title: F-Genome: slide42

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58014.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 3/20/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F10C_A10C_A10c5; Parameter Date performed = 3/22/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F10C_A10C_A10c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 3/20/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 3/22/2007; Parameter Tube label = F10C_A10C_F10c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F10C_A10C_F10c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

treatment_protocol: Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse

tag: Fiber at 10 DPA derived from F-genome


title: F-Genome: slide39

status: Public on Mar 05 2008

type: RNA

city: Athens

first: Alan

middle: R

last: Gingle

state: GA

address: 111 Riverbend Rd.

department: Center for Applied Genetics Technologies

country: USA

institute: University of Georgia

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58011.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = Gal file; Software: type: feature extraction Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 3/21/2007; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 3/21/2007; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite

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

molecule: total RNA

organism: Gossypium herbaceum

source_name: Fiber at 25 DPA derived from A-genome

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 3/12/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = A20C_A25C_A25c5; Parameter Date performed = 3/20/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = A20C_A25C_A25c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Fiber at 25 DPA derived from A-genome

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 25 DPA; Parameter Transgenes = none

source_name: Fiber at 20 DPA derived from A-genome

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 3/12/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 3/20/2007; Parameter Tube label = A20C_A25C_A20c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = A20C_A25C_A20c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Fiber at 20 DPA derived from A-genome

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Tissue type = Fiber 20 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: F-Genome: slide3

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57975.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = Gal file; Software: type: feature extraction Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 12/23/2006; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 12/23/2006; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite

organism: Gossypium longicalyx

source_name: Fiber at 25 DPA derived from F-genome

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 12/15/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F520_F25A_F25c5; Parameter Date performed = 12/22/2006; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F520_F25A_F25c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Fiber at 25 DPA derived from F-genome

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 5 DPA; Parameter Transgenes = none

source_name: Fiber at 20 DPA derived from F-genome

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 12/15/2006; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 12/22/2006; Parameter Tube label = F520_F25A_F20c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F520_F25A_F20c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Fiber at 20 DPA derived from F-genome

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Tissue type = Fiber 25 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: F-Genome: slide2

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57974.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 12/15/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F10A_F20A_F20c5; Parameter Date performed = 12/22/2006; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F10A_F20A_F20c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 20 DPA; Parameter Transgenes = none

source_name: Fiber at 10 DPA derived from F-genome

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 12/15/2006; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 12/22/2006; Parameter Tube label = F10A_F20A_F10c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F10A_F20A_F10c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Tissue type = Fiber 10 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: F-Genome: slide44

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58016.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = Gal file; Software: type: feature extraction Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 3/23/2007; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 3/23/2007; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 3/20/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F25C_A25C_A25c5; Parameter Date performed = 3/22/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F25C_A25C_A25c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 3/20/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 3/22/2007; Parameter Tube label = F25C_A25C_F25c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F25C_A25C_F25c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA


title: F-Genome: slide40

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58012.gif

source_name: Fiber at 5 DPA derived from A-genome

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 3/12/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = A25C_A5C_A5c5; Parameter Date performed = 3/20/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = A25C_A5C_A5c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Fiber at 5 DPA derived from A-genome

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 5 DPA; Parameter Transgenes = none

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 3/12/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 3/20/2007; Parameter Tube label = A25C_A5C_A25c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = A25C_A5C_A25c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Tissue type = Fiber 25 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: F-Genome: slide16

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57988.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = Gal file; Software: type: feature extraction Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 1/3/2007; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 1/3/2007; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 12/29/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F25A_A25A_F25c5; Parameter Date performed = 1/2/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F25A_A25A_F25c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 25 DPA; Parameter Transgenes = none

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 12/29/2006; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 12/22/2006; Parameter Tube label = F25A_A25A_A25c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F25A_A25A_A25c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

treatment_protocol: Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse


title: F-Genome: slide43

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58015.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 3/20/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F20C_A20C_A20c5; Parameter Date performed = 3/22/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F20C_A20C_A20c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 20 DPA; Parameter Transgenes = none

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 3/20/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 3/22/2007; Parameter Tube label = F20C_A20C_F20c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F20C_A20C_F20c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Tissue type = Fiber 20 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: F-genome: slide1

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57973.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 12/15/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F5A_F10A_F10c5; Parameter Date performed = 12/22/2006; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F5A_F10A_F10c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Fiber at 10 DPA derived from F-genome

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 10 DPA; Parameter Transgenes = none

source_name: Fiber at 5 DPA derived from F-genome

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 12/15/2006; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 12/22/2006; Parameter Tube label = F5A_F10A_F5c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F5A_F10A_F5c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Fiber at 5 DPA derived from F-genome

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Tissue type = Fiber 5 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: F-Genome: slide41

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58013.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 3/20/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F5C_A5C_A5c5; Parameter Date performed = 3/22/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F5C_A5C_A5c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 3/20/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 3/22/2007; Parameter Tube label = F5C_A5C_F5c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F5C_A5C_F5c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA


title: F-Genome: slide20

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57992.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = Gal file; Software: type: feature extraction Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 1/29/2007; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 1/29/2007; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 1/22/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F25B_F5B_F25c5; Parameter Date performed = 1/28/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F25B_F5B_F25c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 1/22/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 1/28/2007; Parameter Tube label = F25B_F5B_F5c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F25B_F5B_F5c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA


title: F-Genome: slide14

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57986.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 12/29/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F10A_A10A_F10c5; Parameter Date performed = 1/2/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F10A_A10A_F10c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

source_name: Fiber at 10 DPA derived from A-genome

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 12/29/2006; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 12/22/2006; Parameter Tube label = F10A_A10A_A10c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F10A_A10A_A10c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Fiber at 10 DPA derived from A-genome

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Tissue type = Fiber 10 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: F-Genome: slide38

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58010.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 3/12/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = A10C_A20C_A20c5; Parameter Date performed = 3/20/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = A10C_A20C_A20c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Fiber at 20 DPA derived from A-genome

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 3/12/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 3/20/2007; Parameter Tube label = A10C_A20C_A10c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = A10C_A20C_A10c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA


title: F-Genome: slide13

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57985.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 12/29/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F5A_A5A_F5c5; Parameter Date performed = 1/2/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F5A_A5A_F5c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 5 DPA; Parameter Transgenes = none

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 12/29/2006; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 12/22/2006; Parameter Tube label = F5A_A5A_A5c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F5A_A5A_A5c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Tissue type = Fiber 5 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: F-Genome: slide10

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57982.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 12/29/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F10A_A10A_A10c5; Parameter Date performed = 1/2/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F10A_A10A_A10c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 10 DPA; Parameter Transgenes = none

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 12/29/2006; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 12/22/2006; Parameter Tube label = F10A_A10A_F10c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F10A_A10A_F10c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA


title: F-Genome: slide11

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57983.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 12/29/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F20A_A20A_A20c5; Parameter Date performed = 1/2/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F20A_A20A_A20c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 12/29/2006; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 12/22/2006; Parameter Tube label = F10A_A20A_F20c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F10A_A20A_F20c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Fiber at 20 DPA derived from F-genome


title: F-Genome: slide37

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58009.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 3/12/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = A5C_A10C_A10c5; Parameter Date performed = 3/20/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = A5C_A10C_A10c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 3/12/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 3/20/2007; Parameter Tube label = A5C_A10C_A5c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = A5C_A10C_A5c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Fiber at 5 DPA derived from A-genome


title: mature flavedo

city: Davis

first: Abhaya

middle: M

last: Dandekar

state: CA

address: One Shields Ave

department: Plant Sciences

institute: University of California, Davis

description: no additional information

hyb_protocol: Combimatrix protocols were followed, using fluorolink Cy5-labeled streptavidin

scan_protocol: GenePix scanner used

data_processing: Combimatrix software was used to identify spots and intensities. Avadis Prophetic 3.3 by Strand Genomics (Bangalore, India) was used for microarray statistical analysis. Intensities were converted to log base 2. To confirm correct orientation for each contig, intensities for ‘sense’ and ‘antisense’ versions were compared, with the assumption that ‘sense’ orientation probes would have an aggregate higher intensity across libraries. In the few instances where intensities were very close or conflicted with listed orientations, component ESTs were manually inspected.  Next, the mean of all negative control spots was subtracted from the value of all other spots on the array, with a minimum resulting value of 1. A spike-in-based spot normalization was employed. For each array, the mean of all spike-ins was calculated, ignoring two spike-in concentrations that had fallen to 1 after negative control subtraction. Each mean was then multiplied by a coefficient to make it equal to the highest mean spike-in value. The coefficient used for a given array was then applied to each spot on that array. Following normalization, probes were aggregated by median polishing scripts designed by Strand Genomics.

label: biotin

organism: Citrus sinensis

source_name: Washington navel orange mature flavedo

label_protocol: RNA was amplified and labeled with MessageAmp II aRNA kits (Ambion, Austin, TX), following instructions for single-round amplification and biotinylation with 11-CTP and 16-UTP biotin. 3 micrograms total RNA was used for each sample, calculated by UV spectrometry.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen; Carlsbad, CA), followed by RNA purification using an RNA/DNA cleanup kit (Qiagen; Valencia, CA). RNA concentration and purity were assessed by UV spectrophotometry. The RNA was stored at -80˚C in water.

tag: synonym

value: Citrus sinensis (L.) Osbeck

tag: Tissues dissected from five fruit and pooled; frozen, ground in liquid nitrogen. Mature (220 DAFB) samples collected in previous growing season.


title: mature juice sac

description: no additional information

source_name: Washington navel orange mature juice sac


title: flavedo, 165 DAFB

description: no additional information

source_name: Washington navel orange flavedo, 165 DAFB

tag: Tissues dissected from five fruit and pooled; frozen, ground in liquid nitrogen.


title: albedo, 165 DAFB

description: no additional information

source_name: Washington navel orange albedo, 165 DAFB


title: flavedo, 80 DAFB

description: no additional information

source_name: Washington navel orange flavedo, 80 DAFB


title: albedo, 80 DAFB

description: no additional information

source_name: Washington navel orange albedo, 80 DAFB


title: F-Genome: slide35

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58007.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 3/12/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F20C_F25C_F25c5; Parameter Date performed = 3/20/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F20C_F25C_F25c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Fiber at 25 DPA derived from F-genome

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 25 DPA; Parameter Transgenes = none

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 3/12/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 3/20/2007; Parameter Tube label = F20C_F25C_F20c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F20C_F25C_F20c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA


title: F-Genome: slide9

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57981.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 12/29/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F5A_A5A_A5c5; Parameter Date performed = 1/2/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F5A_A5A_A5c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 5 DPA; Parameter Transgenes = none

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 12/29/2006; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 12/22/2006; Parameter Tube label = F5A_A5A_F5c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F5A_A5A_F5c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA


title: F-Genome: slide34

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58006.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 3/12/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F10C_F20C_F20c5; Parameter Date performed = 3/20/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F10C_F20C_F20c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 20 DPA; Parameter Transgenes = none

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 3/12/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 3/20/2007; Parameter Tube label = F10C_F20C_F10c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F10C_F20C_F10c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Fiber at 10 DPA derived from F-genome

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Tissue type = Fiber 10 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: F-Genome: slide36

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58008.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 3/12/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F25C_F5C_F5c5; Parameter Date performed = 3/20/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F25C_F5C_F5c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Fiber at 5 DPA derived from F-genome

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 3/12/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 3/20/2007; Parameter Tube label = F25C_F5C_F25c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F25C_F5C_F25c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Tissue type = Fiber 25 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: F-Genome: slide48

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58020.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 3/20/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F25C_A25C_F25c5; Parameter Date performed = 3/22/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F25C_A25C_F25c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 3/20/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 3/22/2007; Parameter Tube label = F25C_A25C_A25c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F25C_A25C_A25c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Fiber at 25 DPA derived from A-genome

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Tissue type = Fiber 25 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: F-Genome: slide30

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58002.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = Gal file; Software: type: feature extraction Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 1/30/2007; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 1/30/2007; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 1/28/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F10B_A10B_F10c5; Parameter Date performed = 1/29/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F10B_A10B_F10c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 10 DPA; Parameter Transgenes = none

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 1/28/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 1/29/2007; Parameter Tube label = F10B_A10B_A10c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F10B_A10B_A10c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Fiber at 10 DPA derived from A-genome

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Tissue type = Fiber 10 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: F-Genome: slide29

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58001.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 1/28/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F5B_A5B_F5c5; Parameter Date performed = 1/29/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F5B_A5B_F5c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 5 DPA; Parameter Transgenes = none

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 1/28/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 1/29/2007; Parameter Tube label = F5B_A5B_A5c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F5B_A5B_A5c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Fiber at 5 DPA derived from A-genome

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Tissue type = Fiber 5 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: F-Genome: slide15

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57987.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 12/29/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F20A_A20A_F20c5; Parameter Date performed = 1/2/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F20A_A20A_F20c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Fiber at 20 DPA derived from F-genome

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 12/29/2006; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 12/22/2006; Parameter Tube label = F20A_A20A_A20c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F20A_A20A_A20c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Fiber at 20 DPA derived from A-genome

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Tissue type = Fiber 20 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: F-Genome: slide33

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58005.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 3/12/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F5C_F10C_F10c5; Parameter Date performed = 3/20/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F5C_F10C_F10c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 3/12/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 3/20/2007; Parameter Tube label = F5C_F10C_F5c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F5C_F10C_F5c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Tissue type = Fiber 5 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: whole fruit, 38 DAFB

description: no additional information

source_name: Washington navel orange whole fruit, 38 DAFB

label_protocol: RNA was amplified and labeled with MessageAmp II aRNA kits (Ambion, Austin, TX), following instructions for single-round amplification and biotinylation with 11-CTP and 16-UTP biotin. 3 micrograms total RNA was used for each sample, calculated by UV spectrometry.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen; Carlsbad, CA), followed by RNA purification using an RNA/DNA cleanup kit (Qiagen; Valencia, CA). RNA concentration and purity were assessed by UV spectrophotometry. The RNA was stored at -80˚C in water.

tag: synonym

tag: Tissues dissected from five fruit and pooled; frozen, ground in liquid nitrogen.


title: peel, 38 DAFB

description: no additional information

source_name: Washington navel orange peel, 38 DAFB


title: F-Genome: slide27

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57999.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 1/28/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F20B_A20B_A20c5; Parameter Date performed = 1/29/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F20B_A20B_A20c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 20 DPA; Parameter Transgenes = none

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 1/28/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 1/29/2007; Parameter Tube label = F20B_A20B_F20c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F20B_A20B_F20c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Tissue type = Fiber 20 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: whole fruit, 24 DAFB

description: no additional information

source_name: Washington navel orange whole fruit, 24 DAFB


title: F-Genome: slide12

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57984.gif

source_name: Fiber at 25 DPA derived from A-genome

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 12/29/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F25A_A25A_A25c5; Parameter Date performed = 1/2/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F25A_A25A_A25c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 25 DPA; Parameter Transgenes = none

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 12/29/2006; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 12/22/2006; Parameter Tube label = F25A_A25A_F25c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F25A_A25A_F25c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Fiber at 25 DPA derived from F-genome

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Tissue type = Fiber 25DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: T0016 (parental) vs 43270 (congenic)

status: Public on Mar 04 2008

city: Washington, DC

first: Norman

middle: H

last: Lee

state: DC

address: 2300  I Street, N.W.

department: Pharmacology & Physiology

institute: The George Washington University Medical Center

description: T0016 (parental) vs 43270 (congenic)

hyb_protocol: Printed arrays were pre-hybridized in a prehybridization buffer (5x SSC; 0.1% SDS; 1% BSA) for 45 minutes at 42C. Labeled cDNA samples (one labeled with Cy3 and a second with Cy5) were combined and lyophilized. The lyophilized pellet was resuspended in a hybridization buffer (50% formamide; 5x SSC; 0.1% SDS) and heated to 95C for 5 minutes and immediately snap-cooled. The labeled cDNA was then applied to the pre-hybridzed array under glass coverslip. The array was sealed in a hyb chamber and incubated overnight at 42C. The array was subsequently washed three times in buffers of increasing stringency (Low: 1.0x SSC, 0.2% SDS; Medium: 0.1x SSC, 0.2% SDS; High: 0.1x SSC). The arrays were quickly dried and immediately scanned.

scan_protocol: The hybridized microarray chips were scanned on an Axon GenePix 4000B scanner under the two-color mode for Cy3 and Cy5 fluorophores.

data_processing: The Cy3 and Cy5 images were analyzed through GenePix Pro 4.0 to calculate spot intensities and exported obtaining a .gpr file. The .gpr file was run through TIGR Express Converter to generate a .mev file. The .mev file was through the TIGR MIDAS using a lowess normalization.

organism: Rattus norvegicus

source_name: T0016 (Inbred Dahl salt-sensitive (SS/Jr) rat )

label_protocol: Single-stranded cDNA was generated through reverse transcription of total RNA by Superscript III (Invitrogen) and random primers. Amino-allyl dUTP (in a ratio of 2:3 with dTTP) was incorporated during the reverse transcription. The RNA was then degraded by hydrolysis under alkaline conditions and the amino-allyl cDNA was subsequently purified with PCR Purification columns (Qiagen) substituting a phosphate wash buffer and phosphate elution buffer for the Tris-containing buffers in the kit. The purified sample was lyophilized and resuspended in sodium carbonate buffer and allowed to couple to the Cy3 fluorophore for an hour at room temperature. The reaction was stopped by sodium acetate and then the labeled cDNA was purified to remove uncoupled dye with PCR Purification columns (Qiagen) as per manufacturer's protocol.

extract_protocol: Tissue was processed using Trizol reagent (Invitrogen), and total RNA was extracted using RNeasy columns (Qiagen) according to manufacturer's protocols.

tag: Inbred Dahl salt-sensitive (SS/Jr) adult male rat; tissue

value: kidney

label_protocol: Single-stranded cDNA was generated through reverse transcription of total RNA by Superscript III (Invitrogen) and random primers. Amino-allyl dUTP (in a ratio of 2:3 with dTTP) was incorporated during the reverse transcription. The RNA was then degraded by hydrolysis under alkaline conditions and the amino-allyl cDNA was subsequently purified with PCR Purification columns (Qiagen) substituting a phosphate wash buffer and phosphate elution buffer for the Tris-containing buffers in the kit. The purified sample was lyophilized and resuspended in sodium carbonate buffer and allowed to couple to the Cy5 fluorophore for an hour at room temperature. The reaction was stopped by sodium acetate and then the labeled cDNA was purified to remove uncoupled dye with PCR Purification columns (Qiagen) as per manufacturer's protocol.

tag: Congenic strain S.LEW (5)x6x9 adult male rat; tissue


title: F-Genome: slide28

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58000.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 1/28/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F25B_A25B_A25c5; Parameter Date performed = 1/29/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F25B_A25B_A25c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Fiber at 25 DPA derived from A-genome

source_name: Fiber at 25 DPA derived from F-genome

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 1/28/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 1/29/2007; Parameter Tube label = F25B_A25B_F25c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F25B_A25B_F25c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Tissue type = Fiber 25 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: T0009 (parental) vs 43266 (congenic)

description: T0009 (parental) vs 43266 (congenic)

source_name: T0009 (Inbred Dahl salt-sensitive (SS/Jr) rat )


title: T0010 (parental) vs 43267 (congenic)

description: T0010 (parental) vs 43267 (congenic)

source_name: T0010 (Inbred Dahl salt-sensitive (SS/Jr) rat )


title: F-Genome: slide26

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57998.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 1/28/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F10B_A10B_A10c5; Parameter Date performed = 1/29/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F10B_A10B_A10c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Fiber at 10 DPA derived from A-genome

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 10 DPA; Parameter Transgenes = none

source_name: Fiber at 10 DPA derived from F-genome

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 1/28/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 1/29/2007; Parameter Tube label = F10B_A10B_F10c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F10B_A10B_F10c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Fiber at 10 DPA derived from F-genome

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Tissue type = Fiber 10 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: T0003 (parental) vs 43260 (congenic) oligo

source_name: T0003 (Inbred Dahl salt-sensitive (SS/Jr) rat )