title: T32, 12h, 2.5 uM Al, rep2

description: Medicago truncatula (T32) 12 hours after Al treatment rep2


title: S70, 48h, 2.5 uM Al, rep5

status: Public on Feb 08 2007

type: RNA

city: St Paul

first: Kathryn

middle: A

last: VandenBosch

state: MN

address: Room 250 BioSci 6022 1445 Gortner Ave

department: Plant Biology

country: USA

institute: University of Minnesota

description: Medicago truncatula 48 hours after Al treatment rep5

hyb_protocol: Microarrays for each time point were hybridized to cDNAs from both Al- treated and control roots, with cDNAs from the two different treatments labeled with Cy5 and Cy3 dyes. Each hybridization was repeated at least six times to account for technical variability, with triplicates of each dye combination to control for dye effects. A modified two-step hybridization reaction was performed as described in the 3DNA Array 900 Expression Array Detection Kit (Genisphere).

scan_protocol: Microarray slides were scanned using an GenePix4000B (Axon) two-laser scanner and image analysis was performed using GenePix 5.0 (Axon) software

data_processing: Background-subtracted mean intensities for both tissues were log2 transformed and normalized using lowess and ANOVA

molecule: total RNA

organism: Medicago truncatula

source_name: Medicago truncatula 48 hours after control (-Al) treatment

label_protocol: 11 ug RNA from each of 3 biological replicates was pooled to make a total of 33 ug for cDNA synthesis with a RT Primer for labeling with either Cy3 or Cy5 dye molecules using a 3DNA Array 900 Expression Array Detection Kit for cDNA Microarrays (Genisphere, Inc., Hatfield, PA). cDNA was synthesized following instructions from 3DNA Array 900 Expression Array Detection Kit Appendix A (Genisphere Inc.).

growth_protocol: Medicago truncatula seeds from each line were germinated as previously described (Penmetsa and Cook, 2000). Seedlings with radicles of about 1 cm in length were sown through the mesh bottoms of polypropylene cups. The cups were placed in precut holes of a plastic insert placed over a plastic tub that held 7.3 L of aerated nutrient solution. The nutrient solution contained: 1.2 mM KNO3, 0.8 mM Ca(NO3)2, 0.1 mM NH4H2PO4, 0.2 mM MgSO4, 10 uM FeNaEDTA, 50 uM KCl, 12.5 uM H3BO3, 1 uM MnSO4, 1 uM ZnSO4, 0.5 uM CuSO4, 0.1 uM Na2MoO4, and 0.1 uM NiCl2 (Pence et al., 2000). The pH of the nutrient solution was adjusted to 4.5 using 1 N HCl. Seedlings were grown for 72 h in a growth chamber (light/dark, 14/10 h) under a light intensity of 440 µmol photons m-2 s-1. Al treatment was initiated after 72 h by replacing the control growth solution with an identical solution that contained either 0 uM (control) or 2.5 uM Al added as AlK(SO4)3. The control and treatment solutions were adjusted to pH 4.5. Root tips (approximately 0.5 cm in length) from control and 2.5 uM Al treated seedlings were harvested at 12 and 48 h after Al treatment immediately frozen in liquid nitrogen.

extract_protocol: Root tip samples from 3 independent experimental replicates were collected for the experiment. RNA from frozen root tip samples was isolated using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) following the manufacturer's instructions.

tag: Medicago truncatula; lines - S70; tissue-root tips; age - 4 days; treatment - 48 hours after control (-Al) treatment

source_name: Medicago truncatula 48 hours after 2.5 uM Al treatment

tag: Medicago truncatula; lines - S70; tissue-root tips; age - 4 days; treatment - 48 hours after Al treatment


title: S70, 12h, 2.5 uM Al, rep1

description: Medicago truncatula  12 hours after Al treatment rep1

source_name: Medicago truncatula (S70) 12 hours after 2.5 uM Al treatment

growth_protocol: Medicago truncatula seeds from each line were germinated as previously described (Penmetsa and Cook, 2000). Seedlings with radicles of about 1 cm in length were sown through the mesh bottoms of polypropylene cups. The cups were placed in precut holes of a plastic insert placed over a plastic tub that held 7.3 L of aerated nutrient solution. The nutrient solution contained: 1.2 mM KNO3, 0.8 mM Ca(NO3)2, 0.1 mM NH4H2PO4, 0.2 mM MgSO4, 10 uM FeNaEDTA, 50 uM KCl, 12.5 uM H3BO3, 1 uM MnSO4, 1 uM ZnSO4, 0.5 uM CuSO4, 0.1 uM Na2MoO4, and 0.1 uM NiCl2 (Pence et al., 2000). The pH of the nutrient solution was adjusted to 4.5 using 1 N HCl. Seedlings were grown for 72 h in a growth chamber (light/dark, 14/10 h) under a light intensity of 440 umol photons m-2 s-1. Al treatment was initiated after 72 h by replacing the control growth solution with an identical solution that contained either 0 uM (control) or 2.5 uM Al added as AlK(SO4)3. The control and treatment solutions were adjusted to pH 4.5.  Root tips (approximately 0.5 cm in length) from control and 2.5 uM Al treated seedlings were harvested at 12 and 48 h after Al treatment immediately frozen in liquid nitrogen.

tag: Medicago truncatula; lines - S70; tissue-root tips; age - 4 days; treatment -  12 hours after Al treatment

source_name: Medicago truncatula (S70) 12 hours after control (-Al) treatment

tag: Medicago truncatula; lines - S70; tissue-root tips; age - 4 days; treatment -  12 hours after control (-Al) treatment


title: S70, 12h, 2.5 uM Al, rep3

description: Medicago truncatula (S70) 12 hours after Al treatment rep3


title: T32, 48h, 2.5 uM Al, rep1

description: Medicago truncatula (T32) 48 hours after Al treatment rep1

source_name: Medicago truncatula (T32) 48 hours after 2.5 uM Al treatment

tag: Medicago truncatula; lines - T32; tissue-root tips; age - 4 days; treatment -  48 hours after Al treatment

source_name: Medicago truncatula (T32) 48 hours after control (-Al) treatment

tag: Medicago truncatula; lines - T32; tissue-root tips; age - 4 days; treatment -  48 hours after control (-Al) treatment


title: T32, 48h, 2.5 uM Al, rep2

description: Medicago truncatula (T32) 48 hours after Al treatment rep2


title: T32, 12h, 2.5 uM Al, rep1

description: Medicago truncatula (T32) 12 hours after Al treatment rep1

source_name: Medicago truncatula (T32) 12 hours after 2.5 uM Al treatment

tag: Medicago truncatula; lines - T32; tissue-root tips; age - 4 days; treatment -  12 hours after Al treatment

source_name: Medicago truncatula (T32) 12 hours after control (-Al) treatment

tag: Medicago truncatula; lines - T32; tissue-root tips; age - 4 days; treatment -  12 hours after control (-Al) treatment


title: S70, 12h, 2.5 uM Al, rep6

description: Medicago truncatula (S70) 12 hours after Al treatment rep6


title: T32, 12h, 2.5 uM Al, rep4

description: Medicago truncatula (T32) 12 hours after Al treatment rep4


title: Gastric mucosal scrapings #5

city: Los Angeles

first: Nils

middle: Werner Georg

last: Lambrecht

state: CA

address: 11301 Wilshire Blvd, Bldg.113, Rm.325A

department: Physiology

institute: UCLA

description: Manufacturer's scanner and feature extraction - normalization software

hyb_protocol: Agilent 44K hybridization, 17 hrs

scan_protocol: Agilent scanner and Feature Extraction Software

data_processing: Genespring 7.3

organism: Rattus norvegicus

source_name: rat gastric mucosa

label_protocol: Low RNA Input Fluor Linear Amplification Kit (Agilent Technologies, USA)

extract_protocol: NucleoSpin RNA II (BD Biosciences, USA)

treatment_protocol: free access to food and water

tag: gastric mucosal scrapings, mixed homogenate total RNA isolate


title: Fasting gastric mucosal scrapings #6

treatment_protocol: 24 hr fasted rats, free access to water

tag: gastric mucosal scrapings from 24 hr fasted rats, mixed homogenate total RNA isolate


title: S70, 12h, 2.5 uM Al, rep2

description: Medicago truncatula  (S70) 12 hours after Al treatment rep2


title: Gastric mucosal scrapings #4


title: S70, 48h, 2.5 uM Al, rep2

description: Medicago truncatula 48 hours after Al treatment rep2


title: T32, 12h, 2.5 uM Al, rep5

description: Medicago truncatula (T32) 12 hours after Al treatment rep5


title: Gastric mucosal scrapings #3


title: Fasting gastric mucosal scrapings #5


title: S70, 48h, 2.5 uM Al, rep3

description: Medicago truncatula 48 hours after Al treatment rep3


title: Fasting gastric mucosal scrapings #4


title: CT46 Clock;liver;NONE;C57/BL6x129 mop3 KO;38585

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description: circadian liver_ clock and wt_gcrma

hyb_protocol: standard Affymetrix procedures except for use of a custom 24-channel fluidics machine

scan_protocol: standard Affymetrix procedures

data_processing: gcRMA

label: biotin

organism: Mus musculus

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.


title: CT38 Clock;liver;NONE;C57/BL6x129 mop3 KO;38581

description: circadian liver_ clock and wt_gcrma


title: CT34 Clock;liver;NONE;C57/BL6x129 mop3 KO;38574

description: circadian liver_ clock and wt_gcrma


title: CT30 Clock;liver;NONE;C57/BL6x129 mop3 KO;38573

type: mixed

description: circadian liver_ clock and wt_gcrma

molecule: other


title: CT62;liver;NONE;C57/BL6;37468

description: Circadian Liver_48hr_gcrma


title: CT42 Clock;liver;NONE;C57/BL6x129 mop3 KO;38583

description: circadian liver_ clock and wt_gcrma


title: CT42 Clock;liver;NONE;C57/BL6x129 mop3 KO;38582

description: circadian liver_ clock and wt_gcrma


title: CT38 Clock;liver;NONE;C57/BL6x129 mop3 KO;38580

description: circadian liver_ clock and wt_gcrma


title: CT22 Clock;liver;NONE;38564

description: circadian liver_ clock and wt_gcrma

source_name: CT22 Clock;liver;NONE;38564

tag: CT22 Clock;liver;NONE;38564


title: CT46 Clock;liver;NONE;C57/BL6x129 mop3 KO;38584

description: circadian liver_ clock and wt_gcrma


title: CT26 Clock;liver;NONE;C57/BL6x129 wildtype;38569

description: circadian liver_ clock and wt_gcrma


title: CT30 Clock;liver;NONE;C57/BL6x129 mop3 KO;38572

description: circadian liver_ clock and wt_gcrma


title: CT58;liver;NONE;C57/BL6;37465

description: Circadian Liver_48hr_gcrma


title: CT26 Clock;liver;NONE;C57/BL6x129 wildtype;38568

description: circadian liver_ clock and wt_gcrma


title: CT22 Clock;liver;NONE;38565

description: circadian liver_ clock and wt_gcrma

source_name: CT22 Clock;liver;NONE;38565

tag: CT22 Clock;liver;NONE;38565


title: CT54;liver;NONE;C57/BL6;37464

description: Circadian Liver_48hr_gcrma


title: CT58;liver;NONE;C57/BL6;37466

description: Circadian Liver_48hr_gcrma


title: CT54;liver;NONE;C57/BL6;37463

description: Circadian Liver_48hr_gcrma


title: CT46;liver;NONE;C57/BL6;37460

description: Circadian Liver_48hr_gcrma


title: CT38;liver;NONE;C57/BL6;37455

description: Circadian Liver_48hr_gcrma


title: CT34;liver;NONE;C57/BL6;37454

description: Circadian Liver_48hr_gcrma


title: CT50;liver;NONE;C57/BL6;37462

description: Circadian Liver_48hr_gcrma


title: CT26;liver;NONE;C57/BL6;37450

description: Circadian Liver_48hr_gcrma


title: CT34 Clock;liver;NONE;C57/BL6x129 mop3 KO;38575

description: circadian liver_ clock and wt_gcrma


title: CT42;liver;NONE;C57/BL6;37457

description: Circadian Liver_48hr_gcrma


title: CT42;liver;NONE;C57/BL6;37458

description: Circadian Liver_48hr_gcrma


title: CT30;liver;NONE;C57/BL6;37452

description: Circadian Liver_48hr_gcrma


title: CT38;liver;NONE;C57/BL6;37456

description: Circadian Liver_48hr_gcrma


title: CT46;liver;NONE;C57/BL6;37459

description: Circadian Liver_48hr_gcrma


title: CT62;liver;NONE;C57/BL6;37467

description: Circadian Liver_48hr_gcrma


title: CT34;liver;NONE;C57/BL6;37453

description: Circadian Liver_48hr_gcrma


title: CT50;liver;NONE;C57/BL6;37461

description: Circadian Liver_48hr_gcrma


title: Radiation survivor colony A24

type: genomic

city: Durham

first: Juan Lucas

last: Argueso

state: SP

address: 371 CARL Building, Box 3054

department: Molecular Genetics and Microbiology

institute: Duke University Medical Center

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and that of a radiation survivor colony.

hyb_protocol: DNA was hybridized according to Lemoine et al 2005, Cell 120:587.

scan_protocol: Arrays were scanned with a GenePix 4000B scanner. Red and Green PMT gain were manually adjusted to about equal brightness in each channel. Pixel size was 10um and 2 lines were averaged.

data_processing: The data in the VALUE column was obtained by analyzing the data deposited at the University of North Carolina Microarray database (genome.unc.edu). The data from repeated arrays were collapsed to a single value per spot and centered acoording to the median.  The VALUE corresponds to the Log2 RED/GREEN Normalized ratio based on the Median.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Reference strain genomic DNA

label_protocol: DNA was labelled according to Lemoine et al 2005, Cell 120:587.

extract_protocol: DNA was prepared according to Lemoine et al 2005, Cell 120:587.

tag: Reference strain genomic DNA

source_name: A24 isolate genomic DNA

tag: A24 isolate genomic DNA


title: Radiation survivor colony A20

source_name: A20 isolate genomic DNA

tag: A20 isolate genomic DNA


title: Radiation survivor colony A23

source_name: A23 isolate genomic DNA

tag: A23 isolate genomic DNA


title: Radiation survivor colony A21

source_name: A21 isolate genomic DNA

tag: A21 isolate genomic DNA


title: Radiation survivor colony A19

source_name: A19 isolate genomic DNA

tag: A19 isolate genomic DNA


title: CT22;liver;NONE;C57/BL6;37448

description: Circadian Liver_48hr_gcrma


title: CT18;liver;NONE;C57/BL6;37445

description: Circadian Liver_48hr_gcrma

extract_protocol: Tissues were collected from 5 Clock/Clock mutants at each timepoint except for 34 and 46 hours after the onset of DD, when tissues from 10 Clock/Clock mice were collected and run as independent replicates. Mice were sacrificed by cervical dislocation, and the optic nerves were severed in complete darkness; brain dissection was performed using illumination from an infrared viewer (FJW Industries, Palatine, IL). SCNs were dissected out, pooled at a density of 5 per tube in 100 ?l RNAlater (Ambion, Austin, TX), frozen on dry ice, and stored at –80?C until use.


title: CT26;liver;NONE;C57/BL6;37449

description: Circadian Liver_48hr_gcrma


title: CT30;liver;NONE;C57/BL6;37451

description: Circadian Liver_48hr_gcrma


title: 3am C;Muscles;NONE;C57/BL6 clock KO;38849

description: circadian muscle_clock mutant_24hr_gcrma


title: 3am D;Muscles;NONE;C57/BL6 clock KO;38850


title: 11pm B;Muscles;NONE;C57/BL6 clock KO;38848


title: CT18;liver;NONE;C57/BL6;37446

description: Circadian Liver_48hr_gcrma


title: Radiation survivor colony A22

source_name: A22 isolate genomic DNA

tag: A22 isolate genomic DNA


title: Radiation survivor colony A15

source_name: A15 isolate genomic DNA

tag: A15 isolate genomic DNA


title: Radiation survivor colony A16

source_name: A16 isolate genomic DNA

tag: A16 isolate genomic DNA


title: Radiation survivor colony A14

source_name: A14 isolate genomic DNA

tag: A14 isolate genomic DNA


title: 11pm A;Muscles;NONE;C57/BL6 clock KO;38847


title: Radiation survivor colony A17

source_name: A17 isolate genomic DNA

tag: A17 isolate genomic DNA


title: 7pm B;Muscles;NONE;C57/BL6 clock KO;38846


title: 7pm A;Muscles;NONE;C57/BL6 clock KO;38845


title: Radiation survivor colony A18

source_name: A18 isolate genomic DNA

tag: A18 isolate genomic DNA


title: Radiation survivor colony A11

source_name: A11 isolate genomic DNA

tag: A11 isolate genomic DNA


title: Radiation survivor colony A12

source_name: A12 isolate genomic DNA

tag: A12 isolate genomic DNA


title: Radiation survivor colony A13

source_name: A13 isolate genomic DNA

tag: A13 isolate genomic DNA


title: Radiation survivor colony A10

source_name: A10 isolate genomic DNA

tag: A10 isolate genomic DNA


title: Radiation survivor colony A9

source_name: A9 isolate genomic DNA

tag: A9 isolate genomic DNA


title: 3pm A;Muscles;NONE;C57/BL6 clock KO;38843


title: 11am B;Muscles;NONE;C57/BL6 clock KO;38842


title: 11am A;Muscles;NONE;C57/BL6 clock KO;38841


title: Radiation survivor colony A8

source_name: Reference strain genomic DNA

tag: Reference strain genomic DNA

source_name: A8 isolate genomic DNA

tag: A8 isolate genomic DNA


title: Radiation survivor colony A3

source_name: A3 isolate genomic DNA

tag: A3 isolate genomic DNA


title: Radiation survivor colony A4

source_name: A4 isolate genomic DNA

tag: A4 isolate genomic DNA


title: Radiation survivor colony A2

source_name: A2 isolate genomic DNA

tag: A2 isolate genomic DNA


title: Radiation survivor colony A6

source_name: A6 isolate genomic DNA

tag: A6 isolate genomic DNA


title: 3am A;Muscles;NONE;C57/BL6 clock KO;38837


title: Radiation survivor colony A7

source_name: A7 isolate genomic DNA

tag: A7 isolate genomic DNA


title: Radiation survivor colony A5

source_name: A5 isolate genomic DNA

tag: A5 isolate genomic DNA


title: Radiation survivor colony JW12

source_name: JW12 isolate genomic DNA

tag: JW12 isolate genomic DNA


title: Radiation survivor colony JW13

source_name: JW13 isolate genomic DNA

tag: JW13 isolate genomic DNA


title: 3am B;Muscles;NONE;C57/BL6 clock KO;38838


title: 3pm B;Muscles;NONE;C57/BL6 clock KO;38844


title: Radiation survivor colony A1

source_name: A1 isolate genomic DNA

tag: A1 isolate genomic DNA


title: Radiation survivor colony JW8

source_name: JW8 isolate genomic DNA

tag: JW8 isolate genomic DNA


title: Radiation survivor colony JW9

source_name: JW9 isolate genomic DNA

tag: JW9 isolate genomic DNA


title: Radiation survivor colony JW11

source_name: JW11 isolate genomic DNA

tag: JW11 isolate genomic DNA


title: Radiation survivor colony JW10

source_name: JW10 isolate genomic DNA

tag: JW10 isolate genomic DNA


title: Radiation survivor colony JW7

source_name: JW7 isolate genomic DNA

tag: JW7 isolate genomic DNA


title: CT58B;skeletal muscle;NONE;C57/BL6;30538

description: Circadian muscle48hr_gcrma


title: Radiation survivor colony JW6

source_name: JW6 isolate genomic DNA

tag: JW6 isolate genomic DNA


title: CT50B;skeletal muscle;NONE;C57/BL6;30534

description: Circadian muscle48hr_gcrma


title: 7am A;Muscles;NONE;C57/BL6 clock KO;38839


title: CT58A;skeletal muscle;NONE;C57/BL6;30537

description: Circadian muscle48hr_gcrma


title: CT50A;skeletal muscle;NONE;C57/BL6;30533

description: Circadian muscle48hr_gcrma


title: Heart, MAT1 CKO, 2 wk, sample 4

city: Houston

first: Michael

last: Schneider

state: TX

address: One Baylor Plaza, Room 506D

department: Center for Cardiovascular Development

institute: Baylor College of Medicine

description: Heart, MAT1 CKO, 2 wk, sample 4

hyb_protocol: Samples were hybridized to MG U74Av2 arrays (Affymetrix), and stained with streptavidin-phycoerythrin.

scan_protocol: Fluorescence intensities were captured with an Affimetrix GeneArray 2500 Scanner and quantified with Affymetrix Microarray Suite 5.0.

data_processing: Data were normalized and analyzed using dChip2004 (Li and Wong, 2001).

label: biotin, streptavidin-phycoerythrin

source_name: Heart, MAT1 CKO, 2 wk, sample 4

label_protocol: Samples were labeled with biotinylated nucleotides by reverse transcription.

extract_protocol: RNA was isolated with Trizol (Invitrogen) and purified using RNeasy columns (Qiagen).

tag: Heart, MAT1 CKO, 2 wk, sample 4


title: CT62A;skeletal muscle;NONE;C57/BL6;30539

description: Circadian muscle48hr_gcrma


title: Heart, MAT1 CKO, 2 wk, sample 3

description: Heart, MAT1 CKO, 2 wk, sample 3

source_name: Heart, MAT1 CKO, 2 wk, sample 3

tag: Heart, MAT1 CKO, 2 wk, sample 3


title: 7am B;Muscles;NONE;C57/BL6 clock KO;38840


title: CT42B;skeletal muscle;NONE;C57/BL6;30530

description: Circadian muscle48hr_gcrma


title: CT46B;skeletal muscle;NONE;C57/BL6;30532

description: Circadian muscle48hr_gcrma


title: CT62B;skeletal muscle;NONE;C57/BL6;30540

description: Circadian muscle48hr_gcrma


title: CT54B;skeletal muscle;NONE;C57/BL6;30536

description: Circadian muscle48hr_gcrma


title: CT42A;skeletal muscle;NONE;C57/BL6;30529

description: Circadian muscle48hr_gcrma


title: Heart, MAT1 CKO, 2 wk, sample 2

description: Heart, MAT1 CKO, 2 wk, sample 2

source_name: Heart, MAT1 CKO, 2 wk, sample 2

tag: Heart, MAT1 CKO, 2 wk, sample 2


title: Radiation survivor colony JW3

source_name: Reference strain genomic DNA

tag: Reference strain genomic DNA

source_name: JW3 isolate genomic DNA

tag: JW3 isolate genomic DNA


title: Radiation survivor colony JW4

source_name: JW4 isolate genomic DNA

tag: JW4 isolate genomic DNA


title: Radiation survivor colony JW5

source_name: JW5 isolate genomic DNA

tag: JW5 isolate genomic DNA


title: Heart, MAT1 CKO, 2 wk, sample 1

description: Heart, MAT1 CKO, 2 wk, sample 1

source_name: Heart, MAT1 CKO, 2 wk, sample 1

tag: Heart, MAT1 CKO, 2 wk, sample 1


title: Heart, MAT1 control, 2 wk, sample 3

description: Heart, MAT1 control, 2 wk, sample 3

source_name: Heart, MAT1 control, 2 wk, sample 3

tag: Heart, MAT1 control, 2 wk, sample 3


title: Radiation survivor colony JW2

source_name: JW2 isolate genomic DNA

tag: JW2 isolate genomic DNA


title: Radiation survivor colony JW1

source_name: JW1 isolate genomic DNA

tag: JW1 isolate genomic DNA


title: Control 4

description: This REFxREF array was used to provide a control for the CGH Miner analysis.


title: CT54A;skeletal muscle;NONE;C57/BL6;30535

description: Circadian muscle48hr_gcrma


title: Heart, MAT1 CKO, 4 wk, sample 5

description: Heart, MAT1 CKO, 4 wk, sample 5

source_name: Heart, MAT1 CKO, 4 wk, sample 5

tag: Heart, MAT1 CKO, 4 wk, sample 5


title: Heart, MAT1 control, 2 wk, sample 1

description: Heart, MAT1 control, 2 wk, sample 1

source_name: Heart, MAT1 control, 2 wk, sample 1

tag: Heart, MAT1 control, 2 wk, sample 1


title: CT34B;skeletal muscle;NONE;C57/BL6;30526

description: Circadian muscle48hr_gcrma


title: CT46A;skeletal muscle;NONE;C57/BL6;30531

description: Circadian muscle48hr_gcrma


title: CT38A;skeletal muscle;NONE;C57/BL6;30527

description: Circadian muscle48hr_gcrma


title: Heart, MAT1 CKO, 4 wk, sample 4

description: Heart, MAT1 CKO, 4 wk, sample 4

source_name: Heart, MAT1 CKO, 4 wk, sample 4

tag: Heart, MAT1 CKO, 4 wk, sample 4


title: CT34A;skeletal muscle;NONE;C57/BL6;30525

description: Circadian muscle48hr_gcrma


title: CT26B;skeletal muscle;NONE;C57/BL6;30522

description: Circadian muscle48hr_gcrma


title: Control 3


title: Control 1


title: Heart, MAT1 CKO, 4 wk, sample 3

description: Heart, MAT1 CKO, 4 wk, sample 3

source_name: Heart, MAT1 CKO, 4 wk, sample 3

tag: Heart, MAT1 CKO, 4 wk, sample 3


title: Heart, MAT1 CKO, 4 wk, sample 2

description: Heart, MAT1 CKO, 4wk, sample 2

source_name: Heart, MAT1 CKO, 4wk, sample 2

tag: Heart, MAT1 CKO, 4wk, sample 2


title: CT30A;skeletal muscle;NONE;C57/BL6;30523

description: Circadian muscle48hr_gcrma


title: Heart, MAT1 control, 2 wk, sample 2

description: Heart, MAT1 control, 2 wk, sample 2

source_name: Heart, MAT1 control, 2 wk, sample 2

tag: Heart, MAT1 control, 2 wk, sample 2


title: CT38B;skeletal muscle;NONE;C57/BL6;30528

description: Circadian muscle48hr_gcrma


title: Control 2


title: CT30B;skeletal muscle;NONE;C57/BL6;30524

description: Circadian muscle48hr_gcrma


title: CT26A;skeletal muscle;NONE;C57/BL6;30521

description: Circadian muscle48hr_gcrma


title: CT22B;skeletal muscle;NONE;C57/BL6;30520

description: Circadian muscle48hr_gcrma


title: CT22A;skeletal muscle;NONE;C57/BL6;30519

description: Circadian muscle48hr_gcrma


title: CT18B;skeletal muscle;NONE;C57/BL6;30518

description: Circadian muscle48hr_gcrma


title: Heart, MAT1 control, 4 wk, sample 2

description: Heart, MAT1 control, 4 wk, sample 2

hyb_protocol: Samples were hybridized to MG U74Av2 arrays (Affymetrix) and stained with streptavidin-phycoerythrin.

scan_protocol: Fluorescence intensities were captured with a an Affimetrix GeneArray 2500 Scanner, and quantified with Affymetrix Microarray Suite 5.0.

source_name: Heart, MAT1 control, 4 wk, sample 2

tag: Heart, MAT1 control, 4 wk, sample 2


title: Heart, MAT1 control, 4 wk, sample 3

description: Heart, MAT1 control, 4 wk, sample 3

source_name: Heart, MAT1 control, 4 wk, sample 3

extract_protocol: RNA was isolated using TRIzol (Invitrogen) and RNeasy reagents (Qiagen).

tag: Heart, MAT1 control, 4 wk, sample 3


title: Series 5:  Normal female

status: Public on Feb 07 2007

city: Charlotte

first: Ralph

middle: A.

last: Meyer

state: NC

department: Orthopaedic Research Laboratory

institute: Carolinas Medical Center

description: Experimental design.   Equal amounts of RNA from two mice, matched for genotype and sex were pooled to create each sample for microarray analysis.  Four treatment groups were done:  (1) Normal male mice, (2) Hyp male mice, (3) normal female mice, and (4) Hyp female mice.   Five replicates were done with each replicate containing one sample from each of the four treatment groups for a total of 20 independent samples (40 mice total).  Each replicate was matched for littermates and parallel processing.

hyb_protocol: Samples were processed as described in the Affymetrix GeneChip Expression Analysis Technical Manual (copyright 2004, Affymetrix, Inc., Santa Clara, CA, Rev. 6, Part number 701025, http://www.affymetrix.com).  The fragmented cRNA from the 20 independent samples was hybridized to 20 mouse 430 2.0 GeneChip microarrays (Affymetrix P/N 520029) in Affymetrix hybridization buffer for 16 hours at 45 C.  The hybridized arrays were washed and stained in the Affymetrix Fluidics Station 400 to attach fluorescent labels to the biotin, followed by biotin-labeled antibody, and then a second staining with fluorescent labeling of the biotin.

scan_protocol: Each array was scanned once with the Affymetrix GeneArray Scanner 3000.

data_processing: The data were analyzed with Affymetrix GeneChip Operating System (GCOS) 1.2.  GCOS was used for quality control for each array and to scale the mRNA expression (signal value) of each gene so that the average of all genes is set to 500.  GCOS was used to create a single pivot table with 45,101 genes for all 20 samples.

label: Biotin-labeled cRNA

source_name: Mouse femoral shaft

label_protocol: Samples were processed as described in the Affymetrix GeneChip Expression Analysis Technical Manual (copyright 2004, Affymetrix, Inc., Santa Clara, CA, Rev. 6, Part number 701025, http://www.affymetrix.com).  Samples of RNA were purified on RNeasy columns from Qiagen (Valencia, CA, P/N 74104) and then 8 ug purified RNA were converted to double-stranded cDNA with an Affymetrix One-Cycle cDNA Synthesis Kit (P/N 900431).  The cDNA was then expressed as biotin-labeled cRNA by in vitro transcription (IVT) with the 3' Amplification Reagents for IVT Labeling (Affymetrix P/N 900449).  Each sample was spiked with bioB, bioC, bioD, and cre (Affymetrix P/N 900299).  The biotin-labeled cRNA was fragmented non-enzymatically.

extract_protocol: Samples were processed as described in the Affymetrix GeneChip Expression Analysis Technical Manual (copyright 2004, Affymetrix, Inc., Santa Clara, CA, Rev. 6, Part number 701025, http://www.affymetrix.com).  The sample preparation is described here in brief.  The femora were weighed and homogenized, and total RNA was extracted with TRIzol (Invitrogen Life Technologies, Carlsbad, CA).

treatment_protocol: Normal and X-linked hypophosphatemic, Hyp, mice were bred in our colony on the C57BL/6J background from stock originating from the Jackson Laboratory, Bar Harbor, ME.  The breeders were fed Teklad Mouse Breeder Diet (W) No. 8626 (Harlan, Madison, WI) and tap water ad lib.   Pups were weaned at three weeks of age and fed Teklad Rodent Diet (W) No. 8604 (Harlan).  At five weeks of age, Hyp mice (hemizygous male (Hyp/Y) and heterozygous female (Hyp/+)) and littermate normal (wild type) male and female mice were euthanized, and both femora were harvested.  The femora were cut at the metaphyseal/diaphyseal junction and the diaphyses were flushed with physiological saline to remove as much marrow as possible.  The resulting shafts were frozen in liquid nitrogen and stored at  70 C.


title: Heart, MAT1 CKO, 4 wk, sample 1

description: Heart, MAT1 CKO, 4 wk, sample 1

source_name: Heart, MAT1 CKO, 4 wk, sample 1

tag: Heart, MAT1 CKO, 4 wk, sample 1


title: Heart, MAT1 control, 4 wk, sample 1

description: Heart, MAT1 control, 4 wk, sample 1

source_name: Heart, MAT1 control, 4 wk, sample 1

tag: Heart, MAT1 control, 4 wk, sample 1


title: Series 5:  Hyp female


title: Tumor 7703

city: San Francisco

first: Joan

last: Climent

address: 2340 Sutter St

department: Cancer Research Institute

institute: UCSF Cancer Center

hyb_protocol: 72 hours

scan_protocol: CCD camera

data_processing: UCSF Spot (see Jain et al. 2002)

organism: Homo sapiens

source_name: genomic DNA

label_protocol: Random primer

extract_protocol: Standard DNA extraction

tag: Tumor nº

tag: Age (years)

tag: Hormonal Status

value: POSTMENOPAUSIC

tag: TNMPathol

tag: Stage

value: II

tag: Gender

value: FEMALE

tag: Recurrence Systemic

tag: TREATMENT ADCHEM

tag: DFS(months)

tag: Erval (Oestrogen Receptor expression)

value: POSITIVE

tag: PGRval

tag: normal genome


title: Series 4:  Normal female


title: CT18A;skeletal muscle;NONE;C57/BL6;30517

description: Circadian muscle48hr_gcrma


title: Series 5:  Hyp male


title: Series 3:  Normal male

label_protocol: Samples were processed as described in the Affymetrix GeneChip Expression Analysis Technical Manual (copyright 2004, Affymetrix, Inc., Santa Clara, CA, Rev. 6, Part number 701025, http://www.affymetrix.com).  Samples of RNA were purified on RNeasy columns from Qiagen (Valencia, CA, P/N 74104) and then 8 μg purified RNA were converted to double-stranded cDNA with an Affymetrix One-Cycle cDNA Synthesis Kit (P/N 900431).  The cDNA was then expressed as biotin-labeled cRNA by in vitro transcription (IVT) with the 3? Amplification Reagents for IVT Labeling (Affymetrix P/N 900449).  Each sample was spiked with bioB, bioC, bioD, and cre (Affymetrix P/N 900299).  The biotin-labeled cRNA was fragmented non-enzymatically.


title: Tumor 7676

value: NEGATIVE


title: Series 3:  Hyp female


title: Series 4:  Normal male


title: Series 5:  Normal male


title: Series 4:  Hyp male


title: Series 4:  Hyp female


title: Series 3:  Hyp male


title: Series 2:  Hyp male


title: Series 1:  Hyp male


title: Series 2:  Hyp female


title: Series 1:  Normal Male

label_protocol: Samples were processed as described in the Affymetrix GeneChip Expression Analysis Technical Manual (copyright 2004, Affymetrix, Inc., Santa Clara, CA, Rev. 6, Part number 701025, http://www.affymetrix.com).  Samples of RNA were purified on RNeasy columns from Qiagen (Valencia, CA, P/N 74104) and then 8 μg purified RNA were converted to double-stranded cDNA with an Affymetrix One-Cycle cDNA Synthesis Kit (P/N 900431).  The cDNA was then expressed as biotin-labeled cRNA by in vitro transcription (IVT) with the 3’ Amplification Reagents for IVT Labeling (Affymetrix P/N 900449).  Each sample was spiked with bioB, bioC, bioD, and cre (Affymetrix P/N 900299).  The biotin-labeled cRNA was fragmented non-enzymatically.


title: Series 1:  Normal female


title: Series 3:  Normal female


title: Series 2:  Normal female


title: Series 2:  Normal male


title: Tumor 7271

tag: Erval (Oestrogen Receptor expression) :

tag: PGRval:


title: Series 1:  Hyp female


title: Tumor 7277

value: NoHS(male)

value: MALE


title: Tumor 7222

value: I


title: Tumor 7320

value: PREMENOPAUSIC


title: Tumor 6083

value: :No Treatment


title: Tumor 7059


title: Tumor 7099


title: Tumor 6082


title: Tumor 6211

tag: TNMPathol :

tag: Stage:


title: Tumor 5849


title: Tumor 5839


title: Tumor 5226


title: Tumor 5657


title: Tumor 5173


title: Tumor 5186


title: Tumor 5430

value: PERIMENOPAUSICA


title: Tumor 5222


title: Tumor 5362


title: Tumor 5183


title: Tumor 4645


title: Tumor 5012


title: Tumor 4530


title: Tumor 4729


title: Tumor 4265


title: Tumor 5006


title: Tumor 4204


title: Tumor 4255


title: Tumor 4185


title: Tumor 4079


title: Tumor 4002


title: Tumor 3891


title: Tumor 3453


title: Tumor 3619


title: Tumor 3573


title: Tumor 3249


title: Tumor 3117


title: Tumor 3242


title: Tumor 3217

tag: Hormonal Status :


title: Tumor 3179

tag: Tumor nº


title: Tumor 3190

tag: Age (years)


title: Tumor 2405

tag: Hormonal Status


title: Tumor 2471

tag: TNMPathol


title: Tumor 2769

tag: Stage


title: Tumor 2524

tag: Gender


title: Tumor 2496

tag: Recurrence Systemic


title: Tumor 2325

tag: TREATMENT ADCHEM


title: Tumor 2715

tag: DFS(months)


title: Tumor 2907

tag: Erval (Oestrogen Receptor expression)


title: Tumor 3060

tag: PGRval


title: Tumor 2908

tag: normal genome


title: Tumor 2832


title: Tumor 2910


title: Tumor 2223


title: Tumor 2306


title: Tumor 2034


title: Tumor 2227


title: Tumor 2489


title: Tumor 1962


title: Tumor 1825


title: Tumor 1603


title: Tumor 1339


title: Tumor 1333


title: Tumor 1363


title: Tumor 1219


title: Tumor 1390


title: Tumor 1389


title: Tumor 1105


title: Tumor 1238


title: Tumor 690


title: Tumor 1078


title: Tumor 1475


title: Tumor 954


title: Tumor 1106


title: Tumor 1185


title: Tumor 717


title: Tumor 955


title: Tumor 1184


title: Tumor 1174


title: Tumor 1486


title: Tumor 363


title: Tumor 1388

value: DESCONOCIDO


title: Tumor 665


title: Tumor 444


title: Tumor 276


title: Tumor 333


title: Tumor 360


title: Tumor 1308


title: Tumor 152


title: Tumor 171


title: Tumor 191


title: Tumor 52


title: Tumor 6923


title: Tumor 6996

tag: Erval (Oestrogen Receptor expression) :


title: Tumor 6904

tag: PGRval:


title: Tumor 6843


title: Tumor 6798


title: Tumor 7071


title: Tumor 5799


title: Tumor 6058


title: Tumor 56


title: Tumor 6626


title: Tumor 6743


title: Tumor 133


title: Tumor 6358


title: Tumor 6057


title: Tumor 5660


title: Tumor 5688


title: Tumor 6698


title: Tumor 5699


title: Tumor 5948


title: Tumor 5995


title: Tumor 6631


title: Tumor 6630


title: Tumor 5943


title: Tumor 5973


title: Tumor 5654


title: Tumor 5856


title: Tumor 5588


title: Tumor 5579


title: Tumor 5593


title: Tumor 5471


title: Tumor 5179


title: Tumor 5552


title: Tumor 5117


title: Tumor 5225


title: Tumor 5083


title: Tumor 5067


title: Tumor 5264


title: Tumor 4710


title: Tumor 4632


title: Tumor 4398


title: Tumor 5062


title: Tumor 4445


title: Tumor 4466


title: Tumor 4953


title: Tumor 4284


title: Tumor 4431


title: Tumor 5026


title: Tumor 5057


title: Tumor 5559


title: Tumor 4236


title: Tumor 4216


title: Tumor 3837


title: Tumor 3572


title: Tumor 3359


title: Tumor 3392


title: Tumor 4878


title: Tumor 3236


title: Tumor 3274


title: Tumor 3241


title: Tumor 2584


title: Tumor 4306


title: Tumor 1177

value: IIIB


title: Tumor 2858


title: Tumor 1901


title: Tumor 3377


title: Tumor 1080


title: Tumor 2186


title: Tumor 1579


title: Tumor 1077


title: Tumor 1352


title: Tumor 1163


title: Tumor 3221


title: Tumor 700


title: Tumor 699


title: Tumor 1076


title: Tumor 1143


title: Tumor 1055


title: Tumor 416


title: Tumor 1201


title: Tumor 1144


title: Tumor 1338


title: Tumor 455


title: Tumor 4205


title: Tumor 415


title: PP-2 48 hr 2

description: PP-2 48 hr

hyb_protocol: hybridization followed standard Affymetrix protocols while array washing used a GNF custom machine

scan_protocol: standard Affymetrix procedures using the GeneChip 3000 scanner

source_name: PP-2 48 hr

label_protocol: cDNA synthesis and amplification employed the Affymetrix 3' IVT protocol.

extract_protocol: Normal human epidermal keratinocytes (NHEKs) were treated with DMSO or 9 (alias PP-2) (0.5 uM) and harvested at 12, 24, 36 and 48 h. Total RNA from each sample was isolated and purified with the RNeasy Mini Kit (Qiagen). Total RNA was examined on an Agilent Bioanalyzer and the 28S/18S ratio exceeded 2.0 for all samples.

tag: PP-2 48 hr


title: Tumor 306


title: Tumor 203


title: Tumor 286


title: Tumor 208


title: DMSO 48 hr 2

description: DMSO 48 hr

source_name: DMSO 48 hr

tag: DMSO 48 hr


title: PP-2 48 hr 1

description: PP-2 48 hr


title: DMSO 36 hr 1

description: DMSO 36 hr

source_name: DMSO 36 hr

tag: DMSO 36 hr


title: DMSO 48 hr 1

description: DMSO 48 hr


title: PP-2 36 hr 1

description: PP-2 36 hr

source_name: PP-2 36 hr

tag: PP-2 36 hr


title: PP-2 36 hr 2

description: PP-2 36 hr


title: DMSO 24 hr 2

description: DMSO 24 hr

source_name: DMSO 24 hr

tag: DMSO 24 hr


title: PP-2 24 hr 1

description: PP-2 24 hr

source_name: PP-2 24 hr

tag: PP-2 24 hr


title: DMSO 36 hr 2

description: DMSO 36 hr


title: DMSO 24 hr 1

description: DMSO 24 hr


title: Tumor 49

tag: Tumor nº

tag: Age (years)

tag: Hormonal Status

tag: TNMPathol


title: PP-2 24 hr 2

description: PP-2 24 hr


title: Tumor 139

tag: Stage

tag: Gender

tag: Recurrence Systemic

tag: TREATMENT ADCHEM


title: Tumor 154

tag: DFS(months)

tag: Erval (Oestrogen Receptor expression)

tag: PGRval

tag: normal genome


title: DMSO 12 hr 1

description: DMSO 12 hr

source_name: DMSO 12 hr

tag: DMSO 12 hr


title: PP-2 12 hr 2

description: PP-2 12 hr

source_name: PP-2 12 hr

tag: PP-2 12 hr


title: DMSO 12 hr 2

description: DMSO 12 hr


title: DMSO O hr 1

description: DMSO O hr

source_name: DMSO O hr

tag: DMSO O hr


title: DMSO O hr 2

description: DMSO O hr


title: PP-2 12 hr 1

description: PP-2 12 hr


title: Tumor 19


title: Rice non-coding RNA tiling array

status: Public on Feb 06 2007

type: other

city: New Haven

first: Xiangfeng

last: Wang

state: CT

address: 352 OML, 165 Prospect st

department: MCDB

institute: Yale University

description: non-coding RNA tiling array is designed at a very high resolution of 5-bp to mointoer the non-coding RNA's transcription activity.

hyb_protocol: Provided by NimbleGen Hybridization protocol

scan_protocol: Provided by NimbleGen Scanning protocol

data_processing: refer to "NMPP - a user cunstomized NimbleGen microarray data processing pipeline" by Xiangfeng Wang

organism: Oryza sativa

source_name: rice noncoding RNA tiling array

label_protocol: Provided by NimbleGen Labelling protocol

extract_protocol: on-coding RNA species were isolated from total RNA as previously described (5). Briefly, total RNA isolated from japonica rice leaves using the Trizol method was loaded onto an Qiagen-tip and eluted with 0.6~1.0M NaCl gradient of QRW2 buffer (Qiagen) at 50 oC. Fractions corresponding to tRNAs (sample I) and small RNAs of 80-500 nucleotides (nt) (sample II) were collected. To remove remaining mRNAs and rRNAs, the small RNA fractions were hybridized to a mixture of specifically designed oligos in the binding buffer. Unwanted RNA molecules were targeted and removed by a magnetic bead based process (MicrobExpress kit, Ambion). The enriched non-coding RNA pool was then dephosphorylated with a calf intestine alkaline phosphatase and ligated to a 3' adaptor oligonucleotide by the T4 RNA ligase (5). Small size molecules and excessive adaptors were removed from the ligation products using the mirVana miRNA isolation kit (Ambion) and reverse transcribed at 50 degrees C using the Thermoscript (Invitrogen) and the oligo 3RT as the primer (5). Amino-allyl-modified dCTP was incorporated into the cDNA strand during reverse transcription.

tag: 1Mb tiling array designed from a region (10~11Mb) of rice chromosome 10, and hybridized with non-coding RNA samples.


title: Wild-type (2MBS) b(16012201010080)

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: Wild-type (2MBS)

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004.  Agilent Publication Number:  G4140-90030 V4.1 APRIL 2004.   The manual can be found at  https://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=34961,  or through a WEB search on the manual title.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2505-64120 at 100% PMT in both channels, with a scan resolution of 10um.  A scan window of 61 x 21.6 mm was used, then images were cropped to size and saved in a modified two-color TIFF format.  Images were examined visually for evidence of foreign debris or major failures. Agilent Microarray Scanner User Manual (6.3) http://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=33696

data_processing: Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.

source_name: Wild-type (2MBS) b

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

growth_protocol: The UMRR is provided in a solution of 70% ethanol and 0.1 M sodium acetate. Prepare the UMRR for use as follows: 1.Centrifuge the tube at 12,000 x g for 15 minutes at 4C.  2.Carefully remove the supernatant. 3.Wash the pellet in 70% ethanol. 4.Centrifuge the tube at 12,000 x g for 15 minutes at 4C.  5.Carefully remove the supernatant and air-dry the pellet at room temperature for 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.

extract_protocol: RNA samples from embryonic skin were subjected to LiCl precipitation after Triazol isolation to eliminate genomic DNA contamination. LiCl precipitation was effective for cleaning RNA samples, which is proven in real-time PCR.

tag: Strain

value: male

tag: Age

value: 2 months

tag: Development stage

value: adult

source_name: Universal Mouse Reference RNA

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts

tag: Universale Mouse Reference


title: Wild-type TG (2MBS) 3(16012201010087)

description: Wild-type TG (2MBS)

source_name: Wild-type TG (2MBS) 3

value: C57BL/6J-EDA-A1 transgenic mice

tag: Genetic modification

value: EDA-A1 transgenic mice


title: Wild-type (2MBS) 6(16012201010081)

description: Wild-type (2MBS)

source_name: Wild-type (2MBS) 6


title: Wild-type TG (2MBS) 2(16012201010086)

description: Wild-type TG (2MBS)

source_name: Wild-type TG (2MBS) 2


title: Wild-type TG (2MBS) 1(16012201010085)

description: Wild-type TG (2MBS)

source_name: Wild-type TG (2MBS) 1


title: Rice tissue "XOO", replicate experiment 2

description: CAR: rice carpel; DES: rice developing seed; DKS: rice dark seedling shoot; FLL: rice flag leaf; LSS: rice light seedling shoot; MAL: rice mature leaf; SCC: rice suspension cell; SLR: rice seedling root; WFL: rice whole flower; XOO: rice leaf infected with Xoo.

hyb_protocol: Sample Hybridization protocol provided and performed by NimbleGen.

scan_protocol: Nimblegen. Sample scan protocol provided and performed by NimbleGen.

data_processing: refer to "NMPP, A user-customized NimbleGen Microarray Processing Pipeline", By Xiangfeng Wang

label_protocol: Sample labeling protocol provided and performed by NimbleGen.

growth_protocol: Light- and dark-grown seedlings (only the aerial part used for RNA isolation), suspension cultured cells, and panicles were prepared as previously described (1,2). For collecting other rice materials, seedlings were transferred to soil and maintained under long-day conditions (16 hour light/8 hour dark) at 26-28 degrees C in the greenhouse. After 7 weeks, 50 plants were transferred back into a growth chamber. Mature leaves from 25 plants were inoculated two days later with the pathogen Xanthomonas oryzae pv. oryzae race PXO99 (Xoo) using the leaf clip method (3). As a control, the leaves from another 25 plants were inoculated with distilled H2O. The inoculated leaves were harvested 80 hours post inoculation. During the flowering stage, flag leaves and flowers (florets) were harvested from 25 plants maintained in the greenhouse. Carpel tissue was collected before pollination using approximately 100 plants. Developing seeds were harvested three or four days after pollination using 25 plants. Stress treatments of rice seedlings were carried out as previously described.

extract_protocol: For mRNA collection, plant materials were frozen in liquid nitrogen and homogenized. Total RNA and mRNA were sequentially isolated using the RNeasy Plant Mini kit (Qiagen) and the Oligotex mRNA kit (Qiagen) according to the manufacturer's recommendations. For Northern blot analysis, total RNA was isolated from rice seedlings using the Trizol method (Invitrogen). Low-molecular-weight RNA was enriched and subsequent Northern blot analysis was carried out as previously described.

tag: Oryza. sativa ssp. japonica cv. Nipponbare


title: Rice tissue "DES", replicate experiment 3


title: Rice tissue "XOO", replicate experiment 1


title: Rice tissue "DES", replicate experiment 1


title: Wild-type (2MBS) a(16012201010079)

description: Wild-type (2MBS)

source_name: Wild-type (2MBS) a

tag: Gender


title: Tabby (16.5BS) 3(16012201010078)

description: Tabby (16.5BS)

source_name: Tabby (16.5BS) 3

value: embryo

value: Mutant Mice


title: Tabby (16.5BS) 2(16012201010077)

description: Tabby (16.5BS)

source_name: Tabby (16.5BS) 2


title: Rice tissue "FLL", replicate experiment 3


title: Rice tissue "STA", replicate experiment 2


title: Rice tissue "STA", replicate experiment 1


title: Rice tissue "XOO", replicate experiment 3


title: Rice tissue "FLL", replicate experiment 1


title: Rice tissue "CAR", replicate experiment 1


title: Rice tissue "DES", replicate experiment 2


title: Rice tissue "SCC", replicate experiment 3


title: Tabby (16.5BS) 1(16012201010076)

description: Tabby (16.5BS)

source_name: Tabby (16.5BS) 1


title: Rice tissue "SCC", replicate experiment 2


title: Rice tissue "WFL", replicate experiment 2


title: Rice tissue "FLL", replicate experiment 2


title: Rice tissue "CAR", replicate experiment 2


title: Rice tissue "SCC", replicate experiment 1


title: Rice tissue "WFL", replicate experiment 1


title: Rice tissue "STA", replicate experiment 3


title: Rice tissue "CAR", replicate experiment 3


title: Rice tissue "MAL", replicate experiment 3


title: Wild-type (16.5BS) 3(16012201010075)

description: Wild-type (16.5BS)

source_name: Wild-type (16.5BS) 3


title: Wild-type (16.5BS) 2(16012201010074)

description: Wild-type (16.5BS)

source_name: Wild-type (16.5BS) 2


title: Rice tissue "WFL", replicate experiment 3


title: Rice tissue "DKS", replicate experiment 3


title: Rice tissue "DKS", replicate experiment 1


title: Tabby (18.5FP) c(16012201010063)

description: Tabby (18.5FP)

source_name: Tabby (18.5FP) c


title: Rice tissue "MAL", replicate experiment 2


title: Yeast_WT_H4ac

city: Bethesda

first: Keji

last: Zhao

address: Rockville Pike

institute: NHLBI, NIH

description: The GMAT (Genome-wide MApping Technique) was developed by the combination of ChIP (chromatin immunoprecipitation) and SAGE(serial analysis of gene expression) protocols. Briefly, the chromatin prepared by sonication is subject to immunoprecipitation using specific antibody. DNA from precipitated chromatin is ligated with biotinylated linker and digested with NlaIII restriction enzyme. The DNA fragments with biotinylated linker are isolated and ligated with NlaIII-site specific linker. The DNA is cut with MmeI restriction enzyme to generate 21-base seqeunce tags and ligated each other to form ditags. After removing linkers by NlaIII, isolated ditags are concatenated and determined the sequence. The genomic position of tags is identified by DNA sequences and the detected number of each tag sequence represents the degree of enrichment by means of specific antibody.

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: count number, experimentally detected

label: not applicable

label_protocol: not applicable

extract_protocol: not applicable

tag: wild-type yeast strain, W303

tag: Antibody

value: histone H4 tetraacetylation at K5, K8, K16 and K20


title: Wild-type (16.5BS) 1(16012201010073)

description: Wild-type (16.5BS)

source_name: Wild-type (16.5BS) 1


title: Wild-type (18.5FP) e(16012201010062)

description: Wild-type (16.5FP)

source_name: Wild-type (18.5FP) e


title: Embryonic Drosophila cells, Kc167 cells, HP6 DamID after knock-down of white, replicate 1

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: Embryonic Drosophila cells, Kc167 cells

hyb_protocol: Samples were hybridized to the arrays in a volume of approximately 30 ul (5 mM TRIS, 0.5 mM EDTA, 3X SSC). The following competitors were added: 25 ug DpnI-digested Dam-fusion plasmid DNA, 100 ug yeast tRNA, 20 ug poly (dA-dT). Arrays were washed in four subsequent steps. The respective washing buffers were: 1X SSC/0.03% SDS (arrays were submerged once), 1XSSC (arrays were submerged 15 times), 0.2XSSC (20 minutes), 0.05XSSC (10 minutes).

scan_protocol: Microarrays are scanned in a DNA Microarray Scanner (Model G2505B, Serial number US22502518) from Agilent Technologies, which uses Scan Control software (Version A.6.11). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were scanned at a variable PMT (0-100%) for each channel (Red or Green), a variable resolution (5 or 10 um per pixel) and a suitable scan area.

data_processing: After removal of low quality, redundant or ambiguous proves, hybridization data of 9,993 probes was used for analyses, all measured ratios were log base 2-transformed and normalized to the median value of the entire array

organism: Drosophila melanogaster

source_name: Embryonic Drosophila cells, Kc167 cells, expressing HP6-Dam

label_protocol: Sample labeling was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Full length HP6 was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

extract_protocol: Sample extraction was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

tag: HP6-Dam (EXPERIMENTAL)

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

tag: Dam (REFERENCE)


title: Embryonic Drosophila cells, Kc167 cells, HP6 DamID after knock-down of HP1, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: Tabby (14.5BS) c(16012201010061)

description: Tabby (14.5BS)

source_name: Tabby (14.5BS) c


title: Wild-type (14.5BS) c(16012201010042)

description: Wild-type (14.5BS)

source_name: Wild-type (14.5BS) c

source_name: Universal Mouse Reference RNA


title: Rice tissue "DKS", replicate experiment 2


title: Rice tissue "LSS", replicate experiment 3


title: Embryonic Drosophila cells, Kc167 cells, HP6 DamID after knock-down of HP1, replicate 2

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, HP3 DamID after knock-down of white, replicate 2

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing HP3-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Full length HP3 was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

tag: HP3-Dam (EXPERIMENTAL)


title: Embryonic Drosophila cells, Kc167 cells, HP3 DamID after knock-down of white, replicate 3

description: Embryonic Drosophila cells, Kc167 cells


title: Tabby (13.5BS) 3(16012201010041)

description: Tabby (13.5BS)

source_name: Tabby (13.5BS) 3


title: Embryonic Drosophila cells, Kc167 cells, HP6 DamID after knock-down of white, replicate 2

description: Embryonic Drosophila cells, Kc167 cells


title: Yeast_GCN5_H4ac

tag: GCN5-disrupted mutant, W303 background


title: Rice tissue "MAL", replicate experiment 1


title: Yeast_WT_H3ac

value: histone H3 diaceylation at K9 and K14


title: Embryonic Drosophila cells, Kc167 cells, HP3 DamID after knock-down of HP1, replicate 3

description: Embryonic Drosophila cells, Kc167 cells


title: Rice tissue "LSS", replicate experiment 1


title: Embryonic Drosophila cells, Kc167 cells, HP3 DamID after knock-down of HP1, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: Wild-type (13.5BS) 3(16012201010040)

description: Wild-type (13.5BS)

source_name: Wild-type (13.5BS) 3


title: Tabby (18.5FP) a(16012201010037)

description: Tabby (18.5FP)

source_name: Tabby (18.5FP) a


title: Tabby (18.5FP) b(16012201010038)

description: Tabby (18.5FP)

source_name: Tabby (18.5FP) b


title: Embryonic Drosophila cells, Kc167 cells, Jra DamID, replicate 2

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Jra-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Full length Jra was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

tag: Jra-Dam (EXPERIMENTAL)


title: Rice tissue "LSS", replicate experiment 2


title: Rice tissue "SLR", replicate experiment 3


title: Embryonic Drosophila cells, Kc167 cells, Jra DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, HP3 DamID after knock-down of HP1, replicate 2

description: Embryonic Drosophila cells, Kc167 cells


title: Yeast_GCN5_H3ac


title: Rice tissue "SLR", replicate experiment 2


title: Embryonic Drosophila cells, Kc167 cells, HP3 DamID after knock-down of white, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: Wild-type (18.5FP) d(16012201010035)

description: Wild-type (16.5FP)

source_name: Wild-type (18.5FP) d


title: Embryonic Drosophila cells, Kc167 cells, Jra DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, HP6 DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells


title: Rice tissue "SLR", replicate experiment 1


title: Wild-type (18.5FP) c(16012201010034)

description: Wild-type (16.5FP)

source_name: Wild-type (18.5FP) c


title: Adult E2 Vagina2

city: Okazaki

first: Suzuki

last: Atsuko

state: Aichi

address: 5-1, Higashiyama

department: Okazaki Institute for Integrative Bioscience

country: Japan

institute: National Institute of Natural Science

description: Gene expression data 6h after the injection

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 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: Adult mouse vagina treated with E2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: 60-days-old mice were ovariectomized. 70-day-old mice were injected with oil and which were sacrifeced 6h after the injection.

tag: 70-day-old C57BL/6J mice


title: Embryonic Drosophila cells, Kc167 cells, HP5 DamID, replicate 2

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing HP5-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Full length HP5 was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

tag: HP5-Dam (EXPERIMENTAL)


title: Embryonic Drosophila cells, Kc167 cells, HP5 DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, HP5 DamID, replicate 4

description: Embryonic Drosophila cells, Kc167 cells


title: Adult E2 Vagina1


title: Tabby (14.5BS) b(16012201010032)

description: Tabby (14.5BS)

source_name: Tabby (14.5BS) b


title: Embryonic Drosophila cells, Kc167 cells, HP6 DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: Adult Oil Vagina2

source_name: Adult mouse vagina treated with oil


title: Embryonic Drosophila cells, Kc167 cells, HP5 DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, HP6 DamID, replicate 2

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing HP6-Dam


title: Embryonic Drosophila cells, Kc167 cells, HP4 DamID, replicate 2

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing HP4-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Full length HP4 was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

tag: HP4-Dam (EXPERIMENTAL)

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam


title: Embryonic Drosophila cells, Kc167 cells, HP4 DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells


title: Tabby (14.5BS) a(16012201010031)

description: Tabby (14.5BS)

source_name: Tabby (14.5BS) a

tag: Strain


title: Embryonic Drosophila cells, Kc167 cells, HP4 DamID, replicate 4

description: Embryonic Drosophila cells, Kc167 cells


title: Wild-type (14.5BS) a(16012201010028)

description: Wild-type (14.5BS)

source_name: Wild-type (14.5BS) a

tag: Age

source_name: Universal Mouse Reference RNA


title: Embryonic Drosophila cells, Kc167 cells, HP4 DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: Adult Oil Vagina1


title: Human_R_H3K4me3

tag: human primary CD3+ T cell (resting)

value: histone H3 trimethylation at K4


title: Adult E2 mammary gland2

source_name: Adult mouse mammary gland treated with E2


title: Tabby (13.5BS) 2(16012201010026)

description: Tabby (13.5BS)

source_name: Tabby (13.5BS) 2

tag: Development stage

tag: Universale Mouse Reference


title: Embryonic Drosophila cells, Kc167 cells, HP3 DamID, replicate 4

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing HP3-Dam


title: Embryonic Drosophila cells, Kc167 cells, HP3 DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: Wild-type (14.5BS) b(16012201010029)

description: Wild-type (14.5BS)

source_name: Wild-type (14.5BS) b


title: Embryonic Drosophila cells, Kc167 cells, HP3 DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells


title: Tabby (13.5BS) 1(16012201010025)

description: Tabby (13.5BS)

source_name: Tabby (13.5BS) 1

tag: Genetic modification


title: Adult Oil mammary gland2

source_name: Adult mouse mammary gland treated with oil


title: Human_R_T_H3ac

tag: antibody


title: Adult E2 mammary gland1


title: Wild-type (13.5BS) 2(16012201010023)

description: Wild-type (13.5BS)

source_name: Wild-type (13.5BS) 2

tag: Gender


title: Embryonic Drosophila cells, Kc167 cells, Su(var)3-9 DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Su(var)3-9-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Full length Su(var)3-9 was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

tag: Su(var)3-9-Dam (EXPERIMENTAL)


title: Embryonic Drosophila cells, Kc167 cells, HP1 DamID, replicate 2

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing HP1-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Full length HP1 was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

tag: HP1-Dam (EXPERIMENTAL)


title: Embryonic Drosophila cells, Kc167 cells, HP3 DamID, replicate 2

description: Embryonic Drosophila cells, Kc167 cells

tag: Dam (REFERENCE)


title: Embryonic Drosophila cells, Kc167 cells, Su(var)3-9 DamID, replicate 2

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, HP1 DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, HP1 DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, HP1 DamID, replicate 4

description: Embryonic Drosophila cells, Kc167 cells


title: Rat brain D4(synaptosome) vs C2(extrasynaptosome)_MECS-treated_Replicate 1 and 2

city: Machida-shi

first: Mineo

last: Matsumoto

state: Tokyo

address: 11 Minamiooya

institute: Mitsubishi Kagaku Institute of Life Sciences

description: D4 is a synaptosome fraction purified with the protocol by Bagni et al(J Neurosci, vol.20, page RC76, 2000). C2 is a extrasynaptosome fraction that is a reference of the D4 fraction.

hyb_protocol: The hybridization of the cDNA microarray (Part No. G4105A) was carried out according to the protocol recommended by Agilent Technologies Inc (Palo Alto, CA)

scan_protocol: The microarrays were scanned with an Agilent Microarray Scanner G2565BA. Feature Extraction and Image Analysis software (version A.6.1.1, Agilent Technologies) was used to analyze the hybridization signals of each spot.

data_processing: The LOWESS (LOESS) method was applied to filtering and normalization of the data. The filtering was performed according to the default algorithms of the Feature Extraction software. The geometric mean of Cy5/Cy3 value (FoldChange) for each spot was used to average the data. In other words, the geometric mean in this case is (A1/B1)(B1'/A1')(A2/B2)(B2'/A2'), where A1 is Cy5 (C2) from Replacate 1, B1 is Cy3 (D4) from Replicate 1, A1' is Cy5 (D4) from Replicate 1' of the dye-swap experiment, B1' is Cy3 (C2) from Replicate 1' of the dye-swap experiment, and A2, B2, A2', and B2' represent the equivalent entities in a duplicate experiment (Replicate 2). VALUES are log10 ratios.

label: Cy3 or Cy5 (dye swap experiment)

source_name: Total RNA from the HP fraction, with MECS (maximum electroconvulsive seizure) condition.

label_protocol: RNA (330 ng) from the D4 fraction prepared from one rat was amplified to 6~10 ug of aRNA through 1st-round amplification using MessageAmp aRNA Kit (Ambion #1750, Austin, TX). The reverse transcription labelling with cyanine 3 (Cy3)-dCTP  (cDNA labelling kit, Part No. G2557A) was carried out according to the protocol recommended by Agilent Technologies Inc (Palo Alto, CA). To avoid a dye-specific hybridization preference for each RNA species, cyanine dye-swap hybridization was performed in both Replicate 1 and 2. In this cases, RNA from the HP fraction was labeled with Cy5, not Cy3.

extract_protocol: Trizol procedure

label: Cy5 or Cy3 (dye swap experiment)

source_name: Total RNA from the LP fraction

label_protocol: RNA (330 ng) from the C2 fraction prepared from one rat was amplified to 6~10 ug of aRNA through 1st-round amplification using MessageAmp aRNA Kit (Ambion #1750, Austin, TX). The reverse transcription labelling with cyanine 5 (Cy5)-dCTP  (cDNA labelling kit, Part No. G2557A) was carried out according to the protocol recommended by Agilent Technologies Inc (Palo Alto, CA). To avoid a dye-specific hybridization preference for each RNA species, cyanine dye-swap hybridization was performed in both Replicate 1 and 2. In this cases, RNA from the LP fraction was labeled with Cy3, not Cy5.


title: Embryonic Drosophila cells, Kc167 cells, Su(var)3-9 DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells


title: Wild-type (13.5BS) 1(16012201010022)

description: Wild-type (13.5BS)

source_name: Wild-type (13.5BS) 1


title: Tabby back skin (18.5) #3(251246310059)

description: Tabby back skin

source_name: Tabby back skin (18.5) #3


title: Adult E2 uterus2

source_name: Adult mouse uterus treated with E2


title: Wild-type back skin (18.5)#3(251246310056)

description: Wild-type back skin

source_name: Wild-type back skin (18.5)#3


title: Adult Oil mammary gland1


title: Human_A_T_H3ac

tag: human primary CD3+ T cell (activated with anti-CD3 and anti-CD28 antibodies (1ug/ml) for 24 hr)

tag: Antibody


title: Human_R_H3K27me3

value: histone H3 trimethylation at K27


title: Adult Oil uterus2

source_name: Adult mouse uterus treated with oil


title: Rat brain D4(synaptosome) vs C2(extrasynaptosome)_non-MECS_Replicate 1 and 2

source_name: Total RNA from the HP fraction, without MECS (maximum electroconvulsive seizure) condition.


title: Adult E2 uterus1


title: Tabby back skin (18.5) #1(251246310057)

description: Tabby back skin

source_name: Tabby back skin (18.5) #1

source_name: Universal Mouse Reference RNA


title: Rat brain heavy portion of polysome(HP) vs light portion of polysome(LP)_MECS-treated_Replicate 1 and 2

description: HP is a fraction that is abundant of RNA granule that delivers mRNAs from neuronal soma to dendrites, whereas LP is the reference   fraction.

data_processing: The LOWESS (LOESS) method was applied to filtering and normalization of the data. The filtering was performed according to the default algorithms of the Feature Extraction software. The geometric mean of Cy5/Cy3 value (FoldChange) for each spot was used to average the data. In other words, the geometric mean in this case is (A1/B1)(B1'/A1')(A2/B2)(B2'/A2'), where A1 is Cy5 (LP) from Replacate 1, B1 is Cy3 (HP) from Replicate 1, A1' is Cy5 (HP) from Replicate 1' of the dye-swap experiment, B1' is Cy3 (LP) from Replicate 1' of the dye-swap experiment, and A2, B2, A2', and B2' represent the equivalent entities in a duplicate experiment (Replicate 2). VALUES are log10 ratios.

label_protocol: RNA (1 ug) from the HP fraction prepared from three rats was amplified to yield 10~15 ug of aRNA through 1st-round amplification using MessageAmp aRNA Kit (Ambion #1750, Austin, TX). The reverse transcription labelling with cyanine 3 (Cy3)-dCTP (cDNA labelling kit, Part No. G2557A) was carried out according to the protocol recommended by Agilent Technologies Inc (Palo Alto, CA). To avoid a dye-specific hybridization preference for each RNA species, cyanine dye-swap hybridization was performed in both Replicate 1 and 2. In this cases, RNA from the HP fraction was labeled with Cy5, not Cy3.

tag: heavy portion of polysome(HP)

label_protocol: RNA (1 ug) from the LP fraction prepared from three rats was amplified to yield 10~15 ug of aRNA through 1st-round amplification using MessageAmp aRNA Kit (Ambion #1750, Austin, TX). The reverse transcription labelling with cyanine 5 (Cy5)-dCTP  (cDNA labelling kit, Part No. G2557A) was carried out according to the protocol recommended by Agilent Technologies Inc (Palo Alto, CA). To avoid a dye-specific hybridization preference for each RNA species, cyanine dye-swap hybridization was performed in both Replicate 1 and 2. In this cases, RNA from the LP fraction was labeled with Cy3, not Cy5.

tag: light portion of polysome(LP)


title: Tabby back skin (18.5) #2(251246310058)

description: Tabby back skin

source_name: Tabby back skin (18.5) #2


title: CGH_108_CTB1

status: Public on Feb 05 2007

city: Pamplona

first: Jose Angel

middle: Martinez

state: Navarra

address: PIO XII

country: Spain

institute: CIMA/Universidad De Navarra

description: Genome-wide analysis of DNA-copy number changes of CTB1 cell line.

data_processing: We used ?UCSF SPOT? software (A.N.J. manuscript submitted) to automatically segment the spots based on the DAPI images, perform local background correction and to calculate various measurement parameters, including log2ratios of the total integrated Cy3 and Cy5 intensities for each spot.  We used a second custom program SPROC to associate clone identities and a mapping information file with each spot so that the data could be plotted relative to the position of the BACs on the September, 2000 freeze of the draft human genome sequence (http://genome.ucsc.edu).  SPROC also implements a filtering procedure to reject data based on a number of criteria, including low reference/DAPI signal intensity and low correlation of the Cy3 and Cy5 intensities with a spot.  The SPROC output consists of averaged ratios of the triplicate spots for each clone, standard deviations of the triplicates and plotting position for each clone on the array, as well as other clone information stored in the database, such as STS content.

source_name: CTB1 cell line

tag: Cell line derived from diffuse large B-cell lymphoma without the translocation t(14;18)(q32;q21). Derived from 70-years-old male.

tag: With BCL2 overexpression.

tag: Specimen site

value: pericardial effusion.

source_name: Reference genomic DNA.

tag: Normal female reference genomic DNA.


title: CGH_108_MD903

description: Genome-wide analysis of DNA-copy number changes of MD903 cell line.

source_name: MD903 cell line

tag: Cell line derived from diffuse large B-cell lymphoma without the translocation t(14;18)(q32;q21).Derived from 38-years-old male.


title: CGH_108_K1106

description: Genome-wide analysis of DNA-copy number changes of K1106 cell line.

source_name: K1106 cell line

tag: Cell line derived from primary mediastinal B-cell lymphoma with P16INK4A deletion.


title: CGH_108_CIPULLO

description: Genome-wide analysis of DNA-copy number changes of CIPULLO cell line.

source_name: CIPULLO cell line

tag: Cell line derived from diffuse large B-cell lymphoma without the translocation t(14;18)(q32;q21).


title: CGH_108_RIVA

description: Genome-wide analysis OF DNA-copy number changes of RIVA cell line.

data_processing: We used UCSF SPOT software (A.N.J. manuscript submitted) to automatically segment the spots based on the DAPI images, perform local background correction and to calculate various measurement parameters, including log2ratios of the total integrated Cy3 and Cy5 intensities for each spot.  We used a second custom program SPROC to associate clone identities and a mapping information file with each spot so that the data could be plotted relative to the position of the BACs on the September, 2000 freeze of the draft human genome sequence (http://genome.ucsc.edu).  SPROC also implements a filtering procedure to reject data based on a number of criteria, including low reference/DAPI signal intensity and low correlation of the Cy3 and Cy5 intensities with a spot.  The SPROC output consists of averaged ratios of the triplicate spots for each clone, standard deviations of the triplicates and plotting position for each clone on the array, as well as other clone information stored in the database, such as STS content.

source_name: RIVA cell line


title: CGH_108_SCI1

description: Genome-wide analysis of DNA-copy number changes of SCI1 cell line.

source_name: SCI1 cell line

tag: Cell line derived from diffuse large B-cell lymphoma with the translocation t(14;18)(q32;q21).


title: Wild-type back skin (18.5)#2(251246310055)

description: Wild-type back skin

source_name: Wild-type back skin (18.5)#2

tag: Strain

tag: Age

tag: Development stage

tag: Universale Mouse Reference


title: CGH_108_OCI-LY8

description: Genome-wide analysis OF DNA-copy number changes of OCI-LY8 cell line.

data_processing: We used “UCSF SPOT” software (A.N.J. manuscript submitted) to automatically segment the spots based on the DAPI images, perform local background correction and to calculate various measurement parameters, including log2ratios of the total integrated Cy3 and Cy5 intensities for each spot.  We used a second custom program SPROC to associate clone identities and a mapping information file with each spot so that the data could be plotted relative to the position of the BACs on the September, 2000 freeze of the draft human genome sequence (http://genome.ucsc.edu).  SPROC also implements a filtering procedure to reject data based on a number of criteria, including low reference/DAPI signal intensity and low correlation of the Cy3 and Cy5 intensities with a spot.  The SPROC output consists of averaged ratios of the triplicate spots for each clone, standard deviations of the triplicates and plotting position for each clone on the array, as well as other clone information stored in the database, such as STS content.

source_name: OCI-LY8 cell line

tag: Cell line derived from diffuse large B-cell lymphoma with the translocation t(14;18)(q32;q21). Derived from 58-years-old male.

value: bone marrow


title: CGH_108_ROS50

description: Genome-wide analysis of DNA-copy number changes of ROS50 cell line.

source_name: ROS50 cell line

tag: Cell line derived from diffuse large B-cell lymphoma with the translocation t(14;18)(q32;q21). Derived from 69-years-old male.

tag: With t(8;14)(q24;q32). Overexpresion BCL2 and MYC.

value: peripheral blood.


title: CGH_108_K1718

description: Genome-wide analysis OF DNA-copy number changes of K1718 cell line.

source_name: K1718 cell line

tag: Cell line derived from marginal zone lymphoma (derived from a male).


title: Adult Oil uterus1

tag: 70-day-old C57BL/6J mice


title: CGH_108_MD901

description: Genome-wide analysis of DNA-copy number changes of MD901 cell line.

source_name: MD901 cell line


title: CGH_108_SSK41

description: Genome-wide analysis OF DNA-copy number changes of SSK41 cell line.

source_name: SSK41 cell line

tag: Cell line derived from marginal zone lymphoma (derived from a female).


title: Wild-type back skin (18.5) #1(251246310054)

description: Wild-type back skin

source_name: Wild-type back skin (18.5) #1

tag: Gender


title: Rat brain heavy portion of polysome(HP) vs light portion of polysome(LP)_non-MECS_Replicate 1 and 2

source_name: Total RNA from the HP- and LP fraction, without MECS (maximum electroconvulsive seizure) condition.

label_protocol: RNA (1 ug) from the HP fraction prepared from three rats was amplified to yield 10~15 ug of aRNA through 1st-round amplification using MessageAmp aRNA Kit (Ambion #1750, Austin, TX). The reverse transcription labelling with cyanine 3 (Cy3)-dCTP  (cDNA labelling kit, Part No. G2557A) was carried out according to the protocol recommended by Agilent Technologies Inc (Palo Alto, CA). To avoid a dye-specific hybridization preference for each RNA species, cyanine dye-swap hybridization was performed in both Replicate 1 and 2. In this cases, RNA from the HP fraction was labeled with Cy5, not Cy3.

tag: heavy portion of polysome(HP)

source_name: Total RNA from the LP fraction

tag: light portion of polysome(LP)


title: CGH_108_RL

description: Genome-wide analysis OF DNA-copy number changes of RL cell line.

source_name: RL cell line

tag: Cell line derived from diffuse large B-cell lymphoma with the translocation t(14;18)(q32;q21). Derived from 52-years-old male.

tag: With P53 alteration.

tag: Specimen site

value: ascites

tag: Normal female reference genomic DNA.


title: CGH_108_KARPAS 353

description: Genome-wide analysis of DNA-copy number changes of KARPAS 353 cell line.

source_name: KARPAS 353 cell line

tag: Cell line derived from diffuse large B-cell lymphoma with the translocation t(14;18)(q32;q21).Derived from 60-years-old male.

tag: With P16INK4A deletion, MYC mRNA overexpression and BCL2+.


title: CGH_108_PR1

description: Genome-wide analysis of DNA-copy number changes of PR1 cell line.

source_name: PR1 cell line

tag: Cell line derived from diffuse large B-cell lymphoma with the translocation t(14;18)(q32;q21).

source_name: Reference genomic DNA.


title: CGH_108_KARPAS422

description: Genome-wide analysis OF DNA-copy number changes of KARPAS422 cell line.

source_name: KARPAS422 cell line

tag: Cell line derived from diffuse large B-cell lymphoma with the translocation t(14;18)(q32;q21). Derived from 73-years-old female.

value: pleural effusion.


title: CGH_108_KARPAS231

description: Genome-wide analysis OF DNA-copy number changes of KARPAS231 cell line.

source_name: K231 cell line.

tag: Cell line derived from diffuse large B-cell lymphoma with the translocation t(14;18)(q32;q21) and t(3;11)(q27;q23.1).

tag: Derived from 71-years-old female.

tag: Specimen site:peripheral blood.


title: CGH_108_SUDHL6

description: Genome-wide analysis OF DNA-copy number changes of SUDHL6 cell line.

source_name: SUDHL6 cell line

tag: Cell line derived from diffuse large B-cell lymphoma with the translocation t(14;18)(q32;q21). Derived from 43-years-old female.

value: peritoneal effusion


title: CGH_108_VAL

description: Genome-wide analysis OF DNA-copy number changes of VAL cell line.

source_name: VAL cell line

tag: Cell line derived from diffuse large B-cell lymphoma with the translocation t(14;18)(q32;q21).Derived from 50-years-old female.


title: CGH_108_DOHH2

description: Genome-wide analysis OF DNA-copy number changes of DOHH2 cell line.

source_name: DOHH2 cell line

tag: Cell line derived from diffuse large B-cell lymphoma with the translocation t(14;18)(q32;q21). Derived from 60-years-old male.

tag: With t(8;14)(q24;q32) and P16INK4A deletion.


title: CGH_108_P32

description: Genome-wide analysis OF DNA-copy number changes of P32 cell line.

source_name: P32 cell line

tag: Cell line derived from Burkitt lymphoma (derived from a male).


title: CGH_108_OZ

description: Genome-wide analysis OF DNA-copy number changes of OZ cell line.

source_name: OZ cell line

tag: Cell line derived from diffuse large B-cell lymphoma with the translocation t(14;18)(q32;q21).Derived from 32-years-old male.

tag: With P15INKB and P16INK4A deletions and P53 alteration.


title: CGH_108_BALM9

description: Genome-wide analysis OF DNA-copy number changes of BALM9 cell line.

source_name: BALM9 cell line.

tag: Cell line derived from Burkitt lymphoma (derived from 12-years-old female) with karyotipe 55-56, XX, +1, +7, +10, +11, +16, +17, +20.


title: CGH_108_WIEN133

description: Genome-wide analysis OF DNA-copy number changes of WIEN133 cell line.

source_name: WIEN133 CELL LINE

tag: Cell line derived from Burkitt lymphoma (derived from 12-years-old male) with t(8;14;12)(q24;32;q24), EBV-, BCL7A rearrangement.

tag: Specimen site:bone marrow.


title: CGH_108_SP49

description: Genome-wide analysis OF DNA-copy number changes of SP49 cell line.

source_name: SP49 cell line

tag: Cell line derived from Mantle lymphoma (derived from 58-years old female) with t(11;14)(q13;32).

tag: Normal female reference genomic DNA.


title: CGH_108_SERAPHINA

description: Genome-wide analysis OF DNA-copy number changes of SERAPHINA cell line.

source_name: SERAPHINA cell line

tag: Cell line derived from Burkitt lymphoma (derived from a female)


title: CGH_108_PL29018

description: Genome-wide analysis OF DNA-copy number changes of PL29018 cell line.

source_name: PL29018 cell line.


title: CGH_108_ELIJAH

description: Genome-wide analysis OF DNA-copy number changes of ELIJAH cell line.

source_name: ELIJAH cell line.

tag: Cell line derived from Burkitt lymphoma.


title: CGH_108_NCEB1

description: Genome-wide analysis OF DNA-copy number changes of NCEB1 cell line.

source_name: NCEB1 cell line.

tag: NCEB1 cell line derived from Mantle lymphoma (derived from 57-years-old male) with t(11;14)(q13;q32).


title: CGH_108_Z138

description: Genome-wide analysis OF DNA-copy number changes of Z138 cell line.

source_name: Z138 cell line

tag: Cell line derived from Mantle lymphoma (derived from 70-years-old male) with t(18;14)(q24;32), t(14;18)(q32;q21) and cyclin D1 mRNA overexpression.


title: CGH_108_UPN2

description: Genome-wide analysis of DNA-copy number changes of UPN2 cell line.

source_name: UPN2 cell line

tag: Cell line derived from Mantle lymphoma with t(11;14)(q13;32).


title: CGH_108_HBL2

description: Genome-wide analysis OF DNA-copy number changes of Hbl2 cell line.

source_name: Cell line HBL2

tag: Cell line derived from Mantle Lymphoma (derived from 84-years-old male) with t(11;14)(q13;q32). Specimen site

value: lymp node

source_name: Reference genomic DNA.


title: CGH_108_GRANTA519

description: Genome-wide analysis OF DNA-copy number changes of GRANTA519 cell line.

source_name: G519 Cell line

tag: GRANTA519 cell line derived from Mantle lymphoma (derived from 58-years-old female) with t(11;14) (q13;q32), p15INK4B and P16INK4A deletions and overexpression of CDK4 and cyclin D1

source_name: Reference genomic DNA


title: CGH_108_CA46

description: Genome-wide analysis of DNA-copy number changes of CA46 cell line.

source_name: CA46 cell line

tag: Cell line derived from Burkitt lymphoma with t(8;14)((q24;q32).


title: CGH_108_IRM2

description: Genome-wide analysis OF DNA-copy number changes of IRM2 cell line.

source_name: IRM2 cell line.

tag: Normal reference genomic DNA.


title: CGH_108_MEDB1

description: Genome-wide analysis OF DNA-copy number changes of MEDB1 cell line.

source_name: MEDB1 cell line.

tag: Cell line derived from primary mediastinal B-cell lymphoma.


title: CGH_108_GRANTA 452

description: Genome-wide analysis OF DNA-copy number changes of GRANTA 452 cell line.

source_name: GRANTA 452 cell line

tag: Cell line derived from diffuse large B-cell lymphoma with the translocation t(14;18)(q32;q21).


title: CGH_108_KHM10B

description: Genome-wide analysis OF DNA-copy number changes of KHM10B cell line.

source_name: KHM10B cell line

tag: Cell line derived from Burkitt lymphoma. Derived from 41-years-old male.

tag: Specimen site


title: CGH_108_SP53

description: Genome-wide analysis OF DNA-copy number changes of SP53 cell line.

source_name: SP53 cell line.

tag: Cell line derived from Mantle lymphoma with t(11;14)(q13;32). Derived from 58-years-old male. Specimen site


title: CGH_108_REC1

description: Genome-wide analysis OF DNA-copy number changes of REC1 cell line.

source_name: REC1 CELL LINE

tag: Cell line derived from Mantle lymphoma with t(11;14)(q13;32) (derived from a male).


title: CGH_108_BL41

description: Genome-wide analysis OF DNA-copy number changes of BL41 cell line.

source_name: BL41 cell line


title: CGH_108_JVM2

description: Genome-wide analysis OF DNA-copy number changes of JVM2 cell line.

source_name: JVM2 CELL LINE

tag: Cell line derived from Mantle lymphoma (derived from 63-years-old female) with t(11;14)(q13;32).


title: CGH_108_380

description: Genome-wide analysis OF DNA-copy number changes of 380 cell line.

source_name: 380 cell line.

tag: Cell line derived from diffuse large B-cell lymphoma with the translocation t(14;18)(q32;q21) and with the t(8;14)(q24;q32).


title: CGH_108_JEKO1

description: Genome-wide analysis OF DNA-copy number changes of JEKO1 cell line.

source_name: JOKO1 cell line.

tag: Cell line derived from Mantle lymphoma with t(11;14)(q13;32). Derived from 78-years-old male.


title: CGH_108_NAB2

description: Genome-wide analysis OF DNA-copy number changes of NAB2 cell line.

source_name: NAB2 cell line

tag: Cell line derived from Burkitt lymphoma (derived from a female).

tag: Normal female reference genomic DNA.


title: NHF10-hTERT_sham_6h_C5_21704

status: Public on Feb 01 2007

city: Morrisville

first: Tong

last: Zhou

address: 133 Southcenter Court, Suite 400

department: Clincial Genetics

institute: Gentris Corperation

description: The gene expression level was presented as ratio of sample intensity against reference intensity.

hyb_protocol: 750ng of Cy3 and Cy5-labeled cRNA were used in the hybridization. The labeled cRNA from sham- or IR-treated samples was hybridized with the labeled global reference cRNA on an Agilent 22k human 1A array in a hybridization oven (Robbins Scientific Model 400, 1040-60-1AG) at 60oC for 17 h. Hybridization of sample RNA against reference RNA was done twice with dye swap.

scan_protocol: The arrays were scanned using the Agilent DNA Microarray Scanner with SureScan® Technology.

data_processing: Microarray images were analyzed using Agilent Feature Extraction Software (v7.1). Expression patterns and significant genes were extracted using Extracting Microarray Gene Expression Patterns and Identifying Biologically Significant Genes (EPIG)

source_name: reference RNA

label_protocol: 1 µg of global reference RNA (Stratagene) was converted to cDNA with reverse transcriptase then amplified using T7 RNA polymerase while labeling with Cy3-dUTP (Agilent’s Low RNA Input Linear Amplification Kit). The quality of each labeled cRNA was evaluated using an Agilent 2100 Bioanalyzer prior to hybridization.

extract_protocol: Stratagene protocol for preparation of reference RNA

tag: global reference RNA

source_name: Sample RNA

label_protocol: 1 µg of sample RNA was converted to cDNA with reverse transcriptase then amplified using T7 RNA polymerase while labeling with Cy5-dUTP (Agilent’s Low RNA Input Linear Amplification Kit). The quality of each labeled cRNA was evaluated using an Agilent 2100 Bioanalyzer prior to hybridization.

growth_protocol: Fibroblasts were cultured in DMEM (Invitrogen) supplemented with 2 mM L-glutamine (Invitrogen) and 10% fetal bovine serum (Sigma). All cell lines were maintained at 37oC in a humidified atmosphere of 5% CO2.

extract_protocol: Qiagen RNeasy kit

treatment_protocol: Cells were harvested 6 hr after sham treatment

tag: Normal human fibroblast


title: MIN6 growth at 5.5 mM of glucose and treated at 10 uM of amylin during 24h

status: Public on Feb 02 2007

city: Barcelona

first: Silvia

last: Casas Fontdevila

address: Villarroel, 170

institute: IDIBAPS

description: Murine pancreatic beta cell line MIN6 was growth at 5.5 mM of glucose, 37 ºC, 5% CO2 and was treated at 10 uM of human amylin during 24h

hyb_protocol: According to Affymetrix protocol

scan_protocol: According to Affymetrix protocol

data_processing: Raw data was background adjusted, normalized and summarized by RMA (Affy package version 1.12.2, R version 2.4.0)

label: According to Affymetrix protocol (biotin)

source_name: MIN6, 5.5 mM of glucose,treated at 10 uM of amylin during 24h

label_protocol: According to Affymetrix protocol (biotin labeled cRNA)

extract_protocol: According to the protocol enclosed with the RNeasy Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: 10 uM of human amylin during 24h


title: CGH_108_RCK8

description: Genome-wide analysis OF DNA-copy number changes of RCK8 cell line.

source_name: RCK8 cell line

tag: Cell line derived from diffuse large B-cell lymphoma without the translocation t(14;18)(q32;q21). Derived from 55-years-old male.

value: peritoneal effusion.

source_name: Reference genomic DNA.


title: NHF10-hTERT_1.5Gy_24h_C3_21766

label_protocol: 1 µg of sample RNA was converted to cDNA with reverse transcriptase then amplified using T7 RNA polymerase while labeling with Cy3-dUTP (Agilent’s Low RNA Input Linear Amplification Kit). The quality of each labeled cRNA was evaluated using an Agilent 2100 Bioanalyzer prior to hybridization.

treatment_protocol: Cells were harvested 24 hr after 1.5 Gy iozining radiation treatment

source_name: Reference RNA

label_protocol: 1 µg of global reference RNA (Stratagene) was converted to cDNA with reverse transcriptase then amplified using T7 RNA polymerase while labeling with Cy5-dUTP (Agilent’s Low RNA Input Linear Amplification Kit). The quality of each labeled cRNA was evaluated using an Agilent 2100 Bioanalyzer prior to hybridization.


title: NHF10-hTERT_1.5Gy_24h_C5_21765


title: NHF10-hTERT_sham_6h_C3_21705

treatment_protocol: Cells were harvested 6hr after sham treatment


title: MIN6 growth at 22.7 mM of glucose and treated at 1 uM of amylin during 12h

description: Murine pancreatic beta cell line MIN6 was growth at 22.7 mM of glucose, 37 ºC, 5% CO2 and was treated at 1 uM of human amylin during 12h

source_name: MIN6, 22.7 mM of glucose,treated at 1 uM of amylin during 12h

treatment_protocol: 1 uM of human amylin during 12h


title: NHF10-hTERT_1.5Gy_6h_C5_21708

treatment_protocol: Cells were harvested 6 hr after 1.5 Gy iozining radiation treatment


title: NHF1-hTERT_sham_6h_C5_20077


title: NHF1-hTERT_1.5Gy_6h_C3_20130


title: NHF10-hTERT_1.5Gy_6h_C3_21764


title: NHF3-hTERT_1.5Gy_6h_C3_21250


title: NHF3-hTERT_sham_6h_C5_21395


title: mMAPC-1 #1(251279910286)

status: Public on Jan 26 2007

description: MAPC clone 2 (high Oct4)

source_name: mMAPC-1 #1

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

growth_protocol: BM was plated in 60% low glucose DMEM, 40% MCDB-201 containing 10ng/mL mEGF, hPDGF-BB and 1000 units/ml mouse leukemia inhibitory factor (LIF), 2% screened fetal calf serum (FCS), 1x selenium-insulin-transferrin-ethanolamine (SITE), 0.2 mg/mL linoleic acid-bovine serum albumin (LA-BSA), 0.8 mg/mL bovine serum albumin, 1x chemically defined lipid concentrate and 1x 2-mercaptoethanol, 100 units of penicillin, 1,000 units of streptomycin in a humidified, 5% O2 and 6% CO2, 37oC incubator. After 4 weeks, CD45+ and Ter119+ cells were depleted using a MACS separation CS column, and cells replated at 10 cells/well. Expansion was done by trypsinizing (0.05% trypsin) the cells and replating them every two days at a density of 100-200 cells/cm2. Cells at population doubling >80 were used for gene arrays.

extract_protocol: Total RNA was extracted using Trizol according to Invitrogen's protocol.  Cells were pelleted and 1mL Trizol reagent was added to the cell pellet.

treatment_protocol: BM was plated in 60% low glucose DMEM, 40% MCDB-201 containing 10ng/mL mEGF, hPDGF-BB and 1000 units/ml mouse leukemia inhibitory factor (LIF), 2% screened fetal calf serum (FCS), 1x selenium-insulin-transferrin-ethanolamine (SITE), 0.2 mg/mL linoleic acid-bovine serum albumin (LA-BSA), 0.8 mg/mL bovine serum albumin, 1x chemically defined lipid concentrate and 1x _-mercaptoethanol, 100 units of penicillin, 1,000 units of streptomycin (Cellgro, city) in a humidified, 5% O2 and 6% CO2, 37oC incubator. After 4 weeks, CD45+ and Ter119+ cells were depleted using a MACS separation CS column, and cells replated at 10 cells/well. Expansion was done by trypsinizing (0.05% trypsin) the cells and replating them every two days at a density of 100-200 cells/cm2. Cells at population doubling >80 were used for gene arrays.

tag: Multipotent adult progenitor cells C57BL/6  adult

source_name: Universal Mouse Reference Cell Line Pool

tag: Universale Mouse Reference


title: ESC #1(251279910284)

description: ESC C57BL/6

source_name: ESC #1

growth_protocol: ES cells were grown in standard ES media (15% FCS, LIF, P/S, glutamine, non-essential amino acids, BME, DMEM high glucose) on irradiated MEFs. Cells were plated feeder free before RNA sample collection on culture dish.

tag: mouse embryonic stem cell  C57BL/6 male embryo


title: NHF3-hTERT_sham_6h_C3_21247


title: NHF1-hTERT_1.5Gy_24h_C5_20131


title: NHF1-hTERT_1.5Gy_6h_C5_13867


title: NHF3-hTERT_1.5Gy_6h_C5_21249


title: NHF10-hTERT_1.5Gy_2h_C3_21707

treatment_protocol: Cells were harvested 2 hr after 1.5 Gy iozining radiation treatment


title: NHF3-hTERT_1.5Gy_2h_C5_21397


title: NHF1-hTERT_sham_6h_C3_20078


title: NHF3-hTERT_1.5Gy_24h_C5_21251


title: NHF3-hTERT_1.5Gy_2h_C3_21248


title: NHF1-hTERT_1.5Gy_2h_C3_20128

hyb_protocol: 750ng of Cy3 and Cy5-labeled cRNA were used in the hybridization. The labeled cRNA from sham- or IR-treated samples was hybridized with the labeled global reference cRNA on an Agilent 22k human 1A array in a hybridization oven, Robbins Scientific Model 400, 1040-60-1AG, at 60oC for 17 h. Hybridization of sample RNA against reference RNA was done twice with dye swap.


title: NHF1-hTERT_1.5Gy_2h_C5_20081


title: NHF10-hTERT_1.5Gy_2h_C5_21706


title: NS #1(251279910206)

description: NSC C57BL/6

source_name: NS #1

growth_protocol: Neuroepithelial cells were isolated from the forebrains of E11.5 embryos by dissecting telencephalons and dissociating them into a near single cell suspension.  Neurospheres were grown in N2-plus media and supplemented with 20ng/mL bFGF and EGF.

tag: embryonic neuroepithelial cells C57BL/6 mixed sex embryo


title: NHF3-hTERT_1.5Gy_24h_C3_21252


title: NS #2(251279910277)

description: NSC C57BL/6

source_name: NS #2

treatment_protocol: Neuroepithelial cells were isolated from the forebrains of E11.5 embryos by dissecting telencephalons and dissociating them into a near single cell suspension.


title: mMAPC-1 #2(251279910281)

description: MAPC clone 2 (high Oct4)

source_name: mMAPC-1 #2

tag: multipotent adult progenitor cells C57BL/6  adult


title: 00058464

status: Public on Jan 17 2007

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
Date:2006/02/17
N21 vs I21

hyb_protocol: Agilent : 750.0 ng at 50 degree_C during 16 hours

scan_protocol: Scanned on an GenePix 4000A fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: No normalization performed : VALUE column is the "Ratio of Medians (635/532)" column of Genepix6.0 .gpr file.

source_name: Non-Infected, day=21

label_protocol: Invitrogen - Ulysis

extract_protocol: MirVana

tag: Non-Infected, day=21

source_name: Infected, day=21

tag: Infected, day=21


title: ESC #2(251279910279)

description: ESC C57BL/6

source_name: ESC #2

treatment_protocol: ES cells were grown in standard ES media (15% FCS, LIF, P/S, glutamine, non-essential amino acids, BME, DMEM high glucose) on irradiated MEFs.

tag: mouse embryonic stem cell C57BL/6 male embryo

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).


title: Gastric mucosal scrapings #2

status: Public on Nov 22 2006

description: Manufacturer's scanner and feature extraction - normalization software

hyb_protocol: Agilent 44K hybridization, 17 hrs

scan_protocol: Agilent scanner and Feature Extraction Software

data_processing: Genespring 7.3

source_name: rat gastric mucosa

label_protocol: Low RNA Input Fluor Linear Amplification Kit (Agilent Technologies, USA)

extract_protocol: NucleoSpin RNA II (BD Biosciences, USA)

tag: gastric mucosal scrapings, mixed homogenate total RNA isolate


title: 00058495

description:
Date:2006/02/17
I21 vs N21