title: NoCa14-Mock


title: NoCa14-IR

status: Public on Sep 06 2004

type: RNA

city: Stanford

first: Wan-Jen

last: Hong

state: CA

address: 269 Campus Dr., CCSR Room 1140

department: Medicine/Biochemistry

country: USA

institute: Stanford University School of Medicine

description:
Peripheral blood lymphocytes from a total of 57 patients were immortalized with Epstein-Barr virus.  Fourteen radiation-therapy patients suffered unusual levels of radiation toxicity (RadS).  Thirteen radiation-therapy patients with limited toxicity (RadC) were enrolled as controls.  Fifteen patients diagnosed with skin cancer before age 40 (SkCa) were used as a second group of controls.  Fifteen healthy subjects without any history of cancer (NoCa) were matched to the skin cancer patients and used as a third group of controls.

Cells were exposed to mock treatment (Mock), ultra-violet radiation (UV), or ionizing radiation (IR).  For UV radiation treatment, cells were exposed to 10 J/m^2 and harvested for RNA 24 hours later.  For IR treatment, cells were exposed to 5 Gy of IR and harvested for RNA 4 hours later.  For example, RadS1-Mock refers to cells from radiation sensitive patient 1 exposed to mock treatment.

Data were analyzed with Affymetrix MAS version 4.0.

Normalization – A reference data set was generated by averaging the expression of each gene over all data sets. The data for each hybridization were compared with the reference data set in a cube root scatter plot. A linear least-squares fit to the cube root scatter plot was then used to normalize each hybridization.
Keywords = Gene expression in lymphoid cells of cancer patients

molecule: total RNA

organism: Homo sapiens

source_name: Lymphoblastoid cells immortalized with Epstein-Barr virus


title: NoCa15-IR


title: NoCa13-UV


title: SkCa2-Mock


title: NoCa15-UV


title: NoCa13-IR


title: NoCa12-IR


title: NoCa12-Mock


title: NoCa11-UV


title: SkCa3-IR


title: NoCa11-Mock


title: NoCa12-UV


title: NoCa13-Mock


title: NoCa10-Mock


title: NoCa10-IR


title: NoCa11-IR


title: NoCa10-UV


title: NoCa9-UV


title: NoCa6-Mock


title: NoCa5-UV


title: NoCa8-Mock


title: NoCa9-IR


title: NoCa7-IR


title: NoCa7-Mock


title: NoCa9-Mock


title: NoCa7-UV


title: NoCa6-IR


title: NoCa6-UV


title: NoCa8-IR


title: NoCa4-IR


title: NoCa5-Mock


title: NoCa5-IR


title: NoCa4-Mock


title: NoCa3-IR


title: NoCa3-Mock


title: NoCa3-UV


title: NoCa2-UV


title: NoCa4-UV


title: NoCa2-Mock


title: NoCa1-Mock


title: NoCa1-UV


title: RENT1-2

status: Public on Aug 25 2004

city: Baltimore

first: Joshua

middle: T

last: Mendell

state: MD

address: 733 N. Broadway, BRB 471

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

description: HeLa cells were treated with siRNA directed against RENT1/hUPF1 (as described in Mendell et al., Science, 2002; PubMed ID:12228722).  RNA was isolated using Trizol and Qiagen RNeasy kit.

source_name: HeLa cells treated with RENT1 siRNA


title: RENT1-1


title: 845SFMC

status: Public on Aug 11 2004

city: Cincinnati

first: Michael

last: Barnes

state: OH

address: 3333 Burnet Ave

department: Rheumatology

institute: Cincinnati Childrens Hospital Medical Center

description:
SFMC isolated by Ficoll gradient centrifugation from JSpA patient
Biotinylated cRNA was synthesized from total RNA (Enzo; Farmingdale, NY) and processed according to the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix; Santa Clara, CA).  57 samples: 5 pauciarticular PBMC, 15 polyarticular PBMC, 11 control PMBC, 6 JSpA PBMC, 5 pauciarticular SFMC, 10 polyarticular PBMC, 5 JSpA SFMC classified by course.
Keywords = Juvenile spondyloarthropahty (JSpA), synovial fluid mononuclear cells (SFMC)

source_name: SFMC


title: 872SFMC

description:
SFMC isolated by Ficoll gradient centrifugation from polyarticular JRA patient
Biotinylated cRNA was synthesized from total RNA (Enzo; Farmingdale, NY) and processed according to the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix; Santa Clara, CA).  57 samples: 5 pauciarticular PBMC, 15 polyarticular PBMC, 11 control PMBC, 6 JSpA PBMC, 5 pauciarticular SFMC, 10 polyarticular PBMC, 5 JSpA SFMC classified by course.
Keywords = Polyarticular course, juvenile rheumatoid arthritis (JRA), synovial fluid mononuclear cells (SFMC)


title: 9245SFMC


title: Luciferase control 1

description: HeLa cells were treated with siRNA directed against firefly luciferase (as described in Mendell et al., Science, 2002; PubMed ID:12228722).  RNA was isolated using Trizol and Qiagen RNeasy kit.

source_name: HeLa cells treated with luciferase siRNA


title: 850SFMC


title: 878SFMC


title: NoCa2-IR


title: 18042SFMC


title: 9137SFMC


title: 993SFMC


title: 9272SFMC


title: Luciferase control 2

source_name: HeLa cells treat with luciferase siRNA


title: 18057SFMC


title: 7177SFMC


title: NoCa1-IR

description:
Peripheral blood lymphocytes from a total of 57 patients were immortalized with Epstein-Barr virus.  Fourteen radiation-therapy patients suffered unusual levels of radiation toxicity (RadS).  Thirteen radiation-therapy patients with limited toxicity (RadC) were enrolled as controls.  Fifteen patients diagnosed with skin cancer before age 40 (SkCa) were used as a second group of controls.  Fifteen healthy subjects without any history of cancer (NoCa) were matched to the skin cancer patients and used as a third group of controls.

Cells were exposed to mock treatment (Mock), ultra-violet radiation (UV), or ionizing radiation (IR).  For UV radiation treatment, cells were exposed to 10 J/m^2 and harvested for RNA 24 hours later.  For IR treatment, cells were exposed to 5 Gy of IR and harvested for RNA 4 hours later.  For example, RadS1-Mock refers to cells from radiation sensitive patient 1 exposed to mock treatment.  Data were analyzed with Affymetrix MAS version 4.0.

Normalization – A reference data set was generated by averaging the expression of each gene over all data sets. The data for each hybridization were compared with the reference data set in a cube root scatter plot. A linear least-squares fit to the cube root scatter plot was then used to normalize each hybridization.
Keywords = Gene expression in lymphoid cells of cancer patients


title: 831SFMC


title: 824SFMC


title: 1073SFMC


title: 9264SFMC

description:
SFMC isolated by Ficoll gradient centrifugation from pauciarticular JRA patient
Biotinylated cRNA was synthesized from total RNA (Enzo; Farmingdale, NY) and processed according to the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix; Santa Clara, CA).  57 samples: 5 pauciarticular PBMC, 15 polyarticular PBMC, 11 control PMBC, 6 JSpA PBMC, 5 pauciarticular SFMC, 10 polyarticular PBMC, 5 JSpA SFMC classified by course.
Keywords = Pauciarticular course, juvenile rheumatoid arthritis (JRA), synovial fluid mononuclear cells (SFMC)


title: 1087PBSFMC


title: 817SFMC


title: 1095PBMC

description:
PBMC isolated by Ficoll gradient centrifugation from control
Biotinylated cRNA was synthesized from total RNA (Enzo; Farmingdale, NY) and processed according to the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix; Santa Clara, CA).  57 samples: 5 pauciarticular PBMC, 15 polyarticular PBMC, 11 control PMBC, 6 JSpA PBMC, 5 pauciarticular SFMC, 10 polyarticular PBMC, 5 JSpA SFMC classified by course.
Keywords = Control, peripheral blood mononuclear cell (PBMC)

source_name: PBMC


title: 7118.3PBMC


title: 1087CTRPBMC


title: 9161SFMC


title: 976SFMC


title: 8003SFMC


title: 7021.31PBMC


title: 7113.3PBMC


title: NoCa8-UV


title: 9245PBMC

description:
PBMC isolated by Ficoll gradient centrifugation from JSpA patient
Biotinylated cRNA was synthesized from total RNA (Enzo; Farmingdale, NY) and processed according to the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix; Santa Clara, CA).  57 samples: 5 pauciarticular PBMC, 15 polyarticular PBMC, 11 control PMBC, 6 JSpA PBMC, 5 pauciarticular SFMC, 10 polyarticular PBMC, 5 JSpA SFMC classified by course.
Keywords = Juvenile spondyloarthropathy (JSpA), peripheral blood mononuclear cells (PBMC)


title: 1083PBMC


title: 1082PBMC


title: 7149.3PBMC


title: 1089PBMC


title: 1085PBMC


title: 9150PBMC


title: 845PBMC


title: 872PBMC

description:
PBMC isolated by Ficoll gradient centrifugation from polyaticular course JRA patient
Biotinylated cRNA was synthesized from total RNA (Enzo; Farmingdale, NY) and processed according to the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix; Santa Clara, CA).  57 samples: 5 pauciarticular PBMC, 15 polyarticular PBMC, 11 control PMBC, 6 JSpA PBMC, 5 pauciarticular SFMC, 10 polyarticular PBMC, 5 JSpA SFMC classified by course.
Keywords = Polyarticular course, juvenile rheumatoid arthritis (JRA), peripheral blood mononuclear cells (PBMC)


title: 878PBMC


title: 18057PBMC


title: 9137PBMC


title: 7177PBMC


title: 9272PBMC


title: 912PBMC


title: 894PBMC


title: 1081PBMC


title: 1087PBMC


title: 18042PBMC


title: 801PBMC


title: 19PBMC


title: 831PBMC


title: 850PBMC


title: 1073PBMC


title: 824PBMC


title: 976PBMC

description:
PBMC isolated by Ficoll gradient centrifugation from pauciaticular course JRA patient
Biotinylated cRNA was synthesized from total RNA (Enzo; Farmingdale, NY) and processed according to the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix; Santa Clara, CA).  57 samples: 5 pauciarticular PBMC, 15 polyarticular PBMC, 11 control PMBC, 6 JSpA PBMC, 5 pauciarticular SFMC, 10 polyarticular PBMC, 5 JSpA SFMC classified by course.
Keywords = Pauciarticular course, juvenile rheumatoid arthritis (JRA), peripheral blood mononuclear cells (PBMC)


title: 817PBMC


title: 8003PBMC


title: 9264PBMC


title: JF15dR1

status: Public on Jul 29 2004

city: Austin

first: James

middle: C

last: Fleet

state: TX

address: 1400 Barbara Jordan Blvd

department: Nutritional Sciences

institute: University of Texas at Austin

description:
15 day culture of Caco-2 BBe; 11 d post- confluent; differentiated; RNA isolated by TriReagent; Replicate 1 of 4.
Keywords = intestine
Keywords = colon
Keywords = proliferating

source_name: Caco-2; BBe; intestine


title: JF15dR4

description:
15 day culture of Caco-2 BBe; 11 d post- confluent; differentiated; RNA isolated by TriReagent; Replicate 4 of 4.
Keywords = intestine
Keywords = colon
Keywords = proliferating


title: JF15dR3

description:
15 day culture of Caco-2 BBe; 11 d post- confluent; differentiated; RNA isolated by TriReagent; Replicate 3 of 4.
Keywords = intestine
Keywords = colon
Keywords = proliferating


title: 9161PBMC


title: JF15dR2

description:
15 day culture of Caco-2 BBe; 11 d post- confluent; differentiated; RNA isolated by TriReagent; Replicate 2 of 4.
Keywords = intestine
Keywords = colon
Keywords = proliferating


title: JF8dR1

description:
8 day culture of Caco-2 BBe; 4 d post- confluent; RNA isolated by TriReagent; Replicate 1 of 4.
Keywords = intestine
Keywords = colon
Keywords = proliferating


title: JF2dR4

description:
2 day culture of Caco-2 BBe; 50% confluent; RNA isolated by TriReagent; Replicate 4 of 4.
Keywords = intestine
Keywords = colon
Keywords = proliferating


title: JF8dR2

description:
8 day culture of Caco-2 BBe; 4 d post- confluent; RNA isolated by TriReagent; Replicate 2 of 4.
Keywords = intestine
Keywords = colon
Keywords = proliferating


title: JF8dR3

description:
8 day culture of Caco-2 BBe; 4 d post- confluent; RNA isolated by TriReagent; Replicate 3 of 4.
Keywords = intestine
Keywords = colon
Keywords = proliferating


title: JF8dR4

description:
8 day culture of Caco-2 BBe; 4 d post- confluent; RNA isolated by TriReagent; Replicate 4 of 4.
Keywords = intestine
Keywords = colon
Keywords = proliferating


title: JF2dR3

description:
2 day culture of Caco-2 BBe;
50% confluent;
RNA isolated by TriReagent;
Replicate 3 of 4.
Keywords = intestine
Keywords = colon
Keywords = proliferating


title: JF2dR2

description:
2 day culture of Caco-2 BBe;
50% confluent;
RNA isolated by TriReagent;
Replicate 2 of 4.
Keywords = intestine
Keywords = colon
Keywords = proliferating


title: JF2dR1

description:
2 day cultures of the BBe line of Caco-2
(50% confluent)
Replicate 1 of 4
RNA isolated by TriReagent

source_name: Caco-2, BBe, intestine


title: 106 year old female

status: Public on Jul 21 2004

city: Boston

first: Tao

last: Lu

state: MA

address: 300 Longwood Ave

department: Neurology

institute: The Children's Hospital

description:
The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals.
Keywords = human brain aging

source_name: human frontal cortex


title: 91 year old male


title: 87 year old female


title: 90 year old male


title: 95 year old male


title: 85 year old male


title: 80 year old male


title: 90 year old female


title: 73 year old male


title: 66 year old male


title: 77 year old male


title: 61 year old female


title: 71 year old female


title: 53 year old male


title: 70 year old male


title: 52 year old male


title: 45 year old male


title: 48 year old female


title: 42 year old male


title: 56 year old female


title: 36 year old female


title: 37 year old male


title: 40 year old male


title: 29 year old male


title: 27 year old female


title: 30 year old female


title: 26 year old male


title: NR3BX

status: Public on Jul 14 2004

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

description:
Clinical status: sample from transplant with renal dysfunction without rejection
Age: 61
Sex: Male
Immunosupression: SRL/MMF/P
Histopathology: ATN
Donor type: LD
Scr (mg/dL): 5.2
Days post transplant: 11
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant

source_name: kidney


title: NR8BX

description:
Clinical status: sample from transplant with renal dysfunction without rejection
Age: 22
Sex: Female
Immunosupression: FK/MMF/P
Histopathology: FSGS
Donor type: LD
Scr (mg/dL): 3.3
Days post transplant: 78
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: NR5BX

description:
Clinical status: sample from transplant with renal dysfunction without rejection
Age: 35
Sex: Male
Immunosupression: CsA/MMF/P
Histopathology: ATN
Donor type: CAD
Scr (mg/dL): 6.3
Days post transplant: 16
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: TX5BX

description:
Clinical status: sample from well-functioning transplant with no clinical evidence of rejection
Age: 53
Sex: Female
Immunosupression: CsA/MMF/P
Histopathology: Normal
Donor type: LD
Scr (mg/dL): 1.1
Days post transplant: 689
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: another 26 year old male


title: TX9BX

description:
Clinical status: sample from well-functioning transplant with no clinical evidence of rejection
Age: 44
Sex: Male
Immunosupression: CsA/MMF/P
Histopathology: Normal
Donor type: LD
Scr (mg/dL): 1.8
Days post transplant: 718
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: NR1BX

description:
Clinical status: sample from transplant with renal dysfunction without rejection
Age: 55
Sex: Male
Immunosupression: CsA/MMF/P
Histopathology: CNI toxicity
Donor type: LD
Scr (mg/dL): 1.7
Days post transplant: 456
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: TX4BX

description:
Clinical status: sample from well-functioning transplant with no clinical evidence of rejection
Age: 31
Sex: Female
Immunosupression: CsA/MMF/P
Histopathology: Normal
Donor type: LD
Scr (mg/dL): 1.1
Days post transplant: 651
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: TX6BX

description:
Clinical status: sample from well-functioning transplant with no clinical evidence of rejection
Age: 32
Sex: Male
Immunosupression: CsA/MMF/P
Histopathology: Normal
Donor type: LD
Scr (mg/dL): 1.6
Days post transplant: 776
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: TX3BX

description:
Clinical status: sample from well-functioning transplant with no clinical evidence of rejection
Age: 52
Sex: Male
Immunosupression: CsA/MMF/P
Histopathology: Normal
Donor type: CAD
Scr (mg/dL): 1.2
Days post transplant: 902
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: TX2BX

description:
Clinical status: sample from well-functioning transplant with no clinical evidence of rejection
Age: 56
Sex: Male
Immunosupression: CsA/MMF/P
Histopathology: Normal
Donor type: LD
Scr (mg/dL): 1.3
Days post transplant: 911
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: TX7BX

description:
Clinical status: sample from well-functioning transplant with no clinical evidence of rejection
Age: 46
Sex: Female
Immunosupression: CsA/MMF/P
Histopathology: Normal
Donor type: CAD
Scr (mg/dL): 1.2
Days post transplant: 713
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: TX1BX

description:
Clinical status: sample from well-functioning transplant with no clinical evidence of rejection
Age: 51
Sex: Male
Immunosupression: CsA/MMF/P
Histopathology: Normal
Donor type: CAD
Scr (mg/dL): 1.5
Days post transplant: 932
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: TX10BX

description:
Clinical status: sample from well-functioning transplant with no clinical evidence of rejection
Age: 21
Sex: Male
Immunosupression: CsA/MMF/P
Histopathology: Normal
Donor type: CAD
Scr (mg/dL): 1.5
Days post transplant: 674
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: AR7BX

description:
Clinical status: sample from transplant patient with kidney undergoing acute rejection
Age: 35
Sex: Male
Immunosupression: SRL/MMF/P
Histopathology: Banff IA
Donor type: CAD
Scr (mg/dL): 2.0
Days post transplant: 184
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: AR6BX

description:
Clinical status: sample from transplant patient with kidney undergoing acute rejection
Age: 55
Sex: Male
Immunosupression: SRL/MMF/P
Histopathology: Banff borderline
Donor type: CAD
Scr (mg/dL): 2.9
Days post transplant: 68
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: C7BX

description:
Clinical status: control healthy donor kidney
Age: 36
Sex: Male
Immunosupression: none
Histopathology: none
Donor type: LD
Scr (mg/dL): 1.2
Days post transplant: 0
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: AR2BX

description:
Clinical status: sample from transplant patient with kidney undergoing acute rejection
Age: 28
Sex: Male
Immunosupression: FK/MMF/P
Histopathology: Banff IIA
Donor type: LD
Scr (mg/dL): 5.9
Days post transplant: 1467
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: C6BX

description:
Clinical status: control healthy donor kidney
Age: 44
Sex: Male
Immunosupression: none
Histopathology: none
Donor type: LD
Scr (mg/dL): 0.8
Days post transplant: 0
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: C8BX

description:
Clinical status: control healthy donor kidney
Age: 35
Sex: Female
Immunosupression: none
Histopathology: none
Donor type: LD
Scr (mg/dL): 0.8
Days post transplant: 0
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: C9BX

description:
Clinical status: control healthy donor kidney
Age: 50
Sex: Female
Immunosupression: none
Histopathology: none
Donor type: LD
Scr (mg/dL): 0.6
Days post transplant: 0
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: AR1BX

description:
Clinical status: sample from transplant patient with kidney undergoing acute rejection
Age: 42
Sex: Male
Immunosupression: CsA/MMF/P
Histopathology: Banff IIA
Donor type: CAD
Scr (mg/dL): 12.0
Days post transplant: 285
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: AR5BX

description:
Clinical status: sample from transplant patient with kidney undergoing acute rejection
Age: 26
Sex: Female
Immunosupression: CsA/MMF/P
Histopathology: Banff borderline
Donor type: CAD
Scr (mg/dL): 2.0
Days post transplant: 278
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: AR4BX

description:
Clinical status: sample from transplant patient with kidney undergoing acute rejection
Age: 28
Sex: Female
Immunosupression: FK/MMF/P
Histopathology: Banff IA
Donor type: CAD
Scr (mg/dL): 1.5
Days post transplant: 366
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: AR3BX

description:
Clinical status: sample from transplant patient with kidney undergoing acute rejection
Age: 18
Sex: Male
Immunosupression: CsA/MMF/P
Histopathology: Banff IA
Donor type: CAD
Scr (mg/dL): 2.2
Days post transplant: 119
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: C2BX

description:
Clinical status: control healthy donor kidney
Age: 42
Sex: Male
Immunosupression: none
Histopathology: none
Donor type: LD
Scr (mg/dL): 0.9
Days post transplant: 0
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: C1BX

description:
Clinical status: control healthy donor kidney
Age: 38
Sex: Female
Immunosupression: none
Histopathology: none
Donor type: LD
Scr (mg/dL): 0.8
Days post transplant: 0
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: C5BX

description:
Clinical status: control healthy donor kidney
Age: 39
Sex: Male
Immunosupression: none
Histopathology: none
Donor type: LD
Scr (mg/dL): 1.2
Days post transplant: 0
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: C4BX

description:
Clinical status: control healthy donor kidney
Age: 39
Sex: Female
Immunosupression: none
Histopathology: none
Donor type: LD
Scr (mg/dL): 0.9
Days post transplant: 0
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: TX8BX

description:
Clinical status: sample from well-functioning transplant with no clinical evidence of rejection
Age: 61
Sex: Male
Immunosupression: CsA/MMF/P
Histopathology: Normal
Donor type: CAD
Scr (mg/dL): 0.9
Days post transplant: 733
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: C3BX

description:
Clinical status: control healthy donor kidney
Age: 35
Sex: Female
Immunosupression: none
Histopathology: none
Donor type: LD
Scr (mg/dL): 0.6
Days post transplant: 0
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: NR4PBL

description:
Clinical status: PBL sample from transplant patient with renal dysfunction without rejection
Age: 43
Sex: Male
Immunosupression: CsA/MMF/P
Histopathology: CNI toxicity
Donor type: CAD
Scr (mg/dL): 3.8
Days post transplant: 262
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant

source_name: PBL


title: NR5PBL

description:
Clinical status: PBL sample from transplant patient with renal dysfunction without rejection
Age: 35
Sex: Male
Immunosupression: CsA/MMF/P
Histopathology: ATN
Donor type: CAD
Scr (mg/dL): 6.3
Days post transplant: 16
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: NR1PBL

description:
Clinical status: PBL sample from transplant patient with renal dysfunction without rejection
Age: 55
Sex: Male
Immunosupression: CsA/MMF/P
Histopathology: CNI toxicity
Donor type: LD
Scr (mg/dL): 1.7
Days post transplant: 456
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: TXPBL9

description:
Clinical status: PBL sample from patient with well-functioning transplant with no clinical evidence of rejection
Age: 46
Sex: Male
Immunosupression: SRL/MMF/P
Histopathology: none
Donor type: LD
Scr (mg/dL): 1.2
Days post transplant: 81
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: NR7PBL

description:
Clinical status: PBL sample from transplant patient with renal dysfunction without rejection
Age: 44
Sex: Male
Immunosupression: SRL/MMF/P
Histopathology: ATN
Donor type: CAD
Scr (mg/dL): 6.3
Days post transplant: 40
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: NR8PBL

description:
Clinical status: PBL sample from transplant patient with renal dysfunction without rejection
Age: 22
Sex: Female
Immunosupression: FK/MMF/P
Histopathology: FSGS
Donor type: LD
Scr (mg/dL): 3.3
Days post transplant: 78
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: TXPBL6

description:
Clinical status: PBL sample from patient with well-functioning transplant with no clinical evidence of rejection
Age: 68
Sex: Male
Immunosupression: CsA/MMF/P
Histopathology: none
Donor type: CAD
Scr (mg/dL): 1.7
Days post transplant: 376
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: NR9PBL

description:
Clinical status: PBL sample from transplant patient with renal dysfunction without rejection
Age: 58
Sex: Male
Immunosupression: CsA/MMF/P
Histopathology: ATN
Donor type: CAD
Scr (mg/dL): 5.0
Days post transplant: 47
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: TXPBL8

description:
Clinical status: PBL sample from patient with well-functioning transplant with no clinical evidence of rejection
Age: 61
Sex: Female
Immunosupression: CsA/MMF/P
Histopathology: none
Donor type: CAD
Scr (mg/dL): 0.9
Days post transplant: 1491
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: NR2PBL

description:
Clinical status: PBL sample from transplant patient with renal dysfunction without rejection
Age: 38
Sex: Male
Immunosupression: FK/MMF/P
Histopathology: CNI toxicity
Donor type: LD
Scr (mg/dL): 2.3
Days post transplant: 155
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: NR3PBL

description:
Clinical status: PBL sample from transplant patient with renal dysfunction without rejection
Age: 61
Sex: Male
Immunosupression: SRL/MMF/P
Histopathology: ATN
Donor type: LD
Scr (mg/dL): 5.2
Days post transplant: 11
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: 993PBMC

description:
PBMC isolated by Ficoll gradient centrifugation from polyaticular course JRA patient
Biotinylated cRNA was synthesized from total RNA (Enzo; Farmingdale, NY) and processed according to the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix; Santa Clara, CA).  57 samples: 5 pauciarticular PBMC, 15 polyarticular PBMC, 11 control PMBC, 6 JSpA PBMC, 5 pauciarticular SFMC, 10 polyarticular PBMC, 5 JSpA SFMC classified by course.
Keywords = Polyarticular course, juvenile rheumatoid arthritis (JRA), peripheral blood mononuclear cells (PBMC)


title: TXPBL5

description:
Clinical status: PBL sample from patient with well-functioning transplant with no clinical evidence of rejection
Age: 36
Sex: Female
Immunosupression: CsA/MMF/P
Histopathology: none
Donor type: CAD
Scr (mg/dL): 1.1
Days post transplant: 1278
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: TXPBL3

description:
Clinical status: PBL sample from patient with well-functioning transplant with no clinical evidence of rejection
Age: 65
Sex: Male
Immunosupression: CsA/MMF/P
Histopathology: none
Donor type: CAD
Scr (mg/dL): 1.5
Days post transplant: 213
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: TXPBL4

description:
Clinical status: PBL sample from patient with well-functioning transplant with no clinical evidence of rejection
Age: 65
Sex: Female
Immunosupression: FK/MMF/P
Histopathology: none
Donor type: CAD
Scr (mg/dL): 0.8
Days post transplant: 246
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: TXPBL2

description:
Clinical status: PBL sample from patient with well-functioning transplant with no clinical evidence of rejection
Age: 57
Sex: Female
Immunosupression: FK/MMF/P
Histopathology: none
Donor type: LD
Scr (mg/dL): 1.3
Days post transplant: 42
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: TXPBL1

description:
Clinical status: PBL sample from patient with well-functioning transplant with no clinical evidence of rejection
Age: 38
Sex: Male
Immunosupression: CsA/MMF/P
Histopathology: none
Donor type: CAD
Scr (mg/dL): 1.4
Days post transplant: 461
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: AR5PBL

description:
Clinical status: PBL sample from transplant patient with kidney undergoing acute rejection
Age: 26
Sex: Female
Immunosupression: CsA/MMF/P
Histopathology: Banff borderline
Donor type: CAD
Scr (mg/dL): 2.0
Days post transplant: 278
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: AR4PBL

description:
Clinical status: PBL sample from transplant patient with kidney undergoing acute rejection
Age: 28
Sex: Female
Immunosupression: FK/MMF/P
Histopathology: Banff IA
Donor type: CAD
Scr (mg/dL): 1.5
Days post transplant: 366
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: C6PBL

description:
Clinical status: control healthy blood donor
Age: unknown
Sex: unknown
Immunosupression: none
Histopathology: none
Donor type: NA
Scr (mg/dL): unknown
Days post transplant: NA
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: C5PBL


title: AR6PBL

description:
Clinical status: PBL sample from transplant patient with kidney undergoing acute rejection
Age: 55
Sex: Male
Immunosupression: SRL/MMF/P
Histopathology: Banff borderline
Donor type: CAD
Scr (mg/dL): 2.9
Days post transplant: 68
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: AR3PBL

description:
Clinical status: PBL sample from transplant patient with kidney undergoing acute rejection
Age: 18
Sex: Male
Immunosupression: CsA/MMF/P
Histopathology: Banff IA
Donor type: CAD
Scr (mg/dL): 2.2
Days post transplant: 119
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: C2PBL


title: C1PBL


title: AR2PBL

description:
Clinical status: PBL sample from transplant patient with kidney undergoing acute rejection
Age: 28
Sex: Male
Immunosupression: FK/MMF/P
Histopathology: Banff IIA
Donor type: LD
Scr (mg/dL): 5.9
Days post transplant: 1467
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: C7PBL


title: stem cells, D0-1

status: Public on Jun 10 2004

first: Stephen

middle: R.

last: Lyle

address: 330 Brookline Avenue

department: Pathology

institute: Beth Israel Deaconess Medical Center

description:
Human epithelial stem cells isolated from hair follicle were co-cultured with freshly isolated and cultured dermal papilla cells for up to 5 days in the transwell system. RNAs from the stem cells were isolated at different days of co-cultured (from day 0, 1, 2, and 5) and subjected to genechip microarray analysis.
Keywords = epithelial stem cell
Keywords = co-cultured with dermal papilla

source_name: stem cells, day 1


title: NR2BX

description:
Clinical status: sample from transplant with renal dysfunction without rejection
Age: 38
Sex: Male
Immunosupression: FK/MMF/P
Histopathology: CNI toxicity
Donor type: LD
Scr (mg/dL): 2.3
Days post transplant: 155
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: C8PBL


title: CCFAlmasan_CaPGSE56_6

status: Public on Jun 01 2004

city: Cleveland

first: John

middle: Gilmary

last: Hissong

address: 9500 Euclid Ave.

department: Cancer Biology

institute: Lerner Research Institute Cleveland Clinic Foundation

description:
SUMMARY: Response to radiation in prostate adenocarcinoma with dominant negative p53 function
LNCaP C4-2 cells transfected with pLXSN to stably express p53-suppressing GSE56, total RNA extracted, harvested 6 hr after irradiation to a dose of 10 Sv, Affymetrix HG-U95Av2 GeneChip(R).
DESIGN: The experiment was a response to radiation experiment using LNCaP C4-2 human prostate adenocarcinoma cells with dominant negative p53 function.  Cells were irradiated to a dose of 10 Sv from a Cesium-137 gamma source.  Total RNA was extracted from cells at 6 and 24 hours after irradiation.  The control sample, labeled 0, was collected concurrently with the cells extracted at 24 hr.  It was not irradiated, but was transfected with the pLXSN retrovirus.  After extraction, the samples were processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HG-U95Av2 chip, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual.  Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).
BIOLOGICAL SAMPLE: Cultured LNCaP C4-2 human prostate adenocarcinoma cells transfected with a pLXSN retrovirus (Clontech, Palo Alto, CA) to express GSE56, producing a dominant negative p53 phenotype.  (See Ossovskaya, VS, et. al., PNAS, 93: 10309-10314, PMID: 8816796 and Rokhlin , OW, et.al., Oncogene, 19: 1959-1968, PMID: 10773886.)  The pLXSN retrovirus also contains neo, conferring neomycin resistance.  For transfection into experimental samples, the retrovirus pLXSN was modified to include GSE56.  (The control sample was transfected with the pLXSN retrovirus.)  Transfected LNCaP C4-2 cells were selected for by growing the cells in a neomycin-containing medium.  C4-2 cells are an androgen independent derivative of the LNCaP cell line, described in Thalmann, GN, et.al., Cancer Res., 54:2577-2581, 1994, PMID: 8168083.  (See also Ray, S and Almasan, A, Cancer Res, 63:4713-4723, 2003, PMID: 1290765.)
IRRADIATION:  Harvested at specified intervals after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Mark 1 Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 emits a gamma ray with an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
EXTRACTION:  Total RNA was extracted from cells using the Trizol reagent (GIBCO BRL).
PROCESSING:  Sample processing proceeded as recommended in the Affymetrix GeneChip(R) Expression Analysis Manual.  Double-stranded cDNA was prepared from total RNA using the GIBCO BRL SuperScript Choice system.  An in vitro transcription reaction was used to produce biotin-labeled cRNA using the Enzo BioArray High Yield RNA Transcript Labeling Kit.  The sample was then purified using the QIAGEN RNA MiniKit and then fragmented.  A hybridization mixture was prepared including the fragmented cRNA, the Affymetrix recommended control cocktail and herring sperm DNA.
MICROARRAY:  Affymetrix HG-U95Av2 GeneChip(R).
HYBRIDIZATION: Affymetrix Hybridization Oven 640, Time: 16 hr, Temp: 45 C, Carousel Rotation Speed: 60 rpm.
WASHING AND STAINING:  Affymetrix Fluidics Station 400, EukGE:WS2v4 Protocol.
SCANNING: Affymetrix Agilent 2500 Scanner, Pixel Size: 3 microns, Filter: 570 nm, Scans: 2.  Calibration modified to avoid saturation.  The data recorded below is from the scan after the final antibody stain. (See the Affymetrix technical note, GeneArray(R) Scanner Update, Part 700575 Revision 2.)
DEVICE SPECIFIC ANALYSIS: Affymetrix Microarray Suite 5.0
Algorithm:  Statistical
Corner+  Avg:186, Count:32
Corner-  Avg:11376, Count:32
Background  Avg:53.91, Stdev:1.76, Max:57.4, Min:50.5
Noise  Avg:2.04, Stdev:0.03, Max:2.1, Min:1.9
RawQ  2.07
Alpha1  0.04
Alpha2  0.06
Tau  0.015
Gamma1H  0.0025
Gamma1L  0.0025
Gamma2H  0.003
Gamma2L  0.003
Perturbation  1.1
TGT  300
NF  1.000000
SF  3.343342
SFGene  All
DEVICE INDEPENDENT ANALYSIS: Silicon Genetics' GeneSpring(R) version 6, build 1333.  The Microarray Suite 5 output data was further processed with GeneSpring(R).  Each chip was normalized separately.  Each measurement on the chip was divided by the 50th percentile of all measurements (the median) in that sample.  The percentile was calculated with all normalized measurements above 0.  Values below 0.0 were set to 0.0.
Keywords = Human
Keywords = Prostate
Keywords = Cancer
Keywords = Adenocarcinoma
Keywords = Ionizing Radiation
Keywords = Microarray
Keywords = p53
Keywords = GSE56

source_name: LNCaP C4-2, a human prostate cancer androgen insensitive cell line, transfected to stably express GSE56 which supresses p53 function


title: CCFAlmasan_CaPGSE56_24

description:
SUMMARY: Response to radiation in prostate adenocarcinoma with dominant negative p53 function
LNCaP C4-2 cells transfected with pLXSN to stably express p53-suppressing GSE56, total RNA extracted, harvested 24 hr after irradiation to a dose of 10 Sv, Affymetrix HG-U95Av2 GeneChip(R).
DESIGN: The experiment was a response to radiation experiment using LNCaP C4-2 human prostate adenocarcinoma cells with dominant negative p53 function.  Cells were irradiated to a dose of 10 Sv from a Cesium-137 gamma source.  Total RNA was extracted from cells at 6 and 24 hours after irradiation.  The control sample, labeled 0, was collected concurrently with the cells extracted at 24 hr.  It was not irradiated and was transfected with the pLXSN retrovirus, lacking the inserted GSE56 coding region.  After extraction, the samples were processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HG-U95Av2 chip, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual.  Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).
BIOLOGICAL SAMPLE: Cultured LNCaP C4-2 human prostate adenocarcinoma cells transfected with a pLXSN retrovirus (Clontech, Palo Alto, CA) to express the peptide GSE56, producing a dominant negative p53 phenotype.  (See Ossovskaya, VS, et. al., PNAS, 93: 10309-10314, PMID: 8816796 and Rokhlin , OW, et.al., Oncogene, 19: 1959-1968, PMID: 10773886.)  The pLXSN retrovirus also contains neo, conferring neomycin resistance.  For transfection into experimental samples, the retrovirus pLXSN was modified to include GSE56.  (The control sample was transfected with the pLXSN retrovirus.)  Transfected LNCaP C4-2 cells were selected for by growing the cells in a neomycin-containing medium.  C4-2 cells are an androgen independent derivative of the LNCaP cell line, described in Thalmann, GN, et.al., Cancer Res., 54:2577-2581, 1994, PMID: 8168083.  (See also Ray, S and Almasan, A, Cancer Res, 63:4713-4723, 2003, PMID: 1290765.)
IRRADIATION:  Harvested at specified intervals after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Mark 1 Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 emits a gamma ray with an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
EXTRACTION:  Total RNA was extracted from cells using the Trizol reagent (GIBCO BRL).
PROCESSING:  Sample processing proceeded as recommended in the Affymetrix GeneChip(R) Expression Analysis Manual.  Double-stranded cDNA was prepared from total RNA using the GIBCO BRL SuperScript Choice system.  An in vitro transcription reaction was used to produce biotin-labeled cRNA using the Enzo BioArray High Yield RNA Transcript Labeling Kit.  The sample was then purified using the QIAGEN RNA MiniKit and then fragmented.  A hybridization mixture was prepared including the fragmented cRNA, the Affymetrix recommended control cocktail and herring sperm DNA.
MICROARRAY:  Affymetrix HG-U95Av2 GeneChip(R).
HYBRIDIZATION: Affymetrix Hybridization Oven 640, Time: 16 hr, Temp: 45 C, Carousel Rotation Speed: 60 rpm.
WASHING AND STAINING:  Affymetrix Fluidics Station 400, EukGE:WS2v4 Protocol.
SCANNING: Affymetrix Agilent 2500 Scanner, Pixel Size: 3 microns, Filter: 570 nm, Scans: 2.  Calibration modified to avoid saturation.  The data recorded below is from the scan after the final antibody stain. (See the Affymetrix technical note, GeneArray(R) Scanner Update, Part 700575 Revision 2.)
DEVICE SPECIFIC ANALYSIS: Affymetrix Microarray Suite 5.0
Algorithm:  Statistical
Corner+  Avg:183, Count:32
Corner-  Avg:10631, Count:32
Background  Avg:56.60, Stdev:1.79, Max:60.8, Min:52.1
Noise  Avg:2.11, Stdev:0.09, Max:2.5, Min:1.9
RawQ  2.11
Alpha1  0.04
Alpha2  0.06
Tau  0.015
Gamma1H  0.0025
Gamma1L  0.0025
Gamma2H  0.003
Gamma2L  0.003
Perturbation  1.1
TGT  300
NF  1.000000
SF  3.051127
SFGene  All
DEVICE INDEPENDENT ANALYSIS: Silicon Genetics' GeneSpring(R) version 6, build 1333.  The Microarray Suite 5 output data was further processed with GeneSpring(R).  Each chip was normalized separately.  Each measurement on the chip was divided by the 50th percentile of all measurements (the median) in that sample.  The percentile was calculated with all normalized measurements above 0.  Values below 0.0 were set to 0.0.
Keywords = Human
Keywords = Prostate
Keywords = Cancer
Keywords = Adenocarcinoma
Keywords = Ionizing Radiation
Keywords = Microarray
Keywords = p53
Keywords = GSE56


title: CCFAlmasan_CaPK_24

description:
SUMMARY: Kinetic response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, total RNA extracted, harvested 24 hr after irradiation to a dose of 10 Sv, Affymetrix HG-U95Av2 GeneChip(R).
DESIGN: The experiment was a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 gamma source.  Total RNA was extracted from cells at 1, 2, 4, 6, 8, 12, 16, 20 and 24 hours after irradiation.  The untreated control sample, labeled 0, was collected concurrently with the cells extracted at 24 hr.  After extraction, the samples were processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HG-U95Av2 chip, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual.  Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).
BIOLOGICAL SAMPLE: Cultured LNCaP C4-2 human prostate adenocarcinoma cells.  The derived LNCaP C4-2 cell lines are described in Thalmann, GN, et.al., Cancer Res., 54:2577-2581, 1994, PMID: 8168083.  (See also Ray, S and Almasan, A, Cancer Res, 63:4713-4723, 2003, PMID: 1290765.)  The C4-2 derivative of the LNCaP cell line is androgen independent.
IRRADIATION:  Harvested at specified intervals after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Mark 1 Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 emits a gamma ray with an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
EXTRACTION:  Total RNA was extracted from cells using the Trizol reagent (GIBCO BRL).
PROCESSING:  Sample processing proceeded as recommended in the Affymetrix GeneChip(R) Expression Analysis Manual.  Double-stranded cDNA was prepared from total RNA using the GIBCO BRL SuperScript Choice system.  An in vitro transcription reaction was used to produce biotin-labeled cRNA using the Enzo BioArray High Yield RNA Transcript Labeling Kit.  The sample was then purified using the QIAGEN RNA MiniKit and then fragmented.  A hybridization mixture was prepared including the fragmented cRNA, the Affymetrix recommended control cocktail and herring sperm DNA.
MICROARRAY:  Affymetrix HG-U95Av2 GeneChip(R).
HYBRIDIZATION: Affymetrix Hybridization Oven 640, Time: 16 hr, Temp: 45 C, Carousel Rotation Speed: 60 rpm.
WASHING AND STAINING:  Affymetrix Fluidics Station 400, EukGE:WS2v3 Protocol.
SCANNING: Affymetrix Agilent 2500 Scanner, Pixel Size: 3 microns, Filter: 570 nm, Scans: 2.  Original calibration.  The source of the data recorded below is the scan before the final antibody stain. (See the Affymetrix technical note, GeneArray(R) Scanner Update, Part 700575 Revision 2.)
DEVICE SPECIFIC ANALYSIS: Affymetrix Microarray Suite 5.0
Algorithm:  Statistical
Corner+  Avg:671, Count:32
Corner-  Avg:33802, Count:32
Background  Avg:290.73, Stdev:3.69, Max:299.9, Min:282.0
Noise  Avg:9.27, Stdev:0.27, Max:10.2, Min:8.5
RawQ  12.61
Alpha1  0.04
Alpha2  0.06
Tau  0.015
Gamma1H  0.0025
Gamma1L  0.0025
Gamma2H  0.003
Gamma2L  0.003
Perturbation  1.1
TGT  300
NF  1.000000
SF  1.719597
SFGene  All
DEVICE INDEPENDENT ANALYSIS: Silicon Genetics' GeneSpring(R) version 6, build 1333.  The Microarray Suite 5 output data was further processed with GeneSpring(R).  Each chip was normalized separately.  Each measurement on the chip was divided by the 50th percentile of all measurements (the median) in that sample.  The percentile was calculated with all normalized measurements above 0.  Values below 0.0 were set to 0.0.
Keywords = Human
Keywords = Prostate
Keywords = Cancer
Keywords = Adenocarcinoma
Keywords = Ionizing Radiation
Keywords = Microarray

source_name: LNCaP C4-2 cells, human prostate cancer androgen insensitive cultured cell line


title: C4PBL


title: C3PBL


title: stem cells, D0-5

source_name: stem cells, day 5


title: CCFAlmasan_CaPK_20

description:
SUMMARY: Kinetic response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, total RNA extracted, harvested 20 hr after irradiation to a dose of 10 Sv, Affymetrix HG-U95Av2 GeneChip(R).
DESIGN: The experiment was a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 gamma source.  Total RNA was extracted from cells at 1, 2, 4, 6, 8, 12, 16, 20 and 24 hours after irradiation.  The untreated control sample, labeled 0, was collected concurrently with the cells extracted at 24 hr.  After extraction, the samples were processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HG-U95Av2 chip, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual.  Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).
BIOLOGICAL SAMPLE: Cultured LNCaP C4-2 human prostate adenocarcinoma cells.  The derived LNCaP C4-2 cell lines are described in Thalmann, GN, et.al., Cancer Res., 54:2577-2581, 1994, PMID: 8168083.  (See also Ray, S and Almasan, A, Cancer Res, 63:4713-4723, 2003, PMID: 1290765.)  The C4-2 derivative of the LNCaP cell line is androgen independent.
IRRADIATION:  Harvested at specified intervals after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Mark 1 Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 emits a gamma ray with an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
EXTRACTION:  Total RNA was extracted from cells using the Trizol reagent (GIBCO BRL).
PROCESSING:  Sample processing proceeded as recommended in the Affymetrix GeneChip(R) Expression Analysis Manual.  Double-stranded cDNA was prepared from total RNA using the GIBCO BRL SuperScript Choice system.  An in vitro transcription reaction was used to produce biotin-labeled cRNA using the Enzo BioArray High Yield RNA Transcript Labeling Kit.  The sample was then purified using the QIAGEN RNA MiniKit and then fragmented.  A hybridization mixture was prepared including the fragmented cRNA, the Affymetrix recommended control cocktail and herring sperm DNA.
MICROARRAY:  Affymetrix HG-U95Av2 GeneChip(R).
HYBRIDIZATION: Affymetrix Hybridization Oven 640, Time: 16 hr, Temp: 45 C, Carousel Rotation Speed: 60 rpm.
WASHING AND STAINING:  Affymetrix Fluidics Station 400, EukGE:WS2v3 Protocol.
SCANNING: Affymetrix Agilent 2500 Scanner, Pixel Size: 3 microns, Filter: 570 nm, Scans: 2.  Original calibration.  The source of the data recorded below is the scan before the final antibody stain. (See the Affymetrix technical note, GeneArray(R) Scanner Update, Part 700575 Revision 2.)
DEVICE SPECIFIC ANALYSIS: Affymetrix Microarray Suite 5.0
Algorithm:  Statistical
Corner+  Avg:491, Count:32
Corner-  Avg:33215, Count:32
Background  Avg:320.97, Stdev:2.74, Max:327.9, Min:314.7
Noise  Avg:9.88, Stdev:0.28, Max:11.0, Min:8.9
RawQ  13.38
Alpha1  0.04
Alpha2  0.06
Tau  0.015
Gamma1H  0.0025
Gamma1L  0.0025
Gamma2H  0.003
Gamma2L  0.003
Perturbation  1.1
TGT  300
NF  1.000000
SF  1.501031
SFGene  All
DEVICE INDEPENDENT ANALYSIS: Silicon Genetics' GeneSpring(R) version 6, build 1333.  The Microarray Suite 5 output data was further processed with GeneSpring(R).  Each chip was normalized separately.  Each measurement on the chip was divided by the 50th percentile of all measurements (the median) in that sample.  The percentile was calculated with all normalized measurements above 0.  Values below 0.0 were set to 0.0.
Keywords = Human
Keywords = Prostate
Keywords = Cancer
Keywords = Adenocarcinoma
Keywords = Ionizing Radiation
Keywords = Microarray


title: TXPBL7

description:
Clinical status: PBL sample from patient with well-functioning transplant with no clinical evidence of rejection
Age: 39
Sex: Male
Immunosupression: SRL/MMF/P
Histopathology: none
Donor type: CAD
Scr (mg/dL): 0.9
Days post transplant: 36
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: 81 year old female

description:
The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals.
Keywords = human brain aging


title: AR7PBL

description:
Clinical status: PBL sample from transplant patient with kidney undergoing acute rejection
Age: 35
Sex: Male
Immunosupression: SRL/MMF/P
Histopathology: Banff IA
Donor type: CAD
Scr (mg/dL): 2.0
Days post transplant: 184
Abbreviations used in sample description: Abreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant


title: CCFAlmasan_CaPK_6

description:
SUMMARY: Kinetic response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, total RNA extracted, harvested 6 hr after irradiation to a dose of 10 Sv, Affymetrix HG-U95Av2 GeneChip(R).
DESIGN: The experiment was a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 gamma source.  Total RNA was extracted from cells at 1, 2, 4, 6, 8, 12, 16, 20 and 24 hours after irradiation.  The untreated control sample, labeled 0, was collected concurrently with the cells extracted at 24 hr.  After extraction, the samples were processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HG-U95Av2 chip, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual.  Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).
BIOLOGICAL SAMPLE: Cultured LNCaP C4-2 human prostate adenocarcinoma cells.  The derived LNCaP C4-2 cell lines are described in Thalmann, GN, et.al., Cancer Res., 54:2577-2581, 1994, PMID: 8168083.  (See also Ray, S and Almasan, A, Cancer Res, 63:4713-4723, 2003, PMID: 1290765.)  The C4-2 derivative of the LNCaP cell line is androgen independent.
IRRADIATION:  Harvested at specified intervals after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Mark 1 Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 emits a gamma ray with an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
EXTRACTION:  Total RNA was extracted from cells using the Trizol reagent (GIBCO BRL).
PROCESSING:  Sample processing proceeded as recommended in the Affymetrix GeneChip(R) Expression Analysis Manual.  Double-stranded cDNA was prepared from total RNA using the GIBCO BRL SuperScript Choice system.  An in vitro transcription reaction was used to produce biotin-labeled cRNA using the Enzo BioArray High Yield RNA Transcript Labeling Kit.  The sample was then purified using the QIAGEN RNA MiniKit and then fragmented.  A hybridization mixture was prepared including the fragmented cRNA, the Affymetrix recommended control cocktail and herring sperm DNA.
MICROARRAY:  Affymetrix HG-U95Av2 GeneChip(R).
HYBRIDIZATION: Affymetrix Hybridization Oven 640, Time: 16 hr, Temp: 45 C, Carousel Rotation Speed: 60 rpm.
WASHING AND STAINING:  Affymetrix Fluidics Station 400, EukGE:WS2v3 Protocol.
SCANNING: Affymetrix Agilent 2500 Scanner, Pixel Size: 3 microns, Filter: 570 nm, Scans: 2.  Original calibration.  The source of the data recorded below is the scan before the final antibody stain. (See the Affymetrix technical note, GeneArray(R) Scanner Update, Part 700575 Revision 2.)
DEVICE SPECIFIC ANALYSIS: Affymetrix Microarray Suite 5.0
Algorithm:  Statistical
Corner+  Avg:558, Count:32
Corner-  Avg:37661, Count:32
Background  Avg:318.00, Stdev:2.89, Max:326.7, Min:309.6
Noise  Avg:10.04, Stdev:0.25, Max:10.9, Min:9.3
RawQ  13.34
Alpha1  0.04
Alpha2  0.06
Tau  0.015
Gamma1H  0.0025
Gamma1L  0.0025
Gamma2H  0.003
Gamma2L  0.003
Perturbation  1.1
TGT  300
NF  1.000000
SF  0.930013
SFGene  All
DEVICE INDEPENDENT ANALYSIS: Silicon Genetics' GeneSpring(R) version 6, build 1333.  The Microarray Suite 5 output data was further processed with GeneSpring(R).  Each chip was normalized separately.  Each measurement on the chip was divided by the 50th percentile of all measurements (the median) in that sample.  The percentile was calculated with all normalized measurements above 0.  Values below 0.0 were set to 0.0.
Keywords = Human
Keywords = Prostate
Keywords = Cancer
Keywords = Adenocarcinoma
Keywords = Ionizing Radiation
Keywords = Microarray


title: stem cells, D0-2

source_name: stem cells, day 2


title: CCFAlmasan_CaPK_16

description:
SUMMARY: Kinetic response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, total RNA extracted, harvested 16 hr after irradiation to a dose of 10 Sv, Affymetrix HG-U95Av2 GeneChip(R).
DESIGN: The experiment was a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 gamma source.  Total RNA was extracted from cells at 1, 2, 4, 6, 8, 12, 16, 20 and 24 hours after irradiation.  The untreated control sample, labeled 0, was collected concurrently with the cells extracted at 24 hr.  After extraction, the samples were processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HG-U95Av2 chip, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual.  Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).
BIOLOGICAL SAMPLE: Cultured LNCaP C4-2 human prostate adenocarcinoma cells.  The derived LNCaP C4-2 cell lines are described in Thalmann, GN, et.al., Cancer Res., 54:2577-2581, 1994, PMID: 8168083.  (See also Ray, S and Almasan, A, Cancer Res, 63:4713-4723, 2003, PMID: 1290765.)  The C4-2 derivative of the LNCaP cell line is androgen independent.
IRRADIATION:  Harvested at specified intervals after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Mark 1 Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 emits a gamma ray with an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
EXTRACTION:  Total RNA was extracted from cells using the Trizol reagent (GIBCO BRL).
PROCESSING:  Sample processing proceeded as recommended in the Affymetrix GeneChip(R) Expression Analysis Manual.  Double-stranded cDNA was prepared from total RNA using the GIBCO BRL SuperScript Choice system.  An in vitro transcription reaction was used to produce biotin-labeled cRNA using the Enzo BioArray High Yield RNA Transcript Labeling Kit.  The sample was then purified using the QIAGEN RNA MiniKit and then fragmented.  A hybridization mixture was prepared including the fragmented cRNA, the Affymetrix recommended control cocktail and herring sperm DNA.
MICROARRAY:  Affymetrix HG-U95Av2 GeneChip(R).
HYBRIDIZATION: Affymetrix Hybridization Oven 640, Time: 16 hr, Temp: 45 C, Carousel Rotation Speed: 60 rpm.
WASHING AND STAINING:  Affymetrix Fluidics Station 400, EukGE:WS2v3 Protocol.
SCANNING: Affymetrix Agilent 2500 Scanner, Pixel Size: 3 microns, Filter: 570 nm, Scans: 2.  Original calibration.  The source of the data recorded below is the scan before the final antibody stain. (See the Affymetrix technical note, GeneArray(R) Scanner Update, Part 700575 Revision 2.)
DEVICE SPECIFIC ANALYSIS: Affymetrix Microarray Suite 5.0
Algorithm:  Statistical
Corner+  Avg:518, Count:32
Corner-  Avg:33532, Count:32
Background  Avg:299.71, Stdev:5.77, Max:318.4, Min:288.4
Noise  Avg:9.46, Stdev:0.36, Max:10.7, Min:8.5
RawQ  13.08
Alpha1  0.04
Alpha2  0.06
Tau  0.015
Gamma1H  0.0025
Gamma1L  0.0025
Gamma2H  0.003
Gamma2L  0.003
Perturbation  1.1
TGT  300
NF  1.000000
SF  1.532152
SFGene  All
DEVICE INDEPENDENT ANALYSIS: Silicon Genetics' GeneSpring(R) version 6, build 1333.  The Microarray Suite 5 output data was further processed with GeneSpring(R).  Each chip was normalized separately.  Each measurement on the chip was divided by the 50th percentile of all measurements (the median) in that sample.  The percentile was calculated with all normalized measurements above 0.  Values below 0.0 were set to 0.0.
Keywords = Human
Keywords = Prostate
Keywords = Cancer
Keywords = Adenocarcinoma
Keywords = Ionizing Radiation
Keywords = Microarray


title: CCFAlmasan_CaPK_12

description:
SUMMARY: Kinetic response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, total RNA extracted, harvested 12 hr after irradiation to a dose of 10 Sv, Affymetrix HG-U95Av2 GeneChip(R).
DESIGN: The experiment was a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 gamma source.  Total RNA was extracted from cells at 1, 2, 4, 6, 8, 12, 16, 20 and 24 hours after irradiation.  The untreated control sample, labeled 0, was collected concurrently with the cells extracted at 24 hr.  After extraction, the samples were processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HG-U95Av2 chip, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual.  Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).
BIOLOGICAL SAMPLE: Cultured LNCaP C4-2 human prostate adenocarcinoma cells.  The derived LNCaP C4-2 cell lines are described in Thalmann, GN, et.al., Cancer Res., 54:2577-2581, 1994, PMID: 8168083.  (See also Ray, S and Almasan, A, Cancer Res, 63:4713-4723, 2003, PMID: 1290765.)  The C4-2 derivative of the LNCaP cell line is androgen independent.
IRRADIATION:  Harvested at specified intervals after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Mark 1 Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 emits a gamma ray with an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
EXTRACTION:  Total RNA was extracted from cells using the Trizol reagent (GIBCO BRL).
PROCESSING:  Sample processing proceeded as recommended in the Affymetrix GeneChip(R) Expression Analysis Manual.  Double-stranded cDNA was prepared from total RNA using the GIBCO BRL SuperScript Choice system.  An in vitro transcription reaction was used to produce biotin-labeled cRNA using the Enzo BioArray High Yield RNA Transcript Labeling Kit.  The sample was then purified using the QIAGEN RNA MiniKit and then fragmented.  A hybridization mixture was prepared including the fragmented cRNA, the Affymetrix recommended control cocktail and herring sperm DNA.
MICROARRAY:  Affymetrix HG-U95Av2 GeneChip(R).
HYBRIDIZATION: Affymetrix Hybridization Oven 640, Time: 16 hr, Temp: 45 C, Carousel Rotation Speed: 60 rpm.
WASHING AND STAINING:  Affymetrix Fluidics Station 400, EukGE:WS2v3 Protocol.
SCANNING: Affymetrix Agilent 2500 Scanner, Pixel Size: 3 microns, Filter: 570 nm, Scans: 2.  Original calibration.  The source of the data recorded below is the scan before the final antibody stain. (See the Affymetrix technical note, GeneArray(R) Scanner Update, Part 700575 Revision 2.)
DEVICE SPECIFIC ANALYSIS: Affymetrix Microarray Suite 5.0
Algorithm:  Statistical
Corner+  Avg:602, Count:32
Corner-  Avg:36666, Count:32
Background  Avg:323.28, Stdev:6.29, Max:341.4, Min:311.1
Noise  Avg:10.34, Stdev:0.32, Max:11.3, Min:9.5
RawQ  14.02
Alpha1  0.04
Alpha2  0.06
Tau  0.015
Gamma1H  0.0025
Gamma1L  0.0025
Gamma2H  0.003
Gamma2L  0.003
Perturbation  1.1
TGT  300
NF  1.000000
SF  1.283897
SFGene  All
DEVICE INDEPENDENT ANALYSIS: Silicon Genetics' GeneSpring(R) version 6, build 1333.  The Microarray Suite 5 output data was further processed with GeneSpring(R).  Each chip was normalized separately.  Each measurement on the chip was divided by the 50th percentile of all measurements (the median) in that sample.  The percentile was calculated with all normalized measurements above 0.  Values below 0.0 were set to 0.0.
Keywords = Human
Keywords = Prostate
Keywords = Cancer
Keywords = Adenocarcinoma
Keywords = Ionizing Radiation
Keywords = Microarray


title: CCFAlmasan_CaPGSE56_0

description:
SUMMARY: Response to radiation in prostate adenocarcinoma with dominant negative p53 function.
LNCaP C4-2 cells transfected with an unmodified pLXSN, total RNA extracted, no irradiation, Affymetrix HG-U95Av2 GeneChip(R).
DESIGN: The experiment was a response to radiation experiment using LNCaP C4-2 human prostate adenocarcinoma cells with dominant negative p53 function.  Cells were irradiated to a dose of 10 Sv from a Cesium-137 gamma source.  Total RNA was extracted from cells at 6 and 24 hours after irradiation.  The control sample, labeled 0, was collected concurrently with the cells extracted at 24 hr.  It was not irradiated, but was transfected with the pLXSN retrovirus.  After extraction, the samples were processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HG-U95Av2 chip, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual.  Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).
BIOLOGICAL SAMPLE: Cultured LNCaP C4-2 human prostate adenocarcinoma cells transfected with the pLXSN retrovirus (Clontech, Palo Alto, CA).  (See Ossovskaya, VS, et. al., PNAS, 93: 10309-10314, PMID: 8816796 and Rokhlin , OW, et.al., Oncogene, 19: 1959-1968, PMID: 10773886.)  The pLXSN retrovirus also contains neo, conferring neomycin resistance.  Transfected LNCaP C4-2 cells were selected for by growing the cells in a neomycin-containing medium.  C4-2 cells are an androgen independent derivative of the LNCaP cell line, described in Thalmann, GN, et.al., Cancer Res., 54:2577-2581, 1994, PMID: 8168083.  (See also Ray, S and Almasan, A, Cancer Res, 63:4713-4723, 2003, PMID: 1290765.)
IRRADIATION:  This sample was not irradiated.
EXTRACTION:  Total RNA was extracted from cells using the Trizol reagent (GIBCO BRL).
PROCESSING:  Sample processing proceeded as recommended in the Affymetrix GeneChip(R) Expression Analysis Manual.  Double-stranded cDNA was prepared from total RNA using the GIBCO BRL SuperScript Choice system.  An in vitro transcription reaction was used to produce biotin-labeled cRNA using the Enzo BioArray High Yield RNA Transcript Labeling Kit.  The sample was then purified using the QIAGEN RNA MiniKit and then fragmented.  A hybridization mixture was prepared including the fragmented cRNA, the Affymetrix recommended control cocktail and herring sperm DNA.
MICROARRAY:  Affymetrix HG-U95Av2 GeneChip(R).
HYBRIDIZATION: Affymetrix Hybridization Oven 640, Time: 16 hr, Temp: 45 C, Carousel Rotation Speed: 60 rpm.
WASHING AND STAINING:  Affymetrix Fluidics Station 400, EukGE:WS2v4 Protocol.
SCANNING: Affymetrix Agilent 2500 Scanner, Pixel Size: 3 microns, Filter: 570 nm, Scans: 2.  Calibration modified to avoid saturation.  The data recorded below is from the scan after the final antibody stain. (See the Affymetrix technical note, GeneArray(R) Scanner Update, Part 700575 Revision 2.)
DEVICE SPECIFIC ANALYSIS: Affymetrix Microarray Suite 5.0
Algorithm:  Statistical
Corner+  Avg:167, Count:32
Corner-  Avg:9959, Count:32
Background  Avg:52.81, Stdev:1.65, Max:56.2, Min:49.3
Noise  Avg:1.85, Stdev:0.07, Max:2.0, Min:1.6
RawQ  1.98
Alpha1  0.04
Alpha2  0.06
Tau  0.015
Gamma1H  0.0025
Gamma1L  0.0025
Gamma2H  0.003
Gamma2L  0.003
Perturbation  1.1
TGT  300
NF  1.000000
SF  2.747055
SFGene  All
DEVICE INDEPENDENT ANALYSIS: Silicon Genetics' GeneSpring(R) version 6, build 1333.  The Microarray Suite 5 output data was further processed with GeneSpring(R).  Each chip was normalized separately.  Each measurement on the chip was divided by the 50th percentile of all measurements (the median) in that sample.  The percentile was calculated with all normalized measurements above 0.  Values below 0.0 were set to 0.0.
Keywords = Human
Keywords = Prostate
Keywords = Cancer
Keywords = Adenocarcinoma
Keywords = Ionizing Radiation
Keywords = Microarray
Keywords = p53
Keywords = GSE56

source_name: LNCaP C4-2, a human prostate cancer androgen insensitive cell line, transfected with an unmodified retrovirus, pLXSN, as a control.


title: CCFAlmasan_CaPK_0

description:
SUMMARY: Kinetic response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, total RNA extracted, control: no irradiation, Affymetrix HG-U95Av2 GeneChip(R).
DESIGN: The experiment was a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 gamma source.  Total RNA was extracted from cells at 1, 2, 4, 6, 8, 12, 16, 20 and 24 hours after irradiation.  The untreated control sample, labeled 0, was collected concurrently with the cells extracted at 24 hr.  After extraction, the samples were processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HG-U95Av2 chip, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual.  Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).
BIOLOGICAL SAMPLE:  This unirradiated control sample of cultured LNCaP C4-2 human prostate adenocarcinoma cells was collected at the same time as the 24 hr sample.  The derived LNCaP C4-2 cell lines are described in Thalmann, GN, et.al., Cancer Res., 54:2577-2581, 1994, PMID: 8168083.  (See also Ray, S and Almasan, A, Cancer Res, 63:4713-4723, 2003, PMID: 1290765.)  The C4-2 derivative of the LNCaP cell line is androgen independent.
IRRADIATION:  This sample was not irradiated.
EXTRACTION:  Total RNA was extracted from cells using the Trizol reagent (GIBCO BRL).
PROCESSING:  Sample processing proceeded as recommended in the Affymetrix GeneChip(R) Expression Analysis Manual.  Double-stranded cDNA was prepared from total RNA using the GIBCO BRL SuperScript Choice system.  An in vitro transcription reaction was used to produce biotin-labeled cRNA using the Enzo BioArray High Yield RNA Transcript Labeling Kit.  The sample was then purified using the QIAGEN RNA MiniKit and then fragmented.  A hybridization mixture was prepared including the fragmented cRNA, the Affymetrix recommended control cocktail and herring sperm DNA.
MICROARRAY:  Affymetrix HG-U95Av2 GeneChip(R).
HYBRIDIZATION: Affymetrix Hybridization Oven 640, Time: 16 hr, Temp: 45 C, Carousel Rotation Speed: 60 rpm.
WASHING AND STAINING:  Affymetrix Fluidics Station 400, EukGE:WS2v3 Protocol.
SCANNING: Affymetrix Agilent 2500 Scanner, Pixel Size: 3 microns, Filter: 570 nm, Scans: 2.  Original calibration.  The source of the data recorded below is the scan before the final antibody stain. (See the Affymetrix technical note, GeneArray(R) Scanner Update, Part 700575 Revision 2.)
DEVICE SPECIFIC ANALYSIS: Affymetrix Microarray Suite 5.0
Algorithm:  Statistical
Corner+  Avg:638, Count:32
Corner-  Avg:35477, Count:32
Background  Avg:333.27, Stdev:6.24, Max:345.9, Min:319.4
Noise  Avg:10.11, Stdev:0.34, Max:11.5, Min:9.3
RawQ  13.50
Alpha1  0.04
Alpha2  0.06
Tau  0.015
Gamma1H  0.0025
Gamma1L  0.0025
Gamma2H  0.003
Gamma2L  0.003
Perturbation  1.1
TGT  300
NF  1.000000
SF  0.974060
SFGene  All
DEVICE INDEPENDENT ANALYSIS: Silicon Genetics' GeneSpring(R) version 6, build 1333.  The Microarray Suite 5 output data was further processed with GeneSpring(R).  Each chip was normalized separately.  Each measurement on the chip was divided by the 50th percentile of all measurements (the median) in that sample.  The percentile was calculated with all normalized measurements above 0.  Values below 0.0 were set to 0.0.
Keywords = Human
Keywords = Prostate
Keywords = Cancer
Keywords = Adenocarcinoma
Keywords = Ionizing Radiation
Keywords = Microarray


title: CCFAlmasan_CaPK_8

description:
SUMMARY: Kinetic response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, total RNA extracted, harvested 8 hr after irradiation to a dose of 10 Sv, Affymetrix HG-U95Av2 GeneChip(R).
DESIGN: The experiment was a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 gamma source.  Total RNA was extracted from cells at 1, 2, 4, 6, 8, 12, 16, 20 and 24 hours after irradiation.  The untreated control sample, labeled 0, was collected concurrently with the cells extracted at 24 hr.  After extraction, the samples were processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HG-U95Av2 chip, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual.  Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).
BIOLOGICAL SAMPLE: Cultured LNCaP C4-2 human prostate adenocarcinoma cells.  The derived LNCaP C4-2 cell lines are described in Thalmann, GN, et.al., Cancer Res., 54:2577-2581, 1994, PMID: 8168083.  (See also Ray, S and Almasan, A, Cancer Res, 63:4713-4723, 2003, PMID: 1290765.)  The C4-2 derivative of the LNCaP cell line is androgen independent.
IRRADIATION:  Harvested at specified intervals after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Mark 1 Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 emits a gamma ray with an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
EXTRACTION:  Total RNA was extracted from cells using the Trizol reagent (GIBCO BRL).
PROCESSING:  Sample processing proceeded as recommended in the Affymetrix GeneChip(R) Expression Analysis Manual.  Double-stranded cDNA was prepared from total RNA using the GIBCO BRL SuperScript Choice system.  An in vitro transcription reaction was used to produce biotin-labeled cRNA using the Enzo BioArray High Yield RNA Transcript Labeling Kit.  The sample was then purified using the QIAGEN RNA MiniKit and then fragmented.  A hybridization mixture was prepared including the fragmented cRNA, the Affymetrix recommended control cocktail and herring sperm DNA.
MICROARRAY:  Affymetrix HG-U95Av2 GeneChip(R).
HYBRIDIZATION: Affymetrix Hybridization Oven 640, Time: 16 hr, Temp: 45 C, Carousel Rotation Speed: 60 rpm.
WASHING AND STAINING:  Affymetrix Fluidics Station 400, EukGE:WS2v3 Protocol.
SCANNING: Affymetrix Agilent 2500 Scanner, Pixel Size: 3 microns, Filter: 570 nm, Scans: 2.  Original calibration.  The source of the data recorded below is the scan before the final antibody stain. (See the Affymetrix technical note, GeneArray(R) Scanner Update, Part 700575 Revision 2.)
DEVICE SPECIFIC ANALYSIS: Affymetrix Microarray Suite 5.0
Algorithm:  Statistical
Corner+  Avg:540, Count:32
Corner-  Avg:32728, Count:32
Background  Avg:299.65, Stdev:2.97, Max:309.6, Min:291.6
Noise  Avg:10.08, Stdev:0.35, Max:11.1, Min:9.2
RawQ  13.28
Alpha1  0.04
Alpha2  0.06
Tau  0.015
Gamma1H  0.0025
Gamma1L  0.0025
Gamma2H  0.003
Gamma2L  0.003
Perturbation  1.1
TGT  300
NF  1.000000
SF  1.234287
SFGene  All
DEVICE INDEPENDENT ANALYSIS: Silicon Genetics' GeneSpring(R) version 6, build 1333.  The Microarray Suite 5 output data was further processed with GeneSpring(R).  Each chip was normalized separately.  Each measurement on the chip was divided by the 50th percentile of all measurements (the median) in that sample.  The percentile was calculated with all normalized measurements above 0.  Values below 0.0 were set to 0.0.
Keywords = Human
Keywords = Prostate
Keywords = Cancer
Keywords = Adenocarcinoma
Keywords = Ionizing Radiation
Keywords = Microarray


title: Week 4 - Low Glucose

status: Public on May 31 2004

city: St. Louis

first: Matthew

middle: Alan

last: Roberts

state: MO

address: 1 Checkerboard Square

department: Global Strategic Business Unit and R&D

institute: Nestle Research Center

description: Human muscle cultures were prepared from progenitor satellite cells isolated from a muscle biopsy of a 16-donor subject through an explant-reexplant technique (5). Biopsies were obtained with informed consent and approval of the Human Use Committee of the Hospital Vall d’Hebrón, Barcelona. A batch of cells isolated after 1 explant and 4 consecutive subcultures at dilution (1:3) were induced to differentiate for 15 days and then weekly monitored for the stated parameters. Growth medium was DMEM:MEM-199 3:1, supplemented with 10 % fetal bovine serum (FBS), 10 µg/ml insulin, 2 mM glutamine, 25 ng/ml fibroblast growth factor (FGF) and 10 ng/ml epidermal growth factor (EGF).  Differentiating medium had the same composition except FGF and EGF. Cultures were kept at 37ºC in a humidified 5% CO2 atmosphere.

source_name: muscle biopsy primary cell culture