrophotometer, followed by RNA quality control by RNA Bioanalyzer (Agilent) analyses.

value: U251 glioblastoma

tag: silencing vector


title: GBML18-shControl_Replicate3

description: Gene expression in GBML18-shControl cells.

source_name: GBML18, patient-derived primary human glioblastoma cell line; Control

value: GBML18 glioblastoma

value: shControl


title: U251-shHOXA9_Replicate3


title: U251-shControl_Replicate3

description: Gene expression in U251-shControl cells.

source_name: U251, human glioblastoma cell line; Control


title: U251-shControl_Replicate1


title: GBML18-shHOXA9_Replicate1

description: Gene expression in GBML18-shHOXA9 silenced cells.

source_name: GBML18, patient-derived primary human glioblastoma cell line; HOXA9 silencing


title: U251-shHOXA9_Replicate2


title: GBML18-shHOXA9_Replicate3


title: GBML18-shHOXA9_Replicate2


title: U251-shControl_Replicate2


title: GBML18-shControl_Replicate2


title: Case_2_sibling_2

institute: University Medical Center Utrecht

description:
Genomic DNA extracted from sample was genotyped using Illumina HumanCNV370-QuadV3 DNA Analysis BeadChip.
C2_Sibling2

data_processing: Data processing was done using GenomeStudio (Illumina)


title: U87MG-MSCV Replicate 4

description: Gene expression in glioblastoma U87MG-Control cells.

scan_protocol: Slides were scanned on the Agilent Technologies Scanner G2505B using one color settings for 44K slides. Dye channel was set to Green, and Green PMT at 100% for replicates 1, 3 and 4, and 40% for replicate 2.

source_name: U87MG, human glioblastoma; Control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1000ng of total RNA using the One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling; Agilent) according to the manufacturer’s protocol. cRNA quantification and dye incorporation were checked using a NanoDrop ND-1000 Spectrophotometer and calculated according to the manufacturer’s instructions.

growth_protocol: Cell lines were grown in DMEM supplemented with 10% FBS and 1% Penicillin-Streptomycin, and continuously selected with 500µg/mL G418.

value: U87MG glioblastoma

tag: overexpression vector

value: MSCV-Control


title: U87MG-HOXA9 Replicate 3

description: Gene expression in glioblastoma U87MG-HOXA9 cells.

source_name: U87MG, human glioblastoma; HOXA9 overexpression


title: GBML18-shControl_Replicate1


title: U87MG-MSCV Replicate 3


title: Fallopian tube exposed 20min (Em_26n)

tag: strain

value: exposed in vitro to progesterone


title: U87MG-HOXA9 Replicate 4


title: hTERT/E6/E7-HOXA9 Replicate 4

description: Gene expression in hTERT/E6/E7-HOXA9 overexpressing cells.

source_name: hTERT/E6/E7, immortalized human astrocytes; HOXA9 overexpression

value: hTERT/E6/E7 immortalized human astrocytes


title: U87MG-HOXA9 Replicate 2


title: U87MG-HOXA9 Replicate 1


title: U87MG-MSCV Replicate 1


title: hTERT/E6/E7-HOXA9 Replicate 3


title: hTERT/E6/E7-MSCV Replicate 4

description: Gene expression in hTERT/E6/E7-Control cells.

source_name: hTERT/E6/E7, immortalized human astrocytes; Control


title: hTERT/E6/E7-HOXA9 Replicate 2


title: hTERT/E6/E7-HOXA9 Replicate 1


title: hTERT/E6/E7-MSCV Replicate 3


title: Ab11274, 1.0 ug/mL

type: protein

first: Andrew

last: Gentles

address: 1201 Welch Road

description:
OAEMZL Ab11274
http://www.lifetechnologies.com/us/en/home/life-science/protein-biology/protein-assays-analysis/protein-microarrays/human-protein-microarrays-overview.html
AlexaFluor 647-goat-anti-human IgG
recombinant antibody

hyb_protocol: Performed according to manufacturer's instructions

label: AlexaFluor 647

molecule: protein

source_name: OAEMZL

extract_protocol: The cells were transferred to roller bottles and grown in FreeStyle (Invitrogen) serum-free medium. Supernatants were harvested, and rAbs were purified using protein G beads (Invitrogen) followed by elution with 0.1M glycine (pH 3.0) and neutralization with 1M Tris (pH 8.0).

treatment_protocol: rAb derived form orbital lymphomas were produced in 293T cells

tag: antibody

tag: morphology

value: Orbital Adnexa Marginal Zone lymphoma


title: Ab11274, 0.1 ug/mL

scan_protocol: Performed according to manufacturer's instructions


title: Ab5334, 1.0 ug/mL

description:
OAEMZL Ab5334
http://www.lifetechnologies.com/us/en/home/life-science/protein-biology/protein-assays-analysis/protein-microarrays/human-protein-microarrays-overview.html
AlexaFluor 647-goat-anti-human IgG
recombinant antibody

data_processing: Performed according to manufacturer's instructions


title: Ab4726, 1.0 ug/mL

description:
OAEMZL Ab4726
http://www.lifetechnologies.com/us/en/home/life-science/protein-biology/protein-assays-analysis/protein-microarrays/human-protein-microarrays-overview.html
AlexaFluor 647-goat-anti-human IgG
recombinant antibody

label_protocol: Performed according to manufacturer's instructions


title: Ab5334, 0.1 ug/mL


title: Ab4438, 1.0 ug/mL

description:
OAEMZL Ab4438
http://www.lifetechnologies.com/us/en/home/life-science/protein-biology/protein-assays-analysis/protein-microarrays/human-protein-microarrays-overview.html
AlexaFluor 647-goat-anti-human IgG
recombinant antibody


title: Ab4726, 0.1 ug/mL


title: backcross mouse ID  23711

city: San Francisco

middle: A.

last: Weiss

address: 1450 3rd Street, HD-220

department: Neurology

institute: University of California, San Francisco

description: pooled pair of SCG from single backcross mouse

hyb_protocol: 200 ul of hybridization cocktail were injected into microarrays and hybridized at 45°C for 16 hr at 60 rpm.  Arrays were washed with fluidics station protocol: FS450_0001

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
Expression was based on RMA values assessed using the Bioconductor XPS package in R on only core probes
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: (129xFVBN) F1 x129 backcross mouse

label_protocol: Labeling was performed according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual using kit 900652.

growth_protocol: Superior Cervical Ganglia were dissected from backcrossed mice at time of tumor harvest or 1 year of age

extract_protocol: Total RNA was extracted and purified using the Rneasy mini kit

tag: Sex

tag: tumor

tag: age (days)


title: Ab4438,  0.1 ug/mL


title: hTERT/E6/E7-MSCV Replicate 1

tag: cell type


title: U87MG-MSCV Replicate 2