title: Salt stress, biological rep 3

description: 7-day-old light-grown rice seedlings kept in 200 mM NaCl solution for 3 h at 28 ± 1 degree celsius

treatment_protocol: Seedlings were transferred to a beaker containing 200 mM NaCl solution for 3 h at 28 ± 1 degree celsius


title: Fig S2: Dis IX pdr5 (A15560) DNA (swap)

status: Public on May 17 2007

type: genomic

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

country: USA

institute: University of Washington

description: former name: Disome 9.3 delta pdr5 (channels originally misassigned)

hyb_protocol: Description : 200 ng differentially labeled DNA from the reference strain and the strain of interest were mixed, combined with control targets and hybridization buffer, boiled for 5 minutes, and applied to a microarray consisting of 60mer probes for each yeast open reading frame (Agilent).  Microarrays were rotated at 60?C for 17 hours in a hybridization oven (Agilent).  Arrays were then washed according to the Agilent SSPE wash protocol.

scan_protocol: Pixel Size : 10 Scan Date : 2006-02-23 Scan Time : 10:08:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 8.1.1.1
Datafile type : Agilent result file

molecule: genomic DNA

organism: Saccharomyces cerevisiae

label_protocol: Description : 1 microg HhaI digested DNA was labeled with Klenow polymerase and Cy3- or Cy5-dCTP according to the BioPrime CGH labeling kit (Invitrogen), using half volume reactions.  Yield and dye incorporation were checked with a Nanodrop spectrophotometer.

extract_protocol: Description : To prepare genomic DNA, cells were grown to saturation in selective media. 15 mls of culture were spun down, rinsed and incubated for 60 minutes at 37oC in 1.5 mls of 1 M Sorbitol, 10 mM Na-phosphate, pH 7.0, 10 mM EDTA, 200 mg/ml zymolase and 150 mM b-mercaptoethanol.  Cells were pelleted and incubated in 1.5 mls of 50 mM EDTA, pH 8.0, 0.3% SDS, 200 mg/ml proteinase K and incubated for another 60 minutes at 65oC.  0.6 mls of 5 M KOAc was added and mixture was incubated on ice for 30 min.  The supernatant was subjected to a phenol/chloroform extraction and DNA was precipitated. The DNA was RNAse treated at 37oC for 2 hours (10 mM Tri-HCl, 1mM EDTA, pH 7.5, 1 mg/ml RNAse), followed by another phenol/chloroform extraction, and precipitated with ethanol.

tag: Strain Name

value: Dis IX pdr5 (A15560)

source_name: WT


title: Fig S2: Tris XVI (A18351) DNA (swap)

description: Fig S2: Tris XVI (A18351) DNA (swap)

scan_protocol: Pixel Size : 10 Scan Date : 2007-05-12 Scan Time : 11:32:35 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 9.1.3.1
Datafile type : Agilent result file

source_name: Trisome 16

value: Tris XVI (A18351)


title: Cold stress, biological rep 2

type: RNA

city: New Delhi

first: Akhilesh

middle: K.

last: Tyagi

state: Delhi

address: Benito Juarez Road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi South Campus

description: 7-day-old light-grown rice seedlings kept at 4 ± 1 degree celsius for 3 h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degree celsius on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using script EukGE-WS2v5.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: The data were analyzed with GeneChipOperating Software (GCOS 1.2.1) using Affymetrix default analysis settings and global scaling as normalization method. The mean target intensity of each array was arbitrarily set to 100.

label: Biotin

molecule: total RNA

organism: Oryza sativa

source_name: 7-day-old light-grown rice seedlings

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

growth_protocol: Rice seeds were disinfected with 0.1% HgCl2 for 1 h, thoroughly washed with RO (reverse-osmosis) water and soaked overnight in RO water. Seedlings were grown in RO water, at 28±1 degree celsius for 7 days, in a culture room with a daily photoperiodic cycle of 14 h light and 10 h dark.

extract_protocol: Extraction of total RNA was performed using Trizol, according to the manufacturer's instructions

treatment_protocol: Seedlings were kept at 4±1 degree celsius for 3 h

tag: Supspecies

value: indica, Variety:IR64


title: Fig S2: Dis II (A12685) DNA (swap)

description: former name: Disome 2 (12685)

scan_protocol: Pixel Size : 10 Scan Date : 2006-09-27 Scan Time : 14:41:08 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 9.1.1.1
Datafile type : Agilent result file


title: Salt stress, biological rep 2


title: Drought stress, biological rep 1

description: 7-day-old light-grown rice seedlings dried between folds of tissue paper at 28 ± 1 degree celsius for 3 h

treatment_protocol: Seedlings were dried between folds of tissue paper at 28 ± 1 degree celsius for 3 h


title: Fig S2: Tris I (A18345) DNA (swap)

description: Fig S2: Tris I (A18345) DNA (swap)

scan_protocol: Pixel Size : 10 Scan Date : 2007-05-12 Scan Time : 11:31:05 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B

source_name: Trisome 1


title: Fig S2: Dis I pdr5 (A15550) DNA (swap)

description: former name: Disome 1.1 delta pdr5 (channels originally misassigned)

scan_protocol: Pixel Size : 10 Scan Date : 2006-02-23 Scan Time : 10:24:32 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: Dis I pdr5 (A15550)


title: Fig S2: Dis XIII pdr5 (15567) DNA (swap)

description: former name: Disome 13.2delta pdr5 (channels originally misassigned)

scan_protocol: Pixel Size : 10 Scan Date : 2006-02-23 Scan Time : 11:29:26 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: Dis XIII pdr5 (15567)


title: 7-day-old Seedling, biological rep 3

description: 7-day-old light-grown rice seedlings kept in water for 3 h at 28 ± 1 degree celsius

growth_protocol: Rice seeds were disinfected with 0.1% HgCl2 for 1 h, thoroughly washed with RO (reverse-osmosis) water and soaked overnight in RO water. Seedlings were grown in RO water, at 28±1 degree celsius, in a culture room with a daily photoperiodic cycle of 14 h light and 10 h dark.

treatment_protocol: Seedlings were kept in beaker containing water for 3 h at 28 ± 1 degree celsius


title: Fig S2: Dis X pdr5 (A15562) DNA (swap)

description: former name: Disome 10.2 delta pdr5 (channels originally misassigned)

scan_protocol: Pixel Size : 10 Scan Date : 2006-02-23 Scan Time : 10:00:25 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: Dis X pdr5 (A15562)


title: Fig S2: Dis XII pdr5 (A15566) DNA (swap)

description: former name: Disome 12.7 delta pdr5 (channels originally misassigned)

value: Dis XII pdr5 (A15566)


title: Salt stress, biological rep 1


title: Drought stress, biological rep 3


title: Drought stress, biological rep 2


title: 7-day-old Seedling, biological rep 2


title: Fig 1B: cdc23-1 (A755) batch RNA

description: former name: AA 755 (Cdc23-1, DT=3.9) RNA

hyb_protocol: Description : Equal masses of differentially labeled control and sample cRNA were combined such that each sample contained at least 2.5 pmol dye.  Samples were mixed with control targets, fragmented, combined with hybridization buffer, and applied to a microarray consisting of 60mer probes for each yeast open reading frame (Agilent).  Microarrays were rotated at 60?C for 17 hours in a hybridization oven (Agilent).  Arrays were then washed according to the Agilent SSPE wash protocol, and scanned on an Agilent scanner.

scan_protocol: Pixel Size : 10 Scan Date : 2005-11-08 Scan Time : 11:53:00 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : A.7.5.1
Datafile type : Agilent result file

source_name: WT RNA

label_protocol: Description : 325 ng was used for microarray labeling with the Agilent Low RNA Input Fluorescent Linear Amplification Kit.  Reactions were performed as directed except using half the recommended reaction volume and one quarter the recommended Cy-CTP amount.  Dye incorporation and yield were measured with a Nanodrop spectrophotometer.

extract_protocol: Description : Filters were incubated for 1 hour at 65oC in lysis buffer (10 mM EDTA, 0.5% SDS, and 10 mM Tris, pH 7.5) and acid phenol.  The aqueous phase was further extracted twice with an equal volume of chloroform using phase lock gel (Eppendorf).  Total RNA was then ethanol precipitated and further purified over RNeasy columns (Qiagen). RNA quality was checked using the Bioanalyzer RNA Nano kit.

source_name: 755 RNA

growth_protocol: Description : Cultures were grown overnight at 30C in selective -his/G418 media and then diluted back to OD=0.3 in 250 ml -his/G418 media.  Cultures were grown shaking at 30C to midlog (OD=1.0-1.3) and harvested by vacuum filtration, flash-frozen in liquid nitrogen, and stored at ?80oC until RNA extraction.


title: Fig 1B: cdc28-4 (A2594) batch RNA

description: former name: AA 2594 (Cdc28-4, DT=3.4) RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-11-08 Scan Time : 11:45:05 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig S2: Dis XIII (A12695) DNA

description: former name: AA chr 13 disome (12695 new) DNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-03-23 Scan Time : 11:10:06 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 11311 CC H+W DNA

value: Dis XIII (A12695)


title: 7-day-old Seedling, biological rep 1


title: Fig 1C: Dis VIII (A13628) chem RNA (swap)

description: former name: AA chr 8 disome (13628) P-lim chemostat RNA swap

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-23 Scan Time : 13:16:12 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: Dis VIII (A13628)

growth_protocol: Description : ATR Sixfors fermenters were modified for use as chemostats.  Chemostat cultures were run at 30oC at a working volume of 300 mls, mixed at 400 rpm, and sparged at 5 standard liters per minute with humidified and filter-sterilized air.  The dilution rate was set to 0.17 volumes/hour.  Cultures were run in phosphate limited minimal defined medium containing the following (per liter): 100 mg calcium chloride, 100 mg sodium chloride, 500 mg magnesium sulfate, 5 g ammonium sulfate, 1 g potassium chloride, 500 mg boric acid, 40 mg copper sulfate, 100 mg potassium iodide, 200 mg ferric chloride, 400 mg manganese sulfate, 200 mg sodium molybdate, 400 mg zinc sulfate, 1 mg biotin, 200 mg calcium pantothenate, 1 mg folic acid, 1 mg inositol, 200 mg niacin, 100 mg p-aminobenzoic acid, 200 mg pyridoxine, 100 mg riboflavin, 200 mg thiamine, 50 mg adenine, 50 mg tryptophan, 20 mg uracil, 100 mg lysine, 20 mg methionine, 100 mg leucine, 100 mg G418, and 5 g glucose. Chemostats were inoculated with 1 ml overnight culture grown in chemostat media.  Cultures were maintained in batch for 24 hours, at which time the media flow was switched on.   Cultures were sampled daily for cell density by Coulter count, klett, and absorbance, and were considered to be in steady state when all parameters measurements were the same for two consecutive measurements, which occurred 4 days after inoculation for all cultures.  100 ml of cultures were harvested by vacuum filtration, flash-frozen in liquid nitrogen, and stored at ?80oC until RNA extraction.


title: Fig S2: Dis XI (A13771) DNA

description: former name: AA chr 11 disome (13771) DNA redo

scan_protocol: Pixel Size : 10 Scan Date : 2006-03-23 Scan Time : 10:46:18 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig S2: Dis IV (A15232) DNA

description: former name: AA chr 4 disome (4D1) DNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-11-08 Scan Time : 11:37:11 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 11311 genomic DNA

source_name: chr 4 disome (4D1) genomic DNA


title: Fig S2: Dis XVI pdr5 (A15572) DNA (swap)

description: former name: AA 16.1 ?pdr5 candidate DNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-03-23 Scan Time : 13:52:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 16.1 ?pdr5 DNA

value: Dis XVI pdr5 (A15572)


title: Fig S2: Dis XV (A12697) DNA

description: former name: AA chr 15 disome (12697) DNA redo


title: Fig 1B: cdc15-2 (A2596) batch RNA

description: former name: AA 2596 (Cdc15-2, DT=2.2) RNA


title: Fig S2: Dis VIII, XV, and s-YAC (A15579) DNA (swap)

description: former name: AA 13628 AB DNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-03-23 Scan Time : 14:15:50 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 13628 AB DNA

value: Dis VIII, XV, and s-YAC (A15579)


title: Seed (S3, 5 - 10 dap), biological rep 3

first: Sanjay

last: Kapoor

description: Seed [5 - 10 days after pollination (dap)] from rice plants

source_name: Seed, after pollination from rice plants

growth_protocol: Rice seeds were disinfected with 0.1% HgCl2 for 1 h, thoroughly washed with RO (reverse-osmosis) water and soaked overnight in RO water. Seedlings were grown in RO water, at 28±1 degree celsius, in a culture room with a daily photoperiodic cycle of 14 h light and 10 h dark. After 15 days seedlings were transferred in pots kept in greenhouse

extract_protocol: Extraction of total RNA was performed using modified guanidine hydrochloride method as described (Jain et al., 2006, Biochem Biophys Res Commun, 345, 646-651)

treatment_protocol: Untreated

tag: Subspecies


title: Fig 1AB: Dis XI and XV (A12691) batch RNA 2

description: former name: AA chr 11 + 15 disome (12691) RNA set 2

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-19 Scan Time : 12:50:11 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: Dis XI and XV (A12691)


title: Fig S2: Dis XVI (A12700) DNA

description: former name: AA chr 16 disome (12700) DNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-06-23 Scan Time : 12:18:02 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 12700 genomic DNA

value: Dis XVI (A12700)


title: Seed (S4, 11 - 20 dap), biological rep 2

description: Seed [11 - 20 days after pollination (dap)] from rice plants


title: Fig S2: Dis XII (A12694) DNA (swap)

description: former name: AA chr 12 disome (12694) DNA swap

scan_protocol: Pixel Size : 10 Scan Date : 2005-04-08 Scan Time : 11:30:48 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: Dis XII (A12694)


title: Seed (S1, 0 - 2 dap), biological rep 3

description: Seed [0 - 2 days after pollination (dap)] from rice plants

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000


title: Seed (S5, 21 - 29 dap), biological rep 3

description: Seed [21 - 29 days after pollination (dap)] from rice plants


title: Fig S2: Dis XIII CLN2-3HA (A15239) DNA

description: former name: AA chr 13 disome (13HA.K) DNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-07-20 Scan Time : 10:43:17 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 13HA.K genomic DNA

value: Dis XIII CLN2-3HA (A15239)


title: Seed (S3, 5 - 10 dap), biological rep 2


title: Fig S2: Dis I, VI, and XIII (A15619) DNA

description: former name: AA chr 6 disome (6H1.B) DNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-07-20 Scan Time : 10:35:18 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 6H1.B genomic DNA

value: Dis I, VI, and XIII (A15619)


title: cells grown with 2% oxygen #2

first: Carolina

last: Alvarez

address: 1959 NE Pacific St

department: Microbiology

description: cDNA synthesis, fragmentation, labeling, hybridization, and processing of Pseudomonas aeruginosa GeneChips were carried out as recommended by the manufacturer. Experiments were performed in duplicate with independently prepared samples.

hyb_protocol: As recommended by the manufacturer (Affymetrix)

data_processing: The Affymetrix GeneChip Operating Software Version 1.4 was used for initial data acquisition and processing.

label: Biotinylated GeneChip reagent

organism: Pseudomonas aeruginosa

source_name: strain PAO1 grown with 2% oxygen #2

extract_protocol: Pseudomonas aeruginosa cells were disrupted by sonication and RNA was purified with the RNeasy Mini kit (Qiagen) including DNase treatment on the column.

tag: Pseudomonas aeruginosa strain PAO1 grown with 2% oxygen # 2


title: Seed (S2, 3 - 4 dap), biological rep 3

description: Seed [3 - 4 days after pollination (dap)] from rice plants


title: Fig 1AB: Dis I (A12683) batch RNA 1

description: former name: AA chr 1 disome (12683) RNA set 1

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-19 Scan Time : 12:18:37 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig 1AB: Dis II (A12685) batch RNA 1

description: former name: AA chr 2 disome (12685) RNA set 1

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-19 Scan Time : 12:02:49 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: cells grown with 2% oxygen #1

scan_protocol: As recommended by the manufacturer (Affymetrix)

source_name: strain PAO1 grown with 2% oxygen #1

tag: Pseudomonas aeruginosa strain PAO1 grown with 2% oxygen # 1


title: cells grown with 0% oxygen + 100mM nitrate #1

source_name: strain PAO1 grown with nitrate #1

label_protocol: As recommended by the manufacturer (Affymetrix)

tag: Pseudomonas aeruginosa strain PAO1 grown with nitrate #1


title: cells grown with 0.4% oxygen #1

source_name: strain PAO1 grown with 0.4% oxygen #1

tag: Pseudomonas aeruginosa strain PAO1 grown with 0.4% oxygen # 1


title: Fig 1AB: Dis XV (A12697) batch RNA 2

description: former name: AA chr 15 disome (12697) RNA set 2


title: Seed (S2, 3 - 4 dap), biological rep 2


title: Fig 1AB: Dis X (A12689) batch RNA 2

description: former name: AA chr 10 disome (12689) RNA set 2


title: cells grown with 20% oxygen #2

source_name: strain PAO1 grown with 20% oxygen #2

tag: Pseudomonas aeruginosa strain PAO1 grown with 20% oxygen # 2


title: cells grown with 20% oxygen #1

source_name: strain PAO1 grown with 20% oxygen #1

tag: Pseudomonas aeruginosa strain PAO1 grown with 20% oxygen #1


title: Inflorescence (P6, 22 - 30 cm), biological rep 3

description: Inflorescence (22 - 30 cm) from rice plants

source_name: Inflorescence, immature rice plants


title: Seed (S4, 11 - 20 dap), biological rep 1


title: cells grown with 0% oxygen + 100mM nitrate #2

source_name: strain PAO1 grown with nitrate #2

tag: Pseudomonas aeruginosa strain PAO1 grown with nitrate # 2


title: Seed (S3, 5 - 10 dap), biological rep 1


title: Seed (S4, 11 - 20 dap), biological rep 3


title: cells grown with 0.4% oxygen #2

source_name: strain PAO1 grown with 0.4% oxygen #2

tag: Pseudomonas aeruginosa strain PAO1 grown with 0.4% oxygen # 2


title: Seed (S5, 21 - 29 dap), biological rep 2


title: Seed (S1, 0 - 2 dap), biological rep 2


title: Inflorescence (P6, 22 - 30 cm), biological rep 2


title: Inflorescence (P5, 15 - 22 cm), biological rep 3

description: Inflorescence (15 - 22 cm) from rice plants


title: Seed (S1, 0 - 2 dap), biological rep 1


title: Fig S2: Dis VIII (A13628) DNA

description: former name: AA chr 8 disome (13628) DNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-05-18 Scan Time : 10:05:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: chr 8 disome (13628) DNA


title: Fig 1AB: Dis XII (A12693) batch RNA 1

description: former name: AA chr 12 disome (12693) RNA set 1

value: Dis XII (A12693)


title: Fig S2: Dis VIII and XIV (A15615) DNA

description: former name: AA chr 14? disome DNA

source_name: chr 14 disome? DNA

value: Dis VIII and XIV (A15615)


title: Inflorescence (P6, 22 - 30 cm), biological rep 1


title: Seed (S5, 21 - 29 dap), biological rep 1


title: Seed (S2, 3 - 4 dap), biological rep 1


title: Fig 1AB: Dis II (A12685) batch RNA 2

description: former name: AA chr 2 disome (12685) RNA set 2

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-19 Scan Time : 13:14:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig S2: Dis X (A6869) DNA

description: former name: AA chr 10 disome (6869) DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-09 Scan Time : 13:30:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 11311 genomic DNA

source_name: 6869 genomic DNA


title: Fig 1AB: Dis XI and XV (A12691) batch RNA 1

description: former name: AA chr 11 + 15 disome (12691) RNA set 1

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-19 Scan Time : 11:54:56 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig 1AB: wt (A11311) batch RNA 2

description: former name: AA 11311 RNA set 3

scan_protocol: Pixel Size : 10 Scan Date : 2005-04-29 Scan Time : 12:50:20 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 11311 set 3 RNA


title: Inflorescence (P5, 15 - 22 cm), biological rep 2


title: Inflorescence (P5, 15 - 22 cm), biological rep 1


title: Fig 1AB: Dis XIII (A12695) batch RNA 1

description: former name: AA chr 13 disome (12695) RNA set 1


title: Inflorescence (P4, 10 - 15 cm), biological rep 3

description: Inflorescence (10 - 15 cm) from rice plants


title: Inflorescence (P3, 5 - 10 cm), biological rep 3

description: Inflorescence (5 - 10 cm) from rice plants


title: Inflorescence (P4, 10 - 15 cm), biological rep 1


title: Fig 1AB: Dis XVI (A12700) batch RNA 1

description: former name: AA chr 16 disome (12700) RNA set 3

scan_protocol: Pixel Size : 10 Scan Date : 2005-04-29 Scan Time : 12:10:41 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 12700 set 3 RNA


title: Fig 1AB: Dis I (A12683) batch RNA 2

description: former name: AA chr 1 disome (12683) RNA set 2


title: Fig 1AB: Dis VIII (A13628) batch RNA 1

description: former name: AA chr 8 disome (13628) RNA set 3

scan_protocol: Pixel Size : 10 Scan Date : 2005-04-29 Scan Time : 12:18:35 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: chr8 set 3 RNA


title: Inflorescence (P4, 10 - 15 cm), biological rep 2


title: Fig 5A: YAC-1c (A16854) chem RNA

description: former name: AA YAC 16854 P-lim

scan_protocol: Pixel Size : 10 Scan Date : 2006-12-15 Scan Time : 13:20:37 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: Inflorescence (P3, 5 - 10 cm), biological rep 2


title: Fig 1C: wt (A11311) chem RNA

description: former name: AA 11311 P-lim F18 12/9/6 vs F1 12/6/5

scan_protocol: Pixel Size : 10 Scan Date : 2006-12-15 Scan Time : 13:12:33 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: Fig 1AB: wt (A11311) batch RNA 3

description: former name: AA 11311 RNA set 4

scan_protocol: Pixel Size : 10 Scan Date : 2005-04-29 Scan Time : 12:26:30 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 11311 set 4 RNA


title: Inflorescence (P3, 5 - 10 cm), biological rep 1


title: Inflorescence (P2, 3 - 5 cm), biological rep 3

description: Inflorescence (3 - 5 cm) from rice plants


title: Fig 5A: YAC-7 (A16851) chem RNA

description: former name: AA YAC 16651 P-lim (correct number is 16851)


title: Fig S2: Dis XI and XV (A12691) DNA

description: former name: AA chr 11+15 disome (12691) DNA redo3

scan_protocol: Pixel Size : 10 Scan Date : 2006-07-07 Scan Time : 12:47:48 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Inflorescence (P2, 3 - 5 cm), biological rep 2

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000


title: Fig 5A: YAC-2 (A17392) chem RNA

description: former name: YAC 11.1, AA YAC-2 (A17392) P-lim

scan_protocol: Pixel Size : 10 Scan Date : 2006-11-22 Scan Time : 13:31:44 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: Fig S2: Dis XI pdr5 (A15564) DNA

description: former name: AA Dis5 ?pdr5 (actually Dis11 pdr5, misnamed)

scan_protocol: Pixel Size : 10 Scan Date : 2006-07-07 Scan Time : 11:31:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: Dis5 ?pdr5 7/6/06 DNA

value: Dis XI pdr5 (A15564)


title: Fig 5A: YAC-4 (A17394) chem RNA

description: former name: YAC 2.1, AA YAC-4 (A17394) P-lim


title: Fig 1AB: Dis XIV (A13979) batch RNA 2

description: former name: AA chr 14 disome (13979) set#6 batch RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-01-31 Scan Time : 10:39:38 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: Dis XIV (A13979)


title: Fig 5A: YAC-3 (A17393) chem RNA

description: former name: YAC 4.1, AA YAC-3 (A17393) P-lim

scan_protocol: Pixel Size : 10 Scan Date : 2006-11-22 Scan Time : 13:16:16 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: Fig 1AB: Dis XVI (A12700) batch RNA 2

description: former name: AA chr 16 disome (12700) RNA set 4

scan_protocol: Pixel Size : 10 Scan Date : 2005-04-29 Scan Time : 12:02:44 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 12700 set 4 RNA


title: Fig S2: Dis V pdr5 (A15556) DNA

description: former name: AA Dis11 ?pdr5 1.1A (actually Dis5, misnamed)

scan_protocol: Pixel Size : 10 Scan Date : 2006-07-07 Scan Time : 12:16:10 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: Dis V pdr5 (A15556)


title: Fig 1AB: Dis IV (A12687) batch RNA 2

description: former name: AA chr 4 disome (12687) RNA set 2

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-19 Scan Time : 12:26:30 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig 1C: cdc23-1 (A755) chem RNA

description: former name: AA 755 (cdc23-1) chemostat RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-04-18 Scan Time : 10:14:30 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig 1AB: Dis VIII and XIV (A15615) batch RNA 2

description: former name: AA chr 14+8 disome (14H2-4) set#6 batch RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-01-31 Scan Time : 11:29:46 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 14H2-4 set#6 RNA


title: Fig S2: Dis X (A12689) DNA

description: former name: CC 11311 vs. 12689 H+W DNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-07-21 Scan Time : 10:50:14 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig S2: Dis I (A12683) DNA

description: former name: CC 11311 vs. 12683 H+W DNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-07-21 Scan Time : 10:58:08 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Young inflorescence (P1, upto 3 cm), biological rep 3

description: Young inflorescence (upto 3 cm) from rice plants

source_name: Young inflorescence, immature rice plants

value: indica, Variety:IR64


title: Fig 1C: cdc15-2 (A2596) chem RNA

description: former name: AA 2596 (cdc15-2) chemostat RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-04-18 Scan Time : 10:06:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig 1AB: Dis V (A14479) batch RNA 1

description: former name: AA chr 5 disome RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-06-22 Scan Time : 11:13:51 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 11311 batch RNA (sample that came with disome 5)

source_name: disome 5 batch RNA


title: Fig 1AB: Dis XI and XVI (A12699) batch RNA 1

description: former name: AA chr 11+16 disome (12699) RNA set 1

value: Dis XI and XVI (A12699)


title: Fig S2: wt (A11311) DNA

description: Former name: AA 11311 vs 11311 DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-08 Scan Time : 13:40:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Inflorescence (P2, 3 - 5 cm), biological rep 1

source_name: Inflorescence, immature rice plants


title: Fig 1AB: Dis IX (A13975) batch RNA 2

description: former name: AA chr 9 disome (13975) set#6 batch RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-01-31 Scan Time : 10:47:42 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig 1AB: wt (A11311) batch RNA 4

description: former name: AA 11311 set#5 vs. 11311 set#6 batch RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-01-31 Scan Time : 11:37:52 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig S2: Dis XII (A12693) DNA

description: former name: AA chr 12 disome (12693) DNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-01-14 Scan Time : 10:58:53 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 11311 DNA from earlier experiment


title: Fig 1C: cdc28-4 (A2594) chem RNA

description: former name: AA 2594 (cdc28-4) chemostat RNA


title: Fig 1AB: Dis XI (A13771) batch RNA 2

description: former name: AA chr 11 disome (13771) set#6 batch RNA


title: Young inflorescence (P1, upto 3 cm), biological rep 1

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000


title: SAM, biological rep 3

description: Shoot apical meristem (SAM, upto 0.5 mm) from rice plants at floral transition stage

source_name: Rice plants at floral transition stage


title: SAM, biological rep 2


title: Young inflorescence (P1, upto 3 cm), biological rep 2


title: Fig 1AB: Dis XIII (A12695) batch RNA 2

description: former name: AA chr 13 disome (12695) RNA set 2

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-19 Scan Time : 13:06:00 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig 1AB: Dis XI and XVI (A12699) batch RNA 2

description: former name: AA chr 11+16 disome (12699) RNA set 2


title: Fig 5A: YAC-6 (A17397) chem RNA

description: former name: AA YAC 7.1 P-lim

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-11 Scan Time : 10:37:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: Fig 1AB: Dis XIV (A13979) batch RNA 1

description: former name: AA chr 14 disome (13979) set#5 batch RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-01-31 Scan Time : 12:01:39 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig 1C: Dis XIV (A13979) chem RNA (swap)

description: former name: AA chr 14 disome (13979) P-lim chemostat RNA swap

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-23 Scan Time : 13:39:56 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig 1AB: Dis X (A12689) batch RNA 1

description: former name: AA chr 10 disome (12689) RNA set 1

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-19 Scan Time : 12:42:18 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig 1AB: Dis IX (A13975) batch RNA 1

description: former name: AA chr 9 disome (13975) set#5 batch RNA


title: Fig 1AB: Dis VIII and XIV (A15615) batch RNA 1

description: former name: AA chr 14+8 disome (14H2-4) set#5 batch RNA

source_name: 14H2-4 set#5 RNA


title: Fig 1AB: Dis XI (A13771) batch RNA 1

description: former name: AA chr 11 disome (13771) set#5 batch RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-01-31 Scan Time : 10:55:37 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig 1AB: Dis XV (A12697) batch RNA 1

description: former name: AA chr 15 disome (12697) RNA set 1


title: Fig 1C: Dis XI (A13771) chem RNA (swap)

description: former name: AA chr 11 disome (13771) P-lim chemostat RNA swap


title: SAM, biological rep 1


title: Fig 1C: Dis XI and XVI (A12699) chem RNA

description: former name: AA chr 11+16 disome (12699) phos-lim chemostat RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-01-31 Scan Time : 11:03:31 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig 1C: Dis II (A12685) chem RNA (swap)

description: former name: AA chr 2 disome (12685) P-lim chemostat RNA swap

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-23 Scan Time : 12:26:26 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig S2: Dis II (A6865) DNA

description: former name: AA chr 2 disome (6865) DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-11-10 Scan Time : 14:15:07 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: Dis II (A6865)


title: Fig S2: Dis IX (A13975) DNA (swap)

description: former name: AA chr 9 disome (13975) DNA redo swap

scan_protocol: Pixel Size : 10 Scan Date : 2006-03-15 Scan Time : 11:38:10 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 11311 CC H+W DNA


title: Fig 1AB: Dis IV (A12687) batch RNA 1

description: former name: AA chr 4 disome (12687) RNA set 1

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-19 Scan Time : 12:10:43 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig S2: Dis XI and XVI (A12699) DNA

description: former name: AA chr 11+16 disome (12699) redo DNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-06-29 Scan Time : 09:45:36 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig S2: Dis I (A6863) DNA

description: former name: AA chr 1 disome (6863) DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-11-10 Scan Time : 13:43:14 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig 1AB: Dis XII (A12693) batch RNA 2

description: former name: AA chr 12 disome (12693) RNA set 2


title: Fig S2: Dis XIV (A13979) DNA (swap)

description: former name: AA chr 14 disome (13979) DNA redo swap

scan_protocol: Pixel Size : 10 Scan Date : 2006-03-15 Scan Time : 12:02:17 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Y Leaf, biological rep 3

description: Y Leaf (leaf subtending the shoot apical meristem) from mature rice plants

source_name: Mature rice plants


title: Y Leaf, biological rep 2


title: Fig S2: Dis IV (A12687) DNA (swap)

description: former name: AA chr 4 disome (12687) DNA swap

scan_protocol: Pixel Size : 10 Scan Date : 2005-04-28 Scan Time : 10:58:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Y Leaf, biological rep 1


title: Mature leaf, biological rep 3

description: Leaf from mature rice plants


title: Fig 1AB: Dis VIII (A13628) batch RNA 2

description: former name: AA chr 8 disome (13628) RNA set 4

scan_protocol: Pixel Size : 10 Scan Date : 2005-04-29 Scan Time : 11:46:57 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: chr8 set 4 RNA


title: Fig 1C: Dis XVI (A12700) chem RNA (swap)

description: former name: AA chr 16 disome (12700) P-lim chemostat RNA swap

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-23 Scan Time : 13:08:15 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Mature leaf, biological rep 2

description: Leaf from mature rice plants

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000


title: Root, 7-day-old Seedling, biological rep 3

description: Root of 7-day-old light-grown rice seedlings

source_name: 7-day-old light-grown rice seedlings


title: Fig S2: Dis V (A14479) DNA (swap)

description: former name: AA chr 5 disome (14479) DNA redo swap


title: Mature leaf, biological rep 1

description: Leaf from mature rice plants


title: Root, 7-day-old Seedling, biological rep 2


title: Root, 7-day-old Seedling, biological rep 1


title: Fig 1AB: wt (A11311) batch RNA 1

description: former name: AA 11311 B vs 11311 A RNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-10-19 Scan Time : 12:31:21 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig 1AB: Dis X (A6869) batch RNA 2

description: former name: AA chr 10 disome (6869) RNA set 2

scan_protocol: Pixel Size : 10 Scan Date : 2004-10-14 Scan Time : 11:39:36 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 6869B RNA


title: Fig 1AB: Dis II (A6865) batch RNA 2

description: former name: AA chr 2 disome (6865) RNA set 2

scan_protocol: Pixel Size : 10 Scan Date : 2004-10-14 Scan Time : 11:23:48 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 6865B RNA


title: Fig 1C: Dis XIII (A12695) chem RNA (swap)

description: former name: AA chr 13 disome (12695) P-lim chemostat RNA swap

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-23 Scan Time : 13:32:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: Dis XIII (A12695)


title: Fig 1AB: Dis X (A6869) batch RNA 1

description: former name: AA chr 10 disome (6869) RNA set 1

scan_protocol: Pixel Size : 10 Scan Date : 2004-10-14 Scan Time : 11:31:42 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 6869A RNA


title: Fig 1C: Dis V (A14479) chem RNA (swap)

description: former name: AA chr 5 disome (14479) P-lim chemostat RNA swap

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-23 Scan Time : 12:10:26 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig 1C: Dis XII (A12693) chem RNA (swap)

description: former name: AA chr 12 disome (12693) P-lim chemostat RNA swap


title: Fig 1C: Dis IX (A13975) chem RNA (swap)

description: former name: AA chr 9 disome (13975) P-lim chemostat RNA swap


title: Fig 1C: Dis IV (A12687) chem RNA (swap)

description: former name: AA chr 4 disome (12687) P-lim chemostat RNA swap

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-23 Scan Time : 12:18:21 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig 1C: Dis XV (A12697) chem RNA (swap)

description: former name: AA chr 15 disome (12697) P-lim chemostat RNA swap

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-23 Scan Time : 12:50:14 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig 1C: Dis X (A12689) chem RNA (swap)

description: former name: AA chr 10 disome (12689) P-lim chemostat RNA swap


title: FlagMyc-unsync-midlog

status: Public on May 16 2007

type: other

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

description: High-resolution Flag/Myc rations (using IP for Gal-driven Flag-H3 and constitutive Myc-H3). midlog after Gal induction.

hyb_protocol: Labeled probes were hybridized onto a yeast tiled oligonucleotide microarray [Yuan et al., Science 309, 626 (2005)] at 65°C for 16 hours and washed as described on www.microarrays.org.

scan_protocol: The arrays were scanned at 5 micron resolution with an Axon Laboratories GenePix 4000B scanner running GenePix 5.1. Image analysis and data normalization were performed as previously described [Liu et al., PLoS Biol 3, e328 (2005)].

data_processing: Normalized log2(Cy3/Cy5)

molecule: other

source_name: Myc IP midlog

label_protocol: 3 μg of aRNA produced from the linear amplification were used to label probe

growth_protocol: MDY510 cells were grown in YP + 2% raffinose

extract_protocol: IPed using anti-Myc Ab (Sigma; monoclonal). Amplified with a starting amount of up to 75 ng for ChIP samples, using the DNA linear amplification

treatment_protocol: Cells collected by filtration and resuspended in YP+2% galactose.

tag: Strain

source_name: Flag IP midlog

extract_protocol: IPed using anti-Flag Ab (Sigma; monoclonal). Amplified with a starting amount of up to 75 ng for ChIP samples, using the DNA linear amplification


title: FlagMyc-unsync-t150

description: High-resolution Flag/Myc rations (using IP for Gal-driven Flag-H3 and constitutive Myc-H3). 150min after Gal induction.

source_name: Myc IP 150 minutes

source_name: Flag IP 150 minutes


title: Fig 1AB: Dis II (A6865) batch RNA 1

description: former name: AA chr 2 disome (6865) RNA set 1

scan_protocol: Pixel Size : 10 Scan Date : 2004-10-14 Scan Time : 11:15:42 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 6865A RNA


title: FlagMyc-unsync-t120

description: High-resolution Flag/Myc rations (using IP for Gal-driven Flag-H3 and constitutive Myc-H3). 120min after Gal induction.

source_name: Myc IP 120 minutes

source_name: Flag IP 120 minutes


title: Fig 1C: Dis I (A12683) chem RNA (swap)

description: former name: AA chr 1 disome (12683) P-lim chemostat RNA swap

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-23 Scan Time : 13:47:55 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Fig 1AB: Dis I (A6863) batch RNA 2

description: former name: AA chr 1 disome (6863) RNA set 2

source_name: 6863B RNA


title: FlagMyc-unsync-t45

description: High-resolution Flag/Myc rations (using IP for Gal-driven Flag-H3 and constitutive Myc-H3). 45min after Gal induction.

source_name: Myc IP 45 minutes

source_name: Flag IP 45 minutes


title: FlagMyc-unsync-t60

description: High-resolution Flag/Myc rations (using IP for Gal-driven Flag-H3 and constitutive Myc-H3). 60min after Gal induction.

source_name: Myc IP 60 minutes

source_name: Flag IP 60 minutes


title: FlagMyc-unsync-t90

description: High-resolution Flag/Myc rations (using IP for Gal-driven Flag-H3 and constitutive Myc-H3). 90min after Gal induction.

source_name: Myc IP 90 minutes

source_name: Flag IP 90 minutes


title: FlagMyc-unsync-t2

description: High-resolution Flag/Myc rations (using IP for Gal-driven Flag-H3 and constitutive Myc-H3). 2min after Gal induction.

source_name: Myc IP 2 minutes

source_name: Flag IP 2 minutes


title: Fig 1AB: Dis I (A6863) batch RNA 1

description: former name: AA chr 1 disome (6863) RNA set 1

source_name: 6863A RNA


title: FlagMyc-unsync-t30

description: High-resolution Flag/Myc rations (using IP for Gal-driven Flag-H3 and constitutive Myc-H3). 30min after Gal induction.

source_name: Myc IP 30 minutes

source_name: Flag IP 30 minutes


title: MycFlag-G1-arrest-t150-rep1

description: High-resolution Myc/Flag rations (using IP for Gal-driven Flag-H3 and constitutive Myc-H3). 150min after Gal induction.

source_name: Myc IP 150 minutes rep1

treatment_protocol: Cells arrested with 4μg/mL alpha factor for 3 hours, collected by filtration and resuspended in YP+2% galactose.

source_name: Flag IP 150 minutes rep1


title: MycFlag-G1-arrest-t150-rep2

source_name: Myc IP 150 minutes rep2

source_name: Flag IP 150 minutes rep2


title: MycFlag-G1-arrest-t120-rep1

description: High-resolution Myc/Flag rations (using IP for Gal-driven Flag-H3 and constitutive Myc-H3). 120min after Gal induction.

source_name: Myc IP 120 minutes rep1

source_name: Flag IP 120 minutes rep1


title: MycFlag-G1-arrest-t120-rep2

source_name: Myc IP 120 minutes rep2

source_name: Flag IP 120 minutes rep2


title: Fig S2: Dis IV CLN2-3HA (A15236) DNA

description: former name: AA chr 4 disome (4HAc4B) DNA (incorrectly labeled a swap)

scan_protocol: Pixel Size : 10 Scan Date : 2006-01-26 Scan Time : 10:33:30 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 11311 genomic DNA

source_name: 4HAc4B genomic DNA

value: Dis IV CLN2-3HA (A15236)


title: MycFlag-G1-arrest-t30-rep1

description: High-resolution Myc/Flag rations (using IP for Gal-driven Flag-H3 and constitutive Myc-H3). 30min after Gal induction.

source_name: Myc IP 30 minutes rep1

source_name: Flag IP 30 minutes rep1


title: MycFlag-G1-arrest-t90-rep1

description: High-resolution Myc/Flag rations (using IP for Gal-driven Flag-H3 and constitutive Myc-H3). 90min after Gal induction.

source_name: Myc IP 90 minutes rep1

source_name: Flag IP 90 minutes rep1


title: MycFlag-G1-Agilent-t120-set5

description: Genome-wide Myc/Flag ratios. 120min after Gal induction.

hyb_protocol: was hybridized according to Agilent protocol

scan_protocol: was scanned according to Agilent protocol

source_name: Myc IP 120 minutes set5

source_name: Flag IP 120 minutes set5


title: rpkA mutant; t8; Culture B: Con. Cy3, Exp. Cy5

city: Cologne

first: Ludwig

last: Eichinger

address: Joseph-Stelzmann-Strasse 52

country: Germany

institute: Institute for Biochemistry 1

description: DNA microarrays cotainining 5,423 non-redundant ESTs from the D. discoideum cDNA project (Urushihara et al., 2004), partial sequences of 450 selected genes, probes of the SpotReport-10 Array Validation System (Stratagene, La Jolla, USA) and appropriate positive and negative controls were produced in-house using standard protocols (see also: http://www.uni-koeln.de/medfak/biochemie/transcriptomics/ production.e.shtml). Briefly, probes were amplified by two 100µl PCR reactions in 96-well microtiter plates using standard primers (M13F2: 5’-GTAAAACGACGGCCAGTG-3’, M13R2: 5’-C6-Aminolink-ACCATGATTACGCCAAGC-3’) for the cloned ESTs and gene-specific primers for the selected genes and the positive controls. After analysis by agarose gel electrophoresis (10µl of each reaction) the two reactions were combined, precipitated, solubilised in 11µl 25% DMSO, 1µl separated again by agarose gel electrophoresis and evaluated (Farbrother et al., 2002). Probes were transferred with the proteineer dp pipetting robot (Bruker, Germany) into 384-well microarray plates with cylindrical wells (Abgene, Hamburg, Germany) and printed onto UltraGaps slides (Corning, New York, USA) at 18°C and 45% humidity with a BioRobotics MicroGrid 600 microarray robot (Genomic Solutions, Huntingdon, UK) using MicroSpot 2500 microarraying pins. Each probe was spotted in duplicate, positive and negative controls were spotted 6, 24, 192 or 286 times and the SpotReport controls 96 times. The microarray is composed of three grids with 16 subarrays each and 14,620 spots in total. The complete microarray dataset is available at GEO, http://www.ncbi.nlm.nih.gov/geo; accession number GPL1972.

hyb_protocol: Cy3 and Cy5 labelled targets were mixed, ethanol precipitated and dissolved in 65 µl of hybridisation buffer (Noegel et al., 1985) with 500 µg/ml Fish sperm DNA (Roche, Mannheim, Germany) and 2 µM Oligo dA 18-mer. The hybridisation mix was heated to 80 °C for 10 min, applied to the microarray under a cover-slip and incubated in a hybridisation chamber (Corning, New York, USA) for 15 hours at 37°C. Post-hybridisation washes were performed twice with 2x SSC, 0.1% SDS and once with 0.1x SSC, 0.1% SDS for 5 min each, five times with 0.1x SSC and once with with 0.01x SSC for 5 sec each and dried by centrifugation at 235xg for 5 min. See also Farbrother et al., Cell. Microbiol., 3:438-456, 2006.

scan_protocol: Signal detection was performed with the ScanArray 4000XL confocal laser scanner (PerkinElmer Life Sciences, Wellesley, USA). Images for Cy3 and Cy5 were obtained, spots were detected and quantified with ScanArray Express v2.2 (PerkinElmer Life Sciences), then manually inspected and if necessary corrected. See also Farbrother et al., Cell. Microbiol., 3:438-456, 2006.

data_processing:
For each individual comparison four microarrays were hybridised and analysed. Two imagepairs were produced per microarray slide, one with high laser intensity so that signals for most probes and also some saturated signals were obtained and a second one with lower laser intensity so that none of the signals was saturated. This way the dynamic range of the measurement was expanded. To handle the import and export of microarray data to different analysis programs an Excel Add-In, Array tools (http://www.uni-koeln.de/med-fak/biochemie/ transcriptomics/tools-array.e.shtml), was programmed in Visual Basic. Upon import of two data files of the same microarray scanned with different laser powers the saturated spots of the high laser power scan were replaced by non-saturated spots from the low laser power scan. In addition the import also performed data filtering by flagging SpotReport controls, negative controls, empty spots, spots where only spotting solution was printed and spots whose intensities were below or equal to zero as "Bad". Fluorescence ratios were normalised by LOWESS-norma-lisation using R1.6.2 (BioConductor, http://www.bioconductor.org/). The normalized M values (M = log2 (Intensityexperiment/Intensitycontrol) were transferred into a new worksheet for significance analysis of microarrays (SAM) analysis (Tusher et al., 2001). At the transfer all probes spotted in higher replicates were reduced to double spots by averaging. Furthermore all probes that were flagged "Found" in less than half of the spots, were excluded from SAM analysis. Differentially regulated genes were identified using the one-class SAM method calculating 1000 permutations. The SAM program not only identifies the differentially regulated genes, but also predicts the number of false positives. These are the genes that are falsely reported as differentially expressed. This feature was used in all microarray experiments to set the significance level such, that the 90th percentile of the false discovery rate (FDR) was minimal.
See also Farbrother et al., Cell. Microbiol., 3:438-456, 2006.

molecule: cytoplasmic RNA

organism: Dictyostelium discoideum

source_name: Dictyostelium discoideum AX2

label_protocol: Fairplay indirect labelling kit (Stratagene)

growth_protocol: cells after 8 hours of development on phosphate agar plates

extract_protocol: Qiagen RNeasy kit, isolation of cytoplasmic RNA from animal cells

treatment_protocol: untreated

tag: AX2 cells after 8 hours (t8) of development

source_name: Dictyostelium discoideum rpkA minus mutant

tag: strain AX2 in which the rpkA (seven transmembrane receptor fused to a PIP5 kinase domain) gene has been knocked out by homologous recombination after 8 hours (t8) of development;


title: rpkA mutant; t8; Culture A: Con. Cy5, Exp. Cy3


title: rpkA mutant; t0; Culture B: Con. Cy3, Exp. Cy5

growth_protocol: cells in logarithmic growth phase

tag: AX2 vegetative (t0) cells

tag: strain AX2 in which the rpkA (seven transmembrane receptor fused to a PIP5 kinase domain) gene has been knocked out by homologous recombination


title: MycFlag-G1-Agilent-t150-set5

description: Genome-wide Myc/Flag ratios. 150min after Gal induction.

source_name: Myc IP 150 minutes set5

source_name: Flag IP 150 minutes set5


title: MycFlag-G1-arrest-t90-rep2

source_name: Myc IP 90 minutes rep2

source_name: Flag IP 90 minutes rep2


title: MycFlag-G1-Agilent-t090-set2

description: Genome-wide Myc/Flag ratios. 90min after Gal induction.

source_name: Myc IP 090 minutes set2

source_name: Flag IP 090 minutes set2


title: MycFlag-G1-Agilent-t150-set2

source_name: Myc IP 150 minutes set2

source_name: Flag IP 150 minutes set2


title: MycFlag-G1-Agilent-t120-set2

source_name: Myc IP 120 minutes set2

source_name: Flag IP 120 minutes set2


title: MycFlag-G1-arrest-t60-rep1

description: High-resolution Myc/Flag rations (using IP for Gal-driven Flag-H3 and constitutive Myc-H3). 60min after Gal induction.

source_name: Myc IP 60 minutes rep1

source_name: Flag IP 60 minutes rep1


title: rpkA mutant; t8; Culture B: Con. Cy5, Exp. Cy3


title: rpkA mutant; t0; Culture A: Con. Cy5, Exp. Cy3

tag: strain AX2 in which the rpkA (seven transmembrane receptor fused to a PIP5 kinase domain) gene has been knocked out by homologous recombination.


title: Nuc-vs-Genomic-rep1

type: mixed

description: Genome-wide levels of nucleosomal DNA. Cells were arrested with alpha factor, chromatin digested by MNase and compared to sonicated input.

source_name: Nucleosomal rep1

extract_protocol: Chromatin digested by MNase. Amplified with a starting amount of up to 75 ng for ChIP samples, using the DNA linear amplification

tag: See [Yuan et al., Science 309, 626 (2005)]

source_name: Genomic rep1

extract_protocol: Chromatin sheared by sonication.


title: MycFlag-G1-Agilent-t090-set5

source_name: Myc IP 090 minutes set5

source_name: Flag IP 090 minutes set5


title: Myc-IP-vs-WCE-rep2

description: Genome-wide levels of histone H3. Cells were arrested with alpha factor, chromatin sheared by sonication, and Myc-H3 was IPed and compared to to sonicated input (WCE)

source_name: Myc-H3 IP rep2

extract_protocol: Chromatin sheared by sonication. IPed using anti-Myc Ab (Sigma; monoclonal). Amplified with a starting amount of up to 75 ng for ChIP samples, using the DNA linear amplification

treatment_protocol: Cells arrest with alpha factor. No Galactose induction

value: MDY510, Myc-tagged H3

source_name: WCE rep2


title: PolII-IP-vs-Genomic-t60-rep1

description: Genome-wide PolII occupancy using PolII-IP vs genomic DNA. Yeast grown on Raffinose, arrested for 3 hours using alpha factor, then shifted to Galactose. 60 minutes after Galactose induction

source_name: PolII IP 60 minutes rep1

treatment_protocol: t=60 (3 hours of alpha factor, 60 minutes after galactose shift)

source_name: Genomic 60 minutes rep1


title: PolII-IP-vs-Genomic-t0-rep2

description: Genome-wide PolII occupancy using PolII-IP vs genomic DNA. Yeast grown on Raffinose, arrested for 3 hours using alpha factor. no galactose induction.

source_name: PolII IP 0 minutes rep2

treatment_protocol: t=0 (3 hours of alpha factor, no galactose)

source_name: Genomic 0 minutes rep2


title: MycFlag-G1-Agilent-t060-set5

description: Genome-wide Myc/Flag ratios. 60min after Gal induction.

source_name: Myc IP 060 minutes set5

source_name: Flag IP 060 minutes set5


title: rpkA mutant; t8; culture A: Con. Cy3, Exp. Cy5

source_name: Dictyostelium discoideum AX2

tag: AX2 after 8 hours (t8) of development

source_name: Dictyostelium discoideum rpkA minus mutant


title: Nuc-vs-Genomic-rep2

source_name: Nucleosomal rep2

source_name: Genomic rep2


title: PolII-IP-vs-Genomic-t60-rep2

source_name: PolII IP 60 minutes rep2

source_name: Genomic 60 minutes rep2


title: rpkA mutant; t0; Culture A: Con. Cy3, Exp. Cy5


title: Htz1d-MycFlag-t180-rep1

description: Genome-wide Myc/Flag rations on a Htz1D strains. 180min after Gal induction.

source_name: Htz1d Myc IP 180 minutes rep1

treatment_protocol: Cells arrested with 4μg/mL alpha factor for 4 hours, collected by filtration and resuspended in YP+2% galactose.

value: MDY513, Htz1 deletion,

source_name: Htz1d Flag IP 180 minutes rep1


title: rpkA mutant; t0; Culture B: Con. Cy5, Exp. Cy3

tag: strain AX2 in which the rpkA (seven transmembrane receptor fused to PIP5 kinase domain) gene has been knocked out by homologous recombination.


title: Htz1d-MycFlag-t180-rep2

source_name: Htz1d Myc IP 180 minutes rep2

source_name: Htz1d Flag IP 180 minutes rep2


title: PolII-IP-vs-Genomic-t0-rep1

source_name: PolII IP 0 minutes rep1

source_name: Genomic 0 minutes rep1


title: PANC-1_Treated_BiolRep3

status: Public on May 15 2007

city: Bethesda

first: Margaret

middle: C

last: Cam

state: MD

institute: NIH

description: RNA extracted from the first biological replicate was derived from 3 culture dishes producing enough sample for three technical replicates, whereas RNA from the second and third biological replicates were derived from one culture dish each.

hyb_protocol: Ten micrograms of fragmented target cRNA was used for hybridization of each UniSet Human I Expression Bioarray chip as described in (Ramakrishnan R et al, An assessment of Motorola CodeLinkTM microarray performance for gene expression profiling applications. Nucleic Acids Res. 2002 Apr 1;30(7):e30).

scan_protocol: Processed slides were scanned using an Axon GenePix Scanner with the laser set to 635 nm, and the scan resolution to 10 µm.

data_processing: Slides were scanned using CodeLinkTM Expression Scanning Software, and images for each slide analyzed using the CodeLinkTM Expression Analysis Software

label: streptavidin-Alexa 647

organism: Homo sapiens

source_name: PANC-1 cell line grown in serum-containing media

label_protocol: Five micrograms of total RNA was labeled according to manufacturer's guidelines (Ramakrishnan R et al, An assessment of Motorola CodeLinkTM microarray performance for gene expression profiling applications. Nucleic Acids Res. 2002 Apr 1;30(7):e30).

growth_protocol: PANC-1 cells (American Type Culture Collection, Manassas, VA) were started as passage 1 (passages 3–6 were used for all experiments). Cells were cultured in serum-containing media (SCM), a mixture of DMEM (Cellgro, Mediatech, Herndon, VA) containing 10% FBS.

extract_protocol: TRIzol to isolate total RNA, followed by cleanup using QIAGEN RNeasy Mini Kit.

treatment_protocol: To induce ICA formation, Serum-containing medium (SCM) was removed, cells were exposed for 60–120 s to 0.05% trypsin (CellgroMediatech) at 25°C, to loosen but not detach the cells from their extracellular matrix (ECM) and then cultured in Serum Free Medium (SFM). SFM was DME/F12 medium containing 17.5 mM glucose, 1% BSA (no. 152401, ICN) and insulin— transferrin—selenium (GIBCO).

tag: Human pancreatic carcinoma, epithelial-like cell line

tag: Gender

value: Male


title: PANC-1_Treated_BiolRep1_TechRep2


title: PANC-1_Treated_BiolRep2


title: PANC-1_Treated_BiolRep1_TechRep1


title: Adult vs developmental stages rep 3

city: Baltimore

first: George

last: Dimopoulos

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

description: Assay done for the determination of the adult vs. development specific transcriptome

hyb_protocol: Agilent Technologies

scan_protocol: Axon

data_processing: signal intensity cutoff: 100, Lowess normalization, T-test 0.05

organism: Aedes aegypti

source_name: 4 day old adult female

label_protocol: Agilent Technologies

extract_protocol: Qiagen

tag: 4 day old adult female

source_name: Pool of embryo, larvae (1-4) and pupae

tag: Pool of embryo, larvae (1-4) and pupae


title: Adult Female vs Adult Male rep 2

description: Assay done for the determination of the adult sex specific transcriptome

source_name: 4 day old adult male

tag: 4 day old adult male


title: PANC-1_Control_BiolRep1_TechRep3


title: PANC-1_Control_BiolRep2


title: PANC-1_Treated_BiolRep1_TechRep3


title: PANC-1_Control_BiolRep1_TechRep2

description: RNA was extracted from the first biological replicate which was derived from 3 culture dishes producing enough sample for three technical replicates, whereas the second and third biological replicate was derived from one culture dish each.


title: Adult vs developmental stages rep 2


title: Adult Female vs Adult Male rep 3


title: PANC-1_BiolRep1_TechRep3_2

hyb_protocol: Each Agilent slide contained two sets of coordinate arrays, where samples labeled with the opposite dye (Cy5 and Cy3) configurations were hybridized using the Agilent cDNA Microarray Kit Hybridization Protocol

scan_protocol: Slides were scanned  using the Agilent G2566AA scanner

data_processing: For the Agilent cDNA arrays, the default settings of the Agilent G2566AA Feature Extraction Software (v.A.5.1.1) were used, which selects the LOWESS (locally weighted linear regression curve fit) normalization method.  A second round of normalization included median scaling followed by batch (including dye, RNA extraction batch, slide configuration and array) effect removal using Partek Genomics Solution software.

label_protocol: 10 ug of RNA was labeled using the Agilent Fluorescent Direct Label Kit

source_name: PANC-1 cell line 24 hours after serum withdrawal


title: PANC-1_BiolRep1_TechRep3_1


title: PANC-1_BiolRep1_TechRep2_2


title: PANC-1_BiolRep1_TechRep1_1


title: PANC-1_BiolRep3_2


title: PANC-1_Control_BiolRep1_TechRep1

description: RNA extracted from the first biological replicate was derived from 3 culture dishes producing enough sample for three technical replicates, whereas the second and third biological replicates were derived from one culture dish each.

hyb_protocol: Ten micrograms of fragmented target cRNA was used for hybridization of each UniSet Human I Expression Bioarray chip as described in (Ramakrishnan R et al, An assessment of Motorola CodeLinkTM microarray performance for gene expression profiling applications.  Nucleic Acids Res. 2002 Apr 1;30(7):e30).

data_processing: Slides were scanned using CodeLinkTM Expression Scanning Software and images for each slide analyzed using the CodeLinkTM Expression Analysis Software.

label_protocol: Five micrograms of total RNA was labeled according to manufacturer's guidelines (Ramakrishnan R et al, An assessment of Motorola CodeLinkTM microarray performance for gene expression profiling applications.  Nucleic Acids Res. 2002 Apr 1;30(7):e30).


title: PANC-1_BiolRep2_1


title: PANC-1_BiolRep2_2


title: Adult female vs adult male rep 1


title: PANC-1_BiolRep3_1


title: PANC-1_BiolRep1_TechRep2_1


title: PANC-1_BiolRep1_TechRep1_2


title: PANC-1_Control_BiolRep3


title: Adult vs developmental stages rep 1


title: DLD-1 cell line treated with 5-aza-2’-deoxycytidine, DyeFlip

status: Public on May 14 2007

city: Chiba

first: Satoshi

last: Fukutomi

address: 1-8-1 Inohana Chuoku

department: General Surgery

country: Japan

institute: Chiba University

description: DLD1, DyeFlip

hyb_protocol: Hybridized for 16 h at 42 C. Hybridization buffer and washing protocol was followed by the protocol supplied by Hitach Software Engineering Co., Ltd. Detailed protocols at the DNA Chip Research Inc. website.

scan_protocol: ScanArray HT (PerkinElmer Japan Co., Ltd.) was used for scanning. Array images were analyzed with DNASIS Array (Hitachi Software Engineering Co., Ltd.).

data_processing: This data were analyzed by DNASIS array software(Hitachi Software Engineering), which converted the signal intensity of each spot into text format. Log2-ratios of the median subtracted background intensity levels were analyzed. Data from each microarray were normalized by LOWESS normalization.

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp™  aRNA Amplification Kit (Ambion). CyeDye Coupling and fragmentation were performed as the protocol supplied by Hitach Software Engineering Co., Ltd. Detailed protocols at the DNA Chip Research Inc. website.

growth_protocol: DLD-1 cell line was maintained in RPMI1640. It was supplemented with 10% fetal bovine serum and was cultured under 5% CO2 at 37°C.

extract_protocol: TriZol procedure

treatment_protocol: For demethylation experiments, cells were plated at a density of 2×105 cells/75 cm2 flask and cultured for 24 h, followed by 96 h incubation with 1 μM 5-aza-2’-deoxycytidine (Sigma Chemical Co., St. Louis, MO).

tag: DLD-1 cell line is derived from colorectal adenocarcinoma (Dukes' type C).

source_name: DLD-1 cell line


title: HT-29 cell line treated with 5-aza-2’-deoxycytidine, DyeFlip

description: HT29, DyeFlip

growth_protocol: HT-29 cell line was maintained in RPMI1640. It was supplemented with 10% fetal bovine serum and was cultured under 5% CO2 at 37°C.

tag: HT-29 cell line is derived from colorectal adenocarcinoma.

source_name: HT-29 cell line


title: HT-29 cell line treated with 5-aza-2’-deoxycytidine


title: Dioxin treated MCF7 breast cancer cells [HG-U133B] Exp 2

status: Public on May 12 2007

city: Los Angeles

first: Oliver

last: Hankinson

state: CA

department: Pathology and Laboratory Medicine

institute: UCLA

description: MCF7 human breast cancer cells treated with 100 nM of dioxin to quantify RNA differences in a 2 platform, three replicate experiment

hyb_protocol: 15ug of CRNA was fragmented, fragmented product was checked on gel(average size 100nt), Hybridization cocktail added and hybed on HG_U133B arrays.  Washed with non-stringent wash buffer (A) and stained with SAPE solution.

scan_protocol: HP Genechip Scanner (fixed pixel and wavelength)

data_processing: Probe array type- HG_U133 B. Parameters - defaults. Normalization - all probe sets. Scaling - all probe sets (Target signal - 2500)

label: biotin

source_name: MCF7 human breast cancer cells, dioxin-treated

label_protocol: Enzo Biotin labeling

extract_protocol: Qiagen RNeasy kit

tag: 16 hr dioxin treatment


title: DLD-1 cell line treated with 5-aza-2’-deoxycytidine


title: Dioxin treated MCF7 breast cancer cells [HG-U133B] Exp 3


title: Ecoli_wt_methionine_8uM_DeaNO_Sample1_TechRep2

status: Public on May 11 2007

city: Logan

first: Daniel

middle: R

last: Hyduke

state: UT

address: 4105 Old Main Hill ENGR 402S

department: Biological Engineering

institute: Utah State University

description: Cells were grown in MOPS media/0.5% glucose with methionine (50 ug/mL) and aerobic conditions and treated with DeaNO.

hyb_protocol: Samples were hybridized as specified in the Corning UltraGAPS manual. Slides were blocked and washed as specified in the Corning UltraGAPS manual.

scan_protocol: Slides were scanned immediately after washing with a Virtek/BioRad scanner.

data_processing: Quantification of the scans were performed with ImaGene (Version 6.0.1; BioDiscovery; El Segundo, CA; www.biodiscovery.com); with the results presented in the associated text files. The normalized data VALUE was generated using LOWESS normalization with rank invariant selection, as implemented in lcDNA (receptor.seas.ucla.edu/lcDNA; Hyduke DR, Rohlin L, Kao KC, Liao JC. 2003 A software package for cDNA microarray data normalization and assessing confidence intervals. OMICS 7(3):227-234.)

organism: Escherichia coli

source_name: Ecoli grown in MOPS with methionine (50 ug/mL) prior to DeaNO treatment

label_protocol: Samples were directly labeled by direct incorporation of labeled dCTP.

growth_protocol: Cells grown to mid-log phase in MOPS/0.5% glucose with methionine (50 ug/mL) at 37C and ~250 RPM.

extract_protocol: RNA extracted by hot phenol choloroform folled by Qiagen RNA Midi column.

treatment_protocol: Untreated.

tag: Strain

source_name: Ecoli grown in MOPS with methionine (50 ug/mL) 5 minutes after DeaNO (8 microM ) treatment

treatment_protocol: Samples were treated with DeaNO (8 micromolar) and harvested after 5 minutes.


title: Ecoli_wt_methionine_8uM_DeaNO_Sample2_TechRep2


title: Dioxin treated MCF7 breast cancer cells [HG-U133A] Exp 1

hyb_protocol: 15ug of CRNA was fragmented, fragmented product was checked on gel(average size 100nt), Hybridization cocktail added and hybed on HG_U133A arrays.  Washed with non-stringent wash buffer (A) and stained with SAPE solution.

data_processing: Probe array type- HG_U133 A. Parameters - defaults. Normalization - all probe sets. Scaling - all probe sets (Target signal - 2500)


title: Dioxin treated MCF7 breast cancer cells [HG-U133B] Exp 1


title: Ecoli_wt_8uM_DeaNO_Sample2_TechRep2

description: Cells were grown in MOPS media/0.5% glucose and aerobic conditions and treated with DeaNO.

source_name: Ecoli grown in MOPS prior to DeaNO treatment

growth_protocol: Cells grown to mid-log phase in MOPS/0.5% glucose at 37C and ~250 RPM.

source_name: Ecoli grown in MOPS 5 minutes after DeaNO (8 microM ) treatment


title: DMSO treated MCF7 breast cancer cells [HG-U133A] Exp 1

description: MCF7 human breast cancer cells treated with DMSO and used as a control in a 2 platform, three replicate experiment

source_name: MCF7 human breast cancer cells, DMSO-treated

tag: 16 hr DMSO treatment


title: Ecoli_wt_methionine_8uM_DeaNO_Sample1_TechRep1


title: Ecoli_wt_8uM_DeaNO_Sample2_TechRep1


title: Ecoli_wt_8uM_DeaNO_Sample1_TechRep2_label2

description: Cells were grown in MOPS media/0.5% glucose and aerobic conditions and treated with DeaNO.  The RNA is the same as in Ecoli_wt_8uM_DeaNO_Sample1_TechRep1 found in this series; the RNA was relabeled (using channel 1 for treatment and channel 2 for control) and hybridized for this array.


title: Ecoli_wt_8uM_DeaNO_Sample1_TechRep2


title: Dioxin treated MCF7 breast cancer cells [HG-U133A] Exp 2


title: Dioxin treated MCF7 breast cancer cells [HG-U133A] Exp 3


title: DMSO treated MCF7 breast cancer cells [HG-U133A] Exp 3


title: Ecoli_nsrR_hmpA_8uM_DeaNO_Sample2_TechRep1

source_name: Ecoli with nsrR and hmpA deleted grown in MOPS prior to DeaNO treatment

value: BW25113 / nsrR- hmpA-

source_name: Ecoli with nsrR and hmpA deleted grown in MOPS 5 minutes after DeaNO (8 microM ) treatment


title: DMSO treated MCF7 breast cancer cells [HG-U133B] Exp 3


title: DMSO treated MCF7 breast cancer cells [HG-U133A] Exp 2


title: Ecoli_wt_8uM_DeaNO_Sample1_TechRep1_label2

source_name: Ecoli grown in MOPS 5 minutes after DeaNO (8 microM) treatment.


title: Ecoli_metJ_8uM_DeaNO_Sample2_TechRep2

source_name: Ecoli with metJ deleted grown in MOPS prior to DeaNO treatment

source_name: Ecoli with metJ deleted grown in MOPS 5 minutes after DeaNO (8 microM ) treatment


title: DMSO treated MCF7 breast cancer cells [HG-U133B] Exp 2


title: Ecoli_wt_methionine_8uM_DeaNO_Sample2_TechRep1


title: Ecoli_metJ_8uM_DeaNO_Sample2_TechRep1


title: DMSO treated MCF7 breast cancer cells [HG-U133B] Exp 1


title: Ecoli_norR_8uM_DeaNO_Sample1_TechRep1

source_name: Ecoli with norR deleted grown in MOPS prior to DeaNO treatment

source_name: Ecoli with norR deleted grown in MOPS 5 minutes after DeaNO (8 microM ) treatment


title: Ecoli_iscR_8uM_DeaNO_Sample1_TechRep2

source_name: Ecoli with iscR deleted grown in MOPS prior to DeaNO treatment

source_name: Ecoli with iscR deleted grown in MOPS 5 minutes after DeaNO (8 microM ) treatment


title: Ecoli_metJ_8uM_DeaNO_Sample1_TechRep2


title: Ecoli_nsrR_8uM_DeaNO_Sample1_TechRep2

source_name: Ecoli with nsrR deleted grown in MOPS prior to DeaNO treatment

source_name: Ecoli with nsrR deleted grown in MOPS 5 minutes after DeaNO (8 microM ) treatment


title: Ecoli_norR_8uM_DeaNO_Sample1_TechRep2


title: Ecoli_iscR_8uM_DeaNO_Sample2_TechRep1


title: Ecoli_nsrR_hmpA_8uM_DeaNO_Sample1_TechRep1


title: Ecoli_norR_8uM_DeaNO_Sample2_TechRep1


title: TGC 12-8  passage43 Lif-(251279910300)

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

description: Embryonic germ cells

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.

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)

data_processing: Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See NIA Array Analysis website for details.

organism: Mus musculus

source_name: TGC 12-8  passage43 Lif-

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

growth_protocol: EG grown on gelatin coated, 6-well plates, 300000 cells/well (30000 cells/cm2), in complete ES medium: DMEM, 15% FBS;1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercapto ethanol,penicillin/streptomycin. Cells were incubated at 37 0C; 5% CO2. Medium was changed daily. On the day 3 Trizol was added and RNA extracted.t 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: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 25 ul of DEPC dH2O.

tag: embryonic germ cell

value: male

source_name: Universal Mouse Reference RNA

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: 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: EG-3 passage 9 Lif-(251279910201)

description: TGC(Embryonic germ cells)

source_name: EG-3 passage 9 Lif-

growth_protocol: EG grown on gelatin coated, 6-well plates, 200000 cells/well (20000 cells/cm2), in complete ES medium: DMEM, 15% FBS;1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate,0.1 mM beta-mercapto ethanol,penicillin/streptomycin. Cells were incubated at 37 0C; 5% CO2. Medium was changed daily. On the day 3 Trizol was added and RNA extracted.nt 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: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 30 ul of DEPC dH2O.

value: female


title: Ecoli_iscR_8uM_DeaNO_Sample2_TechRep2


title: Ecoli_nsrR_hmpA_8uM_DeaNO_Sample1_TechRep2


title: Ecoli_norR_8uM_DeaNO_Sample2_TechRep2


title: TGC 8-7 passage7 Lif+,RA(251279910298)

description: Embryonic germ cells

source_name: TGC 8-7 passage7 Lif+,RA

growth_protocol: EG  cells grown on gelatin coated, 6-well plates, 300000 cells/well (30000 cells/cm2), in complete ES medium: DMEM, 15% FBS; LIF (ESGRO) 1000 u/ml; 1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercapto ethanol,  penicillin/streptomycin,retinoic acid 2uM.. Cells were incubated at 37 0C; 5% CO2. Medium was changed daily. On the day 3 Trizol was added and RNA extracted.minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 15 ul of DEPC dH2O.


title: TGC 8-7 passage7 Lif-(251279910297)

description: Embryonic germ cells

source_name: TGC 8-7 passage7 Lif-

growth_protocol: EG  cells grown on gelatin coated, 6-well plates, 300000 cells/well (30000 cells/cm2), in complete ES medium: DMEM, 15% FBS; 1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercapto ethanol,  penicillin/streptomycin. Cells were incubated at 37 0C; 5% CO2. Medium was changed daily. On the day 3 Trizol was added and RNA extracted.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: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 20 ul of DEPC dH2O.


title: TGC 8-7 passage7 Lif+(251279910288)

description: Embryonic germ cells

source_name: TGC 8-7 passage7 Lif+

growth_protocol: EG  cells grown on gelatin coated, 6-well plates, 300000 cells/well (30000 cells/cm2), in complete ES medium: DMEM, 15% FBS; LIF (ESGRO) 1000 u/ml; 1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercapto ethanol,  penicillin/streptomycin. Cells were incubated at 37 0C; 5% CO2. Medium was changed daily. On the day 3 Trizol was added and RNA extracted.temperature for 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.


title: Ecoli_nsrR_8uM_DeaNO_Sample1_TechRep1


title: Ecoli_iscR_8uM_DeaNO_Sample1_TechRep1


title: Ecoli_metJ_8uM_DeaNO_Sample1_TechRep1


title: EG-3 passage 9 Lif+RA(251279910202)

description: TGC(Embryonic germ cells)

source_name: EG-3 passage 9 Lif+RA

growth_protocol: EG grown on gelatin coated, 6-well plates, 200000 cells/well(20000 cells/cm2), in complete ES medium: DMEM, 15% FBS; LIF (ESGRO) 1000 u/ml; 1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercapto ethanol, and penicillin/streptomycin,retinoic acid 2uM. Cells were incubated at 37 0C; 5% CO2. Medium was changed daily. On the day 3 Trizol was added and RNA extracted.or 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.


title: TGC 12-8  passage43 Lif+,RA(251279910301)

description: Embryonic germ cells

source_name: TGC 12-8  passage43 Lif+,RA

growth_protocol: EG grown on gelatin coated, 6-well plates, 300000 cells/well (30000 cells/cm2), in complete ES medium: DMEM, 15% FBS; LIF (ESGRO) 1000 u/ml; 1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercapto ethanol, and penicillin/streptomycin,retinoic acid 2uM. Cells were incubated at 37 0C; 5% CO2. Medium was changed daily. On the day 3 Trizol was added and RNA extracted.r 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.


title: Ecoli_wt_Control_Sample2_TechRep1

description: Cells were grown in MOPS media/0.5% glucose and aerobic conditions and treated with degraded DeaNO.

source_name: E coli grown in MOPS prior to degraded DeaNO treatment

source_name: E coli grown in MOPS 5 minutes after degraded DeaNO exposure.

treatment_protocol: Samples were treated with degraded DeaNO (8 micromolar) and harvested after 5 minutes.


title: EG-3 passage 9 Lif+(251279910200)

description: TGC(Embryonic germ cells)

source_name: EG-3 passage 9 Lif+

growth_protocol: EG grown on gelatin coated, 6-well plates, 200000 cells/well (20000 cells/cm2), in complete ES medium: DMEM, 15% FBS; LIF (ESGRO) 1000 u/ml; 1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercapto ethanol,penicillin/streptomycin. Cells were incubated at 37 0C; 5% CO2. Medium was changed daily. On the day 3 Trizol was added and RNA extracted. at room temperature for 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.


title: EG-1 passage 8 Lif+RA(251279910199)

description: TGC(Embryonic germ cells)

source_name: EG-1 passage 8 Lif+RA

growth_protocol: EG grown on gelatin coated, 6-well plates, 200000 cells/well (20000 cells/cm2), in complete ES medium: DMEM, 15% FBS; LIF (ESGRO) 1000 u/ml; 1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercapto ethanol, and penicillin/streptomycin,retinoic acid 2uM. Cells were incubated at 37 0C; 5% CO2. Medium was changed daily. On the day 3 Trizol was added and RNA extracted.r 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.


title: Ecoli_wt_Control_Sample1_TechRep1


title: Ecoli_wt_Control_Sample1_TechRep2


title: TGC 8.5-5 passage36 Lif+RA(251279910125)

description: TGC(Embryonic germ cells)

source_name: TGC 8.5-5 passage36 Lif+RA

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 50 ul of DEPC dH2O.


title: TGC 12-8  passage43 Lif+(251279910299)

description: Embryonic germ cells

source_name: TGC 12-8  passage43 Lif+


title: TGC 8.5-5 passage36 Lif+(251279910123)

description: TGC(Embryonic germ cells)

source_name: TGC 8.5-5 passage36 Lif+

growth_protocol: EG grown on gelatin coated, 6-well plates, 300000 cells/well (30000 cells/cm2), in complete ES medium: DMEM, 15% FBS; LIF (ESGRO) 1000 u/ml; 1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercapto ethanol,penicillin/streptomycin. Cells were incubated at 37 0C; 5% CO2. Medium was changed daily. On the day 3 Trizol was added and RNA extracted. at room temperature for 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 40 ul of DEPC dH2O.


title: Ecoli_arcA_8uM_DeaNO_Sample2_TechRep2

description: Cells were grown in MOPS media/0.5% glucose and aerobic conditions.  Four independent cultures were combined before hybridization.

source_name: Ecoli with arcA deleted grown in MOPS prior to DeaNO treatment

value: BW25113 / arcA-. Four independent cultures were combined before RNA extraction.

source_name: Ecoli with arcA deleted grown in MOPS 5 minutes after DeaNO (8 microM ) treatment

treatment_protocol: Treated with 8 uM DeaNO and harvested after 5 minutes.


title: EG-1 passage 8 Lif+(251279910197)

description: TGC(Embryonic germ cells)

source_name: EG-1 passage 8 Lif+


title: TGC 8.5-5 passage36 Lif-(251279910124)

description: TGC(Embryonic germ cells)

source_name: TGC 8.5-5 passage36 Lif-

source_name: Universal Mouse Reference RNA


title: TGC 8-8 passage 9 Lif-(251279910121)

description: TGC(Embryonic germ cells)

source_name: TGC 8-8 passage 9 Lif-


title: Ecoli_arcA_8uM_DeaNO_Sample1_TechRep2

description: Cells were grown in MOPS media/0.5% glucose and aerobic conditions.


title: EG-1 passage 8 Lif-(251279910198)

description: TGC(Embryonic germ cells)

source_name: EG-1 passage 8 Lif-


title: Ecoli_wt_Control_Sample2_TechRep2


title: TGC 8-8 passage 9 Lif+RA(251279910122)

description: TGC(Embryonic germ cells)

source_name: TGC 8-8 passage 9 Lif+RA


title: Ecoli_wt_SeOH_Sample2_TechRep2

description: Cells were grown in MOPS media/0.5% glucose and aerobic conditions and treated with serine hydroxymate (1 mg/mL).

source_name: E coli grown in MOPS prior to SeOH (1 mg/mL) treatment

source_name: E coli grown in MOPS 5 minutes after SeOH (1 mg/mL) treatment

treatment_protocol: Treated with 1 mg / mL serine hydroxymate for 5 minutes before harvesting.


title: ES -D3-GL Passage13  LIF+,RA(251279910098)

description: ES

source_name: ES -D3-GL Passage13  LIF+,RA

growth_protocol: ES grown without feeders on gelatin coated, 6-well plates, 100000 cells/well (10000 cells/cm2), in complete ES medium: DMEM, 15% FBS; LIF (ESGRO) 1000 u/ml; 1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercaptoethanol, and penicillin/strepromycin and  1 uM RA.                            refully 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.

tag: embryonic stem cell


title: TGC 8-8 passage 9 Lif+(251279910120)

description: TGC(Embryonic germ cells)

source_name: TGC 8-8 passage 9 Lif+

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 17 ul of DEPC dH2O.


title: Ecoli_wt_8uM_DeaNO_Sample1_TechRep1

source_name: Ecoli grown in MOPS prior to DeaNO treatment

source_name: Ecoli grown in MOPS 5 minutes after DeaNO (8 microM ) treatment


title: ES -D3-GL Passage13  LIF-(251279910097)

description: ES

source_name: ES -D3-GL Passage13  LIF-

growth_protocol: ES grown without feeders on gelatin coated, 6-well plates, 100000 cells/well (10000 cells/cm2), in complete ES medium: DMEM, 15% FBS; 1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercaptoethanol, and penicillin/streptomycin. Cells were incubated at 37 0C; 5% CO2. Medium was changed daily. On the day 3 Trizol was added and RNA extractedllet at room temperature for 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.


title: Ecoli_arcA_8uM_DeaNO_Sample1_TechRep1


title: Ecoli_wt_SeOH_Sample1_TechRep1

growth_protocol: Cells aerobically grown to mid-log phase in MOPS/0.5% glucose at 37C and ~250 RPM.


title: EBRTcH3  Passage5  LIF-(251279910094)

description: ES

source_name: EBRTcH3  Passage5  LIF-

growth_protocol: ES grown without feeders on gelatin coated, 6-well plates, 100000 cells/well (10000 cells/cm2), in complete ES medium: DMEM, 15% FBS;  1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercaptoethanol, and penicillin/streptomycin,Hygromycin(100ug/ml),Blasticidin S(10ug/ml. Cells were incubated at 37 0C; 5% CO2. Medium was changed daily. On the day 3 Trizol was added and RNA extractedemove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.


title: Ecoli_arcA_8uM_DeaNO_Sample2_TechRep1


title: ES-C57BL/6  Passage7 LIF-(251279910070)

description: ES

source_name: ES-C57BL/6  Passage7 LIF-

growth_protocol: ES grown without feeders on gelatin coated, 6-well plates, 100000 cells/well (10000 cells/cm2), in complete ES medium: DMEM, 15% FBS;  1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercaptoethanol, and penicillin/streptomycin. Cells were incubated at 37 0C; 5% CO2. Medium was changed daily. On the day 3 Trizol was added and RNA extractedlet at room temperature for 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.


title: ES -D3-GL Passage13  LIF+(251279910096)

description: ES

source_name: ES -D3-GL Passage13  LIF+

growth_protocol: ES grown without feeders on gelatin coated, 6-well plates, 100000 cells/well (10000 cells/cm2), in complete ES medium: DMEM, 15% FBS; LIF (ESGRO) 1000 u/ml; 1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercaptoethanol, and penicillin/strepromycin.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.


title: Ecoli_wt_SeOH_Sample1_TechRep2

growth_protocol: Cells grown to mid-log phase in MOPS/0.5% glucose at 37C and ~250 RPM.

source_name: E coli grown in MOPS 5 minutes after SeOH treatment


title: EG-1  Lif+(251411710197)

description: (TGC)Embryonic germ cells

source_name: EG-1  Lif+

tag: Embryonic Germ cells

source_name: Universal Mouse Reference Cell Line Pool

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.


title: EG-3  Lif+(251411710198)

description: (TGC)Embryonic germ cells

source_name: EG-3  Lif+


title: EBRTcH3  Passage5  LIF+,RA(251279910095)

description: ES

source_name: EBRTcH3  Passage5  LIF+,RA

source_name: Universal Mouse Reference RNA


title: ES-CC9.3.1 Passage14 LIF+,RA(251279910080)

description: ES

source_name: ES-CC9.3.1 Passage14 LIF+,RA

growth_protocol: ES grown without feeders on gelatin coated, 6-well plates, 100000 cells/well (10000 cells/cm2), in complete ES medium: DMEM, 15% FBS; LIF (ESGRO) 1000 u/ml; 1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate.. 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.


title: MG1.19  Lif+(251411710190)

description: Embryonic stem cells

source_name: MG1.19  Lif+

growth_protocol: ES grown without feeders on gelatin coated, 6-well plates, 100000 cells/well (10000 cells/cm2), in complete ES medium: DMEM, 15% FBS; LIF (ESGRO) 1000 u/ml; 1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate,0.1 mM beta-mercapto ethanol, and penicillin/streptomycin. Cells were incubated at 37 0C; 5% CO2. Medium was changed daily. On the day 3 Trizol was added and RNA extracted. for 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.

tag: Embryonic stem cells


title: ES-CC9.3.1 Passage14 LIF+(251279910078)

description: ES

source_name: ES-CC9.3.1 Passage14 LIF+


title: EBRTcH3  Passage5  LIF+(251279910081)

description: ES

source_name: EBRTcH3  Passage5  LIF+


title: Ecoli_wt_SeOH_Sample2_TechRep1

source_name: E coli grown in MOPS prior to SeOH (1 mg/mL) treatment

source_name: E coli grown in MOPS 5 minutes after SeOH (1 mg/mL) treatment


title: ES-C57BL/6  Passage7 LIF+(251279910069)

description: ES

source_name: ES-C57BL/6  Passage7 LIF+


title: ES-C57BL/6  Passage7 LIF+,RA(251279910071)

description: ES

source_name: ES-C57BL/6  Passage7 LIF+,RA


title: ES-D3-GL   Lif+(251411710187)

description: Embryonic stem cells

source_name: ES-D3-GL   Lif+


title: TGC 8.5-5  Lif+(251411710194)

description: (TGC)Embryonic germ cells

source_name: TGC 8.5-5  Lif+


title: ES-CC9.3.1   Lif+(251411710188)

description: Embryonic stem cells

source_name: ES-CC9.3.1   Lif+

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 10 ul of DEPC dH2O.


title: TGC 12-8  Lif+(251411710196)

description: (TGC)Embryonic germ cells

source_name: TGC 12-8  Lif+


title: TGC 8-8  Lif+(251411710191)

description: (TGC)Embryonic germ cells

source_name: TGC 8-8  Lif+


title: TGC 8-7  Lif+(251411710193)

description: (TGC)Embryonic germ cells

source_name: TGC 8-7  Lif+

source_name: Universal Mouse Reference Cell Line Pool


title: ES-CC9.3.1 Passage14 LIF-(251279910079)

description: ES

source_name: ES-CC9.3.1 Passage14 LIF-


title: ES-129.3  Lif+(251411710186)

description: Embryonic stem cells


title: EBRTcH3   Lif+(251411710189)

description: Embryonic stem cells

source_name: EBRTcH3   Lif+


title: 2198

city: Ottawa

first: Benjamin

last: Tsang

address: 725 Parkdale Avenue

country: Canada

institute: Ottawa Health Research Institute

description: Granulosa cell gene expression associated with oocyte developmental competence

hyb_protocol: According to standard Affymetrix protocol

organism: Rattus norvegicus

source_name: rat ovarian granulosa cells, isolated from ovarian follicles

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen) following the manufacturer’s protocol

tag: eCG treatment for 24 h followed by injection of anti-eCG antiserum for 24 h, then the injection of hCG for 12 h


title: 2199

scan_protocol: According to standard Affymetrix protocol


title: 15 min oxygen depletion

status: Public on May 10 2007

city: Sheffield

first: Jonathan

last: Partridge

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

country: United Kingdom

institute: The University of Sheffield

description: Aerobic cultures were maintained by sparging the chemostat with air (0.4 l min-1). The switch to micro-aerobic conditions was achieved by switching off the air sparging the culture. After a period of 15 min exposure to air cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA before total RNA purification using Qiagen’s Rneasy Midi kit as recommended by manufacturer’s instructions. Data from control samples (aerobic) were used in indirect comparisons with 5 min, 10 min, 15 min and 60 min of oxygen depletion. Dye swaps and biological repeats were carried out giving two biological repeats and two technical repeats (see supplementary files).

hyb_protocol: Labelled cDNA hybridised using the MWG Gene-Frame system. Slides placed in shaking water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.2x SSC and 0.1x SSC, each at 37 °C for 5 min prior to drying and scanning.

scan_protocol: Arrays scanned using an Affymetrix 428 scanner and Imagene version 4 software.

data_processing: Control (aerobic) and 15 min oxygen depletion samples from two biological replicates and two dye swap experiments were compared, LOG2 LOWESS normalized data is shown.

label: Cy3/5 dye swap

source_name: Steady-state continuous cultured control samples in presence of oxygen MG1655

label_protocol: Labelled with Cy3/Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.

extract_protocol: Bacterial cultures flushed directly into QIAGEN RNAprotect before total RNA isolation using QIAGEN RNEasy Midi kit with on column DNAse digestion.

source_name: Steady-state continuous cultured experimental samples after 15 min oxygen depletion.


title: 2197

label_protocol: According to standard Affymetrix protocol


title: 2195

tag: 48 h after equine chorionic gonadotropin (eCG) treatment followed by human chorionic gonadotropin (hCG) injection for 12 h


title: ES-129.3  Lif+(251411710185)

description: Embryonic stem cells


title: ES-C57BL6.9  Lif+(251411710183)

description: Embryonic stem cells

source_name: ES-C57BL6.9  Lif+