title: 2:08 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 15, 2005 12:10:03

source_name: 2:08 saline inflammatory

tag: subject id = 2:08 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:06 saline inflammatory (Cy5)

status: Public on Oct 01 2009

type: RNA

city: RTP

first: John

last: Tomfohr

state: NC

address: 111 T.W. Alexander Dr. P.O. Box 12233

country: USA

institute: NIEHS

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 09:10:35

molecule: total RNA

organism: Homo sapiens

source_name: 2:06 saline inflammatory

tag: subject id = 2:06 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes

source_name: Stratagene Universal Human Reference RNA

tag: Reference RNA


title: 2:06 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, April 19, 2005 09:33:10

source_name: 2:06 LPS inflammatory

tag: subject id = 2:06 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:05 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, April 13, 2005 15:56:13

source_name: 2:05 LPS inflammatory

tag: subject id = 2:05 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:05 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, April 13, 2005 16:11:04

source_name: 2:05 HDM inflammatory

tag: subject id = 2:05 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:10 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, May 26, 2005 14:04:21

source_name: 2:10 saline inflammatory

tag: subject id = 2:10 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:09 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 15, 2005 14:59:27

source_name: 2:09 LPS inflammatory

tag: subject id = 2:09 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:10 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, April 06, 2005 15:51:15

source_name: 2:10 HDM inflammatory

tag: subject id = 2:10 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:10 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, April 06, 2005 15:34:40

source_name: 2:10 LPS inflammatory

tag: subject id = 2:10 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:11 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, May 05, 2005 19:23:09

source_name: 2:11 saline inflammatory

tag: subject id = 2:11 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:09 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 15, 2005 15:35:23

source_name: 2:09 saline inflammatory

tag: subject id = 2:09 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:06 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 08:04:06

source_name: 2:06 HDM inflammatory

tag: subject id = 2:06 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:11 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, May 05, 2005 20:24:11

source_name: 2:11 LPS inflammatory

tag: subject id = 2:11 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:14 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, April 18, 2005 11:22:37

source_name: 2:14 HDM inflammatory

tag: subject id = 2:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:09 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 15, 2005 15:16:57

source_name: 2:09 HDM inflammatory

tag: subject id = 2:09 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:15 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 13:31:49

source_name: 2:15 saline inflammatory

tag: subject id = 2:15 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 2:15 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 09:30:20

source_name: 2:15 HDM inflammatory

tag: subject id = 2:15 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:14 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, April 18, 2005 11:02:03

source_name: 2:14 LPS inflammatory

tag: subject id = 2:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:03 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 15, 2005 10:31:55

source_name: 2:03 HDM inflammatory

tag: subject id = 2:03 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes

source_name: Stratagene Universal Human Reference RNA

tag: Reference RNA


title: 2:11 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, May 05, 2005 21:00:31

source_name: 2:11 HDM inflammatory

tag: subject id = 2:11 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:15 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 20:03:53

source_name: 2:15 LPS inflammatory

tag: subject id = 2:15 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 3:01 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, April 14, 2005 14:30:09

source_name: 3:01 saline inflammatory

tag: subject id = 3:01 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 3:01 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, May 25, 2005 09:04:35

source_name: 3:01 LPS inflammatory

tag: subject id = 3:01 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 3:02 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, April 18, 2005 09:09:12

source_name: 3:02 LPS inflammatory

tag: subject id = 3:02 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 3:01 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, May 25, 2005 09:23:59

source_name: 3:01 HDM inflammatory

tag: subject id = 3:01 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 3:02 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, April 18, 2005 09:42:44

source_name: 3:02 saline inflammatory

tag: subject id = 3:02 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 3:05 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 07:47:11

source_name: 3:05 HDM inflammatory

tag: subject id = 3:05 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 3:02 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, April 18, 2005 09:25:11

source_name: 3:02 HDM inflammatory

tag: subject id = 3:02 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 3:05 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, April 19, 2005 14:41:43

source_name: 3:05 saline inflammatory

tag: subject id = 3:05 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 3:07 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 18:00:51

source_name: 3:07 saline inflammatory

tag: subject id = 3:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 3:07 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, April 26, 2005 12:37:49

source_name: 3:07 LPS inflammatory

tag: subject id = 3:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:15 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, April 26, 2005 14:53:31

source_name: 4:15 saline inflammatory

tag: subject id = 4:15 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:16 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 01, 2005 16:01:42

source_name: 4:16 HDM inflammatory

tag: subject id = 4:16 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:12 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 10:12:07

source_name: 4:12 saline inflammatory

tag: subject id = 4:12 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:12 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 15:21:40

source_name: 4:12 HDM inflammatory

tag: subject id = 4:12 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:15 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 06:12:36

source_name: 4:15 LPS inflammatory

tag: subject id = 4:15 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes

source_name: Stratagene Universal Human Reference RNA

tag: Reference RNA


title: 4:15 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 21:00:59

source_name: 4:15 HDM inflammatory

tag: subject id = 4:15 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:14 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, April 27, 2005 13:43:40

source_name: 4:14 LPS inflammatory

tag: subject id = 4:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:17 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 07:46:42

source_name: 4:17 HDM inflammatory

tag: subject id = 4:17 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:08 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 15, 2005 11:49:09

source_name: 2:08 LPS inflammatory

tag: subject id = 2:08 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:16 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 01, 2005 15:36:11

source_name: 4:16 LPS inflammatory

tag: subject id = 4:16 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:03 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 15, 2004 15:10:55

source_name: 4:03 HDM inflammatory

tag: subject id = 4:03 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:03 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 15, 2004 15:17:24


title: 4:03 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, July 13, 2004 14:32:33

source_name: 4:03 LPS inflammatory

tag: subject id = 4:03 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:17 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 08:39:19

source_name: 4:17 saline inflammatory

tag: subject id = 4:17 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:14 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, April 28, 2005 11:04:15

source_name: 4:14 saline inflammatory

tag: subject id = 4:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:17 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 07:20:35

source_name: 4:17 LPS inflammatory

tag: subject id = 4:17 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:12 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 15:09:42

source_name: 4:12 LPS inflammatory

tag: subject id = 4:12 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:14 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, April 27, 2005 14:15:09

source_name: 4:14 HDM inflammatory

tag: subject id = 4:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 1:12 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, July 02, 2004 08:54:32

source_name: 1:12 HDM inflammatory

tag: subject id = 1:12 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:12 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, July 02, 2004 09:07:08

source_name: 1:12 saline inflammatory

tag: subject id = 1:12 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:12 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, July 02, 2004 08:28:19


title: 1:12 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, July 02, 2004 09:14:20


title: 1:12 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, July 02, 2004 16:17:04

source_name: 1:12 LPS inflammatory

tag: subject id = 1:12 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:03 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, July 13, 2004 14:24:31


title: 1:11 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 21, 2004 12:27:57

source_name: 1:11 saline inflammatory

tag: subject id = 1:11 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 2:14 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, April 18, 2005 11:40:49

source_name: 2:14 saline inflammatory

tag: subject id = 2:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes

source_name: Stratagene Universal Human Reference RNA

tag: Reference RNA


title: Brugia pahangi mature mf vs immature mf slide #32

city: Oshkosh

first: Kathryn

last: Griffiths

state: WI

address: 800 Algoma Blvd

department: Biology and Microbiology

institute: University of Wisconsin Oshkosh

description: Total RNA concentration and purity is obtained from an absorbance ratio at 260nm and 280nm. Total RNA quality is then determined by Agilent 2100 bioanalyzer (Agilent Technologies) according to manufacturer’s recommendations.

hyb_protocol: Hybridization Each sample pair (~24ul) is resuspended in formamide-based hybridization buffer (vial 7-Genisphere) (26ul), and Array 50dT blocker (Genisphere) (2ul). Two hybridizations are carried out in a sequential manner. The primary hybridization is performed by adding 48ul of sample to the microarray under a supported glass coverslip (Erie Scientific) at 43C for 16-20 hours at high humidity in the dark. Prior to the secondary hybridization, slides are gently submerged into 2X SSC, 0.2% SDS (at 43C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation. Secondary hybridization is carried out using the complimentary capture reagents provided in the 3DNA Array 900 kit (Genisphere). For each reaction, the following are added: 3DNA capture reagent with Cy3 (2.5ul), 3DNA capture reagent with Cy5 (2.5ul), SDS-based hybridization buffer (vial 6-Genisphere) (26ul), and nuclease-free water (21ul). The secondary hybridization solution is incubated in the dark at 80C for 10 min. then 50C for 15 min. Hybridization is performed by adding 48ul secondary hybridization solution to the slide under a supported glass coverslip at 65C for 4 hr at high humidity in the dark. At hybridization termination, arrays are gently submerged into 2X SSC, 0.2% SDS (at 65C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation.

scan_protocol: Slides are scanned on a Perkin Elmer ScanArray Express HT scanner to detect Cy3 and Cy5 fluorescence. Laser power is kept constant for Cy3/Cy5 scans and PMT is varied for each experiment based on optimal signal intensity with lowest possible background fluorescence. A low pmt setting scan is also performed to recover signal from saturated elements. Gridding and analysis of images is performed using ScanArray v3.0 (Perkin Elmer).

data_processing: Slides were scanned on a Perkin Elmer ScanArray Express HT scanner to detect Cy3 and Cy5 fluorescence as described by Li et al. B. pahangi data were analyzed by volcano plots (Bartholomay 2007). GeneSpring software (Agilent Technologies, Santa Clara, CA, USA) was used to identify differentially abundant transcripts using a 95% confidence interval over twofold values. To reduce false positives due to only two biological replicates in the B. malayi study, results were filtered using Benjamini and Hochberg false discovery rate (Benjamini 2001).

organism: Brugia pahangi

source_name: Brugia pahangi mature mf sample #3

label_protocol: First strand cDNA is generated by oligo-dT primed reverse transcription (Superscript II; Invitrogen) utilizing the 3DNA Array 900 kit (Genisphere). Modified oligo-dT primers are utilized in which a fluorophore/dendrimer specific oligo sequence is attached to the 5’ end of the dT primer. For cDNA synthesis, 1ul of fluorophore specific oligo-dT primer is added to 2ug of total RNA and the solution is incubated at 80C for 5 minutes then cooled on ice for 2 minutes. To each sample are added RNase inhibitor (Superase-In; Ambion) (0.5ul), 5X first strand buffer (2ul), dNTP mix (10mM each dATP, dCTP, dGTP, and dTTP) (0.5ul), 0.1M DTT (1ul), and Superscript II RNase H- Reverse Transcriptase (0.5ul). Reverse transcription is carried out at 42C for 2 hours. The reaction is terminated by adding 1.0M NaOH/ 100mM EDTA (1.0ul) and incubation at 65C for 10 minutes then neutralized with 2M Tris-HCL, pH 7.5 (1.2ul). For RNA expression level comparison, samples are paired.

extract_protocol: Total mf RNA was isolated by organic extraction with Trizol LS (Invitrogen, Carlsbad, CA USA), followed by column purification using Ambion RNAqueous-Micro® Kit (Applied Biosystems, Foster City, CA USA). RNA integrity was confirmed visually by agarose gel electrophoresis (data not shown), and purity and concentration determined spectrophotometrically (NanoDrop ND-1000, Thermo Fisher Scientific Wilmington, DE USA) and stored at -80° C. Samples were lyophilized under vacuum for transport to the Washington University Genome Sequencing Center, where RNA quality was verified using Agilent 2100 bioanalyzer (Agilent Technologies)

treatment_protocol:
Generation and collection of Brugia mf
Male jirds (Meriones unguiculatus) that had patent intraperitoneal infections for a minimum of 30 days were sacrificed and worms collected by peritoneal flush with sterile, prewarmed RPMI-1640 medium (Lonza, Walkersville, MD USA). Adults and mature mf were maintained in 37°C in RPMI containing 100 μg/mL penicillin and 100 μg/mL streptomycin (Cambrex, Rockland, ME USA). Equivalent numbers of adult worms were randomly assigned to groups and surgically transplanted into the peritoneum of uninfected jirds. To reduce damage due to excess handling, worms were not enumerated. Peritoneal flushes were microscopically examined in small volume increments (2-4 mL) to remove contaminating adult worms and debris, and mature (>30 day old) mf isolated by centrifugation through a Histopaque 1083 (Sigma Chemical Co., St. Louis, MO USA) gradient (Chandrashekar 1984). To collect immature mf, gerbils with transplanted adults were sacrificed after two days, and immature mf (<3 days old) were collected and purified as above. Mf pellets were resuspended in 250 ul of sterile phosphate buffered saline, flash frozen and stored at -80° C. B. pahangi transfers and harvests were performed in triplicate to generate three biological replicates for microarray hybridization, B. malayi transfers and harvests were performed in duplicate.

tag: developmental stage

value: mature mf

source_name: Brugia pahangi immature mf sample #3

value: immature mf


title: Brugia pahangi mature mf vs immature mf slide #29

source_name: Brugia pahangi mature mf sample #2

source_name: Brugia pahangi immature mf sample #2


title: Brugia pahangi mature mf vs immature mf slide #30


title: 1:11 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 16:51:40


title: Brugia pahangi mature mf vs immature mf slide #31


title: 1:11 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 16:43:51

source_name: 1:11 HDM inflammatory

tag: subject id = 1:11 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: Brugia pahangi mature mf vs immature mf slide #28

source_name: Brugia pahangi mature mf sample #1

source_name: Brugia pahangi immature mf sample #1


title: 1:11 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 16:32:06


title: 4:10 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 15, 2004 15:23:40

source_name: 4:10 LPS inflammatory

tag: subject id = 4:10 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:11 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 22:16:21

source_name: 1:11 LPS inflammatory

tag: subject id = 1:11 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:10 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 15, 2004 15:48:14

source_name: 4:10 saline inflammatory

tag: subject id = 4:10 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:11 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 22:02:21


title: 3:07 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, April 26, 2005 12:53:04

source_name: 3:07 HDM inflammatory

tag: subject id = 3:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 1:12 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 17:19:52


title: 4:10 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 15, 2004 15:04:22


title: Brugia malayi mature mf vs immature mf slide #42

organism: Brugia malayi

source_name: Brugia malayi mature mf sample #2

source_name: Brugia malayi immature mf sample #2


title: 4:10 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 28, 2004 13:34:13

tag: subject id = 4:10 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = no


title: 4:10 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 15, 2004 15:29:52

source_name: 4:10 HDM inflammatory

tag: subject id = 4:10 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:10 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 15, 2004 15:35:41

tag: subject id = 4:10 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = no


title: 4:09 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 15, 2004 14:50:32

source_name: 4:09 saline inflammatory

tag: subject id = 4:09 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:09 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 28, 2004 13:25:13


title: 4:09 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 14, 2004 11:15:54

source_name: 4:09 HDM inflammatory

tag: subject id = 4:09 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:16 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, April 27, 2005 13:14:06

source_name: 4:16 saline inflammatory

tag: subject id = 4:16 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes

source_name: Stratagene Universal Human Reference RNA


title: 4:09 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 14, 2004 11:07:30


title: Brugia pahangi mature mf vs immature mf slide #27

description: Total RNA concentration and purity is obtained from an absorbance ratio at 260nm and 280nm.  Total RNA quality is then determined by Agilent 2100 bioanalyzer (Agilent Technologies) according to manufacturer’s recommendations.

hyb_protocol: Hybridization Each sample pair (~24ul) is resuspended in formamide-based  hybridization buffer (vial 7-Genisphere) (26ul),  and Array 50dT blocker (Genisphere) (2ul).  Two hybridizations are carried out in a sequential manner. The primary hybridization is performed by adding 48ul of sample to the microarray under a supported glass coverslip (Erie Scientific) at 43C for 16-20 hours at high humidity in the dark.  Prior to the secondary hybridization, slides are gently submerged into 2X SSC, 0.2% SDS (at 43C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation. Secondary hybridization is carried out using the complimentary capture reagents provided in the 3DNA Array 900 kit (Genisphere).  For each reaction, the following are added: 3DNA capture reagent with Cy3 (2.5ul), 3DNA capture reagent with Cy5 (2.5ul), SDS-based hybridization buffer (vial 6-Genisphere) (26ul), and nuclease-free water (21ul).  The secondary hybridization solution is incubated in the dark at 80C for 10 min. then 50C for 15 min.  Hybridization is performed by adding 48ul secondary hybridization solution to the slide under a supported glass coverslip at 65C for 4 hr at high humidity in the dark. At hybridization termination, arrays are gently submerged into 2X SSC, 0.2% SDS (at 65C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation.

scan_protocol: Slides are scanned on a Perkin Elmer ScanArray Express HT scanner to detect Cy3 and Cy5 fluorescence.  Laser power is kept constant for Cy3/Cy5 scans and PMT is varied for each experiment based on optimal signal intensity with lowest possible background fluorescence. A low pmt setting scan is also performed to recover signal from saturated elements.  Gridding and analysis of images is performed using ScanArray v3.0 (Perkin Elmer).

data_processing: Slides were scanned on a Perkin Elmer ScanArray Express HT scanner to detect Cy3 and Cy5 fluorescence as described by Li et al.  B. pahangi data were analyzed by volcano plots (Bartholomay 2007). GeneSpring software (Agilent Technologies, Santa Clara, CA, USA) was used to identify differentially abundant transcripts using a 95% confidence interval over twofold values. To reduce false positives due to only two biological replicates in the B. malayi study, results were filtered using Benjamini and Hochberg false discovery rate (Benjamini 2001).

label_protocol: First strand cDNA is generated by oligo-dT primed reverse transcription (Superscript II; Invitrogen) utilizing the 3DNA Array 900 kit (Genisphere).  Modified oligo-dT primers are utilized in which a fluorophore/dendrimer specific oligo sequence is attached to the 5’ end of the dT primer.  For cDNA synthesis, 1ul of fluorophore specific oligo-dT primer is added to 2ug of total RNA and the solution is incubated at 80C for 5 minutes then cooled on ice for 2 minutes.  To each sample are added RNase inhibitor (Superase-In; Ambion) (0.5ul), 5X first strand buffer (2ul), dNTP mix (10mM each dATP, dCTP, dGTP, and dTTP) (0.5ul), 0.1M DTT (1ul), and Superscript II RNase H- Reverse Transcriptase (0.5ul).  Reverse transcription is carried out at 42C for 2 hours.  The reaction is terminated by adding 1.0M NaOH/ 100mM EDTA (1.0ul) and incubation at 65C for 10 minutes then neutralized with 2M Tris-HCL, pH 7.5 (1.2ul).  For RNA expression level comparison, samples are paired.

extract_protocol: Total mf RNA was isolated by organic extraction with Trizol LS (Invitrogen, Carlsbad, CA USA), followed by column purification using Ambion RNAqueous-Micro® Kit (Applied Biosystems, Foster City, CA USA). RNA integrity was confirmed visually by agarose gel electrophoresis (data not shown), and purity and concentration determined spectrophotometrically (NanoDrop ND-1000, Thermo Fisher Scientific Wilmington, DE USA) and stored at -80° C.  Samples were lyophilized under vacuum for transport to the Washington University Genome Sequencing Center, where RNA quality was verified using Agilent 2100 bioanalyzer (Agilent Technologies)

treatment_protocol:
Generation and collection of Brugia mf
Male jirds (Meriones unguiculatus) that had patent intraperitoneal infections for a minimum of 30 days were sacrificed and worms collected by peritoneal flush with sterile, prewarmed RPMI-1640 medium (Lonza, Walkersville, MD USA).  Adults and mature mf were maintained in 37°C in RPMI containing 100 μg/mL penicillin and 100 μg/mL streptomycin (Cambrex, Rockland, ME USA).  Equivalent numbers of adult worms were randomly assigned to groups and surgically transplanted into the peritoneum of uninfected jirds.  To reduce damage due to excess handling, worms were not enumerated.  Peritoneal flushes were microscopically examined in small volume increments (2-4 mL) to remove contaminating adult worms and debris, and mature (>30 day old) mf isolated by centrifugation through a Histopaque 1083 (Sigma Chemical Co., St. Louis, MO USA) gradient (Chandrashekar 1984).  To collect immature mf, gerbils with transplanted adults were sacrificed after two days, and immature mf (<3 days old) were collected and purified as above.  Mf pellets were resuspended in 250 ul of sterile phosphate buffered saline, flash frozen and stored at -80° C.  B. pahangi transfers and harvests were performed in triplicate to generate three biological replicates for microarray hybridization, B. malayi transfers and harvests were performed in duplicate.


title: 4:09 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 14, 2004 10:44:38

source_name: 4:09 LPS inflammatory

tag: subject id = 4:09 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: Brugia malayi mature mf vs immature mf slide #39

source_name: Brugia malayi mature mf sample #1

source_name: Brugia malayi immature mf sample #1


title: Brugia malayi mature mf vs immature mf slide #40

data_processing: Slides were scanned on a Perkin Elmer ScanArray Express HT scanner to detect Cy3 and Cy5 fluorescence as described by Li et al. B. pahangi data were analyzed by volcano plots (Bartholomay 2007). GeneSpring software (Agilent Technologies, Santa Clara, CA, USA) was used to identify differentially abundant transcripts using a 95% confidence interval over twofold values. To reduce false positives due to only two biological replicates in the B. malayi study, results were filtered using Benjamini and Hochberg false discovery rate (Benjamini 2001).


title: 4:07 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 07:30:04

source_name: 4:07 HDM inflammatory

tag: subject id = 4:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:07 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 07:37:01

source_name: 4:07 saline inflammatory

tag: subject id = 4:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:02 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, July 02, 2004 15:02:30

source_name: 4:02 HDM inflammatory

tag: subject id = 4:02 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:02 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, July 02, 2004 15:14:49

tag: Reference RNA


title: 1:10 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, August 06, 2004 17:15:26

source_name: 1:10 saline inflammatory

tag: subject id = 1:10 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:07 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 07:44:13


title: 4:02 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, July 02, 2004 15:31:04

source_name: 4:02 saline inflammatory

tag: subject id = 4:02 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:10 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 23:15:58

source_name: 1:10 LPS inflammatory

tag: subject id = 1:10 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:07 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, July 02, 2004 15:47:27

source_name: 4:07 LPS inflammatory

tag: subject id = 4:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:10 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 22:28:19

source_name: 1:10 HDM inflammatory

tag: subject id = 1:10 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:07 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 08:01:58


title: 4:02 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, July 02, 2004 15:23:56


title: 4:02 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, July 02, 2004 13:48:07

source_name: 4:02 LPS inflammatory

tag: subject id = 4:02 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:10 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 21, 2004 14:05:43


title: 4:02 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, July 02, 2004 14:08:23


title: 1:07 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 06:50:08

source_name: 1:07 saline inflammatory

tag: subject id = 1:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:07 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 07:12:39

source_name: 1:07 HDM inflammatory

tag: subject id = 1:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:07 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 06:09:32


title: 1:10 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 22:53:13


title: Brugia malayi mature mf vs immature mf slide #41

data_processing: Slides were scanned on a Perkin Elmer ScanArray Express HT scanner to detect Cy3 and Cy5 fluorescence as described by Li et al. B. pahangi data were analyzed by volcano plots (Bartholomay 2007). GeneSpring software (Agilent Technologies, Santa Clara, CA, USA) was used to identify differentially abundant transcripts using a 95% confidence interval over twofold values. To reduce false positives due to only two biological replicates in the B. malayi study, results were filtered using Benjamini and Hochberg false discovery rate (Benjamini 2001).

source_name: Brugia malayi mature mf sample #2

tag: developmental stage

source_name: Brugia malayi immature mf sample #2


title: 1:07 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 08:32:11

source_name: Stratagene Universal Human Reference RNA

source_name: 1:07 LPS inflammatory

tag: subject id = 1:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:07 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 08:19:42


title: 4:06 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, July 02, 2004 09:36:35

source_name: 4:06 LPS inflammatory

tag: subject id = 4:06 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:09 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 14, 2004 10:53:18

source_name: 4:09 LPS inflammatory


title: 4:06 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, July 02, 2004 09:52:44

source_name: 4:06 HDM inflammatory

tag: subject id = 4:06 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:08 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, July 20, 2004 22:21:11

source_name: 4:08 HDM inflammatory

tag: subject id = 4:08 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:08 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, July 13, 2004 16:04:21

source_name: 4:08 saline inflammatory

tag: subject id = 4:08 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:05 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 08:55:01

source_name: 4:05 saline inflammatory

tag: subject id = 4:05 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:04 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 10:14:42

source_name: 4:04 LPS inflammatory

tag: subject id = 4:04 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:05 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 08:38:12

source_name: 4:05 HDM inflammatory

tag: subject id = 4:05 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes

tag: Reference RNA


title: 4:08 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 09:34:52

source_name: 4:08 LPS inflammatory

tag: subject id = 4:08 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:04 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 09:01:36

source_name: 4:04 saline inflammatory

tag: subject id = 4:04 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:08 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, July 13, 2004 15:40:02


title: 4:05 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 08:47:45


title: 4:04 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 09:23:52


title: 4:08 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 09:45:21


title: 4:04 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 10:28:09

source_name: 4:04 HDM inflammatory

tag: subject id = 4:04 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:06 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, July 02, 2004 10:36:52

source_name: 4:06 saline inflammatory

tag: subject id = 4:06 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = no


title: 4:04 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, July 20, 2004 22:08:49


title: 4:06 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, July 02, 2004 11:14:57

tag: subject id = 4:06 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:08 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, July 13, 2004 15:18:28


title: 1:07 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 08:44:14


title: 4:06 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, July 02, 2004 09:23:51


title: 4:06 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, July 02, 2004 10:14:36

tag: subject id = 4:06 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = no


title: 4:04 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 10:21:03


title: 4:05 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 10:08:26


title: 4:05 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 08:30:47

source_name: 4:05 LPS inflammatory

tag: subject id = 4:05 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:10 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 21, 2004 11:21:24

source_name: 1:10 saline inflammatory

tag: subject id = 1:10 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:09 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 09:19:26

source_name: 1:09 HDM inflammatory

tag: subject id = 1:09 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:09 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 09:12:35

source_name: Stratagene Universal Human Reference RNA

source_name: 1:09 LPS inflammatory

tag: subject id = 1:09 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:09 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 09:26:00


title: 1:09 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 09:05:39


title: 4:01 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 10:55:32

source_name: 4:01 HDM inflammatory

tag: subject id = 4:01 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:09 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 10:27:35

source_name: 1:09 saline inflammatory

tag: subject id = 1:09 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:06 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 08:38:23

source_name: 1:06 HDM inflammatory

tag: subject id = 1:06 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:01 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 08:12:42

source_name: 4:01 LPS inflammatory

tag: subject id = 4:01 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:01 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 10:46:19


title: 4:07 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 28, 2004 13:17:52

source_name: 4:07 LPS inflammatory

tag: subject id = 4:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:06 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 08:28:26


title: 4:01 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 11:02:15


title: 1:03 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 10:06:19

source_name: 1:03 HDM inflammatory

tag: subject id = 1:03 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:09 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 09:11:34

tag: Reference RNA


title: 4:01 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 09:54:24

source_name: 4:01 saline inflammatory

tag: subject id = 4:01 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:04 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 10:38:45

source_name: 1:04 HDM inflammatory

tag: subject id = 1:04 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:06 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 21, 2004 13:56:52

source_name: 1:06 LPS inflammatory

tag: subject id = 1:06 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:04 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 21, 2004 13:50:49

source_name: 1:04 saline inflammatory

tag: subject id = 1:04 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:04 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 10:19:50


title: 4:05 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 08:22:59


title: 1:06 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 08:46:38

source_name: 1:06 saline inflammatory

tag: subject id = 1:06 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 4:01 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 07, 2004 10:01:14


title: 1:03 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, August 06, 2004 19:10:58


title: 1:06 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 11:03:20


title: 1:03 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 21, 2004 13:37:27

source_name: 1:03 saline inflammatory

tag: subject id = 1:03 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:04 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 10:25:47

source_name: 1:04 LPS inflammatory

tag: subject id = 1:04 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:04 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 10:32:30


title: 1:06 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 08:59:26


title: 1:04 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 10:47:48


title: 1:02 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 09:27:25

source_name: 1:02 HDM inflammatory

tag: subject id = 1:02 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = no


title: 1:02 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 09:34:26

tag: subject id = 1:02 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: 1:01 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 09:14:32

source_name: 1:01 LPS inflammatory

tag: subject id = 1:01 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = no


title: 1:02 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 21, 2004 14:21:30

source_name: 1:02 LPS inflammatory

tag: subject id = 1:02 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes

source_name: Stratagene Universal Human Reference RNA


title: 1:03 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, August 06, 2004 17:31:33


title: 1:02 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 09:03:29

source_name: 1:02 saline inflammatory

tag: subject id = 1:02 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes


title: NHEK_DNCB treated_4.5 hr

status: Public on Sep 30 2009

city: Nishinomiya

first: Yoshie

last: Yoshikawa

state: Hyogo

address: 1-1 Mukogawa-cho

department: Genetics

country: Japan

institute: Hyogo College of Medicine

description: NHEK ; purchased from Kurabo (Osaka, Japan)

hyb_protocol: Cy3- or Cy5-labeled probes were mixed, fragmented, and then dissolved in GE hybridization buffer in the Gene Expression Hybridization Kit (Agilent). After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent microarray scanner. Images were quantified using Agilent Feature Extraction Software (ver9.5.3.1).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Expressionist (GeneData AG, Basel, Switzerland) software was used.

source_name: neonatal human epidermal keratinocytes NHEK_DNCB treated_4.5 hr

label_protocol: Total RNAs (each 200ng) were labeled with Cy3- or Cy5- CTP using Agilent Quick Amp Labeling Kit (Agilent Technologies Inc.).

growth_protocol: BDKs and NHEK ; cultured in Defined Keratinocyte-SFM medium （DK-SFM, GIBCO/Invitrogen Co., CA） at 37°C in a humidified atmosphere containing 5% CO2.                                                                             THP-1; cultured in RPMI1640 medium (GIBCO/Invitrogen Co.) containing 10% fetal bovine serum (Equitech-bio Inc., TX, USA) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Isolated using TRIzol reagent (Invitrogen, CA, USA) and purified using an RNeasy kit (QIAGEN, Hilden, Germany).

treatment_protocol: BDKs or NHEK ; seeded at 5 x 105 cells/60 mm φ dish and incubated in medium at 37 °C for 24 hr, and sequentially in MCDB153 medium (Research Institute for the Functional Peptides Co., Ltd, Yamagata, Japan) at 37 °C for 24 hr. 24 hr later, cells were treated with 10 μM DNCB or 0.1% DMSO for 4.5 hr.                      THP-1 ;  seeded at the density of 7 x 105 cells/10 mm φ dish. 24 hr later, cells were treated with 10 μM DNCB or 0.1% DMSO for 4.5 hr.

tag: gender

value: male

source_name: neonatal human epidermal keratinocytes NHEK_DMSO (solvent control) treated_4.5 hr


title: BDK established from donor II_DNCB treated_4.5 hr

description: BDKs ; prepared from plucked hairs using a depilation forceps from the side area of the scalp of adult subjects, who gave written informed consent

source_name: bulge-derived keratinocytes established from donor II_DNCB treated_4.5 hr

value: female

source_name: bulge-derived keratinocytes established from donor II_DMSO (solvent control) treated_4.5 hr


title: THP-1_DNCB treated_4.5 hr

description: THP-1; obtained from Human Sciences Research Resources Bank (Japan Human Sciences Foundation, Tokyo, Japan)

source_name: human monocytic leukemia THP-1_DNCB treated_4.5 hr

source_name: human monocytic leukemia THP-1_DMSO (solvent control) treated_4.5 hr


title: 1:02 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 08:56:53


title: 1:02 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, August 06, 2004 16:59:51

tag: subject id = 1:02 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = no


title: BDK established from donor I_DNCB treated_4.5 hr

source_name: bulge-derived keratinocytes established from donor I_DNCB treated_4.5 hr

source_name: bulge-derived keratinocytes established from donor I_DMSO (solvent control) treated_4.5 hr


title: dysplastic nevus_23_DS

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

country: Italy

institute: Fondo Edo Tempia

description: technical replicate of 23_NORM

hyb_protocol: Equal amounts (0.75 ug) of labeled specimens from sample and reference were put together, fragmented and hybridized to oligonucleotide glass arrays representing 41K human unique genes and transcripts (Human Whole Genome Oligo Microarray Array, Agilent Technologies). All steps were performed using the In Situ Hybridization kit-plus (Agilent Technologies) and following the 60-mer oligo microarray processing protocol (Agilent Technologies). Then, slides were washed with the SSPE wash procedure. For each sample, a dye-swap replicate was performed.

scan_protocol: Slides were scanned with the dual-laser microarray scanner Agilent G2505B

data_processing:
Images were analyzed using Feature Extraction software (Agilent Technologies) version 7.6. Output files containing feature and background intensities and the related statistical parameters for red and green signals were then loaded into the Resolver SE System (Rosetta Biosoftware, Seattle, WA) together with the scan images and the Agilent Human Whole Genome pattern file. Data processing and normalization were performed using the Agilent Human Whole Genome platform-specific error model.  The Log10 (test/ref) ratios are reported in the Sample VALUE column in the data table below.

The final, processed data (those that form the basis of the conclusions of the study) are contained in the file named all_vs_average_nevi.txt which has been linked as a supplementary file on the Series GSE12391 record. Experiments (displastic nevi, melanoma, melanoma metastasis samples) were combined to form ratio experiments, by applying the ratio split with common reference option and calculating ratios over the average of non tumor samples (CMN).
More details: Replicated expression profiles were combined to form ratio experiments where each gene is associated to an expression fold-change and a p-value to assess the statistical significance of its modulation in the sample compared to the reference. New ratio experiments were also built by applying the “ratio split with common reference” option and calculating ratios over the average of non tumor samples (CMN). A “weight by error” divisive clustering algorithm available within the Rosetta Resolver system (with cosine correlation as similarity metrics) was applied to such new ratios to compare their expression profiles. At the same time, data treatment with the LIMMA (LInear Models for MicroArray data) package available within Bioconductor (http://www.bioconductor.org/) was also performed applying normexp background calculation, lowess within-array and A-quantile between-array normalization methods.

source_name: commercial human universal reference

label_protocol: RNA isolated from each fresh tissue and from the human universal reference (BD™ Human Universal Reference Total RNA, Clontech, Palo Alto, CA) was amplified by means of the Amino Allyl MessageAmp II aRNA Kit (Ambion) to obtain amino allyl antisense RNA (aaRNA) following the method developed by Eberwine and coworkers. Two rounds of amplification were performed to obtain the necessary quantity of aaRNA for labeling. Briefly: mRNA was reverse transcribed in cDNA single strand; after the second strand synthesis (in the second round of amplification), cDNA was in vitro transcribed in aaRNA including amino allyl modified nucleotides (aaUTP). Both dsDNA and aaRNA underwent a purification step using columns provided with the kit. Labeling was performed using NHS ester Cy3 or Cy5 dyes (Amersham Biosciences, Buckinghamshire UK) able to react with the modified RNA. mRNA quality was checked by means of RNA 6000 nano chip assays (Agilent Technologies). At least 5 ug of mRNA for each sample were labeled and purified with columns.

extract_protocol: All the samples were homogenized (Ultra – TurraxT8, Ika – Werke, Staufen, Germany) with 600 ul of RNA lysis buffer plus 1% 2-mercaptoethanol, and total RNA was isolated by using RNeasy Mini Kit (Qiagen, Dusseldorf, Germany). TotRNA quality was checked by means of RNA 6000 pico chip assays (Agilent Technologies, Palo Alto, CA) run on the Agilent 2100 bioanalyzer.

tag: Clontech human universal reference

source_name: dysplastic nevus: high atypia

tag: Gender

value: Male

tag: Age


title: dysplastic nevus_8b_DS

description: technical replicate of 8b_NORM


title: 1:01 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 09:06:35

tag: subject id = 1:01 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 1 (2004) | included in published analysis = yes

tag: Reference RNA


title: dysplastic nevus_25b_DS

description: technical replicate of 25b_NORM


title: dysplastic nevus_20_DS

description: technical replicate of 20_NORM

source_name: dysplastic nevus: low atypia


title: dysplastic nevus_26_DS

description: technical replicate of 26_NORM


title: melanoma metastasis_51_DS

description: technical replicate of 51_NORM

source_name: melanoma metastasis site: derma

value: Female


title: dysplastic nevus_25a_DS

description: technical replicate of 25a_NORM


title: dysplastic nevus_22_DS

description: technical replicate of 22_NORM


title: dysplastic nevus_24_DS

description: technical replicate of 24_NORM


title: dysplastic nevus_21_DS

description: technical replicate of 21_NORM


title: melanoma metastasis_50_DS

description: technical replicate of 50_NORM


title: vertical growth phase melanoma_37_DS

description: technical replicate of 37_NORM

source_name: melanoma Clark's level III


title: melanoma metastasis_48_DS

description: technical replicate of 48_NORM

source_name: melanoma metastasis site: node


title: melanoma metastasis_49_DS

description: technical replicate of 49_NORM


title: dysplastic nevus_18_DS

description: technical replicate of 18_NORM


title: vertical growth phase melanoma_17b_DS

description: technical replicate of 17b_NORM


title: radial growth phase melanoma_30_DS

description: technical replicate of 30_NORM

source_name: melanoma Clark's level II


title: melanoma metastasis_47_DS

description: technical replicate of 47_NORM


title: radial growth phase melanoma_27_DS

description: technical replicate of 27_NORM

source_name: melanoma Clark's level I


title: dysplastic nevus_22

description: technical replicate of 22_DS


title: dysplastic nevus_24

description: technical replicate of 24_DS


title: dysplastic nevus_20

description: technical replicate of 20_DS


title: dysplastic nevus_8b

description: technical replicate of 8b_DS


title: dysplastic nevus_23

description: technical replicate of 23_DS


title: common melanocytic nevus_2_DS

description: technical replicate of 2_NORM

source_name: common acquired melanocytic nevus


title: dysplastic nevus_25a

description: technical replicate of 25a_DS


title: dysplastic nevus_21

description: technical replicate of 21_DS


title: dysplastic nevus_18

description: technical replicate of 18_DS


title: melanoma metastasis_48

description: technical replicate of 48_DS


title: vertical growth phase melanoma_37

description: technical replicate of 37_DS


title: melanoma metastasis_47

description: technical replicate of 47_DS


title: melanoma metastasis_49

description: technical replicate of 49_DS


title: common melanocytic nevus_8a_DS

description: technical replicate of 8a_NORM


title: dysplastic nevus_26

description: technical replicate of 26_DS


title: radial growth phase melanoma_28_DS

description: technical replicate of 28_NORM


title: common melanocytic nevus_9a_DS

description: technical replicate of 9a_NORM


title: common melanocytic nevus_3_DS

description: technical replicate of 3_NORM


title: vertical growth phase melanoma_17b

description: technical replicate of 17b_DS


title: dysplastic nevus_25b

description: technical replicate of 25b_DS


title: melanoma metastasis_50

description: technical replicate of 50_DS


title: melanoma metastasis_51

description: technical replicate of 51_DS


title: common melanocytic nevus_17a_DS

description: technical replicate of 17a_NORM


title: radial growth phase melanoma_28

description: technical replicate of 28_DS


title: radial growth phase melanoma_30

description: technical replicate of 30_DS


title: radial growth phase melanoma_27

description: technical replicate of 27_DS


title: common melanocytic nevus_17a

description: technical replicate of 17a_DS


title: gpa1(-)-exp1-161

status: Public on Sep 26 2009

city: Seoul

first: Yong-Sun

last: Bahn

address: 134 Shinchon-dong Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

hyb_protocol: Microarray Hybridization and Washing.  A C. neoformans serotype D 70-mer microarray slide containing 7,936 probes (Duke University) was pre-hybridized at 42°C in 60 ml of pre-hybridization buffer (42.4 ml sterile distilled water, 2 ml 30% BSA (Bobogen), 600 µl 10% SDS, 15 ml 20x SSC (Saline-Sodium Citrate, 3 M NaCl, 0.3 M Na-citrate, pH 7.0)), washed with distilled water and isopropanol, and dried by brief centrifugation (110g, 2 min).  The Cy3- and Cy5-labeled cDNA samples were combined, concentrated through a Microcon30 filter, and vacuum-dried.  The dried cDNA samples were resuspended with 24 µl of 1x hybridization buffer (250 µl 50% formamide, 125 µl 20x SSC, 5 µl 10% SDS, 120 µl dH2O, total 500 µl), added with 1 µl polyA tail DNA (Sigma), further incubated at 100°C for 3 min and allowed to cool for 5 min at room temperature.  The microarray slides were aligned into the hybridization chamber (DieTech), removed of any dust, and covered by coverslide (Marienfeld 22X22).  The Cy3/Cy5-labeled cDNA samples were applied in between coverslide and slides.  To prevent slides from drying, 10 µl of 3x SSC buffer was applied onto the slides, which were subsequently incubated for 16 hr at 42°C.  After incubation, the microarray slides were washed with three different washing buffers (wash buffer 1 (10 ml 20x SSC, 600 µl 10% SDS, 189.4 ml dH2O, preheated at 42°C), wash buffer 2 (3.5 ml 20x SSC, 346.5 ml dH2O), wash buffer 3 (0.88 ml 20x SSC, 349.12 ml dH2O)) for 2, 5, and 5 min, respectively, on an racker.  Three independent DNA microarrays with 3 independent biological replicates were performed, including one-dye swap experiment.

scan_protocol: After hybridization and washing, the microarray slides were scanned with a GenePix 4100A scanner (Axon Instrument) and the signals were analyzed with GenePix Pro (Ver. 6.0) and gal file (http://genome.wustl.edu/activity/ma/cneoformans).

data_processing: Since total RNAs isolated from serotype A C. neoformans strains were hybridized on the microarray slides printed with the serotype D 70-mer oligonucleotide sequences, the serotype A gene sequences were mapped to those of the serotype D using BLASTN.  C. neoformans H99 gene sequences that were updated at 24 November 2008 were downloaded from Broad institute (http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans).  The serotype D C. neoformans JEC21 gene sequences that were updated 27 April 2005 were downloaded from JCVI (ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/c_neoformans/).  The functional category of each C. neoformans H99 gene was assigned using the NCBI KOG database (http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi).  Using the serotype A gene sequence, each S. cerevisiae gene name or ID listed in the supplementary Tables was identified by blastp search (e-value cut-off: e-6). For hierarchical and statistical analysis, data transported from GenePix software were analyzed with GeneSpring (Agilent) by employing LOWESS normalization, reliable gene filtering, clustering (standard correlation and average linkage) and zero-transformation, and ANOVA analysis (P<0.01), and Microsoft Excel software (Microsoft).

organism: Cryptococcus neoformans H99

label_protocol: For cDNA synthesis, the total RNA concentration was adjusted to 1 µg/µl with DEPC-treated water, and 15 µl of the total RNA (15 µg) was added to 1 µl of 5 µg/µl oligo dT (5’-TTTTTTTTTTTTTTTTTTTTV-3’)/pdN6 (IDT, 1:1 mixture of 10 µg/µl, respectively), incubated at 70°C for 10 min, and place on ice for 10 min.  Then 15 µl of cDNA synthesis mixture (3 µl 0.1 M DTT, 0.5 µl RNasin (Intron), 0.6 µl aa-dUTP (5-(3-aminoallyl)-2’-deoxyuridine 5’-triphosphate)/dNTPs (a mixture of 6 µl dTTP (100 mM), 4 µl aa-dUTP (100 mM), 10 µl dATP (100 mM), 10 µl dCTP (100 mM), 10 µl dGTP (100 mM)), 1.5 µl SuperScript reverse transcriptase (Invitrogen), 3 µl SuperScript buffer, 7 µl water) was added and incubated at 42°C for 2 hrs.  Then 10 µl of 1 N NaOH and 10 µl of 0.5 M EDTA (pH 8.0) were added and incubated at 65°C for 15 min.  After incubation, 25 µl of 1 M HEPES buffer (pH 8.0) and 450 µl of DEPE-treated water were added, and the whole mixture was concentrated through a Microcon30 filter (Millipore) and vacuum-dried for 1 hr.  For Cy3 and Cy5 (Amersham) labeling of the prepared cDNA, Cy3 and Cy5 were dissolved in 10 µl DMSO and 1.25 µl of each dye was aliquoted into separate tubes.  The cDNAs prepared as described above were added to 9 µl of 0.05 M Na-bicarbonate (pH 8.0) and incubate at room temperature for 15 min.  The cDNAs prepared from pooled reference RNAs were mixed with Cy3 as a control and the cDNAs prepared from each test RNA (each experimental condition) were mixed with Cy5.  For a dye-swap experiment, control and test RNAs were labeled oppositely.  Each mixture was further incubated at room temperature for 1 hr in the dark and purified by QIAquick PCR purification kit (QIAGEN).

growth_protocol: H99 wild type, ras1(YSB53), aca1(YSB6), gpa1(YSB83), cac1(YSB42), pka1pka2 (YSB200), mutant strains were grown in 50 ml YPD medium at 30°C for 16 hr.  Then 5 ml of the overnight culture was inoculated into a 100 ml of fresh YPD medium and further incubated for 4-5 hr at 30°C until it approximately reaches to the 1.0 of optical density (OD) at 600 nm (OD600nm = 1.0).

extract_protocol: For total RNA isolation, the lyophilized cell pellets were added to 3 ml volume of sterile 3 mm glass bead (SIGMUND LINDER), homogenized by shaking, added to 4 ml of TRizol reagent (Tri reagent, Molecular Research Center), and allowed to incubate at room temperature for 5 min.  Then 800 µl of chloroform was added, incubated for 3 min at room temperature, transferred to 15 ml round-bottom tubes (SPL), and centrifuged by 10,000 rpm at 4°C for 15 min (Hanil rotor No. 7).  Two milliliters of the supernatant was transferred to a new round-bottom tube, 2 ml isopropanol was added, inverted several times, and allowed to incubate for 10 min at room temperature.  Then the mixture was re-centrifuged at 10,000 rpm at 4°C for 10 min, and the pellet was washed with 4 ml of 75% ethanol diluted with diethylpyrocarbonate (DEPC)-treated water and centrifuged at 8,000 rpm at 4°C for 5 min.  The pellet was dried and resuspended with 500 µl DEPC-treated water.  Concentration and purity of total RNA samples were calculated by measuring OD260nm and gel-electrophoresis, respectively.  For control total RNA, all total RNAs prepared from WT, ras1, gpa1, aca1, cac1 and pka1pka2 mutant cells grown in conditions described above were pooled (pooled reference RNAs).

treatment_protocol: 50 ml culture was sampled and rapidly frozen in liquid nitrogen and lyophilized overnight. The lyophilized cells were subsequently used for total RNA isolation.  As biological replicates for DNA microarrays, three independent cultures for each strain and growth condition were prepared for total RNA isolation.

tag: strain

tag: genotype

tag: exposed stress

value: Normal

source_name: pooled total RNA from all strains

tag: reference

value: pooled reference


title: pka1(-)pka2(-)-exp2-dye swap-154

description: pka1(-)pka2(-)-exp2-dye swap-154

value: pka1Δ pka2Δ


title: gpa1(-)-exp2-dye swap-150

description: gpa1(-)-exp2-dye swap-150


title: cac1(-)-exp2-dye swap-152

description: cac1(-)-exp2-dye swap-152


title: cac1(-)-exp3-158


title: gpa1(-)-exp3-156


title: pka1(-)pka2(-)-exp3-160


title: cac1(-)-exp1-165


title: pka1(-)pka2(-)-exp1-148


title: aca1(-)-exp1-162


title: aca1(-)-exp3-157


title: WT(H99)-exp2-dye swap-149

description: WT(H99)-exp2-dye swap-149

source_name: wild-type

value: wild-type


title: WT(H99)-exp3-155


title: common melanocytic nevus_3

description: technical replicate of 3_DS


title: common melanocytic nevus_8a

description: technical replicate of 8a_DS


title: WT(H99)-exp1-147


title: ras1(-)-exp2-dye swap-153

description: ras1(-)-exp2-dye swap-153


title: common melanocytic nevus_2

description: technical replicate of 2_DS


title: common melanocytic nevus_9a

description: technical replicate of 9a_DS


title: aca1(-)-exp2-dye swap-151

description: aca1(-)-exp2-dye swap-151


title: ras1(-)-exp1-166


title: ras1(-)-exp3-159


title: gcn5mst_gcn5_KCl_rep1

status: Public on Sep 20 2009

city: Los Angeles

first: Susan

last: Forsburg

state: CA

address: 1050 Childs Way, RRI 201B

department: Molecular and Computational Biology

institute: University of Southern California

hyb_protocol: See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).

scan_protocol: Slides were scanned using Bio-rad Vers-Array ChipReader. Scanned slides were quantified with Imagene 4.2 software.

data_processing: Quantified data were loaded to GeneSpring software and normalized by lowess normalization

molecule: polyA RNA

organism: Schizosaccharomyces pombe

source_name: mutant ∆gcn5∆mst, 60 min 1 M KCl, 25C, rep 1

growth_protocol: Strain was grown on YES medium at 25C to log phase

tag: cell line

tag: treatment

value: 1 M KCl, 60 minutes

source_name: mutant ∆gcn5, 60 min 1 M KCl, 25C, rep 1


title: mst_wt_KCl_rep1

source_name: wild type, 60 min 1 M KCl, 25C, rep 1

label_protocol: See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).

value: wt

source_name: mutant ∆mst, 60 min 1 M KCl, 25C, rep 1

value: mst


title: gcn5mst_gcn5_KCl_rep2

source_name: mutant ∆gcn5, 60 min 1 M KCl, 25C, rep 2

extract_protocol: See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).

source_name: mutant ∆gcn5∆mst, 60 min 1 M KCl, 25C, rep 2


title: mst_wt_KCl_rep2

source_name: mutant ∆mst, 60 min 1 M KCl, 25C, rep 2

source_name: wild type, 60 min 1 M KCl, 25C, rep 2


title: gcn5elp3mst2_1

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Yeast Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The .CEL files are read into R and processed with RMA (Irizarry et al., 2003) to generate log2 scores of the probe set intensities. The array intensities are then linearly modeled to find coefficients of expression between the various mutants and wt using Limma (Smyth, 2004).

label: biotin

source_name: mutant ∆gcn5∆elp3∆mst2, rep 1

label_protocol: Biotinylated cRNA were prepared according to the MessageAmp II-Biotin Enhanced Single Round protocol (Life technologies / Ambion, TX) from 1 ug total RNA.

growth_protocol: Cells were grown at 30 °C in asynchronous cultures.

extract_protocol: Cells were harvested for Total RNA extraction with hot phenol.

value: mutant ∆gcn5∆elp3∆mst2

tag: replicate

tag: experiment date


title: mst2elp3_2

source_name: mutant ∆mst2∆elp3, rep 2

value: mutant ∆mst2∆elp3


title: elp3_2

source_name: mutant ∆elp3, rep 2

value: mutant ∆elp3


title: mst2elp3_3

source_name: mutant ∆mst2∆elp3, rep 3


title: gcn5elp3_1

source_name: mutant ∆gcn5∆elp3, rep 1

value: mutant ∆gcn5∆elp3


title: elp3_3

source_name: mutant ∆elp3, rep 3


title: gcn5mst2_2

source_name: mutant ∆gcn5∆mst2, rep 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix (One-Cycle) protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix)

value: mutant ∆gcn5∆mst2


title: gcn5mst2_1

source_name: mutant ∆gcn5∆mst2, rep 1


title: mst2_1

source_name: mutant ∆mst2, rep 1

value: mutant ∆mst2


title: gcn5elp3_2

source_name: mutant ∆gcn5∆elp3, rep 2


title: mst2_3

source_name: mutant ∆mst2, rep 3


title: mst2_2

source_name: mutant ∆mst2, rep 2


title: gcn5mst2_3

source_name: mutant ∆gcn5∆mst2, rep 3


title: elp3_1

source_name: mutant ∆elp3, rep 1


title: mst2-ts_2

source_name: temperature sensitive mst1, rep 2

value: temperature sensitive mst1


title: mst2-ts_3

source_name: temperature sensitive mst1, rep 3


title: mst2-ts_1

source_name: temperature sensitive mst1, rep 1


title: mst2elp3_1

source_name: mutant ∆mst2∆elp3, rep 1


title: wt_3

source_name: wild type, rep 3

value: wild type


title: gcn5_2

source_name: mutant ∆gcn5, rep 2

value: mutant ∆gcn5


title: gcn5_1

source_name: mutant ∆gcn5, rep 1


title: wt_2

source_name: wild type, rep 2


title: mst_wt_rep1

source_name: mutant ∆mst, rep 1

source_name: wild type, rep 1


title: gcn5_3

source_name: mutant ∆gcn5, rep 3


title: wt_1


title: mst_wt_rep2

source_name: mutant ∆mst, rep 2


title: 60141_FAaplastic_rep15

status: Public on Sep 15 2009

city: Portland

first: Grover

middle: C

last: Bagby

state: OR

address: 3181 SW Sam Jackson Park Rd.

department: Dept. of Medicine

institute: Oregon Health & Science University

description: Hybridization date: 12/10/02; Array lot: 2006208

hyb_protocol: The arrays were hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 16 hours at 45⁰C, followed by washing, staining with streptavidin-phycoerythrin (SAPE; Molecular Probes, Eugene, OR), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA), and a final staining with SAPE. The staining and washing were performed using two GeneChip Fluidic Station 400s (Affymetrix, Santa Clara, CA) running standard Affymetrix fluidics script.

scan_protocol: The distribution of fluorescent material on the processed array was determined using the Agilent G2500 GeneArray Scanner (Agilent Technologies, Santa Clara, CA). The array image scan was processed using Affymetrix Microarray Suite, version 5.0 (MAS 5.0), which resulted in the generation of raw, probe level data in the CEL file format.

data_processing: The data were processed by GeneSifter software using Robust Multichip Analysis (RMA) that includes a background correction, quantile normalization, and median polish as summarization.

source_name: low-density bone marrow cells from aplastic Fanconi anemia patient

label_protocol: Each total RNA sample was labeled and amplified following the recommended protocol in the Affymetrix GeneChip Expression Analysis Technical Manual, rev. 2 (http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf). Using 4 µg of total RNA as input, messenger RNA was amplified and labeled in two steps. In the first step, mRNA was converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (IDT, Coralville, IA). Double-stranded cDNA was purified by phenol-chloroform-isoamyl alcohol extraction and a standard ethanol precipitation. In the second step, the cDNA was converted to labeled cRNA (the target) using T7 RNA polymerase in the presence of biotinylated UTP and CTP (Enzo, Farmingdale, NY). Unincorporated nucleotides were removed using the RNeasy Mini kit (Qiagen) and was followed by an ethanol precipitation of the labeled target. The target was fragmented to produce a uniform distribution of short cRNAs. 10µg each of fragmented target was combined with hybridization control oligomer (Affymetrix, Santa Clara, CA) and control cRNAs (1.5pM BioB, 5.0pM BioC, 25pM BioD, and 100pM Cre; Affymetrix, Santa Clara, CA), in hybridization buffer and applied to the array.

extract_protocol: Heparinized bone marrow aspiration samples were obtained from patients and normal volunteers after obtaining informed consent. Low-density marrow cells were isolated using Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ), then total RNA was extracted immediately using the RNeasy Mini Kit (QIAGEN, Valencia, CA). RNA was concentrated to approximately 1 ug/ul by precipitation with 3M sodium acetate, pH 5.2, 5 ug of linear polyacrylamide (Sigma, St. Louis, MO), and 2.5 volumes of 100% ethanol. Final RNA pellets were dissolved in nuclease-free water.

tag: disease state

value: Fanconi anemia

tag: cell type

value: low-density bone marrow cells

value: F

tag: age

tag: fa complementation group

value: FANCG


title: 60101_FAaplastic_rep12

tag: gender

value: FANCC


title: 60321_FAaplastic_rep20

description: Hybridization date: 03/06/04; Array lot: 3004864

value: unknown


title: 10231_FAaplastic_rep5

description: Hybridization date: 10/05/04; Array lot: 4003510

value: M

value: FANCA


title: 60181_FAaplastic_rep17

description: Hybridization date: 04/08/03; Array lot: 3000517


title: 60061_FAaplastic_rep9


title: 60071_FAaplastic_rep10


title: 60331_FAaplastic_rep21


title: 60151_FAaplastic_rep16


title: 60031_FAaplastic_rep7


title: 60041_FAaplastic_rep8


title: 60211_FAaplastic_rep18


title: 10061_FAaplastic_rep3

description: Hybridization date: 07/26/02; Array lot: 2003960


title: 60131_FAaplastic_rep14


title: 60091_FAaplastic_rep11


title: 60021_FAaplastic_rep6


title: 10202_FAaplastic_rep4


title: 10171_normal control_rep9

source_name: normal low-density bone marrow cells

value: normal


title: 10031_FAaplastic_rep2


title: 60221_FAaplastic_rep19


title: 10151_normal control_rep8


title: 10181_normal control_rep10


title: 10131_normal control_rep6


title: 60111_FAaplastic_rep13


title: 10141_normal control_rep7


title: 10021_FAaplastic_rep1


title: 10221_normal control_rep11


title: 10121_normal control_rep5


title: 10091_normal control_rep3