title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430025_A

description: Sample name: 5502430025_A


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430034_D

status: Public on May 12 2014

type: RNA

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

country: USA

institute: Rutgers University

description: Sample name: 5502430034_D

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were loaded and background corrected with BeadStudio. The resulting matrix was VST transformed and RSN normalized with lumiT and lumiN functions from lumi package in R.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: prostate tumor/tissue

label_protocol: Amplification and Labeling was done using the Illumina TotalPrep-96 Amplification kit

extract_protocol: RNA was extracted using the MagMAX-96 RNA isolation kit (Ambion). Quality control was performed with Agilent Bioanalyser.(I do not think we used Agilent….)

treatment_protocol: Mice were treated dailly for 5 consecutive days with the indicated drugs and prostate tumor/tissues harvested the fifth day

tag: strain

tag: genotype/variation

tag: cancer type

value: NPK

tag: treatment


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430025_F

description: Sample name: 5502430025_F

value: Sorafenib


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430034_B

description: Sample name: 5502430034_B


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430025_C

description: Sample name: 5502430025_C

value: Docetaxel


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430021_F

description: Sample name: 5502430021_F

value: Testosterone


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430021_D

description: Sample name: 5502430021_D

value: Rapamycin


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430025_D

description: Sample name: 5502430025_D

value: Dasatinib


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430020_E

description: Sample name: 5502430020_E


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430034_A

description: Sample name: 5502430034_A

value: Calcitriol


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430020_F

description: Sample name: 5502430020_F

value: Vehicle


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430021_E

description: Sample name: 5502430021_E


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430020_C

description: Sample name: 5502430020_C


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430021_B

description: Sample name: 5502430021_B


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430025_E

description: Sample name: 5502430025_E


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5513075039_E

description: Sample name: 5513075039_E

value: NP-Ai


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430020_B

description: Sample name: 5502430020_B


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430021_C

description: Sample name: 5502430021_C


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430020_A

description: Sample name: 5502430020_A


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5513075039_D

description: Sample name: 5513075039_D


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5513075039_A

description: Sample name: 5513075039_A


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5502430026_F

description: Sample name: 5502430026_F


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5513075039_B

description: Sample name: 5513075039_B


title: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice) 5502430020_D

description: Sample name: 5502430020_D


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5502430026_E

description: Sample name: 5502430026_E

value: Imatinib


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5502430026_D

description: Sample name: 5502430026_D


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5502430026_A

description: Sample name: 5502430026_A


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5513075039_C

description: Sample name: 5513075039_C


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5502430026_C

description: Sample name: 5502430026_C


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5513075039_F

description: Sample name: 5513075039_F


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5502430026_B

description: Sample name: 5502430026_B


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5316830044_D

description: Sample name: 5316830044_D


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5316830044_E

description: Sample name: 5316830044_E


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5316830025_F

description: Sample name: 5316830025_F


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5316830025_E

description: Sample name: 5316830025_E


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5316830044_A

description: Sample name: 5316830044_A


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5316830025_A

description: Sample name: 5316830025_A


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5316830044_F

description: Sample name: 5316830044_F


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5312759023_D

description: Sample name: 5312759023_D


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5316830044_C

description: Sample name: 5316830044_C


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5316830025_D

description: Sample name: 5316830025_D


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5312759023_B

description: Sample name: 5312759023_B


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5312759023_C

description: Sample name: 5312759023_C


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5316830025_B

description: Sample name: 5316830025_B


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5316830025_C

description: Sample name: 5316830025_C


title: Wild_type 5513075027_A

description: Sample name: 5513075027_A

value: wild-type


title: Wild_type 5513075027_E

description: Sample name: 5513075027_E


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5312759023_A

description: Sample name: 5312759023_A


title: Wild_type 5513075027_B

description: Sample name: 5513075027_B


title: Wild_type 5513075027_F

description: Sample name: 5513075027_F


title: Nkx3.1CreERT2/+; Ptenflox/flox (castrated) (NP-Ai mice) 5312759023_F

description: Sample name: 5312759023_F


title: Wild_type 5513075026_F

description: Sample name: 5513075026_F


title: Wild_type 5513075025_F

description: Sample name: 5513075025_F


title: Wild_type 5513075026_D

description: Sample name: 5513075026_D


title: Wild_type 5513075026_A

description: Sample name: 5513075026_A


title: Wild_type 5513075027_C

description: Sample name: 5513075027_C


title: Wild_type 5513075026_C

description: Sample name: 5513075026_C


title: Wild_type 5513075027_D

description: Sample name: 5513075027_D


title: Wild_type 5513075025_D

description: Sample name: 5513075025_D


title: Wild_type 5513075026_E

description: Sample name: 5513075026_E


title: Wild_type 5513075025_A

description: Sample name: 5513075025_A


title: Wild_type 5513075004_C

description: Sample name: 5513075004_C


title: Wild_type 5513075025_C

description: Sample name: 5513075025_C


title: Wild_type 5513075006_C

description: Sample name: 5513075006_C


title: Wild_type 5513075006_F

description: Sample name: 5513075006_F


title: Wild_type 5513075004_F

description: Sample name: 5513075004_F


title: Wild_type 5513075006_E

description: Sample name: 5513075006_E


title: Pb-TagAPT121 (APT mice) 5312759007_D

description: Sample name: 5312759007_D

value: Pb-TagAPT121 (APT mice)

value: APT


title: Wild_type 5513075004_B

description: Sample name: 5513075004_B


title: Wild_type 5513075025_B

description: Sample name: 5513075025_B


title: Pb-TagAPT121 (APT mice) 5312759007_E

description: Sample name: 5312759007_E


title: Wild_type 5513075006_D

description: Sample name: 5513075006_D


title: Pb-TagAPT121 (APT mice) 5535696007_F

description: Sample name: 5535696007_F


title: Wild_type 5513075006_A

description: Sample name: 5513075006_A


title: Pb-TagAPT121 (APT mice) 5312759020_D

description: Sample name: 5312759020_D


title: Pb-TagAPT121 (APT mice) 5312759020_F

description: Sample name: 5312759020_F


title: Pb-TagAPT121 (APT mice) 5312759007_C

description: Sample name: 5312759007_C


title: Pb-TagAPT121 (APT mice) 5312759020_A

description: Sample name: 5312759020_A


title: Wild_type 5513075004_D

description: Sample name: 5513075004_D


title: Wild_type 5513075006_B

description: Sample name: 5513075006_B


title: Pb-TagAPT121 (APT mice) 5312759020_C

description: Sample name: 5312759020_C


title: Pb-TagAPT121 (APT mice) 5535696008_C

description: Sample name: 5535696008_C


title: Pb-TagAPT121 (APT mice) 5312759007_F

description: Sample name: 5312759007_F


title: Pb-TagAPT121 (APT mice) 5312759007_A

description: Sample name: 5312759007_A


title: Wild_type 5513075004_E

description: Sample name: 5513075004_E


title: Pb-TagAPT121 (APT mice) 5312759018_F

description: Sample name: 5312759018_F


title: Wild_type 5513075004_A

description: Sample name: 5513075004_A


title: Pb-TagAPT121 (APT mice) 5312759020_E

description: Sample name: 5312759020_E


title: Pb-TagAPT121 (APT mice) 5312759018_D

description: Sample name: 5312759018_D


title: Pb-TagAPT121 (APT mice) 5312759018_A

description: Sample name: 5312759018_A


title: Pb-TagAPT121 (APT mice) 5312759003_A

description: Sample name: 5312759003_A


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830047_D

description: Sample name: 5316830047_D

value: B6D2F1/J C57Bl/6J

value: Pb-TagAPT121; Pten+/- (APT-P mice)

value: APT-P


title: Pb-TagAPT121 (APT mice) 5312759003_B

description: Sample name: 5312759003_B


title: Pb-TagAPT121 (APT mice) 5312759020_B

description: Sample name: 5312759020_B


title: Pb-TagAPT121 (APT mice) 5312759002_F

description: Sample name: 5312759002_F


title: Pb-TagAPT121 (APT mice) 5312759002_D

description: Sample name: 5312759002_D


title: Pb-TagAPT121 (APT mice) 5312759003_C

description: Sample name: 5312759003_C


title: Pb-TagAPT121 (APT mice) 5312759002_E

description: Sample name: 5312759002_E


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830047_F

description: Sample name: 5316830047_F


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830047_A

description: Sample name: 5316830047_A


title: Pb-TagAPT121 (APT mice) 5312759003_E

description: Sample name: 5312759003_E


title: Pb-TagAPT121 (APT mice) 5312759002_A

description: Sample name: 5312759002_A


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830042_D

description: Sample name: 5316830042_D


title: Pb-TagAPT121 (APT mice) 5312759002_B

description: Sample name: 5312759002_B


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830042_E

description: Sample name: 5316830042_E


title: Pb-TagAPT121 (APT mice) 5312759018_B

description: Sample name: 5312759018_B


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830042_C

description: Sample name: 5316830042_C


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830047_B

description: Sample name: 5316830047_B


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830042_A

description: Sample name: 5316830042_A


title: Pb-TagAPT121 (APT mice) 5312759018_C

description: Sample name: 5312759018_C


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830041_E

description: Sample name: 5316830041_E


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830041_C

description: Sample name: 5316830041_C


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830041_A

description: Sample name: 5316830041_A


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830043_F

description: Sample name: 5316830043_F


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830042_B

description: Sample name: 5316830042_B


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830041_D

description: Sample name: 5316830041_D


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830042_F

description: Sample name: 5316830042_F


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830047_C

description: Sample name: 5316830047_C


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830043_A

description: Sample name: 5316830043_A


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830040_F

description: Sample name: 5316830040_F


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830043_B

description: Sample name: 5316830043_B


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830040_E

description: Sample name: 5316830040_E


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830043_C

description: Sample name: 5316830043_C


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830040_A

description: Sample name: 5316830040_A


title: ARR2PB-Myc (Myc mice) 5316830051_D

description: Sample name: 5316830051_D

value: FVB

value: ARR2PB-Myc (Myc mice)

value: Myc


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830040_D

description: Sample name: 5316830040_D


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830040_C

description: Sample name: 5316830040_C


title: ARR2PB-Myc (Myc mice) 5316830049_F

description: Sample name: 5316830049_F


title: ARR2PB-Myc (Myc mice) 5316830051_C

description: Sample name: 5316830051_C

value: Docetaxel


title: ARR2PB-Myc (Myc mice) 5316830051_F

description: Sample name: 5316830051_F

value: Sorafenib


title: ARR2PB-Myc (Myc mice) 5316830049_A

description: Sample name: 5316830049_A

value: Rapamycin


title: ARR2PB-Myc (Myc mice) 5316830051_E

description: Sample name: 5316830051_E


title: ARR2PB-Myc (Myc mice) 5316830049_B

description: Sample name: 5316830049_B


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830043_D

description: Sample name: 5316830043_D


title: ARR2PB-Myc (Myc mice) 5316830049_E

description: Sample name: 5316830049_E


title: ARR2PB-Myc (Myc mice) 5316830051_A

description: Sample name: 5316830051_A


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830040_B

description: Sample name: 5316830040_B


title: ARR2PB-Myc (Myc mice) 5316830046_F

description: Sample name: 5316830046_F


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830041_F

description: Sample name: 5316830041_F


title: ARR2PB-Myc (Myc mice) 5316830046_E

description: Sample name: 5316830046_E


title: ARR2PB-Myc (Myc mice) 5316830046_C

description: Sample name: 5316830046_C


title: ARR2PB-Myc (Myc mice) 5316830046_D

description: Sample name: 5316830046_D


title: ARR2PB-Myc (Myc mice) 5316830050_E

description: Sample name: 5316830050_E


title: ARR2PB-Myc (Myc mice) 5316830050_D

description: Sample name: 5316830050_D


title: ARR2PB-Myc (Myc mice) 5316830050_F

description: Sample name: 5316830050_F

value: Testosterone


title: ARR2PB-Myc (Myc mice) 5316830049_C

description: Sample name: 5316830049_C


title: ARR2PB-Myc (Myc mice) 5316830048_D

description: Sample name: 5316830048_D


title: ARR2PB-Myc (Myc mice) 5316830046_B

description: Sample name: 5316830046_B


title: ARR2PB-Myc (Myc mice) 5316830050_C

description: Sample name: 5316830050_C


title: ARR2PB-Myc (Myc mice) 5316830050_B

description: Sample name: 5316830050_B


title: ARR2PB-Myc (Myc mice) 5316830048_A

description: Sample name: 5316830048_A


title: ARR2PB-Myc (Myc mice) 5316830048_F

description: Sample name: 5316830048_F


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139020_C

description: Sample name: 5003139020_C

value: NP


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139020_D

description: Sample name: 5003139020_D

value: Vehicle


title: ARR2PB-Myc (Myc mice) 5316830048_B

description: Sample name: 5316830048_B


title: ARR2PB-Myc (Myc mice) 5316830050_A

description: Sample name: 5316830050_A

value: Dasatinib


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139013_D

description: Sample name: 5003139013_D


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139020_A

description: Sample name: 5003139020_A


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139013_F

description: Sample name: 5003139013_F


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139026_F

description: Sample name: 5003139026_F


title: ARR2PB-Myc (Myc mice) 5316830048_C

description: Sample name: 5316830048_C


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139020_B

description: Sample name: 5003139020_B


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139013_E

description: Sample name: 5003139013_E


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139020_F

description: Sample name: 5003139020_F


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139013_A

description: Sample name: 5003139013_A


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139020_E

description: Sample name: 5003139020_E


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139026_E

description: Sample name: 5003139026_E


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139026_C

description: Sample name: 5003139026_C


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139013_C

description: Sample name: 5003139013_C


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139026_D

description: Sample name: 5003139026_D


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 4968570017_F

description: Sample name: 4968570017_F


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139026_A

description: Sample name: 5003139026_A


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139026_B

description: Sample name: 5003139026_B


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139013_B

description: Sample name: 5003139013_B


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 4968570017_C

description: Sample name: 4968570017_C


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139022_D

description: Sample name: 5003139022_D

value: Calcitriol


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 4968570017_B

description: Sample name: 4968570017_B


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139022_E

description: Sample name: 5003139022_E


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 4968570017_D

description: Sample name: 4968570017_D


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139022_C

description: Sample name: 5003139022_C


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139022_A

description: Sample name: 5003139022_A


title: Aerobic glucose-limited chemostat 0.03h-1 T=72h after B.subtilis pulse-2

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

hyb_protocol: Acquisition and quantification of array images were performed using Affymetrix GeneChip Operating Software (GCOS version 1.2). Before comparison, all arrays were globally scaled to a target value of 100 using the average signal from all gene features. To the 15,531 transcript features on the arrays, a filter was applied to extract 13,746 open reading frames of which there were 13,485 different genes. This discrepancy was due to several genes being represented more than once. To represent the variation in triplicate measurements, the coefficient of variation (S.D. divided by the mean) was calculated. When the genes were ranked according to increasing average intensity, the average coefficient of variation showed a sharp increase for the genes with the lowest expression. Therefore, all genes in which the average expression in all conditions was below 12 were removed from the dataset. Subsequently all remaining values below 12 were set to a value of 12. To assess differential expression, the Significance Analysis of Microarrays (SAM version 1.21) add-in to MicrosoftTM Excel was used for comparisons of replicate array experiments. SAM identifies genes with statistically significant changes in expression by assimilating a set of gene-specific t tests. Each gene is assigned a score on the basis of its change in gene expression relative to the standard deviation of repeated measurements for that gene. Genes with scores greater than a threshold are deemed potentially significant. The percentage of such genes identified by chance is the false discovery rate (FDR). To estimate the FDR, nonsense genes are identified by analyzing permutations of the measurements. The threshold can be adjusted to identify smaller or larger sets of genes, and FDRs are calculated for each set. Here internal SAM parameters for fold-change threshold and the false discovery rate values were set at 2 and 1% respectively. The genes with significantly changed expression in one of the comparisons were arranged in groups via overlapping them in MicrosoftTM Excel.

scan_protocol: Scanning of the Affymetrix Genechip® microarrays was performed with The Affymetrix scanner 3000 following Affymetrix instructions

data_processing: Data were processed with the GeneChip® Operating Software version 1.2 (GCOS 1.2) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity was scaled to 100 with GCOS 1.2

label: biotin

organism: Penicillium chrysogenum

source_name: Glucose-limited chemostat culture -0.03h-1

label_protocol: Double stranded cDNA synthesis was carried out using 10 µg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labelling using the GeneChip IVT labeling Kit (Affymetrix). Finally, labelled cRNA was purified (GeneChip Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridised to Affymetrix custom-made Penicillium chrysogenum GeneChip® microarrays (array code DSM_PENa520255F) at 45ºC for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.

growth_protocol: Chemostat experiments were performed with the industrial high penicillin production strain Penicillium chrysogenum DS17690, kindly donated by DSM Anti-Infectives (Delft, The Netherlands), the DS63171 (velA delta) and the DS67261 (laeA delta). Cultivation medium was prepared as described earlier (van Gulik et al., 2000) and contained 0.25 Cmol/L glucose in presence or absence of 4 mM PAA and was used for the batch and chemostat phase of fermentations, allowing a biomass concentration of about 3 gDW/L. Glucosel-limited chemostat cultivations were performed according to Harris et al. (2009) in a 7 L turbine stirred reactor with a working volume of 1.8 L under aerobic conditions (DO > 70%) and a dilution rate of 0.03 h-1 at 25°C and pH 6.5. Sampling for transcriptome measurements was performed at steady state. Harris DM, van der Krogt ZA, Klaassen P, Raamsdonk LM, Hage S, van den Berg MA, Bovenberg RA, Pronk JT, Daran JM. Exploring and dissecting genome-wide gene expression responses of Penicillium chrysogenum to phenylacetic acid consumption and penicillinG production. BMC Genomics. 2009 Feb 10;10:75. Preculture of B. subtillis were propagated by inoculating 1 ml of B. subtilis glycerol stock in 100 ml of B. subtilis fermentation medium and incubated on shaker at 30oC and 200 rpm for 24 h. A volume of 10 ml of this culture was inoculated in 200 ml of fermentation medium in 1 l shake flasks and incubated at 30oC at speed of 200 rpm. After 24 h of incubation, when culture reached the exponential phase, cells were separated aseptically by centrifuging for 20 min at 4C and 10000 rpm, washed twice with the B. subtilis fermentation medium and re-suspended in 50 ml of P. chrysogenum fermentation medium. When the P. chrysogenum culture reached steady state the bacterial B. subtilis biomass (~ 1.80 g), equal to 1/3rd of the P. chrysogenum biomass was added to the P. chrysogenum bioreactor. The culture was left to coexist for 72h while samples for biomass, metabolites, microscopic observation and transcriptome were taken after 5h, 24h, 48h and 72h of mixed culture.

extract_protocol: For total RNA extraction, half of the pellet was grounded by mortar and pestle under constant cooling with liquid nitrogen. The powder was dissolved in 5 mL of Trizol reagent (Invitrogen) and 1 mL chloroform (Sigma) and mixed well. The two phases were separated by centrifugation (4600 g, 15 min). Total RNA was isolated using a phenol-chloroform extraction method, which consisted of two extraction steps in acid-phenol/chloroform/isoamyl alcohol (5:1, pH 4.8, Ambion, Foster City, USA), followed by a chloroform extraction step. Each time the phases were separated by centrifugation (4600 g, 15 min). Total RNA was precipitated for 30 min at -20ºC in 96% ethanol and 0.3 M sodium acetate. The RNA was collected by centrifugation at 23000 g for 15 min and dissolved in RNAse free H2O.

treatment_protocol: Sampling for transcriptome analysis from chemostat cultures and total RNA extraction was performed as described previously (Piper et al., J Biol Chem. 277:37001-8.).

tag: genetic background

value: P. chrysogenum Wisconsin 54-1255 (ATCC 28089) was obtained from DSM-Anti-Infectives (Delft, The Netherlands) as spores on rice grains

value: Penicillin producer

tag: time

value: 72h after B.subtilis pulse

value: B.subtilis pulse

tag: c-source

value: glucose


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139022_B

description: Sample name: 5003139022_B


title: Aerobic glucose-limited chemostat 0.03h-1 T=72h after B.subtilis pulse-1


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 4968570025_C

description: Sample name: 4968570025_C


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 4968570025_D

description: Sample name: 4968570025_D


title: Aerobic glucose-limited chemostat 0.03h-1 T=48h after B.subtilis pulse-2

value: 48h after B.subtilis pulse


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139022_F

description: Sample name: 5003139022_F


title: Aerobic glucose-limited chemostat 0.03h-1 T=24h after B.subtilis pulse-2

value: 24h after B.subtilis pulse


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 4968570017_A

description: Sample name: 4968570017_A


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 4968570025_A

description: Sample name: 4968570025_A


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 4968570025_B

description: Sample name: 4968570025_B


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 4968570025_F

description: Sample name: 4968570025_F


title: Aerobic glucose-limited chemostat 0.03h-1 T=5h after B.subtilis pulse-2

value: 5h after B.subtilis pulse


title: Aerobic glucose-limited chemostat 0.03h-1 T=48h after B.subtilis pulse-1


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 4968570025_E

description: Sample name: 4968570025_E


title: Aerobic glucose-limited chemostat 0.03h-1 T=0h-2


title: Aerobic glucose-limited chemostat 0.03h-1 T=24h after B.subtilis pulse-1


title: Aerobic glucose-limited chemostat 0.03h-1 T=5h after B.subtilis pulse-1


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139021_F

description: Sample name: 5003139021_F


title: Aerobic glucose-limited chemostat 0.03h-1 T=0h-1


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5038753087_F

description: Sample name: 5038753087_F


title: Pb-TagAPT121; Pten+/- (APT-P mice) 5316830043_E

description: Sample name: 5316830043_E

value: B6D2F1/J C57Bl/6J

value: Pb-TagAPT121; Pten+/- (APT-P mice)

value: APT-P


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139021_C

description: Sample name: 5003139021_C


title: Anaerobic C-limited chemostat DTC 21°C decreasing T-1

description: S. cerevisiae anaerobic C-limited chemostat dilution rate 0.03h-1 DTC 21°C decreasing T-1

hyb_protocol: Hybridization, washing and scanning of Affymetrix chips were done according to manufacturers’ instructions. For each temperature point analysed, microarrays were run on two independent cultures.

data_processing: Processing of expression data (normalization, expression cut-off, etc.) was performed as described previously (Boer et al., J Biol Chem., 278:3265-74; Boender et al., FEMS Yeast Res. 11:603-620.). With the expression data from these 6 time points a time-course differential expression analysis by Empirical analysis of Digital Gene Expression data in R (EDGE, v 1.1.291) was executed (Storey et al., 2005. Proc.Natl.Acad.Sci.U.S.A 102:12837-12842). All genes with a p-value<0.002 were considered to be significantly changed. Genes that were differentially expressed genes under two conditions (e.g. pair-wise comparison between steady-state 12°C versus steady-state 30°C) were identified by first removing probe intensity background using robust multichip analysis (RMA) (Irizarry et al., 2003. Biostatistics. 4:249-264) and quantile-normalizing intensity levels (Bolstad et al., 2003. Bioinformatics. 19:185-193). Subsequently, array groups (two biologically independent arrays per group) that corresponded to the sampling point were compared based on the perfect match probe intensity levels only (Irizarry et al., 2003. Biostatistics. 4:249-264), by performing a per-probe set two-way analysis of variance (with factors ‘probe’ and ‘sampling point’). Adjustment of p-values for multiple testing was done with Šidák step-down adjustment (Ge et al., 2003. Test 12:1-77). Differences with adjusted p-values < 0.05 and a fold difference of two or larger were considered significant.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae   DTC 21°C decreasing T

label_protocol: Processing of total RNA was performed according to Affymetrix’s instructions. RNA target preparation for microarray expression analysis was carried out according the GeneChip 3' IVT Express Kit (Affymetrix, Santa Clara, USA) using 200 ng of total RNA for both pure and mixed cultures. The protocol was carried out with minor modifications, i.e the Affymetrix polyA RNA controls were excluded from the aRNA amplification protocol and the IVT reactions were incubated for 16 h at 40°C. The quality of total RNA, cDNA, cRNA, and fragmented aRNA was checked using the Agilent Bioanalyzer 2100 (Agilent Technologies).

growth_protocol: Anaerobic glucose-limited chemostat cultures were grown in 2-L laboratory bioreactors (Applikon, Schiedam, The Netherlands) with a working volume of 1.4 L and at a dilution rate of 0.03 h-1. The pH was controlled at 5.0 by automatic addition of 2 M KOH and the stirrer speed was kept at 800 rpm. To ensure anaerobic conditions, bioreactors and medium vessels were continuously sparged with pure nitrogen (N2) gas at a flow rate of 0.7 l•min-1 and circa 7 ml•min-1, respectively, and equipped with Norprene® tubing (Saint-Gobain Performance Plastics, Courbevoie, France) and Viton® O-rings (Eriks, Alkmaar, Netherlands). Active temperature regulation was performed by connecting a platinum resistance thermometer, placed in a socket in the bioreactor, to a low-temperature thermostat (Lauda RE304, Lauda-Königshofen, Germany). Steady-state sampling of cultures grown at constant temperatures of 12 or 30°C was performed when biomass dry weight, metabolite levels and carbon-dioxide production rates differed by less than 5% for at least three consecutive volume changes. Considering the diurnal temperature experiments, after three volume changes at a constant temperature of 30°C without significant changes in biomass dry weight, a pre- programmed sinoidal temperature profile (T(°C) = 21+9sin(π/12•t (h) +1.57) was started. This profile was designed to mimic a real-life circadian temperature cycle.Samples were taken during the fifth and/or sixth temperature cycle. To minimize disturbance, sampling volumes did not exceed 5 % of the reactor volume during a single temperature cycle and intervals of at least 3 h were maintained between sampling points.

extract_protocol: Sampling for transcriptome analysis from chemostat cultures and total RNA extraction was performed as described previously (Mendes et al., 2013, Appl.Environ.Microbiol. 79:5949-5961).

value: CEN.PK113-7D (MATa MAL2-8C SUC2 )

value: MATa MAL2-8C SUC2

tag: culture condition

value: anaerobic C-limited chemostat


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139021_A

description: Sample name: 5003139021_A

value: NP

value: Vehicle


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139021_E

description: Sample name: 5003139021_E


title: Anaerobic C-limited chemostat DTC 21°C decreasing T-2

description: S. cerevisiae anaerobic C-limited chemostat dilution rate 0.03h-1 DTC 21°C decreasing T-2

scan_protocol: Hybridization, washing and scanning of Affymetrix chips were done according to manufacturers’ instructions.  For each temperature point analysed, microarrays were run on two independent cultures.

treatment_protocol: Sampling for transcriptome analysis from chemostat cultures and total RNA extraction was performed as described previously (Mendes et al., 2013, Appl.Environ.Microbiol. 79:5949-5961).


title: Anaerobic C-limited chemostat DTC 14.6°C-1

description: S. cerevisiae anaerobic C-limited chemostat dilution rate 0.03h-1 DTC 14.6°C-1

source_name: S. cerevisiae   DTC 14.6°C


title: Anaerobic C-limited chemostat DTC 30°C-2

description: S. cerevisiae anaerobic C-limited chemostat dilution rate 0.03h-1 DTC 30°C-2

source_name: S. cerevisiae   DTC 30°C


title: Anaerobic C-limited chemostat DTC 12°C-1

description: S. cerevisiae anaerobic C-limited chemostat dilution rate 0.03h-1 DTC 12°C-1

source_name: S. cerevisiae   DTC 12°C


title: Anaerobic C-limited chemostat DTC 14.6°C-2

description: S. cerevisiae anaerobic C-limited chemostat dilution rate 0.03h-1 DTC 14.6°C-2


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139021_B

description: Sample name: 5003139021_B


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139028_E

description: Sample name: 5003139028_E

value: Sorafenib


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139021_D

description: Sample name: 5003139021_D


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5038753087_B

description: Sample name: 5038753087_B


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5038753087_A

description: Sample name: 5038753087_A


title: Anaerobic C-limited chemostat DTC 30°C-1

description: S. cerevisiae anaerobic C-limited chemostat dilution rate 0.03h-1 DTC 30°C-1


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139028_F

description: Sample name: 5003139028_F


title: Anaerobic C-limited chemostat DTC 21°C increasing T-2

description: S. cerevisiae anaerobic C-limited chemostat dilution rate 0.03h-1 DTC 21°C increasing T-2

source_name: S. cerevisiae   DTC 21°C increasing T


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5038753087_C

description: Sample name: 5038753087_C


title: Anaerobic C-limited chemostat SS 30°C-2

description: S. cerevisiae anaerobic C-limited chemostat dilution rate 0.03h-1SS 30°C-2

source_name: S. cerevisiae   SS 30°C


title: Anaerobic C-limited chemostat DTC 27.4°C-1

description: S. cerevisiae anaerobic C-limited chemostat dilution rate 0.03h-1 DTC 27.4°C-1

source_name: S. cerevisiae   DTC 27.4°C


title: Anaerobic C-limited chemostat DTC 12°C-2

description: S. cerevisiae anaerobic C-limited chemostat dilution rate 0.03h-1 DTC 12°C-2


title: Anaerobic C-limited chemostat DTC 27.4°C-3

description: S. cerevisiae anaerobic C-limited chemostat dilution rate 0.03h-1 DTC 27.4°C-3


title: Anaerobic C-limited chemostat DTC 27.4°C-2

description: S. cerevisiae anaerobic C-limited chemostat dilution rate 0.03h-1 DTC 27.4°C-2


title: Anaerobic C-limited chemostat SS 30°C-1

description: S. cerevisiae anaerobic C-limited chemostat dilution rate 0.03h-1 SS 30°C-1


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139028_C

description: Sample name: 5003139028_C

value: Imatinib


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139028_D

description: Sample name: 5003139028_D


title: Anaerobic C-limited chemostat SS 12°C-2

description: S. cerevisiae anaerobic C-limited chemostat dilution rate 0.03h-1 SS 12°C-2

source_name: S. cerevisiae   SS 12°C


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139028_B

description: Sample name: 5003139028_B


title: Anaerobic C-limited chemostat DTC 21°C increasing T-1

description: S. cerevisiae anaerobic C-limited chemostat dilution rate 0.03h-1 DTC 21°C increasing T-1


title: Anaerobic C-limited chemostat SS 12°C-1

description: S. cerevisiae anaerobic C-limited chemostat dilution rate 0.03h-1 SS 12°C-1


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5038753087_E

description: Sample name: 5038753087_E


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 4968570019_E

description: Sample name: 4968570019_E


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 4968570019_C

description: Sample name: 4968570019_C


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139028_A

description: Sample name: 5003139028_A


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 4968570019_B

description: Sample name: 4968570019_B


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 4968570019_F

description: Sample name: 4968570019_F


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 4968570019_D

description: Sample name: 4968570019_D


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139030_F

description: Sample name: 5003139030_F


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 4968570019_A

description: Sample name: 4968570019_A


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139030_E

description: Sample name: 5003139030_E


title: Diabetic Sternohyoid 4 (ZDF Study)

city: Cleveland

first: Erik

last: van Lunteren

state: OH

address: 10701 East Boulevard

department: Pulmonary 111J(W)

institute: Cleveland VA Medical Center

description:
18-week-old Diabetic fatty animal for Zucker diabetic fatty rat.

Zucker Diabetic Fatty (ZDF) rats are an animal model of obesity and type 2 diabetes. They were obtained from Charles River Laboratories (Wilmington, MA).

hyb_protocol: 15 ug of biotin-labeled cRNA was used in a 300 ml hybridization cocktail which included spiked transcript controls. 200 ml of cocktail was loaded onto Affymetrix RAE 230A microarrays (Santa Clara, CA) and hybridized for 16 hr at 45oC with agitation. Standard post-hybridization washes and double-stain protocols used an Affymetrix GeneChip Fluidics Station 400.

scan_protocol: Arrays were scanned using a Hewlett Packard Gene Array scanner.

data_processing: Affymetrix GCOS version 1.4 software.

organism: Rattus norvegicus

source_name: Diabetic sternohyoid

label_protocol: 8 ug of RNA was used in a reverse transcription reaction (SuperScript II; Life Technologies, Rockville, MD) to generate first strand cDNA. After second strand synthesis, double strand cDNA was used in an in vitro transcription reaction to generate biotinylated cRNA, which was purified and fragmented.

extract_protocol: Total RNA was extracted using Trizol (GibcoBRL, Rockville, MD), and the RNA pellets were resuspended at 1 mg RNA/ml DEPC-treated water. This was followed by a cleanup protocol with a Qiagen (Valencia, CA) RNeasy Total RNA mini kit.

tag: age

value: 18 weeks

tag: gender

value: male

value: ZDF

tag: tissue

value: sternohyoid

tag: phenotype

value: type 2 diabetes, obesity


title: Diabetic Sternohyoid 3 (ZDF Study)


title: Normal Sternohyoid 3 (ZDF Study)

description:
18-week-old control animal for Zucker diabetic fatty rat.

Zucker Diabetic Fatty (ZDF) rats are an animal model of obesity and type 2 diabetes. They were obtained from Charles River Laboratories (Wilmington, MA).

source_name: Normal sternohyoid

value: control


title: Normal Sternohyoid 6 (ZDF Study)


title: Diabetic Sternohyoid 1 (ZDF Study)


title: Normal Sternohyoid 5 (ZDF Study)


title: Diabetic Sternohyoid 2 (ZDF Study)


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139030_B

description: Sample name: 5003139030_B


title: Diabetic Sternohyoid 5 (ZDF Study)


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 4968570017_E

description: Sample name: 4968570017_E


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139030_D

description: Sample name: 5003139030_D


title: Normal Sternohyoid 4 (ZDF Study)


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139030_A

description: Sample name: 5003139030_A


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139002_F

description: Sample name: 5003139002_F


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139002_E

description: Sample name: 5003139002_E


title: Diabetic Diaphragm 5 (ZDF Study)

description:
18-week-old Diabetic Obese animal for Zucker diabetic fatty rat.

Zucker Diabetic Fatty (ZDF) rats are an animal model of obesity and type 2 diabetes. They were obtained from Charles River Laboratories (Wilmington, MA).

source_name: Diabetic diaphragm

value: diaphragm


title: Normal Sternohyoid 2 (ZDF Study)


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139030_C

description: Sample name: 5003139030_C


title: Normal Sternohyoid 1 (ZDF Study)


title: TMV_33d_3dpi_rep3

city: Singapore

first: Sek Man

last: WONG

state: Singapore

address: 14 Science Drive 4

department: Biological sciences

country: Singapore

institute: National University of Singapore

description: Upper new grown leaf with TMV inoculation, 30 d, 12 dpi, replicate 3

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 65 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09  and Grid: 021113_D_F_20110323) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Nicotiana benthamiana

source_name: post 3 days TMV inoculation (equal to 15 days HLSV inoculation)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: N. benthamiana plants were grown in a growth room with a 16 h photoperiod and 8 h darkness, at a constant temperature of 23°C.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: Twenty-four N. benthamiana plants were used for each batch of cross protection experiment between HLSV and TMV. When they were grown to 6 to 8 newly emerged and fully expanded leaves, 12 plants were inoculated with HLSV by mechanical inoculation. Two leaves on each plant were dusted with carborundum and inoculated with purified HLSV. Another 12 plants were treated with an equal volume of inoculation buffer. Among them, six plants were kept as a negative control and another six plants were used for TMV inoculation.

value: upper new grown leaves


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139002_B

description: Sample name: 5003139002_B


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139002_C

description: Sample name: 5003139002_C


title: Diabetic Diaphragm 1 (ZDF Study)


title: TMV_33d_3dpi_rep2

description: Upper new grown leaf with TMV inoculation, 30 d, 12 dpi, replicate 2


title: Diabetic Diaphragm 4 (ZDF Study)


title: Diabetic Diaphragm 2 (ZDF Study)


title: Diabetic Diaphragm 3 (ZDF Study)


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139002_D

description: Sample name: 5003139002_D


title: TMV_33d_3dpi_rep1

description: Upper new grown leaf with TMV inoculation, 30 d, 12 dpi, replicate 1


title: Normal Diaphragm 6 (ZDF Study)

source_name: Normal diaphragm


title: HLSV+TMV_33d_3dpi_rep3

description: Upper new grown leaf with TMV inoculation with pre-inoculation of HLSV, 30 d, 12 dpi, replicate 3

source_name: post 3 days TMV inoculation (equal to 15 days HLSV inoculation) with HLSV pre-inoculation


title: zebrafish_control_WT_Rep1

city: La Jolla

first: Xin-Xin

middle: I.

last: Zeng

state: CA

address: 9500 Gilman Drive 0380

department: Division OF Biological Sciences

institute: UCSD

hyb_protocol: Hybridization protocol followed standard procedures in the Sloan-Kettering Institute Genomic Core (Protocol EukGE-WS2v4_450).

scan_protocol: Scanning protocol followed standard procedures in the Sloan-Kettering Institute Genomic Core.

data_processing: Initial data processing was done following standard procedures in the Sloan-Kettering Institute Genomic Core.

organism: Danio rerio

source_name: wild-type DMSO-treated sibling_48 hpf

label_protocol: Label protocol was done using standard procedures in the Sloan-Kettering Institute Genomic Core.

growth_protocol: Embryos were collected, grown in blue water (60 mg/mL Instant Ocean and 0.025% methylene blue) at 28.5 degrees Celcius and dechorionated prior to heart dissection and RNA extraction.

extract_protocol: Embryonic zebrafish hearts and surrounding tissues were collected at 48 hpf for microarray analysis using a previously described syringe-based extraction method (Burns and MacRae, 2006). Tissue was preserved in RNAlater solution (Ambion) and total RNA was isolated using a RNAqueous-Micro kit (Ambion).

treatment_protocol: SU5402 incubation was performed as previously described (Marques et al., 2008). A 1 mM stock of SU5402 (Calbiochem) in DMSO was diluted to a working concentration of 10 μM in E3 medium. Up to 20 embryos were treated in glass vials in a final volume of 3 mL. Control embryos were treated with 1% DMSO in E3 medium.

value: wild type

tag: Stage

value: 48 hpf

tag: treated with

value: DMSO

value: heart


title: zebrafish_SU5402 treated_Rep2

source_name: wild-type SU5402-treated sibling_48 hpf


title: zebrafish_control_WT_Rep2


title: HLSV+TMV_33d_3dpi_rep2

description: Upper new grown leaf with TMV inoculation with pre-inoculation of HLSV, 30 d, 12 dpi, replicate 2


title: GF_LPA_8hr-rep2

city: Omaha

first: D.

middle: Roselyn

last: Cerutis

state: NE

address: 2500 California Plaza

department: Oral Biology

institute: Creighton University

description:
Biological replicate 2 of 3. Passage 2 cells treated with or without LPA 18:1 for 8hours. Following treatment, cultured cells from human donors #4, #5 and #6  were pooled (Pool B) for RNA extraction.
251485035142_1_4

hyb_protocol: Proprietary - Miltenyi Biotec, Array G4112F, (GPL6480). The corresponding Cy3- and Cy5- labeled cDNAs were combined (table 3) and hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays 4 x 44K using Agilent’s ecommended hybridization chamber and oven.  Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% N-lauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Proprietary- Miltenyi Biotec, Agilent’s DNA microarray scanner, Agilent Feature Extraction Software v.9.1

data_processing: Miltenyi Biotec designated genes from the microarray experiments which showed > than, or < than 2-fold differences between the signal from the LPA-treated samples and their untreated controls as significantly changed.  The company uses the Rosetta Resolver® gene expression data analysis system (Rosetta Biosoftware, www.rosettabio.com ) and this analysis provides a level of significance of p < 0.01.

organism: Homo sapiens

source_name: donor pool B, LPA+, 8hours

label_protocol: Proprietary - Cy3/Cy5, Miltenyi Biotec, 250 ng of each of the cDNAs were used as template for Cy3 and Cy5 labeling.

growth_protocol: GF isolates (pass 2) from nine young, healthy donors  (25-35 years old) were seeded at 1 x 104 cells / 2 ml / 35mm dish in Dulbecco’s modified Eagle’s medium [(DMEM), Life Technologies Corporation] with 10% defined fetal bovine serum [(FBS), Hyclone] and penicillin/streptomycin.  They were incubated in a 5% CO2, 37 oC humidified atmosphere for two days until they were ~90% confluent.  The cells were then washed four times with serum-free DMEM, and serum-starved for 24 h in serum-free DMEM.

extract_protocol: Each donor’s cells were then trypsinized, washed once with ice-cold phosphate-buffered saline (PBS), held on ice, and counted. The nine donors’ cells were grouped into 3 pools of 3,000 cells, each containing 1,000 cells/donor [A =donors 1-3 (2 M, 1 F), B =donors 4-6 (1M, 2F), and C =donors 7-9 (2M, 1F)]. The pools were lysed directly in Miltenyi Biotec’s (Auburn, CA, USA) proprietary buffer, and quick-frozen on dry ice for shipment to the company.  As we used cells at very low pass to help conserve in vivo influences, Miltenyi subjected the samples to SuperAmpTM  RNA amplification prior to labeling.

treatment_protocol: Oleoyl-LPA (18:1), (Avanti Polar Lipids) stock (1 x 10-2 M) was prepared in 0.25% de-lipidated (fraction V) bovine serum albumin [(BSA), Sigma] in DMEM. Each donor’s cells were individually treated for 2h or 8h with 2 ml 1 x 10-5 M LPA in serum-free DMEM. Untreated controls received an equal volume of 0.25% BSA in serum-free DMEM.

tag: individual

value: donor pool B [donors 4-6 (1M, 2F)]

value: gingiva

tag: cell type

value: fibroblast

tag: stress

value: LPA

source_name: donor pool B, LPA-neg


title: Normal Diaphragm 2 (ZDF Study)

tag: strain


title: GF_LPA_2hr-rep3

description:
Biological replicate 3 of 3. Passage 2 cells treated with or without LPA 18:1 for 2hours. Following treatment, cultured cells from human donors #7, #8 and #9 were pooled (Pool C) for RNA extraction.
251485021888_1_4

source_name: donor pool C, LPA+, 2hours

value: donor pool C [donors 7-9 (2M, 1F)]

source_name: donor pool C, LPA-neg


title: Normal Diaphragm 3 (ZDF Study)

value: 18 weeks


title: Normal Diaphragm 5 (ZDF Study)

value: male


title: HLSV+TMV_33d_3dpi_rep1

description: Upper new grown leaf with TMV inoculation with pre-inoculation of HLSV, 30 d, 12 dpi, replicate 1


title: Normal Diaphragm 4 (ZDF Study)

value: ZDF


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5038753087_D

description: Sample name: 5038753087_D

source_name: prostate tumor/tissue

tag: genotype/variation

value: NP

value: Vehicle


title: HLSV_30d_12dpi_rep3

description: Upper new grown leaf with HLSV inoculation, 30 d, 12 dpi, replicate 3

source_name: post 12 days HLSV inoculation


title: GF_LPA_2hr-rep2

description:
Biological replicate 2 of 3. Passage 2 cells treated with or without LPA 18:1 for 2hours. Following treatment, cultured cells from human donors #4, #5 and #6  were pooled (Pool B) for RNA extraction.
251485035142_1_3

source_name: donor pool B, LPA+, 2hours

value: control


title: zebrafish_SU5402 treated_Rep1


title: Normal Diaphragm 1 (ZDF Study)

value: diaphragm


title: HLSV_30d_12dpi_rep2

description: Upper new grown leaf with HLSV inoculation, 30 d, 12 dpi, replicate 2

value: upper new grown leaves


title: GF_LPA_8hr-rep1

description:
Biological replicate 1 of 3. Passage 2 cells treated with or without LPA 18:1 for 8hours. Following treatment, cultured cells from 3 human donors #1, #2 and #3 were pooled (Pool A) for RNA extraction.
251485035142_1_2

source_name: donor pool A, LPA+, 8hours

value: donor pool A [donors 1-3 (2M, 1F)]

source_name: donor pool A, LPA-neg


title: GF_LPA_2hr-rep1

description:
Biological replicate 1 of 3. Passage 2 cells treated with or without LPA 18:1 for 2hours. Following treatment, cultured cells from human donors #1, #2 and #3 were pooled (Pool A) for RNA extraction.
251485035142_1_1

source_name: donor pool A, LPA+, 2hours


title: HLSV_30d_12dpi_rep1

description: Upper new grown leaf with HLSV inoculation, 30 d, 12 dpi, replicate 1


title: GF_LPA_8hr-rep3

description:
Biological replicate 3 of 3. Passage 2 cells treated with or without LPA 18:1 for 8hours. Following treatment, cultured cells from 3 human donors #7, #8 and #9 were pooled (Pool C) for RNA extraction.
251485035143_1_2

source_name: donor pool C, LPA+, 8hours


title: Nkx3.1CreERT2/+; Ptenflox/flox (NP mice) 5003139002_A

description: Sample name: 5003139002_A

tag: cancer type


title: mock_30d_12dpi_rep3

description: Upper new grown leaf with mock inoculation, 30 d, 12 dpi, replicate 3

source_name: post 12 days mock buffer inoculation


title: mock_30d_12dpi_rep1

description: Upper new grown leaf with mock inoculation, 30 d, 12 dpi, replicate 1


title: mock_30d_12dpi_rep2

description: Upper new grown leaf with mock inoculation, 30 d, 12 dpi, replicate 2


title: Wilms3 siWT1 24h Replicate 1

city: Duesseldorf

first: Brigitte

last: Royer-Pokora

address: Universitätsstr. 1

country: Germany

institute: Institute of Human Genetics and Anthropology, Heinrich-Heine-University Duesseldorf

description: siWT1 vs. control siRNA treated Wilms tumor cells, cell line 3, replicate 1, 24h after transfection

hyb_protocol: 825 ng labeled target and control cRNA were incubated with blocking agent and fragmentation buffer for 30 min at 60°C. Then 2x hybridization buffer (Agilent) was added, samples were applied to microarrays and incubated for 17 hr at 65°C (10rpm).

scan_protocol: scanned on Agilent Technologies Scanner G2505B Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. Control spots are removed.

source_name: Wilms tumor cell line 3, 24h after siWT1 transfection

label_protocol: 250 ng total target and control RNA were reverse transcribed (with spike-In controls) and then labelled with Cyanine 3-CTP or Cyanine 5-CTP following the manufacturer´s instructions (Agilent). Specific activity was determined after a purification step with the RNeasy Mini Kit (Qiagen).

growth_protocol: Wilms tumor cells were cultivated in MSCG media from Lonza.

extract_protocol: Total RNA extracted using Rneasy Mini Kit with QIAshredder (Qiagen) following manufacturer´s instructions

treatment_protocol: 4x 10^4 cells were seeded in 24 wells in MSCG medium (Lonza). After a growth period of 24 h the cells were transfected with 25 pMol WT1-si RNA (combination of Hs_WT1_1_HP and Hs_WT1_8_HP siRNA from Qiagen) and 6µl HighPerfect transfection reagent per 24 well. A non-silencing control (FITC siRNA from Qiagen) was also transfected as described.

tag: cell line

value: Wilms tumor cell line 3

tag: treatment

value: kidney

value: 11 months

source_name: Wilms tumor cell line 3, 24h after control siRNA transfection


title: Wilms3 siWT1 24h Replicate 2

description: siWT1 vs. control siRNA treated Wilms tumor cells, cell line 3, replicate 2, 24h after transfection

tag: time


title: Wilms3 siWT1 48h Replicate 1

description: siWT1 vs. control siRNA treated Wilms tumor cells, cell line 3, replicate 1, 48h after transfection

source_name: Wilms tumor cell line 3, 48h after siWT1 transfection

source_name: Wilms tumor cell line 3, 48h after control siRNA transfection


title: wild type rep1

city: Shanghai

first: dabing

last: zhang

address: Dongchuan Road

country: China

institute: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University,China

description: control 1

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

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

data_processing: The data were analyzed with PARTEK genomic suit 6.4 using RMA normalization

label: boitin

organism: Oryza sativa

source_name: wild type

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (3_ivt_express_kit_manual  Affymetrix).

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

tag: genotype

value: wild type

value: flower

tag: developmental stage


title: wild type rep3

description: control 3


title: shGR-19_rep1

status: Public on May 11 2014

city: Kingston

first: Christopher

last: Mueller

state: Ontario

address: 18 Stuart Street

department: Cancer Research Institute

country: Canada

institute: Queen's University

description: gene expression in cells depleted of GR

hyb_protocol: 1.65 ug of Cy3-labeled cRNA for each sample was fragmented at 60°C for 30 minutes in a reaction volume of 30 uL containing 25X Agilent Fragmentation Buffer and 10X Agilent Blocking Agent following the manufacturer's instructions. 30 uL of 2X GE Hybridization Buffer was added to each fragmentation mix and these were subsequently hybridized to an Agilent Whole Mouse Genome 4 x 44K gene expression microarray (G2519F-014868) for 17 hours at 65°C in a rotating Agilent hybridization oven in accordance with Agilent hybridization protocols. After hybridization, microarrays were washed once at room temperature and once at 37°C, then dried at 30°C before being scanned.

scan_protocol: Slides were scanned using the Agilent DNA Microarray Scanner using the one color scan setting for 4 x 44K array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameter settings for one-colour oligonucleotide microarrays to obtain background subtracted and Processed Signal intensities.

source_name: mammary epithelial cells depleted of endogenous GR expression, shGR-19, replicate 1

label_protocol: A total of 300 ng of quality-checked RNA from each sample (in duplicate) was amplified and labeled with Cyanine-3 (Cy3) using the Agilent QuickAmp kit (Agilent Technologies). Cy3 labeling efficiency and amplification efficient were asses using a NanoDrop-1000 spectrophotometer.

growth_protocol: EPH-4 EV-50 and shGR-19 stable cell lines were cultured in serum-free DMEM/F-12 medium containing 2 ug/mL puromycin.

extract_protocol: RNA was prepared using the GenElute Mammalian Total RNA Miniprep kit (Sigma) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA quality was determined with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: gr-status

value: depleted <50%

tag: tissue origin

value: breast

value: mammary epithelial cells


title: Wilms2 siWT1 24h

description: siWT1 vs. control siRNA treated Wilms tumor cells, cell line 2, 24h after transfection

source_name: Wilms tumor cell line 2, 24h after siWT1 transfection

value: Wilms tumor cell line 2

tag: tissue

tag: gender

tag: age

value: 12 months

source_name: Wilms tumor cell line 2, 24h after control siRNA transfection


title: wild type rep2

description: control 2


title: Wilms3 siWT1 48h Replicate 2

description: siWT1 vs. control siRNA treated Wilms tumor cells, cell line 3, replicate 2, 48h after transfection

value: male


title: osmads6-1 rep3

description: experiment 3


title: Wilms2 siWT1 48h

description: siWT1 vs. control siRNA treated Wilms tumor cells, cell line 2, 48h after transfection

source_name: Wilms tumor cell line 2, 48h after siWT1 transfection

source_name: Wilms tumor cell line 2, 48h after control siRNA transfection


title: shGR-19_rep2

description: gene expression in cells depleted of GR

source_name: mammary epithelial cells depleted of endogenous GR expression, shGR-19, replicate 2


title: osmads6-1 rep1

description: experiment 1


title: EV-50_rep2

description: gene expression in normal mammary cells

source_name: normal mammary epithelial cells, EV-50, replicate 2

value: normal


title: osmads6-1 rep2

description: experiment 2


title: EV-50_rep1

description: gene expression in normal mammary cells

source_name: normal mammary epithelial cells, EV-50, replicate 1


title: Rosette-brc1-2-FR vs Rosette-brc1-2-WL-REP3

city: Campus de Cantoblanco

first: César

last: Poza-Carrión

state: Madrid

address: Darwin 3

country: Spain

institute: CNB-CSIC

description: Biological replicate 3 of 3: brc1-2 plants illuminated with red and far-red light versus brc1-2 plants illuminated with cool white fluorescent light

hyb_protocol: Equal amounts of dye of each aRNA labeled with either Cy3 or Cy5, ranging from 200 to 300 pmol, were mixed with 20 ug of poly(A) and 20 µg of yeast tRNA (Sigma-Aldrich) in a volume of 9 µL. To this volume, 1 µL of RNA fragmentation buffer was added (RNA fragmentation reagents; Ambion) and after 15 min at 70°C, 1 µL of stop solution. Formamide, 20x SSC, 50x Denhardt's, and 20% SDS were added to a final concentration of 50% formamide, 6x SSC, 5x Denhardt's, and 0.5% SDS. This mix was boiled for 3 min at 95°C and then added to the prehybridized slide. Hybridization took place overnight at 37°C in a hybridization chamber. Arrays were then washed for 5 min at 37°C in 0.5x SSC and 0.1% SDS, twice for 5 min at room temperature (21°C) with 0.5x SSC and 0.1% SDS, three times with 0.5x SSC at room temperature, and 5 min with 0.1x SSC. The slides were then drained with a 2000-rpm spin for 2 min. The slides were stored in darkness until they were scanned.

scan_protocol: Images from Cy3 and Cy5 channels were equilibrated and captured with a GenePix 4000B (Molecular Devices) and spots quantified using GenPix 5.1 software (Molecular Devices).

data_processing: Local background was corrected by normexp method with an offset of 50. Background corrected intensities were transformed to log scale (base 2) and normalized by loess for each array (Smyth and Speed, 2003). Finally, to have similar intensity distribution across all arrays, loess-normalized-intensity values were scaled by adjusting their quantiles (Bolstad et al., 2003).

organism: Arabidopsis thaliana

source_name: Rosette brc1-2 WL

label_protocol: RNA was amplified with the MessageAmp aRNA amplification kit from Ambion following the instruction manual. To allow later labeling with Cy fluorophores, aminoallyl UTP (Ambion) was added to the mix of the T7 RNA polymerase-driven aRNA amplification reaction. The amount and quality of aRNA obtained was assessed as before. The aminoallyl-labeled aRNA (10 µg) was incubated in 1 M Na2CO3 with 8 nmol of dye monofunctional NHS ester (Cy3/Cy5) RPN 5661 (Amersham Biosciences) at room temperature in the dark for 1 h. Then, 35 µL of 0.1 M sodium acetate, pH 5.2, was added and incubated for a further 5 min in the dark. The Cy-labeled aRNA was purified with the Megaclear kit from Ambion and measured with the Nanodrop ND-100 spectrophotometer.

growth_protocol: Plants were grown in chambers under controlled conditions (16/8 hr photoperiod). Plants were illuminated with cool-white fluorescent light (200 µmol m-2 s-1) for 4 weeks until the plants had undergone flowering and the bolts were 1cm long.

extract_protocol: RNA from dissected flowering rosettes comprising axillary buds but not rosette leaves were obtained using TRIzol (Invitrogen). The RNA fraction was cleaned using RNeasy midi columns (Qiagen) following manufacturer's protocol.

treatment_protocol: Plants were either maintained in the standard growth conditions or transferred to continuous red and far-red light (R:FR, 0.15) during 8 hours.

tag: condition

value: white light

value: Flowering rosettes comprising axillary buds but not rosette leaves

source_name: Rosette brc1-2 FR

value: red+far red light


title: Rosette-WT-FR vs Rosette-WT-WL-REP2

description: Biological replicate 2 of 3: wild type plants illuminated with red and far-red light versus wild type plants illuminated with cool white fluorescent light

source_name: Rosette WT-WL

source_name: Rosette WT-FR


title: Rosette-WT-FR vs Rosette-WT-WL-REP3

description: Biological replicate 3 of 3: wild type plants illuminated with red and far-red light versus wild type plants illuminated with cool white fluorescent light


title: Rosette-WT-FR vs Rosette-WT-WL-REP1

description: Biological replicate 1 of 3: wild type plants illuminated with red and far-red light versus wild type plants illuminated with cool white fluorescent light


title: Rosette-brc1-2-FR vs Rosette-brc1-2-WL-REP1

description: Biological replicate 1 of 3: brc1-2 plants illuminated with red and far-red light versus brc1-2 plants illuminated with cool white fluorescent light


title: Rosette-brc1-2-FR vs Rosette-brc1-2-WL-REP2

description: Biological replicate 2 of 3: brc1-2 plants illuminated with red and far-red light versus brc1-2 plants illuminated with cool white fluorescent light


title: 84_CL

status: Public on May 10 2014

type: genomic

city: College Station

first: Cole

middle: M

last: McQueeen

address: 4467 VMRB

institute: Texas A&M University

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

molecule: genomic DNA

organism: Equus caballus

source_name: Genomic DNA of Clinical foal

label_protocol: 4 µg of purified genomic DNA was primed with 20 µl of 100 µM panomer at 37°C overnight,

extract_protocol: Genomic DNA isolated via Phenoyl-Cholorofoam-Isoamyl extraction protocol from whole blood

value: whole blood

source_name: Genomic DNA from reference horse


title: 83_SC

source_name: Genomic DNA of Subclinical foal


title: 74_CL


title: 91_UN

source_name: Genomic DNA of Unaffected foal


title: 72_UN


title: 82_UN


title: 71_SC


title: 59_UN


title: 265_SC


title: 35_SC


title: 262_CL


title: 267_SC


title: 256_UN


title: 40_CL


title: 47_CL


title: 272_UN


title: 50_CL


title: 64_CL


title: 51_UN


title: 33_UN


title: 65_SC


title: 37_UN


title: 243_SC


title: 36_SC


title: 247_SC


title: 61_CL


title: 228_SC


title: 25_CL


title: 248_CL


title: 57_UN


title: 264_SC


title: 246_CL


title: 224_UN


title: 229_CL


title: 240_UN


title: 214_CL


title: 252_SC


title: 251_UN


title: 213_CL


title: 203_CL


title: 205_SC


title: 21_SC


title: 195_SC


title: 194_UN


title: 19_CL


title: 176_SC


title: 201_UN


title: normal spleen hyb5193

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

country: Belgium

institute: KULeuven

description: chip #7

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450  (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing:
The data were analyzed with Array Studio version 5.0 (Omicsoft Corporation)
Data were normalized using RMA. Expression values are represented on a log2-scale. Control probes are discarded.

source_name: spleen

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent).  All steps were carried out according to the manufacturers protocol (Affymetrix).

growth_protocol: Patients diagnosed with HSTL were biopsied and tumor tissues were frozen.

treatment_protocol: Frozen tissue sections were immediately dissolved in Trizol.

tag: patient gender

tag: tissue type

value: normal spleen control


title: normal spleen hyb5192

description: chip #6


title: 169_CL


title: 130_UN


title: 147_SC


title: 183_CL


title: 167_SC


title: 158_UN


title: 146_CL


title: 170_SC


title: 202_SC


title: 133_UN


title: 173_SC


title: 128_CL


title: 155_UN


title: 190_UN


title: 112_CL


title: 174_SC


title: Hepatosplenic T-cell lymphoma case7

description: chip #4

tag: patient age

value: 18 yrs

value: Hepatosplenic T cell Lymphoma

tag: medical history

value: kidney Tx for dysplasia

tag: site of involvement of lymphoma

value: S, Pe, BM

value: splenectomy, combined CT

tag: karyotype


title: 123_CL


title: 152_SC


title: Hepatosplenic T-cell lymphoma case5

description: chip #3

value: 52 yrs

value: Crohn’s disease

value: S

value: splenectomy, combined CT, MAB


title: 136_SC


title: 18_UN


title: Hepatosplenic T-cell lymphoma case4

description: chip #2

value: 33 yrs

value: Budd-Chiari syndrome, liver Tx

value: S, L, BM

value: splenectomy


title: 111_CL


title: 103_CL


title: normal spleen hyb5191

description: chip #5


title: Hepatosplenic T-cell lymphoma case1

description: chip #1

value: male

value: 26 yrs

value: splenectomy, allo BMTx


title: FL-0.63/LDN_rep1

status: Public on May 09 2014

city: Aas

first: Tatiana

last: Belova

address: arboretveien 6

department: department of plant science

country: Norway

institute: cigene

description:
sample 15
Ch1 raw data file: 532778_2012-04-13_12-54_Area1_532_grid.pair
Ch2 raw data file: 532778_2012-04-13_11-33_Area1_532_grid.pair

hyb_protocol: Each sample pair was re-suspended in unique Sample Tracking Control and added to 8.7 ul of the hybridization solution mix. Tubes were first incubated at 95C for 5 min, and then at 42C for 5 min. Samples were hybridized to CGH array for 60-72 hours at 42C.

scan_protocol: Slides were washed and immediately scanned using the MS 200 Microarray Skanner according to the array manufacturer's protocol.

data_processing:
probe fluorescence intensities were extracted with the NimbleScan 2.1 software
raw data was normalization by two-dimensional loess spatial normalization followed by log2(test/reference)

organism: Triticum aestivum

source_name: Chinese Spring 7B deletion stock (hexaploid wheat)_Del7BL-7Del1DS-3

label_protocol: 0.5 µg DNA of each sample was labeled using either Cy3 or Cy5-labeled Random Nonamers. Samples were denaturated at 98C for 10 min and chilled on ice for 2 min. The DNA was incubated for 2 hours at 37C with 100 units Klenow Fragment (5'-3' exo-) and dNTP mix(10mM each). After adding stop solution (0.5 M EDTA), samples were precipitated with NaCl and isopropanol and centrifuged at 12,000xg for 10 min. The samples were re-suspended in 25ul of H2O. 20 µg of Cy3 and Cy5 labeled samples were mixed in a 1.5 ml tube and dried in vacuum concentrator on low heat.

extract_protocol: DNA from leaf tissue was isolated by the CTAB method according to Springer NM: Isolation of plant DNA for PCR and genotyping using organics extraction and CTAB. Cold Harbor protocols 2010, 2010(11):pdb prot5515

tag: stock name

value: leaf

organism: Triticum turgidum subsp. durum

source_name: Langdon (LDN) tetraploid wheat

tag: line

value: Langdon

tag: genome

value: intact 7B chromosome


title: FL-0.27/LDN_rep1

description:
sample 19
Ch1 raw data file: 532778_2012-04-13_13-04_Area1_532_grid.pair
Ch2 raw data file: 532778_2012-04-13_11-33_Area1_532_grid.pair

source_name: Chinese Spring 7B deletion stock (hexaploid wheat)_Del7BS-2


title: FL-0.86/LDN_rep1

description:
sample 21
Ch1 raw data file: 532778_2012-04-13_13-04_Area1_635_grid.pair
Ch2 raw data file: 532778_2012-04-13_11-33_Area1_532_grid.pair

source_name: Chinese Spring 7B deletion stock (hexaploid wheat)_Del7BL-3


title: FL-0.63/LDN_rep2

description:
sample 16
Ch1 raw data file: 532778_2012-04-13_12-54_Area1_532_grid.pair
Ch2 raw data file: 532778_2012-04-13_12-14_Area1_532_grid.pair


title: FL-0.79/LDN_rep2

description:
sample 8
Ch1 raw data file: 532778_2012-04-13_12-04_Area1_532_grid.pair
Ch2 raw data file: 532778_2012-04-13_12-14_Area1_532_grid.pair

source_name: Chinese Spring 7B deletion stock (hexaploid wheat)_Del7BL-13


title: FL-0.40/LDN_rep1

description:
sample 13
Ch1 raw data file: 532778_2012-04-13_12-44_Area1_635_grid.pair
Ch2 raw data file: 532778_2012-04-13_11-33_Area1_532_grid.pair

source_name: Chinese Spring 7B deletion stock (hexaploid wheat)_Del7BL-1


title: 104_UN

value: whole blood


title: FL-0.86/LDN_rep2

description:
sample 22
Ch1 raw data file: 532778_2012-04-13_13-04_Area1_635_grid.pair
Ch2 raw data file: 532778_2012-04-13_12-14_Area1_532_grid.pair


title: FL-0.27/LDN_rep2

description:
sample 20
Ch1 raw data file: 532778_2012-04-13_13-04_Area1_532_grid.pair
Ch2 raw data file: 532778_2012-04-13_12-14_Area1_532_grid.pair


title: FL-0.40/LDN_rep2

description:
sample 14
Ch1 raw data file: 532778_2012-04-13_12-44_Area1_635_grid.pair
Ch2 raw data file: 532778_2012-04-13_12-14_Area1_532_grid.pair


title: FL-0.69/LDN_rep1

description:
sample 11
Ch1 raw data file: 532778_2012-04-13_12-44_Area1_532_grid.pair
Ch2 raw data file: 532778_2012-04-13_11-33_Area1_532_grid.pair

source_name: Chinese Spring 7B deletion stock (hexaploid wheat)_Del7BL-5


title: FL-0.79/LDN_rep1

description:
sample 7
Ch1 raw data file: 532778_2012-04-13_12-04_Area1_532_grid.pair
Ch2 raw data file: 532778_2012-04-13_11-33_Area1_532_grid.pair


title: FL-0.45/LDN_rep2

description:
sample 2
Ch1 raw data file: 532778_2012-04-13_11-33_Area1_635_grid.pair
Ch2 raw data file: 532778_2012-04-13_12-14_Area1_532_grid.pair

source_name: Chinese Spring 7B deletion stock (hexaploid wheat)_Del7BL-9


title: DT7BL/LDN_rep1

description:
sample 3
Ch1 raw data file: 532778_2012-04-13_11-54_Area1_532_grid.pair
Ch2 raw data file: 532778_2012-04-13_11-33_Area1_532_grid.pair

source_name: Chinese Spring 7B deletion stock (hexaploid wheat)_DT7BL


title: DT7BS/LDN_rep2

description:
sample 6
Ch1 raw data file: 532778_2012-04-13_11-54_Area1_635_grid.pair
Ch2 raw data file: 532778_2012-04-13_12-14_Area1_532_grid.pair

source_name: Chinese Spring 7B deletion stock (hexaploid wheat)_DT7BS


title: DT7BS/LDN_rep1

description:
sample 5
Ch1 raw data file: 532778_2012-04-13_11-54_Area1_635_grid.pair
Ch2 raw data file: 532778_2012-04-13_11-33_Area1_532_grid.pair


title: FL-0.33/LDN_rep2

description:
sample 18
Ch1 raw data file: 532778_2012-04-13_12-54_Area1_635_grid.pair
Ch2 raw data file: 532778_2012-04-13_12-14_Area1_532_grid.pair

source_name: Chinese Spring 7B deletion stock (hexaploid wheat)_Del7BL-2


title: FL-0.14/LDN_rep2

description:
sample 10
Ch1 raw data file: 532778_2012-04-13_12-04_Area1_635_grid.pair
Ch2 raw data file: 532778_2012-04-13_12-14_Area1_532_grid.pair

source_name: Chinese Spring 7B deletion stock (hexaploid wheat)_Del7BL-14


title: PBMC_WY_subj7

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD Methylation Assay protocol

scan_protocol: Arrays were imaged using HiScan Reader using standard recommended Illumina scanner settings

data_processing: SWAN normalization on IDAT files using library minfi (v1.6.0) in R/Bioconductor, with beta-threshold = 0.001

label: Cy3 and Cy5

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 7

label_protocol: DNAs were prepared in a total volume of 20 μl (1 μg of FF) using a commercial kit EZ DNA Methylation kit (catalog number D5001; Zymo Research Corp, Orange, CA).

growth_protocol: Peripheral blood mononuclear cells from ten healthy Caucasian male blood donors, aged 30, 31, 34, 35, 43, 52, 62, 64, 65 and 66 years, were isolated directly after arrival of the buffy coat (max. 8 hours after donation) by Ficol-paque Plus density gradient centrifugation (Amersham Biosciences, Roosendaal, the Netherlands).  All donors gave full written informed consent.

extract_protocol: Genomic DNA was extracted from the PBMC pellets by using DNeasy Blood and Tissue Kit (Qiagen), including RNAse treatment, according to the manufacturer’s instructions. All samples were quality tested on a Nanodrop spectrophotometer prior to proceeding with the microarrays.

treatment_protocol: Peripheral blood mononuclear cells were incubated in RPMI1640 medium with 2 mmol/L L-glutamine, 10% fetal bovine serum and antibiotics (penicillin and streptomycin) in the presence of 5% CO2 at 37°C at 1.0 × 10^6 cells per ml with either WY14,643 (50 μM) or vehicle (DMSO, 0.05%). After 13 hrs of exposure the cell suspensions were transferred to 15ml tubes and centrifuged for 5 minutes at 1,600rpm at 4°C. The two cell pellets per donor were re-suspended in ice-cold PBS, and each transferred to separate eppendorf tubes for RNA and DNA isolation and again centrifuged for 5 minutes at 5,000rpm at 4°C. After removing the supernatant, pellets for DNA isolation were snap frozen  on dry-ice  and stored at -80°C. The pellets for RNA isolation were resuspended in 700 μL of  Buffer RPE with added B-mercaptoethanol according to manufacturer’s instructions (Qiagen) and passed five times through a 23G needle before freezing at -80°C.

tag: subject

value: 66 yr

tag: age group

value: old

value: cultured peripheral blood mononuclear cells

tag: treatment


title: FL-0.45/LDN_rep1

description:
sample 1
Ch1 raw data file: 532778_2012-04-13_11-33_Area1_635_grid.pair
Ch2 raw data file: 532778_2012-04-13_11-33_Area1_532_grid.pair


title: FL-0.14/LDN_rep1

description:
sample 9
Ch1 raw data file: 532778_2012-04-13_12-04_Area1_635_grid.pair
Ch2 raw data file: 532778_2012-04-13_11-33_Area1_532_grid.pair


title: FL-0.33/LDN_rep1

description:
sample 17
Ch1 raw data file: 532778_2012-04-13_12-54_Area1_635_grid.pair
Ch2 raw data file: 532778_2012-04-13_11-33_Area1_532_grid.pair


title: PBMC_WY_subj10

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 10

value: 30 yr

value: young


title: PBMC_WY_subj12

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 12

value: 31 yr


title: PBMC_WY_subj8

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 8

value: 64 yr


title: PBMC_WY_subj4

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 4

value: 52 yr


title: PBMC_WY_subj6

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 6

value: 65 yr


title: PBMC_WY_subj5

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 5

value: 62 yr


title: FL-0.69/LDN_rep2

description:
sample 12
Ch1 raw data file: 532778_2012-04-13_12-44_Area1_532_grid.pair
Ch2 raw data file: 532778_2012-04-13_12-14_Area1_532_grid.pair

source_name: Langdon (LDN) tetraploid wheat


title: DT7BL/LDN_rep2

description:
sample 4
Ch1 raw data file: 532778_2012-04-13_11-54_Area1_532_grid.pair
Ch2 raw data file: 532778_2012-04-13_12-14_Area1_532_grid.pair


title: PBMC_WY_subj3

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 3

value: male

value: 34 yr


title: Week 4 rep2(ZN46/47)

city: Wuhan

first: Wenxin

last: Li

address: Luojia Hill, Wuchang

institute: Wuhan University

description:
raw data file: 02_ZN43+ZN46-47_Data.xls
The assay started with 2 to 5 μg total RNA sample, which was size fractionated using an YM-100 Microcon centrifugal filter (Millipore). The isolated small RNAs (<300 nt) were 3’-extended with a poly(A) tail using poly(A) polymerase.

hyb_protocol: On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide-coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) or other RNA (control or customer defined sequences) as well as a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were generated from in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 μL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34°C.

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and normalizing the signals using a LOWESS filter (Locally-weighted Regression).

source_name: human embryo_week 4 rep2 (ZN46/47)

label_protocol: After hybridization, detection used fluorescence labeling with tag-specific Cy3 and Cy5 dyes.

extract_protocol: The microRNAs microarray assay was performed using a service provider (LC Sciences). The assay started with 2 to 5 μg total RNA sample, which was size fractionated using an YM-100 Microcon centrifugal filter (Millipore). The isolated small RNAs (<300 nt) were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments. Hybridization was performed overnight on a μParaflo™ microfluidic chip using a microcirculation pump (Atactic Technologies)

tag: developmental stage

value: embryo

value: Week 4


title: Week 4 rep3(ZN75)

description:
raw data file: 04_ZN70+75_Data.xls
The assay started with 2 to 5 μg total RNA sample, which was size fractionated using an YM-100 Microcon centrifugal filter (Millipore). The isolated small RNAs (<300 nt) were 3’-extended with a poly(A) tail using poly(A) polymerase.

source_name: human embryo_week 4 rep3 (ZN75)


title: Week 5 rep1(ZN38)

description:
raw data file: 01_ZN18+ZN38_Data.xls
The assay started with 2 to 5 μg total RNA sample, which was size fractionated using an YM-100 Microcon centrifugal filter (Millipore). The isolated small RNAs (<300 nt) were 3’-extended with a poly(A) tail using poly(A) polymerase.

source_name: human embryo_week 5 rep1 (ZN38)

value: Week 5


title: Week 5 rep2(ZN43)

source_name: human embryo_week 5 rep2 (ZN43)


title: Week 5 rep3(ZN63-1)

description:
raw data file: 03_ZN56+63_1_Data.xls
The assay started with 2 to 5 μg total RNA sample, which was size fractionated using an YM-100 Microcon centrifugal filter (Millipore). The isolated small RNAs (<300 nt) were 3’-extended with a poly(A) tail using poly(A) polymerase.

source_name: human embryo_week 5 rep3 (ZN63-1)


title: Week 6 rep2(ZN70)

source_name: human embryo_week 6 rep2 (ZN70)

value: Week 6


title: Week 6 rep1(ZN61)

description:
raw data file: 05_ZN55+61_Data.xls
The assay started with 2 to 5 μg total RNA sample, which was size fractionated using an YM-100 Microcon centrifugal filter (Millipore). The isolated small RNAs (<300 nt) were 3’-extended with a poly(A) tail using poly(A) polymerase.

source_name: human embryo_week 6 rep1 (ZN61)


title: Week 4 rep1(ZN18)

source_name: human embryo_week 4 rep1 (ZN18)


title: PNS-classIV-kir_116-120h_rep1

city: San Francisco

first: Charlie

last: Kim

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

hyb_protocol: 825 ng of each aRNA hybridized to custom Agilent 4x44k microarrays as per manufacturer's instructions

scan_protocol: Molecular Devices Genepix 4000B scanner at 5 um resolution

data_processing: Software: GenePix 6.0. Ratio normalized, filters: 'B532' <= 350 AND 'B635' <= 350) AND 'F532 % Sat.' <= 60 AND 'F635 % Sat.' <= 60 AND 'F532 CV' <= 80 AND 'F635 CV' <= 80 AND 'Flags' >= 0 AND 'Dia.' >= 50 AND 'Dia.' <= 80 AND ('% > B532+2SD' >= 70 OR '% > B635+2SD' >= 70) AND 'Substance Name' begins with 'f' AND 'Circularity' >= 60

organism: Drosophila melanogaster

source_name: pooled reference amplified RNA from whole animals and sorted populations

label_protocol: 1.5 ug of aRNA coupled to Cy5 (or Cy3 for common pooled reference aRNA) as per standard protocols

growth_protocol: Timed larvae collections on grape juice agar plates

extract_protocol: Dissociated cells isolated by FACS.  Up to 10k cells sorted into Ambion RNAqueous Micro kit lysis buffer.  RNA isolated as per manufacturer's instructions with DNase treatment.  RNA amplified in two rounds with Ambion Aminoallyl MessageAmp II kit.

tag: tissue

value: Whole animal

source_name: Amplified RNA from FACS-sorted PNS neurons (class IV da subset) expressing kir 116-120h

tag: cell type

value: PNS class IV da neurons

tag: marker

value: ppk

tag: age (hours after egg laying)


title: PNS-classIV-kir_116-120h_rep2


title: PBMC_WY_subj1

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 1

tag: gender

tag: age

value: 43 yr

value: cultured peripheral blood mononuclear cells


title: PNS-classIV-kir_116-120h_rep3


title: PBMC_Ctrl_subj5

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 5

value: old


title: PBMC_Ctrl_subj6

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 6


title: PNS-classIV-kir_116-120h_rep4


title: PBMC_WY_subj2

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 2

value: 35 yr

value: young


title: PNS-classIV_116-120h_rep2

source_name: Amplified RNA from FACS-sorted PNS neurons (class IV da subset) 116-120h


title: PNS-classIV_92-96h_rep4

source_name: Amplified RNA from FACS-sorted PNS neurons (class IV da subset) 92-96h


title: PNS-classIV_116-120h_rep1


title: PNS-classIV_68-72h_rep1

source_name: Amplified RNA from FACS-sorted PNS neurons (class IV da subset) 68-72h


title: PNS-classIV_44-48h_rep3

source_name: Amplified RNA from FACS-sorted PNS neurons (class IV da subset) 44-48h


title: PNS-classIV_44-48h_rep2


title: PNS-classIV_68-72h_rep2


title: PNS-classIV_68-72h_rep3


title: PNS-classIV_116-120h_rep3


title: PNS-classIV_92-96h_rep3


title: PNS-classIV_92-96h_rep2


title: PNS-classIV_44-48h_rep4


title: PNS-classIV_116-120h_rep4


title: PBMC_Ctrl_subj7

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 7

value: 66 yr


title: PNS-classIV_92-96h_rep1


title: PNS-classIV_44-48h_rep5


title: PNS-classIV_68-72h_rep4


title: PNS-classIV_44-48h_rep1


title: PBMC_Ctrl_subj3

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 3


title: PNS-classIV_20-24h_rep3

source_name: Amplified RNA from FACS-sorted PNS neurons (class IV da subset) 20-24h


title: PBMC_Ctrl_subj1

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 1


title: PNS-classIV_20-24h_rep2


title: PNS-classIV_20-24h_rep4


title: PBMC_Ctrl_subj8

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 8

value: 64 yr


title: PNS-md-tnt_92-96h_rep4

source_name: Amplified RNA from FACS-sorted PNS neurons (md subset) expressing tnt 92-96h

value: PNS md neurons


title: PBMC_Ctrl_subj2

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 2

value: male


title: PBMC_Ctrl_subj10

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 10

value: 30 yr


title: PBMC_Ctrl_subj4

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 4

value: 52 yr


title: PNS-md_92-96h_rep2

source_name: pooled reference amplified RNA from whole animals and sorted populations

source_name: Amplified RNA from FACS-sorted PNS neurons (md subset) 92-96h AEL


title: PNS-classIV_20-24h_rep1


title: PNS-md-tnt_92-96h_rep2


title: PNS-md_116-120h_rep2

source_name: Amplified RNA from FACS-sorted PNS neurons (md subset) 116-120h AEL


title: PBMC_Ctrl_subj12

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 12

value: 31 yr


title: PNS-md-tnt_92-96h_rep3


title: PNS-md_116-120h_rep3


title: PNS-md_68-72h_rep3

source_name: Amplified RNA from FACS-sorted PNS neurons (md subset) 68-72h AEL


title: PNS-md_116-120h_rep1


title: PNS-md_68-72h_rep2


title: PNS-md_68-72h_rep4


title: PNS-md_116-120h_rep4


title: t12+/+T43_15d_rep3

city: Prague 4

first: David

last: Homolka

address: Videnska 1083

department: Department of Mouse Molecular Genetics

country: Czech Republic

institute: Institute Of Molecular Genetics

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed independently for spermatogenic populations and testicular samples from 15 days old animals. The analysis was done with Bioconductor and R statistics (version 2.12) using the gcRMA method with default settings and custom chip description file (probes were annotated to Entrez identifiers - NCBI build 37) mm430mmentrezg, created by Microarray Lab at the Molecular and Behavioral Neuroscience Institute at the University of Michigan.

source_name: t12+/+T43, testes, 15 ppt

label_protocol: Between 20 to 30 ng of total RNA were used to prepare biotinylated cRNA according to the standard Affymetrix Two-Cycle protocol (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: Mouse lines used in the experiment were C57BL/6J , C57BL/10J, C57BL/10J -Ttf+/+T43H and C57BL/10J - t12+/+T43. All the male mice used for isolation of spermatogenic populations were two months old. 15 days old males were used for comparison of testicular expression.

extract_protocol: Total RNA from individual populations was isolated using RNeasy Micro kit (Qiagen) according to manufacturer‘s protocol. Testicular RNA from 15 days old males was isolated using RNeasy Mini isolation kit (Qiagen) according to manufacturer‘s protocol.

treatment_protocol: Mice were euthanized by cervical dislocation. For isolation of spermatogenic populations the single cell suspension from testicular tubules was prepared and the populations were isolated using fluorescence activated cell sorting of testicular single cell suspension according to ref. (Bastos et al. 2005). Testicular RNA from 15 days old animals was isolated from the testes after removal of tunica.

tag: strain

value: 15 days

value: testes


title: B6_15d_rep2

source_name: C57BL/6J , testes, 15 ppt


title: PNS-md_92-96h_rep1

value: Whole animal


title: PNS-md-tnt_92-96h_rep1


title: PNS-md_44-48h_rep3

source_name: Amplified RNA from FACS-sorted PNS neurons (md subset) 44-48h AEL


title: PNS-md_92-96h_rep3


title: B6_15d_rep1


title: PNS-md_44-48h_rep4


title: PNS-md_44-48h_rep1


title: Ttf+/+T43H_15d_rep2

source_name: Ttf+/+T43H, testes, 15 ppt


title: t12+/+T43_15d_rep2


title: B10_late_pach_rep2

value: adult (2 months)

value: mid-late-pachytene spermatocytes


title: Ttf+/+T43H_15d_rep3


title: PNS-md_68-72h_rep1


title: Ttf+/+T43H_15d_rep1


title: t12+/+T43_15d_rep1


title: B10_pre_pach_rep2

value: pre-mid-pachytene spermatocytes


title: MN-RN2_92-96h_rep4

source_name: Amplified RNA from FACS-sorted motor neurons (RN2 subset) 92-96h AEL

value: Motor neuron subset


title: PNS-md_20-24h_rep1

source_name: Amplified RNA from FACS-sorted PNS neurons (md subset) 20-24h AEL


title: B10_late_pach_rep1


title: MN-RN2_92-96h_rep3


title: PNS-md_20-24h_rep2


title: MN-RN2_20-24h_rep3

source_name: Amplified RNA from FACS-sorted motor neurons (RN2 subset) 20-24h AEL


title: PNS-md_20-24h_rep3


title: B10_pre_pach_rep1


title: MN-RN2_92-96h_rep2


title: MN-RN2_92-96h_rep1


title: t12+/+T43_pre_pach_rep3


title: t12+/+T43_pre_pach_rep2


title: Ttf+/+T43H_pre_pach_rep3


title: MN_92-96h_rep3

source_name: Amplified RNA from FACS-sorted motor neurons 92-96h AEL

value: Motor neurons


title: MN-RN2_20-24h_rep1


title: MN-RN2_20-24h_rep2


title: t12+/+T43_pre_pach_rep1


title: Ttf+/+T43H_pre_pach_rep1


title: Home Cage (HC) 4

city: Atlanta

first: Raul

last: Andero Gali

state: GA

address: 954 Gatewood Rd

department: Department of Psychiatry and Behavioral Sciences

institute: Emory University

description:
1mm punch used
SAMPLE 12

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Mouse amygdala

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

extract_protocol: Total RNA was isolated and purified from the tissue with the RNeasy Mini Kit (Catalog #74106) following the manufacturer instructions (Qiagen)

tag: group

value: Home Cage

tag: Sex

value: adult

value: Bilateral amygdala


title: CNS_92-96h_rep2

source_name: Amplified RNA from FACS-sorted CNS cells 92-96h AEL

value: CNS

value: elav


title: CNS_116-120h_rep1

source_name: Amplified RNA from FACS-sorted CNS cells 116-120h AEL


title: Home Cage (HC) 3

description:
1mm punch used
SAMPLE 11

value: male


title: CNS_116-120h_rep3


title: Home Cage (HC) 2

description:
1mm punch used
SAMPLE 10


title: MN_92-96h_rep1


title: CNS_92-96h_rep3


title: CNS_92-96h_rep1


title: 2hrs after FC 4

description:
1mm punch used
SAMPLE 4

value: 2 hours after Fear Conditioning


title: 30 min after FC 3

description:
1mm punch used
SAMPLE 7

value: 30 minutes Fear Conditioning


title: CNS_68-72h_rep1

source_name: Amplified RNA from FACS-sorted CNS cells 68-72h AEL


title: Home Cage (HC) 1

description:
1mm punch used
SAMPLE 9


title: 30 min after FC 2

description:
1mm punch used
SAMPLE 6


title: CNS_44-48h_rep3

source_name: pooled reference amplified RNA from whole animals and sorted populations

source_name: Amplified RNA from FACS-sorted CNS cells 44-48h AEL


title: Ttf+/+T43H_pre_pach_rep2


title: 30 min after FC 4

description:
1mm punch used
SAMPLE 8


title: 2hrs after FC 1

description:
1mm punch used
SAMPLE 1


title: 2hrs after FC 3

description:
1mm punch used
SAMPLE 3


title: CNS_68-72h_rep2


title: MN_92-96h_rep2


title: CNS_44-48h_rep2


title: CNS_116-120h_rep2


title: CNS_44-48h_rep1


title: 30 min after FC 1

description:
1mm punch used
SAMPLE 5


title: 2hrs after FC 2

description:
1mm punch used
SAMPLE 2


title: CNS_20-24h_rep2

source_name: Amplified RNA from FACS-sorted CNS cells 20-24h AEL


title: CNS_20-24h_rep3


title: CNS_20-24h_rep1


title: muscle_116-120h_rep4

source_name: Amplified RNA from FACS-sorted muscle cells 116-120h AEL

value: Muscle

value: Mhc


title: muscle_116-120h_rep2


title: muscle_92-96h_rep2

source_name: Amplified RNA from FACS-sorted muscle cells 92-96h AEL


title: muscle_92-96h_rep1


title: muscle_92-96h_rep3


title: muscle_20-24h_rep4

source_name: Amplified RNA from FACS-sorted muscle cells 20-24h AEL


title: 1-B6-HSC 3

city: cambridge

first: yaoyu

last: chen

state: Massachusetts

address: 250 Mass ave

department: ONC

institute: NIBR

hyb_protocol: Affymetrix GeneChip eukaryotic hybridization protocol (Affymetrix Inc.)

scan_protocol: GeneChip Scanner 3000 (Affymetrix Inc.)

data_processing: Micorarray Analysis Suite version 5.0 (MAS 5.0) background correction, scaled to 150

label_protocol: Nugen Ovation RNA Amplification System+ WB + FL cDNA Biotin Module V2 (NuGen Lts)

extract_protocol: RNeasy Plus kit (qiagen) following the manufacturers instructions

tag: genotype/variation

value: WT


title: 1-B6-HSC 2


title: 1-SELP-HSC 3

value: SELP -/-


title: 1-SELP-HSC 2


title: DC_B6.CD11-Cre.FasKi_Rep2

city: Chicago

first: Aly

middle: Azeem

last: Khan

state: IL

address: 6045 S. Kenwood Ave.

institute: University of Chicago

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data was processed with GenomeStudio using Illumina default analysis settings.

source_name: Splenic DCs

label_protocol: Total RNA was processed using the Illumina Totalprep kit (Ambion, Life Technologies, Carlsbad, CA) according to the manufacturer’s protocol.

extract_protocol: Total RNA was extracted using guanidinium cesium chloride gradient ultracentrifugation (Chirgwin et al., 1979).

tag: genetic background

value: Splenic DCs

tag: genotype


title: DC_B6.FasKI_Rep1


title: 1-SELP-HSC 1


title: muscle_116-120h_rep1

value: Whole animal


title: 1-B6-HSC 1


title: muscle_116-120h_rep3


title: DC_B6.CD11-Cre.FasKi_Rep1


title: normal-weight male child with FTO allele AA NW32

city: Footscray

first: Sarah

middle: Amandine Caroline

last: Voisin

state: VIC

address: Ballarat Road

department: Institute for Health and Sport

country: Australia

institute: Victoria University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina's iScan reader using standard recommended Illumina scanner settings

data_processing: Genomestudio2009.2 toghether with the methylumi and limma packages from Bioconductor. Probes with detection P-value>0.01 were removed from further analysis together with probes from the sex chromosomes.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from pheripheral whole blood using QiaGen Maxiprep kit

tag: weight category

value: normal-weight

tag: tanner stage

tag: fto allele

value: AA