title: Trout exposed to 10 mg/L crude oil for 24 h, liver replicate 1,2


title: Trout exposed to 0.4 mg/L crude oil for 24 h, liver replicate 3,1

status: Public on Dec 15 2009

type: RNA

city: Bangor

first: Sharon

middle: E.

last: Hook

state: NSW

address: Private Mail Bag 7

department: Centre for Environmental Contaminants Research

country: Australia

institute: CSIRO

description: Biological replicate 3, Technical replicate 1

hyb_protocol: Samples were mixed with 20 µg tRNA and 20 µg Herring Sperm DNA to prevent non specific hybridization, then mixed with 35 µl of modified Genisphere hybridization buffer (50% formamide, 40% 20x SSC, 9% Denhardt’s solution, 1% SDS). This mixture was then applied to the arrays and allowed to hybridize overnight (16 hr) at 45 o C. After hybridization, arrays were washed in SSC/SDS buffers with descending stringency to remove any unhybridized or weakly (nonspecifically) hybridized cDNAs.

scan_protocol: Arrays were scanned using a Perkin Elmer ScanArray Express, with laser power and PMT gain varied to equalize fluorescence intensity between channels and to prevent over saturation of signal intensity.

data_processing: Data were extracted using ScanArray Express software (Perkin Elmer). The median fluorescence intensity with background subtracted was imported Genespring microarray analysis software for further analysis. Data were LOWESS normalized and spots that did not meet a minimum signal intensity were removed.

label: Alexa Fluor 555

molecule: total RNA

organism: Oncorhynchus mykiss

source_name: liver (control)

label_protocol: Labelled using I\nvitrogen’s Superscript cDNA Indirect Labeling kit and the manufacturer's protocol, and Alexa fluors.

extract_protocol: Trizol extraction following the manufacturer's protocol

treatment_protocol: Juvenile Rainbow trout were exposed to the WAF of Crude oil at the specified dose

tag: treatment

value: control

tag: harvested at what time

label: Alexa Fluor 647

source_name: liver (exposed)

value: 0.4 mg/L Crude Oil


title: Trout exposed to 10 mg/L crude oil for 24 h, liver replicate 2,1

description: Biological replicate 2, Technical replicate 1

value: 10 mg/L Crude Oil


title: Trout exposed to 10 mg/L crude oil for 24 h, liver replicate 1,1

description: Biological replicate 1, Technical replicate 1


title: Trout exposed to 10 mg/L crude oil for 24 h, liver replicate 2,2

description: Biological replicate 2, Technical replicate 2


title: Trout exposed to 0.4 mg/L crude oil for 24 h, liver replicate 1,2

description: Biological replicate 1, Technical replicate 2


title: Trout exposed to 0.4 mg/L crude oil for 24 h, liver replicate 3,2

description: Biological replicate 3, Technical replicate 2


title: Trout exposed to 0.4 mg/L crude oil for 24 h, liver replicate 2,1


title: Trout exposed to 10 mg/L crude oil for 24 h, liver replicate 3,1


title: Trout exposed to 10 mg/L crude oil for 96 h then allowed to recover for 96 h, gill replicate 3,2

source_name: gill (control)

source_name: gill (exposed)


title: Trout exposed to 0.4 mg/L crude oil for 24 h, liver replicate 1,1


title: Trout exposed to 0.4 mg/L crude oil for 24 h, liver replicate 2,2


title: Trout exposed to 10 mg/L crude oil for 96 h, gill replicate 2,1


title: Trout exposed to 10 mg/L crude oil for 96 h then allowed to recover for 96 h, gill replicate 3,1


title: Trout exposed to 10 mg/L crude oil for 96 h then allowed to recover for 96 h, gill replicate 2,2


title: Trout exposed to 10 mg/L crude oil for 96 h, gill replicate 3,1


title: Trout exposed to 10 mg/L crude oil for 96 h then allowed to recover for 96 h, gill replicate 2,1


title: Trout exposed to 10 mg/L crude oil for 96 h then allowed to recover for 96 h, gill replicate 1,1


title: Trout exposed to 10 mg/L crude oil for 96 h then allowed to recover for 96 h, gill replicate 1,2


title: Trout exposed to 10 mg/L crude oil for 24 h, gill replicate 3,2


title: Trout exposed to 10 mg/L crude oil for 96 h, gill replicate 1,1


title: Trout exposed to 10 mg/L crude oil for 96 h, gill replicate 1,2


title: Trout exposed to 10 mg/L crude oil for 96 h, gill replicate 3,2


title: Trout exposed to 10 mg/L crude oil for 96 h, gill replicate 2,2


title: Trout exposed to 10 mg/L crude oil for 24 h, gill replicate 3,1


title: Trout exposed to 10 mg/L crude oil for 24 h, gill replicate 2,2


title: Trout exposed to 10 mg/L crude oil for 24 h, gill replicate 2,1


title: caudal 5HT neurons (C+) biological replicate 2

status: Public on Dec 16 2009

city: Cleveland

first: Evan

middle: S.

last: Deneris

state: OH

address: 2109 Adlebert Road

department: Neurosciences

country: USA

institute: Case Western Reserve University

description:
gene expression data from rostral 5HT neurons (R+), rostral non-5HT neurons (R-), caudal 5HT neurons (C+), and caudal non-5HT neurons (C-)
61 den15

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix High Density Genechip Scanner 3000.

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

label: biotin

organism: Mus musculus

source_name: caudal 5HT neurons (C+)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200,000 sorted cells for reach replicate using one round of amplication.

growth_protocol: E12.5 ePet-EYFP neural tubes were dissected into rostral and caudal portions by making incisions at the pontine flexure, mesecephalic flexure, and spinal cord.

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

treatment_protocol: Cells were dissociated by mild trypsin and mechanical trituration with a glass pipette into single cell suspensions. Cells were sorted and 4 populations collected directly into Trizol: (R+. R-, C+, and C).

tag: tissue

value: caudal 5HT neurons

tag: genotype

value: ePet-EYFP

tag: age


title: Trout exposed to 10 mg/L crude oil for 24 h, gill replicate 1,1


title: Trout exposed 1 mg/L gas oil for 96 h replicate 2,3

description: Biological replicate 2, Technical replicate 3

hyb_protocol: Samples were mixed with 20 µg tRNA and 20 µg Herring Sperm DNA to prevent non specific hybridization, then mixed with 35 µl of modified Genisphere hybridization buffer (50% formamide, 40% 20x SSC, 9% Denhardts solution, 1% SDS). This mixture was then applied to the arrays and allowed to hybridize overnight (16 hr) at 45 o C. After hybridization, arrays were washed in SSC/SDS buffers with descending stringency to remove any unhybridized or weakly (nonspecifically) hybridized cDNAs.

treatment_protocol: Juvenile Rainbow trout were exposed to the WAF of each petroleum product at the specified dose

value: 1 mg/L Gas Oil


title: Trout exposed 1 mg/L gas oil for 96 h replicate 3,3

description: Biological replicate 3, Technical replicate 3


title: Trout exposed 1 mg/L gas oil for 96 h replicate 2,2


title: Trout exposed 2 mg/L kerosene for 96 h replicate 3,2

value: 2 mg/L Kerosene


title: Trout exposed 1 mg/L gas oil for 96 h replicate 1.3

description: Biological replicate 1, Technical replicate 3


title: Trout exposed 1 mg/L gas oil for 96 h replicate 3,1


title: Trout exposed 1 mg/L gas oil for 96 h replicate 3,2


title: Trout exposed 2 mg/L kerosene for 96 h replicate 1,2


title: Trout exposed 1 mg/L gas oil for 96 h replicate 1,1


title: Trout exposed 1 mg/L gas oil for 96 h replicate 2,1


title: Trout exposed 1 mg/L gas oil for 96 h replicate 1,2


title: Trout exposed to 10 mg/L crude oil for 24 h, gill replicate 1,2


title: Trout exposed 2 mg/L kerosene for 96 h replicate 2,2


title: Trout exposed 2 mg/L kerosene for 96 h replicate 2,1


title: Trout exposed 2 mg/L kerosene for 96 h replicate 1,1


title: Trout exposed 2 mg/L heavy fuel oil for 96 h replicate 2,2

value: 2 mg/L Heavy Fuel Oil


title: Trout exposed 2 mg/L kerosene for 96 h replicate 2,3


title: Trout exposed 2 mg/L heavy fuel oil for 96 h replicate 3,2


title: Trout exposed 2 mg/L heavy fuel oil for 96 h replicate 3,1


title: Trout exposed 2 mg/L heavy fuel oil for 96 h replicate 2,3


title: Trout exposed 2 mg/L heavy fuel oil for 96 h replicate 3,3


title: Trout exposed 2 mg/L kerosene for 96 h replicate 2,4

description: Biological replicate 2, Technical replicate 4


title: Trout exposed 2 mg/L heavy fuel oil for 96 h replicate 1.3


title: Trout exposed 2 mg/L heavy fuel oil for 96 h replicate 1,1


title: Trout exposed 2 mg/L crude oil for 96 h replicate 3,1

value: 2 mg/L Crude Oil


title: Trout exposed 2 mg/L crude oil for 96 h replicate 2,1


title: Trout exposed 2 mg/L heavy fuel oil for 96 h replicate 1,2


title: Trout exposed 2 mg/L crude oil for 96 h replicate 2,2


title: Trout exposed 2 mg/L crude oil for 96 h replicate 1,2


title: pituitary harvested at 98 days replicate 2 [compressed]

description: Biological replicate 2

hyb_protocol: Samples were mixed with 20 µg tRNA and 20 µg Herring Sperm DNA to prevent non specific hybridization, then mixed with 35 µl of modified “Genisphere” hybridization buffer (50% formamide, 40% 20x SSC, 9% Denhardt’s solution, 1% SDS).  This mixture was then applied to the arrays and allowed to hybridize overnight (16 hr) at 45 o C.  After hybridization, arrays were washed in SSC/SDS buffers with descending stringency to remove any unhybridized or weakly (nonspecifically) hybridized cDNA’s.

data_processing: Data were extracted using ScanArray Express software (Perkin Elmer).  The median fluorescence intensity with background subtracted was imported Genespring microarray analysis software for further analysis.  Data were LOWESS normalized and spots that did not meet a minimum signal intensity were removed.

source_name: pituitary (control)

treatment_protocol: Post Spawned Female Rainbow Trout over the course of a compressed photoperiod

tag: harvested on which day of the normal photoperiod

value: Day 0

source_name: pituitary (test)

value: Day 98


title: pituitary harvested at 44 days replicate 2 [compressed]

description: Biological replicate 2

value: Day 44


title: Trout exposed 2 mg/L crude oil for 96 h replicate 1,1


title: pituitary harvested at 98 days replicate 1 [compressed]

description: Biological replicate 1


title: pituitary harvested at 204 days replicate 3 [compressed]

description: Biological replicate 3

value: Day 204


title: pituitary harvested at 216 days replicate 3 [compressed]

description: Biological replicate 3

value: Day 216


title: pituitary harvested at 51 days replicate 2 [compressed]

description: Biological replicate 2

value: Day 51


title: pituitary harvested at 204 days replicate 2 [compressed]

description: Biological replicate 2


title: pituitary harvested at 216 days replicate 1 [compressed]

description: Biological replicate 1


title: Infant ALL PRED sensitive 6

city: Rotterdam

first: Ronald

last: Stam

address: Dr. Molewaterplein 60

country: Netherlands

institute: Erasmus MC - Sophia Children's Hospital

description: Gene expression data primary infant ALL cells

hyb_protocol: Fragmented cRNA was hybridized to Affymetrix HU133A microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Gene expression data were normalized using dChip, and filtered with a max-min=100, and max/min=4.

organism: Homo sapiens

source_name: Primary infant (<1 year of age) ALL cells in vitro prednisolone sensisitve 6

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

extract_protocol: Total RNA was extracted from leukemic cells using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Primary ALL samples were obtained at diagnosis (before treatment) and processed within 24 hours after sampling. All samples contained >90% leukemic blasts.

tag: sex

value: female

tag: developmental stage

value: Infant

value: <1 year old

tag: cell type

value: Precursor B-cells

tag: disease status

value: acute lymphoblastic leukemia (ALL)

tag: clinical response factor

value: prednisolone sensitive


title: pituitary harvested at 37 days replicate 1 [compressed]

description: Biological replicate 1

value: Day 37


title: pituitary harvested at 216 days replicate 2 [compressed]

description: Biological replicate 2


title: pituitary harvested at 198 days replicate 3 [compressed]

description: Biological replicate 3

value: Day 198


title: pituitary harvested at 37 days replicate 3 [compressed]

description: Biological replicate 3


title: pituitary harvested at 198 days replicate 2 [compressed]

description: Biological replicate 2


title: pituitary harvested at 198 days replicate 1 [compressed]

description: Biological replicate 1


title: pituitary harvested at 192 days replicate 2 [compressed]

description: Biological replicate 2

value: Day 192


title: pituitary harvested at 180 days replicate 2 [compressed]

description: Biological replicate 2

value: Day 180


title: pituitary harvested at 192 days replicate 1 [compressed]

description: Biological replicate 1


title: pituitary harvested at 156 days replicate 2 [compressed]

description: Biological replicate 2

value: Day 156


title: pituitary harvested at 180 days replicate 1 [compressed]

description: Biological replicate 1

value: Day 0


title: pituitary harvested at 148 days replicate 1 [compressed]

description: Biological replicate 1

value: Day 148


title: pituitary harvested at 156 days replicate 3 [compressed]

description: Biological replicate 2


title: pituitary harvested at 148 days replicate 3 [compressed]

description: Biological replicate 3


title: pituitary harvested at 51 days replicate 1 [compressed]

description: Biological replicate 1


title: Ovary harvested at 216 days replicate 1 [compressed]

description: Biological replicate 1

source_name: ovary (control)

source_name: ovary (test)


title: Ovary harvested at 78 days replicate 2 [compressed]

description: Biological replicate 2

value: Day 78


title: pituitary harvested at 133 days replicate 1 [compressed]

description: Biological replicate 1

value: Day 133


title: Ovary harvested at 51 days replicate 2 [compressed]

description: Biological replicate 2


title: Ovary harvested at 51 days replicate 1 [compressed]

description: Biological replicate 1


title: Ovary harvested at 216 days replicate 3 [compressed]

description: Biological replicate 3

value: Day 216


title: pituitary harvested at 156 days replicate 1 [compressed]

description: Biological replicate 1


title: Ovary harvested at 198 days replicate 3 [compressed]

description: Biological replicate 3


title: pituitary harvested at 133 days replicate 3 [compressed]

description: Biological replicate 3


title: pituitary harvested at 44 days replicate 1 [compressed]

description: Biological replicate 1

value: Day 44


title: pituitary harvested at 180 days replicate 3 [compressed]

description: Biological replicate 3


title: pituitary harvested at 148 days replicate 2 [compressed]

description: Biological replicate 2


title: Ovary harvested at 192 days replicate 3 [compressed]

description: Biological replicate 3


title: Ovary harvested at 156 days replicate 3 [compressed]

description: Biological replicate 3


title: Trout exposed 2 mg/L heavy fuel oil for 96 h replicate 2,1

value: control

value: 2 mg/L Heavy Fuel Oil


title: Ovary harvested at 168 days replicate 1 [compressed]

description: Biological replicate 1

value: Day 168


title: Ovary harvested at 216 days replicate 2 [compressed]

description: Biological replicate 2


title: Ovary harvested at 51 days replicate 3 [compressed]

description: Biological replicate 3

value: Day 51


title: Ovary harvested at 112 days replicate 1 [compressed]

description: Biological replicate 1

value: Day 112


title: Ovary harvested at 37 days replicate 3 [compressed]

description: Biological replicate 3


title: Ovary harvested at 37 days replicate 1 [compressed]

description: Biological replicate 1


title: Ovary harvested at 78 days replicate 1 [compressed]

description: Biological replicate 1


title: Ovary harvested at 204 days replicate 3 [compressed]

description: Biological replicate 3

value: Day 204


title: Trout exposed 2 mg/L kerosene for 96 h replicate 1.3

value: 2 mg/L Kerosene


title: Trout exposed 2 mg/L crude oil for 96 h replicate 3,2

value: 2 mg/L Crude Oil


title: Ovary harvested at 78 days replicate 3 [compressed]

description: Biological replicate 3


title: pituitary harvested at 204 days replicate 1 [compressed]

description: Biological replicate 1


title: Ovary harvested at 192 days replicate 2 [compressed]

description: Biological replicate 2

value: Day 192


title: pituitary harvested at 37 days replicate 2 [compressed]

description: Biological replicate 2

value: Day 37


title: Ovary harvested at 204 days replicate 2 [compressed]

description: Biological replicate 2


title: Ovary harvested at 198 days replicate 2 [compressed]

description: Biological replicate 2

value: Day 198


title: Ovary harvested at 192 days replicate 1 [compressed]

description: Biological replicate 1

value: Day 0


title: Ovary harvested at 204 days replicate 1 [compressed]

description: Biological replicate 1


title: Ovary harvested at 180 days replicate 2 [compressed]

description: Biological replicate 2

value: Day 180


title: tnr null adult_3

city: Chapel Hill

first: ingo

last: meier

state: NC

address: 416 Fordham Hall

institute: UNC chapel hill

description: Gene expression data from wild type and Tenascin-R deficient mice

hyb_protocol: 15 µg of fragmented cRNA were incubated with the chip in 200 µl of hybridization solution in Hybridization Oven 640 (Affymetrix) at 45 C for 16 hours

scan_protocol: GeneChips were scanned using  Agilent Technologies laser scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 185.

source_name: mouse adult tenscin-R knockout brain

label_protocol: biotin-labeled cRNA was carried out using the ENZO RNA transcript labeling kit

growth_protocol: The animals were maintained under standard housing conditions (23 C, 40-50 % humidity, food and water ad libitum)

extract_protocol: Total RNA was extracted from the entire brain of Tnr-deficient and wild-type control mice using TRIzol (Invitrogen) according to the manufacturer’s instructions. Further purification of RNA was performed with the RNeasy Mini Kit (Qiagen). Total RNA concentration was determined using a spectrophotometer at 260 nm and 280 nm wavelength. To check RNA integrity, total RNA was separated in a 1% agarose gel containing formaldehyde, and the intensity ratio of 28S and 18S ribosomal RNA bands was assessed after ethidium bromide staining.

treatment_protocol: no treatment, the mice were killed by cervical dislocation (adult) or decapitaion (P7)

tag: gender

value: male

tag: strain

value: 2-3 month

tag: type

value: tnr null


title: a_formosa_carpels_population3

city: Palmerston North

first: Claudia

last: Voelckel

address: Riddet Road

department: Allan Wilson Centre for Molecular Ecology and Evolution

country: New Zealand

institute: Massey University

description: sample_label: SOM0126E

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com. Order number was OID5089.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com. Order number was OID5089.

data_processing: The raw data (.pair file) was subjected to logarithmization, spatial correction (Borevitz et al. Genome Research 13:513-523), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and probe effect removal (by subtracting probe means). R scripts were written by J.O. Borevitz and functions from R packages affy, stats and nlme were used for data analysis.

organism: Aquilegia formosa

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com. Order number was OID5089.

growth_protocol: Flowers were collected from three native A. formosa populations growing in close proximity at Blue Canyon, Sonora Pass (Sierra Nevada).

extract_protocol: Total RNA was isolated (RNeasy kit, Qiagen, USA) from each tissue across the three replicate populations and 40ug of RNA were sent to NimbleGen Systems (Reykjavík, Iceland) for hybridization.

treatment_protocol: Pre-anthesis stage flowers were dissected into the five floral whorls and shock-frozen into liquid nitrogene immediatetly after collection in the field.

value: carpels

tag: population


title: tnr null adult_1


title: tnr null adult_2


title: wild type adult_3

source_name: mouse adult wild type brain

value: wild type


title: pituitary harvested at 192 days replicate 3 [compressed]

description: Biological replicate 3


title: a_formosa_staminodia_population3

description: sample_label: SOM01267

value: staminodia


title: wild type adult_2


title: Ovary harvested at 180 days replicate 1 [compressed]

description: Biological replicate 1


title: Ovary harvested at 168 days replicate 3 [compressed]

description: Biological replicate 3

value: Day 168


title: Ovary harvested at 168 days replicate 2 [compressed]

description: Biological replicate 2


title: a_formosa_carpels_population2

description: sample_label: SOM01269


title: Ovary harvested at 156 days replicate 2 [compressed]

description: Biological replicate 2

value: Day 156


title: tnr null p7_3

source_name: mouse P7 tenscin-R knockout brain


title: Ovary harvested at 112 days replicate 3 [compressed]

description: Biological replicate 3

value: Day 112


title: Ovary harvested at 156 days replicate 1 [compressed]

description: Biological replicate 1


title: tnr null p7_2


title: wild type adult_1


title: a_formosa_petals_population1

description: sample_label: SOM0125Z

value: petals


title: Ovary harvested at 112 days replicate 2 [compressed]

description: Biological replicate 2


title: tnr null p7_4


title: tnr null p7_1


title: a_formosa_staminodia_population2

description: sample_label: SOM01266


title: Ovary harvested at 180 days replicate 3 [compressed]

description: Biological replicate 3


title: a_formosa_carpels_population1

description: sample_label: SOM01268


title: a_formosa_stamens_population2

description: sample_label: SOM01263

value: stamens


title: Liver harvested at 57 days replicate 2 [compressed]

description: Biological replicate 2

source_name: liver (test)

value: Day 57


title: Liver harvested at 98 days replicate 1 [compressed]

description: Biological replicate 1

value: Day 98


title: a_formosa_petals_population2

description: sample_label: SOM01260


title: Liver harvested at 37 days replicate 2 [compressed]

description: Biological replicate 2

value: Day 37


title: wild type p7_3

source_name: mouse P7 wild type brain


title: a_formosa_petals_population3

description: sample_label: SOM01261


title: a_formosa_stamens_population3

description: sample_label: SOM01264


title: Liver harvested at 204 days replicate 3 [compressed]

description: Biological replicate 3

value: Day 204


title: a_formosa_staminodia_population1

description: sample_label: SOM01265


title: a_formosa_sepals_population1

description: sample_label: SOM0125W

value: sepals


title: Liver harvested at 216 days replicate 3 [compressed]

description: Biological replicate 3

value: Day 0

value: Day 216


title: a_formosa_stamens_population1

description: sample_label: SOM01262


title: Liver harvested at 37 days replicate 3 [compressed]

description: Biological replicate 3


title: Liver harvested at 204 days replicate 1 [compressed]

description: Biological replicate 1


title: a_formosa_sepals_population3

description: sample_label: SOM0125Y


title: a_formosa_sepals_population2

description: sample_label: SOM0125X


title: wild type p7_1

value: male


title: Liver harvested at 198 days replicate 1 [compressed]

description: Biological replicate 1

value: Day 198


title: Liver harvested at 57 days replicate 3 [compressed]

description: Biological replicate 3


title: Liver harvested at 192 days replicate 1 [compressed]

description: Biological replicate 1

value: Day 192


title: Liver harvested at 198 days replicate 3 [compressed]

description: Biological replicate 3


title: Liver harvested at 180 days replicate 2 [compressed]

description: Biological replicate 2

value: Day 180


title: Liver harvested at 180 days replicate 3 [compressed]

description: Biological replicate 3


title: Liver harvested at 198 days replicate 2 [compressed]

description: Biological replicate 2


title: Liver harvested at 156 days replicate 1 [compressed]

description: Biological replicate 1


title: Liver harvested at 168 days replicate 3 [compressed]

description: Biological replicate 3


title: Liver harvested at 57 days replicate 1 [compressed]

description: Biological replicate 1


title: Liver harvested at 204 days replicate 2 [compressed]

description: Biological replicate 2


title: Liver harvested at 168 days replicate 2 [compressed]

description: Biological replicate 2


title: Liver harvested at 133 days replicate 2 [compressed]

description: Biological replicate 2

value: Day 133


title: Liver harvested at 156 days replicate 3 [compressed]

description: Biological replicate 3


title: Liver harvested at 112 days replicate 3 [compressed]

description: Biological replicate 3


title: Liver harvested at 112 days replicate 1 [compressed]

description: Biological replicate 1


title: Liver harvested at 98 days replicate 2 [compressed]

description: Biological replicate 2


title: Liver harvested at 112 days replicate 2 [compressed]

description: Biological replicate 2


title: Liver harvested at 180 days replicate 1 [compressed]

description: Biological replicate 1


title: Liver harvested at 216 days replicate 1 [compressed]

description: Biological replicate 1


title: Liver harvested at 133 days replicate 1 [compressed]

description: Biological replicate 1


title: Liver harvested at 37 days replicate 1 [compressed]

description: Biological replicate 1


title: Liver harvested at 168 days replicate 1 [compressed]

description: Biological replicate 1

value: Day 168


title: Liver harvested at 192 days replicate 2 [compressed]

description: Biological replicate 2


title: Liver harvested at 133 days replicate 3 [compressed]

description: Biological replicate 3


title: pituitary harvested at 92 days replicate 3 [normal]

description: Biological replicate 3

treatment_protocol: Post Spawned Female Rainbow Trout over the course of a Normal photoperiod

value: Day 92


title: wild type p7_2

value: wild type


title: Liver harvested at 156 days replicate 2 [compressed]

description: Biological replicate 2

value: Day 256


title: pituitary harvested at 80 days replicate 3 [normal]

description: Biological replicate 3

value: Day 80


title: pituitary harvested at 330 days replicate 3 [normal]

description: Biological replicate 3

value: Day 330


title: Liver harvested at 98 days replicate 3 [compressed]

description: Biological replicate 3

value: Day 98


title: Liver harvested at 216 days replicate 2 [compressed]

description: Biological replicate 2


title: pituitary harvested at 330 days replicate 2 [normal]

description: Biological replicate 2


title: YPS163 120 min vs YPS163 T0 (rep) - 25C to 37C heat shock

city: Madison

first: Audrey

middle: P.

last: Gasch

state: WI

address: 425-g Henry Mall

department: Laboratory of Genetics

institute: University of Wisconsin Madison

description:
25C to 37C heat shock timecourse in YPS163
yg7-35b

hyb_protocol: As indicated in Gasch AP Methods in Enzymology 350: 393-414

scan_protocol: Arrays were scanned on an Axon 4000B scanner

data_processing: Data were extracted using GenePix 6.0.  Data were normalized by regional mean-centering as described by Lyne et al. 2003 BMC Genomics. Values in Sample tables have been adjusted such that a positive log2 value = induced by heat shock, and a negative log2 value = repressed by heat shock

label: Oyster 550 cyanine dye

organism: Saccharomyces cerevisiae

source_name: YPS163 - 120 min after 37C heat shock

label_protocol: Indirect labeling using amino-allyl-dUTP and cyanine dyes from Flownamics (Madison, Wi) as described in Gasch AP Methods in Enzymology 350: 393-414

growth_protocol: Unless otherwise noted, cells were grown at least 3 doublings in log phase in YPD medium at 25C

extract_protocol: Hot-phenol RNA extraction as described in Gasch AP Methods in Enzymology 350: 393-414

treatment_protocol: Heat shock:  cells were grown at 25C, then an aliquot of prewarmed medium was added to each culture to provide 37C upon mixing

label: Oyster cyanine 650 dye

source_name: YPS163 grown at 25C


title: YPS163 60 min vs YPS163 T0 (rep) tech rep - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in YPS163
yg8-49b

source_name: YPS163 - 60 min after 37C heat shock


title: pituitary harvested at 280 days replicate 1 [normal]

description: Biological replicate 1

value: Day 280


title: pituitary harvested at 280 days replicate 3 [normal]

description: Biological replicate 3


title: pituitary harvested at 316 days replicate 3 [normal]

description: Biological replicate 3

value: Day 316


title: pituitary harvested at 260 days replicate 1 [normal]

description: Biological replicate 1

value: Day 260


title: pituitary harvested at 57 days replicate 1 [normal]

description: Biological replicate 1

value: Day 0

value: Day 57


title: pituitary harvested at 260 days replicate 2 [normal]

description: Biological replicate 2


title: pituitary harvested at 330 days replicate 1 [normal]

description: Biological replicate 1


title: YPS163 45 min vs YPS163 T0 (rep) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in YPS163
yg8-99b

source_name: YPS163 - 45 min after 37C heat shock


title: pituitary harvested at 260 days replicate 3 [normal]

description: Biological replicate 3


title: YPS163 30 min vs YPS163 T0 (rep) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in YPS163
yg8-49a

source_name: YPS163 - 30 min after 37C heat shock


title: YPS163 5 min vs YPS163 T0 (rep) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in YPS163
yg8-48b

source_name: YPS163 - 5 min after 37C heat shock


title: YPS163 15 min vs YPS163 T0 (rep) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in YPS163
yg7-34b

source_name: YPS163 - 15 min after 37C heat shock


title: pituitary harvested at 190 days replicate 2 [normal]

description: Biological replicate 2

source_name: pituitary (control)

value: Day 190


title: pituitary harvested at 251 days replicate 2 [normal]

description: Biological replicate 2

source_name: pituitary (test)

value: Day 251


title: YPS163 120 min vs YPS163 T0 (3) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in YPS163
yg7-34a


title: pituitary harvested at 190 days replicate 1 [normal]

description: Biological replicate 1


title: YPS163 60 min vs YPS163 T0 (3) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in YPS163
yg8-48a


title: YPS163 45 min vs YPS163 T0 (3) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in YPS163
yg7-33b


title: pituitary harvested at 92 days replicate 1 [normal]

description: Biological replicate 1


title: YPS163 30 min vs YPS163 T0 (3) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in YPS163
yg8-46b


title: pituitary harvested at 80 days replicate 2 [normal]

description: Biological replicate 2


title: pituitary harvested at 80 days replicate 1 [normal]

description: Biological replicate 1


title: pituitary harvested at 57 days replicate 3 [normal]

description: Biological replicate 3


title: pituitary harvested at 92 days replicate 2 [normal]

description: Biological replicate 2


title: YPS163 15 min vs YPS163 T0 (3) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in YPS163
yg7-33a


title: RM11a 120 min vs RM11a T0 (r1-2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in RM11a
yg9-8a

source_name: RM11-1a - 120 min after 37C heat shock

source_name: RM11-1a grown at 25C


title: RM11a 60 min vs RM11a T0 (r1-2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in RM11a
yg7-95b

source_name: RM11-1a - 60 min after 37C heat shock


title: YPS163 5 min vs YPS163 T0 (3) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in YPS163
yg8-46a


title: pituitary harvested at 316 days replicate 1 [normal]

description: Biological replicate 1


title: RM11a 30 min vs RM11a T0 (r1) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in RM11a
yg7-95a

source_name: RM11-1a - 30 min after 37C heat shock


title: pituitary harvested at 301 days replicate 3 [normal]

description: Biological replicate 3

value: Day 301


title: wild type p7_4

value: male


title: RM11a 15 min vs RM11a T0 (r1-2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in RM11a
yg9-5a

source_name: RM11-1a - 15 min after 37C heat shock


title: pituitary harvested at 301 days replicate 2 [normal]

description: Biological replicate 2


title: RM11a 5 min vs RM11a T0 (r1-2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in RM11a
yg7-96b

source_name: RM11-1a - 5 min after 37C heat shock


title: RM11a 45 min vs RM11a T0 (r1-2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in RM11a
yg9-5b

source_name: RM11-1a - 45 min after 37C heat shock


title: pituitary harvested at 57 days replicate 2 [normal]

description: Biological replicate 2


title: RM11a 60 min vs RM11a T0 (2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in RM11a
yg7-96a


title: pituitary harvested at 190 days replicate 3 [normal]

description: Biological replicate 3


title: pituitary harvested at 301 days replicate 1 [normal]

description: Biological replicate 1


title: RM11a 120 min vs RM11a T0 (2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in RM11a
yg8-77a


title: pituitary harvested at 316 days replicate 2 [normal]

description: Biological replicate 2


title: RM11a 45 min vs RM11a T0 (2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in RM11a
yg9-4b


title: pituitary harvested at 251 days replicate 1 [normal]

description: Biological replicate 1


title: RM11a 30 min vs RM11a T0 (2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in RM11a
yg7-100b


title: pituitary harvested at 251 days replicate 3 [normal]

description: Biological replicate 2


title: ovary harvested at 8 days replicate 2 [normal]

description: Biological replicate 3

source_name: ovary (control)

source_name: ovary (test)

value: Day 8


title: ovary harvested at 8 days replicate 3 [normal]

description: Biological replicate 3


title: ovary harvested at 80 days replicate 3 [normal]

description: Biological replicate 3


title: RM11a 5 min vs RM11a T0 (2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in RM11a
yg7-100a


title: M22 120 min vs M22 T0 (3) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in M22
yg7-45b

source_name: M22 - 120 min after 37C heat shock

source_name: M22 grown at 25C


title: ovary harvested at 8 days replicate 1 [normal]

description: Biological replicate 1


title: ovary harvested at 316 days replicate 3 [normal]

description: Biological replicate 3


title: ovary harvested at 316 days replicate 2 [normal]

description: Biological replicate 2


title: RM11a 15 min vs RM11a T0 (2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in RM11a
yg9-4a


title: M22 60 min vs M22 T0 (3) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in M22
yg7-6b

source_name: M22 - 60 min after 37C heat shock


title: M22 45 min vs M22 T0 (4) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in M22
yg7-45a

source_name: M22 - 45 min after 37C heat shock


title: M22 30 min vs M22 T0 (4) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in M22
yg7-6a

source_name: M22 - 30 min after 37C heat shock


title: M22 15 min vs M22 T0 (3) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in M22
yg8-40a

source_name: M22 - 15 min after 37C heat shock


title: ovary harvested at 280 days replicate 2 [normal]

description: Biological replicate 3


title: ovary harvested at 161 days replicate 2 [normal]

description: Biological replicate 1

value: Day 161


title: ovary harvested at 301 days replicate 2 [normal]

description: Biological replicate 1


title: M22 5 min vs M22 T0 (3) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in M22
yg7-11a

source_name: M22 - 5 min after 37C heat shock


title: M22 60 min vs M22 T0 (2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in M22
yg7-30b


title: M22 45 min vs M22 T0 (2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in M22
yg7-56b


title: M22 120 min vs M22 T0 (2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in M22
yg7-93b


title: ovary harvested at 161 days replicate 1 [normal]

description: Biological replicate 3


title: ovary harvested at 260 days replicate 3 [normal]

description: Biological replicate 3


title: ovary harvested at 80 days replicate 2 [normal]

description: Biological replicate 2


title: ovary harvested at 80 days replicate 1 [normal]

description: Biological replicate 2


title: M22 15 min vs M22 T0 (2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in M22
yg7-42b


title: ovary harvested at 108 days replicate 2 [normal]

description: Biological replicate 2

value: Day 108


title: M22 5 min vs M22 T0 (2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in M22
yg7-29b


title: ovary harvested at 108 days replicate 1 [normal]

description: Biological replicate 1


title: K9 60 min vs K9 T0 (3) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in K9
yg7-29a

source_name: K9 grown at 25C

source_name: K9 - 60 min after 37C heat shock


title: ovary harvested at 301 days replicate 3 [normal]

description: Biological replicate 2


title: ovary harvested at 57 days replicate 3 [normal]

description: Biological replicate 2


title: ovary harvested at 57 days replicate 2 [normal]

description: Biological replicate 1


title: ovary harvested at 316 days replicate 1 [normal]

description: Biological replicate 1


title: M22 30 min vs M22 T0 (2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in M22
yg7-30a


title: K9 45 min vs K9 T0 (3) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in K9
yg8-40b

source_name: K9 - 45 min after 37C heat shock


title: K9 120 min vs K9 T0 (3) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in K9
yg7-42a

source_name: K9 - 120 min after 37C heat shock


title: ovary harvested at 301 days replicate 1 [normal]

description: Biological replicate 1


title: K9 30 min vs K9 T0 (3) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in K9
yg7-11b

source_name: K9 - 30 min after 37C heat shock


title: K9 120 min vs K9 T0 - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in K9
yg8-33a


title: K9 15 min vs K9 T0 (3) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in K9
yg8-33b

source_name: K9 - 15 min after 37C heat shock


title: K9 60 min vs K9 T0 - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in K9
yg7-13a


title: K9 5 min vs K9 T0 (3) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in K9
yg7-13b

source_name: K9 - 5 min after 37C heat shock


title: ovary harvested at 280 days replicate 1 [normal]

description: Biological replicate 2


title: ovary harvested at 280 days replicate 3 [normal]

description: Biological replicate 3


title: K9 30 min vs K9 T0 - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in K9
yg7-10b


title: ovary harvested at 220 days replicate 3 [normal]

description: Biological replicate 3

value: Day 220


title: K9 45 min vs K9 T0 - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in K9
yg8-47b


title: ovary harvested at 57 days replicate 1 [normal]

description: Biological replicate 2


title: ovary harvested at 260 days replicate 1 [normal]

description: Biological replicate 1


title: K9 15 min vs K9 T0 - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in K9
yg8-47a


title: ovary harvested at 220 days replicate 1 [normal]

description: Biological replicate 1


title: ovary harvested at 260 days replicate 2 [normal]

description: Biological replicate 2


title: ovary harvested at 220 days replicate 2 [normal]

description: Biological replicate 2


title: K9 5 min vs K9 T0 - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in K9
yg7-10a


title: DBY8268 120 min vs DBY8268 T0 (2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in DBY8268
yg7-44b

source_name: DBY8268 - 120 min after 37C heat shock

source_name: DBY8268 grown at 25C


title: DBY8268 15 min vs DBY8268 T0 (2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in DBY8268
yg7-55b

source_name: DBY8268 - 15 min after 37C heat shock


title: Liver harvested at 57 days replicate 2 [normal]

description: Biological replicate 2

source_name: liver (control)

source_name: liver (test)


title: ovary harvested at 108 days replicate 3 [normal]

description: Biological replicate 3

source_name: ovary (control)

source_name: ovary (test)


title: Liver harvested at 92 days replicate 3 [normal]

description: Biological replicate 3

value: Day 92


title: DBY8268 30 min vs DBY8268 T0 (2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in DBY8268
yg7-12a

source_name: DBY8268 - 30 min after 37C heat shock


title: DBY8268 60 min vs DBY8268 T0 (2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in DBY8268
yg7-12b

source_name: DBY8268 - 60 min after 37C heat shock


title: DBY8268 45 min vs DBY8268 T0 (2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in DBY8268
yg7-44a

source_name: DBY8268 - 45 min after 37C heat shock


title: Liver harvested at 330 days replicate 2 [normal]

description: Biological replicate 2


title: DBY8268 5 min vs DBY8268 T0 (2) - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in DBY8268
yg7-15b

source_name: DBY8268 - 5 min after 37C heat shock


title: DBY8268 120 min vs DBY8268 T0 - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in DBY8268
yg7-55a


title: Liver harvested at 92 days replicate 2 [normal]

description: Biological replicate 2


title: ovary harvested at 161 days replicate 3 [normal]

description: Biological replicate 1


title: DBY8268 60 min vs DBY8268 T0 - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in DBY8268
yg7-15a


title: DBY8268 15 min vs DBY8268 T0 - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in DBY8268
yg7-94a


title: DBY8268 45 min vs DBY8268 T0 - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in DBY8268
yg7-94b


title: DBY8268 30 min vs DBY8268 T0 - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in DBY8268
yg7-16b


title: Liver harvested at 301 days replicate 3 [normal]

description: Biological replicate 3


title: Liver harvested at 301 days replicate 1 [normal]

description: Biological replicate 1


title: DBY8268 5 min vs DBY8268 T0 - 25C to 37C heat shock

description:
25C to 37C heat shock timecourse in DBY8268
yg7-16a


title: DBY8268 vs YPS163 #2 at 25C

description:
Comparison of YPS163 to DBY8268 at 25C growth
yg11-6b

data_processing: Data were extracted using GenePix 6.0.  Data were normalized by regional mean-centering as described by Lyne et al. 2003 BMC Genomics. Values in Sample tables have been adjusted such that a positive log2 value = higher expressed in non-lab strain relative to DBY8268, and a negative log2 value = expressed lower in non-lab strain relative to DBY8268.

source_name: YPS163 grown at 25C


title: Liver harvested at 301 days replicate 2 [normal]

description: Biological replicate 2


title: Liver harvested at 316 days replicate 3 [normal]

description: Biological replicate 3


title: Liver harvested at 280 days replicate 1 [normal]

description: Biological replicate 1


title: rat 3, day 0 and 10

city: Singapore

first: jinmiao

last: chen

address: Biopolis

country: Singapore

institute: Singapore Immunology Network

description: dye swap

hyb_protocol: 5uL of 10% BSA and 28.5uL of 2X enhanced hybridization buffer (Genisphere, Hatfield, PA) were added to the sample to make the hybridization mix. This was applied to Invitrogen NCode miRNA microarrays containing 1053 miRNAs from 6 species (467 human miRNAs) printed in triplicate. The arrays incubated overnight (18 hours) in a humidified chamber at 52oC and the following morning, serial 15 minute washes were done with 2x SSC/0.2% SDS at 52oC, 2x SSC at room temperature and 0.2X SSC at room temperature.

scan_protocol: GenePix 4200AL

data_processing:
Dye swap was included for each sample and both raw data files are available as supplementary files.  For each raw data file, the sample labeled with Cy3 is listed first (eg. For '0d_10d_iso080407.gpr' the day 0 sample is labeled with Cy3 and day 10 with cy5).
Background subtracted intensities normalized using the Cross-correlation method (Chua et al., 2006) using R scripts.
Chua SW, Vijayakumar P, Nissom PM, Yam CY, Wong VV, Yang H: A novel normalization method for effective removal of systematic variation in microarray data. Nucleic acids research 2006, 34(5):e38.

organism: Rattus norvegicus

source_name: rat 3, day 0

label_protocol: NCode miRNA labeling system

growth_protocol: DMEM (high glucose) + 10%FBS + antibiotics

extract_protocol: PureLink miRNA Isolation kit

value: Wistar

value: hepatic stellate cells

source_name: rat 3, day 10


title: Liver harvested at 220 days replicate 2 [normal]

description: Biological replicate 2


title: Liver harvested at 220 days replicate 3 [normal]

description: Biological replicate 3


title: DBY8268 vs RM11-1a #2 at 25C

description:
Comparison of RM11-1a to DBY8268 at 25C growth
yg11-28b

source_name: RM11-1a grown at 25C


title: Liver harvested at 220 days replicate 1 [normal]

description: Biological replicate 1


title: rat 2, day 0 and 10

description: dye swap

source_name: rat 2, day 0

source_name: rat 2, day 10


title: Liver harvested at 190 days replicate 1 [normal]

description: Biological replicate 1


title: DBY8268 vs YPS163 #1 at 25C

description:
Comparison of YPS613 to DBY8268 at 25C growth
yg11-9b


title: DBY8268 vs M22 #2 at 25C

description:
Comparison of M22 to DBY8268 at 25C growth
yg11-29b

source_name: M22 grown at 25C


title: rat 1, day 0 and 10

description: dye swap

source_name: rat 1, day 0

source_name: rat 1, day 10


title: Liver harvested at 190 days replicate 2 [normal]

description: Biological replicate 2

source_name: liver (control)


title: DBY8268 vs RM11-1a #1 at 25C

description:
Comparison of RM11-1a to DBY8268 at 25C growth
yg11-10a

source_name: DBY8268 grown at 25C


title: DBY8268 vs K9 #1 at 25C

description:
Comparison of K9 to DBY8268 at 25C growth
yg11-29a

source_name: K9 grown at 25C


title: DBY8268 vs M22 #1 at 25C

description:
Comparison of M22 to DBY8268 at 25C growth
yg11-10b


title: Liver harvested at 316 days replicate 2 [normal]

description: Biological replicate 2

source_name: liver (test)


title: Liver harvested at 92 days replicate 1 [normal]

description: Biological replicate 1

value: Day 192


title: Liver harvested at 316 days replicate 1 [normal]

description: Biological replicate 1


title: Liver harvested at 330 days replicate 1 [normal]

description: Biological replicate 1

value: Day 330


title: DBY8268 vs K9 #2 at 25C

description:
Comparison of K9 to DBY8268 at 25C growth
yg11-6a


title: Liver harvested at 280 days replicate 2 [normal]

description: Biological replicate 2

value: Day 280


title: Liver harvested at 57 days replicate 3 [normal]

description: Biological replicate 3


title: Liver harvested at 190 days replicate 3 [normal]

description: Biological replicate 3


title: Liver harvested at 130 days replicate 3 [normal]

description: Biological replicate 3

value: Day 130


title: BPOP 13

city: Lund

first: Fredrik

last: Mertens

address: Lund University Hospital

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

description: Gene expression analysis for breakpoint mapping.

hyb_protocol: Arrays were hybridized and washed according to the manufacturer's instructions (Affymetrix Inc, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned in a GeneChipR scanner 3000 (Affymetrix Inc, Santa Clara, CA, USA).

data_processing: Image analysis was performed using GeneChipR Operating Software (GCOS, Affymetrix). Expression data were normalized, background-corrected and summarized using the RMA algorithm implemented in the Affymetrix Expression Console version 1.0 software.

label: Biotin

source_name: Bone tumor patient

label_protocol: GeneChipR WT Terminal Labelling Kit (Affymetrix Inc, Santa Clara, CA, USA)

extract_protocol: Total RNA was extracted from frozen tumor biopsies using Trizol reagent (Invitrogen, Carlsbad, CA, USA) and Rneasy (Qiagen, Valencia, CA, USA) according to the manufacturer's recommendations. RNA quality and concentration were measured using an Agilent 2100 bioanalyzer and Nanodrop ND-1000, respectively. cDNA was generated with the GeneChipR Whole Transcript (WT) cDNA synthesis and Amplification Kit (Affymetrix) using 300 ng total RNA. Amplified cDNA was fragmented and end-labelled using the GeneChipR WT terminal labelling Kit (Affymetrix). Subsequently, the fragmented and biotinylated cDNA was hybridized to the GeneChipR Human Gene 1.0 ST Arrays (Affymetrix). The arrays were washed and stained on a GeneChipR Fluidics Station 450 (Affymetrix) according to the manufacturer's recommendations.

tag: disease state

value: Bizarre parosteal osteochondromatous proliferation (BPOP)

value: Frozen tumor


title: Liver harvested at 57 days replicate 1 [normal]

description: Biological replicate 1

value: Day 0

value: Day 57


title: Liver harvested at 280 days replicate 3 [normal]

description: Biological replicate 3


title: Osteochondroma 8

value: Osteochondroma


title: Biofilm_Oct11_TR2

status: Public on Dec 14 2009

type: mixed

city: Norwich

first: Sacha

last: Lucchini

address: Colney Lane

department: Molecular Microbiology

country: United Kingdom

institute: Institute of Food Research

description: Intensity ratios of channel 1 (gDNA) divided by channel 2 (cDNA) signals minus respective background signals. Total array is 16 blocks arranged in 4X4 configuration.

hyb_protocol: Slides blocked with DCE according to protocol at PMID 11266573. For hybridisation and washing protocols see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

scan_protocol: Axon GenePix4000A, 10nm resolution scan & see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

data_processing: Data centring was performed by bringing the median ratio (Cy5/Cy3) for each of the 16 blocks to one using the following equation: (Ti) = (Cy5i/Cy3i) - c, where T is the centred ratio, i is the gene index, Cy5 and Cy3 are the red and green intensities and c is the 50th percentile of all Cy5/Cy3 ratios. Flagged features are omitted from the data centring process. Because we used a microarray based on S. Typhimurium strain LT2 to analyse the transcriptional response of a different strain (S. Typhimurium strain SL1344), we removed all the data corresponding to genes present in LT2, but absent from SL1344.

molecule: genomic DNA

organism: Salmonella enterica

source_name: Reference genomic DNA

label_protocol: Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

growth_protocol: S. Typhimurium grown to stationary phase

extract_protocol: Genomic DNA isolated using the Qiagen 'Genomic DNA' Kit (Cat. No.: 19060 for the buffer kit; 10243 for the columns)

value: Salmonella enterica serovar Typhimurium LT2

growth_protocol: Overnight cultures of Salmonella Typhimurium SL1344 grown in CFA broth were standardized to achieve an initial concentration of 10exp6 CFU ml-1 and injected into a stirring influent flask containing 5 L of pre-warmed (25C) sterile CFA medium. The inoculated influent was then pumped through silicon tubing (5 mm internal diameter, Samco Silicon Products Ltd.) at 60 ml h-1 using a peristaltic pump (Minipulse 3, Gilson). The bacteria were allowed to flow through the closed system and either attach to a vertical piece of silicon tubing (1 meter length, 16 mm internal diameter, Samco Silicon Products Ltd.) or flow out into a waste reservoir. The tubing was positioned vertically to collect biofilm cells adherent to the tubing and minimise collecting bacteria that had simply sedimented. Possible backflow of media or bacteria into the influent from the silicon tubing was eliminated using media breaks. The entire system was kept at a constant temperature of 25C and biofilm cells were isolated after 72 h of growth.

extract_protocol: Total RNA isolation protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

value: Salmonella enterica serovar Typhimurium SL1344


title: BPOP 12


title: Biofilm_Oct11_TR1


title: Planktonic_Jul16_TR3

growth_protocol: Overnight cultures of SL1344 grown in CFA broth were standardized to achieve an initial concentration of 106 CFU ml-1 and injected into a stirring influent flask containing 5 L of pre-warmed (25°C) sterile CFA medium. The inoculated influent was then pumped through silicon tubing (5 mm internal diameter, Samco Silicon Products Ltd.) at 60 ml h-1 using a peristaltic pump (Minipulse 3, Gilson). The bacteria were allowed to flow through the closed system and either attach to a vertical piece of silicon tubing (1 meter length, 16 mm internal diameter, Samco Silicon Products Ltd.) or flow out into a waste reservoir. Possible backflow of media or bacteria into the influent from the silicon tubing was eliminated using media breaks. Planktonic cells were removed after 72 h of growth from the influent vessel to avoid any contamination with biofilm cells. The entire system was kept at a constant temperature of 25°C.


title: Subungual exostosis 1

value: Subungual exostosis


title: Planktonic_Jul16_TR1

description: Intensity ratios of channel 2 (cDNA) divided by channel 1 (gDNA) signals minus respective background signals. Total array is 16 blocks arranged in 4X4 configuration.


title: Biofilm_Oct11_TR3


title: Biofilm_Ju16_TR2


title: Planktonic_Jul16_TR4


title: Planktonic_Oct11_TR1


title: Planktonic_Jul16_TR2


title: Planktonic_Jul5_TR4


title: Osteochondroma 7


title: Biofilm_Jul16_TR1


title: Biofilm_Jul5_TR4


title: Biofilm_Jul5_TR1


title: Planktonic_Jul5_TR3


title: Biofilm_Jul5_TR3


title: Planktonic_Oct11_TR2


title: Biofilm_Jul5_TR2


title: Planktonic_Jun25_TR1


title: Planktonic_Jul5_TR2


title: Biofilm_Jun25_TR1


title: M145E-F134-F202-60 h

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

institute: The Genome Analysis Centre

description: Medium F134, F202 is the run identifier of the fermentation run from which the samples were taken.

hyb_protocol: 3 µg of cDNA were hybridized for 16 hr at 50°C on ScoeA32a520627F.Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: RMA

organism: Streptomyces coelicolor

label_protocol: Biotinylated cDNA were prepared after fragmentation according to the standard Affymetrix protocol from 3 µg total RNA (Prokaryotic Sample and Array Processing, Technical Manual 701030 Rev. 5, 2004, Affymetrix).

extract_protocol: Total RNA isolation was performed via phenol extraction and RNeasy Midi Kit (Qiagen, 2001) according to manufacturer's instruction.

value: wt

tag: time point


title: Planktonic_Jul5_TR1


title: M145E-F134-F202-34 h


title: M145E-F134-F202-46 h


title: M145E-F134-F202-35 h


title: M145E-F134-F202-37 h


title: M145E-F134-F202-40 h


title: M145E-F134-F202-32 h


title: M145E-F134-F202-48 h


title: M145E-F134-F202-28 h


title: M145E-F134-F202-24 h


title: M145E-F134-F202-36 h


title: M145E-F134-F202-44 h


title: M145E-F134-F202-38 h


title: M145E-F134-F201-48 h

description: Medium F134, F201 is the run identifier of the fermentation run from which the samples were taken.


title: M145E-F134-F202-39 h


title: M145E-F134-F202-42 h


title: M145E-F134-F201-40 h


title: M145E-F134-F201-28 h


title: M145E-F134-F201-60 h


title: M145E-F134-F201-44 h


title: M145E-F134-F201-36 h


title: M145E-F134-F201-32 h


title: M145E-F134-F199-58 h

description: Medium F134, F199 is the run identifier of the fermentation run from which the samples were taken.


title: M145E-F134-F199-54 h


title: M145E-F134-F199-60 h


title: M145E-F134-F199-50 h


title: M145E-F134-F199-46 h


title: M145E-F134-F199-43 h


title: M145E-F134-F199-44 h


title: M145E-F134-F199-56 h


title: M145E-F134-F199-52 h


title: M145E-F134-F199-48 h


title: M145E-F134-F199-42 h


title: Control testis - postpartum development - N 27 day B

city: Canterbury

first: Peter

middle: James

last: Ellis

state: Kent

address: Stacey Building

department: School of Biosciences

institute: University of Kent

description: no additional information

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with BeadStudio

source_name: Testis, age-matched controls, postnatal developmental series

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

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

treatment_protocol: For the two rescue series, testosterone propionate was administered as a single intraperitoneal injection at 19 days post partum

tag: genotype/variation

value: WT

value: testis

tag: age post partum

value: 27 days

tag: testosterone dose

tag: time post testosterone injection


title: Control testis - postpartum development - N 19 day B

description: no additional information

tag: tissue

value: 19 days


title: M145E-F134-F199-41 h

tag: genotype


title: M145E-F134-F199-37 h


title: M145E-F134-F199-38 h


title: Control testis - postpartum development - N 19 day A

description: no additional information


title: M145E-F134-F199-35 h


title: M145E-F134-F199-40 h


title: M145E-F134-F199-39 h


title: M145E-F134-F199-36 h


title: M145E-F134-F199-34 h


title: Control testis - postpartum development - N 8 day B

description: no additional information

value: 8 days


title: Control testis - postpartum development - N 13 day A

description: no additional information

value: 13 days


title: M145E-F134-F199-32 h


title: M145E-F134-F199-33 h


title: Control testis - postpartum development - N 13 day B

description: no additional information


title: LuRKO testis - postpartum development - 27 day A

description: no additional information

source_name: Testis, LH receptor knockout, postnatal developmental series

value: LuRKO


title: Control testis - postpartum development - N 3 day A

description: no additional information

value: 3 days


title: M145E-F134-F199-31 h


title: Control testis - postpartum development - N 8 day A

description: no additional information


title: Control testis - postpartum development - N 3 day B

description: no additional information


title: M145E-F134-F199-29 h


title: M145E-F134-F199-30 h


title: LuRKO testis - postpartum development - 19 day A

description: no additional information


title: LuRKO testis - postpartum development - 19 day B

description: no additional information


title: LuRKO testis - postpartum development - 13 day B

description: no additional information


title: M145E-F134-F199-28 h


title: LuRKO testis - postpartum development - 13 day A

description: no additional information


title: M145E-F134-F199-23 h


title: LuRKO testis - postpartum development - 8 day B

description: no additional information


title: LuRKO testis - postpartum development - 8 day A

description: no additional information


title: LuRKO d19 testis + testosterone, 24h post injection - Veh only A

description: no additional information

source_name: Testis, LH receptor knockout, dose/response to testosterone treatment given at 19 days post partum, assayed 24h post injection

value: 19 days + 34 hrs

value: Vehicle only

value: 24 hrs


title: LuRKO d19 testis + testosterone, 24h post injection - 250ngA

description: no additional information

value: 19 days + 24 hrs


title: LuRKO testis - postpartum development - 3 day B

description: no additional information


title: M145E-F134-F199-24 h


title: LuRKO d19 testis + testosterone, 24h post injection - 250ngB

description: no additional information


title: M145E-F134-F201-24 h


title: LuRKO d19 testis + testosterone, 24h post injection - Veh only B

description: no additional information


title: LuRKO d19 testis + testosterone, 24h post injection - 2.5ug B

description: no additional information


title: LuRKO testis - postpartum development - 3 day A

description: no additional information


title: M145E-F134-F199-21 h


title: LuRKO d19 testis + testosterone, 24h post injection - 2.5ugA

description: no additional information


title: M145E-F134-F199-20 h


title: LuRKO d19 testis + testosterone, 24h post injection - 25ugB

description: no additional information


title: M145E-F134-F199-26 h


title: M145E-F134-F199-22 h


title: LuRKO d19 testis + 2.5mg testosterone  - 48hB

description: no additional information

source_name: Testis, LH receptor knockout, 19 days post partum, treated with 2.5mg testosterone, response timecourse

value: 19 days + 48 hrs

value: 48 hrs


title: LuRKO d19 testis + testosterone, 24h post injection - 25ugA

description: no additional information


title: LuRKO d19 testis + 2.5mg testosterone  - 48hA

description: no additional information


title: KLF2-4 [kinome]

status: Public on Dec 11 2009

type: protein

city: Amsterdam

first: Anton

middle: J

last: Horrevoets

address: van der Boechorststraat 7

department: Molecular Cell Biology

institute: VU University Medical Center

description: total cell protein lysate assayed for protein kinases

hyb_protocol: Kinexus service

scan_protocol: Kinexus service

data_processing: Interarray quantile normalization performed by Kinexus service

label: proprietary KINEX

molecule: protein

source_name: umbilical vein endothelial cells transduced with KLF2-expressing lentivirus

label_protocol: Kinexus service

growth_protocol: Human umbilical vein endothelial cells were grown in fibronectin coated tissue culture, using standard medium M199+20% FBS + ECGS

extract_protocol: Protein was isolated according to the KINEXUS protocol (available on KINEXUS website)

treatment_protocol: Cells were transduced by lentiviral vectors expressing no protein (mock) or  Krueppel-like factor 2, and total cell protein was isolated at  72 h after transduction

value: umbilical vein endothelial cell

tag: protocol


title: LuRKO d19 testis + 2.5mg testosterone  - 12hA

description: no additional information

value: 19 days + 12 hrs

value: 12 hrs


title: LuRKO d19 testis + 2.5mg testosterone  - 12hB

description: no additional information


title: LuRKO d19 testis + 2.5mg testosterone  - 8hB

description: no additional information

value: 19 days + 8 hrs

value: 8 hrs


title: LuRKO d19 testis + 2.5mg testosterone  - 4hB

description: no additional information

value: testis

value: 19 days + 4 hrs

value: 4 hrs


title: LuRKO d19 testis + 2.5mg testosterone  - 8hA

description: no additional information


title: KLF2-3 [kinome]


title: LuRKO d19 testis + 2.5mg testosterone  - 2hA

description: no additional information

value: 19 days + 2 hrs

value: 2 hrs


title: mock-3 [kinome]

source_name: umbilical vein endothelial cells transduced with mock lentivirus

value: mock-transduced


title: mock-4 [kinome]


title: KLF2-1 [kinome]


title: KLF2-2 [kinome]


title: mock-2 [kinome]


title: LuRKO d19 testis + 2.5mg testosterone  - 4hA

description: no additional information

value: LuRKO


title: LuRKO d19 testis + 2.5mg testosterone  - 24hB

description: no additional information


title: mock-1 [kinome]


title: 72 H KLF2 EXPRESSION,ISOLATE 3

description: KLF2 TRANSDUCED CELLS COMPARED TO MOCK TRANSDUCED CELLS 72 H AFTER LENTIVIRAL TRANSDUCTION

hyb_protocol: hyb chamber, overnight, 37 C, 40% formaldehyde

scan_protocol: Agilent-II scanner

data_processing: Feature extraction by ScanArray v6, values excluded if <2x noise, then loes normalized ratios KLF2/mock samples (Limma package Bioconductor) were processed by interarray Quantile normalization (Bioconductor)

source_name: UMBILICAL VEIN ENDOTHELIAL CELL

label_protocol: RNA was amplified and aminoallyl-labelled using Ambion MessageAmp kit, then Labelled with Cy3 and Cy5 monoreactive dyes

extract_protocol: RNA was isolated using Stratagene RNAeasy kits and QC by Agilent Bioanalyzer, RIN scores > 8

treatment_protocol: Cells were transduced by lentiviral vectors expressing no protein (mock) or  Krueppel-like factor 2, and total RNA was isolated at the indicated times 24, 48 and 72 h after transduction

tag: time

tag: isolate


title: EB_mm6_dedicated_2

city: Stockholm

first: Rolf

last: Ohlsson

address: Nobels väg 16

department: Microbiology, Tumour and Cell biology

institute: Karolinska Institute

description: Circular Chromosome Conformation Capture (4C) experiments were performed on mouse embryonic cell line (R1) and in-vitro derived embryoid bodies taking H19 ICR as a bait.

hyb_protocol: Standard Nimblegen Protocols located at http://www.nimblegen.com/products/lit/lit.html

data_processing:
Regular Tukey Biweight Scaling by NimblGen Inc.
http://www.nimblegen.com/products/lit/lit.html

molecule: other

source_name: 4C DNA, Differentiated ES cells, 12 days

extract_protocol: Amplified product of 4C (Circular Chromosome Conformation Capture, Zhao et al, Nat Gen., 2006) experiment.

tag: 4C DNA, Differentiated R1 cell-line, 12 days, LIF withdrawal method.

source_name: Input DNA, Differentiated ES cells, 12 days

extract_protocol: Mbo1 digested genomic DNA

tag: Input DNA, Differentiated R1 cell-line, 12 days, LIF withdrawal method.


title: Control testis - postpartum development - N 27 day A

description: no additional information

value: WT

value: 27 days


title: 72 H KLF2 EXPRESSION,ISOLATE 3, REVERSE LABEL

tag: cell type


title: 72 H KLF2 EXPRESSION,ISOLATE 2, REVERSE LABEL


title: B73 high N (ref) rep5 vs IHP high N rep5

city: Urbana

first: Stephen

middle: Patrick

last: Moose

state: IL

address: 1201 W Gregory

department: Crop Sciences

institute: University of Illinois at Urbana-Champaign

hyb_protocol: Hybridizations were performed overnight in custom designed cassettes in 42 degree water bath, followed by 3 washes.

scan_protocol: Scanned on a Genepix 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA). Used GenePix Pro 6.0 (Molecular Devices Corporation) for spotfinding.

data_processing: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

organism: Zea mays

source_name: B73 high N (ref) rep5

label_protocol: The Amino Allyl MessageAmp™ II aRNA Amplification kit (Ambion, Austin, TX) with Cyanine-3 and -5 (GE Healthcare Bio-Sciences Corp., Piscataway, NJ) dyes were used to amplify and label samples.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen, Carlsbad, CA) then Rneasy purification kit (Qiagen, Valencia, CA).

value: leaf

tag: treatment

value: high N (14mM NO3-)

tag: age

value: V8 growth stage

source_name: IHP high N rep5


title: ES_mm6_dedicated_2

scan_protocol: Standard Nimblegen Protocols located at http://www.nimblegen.com/products/lit/lit.html

source_name: 4C DNA, Embryonic stem cells

tag: 4C DNA, R1 cell-line, cultured on feeder cells.

source_name: Input DNA, Embryonic stem cells

tag: Input DNA, R1 cell-line, cultured on feeder cells


title: B73 high N (ref) rep3 vs IHP high N rep3

source_name: B73 high N (ref) rep3

source_name: IHP high N rep3


title: 72 H KLF2 EXPRESSION,ISOLATE 2

value: umbilical vein endothelial cell


title: 72 H KLF2 EXPRESSION,ISOLATE 1


title: 72 H KLF2 EXPRESSION,ISOLATE 1, REVERSE LABEL


title: IHP high N rep4 vs B73 high N (ref) rep4

source_name: IHP high N rep4

source_name: B73 high N (ref) rep4


title: 48 H KLF2 EXPRESSION,ISOLATE 3, REVERSE LABEL

description: KLF2 TRANSDUCED CELLS COMPARED TO MOCK TRANSDUCED CELLS 48 H AFTER LENTIVIRAL TRANSDUCTION


title: IHP high N rep1 vs B73 high N (ref) rep1

source_name: IHP high N rep1

source_name: B73 high N (ref) rep1


title: B73 high N (ref) rep2 vs IHP high N rep2

source_name: B73 high N (ref) rep2

source_name: IHP high N rep2


title: B73 high N (ref) rep2 vs B73 low N rep2

description: B73 high N (ref) rep2 vs B73 low N rep2

source_name: B73 low N rep2

value: low N (1 mM NO3-)


title: B73 low N rep4 vs B73 high N (ref) rep4

description: B73 low N rep4 vs B73 high N (ref) rep4

source_name: B73 low N rep4


title: ES_mm6_dedicated_1

label_protocol: Standard Nimblegen Protocols located at http://www.nimblegen.com/products/lit/lit.html

tag: 4C DNA, R1 cell-line, grown on feeder cells.

tag: Input DNA, R1 cell-line, grown on feeder cells.


title: 48 H KLF2 EXPRESSION,ISOLATE 3

source_name: UMBILICAL VEIN ENDOTHELIAL CELL


title: EB_mm6_dedicated_1

source_name: 4C DNA, Differentiated ES cells, 12 days


title: B73 low N rep1 vs B73 high N (ref) rep1

description: B73 low N rep1 vs B73 high N (ref) rep1

source_name: B73 low N rep1


title: MDI induction of Lithium treated preadipocytes D-3

city: Guangzhou

first: Qin

last: Limei

address: North Third road

country: China

institute: SunYatsen University

description: microRNA expression in MDI induction of Lithium treated preadipocytes

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 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Scan Control software，using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Agilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190-0456) 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: The 3T3-L1 (ATCC, CL-173TM) pre-adipocyte cell line was maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (Gibco, USA) at 37 ℃ and 5% CO2–air.

extract_protocol: Total RNA were extracted using mirVana™ miRNA Isolation (Ambion, Inc., Austin, TX) according to the manufacturer’s instructions. The RNA quality was tested with the Agilent Bioanalyzer 2000.

treatment_protocol: In the model that WNT signaling is suppressed, 3T3-L1 cells were allowed to reach confluence and then exposed to MDI medium for 3 days, which contained 3-isobutyl-1-methylxanthine (0.5 M), dexamethasone (1μM), and insulin (1.75 M), then cultured only in high-glucose DMEM, 10% FBS and insulin alone for the following 2 days, then subsequently cultured with high-glucose DMEM and 10% FBS for 2 days until 7th days of the end of checkpoint. In the model that WNT signaling is activated, Lithium (LiCl) was added into the medium at a concentration of 25mM; To further determine if the WNT signaling was activated, cell was treated with MDI differentiation (i.e. Li+MDI treatment) to see if the cell could differentiate into mature adipocyte.

tag: cell line


title: B73 low N rep3 vs B73 high N (ref) rep3

description: B73 low N rep3 vs B73 high N (ref) rep3

source_name: B73 low N rep3


title: 48 H KLF2 EXPRESSION,ISOLATE 2, REVERSE LABEL


title: B73 high N (ref) rep5 vs B73 low N rep5

description: B73 high N (ref) rep5 vs B73 low N rep5

source_name: B73 high N (ref) rep5

source_name: B73 low N rep5


title: MDI induction of Lithium treated preadipocytes D-2


title: B73 high N (ref) rep3 vs IHP low N rep3

description: B73 high N (ref) rep3 vs IHP low N rep3

source_name: IHP low N rep3


title: IHP low N rep5 vs B73 high N (ref) rep5

description: IHP low N rep5 vs B73 high N (ref) rep5

source_name: IHP low N rep5


title: B73 high N (ref) rep4 vs IHP low N rep4

description: B73 high N (ref) rep4 vs IHP low N rep4

source_name: IHP low N rep4


title: IHP low N rep1 vs B73 high N (ref) rep1

description: IHP low N rep1 vs B73 high N (ref) rep1

source_name: IHP low N rep1


title: 48 H KLF2 EXPRESSION,ISOLATE 1, REVERSE LABEL


title: 48 H KLF2 EXPRESSION,ISOLATE 2


title: IHP low N rep2 vs B73 high N (ref) rep2

description: IHP low N rep2 vs B73 high N (ref) rep2

source_name: IHP low N rep2


title: MDI induction of Lithium treated preadipocytes D-1


title: 48 H KLF2 EXPRESSION,ISOLATE 1


title: Lithium treated preadipocytes C-3

description: microRNA expression in Lithium treated preadipocytes

source_name: Lithium treated preadipocytes


title: IHP high N rep1 vs IHP low N rep1

description: IHP high N rep1 vs IHP low N rep1

source_name: IHP high N rep1


title: IHP low N rep2 vs IHP high N rep2

description: IHP low N rep2 vs IHP high N rep2


title: mature adipocytes (MDI induction) B-3

description: microRNA expression in mature adipocytes

source_name: mature adipocytes (MDI induction)


title: Lithium treated preadipocytes C-1


title: Lithium treated preadipocytes C-2


title: mature adipocytes (MDI induction) B-1


title: mature adipocytes (MDI induction) B-2


title: LuRKO d19 testis + 2.5mg testosterone  - 2hB

description: no additional information

source_name: Testis, LH receptor knockout, 19 days post partum, treated with 2.5mg testosterone, response timecourse

tag: genotype/variation

tag: age post partum

tag: testosterone dose


title: 24 H KLF2 EXPRESSION,ISOLATE 3

description: KLF2 TRANSDUCED CELLS COMPARED TO MOCK TRANSDUCED CELLS 24 H AFTER LENTIVIRAL TRANSDUCTION


title: 24 H KLF2 EXPRESSION,ISOLATE 3, REVERSE LABEL


title: 24 H KLF2 EXPRESSION,ISOLATE 1


title: 24 H KLF2 EXPRESSION,ISOLATE 1, REVERSE LABEL


title: preadipocytes A-2

description: microRNA expression in preadipocyte

source_name: preadipocytes


title: preadipocytes A-1

description: microRNA expression in preadipocyte


title: 24 H KLF2 EXPRESSION,ISOLATE 2


title: Reference vs Genotype3 rep1 dye swap

description: Reference vs Genotype3 rep1 dye swap

source_name: Oba super 1

extract_protocol: Total RNA was isolated using LS TRIzol (Invitrogen, Carlsbad, CA), digested by DNAse,  then Rneasy purification kit (Qiagen, Valencia, CA).

tag: genotype

value: Oba super 1

value: at Anthesis

tag: tissue

value: Earshoot


title: preadipocytes A-3

description: microRNA expression in preadipocyte


title: 24 H KLF2 EXPRESSION,ISOLATE 2, REVERSE LABEL

source_name: UMBILICAL VEIN ENDOTHELIAL CELL

tag: time

tag: protocol


title: Reference vs Genotype2 rep2 dye swap

description: Reference vs Genotype2 rep2 dye swap


title: Reference vs Genotype3 rep2

description: Reference vs Genotype3 rep2


title: Reference vs Genotype3 rep2 dye swap

description: Reference vs Genotype3 rep2 dye swap


title: IHP low N rep3 vs IHP high N rep3

description: IHP low N rep3 vs IHP high N rep3

source_name: IHP high N rep3


title: IHP low N rep4 vs IHP high N rep4

description: IHP low N rep4 vs IHP high N rep4

source_name: IHP high N rep4


description: B73 high N (ref) rep5 vs IHP high N rep5

source_name: IHP high N rep5


description: IHP high N rep4 vs B73 high N (ref) rep4

source_name: B73 high N (ref) rep4


title: Reference vs Genotype2 rep2

description: Reference vs Genotype2 rep2


description: B73 high N (ref) rep2 vs IHP high N rep2

source_name: B73 high N (ref) rep2

source_name: IHP high N rep2


description: IHP high N rep1 vs B73 high N (ref) rep1

source_name: B73 high N (ref) rep1


title: Reference vs Genotype2 rep1

description: Reference vs Genotype2 rep1


title: Reference vs Genotype3 rep1

description: Reference vs Genotype3 rep1


title: Reference vs Genotype2 rep1 dye swap

description: Reference vs Genotype2 rep1 dye swap


title: Reference vs Genotype1 rep2 dye swap

description: Reference vs Genotype1 rep2 dye swap


title: Reference vs Genotype1 rep2

description: Reference vs Genotype1 rep2


title: B73 high N (ref) rep5 vs B73 low N rep5

description: B73 high N (ref) rep5 vs B73 low N rep5

source_name: B73 high N (ref) rep5

source_name: B73 low N rep5


title: B73 high N (ref) rep3 vs IHP low N rep3

description: B73 high N (ref) rep3 vs IHP low N rep3

source_name: B73 high N (ref) rep3

source_name: IHP low N rep3


title: B73 high N (ref) rep2 vs B73 low N rep2

description: B73 high N (ref) rep2 vs B73 low N rep2

source_name: B73 low N rep2


title: IHP low N rep1 vs B73 high N (ref) rep1

description: IHP low N rep1 vs B73 high N (ref) rep1

source_name: IHP low N rep1


title: B73 low N rep4 vs B73 high N (ref) rep4

description: B73 low N rep4 vs B73 high N (ref) rep4

source_name: B73 low N rep4


title: IHP low N rep2 vs B73 high N (ref) rep2

description: IHP low N rep2 vs B73 high N (ref) rep2

source_name: IHP low N rep2


title: Reference vs Genotype1 rep1

description: Reference vs Genotype1 rep1

source_name: Oba super 1


title: B73 low N rep1 vs B73 high N (ref) rep1

description: B73 low N rep1 vs B73 high N (ref) rep1

source_name: B73 low N rep1


title: B73 low N rep3 vs B73 high N (ref) rep3

description: B73 low N rep3 vs B73 high N (ref) rep3

source_name: B73 low N rep3


title: IHP low N rep5 vs B73 high N (ref) rep5

description: IHP low N rep5 vs B73 high N (ref) rep5

source_name: IHP low N rep5


title: IRLP rep2 vs ILP rep2

source_name: Total RNA from Illinois Reverse Low Protein labeled with Cyanine-5 (red)

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen, Carlsbad, CA), digested by DNAse, then Rneasy purification kit (Qiagen, Valencia, CA).

value: Illinois Reverse Low Protein line

value: 8 Days after Pollination

source_name: Total RNA from Illinois Low Protein labeled with Cyanine-3 (green)

value: Illinois Low Protein line


title: IRLP rep2 vs ILP rep2 dye swap

source_name: Total RNA from Illinois Low Protein labeled with Cyanine-5 (red)

source_name: Total RNA from Illinois Reverse Low Protein labeled with Cyanine-3 (green)


title: M145E-F134-F199-27 h

tag: time point

value: wt


title: IHP low N rep2 vs IHP high N rep2

description: IHP low N rep2 vs IHP high N rep2

source_name: IHP high N rep2


title: IHP rep1 vs ILP rep1 dye swap

source_name: Total RNA from Illinois High Protein labeled with Cyanine-3 (green)

value: Illinois High Protein line


title: IRLP rep1 vs ILP rep1 dye swap


title: IRHP rep1 vs ILP rep1

source_name: Total RNA from Illinois Reverse High Protein labeled with Cyanine-5 (red)

value: Illinois Reverse High Protein line


title: IRLP rep1 vs ILP rep1


title: IRHP rep2 vs ILP rep2


title: IRHP rep2 vs ILP rep2 dye swap

source_name: Total RNA from Illinois Reverse High Protein labeled with Cyanine-3 (green)


title: IHP rep1 vs ILP rep1

source_name: Total RNA from Illinois High Protein labeled with Cyanine-5 (red)


title: B73 high N (ref) rep4 vs IHP low N rep4

description: B73 high N (ref) rep4 vs IHP low N rep4

source_name: B73 high N (ref) rep4

source_name: IHP low N rep4


title: IHP low N rep3 vs IHP high N rep3

description: IHP low N rep3 vs IHP high N rep3

source_name: IHP low N rep3

source_name: IHP high N rep3


title: Reference vs Genotype1 rep1 dye swap

description: Reference vs Genotype1 rep1 dye swap

source_name: Oba super 1


title: IHP rep2 vs ILP rep2


title: IHP high N rep1 vs IHP low N rep1

description: IHP high N rep1 vs IHP low N rep1

source_name: IHP high N rep1

source_name: IHP low N rep1


title: Reference vs Genotype3 rep2 dye swap

description: Reference vs Genotype3 rep2 dye swap


title: IHP rep2 vs ILP rep2 dye swap


title: Reference vs Genotype3 rep1

description: Reference vs Genotype3 rep1


title: Reference vs Genotype3 rep1 dye swap

description: Reference vs Genotype3 rep1 dye swap


title: Reference vs Genotype3 rep2

description: Reference vs Genotype3 rep2


title: Rice-9804, biological rep3

city: Beijing

first: Meirong

last: Xu

state: Beijing

address: 12 South Zhong-Guan-Cun St.

department: Institute of Crop Sciences

institute: Chinese academy of agricultural sciences

description: Japonica, 9804, recipent of transformation

hyb_protocol: RNA from the three independent replicate samples of each treatment were used for hybridization to the Affymetrix Genechips® Rice Genome Array chips, which contain probes to query 51,279 transcripts from two rice cultivars, including 48,564 japonica transcripts and 1,260 indica transcripts from Affymetrix (Santa Clara, CA).Hybridization to the arrays and quality control checks were carried out at the Company of CapitalBio Corporation, Beijing. (Affymetrix GeneChip Expression Analysis g of this fragmented target cRNA wasmTechnical Manual).

scan_protocol: standard Affymetrix protocol

data_processing: MaAS 5.0

organism: Oryza sativa

source_name: Japonica, 9804, leaf

label_protocol: Biotin labeled cRNA was produced with 5 ug of total RNA as starting material for each sample reaction.

growth_protocol: Seeds were sown in the seedling nursery, and ten of 30-days-old seedlings of each line were transplanted into an isolated screening house at a spacing of 25×20 cm with 1 seedling per hill in the Fujian Academy of Agricultural Sciences.

extract_protocol: The total RNA was extracted from each frozen leaf sample using the TRIZOL reagent according to the instruction, and then purified and concentrated using the Qiagen RNeasy MinElute Cleanup kit. RNA was quality-checked and quantified using a Bioanalyzer 2100 (Agilent Technologies, Cheadle, UK).

treatment_protocol: All inoculated flag leaves from three plants of 9804-Rxo1 and 9804 were collected two days post-inoculation (dpi), and the flag leaves from three non-inoculated check plants of 9804-Rxo1 and 9804 were also sampled at the same time point as control. The collected leaves were immediately frozen in liquid nitrogen, and then kept at -70°C. The flag leaves from non-inoculated check plants of 9804 were sampled at the same time point as control. The collected leaves were immediately frozen in liquid nitrogen, and then kept at -70°C.

value: Japonica, 9804

tag: developmental stage

value: booting stage


title: Reference vs Genotype2 rep2 dye swap

description: Reference vs Genotype2 rep2 dye swap


title: Rice-9804, biological rep1


title: Reference vs Genotype1 rep2 dye swap

description: Reference vs Genotype1 rep2 dye swap


title: Reference vs Genotype2 rep1 dye swap

description: Reference vs Genotype2 rep1 dye swap


title: Rice-9804, biological rep2


title: Rice-9804-Xoc, biological rep3

source_name: Japonica, 9804, leaf, Xoc, 2 dpi


title: Rice-9804-Rxo1, biological rep3

description: A homozygous T4 line containing a single copy of Rxo1 from transgenic 9804 plants (the standard Agrobacterium mediated transformation system)

source_name: 9804 carrying the maize resistance gene Rxo1, leaf, CK

value: Japonica, 9804 carrying the maize resistance gene Rxo1


title: Rice-9804-Rxo1, biological rep2

value: leaf


title: Reference vs Genotype2 rep1

description: Reference vs Genotype2 rep1


title: Reference vs Genotype2 rep2

description: Reference vs Genotype2 rep2


title: Reference vs Genotype1 rep2

description: Reference vs Genotype1 rep2


title: Rice-9804-Xoc, biological rep2


title: Reference vs Genotype1 rep1

description: Reference vs Genotype1 rep1


title: Rice-9804-Xoc, biological rep1


title: IRHP rep2 vs ILP rep2 dye swap

source_name: Total RNA from Illinois Low Protein labeled with Cyanine-5 (red)


title: Rice-9804-Rxo1, biological rep1


title: Rice-9804-Rxo1-Xoc, biological rep1

source_name: 9804 carrying the maize resistance gene Rxo1, leaf, Xoc, 2 dpi


title: IRLP rep2 vs ILP rep2 dye swap

source_name: Total RNA from Illinois Reverse Low Protein labeled with Cyanine-3 (green)


title: Reference vs Genotype1 rep1 dye swap

description: Reference vs Genotype1 rep1 dye swap


title: IRHP rep2 vs ILP rep2

source_name: Total RNA from Illinois Low Protein labeled with Cyanine-3 (green)


title: Rice-9804-Rxo1-Xoc, biological rep3


title: IRHP rep1 vs ILP rep1

source_name: Total RNA from Illinois Reverse High Protein labeled with Cyanine-5 (red)


title: IRLP rep2 vs ILP rep2

source_name: Total RNA from Illinois Reverse Low Protein labeled with Cyanine-5 (red)


title: Rice-9804-Rxo1-Xoc, biological rep2


title: IHP rep1 vs ILP rep1

source_name: Total RNA from Illinois High Protein labeled with Cyanine-5 (red)


title: IRLP rep1 vs ILP rep1 dye swap


title: IRLP rep1 vs ILP rep1