title: female FSHD #4_U133B_S1

description: female FSHD #4_U133B_S1

tag: female,  FSHD #4


title: male 21.5 yr_U133A_S1

status: Public on Mar 08 2008

type: RNA

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

country: USA

institute: University of Rochester

description: male 21.5 yr_U133A_S1

hyb_protocol: Hybridization, washing, and staining with phycoerythrin-streptavidin were done with an Affymetrix hybridization oven and fluidics station as recommended by Affymetrix

scan_protocol: Arrays were scanned with an Affymetrix scanner after signal enhancement with biotinylated anti-streptavidin antibody

data_processing: GCRMA normalization was done using Bioconductor package

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: vastus lateralis muscle, before (S1) antibody enhancement, normal, U133A

label_protocol: Biotinylated cRNA was prepared from 5 ug total RNA using the BioArray kit (Enzo Life Sciences) according to manufacturer's instructions

growth_protocol: not applicable

extract_protocol: RNA was extracted from frozen biopsy specimens in Tri-Reagent according to the manufacturer's recommended protocol

treatment_protocol: not applicable

tag: male, 21.5 yr, normal


title: female FSHD #6_U133B_S1

description: female FSHD #6_U133B_S1

source_name: vastus lateralis muscle, before (S1) antibody enhancement, FSHD, U133B

tag: female,  FSHD #6


title: male 74.5 yr_U133A_S1

description: male 74.5 yr_U133A_S1

tag: male, 74.5 yr, normal


title: male 73.5 yr_U133A_S1

description: male 73.5 yr_U133A_S1

tag: male, 73.5 yr, normal


title: female FSHD #1_U133B_S1

description: female FSHD #1_U133B_S1

tag: female,  FSHD #1


title: female FSHD #7_U133B_S1

description: female FSHD #7_U133B_S1

tag: female,  FSHD #7


title: male FSHD #9_U133B_S1

description: male FSHD #9_U133B_S1

tag: male,  FSHD #9


title: female FSHD #5_U133B_S1

description: female FSHD #5_U133B_S1

tag: female,  FSHD #5


title: male 69.2 yr_U133A_S1

description: male 69.2 yr_U133A_S1

tag: male, 69.2 yr, normal


title: male FSHD #10_U133B_S1

description: male FSHD #10_U133B_S1

tag: male,  FSHD #10


title: male 69.6 yr_U133A_S1

description: male 69.6 yr_U133A_S1

tag: male, 69.6 yr, normal


title: male 24.2 yr_U133A_S1

description: male 24.2 yr_U133A_S1

tag: male, 24.2 yr, normal


title: male FSHD #7_U133B_S1

description: male FSHD #7_U133B_S1

tag: male,  FSHD #7


title: male 23.4 yr_U133A_S1

description: male 23.4 yr_U133A_S1

tag: male, 23.4 yr, normal


title: female FSHD #2_U133B_S1

description: female FSHD #2_U133B_S1

tag: female,  FSHD #2


title: male 26.2 yr_U133A_S1

description: male 26.2 yr_U133A_S1

tag: male, 26.2 yr, normal


title: male FSHD #4_U133B_S1

description: male FSHD #4_U133B_S1

tag: male,  FSHD #4


title: male 25.1 yr_U133A_S1

description: male 25.1 yr_U133A_S1

tag: male, 25.1 yr, normal


title: male FSHD #8_U133B_S1

description: male FSHD #8_U133B_S1

tag: male,  FSHD #8


title: male 27.1 yr_U133A_S1

description: male 27.1 yr_U133A_S1

tag: male, 27.1 yr, normal


title: male 25.2 yr_U133A_S1

description: male 25.2 yr_U133A_S1

tag: male, 25.2 yr, normal


title: male FSHD #5_U133B_S1

description: male FSHD #5_U133B_S1

tag: male,  FSHD #5


title: male FSHD #3_U133B_S1

description: male FSHD #3_U133B_S1

tag: male,  FSHD #3


title: male FSHD #6_U133B_S1

description: male FSHD #6_U133B_S1

tag: male,  FSHD #6


title: female 65.9 yr_U133B_S1

description: female 65.9 yr_U133B_S1

source_name: vastus lateralis muscle, before (S1) antibody enhancement, normal, U133B

tag: female, normal,  65.9 yr


title: Exp A, Animal #249, 500mg/kg D-Serine

city: WPAFB

first: Molly

last: Davidson

state: OH

address: 2729 R Street, Bldg 837

institute: AFRL/RHPB

description: Gene expression data from male F344 rats treated with a single dose of 500mg/kg D-Serine for 96 hours

hyb_protocol: Hybridization was performed at 45°C for 16 h in an Affymetrix hybridization oven with constant end over end rotation at 60 RPM.

scan_protocol: GeneChips were scanned in the Affymetrix GeneChip Scanner 3000 using the Affymetrix GeneChip Operating Software (GCOS, version 1.2).

data_processing: Data obtained from the Affymetrix GeneChip Scanner 3000 was processed using the statistical algorithm of the Affymetrix GCOS.  The gene expression signal was scaled using "All Probe Sets Scaling" with a target intensity of 500.

organism: Rattus norvegicus

source_name: Brain tissue from Fisher 344 male rat, Animal #249, 500mg/kg D-Serine

label_protocol: Microarrays were stained in the Affymetrix GeneChip Fluidics Station 450 using the EukGE_Ws2v5 protocol.

extract_protocol: Total RNA was isolated from brain tissue using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA).  Frozen tissues were homogenized in lysis buffer containing guanidinium thiocyanate and -mercaptoethanol.  Extraction and purification of total RNA from tissue

treatment_protocol: Male Fisher 344 rats aged 11-12 weeks were treated with various doses (0, 5, 20, 50, 200 & 500 mg/kg) of d-serine and terminally sacrificed 96 hours post-exposure.  An approximate 30mg-section of the forebrain was processed for total RNA isolation.

tag: Sex

value: male

tag: Age

value: adult (11-12 weeks)


title: female 67.9 yr_U133B_S1

description: female 67.9 yr_U133B_S1

tag: female, normal,  67.9 yr


title: Exp A, Animal #247, 500mg/kg D-Serine

source_name: Brain tissue from Fisher 344 male rat, Animal #247, 500mg/kg D-Serine


title: Exp A, Animal #256, 200mg/kg D-Serine

description: Gene expression data from male F344 rats treated with a single dose of 200mg/kg D-Serine for 96 hours

source_name: Brain tissue from Fisher 344 male rat, Animal #256, 200mg/kg D-Serine


title: Exp A, Animal #248, 500mg/kg D-Serine

source_name: Brain tissue from Fisher 344 male rat, Animal #248, 500mg/kg D-Serine


title: Exp A, Animal #255, 200mg/kg D-Serine

source_name: Brain tissue from Fisher 344 male rat, Animal #255, 200mg/kg D-Serine


title: male FSHD #2_U133B_S1

description: male FSHD #2_U133B_S1

tag: male,  FSHD #2


title: female 67.3 yr_U133B_S1

description: female 67.3 yr_U133B_S1

tag: female, normal,  67.3 yr


title: female 66.6 yr_U133B_S1

description: female 66.6 yr_U133B_S1

tag: female, normal,  66.6 yr


title: male FSHD #1_U133B_S1

description: male FSHD #1_U133B_S1

tag: male,  FSHD #1


title: female 68.4 yr_U133B_S1

description: female 68.4 yr_U133B_S1

tag: female, normal,  68.4 yr


title: Exp A, Animal #259, 50mg/kg D-Serine

description: Gene expression data from male F344 rats treated with a single dose of 50mg/kg D-Serine for 96 hours

source_name: Brain tissue from Fisher 344 male rat, Animal #259, 50mg/kg D-Serine


title: Exp A, Animal #254, 200mg/kg D-Serine

source_name: Brain tissue from Fisher 344 male rat, Animal #254, 200mg/kg D-Serine


title: Exp A, Animal #258, 50mg/kg D-Serine

source_name: Brain tissue from Fisher 344 male rat, Animal #258, 50mg/kg D-Serine


title: female 71.4 yr_U133B_S1

description: female 71.4 yr_U133B_S1

tag: female, normal,  71.4 yr


title: Exp A, Animal #251, 500mg/kg D-Serine

source_name: Brain tissue from Fisher 344 male rat, Animal #251, 500mg/kg D-Serine


title: Exp A, Animal #253, 200mg/kg D-Serine

source_name: Brain tissue from Fisher 344 male rat, Animal #253, 200mg/kg D-Serine


title: Exp A, Animal #261, 50mg/kg D-Serine

source_name: Brain tissue from Fisher 344 male rat, Animal #261, 50mg/kg D-Serine


title: female 29.8 yr_U133B_S1

description: female 29.8 yr_U133B_S1

tag: female, normal,  29.8 yr


title: female 70.7 yr_U133B_S1

description: female 70.7 yr_U133B_S1

tag: female, normal,  70.7 yr


title: female 20.1 yr_U133B_S1

description: female 20.1 yr_U133B_S1

tag: female, normal,  20.1 yr


title: female 22.5 yr_U133B_S1

description: female 22.5 yr_U133B_S1

tag: female, normal,  22.5 yr


title: female 65.1 yr_U133B_S1

description: female 65.1 yr_U133B_S1

tag: female, normal,  65.1 yr


title: Exp A, Animal #257, 50mg/kg D-Serine

source_name: Brain tissue from Fisher 344 male rat, Animal #257, 50mg/kg D-Serine


title: female 24.4 yr_U133B_S1

description: female 24.4 yr_U133B_S1

tag: female, normal,  24.4 yr


title: female 26.5 yr_U133B_S1

description: female 26.5 yr_U133B_S1

tag: female, normal,  26.5 yr


title: Exp A, Animal #263, 20mg/kg D-Serine

description: Gene expression data from male F344 rats treated with a single dose of 20mg/kg D-Serine for 96 hours

source_name: Brain tissue from Fisher 344 male rat, Animal #263, 20mg/kg D-Serine


title: Exp A, Animal #271, 5mg/kg D-Serine

description: Gene expression data from male F344 rats treated with a single dose of 5mg/kg D-Serine for 96 hours

source_name: Brain tissue from Fisher 344 male rat, Animal #271, 5mg/kg D-Serine


title: male 75.1 yr_U133B_S1

description: male 75.1 yr_U133B_S1

tag: male, normal,  75.1 yr


title: female 21.5 yr_U133B_S1

description: female 21.5 yr_U133B_S1

tag: female, normal,  21.5 yr


title: Exp A, Animal #269, 5mg/kg D-Serine

source_name: Brain tissue from Fisher 344 male rat, Animal #269, 5mg/kg D-Serine

tag: Sex

tag: Age


title: Exp A, Animal #265, 20mg/kg D-Serine

source_name: Brain tissue from Fisher 344 male rat, Animal #265, 20mg/kg D-Serine


title: Exp A, Animal #266, 20mg/kg D-Serine

source_name: Brain tissue from Fisher 344 male rat, Animal #266, 20mg/kg D-Serine


title: male 71.2 yr_U133B_S1

description: male 71.2 yr_U133B_S1

source_name: vastus lateralis muscle, before (S1) antibody enhancement, normal, U133B

tag: male, normal,  71.2 yr


title: Exp A, Animal #245, control (0mg/kg) D-Serine

description: Gene expression data from male F344 rats treated with a single dose of vehicle, i.e. control, 0mg/kg, for 96 hours

source_name: Brain tissue from Fisher 344 male rat, Animal #245, control (0mg/kg) D-Serine


title: male 74.5 yr_U133B_S1

description: male 74.5 yr_U133B_S1

tag: male, normal,  74.5 yr


title: male 73.5 yr_U133B_S1

description: male 73.5 yr_U133B_S1

tag: male, normal,  73.5 yr


title: Exp A, Animal #270, 5mg/kg D-Serine

source_name: Brain tissue from Fisher 344 male rat, Animal #270, 5mg/kg D-Serine


title: male 69.6 yr_U133B_S1

description: male 69.6 yr_U133B_S1

tag: male, normal,  69.6 yr


title: Exp A, Animal #244, control (0mg/kg) D-Serine

source_name: Brain tissue from Fisher 344 male rat, Animal #244, control (0mg/kg) D-Serine


title: Exp A, Animal #262, 20mg/kg D-Serine

source_name: Brain tissue from Fisher 344 male rat, Animal #262, 20mg/kg D-Serine


title: male 68.4 yr_U133B_S1

description: male 68.4 yr_U133B_S1

tag: male, normal,  68.4 yr


title: female 23.5 yr_U133B_S1

description: female 23.5 yr_U133B_S1

tag: female, normal,  23.5 yr


title: male 67.2 yr_U133B_S1

description: male 67.2 yr_U133B_S1

tag: male, normal,  67.2 yr


title: male 69.2 yr_U133B_S1

description: male 69.2 yr_U133B_S1

tag: male, normal,  69.2 yr


title: male 21.5 yr_U133B_S1

description: male 21.5 yr_U133B_S1

tag: male, normal,  21.5 yr


title: Exp A, Animal #267, 5mg/kg D-Serine

source_name: Brain tissue from Fisher 344 male rat, Animal #267, 5mg/kg D-Serine


title: male 25.2 yr_U133B_S1

description: male 25.2 yr_U133B_S1

tag: male, normal,  25.2 yr


title: WT_t_H_4

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description: 1814655087_A: array designation within the raw data file linked to the Series record

hyb_protocol: According to Illumina Protocol

scan_protocol: Illumina BeadScan

data_processing:
Raw data was analyzed using Bioconductor packages
(www.bioconductor.org). Data was normalized using quantile
normalization. Analysis of differential expression was performed using a
linear model fitting (LIMMA package, Smyth 2005).

label: Biotin

organism: Mus musculus

source_name: WT mouse, treated with compound 106

label_protocol: According to Illumina Protocol

extract_protocol: RNeasy Fibrous Tissue Mini Kit (Qiagen)

tag: Heart from WT mouse, treated with compound 106, replicate #4


title: WT_t_H_3

description: 1842779045_H: array designation within the raw data file linked to the Series record

tag: Heart from WT mouse, treated with compound 106, replicate #3


title: Exp A, Animal #246, control (0mg/kg) D-Serine

source_name: Brain tissue from Fisher 344 male rat, Animal #246, control (0mg/kg) D-Serine


title: male 23.4 yr_U133B_S1

description: male 23.4 yr_U133B_S1

tag: male, normal,  23.4 yr


title: WT_t_CB_1

description: 1729240211_G: array designation within the raw data file linked to the Series record

extract_protocol: RNeasy Lipid Tissue Mini Kit (Qiagen)

tag: Cerebellum from WT mouse, treated with compound 106, replicate #1


title: male 24.2 yr_U133B_S1

description: male 24.2 yr_U133B_S1

tag: male, normal,  24.2 yr


title: male 25.1 yr_U133B_S1

description: male 25.1 yr_U133B_S1

tag: male, normal,  25.1 yr


title: WT_t_H_2

description: 1745080040_C: array designation within the raw data file linked to the Series record

tag: Heart from WT mouse, treated with compound 106, replicate #2


title: WT_t_CB_4

description: 1729240087_D: array designation within the raw data file linked to the Series record

tag: Cerebellum from WT mouse, treated with compound 106, replicate #4


title: female FSHD #9_U133B_S2

description: female FSHD #9_U133B_S2

source_name: vastus lateralis muscle, after (S2) antibody enhancement, FSHD, U133B

tag: female,  FSHD #9


title: male 26.2 yr_U133B_S1

description: male 26.2 yr_U133B_S1

tag: male, normal,  26.2 yr


title: female FSHD #8_U133B_S2

description: female FSHD #8_U133B_S2

tag: female,  FSHD #8


title: female FSHD #6_U133B_S2

description: female FSHD #6_U133B_S2

tag: female,  FSHD #6


title: female FSHD #7_U133B_S2

description: female FSHD #7_U133B_S2

tag: female,  FSHD #7


title: WT_t_H_1

description: 1745080023_F: array designation within the raw data file linked to the Series record

tag: Heart from WT mouse, treated with compound 106, replicate #1


title: male 27.1 yr_U133B_S1

description: male 27.1 yr_U133B_S1

tag: male, normal,  27.1 yr


title: WT_t_B_4

description: 1729240124_D: array designation within the raw data file linked to the Series record

tag: Brain from WT mouse, treated with compound 106, replicate #4


title: WT_t_CB_3

description: 1729240211_B: array designation within the raw data file linked to the Series record

tag: Cerebellum from WT mouse, treated with compound 106, replicate #3


title: WT_t_CB_2

description: 1729240087_H: array designation within the raw data file linked to the Series record

tag: Cerebellum from WT mouse, treated with compound 106, replicate #2


title: WT_t_B_2

description: 1729240124_H: array designation within the raw data file linked to the Series record

tag: Brain from WT mouse, treated with compound 106, replicate #2


title: WT_t_B_3

description: 1729240087_A: array designation within the raw data file linked to the Series record

tag: Brain from WT mouse, treated with compound 106, replicate #3


title: female FSHD #5_U133B_S2

description: female FSHD #5_U133B_S2

tag: female,  FSHD #5


title: WT_c_H_3

description: 1814655035_H: array designation within the raw data file linked to the Series record

source_name: WT mouse, control-treated

tag: Heart from WT mouse, control-treated, replicate #3


title: Exp A, Animal #243, control (0mg/kg) D-Serine

source_name: Brain tissue from Fisher 344 male rat, Animal #243, control (0mg/kg) D-Serine

tag: Sex

tag: Age


title: female FSHD #3_U133B_S2

description: female FSHD #3_U133B_S2

tag: female,  FSHD #3


title: female FSHD #4_U133B_S2

description: female FSHD #4_U133B_S2

tag: female,  FSHD #4


title: WT_c_H_2

description: 1814655036_E: array designation within the raw data file linked to the Series record

tag: Heart from WT mouse, control-treated, replicate #2


title: WT_t_B_1

description: 1729240124_F: array designation within the raw data file linked to the Series record

tag: Brain from WT mouse, treated with compound 106, replicate #1


title: male FSHD #10_U133B_S2

description: male FSHD #10_U133B_S2

tag: male,  FSHD #10


title: female FSHD #2_U133B_S2

description: female FSHD #2_U133B_S2

tag: female,  FSHD #2


title: WT_c_H_4

description: 1745080023_H: array designation within the raw data file linked to the Series record

tag: Heart from WT mouse, control-treated, replicate #4


title: WT_c_H_1

description: 1814655036_B: array designation within the raw data file linked to the Series record

tag: Heart from WT mouse, control-treated, replicate #1


title: female FSHD #1_U133B_S2

description: female FSHD #1_U133B_S2

tag: female,  FSHD #1


title: WT_c_CB_3

description: 1729240087_F: array designation within the raw data file linked to the Series record

tag: Cerebellum from WT mouse, control-treated, replicate #3


title: male FSHD #9_U133B_S2

description: male FSHD #9_U133B_S2

tag: male,  FSHD #9


title: male FSHD #8_U133B_S2

description: male FSHD #8_U133B_S2

tag: male,  FSHD #8


title: male FSHD #5_U133B_S2

description: male FSHD #5_U133B_S2

tag: male,  FSHD #5


title: WT_c_CB_1

description: 1729240211_F: array designation within the raw data file linked to the Series record

tag: Cerebellum from WT mouse, control-treated, replicate #1


title: WT_c_CB_2

description: 1729240087_G: array designation within the raw data file linked to the Series record

tag: Cerebellum from WT mouse, control-treated, replicate #2


title: male FSHD #6_U133B_S2

description: male FSHD #6_U133B_S2

tag: male,  FSHD #6


title: male FSHD #4_U133B_S2

description: male FSHD #4_U133B_S2

tag: male,  FSHD #4


title: male FSHD #7_U133B_S2

description: male FSHD #7_U133B_S2

tag: male,  FSHD #7


title: WT_c_B_3

description: 1814655011_E: array designation within the raw data file linked to the Series record

tag: Brain from WT mouse, control-treated, replicate #3


title: WT_c_B_1

description: 1814655011_B: array designation within the raw data file linked to the Series record

tag: Brain from WT mouse, control-treated, replicate #1


title: WT_c_B_4

description: 1729240124_C: array designation within the raw data file linked to the Series record

tag: Brain from WT mouse, control-treated, replicate #4


title: male FSHD #3_U133B_S2

description: male FSHD #3_U133B_S2

tag: male,  FSHD #3


title: male FSHD #2_U133B_S2

description: male FSHD #2_U133B_S2

tag: male,  FSHD #2


title: female 67.9 yr_U133B_S2

description: female 67.9 yr_U133B_S2

source_name: vastus lateralis muscle, after (S2) antibody enhancement, normal, U133B

tag: female, normal,  67.9 yr


title: KIKI_t_H_4

description: 1814655035_F: array designation within the raw data file linked to the Series record

source_name: KIKI mouse, treated with compound 106

tag: Heart from KIKI mouse, treated with compound 106, replicate #4


title: WT_c_B_2

description: 1814655011_C: array designation within the raw data file linked to the Series record

tag: Brain from WT mouse, control-treated, replicate #2


title: KIKI_t_H_3

description: 1745080023_D: array designation within the raw data file linked to the Series record

tag: Heart from KIKI mouse, treated with compound 106, replicate #3


title: KIKI_t_CB_4

description: 1729240124_A: array designation within the raw data file linked to the Series record

tag: Cerebellum from KIKI mouse, treated with compound 106, replicate #4


title: female 65.9 yr_U133B_S2

description: female 65.9 yr_U133B_S2

tag: female, normal,  65.9 yr


title: male FSHD #1_U133B_S2

description: male FSHD #1_U133B_S2

tag: male,  FSHD #1


title: KIKI_t_H_1

description: 1814655035_G: array designation within the raw data file linked to the Series record

tag: Heart from KIKI mouse, treated with compound 106, replicate #1


title: female 68.4 yr_U133B_S2

description: female 68.4 yr_U133B_S2

tag: female, normal,  68.4 yr


title: KIKI_t_CB_3

description: 1729240087_E: array designation within the raw data file linked to the Series record

tag: Cerebellum from KIKI mouse, treated with compound 106, replicate #3


title: female 67.3 yr_U133B_S2

description: female 67.3 yr_U133B_S2

tag: female, normal,  67.3 yr


title: KIKI_t_H_2

description: 1814655036_G: array designation within the raw data file linked to the Series record

tag: Heart from KIKI mouse, treated with compound 106, replicate #2


title: KIKI_t_CB_2

description: 1814655011_H: array designation within the raw data file linked to the Series record

tag: Cerebellum from KIKI mouse, treated with compound 106, replicate #2


title: KIKI_t_B_2

description: 1729240087_C: array designation within the raw data file linked to the Series record

tag: Brain from KIKI mouse, treated with compound 106, replicate #2


title: KIKI_t_B_4

description: 1729240211_A: array designation within the raw data file linked to the Series record

tag: Brain from KIKI mouse, treated with compound 106, replicate #4


title: female 20.1 yr_U133B_S2

description: female 20.1 yr_U133B_S2

tag: female, normal,  20.1 yr


title: female 65.1 yr_U133B_S2

description: female 65.1 yr_U133B_S2

tag: female, normal,  65.1 yr


title: KIKI_t_B_3

description: 1729240124_B: array designation within the raw data file linked to the Series record

tag: Brain from KIKI mouse, treated with compound 106, replicate #3


title: female 21.5 yr_U133B_S2

description: female 21.5 yr_U133B_S2

tag: female, normal,  21.5 yr


title: female 66.6 yr_U133B_S2

description: female 66.6 yr_U133B_S2

tag: female, normal,  66.6 yr


title: KIKI_t_CB_1

description: 1814655011_F: array designation within the raw data file linked to the Series record

tag: Cerebellum from KIKI mouse, treated with compound 106, replicate #1


title: female 24.4 yr_U133B_S2

description: female 24.4 yr_U133B_S2

tag: female, normal,  24.4 yr


title: KIKI_c_H_3

description: 1814655087_G: array designation within the raw data file linked to the Series record

source_name: KIKI mouse, control-treated

tag: Heart from KIKI mouse, control-treated, replicate #3


title: KIKI_c_CB_3

description: 1729240211_D: array designation within the raw data file linked to the Series record

tag: Cerebellum from KIKI mouse, control-treated, replicate #3


title: KIKI_t_B_1

description: 1814655011_A: array designation within the raw data file linked to the Series record

tag: Brain from KIKI mouse, treated with compound 106, replicate #1


title: female 71.4 yr_U133B_S2

description: female 71.4 yr_U133B_S2

tag: female, normal,  71.4 yr


title: KIKI_c_H_4

description: 1814655087_E: array designation within the raw data file linked to the Series record

tag: Heart from KIKI mouse, control-treated, replicate #4


title: female 70.7 yr_U133B_S2

description: female 70.7 yr_U133B_S2

tag: female, normal,  70.7 yr


title: female 29.8 yr_U133B_S2

description: female 29.8 yr_U133B_S2

tag: female, normal,  29.8 yr


title: female 22.5 yr_U133B_S2

description: female 22.5 yr_U133B_S2

tag: female, normal,  22.5 yr


title: male 75.1 yr_U133B_S2

description: male 75.1 yr_U133B_S2

tag: male, normal,  75.1 yr


title: female 23.5 yr_U133B_S2

description: female 23.5 yr_U133B_S2

tag: female, normal,  23.5 yr


title: male 71.2 yr_U133B_S2

description: male 71.2 yr_U133B_S2

tag: male, normal,  71.2 yr


title: KIKI_c_H_1

description: 1745080023_G: array designation within the raw data file linked to the Series record

tag: Heart from KIKI mouse, control-treated, replicate #1


title: KIKI_c_CB_4

description: 1814655011_D: array designation within the raw data file linked to the Series record

tag: Cerebellum from KIKI mouse, control-treated, replicate #4


title: KIKI_c_B_4

description: 1729240211_E: array designation within the raw data file linked to the Series record

tag: Brain from KIKI mouse, control-treated, replicate #4


title: WT_c_CB_4

description: 1729240211_C: array designation within the raw data file linked to the Series record

tag: Cerebellum from WT mouse, control-treated, replicate #4


title: T cell TGFB rep3

type: other

city: Stanford

first: Michael

middle: George

last: Kattah

address: 269 Campus Dr., CCSR 2250

department: Medicine

institute: Stanford University

description: Biological replicate 3 of 3 (dye-swap)

hyb_protocol: Tags were hybridized in hybridization buffer [20μg salmon sperm DNA (Invitrogen), 25μg yeast tRNA (Invitrogen), 4X SSC, 0.1% SDS] on spotted Codelink slides in in a microarray hybridization chamber (Corning) in a 47.5 C circulating water bath (GE Healthcare) for 16-20 h.  After hybridization, slides were washed three times for 5 min in 1x TNT wash buffer [(100 mM Tris-HCl pH 8.0, 150 mM sodium chloride, 0.05% Tween-20 (Sigma Aldrich), 2 mM EDTA], washed once for 5 min in 0.5x TNT wash buffer, rinsed for <1 s in ddH2O and centrifuged to dryness at 600 x g for  5 min.

scan_protocol: Scanned on an GenePix 4000B scanner. Images were quantified using GenePix Pro 5.0.1.24

data_processing: We averaged the median of 635nm/532nm ratios from replicate features.  The fold-change for each tag was calculated by taking the log2 of the ratios.  We applied a low-intensity cut-off filter during analysis as follows:  spots with over 3% of the pixels exhibiting fluorescent intensities less than two standard deviations above background in both 635nm and 532nm channels were set to a fold-change of zero.  The arrays were median-centered by subtracting the median log value, and analyzed by one class "significance analysis of microarrays" to identify markers with statistically-significant differences.  Because the HIT reaction is 48-plex, each 48-plex data set was analyzed separately.  Tags that had a fold-change of zero in all of the samples were deleted prior to SAM analysis.  For the dye-swap column (D3 TGF-β / D3), the parity of each fold-change was reversed.

molecule: other

source_name: Activated T cells Donor 3 with TGF-β

label_protocol: RNA tags were amplified in amplification mix [250 U T7 RNA Polymerase-Plus (Ambion), 1x transcription buffer (Ambion),  0.5 mM ATP, 0.5 mM CTP, 0.5 mM GTP, 0.33 mM UTP, and 0.17 mM Cy3-UTP  or 0.17 mM Cy5-UTP (PerkinElmer)] for 4-6 hours at 37 C

growth_protocol: Cells were cultured in complete X-VIVO 15 media (Lonza) [X-VIVO 15 supplemented with 10% heat-inactivated FCS (Omega Scientific), 100 units/ml penicillin/streptomycin (Invitrogen), 14.3 μM β-mercaptoethanol (Sigma-Aldrich), and L-glutamine (Invitrogen)].  For FOXP3-induction by TGF-β, cells were cultured with 5 ng/ml of TGF-β (R&D Systems) at a density of 2 x 10^6 cells/ml with 1 x 10^6 anti-CD3/anti-CD28/anti-CD2 coated beads/well (Miltenyi Biotec) in 24-well plates (Falcon).  Cells were first transferred to a 12-well plate (Falcon) at 72 h, and then to small culture flasks at 96 h, and finally analyzed at 120 h.  Prior to surface marker analysis, beads were removed using a Dynal MPC-S magnet (Invitrogen).

extract_protocol: After staining with DNA-antibody conjugates, RNA was amplified and labeled as described below, and then the amplified labeled RNA tags were purified using mirVana (Ambion)

treatment_protocol: activated in the presence of TGF-β

tag: Normal human donor purified primary naïve CD4+ helper T cells

source_name: Activated T cells Donor 3 without TGF-β

treatment_protocol: activated in the absence of TGF-β


title: T cell TGFB rep2

description: Biological replicate 2 of 3

source_name: Activated T cells Donor 2 without TGF-β

source_name: Activated T cells Donor 2 with TGF-β


title: male 73.5 yr_U133B_S2

description: male 73.5 yr_U133B_S2

tag: male, normal,  73.5 yr


title: male 67.2 yr_U133B_S2

description: male 67.2 yr_U133B_S2

tag: male, normal,  67.2 yr


title: male 74.5 yr_U133B_S2

description: male 74.5 yr_U133B_S2

tag: male, normal,  74.5 yr


title: female 26.5 yr_U133B_S2

description: female 26.5 yr_U133B_S2

tag: female, normal,  26.5 yr


title: KIKI_c_CB_2

description: 1729240124_G: array designation within the raw data file linked to the Series record

tag: Cerebellum from KIKI mouse, control-treated, replicate #2


title: KIKI_c_H_2

description: 1814655036_H: array designation within the raw data file linked to the Series record

tag: Heart from KIKI mouse, control-treated, replicate #2


title: male 68.4 yr_U133B_S2

description: male 68.4 yr_U133B_S2

tag: male, normal,  68.4 yr


title: KIKI_c_B_3

description: 1729240087_B: array designation within the raw data file linked to the Series record

tag: Brain from KIKI mouse, control-treated, replicate #3


title: KIKI_c_B_2

description: 1729240124_E: array designation within the raw data file linked to the Series record

tag: Brain from KIKI mouse, control-treated, replicate #2


title: KIKI_c_CB_1

description: 1729240211_H: array designation within the raw data file linked to the Series record

tag: Cerebellum from KIKI mouse, control-treated, replicate #1


title: KIKI_c_B_1

description: 1814655011_G: array designation within the raw data file linked to the Series record

tag: Brain from KIKI mouse, control-treated, replicate #1


title: T cell vs. T cell, freeze thaw T_T_FT

description: Jurkat T cells versus Jurkat T cells with a frozen HIT cocktail

data_processing: We averaged the median of 635nm/532nm ratios from replicate features.  The fold-change for each tag was calculated by taking the log2 of the ratios.  We applied a low-intensity cut-off filter during analysis as follows:  spots with over 30% of the pixels exhibiting fluorescent intensities less than two standard deviations above background in both 635nm and 532nm channels were set to a fold-change of zero.  The arrays were median-centered by subtracting the median log value.

source_name: Jurkat T cell line

growth_protocol: We cultured Jurkat T cells (clone E6-1) and OCI B cells2 in complete RPMI-1640 [RPMI-1640 supplemented with 10% heat-inactivated FCS (Omega Scientific), 2  mM L-glutamine, 25 mM HEPES, 1 mM sodium pyruvate, and 100 U/ml of penicillin streptomycin].

tag: Jurkat T cell line


title: B cell vs. B cell, freeze thaw B_B_FT

description: OCI B cells versus OCI B cells with a frozen HIT cocktail

source_name: OCI B cell line

tag: OCI B cell line


title: T cell TGFB rep1

description: Biological replicate 1 of 3

source_name: Activated T cells Donor 1 without TGF-β

source_name: Activated T cells Donor 1 with TGF-β


title: male 69.6 yr_U133B_S2

description: male 69.6 yr_U133B_S2

tag: male, normal,  69.6 yr


title: male 69.2 yr_U133B_S2

description: male 69.2 yr_U133B_S2

tag: male, normal,  69.2 yr


title: male 21.5 yr_U133B_S2

description: male 21.5 yr_U133B_S2

tag: male, normal,  21.5 yr


title: male 23.4 yr_U133B_S2

description: male 23.4 yr_U133B_S2

tag: male, normal,  23.4 yr


title: T cell vs. B cell, freeze-thaw T_B_FT

description: Jurkat T cells versus OCI B cells with a frozen HIT cocktail


title: B cell vs. T cell, freeze-thaw B_T_FT

description: OCI B cells versus Jurkat T cells with a frozen HIT cocktail


title: B cell vs. T cell B_T

description: OCI B cells versus Jurkat T cells with a freshly-prepared HIT cocktail


title: B cell vs. B cell B_B

description: OCI B cells versus OCI B cells with a freshly-prepared HIT cocktail


title: T cell vs. B cell T_B

description: Jurkat T cells versus OCI B cells with a freshly-prepared HIT cocktail


title: male 25.1 yr_U133B_S2

description: male 25.1 yr_U133B_S2

tag: male, normal,  25.1 yr


title: male 26.2 yr_U133B_S2

description: male 26.2 yr_U133B_S2

tag: male, normal,  26.2 yr


title: GAT201 overexpression_37degress_YNB_rep2

status: Public on Mar 07 2008

city: San Francisco

first: Oliver

middle: W.

last: Liu

department: Biochemistry and Biophysics

institute: UCSF

description: Platform GPL4522, biological replicate 2 of 4

hyb_protocol: Microarrays were post-proccessed and hybridized as previously described (Derisi JL, Iyer VR, Brown PO, 1997)

scan_protocol: Arrays were scanned on an Axon 4000B Scanner using SpotReader software

data_processing: Data was bulk-normalized using NOMAD software (available from http://ucsf-nomad.sourceforge.net). Ratios were converted into log scale (base 2).

organism: Cryptococcus neoformans

label_protocol: cDNA reverse transcribed from total RNA with aminoallyl-dUTP was coupled to Cy3-dye or Cy5-dye per manufacturer (Amersham Biosciences) instructions.

growth_protocol: Cultures were inoculated from a single colony and grown overnight in YNB at 37 degrees.  Cultures were diluted back to an OD600 of 0.1 using YNB prewarmed to 37 degrees, grown at 37 degrees, and harvested at an OD600 of 1.0

extract_protocol: Culture was collected by centrifugation, lyophilized, then total RNA was extracted using TRIzol Reagent (Invitrogen). Total RNA was treated for 1 hr with DNase I, followed by two chloroform extractions and resuspension in DEPC treated water. ~150 ug of total RNA was reverse-transcribed with oligo dT to prime and using a (1:1) mix of aminallyl-dUTP to dTTP in a dNTP mix.

treatment_protocol: 37 degrees in minimal media (YNB)

tag: Serotype A (H99) background

tag: exponential growth in YNB at 37 degrees

tag: pRPL2b (ribosomal protein promoter) inserted upstream of genomic locus of GAT201


title: GAT201 overexpression_37degress_YNB_rep1

description: Platform GPL4522, biological replicate 1 of 4


title: male 27.1 yr_U133B_S2

description: male 27.1 yr_U133B_S2

tag: male, normal,  27.1 yr


title: male 25.2 yr_U133B_S2

description: male 25.2 yr_U133B_S2

tag: male, normal,  25.2 yr


title: GAT201 overexpression_37degress_YNB_rep3

description: Platform GPL4522, biological replicate 3 of 4


title: T cell vs. T cell T_T

description: Jurkat T cells versus Jurkat T cells with a freshly-prepared HIT cocktail


title: GAT201 overexpression_37degress_YNB_rep4

description: Platform GPL4522, biological replicate 4 of 4


title: male 24.2 yr_U133B_S2

description: male 24.2 yr_U133B_S2

tag: male, normal,  24.2 yr


title: Day 7, Sham, Replicate 2

status: Public on Mar 05 2008

city: San Antonio

first: Xinyu

last: Wang

state: TX

address: 3400 Rawley E. Chambers Ave., Bldg. 3611

institute: US Army Institute of Surgical Research

description: Intensity data plus the flags are highlighted in yellow in each raw data (.gpr) file.

hyb_protocol: 750 ng of labeled, amplified cRNA was fragmented with according to Agilent's procotol at 60 degrees for 30 and 2X hybridization buffered added.  Hybridization was accomplished with the Agilent hybridization chamber in a Robbin's Scientific oven for 17 hrs.

scan_protocol: Microarray image segmentation analysis was performed with an Axon 4000B and GenePix 6.0 software and the resulting Cy-3 and Cy-5 intensities recovered from each ligament for further analysis.

data_processing: The Cy 3 and Cy5 pixel intensities minus background were extracted and placed in a single flat file and each microarray sample treated as a single dye labeled specimen. Statistical analyses were performed using BRB ArrayTools developed by Dr. Richard Simon and Amy Peng Lam.

source_name: Medial collateral ligament

label_protocol: Microarray analysis was performed using the Agilent (Santa Clara, CA) low-input labeling system and the Cy-3 or Cy-5 labeled RNA applied to the rat whole genome chip (Agilent).

extract_protocol: Prior to total RNA isolation, all ligaments were lyophilized. The dried ligaments were minced with a scapel blade and placed in 1 ml of TRI™ Reagent.  The process yields 0.5-3 µg per specimen, the injured specimens yielding more RNA. The resulting RNA was quantified on a Nanodrop spectrophotometer and quality assessed by gel electrophoresis.

treatment_protocol: Adult male Sprague-Dawley rats were randomly assigned to two groups: injured and control. Five animals per time point per group were used for gene expression analysis and an additional animal from the sham and injury group at each time point was fixed in formalin and evaluated histologically following paraffin embedding and hematoxylin and eosin stain.. After receiving buprenorphine subcutaneously 15 minutes prior to surgery (0.1 mg/kg), the injured group underwent general anesthesia for the surgery, Anesthesia was induced by placing rats into a Plexiglas chamber flushed with 1-3% Isoflurane and oxygen and they were then maintained at 1-3% Isoflurane with a nose cone on a Bain circuit (with dead space-eliminating rodent anesthesia circuit) hooked to the rodent gas anesthesia machine (VetEquip, Inc., Pleasanton, CA). Respiration was monitored during this 10-20 minute procedure. After the surgery, analgesia (buprenorphine; 0.1 mg/kg SC every 12 hours) was administered for discomfort associated with the surgery for the first 72 hr and as needed. The sham control groups were exposed to the same analgesi/anesthesia regime and a bilateral sham surgery was performed but the ligament was not severed. Animals from each group were sacrificed sequentially on the following schedule: Day 1, 2, 4, 7, 10, and 14. Tissue from the MCLs were harvested under anesthesia and frozen in liquid nitrogen prior to RNA isolation or fixed in 10% formalin and then euthanasia was performed. A group of five rats that were not manipulated any way served as controls for both sham and injured rats.  Eight ligaments were treated with 0.1% collagenase in Delbecco's Modified Eagle's Medium (DMEM: Invitrogen, Carlsbad, CA)) for 3 h, rinsed in complete medium (10% fetal bovine serum; FBS (Hyclone) in DMEM and cultured for two weeks until confluent. Immunostaining for rat proyl hydroxylase confirmed the fibroblast origin of these cells. Rat ligament fibroblasts (RLF) were subcultivated with 0.1% Trypsin/EDTA (Invitrogen) into 6-well multiplates (Corning, Ithaca, NY) until 90% confluent RNA was isolated with TRI™ Reagent as for ligaments.

tag: Sprague-Dawley, male, medial collateral ligament


title: Day 7, Sham, Replicate 1

growth_protocol: Five animals per time point per group were used for gene expression analysis and an additional animal from the sham and injury group at each time point was fixed in formalin and evaluated histologically following paraffin embedding and hematoxylin and eosin stain.. After receiving buprenorphine subcutaneously 15 minutes prior to surgery (0.1 mg/kg), the injured group underwent general anesthesia for the surgery, Anesthesia was induced by placing rats into a Plexiglas chamber flushed with 1-3% Isoflurane and oxygen and they were then maintained at 1-3% Isoflurane with a nose cone on a Bain circuit (with dead space-eliminating rodent anesthesia circuit) hooked to the rodent gas anesthesia machine (VetEquip, Inc., Pleasanton, CA). Respiration was monitored during this 10-20 minute procedure. After the surgery, analgesia (buprenorphine; 0.1 mg/kg SC every 12 hours) was administered for discomfort associated with the surgery for the first 72 hr and as needed. The sham control groups were exposed to the same analgesi/anesthesia regime and a bilateral sham surgery was performed but the ligament was not severed. Animals from each group were sacrificed sequentially on the following schedule: Day 1, 2, 4, 7, 10, and 14. Tissue from the MCLs were harvested under anesthesia and frozen in liquid nitrogen prior to RNA isolation or fixed in 10% formalin and then euthanasia was performed. A group of five rats that were not manipulated any way served as controls for both sham and injured rats.


title: Day 10, Severed, Replicate 2


title: Day 7, Severed, Replicate 3


title: Day 4, Severed, Replicate 5


title: Day 4, Sham, Replicate 5


title: Day 7, Sham, Replicate 3


title: Day 4, Sham, Replicate 4


title: Day 4, Sham, Replicate 1


title: Day 10, Severed, Replicate 1


title: Day 7, Severed, Replicate 2


title: Day 4, Severed, Replicate 3


title: Day 4, Severed, Replicate 4


title: Day 4, Sham, Replicate 3


title: Day 2, Sham, Replicate 4


title: Day 4, Severed, Replicate 2


title: wild type time 0 min vs. wild type time 2 hours upon 100 µM farnesol dye swap

status: Public on Mar 06 2008

city: Ribeirao Preto

first: Gustavo

middle: Henrique

last: Goldman

state: Sao Paulo

address: Avenida do Café, s/n

department: Departament of Pharmaceutical Sciences

country: Brazil

institute: Faculty of Pharmaceutical Sciences of Ribeirao Preto

description: This hybridization used the wild type RNA from time point zero (16 hours grown) as reference. The test RNA was obtained from a 16 hours culture treated for 2 hours with 100 µM farnesol.

hyb_protocol: Labelled cDNAs were mixed with 8 µl Liquid block RPN3601 Batch 24 (GE Health Care), 5.5 µl SDS 2% and 19 µl SSC (20X) and the volume adjusted to 110 µl. Slides were hybridized overnight (42°C) in a Gene-Tac Hybridization Station (Genomic Solutions, Inc.) and washed in 2 X SSC 0,5% SDS, 0,5 X SSC and 0.05X SSC. All washing steps consisted of 1 min of flow, followed by 5 min of incubation.

scan_protocol: Slides were dried by centrifugation and subjected to fluorescent detection with a GMS 418 Array Scanner (Affymetrix Inc., Santa Clara, CA).

data_processing: TIFF images generated were analyzed using TIGR Spotfinder (http://www.tigr.org/software/) to obtain relative transcript levels. Spotfinder uses a dynamic thresholding algorithm to identify spots and calculate local background and integrated fluorescence intensity for each of the Cy3 and Cy5 channels. This software was also useful in eliminating questionable spots (those for which shape deviates significantly from that of a true circle, or those with a low signal-to-noise ratio). Spots with very low intensity in one channel (and thus aberrantly high or low expression ratios) were removed and eliminated from future analyses. Data was normalized using a local regression technique LOWESS (LOcally WEighted Scatterplot Smoothing) for hybridizations with RNA-based samples and SD regularization of the Cy5/Cy3 ratio across all sectors (blocks) of the array using a software tool MIDAS (http://www.tigr.org/softlab). Following normalization, the values for each gene's in-slide replicates were averaged (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects. Differentially expressed genes at the 95% confidence level were determined using intensity-dependent Z-scores (with Z=1.96) as implemented in MIDAS and the union of all genes identified at each time point were considered significant in this experiment. The resulting data were organized and visualized based on similar expression vectors in genes using Euclidean distance and hierarchical clustering with average linkage clustering method to view the whole data set and k-means to group the genes in 60 clusters with TIGR MEV (multi experiment viewer), also available at http://www.tigr.org/software.

organism: Aspergillus nidulans

source_name: wild type conidia grown for 16 hours

label_protocol: The RNA samples were extracted with Trizol and further purified with the RNA easy kit (Qiagen, Germany) and directly labelled by incorporation of Cy5-dUTP (GE Health Care). Briefly, 30 µg of total RNA were mixed with 20 µg of Randon Primer Hexamers (GE Health Care), 100 pmol of oligo dTV (Invitrogen) and 40 U of RNAse Out (Invitrogen) in a volume of 13 µl and heated to 70°C for 5 minutes. The tubes were briefly chilled to 4°C for 5 minutes and mixed with 5 µl of 5X first-strand buffer (Invitrogen), 2 µl DTT (Invitrogen), 2 µl dNTP (5 mM dATP, 5 mM dCTP, 5 mM dGTP, 2 mM dTTP), 2 µl of Suprescript II (Invitrogen) and 1 µl of Cy5-dUTP (25 nmol). The reaction was then incubated at 25°C for 5 minutes and at 42°C for 3 hours. The RNA was degraded by adding 2.5 µl EDTA (0.5 M, pH 8) and 5 µl NaOH (1M) following an incubation at 37°C for 40 minutes. The resulting first strand cDNA was purified and concentrated using a Microcon YM-50 cartridge.

extract_protocol: At each time point the germlings were harvested by centrifugation and quickly frozen in liquid nitrogen. For total RNA isolation, the germlings were disrupted by grinding in liquid nitrogen and total RNA was extracted with Trizol reagent (Invitrogen). Ten micrograms of RNA from each treatment were then fractionated in 2.2 M formaldehyde, 1.2% agarose gel, stained with ethidium bromide, and then visualized with UV-light. The presence of intact 25S and 17S ribosomal RNA bands was used as a criterion to assess the integrity of the RNA.

tag: For the microarray experiments, 1.0 x 1010 conidia/ml of A. nidulans wild type (GR5) were used to inoculate 400 ml of pre-warmed liquid cultures (YG) in 1000-ml erlenmeyer flasks that were incubated in a reciprocal shaker (250 rpm) at 37°C for 12 hours. After this period, the germlings were exposed or not (timepoint 0 min) to 100 µM farnesol for 2 hours at 37°C. Germilings were harvested by centrifugation and total RNA was extracted. Hybridization experiments were competitive using probes derived from wild type strain exposed to farnesol for 2 hours using the timepoint zero (control) as the reference RNA for every hybridizantion. Normalized signal intensities were used to generate relative hybridization ratios (query/reference).

source_name: wild type conidia grown for 16 hours plus 2 hours upon 100 µM farnesol

label_protocol: The RNA samples were extracted with Trizol and further purified with the RNA easy kit (Qiagen, Germany) and directly labelled by incorporation of Cy3-dUTP (GE Health Care). Briefly, 30 µg of total RNA were mixed with 20 µg of Randon Primer Hexamers (GE Health Care), 100 pmol of oligo dTV (Invitrogen) and 40 U of RNAse Out (Invitrogen) in a volume of 13 µl and heated to 70°C for 5 minutes. The tubes were briefly chilled to 4°C for 5 minutes and mixed with 5 µl of 5X first-strand buffer (Invitrogen), 2 µl DTT (Invitrogen), 2 µl dNTP (5 mM dATP, 5 mM dCTP, 5 mM dGTP, 2 mM dTTP), 2 µl of Suprescript II (Invitrogen) and 1 µl of Cy3-dUTP (25 nmol). The reaction was then incubated at 25°C for 5 minutes and at 42°C for 3 hours. The RNA was degraded by adding 2.5 µl EDTA (0.5 M, pH 8) and 5 µl NaOH (1M) following an incubation at 37°C for 40 minutes. The resulting first strand cDNA was purified and concentrated using a Microcon YM-50 cartridge.


title: wild type time 0 min vs. wild type time 2 hours upon 100 µM farnesol


title: Day 4, Sham, Replicate 2


title: Day 2, Sham, Replicate 3


title: Day 4, Severed, Replicate 1


title: Day 2, Sham, Replicate 2


title: Day 2, Sham, Replicate 1


title: Day 2, Severed, Replicate 5


title: Day 2, Severed, Replicate 3


title: Day 2, Sham, Replicate 5


title: Day 1, Sham, Replicate 4


title: Day 2, Severed, Replicate 2


title: Day 1, Sham, Replicate 5


title: Day 1, Severed, Replicate 4


title: Rat Ligament, No Manipulation, Replicate 5


title: Day 2, Severed, Replicate 4


title: Day 1, Sham, Replicate 3


title: Day 1, Severed, Replicate 3


title: Day 1, Severed, Replicate 5


title: Rat Universal Reference RNA, Cy3 labeled, replicate 2

source_name: Rat universal reference RNA

tag: Rat Universal Reference RNA, Stratagene (740200)


title: Rat Universal Reference RNA, Cy3 labeled, replicate 1


title: Day 2, Severed, Replicate 1


title: Rat Universal Reference RNA, Cy5 labeled, replicate 3


title: Rat Ligament, No Manipulation, Replicate 2


title: Day 1, Severed, Replicate 2


title: Day 1, Sham, Replicate 1


title: Day 1, Severed, Replicate 1


title: Day 1, Sham, Replicate 2


title: Rat Universal Reference RNA, Cy3 labeled, replicate 3


title: Rat Ligament, No Manipulation, Replicate 4


title: Rat Ligament, No Manipulation, Replicate 1


title: Rat Ligament,Fibroblasts, Passage 7

source_name: Culture medial collateral ligament


title: Rat Ligament, No Manipulation, Replicate 3


title: Rat Ligament,Fibroblasts, Passage 3


title: Day 7, Severed, Replicate 1


title: Rat Ligament,Fibroblasts, Passage 5


title: Rat Universal Reference RNA, Cy5 labeled, replicate 1


title: Rat Universal Reference RNA, Cy5 labeled, replicate 2


title: Rat Ligament,Fibroblasts, Passage 4


title: Rat Ligament,Fibroblasts, Passage 6


title: Day 14, Sham, Replicate 5


title: Day 14, Severed, Replicate 4


title: Day 14, Sham, Replicate 3


title: Day 14, Severed, Replicate 1


title: Day 14, Severed, Replicate 3


title: Day 14, Sham, Replicate 1


title: Day 14, Sham, Replicate 4


title: Day 10, Sham, Replicate 3


title: Day 10, Sham, Replicate 4


title: Day 10, Sham, Replicate 1


title: Day 10, Sham, Replicate 5


title: Day 10, Severed, Replicate 4


title: Day 14, Severed, Replicate 2


title: Day 14, Sham, Replicate 2


title: Day 10, Severed, Replicate 3


title: Day 10, Severed, Replicate 5


title: Day 10, Sham, Replicate 2


title: Day 14, Severed, Replicate 5


title: 13561409 - MSA vs LCA

city: Evry Cedex

first: Agnes

last: Yu

address: 2 rue Gaston Cremieux CP 5708

department: URGV

country: France

institute: INRA

description: Effect of carnitine on the transcriptome of A. thaliana ?

hyb_protocol: LCA Cy5 / MSA Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: LCA

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: plantlet - medium : MS + L-carnitine 5 mM hygrometry : 40% temperature : 24°C light : 150 umol photons/m2/sec photoperiod 16h

extract_protocol: Pool of extract, LC1:350ng, LC2:350ng, LC3:350ng.

treatment_protocol: no treatment

tag: Arabidopsis thaliana (columbia)  - age:144hourdev.stage (Boyes et al. Plant Cell 2001):boyes = 1.0

source_name: MSA

growth_protocol: plantlet - medium : MS hygrometry : 40% temperature : 24°C light : 150 umol photons/m2/sec photoperiod 16h

extract_protocol: Pool of extract, MS1:350ng, MS2:350ng, MS3:350ng.


title: F-Genome: slide7

city: Athens

first: Alan

middle: R

last: Gingle

state: GA

address: 111 Riverbend Rd.

department: Center for Applied Genetics Technologies

institute: University of Georgia

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57979.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 = 12/29/2006; 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 = 12/29/2006; 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

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

organism: 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 = 12/23/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = A20A_A25A_A25c5; Parameter Date performed = 12/28/2006; 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 = A20A_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: 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 = 12/23/2006; 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 = A20A_A25A_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 = A20A_A25A_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: slide23

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57995.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 = 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 = 1/22/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = A20B_A25B_A20c5; 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 = A20B_A25B_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 = 1/22/2007; 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 = A20B_A25B_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 = A20B_A25B_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: 13561405 - LCA vs MSA

hyb_protocol: MSA Cy5 / LCA Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: F-Genome: slide6

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57978.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 = 12/23/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = A10A_A20A_A20c5; Parameter Date performed = 12/28/2006; 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 = A10A_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

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 = 12/23/2006; 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 = A10A_A20A_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 = A10A_A20A_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: slide22

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57994.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 = 1/22/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = A10_A20_A10c5; 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 = A10_A20_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 = 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 = A10B_A20B_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 = A10B_A20B_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


title: F-Genome: slide21

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57993.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 = 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 = A5B_A10B_A5c5; 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 = A5B_A10B_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 = 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 = A5B_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 = A5B_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


title: F-Genome: slide46

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58018.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

organism: Gossypium longicalyx

source_name: Fiber at 10 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 = 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_F10c5; 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_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

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_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 = F10C_A10C_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

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


title: F-Genome: slide4

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57976.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

source_name: Fiber at 5 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 = F5_F25A_F5c5; 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 = F5_F25A_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

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 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 = 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 = F5_F25A_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 = F5_F25A_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 25 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: F-Genome: slide17

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57989.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 = 1/22/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F5B_F10B_F5c5; 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 = F5B_F10B_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

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 = F5B_F10B_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 = F5B_F10B_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: slide18

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57990.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 = 1/22/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F10B_F20B_F10c5; 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 = F10B_F20B_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 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 = 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 = F510B_F20B_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 = F510B_F20B_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 20 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: F-Genome: slide45

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58017.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 = F5C_A5C_F5c5; 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_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

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_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 = F5C_A5C_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: slide19

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57991.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 = 1/22/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F20B_F25B_F20c5; 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 = F20B_F25B_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 120 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 = 1/22/2007; 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 = F20B_F25B_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 = F20B_F25B_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: slide47

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58019.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 = F20C_A20C_F20c5; 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_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 = 3/20/2007; 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_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 = F20C_A20C_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: slide5

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57977.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 = 12/23/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = A5A_A10A_A10c5; Parameter Date performed = 12/28/2006; 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 = A5A_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: 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

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 = 12/23/2006; 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 = A5A_A10A_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 = A5A_A10A_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


title: 13557359 - LCB vs MSB

hyb_protocol: MSB Cy5 / LCB Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: MSB

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

extract_protocol: Pool of extract, MS4:350ng, MS6:350ng, MS5:350ng.

tag: Arabidopsis thaliana (columbia)  - age:144hourdev.stage (Boyes et al. Plant Cell 2001):boyes = 1.0

source_name: LCB

extract_protocol: Pool of extract, LC4:350ng, LC6:350ng, LC5:350ng.


title: 13557352 - MSB vs LCB

hyb_protocol: LCB Cy5 / MSB Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.