title: Chicken liver, d42 cockerel, 24 hr re-fed, replicate 5

status: Public on Apr 01 2008

city: Newark

first: Larry

middle: Albert

last: Cogburn

state: DE

address: 531 South College Ave.

department: Animal and Food Sciences

institute: University of Delaware

hyb_protocol: Each chicken oligo microarray was baked for 90 min at 90 degrees Celsius prior to use. The slide was pre-treated for 45 min at 42 degrees Celsius in pre-hybridization solution containing 5x SSC, 0.1 % SDS and 1 % BSA and followed by dipping for 5 min in 2x SSC and then 0.2x SSC. The slide was dried by centrifugation (5 min at 1,000 x g). An aliquot of 8 micrograms of purified labeled aRNA samples was fragmented in 1x fragmentation buffer (Ambion, Austin, TX) for 15 min at 70 degrees Celsius. The reaction was then terminated by adding stop solution and dried down in a SpeedVac (not over dried). Each fragmented aRNA sample was reconstituted prior to hybridization in 30 microliters of pre-warmed DIG Easy Hyb solution (Roche Diagnostics Corporation, Indianapolis, IN). All reference aRNA samples within the same hybridization day were pooled together, equally aliquoted (30 microliters) and co-hybridized with each target sample on a slide. The target and reference aRNA samples were mixed with 2.5 microliters of 10 mg/ml yeast tRNA and 2.5 microliters of 10 mg/ml salmon testes DNA (Sigma, Louis, MO). The reference/target mixture (65 microliters) was denatured for 2 min at 94 degrees Celsius, cooled at room temperature, carefully loaded onto the middle of a pre-treated slide held in a hybridization chamber (Corning #2551, Lowell, MA) and overlaid with a 22 x 65 mm LifterSlip (Erie Scientific, Portsmouth, NH). The sealed hybridization chamber was incubated overnight (14-16 hours) at 42 degrees Celsius in a water bath under a light-tight box. On the following day, the cover slip was flushed off in wash solution #1 and the slide was sequentially washed with pre-warmed wash solution #1 (1x SSC, 0.2% SDS, and 0.5% DTT) at 42 degrees Celsius for 10 min, then washed in solution #2 (0.1 x SSC, 0.2% SDS, and 0.5% DTT) for 5 min at room temperature, and finally washed in solution #3 (0.1 x SSC and 0.5% DTT) for 1 min at room temperature. The slide was subsequently rinsed in MilliQ water and dried by centrifugation. The slide was stored until scanning in an individual 50 ml tube covered in aluminum foil and flooded with pure nitrogen gas.

scan_protocol: For each slide, a high-resolution TIFF image file was generated using a GenePix 4000B microarray scanner and analyzed with GenePix Pro V4.1 software (Axon Laboratories, Palo Alto, CA). The TIFF image was acquired at 10 micron resolution by simultaneous scanning at two wavelengths [532 nm (green) and 635 nm (red)]. The PMT count ratio (635/532) was adjusted to 1 in a preview scan at low resolution.

data_processing: The TIFF image was further analyzed with GenePix Pro software which generated a GenePix report (gpr) file. Loess normalization was used in processing of microarray data (Smyth, G. K., and Speed, T. P. (2003) Normalization of cDNA microarray data. Methods 31, 265–273).

label: Alexa Fluor 555 carboxylic acid, succinimidyl ester (Invitrogen, Eugene, OR)

organism: Gallus gallus

source_name: Chick liver, cockerel

label_protocol: The dye labeling was performed according to the instructions for dye coupling and labeled aRNA cleanup with the Amino Allyl MessageAmp™ II aRNA Amplification Kit. Essentially, twenty micrograms of aRNA was dried down to a minimal volume (but not over-dried) in a SpeedVac concentrator, reconstituted in 9 microliters of coupling buffer and mixed with 11 microliters of prepared dye, a 60 microgram aliquot of Alexa 555 freshly dissolved in DMSO. The coupling reaction took place in the dark for one hour at room temperature. Dye incorporation and the concentration of purified labeled aRNA were determined by a NanoDrop and the incorporation efficiency was calculated with a web tool (www.ambion.com/tools/dye).

growth_protocol: Fertile eggs (Ross x Ross) were obtained from a commercial broiler breeder (Allen's Hatchery, Seaford DE) and incubated in the animal facility at Department of Animal and Avian Sciences, University of Maryland (College Park MD). The eggs were incubated under standard conditions (37.5 degrees Celsius and 60% relative humidity) with automatic rotation every hour. The eggs were transferred to a hatchling incubator on embryonic day 18 (e18), where e0 is defined as the start of incubation. All chicks used in this experiment were hatched within a 4-hour period on e21. Chicks were sexed at hatch and only male chicks were used to simplify the experimental design. All chicks were raised under a controlled environment. A brooder lamp and fresh litter were used for brooding at a density of one bird per sq ft during the first two weeks. After 14 days of age, the birds were housed at density of one bird per two sq ft. The housing was maintained with a photoperiod of 16 hr light and 8 hr dark. Water and feed were provided ad libitum with a commercial starter ration for the first three week and a commercial grower-finish ration after three week. Cockerels were weighed on day 37 (d37) and randomly assigned (within one standard deviation of body weight for the entire group) to six treatment groups: fully fed (FF), 16 hr fasted (16hFAST), 48 hr fasted (48hFAST), 4 hr re-fed (4hREFED), 24 hr re-fed (24hREFED) and 48 hr re-fed (48hREFED). All cockerels were killed for tissue sampling on d42 after receiving one of the six treatments.

extract_protocol: Total RNA from frozen liver sample was isolated using a RNeasy Midi kit (Qiagen, Valencia, CA) following the manufacturer's protocol. The quantity of extracted total RNA was determined using a NanoDrop spectrophotometer (Wilmington, DE), and RNA quality was examined by microcapillary electrophoresis on a BioAnalyzer 2100 (Agilent, Wilmington, DE). RNA amplification was performed with an Amino Allyl MessageAmp™ II aRNA Amplification Kit according to the manufacturer’s instruction (Ambion, Austin, TX). A single round of RNA amplification was performed with 4 micrograms of total RNA. In vitro transcription (IVT) of amino allyl-modified aRNA was performed for 14 hr at 37 degrees Celsius. Integrity of aRNA was determined by a BioAnalyzer using the RNA 6000 Nano Assay kit and the concentration of aRNA with a NanoDrop ND-1000 spectrophotometer prior to the aRNA-dye coupling reaction.

treatment_protocol: Liver sample from a 42 day old cockerel, 24 hr re-fed after 48 hr fast (24hREFED), was excised immediately after slaughter, snap frozen in liquid nitrogen, and stored at -80 degrees Celsius until RNA isolation.

tag: Chicken liver, cockerel, 42 day old, 24 hr re-fed after 48 hr fast.

label: Alexa Fluor 647 carboxylic acid, succinimidyl ester (Invitrogen, Eugene, OR)

source_name: Reference aRNA pool

label_protocol: The same as described above for Ch1 except for Alexa 647 was used for dye coupling reaction.

growth_protocol: The same as described above for Ch1.

extract_protocol: The same as described above for Ch1.

treatment_protocol: The reference aRNA pool was made from all 30 samples derived from six treatment groups [5 liver samples per treatment group] including (1) FF, (2) 16hFAST, (3) 48hFAST, (4) 4hREFED, (5) 24hREFED and (6) 48hREFED.

tag: The reference aRNA pool was made from an equal amount of high quality aRNA from all 30 samples used in this experiment.


title: Chicken liver, d42 cockerel, fed, replicate 4

type: RNA

country: USA

molecule: total RNA

label_protocol: The dye labeling was performed according to the instructions for dye coupling and labeled aRNA cleanup with the Amino Allyl MessageAmp™ II aRNA Amplification Kit. Essentially, twenty micrograms of aRNA was dried down to a minimal volume (but not over-dried) in a SpeedVac concentrator, reconstituted in 9 microliters of coupling buffer and mixed with 11 microliters of prepared dye, a 60 microgram aliquot of Alexa 555 freshly dissolved in DMSO. The coupling reaction took place in the dark for one hour at room temperature. Dye incorporation and the concentration of purified labeled aRNA were determined by NanoDrop and the incorporation efficiency was calculated with a web tool (www.ambion.com/tools/dye).

extract_protocol: Total RNA from frozen liver sample was isolated using a RNeasy Midi kit (Qiagen, Valencia, CA) following the manufacturer's protocol. The quantity of extracted total RNA was determined using a NanoDrop spectrophotometer (Wilmington, DE), and RNA quality was examined by microcapillary electrophoresis on a BioAnalyzer 2100 (Agilent, Wilmington, DE). RNA amplification was performed with an Amino Allyl MessageAmp™ II aRNA Amplification Kit according to the manufacturer’s instruction (Ambion, Austin, TX). A single round of RNA amplification was performed with 4 micrograms of total RNA. In vitro transcription (IVT) of amino allyl-modified aRNA was performed for 14 hr at 37 degrees Celsius. Integrity of aRNA was determined by a BioAnalyzer using the RNA 6000 Nano Assay kit and the concentration of aRNA measured with a NanoDrop ND-1000 spectrophotometer prior to the aRNA-dye coupling reaction.

treatment_protocol: Liver sample from a 42 day old cockerel, fully fed (FF), was excised immediately after slaughter, snap frozen in liquid nitrogen, and stored at -80 degrees Celsius until RNA isolation.

tag: Chicken liver, cockerel, 42 day old, fed

treatment_protocol: The reference aRNA pool was made from all 30 samples derived from the six treatment groups [5 liver samples per treatment group] including (1) FF, (2) 16hFAST, (3) 48hFAST, (4) 4hREFED, (5) 24hREFED and (6) 48hREFED.


title: Chicken liver, d42 cockerel, 48 hr re-fed, replicate 4

growth_protocol: Fertile eggs (Ross x Ross) were obtained from a commercial broiler breeder (Allen's Hatchery, Seaford DE) and incubated in the animal facility at Department of Animal and Avian Sciences, University of Maryland (College Park MD). The eggs were incubated under standard conditions (37.5 degrees Celsius and 60% relative humidity) with automatic rotation every hour. The eggs were transferred to a hatchling incubator on embryonic day 18 (e18), where e0 is defined as the start of incubation. All chicks used in this experiment were hatched within a 4-hour period on e21. Chicks were sexed at hatch and only male chicks were used to simplify the experimental design. All chicks were raised under a controlled environment. A brooder lamp and fresh litter were used for brooding at a density of one bird per sq ft during the first two weeks. After 14 days of age, the birds were housed at density of one bird per sq ft. The housing was maintained with a photoperiod of 16 hr light and 8 hr dark. Water and feed were provided ad libitum with a commercial starter ration for the first three week and a commercial grower-finish ration after three week. Cockerels were weighed on day 37 (d37) and randomly assigned (within one standard deviation of body weight for the entire group) to six treatment groups: fully fed (FF), 16 hr fasted (16hFAST), 48 hr fasted (48hFAST), 4 hr re-fed (4hREFED), 24 hr re-fed (24hREFED) and 48 hr re-fed (48hREFED). All cockerels were killed for tissue sampling on d42 after receiving one of the six treatments.

treatment_protocol: Liver samples from a 42 day old cockerel, 48 hr re-fed after 48 hr fast (48hREFED), was excised immediately after slaughter, snap frozen in liquid nitrogen, and stored at -80 degrees Celsius until RNA isolation.

tag: Chicken liver, cockerel, 42 day old, 48 hr re-fed after 48 hr fast.


title: Chicken liver, d42 cockerel, 16 hr fast, replicate 3

description: Chicken liver, d42 cockerel, fed, replicate 3

treatment_protocol: Liver sample from a 42 day old cockerel, fasted for 16 hr prior to tissue sampling (16hFAST), was excised immediately after slaughter, snap frozen in liquid nitrogen, and stored at -80 degrees Celsius until RNA isolation.

tag: Chicken liver, cockerel, 42 day old, 16 hr fasted


title: Chicken liver, d42 cockerel, 4 hr re-fed, replicate 4

treatment_protocol: Liver sample from a 42 day old cockerel, 4 hr re-fed after 48 hr fast (4hREFED), was excised immediately after slaughter, snap frozen in liquid nitrogen, and stored at -80 degrees Celsius until RNA isolation.

tag: Chicken liver, cockerel, 42 day old, 4 hr re-fed after 48 hr fast.


title: Chicken liver, d42 cockerel, 48 hr re-fed, replicate 3


title: Chicken liver, d42 cockerel, 24 hr re-fed, replicate 4


title: Chicken liver, d42 cockerel, 4 hr re-fed, replicate 5


title: Chicken liver, d42 cockerel, 48 hr fast, replicate 5

treatment_protocol: Liver sample from a 42 day old cockerel, fasted for 48 hr prior to tissue sampling (48hFAST), was excised immediately after slaughter, snap frozen in liquid nitrogen, and stored at -80 degrees Celsius until RNA isolation.

tag: Chicken liver, cockerel, 42 day old, 48 hr fasted


title: Chicken liver, d42 cockerel, fed, replicate 3


title: Chicken liver, d42 cockerel, 48 hr re-fed, replicate 2


title: Chicken liver, d42 cockerel, 16 hr fast, replicate 4

description: Chicken liver, d42 cockerel, fed, replicate 4


title: Chicken liver, d42 cockerel, fed, replicate 5


title: Chicken liver, d42 cockerel, 4 hr re-fed, replicate 3


title: Chicken liver, d42 cockerel, 48 hr fast, replicate 2


title: Chicken liver, d42 cockerel, 16 hr fast, replicate 5

description: Chicken liver, d42 cockerel, fed, replicate 5


title: Chicken liver, d42 cockerel, 48 hr fast, replicate 3


title: Chicken liver, d42 cockerel, 48 hr re-fed, replicate 5


title: Chicken liver, d42 cockerel, 48 hr fast, replicate 4


title: Chicken liver, d42 cockerel, 24 hr re-fed, replicate 2


title: Chicken liver, d42 cockerel, 16 hr fast, replicate 2

description: Chicken liver, d42 cockerel, fed, replicate 2


title: Chicken liver, d42 cockerel, fed, replicate 2


title: Chicken liver, d42 cockerel, 4 hr re-fed, replicate 2


title: Chicken liver, d42 cockerel, 24 hr re-fed, replicate 3


title: Chicken liver, d42 cockerel, 4 hr re-fed, replicate 1


title: Chicken liver, d42 cockerel, 24 hr re-fed, replicate 1


title: Chicken liver, d42 cockerel, 48 hr re-fed, replicate 1


title: Chicken liver, d42 cockerel, 48 hr fast, replicate 1


title: Chicken liver, d42 cockerel, fed, replicate 1


title: Chicken liver, three day old, 24hr re-fed, replicate 5

hyb_protocol: Each chicken oligo microarray was baked for 90 min at 90 degrees Celsius prior to use. The slide was pre-treated for 45 min at 42 degrees Celsius in pre-hybridization solution containing 5x SSC, 0.1 % SDS and 1 % BSA and followed by dipping for 5 min in 2x SSC and then 0.2x SSC. The slide was dried by centrifugation (5 min at 1,000 x g). An aliquot of five micrograms of purified labeled aRNA samples was fragmented in 1x fragmentation buffer (Ambion, Austin, TX) for 15 min at 70 degrees Celsius. The reaction was then terminated by adding stop solution and dried down in a SpeedVac (not over dried). Each fragmented aRNA sample was reconstituted prior to hybridization in 30 microliters of pre-warmed DIG Easy Hyb solution (Roche Diagnostics Corporation, Indianapolis, IN). All reference aRNA samples within the same hybridization day were pooled together, equally aliquoted (30 microliters) and co-hybridized with each target sample on a slide. The target and reference aRNA samples were mixed with 2.5 microliters of 10 mg/ml yeast tRNA and 2.5 microliters of 10 mg/ml salmon testes DNA (Sigma, Louis, MO). The reference/target mixture (65 microliters) was denatured for 2 min at 94 degrees Celsius, cooled at room temperature, carefully loaded onto the middle of a pre-treated slide held in a hybridization chamber (Corning #2551, Lowell, MA) and overlaid with a 22 x 65 mm LifterSlip (Erie Scientific, Portsmouth, NH). The sealed hybridization chamber was incubated overnight (14-16 hours) at 42 degrees Celsius in a water bath under a light-tight box. On the following day, the cover slip was flushed off in wash solution #1 and the slide was sequentially washed with pre-warmed wash solution #1 (1x SSC, 0.2% SDS, and 0.5% DTT) at 42 degrees Celsius for 10 min, then washed in solution #2 (0.1 x SSC, 0.2% SDS, and 0.5% DTT) for 5 min at room temperature, and finally washed in solution #3 (0.1 x SSC and 0.5% DTT) for 1 min at room temperature. The slide was subsequently rinsed in MilliQ water and dried by centrifugation. The slide was stored until scanning in individual 50 ml tubes covered in aluminum foil and flooded with pure nitrogen gas.

scan_protocol: For each slide, a high-resolution TIFF image file was generated using a GenePix 4000B microarray scanner and analyzed with GenePix Pro V4.1 software (Axon Laboratories, Palo Alto, CA). The TIFF image was acquired at 10 micron resolution by simultaneous scanning at two wavelengths [532 nm (green) and 635 nm (red)]. The PMT count ratio (635/532) was adjusted to 1 during preview at low resolution scanning.

data_processing: The TIFF image was further analyzed with GenePix Pro software which generated a GenePix report (gpr) file. Loess normalization was used in processing of microarray data (Smyth, G. K., and Speed, T. P. (2003) Normalization of cDNA microarray data. Methods 31, 265–273)

source_name: Chick liver

label_protocol: The dye labeling was performed according to the instructions for dye coupling and labeled aRNA cleanup with the Amino Allyl MessageAmp™ II aRNA Amplification Kit. Essentially, twenty micrograms of aRNA was dried down to a minimal volume (but not over-dried) in a SpeedVac concentrator, reconstituted in 9 microliters of coupling buffer and mixed with 11 microliters of prepared dye, 60 micrograms aliquot of Alexa 555 freshly dissolved in DMSO. The coupling reaction took place in the dark for one hour at room temperature. Dye incorporation and the concentration of purified labeled aRNA were determined with a NanoDrop and the incorporation efficiency was calculated with a web tool (www.ambion.com/tools/dye).

growth_protocol: Fertile eggs (Ross x Ross) were obtained from a commercial broiler breeder (Allen's Hatchery, Seaford DE) and incubated in the animal facility Department of Animal and Avian Sciences, University of Maryland (College Park MD). The eggs were incubated under standard conditions (37.5 degrees Celsius and 60% relative humidity) with automatic rotation every hour. The eggs were transferred to a hatchling incubator on embryonic day 18 (e18), where e0 is defined as the start of incubation. All chicks used in this experiment were hatched within a 4-hour period on e21 and given free access to water. After hatchling, sexed male chicks were assigned to ten treatment groups. Chicks in this treatment (D3_24H_REFED) group were since hatchling brooded with no access to feed for 48 hr and were subsequently provided with feed for 24 hr prior to the time of tissue sampling.

extract_protocol: Total RNA from frozen liver sample was isolated using a RNeasy Midi kit (Qiagen, Valencia, CA) following the manufacturer's protocol. The quantity of extracted total RNA was determined using a NanoDrop spectrophotometer (Wilmington, DE), and RNA quality was examined by microcapillary electrophoresis on a BioAnalyzer 2100 (Agilent, Wilmington, DE). The RNA amplification was performed with an Amino Allyl MessageAmp™ II aRNA Amplification Kit according to manufacturer’s instruction (Ambion, Austin, TX). A single round of RNA amplification was performed with 4 micrograms of total RNA. In vitro transcription (IVT) of amino allyl-modified aRNA was performed for 14 hr at 37 degrees Celsius. Integrity of aRNA was determined by a BioAnalyzer using the RNA 6000 Nano Assay kit and the concentration of aRNA with a NanoDrop ND-1000 spectrophotometer prior to the aRNA-dye coupling reaction.

treatment_protocol: Liver samples from three day chick, 24 hr re-fed after 48 hr fast (D3_24H_REFED), were excised immediately after slaughter, snap frozen in liquid nitrogen, and stored at -80 degrees Celsius until RNA isolation.

treatment_protocol: The reference aRNA pool was made from all 50 samples came from ten treatment groups (5 liver samples per treatment group) including newly hatched (D0), 1-day old fed (D1FED), 1-day old fasted (D1FAST), 2-day old fed (D2FED), 2-day old fasted (D2FAST), 4-hour re-fed after 2-day fast (D2_4H_REFED), 3-day old fed (D3FED), 24-hour re-fed after 2-day fast (D3_24H_REFED), 4-day old fed (D4FED), 48-hour re-fed after 2-day fast (D4_48H_REFED).

tag: The reference aRNA pool was made from an equal amount of high quality aRNA from all 50 samples used in this experiment.


title: Chicken liver, three day old, fed, replicate 5

growth_protocol: Fertile eggs (Ross x Ross) were obtained from a commercial broiler breeder (Allen's Hatchery, Seaford DE) and incubated in the animal facility Department of Animal and Avian Sciences, University of Maryland (College Park MD). The eggs were incubated under standard conditions (37.5 degrees Celsius and 60% relative humidity) with automatic rotation every hour. The eggs were transferred to a hatchling incubator on embryonic day 18 (e18), where e0 is defined as the start of incubation. All chicks used in this experiment were hatched within a 4-hour period on e21 and given free access to water. After hatchling, sexed male chicks were assigned to ten treatment groups. Chicks assigned to this treatment (D3FED) group were immediately provided a commercial starter ration ad libitum until the time of tissue sampling.

treatment_protocol: Liver samples from three day old chick fed (D3FED) were excised immediately after slaughter, snap frozen in liquid nitrogen, and stored at -80 degrees Celsius until RNA isolation.

tag: Chicken liver, three day old, fed


title: Chicken liver, d42 cockerel, 16 hr fast, replicate 1

description: Chicken liver, d42 cockerel, fed, replicate 1


title: Chicken liver, four day old, 48hr re-fed, replicate 5

growth_protocol: Fertile eggs (Ross x Ross) were obtained from a commercial broiler breeder (Allen's Hatchery, Seaford DE) and incubated in the animal facility Department of Animal and Avian Sciences, University of Maryland (College Park MD). The eggs were incubated under standard conditions (37.5 degrees Celsius and 60% relative humidity) with automatic rotation every hour. The eggs were transferred to a hatchling incubator on embryonic day 18 (e18), where e0 is defined as the start of incubation. All chicks used in this experiment were hatched within a 4-hour period on e21 and given free access to water. After hatchling, sexed male chicks were assigned to ten treatment groups. Chicks in this treatment (D4_48H_REFED) group were since hatchling brooded with no access to feed for 48 hr and were subsequently provided with feed for 48 hr prior to the time of tissue sampling.

treatment_protocol: Liver samples from four day chick, 48 hr re-fed after 48 hr fast (D4_48H_REFED), were excised immediately after slaughter, snap frozen in liquid nitrogen, and stored at -80 degrees Celsius until RNA isolation.


title: Chicken liver, two day old, fast, replicate 5

growth_protocol: Fertile eggs (Ross x Ross) were obtained from a commercial broiler breeder (Allen's Hatchery, Seaford DE) and incubated in the animal facility Department of Animal and Avian Sciences, University of Maryland (College Park MD). The eggs were incubated under standard conditions (37.5 degrees Celsius and 60% relative humidity) with automatic rotation every hour. The eggs were transferred to a hatchling incubator on embryonic day 18 (e18), where e0 is defined as the start of incubation. All chicks used in this experiment were hatched within a 4-hour period on e21 and given free access to water. After hatchling, sexed male chicks were assigned to ten treatment groups. Chicks assigned to this treatment (D2FAST) group were since hatchling (48 hr) brooded with no access to feed until the time of tissue sampling.

treatment_protocol: Liver samples from two day chick, fasted for 48 hr (D2FAST), were excised immediately after slaughter, snap frozen in liquid nitrogen, and stored at -80 degrees Celsius until RNA isolation.

tag: Chicken liver, two day old, fast


title: Chicken liver, two day old, 4hr re-fed, replicate 5

growth_protocol: Fertile eggs (Ross x Ross) were obtained from a commercial broiler breeder (Allen's Hatchery, Seaford DE) and incubated in the animal facility Department of Animal and Avian Sciences, University of Maryland (College Park MD). The eggs were incubated under standard conditions (37.5 degrees Celsius and 60% relative humidity) with automatic rotation every hour. The eggs were transferred to a hatchling incubator on embryonic day 18 (e18), where e0 is defined as the start of incubation. All chicks used in this experiment were hatched within a 4-hour period on e21 and given free access to water. After hatchling, sexed male chicks were assigned to ten treatment groups. Chicks assigned to this treatment (D2_4H_REFED) group were since hatchling brooded with no access to feed for 48 hr and were subsequently provided with feed for 4 hr prior to the time of tissue sampling.

treatment_protocol: Liver samples from two day chick, 4 hr re-fed after 48 hr fast (D2_4H_REFED), were excised immediately after slaughter, snap frozen in liquid nitrogen, and stored at -80 degrees Celsius until RNA isolation.

tag: Chicken liver, two day old, 4hr re-fed


title: Chicken liver, one day old, fed, replicate 5

growth_protocol: Fertile eggs (Ross x Ross) were obtained from a commercial broiler breeder (Allen's Hatchery, Seaford DE) and incubated in the animal facility Department of Animal and Avian Sciences, University of Maryland (College Park MD). The eggs were incubated under standard conditions (37.5 degrees Celsius and 60% relative humidity) with automatic rotation every hour. The eggs were transferred to a hatchling incubator on embryonic day 18 (e18), where e0 is defined as the start of incubation. All chicks used in this experiment were hatched within a 4-hour period on e21 and given free access to water. After hatchling, sexed male chicks were assigned to ten treatment groups. The chicks assigned to this treatment (D1FED) group were immediately provided a commercial starter ration ad libitum until the time of tissue sampling.

treatment_protocol: Liver samples from one day old chick fed (D1FED) were excised immediately after slaughter, snap frozen in liquid nitrogen, and stored at -80 degrees Celsius until RNA isolation.

tag: Chicken liver, one day old, fed


title: Chicken liver, one day old, fast, replicate 5

growth_protocol: Fertile eggs (Ross x Ross) were obtained from a commercial broiler breeder (Allen's Hatchery, Seaford DE) and incubated in the animal facility Department of Animal and Avian Sciences, University of Maryland (College Park MD). The eggs were incubated under standard conditions (37.5 degrees Celsius and 60% relative humidity) with automatic rotation every hour. The eggs were transferred to a hatchling incubator on embryonic day 18 (e18), where e0 is defined as the start of incubation. All chicks used in this experiment were hatched within a 4-hour period on e21 and given free access to water. After hatchling, sexed male chicks were assigned to ten treatment groups. Chicks assigned to this treatment (D1FAST) group were since hatchling brooded with no access to feed until the time of tissue sampling.

treatment_protocol: Liver samples from one day chick, fasted (D1FAST), were excised immediately after slaughter, snap frozen in liquid nitrogen, and stored at -80 degrees Celsius until RNA isolation.

tag: Chicken liver, one day old, fast


title: Chicken liver, two day old, fed, replicate 5

growth_protocol: Fertile eggs (Ross x Ross) were obtained from a commercial broiler breeder (Allen's Hatchery, Seaford DE) and incubated in the animal facility Department of Animal and Avian Sciences, University of Maryland (College Park MD). The eggs were incubated under standard conditions (37.5 degrees Celsius and 60% relative humidity) with automatic rotation every hour. The eggs were transferred to a hatchling incubator on embryonic day 18 (e18), where e0 is defined as the start of incubation. All chicks used in this experiment were hatched within a 4-hour period on e21 and given free access to water. After hatchling, sexed male chicks were assigned to ten treatment groups. Chicks assigned to this treatment (D2FED) group were immediately provided a commercial starter ration ad libitum until (48 hr) the time of tissue sampling.

treatment_protocol: Liver samples from two day old chick, fully fed (D2FED), were excised immediately after slaughter, snap frozen in liquid nitrogen, and stored at -80 degrees Celsius until RNA isolation.

tag: Chicken liver, two day old, fed


title: Chicken liver, newly hatched, replicate 5

description: Newly hatched chicken liver, replicate 5

growth_protocol: Fertile eggs (Ross x Ross) were obtained from a commercial broiler breeder (Allen's Hatchery, Seaford DE) and incubated in the animal facility Department of Animal and Avian Sciences, University of Maryland (College Park MD). The eggs were incubated under standard conditions (37.5 degrees Celsius and 60% relative humidity) with automatic rotation every hour. The eggs were transferred to a hatchling incubator on embryonic day 18 (e18), where e0 is defined as the start of incubation. All chicks used in this experiment were hatched within a 4-hour period on e21 and given free access to water. After hatchling, sexed male chicks were assigned to ten treatment groups. Chicks in this treatment (D0) group had since hatchling (4 hr) no access to feed prior to the time of tissue sampling.

treatment_protocol: Liver samples from newly hatched chicks, 4 hr post hatch (D0) were excised immediately after slaughter, snap frozen in liquid nitrogen, and stored at -80 degrees Celsius until RNA isolation.

tag: Chicken liver, newly hatched, not fed


title: Leaf_Water Control_Rep 1_48 h After Treatment

status: Public on Apr 03 2008

first: John

middle: K

last: Lindsay

state: Quebec

address: 21111 Lakeshore Rd

department: Plant Science

country: Canada

institute: McGill University

description: All steps followed Affymetrix guidelines and protocols.

hyb_protocol: The cRNA quality was determined using a 2100 BioAnalyzer equipped with an RNA Nano LabChip, overnight hybridization of the chip utilized 15 µg of fragmented cRNA and the staining and washes were performed using an Affymetrix GeneChip Fluidics Station 450 robot, following the manufacturer's protocols.

scan_protocol: The microarray chips were scanned with an Affymetrix GeneChip Scanner 3000 7G, following the manufacturer's protocols.

data_processing: Robust multi-array average (RMA) analysis was performed on the .CEL files (with normalization and suppression of background noise). The base 2 logarithm of RMA signals were median-centered so that the median log-scale expression measure for each GeneChip was zero.

label: biotin

organism: Glycine max

source_name: First trifoliolate leaf, 48h after sprayed with water control

label_protocol: 3.5 µg was used to synthesize labeled target cRNA using the GeneChip HT One-Cycle Target Labeling and Controls kit (Affymetrix). cRNA were labelled with biotin, stained with Streptavidin-phycoerythrin  (SAPE) and detected with Biotinylated anti-streptavidin antibody.

growth_protocol: Soybean cultivar (cv.) Ontario Agricultural College (OAC) Bayfield seeds were surface-sterilized in 25% v/v sodium hypochlorite (Javex) for 2 min and then washed five times with distilled water (dH2O).  The seeds were then spread evenly on a 5 cm thick bed of autoclaved vermiculite in a large plastic tray (54 x 28 x 6.5 cm) with holes at the bottom, to allow drainage of excess water, and then covered with 1 cm of vermiculite. The tray, with seeds, was placed in a growth chamber with a 16 h photoperiod (25 ºC) and an 8 h period of darkness (20 ºC).  The germination/rooting medium was kept moist through regular additions of dH2O.  When the cotyledons had emerged and separated (V1 growth stage) the seedlings were transferred to 5 cm pots containing a mixture of Pro-Mix (sphagnum peat moss) and perlite, as growth media.  Each seedling was transferred to an individual pot and returned to the growth chamber under the conditions described above.  The seedlings were watered with ½ strength Hoagland’s solution every day.

extract_protocol: Frozen leaf tissue was rapidly ground with a mortar and pestle chilled with liquid N2 that had been placed in a -20 ºC freezer for 4 h prior to RNA extraction.  Total RNA was extracted from ~100 mg of finely-ground, frozen tissue using the Qiagen RNeasy® Plant Mini Kit for total RNA isolation, with an on-column DNase digestion via the RNase-free DNase Set, according to the manufacturer’s instructions. Samples were stored at -80 oC until use.

treatment_protocol: Once the soybean plants had reached the V1 stage of development, the first trifoliolate leaf of each plant was sprayed with 2 mL of sterilized dH2O, containing 0.02% Tween 20. 48 h later, the first trifoliolate leaf was harvested, immediately submerged in liquid N2, and stored at -80 ºC until extraction. Water CONTROL, 1 of 3 replicates.

tag: Soybean cv. OAC Bayfield, V1 stage of development, first trifoliolate leaf.


title: Chicken liver, four day old, 48hr re-fed, replicate 4


title: Chicken liver, four day old, fed, replicate 4

growth_protocol: Fertile eggs (Ross x Ross) were obtained from a commercial broiler breeder (Allen's Hatchery, Seaford DE) and incubated in the animal facility Department of Animal and Avian Sciences, University of Maryland (College Park MD). The eggs were incubated under standard conditions (37.5 degrees Celsius and 60% relative humidity) with automatic rotation every hour. The eggs were transferred to a hatchling incubator on embryonic day 18 (e18), where e0 is defined as the start of incubation. All chicks used in this experiment were hatched within a 4-hour period on e21 and given free access to water. After hatchling, sexed male chicks were assigned to ten treatment groups. Chicks assigned to this treatment (D4FED) group were immediately provided a commercial starter ration ad libitum until the time of tissue sampling.

treatment_protocol: Liver samples from four day old chick, fed (D4FED), were excised immediately after slaughter, snap frozen in liquid nitrogen, and stored at -80 degrees Celsius until RNA isolation.

tag: Chicken liver, four day old, fed


title: Chicken liver, one day old, fast, replicate 4


title: Striatum from cocaine treated control animal, biological rep. 3

city: Heidelberg

first: Jan

last: Rodriguez Parkitna

address: Im Neuenheimer Feld 581

country: Germany

institute: German Cancer Research Center

description: Gene expression data from control animals treated with cocaine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on mouse 430A 2.0 arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Analysis of array data was performed using the R 2.4.1/Bioconductor 1.9 (Gentleman et al. 2004) . Data was normalized and expression values were computed using the gcrma method.

organism: Mus musculus

source_name: The striatum including nucleus accumbens from cocaine treated control animal

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 5 to 6 week-old littermate female mice were single-caged and handled for 5 days

extract_protocol: Whole brains were removed and placed in RNAlater (Ambion) overnight. Brains were sliced into 150 μm-thick vibratome sections and the striatum including the nucleus accumbens was excised with thin needles. Total RNA was prepared with Rneasy RNA Mini kit (Qiagen) and its quality was assessed on RNA LabChips (Agilent).

treatment_protocol: Intra peritoneal injection of 25 mg/kg cocaine, animals were sacrificed one hour after the injection

tag: Female, mixed background C57Bl6 and 129, Cre-, Creb1 flox/flox, Crem +/-


title: Chicken liver, two day old, 4hr re-fed, replicate 4


title: Chicken liver, three day old, fed, replicate 4


title: Chicken liver, three day old, 24hr re-fed, replicate 4


title: Chicken liver, two day old, fed, replicate 4


title: Chicken liver, four day old, fed, replicate 3


title: Chicken liver, four day old, 48hr re-fed, replicate 3


title: Chicken liver, one day old, fed, replicate 4


title: Chicken liver, four day old, fed, replicate 5


title: Chicken liver, two day old, fast, replicate 4


title: Chicken liver, one day old, fast, replicate 3


title: Chicken liver, two day old, fed, replicate 3


title: Chicken liver, two day old, 4hr re-fed, replicate 3


title: Hippocampi from saline treated mutant animal, biological rep. 3

description: Gene expression data from mutant animals treated with saline

hyb_protocol: Following fragmentation, 10 mg of cRNA were hybridized for 16 hr at 45C on mouse GPL81 arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: Pooled hippocampi from 3 saline treated mutant animals

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 mg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 5 to 6 week-old littermate male and female mice were single-caged and handled for 5 days

extract_protocol: Hippocampi were removed and placed in RNAlater (Ambion) overnight. Total RNA was prepared with Absolutely RNA Miniprep kit (Stratagene) and its quality was assessed on RNA LabChips (Agilent). RNA samples from 3 animals were pooled before labelling.

treatment_protocol: Intra peritoneal injection of 20 mg/kg kainate, animals were sacrificed one hour after the injection

tag: Mixed background C57Bl6 and 129, Cre+, Creb1 flox/flox, Crem -/-


title: Chicken liver, four day old, 48hr re-fed, replicate 2


title: Chicken liver, two day old, 4hr re-fed, replicate 2


title: Chicken liver, one day old, fed, replicate 3


title: Chicken liver, two day old, fast, replicate 2


title: Chicken liver, newly hatched, replicate 3

description: Newly hatched chicken liver, replicate 3


title: Chicken liver, four day old, fed, replicate 2


title: Chicken liver, two day old, fed, replicate 2


title: Chicken liver, two day old, fast, replicate 3


title: Chicken liver, three day old, 24hr re-fed, replicate 2


title: Chicken liver, three day old, fed, replicate 1

hyb_protocol: Each chicken oligo microarray was baked for 90 min at 90 degrees Celsius prior to use. The slide was pre-treated for 45 min at 42 degrees Celsius in pre-hybridization solution containing 5x SSC, 0.1 % SDS and 1 % BSA and followed by dipping for 5 min in 2x SSC and then 0.2x SSC. The slide was dried by centrifugation (5 min at 1,000 x g). An aliquot of five micrograms of purified labeled aRNA samples was fragmented in 1x fragmentation buffer (Ambion, Austin, TX) for 15 min at 70 degrees Celsius. The reaction was then terminated by adding stop solution and dried down in a SpeedVac (not over dried). Each fragmented aRNA sample was reconstituted prior to hybridization in a 30 microliters of pre-warmed DIG Easy Hyb solution (Roche Diagnostics Corporation, Indianapolis, IN). All reference aRNA samples within the same hybridization day were pooled together, equally aliquoted (30 microliters) and co-hybridized with each target sample on a slide. The target and reference aRNA samples were mixed with 2.5 microliters of 10 mg/ml yeast tRNA and 2.5 microliters of 10 mg/ml salmon testes DNA (Sigma, Louis, MO). The reference/target mixture (65 microliters) was denatured for 2 min at 94 degrees Celsius, cooled at room temperature, carefully loaded onto the middle of a pre-treated slide held in a hybridization chamber (Corning #2551, Lowell, MA) and overlaid with a 22 x 65 mm LifterSlip (Erie Scientific, Portsmouth, NH). The sealed hybridization chamber was incubated overnight (14-16 hours) at 42 degrees Celsius in a water bath under a light-tight box. On the following day, the cover slip was flushed off in wash solution #1 and the slide was sequentially washed with pre-warmed wash solution #1 (1x SSC, 0.2% SDS, and 0.5% DTT) at 42 degrees Celsius for 10 min, then washed in solution #2 (0.1 x SSC, 0.2% SDS, and 0.5% DTT) for 5 min at room temperature, and finally washed in solution #3 (0.1 x SSC and 0.5% DTT) for 1 min at room temperature. The slide was subsequently rinsed in MilliQ water and dried by centrifugation. The slide was stored until scanning in individual 50 ml tubes covered in aluminum foil and flooded with pure nitrogen gas.


title: Chicken liver, three day old, 24hr re-fed, replicate 1


title: Chicken liver, newly hatched, replicate 2

description: Newly hatched chicken liver, replicate 2


title: Chicken liver, four day old, 48hr re-fed, replicate 1


title: Chicken liver, two day old, fed, replicate 1


title: Chicken liver, four day old, fed, replicate 1

treatment_protocol: Liver samples from four day old chick fed (D4FED) were excised immediately after slaughter, snap frozen in liquid nitrogen, and stored at -80 degrees Celsius until RNA isolation.


title: Chicken liver, one day old, fast, replicate 2


title: Chicken liver, two day old, 4hr re-fed, replicate 1


title: Chicken liver, newly hatched, replicate 4

description: Newly hatched chicken liver, replicate 4


title: Chicken liver, two day old, fast, replicate 1


title: Chicken liver, one day old, fed, replicate 2


title: Chicken liver, one day old, fast, replicate 1


title: Chicken liver, three day old, fed, replicate 2


title: Chicken liver, newly hatched, replicate 1

description: Newly hatched chicken liver, replicate 1


title: Chicken liver, one day old, fed, replicate 1


title: D18.2.H253.32

city: Lisbon

first: Joana

last: Cardoso

address: Av. Prof Egaz Moniz

country: Portugal

institute: Faculty of Medicine

hyb_protocol: Each labeling reaction was purified with the CyScribe GFX purification kit (Amersham Biosciences, Amersham, UK). Subsequently, both labeled cDNAs were hybridized on a human 18K cDNA microarray encompassing 19,200 spots (representing 18,432 independent cDNAs) produced and obtained from The Netherlands Cancer Institute Microarray Facility (Amsterdam, The Netherlands), according to manyfacturer´s protocol.

scan_protocol: Sixteen-bit fluorescent images from the expression arrays were acquired with an Agilent DNA Microarray Scanner (Agilent Technologies, Inc., Palo Alto, CA).

data_processing: The resulting TIFF images were analyzed with the software GenePix Pro 4.0 (Axon Instruments, Union City, CA) and a unique .gpr file was generated for each sample. Each .gpr file was directly loaded into the R environment using the marray package to extract the background-corrected Cy3 and Cy5 median raw intensity per spot. Intensity data was normalized with the variance stabilization and normalization function implemented in the vsn package (http://www.R-project.org/).

organism: Homo sapiens

source_name: laser capture microdissected colorectal tissue; PATIENT: D18; HISTOLOGY: Tumor; MUTATION: APC

label_protocol: Each total RNA microdissected sample that passed the quality controls was linearly amplified with two rounds of amplification using the MessageAmp kit (Ambion, Huntingdon, UK), according to manufacturer’s protocol. One µg aliquots of target and reference aRNA were labeled with Cy5-dUTP and Cy3-dUTP respectively (Amersham Biosciences, Amersham, UK) by reverse transcription using the CyScribe First Strand cDNA Labeling kit (Amersham Biosciences, Amersham, UK).

extract_protocol: As described at Cardoso J, Molenaar L, de Menezes RX, van Leerdam M, Rosenberg C, Moslein G, Sampson J, Morreau H, Boer JM, Fodde R: Chromosomal instability in MYH- and APC-mutant adenomatous polyps, Cancer Res 2006, 66:2514-2519.

tag: ARRAY

tag: PATIENT

tag: HISTOLOGY

value: Tumor

tag: MUTATION

value: APC


title: UK3.2H.H253.36

source_name: laser capture microdissected colorectal tissue; PATIENT: UK3; HISTOLOGY: Tumor; MUTATION: MYH

value: MYH


title: D18.10.H253.33


title: UK3.2.H253.35


title: UK2_2(L)H253_24

source_name: laser capture microdissected colorectal tissue; PATIENT: UK2; HISTOLOGY: Tumor; MUTATION: MYH


title: UK1_3(N)H253_22

source_name: laser capture microdissected colorectal tissue; PATIENT: UK1; HISTOLOGY: Normal; MUTATION: MYH

value: Normal


title: UK3_1(L)H253_25


title: D18.10N.H253.34

source_name: laser capture microdissected colorectal tissue; PATIENT: D18; HISTOLOGY: Normal; MUTATION: APC


title: D15.16.H253.30

source_name: laser capture microdissected colorectal tissue; PATIENT: D15; HISTOLOGY: Tumor; MUTATION: APC


title: D15.17.H253.31

source_name: laser capture microdissected colorectal tissue; PATIENT: D15; HISTOLOGY: Normal; MUTATION: APC


title: UK2_1(L)H253_23


title: D15.1.H253.28


title: L2_2H210.31

source_name: laser capture microdissected colorectal tissue; PATIENT: L2; HISTOLOGY: Tumor; MUTATION: APC


title: UK1_2(L)H253_16

source_name: laser capture microdissected colorectal tissue; PATIENT: UK1; HISTOLOGY: Tumor; MUTATION: MYH


title: D1_39N(Na)H210_84

source_name: laser capture microdissected colorectal tissue; PATIENT: D1; HISTOLOGY: Normal; MUTATION: APC


title: D1_55(L)H210_86

source_name: laser capture microdissected colorectal tissue; PATIENT: D1; HISTOLOGY: Tumor; MUTATION: APC


title: D1_46(L)H210_85


title: D15.2.H253.29


title: D1_26(L)H210_82


title: D1_56(N)H210_87


title: D5_11(i)H210_73

source_name: laser capture microdissected colorectal tissue; PATIENT: D5; HISTOLOGY: Tumor; MUTATION: APC


title: D9_38(L)H210_9

source_name: laser capture microdissected colorectal tissue; PATIENT: D9; HISTOLOGY: Tumor; MUTATION: APC


title: D9_32(vL)H210_8


title: D9_44D(L-i)H210_7


title: D12_13(L-i)H210_70

source_name: laser capture microdissected colorectal tissue; PATIENT: D12; HISTOLOGY: Tumor; MUTATION: APC


title: D12_45(i)H210_72


title: D12_29(L)H210_71


title: D1_39D(L-i)H210_83


title: D12_2N(Na/H)H210_69

source_name: laser capture microdissected colorectal tissue; PATIENT: D12; HISTOLOGY: Normal; MUTATION: APC


title: D12_19(L)H210_61


title: D5_6(Na/H)H210_55

source_name: laser capture microdissected colorectal tissue; PATIENT: D5; HISTOLOGY: Normal; MUTATION: APC


title: D12_2(L)H210_57


title: D5_14(Na)H210_56


title: D12_5(L)H210_60


title: D5_8D(L)H210_53


title: D12_3(i)H210_58


title: D5_4(L-i)H210_52


title: Chicken liver, three day old, 24hr re-fed, replicate 3

source_name: Chick liver

source_name: Reference aRNA pool


title: Chicken liver, three day old, fed, replicate 3


title: D5_1(i)H210_50


title: D5_2(L-i)H210_51


title: D5_8H(H)H210_54


title: NC1(N)H210_42

source_name: laser capture microdissected colorectal tissue; PATIENT: NC1; HISTOLOGY: Normal; MUTATION: NC

value: NC


title: D2_11N(Na/H)H210_49

source_name: laser capture microdissected colorectal tissue; PATIENT: D2; HISTOLOGY: Normal; MUTATION: APC


title: L2_12(N)H210_37

source_name: laser capture microdissected colorectal tissue; PATIENT: L2; HISTOLOGY: Normal; MUTATION: APC


title: D8_2N(H)H210_40

source_name: laser capture microdissected colorectal tissue; PATIENT: D8; HISTOLOGY: Normal; MUTATION: MYH


title: L2_13(L-i)H210_38


title: D8_3(L-i)H210_41

source_name: laser capture microdissected colorectal tissue; PATIENT: D8; HISTOLOGY: Tumor; MUTATION: MYH


title: NC2(N)H210_43

source_name: laser capture microdissected colorectal tissue; PATIENT: NC2; HISTOLOGY: Normal; MUTATION: NC


title: D8_1D(L)H210_39


title: L2_7(L-i)H210_34

source_name: laser capture microdissected colorectal tissue; PATIENT: L2; HISTOLOGY: Tumor; MUTATION: APC


title: NC3(N)H210_44

source_name: laser capture microdissected colorectal tissue; PATIENT: NC3; HISTOLOGY: Normal; MUTATION: NC


title: L2_11(N)H210_36


title: L2_10(L)H210_35


title: L2_4(L)H210_33


title: D2_9(L)H210_29

source_name: laser capture microdissected colorectal tissue; PATIENT: D2; HISTOLOGY: Tumor; MUTATION: APC


title: L2_3(L-i)H210_32


title: D2_2(L)H210_24


title: D5_52Q(L)H210_23


title: D2_8(Na/H)H210_28


title: D2_11D(L)H210_30


title: D9_44N(Na/H)H210_15

source_name: laser capture microdissected colorectal tissue; PATIENT: D9; HISTOLOGY: Normal; MUTATION: APC


title: RE1_4(N)H253_6

source_name: laser capture microdissected colorectal tissue; PATIENT: RE1; HISTOLOGY: Normal; MUTATION: MYH


title: D9_26(L)H210_14

source_name: laser capture microdissected colorectal tissue; PATIENT: D9; HISTOLOGY: Tumor; MUTATION: APC


title: SV12-72, SV40EA transfected

city: Hiroshima

first: Keiko

last: Hiyama

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Research Institute for Radiation Biology and Medicine

country: Japan

institute: Hiroshima University

description: mortal lifespan, transformed

hyb_protocol: The synthesized 10 microgram of cRNA, quantified by spectrometry and qualified using an Agilent 2100 Bioanalyzer, was then fragmented and hybridized to each array. After 16hr hybridization, arrays were rinsed with 0.75 x TNT buffer for 1 h, labeled with Streptavidin-Cy5 at room temperature for 30 min, rinsed again with TNT buffer and 0.05% Tween 20, and dried by centrifugation.

scan_protocol: Each microarray was scanned using using an Agilent DNA Microarray Scanner.

data_processing: Expression levels were quantified by CodeLink Expression Analysis Software (GE Healthcare) and normalized to the median expression value of the whole array spots using GeneSpringTM GX (Agilent Technologies).

source_name: human fetal lung fibroblast TIG-1 clone SV12 transfected with SV40EA

label_protocol: The first-strand cDNA was generated from 1 microgram of total RNA using reverse transcriptase and a T7 primer using the CodeLink Expression Assay Reagent Kit, and then second-strand cDNA was produced using DNA polymerase mix and RNase H. cRNA (complementary RNA) was generated via an in vitro transcription reaction using T7 RNA polymerase and biotin-11-UTP.

growth_protocol: Cells were cultured in Dulbecco's modified Eagle's minimal essential medium (DMEM; Sigma-Aldrich Japan, Tokyo, Japan) containing 10% heat-inactivated fetal bovine serum (FBS; BioWhittaker, Verviers, Belgium) in a humidified atmosphere of 5% CO2.

extract_protocol: Total RNA was extracted from the frozen cultured cell pellets using QIAGEN RNeasy mini kit (QIAGEN, Inc., Valencia, CA), respectively, according to the manufacturer's protocols. The quality of the RNA was checked using Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: SV40 early antigens (SV40EA) expression vector was transfected to TIG-1 and isolated as a G418 resistant clone. Exponentially growing cultured cells were collected using trypsin followed by rinse with PBS, and freezed until use.

tag: human fetal lung fibroblast TIG-1 clone SV12 at 72 PDL transfected with SV40EA


title: ST11-106, TERT and SV40EA transfected

description: immortal lifespan, transformed

source_name: human fetal lung fibroblast TIG-1 clone ST11 transfected with TERT and SV40EA

treatment_protocol: TERT expression vector and SV40 early antigens (SV40EA) expression vector was transfected to TIG-1 and isolated as a G418 resistant clone. Exponentially growing cultured cells were collected using trypsin followed by rinse with PBS, and freezed until use.

tag: human fetal lung fibroblast TIG-1 clone ST11 at 106 PDL transfected with TERT and SV40EA


title: UK2_5N(Na)H253_211

source_name: laser capture microdissected colorectal tissue; PATIENT: UK2; HISTOLOGY: Normal; MUTATION: MYH


title: RE1_1(L-i)H253_4

source_name: laser capture microdissected colorectal tissue; PATIENT: RE1; HISTOLOGY: Tumor; MUTATION: MYH


title: ST11-65, TERT and SV40EA transfected

description: immortal-competent lifespan, transformed

tag: human fetal lung fibroblast TIG-1 clone ST11 at 65 PDL transfected with TERT and SV40EA


title: D2_7(L-i)H210_27


title: UK2_3(L)H253_17

source_name: laser capture microdissected colorectal tissue; PATIENT: UK2; HISTOLOGY: Tumor; MUTATION: MYH


title: UK2_5(L)H253_20


title: D9_25(N/Na)H210_11


title: D9_16(L-i)H210_10


title: D9_35(L)H210_13


title: TERT6-85, TERT transfected

description: immortal-competent lifespan

source_name: human fetal lung fibroblast TIG-1 clone TERT6 transfected with TERT

treatment_protocol: Exponentially growing cultured cells were collected using trypsin followed by rinse with PBS, and freezed until use.

tag: human fetal lung fibroblast TIG-1 clone TERT6 at 85 PDL transfected with TERT


title: UK2_4(L)H253_18


title: UK2_4N(Na)H253_19


title: RE1_2(L-i)H253_5


title: D9_28(L-i)H210_12


title: TIG-1-45, parent

description: mortal lifespan

source_name: human fetal lung fibroblast TIG-1

tag: normal human fetal lung fibroblast at 45 PDL  before gene transfection


title: SV12-68, SV40EA transfected

description: mortal lifespan, transformed

tag: human fetal lung fibroblast TIG-1 clone SV12 at 68 PDL transfected with SV40EA


title: UK1_1(L)H253_15

source_name: laser capture microdissected colorectal tissue; PATIENT: UK1; HISTOLOGY: Tumor; MUTATION: MYH


title: D2_4(L-i)H210_25


title: D2_5(L)H210_26


title: D18_1i_H253_14

source_name: laser capture microdissected colorectal tissue; PATIENT: D18; HISTOLOGY: Tumor; MUTATION: APC


title: TIG-1-45, parent, Agilent

description: mortal lifespan

hyb_protocol: The synthesized 1.5 microgram of cRNA, quantified by spectrometry and qualified using an Agilent 2100 Bioanalyzer, was then fragmented and hybridized to each array. After 17hr hybridization, arrays were washed according to the manufacturer's recommended protocol.

scan_protocol: Each microarray was scanned using an Agilent DNA Microarray Scanner.

data_processing: Expression levels were quantified by Agilent Feature Extraction software ver. 9.1. and normalized to the median expression value of the whole array spots using GeneSpringTM GX (Agilent Technologies).

label_protocol: The cDNA was generated from 0.6 microgram of total RNA using reverse transcriptase and a T7 primer using Agilent Low RNA Input Linear Amplification Kit PLUS, One-color (Agilent). cRNA (complementary RNA) was generated via an in vitro transcription reaction using T7 RNA polymerase and cyanine 3-labeled CTP


title: TERT6-65, TERT transfected

description: immortal-competent lifespan

tag: human fetal lung fibroblast TIG-1 clone TERT6 at 65 PDL transfected with TERT


title: TERT6-217, TERT transfected, Agilent

description: immortal lifespan

treatment_protocol: TERT expression vector was transfected to TIG-1 and isolated as a G418 resistant clone. Exponentially growing cultured cells were collected using trypsin followed by rinse with PBS, and freezed until use.

tag: human fetal lung fibroblast TIG-1 clone TERT6 at 217 PDL transfected with TERT


title: ST11-196, TERT and SV40EA transfected, Agilent

description: immortal lifespan, transformed

treatment_protocol: TERT expression vector and SV40 early antigens (SV40EA) expression vector were co-transfected to TIG-1 and isolated as a G418 resistant clone. Exponentially growing cultured cells were collected using trypsin followed by rinse with PBS, and freezed until use.

tag: human fetal lung fibroblast TIG-1 clone ST11 at 196 PDL transfected with TERT and SV40EA


title: TERT6-65, TERT transfected, Agilent

description: mortal lifespan


title: Prdm6 yolk sacs_rep11

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.0: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

source_name: Prdm6 -/- yolk

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: Prdm6 -/- yolk sac, E10.5, Y988

source_name: Prdm6 +/+


title: Prdm6 yolk sacs_rep4

source_name: Prdm6 -/-

tag: Prdm6 -/- yolk sac, E10.5, Y964


title: Prdm6 yolk sacs_rep3


title: Prdm6 yolk sacs_rep1

tag: Prdm6 -/- yolk sac, E10.5, Y962


title: Prdm6 yolk sacs_rep12


title: Prdm6 yolk sacs_rep10

tag: Prdm6 -/- yolk sac, E10.5, Y984


title: Prdm6 yolk sacs_rep9


title: O55:H7 st58 replicate 2

type: genomic

city: Kiyotake

first: Atsushi

last: Iguchi

address: Oaza-kihara 5220

institute: Miyazaki university

description: This study investigated the genotypic differences and phylogenetic relationships between typical and atypical O55:H7 strains

hyb_protocol: The Cy5-labeled and the Cy3-labeled DNA preparations (15 µl for each) were mixed with a 90-µl hybridization solution containing 6.4 x SSC, 0.64 % sodium dodecyl sulfate (SDS), and 1.3 mg/ml  yeast tRNA.  After incubation at 96ºC for 2 min, the denatured sample was applied to a microarray slide and incubated on an ArrayBooster hybridization apparatus (Advalytix AG, Brunnthal, Germany) at 50ºC for 16 h.  The slide was then washed twice in 2x SSC/0.2% SDS at room temperature for 10 min, twice in 0.2x SSC/0.2% SDS at 50ºC for 5 min, and twice in 0.2x SSC at room temperature for 10 min.  Finally, the slide was briefly rinsed with ethanol and dried by centrifugation.

scan_protocol: Scanned with a FLA-8000 scanner (Fuji Photofilm, Tokyo, Japan).  The obtained data were analyzed by the ArrayVision 8.0 software (Imaging Research).

data_processing: Spots with reference signal intensities lower than the local background (LBG)  plus 5 standard deviations or with some spotting abnormalities were removed from analysis. Signal intensities of other spots were corrected by subtracting the LBG.

molecule: genomic DNA

organism: Escherichia coli

source_name: Genomic DNA from O55:H7 strain st58

label_protocol: First, 3 µg of genomic DNA was labeled with aminoallyl-modified dUTP (Sigma) using the Bioprime DNA Labeling System (Invitrogen).  DNAs were not sheared or digested by restriction enzymes prior to the labeling.  The aminoallyl-labeled DNA was purified by Microcon YM-30 (Millipore), dried in a speed-vac, and resuspended in 10 µl of 50 mM NaHCO3.  After adding 10 µl of dimethyl sulfoxide solution containing Cy3 or Cy5 monofunctional reactive dye (Amersham), the sample was incubated at room temperature in the dark for 1 h to allow the dye to couple with DNA.  The fluorescently labeled DNA was finally purified by the Qiaquick PCR purification kit (Qiagen) into 30 µl elution buffer provided by the manufacturer.

growth_protocol: Cells were grown to the stationary phase at 37ºC in Luria-Bertani medium.

extract_protocol: Genomic DNA was purified using the Genomic-tip 100/G and Genomic DNA buffer set (Qiagen) according to the manufacturer's instruction.

tag: Enteropathogenic E. coli

source_name: O157 strain Sakai

tag: Enteroheamorragic E. coli


title: O55:H6 ICC221 replicate 1

source_name: Genomic DNA from O55:H6 strain ICC221


title: O55:H6 ICC221 replicate 2


title: O55:H7 st58 replicate 1


title: Prdm6 yolk sacs_rep7

tag: Prdm6 -/- yolk sac, E10.5, Y980


title: O55:H6 ICC222 replicate 1

source_name: Genomic DNA from O55:H6 strain ICC222


title: O55:H7 WC416 replicate 2

source_name: Genomic DNA from O55:H7 strain WC416


title: O55:H6 ICC219 replicate 1

source_name: Genomic DNA from O55:H6 strain ICC219


title: Prdm6 yolk sacs_rep6

tag: Prdm6 -/- yolk sac, E10.5, Y975


title: Prdm6 yolk sacs_rep2


title: O55:H6 ICC222 replicate 2


title: O55:H7 WC416 replicate 1


title: O55:H7 WC211 replicate 2

source_name: Genomic DNA from O55:H7 strain WC211


title: O55:H7 st957 replicate 2

source_name: Genomic DNA from O55:H7 strain st957


title: O55:H6 ICC219 replicate 2


title: Prdm6 yolk sacs_rep8


title: O55:H7 st957 replicate 1


title: O55:H7 TB182A replicate 2

source_name: Genomic DNA from O55:H7 strain TB182A


title: Prdm6 yolk sacs_rep5


title: cDNA array wt-3+wt+3 set2(dyeswap)

city: Beijing

first: Yu-Xian

last: Zhu

address: 5# Summer Palace Road

country: China

institute: College of life sciences, Peking University

description: Comparison of gene expression profiles of -3 DPA wild-type and 3 DPA wild-type upland cotton ovules.

hyb_protocol: Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy-dye incorporation and mixed with 30 ¦ÌL hybridization solution (50% formamide, 1x hybridization buffer; Amersham Biosciences). DNA in hybridization solution was denatured at 95¡ãC for 3 min prior to loading onto a microarray. Arrays were hybridized at 42¡ãC overnight and washed with two consecutive solutions (0.2% SDS, 2x SSC at 42¡ãC for 5 min, and 0.2x SSC for 5 min) at room temperature.

scan_protocol: Arrays were scanned with a LuxScanTM 10K/A scanner (CapitalBio), and obtained images were analyzed with GenePix 4.0(Axon).

data_processing: Signal intensities for each spot were calculated by subtracting local background (based on the median intensity of the area surrounding each spot) from total intensities. Raw data was global scaled making the average signal intensity of arrays was equal , allowing comparison among chips. Weak spots (signal intensity smaller than 400 in all samples)were removed from further analysis and negative value was converted to 10. The preprocessed data was loaded into MAANOVA under R environment for rLowess normalization within each slide, and multiple testing by fitting fixed effects ANOVA model[4]. Microarray spots with FDR-corrected P values <0.01 in the F-test and expression between the two samples differed by 2-fold from their average expression across the technical and biological replicates of the samples were considered to be significant.

organism: Gossypium hirsutum

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine's linear RNA amplification method and subsequent enzymatic reaction. In detail, double-stranded cDNAs (containing the T7 RNA polymerase promoter sequence) were synthesized from 10 ¦Ìg total RNA using the cDNA synthesis system according to the manufacturer's protocol (TaKaRa). A T7-oligo(dT) primer (5'-AAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGCGCTTTTTTTTTTTTTTTTT-3') was used instead of the poly-T primer provided in the kit. After completion of double-stranded cDNA synthesis, cDNA products were purified using a PCR purification kit (Qiagen) and eluted with 60 ¦ÌL elution buffer. One-half of the eluted double-stranded cDNA products were vacuum evaporated to 8 ¦ÌL and subjected to 20-¦ÌL in vitro transcription reactions at 37¡ãC for 3 h using the T7 RiboMAX Express large scale RNA production system (Promega). The amplified RNA was purified using the RNeasy mini kit (Qiagen). Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 2 ¦Ìg amplified RNA was mixed with 2 ¦Ìg random hexamers, denatured at 70¡ãC for 5 min, and cooled on ice. Then, 4 ¦ÌL of first-strand buffer, 2 ¦ÌL of 0.1 M DTT, 1 ¦ÌL 10 mM dNTP, and 1.5 ¦ÌL SuperScript II (Invitrogen) were added. The mixtures were incubated at 25¡ãC for 10 min, then at 42¡ãC for 60 min. The cDNA products were purified using a PCR purification kit (Qiagen) and vacuum evaporated to 10 ¦ÌL. Klenow enzyme (1 ¦ÌL; TaKaRa) was then added, and the reaction was performed at 37¡ãC for 60 min.

extract_protocol: Labeled cDNA was purified with a PCR purification kit (Qiagen) and resuspended in elution buffer.

tag: -3 DPA wild-type upland cotton ovules

tag: 3 DPA wild-type upland cotton ovules


title: cDNA array wt-3+wt+3 set2

description: Comparison of gene expression profiles of 3 DPA wild-type and -3 DPA wild-type upland cotton ovules.


title: O55:H7 WC211 replicate 1


title: O55:H7 TB182A replicate 1


title: cDNA array wt-3+wt+2 set1

description: Comparison of gene expression profiles of 2 DPA wild-type and -3 DPA wild-type upland cotton ovules.

tag: 2 DPA wild-type upland cotton ovules


title: cDNA array wt-3+wt+2 set1(dyeswap)

description: Comparison of gene expression profiles of -3 DPA wild-type and 2 DPA wild-type upland cotton ovules.


title: cDNA array wt-3+wt+3_mix set4(dyeswap)

description: Comparison of gene expression profiles of -3 DPA wild-type and 3 DPA wild-type(mix) upland cotton ovules.


title: cDNA array wt-3+wt+1 set1(dyeswap)

description: Comparison of gene expression profiles of -3 DPA wild-type and 1 DPA wild-type upland cotton ovules.

tag: 1 DPA wild-type upland cotton ovules


title: cDNA array wt-3+wt+1_mix set4(dyeswap)

description: Comparison of gene expression profiles of -3 DPA wild-type and 1 DPA wild-type(mix) upland cotton ovules.


title: cDNA array wt-3+wt+3 set3(dyeswap)


title: cDNA array wt-3+wt+3_mix set4

description: Comparison of gene expression profiles of 3 DPA wild-type(mix) and -3 DPA wild-type upland cotton ovules.

tag: 3 DPA wild-type(mix) upland cotton ovules


title: cDNA array wt-3+wt+1 set3

description: Comparison of gene expression profiles of 1 DPA wild-type and -3 DPA wild-type upland cotton ovules.


title: cDNA array wt-3+wt+2_mix set4(dyeswap)

description: Comparison of gene expression profiles of -3 DPA wild-type and 2 DPA wild-type(mix) upland cotton ovules.


title: cDNA array wt-3+wt+3 set1


title: cDNA array wt-3+wt+2 set3


title: cDNA array wt-3+wt+3 set1(dyeswap)


title: cDNA array wt-3+wt+2 set2


title: cDNA array wt-3+wt+0_mix set4(dyeswap)

description: Comparison of gene expression profiles of -3 DPA wild-type and 0 DPA wild-type(mix) upland cotton ovules.


title: cDNA array wt-3+wt+1 set2


title: cDNA array wt-3+wt+3 set3


title: cDNA array wt-3+wt+2 set3(dyeswap)


title: cDNA array wt-3+wt+1_mix set4

description: Comparison of gene expression profiles of 1 DPA wild-type(mix) and -3 DPA wild-type upland cotton ovules.

tag: 1 DPA wild-type(mix) upland cotton ovules


title: cDNA array wt-3+wt+0_mix set4

description: Comparison of gene expression profiles of 0 DPA wild-type(mix) and -3 DPA wild-type upland cotton ovules.

tag: 0 DPA wild-type(mix) upland cotton ovules


title: cDNA array wt-3+wt+1 set2(dyeswap)


title: cDNA array wt-3+wt+1 set1


title: cDNA array wt-3+wt+2_mix set4

description: Comparison of gene expression profiles of 2 DPA wild-type(mix) and -3 DPA wild-type upland cotton ovules.

tag: 2 DPA wild-type(mix) upland cotton ovules


title: cDNA array wt-3+wt+1 set3(dyeswap)


title: cDNA array wt-3+wt+2 set2(dyeswap)


title: cDNA array wt-3+wt+0 set3(dyeswap)

description: Comparison of gene expression profiles of -3 DPA wild-type and 0 DPA wild-type upland cotton ovules.

tag: 0 DPA wild-type upland cotton ovules


title: cDNA array wt-3+wt+0 set2

description: Comparison of gene expression profiles of 0 DPA wild-type and -3 DPA wild-type upland cotton ovules.


title: cDNA array wt-3+fl-3 set2(dyeswap)

description: Comparison of gene expression profiles of -3 DPA wild-type and -3 DPA fl-mutant upland cotton ovules.

tag: -3 DPA fl-mutant upland cotton ovules


title: cDNA array wt-3+wt+0 set3


title: cDNA array wt-3+fl-3 set1(dyeswap)


title: cDNA array wt-3+wt+0 set1


title: cDNA array wt-3+fl-3 set1

description: Comparison of gene expression profiles of -3 DPA fl-mutant and -3 DPA wild-type upland cotton ovules.


title: cDNA array wt-3+fl-3 set2


title: cDNA array wt-3+fl+3 set2(dyeswap)

description: Comparison of gene expression profiles of -3 DPA wild-type and 3 DPA fl-mutant upland cotton ovules.

tag: 3 DPA fl-mutant upland cotton ovules


title: WT_normal_62

city: Rotterdam

first: Claudia

last: Gaspar

address: Dr. Molenwaterplein 40, PO Box 2040

department: Experimental Pathology

country: Netherlands

institute: ErasmusMC

description: C57Bl6/J, normal intestinal epithelial cells

hyb_protocol: Standard Affymetrix protocols.

scan_protocol: Standard Affymetrix protocols.

data_processing: Data analysis was performed using R Statistical Computing software v2.4.1 complemented with Bioconductor Packages: affy,and vsn. Cel files were uploaded and summarized using the affy package and normalized with vsn at the probe level.

label: Biotin

label_protocol: Protocol released by Affymetrix: Small Sample Labeling Protocol vII.

growth_protocol: Animals kept ad libitum under spf conditions.

extract_protocol: RNA was extracted from LCM cells using RNeasy Mini (QIAGEN) with DNase digestion on the column.

tag: Strain

tag: Gender

value: Male

tag: Age

value: 8 months

tag: Tissue

value: Intestine


title: cDNA array wt-3+fl+3 set2

description: Comparison of gene expression profiles of 3 DPA fl-mutant and -3 DPA wild-type upland cotton ovules.


title: cDNA array wt-3+wt+0 set1(dyeswap)


title: wild-type strain_CS medium_2

status: Public on Mar 31 2008

city: Toyonaka

first: Takushi

last: Ooga

state: Osaka

address: Machikaneyama 1-1

department: Department of Biology

institute: Osaka University

description: no additional information

hyb_protocol: 3’-terminal-labeled cDNA (2 micro g) was hybridized to a TTHB8401 GeneChip (Affymetrix, Santa Clara, CA). The array was incubated for 16 h at 50oC in a solution comprising 180 mM MES, pH 6.6, 40 mM EDTA, 0.02% Tween 20, 7% dimethyl sulfoxide, 1 mg of herring sperm DNA (Promega), 0.5 mg of bovine serum albumin (BSA), the recommended amount of Eukaryotic Hybridization Control (Affymetrix), and Control Oligo B2 for the alignment signal (Affymetrix), and then the array was automatically washed and stained with streptavidin-phycoerythrin (Invitrogen) by using a GeneChip Fluidics Station, 450XP (Affymetrix).

scan_protocol: The Probe Array was scanned with a GeneArray Scanner (Affymetrix).

data_processing: The image data was scaled to the target intensity by one-step Tukey’s biweight algorithm using GeneChip Operating software, version 1.0 (Affymetrix, Santa Clara, CA).

organism: Thermus thermophilus HB8

source_name: wild-type strain on CS medium for 800 min

label_protocol: cDNA was synthesized with SuperScript II (Invitrogen) reverse transcriptase in the presence of RNase inhibitor SUPERase (Ambion) and 6 base random primers (Invitrogen). The cDNA was fragmented with 35 units of DNase I (GE Healthcare Bio-Science Corp.) at 37oC for 10 min, and after inactivation at 98oC for 10 min, the cDNA fragments were labeled with biotin-dideoxy UTP, using terminal transferase according to the manufacturer’s instructions (ENZO Biochem. Inc., Farmingdale, NY).

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70oC for 6 h in 5 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl which was adjusted to pH 7.2 with NaOH. The cells were inoculated into 5ml of fresh TR medium while the logarithm growth phase (OD600nm = 0.5), and this inoculation was repeated again. When the OD600nm of final preculture reached 0.5, 2 ml of culture was inoculated into 200 ml fresh CS medium containing 2% Sucrose, 2% sodium glutamate, 0.055% K2HPO4, 0.018% KH2PO4, 0.2% NaCL, 0.05% (NH4)2SO4, 0.125% MgCl2 6H2O, 0.0025% CaCl2 2H2O, 0.001% FeSO4 7H2O, 0.00012% NaMoO3 2H2O, 0.00001% VOSO4 xH2O, 0.00005% MnCl2 4H2O, 0.000006% ZnSO4 7H2O, 0.0000015% 5H2O, 0.00008% CoCl2 6H2O, 0.000002% NiCl2 2H2O, 0.0001% Biotin, and 0.001% Thiamin which was adjusted to pH 7.0 with NaOH. The cells were cultured at 70oC for 800 minutes.

extract_protocol: Crude RNA was extracted by the addition of 1.4 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol to the cell pellet. This mixture was incubated at 65oC for 5 min, chilled on ice for 5 min, and then centrifuged at 4oC. Then, 750 micro l of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase. After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform. The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol. The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 40 micro l of water. The RNA was treated with DNase I (Ambion, Austin, TX) at 37oC for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70oC for 5 min. Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

treatment_protocol: The 20 ml of culture was centrifuged by 10000 rpm, 4oC, and 5minutes. After the removal of supernatant, cell pellet was frozen by using liquid nitrogen.

tag: wild-type strain, CS medium, 800 min after the start of inoculation


title: cDNA array wt-3+fl+3 set3(dyeswap)


title: cDNA array wt-3+fl-3 set3


title: cDNA array wt-3+fl-3 set3(dyeswap)


title: Apc1638N_tumor_2

description: Apc1638N, C57Bl6/J, intestinal tumor

source_name: Apc1638N, C57Bl6/J, intestinal tumor

value: Intestinal tumor


title: cDNA array wt-3+fl+3 set1(dyeswap)


title: Apc1638N_tumor_16

description: Apc1638N, C57Bl6/J, intestinal tumor


title: cDNA array wt-3+fl+3 set3


title: WT_normal_36

source_name: C57Bl6/J, normal intestinal epithelial cells


title: wild-type strain_CS medium_3

description: no additional information


title: wild-type strain_CS medium_4

description: no additional information


title: wild-type strain_CS medium_1

description: no additional information


title: Apc1638N_tumor_18

description: Apc1638N, C57Bl6/J, intestinal tumor


title: TTHA1939 deletion mutant strain_CS medium_2

description: no additional information

source_name: TTHA1939 deletion mutant strain on CS medium for 800 min

growth_protocol: The T. thermophilus HB8 TTHA1939 deletion mutant strain was pre-cultured at 70oC for 6 h in 5 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl which was adjusted to pH 7.2 with NaOH. The cells were inoculated into 5ml of fresh TR medium while the logarithm growth phase (OD600nm = 0.5), and this inoculation was repeated again. When the OD600nm of final preculture reached 0.5, 2 ml of culture was inoculated into 200 ml fresh CS medium containing 2% Sucrose, 2% sodium glutamate, 0.055% K2HPO4, 0.018% KH2PO4, 0.2% NaCL, 0.05% (NH4)2SO4, 0.125% MgCl2 6H2O, 0.0025% CaCl2 2H2O, 0.001% FeSO4 7H2O, 0.00012% NaMoO3 2H2O, 0.00001% VOSO4 xH2O, 0.00005% MnCl2 4H2O, 0.000006% ZnSO4 7H2O, 0.0000015% 5H2O, 0.00008% CoCl2 6H2O, 0.000002% NiCl2 2H2O, 0.0001% Biotin, and 0.001% Thiamin which was adjusted to pH 7.0 with NaOH. The cells were cultured at 70oC for 800 minutes.

tag: TTHA1939 deletion mutant strain, CS medium, 800 min after the start of inoculation


title: cDNA array wt-3+wt+0 set2(dyeswap)

tag: -3 DPA wild-type upland cotton ovules


title: TTHA1939 deletion mutant strain_CS medium_4

description: no additional information


title: TTHA1939 deletion mutant strain_CS medium_3

description: no additional information


title: TTHA1939 deletion mutant strain_CS medium_1

description: no additional information

source_name: TTHA1939 deletion mutant strain on CS medium


title: cDNA array wt-3+fl+3 set1


title: Metastatic Sarcoma Replicate 1

city: Sydney

first: Paromita (Romi)

last: Das Gupta

state: NSW

address: High St, Randwick

department: Dept Surgery

country: Australia

institute: Prince of Wales Hospital

description: Biologic replicate 1 of 3(Metastatic tumour)

hyb_protocol: 50ul DIG EasyHyp was added to each cDNA reaction and the Alexa Fluor 555- and 647 labelled samples were combined. Herring sperm DNA and Yeast tRNA was added. The combined sample was placed on the slide and hybridized overnight at 37deg in a humidified chamber. The slides were then subjected to sequential washes before scanning.

scan_protocol: Scanned on GenePix 4000B laser scanner (Axon Instruments, Molecular Devices).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. GeneSpring software was used.

label: Alexa Fluor 647 (Cy 5)

source_name: Total RNA from Metastatic sarcoma cell line GCT

label_protocol: Total RNA was reverse transcribed using the SuperScriptII Indirect labelling system and Alexa Fluor 555 (Cy3) and Alexa Fluor 647 (Cy5) as the fluorescent dyes. 20ug of RNA was used for sarcoma and reference cell lines in each experiment. 20ug RNA was primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 4ul SuperScript III RTase (Invitrogen), 6ul 5X 1st srand buffer, 3ul 0.1MDTT, 3ul dNTP mix, 2ul RNAaseOUT.

growth_protocol: Cells cultured in DMEM supplemented with 10%FCS plus penicillin and streptomycin. Harvested for RNA extraction at 70-80% confluence.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: No additional treatment.

tag: GCT cell line (TIB-223)

tag: Metastatic Malignant Fibrous Histiocytoma

tag: RNA extracted at 70-80% confluence

label: Alexa Fluor 555 (Cy 3)

source_name: Total RNA from Normal Fibroblast cell line

tag: MRC5 cell line (CCL-171)


title: Low Grade Sarcoma Replicate 4

description: Biologic replicate 4 of 4(Low grade tumour)

source_name: Total RNA from Low grade Fibrosarcoma cell line SW687

tag: SW684 cell line (HTB-91)

tag: Low grade Fibrosarcoma


title: Metastatic Sarcoma Replicate 2

description: Biologic replicate 2 of 3(Metastatic tumour)


title: High Grade Sarcoma Replicate 4

description: Biologic replicate 4 of 4(High grade tumour)

source_name: Total RNA from High grade Fibrosarcoma cell line HT1083

tag: HT1080 cell line (CCL-121)

tag: High grade Fibrosarcoma


title: Low Grade Sarcoma Replicate 1

description: Biologic replicate 1 of 4(Low grade tumour)

source_name: Total RNA from Low grade Fibrosarcoma cell line SW684


title: Liver 25% carb Male fish54

city: Davis

first: Matt

middle: L

last: Settles

state: CA

address: 451 Health Sciences Sr

department: Genome Center

institute: University of California, Davis

hyb_protocol: Microarrays were hybridized with fragmented biotinylated cRNA for 16 h at 45°C with constant rotation (45 r.p.m.), and processed using the Affymetrix GeneChip Fluidic Station 450. Streptavidin-conjugated phycoerythrin (SAPE) was used for staining, followed by amplification using a biotinylated anti-streptavidin antibody.  This was followed by another round of SAPE prior to scanning using a GeneChip Scanner 3000 (Affymetrix).

scan_protocol: Scanning was performed using a GeneChip Scanner 3000 (Affymetrix)

data_processing: After hybridization and quality control, probesets were filtered based on the following criteria:  First, probesets were eliminated that were not classified as present in all arrays of any one combination of sex and treatment using PMA calls.  Second, four separate normalizations of the data (MAS 5, RMA, GCRMA, and PLIER) were performed, and only those probesets that were above the 95th percentile of the background for all four normalizations were retained.  The distribution of background intensity values in each case was determined using the negative control probes on the microarray.  Ultimately, 6,165 probesets passed the filter criteria and were used in subsequent analyses.  Arrays were then clustered based on expression levels of all expressed genes in our filtered set to test for the presence of outlier arrays.  In this case, one sample (a male from the 25% carbohydrate treatment) did not cluster with the other arrays and was removed out of concern that this sample harbored contamination from other tissues.

organism: Danio rerio

source_name: Liver Male 25%carb

label_protocol: For each array, up to 10 mg of total RNA were converted to cDNA.  Biotinylated cRNA was then produced in vitro using the GeneChip expression 3′ amplification one-cycle target labeling kit (Affymetrix)

extract_protocol: Extraction using TRIZOL following manufacturer's protocol

tag: adult livers

tag: Seacrest Farms strain


title: Liver 25% carb Male fish52


title: High Grade Sarcoma Replicate 1

description: Biologic replicate 1 of 4(High grade tumour)

source_name: Total RNA from High grade Fibrosarcoma cell line HT1080


title: Liver 0% carb Male fish26

source_name: Liver Male 0%carb


title: Liver 25% carb Female fish51

source_name: Liver Female 25%carb


title: Low Grade Sarcoma Replicate 3

description: Biologic replicate 3 of 4(Low grade tumour)

source_name: Total RNA from Low grade Fibrosarcoma cell line SW686


title: Liver 0% carb Male fish30


title: Metastatic Sarcoma Replicate 3

description: Biologic replicate 3 of 3(Metastatic tumour)


title: High Grade Sarcoma Replicate 3

description: Biologic replicate 3 of 4(High grade tumour)

source_name: Total RNA from High grade Fibrosarcoma cell line HT1082


title: Liver 0% carb Male fish11


title: High Grade Sarcoma Replicate 2

description: Biologic replicate 2 of 4(High grade tumour)

source_name: Total RNA from High grade Fibrosarcoma cell line HT1081


title: Liver 0% carb Male fish66


title: Liver 25% carb Female fish24


title: Liver 0% carb Female fish8

source_name: Liver Female 0%carb


title: Liver 0% carb Female fish27


title: Liver 25% carb Female fish49


title: Liver 25% carb Male fish53


title: Liver 25% carb Female fish20


title: Liver 0% carb Female fish25


title: Liver 0% carb Female fish10


title: Low Grade Sarcoma Replicate 2

description: Biologic replicate 2 of 4(Low grade tumour)

source_name: Total RNA from Low grade Fibrosarcoma cell line SW685


title: Liver 25% carb Female fish3


title: Liver 0% carb Female fish7


title: slr-2(ku297) worms at L1 stage, third replicate

status: Public on Mar 30 2008

city: Laramie

first: David

last: Fay

state: WY

address: 1000 E. University Dept. 3944

department: MOLB

institute: University of Wyoming

description: slr-2(ku297) larvae

hyb_protocol: according to Affymetrix protocol

scan_protocol: according to Affymetrix protocol

data_processing: expression values were generated using RMA

organism: Caenorhabditis elegans

source_name: RNA from larval C. elegans population

label_protocol: 2.5 ug total RNA were used for cDNA synthesis. cDNA synthesis, cRNA synthesis, fragmentation and labeling were performed according to Affymetrix protocol.

growth_protocol: Worms were grown on NGM plates spotted with OP50 at 20 oC.

extract_protocol: Total RNA was extracted with phenol, cleaned with phenol:chlorophorm:isoamyl alcohol (25:24:1), and then with chlorophorm:isoamyl alcohol (24:1). Total RNA was precipitated overnight at 4 oC with 4M lithium acetate and DNAseI treated before purification on RNEasy minicolumns from Qiagen.

tag: slr-2(ku297) L1 larvae


title: slr-2(ku297) worms at L1 stage, second replicate

description: slr-2(ku297) larvae


title: HIMAC_4023

status: Public on Mar 29 2008

city: Tsukuba

first: Randeep

last: Rakwal

state: Ibaraki

address: AIST WEST, Onagawa 16-1

institute: AIST

description:
Keyword = rice
Keyword = Irradiation

hyb_protocol: Standard protocol of Gene Expression Hybridization Kit from Agilent Technologies

scan_protocol: Standard protocol of Gene Pix Scanner

data_processing: Gene Pix 4000 scanner

organism: Oryza sativa

label_protocol: Standard Protocol of Agilent Low RNA Input Fluorescent Linear Amplification Kit

growth_protocol: Plants were grown in growth chamber in MS medium for 7 days

extract_protocol: TRIZOL Reagent method

treatment_protocol: Healthy seedlings, control

tag: Non-irradiated shoots

treatment_protocol: Irradiated for 2 h 35 minutes

tag: Irradiated shoots


title: RatFemur_ProliferativeZone_46d

status: Public on Mar 28 2008

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

hyb_protocol: Affymetrix FS450_0004

scan_protocol: Affymetrix GeneChip 7G

data_processing:
Initial analysis - MAS5/GCOS
Final analysis - RMA

organism: Rattus norvegicus

source_name: 46 day old rat femur

label_protocol: Nugen Ovation

extract_protocol: Qiagen RNeasy

tag: Normal proliferative zone laser-dissected from femur


title: RatFemur_PerichondralZone_46d

tag: Age 46d

tag: Male

tag: Normal perichondral zone laser-dissected from femur


title: HIMAC_4022

description:
Keyword = rice
Keyword = Irradiation


title: RatFemur_PerichondralZone_42d

source_name: 42 day old rat femur

tag: Age 42d


title: slr-2(ku297) worms at L1 stage, first replicate

description: slr-2(ku297) larvae


title: RatFemur_ReserveZone_42d

tag: Normal reserve zone laser-dissected from femur


title: Day-7EB-Exp4

city: Santiago

first: Dario

last: Sepulveda

state: RM

address: Beacuhef 861

department: Chemical Engineering and Biotechnology

country: Chile

institute: Universidad de Chile

description: R1_Embryonic_Stem_Cell_Embryoid_Body_Day_7_BiolRep1

hyb_protocol: Agilent 60-mer oligo microarray processing protocol

scan_protocol: Slides were scanned using the Agilent Microarray Scanner G2565BA Agilent’s Feature Extraction software (G2567AA, version 7.2) was used to identify spot and feature outliers. Spot quality was assessed and, if not discarded, multiple spots of the same gene were averaged (geometric mean).

data_processing: SNNLERM-algorithm was used to calculate normalized signal intensity ratios and confidence levels

source_name: embryonic stem cell, embryoid body, day 7

label_protocol: Low RNA input Fluorescent linear amplification kit

growth_protocol: Standard growth protocol.

extract_protocol: Total Rna Isolation mini-kit from Agilent

treatment_protocol: medium used was ES-Diff (Same as ES-MEM but without sodium pyruvate and without LIF). Three conditions were used for cell differentiation: Embryoid Body (EB) formation, where the cells were cultured in non-adherent plastic dishes, Gelatin coated plates (GEL) where cells were cultured on plates coated with a solution at 0.1% gelatin and Matrigel coated plates (MAT) where the plates were treated with a 0.1% protein Matrigel

tag: embryoid body formation

growth_protocol: cells were cultured on gelatin-coated flasks in ES-MEM medium (DMEM high glucose, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 100 mM 2-ME, 2 mM L-glutamine, 15% fetal bovine serum, penicillin/streptomycin 50 mg/ml each, and 1000 U LIF/ml). All  cell cultures were carried out in a humidified incubator at 37ºC with 5% CO2

tag: total RNA was pooled from R1 cells differentiating with embryoid body formation protocol. Samples of equal amounts of RNA from days 1 through 7 were mixed, and this was used as REFERENCE RNA.


title: RatFemur_ReserveZone_46d


title: Day-7EB-Exp1rep

description: R1_Embryonic_Stem_Cell_Embryoid_Body_Day_7_TechRep1


title: Day-7EB-Exp6

description: R1_Embryonic_Stem_Cell_Embryoid_Body_Day_7_BiolRep2


title: Day-5Mat-Exp6

description: R1_Embryonic_Stem_Cell_Matrigel_Coating_plate_Day_5_BiolRep2

source_name: embryonic stem cell, Matrigel coating, day 5

tag: differentiation on a Matrigel coated plate


title: Day-7Mat-Exp6

description: R1_Embryonic_Stem_Cell_Matrigel_Coating_plate_Day_7_BiolRep2

source_name: embryonic stem cell, Matrigel coating, day 7


title: Day-7EB-Exp1

description: R1_Embryonic_Stem_Cell_Embryoid_Body_Day_7


title: Day-5Mat-Exp1rep

description: R1_Embryonic_Stem_Cell_Matrigel_Coating_plate_Day_5_TechRep1


title: Day-7EB-Exp6-rep

description: R1_Embryonic_Stem_Cell_Embryoid_Body_Day_7_BiolRep2_TechRep1


title: RatFemur_ProliferativeZone_42d


title: Day-5Gel-Exp4

description: R1_Embryonic_Stem_Cell_Gelatin_Coating_plate_Day_5_BiolRep1

source_name: embryonic stem cell, gelatin coating, day 5

tag: differentiation on a gelatin coated plate


title: RatFemur_HypertrophicZone_42d

tag: Normal hypertropic zone laser-dissected from femur


title: Day-5Mat-Exp4

description: R1_Embryonic_Stem_Cell_Matrigel_Coating_plate_Day_5_BiolRep1


title: Day-7Gel-Exp1

description: R1_Embryonic_Stem_Cell_Gelatin_Coating_plate_Day_7

source_name: embryonic stem cell, gelatin coating, day 7


title: Day-7Gel-Exp4

description: R1_Embryonic_Stem_Cell_Gelatin_Coating_plate_Day_7_BiolRep1


title: Day-5Mat-Exp1

description: R1_Embryonic_Stem_Cell_Matrigel_Coating_plate_Day_5


title: Day-7Mat-Exp1

description: R1_Embryonic_Stem_Cell_Matrigel_Coating_plate_Day_7


title: Gene expression changes in met1-RNAi lines of Arabidopsis suecica

city: Bethesda

first: Misook

last: Ha

state: MD

address: NIH

institute: National Heart Lung Blood Institute

description: 4 replicates with dye-swap experiments

hyb_protocol: Each lyophilized probe was re-suspended in 40 μL of hybridization solution (0.25 M Na2HPO4, 0.25 M NaH2PO4, pH 7.4, and 3.5% SDS, w/v). The solution was heated for 2 min at 95 °C, chilled immediately in ice, and applied directly to the array. After covering the array with a 24 × 40 mm coverslip (Sigma, St Louis, MO), the slide was placed in a microarray hybridization chamber (Corning Incorporated, Corning, NY). Hybridization was performed overnight (16 h) at 60 °C in a hybridization oven. After hybridization, the slides were washed for 2 min in 2× SSC, 0.03% (w/v) SDS, 2 min in 0.2× SSC, and 2 min in 0.05× SSC. Immediately after the last wash, the slides were dried by centrifugation (3 min at 500 r.p.m.).

scan_protocol: Slides were scanned using Genepix 4000B

data_processing:
The notation Xijkplm is used to denote the mth replicate spot of gene l with feature type p under target condition k labelled with dye j on slide i. After log transformation, Yijkplm = log(Xijkplm).
The anova model for this situation is given by:
Yijkplm = µ + Si + Dj + Tk + Fp + Gl + TFkp + SGil + DGjl + TGkl + FGpl + TFGkpl + ijkplm,where µ represents the overall mean effect, S, D, T, F and G represent main effects from the slide, dye, target (e.g. A.thaliana genome vs. A.arenosa genome), feature type (e.g. oligo vs. gene) and gene, respectively. The interaction terms TF, SG, DG, TG, FG and TFG represent target by feature type, array by gene, dye by gene, target by gene, feature type by gene, and target by feature type by gene interactions, and ijkplm denotes the random error and is used to test for significance of main and interaction effects in the model. Due to confounding and/or aliasing issues involving the slide, dye and target terms, not all two-way interactions are included in the model. The model residuals are assumed to be normally distributed with a common variance (i.e. ijkplm i.i.d. N(0, σ2)). Also, a per gene variance is assumed (i.e. ijkplm independent.
Hypothesis testing
The presence of differential expression in a microarray expression is represented by significant differences in T + TG terms for a particular gene. The following hypotheses are tested to determine whether a gene, g, has undergone differential expression between targets t and t' (e.g. A.thaliana RNA vs. A. arenosa RNA).
H0: Tt + TGtg = Tt' + TGt'g
A standard t-test statistic is used for this comparison, based on the normality assumption for the residuals. To control for multiple testing errors, both Holm's and the false discovery rate (FDR) were employed. Holm's sequential adjustment provides strong control of the family-wise error rate (FWER) below level α with greater power than the standard Bonferroni method (Hochberg and Tamhane, 1987). The false discovery rate (FDR) controlling method of Benjamini and Hochberg (Benjamini and Hochberg, 1995) provides weak control of the FWER, and controls the FDR below level α. The FDR is defined as the expected proportion of incorrect rejections of H0, relative to the total number of rejections. The significance level α= 0.05 was chosen for this study.

label: Cy3 and Cy5, dye swap

molecule: polyA RNA

organism: Arabidopsis suecica

source_name: Leaf tissue

label_protocol: We used 500 ng of mRNA in each labeling reaction using Cy3- or Cy5-dCTP (Amersham Biosciences). The Cy3-dCTP reaction was mixed with the Cy5-dCTP reaction for one hybridization, and then an equal amount of RNA samples was reversely labeled for another hybridization.

extract_protocol: RNA was extracted using TRIzol reagent (Invitrogen Life Technologies), following the manufacture instruction.

tag: Reduced DNA methylation in the genome of Arabidopsis suecica.

tag: met1-RNAi lines of Arabidopsis suecica

tag: Leaf tissue

tag: Natural allopolyploid, 2n=4x=26


title: Day-7Gel-Exp6

description: R1_Embryonic_Stem_Cell_Gelatin_Coating_plate_Day_7_BiolRep2


title: Day-7Mat-Exp4

description: R1_Embryonic_Stem_Cell_Matrigel_Coating_plate_Day_7_BiolRep1


title: RatFemur_HypertrophicZone_46d


title: Day-5Gel-Exp6

description: R1_Embryonic_Stem_Cell_Gelatin_Coating_plate_Day_5_BiolRep2


title: Day-5Gel-Exp4rep

description: R1_Embryonic_Stem_Cell_Gelatin_Coating_plate_Day_5_BiolRep1_TechRep1


title: Day-5EB-Exp1

description: R1_Embryonic_Stem_Cell_Embryoid_Body_Day_5

source_name: embryonic stem cell, embryoid body, day 5


title: Day-5EB-Exp1rep

description: R1_Embryonic_Stem_Cell_Embryoid_Body_Day_5_TechRep1


title: Day-5EB-Exp4

description: R1_Embryonic_Stem_Cell_Embryoid_Body_Day_5_BiolRep1


title: Day-3EB-Exp1

description: R1_Embryonic_Stem_Cell_Embryoid_Body_Day_3

source_name: embryonic stem cell, embryoid body, day 3


title: Day-5EB-Exp6

description: R1_Embryonic_Stem_Cell_Embryoid_Body_Day_5_BiolRep2


title: Day-0-Exp6

description: R1_Embryonic_Stem_Cell_Undifferentiated_BiolRep2

source_name: embryonic stem cell, day 0

tag: undifferentiated R1 cells


title: Day-3Mat-Exp6rep

description: R1_Embryonic_Stem_Cell_Matrigel_Coating_plate_Day_3_BiolRep2_TechRep1

source_name: embryonic stem cell, Matrigel coating, day 3


title: Day-3EB-Exp6

description: R1_Embryonic_Stem_Cell_Embryoid_Body_Day_3_BiolRep2


title: Day-3EB-Exp4

description: R1_Embryonic_Stem_Cell_Embryoid_Body_Day_3_BiolRep1


title: Day-3Gel-Exp4

description: R1_Embryonic_Stem_Cell_Gelatin_Coating_plate_Day_3_BiolRep1

source_name: embryonic stem cell, gelatin coating, day 3


title: Day-3Mat-Exp6

description: R1_Embryonic_Stem_Cell_Matrigel_Coating_plate_Day_3_BiolRep2


title: Day-0-Exp4

description: R1_Embryonic_Stem_Cell_Undifferentiated_BiolRep1


title: Day-3Gel-Exp1

description: R1_Embryonic_Stem_Cell_Gelatin_Coating_plate_Day_3


title: Day-3Mat-Exp4

description: R1_Embryonic_Stem_Cell_Matrigel_Coating_plate_Day_3_BiolRep1


title: Day-0-Exp1