title: Hapatic_5715

description:
Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59464.gif; format: GIF

source_name: Amplified universal human reference

tag: Amplified universal human reference

source_name: clonetic cells Hepatic fibroblasts #5715


title: DTG_heart_on2w/off2d_rep4_chip430A

status: Public on Aug 25 2006

type: RNA

city: Boston

first: Stephan

last: Schiekofer

state: MA

address: 700 Albany Street, W611

department: Molecular Cardiology

country: USA

institute: Boston University School of Medicine

description: heart tissue from Tet-myrAkt1/?MHC-tTA mice after 2 weeks of Akt induction followed by 2 days of Akt repression

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: heart tissue

label_protocol: standard Affymetrix procedures

extract_protocol: Ultraspec(TM)-II RNA Isolation System

tag: Strain

value: Tet-myrAkt1/?MHC-tTA, Gender:male, Age:14 weeks + 2 days, Tissue:heart tissue


title: Lung_6114

city: Stanford

first: Howard

last: Chang

state: CA

address: CCSR 2142

department: Dermatology

institute: Stanford University

description:
Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59465.gif; format: GIF

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Homo sapiens

source_name: clonetic cells Lung fibroblasts #6114

tag: clonetic cells Lung fibroblasts #6114


title: Wild type murine bone marrow-derived macrophages stimulated with LPS (100 ng/ml) and IL-10 (10 ng/ml), biol. rep2 T180

city: Memphis

first: Peter

middle: J

last: Murray

state: TN

address: 332 Nth Lauderdale

department: Infectious Diseases

institute: St. Jude Children's Research Hospital

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: BMDMs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: BMDMs differentiated from bone marrow in mCSF (CSF-1).  Samples grown fro 7 days and rested in complete DMEM for 1 hr prior to Trizol processing

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

treatment_protocol: LPS+IL-10 180 minutes

tag: Time point 180 minutes post-stimulation


title: KAX3_bio2_tc1_hour12

city: Houston

first: Ezgi

last: Booth

state: TX

address: S430, One Baylor Plaza

institute: Baylor College of Medicine

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with KAX3 strain from 12 hrs of development labeled with Cy5.

hyb_protocol: Labeled cDNA in PerfectHybTM Plus Hybridization buffer (SIGMA H-7033) was hybridized to the arrays after heat treatment (95°C, 2 min) using a GeneTAC hybridization station (Genomic Solutions) according to the manufacturer's recommended protocol as indicated below.Labeled cDNA was hybridized to the arrays using a GeneTAC automatic hybridization station (Genomic Solutions) for 2 hours at 65°C. Arrays were sequentially washed with 3 solutions, 2x SSC, 0.5% SDS; 0.5x SSC, 0.5% SDS; 0.1x SSC, for 30 sec at room temperature twice each.

scan_protocol: The arrays were scanned with a ScanArrayLite scanner (Perkin Elmer) according to the manufacturer's recommended protocol. PMT and Laser settings were not recorded.All images were processed with the ImaGene software package (BioDiscovery, Inc.).

data_processing: After quantiation the normalization is implemented in 6 distinct steps: thresholding, quantile adjustment of single channel values, bias adjustment, averaging of on-chip replicates, by-signal-size variance estimation and scaling of the final values using the estimated by-signal-size variance. For more details see Van Driessche, et al.(2005). "Epistasis analysis with global transcriptional phenotypes" Nat Genet 37(5):471-7.

organism: Dictyostelium discoideum

source_name: Dictyostelium discoideum_KAX3

label_protocol: Total RNA (10 µg) was mixed with 1 µg of labeled [dT(18)] primer in 13 µl of water, incubated at 70°C for 10 minutes and on ice for 2-5 minutes. Reaction buffer (Gibco-BRL), 0.1M DTT, 0.5 mM of each dNTP and 200U Superscript II (Gibco-BRL) were added and the reaction was incubated at 42°C for 2 hours. Experimental RNA samples were labeled with Alexa 647 primers and the reference RNA sample was labeled with Cy3. Both of the primers were HPLC-purified by the manufacturer (Operon Technologies). Reverse transcription reactions were terminated with 0.1M EDTA. RNA was degraded by adding 0.3 N NaOH and incubating at 60°C for 20 minutes. The reaction was neutralized with 0.4 M Tris.HCl pH7.6. Labeled cDNA was purified by ethanol precipitation, resuspended in 10 µl of DDW and mixed with 130 µl of PerfectHybTM Plus Hybridization buffer (SIGMA H-7033).

extract_protocol: RNA samples prepared from developing KAX3 cells at 12 hr using TRIZOL(Invitrogen)

tag: 'strain:AX4', 'development:filter','biological replication:2','technical replication:1','time point:12 hr'

extract_protocol: RNA samples prepared from vegetative wild type cells and from 6 developmental times (0, 3, 6, 12, 17, 24 hours) using TRIZOL(Invitrogen)

tag: 'strain:AX4', 'development:filter','biological replication:2','technical replication:1','time point:0, 3, 6, 12, 17, 24 hr'


title: Wild type murine bone marrow-derived macrophages stimulated with LPS (100 ng/ml) and IL-10 (10 ng/ml), biol. rep1 T180


title: KAX3_bio2_tc1_hour18

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with KAX3 strain from 18 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing KAX3 cells at 18 hr collected using TRIZOL(Invitrogen)

tag: 'strain:KAX3', 'development:filter','biological replication:2','technical replication:1','time point:18  hr'


title: smkA_bio1_tc2_hour12

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with smkA- strain from 12 hrs of development labeled with Cy5.

source_name: Dictyostelium discoideum_smkA-

extract_protocol: RNA samples prepared from developing smkA- cells at 12 hr using TRIZOL(Invitrogen)

tag: 'strain:smkA-'development:filter','biological replication:1','technical replication:2','time point:12 hr'

tag: 'strain:AX4', 'development:filter','biological replication:1','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: KAX3_bio2_tc2_hour18

extract_protocol: RNA samples prepared from developing KAX3 cells at 18 hr using TRIZOL(Invitrogen)

tag: 'strain:KAX3', 'development:filter','biological replication:2','technical replication:2','time point:18 hr'

tag: 'strain:AX4', 'development:filter','biological replication:2','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: DTG_heart_on2w/off2d_rep3_chip430A


title: DTG_heart_on2w/off2d_rep2_chip430A


title: DTG_heart_on6w_rep2_chip430A

description: heart tissue from Tet-myrAkt1/?MHC-tTA mice after 6 weeks of Akt induction

value: Tet-myrAkt1/?MHC-tTA, Gender:male, Age:18 weeks, Tissue:heart tissue


title: KAX3_bio2_tc1_hour6

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with KAX3 strain from 6 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing KAX3 cells at 6 hr using TRIZOL(Invitrogen)

tag: 'strain:KAX3', 'development:filter','biological replication:2','technical replication:1','time point:6 hr'


title: KAX3_bio2_tc1_hour0

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with KAX3 strain from 0 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing KAX3 at 0 hr using TRIZOL(Invitrogen)

tag: 'strain:KAX3', 'development:filter','biological replication:2','technical replication:1','time point:0 hr'

tag: 'strain:AX4', 'development:filter','biological replication:1','technical replication:1','time point:0, 3, 6, 12, 17, 24 hr'


title: DTG_heart_on2w/off2d_rep1_chip430A


title: Wild type murine bone marrow-derived macrophages stimulated with LPS (100 ng/ml) and IL-10 (10 ng/ml), biol. rep1 T45

treatment_protocol: LPS 45 minutes

tag: Time point 45 minutes post-stimulation


title: KAX3_bio1_tc2_hour18

tag: 'strain:KAX3', 'development:filter','biological replication:1','technical replication:2','time point:18 hr'


title: 100-54_D_wrist

description:
Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59462.gif; format: GIF

source_name: L forearm, dorsal, wrist

tag: L forearm, dorsal, wrist


title: 4938_skeletal_muscle

description:
Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59461.gif; format: GIF

tag: Amplified universal human reference

source_name: 4938_skeletal_muscle clonetic cells

tag: 4938_skeletal_muscle clonetic cells


title: Lung_6122

description:
Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59463.gif; format: GIF

source_name: clonetic cells lung fibroblasts #6122

tag: clonetic cells lung fibroblasts #6122


title: DTG_heart_on2w_rep4_chip430A

description: heart tissue from Tet-myrAkt1/?MHC-tTA mice after 2 weeks of Akt induction

tag: Strain

value: Tet-myrAkt1/?MHC-tTA, Gender:male, Age:14 weeks, Tissue:heart tissue


title: DTG_heart_on2w_rep3_chip430A


title: KAX3_bio1_tc2_hour12

tag: 'strain:KAX3', 'development:filter','biological replication:1','technical replication:2','time point:12 hr'


title: 100-52_D_Elbow

description:
Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59460.gif; format: GIF

source_name: 100-52 L forearm, dorsal, elbow

tag: 100-52 L forearm, dorsal, elbow


title: Wild type murine bone marrow-derived macrophages stimulated with LPS (100 ng/ml) and IL-10 (10 ng/ml), biol. rep2 T45


title: KAX3_bio1_tc2_hour6

tag: 'strain:KAX3', 'development:filter','biological replication:1','technical replication:2','time point:6 hr'


title: Wild type murine bone marrow-derived macrophages stimulated with LPS (100 ng/ml), biol. rep2	T45


title: Mek_bio2_tc1_hour6

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with Mek1- strain from 6 hrs of development labeled with Cy5.

source_name: Dictyostelium discoideum_Mek1-

extract_protocol: RNA samples prepared from developing Mek1- cells at 6 hr using TRIZOL(Invitrogen)

tag: strain:Mek1-', 'development:filter','biological replication:2','technical replication:1','time point:6 hr'

tag: 'strain:AX4', 'development:filter','biological replication:2','technical replication:1','time point:0, 3, 6, 12, 17, 24 hr'


title: KAX3_bio1_tc2_hour0

tag: 'strain:KAX3', 'development:filter','biological replication:1','technical replication:2','time point:0 hr'

tag: 'strain:AX4', 'development:filter','biological replication:1','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: S97.8_D4digit

description:
Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59710.gif; format: GIF

source_name: Amplified Universal Human Reference messge amp II

source_name: Total RNA from S97.8 fibroblasts dorsal 4th digit


title: Wild type murine bone marrow-derived macrophages stimulated with LPS (100 ng/ml), biol. rep1	T45


title: KAX3_bio1_tc1_hour18

hyb_protocol: Labeled cDNA in PerfectHybTM Plus Hybridization buffer (SIGMA H-7033) was hybridized to the arrays after heat treatment (95°C, 2 min) using a GeneTAC hybridization station (Genomic Solutions) according to the manufacturer's recommended protocol as indicated below.Labeled cDNA was hybridized to the arrays using a GeneTAC automatic hybridization station (Genomic Solutions) for 2 hours at 65C.  Arrays were sequentially washed with 3 solutions, 2x SSC, 0.5% SDS; 0.5x SSC, 0.5% SDS; 0.1x SSC, for 30 sec at room temperature twice each.

scan_protocol: The arrays were scanned with a ScanArrayLite scanner (Perkin Elmer) according to the manufacturer's recommended protocol.  PMT and Laser settings were not recorded.All images were processed with the ImaGene software package (BioDiscovery, Inc.).

label_protocol: Total RNA (10 µg) was mixed with 1 µg of labeled [dT(18)] primer in 13 µl of water, incubated at 70°C for 10 minutes and on ice for 2-5 minutes.  Reaction buffer (Gibco-BRL), 0.1M DTT, 0.5 mM of each dNTP and 200U Superscript II (Gibco-BRL) were added and the reaction was incubated at 42°C for 2 hours.  Experimental RNA samples were labeled with Alexa 647 primers and the reference RNA sample was labeled with Cy3.  Both of the primers were HPLC-purified by the manufacturer (Operon Technologies).  Reverse transcription reactions were terminated with 0.1M EDTA.  RNA was degraded by adding 0.3 N NaOH and incubating at 60°C for 20 minutes.  The reaction was neutralized with 0.4 M Tris.HCl pH7.6.  Labeled cDNA was purified by ethanol precipitation, resuspended in 10 µl of DDW and mixed with 130 µl of PerfectHybTM Plus Hybridization buffer (SIGMA H-7033).

extract_protocol: RNA samples prepared from developing KAX3 cells at 18 hours using TRIZOL(Invitrogen)

tag: 'strain:KAX3', 'development:filter','biological replication:1','technical replication:1','time point:18 hr'


title: Wild type murine bone marrow-derived macrophages stimulated with LPS (100 ng/ml), biol. rep2	T180

treatment_protocol: LPS 180 minutes

tag: Time point 180 minutes post-stimulation


title: 100-64_V_wrist

description:
Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59459.gif; format: GIF

source_name: Ventral wrist

tag: Ventral wrist


title: DTG_heart_control_rep4_chip430A

description: heart tissue from Tet-myrAkt1/?MHC-tTA mice before Akt induction

value: Tet-myrAkt1/?MHC-tTA, Gender:male, Age:12 weeks, Tissue:heart tissue


title: Murine bone marrow-derived macrophages at T0, biol. rep4

source_name: resting BMDMs

treatment_protocol: BMDMs differentiated frombone marrow in L cell conditioned media as a source of mCSF (CSF-1).  Samples grown fro 7 days and rested in complete DMEM for 1 hr prior to Trizol processing


title: Wild type murine bone marrow-derived macrophages stimulated with LPS (100 ng/ml), biol. rep1	T180


title: DTG_heart_on2w_rep2_chip430A


title: DTG_heart_on2w_rep1_chip430A


title: S97.6_D2digit

description:
Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59709.gif; format: GIF

tag: Amplified Universal Human Reference messge amp II

source_name: Total RNA from S97.6 fibroblasts dorsal 2nd digit


title: KAX3_bio1_tc1_hour12

extract_protocol: RNA samples prepared from KAX3 cells developed and collected at 12 hours using TRIZOL(Invitrogen)

tag: 'strain:KAX3', 'development:filter','biological replication:1','technical replication:1','time point:12 hr'

tag: 'strain:AX4', 'development:filter','biological replication:1','technical replication:1','time point:0, 3, 6, 12, 17, 24 hr'


title: DTG_heart_control_rep3_chip430A


title: KAX3_bio1_tc1_hour6

extract_protocol: RNA samples prepared from KAX3 cells developed and collected at 0 hr using TRIZO(Invitrogen)

tag: 'strain:KAX3', 'development:filter','biological replication:1','technical replication:1','time point:6 hr'

source_name: Dictyostelium discoideum_AX4

tag: 'strain:AX4', 'development:filter','biological replication:1','technical replication:1','time point:0 hr(pool 0,3,6,12,17,24hr)'


title: Aorta_5673

description:
Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59473.gif; format: GIF

source_name: Amplifiied Human Universal Reference

tag: Amplifiied Human Universal Reference

source_name: Clonetic Cells Aorta fibroblasts #5763

tag: Clonetic Cells Aorta fibroblasts #5763


title: DTG_heart_control_rep2_chip430A

source_name: heart tissue

tag: Strain


title: Murine bone marrow-derived macrophages at T0, biol. rep2

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.


title: DTG_heart_control_rep1_chip430A


title: S97.5_D1digit

description:
Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59708.gif; format: GIF

source_name: Total RNA from S97.5 fibroblasts dorsal 1st digit


title: Murine bone marrow-derived macrophages at T0, biol. rep1


title: KAX3_bio1_tc1_hour0

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with KAX3 strain from 0 hrs of development labeled with Cy5

hyb_protocol: Labeled cDNA in PerfectHybTM Plus Hybridization buffer (SIGMA H-7033) was hybridized to the arrays after heat treatment (95°C, 2 min) using a GeneTAC hybridization station (Genomic Solutions) according to the manufacturer's recommended protocol as indicated below.Labeled cDNA was hybridized to the arrays using a GeneTAC automatic hybridization station (Genomic Solutions) for 2 hours at 65°C.  Arrays were sequentially washed with 3 solutions, 2x SSC, 0.5% SDS; 0.5x SSC, 0.5% SDS; 0.1x SSC, for 30 sec at room temperature twice each.

source_name: Dictyostelium discoideum_KAX3

extract_protocol: RNA samples prepared from developing KAX3 cells at 0 hrs of development using TRIZOL(Invitrogen)

tag: strain:KAX3', 'development:filter','biological replication:1','technical replication:1','time point:0 hr'

source_name: Dictyostelium Discoedium_KAX3

tag: 'strain:AX4', 'development:filter','biological replication:1','technical replication:1','time point:0 hr'


title: 3000132352B_adultworm_male_52_right

status: Public on Aug 24 2006

city: Campos dos Goytacazes

first: Thiago

middle: Motta

last: Venancio

state: RJ

address: Av Alberto Lamego 2000

country: Brazil

institute: UENF

description: Raw intensity values were extracted from images with ArrayVision. An individual spot background was extracted for each spot using the following software settings: Background: Mean; Enable background subtraction; corners between spots; mode: individual.

data_processing: Spot signals below individual spot background are marked ?null? in the VALUE column. The last line of each of 12 subarrays contained a set of Lucidea Universal scorecard controls (GE Healthcare), which include 2 negative controls per set, totalizing 48 negative control spots per slide that were used as a cutoff value for filtering out low intensity spot signals. Low intensity data points below the average plus 2 standard deviations of the negative control signal were filtered out and are marked ?null? in the VALUE column. Positive and negative external controls were excluded and are marked ?null? in the VALUE column. Data intensity from each array was normalized by a factor proportional to the total intensity of the slide, excluding positive and negative external controls.

molecule: polyA RNA

organism: Schistosoma mansoni

source_name: adult worm, male, sample 52

label_protocol: Fluorescently labeled cDNA targets were generated using Superscript-plus indirect cDNA labeling system (Invitrogen), according to the manufacturer instructions.

extract_protocol: Extractions of mRNA were performed with MAC magnetic beads isolation kits (Miltenyi Biotec) using approximately 300 mg of worm tissue.

treatment_protocol: Worms were conserved in RNAlater (Ambion) according to the manufacturer instructions. Materials from 3 perfusions performed at different dates were pooled, and male and female parasites were separated manually.

tag: Gender

value: male Gender:female

tag: Tissue

value: whole worm

tag: Life cycle stage

value: adult worms obtained from portal perfusion of hamsters 7 to 8 weeks after infection.


title: 3000132351B_adultworm_female_51_right

data_processing: Spot signals below individual spot background are marked 'null' in the VALUE column. The last line of each of 12 subarrays contained a set of Lucidea Universal scorecard controls (GE Healthcare), which include 2 negative controls per set, totalizing 48 negative control spots per slide that were used as a cutoff value for filtering out low intensity spot signals. Low intensity data points below the average plus 2 standard deviations of the negative control signal were filtered out and are marked 'null' in the VALUE column. Positive and negative external controls were excluded and are marked 'null' in the VALUE column. Data intensity from each array was normalized by a factor proportional to the total intensity of the slide, excluding positive and negative external controls.

source_name: adult worm, female, sample 51


title: 3000132352_adultworm_male_52_left


title: 3000132351_adultworm_female_51_left


title: 3000132346B_adultworm_male_46_right

source_name: adult worm, male, sample 46


title: Murine bone marrow-derived macrophages at T0, biol. rep3


title: 100-53_D_1/2_elbwnwrst

description:
Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59456.gif; format: GIF

source_name: Amplified universal human reference

tag: Amplified universal human reference

source_name: L forearm, dorsal, 1/2 way between elbow and wrist


title: 3000132346_adultworm_male_46_left


title: 3000132345B_adultworm_female_45_right

source_name: adult worm, female, sample 45


title: 3000132344B_adultworm_female_44_right

source_name: adult worm, female, sample 44


title: 3000132344_adultworm_female_44_left


title: 100-55.2_D_digit3and4

description:
Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59472.gif; format: GIF

source_name: Poly A RNA L hand, dorsal, medial (V of digit 4 and 4)


title: 3000132343B_adultworm_male_43_right

source_name: adult worm, male, sample 43


title: S97.3_DForearm

description:
Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59707.gif; format: GIF

source_name: Amplified Universal Human Reference messge amp II

source_name: Total RNA from S97.3 fibroblasts D forearm


title: 3000132343_adultworm_male_43_left


title: Sup fraction for the analysis of Distibution of Rec8 in pds5 deletion mutant.

status: Public on Aug 23 2006

type: genomic

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

country: Japan

institute: The University of Tokyo

description: Sup fraction for the normalization of Rec8 distribution in pds5 deletion mutant.

data_processing: Data was processed following the protocol provided by Affymetrix (GCOS ver 1.4).

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: Sup fraction (equal to Whole cell extract DNA)

tag: S.pombe strain deleted for pds5 was used.


title: 100-55.1_D_digit1and2

description:
Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59471.gif; format: GIF

source_name: Amplifiied Human Universal Reference

source_name: Poly A RNA L hand, dorsal, lateral (V of digit 1 and 2)


title: Rec8 distribution in meiosis w/o Pds5

description: Rec8 distribution on whole chr2 and part of chr3.

source_name: Chromatin-immunoprecipitated DNA

tag: Pds5 deleted pombe strain was used.


title: T6 versus T4 B10_0055 29T4a_v_29T6a

city: Urbana

first: Elizabeth

middle: A

last: Ainsworth

state: IL

address: 147 ERML, 1201 W. Gregory Drive

department: Photosynthesis Research Unit

institute: USDA/ARS

description: Replicate 1

hyb_protocol: Hegde P et al Biotechniques 2000 29:548-56

scan_protocol: scanner: Perkin-Elmer ScanArray Express Software: Imagene 6.1

data_processing:
local background subtracted from each spot
natural log of the background corrected median signal was used

organism: Glycine max

source_name: Pooled 4th trifoliate leaves from 6 plants grown at elevated CO2 in ring 29

label_protocol: Indirect incorporation using aa-dUTP

growth_protocol: Elevated CO2 at SoyFACE

extract_protocol: SDS/Phenol Chloroform Method

tag: Cultivar

value: Pioneer 93B15

tag: Grown at elevated CO2

tag: Fully Expanded leaves

source_name: Pooled 6th trifoliate leaves from 6 plants grown at elevated CO2 in ring 29

treatment_protocol: Elevated CO2 at SoyFACE

tag: Growing leaves


title: T6 versus T4 C04_0055 20T6b_v_20T4b

description: Replicate 2

source_name: Pooled 6th trifoliate leaves from 6 plants grown at elevated CO2 in ring 20

source_name: Pooled 4th trifoliate leaves from 6 plants grown at elevated CO2 in ring 20


title: Aorta_5640

description:
Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59470.gif; format: GIF

source_name: Clonetic cells aorta fibroblasts #5640

tag: Clonetic cells aorta fibroblasts #5640


title: T6 versus T4 A10_0050 29T4b_v_29T6b

description: Replicate 1

tag: Fully expanded leaves


title: T6 versus T4 C07_0035 20T6a_v_20T4a

description: Replicate 2


title: T6 versus T4 C02_0050 29T6a_v_29T4a

description: Replicate 1


title: Rec8 distribution in meiosis in wild type strain.

description: Rec8 distribution in wild type strain.

tag: Wild type S.pombe strain was used.


title: Sup fraction for the analysis of Distibution of Rec8 in wild type.

description: Sup fraction for the normalization of Rec8 distribution.


title: T6 versus T4 B02_0055 20T4b_v_20T6b

description: Replicate 1


title: T6 versus T4 B09_0045 20T6b_v_20T4b

description: Replicate 2


title: T6 versus T4 A08_0055 20T4a_v_20T6a

description: Replicate 1


title: Lung_6508

description:
Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59455.gif; format: GIF

source_name: Amplified universal human reference

source_name: clonetic lung fibroblasts #6508

tag: clonetic lung fibroblasts #6508


title: T6 versus T4 E03_0045 20T4b_v_20T6b

description: Replicate 1


title: T6 versus T4 B04_0035 21T4b_v_21T6b

description: Replicate 1

source_name: Pooled 4th trifoliate leaves from 6 plants grown at elevated CO2 in ring 21

source_name: Pooled 6th trifoliate leaves from 6 plants grown at elevated CO2 in ring 21


title: T6 versus T4 C05_0035 21T4b_v_21T6b

description: Replicate 2


title: T6 versus T4 B10_0050 29T4a_v_29T6a

description: Replicate 2


title: T6 versus T4 D05_0045 21T4b_v_21T6b

description: Replicate 2


title: Patient MKS Normal RNA_rep1 (MKS485)

city: Pittsburgh

first: Mandal.

middle: K.

last: Singh

state: PA

address: 3460 Fifth Ave

department: Transplant

institute: Childrens Hospital of Pittsburgh

description: Bitynylated cRNA is probe is prepared and hybridization is carried out following the Codelink protocols and reagents

hyb_protocol: Standard CodeLink procedures

scan_protocol: Standard CodeLink procedures

data_processing: Normalized intensities analysed by by SAM using two fold cutoff.

label: Biotin

source_name: Patient MKS Normal RNA_rep1

label_protocol: The Codelink Reagents for IVT kit is used to label 2 µg of total RNA to produce UTP-biotinylated cRNA targets.

extract_protocol: PBMC total RNA is prepared by RNAeasy protocol. RNA quality checked on bioanalyzer.

tag: PBMC


title: T6 versus T4 B08_0050 20T4a_v_20T6a

description: Replicate 1


title: T6 versus T4 C01_0035 21T4a_v_21T6a

description: Replicate 1


title: T6 versus T4 B08_0055 25T6b_v_25T4b

description: Replicate 2

source_name: Pooled 6th trifoliate leaves from 6 plants grown at ambient CO2 in ring 25

growth_protocol: Ambient CO2 at SoyFACE

tag: Grown at ambient CO2

source_name: Pooled 4th trifoliate leaves from 6 plants grown at ambient CO2 in ring 25

treatment_protocol: Ambient CO2 at SoyFACE

tag: fully expanded leaves


title: T6 versus T4 B06_0050 21T4a_v_21T6a

description: Replicate 2


title: Patient MKS Normal RNA_rep1 (MKS481)


title: T6 versus T4 E09_0045 20T6a_v_20T4a

description: Replicate 2


title: T6 versus T4 C02_0055 25T6a_v_25T4a

description: Replicate 2


title: T6 versus T4 D08_0035 25T4a_v_25T6a

description: Replicate 1


title: Patient DT Acute RNA_rep2 (DT495 Acute)

source_name: Patient DT Acute RNA_rep2


title: T6 versus T4 E02_0035 25T4b_v_25T6b

description: Replicate 1


title: T6 versus T4 A07_0045 21T6b_v_21T4b

description: Replicate 1


title: T6 versus T4 A10_0055 24T6a_v_24T4a

description: Replicate 2

source_name: Pooled 6th trifoliate leaves from 6 plants grown at ambient CO2 in ring 24

source_name: Pooled 4th trifoliate leaves from 6 plants grown at ambient CO2 in ring 24


title: T6 versus T4 B04_0055 24T6b_v_24T4b

description: Replicate 2


title: T6 versus T4 B01_0045 21T6a_v_21T4a

description: Replicate 1


title: T6 versus T4 C08_0055 24T4a_v_24T6a

description: Replicate 1

source_name: Pooled 6th trifoliate leaves from 6 plants grown at ambient CO2 in ring 17


title: T6 versus T4 A08_0050 25T6A_V_25T4A

description: Replicate 2


title: T6 versus T4 A10_0035 21T4a_v_21T6a

description: Replicate 2


title: Patient DT Late Chronic RNA_rep2 (DT493 LChronic)

source_name: Patient DT Late Chronic RNA_rep2


title: T6 versus T4 B02_0035 17T6b_v_17T4b

description: Replicate 2

source_name: Pooled 4th trifoliate leaves from 6 plants grown at ambient CO2 in ring 17


title: T6 versus T4 B02_0050 25T6B_V_25T4B

description: Replicate 2


title: Patient DT Late Chronic RNA_rep1 (DT492 LChronic)

source_name: Patient DT Late Chronic RNA_rep1


title: T6 versus T4 C03_0035 17T6b_v_17T4b

description: Replicate 1


title: T6 versus T4 C05_0045 25T4A_V_25T6A

description: Replicate 1


title: Elevated CO2 versus ambient CO2 B09_0055 29T6b_v_25T6b

description: Replicate 2

source_name: Pooled 6th trifoliate leaves from 6 leaves grown at elevated CO2 in Ring 29

source_name: Pooled 6th trifoliate leaves from 6 leaves grown at ambient CO2 in Ring 25

tag: growing leaves


title: Patient DT Chronic RNA_rep1 (DT490 Chronic)

source_name: Patient DT Chronic RNA_rep1


title: Elevated CO2 versus ambient CO2 D09_0035 25T6A_v_29T6A

description: Replicate 1


title: T6 versus T4 C09_0045 25T4B_V_25T6B

description: Replicate 1


title: Elevated CO2 versus ambient CO2 C03_0055 29T6a_v_25T6a

description: Replicate 2


title: T6 versus T4 B08_0035 17T6a_v_17T4a

description: Replicate 1


title: T6 versus T4 C01_0050 24T6B_V_24T4B

description: Replicate 2


title: T6 versus T4 B08_0034 17T6a_v_17T4a

description: Replicate 2


title: Elevated CO2 versus ambient CO2 E03_0035 25T6B_v_29T6B

description: Replicate 1


title: Elevated CO2 versus ambient CO2 D04_0035 24T6B_v_20T6B

description: Replicate 2

source_name: Pooled 6th trifoliate leaves from 6 leaves grown at ambient CO2 in Ring 24

source_name: Pooled 6th trifoliate leaves from 6 leaves grown at elevated CO2 in Ring 20


title: Patient DT Acute RNA_rep2 (DT489 Acute)


title: Elevated CO2 versus ambient CO2 C10_0035 24T6A_v_20T6A

description: Replicate 2


title: T6 versus T4 E01_0045 24T6A_V_24T4A

description: Replicate 2


title: T6 versus T4 C07_0055 24T4b_v_24T6b

description: Replicate 1


title: Elevated CO2 versus ambient CO2 B05_0055 20T6B_v_24T6B

description: Replicate 1


title: Elevated CO2 versus ambient CO2 B01_0055 20T6A_v_24T6A

description: Replicate 1


title: T6 versus T4 C01_0045 24T4B_V_24T6B

description: Replicate 1


title: Patient DT Pre RNA_rep2 (DT487 Pre)

source_name: Patient DT Pre RNA_rep2


title: T6 versus T4 B07_0045 24T4A_V_24T6A

description: Replicate 1


title: Elevated CO2 versus ambient CO2 C06_0035 21T6b_v_17T6b

description: Replicate 2

source_name: Pooled 6th trifoliate leaves from 6 leaves grown at elevated CO2 in Ring 21

source_name: Pooled 6th trifoliate leaves from 6 leaves grown at ambient CO2 in Ring 17


title: Elevated CO2 versus ambient CO2 B06_0035 21T6b_v_17T6b

description: Replicate 1


title: Elevated CO2 versus ambient CO2 B01_0035 21T6a_v_17T6a

description: Replicate 1


title: Patient DT Chronic RNA_rep2 (DT491 Chronic)

source_name: Patient DT Chronic RNA_rep2


title: T6 versus T4 D07_0045 17T4B_V_17T6B

description: Replicate 2


title: Patient TP Chronic RNA_rep2 (TP144 Chronic)

source_name: Patient TP Chronic RNA_rep2


title: Elevated CO2 versus ambient CO2 C02_0035 21T6a_v_17T6a

description: Replicate 2


title: T6 versus T4 A09_0045 17T4B_V_17T6B

description: Replicate 1


title: Elevated CO2 versus ambient CO2 Block3_BioRep1_Amb_FE_vs_Ele_FE_2

description: Replicate 2

source_name: Pooled 4th trifoliate leaves from 6 leaves grown at elevated CO2 in Ring 29

source_name: Pooled 4th trifoliate leaves from 6 leaves grown at ambient CO2 in Ring 25


title: Elevated CO2 versus ambient CO2 Block1_BioRep2_Amb_FE_vs_Ele_FE_2

description: Replicate 2

source_name: Pooled 4th trifoliate leaves from 6 leaves grown at ambient CO2 in Ring 17

source_name: Pooled 4th trifoliate leaves from 6 leaves grown at elevated CO2 in Ring 21


title: Patient DT Acute RNA_rep1 (DT48Acute)

source_name: Patient DT Acute RNA_rep1


title: Elevated CO2 versus ambient CO2 Block3_BioRep1_Amb_FE_vs_Ele_FE

description: Replicate 1


title: Patient DT Pre RNA_rep1 (DT486 Pre)

source_name: Patient DT Pre RNA_rep1


title: T6 versus T4 D03_0045 17T4A_V_17T6A

description: Replicate 2

source_name: Pooled 4th trifoliate leaves from 6 plants grown at ambient CO2 in ring 17

source_name: Pooled 6th trifoliate leaves from 6 plants grown at ambient CO2 in ring 17


title: T6 versus T4 B03_0045 17T4A_V_17T6A

description: Replicate 1


title: Patient TP acute RNA_rep1 (TP140Acute)

source_name: Patient TP Acute RNA_rep1


title: Patient TP Chronic RNA_rep1 (TP142 Chronic)

source_name: Patient TP Chronic RNA_rep1


title: Patient TP acute RNA_rep2 (TP141Acute)

source_name: Patient TP Acute RNA_rep2


title: Elevated CO2 versus ambient CO2 Block2_BioRep1_Amb_FE_vs_Ele_FE_2

description: Replicate 2

data_processing: local background subtracted from each spot

source_name: Pooled 4th trifoliate leaves from 6 leaves grown at elevated CO2 in Ring 20

source_name: Pooled 4th trifoliate leaves from 6 leaves grown at ambient CO2 in Ring 24


title: Elevated CO2 versus ambient CO2 B03_0050 29T6b_V_25T6b

description: Replicate 2

source_name: Pooled 6th trifoliate leaves from 6 leaves grown at elevated CO2 in Ring 29

source_name: Pooled 6th trifoliate leaves from 6 leaves grown at ambient CO2 in Ring 25


title: Elevated CO2 versus ambient CO2 Block1_BioRep1_Amb_FE_vs_Ele_FE

description: Replicate 1


title: Elevated CO2 versus ambient CO2 Block2_BioRep1_Amb_FE_vs_Ele_FE

description: Replicate 1


title: Patient TP Pre RNA_rep1 (TP137Pre)

source_name: Patient TP Pre RNA_rep1


title: Elevated CO2 versus ambient CO2 Block1_BioRep1_Amb_FE_vs_Ele_FE_2

description: Replicate 2


title: Elevated CO2 versus ambient CO2 C10_0045 25T6a_V_29T6a

description: Replicate 1


title: PatientMH Chronic RNA_rep2 (MHchronic136 Chronic)

source_name: PatientMH Chronic RNA_rep2


title: PatientMH Chronic RNA_rep1 (MH135 Chronic)

source_name: PatientMH Chronic RNA_rep1


title: Elevated CO2 versus ambient CO2 C10_0045 25T6b_V_29T6b

description: Replicate 1


title: Elevated CO2 versus ambient CO2 C02_0045 24T6b_V_20T6b

description: Replicate 2

source_name: Pooled 6th trifoliate leaves from 6 leaves grown at ambient CO2 in Ring 24

source_name: Pooled 6th trifoliate leaves from 6 leaves grown at elevated CO2 in Ring 20


title: PatientMH Acute RNA_rep2 (MH130Acute)

source_name: PatientMH Acute RNA_rep2


title: Elevated CO2 versus ambient CO2 Block2_BioRep2_Amb_FE_vs_Ele_FE_2

description: Replicate 2


title: Elevated CO2 versus ambient CO2 B08_0045 24T6a_V_20T6a

description: Replicate 2


title: PatientMH Acute RNA_rep1 (MH128Acute)

source_name: PatientMH Acute RNA_rep1


title: Elevated CO2 versus ambient CO2 Block2_BioRep2_Amb_FE_vs_Ele_FE

description: Replicate 1


title: PatientMH Pre RNA_rep2 (MKH127Pre)

source_name: PatientKF Pre RNA_rep2


title: Elevated CO2 versus ambient CO2 E06_0045 20T6b_V_24T6b

description: Replicate 1


title: Elevated CO2 versus ambient CO2 E02_0045 20T6a_V_24T6a

description: Replicate 1


title: PatientMH Pre RNA_rep1 (MH126Pre)

source_name: PatientKF Pre RNA_rep1


title: PatientKF Chronic RNA_rep2 (KF124 Chronic)

source_name: PatientKF Chronic RNA_rep2


title: Elevated CO2 versus ambient CO2 D08_0045 21T6b_v_17T6b

description: Replicate 2

source_name: Pooled 6th trifoliate leaves from 6 leaves grown at elevated CO2 in Ring 21

source_name: Pooled 6th trifoliate leaves from 6 leaves grown at ambient CO2 in Ring 17


title: Elevated CO2 versus ambient CO2 Block1_BioRep2_Amb_FE_vs_Ele_FE

description: Replicate 1

source_name: Pooled 4th trifoliate leaves from 6 leaves grown at ambient CO2 in Ring 17

source_name: Pooled 4th trifoliate leaves from 6 leaves grown at elevated CO2 in Ring 21


title: PatientKF Chronic RNA_rep1 (KF122 Chronic)

source_name: PatientKF Chronic RNA_rep1


title: Patient TP Pre RNA_rep2 (TP138Pre)

source_name: Patient TP Pre RNA_rep2


title: Elevated CO2 versus ambient CO2 E07_0045 17T6b_V_21T6b

description: Replicate 1


title: Elevated CO2 versus ambient CO2 D04_0045 21T6a_v_17T6a

description: Replicate 2


title: Elevated CO2 versus ambient CO2 B04_0045 17T6a_V_21T6a

description: Replicate 1


title: Elevated CO2 versus ambient CO2 1088_Block2_BioRep1_Amb_FE_vs_Ele_FE_2

description: Replicate 2

source_name: Pooled 4th trifoliate leaves from 6 leaves grown at ELEVATED CO2 in Ring 20

source_name: Pooled 4th trifoliate leaves from 6 leaves grown at ambient CO2 in Ring 24


title: PatientKF Pre RNA_rep2 (KF119Pre)


title: PatientKF Pre RNA_rep1 (KF118Pre)


title: Elevated CO2 versus ambient CO2 1088_Block2_BioRep2_Amb_FE_vs_Ele_FE

description: Replicate 1

source_name: Pooled 4th trifoliate leaves from 6 leaves grown at elevated CO2 in Ring 20


title: PatientDD Chronic RNA_rep2 (DD117 Chronic)

source_name: PatientDD Chronic RNA_rep2


title: Elevated CO2 versus ambient CO2 1088_Block1_BioRep2_Amb_FE_vs_Ele_FE_2

description: Replicate 2


title: Elevated CO2 versus ambient CO2 1088_Block1_BioRep1_Amb_FE_vs_Ele_FE_2

description: Replicate 2


title: PatientDD Chronic RNA_rep1 (DD116 Chronic)

source_name: PatientDD Chronic RNA_rep1


title: Elevated CO2 versus ambient CO2 1088_Block2_BioRep2_Amb_FE_vs_Ele_FE_2

description: Replicate 1


title: PatientDD Acute RNA_rep2 (DD114Acute)

source_name: PatientDD Acute RNA_rep2


title: PatientDD Acute RNA_rep1 (DD112Acute)

source_name: PatientDD Acute RNA_rep1


title: Elevated CO2 versus ambient CO2 1088_Block2_BioRep1_Amb_FE_vs_Ele_FE

description: Replicate 1


title: PatientKF Acute RNA_rep2 (KF121Acute)

source_name: PatientKF Acute RNA_rep2


title: Elevated CO2 versus ambient CO2 1088_Block1_BioRep1_Amb_FE_vs_Ele_FE

description: Replicate 1


title: PatientDD Pretreatment RNA_rep2 (DD111Pre)

source_name: PatientDD Pretreatment RNA_rep2


title: PatientDD Pretreatment RNA_rep1 (DD109Pre)

source_name: PatientDD Pretreatment RNA_rep1


title: Elevated CO2 versus ambient CO2 1088_Block3_BioRep2_Amb_FE_vs_Ele_FE

description: Replicate 1

source_name: Pooled 4th trifoliate leaves from 6 leaves grown at ambient CO2 in Ring 25

tag: Fully ambient leaves

source_name: Pooled 4th trifoliate leaves from 6 leaves grown at elevated CO2 in Ring 29


title: PatientKF Acute RNA_rep1 (KF120Acute)

source_name: PatientKF Acute RNA_rep1


title: Elevated CO2 versus ambient CO2 1088_Block3_BioRep1_Amb_FE_vs_Ele_FE

description: Replicate 1


title: i4-072A-750700_Yap1A

status: Public on Aug 21 2006

city: University Park

first: Frank

last: Pugh

address: 452 North Frear Laboratory

department: Biochemistry and Molecular Biology

institute: The Pennsylvania State University

description:
Strains were grown in YPD media at 25ûC to OD600 = ~0.8. Then the cultures were shifted to 37ûC for 15 min. ( by adding an equal volume of heated media for the heat shocked set), or mock treated at 25ûC for 15 min. (by adding an equal volume of 25ûC media for the mock treated set).  After 15 min. incubation, cells were brought back to 25ûC and simultaneously cross-linked with 1% formaldehyde for 2 hours.  Cross-linkage was quenched with 0.25M Glycine for 5 minutes. Cells were harvested at 4ûC.  See methods and publication for details on chromatin immunprecipitation, non-specific amplification and intergenic array hybridization.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.
Keywords = Saccharomyces cerevisiae

organism: Saccharomyces cerevisiae

source_name: Yap1-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Yap1-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-072B-700700_Yap1B

source_name: Yap1-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Yap1-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-064B-650700_Tup1D

source_name: Tup1-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Tup1-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-049B-750770_Tup1B


title: Elevated CO2 versus ambient CO2 1088_Block1_BioRep2_Amb_FE_vs_Ele_FE

description: Replicate 1

source_name: Pooled 4th trifoliate leaves from 6 leaves grown at elevated CO2 in Ring 21

growth_protocol: elevated CO2 at SoyFACE

source_name: Pooled 4th trifoliate leaves from 6 leaves grown at ambient CO2 in Ring 17


title: i4-064A-700700_Tup1C

source_name: Tup1-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Tup1-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-049A-750750_Tup1A


title: i4-047B-800750_Toa2B

source_name: Toa2-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Toa2-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-047A-800750_Toa2A

source_name: Toa2-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Toa2-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-081B-750720_Tfa1B

source_name: Tfa1-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Tfa1-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-081A-750700_Tfa1A

source_name: Tfa1-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Tfa1-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-076B-750700_Taf9B

source_name: Taf9-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Taf9-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-076A-750700_Taf9A

source_name: Taf9-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Taf9-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-068A-720720_Taf6A

source_name: Taf6-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Taf6-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-070B-720720_Swr1B

source_name: Swr1-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Swr1-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-070A-720720_Swr1A

source_name: Swr1-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Swr1-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-073B-700700_Ssl2B

source_name: Ssl2-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Ssl2-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-073A-700700_Ssl2A

source_name: Ssl2-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Ssl2-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-074A-700720_Msn2C

source_name: Msn2-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Msn2-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-054B-750750_Med2B

source_name: Med2-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Med2-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-062A-700680_Med2C

source_name: Med2-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Med2-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-054A-800750_Med2A


title: i4-087B-710700_Ifh1B

source_name: Ifh1-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Ifh1-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-062B-700680_Med2D


title: i4-087A-730700_Ifh1A

source_name: Ifh1-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Ifh1-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-074B-720700_Msn2D

source_name: Msn2-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Msn2-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-085A-750700_Tfg1C

source_name: Tfg1-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Tfg1-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-079A-750700_Htb2A

source_name: Htb2-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Htb2-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-041B-720750_Tfg1B


title: i4-041A-720750_Tfg1A

source_name: Tfg1-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Tfg1-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-046B-750750_Taf5B

source_name: Taf5-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Taf5-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-046A-750750_Taf5A

source_name: Taf5-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Taf5-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-068B-720720_Taf6B

source_name: Taf6-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Taf6-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-020A-750750_Sua7A

source_name: Sua7-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Sua7-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-020B-750680_Sua7B

source_name: Sua7-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Sua7-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-043B-720720_Rsc2B

source_name: Rsc2-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Rsc2-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-043A-750720_Rsc2A

source_name: Rsc2-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Rsc2-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-079B-700710_Htb2B

source_name: Htb2-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Htb2-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-040B-720720_Rap1B

source_name: Rap1-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Rap1-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-009B-710700_polyTBPB

source_name: BY4741 Mock Treated Purified ChIP DNA (polyclonal TBP Ab) (CH1)

source_name: BY4741 Heat Shocked Purified ChIP DNA (polyclonal TBP Ab) (CH2)


title: i4-009A-700750_polyTBPA

source_name: BY4741 Heat Shocked Purified ChIP DNA (polyclonal TBP Ab) (CH1)

source_name: BY4741 Mock Treated Purified ChIP DNA (polyclonal TBP Ab) (CH2)


title: i4-027A-800700_Sua7C


title: i4-008B-700700_PolIID

source_name: BY4741 Mock Treated Purified ChIP DNA (Anti-Pol II 8WG16 Ab) (CH1)

source_name: BY4741 Heat Shocked Purified ChIP DNA (Anti-Pol II 8WG16 Ab) (CH2)


title: i4-008A-700700_PolIIC

source_name: BY4741 Heat Shocked Purified ChIP DNA (Anti-Pol II 8WG16 Ab) (CH1)

source_name: BY4741 Mock Treated Purified ChIP DNA (Anti-Pol II 8WG16 Ab) (CH2)


title: i4-006B-650680_PolIIB


title: i4-006A-700680_PolIIA


title: i4-022B-680680_Rpo21B

source_name: Rpo21-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Rpo21-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-023B-680680_Hxk1B

source_name: Hxk1-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Hxk1-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-023A-680680_Hxk1A

source_name: Hxk1-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Hxk1-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-044A-680680_Htz1A

source_name: Htz1-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Htz1-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-022A-700700_Rpo21A

source_name: Rpo21-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Rpo21-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-060B-680680_Hta2B

source_name: Hta2-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Hta2-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-044B-680680_Htz1B

source_name: Htz1-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Htz1-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-039A-680680_Hht2A

source_name: Hht2-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Hht2-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-039B-680680_Hht2B

source_name: Hht2-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Hht2-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-060A-680680_Hta2A

source_name: Hta2-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Hta2-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-040A-720720_Rap1A

source_name: Rap1-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Rap1-TAP Mock Treated Purified ChIP DNA (CH2)


title: i4-038B-680680_Hhf1B

source_name: Hhf1-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Hhf1-TAP Heat Shocked Purified ChIP DNA (CH2)


title: Mast cells-6hr_donar_3

city: Singapore

first: Jayapal

last: Manikandan

country: Singapore

institute: NUS

description: Human umbilical cord blood derived mast cells- IgE sensitized for 12 hrs- crosslinked Fce receptor for 6 hrs

source_name: mast cells-crosslinked 6 hrs


title: Mast cells-12hr_Donar_3

description: Human umbilical cord blood derived mast cells- IgE sensitized for 12 hrs- crosslinked Fce receptor for 12hrs

source_name: Mast cells-crosslinked 12 hrs


title: Mast cells-6hr_donar_4


title: mast cells -2hr_Donar_4

description: Human umbilical cord blood derived mast cells- IgE sensitized for 12 hrs- crosslinked Fce receptor for 2 hrs

source_name: mast cells- crosslinked 2 hr


title: i4-051B-770750_Bur6A

source_name: Bur6-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Bur6-TAP Mock Treated Purified ChIP DNA (CH2)


title: Fxb15 bgeo-KI MEF transfected with the four factors but not selected with G418 (FBX15 KO MEF-4 factors)

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

description: Fbx15 bgeo-KI MEF were transfected with retroviral vectors for the four factors. However, cells were not selected with G418, thus no iPS clones was observed.

data_processing: gProcessedSiganl value calculated by Agilent Microarray Scanner Feature Extraction Software

tag: G418 sensitive

tag: non ES-like


title: NIH3T3 cells transformed with HRasV12 (NIH3T3-HRasV12)

description: NIH3T3 cells were transformed with a retroviral vector for a constitutively active HRas mutant (HRasV12).

source_name: NIH3T3 cells transformed with HRasV12

tag: wild-type for Fbx15 locus

tag: nullipotent


title: mast cells -2hr_Donar_3


title: i4-051A-750750_Bur6B

source_name: Bur6-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Bur6-TAP Heat Shocked Purified ChIP DNA (CH2)


title: IgE Sensitized_Donar_4

description: Human umbilical cord blood derived mast cells- IgE sensitized for 12 hrs

source_name: IgE sensitized mast cells


title: IgE Sensitized_Donar_3


title: Elevated CO2 versus ambient CO2 A09_0050 29T6a_V_25T6a

description: Replicate 2

source_name: Pooled 6th trifoliate leaves from 6 leaves grown at elevated CO2 in Ring 29

tag: Cultivar

source_name: Pooled 6th trifoliate leaves from 6 leaves grown at ambient CO2 in Ring 25


title: i4-021B-680680_Bdf1B

source_name: Bdf1-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Bdf1-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-021A-680680_Bdf1A

source_name: Bdf1-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Bdf1-TAP Mock Treated Purified ChIP DNA (CH2)


title: Mast Cell_Control 3

description: Human umbilical cord blood derived mast cells

source_name: Mast cells


title: Mast Cell_Control4

source_name: Mast cell


title: Induced pluripotent-like stem (iPS) cells derived from Fbx15 bgeo-KI MEF by three factors (iPS-MEF3-2)

description: Retroviral vectors for the 3 factors were transfected into Fbx15 bgeo-KI MEF. Cells were cultured with ES cell condition and selected with G418 for 16 days.

source_name: induced pluripotent-like stem (iPS) cells derived from Fbx15 bgeo-KI MEF by three factors

tag: more clumpy than ES cells


title: Mast cells-12hr_Donar1

source_name: Mast cells-crosslinked 12 hrs


title: Mast Cells-12hr_Donar2

source_name: Mast Cells_Crosslinked 12 hrs


title: i4-024B-650650_AcH3D

source_name: BY4741 Mock Treated Purified ChIP DNA (Anti-AcH3 K9,14 Ab) (CH1)

source_name: BY4741 Heat Shocked Purified ChIP DNA (Anti-AcH3 K9,14 Ab) (CH2)


title: Mast cells-12hr_Donar_4


title: Mast cells-6 hr_donar2

source_name: Mast cells-crosslinked for 6 hrs


title: i4-038A-680680_Hhf1A

source_name: Hhf1-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Hhf1-TAP Mock Treated Purified ChIP DNA (CH2)


title: Mast cells-6hr_donar1

source_name: mast cells-crosslinked 6 hrs


title: Induced pluripotent-like stem (iPS) cells derived from Fbx15 bgeo-KI MEF by 10 factors (iPS-MEF10-6)

description: Retroviral vectors for the 10 factors were transfected into Fbx15 bgeo-KI MEF. Cells were cultured with ES cell condition and selected with G418 for 16 days.

source_name: induced pluripotent-like stem (iPS) cells derived from Fbx15 bgeo-KI MEF by 10 factors

tag: ES-like phenotypes


title: i4-024A-680680_AcH3C

source_name: BY4741 Heat Shocked Purified ChIP DNA (Anti-AcH3 K9,14 Ab) (CH1)

source_name: BY4741 Mock Treated Purified ChIP DNA (Anti-AcH3 K9,14 Ab) (CH2)


title: Mast cells-2hr -Donar 2

source_name: mast cells- crosslinked Fce receptor for 2 hrs


title: IgE sensitized-Donar2

source_name: mast cells- IgE sensitized


title: mast cells -2hr_Donar1

source_name: mast cells-  crosslinked 2 hr


title: IgE Sensitized_Donar1

source_name: IgE sensitized mast cells


title: Mast cell-control 2

source_name: mast cells


title: Mast cell-control 1


title: i4-012A-700680_AcH3A


title: Wild-type MEF spontaneously immortilized and expressing KRasV12 (MEF-KRasV12)

description: MEF cells were spontaneously transformed before transfected with a retroviral vector for a constitutively

source_name: wild-type MEF spontaneously immortilized and expressing KRasV12

tag: Wild-type for Fbx15 locus


title: Bull 19 months, LT_02604, Replicate4

status: Public on Aug 19 2006

city: Saint-Genès-Champanelle

first: Isabelle

last: CASSAR-MALEK

address: Theix

department: Centre de Clermont-Fd/Theix

country: France

institute: INRA

description: Longissimus thoracis (LT) muscle of Charolais bull calves at 19 months of age. The animals has a low growth potential (IC-). This muscle gives a meat which is of average tenderness (T), juiciness (Jm) and flavor (Fm)

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were normalized and scalled. This procedure is done with MADSCAN tool.

organism: Bos taurus

source_name: Bull 19 months, LT_02604

tag: Charolais 2003, Bull 19 months IC-, T, Jm, Fm, Muscle LT

source_name: Pool of 5 samples (muscle LT) of 19 months bulls

tag: Pool of 5 samples(muscle LT) of 19 months bulls


title: Bull 19 months, LT_02604, Replicate3


title: Induced pluripotent-like stem (iPS) cells derived from Fbx15 bgeo-KI MEF by three factors (iPS-MEF3-3)

source_name: induced pluripotent-like stem (iPS) cells derived from Fbx15 bgeo-KI MEF by three factors


title: Bull 19 months, LT_02604, Replicate2


title: Bull 19 months, LT_02604, Replicate1


title: Bull 19 months, LT_02597, Replicate3

source_name: Bull 19 months, LT_02597


title: Bull 19 months, LT_02597, Replicate1


title: Bull 19 months, LT_02597, Replicate2


title: Bull 19 months, LT_02597, Replicate4


title: Bull 15 months, LT_02595, rep3

description: Longissimus thoracis (LT) muscle from Charolais bull calf at 15 months of age. The animal has a high growth potential (IC+). This muscle gives a meat which is of average tenderness (Tm), juiciness (Jm) and flavor (Fm).

source_name: Bull 15 months, LT_02595

tag: Charolais 2003, Bull 15 months IC+, Tm, Jm, Fm, Muscle LT

tag: Pool of 5 samples (muscle LT) of 19 months bulls


title: Bull 15 months, LT_02595, rep1


title: Bull 15 months, LT_02587, rep4

description: Longissimus thoracis (LT) muscle from Charolais bull calf at 15 months of age. The animal has a low growth potential (IC-). This muscle gives a meat which is tasty (F+) and of average tenderness (Tm) and juiciness (Jm).

source_name: Bull 15 months, LT_02587

tag: Charolais 2003, Bull 15 months IC-, Tm, Jm, F+, Muscle LT


title: Bull 15 months, LT_02595, rep4


title: Bull 15 months, LT_02587, rep3


title: i4-012B-640660_AcH3B

source_name: BY4741 Mock Treated Purified ChIP DNA (Anti-AcH3 K9,14 Ab) (CH1)

source_name: BY4741 Heat Shocked Purified ChIP DNA (Anti-AcH3 K9,14 Ab) (CH2)


title: Bull 19 months, LT_02547, Replicate4

description: Longissimus thoracis (LT) muscle of Charolais bull calves at 19 months of age. This muscle gives a meat which is flavored (Fm+) and which is of average tenderness (T) and juiciness (Jm)

source_name: Bull 19 months, LT_02547

tag: Charolais 2003, Bull 19 months, T, Jm, Fm+, Muscle LT


title: Bull 19 months, LT_02547, Replicate3


title: Bull 15 months, LT_02587, rep1


title: Bull 19 months, LT_02594, Replicate3

description: Longissimus thoracis (LT) muscle of Charolais bull calves at 19 months of age. This muscle gives a meat which is not tender (T-) and not flavored (Fm-) and which is of average juiciness (Jm)

source_name: Bull 19 months, LT_02594

tag: Charolais 2003, Bull 19 months, T-, Jm, Fm-, Muscle LT


title: Bull 19 months, LT_02594, Replicate2


title: Bull 19 months, LT_02594, Replicate1


title: Bull 19 months, LT_02588, Replicate4

description: Longissimus thoracis (LT) muscle of Charolais bull calves at 19 months of age. This muscle gives a meat which is tender (T+) and which is of average Flavor (Fm) and juiciness (Jm)

source_name: Bull 19 months, LT_02588

tag: Charolais 2003, Bull 19 months, T+, Jm, Fm, Muscle LT


title: Bull 15 months, LT_02587, rep2


title: Bull 15 months, LT_02582, rep1

description: Longissimus thoracis (LT) muscle from Charolais bull calf at 15 months of age. The animal has a low growth potential (IC-). This muscle gives a meat which is not tender (T-), tasty (F-) and of average juiciness (Jm).

source_name: Bull 15 months, LT_02582

tag: Charolais 2003, Bull 15 months IC-, T-, Jm, F-, Muscle LT


title: Bull 19 months, LT_02588, Replicate3


title: Bull 15 months, LT_02578, rep4

description: Longissimus thoracis (LT) muscle from Charolais bull calf at 15 months of age. The animal has a high growth potential (IC+). This muscle gives a meat which is juicier (J+) and of average tenderness (Tm) and flavor (Fm).

source_name: Bull 15 months, LT_02578

tag: Charolais 2003, Bull 15 months IC+, Tm, J+, Fm, Muscle LT


title: Bull 15 months, LT_02595, rep2


title: Bull 15 months, LT_02578, rep2


title: Bull 15 months, LT_02582, rep2


title: Bull 19 months, LT_02588, Replicate1


title: Bull 15 months, LT_02585, rep4

description: Longissimus thoracis (LT) muscle from Charolais bull calf at 15 months of age. The animal has a low growth potential (IC-). This muscle gives a meat which is not tender (T-), juicier (J-) and tasty (F-).

source_name: Bull 15 months, LT_02585

tag: Charolais 2003, Bull 15 months IC-, T-, J-, F-, Muscle LT


title: Bull 15 months, LT_02578, rep1


title: Bull 15 months, LT_02585, rep3


title: Bull 19 months, LT_02594, Replicate4


title: Bull 19 months, LT_02567, Replicate4

description: Longissimus thoracis (LT) muscle of Charolais bull calves at 19 months of age. The animals has a low growth potential (IC-). This muscle gives a meat which is not juicy (Jm-) and not flavored (Fm-) and which is of average tenderness (T)

source_name: Bull 19 months, LT_02567

tag: Charolais 2003, Bull 19 months IC-, T, Jm-, Fm-, Muscle LT


title: Bull 15 months, LT_02585, rep1


title: Bull 19 months, LT_02567, Replicate2


title: Bull 19 months, LT_02567, Replicate3


title: Bull 15 months, LT_02585, rep2


title: Bull 15 months, LT_02582, rep4


title: Bull 15 months, LT_02576, rep4

description: Longissimus thoracis (LT) muscle from Charolais bull calf at 15 months of age. The animal has a mean growth potential (ICm). This muscle gives a meat which is of average tenderness (Tm), juiciness (Jm) and flavor (Fm).

source_name: Bull 15 months, LT_02576

tag: Charolais 2003, Bull 15 months ICm, Tm, Jm, Fm, Muscle LT


title: Bull 15 months, LT_02566, rep4

source_name: Bull 15 months, LT_02566


title: Bull 15 months, LT_02582, rep3


title: Bull 15 months, LT_02576, rep3


title: Bull 15 months, LT_02566, rep3


title: Bull 15 months, LT_02576, rep1


title: Bull 15 months, LT_02578, rep3


title: Bull 19 months, LT_02567, Replicate1


title: Bull 15 months, LT_02566, rep2


title: Bull 19 months, LT_02588, Replicate2


title: Bull 15 months, LT_02566, rep1


title: Bull 15 months, LT_02575, rep4

source_name: Bull 15 months, LT_02575


title: Bull 15 months, LT_02575, rep3

source_name: Pool of 5 samples (muscle LT) of 19 months bulls


title: Bull 15 months, LT_02575, rep1


title: Bull 19 months, LT_02560, Replicate2

description: Longissimus thoracis (LT) muscle of Charolais bull calves at 19 months of age. The animals has a low growth potential (IC-). This muscle gives a meat which is not juicy (Jm-) and which is of average tenderness (T) and flavor (Fm)

source_name: Bull 19 months, LT_02560

tag: Charolais 2003, Bull 19 months IC-, T, Jm-, Fm, Muscle LT


title: Bull 19 months, LT_02560, Replicate4


title: Bull 15 months, LT_02575, rep2


title: Bull 15 months, LT_02576, rep2


title: Bull 19 months, LT_02560, Replicate1


title: i4-027B-750750_Sua7D

description:
Strains were grown in YPD media at 25ûC to OD600 = ~0.8. Then the cultures were shifted to 37ûC for 15 min. ( by adding an equal volume of heated media for the heat shocked set), or mock treated at 25ûC for 15 min. (by adding an equal volume of 25ûC media for the mock treated set).  After 15 min. incubation, cells were brought back to 25ûC and simultaneously cross-linked with 1% formaldehyde for 2 hours.  Cross-linkage was quenched with 0.25M Glycine for 5 minutes. Cells were harvested at 4ûC.  See methods and publication for details on chromatin immunprecipitation, non-specific amplification and intergenic array hybridization.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.
Keywords = Saccharomyces cerevisiae

source_name: Sua7-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Sua7-TAP Heat Shocked Purified ChIP DNA (CH2)


title: Bull 19 months, LT_02562, Replicate4

description: Longissimus thoracis (LT) muscle of Charolais bull calves at 19 months of age. This muscle gives a meat which is of average tenderness (T), Flavor (Fm) and juiciness (Jm)

source_name: Bull 19 months, LT_02562

tag: Charolais 2003, Bull 19 months, T, Jm, Fm, Muscle LT


title: Bull 19 months, LT_02544, Replicate4

description: Longissimus thoracis (LT) muscle of Charolais bull calves at 19 months of age. The animals has a low growth potential (IC-). This muscle gives a meat which is tender (T+), juicy (Jm+) and flavored (Fm+).

source_name: Bull 19 months, LT_02544

tag: Charolais 2003, Bull 19 months IC-, T+, Jm+, Fm+, Muscle LT


title: Bull 19 months, LT_02562, Replicate2


title: Bull 19 months, LT_02544, Replicate2


title: Bull 15 months, LT_02556, rep4

description: Longissimus thoracis (LT) muscle from Charolais bull calf at 15 months of age. The animal has a mean growth potential (ICm). This muscle gives a meat which is tender (T+), not juicier (J-) and of average flavor (Fm).

source_name: Bull 15 months, LT_02556

tag: Charolais 2003, Bull 15 months ICm, T+, J-, Fm, Muscle LT


title: Bull 19 months, LT_02544, Replicate3


title: Bull 19 months, LT_02562, Replicate1


title: Bull 15 months, LT_02556, rep3


title: Bull 19 months, LT_02560, Replicate3


title: Bull 19 months, LT_02540, Replicate3

description: Longissimus thoracis (LT) muscle of Charolais bull calves at 19 months of age. The animals has a low growth potential (IC-). This muscle gives a meat which is of average tender (T), juiciness (Jm) and flavor (Fm).

source_name: Bull 19 months, LT_02540

tag: Charolais 2003, Bull 19 months IC-, T, Jm, Fm, Muscle LT


title: Bull 19 months, LT_02540, Replicate4

tag: Pool of 5 samples(muscle LT) of 19 months bulls


title: Bull 15 months, LT_02556, rep1


title: Bull 19 months, LT_02544, Replicate1


title: Bull 15 months, LT_02556, rep2


title: Bull 19 months, LT_02540, Replicate2


title: Bull 19 months, LT_02540, Replicate1


title: Bull 15 months, LT_02555, rep4

source_name: Bull 15 months, LT_02555


title: Bull 19 months, LT_02562, Replicate3


title: Bull 15 months, LT_02555, rep3


title: Bull 15 months, LT_02538, rep4

source_name: Bull 15 months, LT_02538

tag: Charolais 2003, Bull 15 months IC+, Tm, Jm, Fm, Muscle LT


title: Bull 15 months, LT_02555, rep2

tag: Pool of 5 samples (muscle LT) of 19 months bulls


title: Bull 15 months, LT_02538, rep2


title: Bull 15 months, LT_02538, rep3


title: Bull 15 months, LT_02538, rep1


title: Bull 15 months, LT_02551, rep4

description: Longissimus thoracis (LT) muscle from Charolais bull calf at 15 months of age. The animal has a low growth potential (IC-). This muscle gives a meat which is of average tenderness (Tm), juiciness (Jm) and flavor (Fm).

source_name: Bull 15 months, LT_02551

tag: Charolais 2003, Bull 15 months IC-, Tm, Jm, Fm, Muscle LT


title: Bull 19 months, LT_02533, Replicate3

description: Longissimus thoracis (LT) muscle of Charolais bull calves at 19 months of age. The animals has a high growth potential (IC+). This muscle gives a meat which is juiciness (Jm+) and which is of average tender (T) and flavor (Fm).

source_name: Bull 19 months, LT_02533

tag: Charolais 2003, Bull 19 months IC+, T, Jm+, Fm, Muscle LT


title: Bull 15 months, LT_02551, rep2


title: Bull 15 months, LT_02551, rep1


title: Bull 19 months, LT_02533, Replicate2


title: Bull 15 months, LT_02551, rep3


title: Bull 19 months, LT_02533, Replicate4


title: Bull 15 months, LT_02548, rep4

description: Longissimus thoracis (LT) muscle from Charolais bull calf at 15 months of age. The animal has a mean growth potential (ICm). This muscle gives a meat which is tender (T+), juicier (J+) and tasty (F+).

source_name: Bull 15 months, LT_02548

tag: Charolais 2003, Bull 15 months ICm, T+, J+, F+, Muscle LT


title: Bull 15 months, LT_02548, rep3


title: Bull 15 months, LT_02555, rep1


title: Bull 19 months, LT_02531, Replicate4

description: Longissimus thoracis (LT) muscle of Charolais bull calves at 19 months of age. The animals has a high growth potential (IC+). This muscle gives a meat which is not tender (T-) and which is of average juiciness (Jm) and flavor (Fm).

source_name: Bull 19 months, LT_02531

tag: Charolais 2003, Bull 19 months IC+, T-, Jm, Fm, Muscle LT


title: Bull 19 months, LT_02533, Replicate1


title: Bull 19 months, LT_02531, Replicate3


title: Bull 15 months, LT_02548, rep2


title: Bull 19 months, LT_02531, Replicate2


title: Gamma Radiation Response, Array 07997

status: Public on Aug 18 2006

city: Seattle

first: Nitin

last: Baliga

state: WA

address: 1441 North 34th St.

institute: Institute for Systems Biology

description: Post Gamma irradiation (2500Gy) 240 min vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35[optional]

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details

data_processing: AnalyzerDG software for spotfinding.  see http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details

label: Alexa 546

organism: Halobacterium salinarum NRC-1

source_name: Halobacterium NRC-1, reference

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1

extract_protocol: Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.

tag: Halobacterium NRC-1 grown in standard growth media

label: Alexa 647

source_name: Halobacterium NRC-1, Post gamma irradiation, 240 min

growth_protocol: Mid-log phase (OD600-0.4 - 0.7) Halobacterium NRC-1 control culture

tag: Halobacterium NRC-1 control culture in standard growth media at 42 C after gamma irradiation (60Co source) 2500 Gy.


title: Gamma Radiation Response, Array 07996

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35[optional]


title: Bull 19 months, LT_02531, Replicate1


title: Bull 19 months, LT_02547, Replicate1

description: Longissimus thoracis (LT) muscle of Charolais bull calves at 19 months of age. This muscle gives a meat which is flavored (Fm+) and which is of average tenderness (T) and juiciness (Jm)

source_name: Bull 19 months, LT_02547

tag: Charolais 2003, Bull 19 months, T, Jm, Fm+, Muscle LT


title: Gamma Radiation Response, Array 07995

description: Post Gamma irradiation (2500Gy) 120 min vs. reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

source_name: Halobacterium NRC-1, Post gamma irradiation, 120 min


title: Gamma Radiation Response, Array 07998

description: Gamma Control 40 min vs. reference

source_name: Halobacterium NRC-1, Control 40 min

tag: Halobacterium NRC-1 control culture in standard growth media at 42 C.


title: Gamma Radiation Response, Array 07994


title: Gamma Radiation Response, Array 07992

description: Post Gamma irradiation (2500Gy) 60 min vs. reference

source_name: Halobacterium NRC-1, Post gamma irradiation, 60 min


title: Gamma Radiation Response, Array 07990

description: Post Gamma irradiation (2500Gy) 50 min vs. reference

source_name: Halobacterium NRC-1, Post gamma irradiation, 50 min


title: Gamma Radiation Response, Array 07991


title: Gamma Radiation Response, Array 07993


title: Gamma Radiation Response, Array 07989

description: Post Gamma irradiation (2500Gy) 40 min vs. reference

source_name: Halobacterium NRC-1, Post gamma irradiation, 40 min


title: Gamma Radiation Response, Array 07986

description: Post Gamma irradiation (2500Gy) 30 min vs. reference

source_name: Halobacterium NRC-1, Post gamma irradiation, 30 min


title: Bull 15 months, LT_02548, rep1

source_name: Pool of 5 samples (muscle LT) of 19 months bulls


title: Gamma Radiation Response, Array 07988


title: Bull 19 months, LT_02547, Replicate2


title: Gamma Radiation Response, Array 07985

description: Post Gamma irradiation (2500Gy) 20 min vs. reference

source_name: Halobacterium NRC-1, Post gamma irradiation, 20 min


title: Gamma Radiation Response, Array 07983

description: Post Gamma irradiation (2500Gy) 10 min vs. reference

source_name: Halobacterium NRC-1, Post gamma irradiation, 10 min


title: Gamma Radiation Response, Array 07981

description: Post Gamma irradiation (2500Gy) 0 min vs. reference

source_name: Halobacterium NRC-1, Post gamma irradiation, 0 min


title: Gamma Radiation Response, Array 07980


title: Gamma Radiation Response, Array 07984


title: Gamma Radiation Response, Array 07979

description: Gamma Control 240 min vs. reference

source_name: Halobacterium NRC-1, Control 240 min


title: Gamma Radiation Response, Array 07976

description: Gamma Control 120 min vs. reference

source_name: Halobacterium NRC-1, Control 120 min


title: Gamma Radiation Response, Array 07978

description: Gamma Control 240 min vs. reference


title: Gamma Radiation Response, Array 07977

description: Gamma Control 120 min vs. reference


title: Gamma Radiation Response, Array 07936

description: Gamma Control 30 min vs. reference

source_name: Halobacterium NRC-1, Control 30 min


title: Gamma Radiation Response, Array 07975

description: Gamma Control 50 min vs. reference

source_name: Halobacterium NRC-1, Control 50 min


title: Gamma Radiation Response, Array 07937

description: Gamma Control 30 min vs. reference

source_name: Halobacterium NRC-1, reference


title: Gamma Radiation Response, Array 07973

description: Gamma Control 50 min vs. reference


title: Gamma Radiation Response, Array 07972

description: Gamma Control 50 min vs. reference


title: Gamma Radiation Response, Array 07935

description: Gamma Control 20 min vs. reference

source_name: Halobacterium NRC-1, Control 20 min


title: Gamma Radiation Response, Array 07934

description: Gamma Control 20 min vs. reference


title: Gamma Radiation Response, Array 07908

description: Gamma Control 10 min vs. reference

source_name: Halobacterium NRC-1, Control 10 min


title: Gamma Radiation Response, Array 07907

description: Gamma Control 10 min vs. reference


title: Gamma Radiation Response, Array 07982


title: Gamma Radiation Response, Array 07905

description: Gamma Control 0 min vs. reference

source_name: Halobacterium NRC-1, Control 0 min


title: Gamma Radiation Response, Array 07906

description: Gamma Control 0 min vs. reference


title: Gamma Radiation Response, Array 7006

label: Alexa 532


title: Gamma Radiation Response, Array 7004


title: Gamma Radiation Response, Array 7005


title: Gamma Radiation Response, Array 7007


title: Gamma Radiation Response, Array 7003


title: Gamma Radiation Response, Array 7002


title: Gamma Radiation Response, Array 6999

description: Gamma Control 960 min vs. reference

source_name: Halobacterium NRC-1, Control 960 min


title: Gamma Radiation Response, Array 07974

description: Gamma Control 60 min vs. reference

source_name: Halobacterium NRC-1, Control 60 min


title: Gamma Radiation Response, Array 6998

description: Gamma Control 960 min vs. reference


title: Gamma Radiation Response, Array 07971

description: Gamma Control 40 min vs. reference

source_name: Halobacterium NRC-1, Control 40 min


title: Gamma Radiation Response, Array 6997

description: Gamma Control 240 min vs. reference


title: Gamma Radiation Response, Array 6994

description: Gamma Control 60 min vs. reference


title: Gamma Radiation Response, Array 6996

description: Gamma Control 240 min vs. reference


title: Gamma Radiation Response, Array 6995

description: Gamma Control 60 min vs. reference


title: Gamma Radiation Response, Array 07001

source_name: Halobacterium NRC-1, Post gamma irradiation, 40 min


title: Gamma Radiation Response, Array 07008

source_name: Halobacterium NRC-1, Post gamma irradiation, 30 min


title: Gamma Radiation Response, Array 6989

description: Gamma Control 00 min vs. reference

source_name: Halobacterium NRC-1, Control 00 min


title: Gamma Radiation Response, Array 6988

description: Gamma Control 00 min vs. reference


title: Gamma Radiation Response, Array 06993

description: Gamma Control 30 min vs. reference


title: Gamma Radiation Response, Array 07000


title: Gamma Radiation Response, Array 06991

description: Gamma Control 10 min vs. reference


title: Gamma Radiation Response, Array 06990

description: Gamma Control 10 min vs. reference


title: Gamma Radiation Response, Array 06984

description: Post Gamma irradiation (2500Gy) 480 min vs. reference

source_name: Halobacterium NRC-1, Post gamma irradiation, 480 min


title: Gamma Radiation Response, Array 06987

description: Post Gamma irradiation (2500Gy) 960 min vs. reference

source_name: Halobacterium NRC-1, Post gamma irradiation, 960 min


title: Gamma Radiation Response, Array 6986


title: Gamma Radiation Response, Array 06760

source_name: Halobacterium NRC-1, Post gamma irradiation, 240 min


title: Gamma Radiation Response, Array 06758

source_name: Halobacterium NRC-1, Post gamma irradiation, 120 min


title: Gamma Radiation Response, Array 06985


title: Drosophila SL2_C2 versus C3_ replicate 2

first: Meghana

middle: M

last: Kulkarni

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: First, the total RNA is reverse transcribed using the included deoxynucleotide triphosphate mix and special Cy3/Cy5 RTdT primers. Thus, total RNA from the D1- and C1- treated samples were reverse transcribed using complementary Cy3 and Cy5 RTdT primers. Similarly total RNA from C2- and C3- treated samples were reverse transcribed using complementary Cy3/Cy5 RTdT primers (see Table 1 above). Then, the complementary cDNAs were mixed (D1 and C1; C2 and C3) and hybridized to the cDNA array. Cy3/Cy5 Fluorescent 3DNA reagents are then hybridized to the microarray in a second hybridization step. The Cy3 and Cy5 fluorescent 3DNA reagents will hybridize to the cDNA because they include a 'capture sequence' that is complementary to a sequence on the 5' end of the Cy3/Cy5 RT primer respectively. Each competitive hybridization was independently performed in triplicate including a color-flip to preclude dye bias.

scan_protocol: Post hybridization the microarrays were scanned using PMT-adjusted Axon's GenePix 4000B microarray scanner. GenePix Pro 5.0 was used for raw intensity value calculations.

data_processing: GenePix Results files (.GPR) were used as input for MIDAS V2.19 software (Saeed et al. 2003) to normalize the raw cDNA microarray signals by LOWESS method. We used t-test followed by the false discovery rate (FDR) adjustment to detect differentially expressed genes. The FDR adjusted p-value cutoff was 0.01. We calculated the base 2 log of the fold-changes. The clustering was performed by a hierarchical clustering algorithm with the centroid-linkage method.

organism: Drosophila melanogaster

source_name: Drosophila melanogaster SL2 culture cells, SL2 cells treated with double-stranded RNA (dsRNA)

label_protocol: 25 microgms of total RNA from Drosophila SL2 cells treated with C2 dsRNAs targeting the PP2A-B' gene were reverse transcribed and labeled using Superscript RT II (Invitrogen) and Genisphere's 3DNA Array 350 labeling kit.

growth_protocol: Drosophila Schneider SL2 cells were cultured in Schneider's medium (GibcoBRL) supplemented with 10% fetal bovine serum (JRH Bioscience) and Penicillin-Streptomycin (GibcoBRL) at 25 degree C, unless noted otherwise. 4x106 SL2 cells were seeded in each well of a 6-well cell culture dish (Falcon) in 1ml of serum-free media and treated with 15 microgms of dsRNA at room temperature for 45 min. After 45 min, 2 ml of serum-supplemented Schneider's medium was added and cells were further incubated for 72 hr. For expression profiling experiments three independent treatments were setup for each dsRNA.

extract_protocol: Total RNA was isolated by Trizol according to the manufacturer's specifications (GibcoBRL), purified with RNeasy columns (Qiagen) and quality was assessed using the Agilent Bioanalyzer according to manufacturer's specifications (Agilent)

treatment_protocol: SL2 cells treated with C2 dsRNA targeting all splice forms of the PP2A-B' gene

tag: Drosophila melanogaster SL2 culture cells, SL2 cells embryonically derived

label_protocol: 25 microgms of total RNA from Drosophila SL2 cells treated with C3 dsRNAs targeting the PP2A-B' gene were reverse transcribed and labeled using Superscript RT II (Invitrogen) and Genisphere's 3DNA Array 350 labeling kit.

growth_protocol: Drosophila Schneider SL2 cells were cultured in Schneider's medium (GibcoBRL) supplemented with 10% fetal bovine serum (JRH Bioscience) and Penicillin-Streptomycin (GibcoBRL) at 25 degree C, unless noted otherwise. 4x106 SL2 cells were seeded in each well of a 6-well cell culture dish (Falcon) in 1ml of serum-free media and treated with 15 microgmsof dsRNA at room temperature for 45 min. After 45 min, 2 ml of serum-supplemented Schneider's medium was added and cells were further incubated for 72 hr. For expression profiling experiments three independent treatments were setup for each dsRNA.

treatment_protocol: SL2 cells treated with C3 dsRNA targeting all splice forms of the PP2A-B' gene


title: Drosophila SL2_C2 versus C3_ replicate 1

hyb_protocol: First, the total RNA is reverse transcribed using the included deoxynucleotide triphosphate mix and special Cy3/Cy5 RTdT primers. Thus, total RNA from the D1- and C1- treated samples were reverse transcribed using complementary Cy3 and Cy5 RTdT primers. Similarly total RNA from C2- and C3- treated samples were reverse transcribed using complementary Cy3/Cy5 RTdT primers (see Table 1 above). Then, the complementary cDNAs were mixed (D1 and C1; C2 and C3) and hybridized to the cDNA array. Cy3/Cy5 Fluorescent 3DNA reagents are then hybridized to the microarray in a second hybridization step. The Cy3 and Cy5 fluorescent 3DNA reagents will hybridize to the cDNA because they include a 'capture sequence' that is complementary to a sequence on the 5' end of the Cy3/Cy5 RT primer respectively. Each competitive hybridization was independently performed in triplicate including a color-flip to preclude dye bias.


title: Gamma Radiation Response, Array 06759


title: Drosophila SL2_C1 versus D1_ replicate 3

label_protocol: 25 microgms of total RNA from Drosophila SL2 cells treated with C1 dsRNAs targeting the PP2A-B' gene were reverse transcribed and labeled using Superscript RT II (Invitrogen) and Genisphere's 3DNA Array 350 labeling kit.

treatment_protocol: SL2 cells treated with C1 dsRNA targeting the PP2A-B' gene

label_protocol: 25 microgms of total RNA from Drosophila SL2 cells treated with D1 dsRNAs targeting the PP2A-B' gene were reverse transcribed and labeled using Superscript RT II (Invitrogen) and Genisphere's 3DNA Array 350 labeling kit.

treatment_protocol: SL2 cells treated with D1 dsRNA targeting the PP2A-B' gene


title: Gamma Radiation Response, Array 06755


title: Drosophila SL2_C1 versus D1_ replicate 2

tag: Drosophila melanogaster SL2 culture cells, SL2 cells ebryonically derived


title: Gamma Radiation Response, Array 06756

source_name: Halobacterium NRC-1, Post gamma irradiation, 60 min


title: Normal pool vs MAM S49N 57a - mAdbID:48976

status: Public on Aug 17 2006

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

description: mAdb experiment ID: 48976

hyb_protocol: Sample Hybridization Protocol Other: Prior to hybridization, microarrays were pre-hybridized at 42C for 1 hour in pre-hybridization buffer containing 5X SSC, 0.1% SDS and 1% BSA, followed by washes at room temperature in water 2 min, isopropanol 2 min, and centrifugation 2 min at 700 rpm. Concentrated probes were hybridized to microarrays in hybridization buffer (50% formamide, 10X SSC, and 0.2% SDS pre-warmed to 42C) overnight at 42C. After 16 hours, slides were washed in 1X SSC containing 0.1% SDS, 1X SSC, 0.2X SSC for 2 min each and 0.05X SSC for 15 seconds.

data_processing: The expression data were filtered based on channel intensities, spot size and flags (missing data) and the Cye5/Cye3 ratios were calculated and normalized to the median centering of the log-ratio of all genes on the array.

source_name: Pooled Normal

label_protocol:
Cy3 Sample Labeling Protocol
Other: Isolated RNA (40 ug) was reverse transcribed by oligo dT-primed polymerization using Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA). The targets were coupled to Cye3-(normal pool) conjugated deoxynucleotides (Amersham Biosciences, Piscataway, NJ) for 1 hour at room temperature, followed by probe clean-up using the Qiaquick PCR Purification Kit (Qiagen, Valencia, CA). Probes were combined and concentrated using Microcon YM-30 columns (Millipore, Billerica, MA).

tag: Tissue

value: liver

tag: Other

value: A pooled RNA sample from 8 normal liver tissues was used as a common reference.

source_name: MAM S49N 57a

label_protocol:
Cy5 Sample Labeling Protocol
Other: Isolated RNA (40 ug) was reverse transcribed by oligo dT-primed polymerization using Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA). The targets were coupled to Cye5-(MIM or MAM) conjugated deoxynucleotides (Amersham Biosciences, Piscataway, NJ) for 1 hour at room temperature, followed by probe clean-up using the Qiaquick PCR Purification Kit (Qiagen, Valencia, CA). Probes were combined and concentrated using Microcon YM-30 columns (Millipore, Billerica, MA).

tag: Disease state

value: Hepatocellular Carcinoma


title: Gamma Radiation Response, Array 07987

source_name: Halobacterium NRC-1, reference


title: Gamma Radiation Response, Array 06761


title: Gamma Radiation Response, Array 06992

description: Gamma Control 30 min vs. reference

source_name: Halobacterium NRC-1, Control 30 min


title: Normal pool vs MAM S42N 55a - mAdbID:48972

description: mAdb experiment ID: 48972

source_name: MAM S42N 55a


title: Normal pool vs MIM S34N 61a - mAdbID:48716

description: mAdb experiment ID: 48716

source_name: MIM S34N 61a


title: Normal pool vs MAM S51N 59a - mAdbID:48710

description: mAdb experiment ID: 48710

source_name: MAM S51N 59a


title: Gamma Radiation Response, Array 06757


title: Normal pool vs MAM S47N 60a - mAdbID:48712

description: mAdb experiment ID: 48712

source_name: MAM S47N 60a


title: Normal pool vs MAM 45N 69a - mAdbID:48605

description: mAdb experiment ID: 48605

source_name: MAM 45N 69a


title: Normal pool vs MAM S46N 56a - mAdbID:48975

description: mAdb experiment ID: 48975

source_name: MAM S46N 56a


title: Normal pool vs MIM S33N 62a - mAdbID:48722

description: mAdb experiment ID: 48722

source_name: MIM S33N 62a


title: Normal pool vs MIM S25N 63a - mAdbID:48726

description: mAdb experiment ID: 48726

source_name: MIM S25N 63a


title: Normal pool vs MIM 12N 67b - mAdbID:48597

description: mAdb experiment ID: 48597

source_name: MIM 12N 67b


title: Normal pool vs MIM 26N 66b - mAdbID:48603

description: mAdb experiment ID: 48603

source_name: MIM 26N 66b


title: Normal pool vs MAM S57N 58a - mAdbID:48709

description: mAdb experiment ID: 48709

source_name: MAM S57N 58a


title: Normal pool vs MAM 44N 65b - mAdbID:48604

description: mAdb experiment ID: 48604

source_name: MAM 44N 65b


title: Drosophila SL2_C1 versus D1_ replicate 1

description: First, the total RNA is reverse transcribed using the included deoxynucleotide triphosphate mix and special Cy3/Cy5 RTdT primers. Thus, total RNA from the D1- and C1- treated samples were reverse transcribed using complementary Cy3 and Cy5 RTdT primers. Similarly total RNA from C2- and C3- treated samples were reverse transcribed using complementary Cy3/Cy5 RTdT primers (see Table 1 above). Then, the complementary cDNAs were mixed (D1 and C1; C2 and C3) and hybridized to the cDNA array. Cy3/Cy5 Fluorescent 3DNA reagents are then hybridized to the microarray in a second hybridization step. The Cy3 and Cy5 fluorescent 3DNA reagents will hybridize to the cDNA because they include a “capture sequence” that is complementary to a sequence on the 5’ end of the Cy3/Cy5 RT primer respectively. Each competitive hybridization was independently performed in triplicate including a color-flip to preclude dye bias.

scan_protocol: Post hybridization the microarrays were scanned using PMT-adjusted Axon’s GenePix 4000B microarray scanner. GenePix Pro 5.0 was used for raw intensity value calculations.

source_name: Drosophila melanogaster SL2 culture cells, SL2 cells treated with double-stranded RNA (dsRNA)

label_protocol: 25 microgms of total RNA from Drosophila SL2 cells treated with C1 dsRNAs targeting the PP2A-B’ gene were reverse transcribed and labeled using Superscript RT II (Invitrogen) and Genisphere’s 3DNA Array 350 labeling kit.

growth_protocol: Drosophila Schneider SL2 cells were cultured in Schneider’s medium (GibcoBRL) supplemented with 10% fetal bovine serum (JRH Bioscience) and Penicillin-Streptomycin (GibcoBRL) at 25 degree C, unless noted otherwise. 4x106 SL2 cells were seeded in each well of a 6-well cell culture dish (Falcon) in 1ml of serum-free media and treated with 15 microgms of dsRNA at room temperature for 45 min. After 45 min, 2 ml of serum-supplemented Schneider’s medium was added and cells were further incubated for 72 hr. For expression profiling experiments three independent treatments were setup for each dsRNA.

extract_protocol: Total RNA was isolated by Trizol according to the manufacturer’s specifications (GibcoBRL), purified with RNeasy columns (Qiagen) and quality was assessed using the Agilent Bioanalyzer according to manufacturer’s specifications (Agilent)

tag: Drosophila melanogaster SL2 culture cell, SL2 cells, embryonically derived

label_protocol: 25 microgms of total RNA from Drosophila SL2 cells treated with D1 dsRNAs targeting the PP2A-B’ gene were reverse transcribed and labeled using Superscript RT II (Invitrogen) and Genisphere’s 3DNA Array 350 labeling kit.

growth_protocol: Drosophila Schneider SL2 cells were cultured in Schneider’s medium (GibcoBRL) supplemented with 10% fetal bovine serum (JRH Bioscience) and Penicillin-Streptomycin (GibcoBRL) at 25 degree C, unless noted otherwise. 4x106 SL2 cells were seeded in each well of a 6-well cell culture dish (Falcon) in 1ml of serum-free media and treated with 15 microgmsof dsRNA at room temperature for 45 min. After 45 min, 2 ml of serum-supplemented Schneider’s medium was added and cells were further incubated for 72 hr. For expression profiling experiments three independent treatments were setup for each dsRNA.


title: Normal pool vs MAM S41N 54a - mAdbID:48966

description: mAdb experiment ID: 48966

source_name: Pooled Normal

source_name: MAM S41N 54a


title: Normal pool vs MIM 19N 74b - mAdbID:48596

description: mAdb experiment ID: 48596

source_name: MIM 19N 74b


title: Normal pool vs MIM S21N 76b - mAdbID:48370

description: mAdb experiment ID: 48370

source_name: MIM S21N 76b


title: Normal pool vs MIM S23N 75b - mAdbID:48384

description: mAdb experiment ID: 48384

source_name: MIM S23N 75b


title: Normal pool vs MAM S52N 79b - mAdbID:48358

description: mAdb experiment ID: 48358

source_name: MAM S52N 79b


title: CML-BM 9

city: Duesseldorf

first: Michael

last: Rosskopf

address: Universitaetsstrasse 1

department: Bioinformatics

country: Germany

institute: University of Duesseldorf

description: bone marrow CD34+ cells

data_processing: Using the affy package of functions of statistical scripting language 'R' integrated into the Bioconductor project data from cel files of each sample were normalized by variance stabilizing transformations (VSN) Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics 2002;18:96-104.

label: Biotin/Streptavidin-PE

source_name: bone marrow

tag: age	54

tag: gender	male

tag: disease	CML

tag: disease phase	chronic phase

tag: previous therapy	no

tag: bcr-abl/G6PDH ratio (%)	5.7

tag: leukocyte count (/nl)	52.2

tag: hemoglobin (g/dl)	9.3

tag: platelet count (/nl)	388


title: Normal pool vs MIM S14N 80a - mAdbID:48087

description: mAdb experiment ID: 48087

source_name: MIM S14N 80a


title: Normal pool vs MAM S55N 77a - mAdbID:48369

description: mAdb experiment ID: 48369

source_name: MAM S55N 77a


title: Platelet activating receptor factor and innate immunity: 251186821694

city: San Antonio

first: Deepak

last: Kaushal

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

description: Replicate two: differential expression analysis of CW treatment on RBEC6 cells

organism: Rattus norvegicus

source_name: Lyt44+TNF Replicate 2

extract_protocol: Qiagen RNeasy

tag: Cy3 labeled aa-cDNA from Lyt44+TNF Replicate 2 RNA

source_name: CW+TNF Replicate 2

tag: Cy5 labeled aa-cDNA from CW+TNF Replicate 2 RNA


title: Somatic fibroblasts

city: Beaverton

first: James

middle: Anthony

last: Byrne

state: OR

address: 505 NW 185th Ave

department: Reproductive Sciences

institute: ONPRC

description: Probe level measurements produced by Affymetrix Microarray Suite 5.0. Analysis performed at level of raw signal. (See Affymetrix Microarray Suite 5.0 reference on web site for description).

scan_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001).Scanning Hardware – HP GeneArray Scanner

data_processing: MAS 5.0; Data was normalized with Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)

organism: Macaca mulatta

source_name: Adult somatic skin fibroblasts

growth_protocol: Fibroblasts were grown at 37°C in 5% CO2 atmosphere in Dulbecco’s Modified Eagle’s Medium (DMEM) (Invitrogen) supplemented with 10% foetal bovine serum (FBS) (Hyclone).

extract_protocol: Total RNA was isolated using the Invitrogen RNA purification kit (Cat No.12183-018) with the optional DNase I treatment.

treatment_protocol: Confluent fibroblasts were trypsinized for total RNA purification.

tag: Adult rhesus macaque skin fibroblasts.


title: CML-BM 8

description: bone marrow CD34+ cells

tag: age	55

tag: bcr-abl/G6PDH ratio (%)	25.8

tag: leukocyte count (/nl)	206

tag: hemoglobin (g/dl)	10.1

tag: platelet count (/nl)	331


title: Platelet activation factor receptor and innate immunity: 251186821693

source_name: Lyt44 + TNF Replicate 1

tag: cy3 labeled aa-cDNA from Lyt44 + TNF Replicate 1 RNA

source_name: CW +TNF Replicate 1

tag: cy5 labeled aa-cDNA from CW + TNF Replicate 1 RNA


title: CML-BM 6

description: bone marrow CD34+ cells

tag: age	64

tag: gender	male

tag: disease	CML

tag: bcr-abl/G6PDH ratio (%)	7.1

tag: leukocyte count (/nl)	38.3

tag: hemoglobin (g/dl)	14.1

tag: platelet count (/nl)	212


title: Platelet activating factor receptor and innate immunity: 16011868021377

source_name: Neurons Replicate 2

tag: cy3 labeled aa-cDNA from Neurons Replicate 2 RNA

source_name: Neurons + CW Replicate 2

tag: cy5 labeled aa-cDNA from Neurons + CW Replicate 2 RNA


title: ORMES7

hyb_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)

source_name: Rhesus monkey embryonic stem cell lines ORMES7

growth_protocol: ORMES cells were grown at 37°C in 5% CO2 atmosphere on mitotically inactivated mouse embryonic fibroblasts (MEF) feeder cells in Dulbecco’s Modified Eagle’s Medium/F12 (DMEM/F12) (Invitrogen) supplemented with 15% foetal bovine serum (FBS) (Hyclone), 0.1 mM ß-mercaptoethanol (Sigma), 1% nonessential amino acids (Invitrogen), 4ng/ml FGF2, 2 mM L-glutamine (Invitrogen) and a pH of 7.2 (altered with 4N NaOH). ES cell colonies were manually passaged every 4-5 days.

treatment_protocol: Embryonic stem cells with good morphology were manually removed from culture for total RNA purification.

tag: Undifferentiated rhesus monkey Oregon Rhesus Macaque Embryonic Stem (ORMES) cell line 7.


title: ORMES9

source_name: Rhesus monkey embryonic stem cell lines ORMES9

label_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)

tag: Undifferentiated rhesus monkey Oregon Rhesus Macaque Embryonic Stem (ORMES) cell line 9.


title: CML-BM 5

description: bone marrow CD34+ cells

tag: age	69

tag: gender	female

tag: disease phase	chronic phase

tag: previous therapy	no

tag: bcr-abl/G6PDH ratio (%)	8.2

tag: leukocyte count (/nl)	9

tag: hemoglobin (g/dl)	14.3

tag: platelet count (/nl)	283


title: CML-BM 7

description: bone marrow CD34+ cells

tag: age	28

tag: disease	CML

tag: bcr-abl/G6PDH ratio (%)	11.2

tag: leukocyte count (/nl)	164

tag: hemoglobin (g/dl)	9.5

tag: platelet count (/nl)	842


title: CML-BM 4

description: bone marrow CD34+ cells

tag: age	52

tag: gender	male

tag: bcr-abl/G6PDH ratio (%)	4.4

tag: leukocyte count (/nl)	30.5

tag: hemoglobin (g/dl)	12.8

tag: platelet count (/nl)	359


title: Platelet activating factor receptor and innate immunity: 251186829677

description: Replicate three: differential expression analysis of CW + TNF treatment compared to Lyt44 + TNF treatment

source_name: Lyt44+TNF Replicate 3

tag: cy3 labeled aa-cDNA from Lyt44+TNF Replicate 3 RNA

source_name: CW+TNF Replicate 3

tag: cy5 labeled aa-cDNA from CW+TNF Replicate 3 RNA


title: Platelet activating factor receptor and innate immunity: 251186821865

source_name: Neurons Replicate 1

tag: cy3 labeled aa-cDNA from Neurons Replicate 1 RNA

source_name: Neurons + CW Replicate 1

tag: cy5 labeled aa-cDNA from Neurons + CW Replicate 1 RNA


title: ORMES6_biological repC

source_name: Rhesus monkey embryonic stem cell lines ORMES6C

tag: Undifferentiated rhesus monkey Oregon Rhesus Macaque Embryonic Stem (ORMES) cell line 6, biological replicate C (passage 31).


title: CML-BM 3

description: bone marrow CD34+ cells

source_name: bone marrow

tag: age	40

tag: gender	female

tag: disease phase	chronic phase

tag: previous therapy	no

tag: bcr-abl/G6PDH ratio (%)	9.5

tag: leukocyte count (/nl)	129

tag: hemoglobin (g/dl)	9.4

tag: platelet count (/nl)	261