title: Spore germination_3 hours

description: S. cerevisiae spores, 3 hours after the transfer to YPD


title: Spore germination_3 hours and 15 minutes

status: Public on Dec 23 2007

type: RNA

city: Rehovot

first: Naama

last: Barkai

address: P.O box 26

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute of Science

description: S. cerevisiae spores, 3 hours and 15 minutes after the transfer to YPD

hyb_protocol: For each hybridization, labeled Cy3 and Cy5 were combined together with the following blockers: 5µg Herring sperm (Promega), 5 µg tRNA (Gibco) and 17.5µg Poly A (Synthesized oligos with the length of 40, 50 and 60), and concentrated to 25µl using Microcon (Millipore). 25 µl of hybridization x2 solution (10x SSC, 50% formamide and 0.2% SDS) was added. Microarrays containing all yeast ORFs (purchased from the Microarray Centre, University Health Network, Ontario) were pre-hybridized by incubating in a solution containing 1% BSA, 25% formamide, 5x SSC and 0.1% SDS at 42 C for 45 minutes. The slides were washed with DDW and dried by centrifugation (3 minutes, 2000 rpm). The labeled sample with the blockers, was boiled for 5 minutes, centrifuged for 1 minute and hybridized on the slide. The slides were placed in hybridization chamber (Corning) and incubated over night at 42 C. The slides were washed for 5 minutes at 42 C with a solution containing 2x SSC and 0.1% SDS. Additional wash was performed at room temperature with a solution containing 0.1x SSC and 0.1% SDS, followed by 3 additional washes at room temperature in 0.1x SSC solution.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 using ScanArray 4000 scanner (Packard BioScience) and image intensity data were extracted and analyzed with QuantArray analysis software.

data_processing: For each array, bad spots were omitted from the analysis. For each spot, the Quantarray program outputs the level of signal intensity and background fluorescence. As a first step, we re-defined the spot intensity by subtracting the spot-specific background. For each channel (Cy3 or Cy5) we then calculated the value of background signal, defined by the mean (intensity-background) of the controlled spots printed with 3x SSC buffer. All intensity values below this background level were reset to this background level. The data for each spot was then transformed into a log2-ratios. The data was normalized by subtracting from each log2ratio the median. Values of duplicates were averaged.

molecule: total RNA

organism: Saccharomyces cerevisiae

label_protocol: Samples and reference cDNA were synthesized from total RNA and labeled with Cy3 and Cy5 by the indirect amino-allyl method as described below. Total RNA (20 µg) was annealed with 4 µg oligo dT12-18 and reverse transcribed into cDNA with M-MLV Reverse Transcriptase RNase H Minus (Promega) for 2 hours at 45°C in the presence of 2.5mM MgCl2, 0.5 mM of dATP, dCTP and dGTP, 0.1mM dTTP, 0.4mM amino-allyl dUTP. Additional 400U M-MLV Reverse Transcriptase RNase H Minus was added and incubated for another 2 hours. The reaction was terminated by incubation at 70°C for 15 minutes and RNA was degraded by adding 10 µM 1N NaOH and incubation at 65 C for 30 minutes. The sample was neutralized by titrating with 1M HCl. cDNA was purified by ethanol precipitation, resuspended in 10 µl 0.1M Sodium Carbonate buffer pH 9.3. Cy5 or Cy3 were added to experimental or reference sample, respectively, and incubated at 25 C for 1 hour. Labeled cDNA was purified by Strataprep PCR purification kit (Stratagene) according to the manufactures instructions. Dye incorporation was measured using a spectrophotometer.

extract_protocol: Cells were flash frozen in liquid Nitrogen. Total RNA was extracted using RNeasy Midi kit (QIAGEN)

tag: Strain

value: SK1 wild type

source_name: S. cerevisiae, logarithmic growing, haploid cells

value: SK1 wild type haploid cells, Mating types and growth conditions:Mata and Matα cells were grown separately in YPD.


title: Spore germination_1 hour and 45 minutes

description: S. cerevisiae spores, 1 hour and 45 minutes after the transfer to YPD


title: Spore germination_2 hours

description: S. cerevisiae spores, 2 hours after the transfer to YPD


title: Spore germination_4 hours and 15 minutes

description: S. cerevisiae spores, 4 hours and 15 minutes after the transfer to YPD


title: Spore germination_3 hours and 45 minutes

description: S. cerevisiae spores, 3 hours and 45 minutes after the transfer to YPD


title: Spore germination_2 hours and 15 minutes

description: S. cerevisiae spores, 2 hours and 15 minutes after the transfer to YPD


title: Spore germination_2 hours and 45 minutes

description: S. cerevisiae spores, 2 hours and 45 minutes after the transfer to YPD


title: Spores_incubation in different nutrients_SPO

description: S. cerevisiae spores

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 using Aginlet's DNA microarray scanner and image intensity data were extracted and analyzed with SpotReader (Niles Scientific) analysis software.

data_processing: Background intensity was subtracted using a Bayesian correction, and the ratios of the two dyes were log2-transformed. Log2 ratios were then corrected for intensity-dependant and spatial-dependant biases by subtracting a Lowess curve followed by a median filter. The two spots corresponding to each gene were then averaged, and genes for which the two spots were significantly different were declared as 'missing values' (along with other genes which were flagged by the image analysis software or removed by manual inspection).

source_name: S. cerevisiae spores


title: Spore germination_1 hour and 15 minutes

description: S. cerevisiae spores, 1 hour and 15 minutes after the transfer to YPD


title: control AMG B liver 0 mg/kg 4 day #13

city: Thousand Oaks

first: Tiffany

last: Day

state: CA

address: One Amgen Center Drive

country: USA

institute: Amgen

description: control AMG B liver 0 mg/kg 4 day #13

hyb_protocol: Fragmented biotin labeled cRNA and hybÆd 15ug per array for 16hrs at 45C with rotation at 50rpm. Affymetrix Rat Genome 230 2.0 Array

scan_protocol: Scanned on Affymetrix GeneChip 3000 scanner.

data_processing: Rosetta Resovler Normalization Pipeline Convert to Z-Scores

label: biotin

organism: Rattus norvegicus

source_name: Rat liver 0mg/kg 4 day

label_protocol: Eukaryotic One-Cycle Target Labeling. 5ug total RNA to start.

extract_protocol: Qiagen RNeasy midi kits

tag: Sprague Dawley rat; Gender

value: male; Age:8 to 10 weeks; Tissue:liver


title: AMG B liver 3 mg/kg 4 day #19

description: AMG B liver 3 mg/kg 4 day #19

source_name: Rat liver 3mg/kg 4 day


title: AMG B liver 60 mg/kg 14 day #35

description: AMG B liver 60 mg/kg 14 day #35

source_name: Rat liver 60mg/kg 14 day


title: control AMG B liver 0 mg/kg 4 day #14

description: control AMG B liver 0 mg/kg 4 day #14


title: AMG B liver 3 mg/kg 14 day #31

description: AMG B liver 3 mg/kg 14 day #31

source_name: Rat liver 3mg/kg 14 day


title: control AMG B liver 0 mg/kg 1 day #3

description: control AMG B liver 0 mg/kg 1 day #3

source_name: Rat liver 0mg/kg 1 day


title: AMG B liver 3 mg/kg 14 day #30

description: AMG B liver 3 mg/kg 14 day #30


title: control AMG B liver 0 mg/kg 14 day #27

description: control AMG B liver 0 mg/kg 14 day #27

source_name: Rat liver 0mg/kg 14 day


title: AMG B liver 3 mg/kg 4 day #17

description: AMG B liver 3 mg/kg 4 day #17


title: AMG B liver 3 mg/kg 1 day #5

description: AMG B liver 3 mg/kg 1 day #5

source_name: Rat liver 3mg/kg 1 day


title: AMG B liver 3 mg/kg 4 day #18

description: AMG B liver 3 mg/kg 4 day #18


title: control AMG B liver 0 mg/kg 4 day #15

description: control AMG B liver 0 mg/kg 4 day #15


title: AMG B liver 3 mg/kg 4 day #20

description: AMG B liver 3 mg/kg 4 day #20


title: AMG B liver 3 mg/kg 1 day #6

description: AMG B liver 3 mg/kg 1 day #6


title: AMG B liver 3 mg/kg 14 day #29

description: AMG B liver 3 mg/kg 14 day #29


title: AMG B liver 3 mg/kg 1 day #7

description: AMG B liver 3 mg/kg 1 day #7


title: control AMG B liver 0 mg/kg 1 day #4

description: control AMG B liver 0 mg/kg 1 day #4


title: control AMG B liver 0 mg/kg 14 day #28

description: control AMG B liver 0 mg/kg 14 day #28


title: AMG B liver 3 mg/kg 1 day #8

description: AMG B liver 3 mg/kg 1 day #8


title: AMG B liver 60 mg/kg 1 day #11

description: AMG B liver 60 mg/kg 1 day #11

source_name: Rat liver 60mg/kg 1 day


title: AMG B liver 60 mg/kg 1 day #10

description: AMG B liver 60 mg/kg 1 day #10


title: control AMG B liver 0 mg/kg 1 day #2

description: control AMG B liver 0 mg/kg 1 day #2


title: AMG B liver 60 mg/kg 1 day #9

description: AMG B liver 60 mg/kg 1 day #9


title: control AMG B liver 0 mg/kg 4 day #16

description: control AMG B liver 0 mg/kg 4 day #16


title: control AMG B liver 0 mg/kg 1 day #1

description: control AMG B liver 0 mg/kg 1 day #1


title: AMG B liver 3 mg/kg 14 day #32

description: AMG B liver 3 mg/kg 14 day #32


title: control AMG B liver 0 mg/kg 14 day #25

description: control AMG B liver 0 mg/kg 14 day #25


title: control AMG B liver 0 mg/kg 14 day #26

description: control AMG B liver 0 mg/kg 14 day #26


title: AMG B liver 60 mg/kg 14 day #36

description: AMG B liver 60 mg/kg 14 day #36


title: AMG B liver 60 mg/kg 14 day #33

description: AMG B liver 60 mg/kg 14 day #33


title: AMG A liver 30 mg/kg 14 day #3034

description: AMG A liver 30 mg/kg 14 day #3034

hyb_protocol: Fragmented biotin labeled cRNA and hybÆd 15ug per array for 16hrs at 45C with rotation at 50rpm.  Affymetrix Rat Expression Array 230A

source_name: Rat liver 30mg/kg 14 day


title: AMG A liver 3 mg/kg 4 day #3017

description: AMG A liver 3 mg/kg 4 day #3017


title: AMG A liver 3 mg/kg 1 day #3015

description: AMG A liver 3 mg/kg 1 day #3015


title: AMG B liver 60 mg/kg 4 day #24

description: AMG B liver 60 mg/kg 4 day #24

source_name: Rat liver 60mg/kg 4 day


title: AMG A liver 30 mg/kg 14 day #3036

description: AMG A liver 30 mg/kg 14 day #3036


title: AMG B liver 60 mg/kg 1 day #12

description: AMG B liver 60 mg/kg 1 day #12


title: AMG A liver 30 mg/kg 1 day #3025

description: AMG A liver 30 mg/kg 1 day #3025

source_name: Rat liver 30mg/kg 1 day


title: AMG A pancreas 30 mg/kg 14 day #3033

description: AMG A pancreas 30 mg/kg 14 day #3033

source_name: Rat pancreas 30mg/kg 14 day

value: male; Age:8 to 10 weeks; Tissue:pancreas


title: AMG B liver 60 mg/kg 4 day #21

description: AMG B liver 60 mg/kg 4 day #21


title: AMG A liver 3 mg/kg 4 day #3018

description: AMG A liver 3 mg/kg 4 day #3018


title: control pancreas 0 mg/kg 14 day #3011

description: control pancreas 0 mg/kg 14 day #3011

source_name: Rat pancreas 0mg/kg 14 day


title: AMG B liver 60 mg/kg 14 day #34

description: AMG B liver 60 mg/kg 14 day #34


title: AMG A liver 3 mg/kg 4 day #3020

description: AMG A liver 3 mg/kg 4 day #3020


title: AMG B liver 60 mg/kg 4 day #23

description: AMG B liver 60 mg/kg 4 day #23


title: AMG B pancreas 3 mg/kg 14 day #30

description: AMG B pancreas 3 mg/kg 14 day #30

source_name: Rat pancreas 3mg/kg 14 day


title: AMG B pancreas 60 mg/kg 14 day #33

description: AMG B pancreas 60 mg/kg 14 day #33

source_name: Rat pancreas 60mg/kg 14 day


title: AMG A liver 30 mg/kg 1 day #3026

description: AMG A liver 30 mg/kg 1 day #3026


title: AMG A liver 30 mg/kg 1 day #3027

description: AMG A liver 30 mg/kg 1 day #3027


title: AMG B liver 60 mg/kg 4 day #22

description: AMG B liver 60 mg/kg 4 day #22


title: AMG A pancreas 30 mg/kg 14 day #3034

description: AMG A pancreas 30 mg/kg 14 day #3034


title: AMG A liver 30 mg/kg 14 day #3033

description: AMG A liver 30 mg/kg 14 day #3033


title: AMG A liver 30 mg/kg 4 day #3029

description: AMG A liver 30 mg/kg 4 day #3029

source_name: Rat liver 30mg/kg 4 day


title: control pancreas 0 mg/kg 14 day #3009

description: control pancreas 0 mg/kg 14 day #3009


title: AMG A liver 3 mg/kg 1 day #3016

description: AMG A liver 3 mg/kg 1 day #3016


title: AMG B pancreas 3 mg/kg 14 day #29

description: AMG B pancreas 3 mg/kg 14 day #29


title: AMG B pancreas 60 mg/kg 14 day #35

description: AMG B pancreas 60 mg/kg 14 day #35


title: AMG A liver 3 mg/kg 14 day #3024

description: AMG A liver 3 mg/kg 14 day #3024


title: AMG B pancreas 60 mg/kg 14 day #36

description: AMG B pancreas 60 mg/kg 14 day #36


title: AMG B pancreas 3 mg/kg 14 day #31

description: AMG B pancreas 3 mg/kg 14 day #31


title: AMG B pancreas 3 mg/kg 14 day #32

description: AMG B pancreas 3 mg/kg 14 day #32


title: AMG A liver 3 mg/kg 14 day #3022

description: AMG A liver 3 mg/kg 14 day #3022


title: control pancreas 0 mg/kg 14 day #27

description: control pancreas 0 mg/kg 14 day #27


title: AMG B pancreas 60 mg/kg 14 day #34

description: AMG B pancreas 60 mg/kg 14 day #34


title: AMG A liver 3 mg/kg 14 day #3021

description: AMG A liver 3 mg/kg 14 day #3021


title: AMG A liver 30 mg/kg 4 day #3030

description: AMG A liver 30 mg/kg 4 day #3030


title: AMG A liver 3 mg/kg 1 day #3014

description: AMG A liver 3 mg/kg 1 day #3014


title: control AMG A liver 0 mg/kg 4 day #3007

description: control AMG A liver 0 mg/kg 4 day #3007


title: AMG A pancreas 30 mg/kg 14 day #3036

description: AMG A pancreas 30 mg/kg 14 day #3036


title: control pancreas 0 mg/kg 14 day #26

description: control pancreas 0 mg/kg 14 day #26


title: AMG A liver 30 mg/kg 4 day #3031

description: AMG A liver 30 mg/kg 4 day #3031


title: control pancreas 0 mg/kg 14 day #28

description: control pancreas 0 mg/kg 14 day #28


title: AMG A pancreas 3 mg/kg 14 day #3021

description: AMG A pancreas 3 mg/kg 14 day #3021


title: AMG A pancreas 3 mg/kg 14 day #3024

description: AMG A pancreas 3 mg/kg 14 day #3024


title: AMG A pancreas 30 mg/kg 14 day #3035

description: AMG A pancreas 30 mg/kg 14 day #3035


title: AMG A liver 3 mg/kg 4 day #3019

description: AMG A liver 3 mg/kg 4 day #3019


title: control pancreas 0 mg/kg 14 day #25

description: control pancreas 0 mg/kg 14 day #25


title: control AMG B adrenal 0 mg/kg 4 day #14

description: control AMG B adrenal 0 mg/kg 4 day #14

source_name: Rat adrenal 0mg/kg 4 day

value: male; Age:8 to 10 weeks; Tissue:adrenal


title: control pancreas 0 mg/kg 14 day #3012

description: control pancreas 0 mg/kg 14 day #3012


title: AMG A liver 30 mg/kg 4 day #3032

description: AMG A liver 30 mg/kg 4 day #3032


title: AMG B adrenal 3 mg/kg 4 day #18

description: AMG B adrenal 3 mg/kg 4 day #18

source_name: Rat adrenal 3mg/kg 4 day


title: AMG A pancreas 3 mg/kg 14 day #3022

description: AMG A pancreas 3 mg/kg 14 day #3022


title: control AMG A liver 0 mg/kg 1 day #3002

description: control AMG A liver 0 mg/kg 1 day #3002


title: control pancreas 0 mg/kg 14 day #3010

description: control pancreas 0 mg/kg 14 day #3010


title: AMG A liver 30 mg/kg 14 day #3035

description: AMG A liver 30 mg/kg 14 day #3035


title: AMG B adrenal 60 mg/kg 1 day #12

description: AMG B adrenal 60 mg/kg 1 day #12

source_name: Rat adrenal 60mg/kg 1 day


title: AMG B adrenal 60 mg/kg 4 day #24

description: AMG B adrenal 60 mg/kg 4 day #24

source_name: Rat adrenal 60mg/kg 4 day


title: control AMG A liver 0 mg/kg 14 day #3009


title: AMG A liver 30 mg/kg 1 day #3028

description: AMG A liver 30 mg/kg 1 day #3028


title: AMG B adrenal 60 mg/kg 1 day #11

description: AMG B adrenal 60 mg/kg 1 day #11


title: AMG B adrenal 3 mg/kg 1 day #6

description: AMG B adrenal 3 mg/kg 1 day #6

source_name: Rat adrenal 3mg/kg 1 day


title: control AMG B adrenal 0 mg/kg 1 day #3

description: control AMG B adrenal 0 mg/kg 1 day #3

source_name: Rat adrenal 0mg/kg 1 day


title: control AMG A liver 0 mg/kg 4 day #3005

description: control AMG A liver 0 mg/kg 4 day #3005

source_name: Rat liver 0mg/kg 4 day


title: control AMG B adrenal 0 mg/kg 4 day #13

description: control AMG B adrenal 0 mg/kg 4 day #13


title: AMG B adrenal 60 mg/kg 1 day #9

description: AMG B adrenal 60 mg/kg 1 day #9


title: AMG B adrenal 3 mg/kg 1 day #7

description: AMG B adrenal 3 mg/kg 1 day #7


title: control AMG B adrenal 0 mg/kg 1 day #4

description: control AMG B adrenal 0 mg/kg 1 day #4


title: AMG A liver 3 mg/kg 14 day #3023

description: AMG A liver 3 mg/kg 14 day #3023

source_name: Rat liver 3mg/kg 14 day


title: AMG B adrenal 60 mg/kg 4 day #22

description: AMG B adrenal 60 mg/kg 4 day #22


title: AMG A liver 3 mg/kg 1 day #3013

description: AMG A liver 3 mg/kg 1 day #3013

source_name: Rat liver 3mg/kg 1 day


title: control AMG A liver 0 mg/kg 4 day #3008

description: control AMG A liver 0 mg/kg 4 day #3008


title: AMG B adrenal 3 mg/kg 4 day #17

description: AMG B adrenal 3 mg/kg 4 day #17


title: control AMG B adrenal 0 mg/kg 1 day #1

description: control AMG B adrenal 0 mg/kg 1 day #1


title: AMG A pancreas 3 mg/kg 14 day #3023

description: AMG A pancreas 3 mg/kg 14 day #3023


title: Spore germination_7 hours

description: S. cerevisiae spores, 7 hours after the transfer to YPD

source_name: S. cerevisiae, logarithmic growing, haploid cells


title: control AMG A liver 0 mg/kg 1 day #3004

description: control AMG A liver 0 mg/kg 1 day #3004

source_name: Rat liver 0mg/kg 1 day


title: AMG B adrenal 3 mg/kg 4 day #20

description: AMG B adrenal 3 mg/kg 4 day #20


title: AMG B adrenal 3 mg/kg 1 day #5

description: AMG B adrenal 3 mg/kg 1 day #5


title: Spore germination_6 hours and 15 minutes

description: S. cerevisiae spores, 6 hours and 15 minutes after the transfer to YPD


title: control AMG A liver 0 mg/kg 1 day #3003

description: control AMG A liver 0 mg/kg 1 day #3003


title: control AMG A liver 0 mg/kg 4 day #3006

description: control AMG A liver 0 mg/kg 4 day #3006


title: AMG B adrenal 60 mg/kg 1 day #10

description: AMG B adrenal 60 mg/kg 1 day #10


title: control AMG B adrenal 0 mg/kg 1 day #2

description: control AMG B adrenal 0 mg/kg 1 day #2


title: Spore germination_6 hours

description: S. cerevisiae spores, 6 hours after the transfer to YPD


title: control AMG B adrenal 0 mg/kg 4 day #16

description: control AMG B adrenal 0 mg/kg 4 day #16


title: AMG B adrenal 3 mg/kg 1 day #8

description: AMG B adrenal 3 mg/kg 1 day #8


title: AMG B adrenal 3 mg/kg 4 day #19

description: AMG B adrenal 3 mg/kg 4 day #19


title: AMG B adrenal 60 mg/kg 14 day #35

description: AMG B adrenal 60 mg/kg 14 day #35

source_name: Rat adrenal 60mg/kg 14 day


title: AMG B adrenal 60 mg/kg 4 day #21

description: AMG B adrenal 60 mg/kg 4 day #21


title: control AMG A liver 0 mg/kg 14 day #3011

source_name: Rat liver 0mg/kg 14 day


title: Spore germination_5 hours and 15 minutes

description: S. cerevisiae spores, 5 hours and 15 minutes after the transfer to YPD


title: Spore germination_5 hours

description: S. cerevisiae spores, 5 hours after the transfer to YPD


title: control AMG A liver 0 mg/kg 14 day #3010


title: AMG B adrenal 60 mg/kg 14 day #34

description: AMG B adrenal 60 mg/kg 14 day #34


title: Spore germination_5 hours and 30 minutes

description: S. cerevisiae spores, 5 hours and 30 minutes after the transfer to YPD


title: AMG B adrenal 60 mg/kg 4 day #23

description: AMG B adrenal 60 mg/kg 4 day #23


title: AMG B adrenal 60 mg/kg 14 day #36

description: AMG B adrenal 60 mg/kg 14 day #36


title: AMG B adrenal 3 mg/kg 14 day #30

description: AMG B adrenal 3 mg/kg 14 day #30

source_name: Rat adrenal 3mg/kg 14 day


title: control AMG B adrenal 0 mg/kg 4 day #15

description: control AMG B adrenal 0 mg/kg 4 day #15


title: control adrenal 0 mg/kg 14 day #26

description: control adrenal 0 mg/kg 14 day #26

source_name: Rat adrenal 0mg/kg 14 day


title: control AMG A liver 0 mg/kg 1 day #3001

description: control AMG A liver 0 mg/kg 1 day #3001


title: AMG B adrenal 60 mg/kg 14 day #33

description: AMG B adrenal 60 mg/kg 14 day #33


title: AMG B adrenal 3 mg/kg 14 day #31

description: AMG B adrenal 3 mg/kg 14 day #31


title: AMG B adrenal 3 mg/kg 14 day #32

description: AMG B adrenal 3 mg/kg 14 day #32


title: Spore germination_4 hours

description: S. cerevisiae spores, 4 hours after the transfer to YPD


title: control adrenal 0 mg/kg 14 day #25

description: control adrenal 0 mg/kg 14 day #25


title: Spore germination_3 hours and 30 minutes

description: S. cerevisiae spores, 3 hours and 30 minutes after the transfer to YPD


title: control AMG A liver 0 mg/kg 14 day #3012


title: Spore germination_1 hour and 30 minutes

description: S. cerevisiae spores, 1 hour and 30 minutes after the transfer to YPD


title: Spore germination_2 hours and 30 minutes

description: S. cerevisiae spores, 2 hours and 30 minutes after the transfer to YPD


title: Spore germination_1 hour

description: S. cerevisiae spores, 1 hour after the transfer to YPD


title: Spore germination_4 hours and 45 minutes

description: S. cerevisiae spores, 4 hours and 45 minutes after the transfer to YPD


title: Spore germination_4 hours and 30 minutes

description: S. cerevisiae spores, 4 hours and 30 minutes after the transfer to YPD


title: control adrenal 0 mg/kg 14 day #27

description: control adrenal 0 mg/kg 14 day #27


title: AMG A adrenal 30 mg/kg 14 day #3034

description: AMG A adrenal 30 mg/kg 14 day #3034

source_name: Rat adrenal 30mg/kg 14 day


title: Spore germination_0 minutes

description: S. cerevisiae spores, immediately after the transfer to YPD


title: control adrenal 0 mg/kg 14 day #3012

description: control adrenal 0 mg/kg 14 day #3012


title: AMG A adrenal 3 mg/kg 14 day #3024

description: AMG A adrenal 3 mg/kg 14 day #3024


title: control adrenal 0 mg/kg 14 day #3010

description: control adrenal 0 mg/kg 14 day #3010


title: AMG A adrenal 30 mg/kg 14 day #3033

description: AMG A adrenal 30 mg/kg 14 day #3033


title: control adrenal 0 mg/kg 14 day #3011

description: control adrenal 0 mg/kg 14 day #3011


title: AMG B adrenal 3 mg/kg 14 day #29

description: AMG B adrenal 3 mg/kg 14 day #29


title: control adrenal 0 mg/kg 14 day #28

description: control adrenal 0 mg/kg 14 day #28


title: control adrenal 0 mg/kg 14 day #3009

description: control adrenal 0 mg/kg 14 day #3009


title: AMG A adrenal 30 mg/kg 14 day #3036

description: AMG A adrenal 30 mg/kg 14 day #3036


title: OCI-Ly10 JAK inhibitor I 6h-2 - mAdbID:86901

status: Public on Dec 21 2007

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

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

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 86901

hyb_protocol: NCI cDNA Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 µl COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), for 1 minute in 0.05X SSC, and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 800;; 710 ScanPower: 100;; 100 LaserPower: 3.12174;; 3.45439 Temperature: 31.2098

data_processing:
mAdb Data Processing Protocol (v. 1)
Calculation Method: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

organism: Homo sapiens

label_protocol:
Cy3 Labeling Protocol
Other: Isolated RNA (50 ug) was reverse transcribed by oligo dT-primed polymerization using Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA). The targets were coupled to Cy3-conjugated deoxynucleotides (Amersham Biosciences, Piscataway, NJ) for 1 hour at room temperature. Probes were combined and concentrated using Microcon YM-30 columns (Millipore, Billerica, MA).

extract_protocol:
Trizol Reagent Extraction Protocol
Extraction method: Trizol Reagent
Other: Total RNA was prepared using the Trizol reagent (Gibco BRL) according to manufacturer's instructions.

tag: Cell line

value: OCI-Ly10 Cell Line

source_name: OCI-Ly10 JAK inhibitor I 6h

label_protocol:
Cy5 Labeling Protocol
Other: Isolated RNA (50 ug) was reverse transcribed by oligo dT-primed polymerization using Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA). The targets were coupled to Cy5-conjugated deoxynucleotides (Amersham Biosciences, Piscataway, NJ) for 1 hour at room temperature. Probes were combined and concentrated using Microcon YM-30 columns (Millipore, Billerica, MA).

treatment_protocol:
Treatment type: compound
Agent: JAK inhibitor
Treatment dose: 5 uM
Treatment time: 6h
In-vivo treatment: OCI-Ly10 cells were treated with JAK inhibitor I for 6 hour.


title: AMG A adrenal 30 mg/kg 14 day #3035

description: AMG A adrenal 30 mg/kg 14 day #3035


title: OCI-Ly3 IL-10 24h-1 - mAdbID:60815

description: mAdb experiment ID: 60815

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 760;; 700 ScanPower: 100;; 100 LaserPower: 1.63976;; 1.96661 Temperature: 35.6821

value: OCI-Ly3 Cell Line

source_name: OCI-Ly3 IL-10 24h

treatment_protocol:
Treatment type: compound
Agent: IL-10
Treatment dose: 50 ng/ml
Treatment time: 24h
In-vivo treatment: OCI-Ly3 cells were treated with IL-10 for 24 hour.


title: OCI-Ly10 STAT3 siRNA SMARTpool vs. no siRNA 8h - mAdbID:63497

description: mAdb experiment ID: 63497

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 680;; 700 ScanPower: 100;; 100 LaserPower: 1.03275;; 1.6126 Temperature: 31.4008

source_name: Control Solution T - 8 hour

treatment_protocol:
Treatment time: 8h
In-vivo treatment: OCI-Ly10 cells were transfected with no siRNA using the Amaxa electroporator. In brief, 8X10^6 cells were used for each time point. Cells were pelleted and resuspended in Solution T (Amaxa) and RNAi. After transferring cells to the cuvettes, they were electroporated using the program A-23. Cells were then transferred to pre-warm medium and incubated for 8 hours before harvest.

source_name: STAT3 siRNA SMARTpool - 8 hour

treatment_protocol:
Treatment type: compound
Agent: STAT3 siRNA
Treatment time: 8h
In-vivo treatment: OCI-Ly10 cells were transfected with 4uM STAT3 siRNA SMARTpool (Dharmacon) using the Amaxa electroporator. In brief, 8X10^6 cells were used for each time point. Cells were pelleted and resuspended in Solution T (Amaxa) and RNAi. After transferring cells to the cuvettes, they were electroporated using the program A-23. Cells were then transferred to pre-warm medium and incubated for 8 hours before harvest.


title: AMG A adrenal 3 mg/kg 14 day #3023

description: AMG A adrenal 3 mg/kg 14 day #3023


title: OCI-Ly10 STAT3 siRNA SMARTpool vs. no siRNA 24h-1 - mAdbID:63498

description: mAdb experiment ID: 63498

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 700;; 700 ScanPower: 100;; 100 LaserPower: 1.07181;; 1.60802 Temperature: 31.976

source_name: Control Solution T - 24 hour

treatment_protocol:
Treatment time: 24h
In-vivo treatment: OCI-Ly10 cells were transfected with no siRNA using the Amaxa electroporator. In brief, 8X10^6 cells were used for each time point. Cells were pelleted and resuspended in Solution T (Amaxa) and RNAi. After transferring cells to the cuvettes, they were electroporated using the program A-23. Cells were then transferred to pre-warm medium and incubated for 24 hours before harvest.

source_name: STAT3 siRNA SMARTpool - 24 hour

treatment_protocol:
Treatment type: compound
Agent: STAT3 siRNA
Treatment time: 24h
In-vivo treatment: OCI-Ly10 cells were transfected with 4uM STAT3 siRNA SMARTpool (Dharmacon) using the Amaxa electroporator. In brief, 8X10^6 cells were used for each time point. Cells were pelleted and resuspended in Solution T (Amaxa) and RNAi. After transferring cells to the cuvettes, they were electroporated using the program A-23. Cells were then transferred to pre-warm medium and incubated for 24 hours before harvest.


title: OCI-Ly10 STAT3 siRNA SMARTpool vs. no siRNA 48h-2 - mAdbID:63279

description: mAdb experiment ID: 63279

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 690;; 750 ScanPower: 100;; 100 LaserPower: 1.2772;; 1.92907 Temperature: 36.0251

source_name: Control Solution T - 48 hour

treatment_protocol:
Treatment time: 48h
In-vivo treatment: OCI-Ly10 cells were transfected with no siRNA using the Amaxa electroporator. In brief, 8X10^6 cells were used for each time point. Cells were pelleted and resuspended in Solution T (Amaxa) and RNAi. After transferring cells to the cuvettes, they were electroporated using the program A-23. Cells were then transferred to pre-warm medium and incubated for 48 hours before harvest.

source_name: STAT3 siRNA SMARTpool - 48 hour

treatment_protocol:
Treatment type: compound
Agent: STAT3 siRNA
Treatment time: 48h
In-vivo treatment: OCI-Ly10 cells were transfected with 4uM STAT3 siRNA SMARTpool (Dharmacon) using the Amaxa electroporator. In brief, 8X10^6 cells were used for each time point. Cells were pelleted and resuspended in Solution T (Amaxa) and RNAi. After transferring cells to the cuvettes, they were electroporated using the program A-23. Cells were then transferred to pre-warm medium and incubated for 48 hours before harvest.


title: OCI-Ly10 JAK inhibitor I 3h-1 - mAdbID:75045

description: mAdb experiment ID: 75045

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000A [47890] ScanPower: 100;; 100 LaserPower: 1.22;; 1.9 Temperature: 35.86

source_name: OCI-Ly10 JAK inhibitor I 3h

treatment_protocol:
Treatment type: compound
Agent: JAK inhibitor
Treatment dose: 5 uM
Treatment time: 3h
In-vivo treatment: OCI-Ly10 cells were treated with JAK inhibitor I for 3 hour.


title: AMG A adrenal 3 mg/kg 14 day #3021

description: AMG A adrenal 3 mg/kg 14 day #3021


title: AMG A adrenal 3 mg/kg 14 day #3022

description: AMG A adrenal 3 mg/kg 14 day #3022


title: OCI-Ly3 IL-10 3h-1 - mAdbID:60813

description: mAdb experiment ID: 60813

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 780;; 730 ScanPower: 100;; 100 LaserPower: 1.66;; 1.96 Temperature: 35.2

source_name: OCI-Ly3 IL-10 3h

treatment_protocol:
Treatment type: compound
Agent: IL-10
Treatment dose: 50 ng/ml
Treatment time: 3h
In-vivo treatment: OCI-Ly3 cells were treated with IL-10 for 3 hour.


title: OCI-Ly10 JAK inhibitor I 6h-1 - mAdbID:75046

description: mAdb experiment ID: 75046

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000A [47890] ScanPower: 100;; 100 LaserPower: 1.18534;; 1.90374 Temperature: 36.0859


title: OCI-Ly10 JAK inhibitor I 3h-2 - mAdbID:86900

description: mAdb experiment ID: 86900

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 800;; 740 ScanPower: 100;; 100 LaserPower: 3.09;; 2.87 Temperature: 30.78


title: OCI-Ly3 IL-10 6h-1 - mAdbID:60814

description: mAdb experiment ID: 60814

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 760;; 700 ScanPower: 100;; 100 LaserPower: 1.67;; 1.97 Temperature: 35.43

source_name: OCI-Ly3 IL-10 6h

treatment_protocol:
Treatment type: compound
Agent: IL-10
Treatment dose: 50 ng/ml
Treatment time: 6h
In-vivo treatment: OCI-Ly3 cells were treated with IL-10 for 6 hour.


title: OCI-Ly10 iIkBsr 24h - mAdbID:60576

description: mAdb experiment ID: 60576

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 760;; 700 ScanPower: 100;; 100 LaserPower: 1.88726;; 2.0542 Temperature: 39.8529

source_name: OCI-Ly10 iIkBsr control

value: OCI-Ly10 iIkBsr Cell Line

source_name: OCI-Ly10 iIkBsr dox (24h)

treatment_protocol:
Treatment type: compound
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 24h
In-vivo treatment: Cells transfected with inducible IkB super-repressor were treated with doxycycline for 24 hour.


title: OCI-Ly10 iIkBsr 3h - mAdbID:60574

description: mAdb experiment ID: 60574

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 770;; 740 ScanPower: 100;; 100 LaserPower: 1.84;; 2.16 Temperature: 39.58

source_name: OCI-Ly10 iIkBsr dox (3h)

treatment_protocol:
Treatment type: compound
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 3h
In-vivo treatment: Cells transfected with inducible IkB super-repressor were treated with doxycycline for 3 hour.


title: OCI-Ly3 IL-10 1h-1 - mAdbID:60812

description: mAdb experiment ID: 60812

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 810;; 730 ScanPower: 100;; 100 LaserPower: 1.59;; 1.97 Temperature: 34.89

source_name: OCI-Ly3 IL-10 1h

treatment_protocol:
Treatment type: compound
Agent: IL-10
Treatment dose: 50 ng/ml
Treatment time: 1h
In-vivo treatment: OCI-Ly3 cells were treated with IL-10 for 1 hour.


title: OCI-Ly3 IL-10 96h - mAdbID:60707

description: mAdb experiment ID: 60707

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 770;; 710 ScanPower: 100;; 100 LaserPower: 1.60436;; 2.00507 Temperature: 35.8979

source_name: OCI-Ly3 IL-10 96h

treatment_protocol:
Treatment type: compound
Agent: IL-10
Treatment dose: 50 ng/ml
Treatment time: 96h
In-vivo treatment: OCI-Ly3 cells were treated with IL-10 for 96 hour.


title: OCI-Ly10 iIkBsr 6h - mAdbID:60575

description: mAdb experiment ID: 60575

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 760;; 740 ScanPower: 100;; 100 LaserPower: 1.89;; 2.26 Temperature: 39.69

source_name: OCI-Ly10 iIkBsr dox (6h)

treatment_protocol:
Treatment type: compound
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 6h
In-vivo treatment: Cells transfected with inducible IkB super-repressor were treated with doxycycline for 6 hour.


title: OCI-Ly10 STAT3 siRNA SMARTpool vs. no siRNA 48h-1 - mAdbID:63499

description: mAdb experiment ID: 63499

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 700;; 710 ScanPower: 100;; 100 LaserPower: 1.08493;; 1.62358 Temperature: 32.7892


title: OCI-Ly3 iIkBsr 1.5h - mAdbID:58869

description: mAdb experiment ID: 58869

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 770;; 710 ScanPower: 100;; 100 LaserPower: 1.77;; 2 Temperature: 39.44

source_name: OCI-Ly3 iIkBsr control

value: OCI-Ly3 iIkBsr Cell Line

source_name: OCI-Ly3 iIkBsr dox (1.5h)

treatment_protocol:
Treatment type: compound
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 1.5h
In-vivo treatment: Cells transfected with inducible IkB super-repressor were treated with doxycycline for 1.5 hour.


title: OCI-Ly10 iIkBsr 1.5h - mAdbID:60573

description: mAdb experiment ID: 60573

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 770;; 710 ScanPower: 100;; 100 LaserPower: 1.84;; 2.16 Temperature: 39.39

source_name: OCI-Ly10 iIkBsr dox (1.5h)


title: OCI-Ly3 IL-10 24h-2 - mAdbID:60298

description: mAdb experiment ID: 60298

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 680;; 670 ScanPower: 100;; 100 LaserPower: 1.61199;; 2.03528 Temperature: 34.0006

source_name: OCI-Ly3 IL-10 24h


title: OCI-Ly3 IL-10 3h-2 - mAdbID:60296

description: mAdb experiment ID: 60296

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 710;; 700 ScanPower: 100;; 100 LaserPower: 1.56;; 2.07 Temperature: 33.2


title: OCI-Ly3 iIkBsr 6h-2 - mAdbID:58874

description: mAdb experiment ID: 58874

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 760;; 710 ScanPower: 100;; 100 LaserPower: 1.73;; 2 Temperature: 39.18

source_name: OCI-Ly3 iIkBsr dox (6h)


title: OCI-Ly3 iIkBsr 2h-1 - mAdbID:57874

description: mAdb experiment ID: 57874

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 750;; 750 ScanPower: 100;; 100 LaserPower: 1.62;; 2.08 Temperature: 36.26

source_name: OCI-Ly3 iIkBsr dox (2h)

treatment_protocol:
Treatment type: compound
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 2h
In-vivo treatment: Cells transfected with inducible IkB super-repressor were treated with doxycycline for 2 hour.


title: OCI-Ly3 iIkBsr 4h-2 - mAdbID:58873

description: mAdb experiment ID: 58873

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 740;; 710 ScanPower: 100;; 100 LaserPower: 1.7;; 2.01 Temperature: 38.91

source_name: OCI-Ly3 iIkBsr dox (4h)

treatment_protocol:
Treatment type: compound
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 4h
In-vivo treatment: Cells transfected with inducible IkB super-repressor were treated with doxycycline for 4 hour.


title: OCI-Ly3 IL-10 6h-2 - mAdbID:60297

description: mAdb experiment ID: 60297

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 700;; 670 ScanPower: 100;; 100 LaserPower: 1.56;; 1.99 Temperature: 33.63


title: OCI-Ly3 IL-10 48h - mAdbID:60706

description: mAdb experiment ID: 60706

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 750;; 710 ScanPower: 100;; 100 LaserPower: 1.64;; 2.01 Temperature: 35.6

source_name: OCI-Ly3 IL-10 48h

treatment_protocol:
Treatment type: compound
Agent: IL-10
Treatment dose: 50 ng/ml
Treatment time: 48h
In-vivo treatment: OCI-Ly3 cells were treated with IL-10 for 48 hour.


title: OCI-Ly3 iIkBsr 6h-1 - mAdbID:57876

description: mAdb experiment ID: 57876

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 750;; 740 ScanPower: 100;; 100 LaserPower: 1.67516;; 2.13263 Temperature: 36.9654


title: OCI-Ly10 STAT3 siRNA SMARTpool vs. no siRNA 24h-2 - mAdbID:63278

description: mAdb experiment ID: 63278

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 710;; 740 ScanPower: 100;; 100 LaserPower: 1.26041;; 1.93976 Temperature: 35.5881

source_name: Control Solution T - 24 hour

source_name: STAT3 siRNA SMARTpool - 24 hour


title: OCI-Ly3 iIkBsr 2h-2 - mAdbID:58870

description: mAdb experiment ID: 58870

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 780;; 720 ScanPower: 100;; 100 LaserPower: 1.73;; 2.01 Temperature: 38.32


title: OCI-Ly3 iIkBsr 4h-1 - mAdbID:57875

description: mAdb experiment ID: 57875

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 760;; 740 ScanPower: 100;; 100 LaserPower: 1.65;; 2.09 Temperature: 36.59


title: OCI-Ly10 IL-6 6h-1 - mAdbID:35680

description: mAdb experiment ID: 35680

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 670;; 710 ScanPower: 100;; 100 LaserPower: 1.29;; 2.17 Temperature: 38.65

source_name: OCI-Ly10 IL-6 6h

treatment_protocol:
Treatment type: compound
Agent: IL-6
Treatment dose: 50 ng/ml
Treatment time: 6h
In-vivo treatment: OCI-Ly10 cells were treated with IL-6 for 6 hour.


title: OCI-Ly10 IL-6 1h-2 - mAdbID:35437

description: mAdb experiment ID: 35437

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 650;; 620 ScanPower: 100;; 100 LaserPower: 1.67;; 1.94 Temperature: 38.18

source_name: OCI-Ly10 IL-6 1h

treatment_protocol:
Treatment type: compound
Agent: IL-6
Treatment dose: 50 ng/ml
Treatment time: 1h
In-vivo treatment: OCI-Ly10 cells were treated with IL-6 for 1 hour.


title: OCI-Ly10 IL-6 30 min - mAdbID:35677

description: mAdb experiment ID: 35677

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 640;; 710 ScanPower: 100;; 100 LaserPower: 1.28;; 1.82 Temperature: 38.19

source_name: OCI-Ly10 IL-6 30 min

treatment_protocol:
Treatment type: compound
Agent: IL-6
Treatment dose: 50 ng/ml
Treatment time: 30 min
In-vivo treatment: OCI-Ly10 cells were treated with IL-6 for 30 minutes.


title: OCI-Ly3 iIkBsr 3h - mAdbID:58871

description: mAdb experiment ID: 58871

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 730;; 710 ScanPower: 100;; 100 LaserPower: 1.69;; 2.01 Temperature: 38.66

source_name: OCI-Ly3 iIkBsr dox (3h)


title: OCI-Ly10 IL-6 3h-1 - mAdbID:35679

description: mAdb experiment ID: 35679

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 690;; 690 ScanPower: 100;; 100 LaserPower: 1.28;; 2.28 Temperature: 38.48

source_name: OCI-Ly10 IL-6 3h

treatment_protocol:
Treatment type: compound
Agent: IL-6
Treatment dose: 50 ng/ml
Treatment time: 3h
In-vivo treatment: OCI-Ly10 cells were treated with IL-6 for 3 hour.


title: OCI-Ly3 iIkBsr 1h - mAdbID:57873

description: mAdb experiment ID: 57873

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 760;; 750 ScanPower: 100;; 100 LaserPower: 1.66;; 2.09 Temperature: 35.95

source_name: OCI-Ly3 iIkBsr dox (1h)

treatment_protocol:
Treatment type: compound
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 1h
In-vivo treatment: Cells transfected with inducible IkB super-repressor were treated with doxycycline for 1 hour.


title: OCI-Ly10 IL-6 24h - mAdbID:35681

description: mAdb experiment ID: 35681

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 670;; 710 ScanPower: 100;; 100 LaserPower: 1.2949;; 2.19611 Temperature: 38.7908

source_name: OCI-Ly10 IL-6 24h

treatment_protocol:
Treatment type: compound
Agent: IL-6
Treatment dose: 50 ng/ml
Treatment time: 24h
In-vivo treatment: OCI-Ly10 cells were treated with IL-6 for 24 hour.


title: OCI-Ly10 IL-6 1h-1 - mAdbID:35678

description: mAdb experiment ID: 35678

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 640;; 710 ScanPower: 100;; 100 LaserPower: 1.28;; 1.77 Temperature: 38.35


title: OCI-Ly10 IL-6 3h-2 - mAdbID:35440

description: mAdb experiment ID: 35440

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 650;; 620 ScanPower: 100;; 100 LaserPower: 1.68;; 1.96 Temperature: 38.48


title: OCI-Ly3 IL-10 1h-2 - mAdbID:60295

description: mAdb experiment ID: 60295

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 730;; 710 ScanPower: 100;; 100 LaserPower: 1.6;; 1.99 Temperature: 32.73

source_name: OCI-Ly3 IL-10 1h


title: OCI-Ly10 IL-6 6h-2 - mAdbID:35451

description: mAdb experiment ID: 35451

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 650;; 620 ScanPower: 100;; 100 LaserPower: 1.7;; 1.96 Temperature: 38.71


title: placentome 1985, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy5.

city: Champaign

first: Robin

middle: Edward

last: Everts

state: IL

address: 1201 West Gregory Drive

department: Animal Sciences

institute: UIUC

description:
The cDNA from placentome RNA and the reference standard was coupled with Cy5 or Cy3 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner dual-laser confocal scanner and images were processed using GenePix 6.0 (Axon Instruments, Inc., CA).
Keywords = placentome
Keywords = cow
Keywords = term pregnancy
Keywords = microarray

hyb_protocol: Each Cy5-labeled sample was combined with a Cy3-labeled reference, vacuum dried, and resuspended in 40 µl of ddH2O containing 10 µg of bovine Cot1 DNA, 20 µg oligo dT.  After denaturation for 3 min at 94°C and reannealing for 10 min at 60°C, 40 µl of 2x hybridization buffer (50% formamide, 10x SSC, 02% SDS) was added and the mixture was hybridized to the microarray for 40 hrs. Microarrays were subsequently washed in a series of SSC/SDS washes (1xSSC/0.2% SDS, 0.1xSS/0.2% SDS, 0.1xSSC)to remove unbound cDNA.  After washing, arrays were dried by centrifugation and stored in argon gas until scanning (max. ~1 hr).

scan_protocol: The microarray image was acquired using a GenePix 4000B scanner and analyzed using GenePix Pro 6.0 using the autobalance feature and a saturation threshold of 0.05%. Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner dual-laser confocal scanner and images were processed using GenePix 6.0 (Axon Instruments, Inc., CA).

data_processing: Values are raw log2 transformed ratios, no normalizations are performed, and only GenePix flagging is performed.

organism: Bos taurus

source_name: placentome 1985, type: AI, phenotype: normal, sex: male, term: term, labeled with Cy5

label_protocol: The RNA (10 µg) was annealed with 6 µg random N6, and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 46°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column.  The cDNA was covalently coupled with Cy5-monoreactive dye in 50 mM sodium bicarbonate, pH 9.0. The Cy5-labeled cDNA was purified with a QIAquick PCR purification column. Each labeled sample was analyzed using a spectrophotometer to assess dye incorporation.

extract_protocol: RNA isolation was accomplished using Trizol.

tag: placentome total RNA was isolated by Trizol

source_name: reference standard RNA, labeled with Cy3

label_protocol: The RNA (10 µg) was annealed with 6 µg random N6, and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 46°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column. The cDNA was covalently coupled Cy3-monoreactive dye in 50 mM sodium bicarbonate, pH 9.0. The Cy3-labeled cDNA was purified with a QIAquick PCR purification column. Each labeled reference was analyzed using a spectrophotometer to assess dye incorporation.

tag: reference total RNA was isolated by Trizol and consists of equal amounts total RNA extracted from EBTr, MDBK, and BL30 cell lines, and brain tissue


title: placentome 1985, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy3.

description:
The cDNA from placentome RNA and the reference standard was coupled with Cy3 or Cy5 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner dual-laser confocal scanner and images were processed using GenePix 6.0 (Axon Instruments, Inc., CA).
Keywords = placentome
Keywords = cow
Keywords = term pregnancy
Keywords = microarray

hyb_protocol: Each Cy3-labeled sample was combined with a Cy5-labeled reference, vacuum dried, and resuspended in 40 µl of ddH2O containing 10 µg of bovine Cot1 DNA, 20 µg oligo dT.  After denaturation for 3 min at 94°C and reannealing for 10 min at 60°C, 40 µl of 2x hybridization buffer (50% formamide, 10x SSC, 02% SDS) was added and the mixture was hybridized to the microarray for 40 hrs. Microarrays were subsequently washed in a series of SSC/SDS washes (1xSSC/0.2% SDS, 0.1xSS/0.2% SDS, 0.1xSSC)to remove unbound cDNA.  After washing, arrays were dried by centrifugation and stored in argon gas until scanning (max. ~1 hr).

scan_protocol: The microarray image was acquired using a GenePix 4000B scanner and analyzed using GenePix Pro 6.0 using the autobalance feature and a saturation threshold of 0.05%.

source_name: reference standard RNA, labeled with Cy5

label_protocol: The reference RNA (10 µg) was annealed with 6 µg random N6, and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 46°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column. The cDNA was covalently coupled separately with Cy5-monoreactive dye in 50 mM sodium bicarbonate, pH 9.0. The Cy5-labeled cDNA was purified with a QIAquick PCR purification column. The labeled reference was analyzed using a spectrophotometer to assess incoproration of dyes.

source_name: placentome 1985, type: AI, phenotype: normal, sex: male, term: term, labeled with Cy3

label_protocol: The sample RNA (10 µg) was annealed with 6 µg random N6, and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 46°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column. The cDNA was covalently coupled separately with Cy3-monoreactive dye in 50 mM sodium bicarbonate, pH 9.0. The Cy3-labeled cDNA was purified with a QIAquick PCR purification column. The labeled sample was analyzed using a spectrophotometer to assess incoproration of dyes.

tag: placentome total RNA isolated by Trizol


title: placentome 9674, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy3.

source_name: placentome 9674, type: AI, phenotype: normal, sex: male, term: term, labeled with Cy3


title: placentome 1039, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy5.

source_name: placentome 1039, type: AI, phenotype: normal, sex: male, term: term, labeled with Cy5


title: placentome 8856, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy5.

source_name: placentome 8856, type: AI, phenotype: normal, sex: male, term: term, labeled with Cy5


title: placentome 9674, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy5.

source_name: placentome 9674, type: AI, phenotype: normal, sex: male, term: term, labeled with Cy5


title: placentome 9026, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy3.

source_name: placentome 9026, type: AI, phenotype: normal, sex: male, term: term, labeled with Cy3


title: placentome 8856, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy3.

source_name: placentome 8856, type: AI, phenotype: normal, sex: male, term: term, labeled with Cy3


title: placentome 44, term parturition with other phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 44, type: NT, phenotype: other, sex: female, term: term, labeled with Cy3


title: placentome 1039, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy3.

source_name: placentome 1039, type: AI, phenotype: normal, sex: male, term: term, labeled with Cy3


title: placentome 46, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 46, type: NT, phenotype: normal, sex: female, term: term, labeled with Cy5


title: placentome 44, term parturition with other phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 44, type: NT, phenotype: other, sex: female, term: term, labeled with Cy5


title: placentome 9026, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy5.

source_name: placentome 9026, type: AI, phenotype: normal, sex: male, term: term, labeled with Cy5


title: placentome 46, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 46, type: NT, phenotype: normal, sex: female, term: term, labeled with Cy3


title: placentome 40, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 40, type: NT, phenotype: normal, sex: female, term: term, labeled with Cy5


title: placentome 38, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 38, type: NT, phenotype: normal, sex: female, term: term, labeled with Cy5


title: placentome 36, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 36, type: IVF, phenotype: normal, sex: female, term: term, labeled with Cy3


title: placentome 37, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: reference standard RNA, labeled with Cy5

source_name: placentome 37, type: NT, phenotype: normal, sex: female, term: term, labeled with Cy3


title: placentome 37, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 37, type: NT, phenotype: normal, sex: female, term: term, labeled with Cy5

source_name: reference standard RNA, labeled with Cy3


title: placentome 40, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 40, type: NT, phenotype: normal, sex: female, term: term, labeled with Cy3


title: placentome 36, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 36, type: IVF, phenotype: normal, sex: female, term: term, labeled with Cy5


title: placentome 38, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 38, type: NT, phenotype: normal, sex: female, term: term, labeled with Cy3


title: placentome 35, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 35, type: NT, phenotype: normal, sex: female, term: term, labeled with Cy3


title: placentome 33, preterm parturition with normal phenotype; male calf.  cDNA labeled with dye Cy5.

description:
The cDNA from placentome RNA and the reference standard was coupled with Cy5 or Cy3 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner dual-laser confocal scanner and images were processed using GenePix 6.0 (Axon Instruments, Inc., CA).
Keywords = placentome
Keywords = cow
Keywords = preterm pregnancy
Keywords = microarray

source_name: placentome 33, type: AI, phenotype: normal, sex: male, term: preterm, labeled with Cy5


title: placentome 32, term parturition with other phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 32, type: NT, phenotype: other, sex: female, term: term, labeled with Cy3


title: placentome 33, preterm parturition with normal phenotype; male calf.  cDNA labeled with dye Cy3.

description:
The cDNA from placentome RNA and the reference standard was coupled with Cy3 or Cy5 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner dual-laser confocal scanner and images were processed using GenePix 6.0 (Axon Instruments, Inc., CA).
Keywords = placentome
Keywords = cow
Keywords = preterm pregnancy
Keywords = microarray

source_name: placentome 33, type: AI, phenotype: normal, sex: male, term: preterm, labeled with Cy3


title: placentome 35, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 35, type: NT, phenotype: normal, sex: female, term: term, labeled with Cy5


title: placentome 32, term parturition with other phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 32, type: NT, phenotype: other, sex: female, term: term, labeled with Cy5


title: placentome 31, term parturition with hydrops phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 31, type: NT, phenotype: hydrops, sex: female, term: term, labeled with Cy3


title: placentome 27, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy5.

source_name: placentome 27, type: IVF, phenotype: normal, sex: male, term: term, labeled with Cy5


title: placentome 29, preterm parturition with normal phenotype; male calf.  cDNA labeled with dye Cy5.

source_name: placentome 29, type: AI, phenotype: normal, sex: male, term: preterm, labeled with Cy5


title: placentome 28, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 28, type: NT, phenotype: normal, sex: female, term: term, labeled with Cy3


title: placentome 23, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy5.

source_name: placentome 23, type: IVF, phenotype: normal, sex: male, term: term, labeled with Cy5


title: placentome 22, term parturition with other phenotype; male calf.  cDNA labeled with dye Cy5.

source_name: placentome 22, type: IVF, phenotype: other, sex: male, term: term, labeled with Cy5


title: placentome 23, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy3.

source_name: reference standard RNA, labeled with Cy5

source_name: placentome 23, type: IVF, phenotype: normal, sex: male, term: term, labeled with Cy3


title: placentome 26, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy3.

source_name: placentome 26, type: IVF, phenotype: normal, sex: male, term: term, labeled with Cy3


title: placentome 29, preterm parturition with normal phenotype; male calf.  cDNA labeled with dye Cy3.

source_name: placentome 29, type: AI, phenotype: normal, sex: male, term: preterm, labeled with Cy3


title: placentome 20, term parturition with other phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 20, type: NT, phenotype: other, sex: female, term: term, labeled with Cy5

source_name: reference standard RNA, labeled with Cy3


title: placentome 28, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 28, type: NT, phenotype: normal, sex: female, term: term, labeled with Cy5


title: placentome 24, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy3.

source_name: placentome 24, type: IVF, phenotype: normal, sex: male, term: term, labeled with Cy3


title: placentome 21, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 21, type: NT, phenotype: normal, sex: female, term: term, labeled with Cy5


title: placentome 27, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy3.

source_name: placentome 27, type: IVF, phenotype: normal, sex: male, term: term, labeled with Cy3


title: placentome 21, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 21, type: NT, phenotype: normal, sex: female, term: term, labeled with Cy3


title: placentome 22, term parturition with other phenotype; male calf.  cDNA labeled with dye Cy3.

source_name: placentome 22, type: IVF, phenotype: other, sex: male, term: term, labeled with Cy3


title: placentome 31, term parturition with hydrops phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 31, type: NT, phenotype: hydrops, sex: female, term: term, labeled with Cy5


title: placentome 19, term parturition with other phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 19, type: NT, phenotype: other, sex: female, term: term, labeled with Cy3


title: placentome 24, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy5.

source_name: placentome 24, type: IVF, phenotype: normal, sex: male, term: term, labeled with Cy5


title: placentome 16, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 16, type: NT, phenotype: normal, sex: female, term: term, labeled with Cy5


title: placentome 19, term parturition with other phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 19, type: NT, phenotype: other, sex: female, term: term, labeled with Cy5


title: placentome 20, term parturition with other phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: reference standard RNA, labeled with Cy5

source_name: placentome 20, type: NT, phenotype: other, sex: female, term: term, labeled with Cy3


title: placentome 26, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy5.

source_name: placentome 26, type: IVF, phenotype: normal, sex: male, term: term, labeled with Cy5


title: placentome 14, term parturition with other phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 14, type: NT, phenotype: other, sex: female, term: term, labeled with Cy3


title: placentome 15, preterm parturition with normal phenotype; male calf.  cDNA labeled with dye Cy5.

source_name: placentome 15, type: AI, phenotype: normal, sex: male, term: preterm, labeled with Cy5


title: placentome 15, preterm parturition with normal phenotype; male calf.  cDNA labeled with dye Cy3.

source_name: placentome 15, type: AI, phenotype: normal, sex: male, term: preterm, labeled with Cy3


title: placentome 16, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 16, type: NT, phenotype: normal, sex: female, term: term, labeled with Cy3


title: placentome 14, term parturition with other phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 14, type: NT, phenotype: other, sex: female, term: term, labeled with Cy5

source_name: reference standard RNA, labeled with Cy3


title: placentome 13, term parturition with hydrops phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 13, type: NT, phenotype: hydrops, sex: female, term: term, labeled with Cy3


title: 20_MLY61_SLAM

city: Washington

first: Dzung

last: Thach

state: DC

address: 4555 Overlook Ave SW

department: Center for Biomolecular Science and Engineering

institute: Naval Research Laboratory

description: wildtype diploid yeast strains grown on low nitrogen starved maltose media

hyb_protocol: The cocktail was hybridized onto the GeneChip® Yeast Genome S98 (YG_S98) microarray (Affymetrix) which contains probe sets for 6,400 genes of the S. cerevisiae S288C strain identified in the Saccharomyces Genome Database (SGD) as of December 1998 and 600 additional probe sets for putative open reading frames (ORFs) identified by SAGE analysis, mitochondrial proteins, TY proteins, plasmids, and a small number of ORFs for strains other than S288C. Hybridization was carried out for 16 h at 45 °C with rotation at 60 rpm. The microarrays were then washed and stained using the Affymetrix GeneChip Fluidics Station 450 and scanned using the GeneChip Scanner 3000.

scan_protocol: The microarrays were then washed and stained using the Affymetrix GeneChip Fluidics Station 450 and scanned using the GeneChip Scanner 3000.   GeneChip® Operating Software 1.2 (GCOS 1.2) (Affymetrix) was used to acquire and process array images, determine the quantity and presence or absence of a transcript using the Microarray Suite 5.0 (MAS5) algorithm, and generated the Report files summarizing the quality of target detection for each microarray.

data_processing: Data Acquisition, Integration, and Analysis: GeneChip® Operating Software 1.2 (GCOS 1.2) (Affymetrix) was used to acquire and process array images, determine the quantity and presence or absence of a transcript using the Microarray Suite 5.0 (MAS5) algorithm, and generated the Report files summarizing the quality of target detection for each microarray. We used the RMA (robust multi-chip analysis) transcript quantities because this method improved detection of differentially expressed transcripts compared to the MAS5 algorithm{Irizarry, 2003 #78}. However, MAS5 present and absent calls were still used for the filtering of probe sets. Arraytools 3.3.0 developed by Simon and Lam (http://linus.nci.nih.gov/BRB-ArrayTools.html) was used to calculate RMA (robust multi-chip analysis) transcript quantities, integrate transcript data with experimental information such as yeast mutant strains and growth conditions, and to determine differentially expressed transcripts via ANOVA (analysis of variance) and the random variance model.   JMP software (SAS) was used to join various data sets together, perform statistical quality control, and determined relations among variables. For joining transcript and protein data, probe set identifiers were mapped to SwissProt identifiers via NetAffx {Liu, 2003 #79} and subsequently matched and joined to protein identifiers from mass spectrometry data output by Pro Group{Applied-Biosystems, 2006 #75}. DAVID 2.0{Dennis, 2003 #77} was used to convert Affymetrix probe set identifiers and Pro Group SwissProt protein identifiers to yeast open reading frames (ORFs) or Saccharomyces Genome Database (SGD) identifiers for input into the SGD GO Term Finder tool (http://db.yeastgenome.org/cgi-bin/GO/goTermFinder) to group up-regulated or down-regulated transcripts or proteins into biological processes. The yeast ORFs derived from DAVID 2.0 were also used for input into the Retrieve Sequence (http://rsat.ccb.sickkids.ca/) tool to obtain sequences for promoter analysis. Up-regulated or down-regulated transcripts from each class comparison were input into the promoter analysis tool {Tompa, 2005 #82; van Helden, 2000 #83}. Promoter analysis was performed on -800 to -1 sequence before the start codons of genes expressing differential transcripts. Sequential putative oligomer or dyad sequences were searched against known transcription factor consensus binding sequences using the Search Putative Sites (http://rulai.cshl.edu/SCPD/searchputative.html) and the Search Existing Motif tools (http://rulai.cshl.edu/SCPD/searchmotif.html) from The Promoter Database of S. cerevisiae (http://rulai.cshl.edu/SCPD/). Matches consist of 6 to 8 basepair identity in a transcription factor’s known/consensus binding site.

label_protocol: Target Preparation and Hybridization to Arrays: Eight µg of RNA were concentrated via ethanol precipitation as previously described{Thach, 2003 #81}. All subsequent steps were as described in the GeneChip Expression Analysis Technical Manual version 701021 Rev. 3 (Affymetrix). Briefly, for each sample, the purified, concentrated RNA was reverse-transcribed using a poly-T primer with a T7 RNA-polymerase promoter sequence into double stranded cDNA followed by linear amplification via in vitro transcription (BioArray High Yield IVT kit, ENZO) to yield an antisense cRNA labeled with biotin. The purified biotinylated cRNA was fragmented by magnesium ions and heat and mixed with the hybridization cocktail that contained biotinylated cRNA controls with known concentrations to monitor the quality of the hybridization procedure.

growth_protocol: Yeast strains, media and growth conditions   Diploid strains MLY61 a/alpha (ura3-52/ura3-52 MATa/alpha) and MLY132 a/alpha (delta gpa2::G418/delta gpa2::G418 ura3-52/ura3-52 MATa/alpha) were obtained from J. Heitman, Duke University{Lorenz, 2000 #19; Lorenz, 1997 #33}. Standard YPM media were used as described{Sherman, 1991 #36}. Synthetic low ammonium media consisting of SLAM (0.17% Yeast Nitrogen Base without ammonium sulfate or amino acids, 50 µM ammonium sulfate, 2% maltose) were used when switching to low nitrogen pseudohyphal inducing conditions{Lorenz, 2000 #19; Lorenz, 1997 #33}. Similar to a previously described method{Pan, 2000 #37}, strains were grown to an OD600 of 1.0 in YPM media. Approximately 200 OD600 units were collected by filtering followed by resuspension in 10 mL RNAlater (Ambion) for <30 min, pelleted by centrifugation, flash frozen and stored at –80 °C. Strains were also grown to an OD600 of 1.0 in YPM media and approximately 200 O.D. were collected by filtration and transferred to SLAM media for 2 h at 30 °C prior to collection as above.

extract_protocol: Expression profiling analyses    RNA Isolation: The RibopureTM-Yeast kit (Ambion) was used to extract total RNA from yeast cells. Briefly, for each RNAlater-treated sample, cells were pelleted in a microtube and any remaining RNAlater removed. Then lysis buffer, 10% SDS, and 25:24:1 phenol:chloroform:isoamyl alcohol were used to resuspend the pellet, and the mixture was transferred to a screw cap microtube with Zirconia beads (BioSpec Products) to disrupt the yeast cells by vortexing. The lysate was centrifuged, and the upper aqueous layer transferred to 15 mL conical tubes with Binding Buffer and 100% ethanol. The mixture was drawn through a filter cartridge to capture the RNA, followed by washing and elution. To remove contaminating DNA, 50 µL of the eluted RNA was treated with 10 µL of 10X DNase I buffer and 4 µL of 8 units µL-1 DNase I. The reaction was mixed, incubated at 37 °C for 30 min, followed by addition of 0.1 volume DNase Inactivation Reagent. After 5 min at room temperature, the mixture was spun through a spin column (Qiagen) to remove the DNase binding beads in the DNase Inactivation Reagent. The quality/quantity of purified yeast total RNA was determined by separating 1 µL from each sample on a Bioanalyzer 2100 (Agilent).

tag: wildtype MLY61 transferred to low nitrogen SLAM media


title: 22_MLY61_YPM

description: wildtype diploid yeast strains grown on rich nitrogen maltose media

tag: wildtype MLY61 grown in YPM media


title: placentome 13, term parturition with hydrops phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 13, type: NT, phenotype: hydrops, sex: female, term: term, labeled with Cy5


title: placentome 12, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy5.

source_name: placentome 12, type: IVF, phenotype: normal, sex: male, term: term, labeled with Cy5


title: placentome 7, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 7, type: IVF, phenotype: normal, sex: female, term: term, labeled with Cy3


title: placentome 10, term parturition with hydrops phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 10, type: NT, phenotype: hydrops, sex: female, term: term, labeled with Cy3


title: placentome 2, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 2, type: NT, phenotype: normal, sex: female, term: term, labeled with Cy5


title: 18_MLY61_YPM


title: placentome 5, preterm parturition with normal phenotype; male calf.  cDNA labeled with dye Cy3.

source_name: placentome 5, type: AI, phenotype: normal, sex: male, term: preterm, labeled with Cy3


title: placentome 2, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 2, type: NT, phenotype: normal, sex: female, term: term, labeled with Cy3


title: placentome 5, preterm parturition with normal phenotype; male calf.  cDNA labeled with dye Cy5.

source_name: placentome 5, type: AI, phenotype: normal, sex: male, term: preterm, labeled with Cy5


title: placentome 4, preterm parturition with normal phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: reference standard RNA, labeled with Cy5

source_name: placentome 4, type: IVF, phenotype: normal, sex: female, term: preterm, labeled with Cy3


title: placentome 12, term parturition with normal phenotype; male calf.  cDNA labeled with dye Cy3.

source_name: placentome 12, type: IVF, phenotype: normal, sex: male, term: term, labeled with Cy3


title: placentome 1, preterm parturition with hydrops phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 1, type: NT, phenotype: hydrops, sex: female, term: preterm, labeled with Cy5


title: placentome 1, preterm parturition with hydrops phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 1, type: NT, phenotype: hydrops, sex: female, term: preterm, labeled with Cy3


title: placentome 3, preterm parturition with hydrops phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 3, type: NT, phenotype: hydrops, sex: female, term: preterm, labeled with Cy3


title: placentome 6, preterm parturition with hydrops phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 6, type: NT, phenotype: hydrops, sex: female, term: preterm, labeled with Cy5


title: 24_MLY61_SLAM


title: placentome 3, preterm parturition with hydrops phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 3, type: NT, phenotype: hydrops, sex: female, term: preterm, labeled with Cy5

source_name: reference standard RNA, labeled with Cy3


title: placentome 6, preterm parturition with hydrops phenotype; female calf.  cDNA labeled with dye Cy3.

source_name: placentome 6, type: NT, phenotype: hydrops, sex: female, term: preterm, labeled with Cy3


title: 16_MLY61_SLAM


title: Rat070216_GENonIMCD_3

first: Panapat

last: Uawithya

address: 9000 Rockville pike Bldg 10 Rm 6N306

department: NHLBI

institute: NIH

description: profiling of gene expression in inner medulla collecting duct cell of rat

hyb_protocol: Labeled cRNA were hybridized to Rat 230 2.0 Array in Affymetrix Hybridization Oven 640 and washed in GeneChip® Fluidics Station 450 according to the manufacturer's recomended protocols.

scan_protocol: Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recomended protocols

data_processing: Affymetrix default parameters

source_name: Inner Medulla, non collecting duct cells  of rat

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocols.

extract_protocol: Total RNA were extracted by using Trizol reagent according to manufacturer's protocols.

treatment_protocol: Rats were injected with 1mg furosemide intraperitoneum 30 minutes before decapitation. Inner Medulla were excised and digested with collagenase B and hyarulonidase for 75 minutes at 37 degree celcius.

value: Sprague-Dawley

tag: Sex

value: Male

tag: Age

value: 10 weeks old

tag: Tissue

value: inner medulla, non collecting duct cells


title: placentome 4, preterm parturition with normal phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 4, type: IVF, phenotype: normal, sex: female, term: preterm, labeled with Cy5


title: 12_MLY132_SLAM

description: Gpa2p deficient diploid yeast strains grown on low nitrogen starved maltose media

tag: gpa2 deletion mutant MLY132 transferred to low nitrogen SLAM media


title: 14_MLY61_YPM


title: Rat070216_GENonIMCD_2

source_name: Inner medulla non collecting duct cells of rat


title: PTX 48H B

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

description: cDNA CNIO Oncochip Array

data_processing: GenePix 6.0

source_name: MCF7 + paclitaxel 48h

tag: MCF7 + paclitaxel 100 nM 48h

source_name: Universal Human Reference RNA

tag: Reference RNA


title: 04_MLY132_SLAM


title: 08_MLY132_SLAM


title: 06_MLY132_YPM

description: Gpa2p deficient diploid yeast strains grown on rich nitrogen maltose media

tag: gpa2 deletion mutant MLY132 grown in YPM media


title: Rat070216_GENonIMCD_1

value: Inner medulla, non collecting duct cells


title: PTX 8H A

description: cDNA CNIO Oncochip Array

data_processing: GenePix 6.0 - log2 ratio

source_name: MCF7 + paclitaxel 8h

tag: MCF7 + paclitaxel 100 nM 8h


title: PTX 8H B

description: cDNA CNIO Oncochip Array

tag: paclitaxel 100 nM 8h

source_name: Universal Human Reference Pool


title: Rat070216_GEIMCD_2

source_name: inner medulla collecting duct cells of rat

tag: Strain

value: inner medulla collecting duct cells


title: Rat070216_GEIMCD_3

source_name: Inner medulla collecting duct cells of rat


title: Rat070216_GEIMCD_1

value: 6 Weeks old


title: placentome 7, term parturition with normal phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 7, type: IVF, phenotype: normal, sex: female, term: term, labeled with Cy5


title: PTX 48H A

description: cDNA CNIO Oncochip Array

tag: MCF7 cells + paclitaxel 100 nM 48h


title: Control A

description: cDNA CNIO Oncochip Array

source_name: MCF7 control

tag: MCF7 breast adenocarcinoma cells

tag: RNA Reference Pool


title: 02_MLY132_YPM

tag: gpa2 deletion mutant MYL132 grown in YPM media


title: Control B

description: cDNA CNIO Oncochip Array

source_name: MCF7 Control

tag: MCF7 Control cells


title: Glucocorticoid receptor isoform D treated for 24 hr, replicate 3

status: Public on Dec 20 2007

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: U-2 OS cells were transfected with the BD Clontech pTET-OFF regulatory plasmid to establish the U-OFF parental cell line. MluI and EcoRV ends were generated onto the coding region of hGR-alpha, -A, -B, -C, or -D using PCR amplification of the pCMVhGR-alpha or -A plasmid. The pTRE2hyg vector was digested with MluI and EcoRV and the two DNAs were ligated to form the pTRE2hGR-alpha,-A, -B, -C, or -D plasmid (Lu and Cidlowski). Each DNA construct was individually transfected into the U-OFF cells and clones were selected which stably expressed either hGR-alpha, -A, -B, -C, or -D using 200 microg/ml of geneticin and 500 mircorg/ml of hygromycin. Several clones were obtained for each receptor, and the receptor levels were compared using western blot analyses. In these cell lines, the expression of hGR can be repressed by the addition of tetracycline or the derivative doxycycline to the media. U-2 OS (human osteosarcoma) cells were maintained in DMEM/F-12 supplemented with 10% FCS:CS, 2 mM glutamine and pen-strep and selected clones were maintained in the same media with the addition of 200 microg/ml Geneticin and 200 mircrog/ml hygromycin. All cells were maintained in a humidified, 5% CO2 atmosphere.

hyb_protocol: For each sample, 1.5ug of Cy3 labeled cRNAs were fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven at 65 degrees at 4 RPM.

scan_protocol: Slides were washed with 6X SSPE + 0.005% N-lauroyl sarcosine for 1 minute then 0.06X SSPE + 0.005% N-lauroyl sracosine for 1 minute at 37 degrees.  The slides were dried by slowly removing from second wash solution and then scanned with an Agilent G2565 Scanner (10micron and with XDR) and processed with Agilent Feature Extraction v9.1.

data_processing: The resulting files were imported into the Rosetta Resolver system (Version 6.0).  This system performs data pre-processing and error modeling.  Resolver generated log2 intensities were saved and exported.  In addition, Resolver generated fold-changes and p values, based on ratios built in the system, were exported for further analysis.

source_name: U-2 OS cells expressing glucocorticoid receptor isoform D

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer's protocol.

growth_protocol: Cells were grown in DMEM-F12 medium, supplemented with 10% Fetal Bovine Serum.

extract_protocol: The RNeasy RNA extraction kit, with on column DNAse digestion (Qiagen) was used, according to manufacturer's protocol.

treatment_protocol: Cells were treated with 100 nM dexamethasone for 24 hr.

tag: Human osteosarcoma, female


title: 10_MLY132_YPM


title: Glucocorticoid receptor isoform D treated for 24 hr, replicate 1


title: Glucocorticoid receptor isoform C treated for 24 hr, replicate 2

source_name: U-2 OS cells expressing glucocorticoid receptor isoform C


title: Glucocorticoid receptor isoform B treated for 24 hr, replicate 1

source_name: U-2 OS cells expressing glucocorticoid receptor isoform B


title: Glucocorticoid receptor isoform C treated for 24 hr, replicate 3


title: Glucocorticoid receptor isoform alpha treated for 24 hr, replicate 2

source_name: U-2 OS cells expressing glucocorticoid receptor isoform alpha


title: Glucocorticoid receptor isoform B treated for 24 hr, replicate 2


title: Glucocorticoid receptor isoform D treated for 12 hr, replicate 1

treatment_protocol: Cells were treated with 100 nM dexamethasone for 12 hr.


title: Glucocorticoid receptor isoform alpha treated for 24 hr, replicate 3


title: Glucocorticoid receptor isoform A treated for 24 hr, replicate 3

source_name: U-2 OS cells expressing glucocorticoid receptor isoform A


title: placentome 10, term parturition with hydrops phenotype; female calf.  cDNA labeled with dye Cy5.

source_name: placentome 10, type: NT, phenotype: hydrops, sex: female, term: term, labeled with Cy5

tag: placentome total RNA was isolated by Trizol

source_name: reference standard RNA, labeled with Cy3

tag: reference total RNA was isolated by Trizol and consists of equal amounts total RNA extracted from EBTr, MDBK, and BL30 cell lines, and brain tissue


title: Glucocorticoid receptor isoform A treated for 24 hr, replicate 1


title: Glucocorticoid receptor isoform C treated for 24 hr, replicate 1


title: Glucocorticoid receptor isoform A treated for 24 hr, replicate 2


title: Glucocorticoid receptor isoform alpha treated for 24 hr, replicate 1


title: Glucocorticoid receptor isoform D treated for 12 hr, replicate 2


title: Glucocorticoid receptor isoform D treated for 12 hr, replicate 3


title: Glucocorticoid receptor isoform B treated for 12 hr, replicate 3


title: Glucocorticoid receptor isoform D treated for 24 hr, replicate 2


title: Glucocorticoid receptor isoform B treated for 24 hr, replicate 3


title: Glucocorticoid receptor isoform C treated for 12 hr, replicate 2


title: Glucocorticoid receptor isoform B treated for 12 hr, replicate 1


title: Glucocorticoid receptor isoform A treated for 12 hr, replicate 3


title: Glucocorticoid receptor isoform B treated for 12 hr, replicate 2


title: Glucocorticoid receptor isoform C treated for 12 hr, replicate 3


title: Glucocorticoid receptor isoform A treated for 12 hr, replicate 1


title: Glucocorticoid receptor isoform alpha treated for 12 hr, replicate 1


title: Glucocorticoid receptor isoform C treated for 12 hr, replicate 1


title: Glucocorticoid receptor isoform A treated for 12 hr, replicate 2


title: Glucocorticoid receptor isoform D treated for 6 hr, replicate 3

treatment_protocol: Cells were treated with 100 nM dexamethasone for 6 hr.


title: Glucocorticoid receptor isoform alpha treated for 12 hr, replicate 2


title: Glucocorticoid receptor isoform C treated for 6 hr, replicate 3


title: Glucocorticoid receptor isoform B treated for 6 hr, replicate 3


title: Glucocorticoid receptor isoform D treated for 6 hr, replicate 1


title: Glucocorticoid receptor isoform alpha treated for 12 hr, replicate 3


title: Glucocorticoid receptor isoform C treated for 6 hr, replicate 2


title: Glucocorticoid receptor isoform B treated for 6 hr, replicate 1


title: Glucocorticoid receptor isoform B treated for 6 hr, replicate 2


title: Glucocorticoid receptor isoform C treated for 6 hr, replicate 1


title: Glucocorticoid receptor isoform alpha treated for 6 hr, replicate 3


title: Glucocorticoid receptor isoform A treated for 6 hr, replicate 3


title: Glucocorticoid receptor isoform alpha treated for 6 hr, replicate 2


title: DNAse treated CD4+ T-cells on Solexa

type: genomic

first: Sean

last: Davis

address: 37 Convent Drive, Room 6138

description: CD4+ T-cells treated with DNAse and then subjected to high-throuput sequencing

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: Sequences were read and raw counts reported.  Alignments to build 35 are reported for unique matches only.

label: not applicable

molecule: genomic DNA

source_name: CD4+ T-cells, DNAse Treated

label_protocol: not applicable

extract_protocol: Intact nuclei from primary human CD4+ T cells were prepared and digested with DNaseI, and prepared for Dnase-seq as previously described (Crawford et al., 2006a; Crawford et al., 2004; Crawford et al., 2006b).

tag: Treatment

value: DNAse;Tissue:CD4+ T-cells


title: SK0019-003_StyI

city: Toronto

first: Christian

middle: R.

last: Marshall

state: ON

address: 101 College St.

department: Genetics & Genome Biology

country: Canada

institute: The Hospital for Sick Children

description: SNP data from proband with abnormal karyotype

hyb_protocol: Following fragmentation, 90 ug of genomic DNA were hybridized for 16 hr at 49C on either the GeneChip® Mapping NspI or StyI chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were processed using GCOS software. Genotypes were analyzed with GTYPE using Affymetrix defaults.

source_name: lymphoblast or blood

label_protocol: Biotinylated genomic DNA were prepared according to the standard Affymetrix protocol from 90 ug PCR product (GeneChip® Mapping 500K Assay Manual, 2005, Affymetrix).

growth_protocol: Not Applicable

extract_protocol: DNA was extracted from blood or lymphoblast using a standard phenol/chloroform method. 500ng of genomic DNA was used for subsequent PCR complexity reduction (GeneChip® Mapping 500K Assay Manual, 2005, Affymetrix)

treatment_protocol: Not Applicable

tag: Family ID

tag: DNA ID

tag: Gender

value: M

tag: Family Type

value: SPX

tag: Individual Type

value: proband


title: Glucocorticoid receptor isoform D treated for 0 hr, replicate 3

treatment_protocol: Cells were not treated.


title: Glucocorticoid receptor isoform alpha treated for 6 hr, replicate 1


title: Glucocorticoid receptor isoform C treated for 0 hr, replicate 2


title: SK0019-003_NspI


title: Glucocorticoid receptor isoform A treated for 6 hr, replicate 1


title: Glucocorticoid receptor isoform D treated for 0 hr, replicate 1


title: Glucocorticoid receptor isoform A treated for 6 hr, replicate 2


title: Glucocorticoid receptor isoform B treated for 0 hr, replicate 3


title: Glucocorticoid receptor isoform B treated for 0 hr, replicate 2


title: Glucocorticoid receptor isoform C treated for 0 hr, replicate 3


title: Glucocorticoid receptor isoform A treated for 0 hr, replicate 3


title: Glucocorticoid receptor isoform D treated for 0 hr, replicate 2


title: Glucocorticoid receptor isoform A treated for 0 hr, replicate 1


title: Glucocorticoid receptor isoform B treated for 0 hr, replicate 1


title: Glucocorticoid receptor isoform C treated for 0 hr, replicate 1


title: Glucocorticoid receptor isoform D treated for 6 hr, replicate 2


title: Glucocorticoid receptor isoform alpha treated for 0 hr, replicate 2


title: Glucocorticoid receptor isoform alpha treated for 0 hr, replicate 3


title: PCR_ovoid_2_4

city: Jouy en Josas

first: Isabelle

last: Hue

address: Domaine de Vilvert

department: PHASE

institute: INRA

description: amplification mode=PCR  biological material=ovoid embryo  target replicate=2  array replicate=4.  As advised by N'Guyen (1995), we first determined the amount of labelled target to be used for each hybridisation so that no additional signal appeared but the intensity of the positive signals increased when the amount of target did. (50, 125, 250 and 500ng for aRNA or cDNA labelled targets). On this basis, 125ng of each target has been hybridised to each array.

hyb_protocol: Prehybridisation in ExpressHybTM Hybridization Solution (Clontech) at 68°C during 1h (14ml). Hybridisation using new ExpressHybTM Hybridization Solution (Clontech) at 68°C overnight (10ml). Arrays were washed four times in 2X SSC, 1% SDS and once in 0.1X SSC, 0.5% SDS at 68°C for 30 min each. They were then exposed to phosphor-screens (Amersham) for 7 days.

scan_protocol: Scanner: STORM 760 from Molecular Dynamics. Raw data set : Feature extraction with Imagene 5.1 software from BioDiscovery (Proteigene)

data_processing: Intensity: Signal Mean, Normalization: Signal mean were log2 transformed and normalized by the mean of the all intensities on the array. For the statistical analyses described on the paper, the mean of the 4 array_replicates was done for each target_replicate and the data was standardized by gene. Furthermore, for the valid spots analysis, we consider the Flag column from Imagene 5.1 Software (flag=0 corresponds to a valid signal compare to his own local background whereas flag=2 corresponds to an non valid signal, ie: background>Signal Mean)

source_name: Embryonic tissues immediately snap-frozen. Total RNA extracted with RNA-PlusTM (QBioGene). RNA quality verified by intact ribosomal bands on a 1% agarose gel (28S and 18S) and A260/280 absorbance ratios.

label_protocol: aRNA was retro-transcribed and directly labelled with [alpha-33P]dATP as described for polyA+RNA (Decraene, 1999). 500ng of aRNA was mixed with 500ng of random hexamers in a volume of 25µl. The mixture was incubated at 70°C for 10 min and chilled on ice. cDNA was synthesised by the addition of 5µl 10X PCR buffer, 5µl 25mM MgCl2, 5µl 0,1 mM DTT, 2,5µl 10mM mix dGTP, dCTP and dTTP, 2,5µl water, 50µCi [alpha-33P]dATP and 200U Superscript II (Invitrogen) at 42°C for 50min. The RNA template was removed by the addition of 1µl RNAse H- and incubation at 37°C for 20 min. PCR-amplified cDNA was labelled with [alpha-33P]dATP using random hexamers and Klenow included in Atlas SMART Probe Amplification kit (Clontech). 500ng of amplified cDNA was mixed with 500ng random hexamers in a volume of 34µl. The mixture was incubated at 98°C for 8 min and at 50°C for 3 min. After addition of 5µl 10X buffer, 5µl dNTPs for ATP label, 5µl [alpha-33P]dATP and 1µl Klenow, the reaction mixture was incubated at 50°C for 30 min and stopped with 2µl 0,5M EDTA. Labelled targets were then purified on Sephadex columns (G-50).

extract_protocol: IVT amplified RNA from each sample was synthesized with the MessageAmpTM aRNA Kit (Ambion) according to the manufacturer instructions (RT on 1µg total RNA, IVT during 10h). aRNA was purified on Mini Quick Spin RNA columns (Roche Diagnostic) and its quality verified on RNA 6000 lab-chips (BioAnalyser 2100; Agilent Technologies). PCR amplified cDNA was prepared as described (Revel, 1995; Pacheco-Trigon, 2002) with few modifications. Briefly, 1µg total RNA was incubated with 1µl 10µM oligo(dT), 1µl 10 mM dNTPs, 1µl 10% NP40, 1µl 20mM DTT, 2µl first-strand buffer 5X, 1µl RNAse inhibitor (Ambion) at 65°C for 2 min, at room temperature for 3 min and cooled on ice. cDNA was synthesised by the addition of 200U Superscript II (Invitrogen) and 2U AMV (Gibco BRL) and incubation at 42°C for 30 min. First-strand cDNA were poly(dG)-tailed by incubation with 1µl 20mM dGTP, 4µl TdT buffer 5x, 2,5µl water, 2,5µl TdT enzyme (Promega) at 37°C for 1h. The first PCR was performed in a volume of 50µl using 1/10 of the RT and the secondPCR was performed on 1/4 of the first PCR. Samples were incubated at 94°C for 10min before the two rounds of PCR cycles (12 cycles each; 94°C for 2 min, 63°C for 50 sec and 72°C for 6 min). PCR products were then purified using Qiaquick PCR purification (Qiagen) and their quality verified on DNA 7500 lab-chips (BioAnalyser 2100; Agilent Technologies).

treatment_protocol: Tissues were collected and immediately snap-frozen. Total RNA from ovoid (n=4), tubular (n=4) and filamentous (n=4) embryos was extracted with RNA-PlusTM (QBioGene). RNA quality was first verified by intact ribosomal bands on a 1% agarose gel (28S and 18S) and A260/280 absorbance ratios.

tag: Day of pregnancy

tag: Somatic tissue

value: no

tag: Embryo

value: yes

tag: Additional data

value: Embryo (or blastocyst) size:1 to 12 mm (ovoid stage), 50-60 mm (tubular stage), 140-160 mm (filamentous early stage). Pregnant cows from Charolais breed. Animals humanly put down in accredited experimental slaughterhouse of INRA under the supervision of veterinary services.


title: PCR_ovoid_1_2

description: amplification mode=PCR  biological material=ovoid embryo  target replicate=1  array replicate=2.  As advised by N'Guyen (1995), we first determined the amount of labelled target to be used for each hybridisation so that no additional signal appeared but the intensity of the positive signals increased when the amount of target did. (50, 125, 250 and 500ng for aRNA or cDNA labelled targets). On this basis, 125ng of each target has been hybridised to each array.


title: PCR_ovoid_1_4

description: amplification mode=PCR  biological material=ovoid embryo  target replicate=1  array replicate=4.  As advised by N'Guyen (1995), we first determined the amount of labelled target to be used for each hybridisation so that no additional signal appeared but the intensity of the positive signals increased when the amount of target did. (50, 125, 250 and 500ng for aRNA or cDNA labelled targets). On this basis, 125ng of each target has been hybridised to each array.


title: PCR_ovary_3_1

description: amplification mode=PCR  biological material=ovary  target replicate=3  array replicate=1.  As advised by N'Guyen (1995), we first determined the amount of labelled target to be used for each hybridisation so that no additional signal appeared but the intensity of the positive signals increased when the amount of target did. (50, 125, 250 and 500ng for aRNA or cDNA labelled targets). On this basis, 125ng of each target has been hybridised to each array.

source_name: Ovary pieces immediately snap-frozen. Total RNA extracted with RNA-PlusTM (QBioGene). RNA quality  verified by intact ribosomal bands on a 1% agarose gel (28S and 18S) and A260/280 absorbance ratios.


title: DNAse treated CD4+ T-cells on 454 sequencer

data_processing: Sequences were read and raw counts reported.


title: IVT_ovoid_2_2

description: amplification mode=IVT  biological material=ovoid embryo  target replicate=2  array replicate=2.  As advised by N'Guyen (1995), we first determined the amount of labelled target to be used for each hybridisation so that no additional signal appeared but the intensity of the positive signals increased when the amount of target did. (50, 125, 250 and 500ng for aRNA or cDNA labelled targets). On this basis, 125ng of each target has been hybridised to each array.


title: IVT_tubular_2_1

description: amplification mode=IVT  biological material=tubular embryo  target replicate=2  array replicate=1.  As advised by N'Guyen (1995), we first determined the amount of labelled target to be used for each hybridisation so that no additional signal appeared but the intensity of the positive signals increased when the amount of target did. (50, 125, 250 and 500ng for aRNA or cDNA labelled targets). On this basis, 125ng of each target has been hybridised to each array.


title: Glucocorticoid receptor isoform alpha treated for 0 hr, replicate 1


title: PCR_ovoid_2_1

description: amplification mode=PCR  biological material=ovoid embryo  target replicate=2  array replicate=1.  As advised by N'Guyen (1995), we first determined the amount of labelled target to be used for each hybridisation so that no additional signal appeared but the intensity of the positive signals increased when the amount of target did. (50, 125, 250 and 500ng for aRNA or cDNA labelled targets). On this basis, 125ng of each target has been hybridised to each array.


title: PCR_tubular_1_2

description: amplification mode=PCR  biological material=tubular embryo  target replicate=1  array replicate=2.  As advised by N'Guyen (1995), we first determined the amount of labelled target to be used for each hybridisation so that no additional signal appeared but the intensity of the positive signals increased when the amount of target did. (50, 125, 250 and 500ng for aRNA or cDNA labelled targets). On this basis, 125ng of each target has been hybridised to each array.


title: PCR_ovoid_2_3

description: amplification mode=PCR  biological material=ovoid embryo  target replicate=2  array replicate=3.  As advised by N'Guyen (1995), we first determined the amount of labelled target to be used for each hybridisation so that no additional signal appeared but the intensity of the positive signals increased when the amount of target did. (50, 125, 250 and 500ng for aRNA or cDNA labelled targets). On this basis, 125ng of each target has been hybridised to each array.


title: Glucocorticoid receptor isoform A treated for 0 hr, replicate 2


title: PCR_ovary_1_3

description: amplification mode=PCR  biological material=ovary  target replicate=1  array replicate=3.  As advised by N'Guyen (1995), we first determined the amount of labelled target to be used for each hybridisation so that no additional signal appeared but the intensity of the positive signals increased when the amount of target did. (50, 125, 250 and 500ng for aRNA or cDNA labelled targets). On this basis, 125ng of each target has been hybridised to each array.


title: PCR_filamentous_2_1

description: amplification mode=PCR  biological material=filamentous embryo  target replicate=2  array replicate=1.  As advised by N'Guyen (1995), we first determined the amount of labelled target to be used for each hybridisation so that no additional signal appeared but the intensity of the positive signals increased when the amount of target did. (50, 125, 250 and 500ng for aRNA or cDNA labelled targets). On this basis, 125ng of each target has been hybridised to each array.

source_name: Embryonic tissues immediately snap-frozen. Total RNA extracted with RNA-PlusTM (QBioGene). RNA quality verified by intact ribosomal bands on a 1% agarose gel (28S and 18S) and A260/280 absorbance ratios


title: PCR_tubular_1_1

description: amplification mode=PCR  biological material=tubular embryo  target replicate=1  array replicate=1.  As advised by N'Guyen (1995), we first determined the amount of labelled target to be used for each hybridisation so that no additional signal appeared but the intensity of the positive signals increased when the amount of target did. (50, 125, 250 and 500ng for aRNA or cDNA labelled targets). On this basis, 125ng of each target has been hybridised to each array.


title: PCR_tubular_2_3

description: amplification mode=PCR  biological material=tubular embryo  target replicate=2  array replicate=3.  As advised by N'Guyen (1995), we first determined the amount of labelled target to be used for each hybridisation so that no additional signal appeared but the intensity of the positive signals increased when the amount of target did. (50, 125, 250 and 500ng for aRNA or cDNA labelled targets). On this basis, 125ng of each target has been hybridised to each array.