title: 12-0007-04A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_biopsyGrade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_Cy3: 12-0007-04A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 12-0002-03A

status: Public on Sep 01 2005

type: RNA

city: South San Francisco

first: Expression

last: Diagnostics

state: CA

address: 750 Gateway Boulevard, Suite H

country: USA

institute: XDx Inc

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_biopsyGrade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_Cy3: 12-0002-03A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response

molecule: total RNA

organism: Homo sapiens

source_name: Cy5 reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors


title: 12-0013-01A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_biopsyGrade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_Cy3: 12-0013-01A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 12-0012-03A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 1A Consensus_Biopsy_Grade: 0
Sample_biopsyGrade: Local_Biopsy_Grade: 1A Consensus_Biopsy_Grade: 0
Sample_Cy3: 12-0012-03A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 331_28_3

city: Tucson

first: Therese

middle: Ann

last: Markow

state: AZ

address: 310 Biosciences West

department: EEB

institute: University of Arizona

description:
This sample is set 3 on Slide 28, part of a "Dye flip" experiment with Slide 25. Each slide contains three sets of replicate spots.
Keywords = dietary shifts
Keywords = ecological genomics

organism: Drosophila melanogaster

source_name: experimental (switched to banana)

source_name: control (cornmeal diet)


title: 331_25_3

description:
This sample is set 3 on Slide 25, part of a "Dye flip" experiment with Slide 28. Each slide contains three sets of replicate spots.
Keywords = dietary shifts
Keywords = ecological genomics


title: 12-0002-02A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 1B Consensus_Biopsy_Grade: 1A
Sample_biopsyGrade: Local_Biopsy_Grade: 1B Consensus_Biopsy_Grade: 1A
Sample_Cy3: 12-0002-02A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 12-0001-03A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 1A Consensus_Biopsy_Grade: 0
Sample_biopsyGrade: Local_Biopsy_Grade: 1A Consensus_Biopsy_Grade: 0
Sample_Cy3: 12-0001-03A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 12-0001-02A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 1A Consensus_Biopsy_Grade: 0
Sample_biopsyGrade: Local_Biopsy_Grade: 1A Consensus_Biopsy_Grade: 0
Sample_Cy3: 12-0001-02A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 12-0001-01A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 3A Consensus_Biopsy_Grade: 1A
Sample_biopsyGrade: Local_Biopsy_Grade: 3A Consensus_Biopsy_Grade: 1A
Sample_Cy3: 12-0001-01A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 12-0013-02A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 1A Consensus_Biopsy_Grade: 1A
Sample_biopsyGrade: Local_Biopsy_Grade: 1A Consensus_Biopsy_Grade: 1A
Sample_Cy3: 12-0013-02A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 12-0010-05A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 1A Consensus_Biopsy_Grade: n/a
Sample_biopsyGrade: Local_Biopsy_Grade: 1A Consensus_Biopsy_Grade: n/a
Sample_Cy3: 12-0010-05A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 12-0001-04A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_biopsyGrade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_Cy3: 12-0001-04A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 12-0010-04A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_biopsyGrade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_Cy3: 12-0010-04A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 331_25_1

description:
This sample is set 1 on Slide 25, part of a "Dye flip" experiment with Slide 28. Each slide contains three sets of replicate spots.
Keywords = dietary shifts
Keywords = ecological genomics


title: 331_25_2

description:
This sample is set 2 on Slide 25, part of a "Dye flip" experiment with Slide 28. Each slide contains three sets of replicate spots.
Keywords = dietary shifts
Keywords = ecological genomics


title: 12-0010-03A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: n/a
Sample_biopsyGrade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: n/a
Sample_Cy3: 12-0010-03A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 331_28_2

description:
This sample is set 2 on Slide 28, part of a "Dye flip" experiment with Slide 25. Each slide contains three sets of replicate spots.
Keywords = dietary shifts
Keywords = ecological genomics


title: 331_28_1

description:
This sample is set 1 on Slide 28, part of a "Dye flip" experiment with Slide 25. Each slide contains three sets of replicate spots.
Keywords = dietary shifts
Keywords = ecological genomics


title: 331_30_3

description:
This sample is set 3 on Slide 30, part of a "Dye flip" experiment with Slide 29. Each slide contains three sets of replicate spots.
Keywords = dietary shifts
Keywords = ecological genomics


title: 12-0007-02A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 1A Consensus_Biopsy_Grade: 0
Sample_biopsyGrade: Local_Biopsy_Grade: 1A Consensus_Biopsy_Grade: 0
Sample_Cy3: 12-0007-02A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 331_29_3

description:
This sample is set 3 on Slide 29, part of a "Dye flip" experiment with Slide 30. Each slide contains three sets of replicate spots.
Keywords = dietary shifts
Keywords = ecological genomics


title: 331_30_1

description:
This sample is set 1 on Slide 30, part of a "Dye flip" experiment with Slide 29. Each slide contains three sets of replicate spots.
Keywords = dietary shifts
Keywords = ecological genomics


title: 331_30_2

description:
This sample is set 2 on Slide 30, part of a "Dye flip" experiment with Slide 29. Each slide contains three sets of replicate spots.
Keywords = dietary shifts
Keywords = ecological genomics


title: ThyDNWT

city: New York

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: double negative thymocyte isolated from RAG1 mutant mice

organism: Mus musculus

source_name: Total RNA


title: 12-0007-09A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 1B Consensus_Biopsy_Grade: 1B
Sample_biopsyGrade: Local_Biopsy_Grade: 1B Consensus_Biopsy_Grade: 1B
Sample_Cy3: 12-0007-09A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 331_29_1

description:
This sample is set 1 on Slide 29, part of a "Dye flip" experiment with Slide 30. Each slide contains three sets of replicate spots.
Keywords = dietary shifts
Keywords = ecological genomics


title: Rag T-cell

description: double negative thymocyte isolated from RAG1 deficient mutant mice


title: 331_29_2

description:
This sample is set 2 on Slide 29, part of a "Dye flip" experiment with Slide 30. Each slide contains three sets of replicate spots.
Keywords = dietary shifts
Keywords = ecological genomics


title: 12-0006-04A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 1A Consensus_Biopsy_Grade: 0
Sample_biopsyGrade: Local_Biopsy_Grade: 1A Consensus_Biopsy_Grade: 0
Sample_Cy3: 12-0006-04A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 331_3_1

description:
This sample is set 1 on Slide 3, part of a "Dye flip" experiment with Slide 2. Each slide contains three sets of replicate spots.
Keywords = dietary shifts
Keywords = ecological genomics


title: 12-0006-03A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_biopsyGrade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_Cy3: 12-0006-03A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 331_3_2

description:
This sample is set 2 on Slide 3, part of a "Dye flip" experiment with Slide 2. Each slide contains three sets of replicate spots.
Keywords = dietary shifts
Keywords = ecological genomics


title: RagEuxl-Tcell

description: double negative thymocyte isolated from RAG1/Ezh2 double mutant mice

source_name: total RNA


title: 12-0003-03A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_biopsyGrade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_Cy3: 12-0003-03A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 331_2_2

description:
This sample is set 2 on Slide 2, part of a "Dye flip" experiment with Slide 3. Each slide contains three sets of replicate spots.
Keywords = dietary shifts
Keywords = ecological genomics


title: 12-0002-04B

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_biopsyGrade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_Cy3: 12-0002-04B
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 12-0001-05A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_biopsyGrade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_Cy3: 12-0001-05A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 2204DNWT

description: double negative thymocyte isolated from RAG1 defificient mice


title: 331_2_1

description:
This sample is set 1 on Slide 2, part of a "Dye flip" experiment with Slide 3. Each slide contains three sets of replicate spots.
Keywords = dietary shifts
Keywords = ecological genomics


title: 2205DNMT


title: 12-0001-08A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 1B Consensus_Biopsy_Grade: n/a
Sample_biopsyGrade: Local_Biopsy_Grade: 1B Consensus_Biopsy_Grade: n/a
Sample_Cy3: 12-0001-08A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 5B

status: Public on Aug 31 2005

city: Aberdeen Proving Ground

first: James

middle: F

last: Dillman

state: MD

address: 3100 Ricketts Point Rd

department: Cell and Molecular Biology Branch

institute: U.S. Army Medical Research Institute of Chemical Defense

description:
phosgene exposed mouse lung
CG
32 mg
0.5
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC

source_name: lung


title: 6B


title: 5A

description:
phosgene exposed mouse lung
CG
32 mg
0.5
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 4B


title: 4A


title: 331_3_3

description:
This sample is set 3 on Slide 3, part of a "Dye flip" experiment with Slide 2. Each slide contains three sets of replicate spots.
Keywords = dietary shifts
Keywords = ecological genomics


title: ThyDNEx1


title: 12-0006-05A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_biopsyGrade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_Cy3: 12-0006-05A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 12-0003-02A

description:
PBMC blood sample (CPT, Becton-Dickinson) of cardiac transplant patient.
Samples were frozen in lysis byffer (RLT, Qiuagen) within 2 hours of phlebotomy.
Arrays were scanned on an Agilent scanner. GenePix software was used for image processing.
Biopsy grade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_biopsyGrade: Local_Biopsy_Grade: 0 Consensus_Biopsy_Grade: 0
Sample_Cy3: 12-0003-02A
Sample_Cy5: reference pool of amplified RNA from PBMC samples of 50 randomly selected blood donors
Sample_keywords: Transplantation, Graft Rejection, Heart Transplantation,  Immune Response


title: 48A

description:
phosgene exposed mouse lung
CG
32 mg
72
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 41A

description:
phosgene exposed mouse lung
CG
32 mg
48
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 47B

description:
phosgene exposed mouse lung
CG
32 mg
72
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 6A


title: 47A


title: 42A


title: 40A


title: 40B

description:
phosgene exposed mouse lung
CG
32 mg
48
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 42B


title: 46B


title: 36A

description:
phosgene exposed mouse lung
CG
32 mg
24
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 36B

description:
phosgene exposed mouse lung
CG
32 mg
24
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 35B


title: 331_2_3

description:
This sample is set 3 on Slide 2, part of a "Dye flip" experiment with Slide 3. Each slide contains three sets of replicate spots.
Keywords = dietary shifts
Keywords = ecological genomics


title: 35A


title: 30A

description:
phosgene exposed mouse lung
CG
32 mg
12
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 34A


title: 48B


title: 30B

description:
phosgene exposed mouse lung
CG
32 mg
12
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 29B


title: 28A


title: 34B


title: 22A

description:
phosgene exposed mouse lung
CG
32 mg
8
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 46A


title: 29A


title: 24B


title: 18A

description:
phosgene exposed mouse lung
CG
32 mg
4
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 16A


title: 17A

description:
phosgene exposed mouse lung
CG
32 mg
4
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 28B


title: 159B

description:
phosgene exposed mouse lung
Air
1
72
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 23A


title: 16B


title: 159A

description:
phosgene exposed mouse lung
Air
1
72
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 156B

description:
phosgene exposed mouse lung
Air
1
48
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 156A

description:
phosgene exposed mouse lung
Air
1
48
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 155B

description:
phosgene exposed mouse lung
Air
1
8
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 155A

description:
phosgene exposed mouse lung
Air
1
8
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 17B


title: 157A


title: 152A

description:
phosgene exposed mouse lung
None
None
0
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 142A


title: 147A


title: 153A

description:
phosgene exposed mouse lung
None
None
0
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 154A


title: 147B


title: 152B


title: 139B


title: 153B


title: 139A


title: 130B

description:
phosgene exposed mouse lung
Air
1
12
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 130A

description:
phosgene exposed mouse lung
Air
1
12
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 136B

description:
phosgene exposed mouse lung
Air
1
24
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 135A

description:
phosgene exposed mouse lung
Air
1
24
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 134B


title: 134A


title: 136A


title: 135B


title: 12A

description:
phosgene exposed mouse lung
CG
32 mg
1
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 129B


title: 24A

description:
phosgene exposed mouse lung
CG
32 mg
8
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 128B


title: 128A


title: 12B

description:
phosgene exposed mouse lung
CG
32 mg
1
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 122A


title: 41B

description:
phosgene exposed mouse lung
CG
32 mg
48
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 122B


title: 118B

description:
phosgene exposed mouse lung
Air
1
4
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 11A


title: 123B


title: 116A


title: 129A


title: 117A

description:
phosgene exposed mouse lung
Air
1
4
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 123A


title: 118A


title: 117B


title: 112A

description:
phosgene exposed mouse lung
Air
1
1
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 111A


title: 112B

description:
phosgene exposed mouse lung
Air
1
1
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 110A


title: 110B


title: 106A

description:
phosgene exposed mouse lung
Air
1
0.5
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 10A


title: 106B

description:
phosgene exposed mouse lung
Air
1
0.5
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 10B


title: 111B


title: 157B

description:
phosgene exposed mouse lung
Air
1
48
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: 105B


title: 104A


title: Rat R73: JA vs Normal(pooled)

status: Public on Aug 25 2005

city: Baltimore

first: Irene

last: Kim

address: 720 Rutland Avenue

department: Medicine

institute: Johns Hopkins University

description: Sample R73 represents the cohybridization of labeled extracts JA_Cy5 and Normal(pooled)_Cy3 to a rat 8Kx2 cDNA array.  Dyeswap of sample R72.

organism: Rattus norvegicus

source_name: JA is a reflux induced esophageal tumor cell line.

source_name: Normal(pooled) is a 1:1 mixture of Normal1_esophageal cell line + Normal2_esophageal cell line.


title: 105A


title: 104B


title: Rat R74: Amy vs Normal(pooled)

description: Sample R74 represents the cohybridization of labeled extracts Amy_Cy3 and Normal(pooled)_Cy5 to a rat 8Kx2 cDNA array.  Dyeswap of sample R75.

source_name: Amy is a reflux induced esophageal tumor cell line.


title: Rat R71: JB vs Normal(pooled)

description: Sample R71 represents the cohybridization of labeled extracts JB_Cy5 and Normal(pooled)_Cy3 to a rat 8Kx2 cDNA array.  Dyeswap of sample R70.

source_name: JB is a reflux induced esophageal tumor cell line.


title: Rat R72: JA vs Normal(pooled)

description: Sample R72 represents the cohybridization of labeled extracts JA_Cy3 and Normal(pooled)_Cy5 to a rat 8Kx2 cDNA array.  Dyeswap of sample R73.


title: DATA:ipe-249; ch1: Pool2: cy3; ch2: Stem 4_2: cy5

status: Public on Aug 24 2005

city: Campinas

first: Renato

last: Vicentini

state: SP

address: Cidade Universitaria "Zeferino Vaz"

department: Centro de Biologia Molecular e Engenharia Genetica - CBMEG

country: Brazil

institute: Universidade Estadual de Campinas - UNICAMP

description:
Origin: Sugarcane
Channel_1: Equimolar pool of tissue extracts (root, lateral bud, leaf, stem1, stem4 and flower) used as common reference.
Channel_2: The fourth internode , visible after leaf removal and counted from top of the plant was collected from a single 14 month old field grown plant of the commercial variety SP80-3280. The nodal region was discarded and the tissue was divided in small pieces that were frozen in liquid nitrogen and stored at -80oC
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

organism: Saccharum officinarum

source_name: Pool2: cy3

source_name: Stem 4_2: cy5


title: Rat R75: Amy vs Normal(pooled)

description: Sample R75 represents the cohybridization of labeled extracts Amy_Cy5 and Normal(pooled)_Cy3 to a rat 8Kx2 cDNA array.  Dyeswap of sample R74.


title: Rat R70: JB vs Normal(pooled)

description: Sample R70 represents the cohybridization of labeled extracts JB_Cy3 and Normal(pooled)_Cy5 to a rat 8Kx2 cDNA array.  Dyeswap of sample R71.


title: DATA:ipe-244; ch1: Root2: cy3; ch2: Pool2: cy5

description:
Origin: Sugarcane
Channel_1: Single eyed seed setts from 14 months old field grown plants were planted in 200 ml plastic cups containing moist white sand without any treatment. Adventitious roots were collected 12 days after planting, frozen in liquid nitrogen and stored at -80oC.
Channel_2: Equimolar pool of tissue extracts (root, lateral bud, leaf, stem1, stem4 and flower) used as common reference.
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.
Sample_characteristics_ch1: Origin: Root

source_name: Root2: cy3

source_name: Pool2: cy5


title: DATA:ipe-248; ch1: Pool2: cy3; ch2: LV-c: cy5

description:
Channel_1:Equimolar pool of tissue extracts (root, lateral bud, leaf, stem1, stem4 and flower) used as common reference.
Channel_2: First leaf with a visible dewlap (leaf+1) from a single field grown plant of the commercial variety SP80-3280.
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: LV-c: cy5


title: DATA:ipe-252; ch1: Pool2: cy3; ch2: Stem1: cy5

description:
Origin: Sugarcane
Channel_1: Equimolar pool of tissue extracts (root, lateral bud, leaf, stem1, stem4 and flower) used as common reference.
Channel_2: The first and second formed internodes , visible after leaf removal and counted from top of the plant  were collected from a single 12 month old field grown plant of the commercial variety SP80-3280. The nodal region was discarded and the internodes were sectioned in small pieces that were frozen in liquid nitrogen and stored at -80oC
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Stem1: cy5


title: DATA:ipe-250; ch1: Pool2: cy3; ch2: Lateral Bud: cy5

description:
Origin: Sugarcane
Channel_1: Equimolar pool of tissue extracts (root, lateral bud, leaf, stem1, stem4 and flower) used as common reference.
Channel_2: Variety: SP80-3280 Single eyed seed setts from 12 months old field grown plants were treated with the fungicide Benlate (Benomyl) and the insecticide Decis (Deltamethrin)and placed on top of wet paper towels to germinate under dark and moist conditions. Temperature was kept constant at 25oC. After 10 days, lateral buds were collected and frozen in liquid nitrogen and stored at -80oC.
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Lateral Bud: cy5


title: DATA:ipe-246; ch1: Pool2: cy3; ch2: Stem 4_2: cy5


title: DATA:ipe-247; ch1: Root2: cy3; ch2: Pool2: cy5


title: DATA:ipe-251; ch1: Pool2: cy3; ch2: Flower: cy5

description:
Origin: Sugarcane
Channel_1: Equimolar pool of tissue extracts (root, lateral bud, leaf, stem1, stem4 and flower) used as common reference.
Channel_2: Variety: SP87-342 Sampling date: 05/09/2003 Planting date: 08/26/2002 as single stools from potted plants Tissue: Inflorescence Tissue description: Several immature inflorescences with lengths varying between 5 and 30 cm were sampled and stored at -80oC. Small pieces of the inflorescences containing all its different tissue types were pooled from freezer for RNA extraction.
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Flower: cy5


title: 23B

description:
phosgene exposed mouse lung
CG
32 mg
8
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: DATA:ipe-243; ch1: Stem1_2: cy3; ch2: Pool2: cy5

description:
Origin: Sugarcane
Channel_1: The first and second formed internodes , visible after leaf removal and counted from top of the plant  were collected from a single 14 month old field grown plant of the commercial variety SP80-3280. The nodal region was discarded and the internodes were sectioned in small pieces that were frozen in liquid nitrogen and stored at -80oC
Channel_2: Equimolar pool of tissue extracts (root, lateral bud, leaf, stem1, stem4 and flower) used as common reference.
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Stem1_2: cy3


title: DATA:ipe-245; ch1: Pool2: cy3; ch2: Leaf 1: cy5

description:
Origin: Sugarcane
Channel_1: Equimolar pool of tissue extracts (root, lateral bud, leaf, stem1, stem4 and flower) used as common reference.
Channel_2: The first leaf with a visible dewlap (leaf+1) was collected from a single 12 month old field grown plant of the commercial variety SP80-3280. The leaf was sectioned in small 1-2 cm pieces that were frozen in liquid nitrogen and stored at -80oC
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Leaf 1: cy5


title: DATA:ipe-240; ch1: Pool2: cy3; ch2: Lateral Bud: cy5


title: DATA:ipe-241; ch1: Flower2: cy3; ch2: Pool2: cy5

description:
Origin: Sugarcane
Channel_1: Variety: SP87-342 Sampling date: 08/05/2003 Planting date: 08/26/2002 as single stools from potted plants Tissue: Inflorescence Tissue description: Immature inflorescences with approximately 50 cm in length were collected. Pieces of different parts along their lengths were sampled and stored together. RNA extraction was done on this material.
Channel_2: Equimolar pool of tissue extracts (root, lateral bud, leaf, stem1, stem4 and flower) used as common reference.
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Flower2: cy3


title: 18B

description:
phosgene exposed mouse lung
CG
32 mg
4
chip replicate A
Keywords = phosgene, lung, toxic industrial chemical, TIC


title: DATA:ipe-238; ch1: Pool2: cy3; ch2: LV-c: cy5

description:
Channel_1: Equimolar pool of tissue extracts (root, lateral bud, leaf, stem1, stem4 and flower) used as common reference.
Channel_2: First leaf with a visible dewlap (leaf+1) from a single field grown plant of the commercial variety SP80-3280.
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.


title: DATA:ipe-233; ch1: Lateral Bud_2: cy3; ch2: Pool2: cy5

description:
Origin: Sugarcane
Channel_1: Single eyed seed setts from 14 months old field grown plants were planted in 200 ml plastic cups containing moist white sand without any treatment. Lateral buds were excised 12 days after planting, frozen in liquid nitrogen and stored at -80oC.
Channel_2: Equimolar pool of tissue extracts (root, lateral bud, leaf, stem1, stem4 and flower) used as common reference.
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Lateral Bud_2: cy3


title: DATA:ipe-239; ch1: Pool2: cy3; ch2: Stem1: cy5


title: DATA:ipe-235; ch1: Pool2: cy3; ch2: Root: cy5

description:
Origin: Sugarcane
Channel_1: Equimolar pool of tissue extracts (root, lateral bud, leaf, stem1, stem4 and flower) used as common reference.
Channel_2: Variety: SP80-3280 Single eyed seed setts from 12 months old field grown plants were treated with the fungicide Benlate (Benomyl) and the insecticide Decis (Deltamethrin)and placed on top of wet paper towels to germinate under dark and moist conditions. Temperature was kept constant at 25oC. After 10 days, adventitious roots were collected and frozen in liquid nitrogen and stored at -80oC.
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
Channel_1 RNA extraction: Trizol; Channel_2 RNA extraction: Guanidine-HCl
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Root: cy5


title: DATA:ipe-236; ch1: Pool2: cy3; ch2: Flower: cy5


title: DATA:ipe-232; ch1: Pool2: cy3; ch2: Leaf 1: cy5


title: DATA:ipe-226; ch1: Pool2: cy3; ch2: LV-b: cy5

source_name: LV-b: cy5


title: DATA:ipe-221; ch1: Root: cy3; ch2: Pool1: cy5

description:
Origin: Sugarcane
Channel_1: Variety: SP80-3280 Single eyed seed setts from 12 months old field grown plants were treated with the fungicide Benlate (Benomyl) and the insecticide Decis (Deltamethrin)and placed on top of wet paper towels to germinate under dark and moist conditions. Temperature was kept constant at 25oC. After 10 days, adventitious roots were collected and frozen in liquid nitrogen and stored at -80oC.
Channel_2: Equimolar pool of tissue extracts (root, lateral bud, leaf*, stem1, and flower) used as common reference.  *low quality
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Guanidine-HCl
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Root: cy3

source_name: Pool1: cy5


title: DATA:ipe-222; ch1: Lateral Bud: cy3; ch2: Pool1: cy3

description:
Origin: Sugarcane
Channel_1: Variety: SP80-3280 Single eyed seed setts from 12 months old field grown plants were treated with the fungicide Benlate (Benomyl) and the insecticide Decis (Deltamethrin)and placed on top of wet paper towels to germinate under dark and moist conditions. Temperature was kept constant at 25oC. After 10 days, lateral buds were collected and frozen in liquid nitrogen and stored at -80oC.
Channel_2: Equimolar pool of tissue extracts (root, lateral bud, leaf*, stem1, and flower) used as common reference.  *low quality
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.
Sample_label_ch1: cy3
Sample_label_ch2: cy3

source_name: Lateral Bud: cy3

source_name: Pool1: cy3


title: DATA:ipe-218; ch1: Pool1: cy3; ch2: Stem4: cy5

description:
Origin: Sugarcane
Channel_1: Equimolar pool of tissue extracts (root, lateral bud, leaf*, stem1, and flower) used as common reference.  *low quality
Channel_2: The fourth internode , visible after leaf removal and counted from top of the plant was collected from a single 12 month old field grown plant of the commercial variety SP80-3280. The nodal region was discarded and the tissue was sectioned in small pieces that were frozen in liquid nitrogen and stored at -80oC
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Stem4: cy5


title: DATA:ipe-213; ch1: Pool1: cy3; ch2: Lateral Bud: cy5

description:
Origin: Sugarcane
Channel_1: Equimolar pool of tissue extracts (root, lateral bud, leaf*, stem1, and flower) used as common reference.  *low quality
Channel_2: Variety: SP80-3280 Single eyed seed setts from 12 months old field grown plants were treated with the fungicide Benlate (Benomyl) and the insecticide Decis (Deltamethrin)and placed on top of wet paper towels to germinate under dark and moist conditions. Temperature was kept constant at 25oC. After 10 days, lateral buds were collected and frozen in liquid nitrogen and stored at -80oC.
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.


title: DATA:ipe-229; ch1: Lateral Bud_2: cy3; ch2: Pool2: cy5


title: DATA:ipe-219; ch1: Stem1: cy3; ch2: Pool1: cy5

description:
Origin: Sugarcane
Channel_1: The first and second formed internodes , visible after leaf removal and counted from top of the plant  were collected from a single 12 month old field grown plant of the commercial variety SP80-3280. The nodal region was discarded and the internodes were sectioned in small pieces that were frozen in liquid nitrogen and stored at -80oC
Channel_2: Equimolar pool of tissue extracts (root, lateral bud, leaf*, stem1, and flower) used as common reference.  *low quality
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Stem1: cy3


title: DATA:ipe-228; ch1: Pool2: cy3; ch2: LV-a: cy5

source_name: Pool2: cy3

source_name: LV-a: cy5


title: DATA:ipe-230; ch1: Stem1_2: cy3; ch2: Pool2: cy5

source_name: Pool2: cy5


title: DATA:ipe-216; ch1: Leaf 2: cy3; ch2: Pool1: cy5

description:
Origin: Sugarcane
Channel_1: The first leaf with a visible dewlap (leaf+1) was collected from a single 14 month old field grown plant of the commercial variety SP80-3280. The leaf was sectioned in small 1-2 cm pieces that were frozen in liquid nitrogen and stored at -80oC
Channel_2: Equimolar pool of tissue extracts (root, lateral bud, leaf*, stem1, and flower) used as common reference.  *low quality
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Leaf 2: cy3


title: DATA:ipe-214; ch1: Pool1: cy3; ch2: Root: cy5

description:
Origin: Sugarcane
Channel_1: Equimolar pool of tissue extracts (root, lateral bud, leaf*, stem1, and flower) used as common reference.  *low quality
Channel_2: Variety: SP80-3280 Single eyed seed setts from 12 months old field grown plants were treated with the fungicide Benlate (Benomyl) and the insecticide Decis (Deltamethrin)and placed on top of wet paper towels to germinate under dark and moist conditions. Temperature was kept constant at 25oC. After 10 days, adventitious roots were collected and frozen in liquid nitrogen and stored at -80oC.
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
Channel_1 RNA extraction: Trizol; Channel_2 RNA extraction: Guanidine-HCl
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.


title: DATA:ipe-237; ch1: Pool2: cy3; ch2: LV-a: cy5


title: DATA:ipe-225; ch1: Leaf 1: cy3; ch2: Pool1: cy5

description:
Origin: Sugarcane
Channel_1: The first leaf with a visible dewlap (leaf+1) was collected from a single 12 month old field grown plant of the commercial variety SP80-3280. The leaf was sectioned in small 1-2 cm pieces that were frozen in liquid nitrogen and stored at -80oC
Channel_2: Equimolar pool of tissue extracts (root, lateral bud, leaf*, stem1, and flower) used as common reference.  *low quality
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Leaf 1: cy3


title: DATA:ipe-231; ch1: Pool2: cy3; ch2: Root: cy5


title: DATA:ipe-227; ch1: Pool2: cy3; ch2: LV-b: cy5


title: DATA:ipe-223; ch1: Flower: cy3; ch2: Pool1: cy5

description:
Origin: Sugarcane
Channel_1: Variety: SP87-342 Sampling date: 05/09/2003 Planting date: 08/26/2002 as single stools from potted plants Tissue: Inflorescence Tissue description: Several immature inflorescences with lengths varying between 5 and 30 cm were sampled and stored at -80oC. Small pieces of the inflorescences containing all its different tissue types were pooled from freezer for RNA extraction.
Channel_2: Equimolar pool of tissue extracts (root, lateral bud, leaf*, stem1, and flower) used as common reference.  *low quality
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Flower: cy3


title: DATA:ipe-217; ch1: Pool1: cy3; ch2: Flower: cy5

description:
Origin: Sugarcane
Channel_1: Equimolar pool of tissue extracts (root, lateral bud, leaf*, stem1, and flower) used as common reference.  *low quality
Channel_2: Variety: SP87-342 Sampling date: 05/09/2003 Planting date: 08/26/2002 as single stools from potted plants Tissue: Inflorescence Tissue description: Several immature inflorescences with lengths varying between 5 and 30 cm were sampled and stored at -80oC. Small pieces of the inflorescences containing all its different tissue types were pooled from freezer for RNA extraction.
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Flower: cy5


title: DATA:ipe-215; ch1: Pool1: cy3; ch2: Flower: cy5


title: DATA:ipe-220; ch1: Pool1: cy3; ch2: Root: cy5


title: DATA:ipe-224; ch1: Stem1: cy3; ch2: Pool1: cy5


title: DATA:ipe-211; ch1: Stem4: cy3; ch2: Pool1: cy5

description:
Origin: Sugarcane
Channel_1: The fourth internode , visible after leaf removal and counted from top of the plant was collected from a single 12 month old field grown plant of the commercial variety SP80-3280. The nodal region was discarded and the tissue was sectioned in small pieces that were frozen in liquid nitrogen and stored at -80oC
Channel_2: Equimolar pool of tissue extracts (root, lateral bud, leaf*, stem1, and flower) used as common reference.  *low quality
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Stem4: cy3


title: DATA:ipe-210; ch1: Flower: cy3; ch2: Pool1: cy5


title: DATA:ipe-207; ch1: Pool1: cy3; ch2: Leaf 1: cy5

description:
Origin: Sugarcane
Channel_1: Equimolar pool of tissue extracts (root, lateral bud, leaf*, stem1, and flower) used as common reference.  *low quality
Channel_2: The first leaf with a visible dewlap (leaf+1) was collected from a single 12 month old field grown plant of the commercial variety SP80-3280. The leaf was sectioned in small 1-2 cm pieces that were frozen in liquid nitrogen and stored at -80oC
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Leaf 1: cy5


title: DATA:ipe-206; ch1: Root: cy3; ch2: Pool1: cy5


title: DATA:ipe-204; ch1: Lateral Bud: cy3; ch2: Pool1: cy5

description:
Origin: Sugarcane
Channel_1: Variety: SP80-3280 Single eyed seed setts from 12 months old field grown plants were treated with the fungicide Benlate (Benomyl) and the insecticide Decis (Deltamethrin)and placed on top of wet paper towels to germinate under dark and moist conditions. Temperature was kept constant at 25oC. After 10 days, lateral buds were collected and frozen in liquid nitrogen and stored at -80oC.
Channel_2: Equimolar pool of tissue extracts (root, lateral bud, leaf*, stem1, and flower) used as common reference.  *low quality
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.


title: DATA:ipe-208; ch1: Pool1: cy3; ch2: Lateral Bud: cy5

source_name: Lateral Bud: cy5


title: DATA:ipe-212; ch1: Pool1: cy3; ch2: Leaf 1: cy5


title: DATA:ipe-205; ch1: Pool1: cy3; ch2: Stem4: cy5


title: Male 1 chip A

status: Public on Aug 23 2005

city: Denver

first: Melanie

last: Gubbels

state: CO

institute: University of Colorado Health Sciences Center

description:
Goal of experimet: Identification of differentially expressed immune genes from male and female BWF1 lupus-prone mice.  (Female incidence is higher than male--attempting to find sex hormone regulated genes that may contribute to this difference)
Keywords = disease-prone (female) vs not disease prone (male)

source_name: Whole spleen taken at 4 months of age


title: Male 4 chip A


title: Male 1 chip B

description:
Goal of experimet: Identification of differentially expressed immune genes from male and female BWF1 lupus-prone mice. (Female incidence is higher than male--attempting to find sex hormone regulated genes that may contribute to this difference)
Keywords = disease-prone (female) vs not disease prone (male)


title: DATA:ipe-202; ch1: Leaf 2: cy3; ch2: Pool1: cy5


title: Male 2 chip A


title: DATA:ipe-198; ch1: Pool1: cy3; ch2: Leaf 2: cy5

description:
Origin: Sugarcane
Channel_1: Equimolar pool of tissue extracts (root, lateral bud, leaf*, stem1, and flower) used as common reference.  *low quality
Channel_2: The first leaf with a visible dewlap (leaf+1) was collected from a single 14 month old field grown plant of the commercial variety SP80-3280. The leaf was sectioned in small 1-2 cm pieces that were frozen in liquid nitrogen and stored at -80oC
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Leaf 2: cy5


title: DATA:ipe-200; ch1: Stem4: cy3; ch2: Pool1: cy5

source_name: Pool1: cy5


title: IPF lung biopsy E32

status: Public on Aug 08 2005

city: Pittsburgh

first: Thomas

last: Richards

state: PA

institute: University of Pittsburgh

description: CodeLink Normalized Intensity, IPF lung biopsy E32.  Archived lung tissues of patients with IPF were obtained from the tissue bank of the Department of Pathology at the University of Pittsburgh.  The diagnosis of IPF was confirmed by open lung biopsy. All patients fulfilled the criteria of the American Thoracic Society and European Respiratory Society for the diagnosis of IPF.

source_name: IPF lung biopsy


title: IPF lung biopsy E286

description: CodeLink Normalized Intensity, IPF lung biopsy D286.  Archived lung tissues of patients with IPF were obtained from the tissue bank of the Department of Pathology at the University of Pittsburgh.  The diagnosis of IPF was confirmed by open lung biopsy. All patients fulfilled the criteria of the American Thoracic Society and European Respiratory Society for the diagnosis of IPF.


title: DATA:ipe-203; ch1: Pool1: cy3; ch2: Stem1: cy5

description:
Origin: Sugarcane
Channel_1: Equimolar pool of tissue extracts (root, lateral bud, leaf*, stem1, and flower) used as common reference.  *low quality
Channel_2: The first and second formed internodes , visible after leaf removal and counted from top of the plant  were collected from a single 12 month old field grown plant of the commercial variety SP80-3280. The nodal region was discarded and the internodes were sectioned in small pieces that were frozen in liquid nitrogen and stored at -80oC
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Pool1: cy3

source_name: Stem1: cy5


title: IPF lung biopsy E46

description: CodeLink Normalized Intensity, IPF lung biopsy E46.  Archived lung tissues of patients with IPF were obtained from the tissue bank of the Department of Pathology at the University of Pittsburgh.  The diagnosis of IPF was confirmed by open lung biopsy. All patients fulfilled the criteria of the American Thoracic Society and European Respiratory Society for the diagnosis of IPF.


title: DATA:ipe-197; ch1: Leaf 1: cy3; ch2: Pool1: cy5


title: Female 2 chip A


title: Scleroderma lung biopsy E488

description: CodeLink Normalized Intensity, IPF lung biopsy E488.  Archived lung tissues of patients with IPF were obtained from the tissue bank of the Department of Pathology at the University of Pittsburgh.  The diagnosis of IPF was confirmed by open lung biopsy. All patients fulfilled the criteria of the American Thoracic Society and European Respiratory Society for the diagnosis of IPF.

source_name: lung biopsy


title: IPF lung explant E465

description:
CodeLink Normalized Intensity, IPF lung explant E465.  Archived lung tissues of patients with IPF were obtained from
the tissue bank of the Department of Pathology at the
University of Pittsburgh.  The diagnosis of IPF was confirmed by open lung biopsy.
All patients fulfilled the criteria of the American Thoracic Society and
European Respiratory Society for the diagnosis of IPF.

source_name: IPF lung explant


title: DATA:ipe-201; ch1: Pool1: cy3; ch2: Leaf 2: cy5


title: IPF lung explant E54

description: CodeLink Normalized Intensity, IPF lung explant E54.  Archived lung tissues of patients with IPF were obtained from the tissue bank of the Department of Pathology at the University of Pittsburgh.  The diagnosis of IPF was confirmed by open lung biopsy. All patients fulfilled the criteria of the American Thoracic Society and European Respiratory Society for the diagnosis of IPF.


title: Female 4 chip A


title: Female 4 chip B


title: DATA:ipe-199; ch1: Pool1: cy3; ch2: Stem1: cy5


title: Female 3 chip B


title: IPF lung biopsy D810

description: CodeLink Normalized Intensity, IPF lung biopsy D810.  Archived lung tissues of patients with IPF were obtained from the tissue bank of the Department of Pathology at the University of Pittsburgh.  The diagnosis of IPF was confirmed by open lung biopsy. All patients fulfilled the criteria of the American Thoracic Society and European Respiratory Society for the diagnosis of IPF.


title: DATA:ipe-242; ch1: Flower2: cy3; ch2: Pool2: cy5

description:
Origin: Sugarcane
Channel_1: Variety: SP87-342 Sampling date: 08/05/2003 Planting date: 08/26/2002 as single stools from potted plants Tissue: Inflorescence Tissue description: Immature inflorescences with approximately 50 cm in length were collected. Pieces of different parts along their lengths were sampled and stored together. RNA extraction was done on this material.
Channel_2: Equimolar pool of tissue extracts (root, lateral bud, leaf, stem1, stem4 and flower) used as common reference.
Hybridization:  micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

source_name: Flower2: cy3


title: Male 3 chip A


title: gd T cell clone 61.1G11 stimulated with ConA/IL-2

city: Pullman

first: Kevin

middle: Karl

last: Lahmers

state: WA

department: Veterinary Microbiology and Pathology

institute: Washington State University

description: Stimulation of antigen specific clone with ConA/IL-2

organism: Bos taurus

source_name: gd T cell clone 61.1G11


title: Exp 1 comparing gd and ab T cell clones

description: Comparison of bovine T cell clones stimulated with ConA/IL-2

source_name: gd T cell clone 61.1G9

source_name: ab T cell clone 61.1C8


title: ab T cell clone 61.10.2D7 stimulated with ConA/IL-2

source_name: ab T cell clone 61.10.2D7


title: Exp 2 comparing gd and ab T cell clones


title: Female 3 chip A


title: IPF lung explant E396

description:
CodeLink Normalized Intensity, IPF lung explant E396.  Archived lung tissues of patients with IPF were obtained from
the tissue bank of the Department of Pathology at the
University of Pittsburgh.  The diagnosis of IPF was confirmed by open lung biopsy.
All patients fulfilled the criteria of the American Thoracic Society and
European Respiratory Society for the diagnosis of IPF.


title: IPF lung explant C498

description:
CodeLink Normalized Intensity, IPF lung explant C498.  Archived lung tissues of patients with IPF were obtained from the tissue bank of the Department of Pathology at the
University of Pittsburgh.  The diagnosis of IPF was confirmed by open lung biopsy. All patients fulfilled the criteria of the American Thoracic Society and
European Respiratory Society for the diagnosis of IPF.


title: MCTD lung explant C899

description:
CodeLink Normalized Intensity, IPF lung explant C899.  Archived lung tissues of patients with IPF were obtained from
the tissue bank of the Department of Pathology at the
University of Pittsburgh.  The diagnosis of IPF was confirmed by open lung biopsy.
All patients fulfilled the criteria of the American Thoracic Society and
European Respiratory Society for the diagnosis of IPF.

source_name: MCTD (Mixed Tissue Connective Disorder) lung explant


title: IPF lung explant D669

description:
CodeLink Normalized Intensity, IPF lung explant D669.  Archived lung tissues of patients with IPF were obtained from
the tissue bank of the Department of Pathology at the
University of Pittsburgh.  The diagnosis of IPF was confirmed by open lung biopsy.
All patients fulfilled the criteria of the American Thoracic Society and
European Respiratory Society for the diagnosis of IPF.


title: IPF lung explant E144

description:
CodeLink Normalized Intensity, IPF lung explant E144.  Archived lung tissues of patients with IPF were obtained from
the tissue bank of the Department of Pathology at the
University of Pittsburgh.  The diagnosis of IPF was confirmed by open lung biopsy.
All patients fulfilled the criteria of the American Thoracic Society and
European Respiratory Society for the diagnosis of IPF.


description:
CodeLink Normalized Intensity, normal histology lung tissue sample B301.
Normal histology lung tissues were resected from patients with lung cancer were used as controls.

source_name: normal histology lung tissue


title: IPF lung explant D312

description:
CodeLink Normalized Intensity, IPF lung explant D312.  Archived lung tissues of patients with IPF were obtained from
the tissue bank of the Department of Pathology at the
University of Pittsburgh.  The diagnosis of IPF was confirmed by open lung biopsy.
All patients fulfilled the criteria of the American Thoracic Society and
European Respiratory Society for the diagnosis of IPF.


description:
CodeLink Normalized Intensity, normal histology lung tissue sample E634.
Normal histology lung tissues resected from patients with lung cancer were used as controls.


description:
CodeLink Normalized Intensity, normal histology lung tissue sample E642.
Normal histology lung tissues resected from patients with lung cancer were used as controls.


title: IPF lung explant D313

description:
CodeLink Normalized Intensity, IPF lung explant D313.  Archived lung tissues of patients with IPF were obtained from
the tissue bank of the Department of Pathology at the
University of Pittsburgh.  The diagnosis of IPF was confirmed by open lung biopsy.
All patients fulfilled the criteria of the American Thoracic Society and
European Respiratory Society for the diagnosis of IPF.


description:
CodeLink Normalized Intensity, normal histology lung tissue sample E406.
Normal histology lung tissues resected from patients with lung cancer were used as controls.


description:
CodeLink Normalized Intensity, normal histology lung tissue sample E628.
Normal histology lung tissues resected from patients with lung cancer were used as controls.


title: IPF lung explant B438

description:
CodeLink Normalized Intensity, IPF lung explant B438.  Archived lung tissues of patients with IPF were obtained from the tissue bank of the Department of Pathology at the
University of Pittsburgh.  The diagnosis of IPF was confirmed by open lung biopsy. All patients fulfilled the criteria of the American Thoracic Society and
European Respiratory Society for the diagnosis of IPF.


description:
CodeLink Normalized Intensity, normal histology lung tissue sample B167.
Normal histology lung tissues were resected from patients with lung cancer were used as controls.


description:
CodeLink Normalized Intensity, normal histology lung tissue sample B160.
Normal histology lung tissues were resected from patients with lung cancer were used as controls.


title: normal histology lung tissue sample B54

description:
CodeLink Normalized Intensity, normal histology lung tissue sample B54.
Normal histology lung tissues were resected from patients with lung cancer were used as controls.


title: normal histology lung tissue sample E325

description:
CodeLink Normalized Intensity, normal histology lung tissue sample B54.
Normal histology lung tissues resected from patients with lung cancer were used as controls.


description: CodeLink Normalized Intensity, normal histology lung tissue sample B210.


description: CodeLink Normalized Intensity, normal histology lung tissue sample B141.  Normal histology lung tissues resected from patients with lung cancer were used as controls.


title: GC2_MZ650_MZ630_5D550_3

status: Public on Aug 06 2005

type: genomic

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description:
genomic comparison MZ650/MZ630
User - PCheng
Date_of_Scan = Tue Nov 23 12:41:48 2004

molecule: genomic DNA

organism: Salmonella enterica subsp. enterica

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT8 MZ650 gDNA

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT4 MZ630 gDNA


title: GC2_SARB12_MZ630_5D633_2

description:
genomic comparison SARB12/MZ630
User - PCheng
Date_of_Scan = Wed Jan 12 11:26:32 2005

source_name: Salmonella enterica subsp. enterica serovar Dublin SARB12 gDNA


title: GC2_SARB13_MZ630_5D634_3

description:
genomic comparison SARB13/MZ630
User - PCheng
Date_of_Scan = Wed Jan 12 14:50:25 2005

source_name: Salmonella enterica subsp. enterica serovar Dublin SARB13 gDNA


title: GC2_MZ650_MZ630_5D550_2


title: GC2_SARB13_MZ630_5D634_1


title: GC2_SARB12_MZ630_5D633_1


title: GC2_99117_MZ630_5D621_3

description:
genomic comparison 99117/MZ630
User - PCheng
Date_of_Scan = Thu Jan 06 14:01:20 2005

source_name: Salmonella enterica subsp. enterica serovar Gallinarum biovar Pullorum 99117 gDNA


title: GC2_SARB12_MZ630_5D633_3


title: GC2_99117_MZ630_5D621_2


title: GC2_SARB13_MZ630_5D634_2


title: GC2_MZ650_MZ630_5D550_1


title: GC2_99113_MZ630_5D620_3

description:
genomic comparison 99113/MZ630
User - PCheng
Date_of_Scan = Thu Jan 06 13:01:32 2005

source_name: Salmonella enterica subsp. enterica serovar Gallinarum biovar Pullorum 99113 gDNA


title: GC2_99117_MZ630_5D621_1


title: GC2_MZ638_MZ630_5D552_3

description:
genomic comparison MZ638/MZ630
User - PCheng
Date_of_Scan = Tue Nov 30 12:56:27 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT6a MZ638 gDNA


title: GC2_MZ635_MZ630_5D551_2

description:
genomic comparison MZ635/MZ630
User - PCheng
Date_of_Scan = Tue Nov 30 11:07:10 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT7a MZ635 gDNA


title: GC2_MZ638_MZ630_5D552_2


title: GC2_99113_MZ630_5D620_1


title: GC2_MZ635_MZ630_5D551_3


title: GC2_99113_MZ630_5D620_2


title: GC2_17368L_MZ630_5D451_3

description:
genomic comparison 17368L/MZ630
User - PCheng
Date_of_Scan = Tue Sep 21 10:16:00 2004

source_name: Salmonella enterica subsp. enterica serovar Gallinarum biovar Pullorum 17368L gDNA


title: GC2_MZ638_MZ630_5D552_1


title: GC2_7865L_MZ630_5D452_3

description:
genomic comparison 7865L/MZ630
User - PCheng
Date_of_Scan = Tue Sep 21 11:13:28 2004

source_name: Salmonella enterica subsp. enterica serovar Gallinarum biovar Pullorum 7865L gDNA


title: GC2_MZ635_MZ630_5D551_1


title: GC2_MZ747_MZ630_5D363_3

description:
genomic comparison MZ747/MZ630
User - sporwollik
Date_of_Scan = Tue Aug 17 16:32:37 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT8 MZ747 gDNA


title: GC2_MZ648_MZ630_5D549_3

description:
genomic comparison MZ648/MZ630
User - PCheng
Date_of_Scan = Tue Nov 23 11:56:20 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT1 MZ648 gDNA


title: GC2_MZ748_MZ630_5D364_2

description:
genomic comparison MZ748/MZ630
User - csantiviago
Date_of_Scan = Wed Aug 18 13:38:17 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT13a MZ748 gDNA


title: GC2_7865L_MZ630_5D452_2


title: GC2_7865L_MZ630_5D452_1


title: GC2_17368L_MZ630_5D451_2


title: GC2_MZ747_MZ630_5D363_2


title: GC2_MZ748_MZ630_5D364_3


title: GC2_17368L_MZ630_5D451_1


title: GC2_MZ747_MZ630_5D363_1


title: GC2_MZ748_MZ630_5D364_1


title: GC2_MZ648_MZ630_5D549_2


title: GC2_MZ648_MZ630_5D549_1


title: GC2_MZ749_MZ630_5D361_3

description:
genomic comparison MZ749/MZ630
User - csantiviago
Date_of_Scan = Thu Aug 19 11:27:28 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT4b MZ749 gDNA


title: GC2_MZ749_MZ630_5D361_1


title: GC2_SgJ91_MZ630_5D169_3

description:
genomic comparison SgJ91/MZ630
User - PCheng
Date_of_Scan = Thu May 27 11:43:39 2004

source_name: Salmonella enterica subsp. enterica serovar Gallinarum biovar Gallinarum SgJ91 gDNA


title: GC2_MZ749_MZ630_5D361_2


title: GC2_SgJ91_MZ630_5D169_2


title: GC2_MZ743_MZ630_5D360_2

description:
genomic comparison MZ743/MZ630
User - csantiviago
Date_of_Scan = Thu Aug 14 16:32:01 2003

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT6a MZ743 gDNA


title: GC2_MZ750_MZ630_5D358_2

description:
genomic comparison MZ750/MZ630
User - csantiviago
Date_of_Scan = Wed Aug 18 18:57:41 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT8 MZ750 gDNA


title: GC2_MZ750_MZ630_5D358_3


title: GC2_SARB51_MZ630_5D137_3

description:
genomic comparison SARB51/MZ630
User - PCheng
Date_of_Scan = Tue May 18 14:48:42 2004

source_name: Salmonella enterica subsp. enterica serovar Galinarum biovar Pullorum SARB51 gDNA


title: GC2_SgJ91_MZ630_5D169_1

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT4 MZ630 gDNA


title: GC2_MZ750_MZ630_5D358_1


title: GC2_SARB51_MZ630_5D137_1


title: GC2_MZ746_MZ630_5D357_1

description:
genomic comparison MZ746/MZ630
User - csantiviago
Date_of_Scan = Wed Aug 18 12:24:23 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT13a MZ746 gDNA


title: GC2_MZ743_MZ630_5D360_3


title: GC2_MZ743_MZ630_5D360_1


title: GC2_MZ746_MZ630_5D357_3


title: GC2_SGSC2377_MZ630_5D338_3

description:
genomic comparison SGSC2377/MZ630
User - PCheng
Date_of_Scan = Fri Aug 20 10:48:02 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT8 SGSC2377 gDNA


title: GC2_SARB20_MZ630_5D178_3

description:
genomic comparison SARB20/MZ630
User - PCheng
Date_of_Scan = Thu Jun 17 10:29:37 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis RDNC SARB20 gDNA


title: GC2_MZ634_MZ630_5D136_2

description:
genomic comparison MZ634/MZ630
User - PCheng
Date_of_Scan = Tue May 18 10:47:58 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT4 MZ634 gDNA


title: GC2_MZ746_MZ630_5D357_2


title: GC2_MZ634_MZ630_5D136_1


title: GC2_SARB20_MZ630_5D178_2


title: GC2_SGSC2377_MZ630_5D338_2


title: GC2_SGSC2377_MZ630_5D338_1


title: GC2_MZ634_MZ630_5D136_3


title: GC2_MZ649_MZ630_5D177_1

description:
genomic comparison MZ649/MZ630
User - PCheng
Date_of_Scan = Thu Aug 14 16:32:01 2003

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT2 MZ649 gDNA


title: GC2_MZ637_MZ630_5D336_2

description:
genomic comparison MZ637/MZ630
User - PCheng
Date_of_Scan = Fri Aug 20 14:36:59 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT5 MZ637 gDNA


title: GC2_MZ649_MZ630_5D177_3


title: GC2_MZ637_MZ630_5D336_3


title: GC2_SARB52_MZ630_5D176_3

description:
genomic comparison SARB52/MZ630
User - PCheng
Date_of_Scan = Fri Jun 11 12:12:03 2004

source_name: Salmonella enterica subsp. enterica serovar Gallinarum biovar Pullorum SARB52 gDNA


title: GC2_SARB20_MZ630_5D178_1


title: GC2_MZ636_MZ630_5D335_3

description:
genomic comparison MZ636/MZ630
User - PCheng
Date_of_Scan = Fri Aug 20 13:32:40 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT4b MZ636 gDNA


title: GC2_MZ637_MZ630_5D336_1


title: GC2_SARB17_MZ630_5D174_3

description:
genomic comparison SARB17/MZ630
User - PCheng
Date_of_Scan = Thu Jun 10 11:17:53 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis RDNC SARB17 gDNA


title: GC2_SARB52_MZ630_5D176_2


title: GC2_SARB17_MZ630_5D174_2


title: GC2_MZ636_MZ630_5D335_2


title: GC2_SARB52_MZ630_5D176_1


title: GC2_MZ636_MZ630_5D335_1


title: GC2_MZ745_MZ630_5D269_2

description:
genomic comparison MZ745/MZ630
User - csantiviago
Date_of_Scan = Wed Aug 18 17:19:01 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT35 MZ745 gDNA


title: GC2_MZ655_MZ630_5D173_2

description:
genomic comparison MZ655/MZ630
User - PCheng
Date_of_Scan = Fri May 28 11:09:43 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT23 MZ655 gDNA


title: GC2_MZ745_MZ630_5D269_3


title: GC2_MZ655_MZ630_5D173_3


title: GC2_MZ744_MZ630_5D268_1

description:
genomic comparison MZ744/MZ630
User - csantiviago
Date_of_Scan = Wed Aug 18 14:51:32 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT13a MZ744 gDNA


title: GC2_MZ672_MZ630_5D172_2

description:
genomic comparison MZ672/MZ630
User - PCheng
Date_of_Scan = Fri May 28 10:36:49 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis MZ672 gDNA


title: GC2_MZ672_MZ630_5D172_1


title: GC2_Sg9_MZ630_5D170_3

description:
genomic comparison Sg9/MZ630
User - PCheng
Date_of_Scan = Thu May 27 14:08:49 2004

source_name: Salmonella enterica subsp. enterica serovar Gallinarum biovar Gallinarum Sg9 gDNA


title: GC2_MZ744_MZ630_5D268_3


title: GC2_MZ745_MZ630_5D269_1


title: GC2_MZ672_MZ630_5D172_3


title: GC2_Sg9_MZ630_5D170_2


title: GC2_MZ744_MZ630_5D268_2


title: GC2_MZ646_MZ630_5D099_2

description:
genomic comparison MZ646/MZ630
User - PCheng
Date_of_Scan = Thu Jun 03 13:02:53 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT25 MZ646 gDNA


title: GC2_MZ655_MZ630_5D173_1


title: GC2_MZ646_MZ630_5D099_3


title: GC2_21027_MZ630_4D009_1

description:
genomic comparison 21027/MZ630
User - PCheng
Date_of_Scan = Wed Sep 10 13:32:51 2003

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT13a 21027 gDNA


title: GC2_21046_MZ630_4D010_3

description:
genomic comparison 21046/MZ630
User - PCheng
Date_of_Scan = Thu Sep 11 09:30:24 2003

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT13a 21046 gDNA

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT4 MZ630 gDNA


title: GC2_SARB18_MZ630_5D041_3

description:
genomic comparison SARB18/MZ630
User - PCheng
Date_of_Scan = Fri May 28 13:52:20 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT4 SARB18 gDNA


title: GC2_MZ647_MZ630_5D096_2

description:
genomic comparison MZ647/MZ630
User - PCheng
Date_of_Scan = Thu Jun 03 14:34:24 2004

source_name: Salmonella enterica subsp. enterica serovar Dublin MZ647 gDNA


title: GC2_21027_MZ630_4D009_3


title: GC2_MZ646_MZ630_5D099_1


title: GC2_MZ649_MZ630_5D177_2


title: GC2_SARB16_MZ630_5D013_2

description:
genomic comparison SARB16/MZ630
User - PCheng
Date_of_Scan = Tue May 25 14:33:29 2004

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT13a SARB16 gDNA


title: GC2_SARB18_MZ630_5D041_1


title: GC2_MZ647_MZ630_5D096_3


title: GC2_SARB18_MZ630_5D041_2


title: GC2_MZ647_MZ630_5D096_1


title: GC2_SARB16_MZ630_5D013_3


title: GC2_21027_MZ630_4D009_2


title: GC2_21046_MZ630_4D010_1


title: GC2_SARB16_MZ630_5D013_1


title: BxPC-3-vector_UA62001

status: Public on Aug 01 2005

city: Phoenix

first: Hong

last: Wang

address: 445 N 5th Street

department: Translational Drug Development Division

institute: Translational Genomics Research Institute

description:
empty vector expressed in pancreatic cancer BxPC-3 cell lines
Keywords = Agilent microarray and drug treatment

source_name: BxPC-3-vector cells, control for 24 hours, labeled with cy5

source_name: BxPC-3-vector cells treated with UA62001 for 24 hours, labeled with cy3


title: GC2_21046_MZ630_4D010_2


title: HDEC with ACA sera, time 24 hours

status: Public on Jul 30 2005

city: Boston

first: Syed

middle: S

last: Ahmed

state: MA

address: 715 Albany Street

institute: Boston University School of Medicine

description:
Human dermal endothelial cells exposed to 10% human control sera
Cells were plated in T75 flasks and grown to subconfluence and serum was removed at designated time point and cells were rinsed three times with PBS prior to extraction of RNA for microarray studies.
The cDNA from HDEC exposed to ACA SSc sera and that from Human Universal RNA (Stratagene, La Jolla, California) as a common probe across all the arrays (reference-experimental design) was covalently coupled with separate Cy5 and Cy3 monoreactive fluors.
RNA was extracted from the cell cultures using TRIzol (Invitrogen, Carlsbad, California).  The RNA was DNase I-treated (Invitrogen) and purified on an RNeasy column (Qiagen, Valencia, California) with purity being assessed by UV absorbance (260/280 ratio >1.8) and by agarose gel analysis.  We utilized the hapten-antibody method (Micromax TSA kit, Perkin-Elmer, Boston, Massachusetts) for labeling of the probes with Cy3 and Cy5 which required a minimum of ~5 mg of input total RNA.
After drying, the array images were acquired on a confocal dual-laser scanner (Lumonics ScanArray Lite, Perkin-Elmer) equipped with Scanarray and Quantarray software (Perkin-Elmer).  Background corrected intensity expression levels were normalized per channel using Cluster as follows:  one cycle of log transformation, five cycles of median centering of genes, and five cycles of normalizing genes to generate a log-transformed, median polished, and normal (magnitudes close to 1.0) dataset.  Arrays (representing sequential serum incubation times) were not adjusted.
Hierarchical correlation (centered) complete linkage clustering was performed of genes using Cluster and illustrated in heat maps by TreeView.  Pathway Analysis:  a Gene Microarray Pathway Profiler (GenMAPP) http://www.genmapp.org/) was utilized to visualize gene expression data on maps representing biological pathways and groupings of genes pertinent to apoptosis, angiogenesis, and autoantigens.  Fold ratios were calculated by dividing normalized gene expression data for HDEC exposed to either control sera or SSc sera (at 1, 6, 12, and 24 hours) by normalized gene expression data for HDEC exposed to control sera for 5 minutes.  A difference of three-fold was arbitrarily chosen to enable GenMAPP to assign colors representing upregulation and downregulation in pathways of biological significance and narrow the number of genes analyzed to < 500.  The intention was to utilize Cluster, TreeView, and GenMAPP to qualitatively illustrate the patterns of gene expression induced in HDEC by sequential serum stimulation.
Triplicate sets of data were averaged and experimental data was normalized by dividing with respective spot intensity for reference RNA
Keywords = human dermal endothelial cell, scleroderma

source_name: HDEC with ACA sera, 24 hours

source_name: Universal human reference RNA


title: GC2_SARB17_MZ630_5D174_1

source_name: Salmonella enterica subsp. enterica serovar Enteritidis RDNC SARB17 gDNA


title: HDEC with ACA sera, time 12 hours

source_name: HDEC with ACA sera, 12 hours


title: HDEC with SCL70 sera, time 12 hours

description:
Human dermal endothelial cells exposed to 10% human control sera
Cells were plated in T75 flasks and grown to subconfluence and serum was removed at designated time point and cells were rinsed three times with PBS prior to extraction of RNA for microarray studies.
The cDNA from HDEC exposed to SCL70 SSc sera and that from Human Universal RNA (Stratagene, La Jolla, California) as a common probe across all the arrays (reference-experimental design) was covalently coupled with separate Cy5 and Cy3 monoreactive fluors.
RNA was extracted from the cell cultures using TRIzol (Invitrogen, Carlsbad, California).  The RNA was DNase I-treated (Invitrogen) and purified on an RNeasy column (Qiagen, Valencia, California) with purity being assessed by UV absorbance (260/280 ratio >1.8) and by agarose gel analysis.  We utilized the hapten-antibody method (Micromax TSA kit, Perkin-Elmer, Boston, Massachusetts) for labeling of the probes with Cy3 and Cy5 which required a minimum of ~5 mg of input total RNA.
After drying, the array images were acquired on a confocal dual-laser scanner (Lumonics ScanArray Lite, Perkin-Elmer) equipped with Scanarray and Quantarray software (Perkin-Elmer).  Background corrected intensity expression levels were normalized per channel using Cluster as follows:  one cycle of log transformation, five cycles of median centering of genes, and five cycles of normalizing genes to generate a log-transformed, median polished, and normal (magnitudes close to 1.0) dataset.  Arrays (representing sequential serum incubation times) were not adjusted.
Hierarchical correlation (centered) complete linkage clustering was performed of genes using Cluster and illustrated in heat maps by TreeView.  Pathway Analysis:  a Gene Microarray Pathway Profiler (GenMAPP) http://www.genmapp.org/) was utilized to visualize gene expression data on maps representing biological pathways and groupings of genes pertinent to apoptosis, angiogenesis, and autoantigens.  Fold ratios were calculated by dividing normalized gene expression data for HDEC exposed to either control sera or SSc sera (at 1, 6, 12, and 24 hours) by normalized gene expression data for HDEC exposed to control sera for 5 minutes.  A difference of three-fold was arbitrarily chosen to enable GenMAPP to assign colors representing upregulation and downregulation in pathways of biological significance and narrow the number of genes analyzed to < 500.  The intention was to utilize Cluster, TreeView, and GenMAPP to qualitatively illustrate the patterns of gene expression induced in HDEC by sequential serum stimulation.
Triplicate sets of data were averaged and experimental data was normalized by dividing with respective spot intensity for reference RNA
Keywords = human dermal endothelial cell, scleroderma

source_name: HDEC with SCL70 sera, 12 hours


title: HDEC with SCL70 sera, time 6 hours

source_name: HDEC with SCL70 sera, 6 hours


title: BxPC-3-DPC4_UA62001

description:
Wildtype DPC4 reexpress in pancreatic cancer BxPC-3 cell lines
Keywords = Agilent microarray and drug treatment

source_name: BxPC-3-DPC4 cells, control for 24 hours and labeled with cy5

source_name: BxPC-3-DPC4 cells treated with UA62001 for 24 hours and labeled with cy3


title: HDEC with SCL70 sera, time 24 hours

source_name: HDEC with SCL70 sera, 24 hours


title: HDEC with ACA sera, time 1 hour

source_name: HDEC with ACA sera, 1 hour


title: HDEC with ACA sera, time 6 hours

source_name: HDEC with ACA sera, 6 hours


title: HDEC with control sera, time 12 hours

description:
Human dermal endothelial cells exposed to 10% human control sera
Cells were plated in T75 flasks and grown to subconfluence and serum was removed at designated time point and cells were rinsed three times with PBS prior to extraction of RNA for microarray studies.
The cDNA from HDEC exposed to control sera and that from Human Universal RNA (Stratagene, La Jolla, California) as a common probe across all the arrays (reference-experimental design) was covalently coupled with separate Cy5 and Cy3 monoreactive fluors.
RNA was extracted from the cell cultures using TRIzol (Invitrogen, Carlsbad, California).  The RNA was DNase I-treated (Invitrogen) and purified on an RNeasy column (Qiagen, Valencia, California) with purity being assessed by UV absorbance (260/280 ratio >1.8) and by agarose gel analysis.  We utilized the hapten-antibody method (Micromax TSA kit, Perkin-Elmer, Boston, Massachusetts) for labeling of the probes with Cy3 and Cy5 which required a minimum of ~5 mg of input total RNA.
After drying, the array images were acquired on a confocal dual-laser scanner (Lumonics ScanArray Lite, Perkin-Elmer) equipped with Scanarray and Quantarray software (Perkin-Elmer).  Background corrected intensity expression levels were normalized per channel using Cluster as follows:  one cycle of log transformation, five cycles of median centering of genes, and five cycles of normalizing genes to generate a log-transformed, median polished, and normal (magnitudes close to 1.0) dataset.  Arrays (representing sequential serum incubation times) were not adjusted.
Hierarchical correlation (centered) complete linkage clustering was performed of genes using Cluster and illustrated in heat maps by TreeView.  Pathway Analysis:  a Gene Microarray Pathway Profiler (GenMAPP) http://www.genmapp.org/) was utilized to visualize gene expression data on maps representing biological pathways and groupings of genes pertinent to apoptosis, angiogenesis, and autoantigens.  Fold ratios were calculated by dividing normalized gene expression data for HDEC exposed to either control sera or SSc sera (at 1, 6, 12, and 24 hours) by normalized gene expression data for HDEC exposed to control sera for 5 minutes.  A difference of three-fold was arbitrarily chosen to enable GenMAPP to assign colors representing upregulation and downregulation in pathways of biological significance and narrow the number of genes analyzed to < 500.  The intention was to utilize Cluster, TreeView, and GenMAPP to qualitatively illustrate the patterns of gene expression induced in HDEC by sequential serum stimulation.
Triplicate sets of data were averaged and experimental data was normalized by dividing with respective spot intensity for reference RNA
Keywords = human dermal endothelial cell, scleroderma

source_name: HDEC with control sera, 12 hours


title: GC2_Sg9_MZ630_5D170_1

source_name: Salmonella enterica subsp. enterica serovar Gallinarum biovar Gallinarum Sg9 gDNA

source_name: Salmonella enterica subsp. enterica serovar Enteritidis PT4 MZ630 gDNA


title: HDEC with control sera, time 1 hour

source_name: HDEC with control sera, 1 hour


title: HDEC with control sera, time 5 minutes

source_name: HDEC with control sera, 5 minutes


title: PAVEC 20 48 vs. PAEC 20 48 Slide_2_Array_2

city: Atlanta

first: Jonathan

middle: T

last: Butcher

state: GA

address: 315 Ferst Dr.

department: Mechanical Engineering

institute: Georgia Institute of Technology

description:
Porcine aortic and aortic valve endothelial cells isolated through collagenase digestion, cultured in DMEM with 10% FBS, 1% Pen-strep, and 1% L-glut.  Cells used at passage 5.
After experiments, cells were harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents.
Total RNA from shear and control experiments were independently reverse-transcribed and labeled (Cy3 and Cy5) according to the Agilent Fluorescent Direct Label Protocol.  Samples were then hybridized overnight at 65C.
green is PAVEC shear, red is PAEC shear
Fluorescent array images were collected for both Cy3 and Cy5 with the Agilent Array Scanner.  Using the Agilent Feature Extraction Software, spots were identified, measured for fluorescence intensity, local background, and arraywide parameters used to normalize the signals.  Outliers and saturated spots were rejected according to 1.42xIQR, and local backgroud subtracted from the signals.  Signals were then normalized to remove dye bias and arraywide drift in flourescence.
Sample statistics were conducted using two factor mixed ANOVA with P<0.005 considered significant.  Only samples with measurable intensities in both channels for all six arrays were included in the analysis.
Keywords = aortic valve endothelial, shear stress

organism: Sus scrofa

source_name: Aortic valve endothelial cells exposed to 48 hours of 20 dynes/cm2 steady laminar shear stress

source_name: Aortic endothelial cells exposed to 48 hours of 20 dynes/cm2 steady laminar shear stress


title: PAVEC 20 48 vs. PAEC 20 48 Slide_3_Array_1


title: HDEC with control sera, time 6 hours

source_name: HDEC with control sera, 6 hours

source_name: Universal human reference RNA


title: HDEC with control sera, time 24 hours

source_name: HDEC with control sera, 24 hours


title: PAVEC 20 48 vs. PAEC 20 48 Slide_2_Array_1


title: PAVEC 20 48 vs. PAEC 20 48 Slide_3_Array_2


title: PAVEC 20 48 vs. PAEC 20 48 Slide_1_Array_1


title: PAVEC C 48 vs. PAEC C 48 Slide_2_Array_2

description:
Porcine aortic and aortic valve endothelial cells isolated through collagenase digestion, cultured in DMEM with 10% FBS, 1% Pen-strep, and 1% L-glut.  Cells used at passage 5.
After experiments, cells were harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents.
Total RNA from shear and control experiments were independently reverse-transcribed and labeled (Cy3 and Cy5) according to the Agilent Fluorescent Direct Label Protocol.  Samples were then hybridized overnight at 65C.
green is PAVEC static control, red is PAEC static control
Fluorescent array images were collected for both Cy3 and Cy5 with the Agilent Array Scanner.  Using the Agilent Feature Extraction Software, spots were identified, measured for fluorescence intensity, local background, and arraywide parameters used to normalize the signals.  Outliers and saturated spots were rejected according to 1.42xIQR, and local backgroud subtracted from the signals.  Signals were then normalized to remove dye bias and arraywide drift in flourescence.
Sample statistics were conducted using two factor mixed ANOVA with P<0.005 considered significant.  Only samples with measurable intensities in both channels for all six arrays were included in the analysis.
Keywords = aortic valve endothelial, shear stress

source_name: Aortic valve endothelial cells in 48 hour static culture

source_name: Aortic endothelial cells in 48 hour static culture


title: PAVEC C 48 vs. PAEC C 48 Slide_2_Array_1


title: PAVEC 20 48 vs. PAEC 20 48 Slide_1_Array_2


title: PAVEC C 48 vs. PAEC C 48 Slide_3_Array_1


title: PAVEC C 48 vs. PAEC C 48 Slide_1_Array_2


title: PAEC 20 48 vs. PAEC C 48 Slide_1_Array_2

description:
Porcine aortic endothelial cells isolated through collagenase digestion, cultured in DMEM with 10% FBS, 1% Pen-strep, and 1% L-glut.  Cells used at passage 5.
After experiments, cells were harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents.
Total RNA from shear and control experiments were independently reverse-transcribed and labeled (Cy3 and Cy5) according to the Agilent Fluorescent Direct Label Protocol.  Samples were then hybridized overnight at 65C.
green is PAEC shear, red is PAEC static control
Fluorescent array images were collected for both Cy3 and Cy5 with the Agilent Array Scanner.  Using the Agilent Feature Extraction Software, spots were identified, measured for fluorescence intensity, local background, and arraywide parameters used to normalize the signals.  Outliers and saturated spots were rejected according to 1.42xIQR, and local backgroud subtracted from the signals.  Signals were then normalized to remove dye bias and arraywide drift in flourescence.
Sample statistics were conducted using two factor mixed ANOVA with P<0.005 considered significant.  Only samples with measurable intensities in both channels for all six arrays were included in the analysis.
Keywords = aortic endothelial, shear stress


title: PAEC 20 48 vs. PAEC C 48 Slide_3_Array_2


title: PAEC 20 48 vs. PAEC C 48 Slide_1_Array_1


title: PAEC 20 48 vs. PAEC C 48 Slide_2_Array_1


title: PAEC 20 48 vs. PAEC C 48 Slide_3_Array_1


title: PAVEC 20 48 vs. PAVEC C 48 Slide_3_Array_2

description:
Porcine aortic valve endothelial cells isolated through collagenase digestion, cultured in DMEM with 10% FBS, 1% Pen-strep, and 1% L-glut.  Cells used at passage 5.
After experiments, cells were harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents.
Total RNA from shear and control experiments were independently reverse-transcribed and labeled (Cy3 and Cy5) according to the Agilent Fluorescent Direct Label Protocol.  Samples were then hybridized overnight at 65C.
green is PAVEC shear, red is PAVEC static control
Fluorescent array images were collected for both Cy3 and Cy5 with the Agilent Array Scanner.  Using the Agilent Feature Extraction Software, spots were identified, measured for fluorescence intensity, local background, and arraywide parameters used to normalize the signals.  Outliers and saturated spots were rejected according to 1.42xIQR, and local backgroud subtracted from the signals.  Signals were then normalized to remove dye bias and arraywide drift in flourescence.
Sample statistics were conducted using two factor mixed ANOVA with P<0.005 considered significant.  Only samples with measurable intensities in both channels for all six arrays were included in the analysis.
Keywords = aortic valve endothelial, shear stress


title: PAEC 20 48 vs. PAEC C 48 Slide_2_Array_2


title: PAVEC C 48 vs. PAEC C 48 Slide_3_Array_2


title: PAVEC C 48 vs. PAEC C 48 Slide_1_Array_1


title: PAVEC 20 48 vs. PAVEC C 48 Slide_3_Array_1


title: PAVEC 20 48 vs. PAVEC C 48 Slide_2_Array_2


title: HDEC with SCL70 sera, time 1 hour

source_name: HDEC with SCL70 sera, 1 hour


title: PAVEC 20 48 vs. PAVEC C 48 Slide_2_Array_1


title: GC2_SARB51_MZ630_5D137_2

description:
genomic comparison SARB51/MZ630
User - PCheng
Date_of_Scan = Tue May 18 14:48:42 2004

source_name: Salmonella enterica subsp. enterica serovar Galinarum biovar Pullorum SARB51 gDNA


title: 2091N

status: Public on Jul 20 2005

city: Tel Aviv

first: Elinor

last: Dehan

country: Israel

institute: Tel Aviv University

description: Normal tissue adjacent to sample 2091T

source_name: Lung Normal


title: 2092N

description: Normal tissue adjacent to sample 2092T


title: 2075N

description: Normal tissue adjacent to sample 2075T


title: 2073N

description: Normal tissue adjacent to sample 2073T


title: 2079N

description: Normal tissue adjacent to sample 2079T


title: 2097T

description: Squamous Cell Carcinoma. Male. Stage 1.

source_name: Lung Cancer


title: 2093T

description: Adenocarcinoma. Female. Stage 1.


title: 2065N

description: Normal tissue adjacent to sample 2065T


title: PAVEC 20 48 vs. PAVEC C 48 Slide_1_Array_1


title: PAVEC 20 48 vs. PAVEC C 48 Slide_1_Array_2


title: 2000N_1

description: Commercial normal lung RNA

source_name: Normal Lung


title: 2099T

description: Squamous Cell Carcinoma. Male. Stage 2.


title: 2068T

description: Squamous Cell Carcinoma. Male. Stage 2.


title: 2059N

description: Normal tissue adjacent to sample 2059T


title: 2000N_2

description: Commercial normal lung RNA


title: 2082T

description: Colon Metastasis. Female.


title: 2091T

description: Squamous Cell Carcinoma. Male. Stage 3.


title: lung - N. brasiliensis infection

status: Public on Jul 27 2005

city: San Francisco

first: David

last: Voehringer

address: 521, Parnassus Ave

department: Medicine, Infectious diseases

institute: HHMI

description:
RNA was extracted from total lung tissue of wt or stat6 deficient mice (3 mice each) on day 9 after N. brasiliensis infection, transcribed in cDNA incorporating aminoallyl-dUTP. WT samles were labeled with Cy5 and Stat6-deficient samples with Cy3 and hybridized to spotted oligonucleotide arrays
Lot batch = platform GPL929

source_name: Total lung tissue from N. brasiliensis infected wild-type mice

source_name: Total lung tissue from N. brasiliensis infected Stat6-deficient mice


title: 2081T

description: Squamous Cell Carcinoma. Male. Stage 1.


title: 2083T

description: Squamous Cell Carcinoma. Female. Stage 1.


title: 2092T

description: Squamous Cell Carcinoma. Male. Stage 3.


title: 2086T

description: Renal Metastasis. Male.


title: 2087T

description: Squamous Cell Carcinoma. Male. Stage 1.


title: 2076T

description: Squamous Cell Carcinoma. Male. Stage 1.


title: 2090T

description: AdenoSquamous. Male. Stage 1.


title: 2079T

description: Squamous Cell Carcinoma. Male. Stage 3.


title: 2080T

description: Renal Metastasis. Male.


title: small intestine - N. brasiliensis infection

description:
Total RNA was extracted from small intestine of wt or stat6 deficient mice (3 mice per group) on day 9 after N. brasiliensis infection, transcribed in cDNA incorporating aminoallyl-dUTP, labeled with Cy5 (WT sample) or Cy3 (stat6-deficient sample) and hybridized to spotted oligonucleotide arrays.
Lot batch = platform GPL929

source_name: small intestine from N. brasiliensis infected wt mice

source_name: small intestine from N. brasiliensis infected stat6 deficient mice


title: 2075T

description: Squamous Cell Carcinoma. Male. Stage 2.


title: 2073T

description: Squamous Cell Carcinoma. Male. Stage 2.


title: 2069T

description: Squamous Cell Carcinoma. Male. Stage 3.


title: 2062T

description: Adenocarcinoma. Male. Stage 1.


title: 2022T

description: Adenocarcinoma. Male. Stage 2.


title: 2002T

description: Adenocarcinoma. Male. Stage 1.


title: 2009T

description: Squamous Cell Carcinoma. Male. Stage 1.


title: 2001T

description: Squamous Cell Carcinoma. Femeale. Stage 2.


title: 2014T

description: Squamous Cell Carcinoma. Male. Stage 1.


title: 2010T

description: Adenocarcinoma . Femeale. Stage 2.


title: 2011T

description: Squamous Cell Carcinoma. Femeale. Stage 1.


title: 1287_RNT1_5_2

status: Public on Jul 19 2005

city: Los Angeles

first: Guillaume

middle: Francois

last: Chanfreau

address: 607 Charles E. Young Drive East

department: Chemistry and Biochemistry

institute: UCLA

description: Strain background is BMA64 with RNT1 gene deleted with the TRP marker Media is SD -Trp (synthetic dextrose minimal media missing tryptophan) Cells were grown until midlog and harvested at OD600=0.4; MAS5 (Statistical Algorithm) Scaling:All Probe Sets Target Signal 500;Normalization:All Probe Sets; Alpha1=0.04; Alpha2=0.06; Tau=0.015

organism: Saccharomyces cerevisiae

source_name: Rnt1 knockout BMA64


title: 2020T

description: Adenocarcinoma. Femeale. Stage 3.


title: 1286_RNT1_4


title: 1285_RNT1_3


title: 2017T

description: Adenocarcinoma. Femeale. Stage 3.


title: 1280_BMA_3

description: Strain background is BMA64 with plasmid expressing TRP marker Media is SD -Trp (synthetic dextrose minimal media missing tryptophan) Cells were grown until midlog and harvested at OD600=0.4; MAS5 (Statistical Algorithm) Scaling:All Probe Sets Target Signal 500;Normalization:All Probe Sets; Alpha1=0.04; Alpha2=0.06; Tau=0.015

source_name: Wild-type BMA64


title: 1284_RNT1_2


title: 1278_BMA_1


title: 1281_BMA_4


title: 1279_BMA_2


title: 24 hours

status: Public on Jul 18 2005

first: Damian

last: LaGamba

address: 220 Longwood Ave.

department: Cell Biology

institute: Harvard Medical School

description:
Palate medial edge epithelium from CF-1 ED13.5 mouse embryos.
Palatal shelves were placed together in culture for 24 hours post initial contact.
Epithelium was isolated using Dispase II (Roche) enzyme.
RNA isolation was performed using RNeasy Mini kit (Qiagen).
RNA amplification and labeling was performed using RiboAmp RNA amplification kit (Arcturus) and ENZO Bioarray high yield labeling kit (Affymetrix). Hybridization, fluidics, scanning were performed at the Biopolymers facility at Harvard Medical School: Department of Genetics. Data analysis was conducted with Microarray Suite 5.0 (Affymetrix) and GeneSpring 6.0 (Silicon Genetics) software.

source_name: Fused palate medial edge epithelium undergoing epithelial-mesenchymal transformation


title: 1282_BMA_5