title: NA21379/NA12878

value: lymphoblast cell line NA21379

value: Northwest European American from Utah (HapMap code:CEU)


title: NA21300/NA12878

status: Public on Feb 01 2011

type: genomic

city: Seattle

first: Catarina

middle: D

last: Campbell

state: WA

address: 3720 15th Avenue NE

department: Genome Sciences

country: USA

institute: Univerisity of Washington

hyb_protocol: The hybridization protocol was performed per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf) with 5 ug of labelled test sample and 5 ug of labelled reference sample (NA12878)

scan_protocol: The scan protocol was performed using the Agilent Scanner per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf).

data_processing: The data were processed using the Agilent Feature Extraction software 10.5.1.1 using program defaults (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf) except that 3000 probes through out the genome were used for dye normalization.

molecule: genomic DNA

organism: Homo sapiens

source_name: lymphoblast cell line DNA [test]

label_protocol: 250 ng of genomic DNA (unsonicated) was labeled by Klenow using random priming with Cy3/Cy5 nonamers (for test and reference samples, respectively) using Nimblegen labelling kit but with the following changes: reagents were scaled to the smaller amount of input DNA and with DNA labeling occurring overnight.

extract_protocol: DNA was extracted from lymphoblast cell lines by Coriell Repositories (http://ccr.coriell.org/)

tag: gender

value: Female

tag: cell line

value: lymphoblast cell line NA21300

tag: ethnicity

value: Maasai from Kinyawa, Kenya (HapMap code:MKK)

source_name: lymphoblast cell line DNA [reference]

value: female

value: lymphoblast cell line NA12878


title: NA21357/NA12878

value: lymphoblast cell line NA21357


title: NA21320/NA12878

value: lymphoblast cell line NA21320


title: NA20818/NA12878

value: lymphoblast cell line NA20818

value: Toscani from Italy (HapMap code:TSI)


title: NA21297/NA12878

value: lymphoblast cell line NA21297


title: NA20819/NA12878

value: lymphoblast cell line NA20819


title: NA20807/NA12878

value: lymphoblast cell line NA20807


title: NA20828/NA12878

value: lymphoblast cell line NA20828


title: NA20816/NA12878

value: Male

value: lymphoblast cell line NA20816


title: NA20813/NA12878

value: lymphoblast cell line NA20813


title: NA20815/NA12878

value: lymphoblast cell line NA20815

value: Northwest European American from Utah (HapMap code:CEU)


title: NOD/LtJTCE liver sample batch 6

type: RNA

city: Chapel Hill

first: Blair

middle: Urquhart

last: Bradford

state: NC

address: 135 Dauer Dr.  CB 7431

department: Environmental Sciences and Engineering

institute: University of North Carolina

description: liver sample batch 6

hyb_protocol: Aglient Hybridization kit catalog # 5190-0404 was followed per manufacturer's instruction

scan_protocol: Agilent scanner G2505A model

data_processing:
Feature Extraction Agilent .  Data was filtered by only accepting those genes with 70% or more values present.
sample batch normalization: Samples were run by batch with the same sample used for batch normalization by COMBAT.

label: cy 3

molecule: total RNA

organism: Mus musculus

source_name: Pooled mouse tissue

label_protocol: Low RNA Input Fluuorescent Linear Amp Kit (Agilent 5184-3253) per manufacturer's instruction.

extract_protocol: Total RNA was extracted from liver using Qiagen mini kit per manufacturer's instruction.  Reference samples were pooled RNA from several organs from C57Bl/6J male mouse.

treatment_protocol: Fed male mice age 7-9 weeks were given 2100 mg/kg trichloroethylene in corn oil (10 ml/kg) by gavage or corn oil as vehicle

tag: strain

value: male

label: Cy 5

source_name: liver

value: NOD/LtJ

tag: treatment

value: TCE


title: NA20811/NA12878

value: lymphoblast cell line NA20811

value: female

value: lymphoblast cell line NA12878


title: NA20826/NA12878

value: Female

value: lymphoblast cell line NA20826


title: NA20805/NA12878

value: lymphoblast cell line NA20805

value: Toscani from Italy (HapMap code:TSI)


title: NA21339/NA12878

value: lymphoblast cell line NA21339

value: Maasai from Kinyawa, Kenya (HapMap code:MKK)


title: KK/HIJTCE liver sample batch 6

description: liver sample batch 6

value: KK/HIJ


title: NA20808/NA12878

value: lymphoblast cell line NA20808


title: NA20812/NA12878

value: Male

value: lymphoblast cell line NA20812


title: NA20802/NA12878

value: lymphoblast cell line NA20802

value: Northwest European American from Utah (HapMap code:CEU)


title: FVB/NJ Vehicle liver sample batch 6

description: liver sample batch 6

value: male

value: FVB/NJ

value: vehicle control


title: DBA/2JTCE liver sample batch 6

description: liver sample batch 6

value: TCE


title: 129S1/SvImJ Vehicle liver sample batch 6

description: liver sample batch 6


title: MOLF/EiJ Vehicle liver sample batch 6

description: liver sample batch 6

value: MOLF/EiJ


title: NA20810/NA12878

value: lymphoblast cell line NA20810

value: female

value: lymphoblast cell line NA12878


title: c57BL/6JTCE liver sample batch 6

description: liver sample batch 6


title: NA20806/NA12878

value: lymphoblast cell line NA20806

value: Toscani from Italy (HapMap code:TSI)


title: NA20799/NA12878

value: Female

value: lymphoblast cell line NA20799


title: NA20800/NA12878

value: lymphoblast cell line NA20800


title: NA20797/NA12878

value: lymphoblast cell line NA20797


title: NA20809/NA12878

value: Male

value: lymphoblast cell line NA20809


title: C3H/HeJ Vehicle liver sample batch 6

description: liver sample batch 6


title: CAST/EiJ Vehicle liver sample batch 6

description: liver sample batch 6

value: CAST/EiJ


title: NA20798/NA12878

value: lymphoblast cell line NA20798

value: Northwest European American from Utah (HapMap code:CEU)


title: NA20795/NA12878

value: lymphoblast cell line NA20795


title: B6C3F1/JTCE liver sample batch 6

description: liver sample batch 6

value: male

value: TCE


title: BTBR+tf/JTCE liver sample batch 6

description: liver sample batch 6

value: BTBR+tf/J


title: NA20787/NA12878

value: lymphoblast cell line NA20787

value: female


title: NA20796/NA12878

value: lymphoblast cell line NA20796

value: lymphoblast cell line NA12878


title: NA20792/NA12878

value: lymphoblast cell line NA20792

value: Toscani from Italy (HapMap code:TSI)


title: NA20786/NA12878

value: Female

value: lymphoblast cell line NA20786


title: NA21295/NA12878

value: Male

value: lymphoblast cell line NA21295

value: Maasai from Kinyawa, Kenya (HapMap code:MKK)


title: c57BL/6JTCE liver sample batch 5

description: liver sample batch 5


title: NZW/LacJ Vehicle liver sample batch 5

description: liver sample batch 5

value: NZW/LacJ

value: vehicle control


title: NA20801/NA12878

value: lymphoblast cell line NA20801

value: Northwest European American from Utah (HapMap code:CEU)


title: C3H/HeJ Vehicle liver sample batch 5

description: liver sample batch 5

value: male


title: DBA/2JTCE_5 liver sample batch 5

description: liver sample batch 5

value: TCE


title: CAST/EiJ Vehicle liver sample batch 5

description: liver sample batch 5

value: CAST/EiJ


title: NA20785/NA12878

value: lymphoblast cell line NA20785

value: female


title: PWD/PhJTCE liver sample batch 5

description: liver sample batch 5

value: PWD/PhJ


title: NA20775/NA12878

value: lymphoblast cell line NA20775

value: lymphoblast cell line NA12878


title: B6C3F1/JTCE liver sample batch 5

description: liver sample batch 5


title: MOLF/EiJ Vehicle liver sample batch 5

description: liver sample batch 5

value: MOLF/EiJ


title: NA20783/NA12878

value: lymphoblast cell line NA20783

value: Toscani from Italy (HapMap code:TSI)


title: NA20770/NA12878

value: Male

value: lymphoblast cell line NA20770


title: NA20773/NA12878

value: Female

value: lymphoblast cell line NA20773


title: NA20768/NA12878

value: lymphoblast cell line NA20768


title: NA20761/NA12878

value: lymphoblast cell line NA20761

value: Northwest European American from Utah (HapMap code:CEU)


title: NA20771/NA12878

value: lymphoblast cell line NA20771


title: NA20774/NA12878

value: lymphoblast cell line NA20774


title: NA20760/NA12878

value: lymphoblast cell line NA20760


title: BTBR+tf/JTCE liver sample batch 5

description: liver sample batch 5

value: male

value: BTBR+tf/J

value: TCE


title: BALB/cByJ Vehicle liver sample batch 5

description: liver sample batch 5

value: BALB/cByJ

value: vehicle control


title: PWD/PhJTCE liver sample batch 4

description: liver sample batch 4

value: PWD/PhJ


title: NA20765/NA12878

value: lymphoblast cell line NA20765

value: Toscani from Italy (HapMap code:TSI)

value: female

value: lymphoblast cell line NA12878


title: NA20759/NA12878

value: Male

value: lymphoblast cell line NA20759


title: NZW/LacJ Vehicle liver sample batch 4

description: liver sample batch 4

value: NZW/LacJ


title: NA20766/NA12878

value: Female

value: lymphoblast cell line NA20766

value: Northwest European American from Utah (HapMap code:CEU)


title: AKR/J Vehicle liver sample batch 5

description: liver sample batch 5

value: AKR/J


title: 129S1/SvImJ Vehicle liver sample batch 5

description: liver sample batch 5

value: male


title: NOD/LtJTCE liver sample batch 4

description: liver sample batch 4

value: NOD/LtJ


title: DBA/2JTCE liver sample batch 5

description: liver sample batch 5

value: TCE


title: KK/HIJTCE liver sample batch 4

description: liver sample batch 4

value: KK/HIJ


title: FVB/NJ Vehicle liver sample batch 4

description: liver sample batch 4

value: FVB/NJ

value: vehicle control


title: MOLF/EiJ Vehicle liver sample batch 4

description: liver sample batch 4

value: MOLF/EiJ


title: NA20752/NA12878

value: lymphoblast cell line NA20752

value: Toscani from Italy (HapMap code:TSI)


title: NA20757/NA12878

value: lymphoblast cell line NA20757

value: female

value: lymphoblast cell line NA12878


title: NA20756/NA12878

value: lymphoblast cell line NA20756


title: NA20758/NA12878

value: Male

value: lymphoblast cell line NA20758


title: DBA/2JTCE liver sample batch 4

description: liver sample batch 4


title: NA20589/NA12878

value: Female

value: lymphoblast cell line NA20589

value: Northwest European American from Utah (HapMap code:CEU)


title: NA20754/NA12878

value: lymphoblast cell line NA20754


title: CAST/EiJ Vehicle liver sample batch 4

description: liver sample batch 4

value: male

value: CAST/EiJ


title: c57BL/6JTCE liver sample batch 4

description: liver sample batch 4

value: TCE


title: B6C3F1/JTCE liver sample batch 4

description: liver sample batch 4


title: NA20753/NA12878

value: lymphoblast cell line NA20753


title: BTBR+tf/JTCE liver sample batch 4

description: liver sample batch 4

value: BTBR+tf/J


title: NA20586/NA12878

value: lymphoblast cell line NA20586


title: PWD/PhJ Vehicle liver sample batch 3

description: liver sample batch 3

value: PWD/PhJ

value: vehicle control


title: NZW/LacJTCE liver sample batch 3

description: liver sample batch 3

value: NZW/LacJ


title: A/JTCE liver sample batch 4

description: liver sample batch 4

value: A/J


title: 129S1/SvImJ Vehicle liver sample batch 4

description: liver sample batch 4


title: NA20588/NA12878

value: lymphoblast cell line NA20588

value: Toscani from Italy (HapMap code:TSI)

value: female

value: lymphoblast cell line NA12878


title: BALB/cByJ Vehicle liver sample batch 4

description: liver sample batch 4

value: BALB/cByJ


title: KK/HIJTCE liver sample batch 5

description: liver sample batch 5

value: KK/HIJ


title: A/JTCE liver sample batch 6

description: liver sample batch 6


title: NA20582/NA12878

value: Female

value: lymphoblast cell line NA20582

value: Northwest European American from Utah (HapMap code:CEU)


title: NA20585/NA12878

value: lymphoblast cell line NA20585


title: NA20543/NA12878

value: Male

value: lymphoblast cell line NA20543


title: NA20542/NA12878

value: lymphoblast cell line NA20542


title: NA20581/NA12878

value: lymphoblast cell line NA20581


title: NOD/LtJ Vehicle liver sample batch 3

description: liver sample batch 3

value: male

value: NOD/LtJ

value: vehicle control


title: NA20772/NA12878

value: lymphoblast cell line NA20772


title: NA20540/NA12878

value: lymphoblast cell line NA20540

value: Toscani from Italy (HapMap code:TSI)


title: NA20544/NA12878

value: lymphoblast cell line NA20544

value: female

value: lymphoblast cell line NA12878


title: BALB/cByJ Vehicle liver sample batch 3

description: liver sample batch 3

value: BALB/cByJ


title: c57BL/6J Vehicle liver sample batch 3

description: liver sample batch 3


title: BTBR+tf/J Vehicle liver sample batch 3

description: liver sample batch 3

value: BTBR+tf/J


title: C3H/HeJTCE liver sample batch 3

description: liver sample batch 3

value: TCE


title: CAST/EiJTCE liver sample batch 3

description: liver sample batch 3

value: CAST/EiJ


title: MOLF/EiJTCE liver sample batch 3

description: liver sample batch 3

value: MOLF/EiJ


title: FVB/NJTCE liver sample batch 3

description: liver sample batch 3

value: FVB/NJ


title: DBA/2J Vehicle liver sample batch 3

description: liver sample batch 3


title: BALB/cByJTCE liver sample batch 3

description: liver sample batch 3


title: NA20541/NA12878

value: Female

value: lymphoblast cell line NA20541

value: Northwest European American from Utah (HapMap code:CEU)


title: NA20533/NA12878

value: lymphoblast cell line NA20533


title: NA20778/NA12878

value: Male

value: lymphoblast cell line NA20778


title: NA20804/NA12878

value: lymphoblast cell line NA20804


title: NA20769/NA12878

value: lymphoblast cell line NA20769

value: Toscani from Italy (HapMap code:TSI)


title: NA20532/NA12878

value: lymphoblast cell line NA20532

value: female


title: NA20535/NA12878

value: lymphoblast cell line NA20535

value: lymphoblast cell line NA12878


title: NA20531/NA12878

value: lymphoblast cell line NA20531


title: NA20536/NA12878

value: lymphoblast cell line NA20536


title: B6C3F1/J Vehicle liver sample batch 3

description: liver sample batch 3

value: male

value: vehicle control


title: NA20534/NA12878

value: lymphoblast cell line NA20534


title: NA20538/NA12878

value: lymphoblast cell line NA20538


title: NA20528/NA12878

value: lymphoblast cell line NA20528

value: Northwest European American from Utah (HapMap code:CEU)


title: NA20530/NA12878

value: Female

value: lymphoblast cell line NA20530


title: AKR/JTCE liver sample batch 3

description: liver sample batch 3

value: AKR/J

value: TCE


title: NA20526/NA12878

value: lymphoblast cell line NA20526

value: Toscani from Italy (HapMap code:TSI)


title: AKR/J Vehicle liver sample batch 3

description: liver sample batch 3


title: 129S1/SvImJTCE liver sample batch 3

description: liver sample batch 3


title: NA20527/NA12878

value: Male

value: lymphoblast cell line NA20527

value: female


title: PWD/PhJ Vehicle liver sample batch 2

description: liver sample batch 2

value: PWD/PhJ


title: NOD/LtJ Vehicle liver sample batch 2

description: liver sample batch 2

value: NOD/LtJ


title: UVB-2L_E~6TC_E_Cy5-Rep2-6TC_E

city: Stanford

first: John

middle: F

last: Fernandes

state: CA

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

description: Ear, 4h exp to 2 leaves compared to 6h

hyb_protocol: 750 ng of each labeled target cRNA were hybridized for 17 h at 60C.

scan_protocol: Slides were scanned on an Agilent G2565AA microarray scanner as indicated in the manual.  Images were processed with the Agilent Feature Extraction software.

data_processing: After removal of spots flagged by Feature Extraction as below background or saturated or outliers, dye normalized values for each channel from Feature Extraction were normalized again to the median array intensity.  Average intensities were then calculated for probes with at least 3 of 4 good intensities.

organism: Zea mays

label_protocol: Total RNA (500 ng) was amplified & labeled with Cy5 using Agilent Low RNA Input Fluorescent Linear Amplification Kit.

growth_protocol: Plants were grown and dissected at the Stanford field; tissues were collected and frozen in liquid nitrogen immediately.

extract_protocol: Total RNA was extracted from 30 - 60 mg of frozen tissues with Qiagen RNeasy Mini kit, digested with DNase I, and cleaned up with RNeasy columns.

tag: sample type

value: shielded ear sample

tag: bio rep

tag: exposure hours

value: UVB


title: A/J Vehicle liver sample batch 3

description: liver sample batch 3

value: male

value: A/J

value: vehicle control


title: NZW/LacJTCE liver sample batch 2

description: liver sample batch 2

value: NZW/LacJ


title: NA20529/NA12878

value: Female

value: lymphoblast cell line NA20529

value: lymphoblast cell line NA12878

value: Northwest European American from Utah (HapMap code:CEU)


title: NA20522/NA12878

value: lymphoblast cell line NA20522


title: KK/HIJ Vehicle liver sample batch 2

description: liver sample batch 2

value: KK/HIJ


title: NA20524/NA12878

value: Male

value: lymphoblast cell line NA20524

value: Toscani from Italy (HapMap code:TSI)


title: MOLF/EiJTCE liver sample batch 2

description: liver sample batch 2

value: MOLF/EiJ

value: TCE


title: NA20525/NA12878

value: lymphoblast cell line NA20525

value: female


title: UVB-2L_E~6TC_E_Cy5-Rep1-2L_E

description: Ear, 6h exp to 2 leaves compared to 4h

value: shielded ear sample

tag: tissue

value: 2 leaves

value: UVB


title: NZW/LacJ Vehicle liver sample batch 2

description: liver sample batch 2

value: male

value: NZW/LacJ

value: vehicle control


title: UVB-1TC_E~2TC_E_Cy5-Rep2-2TC_E

description: Ear, 1h exp to 2 leaves compared to 2h


title: NOD/LtJTCE liver sample batch 2

description: liver sample batch 2

value: NOD/LtJ


title: UVB-2L_E~2TC_E_Cy5-Rep2-2L_E

description: Ear, 2h exp to 2 leaves compared to 4h


title: DBA/2J Vehicle liver sample batch 2

description: liver sample batch 2


title: FVB/NJTCE liver sample batch 2

description: liver sample batch 2

value: FVB/NJ


title: NA20521/NA12878

value: lymphoblast cell line NA20521

value: lymphoblast cell line NA12878

value: Northwest European American from Utah (HapMap code:CEU)


title: UVB-1TC_E~2TC_E_Cy5-Rep1-1TC_E

description: Ear, 2h exp to 2 leaves compared to 1h


title: c57BL/6J Vehicle liver sample batch 2

description: liver sample batch 2


title: UVB-3L_E~A_E_Cy5-Rep2-A_E

description: Ear at 4h, 3 leaves exp compared to  leaves

value: whole plant


title: UVB-1TC_E~N_E_Cy5-Rep1-N_E

description: Ear, 1h exp to 2 leaves compared to 4h

value: no exposure


title: UVB-1TC_E~N_E_Cy5-Rep2-1TC_E

description: Ear, 1h exp to 2 leaves compared to no exposure


title: CAST/EiJTCE liver sample batch 2

description: liver sample batch 2

value: CAST/EiJ


title: C3H/HeJTCE liver sample batch 2

description: liver sample batch 2

value: TCE


title: BTBR+tf/J Vehicle liver sample batch 2

description: liver sample batch 2

value: BTBR+tf/J


title: BALB/cByJTCE liver sample batch 2

description: liver sample batch 2

value: BALB/cByJ


title: UVB-3L_E~A_E_Cy5-Rep1-3L_E

description: Ear at 4h,  leaves exp compared to 3 leaves

value: shielded ear sample

value: 3 leaves

tag: number


title: UVB-2L_E~3L_E_Cy5-Rep2-3L_E

description: Ear at 4h, 2 leaves exp compared to 3 leaves

value: UVB


title: UVB-1L_E~2L_E_Cy5-Rep2-2L_E

description: Ear at 4h, 1 leaves exp compared to 2 leaves

value: 2 leaves


title: UVB-1L_E~2L_E_Cy5-Rep1-1L_E

description: Ear at 4h, 2 leaves exp compared to 1 leaves

value: 1 leaf


title: A/J Vehicle liver sample batch 2

description: liver sample batch 2

value: male

value: A/J

value: vehicle control


title: AKR/JTCE liver sample batch 2

description: liver sample batch 2

value: AKR/J


title: UVB-1L_E~N_E_Cy5-Rep1-N_E

description: Ear at 4h, 1 leaves exp compared to no exposure


title: UVB-1L_E~N_E_Cy5-Rep2-1L_E

description: Ear at 4h, No exp compared to 1 leaves


title: UVB-2L_E~FV_E_Cy5-Rep4-FV_E

description: Ear at 4h, 2 leaves exp compared to whole plant field exp

value: field exposure


title: NZW/LacJTCE liver sample batch 1

description: liver sample batch 1

value: NZW/LacJ


title: 129S1/SvImJTCE liver sample batch 2

description: liver sample batch 2


title: B6C3F1/J Vehicle liver sample batch 2

description: liver sample batch 2


title: NOD/LtJ Vehicle liver sample batch 1

description: liver sample batch 1

value: NOD/LtJ


title: PWD/PhJ Vehicle liver sample batch 1

description: liver sample batch 1

value: PWD/PhJ


title: UVB-2L_E~FV_E_Cy5-Rep3-2L_E

description: Ear at 4h, whole plant field exp compared to 2 leaves


title: MOLF/EiJTCE liver sample batch 1

description: liver sample batch 1

value: MOLF/EiJ


title: UVB-2TC_IR~2TC_S_Cy5-Rep4-2TC_S

description: Irrad. Leaf compared to Shielded Leaf at 2h exp to 2 leaves

value: Shielded leaf sample


title: PWD/PhJTCE liver sample batch 1

description: liver sample batch 1

value: TCE


title: FVB/NJ Vehicle liver sample batch 1

description: liver sample batch 1

value: FVB/NJ


title: UVB-2L_E~FV_E_Cy5-Rep1-2L_E

value: shielded ear sample


title: UVB-2L_E~FV_E_Cy5-Rep2-FV_E


title: KK/HIJ Vehicle liver sample batch 1

description: liver sample batch 1

value: KK/HIJ


title: UVB-2TC_IR~2TC_S_Cy5-Rep3-2TC_IR

description: Shielded Leaf compared to Irrad. Leaf at 2h exp to 2 leaves

value: irradiated leaf sample

value: UVB


title: FVB/NJTCE liver sample batch 1

description: liver sample batch 1


title: NA20539/NA12878

value: Male

value: lymphoblast cell line NA20539

value: Toscani from Italy (HapMap code:TSI)

value: female

value: lymphoblast cell line NA12878

value: Northwest European American from Utah (HapMap code:CEU)


title: UVB-2TC_IR~2TC_S_Cy5-Rep2-2TC_IR


title: UVB-2TC_IR~2TC_S_Cy5-Rep1-2TC_S


title: UVB-2L_E~2TC_E_Cy5-Rep1-2TC_E

description: Ear, 4h exp to 2 leaves compared to 2h


title: BALB/cByJTCE liver sample batch 1

description: liver sample batch 1

value: male

value: BALB/cByJ


title: UVB-1TC_IR~1TC_S_Cy5-Rep1-1TC_IR

description: Shielded Leaf compared to Irrad. Leaf at 1h exp to 2 leaves


title: BTBR+tf/J Vehicle liver sample batch 1

description: liver sample batch 1

value: BTBR+tf/J

value: vehicle control


title: UVB-6TC_IR~6TC_S_Cy5-Rep1-6TC_S

description: Irrad. Leaf compared to Shielded Leaf at 6h exp to 2 leaves

value: Shielded leaf sample


title: DBA/2J Vehicle liver sample batch 1

description: liver sample batch 1


title: UVB-1TC_IR~1TC_S_Cy5-Rep2-1TC_S

description: Irrad. Leaf compared to Shielded Leaf at 1h exp to 2 leaves


title: UVB-6TC_IR~6TC_S_Cy5-Rep2-6TC_IR

description: Shielded Leaf compared to Irrad. Leaf at 6h exp to 2 leaves


title: CAST/EiJTCE liver sample batch 1

description: liver sample batch 1

value: CAST/EiJ

value: TCE


title: C3H/HeJTCE liver sample batch 1

description: liver sample batch 1


title: UVB-1TC_S~2TC_S_Cy5-Rep2-2TC_S

description: Shielded Leaf, 1h exp to 2 leaves compared to 2h


title: C3H/HeJ Vehicle liver sample batch 1

description: liver sample batch 1


title: 129S1/SvImJTCE liver sample batch 1

description: liver sample batch 1


title: A/J Vehicle liver sample batch 1

description: liver sample batch 1

value: A/J


title: UVB-1TC_S~2TC_S_Cy5-Rep1-1TC_S

description: Shielded Leaf, 2h exp to 2 leaves compared to 1h


title: UVB-1TC_IR~2TC_IR_Cy5-Rep1-1TC_IR

description: Irrad. Leaf, 2h exp to 2 leaves compared to 1h


title: UVB-FV_IR~FV_S_Cy5-Rep1-FV_IR

description: Shielded Leaf compared to Irrad. Leaf at 4h of full-plant, field exposure

value: field exposure


title: B6C3F1/J Vehicle liver sample batch 1

description: liver sample batch 1


title: UVB-2L_S~FV_S_Cy5-Rep2-FV_S

description: Shielded Leaf at 4h, 2 leaves exp compared to whole plant field exp


title: UVB-2L_S~FV_S_Cy5-Rep1-2L_S

description: Shielded Leaf at 4h, whole plant field exp compared to 2 leaves

value: 2 leaves


title: UVB-FV_IR~FV_S_Cy5-Rep2-FV_S

description: Irrad. Leaf compared to Shielded Leaf at 4h of full-plant, field exposure


title: UVB-2L_S~2TC_S_Cy5-Rep2-2L_S

description: Shielded Leaf, 2h exp to 2 leaves compared to 4h

value: UVB


title: AKR/JTCE liver sample batch 1

description: liver sample batch 1

value: AKR/J


title: UVB-2L_S~6TC_S_Cy5-Rep1-2L_S

description: Shielded Leaf, 6h exp to 2 leaves compared to 4h


title: UVB-1TC_IR~2TC_IR_Cy5-Rep2-2TC_IR

description: Irrad. Leaf, 1h exp to 2 leaves compared to 2h

value: irradiated leaf sample


title: UVB-2L_IR~2TC_IR_Cy5-Rep2-2L_IR

description: Irrad. Leaf, 2h exp to 2 leaves compared to 4h


title: UVB-2L_S~6TC_S_Cy5-Rep2-6TC_S

description: Shielded Leaf, 4h exp to 2 leaves compared to 6h


title: UVB-2L_S~2TC_S_Cy5-Rep1-2TC_S

description: Shielded Leaf, 4h exp to 2 leaves compared to 2h


title: UVB-2L_IR~6TC_IR_Cy5-Rep2-2L_IR

description: Irrad. Leaf, 6h exp to 2 leaves compared to 4h


title: UVB-2L_IR~2TC_IR_Cy5-Rep1-2TC_IR

description: Irrad. Leaf, 4h exp to 2 leaves compared to 2h


title: ecdysonelss mutant at 22 degrees vs 29 degrees replicate 5

city: Athens

first: Melissa

last: Davis

state: GA

address: 500 DW Brooks Dr S 270C

department: Genetics  and MCG/UGA Medical Partnership

institute: University of Georgia

description: ecdysoneless 22 vs ecdysoneless 29 on slide 34 0801

hyb_protocol: Microarray hybridization   The hybridization protocol described here is to be used with microarrays printed with double-stranded DNA.  (For arrays with single-stranded DNA, the amplification and labeling method should be modified) Sample array hybridization.  The hybridization procedure here is for microarrays to be covered with 22mm x 40mm cover slip.  If other sizes of arrays are used, the hybridization volume should be adjusted accordingly.  DieTech hybridization chambers were used here, however the procedure is very similar for other chambers. 1.	Add the following to the 21.9 ul labeled sample (to a 28.6 ul final volume) a.	4.05 ul 20x SSC (final concentration to be ~ 2.83x SSC) b.	1.64 ul 5mg/ml yeast tRNA or 10mg/ml polyA (0.22 um filtered) c.	(Mix now by gently tapping the tube before adding SDS) d.	 0.99 ul 5% SDS (0.22 um filtered) (Mix well by gently tapping the tube) 2.	Denature sample in boiling water for 2 min. 3.	Centrifuge at ~ 12,000 g for 10 min, cool at room temperature for ~ 2 min.  Measure volume.  If the volume is less than 27 ul, adjust it to 28.6 ul with H2O.  It is OK if it is only ~ 1 ul short of 28.6 ul. 4.	 Add 10-15 ul of 2.83x SSC in the each of the two reservoirs of a Die-Tech hybridization chamber.  Set a 100 ul pipette at 28 ul and apply to array. Place and adjust the position of the cover slip on the array using a pipette tip to squarely cover the DNA area.  Put 3-4 droplets of 2.83x SSC on each ends of the slide outside of the Parafilm strips, total ~28 ul.  Put on the chamber over and tighten it with the provided screws.  Incubate in a water bath at ~42°C for 10 min. to adjust temperature.  Then move to another water bath at 64 °C, incubate for 15-18 hours. Washing and scanning microarrays. Prepare Washing Solution in 4 staining dishes (6cmH x 7.5cmW x 9.5cmL, Wheaton Cat. No.: 900200).  Put a slide rack (the matching glass rack for the staining dishes) in the Wash 1A dish and the Wash 2 dish.  Note 1: All washes are done at room temperature.  (do not add SDS into Wash Solution 1A until just prior to the initial use)  All the procedures here need be done swiftly.  After washing, microarrays are to be dried using a centrifuge with swing bucket rotor that takes slide racks.   Microarray Wash Solutions done in sequence of solution numbers: 1A = 1.14 x SSC, 0.0285% SDS; 1B = 1.14 x SSC; 2 = 0.228 x SSC; 3 = 0.057 x SSC

scan_protocol: Array Scanning The scanning method here uses a GenePix 4000 scanner (Axon Instrument) as an example. Scan per manufacturer’s instruction.  Usually the intensity where the histogram curve intersecting the X (intensity) axis is best kept at approximately 35,000, which should keep most features within dynamic range.  Keep the histogram curves from both channels as close a possible, which usually correlated to an intensity ratio of 1.  The resulting image is then analyzed using the GenePix Pro software provided by Axon Instruments per manufacturer’s instructions.

data_processing:
Statistical analysis of microarray data
 Data filtering, normalization and extraction from GenePix Pro.
1.	During the image analysis, GenePix Pro software recognizes the spots representing genes (called features) on an array.  Then the intensity of the red and green channel (pseudo-colors representing the Cy5 channel (635 nm wavelength) and Cy3 channel (532 nm wavelength), respectively) in each feature is quantified and registered as the expression reading of the gene represented.  The ratio of the intensities between two channels is registered as the relative ratio of expression level of this gene in the two samples that hybridized on the array.  The identity of the gene represented by a spot is determined by tracing back to the identity of the original DNA sample used to make the microarray.
2.	In the case of using GenePix Pro software, there is an automatic flagging process in which the software identifies the spots that are of poor quality and flags them as bad (flag value less than 0).
3.	We also apply another data filter to eliminate features whose quality is doubtful.  In the formula of this filter, for a spot to pass quality control, 3 conditions need to be met: (1) There is no negative automatic or manual flags during image processing using GenePix Pro software.  (2) For this spot, in at least 1 channel, the intensities of at least 75% of the pixels are one standard deviation above background.  (3) The net signal-to-noise ratio should be at least 1 in at least one channel.  For a channel, the net signal-to-noise ratio is: [(Feature Intensity) – (Background Intensity)]/ (Background Intensity).  The Feature Intensity is the median signal intensity reading of a spot (feature).  The Background Intensity is the bigger value of two: the median of median background intensity of all the spots on the whole array, and median background intensity of this particular spot.
4.	After data filtering, the intensity ratios (“Ratio of Medians” in the GenePix Pro result file) of every spots are then normalized using the normalization method (calculation based on “Ratio of Medians”) from GenePix Pro software.  This normalization method is based on removal of all spots whose “Ratio of Medians” value is >10-fold and then calculation of the average ratio of medians and multiplication of each value by the resulting correction factor (“Normalization Factor-Medians”) such that the average of the corrected “ratios of medians” equals 1.0.  The normalized Ratio of Medians is the product of Ratio of Medians and the Normalization Factor-Medians.  All subsequent analyses use the normalized Ratio of Medians as the value of gene expression.  A log base 2 transformation of the ratios was performed before further analysis.
Statistical analysis of extracted array data.
1.	At least 3 biological repeats are required to provide statistical power. The models used for significant genelists includes: t-test, t-test combined with fold-cutoff, ANOVA, ANOVA combined with fold-cutoff were used to define significant gene lists.  The formulas for these tests are available in many statistical books, such as Biometry by Sokal and Rohlf (1995).
2.	In the case of comparison of samples from two experimental conditions (for example, normal vs. mutant), t-test or fold-cutoff was used.  In the method a gene is considered significant if it passes a t-test with a certain p-value score, and its expression level is different between the 2 samples by certain fold.  One such example a t-test score of p-value 0.05, plus a 2- fold change in expression level.  Examples of this method could be found in Li and White (2003).
3.	For a time-course experiment (or comparisons between 3 or more timepoints or developmental stages) with at least 3 repeats per time point, one-way ANOVA was the suitable statistical model utilized to it test whether a gene is changed significantly along the time.  Examples of this method could be found in White et al. (2002) and Li and White (2003).

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: ecdysonelss mutant at 22 degrees (REF)

label_protocol:
Labeling of poly-A selected RNA
1.	labeling reactions were set up on ice in two 0.2 ml PCR tubes (two samples for one microarray):
a.	Mix 4.5 ug mRNA and 2.5 ul Random hexamer (3 ug/ul).
b.	Adjust volume to 15.4 ul (either by adding nuclease-free H2O or by partially drying (heating at 70°C with cap open), mix well by pipetting.
c.	Transfer to a preheated PCR machine to denature at 70°C for 10 min.  Then cool on ice for 2 min.
d.	Add 9.6 ul ice-cold Labeling Mixture (6 ul 5x SuperScript II first strand buffer + 3 ul  0.1M DTT +  0.6 ul  Labeling dNTP mix (25mM dATP, dCTP, dGTP, and 10mM dTTP))
2.	Add 3 ul Cy3-dUTP (1 mM) or 3 ul Cy5-dUTP (1 mM) (ice-cold) to the corresponding samples.  Then add 2 ul SuperScript II (200 U/ul) to each sample.  Mix well by pipeting while on ice.  Incubate the complete mixture for 3 min. at room temperature.  Then transfer to a preheated PCR machine to incubate at 42° C for 120 min.
3.	Cool the reaction to room temperature then add 15 ul RNA Degradation Solution (0.1 M NaOH, 2 mM EDTA), immediately mix well by pipetting 3-4 times, transfer to a preheated PCR machine to incubate at 65°C for 9 min. to degrade RNA and stop the reaction.
4.	Prepare a new 1.5 ml microcentrifuge tube with 10 ul H2O and 10 ul 3M NaAcetate (pH ~5). Transfer both the cy3 reaction and the cy5 reaction to the 1.5 ml microcentrifuge tube already.  Note: Cy5 is not stable at basic condition so this neutralization needs to be done quickly after the RNA degradation.
5.	Purify labeled cDNA using QIAquick PCR Purification Kit (follow manufacturer product insert protocol).

extract_protocol:
RNA extraction
1.	Samples were collected and frozen in TRIzol and homogenized by pestle (Kontes disposable pellet pestle, Fisher Cat. No. K749521-0590).  Then incubate for 5 min. at room temperature.  After this step the sample can be stored at -80°C for at least 3 month.  TRIzol disables RNases.
2.	Add 5 µg linear polyacrylamide (LPA, GenElute from Sigma) as carrier to the sample tube. (If the number of animals in a given collection allowed RNA yield more than 5 ug, LPA was not added.)  Vortex for 10 seconds.  Then transfer the sample to the pre-spun Phase Lock Gel tubes (pre-spin to ensure gel is pelleted at the bottom).
3.	Add 60 ul chloroform and shake vigorously for 15 seconds by hands.  Note: Do not vortex.  Then centrifuge samples at 11,000 to 12,000 g (no more than 12,000 g) for 10 min. at 2–8.  Transfer the aqueous phase (~ 200 ul) to a clean nuclease-free tube.
4.	Add 0.7-0.8 volumes of isopropanol (~160 µl), mix well by shaking and vortexing.  Precipitate overnight at -20ºC.
5.	Centrifuge at 12,000 ~ 14,000 g for 30 min. at 4ºC.  Carefully remove the supernatant by pipette.  Add 500 µl 75% ethanol (room temperature) to wash the pellet by shaking.   Centrifuge at 12,000 ~ 14,000 g for 5 min. at room temperature.  Carefully remove the supernatant by pipette then spin at 12,000 ~ 14,000 g for 15 seconds to collect all residual liquid at the bottom.  Carefully remove the supernatant with a 10 ul pipette tip.  Air-dry (sitting the tubes on bench) the pellet for 1-1.5 min.
6.	Redissolve the pellet in 5 µl (4 ul if it is clear that 20% of the yield isn’t enough for a spectrometer measurement.) nuclease-free water.  (optionally:  Heat the tube in a heat block at 55°C for 30 seconds if the pellet does not disappear immediately.
7.	1 ul of the solution  was used for nanodrop spectrometer measurement.  The sample’s OD260nm/OD280nm ratio is usually > 1.8.
8.	When extracting RNA from whole animal samples and the RNA yield is expected to be > 5 ug, resuspend the pellet in 105 ul of nuclease- free water and clean up the RNA using an RNeasy column from Qaigen using the manufacturer’s protocol as described in the product insert.

tag: developmental stage

value: wpp

tag: mutant

value: ecdysoneless

tag: temperature

value: 22 Celsius

source_name: ecdysonelss mutant at 29 degrees (EXP)

value: 29 Celsius


title: UVB-2L_IR~6TC_IR_Cy5-Rep1-6TC_IR

description: Irrad. Leaf, 4h exp to 2 leaves compared to 6h


title: UVB-2L_S~N_IR_Cy5-Rep2-2L_S

description: Irrad. Leaf at 4h, no exposure compared to 2 leaves exp


title: UVB-2L_IR~2L_S_Cy5-Rep4-2L_S

description: Irrad. Leaf compared to Shielded Leaf at 4h exp to 2 leaves


title: UVB-2L_IR~2L_S_Cy5-Rep2-2L_S


title: UVB-2L_S~N_IR_Cy5-Rep1-N_IR

description: Shielded Leaf at 4h, 2 leaves exp compared to no exposure

value: no exposure


title: AKR/J Vehicle liver sample batch 6

description: liver sample batch 6

value: male


title: UVB-2L_IR~2L_S_Cy5-Rep3-2L_IR

description: Shielded Leaf compared to Irrad. Leaf at 4h exp to 2 leaves


title: UVB-2L_IR~FV_IR_Cy5-Rep1-2L_IR

description: Irrad. Leaf at 4h, field-grown with 2 leaves exp compared to 2 leaves


title: UVB-2L_IR~2L_S_Cy5-Rep1-2L_IR


title: UVB-A_IR~N_IR_Cy5-Rep1-A_IR

description: whole plant exp for 4h compared to no exposure

value: whole plant


title: UVB-2L_IR~A_IR_Cy5-Rep2-2L_IR

description: Irrad. Leaf at 4h, whole plant exp compared to 2 leaves


title: UVB-1L_IR~1L_S_Cy5-Rep2-1L_S

description: Irrad. Leaf compared to Shielded Leaf at 4h exp to 1 leaves

value: 1 leaf


title: UVB-2L_S~3L_S_Cy5-Rep1-2L_S

description: Shielded Leaf at 4h, 3 leaves exp compared to 2 leaves

value: Shielded leaf sample


title: UVB-2L_IR~FV_IR_Cy5-Rep2-FV_IR

description: Irrad. Leaf at 4h, 2 leaves exp compared to field-grown with 2 leaves


title: UVB-2L_IR~3L_IR_Cy5-Rep1-2L_IR

description: Irrad. Leaf at 4h, 3 leaves exp compared to 2 leaves


title: UVB-2L_IR~A_IR_Cy5-Rep1-A_IR

description: Irrad. Leaf at 4h, 2 leaves exp compared to whole plant


title: UVB-1L_S~2L_S_Cy5-Rep1-1L_S

description: Shielded Leaf at 4h, 2 leaves exp compared to 1 leaves


title: UVB-2L_S~3L_S_Cy5-Rep2-3L_S

description: Shielded Leaf at 4h, 2 leaves exp compared to 3 leaves

value: 3 leaves


title: UVB-3L_IR~3L_S_Cy5-Rep2-3L_S

description: Irrad. Leaf compared to Shielded Leaf at 4h exp to 3 leaves


title: UVB-A_IR~N_IR_Cy5-Rep2-N_IR


title: UVB-3L_IR~3L_S_Cy5-Rep1-3L_IR

description: Shielded Leaf compared to Irrad. Leaf at 4h exp to 3 leaves


title: UVB-2L_IR~3L_IR_Cy5-Rep2-3L_IR

description: Irrad. Leaf at 4h, 2 leaves exp compared to 3 leaves


title: UVB-2L_E~3L_E_Cy5-Rep1-2L_E

description: Ear at 4h, 3 leaves exp compared to 2 leaves

value: shielded ear sample


title: UVB-1L_IR~1L_S_Cy5-Rep1-1L_IR

description: Shielded Leaf compared to Irrad. Leaf at 4h exp to 1 leaves


title: UVB-2L_E~6TC_E_Cy3-Rep2-2L_E

description: Ear, 4h exp to 2 leaves compared to 6h


title: UVB-1TC_E~2TC_E_Cy3-Rep1-2TC_E

description: Ear, 2h exp to 2 leaves compared to 1h


title: UVB-1L_IR~2L_IR_Cy5-Rep1-1L_IR

description: Irrad. Leaf at 4h, 2 leaves exp compared to 1 leaves


title: UVB-1L_S~2L_S_Cy5-Rep2-2L_S

description: Shielded Leaf at 4h, 1 leaves exp compared to 2 leaves


title: UVB-1L_IR~2L_IR_Cy5-Rep2-2L_IR

description: Irrad. Leaf at 4h, 1 leaves exp compared to 2 leaves


title: UVB-1TC_E~2TC_E_Cy3-Rep2-1TC_E

description: Ear, 1h exp to 2 leaves compared to 2h


title: UVB-2L_E~6TC_E_Cy3-Rep1-6TC_E

description: Ear, 6h exp to 2 leaves compared to 4h


title: UVB-1TC_E~N_E_Cy3-Rep2-N_E

description: Ear, 1h exp to 2 leaves compared to no exposure


title: UVB-2L_E~2TC_E_Cy3-Rep1-2L_E

description: Ear, 4h exp to 2 leaves compared to 2h


title: UVB-2L_E~2TC_E_Cy3-Rep2-2TC_E

description: Ear, 2h exp to 2 leaves compared to 4h


title: UVB-1TC_E~N_E_Cy3-Rep1-1TC_E

description: Ear, 1h exp to 2 leaves compared to 4h


title: UVB-3L_E~A_E_Cy3-Rep2-3L_E

description: Ear at 4h, 3 leaves exp compared to  leaves


title: UVB-2L_E~3L_E_Cy3-Rep2-2L_E

description: Ear at 4h, 2 leaves exp compared to 3 leaves


title: UVB-1L_E~2L_E_Cy3-Rep1-2L_E

description: Ear at 4h, 2 leaves exp compared to 1 leaves


title: UVB-2L_E~3L_E_Cy3-Rep1-3L_E


title: UVB-1L_E~N_E_Cy3-Rep2-N_E

description: Ear at 4h, No exp compared to 1 leaves


title: UVB-1L_E~N_E_Cy3-Rep1-1L_E

description: Ear at 4h, 1 leaves exp compared to no exposure


title: UVB-2L_E~FV_E_Cy3-Rep2-2L_E

description: Ear at 4h, 2 leaves exp compared to whole plant field exp


title: UVB-2TC_IR~2TC_S_Cy3-Rep2-2TC_S

description: Shielded Leaf compared to Irrad. Leaf at 2h exp to 2 leaves


title: UVB-2L_E~FV_E_Cy3-Rep1-FV_E

description: Ear at 4h, whole plant field exp compared to 2 leaves


title: UVB-2L_E~FV_E_Cy3-Rep4-2L_E


title: UVB-2TC_IR~2TC_S_Cy3-Rep4-2TC_IR

description: Irrad. Leaf compared to Shielded Leaf at 2h exp to 2 leaves


title: UVB-2TC_IR~2TC_S_Cy3-Rep1-2TC_IR


title: UVB-1L_E~2L_E_Cy3-Rep2-1L_E

description: Ear at 4h, 1 leaves exp compared to 2 leaves


title: UVB-2L_E~FV_E_Cy3-Rep3-FV_E


title: UVB-3L_E~A_E_Cy3-Rep1-A_E

description: Ear at 4h,  leaves exp compared to 3 leaves


title: UVB-6TC_IR~6TC_S_Cy3-Rep2-6TC_S

description: Shielded Leaf compared to Irrad. Leaf at 6h exp to 2 leaves


title: UVB-2TC_IR~2TC_S_Cy3-Rep3-2TC_S


title: UVB-6TC_IR~6TC_S_Cy3-Rep1-6TC_IR

description: Irrad. Leaf compared to Shielded Leaf at 6h exp to 2 leaves


title: UVB-1TC_S~2TC_S_Cy3-Rep1-2TC_S

description: Shielded Leaf, 2h exp to 2 leaves compared to 1h


title: UVB-2L_S~FV_S_Cy3-Rep2-2L_S

description: Shielded Leaf at 4h, 2 leaves exp compared to whole plant field exp


title: UVB-1TC_IR~2TC_IR_Cy3-Rep2-1TC_IR

description: Irrad. Leaf, 1h exp to 2 leaves compared to 2h


title: UVB-1TC_S~2TC_S_Cy3-Rep2-1TC_S

description: Shielded Leaf, 1h exp to 2 leaves compared to 2h


title: UVB-1TC_IR~1TC_S_Cy3-Rep1-1TC_S

description: Shielded Leaf compared to Irrad. Leaf at 1h exp to 2 leaves


title: UVB-FV_IR~FV_S_Cy3-Rep1-FV_S

description: Shielded Leaf compared to Irrad. Leaf at 4h of full-plant, field exposure


title: UVB-1TC_IR~2TC_IR_Cy3-Rep1-2TC_IR

description: Irrad. Leaf, 2h exp to 2 leaves compared to 1h


title: UVB-2L_S~2TC_S_Cy3-Rep1-2L_S

description: Shielded Leaf, 4h exp to 2 leaves compared to 2h


title: UVB-2L_S~FV_S_Cy3-Rep1-FV_S

description: Shielded Leaf at 4h, whole plant field exp compared to 2 leaves


title: UVB-1TC_IR~1TC_S_Cy3-Rep2-1TC_IR

description: Irrad. Leaf compared to Shielded Leaf at 1h exp to 2 leaves


title: UVB-FV_IR~FV_S_Cy3-Rep2-FV_IR

description: Irrad. Leaf compared to Shielded Leaf at 4h of full-plant, field exposure


title: UVB-2L_S~6TC_S_Cy3-Rep1-6TC_S

description: Shielded Leaf, 6h exp to 2 leaves compared to 4h


title: UVB-2L_IR~2TC_IR_Cy3-Rep2-2TC_IR

description: Irrad. Leaf, 2h exp to 2 leaves compared to 4h


title: UVB-2L_IR~2TC_IR_Cy3-Rep1-2L_IR

description: Irrad. Leaf, 4h exp to 2 leaves compared to 2h


title: UVB-2L_S~6TC_S_Cy3-Rep2-2L_S

description: Shielded Leaf, 4h exp to 2 leaves compared to 6h


title: UVB-2L_IR~6TC_IR_Cy3-Rep2-6TC_IR

description: Irrad. Leaf, 6h exp to 2 leaves compared to 4h


title: RRE2_SKY_HCl45_03_7DE1571

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: biological replicate, Date of Scan Fri Apr 24 11:39:30 2009

hyb_protocol: overnight hyb on Corning UltraGAPS slides at 42°C in 25% formamide / 5xSSC / 0.1% BSA

scan_protocol: Perkin Elmer ScanArray 5000 scanner, image acquisition with ScanArray Express 3.0.1 software, spot quantification using Quantarray 3.0 software, adaptive quantification, protocol STv5_SP040504_adapforsmallpins_040817

data_processing: normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal.

organism: Salmonella enterica subsp. enterica serovar Kentucky

source_name: SKY 3795 total RNA after 10min exposure to HCl pH4.5 in TSB

label_protocol: incorporation of Cy5-dCTP with Superscript RT and random hexamers

extract_protocol: RNeasy kit (QIAGEN)

value: Salmonella Kentucky 3795

tag: condition

value: log phase culture after 10min exposure to acidic conditions HCl pH4.5

tag: medium

value: TSB

source_name: SKY 3795 total RNA in TSB

label_protocol: incorporation of Cy3-dCTP with Superscript RT and random hexamers

value: log phase culture


title: RRE2_SKY_HCl55_03_7DE1573

description: biological replicate, Date of Scan Wed Apr 01 14:08:48 2009

source_name: SKY 3795 total RNA after 10min exposure to HCl pH5.5 in TSB

value: log phase culture after 10min exposure to acidic conditions HCl pH5.5


title: UVB-2L_S~2TC_S_Cy3-Rep2-2TC_S

description: Shielded Leaf, 2h exp to 2 leaves compared to 4h

value: UVB


title: RRE2_SKY_HCl55_01_7DE1542

description: biological replicate, Date of Scan Wed Oct 14 08:44:26 2009


title: UVB-2L_IR~6TC_IR_Cy3-Rep1-2L_IR

description: Irrad. Leaf, 4h exp to 2 leaves compared to 6h

value: irradiated leaf sample

value: 2 leaves


title: UVB-2L_IR~2L_S_Cy3-Rep2-2L_IR

description: Irrad. Leaf compared to Shielded Leaf at 4h exp to 2 leaves


title: RRE2_SEN_HCl45_03_7DE1558

description: biological replicate, Date of Scan Fri Jan 23 12:09:53 2009

organism: Salmonella enterica subsp. enterica serovar Enteritidis

source_name: SEN NalR total RNA after 10min exposure to HCl pH4.5 in TSB

value: Salmonella Enteritidis NalR

source_name: SEN NalR total RNA in TSB


title: UVB-2L_IR~2L_S_Cy3-Rep4-2L_IR


title: UVB-2L_IR~2L_S_Cy3-Rep3-2L_S

description: Shielded Leaf compared to Irrad. Leaf at 4h exp to 2 leaves


title: RRE2_SEN_HCl45_02_7DE1557

description: biological replicate, Date of Scan Fri Jan 30 11:08:39 2009


title: UVB-2L_IR~2L_S_Cy3-Rep1-2L_S


title: RRE2_SEN_HCl45_01_7DE1556

description: biological replicate, Date of Scan Tue Jan 27 12:04:49 2009


title: UVB-2L_S~N_IR_Cy3-Rep1-2L_S

description: Shielded Leaf at 4h, 2 leaves exp compared to no exposure


title: RRE2_SKY_CH3COOH55_02r_7DE1539

description: biological replicate, Date of Scan Thu Aug 27 11:59:09 2009

source_name: SKY 3795 total RNA after 10min exposure to acetic acid pH5.5 in TSB

value: log phase culture after 10min exposure to acidic conditions acetic acid pH5.5


title: RRE2_SKY_HCl55_02_7DE1544

description: biological replicate, Date of Scan Wed Oct 14 09:43:52 2009


title: UVB-2L_IR~FV_IR_Cy3-Rep2-2L_IR

description: Irrad. Leaf at 4h, 2 leaves exp compared to field-grown with 2 leaves


title: RRE2_SKY_HCl45_02_7DE1562

description: biological replicate, Date of Scan Wed Feb 04 12:52:16 2009


title: RRE2_SKY_CH3COOH55_01_7DE1572

description: biological replicate, Date of Scan Wed Apr 01 11:46:10 2009


title: UVB-2L_S~N_IR_Cy3-Rep2-N_IR

description: Irrad. Leaf at 4h, no exposure compared to 2 leaves exp

value: no exposure


title: RRE2_SEN_HCl55_03_7DE1560

description: biological replicate, Date of Scan Wed Feb 11 09:01:09 2009

source_name: SEN NalR total RNA after 10min exposure to HCl pH5.5 in TSB


title: RRE2_SEN_HCl55_01_7DE1538

description: biological replicate, Date of Scan Wed Oct 14 08:14:34 2009


title: UVB-2L_IR~FV_IR_Cy3-Rep1-FV_IR

description: Irrad. Leaf at 4h, field-grown with 2 leaves exp compared to 2 leaves

value: field exposure


title: RRE2_SEN_HCl55_02_7DE1543

description: biological replicate, Date of Scan Wed Oct 14 09:14:49 2009


title: RRE2_SKY_CH3COOH55_03_7DE1533

description: biological replicate, Date of Scan Thu Aug 20 14:00:02 2009


title: UVB-3L_IR~3L_S_Cy3-Rep1-3L_S

description: Shielded Leaf compared to Irrad. Leaf at 4h exp to 3 leaves


title: RRE2_SKY_CH3COOH55_03r_7DE1534

description: biological replicate, Date of Scan Thu Aug 20 14:17:25 2009


title: RRE2_SEN_CH3COOH55_03r_7DE1532

description: biological replicate, Date of Scan Thu Aug 20 14:40:34 2009

source_name: SEN NalR total RNA after 10min exposure to acetic acid pH5.5 in TSB


title: RRE2_SEN_CH3COOH55_03_7DE1531

description: biological replicate, Date of Scan Fri Aug 14 09:00:57 2009


title: UVB-3L_IR~3L_S_Cy3-Rep2-3L_IR

description: Irrad. Leaf compared to Shielded Leaf at 4h exp to 3 leaves


title: UVB-2L_IR~A_IR_Cy3-Rep1-2L_IR

description: Irrad. Leaf at 4h, 2 leaves exp compared to whole plant


title: UVB-2L_IR~A_IR_Cy3-Rep2-A_IR

description: Irrad. Leaf at 4h, whole plant exp compared to 2 leaves

value: whole plant


title: UVB-A_IR~N_IR_Cy3-Rep2-A_IR

description: whole plant exp for 4h compared to no exposure


title: UVB-A_IR~N_IR_Cy3-Rep1-N_IR


title: Kidney Mouse 172

city: Bar Harbor

first: Rachael

middle: S

last: Hageman

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

hyb_protocol: 2.3µg of biotin-labeled and fragmented cDNA was then hybridized onto GeneChip® Mouse Gene 1.0 ST Arrays (Affymetrix) for 16 hours at 45°C.  Post-hybridization staining and washing were performed according to manufacturer’s protocols using the Fludics Station 450 instrument (Affymetrix).

scan_protocol: The arrays were scanned with a GeneChipTM Scanner 3000 laser confocal slide scanner.

data_processing:
Data were imported into R (http://www.r-project.org/) and processed using the affy package from Bioconductor (http://www.bioconductor.org/). The data were normalized using robust multi-array average (rma) expression with no background correction.
A custom cdf file mogene10stvmmenstcdfV11.0.1 was obtained from Brainarray (http://brainarray.mbni.med.umich.edu/brainarray/default.asp).

label: biotin

source_name: Kidney

label_protocol: Labeling occurs by terminal deoxynucleotidyl  transferase (TdT) where biotin is added by a Affymetrix Labeling Reagent.

growth_protocol: Mice were housed in a climate-controlled facility with a 14-hour:10-hour light-dark cycle with free access to food and water throughout the experiment. After weaning, mice were maintained on a chow diet (5K52 LabDiet®, St. Louis, MO). F2 mice were tail-tipped at 2 weeks of age.

extract_protocol: Tissue samples were stored in RNAlater (Ambion, Austin TX) following dissection and later homogenized in TRIzolTM (Invitrogen, Carlsbad, CA).  Total RNA was isolated by TRIzolPlus TM methods according to the manufacturer’s protocols, and quality was assessed using an Agilent 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Palo Alto, CA).  Following reverse transcription with random primers-T7 primers (Affymetrix, Santa Clara, Ca), double stranded cDNA was synthesized with the GeneChip® WT cDNA Synthesis and Amplification Kit (Affymetrix, Santa Clara, Ca).  In an in vitro trancription (IVT) reaction with T7 RNA polymerase, the cDNA was linearly amplified to generate cRNA.  In the second cycle of cDNA synthesis, random primers are used to generate single stranded DNA in the sense orientation.  Incorporation of dUTP in the cDNA synthesis step allows for the fragmentation of the cDNA strand utilizing uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognizes the dUTP and allows for breakage at these residues.

treatment_protocol: The mice were housed individually for 3 days prior to the tissue collection and fasted for 4 hours on the day of the collection. There was no treatment group, all mice were in the same conditions.

value: MRL/MpJ x SM/J F2

value: male

tag: age

value: 13 weeks


title: RRE2_SKY_HCl45_01_7DE1407

description: biological replicate, Date of Scan Wed Aug 20 12:46:51 2008


title: UVB-2L_IR~3L_IR_Cy3-Rep2-2L_IR

description: Irrad. Leaf at 4h, 2 leaves exp compared to 3 leaves


title: Kidney Mouse 170


title: Kidney Mouse 169


title: UVB-2L_S~3L_S_Cy3-Rep1-3L_S

description: Shielded Leaf at 4h, 3 leaves exp compared to 2 leaves

value: Shielded leaf sample

value: 3 leaves


title: UVB-1L_S~2L_S_Cy3-Rep2-1L_S

description: Shielded Leaf at 4h, 1 leaves exp compared to 2 leaves

value: 1 leaf


title: UVB-2L_IR~3L_IR_Cy3-Rep1-3L_IR

description: Irrad. Leaf at 4h, 3 leaves exp compared to 2 leaves


title: RRE2_SKY_CH3COOH55_02_7DE1530

description: biological replicate, Date of Scan Thu Aug 27 11:46:28 2009

value: Salmonella Kentucky 3795

value: TSB


title: Kidney Mouse 165


title: Kidney Mouse 171


title: Kidney Mouse 168


title: RRE2_SEN_CH3COOH55_01_7DE1405

description: biological replicate, Date of Scan Tue Mar 24 11:46:25 2009

value: log phase culture


title: UVB-2L_S~3L_S_Cy3-Rep2-2L_S

description: Shielded Leaf at 4h, 2 leaves exp compared to 3 leaves

value: UVB


title: Kidney Mouse 167


title: UVB-1L_S~2L_S_Cy3-Rep1-2L_S

description: Shielded Leaf at 4h, 2 leaves exp compared to 1 leaves


title: UVB-1L_IR~1L_S_Cy3-Rep2-1L_IR

description: Irrad. Leaf compared to Shielded Leaf at 4h exp to 1 leaves

value: irradiated leaf sample


title: UVB-1L_IR~2L_IR_Cy3-Rep1-2L_IR

description: Irrad. Leaf at 4h, 2 leaves exp compared to 1 leaves

value: 2 leaves


title: Kidney Mouse 166


title: Kidney Mouse 164


title: Kidney Mouse 163


title: Kidney Mouse 162


title: UVB-1L_IR~2L_IR_Cy3-Rep2-1L_IR

description: Irrad. Leaf at 4h, 1 leaves exp compared to 2 leaves


title: Kidney Mouse 161


title: Kidney Mouse 157


title: UVB-1L_IR~1L_S_Cy3-Rep1-1L_S

description: Shielded Leaf compared to Irrad. Leaf at 4h exp to 1 leaves


title: Kidney Mouse 158


title: Kidney Mouse 159


title: Kidney Mouse 155


title: Kidney Mouse 156


title: Kidney Mouse 153


title: Kidney Mouse 150


title: Kidney Mouse 151


title: Kidney Mouse 154


title: Kidney Mouse 160


title: Patient 166

city: Cambridge

first: Nicholas

middle: B

last: Shannon

address: Robinson Way

department: Oncology

country: United Kingdom

institute: Cambridge Research Institute

description: sample id: D166

hyb_protocol: Pre-hybridization mixture was prepared using 50µl of Cy3-labeled test DNA, 50µl of Cy5-labeled reference DNA, 10mg Human Cot-1 DNA (Invitrogen, Carlsbad, CA, USA) and precipitated using 0.1 volume of 3 M sodium acetate pH 5.2 and 2.5 volume of ice-cold 100% ethanol, followed by centrifugation for 30 minutes at 14000 rpm and 4°C. The pellet was re-dissolved in 13 ml of yeast tRNA (100 mg/ml, Invitrogen, Carlsbad, CA, USA) and 26 ml of 20% SDS. 105µl of hybridization solution (4.3% (w/v) dextran sulphate (GE Healthcare, Little Chalfont, UK), 50% (v/v) ultra pure de-ionised formamide (Invitrogen, Carlsbad, CA, USA), 2.9x saline-sodium citrate (SSC) pH 7.0 (Sigma Aldrich, Paisley, UK)) was added and gently mixed. The hybridization mixture was then denatured (73°C, 10 minutes) and incubated (37°C, 60 minutes). Slide hybridization and washing were undertaken using a GeneTAC/HybArray12 hybridization station (Genomic Solutions, Huntingdon, UK), performed for 38 hours at 37°C using a continuous agitation mode. After hybridization, slides were washed for 6 cycles (flow for 10 seconds, hold for 20 seconds) with 50% (v/v) formamide/2x SSC (VWR International, Lutterworth, UK), 2 cycles with phosphate-buffer (0.1 M Na2HPO4, pH 8.0, 0.1% (v/v) Igepal CA630 (Sigma Aldrich, Paisley, UK)), 2 cycles with 0.2x SSC and 2 cycles with 0.1x SSC. Slides were then further washed with 0.01x SSC for 5 minutes whilst rocking and dried by centrifugation (1000 g, 3 minutes).

scan_protocol: The slides were scanned using an Agilent G2505B Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA). Laser power was set at 100%, PMT (photo multiplier tube) set at 100% and the split and rotate TIFF mode selected. Red and green channel TIFF format images were collected.

data_processing: Spot detection, intensity assessment analysis and quality control were fully automated using BlueFuse version 3.4 Build 5836 (BlueGnome, Cambridge, UK). Spots were excluded if the quality flag was <1 or the confidence level <0.1. Oligonucleotides from the human library were mapped to the human genome build NCBI35. Oligonucleotide sequences and mapping are available from Compugen, San Jose, CA, USA. The raw data were analyzed using snapCGH package of Bioconductor (http://www.bioconductor.org/) and re-scaled using global median normalization to account for the differences in individual hybridization intensities. MA plots were constructed to show the relationship between A (the “average signal” [0.5 x (log R + log G)], where R is the background subtracted red signal, G the background subtracted green and M the log2 R/G ratio. Each plot was reviewed by 2 independent reviewers (Rees JR and Chin SF). A cut-off of 2 times the standard deviation (SD, 0.29) above/below the mean log2 ratio (0.03) was employed for genomic gains/losses covering at least 5 oligonucleotides. A cut off of 3 SD from the mean was set for detection of high-level gains or amplifications and homozygous deletions (HDs).      Spot detection, intensity assessment analysis and quality control were fully automated using BlueFuse version 3.4 Build 5836 (BlueGnome, Cambridge, UK). Spots were excluded if the quality flag was <1 or the confidence level <0.1. Oligonucleotides from the human library were mapped to the human genome build NCBI35. Oligonucleotide sequences and mapping are available from Compugen, San Jose, CA, USA. The raw data were analyzed using snapCGH package of Bioconductor (http://www.bioconductor.org/) and re-scaled using global median normalization to account for the differences in individual hybridization intensities. MA plots were constructed to show the relationship between A (the “average signal” [0.5 x (log R + log G)], where R is the background subtracted red signal, G the background subtracted green and M the log2 R/G ratio. Each plot was reviewed by 2 independent reviewers (Rees JR and Chin SF). A cut-off of 2 times the standard deviation (SD, 0.29) above/below the mean log2 ratio (0.03) was employed for genomic gains/losses covering at least 5 oligonucleotides. A cut off of 3 SD from the mean was set for detection of high-level gains or amplifications and homozygous deletions (HDs).

source_name: esophageal adenocarcinoma

label_protocol: DNA labeling was performed using the BioPrime DNA labeling kit reagents (Invitrogen, Carlsbad, CA, USA) and according to protocols described previously (van den Ijssel, P et. al, 2005). 300ng of genomic DNA was mixed with 20µl of 2.5x random primer and miliQ water to a total volume of 42 µl. After the mixture was denatured, Cy3-dCTP (test sample) or Cy5-dCTP (pooled reference sample) and exo-klenow DNA polymerase were added to the mixture and incubated for 16 hours at 37°C. After removing unincorporated Cy3 and Cy5 using ProbeQuant G-50 Micro Spin Columns (GE Healthcare, Little Chalfont, UK), labeled DNA was collected in microfuge tubes. 5 dye-swap experiments were undertaken whereby the test sample was labeled with Cy5 and the reference sample with Cy3 to compare the consistency of data derived.

extract_protocol: On average, 10 30µm cryostat sections were prepared for the extraction of genomic DNA from tumor samples embedded in optimal cutting temperature mounting medium. DNA extracted was then cleaned using phenol:chloroform:isoamyl alcohol and precipitated using ethanol and sodium acetate.

tag: sex

value: Female

value: 89 years

tag: chemo-treated

value: No

tag: histological differentiation

value: Moderate

tag: days to death or last seen alive

source_name: pooled reference sample

tag: reference

value: pooled reference sample


title: Kidney Mouse 148

tag: strain

value: MRL/MpJ x SM/J F2

tag: gender


title: Patient 155

description: sample id: D155

value: Male

value: 51 years

value: Well


title: Patient 160

description: sample id: D160

value: 64 years

value: Poorly


title: Patient 154

description: sample id: D154

value: 71 years


title: Kidney Mouse 145

value: male

value: 13 weeks


title: Kidney Mouse 147


title: Kidney Mouse 149


title: Patient 167

description: sample id: D167

value: 77 years


title: Patient 156

description: sample id: D156

value: 72 years


title: Kidney Mouse 146


title: Patient 161

description: sample id: D161

value: 66 years


title: Patient 143

description: sample id: D143


title: Patient 141

description: sample id: D141

value: Female

value: 74 years


title: Kidney Mouse 144


title: Kidney Mouse 140


title: Kidney Mouse 143


title: Kidney Mouse 141


title: Kidney Mouse 142


title: Patient 139

description: sample id: D139

value: 70 years

value: No


title: Patient 138

description: sample id: D138

value: 75 years

value: Yes

value: pooled reference sample


title: RRE2_SEN_CH3COOH55_02_7DE1561

description: biological replicate, Date of Scan Wed Feb 04 12:41:39 2009

value: Salmonella Enteritidis NalR

value: log phase culture after 10min exposure to acidic conditions acetic acid pH5.5

value: TSB

value: log phase culture


title: Patient 129

description: sample id: D129

value: Male

value: 52 years

value: Poorly


title: Patient 121

description: sample id: D121

value: 82 years

value: Moderate


title: Kidney Mouse 138

value: MRL/MpJ x SM/J F2

value: male

value: 13 weeks


title: Kidney Mouse 173


title: Patient 120

description: sample id: D120

value: 65 years


title: Patient 133

description: sample id: D133

value: 78 years

value: No


title: Patient 134

description: sample id: D134


title: Kidney Mouse 135


title: Kidney Mouse 139


title: Kidney Mouse 136


title: Kidney Mouse 137


title: Kidney Mouse 152


title: Patient 126

description: sample id: D126


title: Patient 136

description: sample id: D136

value: 46 years


title: Kidney Mouse 134


title: Patient 107

description: sample id: D107 (missing processed data)

value: Female

value: pooled reference sample


title: Kidney Mouse 133


title: Kidney Mouse 132


title: Kidney Mouse 131


title: Kidney Mouse 129


title: Patient 117

description: sample id: D117

value: 75 years


title: Patient 128

description: sample id: D128


title: Kidney Mouse 127


title: Patient 101

description: sample id: D101

value: 51 years


title: Patient 105

description: sample id: D105


title: Patient 97

description: sample id: D97


title: Patient 115

description: sample id: D115

value: 64 years


title: Kidney Mouse 126


title: Kidney Mouse 130


title: Kidney Mouse 128


title: Kidney Mouse 121


title: Patient 96

description: sample id: D96

value: Male

value: 63 years


title: Kidney Mouse 124


title: Patient 118

description: sample id: D118


title: Patient 86

description: sample id: D86

value: 81 years


title: Kidney Mouse 123


title: Patient 58

description: sample id: D58

value: 68 years

value: Well


title: Patient 51

description: sample id: D51

value: 77 years

value: Moderate


title: Kidney Mouse 119

value: MRL/MpJ x SM/J F2

value: male

value: 13 weeks


title: Kidney Mouse 125


title: Kidney Mouse 122


title: Patient 50

description: sample id: D50

value: 58 years

value: Yes


title: Kidney Mouse 118


title: Patient 54

description: sample id: D54

value: 50 years

value: No


title: Kidney Mouse 120


title: Patient 52

description: sample id: D52

value: 73 years

value: Poorly

value: pooled reference sample


title: Patient 84

description: sample id: D84

value: Male

value: 54 years


title: Patient 53

description: sample id: D53


title: Patient 47

description: sample id: D47

value: 62 years


title: Kidney Mouse 117


title: Kidney Mouse 115


title: Kidney Mouse 112


title: Kidney Mouse 113


title: Kidney Mouse 116


title: Kidney Mouse 114


title: Patient 27

description: sample id: D27

value: 70 years


title: Patient 40

description: sample id: D40

value: 75 years


title: Kidney Mouse 109


title: Patient 36

description: sample id: D36

value: 81 years


title: Kidney Mouse 104


title: Kidney Mouse 111


title: Kidney Mouse 106


title: Patient 43

description: sample id: D43

value: 71 years

value: Moderate


title: Patient 35

description: sample id: D35

value: Female


title: Patient 29

description: sample id: D29

value: 63 years


title: Patient 25

description: sample id: D25

value: 59 years


title: Patient 38

description: sample id: D38


title: Kidney Mouse 110

value: MRL/MpJ x SM/J F2

value: male

value: 13 weeks


title: Patient 37

description: sample id: D37

value: 68 years

value: No

value: Well


title: Kidney Mouse 108


title: Patient 26

description: sample id: D26

value: 78 years

value: Poorly

value: pooled reference sample


title: Kidney Mouse 105


title: Patient 24

description: sample id: D24


title: Kidney Mouse 103


title: Kidney Mouse 107


title: Patient 23

description: sample id: D23

value: Male

value: 64 years


title: Patient 18

description: sample id: D18


title: Patient 2

description: sample id: D2 (missing processed data)


title: Patient 10

description: sample id: D10

value: 51 years


title: Kidney Mouse 101


title: Patient 13

description: sample id: D13


title: Kidney Mouse 100


title: Kidney Mouse 102


title: Patient 4

description: sample id: D4

value: 54 years


title: Patient 3

description: sample id: D3 (missing processed data)


title: Kidney Mouse 99


title: Patient 8

description: sample id: D8


title: Patient 5

description: sample id: D5

value: Moderate


title: Kidney Mouse 94


title: Kidney Mouse 95


title: Kidney Mouse 92


title: Kidney Mouse 89


title: Kidney Mouse 96


title: Kidney Mouse 91


title: Kidney Mouse 97


title: PGC_bFGF replacement_rep2

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

description: Gene expression data from PGCs after bFGF replacement.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Gallus gallus

source_name: PGCs after bFGF replacement

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: Approximately 2 μl of whole blood cells was taken from the dorsal aortae of stage 14–15 (H&H) (50–54 h of incubation) Korean Oge chicken embryos and cultured in medium comprising knockout Dulbecco’s modified Eagle’s medium (Invitrogen, Carlsbad, CA), 7.5% fetal bovine serum (Hyclone, Logan, UT), 2.5% chicken serum (Sigma-Aldrich, St. Louis, MO), 2 mM GlutaMAX-I Supplement (Invitrogen), 1× nucleosides (Millipore, Temecula, CA), 1× nonessential amino acids, β-mercaptoethanol, and 10 ng·ml–1 human bFGF (Sigma-Aldrich).

extract_protocol: Total RNA was extracted from three different treated cell samples using a RNeasy Total RNA Isolation Kit (Qiagen).

treatment_protocol: Cells were collected before and after withdrawal of bFGF for 24h, and 24h after bFGF replacement.

tag: breed

value: Korean Oge (KO)

value: whole blood

tag: cell type

value: primordial germ cells (PGCs)

value: embryonic day 2.5

tag: treatment

value: basic fibroblast growth factor (bFGF) replacement


title: PGC_bFGF replacement_rep3

tag: tissue


title: Kidney Mouse 87

value: MRL/MpJ x SM/J F2

value: male

value: 13 weeks


title: Kidney Mouse 88


title: PGC_bFGF withdrawal_rep3

description: Gene expression data from PGCs after bFGF withdrawal.

source_name: PGCs after bFGF withdrawal

value: basic fibroblast growth factor (bFGF) withdrawal


title: PGC_bFGF replacement_rep1


title: Kidney Mouse 86


title: Kidney Mouse 85


title: Kidney Mouse 90


title: PGC_bFGF withdrawal_rep1


title: Kidney Mouse 98


title: PGC_Raw_rep3

description: Gene expression data from PGCs not subjected to bFGF withdrawal.

source_name: PGCs not subjected to bFGF withdrawal

value: basic fibroblast growth factor (bFGF)


title: Kidney Mouse 84


title: PGC_bFGF withdrawal_rep2


title: PGC_Raw_rep2


title: Kidney Mouse 83


title: Kidney Mouse 80


title: PGC_Raw_rep1


title: Kidney Mouse 82


title: Kidney Mouse 79


title: Marginal zone B-cell lymphoma patient sample 08-821

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

description:
08-821.CEL
Hybridized to 250K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Data acquisition was performed using the GeneChip Operating Software (GCOS) v1.4 and Genotyping Analysis Software (GTYPE) v4.1. Genotype calls were calculated using the BRLMM algorithm. Mapping data for probes were derived from the National Center for Biotechnology Information (NCBI) Human Genome Build 36, as provided by Affymetrix, which was used for all subsequent analyses. The modified Bayesian Piecewise Regression (mBPCR) method was used to estimate the copy number (CN) starting from raw CN values obtained with Affymetrix CNAT 4.01 using a Gaussian bandwidth of 0 Kb and 46 Caucasian normal female samples of the HapMap Project as reference samples.
signal = log2ratio; loh = 0 or 1

label: Biotin

source_name: MZL patient sample 08-821

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: All clinical specimens were derived from involved sites and obtained in the course of routine diagnostic procedures before therapy initiation. Cases were selected based upon the availability of frozen material with a fraction of neoplastic cells in the specimen representing >70% of overall cellularity as determined by morphologic and/or immunophenotypic studies. Genomic DNA was extracted using the QIAamp DNA Mini Kit.

value: marginal zone lymphoma

tag: diagnosis

value: SMZL


title: Kidney Mouse 78


title: Kidney Mouse 81


title: Kidney Mouse 77


title: Kidney Mouse 93


title: Kidney Mouse 75


title: Marginal zone B-cell lymphoma patient sample 08-819

description:
08-819.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-819


title: Kidney Mouse 73


title: Kidney Mouse 71


title: Kidney Mouse 76


title: Marginal zone B-cell lymphoma patient sample 08-817

description:
08-817.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-817


title: Kidney Mouse 72


title: Marginal zone B-cell lymphoma patient sample 08-818

description:
08-818.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-818


title: Kidney Mouse 66


title: Kidney Mouse 70


title: Kidney Mouse 69


title: Kidney Mouse 74


title: Kidney Mouse 68


title: Kidney Mouse 67


title: Marginal zone B-cell lymphoma patient sample 08-814

description:
08-814.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-814


title: Marginal zone B-cell lymphoma patient sample 08-816

description:
08-816.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-816


title: Marginal zone B-cell lymphoma patient sample 08-815

description:
08-815.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-815


title: Marginal zone B-cell lymphoma patient sample 08-810

description:
08-810.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-810


title: Marginal zone B-cell lymphoma patient sample 08-812

description:
08-812.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-812


title: Kidney Mouse 64


title: Marginal zone B-cell lymphoma patient sample 08-806

description:
08-806.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-806


title: Marginal zone B-cell lymphoma patient sample 08-805

description:
08-805.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-805


title: Marginal zone B-cell lymphoma patient sample 08-807

description:
08-807.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-807


title: Kidney Mouse 62

source_name: Kidney


title: Marginal zone B-cell lymphoma patient sample 08-813

description:
08-813.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-813


title: Kidney Mouse 63


title: Kidney Mouse 55


title: Kidney Mouse 60


title: Kidney Mouse 65


title: Kidney Mouse 59


title: Kidney Mouse 58


title: Kidney Mouse 57


title: Marginal zone B-cell lymphoma patient sample 08-808

description:
08-808.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-808


title: Kidney Mouse 56


title: Kidney Mouse 53


title: Kidney Mouse 61


title: Kidney Mouse 50


title: Kidney Mouse 54


title: Marginal zone B-cell lymphoma patient sample 08-802

description:
08-802.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-802


title: Marginal zone B-cell lymphoma patient sample 08-801

description:
08-801.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-801


title: Marginal zone B-cell lymphoma patient sample 08-803

description:
08-803.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-803


title: Kidney Mouse 49


title: Marginal zone B-cell lymphoma patient sample 08-798

description:
08-798.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-798


title: Kidney Mouse 51


title: Marginal zone B-cell lymphoma patient sample 08-800

description:
08-800.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-800


title: Kidney Mouse 48


title: Kidney Mouse 52


title: Marginal zone B-cell lymphoma patient sample 08-799

description:
08-799.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-799


title: Kidney Mouse 47


title: Kidney Mouse 44


title: Kidney Mouse 46


title: Marginal zone B-cell lymphoma patient sample 08-791

description:
08-791.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-791


title: Marginal zone B-cell lymphoma patient sample 08-796

description:
08-796.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-796


title: Kidney Mouse 43


title: Kidney Mouse 45


title: Marginal zone B-cell lymphoma patient sample 08-795

description:
08-795.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-795


title: Kidney Mouse 41


title: Kidney Mouse 42


title: Marginal zone B-cell lymphoma patient sample 08-792

description:
08-792.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-792


title: Kidney Mouse 40


title: Kidney Mouse 37


title: Marginal zone B-cell lymphoma patient sample 08-790

description:
08-790.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-790


title: Marginal zone B-cell lymphoma patient sample 08-788

description:
08-788.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-788


title: Kidney Mouse 32


title: Kidney Mouse 39


title: Marginal zone B-cell lymphoma patient sample 08-804

description:
08-804.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-804


title: Marginal zone B-cell lymphoma patient sample 08-787

description:
08-787.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-787


title: Kidney Mouse 31

source_name: Kidney


title: Kidney Mouse 35


title: Kidney Mouse 30


title: Kidney Mouse 36


title: Kidney Mouse 38


title: Kidney Mouse 33


title: Marginal zone B-cell lymphoma patient sample 08-786

description:
08-786.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-786


title: Kidney Mouse 34


title: Kidney Mouse 29


title: Marginal zone B-cell lymphoma patient sample 08-777

description:
08-777.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-777


title: Kidney Mouse 27


title: Kidney Mouse 26


title: Kidney Mouse 23


title: Kidney Mouse 25


title: Kidney Mouse 24


title: Marginal zone B-cell lymphoma patient sample 08-776

description:
08-776.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-776


title: Kidney Mouse 19


title: Marginal zone B-cell lymphoma patient sample 08-780

description:
08-780.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-780


title: Marginal zone B-cell lymphoma patient sample 08-779

description:
08-779.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-779


title: Marginal zone B-cell lymphoma patient sample 08-785

description:
08-785.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-785


title: Marginal zone B-cell lymphoma patient sample 08-773

description:
08-773.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-773


title: Kidney Mouse 15


title: Kidney Mouse 21


title: Kidney Mouse 16


title: Marginal zone B-cell lymphoma patient sample 08-772

description:
08-772.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-772


title: Kidney Mouse 17


title: Kidney Mouse 18


title: Kidney Mouse 14


title: Marginal zone B-cell lymphoma patient sample 08-774

description:
08-774.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-774


title: Kidney Mouse 28


title: Kidney Mouse 22


title: Kidney Mouse 12


title: Marginal zone B-cell lymphoma patient sample 08-671_4

description:
08-671_4.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-671_4


title: Marginal zone B-cell lymphoma patient sample 08-670

description:
08-670.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-670


title: Marginal zone B-cell lymphoma patient sample 08-768

description:
08-768.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-768


title: Kidney Mouse 11


title: Marginal zone B-cell lymphoma patient sample 08-770

description:
08-770.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-770


title: Kidney Mouse 6


title: Kidney Mouse 10


title: Kidney Mouse 9


title: Kidney Mouse 8


title: Kidney Mouse 3


title: Kidney Mouse 2


title: Kidney Mouse 5


title: Kidney Mouse 7


title: Kidney Mouse 4


title: Kidney Mouse 1


title: NM8

city: Raleigh

first: Marlene

last: Hauck

address: 4700 Hillsborough Street

department: Clinical Sciences

institute: North Carolina State University

hyb_protocol: Following fragmentation, 2 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Canine GeneChip version 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000

data_processing: Data were analyzed with JMPGenomics software (SAS).  Normalization was performed with dChip.

organism: Canis lupus familiaris

source_name: non-metastatic sarcoma

label_protocol: Affymetrix 1-cycle 3' IVT labeling kit

extract_protocol: Rneasy mini-kit from Qiagen

treatment_protocol: Untreated tumors

tag: tissue type

value: Primary tumor

tag: disease group

value: non-metastatic


title: sporadic breast tumor, Invasive Ductal Carcinoma_C069_Q500B2

city: Amsterdam

first: Petra

last: Nederlof

address: Plesmanlaan 121

department: Pathology

country: Netherlands

institute: The Netherlands Cancer Institute

hyb_protocol: hybridization as describe in Joosse SA, van Beers EH, Nederlof PM. Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. BMC Cancer 2007;7:43.

scan_protocol: ImaGene v6.0 software (BioDiscovery Inc) was used to translate the cy5/cy3 intensity ratios into average of the triplicates log2-ratio.

data_processing: average of triplicate Log2 ratios after Lowess pintip normalization

source_name: FFPE primary breast tumor material sporadic case

label_protocol: Sample and reference DNA were labeled with the Cy5- or Cy3-conjugates from the Universal Linkages System (ULS; Kreatech biotechnology, Amsterdam, The Netherlands)

extract_protocol: DNA isolation for arrayCGH was performed as described elsewhere. (20) In short, formalin-fixed paraffin-embedded FFPE tissue of uterine corpus cancer was used. Cases were discarded if the tumor cell percentage was below 70%.  Genomic DNA was isolated from 10*10µm thick paraffin slides. Slides were deparaffinized twice in xylene for 5 minutes, rehydrated in 100% (twice), 90%,70% ethanol and stained with hematoxylin. To remove formalin induced cross-links an overnight incubation in 1M NaSCN at 37°C was performed. Slides were subsequently washed in PBS twice for 10 minutes and air-dried. Tumor cells were collected by macro dissection by scraping from the slides and cells were transferred to a tube containing 200 µl ATL buffer (QIAamp® DNA Mini Kit cat 51304, Qiagen), 27 µl Proteinase-K was added and samples were incubated at 55°C while shaken at 450 rmp for at least 40 hours.  At intervals of 4, 16 and 24 hours additional 27 µl of Proteinase-K was added (Qiagen kit). Further isolation was done following the manufacturers instructions (Qiagen).

value: female

tag: tumor

value: breast canrcinoma

tag: histology

value: LCIS

tag: age at diagnosis

tag: tumor grade

tag: er ihc

value: positive

tag: pr ihc

value: negative

tag: her2 ihc

source_name: genomic DNA from blood from 8 healthy females


title: NM7


title: Marginal zone B-cell lymphoma patient sample 08-668

description:
08-668.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-668


title: Marginal zone B-cell lymphoma patient sample 08-669

description:
08-669.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-669


title: Marginal zone B-cell lymphoma patient sample 08-666

description:
08-666.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-666


title: Marginal zone B-cell lymphoma patient sample 08-665

description:
08-665.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-665


title: Marginal zone B-cell lymphoma patient sample 08-667_3

description:
08-667_3.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-667_3

value: MZL


title: NM5


title: sporadic breast tumor, Invasive Ductal Carcinoma_C065_Q449C1

value: Invasive ductal carcinoma

tag: reference

value: genomic DNA from blood from 8 healthy females


title: sporadic breast tumor, Invasive Ductal Carcinoma_C067_Q449C2


title: sporadic breast tumor, Invasive Ductal Carcinoma_C068_Q449C0


title: sporadic breast tumor, Invasive Ductal Carcinoma_C063_Q500B1


title: NM4


title: sporadic breast tumor, Invasive Ductal Carcinoma_C060_Q425B4


title: sporadic breast tumor, Invasive Lobular Carcinoma_C061_Q449E1

value: Invasive lobular carcinoma


title: NM6


title: Marginal zone B-cell lymphoma patient sample 08-465

description:
08-465.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-465

value: NMZL


title: Marginal zone B-cell lymphoma patient sample 08-664_2

description:
08-664_2.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-664_2


title: NM3


title: Marginal zone B-cell lymphoma patient sample 08-464

description:
08-464.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-464

value: EMZL


title: NM1


title: sporadic breast tumor, Invasive Ductal Carcinoma_C058_Q449D6


title: Kidney Mouse 13

source_name: Kidney

tag: strain

value: MRL/MpJ x SM/J F2

value: male

tag: age

value: 13 weeks


title: sporadic breast tumor, Invasive Ductal Carcinoma_C051_Q427C5

tag: gender


title: sporadic breast tumor, Invasive Ductal Carcinoma_C057_Q427C8


title: NM2


title: sporadic breast tumor, Invasive Ductal Carcinoma_C056_Q455D4


title: sporadic breast tumor, Invasive Ductal Carcinoma_C052_Q425A0


title: Marginal zone B-cell lymphoma patient sample 08-462

description:
08-462.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-462

tag: cell type

value: marginal zone lymphoma


title: Marginal zone B-cell lymphoma patient sample 08-458

description:
08-458.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-458


title: MET3

source_name: metastatic sarcoma

value: Primary tumor

value: metastatic


title: MET5


title: Oral leukoplakia LM416

city: Houston

first: Pierre

last: Saintigny

address: 1515 Holcombe

department: Thoracic / Head and Neck Medical Oncology

institute: The University of Texas M.D. Anderson Cancer Center

description: RNA was extracted and purified from OCT-embedded tissue using the RNeasy Mini Kit (Qiagen) including on-column DNase (Qiagen) digestion as described by the manufacturer's protocol. RNA amplifications were performed using the WT-Amplification™ Pico (NuGEN) kit. For all experiments, the manufacturers' protocols were strictly followed. WT-Ovation™ Pico products (NuGEN) are labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). Each labeled cRNA targets are synthesized according to manufacturer's protocols. The quantity and quality of the amplified cRNA or cDNA were assessed by a ND-1000 spectrophotometer (Nanodrop Technologies), and Agilent Bioanalyzer (Agilent Technologies), respectively. Hybridization mixtures were prepared according to Affymetrix procedures to accommodate 5 μg of cDNA targets from NuGEN amplification. Human Gene 1.ST platform were hybridized, revealed and washed according to the Affymetrix protocol. Gene chips were scanned using a 7 G scanner (Affymetrix) and images (DAT files) were converted to CEL files using GCOS software (Affymetrix).

data_processing: Raw data of microarrays were processed using quantile normalization and RMA algorithm (RMAExpress); expression values were log2 transformed

source_name: Oral leukoplakia

growth_protocol: Biopsies of oral leukoplakia

treatment_protocol: Samples were OCT-embedded and frozen before RNA extraction

tag: Sex

tag: race

value: white

tag: alcohol habits

value: current

tag: smoking habits

value: never

tag: treatment arm

value: 13-cis-retinoic acid

tag: histology at baseline (hyperplasia versus dysplasia)

value: hyperplasia

tag: histology at baseline (breakdown)

tag: p63 expression

value: low expression

tag: podoplanin expression

tag: oral cancer-free survival time (years)

tag: outcome

value: no oral cancer development

tag: time of biopsy

value: biopsy at 3 months after inclusion


title: Oral leukoplakia LM417

hyb_protocol: Hybridization mixtures were prepared according to Affymetrix procedures to accommodate 5 μg of cDNA targets from NuGEN amplification. Human Gene 1.ST platform were hybridized, revealed and washed according to the Affymetrix protocol.

scan_protocol: Gene chips were scanned using a 7 G scanner (Affymetrix) and images (DAT files) were converted to CEL files using GCOS software (Affymetrix).

label_protocol: WT-Ovation™ Pico products (NuGEN) are labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). Each labeled cRNA targets are synthesized according to manufacturer's protocols.

extract_protocol: RNA was extracted and purified from OCT-embedded tissue using the RNeasy Mini Kit (Qiagen) including on-column DNase (Qiagen) digestion as described by the manufacturer's protocol.

value: female

value: retinyl palmitate

value: high expression

value: oral cancer development

value: biopsy at baseline


title: MET4

tag: tissue type

tag: disease group


title: sporadic breast tumor, Invasive Ductal Carcinoma_C049_Q455D0

tag: tumor

value: breast canrcinoma

tag: histology

value: Invasive ductal carcinoma

tag: age at diagnosis

tag: tumor grade

tag: er ihc

value: negative

tag: pr ihc

tag: her2 ihc

tag: reference

value: genomic DNA from blood from 8 healthy females


title: Kidney Mouse 20

tag: strain

value: MRL/MpJ x SM/J F2

tag: gender

value: male

tag: age

value: 13 weeks


title: Marginal zone B-cell lymphoma patient sample 08-457

description:
08-457.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-457

tag: cell type

value: marginal zone lymphoma

tag: diagnosis

value: EMZL


title: Marginal zone B-cell lymphoma patient sample 08-672

description:
08-672.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-672

value: SMZL


title: MET1

value: Primary tumor

value: metastatic


title: MET2


title: Marginal zone B-cell lymphoma patient sample 08-454

description:
08-454.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-454


title: Marginal zone B-cell lymphoma patient sample 08-459

description:
08-459.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-459

value: NMZL


title: Marginal zone B-cell lymphoma patient sample 08-453

description:
08-453.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-453


title: sporadic breast tumor, Invasive Ductal Carcinoma_C048_Q449D8

source_name: FFPE primary breast tumor material sporadic case

value: female

value: positive

source_name: genomic DNA from blood from 8 healthy females


title: Oral leukoplakia LM415

tag: Sex

tag: race

value: white

tag: alcohol habits

value: current

tag: smoking habits

tag: treatment arm

value: 13-cis-retinoic acid

tag: histology at baseline (hyperplasia versus dysplasia)

value: hyperplasia

tag: histology at baseline (breakdown)

tag: p63 expression

value: low expression

tag: podoplanin expression

tag: oral cancer-free survival time (years)

tag: outcome

value: no oral cancer development


title: sporadic breast tumor, Invasive Lobular Carcinoma_C047_Q455D3

tag: tumor

value: breast canrcinoma

tag: histology

value: Invasive lobular carcinoma

tag: age at diagnosis

tag: tumor grade

tag: er ihc

value: negative

tag: pr ihc

tag: her2 ihc

tag: reference

value: genomic DNA from blood from 8 healthy females


title: Marginal zone B-cell lymphoma patient sample 08-390

description:
08-390.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-390

tag: cell type

value: marginal zone lymphoma

tag: diagnosis


title: Marginal zone B-cell lymphoma patient sample 08-449

description:
08-449.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-449

value: EMZL


title: sporadic breast tumor, Invasive Lobular Carcinoma_C046_Q455C9

tag: gender


title: Marginal zone B-cell lymphoma patient sample 08-447

description:
08-447.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-447


title: Oral leukoplakia LM413

tag: Sex

tag: race

tag: alcohol habits

tag: smoking habits

value: never

tag: age

tag: treatment arm

tag: histology at baseline (hyperplasia versus dysplasia)

value: high expression

tag: time of biopsy

value: biopsy at baseline


title: Marginal zone B-cell lymphoma patient sample 08-450

description:
08-450.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-450


title: Oral leukoplakia LM414

value: female

value: beta-carotene

value: dysplasia

tag: histology at baseline (breakdown)

value: moderate dysplasia

tag: p63 expression

tag: podoplanin expression

tag: oral cancer-free survival time (years)

tag: outcome


title: Marginal zone B-cell lymphoma patient sample 08-389

description:
08-389.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-389

value: NMZL


title: sporadic breast tumor, Invasive Ductal Carcinoma_C044_Q427C4

tag: tumor

tag: histology

value: Invasive ductal carcinoma

tag: age at diagnosis

tag: tumor grade

tag: er ihc

value: positive

tag: pr ihc

tag: her2 ihc

tag: reference


title: Marginal zone B-cell lymphoma patient sample 08-257

description:
08-257.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-257

tag: cell type

tag: diagnosis


title: Oral leukoplakia LM410

tag: Sex

value: male

tag: race

value: white

tag: alcohol habits

value: current

tag: smoking habits

tag: age

tag: treatment arm

value: retinyl palmitate

tag: histology at baseline (hyperplasia versus dysplasia)

value: hyperplasia

value: low expression

value: no oral cancer development


title: Oral leukoplakia LM412

value: asian

value: never

value: 13-cis-retinoic acid

tag: histology at baseline (breakdown)

tag: p63 expression

tag: podoplanin expression

tag: oral cancer-free survival time (years)

tag: outcome

tag: time of biopsy


title: sporadic breast tumor, Invasive Ductal Carcinoma_C043_Q425B3

tag: gender

value: female

tag: tumor

value: breast canrcinoma

tag: histology

tag: age at diagnosis

tag: tumor grade

tag: er ihc

value: negative

tag: pr ihc

tag: her2 ihc

value: genomic DNA from blood from 8 healthy females


title: sporadic breast tumor, Invasive Ductal Carcinoma_C042_Q427C2

tag: reference


title: Marginal zone B-cell lymphoma patient sample 08-250

description:
08-250.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-250

tag: cell type

value: marginal zone lymphoma

tag: diagnosis

value: SMZL


title: Oral leukoplakia LM411

tag: Sex

tag: race

tag: alcohol habits

tag: smoking habits

tag: age

tag: treatment arm

tag: histology at baseline (hyperplasia versus dysplasia)

tag: histology at baseline (breakdown)

value: high expression

value: biopsy at baseline


title: Oral leukoplakia LM409

value: white

value: dysplasia

tag: p63 expression

tag: podoplanin expression

tag: oral cancer-free survival time (years)

tag: outcome

tag: time of biopsy


title: sporadic breast tumor, Invasive Ductal Carcinoma_C035_Q449B9

tag: gender

tag: tumor

tag: histology

value: Invasive ductal carcinoma

tag: age at diagnosis

tag: tumor grade

tag: er ihc

tag: pr ihc

tag: her2 ihc


title: Marginal zone B-cell lymphoma patient sample 08-246

description:
08-246.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-246

tag: cell type

tag: diagnosis

value: EMZL


title: Oral leukoplakia LM408

tag: Sex

tag: race

tag: alcohol habits

value: current

tag: smoking habits

tag: age

tag: treatment arm

tag: histology at baseline (hyperplasia versus dysplasia)

value: hyperplasia

value: low expression


title: Marginal zone B-cell lymphoma patient sample 08-245

description:
08-245.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-245


title: Marginal zone B-cell lymphoma patient sample 08-244

description:
08-244.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-244

value: MZL


title: sporadic breast tumor, Invasive Lobular Carcinoma_C034_Q427C0

tag: gender

value: Invasive lobular carcinoma

value: positive

tag: reference


title: Oral leukoplakia LM406

source_name: Oral leukoplakia

value: female

value: former

value: 13-cis-retinoic acid

tag: histology at baseline (breakdown)

value: mild dysplasia

tag: p63 expression

tag: podoplanin expression

tag: oral cancer-free survival time (years)

tag: outcome

value: oral cancer development

tag: time of biopsy

value: biopsy at 3 months after inclusion


title: Oral leukoplakia LM405

value: male

value: never

value: beta-carotene


title: Oral leukoplakia LM407

value: white

value: retinyl palmitate

value: dysplasia


title: Marginal zone B-cell lymphoma patient sample 08-242

description:
08-242.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-242

tag: cell type

value: marginal zone lymphoma

value: SMZL


title: sporadic breast tumor, Invasive Lobular Carcinoma_C037_Q425A2

tag: tumor

value: breast canrcinoma

tag: histology

tag: age at diagnosis

tag: tumor grade

tag: er ihc

tag: pr ihc

tag: her2 ihc

value: negative

value: genomic DNA from blood from 8 healthy females


title: sporadic breast tumor, Invasive Ductal Carcinoma_C036_Q427B8

value: female

value: Invasive ductal carcinoma

value: positive


title: Oral leukoplakia LM404

tag: Sex

tag: race

tag: alcohol habits

value: current

tag: smoking habits

tag: age

tag: treatment arm

value: 13-cis-retinoic acid

tag: histology at baseline (hyperplasia versus dysplasia)

value: hyperplasia

value: low expression

value: high expression

value: biopsy at baseline


title: sporadic breast tumor, Invasive Ductal Carcinoma_C039_Q425B9

tag: gender

tag: reference


title: sporadic breast tumor, Invasive Ductal Carcinoma_C033_Q455D1