title: 4:16 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 29, 2005 08:44:25

source_name: 4:16 LPS epithelial

tag: subject id = 4:16 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = epithelial | batch = 2 (2005) | included in published analysis = no


title: 4:15 saline epithelial (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 epithelial cells

hyb_protocol: Following fragmentation, 750 nanograms of both cRNA samples were hybridized to an Agilent Human Whole Genome Microarray according to the protocols provided by the manufacturer.

scan_protocol: Microarrays were scanned using the Agilent DNA Microarray Scanner (G2565BA).

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, April 26, 2005 10:33:51

molecule: total RNA

organism: Homo sapiens

source_name: 4:15 saline epithelial

label_protocol: Cy3 and Cy5-labeled cRNA was prepared from 50 nanograms of total RNA using the Agilent Low RNA Input Linear Amplification Kit (Palo Alto, CA).

extract_protocol: RNA was extracted using the RNeasy Mini-kit (Qiagen).

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

source_name: Stratagene Universal Human Reference RNA

tag: Reference RNA


title: 4:14 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 01, 2005 15:17:49

source_name: 4:14 saline epithelial

tag: subject id = 4:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = epithelial | batch = 2 (2005) | included in published analysis = no


title: 4:03 LPS epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 14:55:46

source_name: 4:03 LPS epithelial

tag: subject id = 4:03 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 4:14 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, April 28, 2005 11:17:41

source_name: 4:14 LPS epithelial

tag: subject id = 4:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = epithelial | batch = 2 (2005) | included in published analysis = no


title: 4:03 saline epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 08:56:38

source_name: 4:03 saline epithelial

tag: subject id = 4:03 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 4:17 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 19:36:26

source_name: 4:17 saline epithelial

tag: subject id = 4:17 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = epithelial | batch = 2 (2005) | included in published analysis = no


title: 3:07 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 19:38:24

source_name: 3:07 saline epithelial

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


title: 4:03 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 14:47:35


title: 4:17 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 19:00:47

source_name: 4:17 LPS epithelial

tag: subject id = 4:17 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = epithelial | batch = 2 (2005) | included in published analysis = no


title: 4:15 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, April 26, 2005 15:07:23

source_name: 4:15 LPS epithelial

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


title: 4:12 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 10:31:19

source_name: 4:12 LPS epithelial

tag: subject id = 4:12 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = epithelial | batch = 2 (2005) | included in published analysis = no


title: 4:16 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, April 19, 2005 09:19:38

source_name: 4:16 saline epithelial

tag: subject id = 4:16 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = epithelial | batch = 2 (2005) | included in published analysis = no


title: 4:03 HDM epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 15:07:51

source_name: 4:03 HDM epithelial

tag: subject id = 4:03 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 4:03 HDM epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 15:01:45


title: 1:12 saline epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, June 29, 2004 13:05:51

source_name: 1:12 saline epithelial

tag: subject id = 1:12 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 1:12 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 15:16:19


title: 1:12 HDM epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 13:41:35

source_name: 1:12 HDM epithelial

tag: subject id = 1:12 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 1:12 HDM epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 13:48:49


title: 1:12 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 14:39:12

source_name: 1:12 LPS epithelial

tag: subject id = 1:12 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 4:10 HDM epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 14:24:14

source_name: 4:10 HDM epithelial

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


title: 1:11 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 10:28:21

source_name: 1:11 LPS epithelial

tag: subject id = 1:11 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 1:11 HDM epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 10:40:18

source_name: 1:11 HDM epithelial

tag: subject id = 1:11 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = epithelial | batch = 1 (2004) | included in published analysis = no

source_name: Stratagene Universal Human Reference RNA

tag: Reference RNA


title: 1:11 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 22:18:44

source_name: 1:11 saline epithelial

tag: subject id = 1:11 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 4:10 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 14:31:10

source_name: 4:10 saline epithelial

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


title: 1:11 HDM epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 10:46:53


title: 4:10 LPS epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 14:09:58

source_name: 4:10 LPS epithelial

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


title: 4:07 LPS epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, June 29, 2004 14:51:30

source_name: 4:07 LPS epithelial

tag: subject id = 4:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 4:09 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 13:16:18

source_name: 4:09 LPS epithelial

tag: subject id = 4:09 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 1:11 saline epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 13:08:08


title: 4:09 saline epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 13:53:08

source_name: 4:09 saline epithelial

tag: subject id = 4:09 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 4:09 LPS epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 13:22:02


title: 4:07 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, August 04, 2004 10:02:14

source_name: 4:07 saline epithelial

tag: subject id = 4:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 4:07 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, June 29, 2004 13:34:00


title: 1:11 LPS epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 10:34:22


title: 4:09 HDM epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, August 17, 2004 13:24:05

source_name: 4:09 HDM epithelial

tag: subject id = 4:09 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 4:07 HDM epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 10:14:31

source_name: 4:07 HDM epithelial

tag: subject id = 4:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 4:10 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 14:03:06


title: 4:07 saline epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 10:28:54


title: 4:10 HDM epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 14:17:08


title: 1:10 saline epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 10:22:23

source_name: 1:10 saline epithelial

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


title: 4:07 HDM epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 21, 2004 10:47:01


title: 4:09 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 13:46:28


title: 1:12 LPS epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 13:17:03


title: 4:09 HDM epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, August 04, 2004 11:36:26


title: 1:10 HDM epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 10:03:17

source_name: 1:10 HDM epithelial

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


title: 4:02 saline epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, June 29, 2004 13:11:43

source_name: 4:02 saline epithelial

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


title: 4:02 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 14:33:30

source_name: 4:02 LPS epithelial

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


title: 4:10 saline epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 14:40:32


title: 1:07 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 09:29:19

source_name: 1:07 saline epithelial

tag: subject id = 1:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 4:02 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, June 29, 2004 13:17:03


title: 1:10 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 15:54:12

source_name: 1:10 LPS epithelial

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


title: 1:07 saline epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 09:36:40


title: 1:07 HDM epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 09:20:35

source_name: 1:07 HDM epithelial

tag: subject id = 1:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 1:07 HDM epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, July 13, 2004 15:09:26

source_name: Stratagene Universal Human Reference RNA

tag: Reference RNA


title: 4:06 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 14:49:35

source_name: 4:06 saline epithelial

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


title: 1:10 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 10:16:19


title: 4:08 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 13:01:51

source_name: 4:08 saline epithelial

tag: subject id = 4:08 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 1:07 LPS epithelial (Cy5)

description: human airway epithelial cells

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

source_name: 1:07 LPS epithelial

tag: subject id = 1:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 4:06 LPS epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, June 29, 2004 12:59:52

source_name: 4:06 LPS epithelial

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


title: 4:04 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 12:11:32

source_name: 4:04 saline epithelial

tag: subject id = 4:04 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 4:05 HDM epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, August 06, 2004 15:44:57

source_name: 4:05 HDM epithelial

tag: subject id = 4:05 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 1:07 LPS epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 12:14:46


title: 4:06 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 15:09:51


title: 4:06 saline epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 14:57:14


title: 4:04 saline epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, August 06, 2004 15:58:51


title: 4:04 LPS epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 21, 2004 13:23:08

source_name: 4:04 LPS epithelial

tag: subject id = 4:04 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 4:08 saline epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, June 30, 2004 13:10:14


title: 4:04 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 21, 2004 13:16:39


title: 4:08 HDM epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 12:30:47

source_name: 4:08 HDM epithelial

tag: subject id = 4:08 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 1:10 HDM epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 10:10:20


title: 4:05 saline epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 11:48:50

source_name: 4:05 saline epithelial

tag: subject id = 4:05 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 4:05 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, August 04, 2004 09:27:49


title: 4:08 HDM epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 12:24:43


title: 4:02 LPS epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, June 29, 2004 13:26:15


title: 1:10 LPS epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 09:53:15


title: 4:05 LPS epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 11:16:28

source_name: 4:05 LPS epithelial

tag: subject id = 4:05 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 4:05 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, August 04, 2004 09:16:22


title: 1:09 saline epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, June 24, 2004 15:52:32

source_name: 1:09 saline epithelial

tag: subject id = 1:09 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 4:05 HDM epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 11:22:29


title: 1:09 HDM epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, June 24, 2004 15:29:31

source_name: 1:09 HDM epithelial

tag: subject id = 1:09 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 1:09 LPS epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, June 24, 2004 15:23:12

source_name: 1:09 LPS epithelial

tag: subject id = 1:09 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 4:01 HDM epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, August 04, 2004 10:08:40

source_name: 4:01 HDM epithelial

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


title: 1:06 saline epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, June 24, 2004 15:02:20

source_name: 1:06 saline epithelial

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


title: 4:01 HDM epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, August 06, 2004 15:27:38


title: 1:09 HDM epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, June 24, 2004 15:43:31


title: 1:06 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, June 24, 2004 14:53:38


title: 4:01 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 10:58:40

source_name: 4:01 saline epithelial

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


title: 1:06 HDM epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 09:25:53

source_name: Stratagene Universal Human Reference RNA

tag: Reference RNA

source_name: 1:06 HDM epithelial

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


title: 4:01 LPS epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 10:41:21

source_name: 4:01 LPS epithelial

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


title: 4:01 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 10:35:39


title: 1:06 HDM epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 09:18:52


title: 1:04 HDM epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 10:43:43

source_name: 1:04 HDM epithelial

tag: subject id = 1:04 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 1:09 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 10:51:08


title: 1:04 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 10:51:30

source_name: 1:04 LPS epithelial

tag: subject id = 1:04 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 1:04 LPS epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 10:32:13


title: 1:03 HDM epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, June 24, 2004 14:25:03

source_name: 1:03 HDM epithelial

tag: subject id = 1:03 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 1:04 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, June 24, 2004 14:37:24

source_name: 1:04 saline epithelial

tag: subject id = 1:04 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 1:06 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 15:29:09

source_name: 1:06 LPS epithelial

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


title: 1:04 HDM epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 10:21:03


title: 1:04 saline epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, June 24, 2004 15:36:32


title: 1:06 LPS epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 15:23:10


title: 1:03 HDM epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, June 24, 2004 14:05:42


title: 1:09 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, June 24, 2004 15:16:39


title: 1:03 LPS epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, June 28, 2004 15:36:18

source_name: 1:03 LPS epithelial

tag: subject id = 1:03 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 4:01 saline epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, July 01, 2004 11:04:49


title: 1:03 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, July 13, 2004 14:51:54

source_name: 1:03 saline epithelial

tag: subject id = 1:03 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = epithelial | batch = 1 (2004) | included in published analysis = no


title: 1:03 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, June 24, 2004 13:58:34


title: Erbb2 overexpression _10µM Aza_rep8

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.0: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

organism: Mus musculus

source_name: Erbb2 transfected NIH3T3_10µM Aza

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: Erbb2 transfected NIH3T3 cell line with 10µM Azacytidine treatment

source_name: Erbb2 transfected NIH3T3

tag: Erbb2 transfected NIH3T3 cell line without Azacytidine treatment


title: 1:03 saline epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 11:19:44


title: 1:02 HDM epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, July 21, 2004 14:54:51

source_name: 1:02 HDM epithelial

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


title: NIH3T3_10µM Aza_rep4

source_name: NIH3T3 cell line_10µM Aza

tag: NIH3T3 cell line with 10µM Azacytidine treatment

tag: NIH3T3 cell line without Azacytidine treatment


title: 1:02 saline epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 10:53:24

source_name: 1:02 saline epithelial

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


title: 1:02 saline epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 12:04:44


title: Erbb2 overexpression _10µM Aza_rep5


title: Erbb2 overexpression _10µM Aza_rep6


title: Erbb2 overexpression _10µM Aza_rep3


title: NIH3T3_10µM Aza_rep3


title: Erbb2 overexpression _10µM Aza_rep1


title: Erbb2 overexpression _5µM Aza_rep2

source_name: Erbb2 transfected NIH3T3 _5µM Aza

tag: Erbb2 transfected NIH3T3 cell line with 5µM Azacytidine treatment


title: Erbb2 overexpression _10µM Aza_rep2


title: 1:01 LPS epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 11:30:19

source_name: 1:01 LPS epithelial

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

tag: Reference RNA


title: Erbb2 overexpression _10µM Aza_rep4


title: 1:01 HDM epithelial (Cy5)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 11:58:31

source_name: 1:01 HDM epithelial

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

source_name: Stratagene Universal Human Reference RNA


title: 1:01 HDM epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 12:11:20


title: Erbb2 overexpression _10µM Aza_rep7


title: Erbb2 overexpression _5µM Aza_rep4


title: Erbb2 overexpression _5µM Aza_rep3


title: NIH3T3 cell line_10µM Aza


title: NIH3T3_10µM Aza_rep2


title: 87_R

status: Public on Sep 30 2009

city: Albany

first: Debbie

last: Laudencia-Chingcuanco

state: CA

address: 800 Buchanan Street

department: Western Regional Research Center

institute: USDA-ARS

description: This study looked at 7835 genes in wheat caryopses.

hyb_protocol: Hybridization was carried out using the Pronto! Hybridization kit reagents (Corning Inc, NY) following the supplied protocol.

scan_protocol: Hybridized slides were scanned using a Genepix 4000B microarray scanner and raw spot fluorescence intensities were collected using GenePix Pro version 5.0.

data_processing: The logarithms (base 2) of the original intensity values, not the ratios, for each probe obtained from each fluorescent channel were used.  To reduce any dye bias introduced during RNA labeling, the global median value of all the signals per channel on each individual array was subtracted from each spot raw intensity signal and divided by the standard deviation. The expression values per gene were centered based on the median value of expression of the gene across all time-points. We used SAS PROC STDIZE to normalize the data set by array and then by gene for all samples.

label: Alexa  647

organism: Triticum aestivum

source_name: developing caryopsis from timepoint 14 and BiolRep1

label_protocol: Ten microgram of total RNA was indirectly labeled with Alexa 555 and Alexa 647 fluorophores (Molecular Probes Inc) using the protocol recommended by the manufacturer.

extract_protocol: Total RNA was extracted from developing grains using TRIZOL (Invitrogen), treated with RQ1 DNAse (Promega) and was re-purified using RNA Easy columns (QIAGEN).

tag: RNA Sample ID:3

tag: TimePoint (DPA)

tag: Array ID


title: 1:01 LPS epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 11:50:42


title: 87_G

label: Alexa  555

source_name: developing caryopsis from timepoint 21 and BiolRep1

tag: RNA Sample ID:4


title: 88_R


title: Erbb2 overexpression _5µM Aza_rep1


title: 84_G

source_name: developing caryopsis from timepoint 35 and BiolRep1

tag: RNA Sample ID:6


title: 88_G

source_name: developing caryopsis from timepoint 28 and BiolRep1

tag: RNA Sample ID:5


title: 86_R

source_name: developing caryopsis from timepoint 7 and BiolRep1

tag: RNA Sample ID:2


title: 85_R

source_name: developing caryopsis from timepoint 3 and BiolRep1

tag: RNA Sample ID:1


title: 81_R

source_name: developing caryopsis from timepoint 7 and BiolRep2

tag: RNA Sample ID:8


title: 86_G


title: 83_R


title: 84_R


title: 82_G


title: 85_G


title: 1:02 HDM epithelial (Cy3)

description: human airway epithelial cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 25, 2004 11:08:08

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


title: 81_G

source_name: developing caryopsis from timepoint 14 and BiolRep2

tag: RNA Sample ID:9


title: 83_G


title: 82_R

source_name: developing caryopsis from timepoint 3 and BiolRep2

tag: RNA Sample ID:7


title: 77_R


title: 79_R

source_name: developing caryopsis from timepoint 21 and BiolRep2

tag: RNA Sample ID:10


title: 80_R


title: 80_G


title: 78_G


title: 78_R


title: 76_R

source_name: developing caryopsis from timepoint 28 and BiolRep2

tag: RNA Sample ID:11


title: 77_G


title: 79_G


title: 76_G

source_name: developing caryopsis from timepoint 35 and BiolRep2

tag: RNA Sample ID:12


title: 75_G


title: 75_R


title: 74_G


title: 73_R


title: 74_R


title: 73_G


title: 69_R

source_name: developing caryopsis from timepoint 14 and BiolRep1_DS


title: 69_G

source_name: developing caryopsis from timepoint 7 and BiolRep1_DS


title: 71_G


title: 71_R


title: 70_G

source_name: developing caryopsis from timepoint 3 and BiolRep1_DS


title: 72_G


title: 67_R

source_name: developing caryopsis from timepoint 28 and BiolRep1_DS


title: 72_R


title: 70_R


title: 64_G

source_name: developing caryopsis from timepoint 35 and BiolRep1_DS


title: 68_G


title: 68_R

source_name: developing caryopsis from timepoint 21 and BiolRep1_DS


title: 65_G


title: 64_R


title: 65_R


title: 63_R


title: 67_G


title: 66_G


title: 62_R

source_name: developing caryopsis from timepoint 3 and BiolRep3

tag: RNA Sample ID:13


title: 61_G

source_name: developing caryopsis from timepoint 14 and BiolRep3

tag: RNA Sample ID:15


title: 61_R

source_name: developing caryopsis from timepoint 7 and BiolRep3

tag: RNA Sample ID:14


title: 66_R

tag: TimePoint (DPA)


title: 60_G

source_name: developing caryopsis from timepoint 21 and BiolRep3

tag: RNA Sample ID:16

tag: Array ID


title: 63_G


title: 62_G


title: 58_G

source_name: developing caryopsis from timepoint 35 and BiolRep3

tag: RNA Sample ID:18


title: 57_R


title: 57_G


title: 58_R

source_name: developing caryopsis from timepoint 28 and BiolRep3

tag: RNA Sample ID:17


title: 55_R


title: 59_R


title: 55_G


title: 53_G

tag: RNA Sample ID:3


title: 30_R

source_name: developing caryopsis from timepoint 28 and BiolRep3_DS


title: 53_R

tag: RNA Sample ID:6


title: 56_R


title: 31_G

source_name: developing caryopsis from timepoint 14 and BiolRep3_DS


title: 60_R


title: 59_G


title: 31_R

source_name: developing caryopsis from timepoint 35 and BiolRep3_DS


title: 54_R


title: 54_G


title: 28_R

source_name: developing caryopsis from timepoint 3 and BiolRep3_DS


title: 28_G


title: 29_R

source_name: developing caryopsis from timepoint 21 and BiolRep3_DS


title: 26_R


title: 30_G

source_name: developing caryopsis from timepoint 7 and BiolRep3_DS


title: 56_G


title: 27_R


title: 25_R


title: 26_G


title: 25_G


title: 24_R


title: 24_G


title: 27_G


title: 19_G

source_name: developing caryopsis from timepoint 35 and BiolRep2_DS


title: 18_R


title: 18_G

source_name: developing caryopsis from timepoint 28 and BiolRep2_DS


title: 19_R

source_name: developing caryopsis from timepoint 3 and BiolRep2_DS


title: 22_G

source_name: developing caryopsis from timepoint 14 and BiolRep2_DS


title: 29_G


title: 22_R


title: 23_R


title: 23_G


title: 21_R


title: 17_R


title: 12_R

source_name: developing caryopsis from timepoint 7 and BiolRep2_DS

tag: RNA Sample ID:8


title: 16_G


title: 20_R

source_name: developing caryopsis from timepoint 21 and BiolRep2_DS


title: 21_G


title: 20_G


title: 13_G


title: 17_G


title: 13_R


title: 12_G


title: 16_R


title: HI_155087_HK1246Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

status: Public on Sep 09 2009

type: genomic

city: Rockville

first: Chun-Hua

last: Wan

state: MD

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

description: Haemophilus influenzae(Hi) is a gram-negative rod shaped bacterium that lives symbiotically in the upper respiratory tract of humans. Capsulated Hi, as well as non-capsulated strains are known to cause a number of significant infections. Recognizing and understanding the links between the phenotypic traits and the genetic background has paramount epidemiological and clinical importance. To date, a panoply of microbiological and molecular biology tools have been developed and utilized by researchers aimed at identifying the evolutionary links among strains and isolates. Comparative genomic hybridization (CGH) has been shown to be a useful tool for screening strains for their genetic content. However, there is a major limitation when CGH is conducted on a microarray based on a single reference genome. CGH results report which genes are present or absent relative to the genome. Hence the information about novel genetic content that the query strain possesses remains obscure. We report here the construction of the first Hi pan-genome microarray representing ca. 4600 features by 70-mers. In addition to those from the Rd strain, new features originate from the unfinished genome sequences present in NCBI database and from our novel gene discovery project efforts using strain HK1212. Genomes of 20 strains belonging to different phylogenetic lineages were screened for their gene loss and gain utilizing the species microarray.

hyb_protocol: Epoxy coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 degree Celcius for 45 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and spun dry.  Equal concentrations of DNA probe from the appropriate Cy3 and Cy5 labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were denatured to 95 degree Celcius prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 degree Celcius.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature.

scan_protocol: Scanned on Axon GenePix 4000 scanner.  PMT values were optimized during scanning to balance channel intensities.

data_processing:
Data Processing Procedures:
1. Use software suite TM4 (www.tm4.org) to analyze spotted arrays.
2. Use Spotfinder with background correction to compute the spot intensities of the hybridized arrays.
3. Perform the following filtering steps:
All PFGRC arrays used in this study have 3 types of spots.
(1). Species spot: oligos designed for the species under investigation.
(2). Reserved spot or control spot: oligos designed from Arabidopsis genes as controls.
(3). Empty spots: no oligos or any DNA.
Step 1: Identify the replicates.
Sort the .mev file from Spotfinder by oligo_id.
Step 2: Identify the outliers within each set of replicates for each channel.
Outliers are identified using the Sprents method (The Handbook of Parametric and Nonparametric Statistical Procedures, Third Edition by David J. Sheskin, PP 400-402).
|Xi - M|/MAD > Max
Xi = Each intensity value from the set of replicates.
M = Median intensity value from the set of replicates.
MAD = Median absolute deviation.
Max = the critical value that the result of the inequality must exceed in order to conclude that the Xi value is an outlier. The value of 5 was used for Max.
Step 3: Replace the outliers.
Replace the outliers by the value closest to them from the tail that they occur. For example, if the outlier identified is the highest value in channel A, that value will be replaced by the next highest value of its replicate set in channel A.
Step 4: Subtract the 95th percentile of the reserved spots.
Calculate the 95th percentile of all the reserved spots and subtract that value from all the species spots and reserved spots.
Step 5: Replace zero (0) by one (1).
After subtracting the 95th percentile of the reserved spots, if one of the channel intensities is less than zero (0), replace that value by one (1); If both channels become less than zero (0), set both channels to zero (0).
Step 6. Output the filtered .mev file.
4. Use Midas X for CGH normalization:
1). Plot the histogram of the Log2 ratio data (Reference/Query) from the filtered .mev file, and identify the central peak containing oligos predicted to be shared by both the reference and query strains.
2). Fit a Gaussian curve to the central peak by 'tweaking' the log ratio mean and by shrinking or stretching the standard deviation of the curve to find the smallest least square difference.
3). Perform Log Mode Centering normalization on the channel that contains the query sample only (either Cy3 or Cy5).
4). Log 2 transform reference to query ratios and calculate Z scores using the standard deviation obtained from the Gaussian curve fitted to the data during normalization, for each log 2 ratio.
5). Assign percentile values to the oligos based on the distribution of the Z scores.
4). Output the normalized *.mev file.
5. Re-calculate the value of log 2 ratio (Reference/Query) from the normalized .mev file:
1). If both channels (IA and IB) are zero, assign REF_QUERY_RATIO_LOG2 "null" (i.e., the column REF_QUERY_RATIO_LOG2 of the Sample data file).
2). If one channel is zero and the other is not zero, substitute the zero with one (1) and then, assign REF_QUERY_RATIO_LOG2 log 2 (IA/IB) if IA is the reference genome or log 2 (IB/IA) if IB is the reference genome.
3). If neither channel is zero, assign REF_QUERY_RATIO_LOG2 log 2 (IA/IB) if IA is the
reference genome or log 2 (IB/IA) if IB is the reference genome.

VALUE represents the log2 ratio of the normalized query:reference intensities (inverse of REF_QUERY_RATIO_LOG2).

molecule: genomic DNA

organism: Haemophilus influenzae

label_protocol: 4ug of genomic DNA was labeled at 37 degree Celcius overnight using DNA polymerase I Klenow fragment (New England Biolabs), a 25X 2:1 amino allyl dUTP (Ambion) dNTP mix, and random hexamers (Invitrogen).  Labeled DNA was purified with Qiaquick PCR purification kit (QIAGEN).

growth_protocol: Cells grown in Brain Heart Infusion supplemented with growth factors that are present in blood, specifically hemin and NAD.

extract_protocol: Epicentre MasterPure DNA Extraction Kit

treatment_protocol: None, wild type strains were the focus of the study.

tag: HK1246 is Query Strain.

tag: KW20 is Reference Strain.


title: HI_156028_HK368Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK368is Query Strain.


title: HI_155085_HK715Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK715 is Query Strain.


title: HI_120550_HK367Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

extract_protocol: Epicentre MasterPure DNA Extraction Kit.

tag: HK367 is Query Strain.


title: HI_155084_HK1212Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK1212 is Query Strain.


title: HI_120549_HK1220Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK1220 is Query Strain.


title: HI_155082_HK1136Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK1136 is Query Strain.


title: HI_155083_HK1210Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK1210 is Query Strain.


title: HI_155086_HK2122Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK2122 is Query Strain.


title: HI_156026_HK1240Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK1240 is Query Strain.


title: HI_120576_HK2122Cy3_KW20Cy5_new_MDS.mev.refIsIB.out


title: HI_120518_HK1210Cy3_KW20Cy5_new_MDS.mev.refIsIB.out


title: HI_155077_HK389Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK389 is Query Strain.


title: HI_120570_HK870Cy3KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK870 is Query Strain..

tag: KW20 is Reference Strain


title: HI_120566_HK870Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK870 is Query Strain.


title: HI_120520_HK1240Cy3_KW20Cy5_new_MDS.mev.refIsIB.out


title: HI_155081_HK61Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK61 is Query Strain.


title: HI_155080_HK1219_2Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK1219 is Query Strain.


title: HI_120558_HK2067Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK2067 is Query Strain.


title: HI_120513_HK1214Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK1214 is Query Strain.

tag: KW20 is Reference Strain.


title: HI_120519_HK295Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK295 is Query Strain.


title: HI_120552_HK1214Cy3_KW20Cy5_new_MDS.mev.refIsIB.out


title: HI_120338_HK1220Cy3_KW20Cy5_new_MDS.mev.refIsIB.out


title: HI_120574_HK1141Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK1141 is Query Strain.


title: HI_120505_HK1246Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK1246 is Query Strain.


title: HI_120517_HK1212Cy3KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK1212 is Query Strain.


title: HI_120511_HK2111Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK2111  is Query Strain.


title: HI_155076_HK635Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK635 is Query Strain.


title: HI_155088_HK1141Cy3_KW20Cy5_new_MDS.mev.refIsIB.out


title: HI_119895_HK61Cy3_KW20Cy5_new_MDS.mev.refIsIB.out


title: HI_119893_HK715Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK715 is Query Strain.


title: HI_119747_HK1219.2Cy3_KW20Cy5_new_MDS.mev.refIsIB.out


title: HI_119744_HK367Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK367 is Query Strain.


title: HI_119606_HK295Cy3_KW20Cy5_new_MDS.mev.refIsIB.out


title: HI_156027_HK1212Cy5_KW20Cy3_new_MDS.mev.refIsIA.out


title: HI_120516_HK1136Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK1136 is Query Strain.


title: HI_120507_HK1220Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK1220 is Query Strain.


title: HI_155094_HK368Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK368 is Query Strain.


title: HI_119746_HK2067Cy3_KW20Cy5_new_MDS.mev.refIsIB.out


title: HI_119892_HK368Cy3_KW20Cy5_new_MDS.mev.refIsIB.out


title: HI_120577_HK367Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: K367 is Query Strain.


title: HI_155100_HK1219_2Cy5_KW20Cy3_new_MDS.mev.refIsIA.out


title: HI_155074_HK1240Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK1240 is Query Strain.


title: HI_155098_HK61Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK61 is Query Strain.


title: HI_119737_HK389Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK389 is Query Strain.


title: HI_119897_HK1136Cy3_KW20Cy5_new_MDS.mev.refIsIB.out


title: HI_119608_HK2111Cy3_KW20Cy5_new_MDS.mev.refIsIB.out

tag: HK2111 is Query Strain.


title: HI_120575_HK870Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: KW20 is Reference Strain.

tag: HK870 is Query Strain.


title: HI_120525_HK715Cy5_KW20Cy3_new_MDS.mev.refIsIA.out


title: HI_155097_HK1246Cy5_KW20Cy3_new_MDS.mev.refIsIA.out


title: HI_155091_HK1136Cy5_KW20Cy3_new_MDS.mev.refIsIA.out


title: HI_120504_HK2111Cy5KW20Cy3_new_MDS.mev.refIsIA.out


title: HI_120551_HK2122Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK2122 is Query Strain.


title: HI_120502_HK1214Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK1214 is Query Strain.


title: HI_119738_HK635Cy3_KW20Cy5_new_MDS.mev.refIsIB.out


title: HI_120524_HK1212Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK1212 is Query Strain.


title: HI_155093_HK389Cy5_KW20Cy3_new_MDS.mev.refIsIA.out


title: HI_120506_HK1240Cy5_KW20Cy3_new_MDS.mev.refIsIA.out


title: HI_155092_HK635Cy5_KW20Cy3_new_MDS.mev.refIsIA.out


title: HI_120397_HK1246Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK1246 is Query Strain.


title: HI_120122_HK1141Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK1141 is Query Strain.


title: HI_120120_HK1210Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK1210 is Query Strain.


title: HI_120395_HK295Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK295 is Query Strain.


title: HI_120328_hk1210Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: hk1210 is Query Strain.


title: HI_120331_HK870Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK870  is Query Strain.


title: HI_155099_KW20_self_self_new_MDS.mev.refIsIA.out

tag: KW20 in Channel 1 (A) is used as Reference Strain in the compute for VALUE in the

tag: Sample data file.  This is a self-self hybridization.

tag: The Haemophilus influenzae pan-genome array is designed from multiple genomes, of

tag: which were completely or partially sequenced, as well as through sampling through

tag: novel gene discovery.  The rd strain (KW20) genome is the reference genome for these

tag: experiments, and many of the oligos on the array are from this sequenced genome.  To

tag: better understand the array properties a self to self hybridization with KW20

tag: genomic DNA, KW20 probes were synthesized, coupled with Cy3 and Cy5 dyes, and

tag: subsequently hybridized against each other.  The rationale behind that self to self

tag: hybridization are as follows:

tag: 1.  The quality of the KW20 oligos spotted on the array can be determined

tag: 2.  Dye bias effects can be examined

tag: 3.  The effects of cross-hybridization can be examined

tag: 4.  Evaluate ranges of signal values, and determine thresholds

tag: KW20 in Channel 2 (B) is used as Query Strain in the compute for VALUE in the Sample


title: HI_120118_KW20_self_self_new_MDS.mev.refIsIA.out

tag: KW20 in Channel 1 (A) is used as Reference Strain in the compute for VALUE in the Sample data file.  This is a self-self hybridization.

tag: The Haemophilus influenzae pan-genome array is designed from multiple genomes, of which were completely or partially sequenced, as well as through sampling through novel gene discovery.  The rd strain (KW20) genome is the reference genome for these experiments, and many of the oligos on the array are from this sequenced genome.  To better understand the array properties a self to self hybridization with KW20 genomic DNA, KW20 probes were synthesized, coupled with Cy3 and Cy5 dyes, and subsequently hybridized against each other.  The rationale behind that self to self hybridization are as follows:

tag: KW20 in Channel 2 (B) is used as Query Strain in the compute for VALUE in the Sample data file.  This is a self-self hybridization.


title: HI_119894_HK61Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: KW20 is Reference Strain.

tag: HK61 is Query Strain.


title: HI_120540_KW20_self_self_new_MDS.mev.refIsIA.out


title: HI_120396_HK2111Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK2111 is Query Strain.


title: HI_119891_HK368Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK368 is Query Strain.


title: BC11979

status: Public on Sep 02 2009

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

country: France

institute: Institut Paoli-Calmettes

hyb_protocol: see Affymetrix standard protocols

scan_protocol: see Affymetrix standard protocols

data_processing: RMA. Controls were removed, like all genes with low and poorly measured expression as defined by an expression value inferior to 100 units in all samples. Data were then log2 transformed.

label: biotin

source_name: Breast cancer

label_protocol: see Affymetrix standard protocols

extract_protocol: Guanidinium isothiocyanate and centrifugation over a cesium chloride gradient.

tag: center

value: IPC

tag: type

value: IBC

tag: age of diagnosis (year)

tag: molecular subtype

tag: histology

value: DUC

tag: pt

tag: pn

value: pos

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

value: neg

tag: pr ihc status

tag: p53 ihc status

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: erbb2p ihc status

tag: igf1r ihc status

tag: egfr ihc status

tag: top2a ihc status

tag: foxa1 ihc status

tag: mfs

tag: mfsdel (month)


title: HI_120563_KW20_self_self_new_MDS.mev.refIsIA.out

tag: KW20 in Channel 1 (A) is used as Reference Strain in the compute for VALUE in the

tag: Sample data file.  This is a self-self hybridization.

tag: The Haemophilus influenzae pan-genome array is designed from multiple genomes, of

tag: which were completely or partially sequenced, as well as through sampling through

tag: novel gene discovery.  The rd strain (KW20) genome is the reference genome for these

tag: experiments, and many of the oligos on the array are from this sequenced genome.  To

tag: better understand the array properties a self to self hybridization with KW20

tag: genomic DNA, KW20 probes were synthesized, coupled with Cy3 and Cy5 dyes, and

tag: subsequently hybridized against each other.  The rationale behind that self to self

tag: hybridization are as follows:

tag: 1.  The quality of the KW20 oligos spotted on the array can be determined

tag: 2.  Dye bias effects can be examined

tag: 3.  The effects of cross-hybridization can be examined

tag: 4.  Evaluate ranges of signal values, and determine thresholds

tag: KW20 in Channel 2 (B) is used as Query Strain in the compute for VALUE in the Sample


title: HI_119601_HK295Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

scan_protocol: SCAN PROTOCOL:  Scanned on Axon GenePix 4000 scanner.  PMT values were optimized during scanning to balance channel intensities.

tag: KW20 is Reference Strain.

tag: HK295 is Query Strain.


title: HI_119739_HK635Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK635 is Query Strain.


title: HI_119750_2067Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK2067 is Query Strain.


title: HI_119742_HK1219.2Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK1219 is Query Strain.


title: HI_119740_HK389Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK389 is Query Strain.


title: HI_119604_HK1214Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK1214 is Query Strain.


title: HI_119602_HK1220Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK1220 is Query Strain.


title: HI_120119_HK2122Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK2122 is Query Strain.


title: HI_120335_HK715Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK715 is Query Strain.


title: HI_119741_HK2067Cy5_KW20Cy3_new_MDS.mev.refIsIA.out


title: NB2

source_name: Normal Breast

tag: center

tag: type

tag: age of diagnosis (year)

tag: molecular subtype

tag: histology

tag: pt

tag: pn

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: erbb2p ihc status

tag: igf1r ihc status

tag: egfr ihc status

tag: top2a ihc status

tag: foxa1 ihc status

tag: mfs

tag: mfsdel (month)


title: NB1

tag: center

tag: type

tag: age of diagnosis (year)

tag: molecular subtype

tag: histology

tag: pt


title: NB4

tag: pn

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status


title: Erbb2 transfected NIH3T3_tet-off_7d_rep3

status: Public on Sep 01 2009

source_name: Erbb2 transfected NIH3T3_tet-off_7d

tag: Erbb2 transfected NIH3T3 cell line 7d after tetracycline treatment (tet-off) to stop Erbb2 overexpression

source_name: Erbb2 transfected NIH3T3 cells – untreated

tag: Erbb2 transfected NIH3T3 cell line before tetracycline treatment


title: Erbb2 transfected NIH3T3_untreated_rep3


title: NB3

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: erbb2p ihc status

tag: igf1r ihc status

tag: egfr ihc status

tag: top2a ihc status

tag: foxa1 ihc status


title: HI_119749_HK367Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: KW20 is Reference Strain.

tag: HK367 is Query Strain.


title: Erbb2 transfected NIH3T3_tet-off_7d_rep4


title: Erbb2 transfected NIH3T3_untreated_rep4


title: Erbb2 transfected NIH3T3_tet-off_7d_rep1


title: HI_119609_HK1141Cy5_KW20Cy3_new_MDS.mev.refIsIA.out

tag: HK1141 is Query Strain.


title: Erbb2 transfected NIH3T3_tet-off_5d_rep3

source_name: Erbb2 transfected NIH3T3_tet-off_5d

tag: Erbb2 transfected NIH3T3 cell line 5d after tetracycline treatment (tet-off) to stop Erbb2 overexpression


title: Erbb2 transfected NIH3T3_tet-off_7d_rep2


title: Erbb2 transfected NIH3T3_tet-off_3d_rep1

source_name: Erbb2 transfected NIH3T3_tet-off_3d

tag: Erbb2 transfected NIH3T3 cell line 3d after tetracycline treatment (tet-off) to stop Erbb2 overexpression


title: Erbb2 transfected NIH3T3_tet-off_5d_rep4


title: Erbb2 transfected NIH3T3_tet-off_12h_rep4

source_name: Erbb2 transfected NIH3T3_tet-off_12h

tag: Erbb2 transfected NIH3T3 cell line 12h after tetracycline treatment (tet-off) to stop Erbb2 overexpression


title: Erbb2 transfected NIH3T3_tet-off_5d_rep2


title: Erbb2 transfected NIH3T3_tet-off_3d_rep4


title: Erbb2 transfected NIH3T3_tet-off_24h_rep4

source_name: Erbb2 transfected NIH3T3_tet-off_24h

tag: Erbb2 transfected NIH3T3 cell line 24h after tetracycline treatment (tet-off) to stop Erbb2 overexpression


title: Erbb2 transfected NIH3T3_tet-off_5d_rep1


title: Erbb2 transfected NIH3T3_tet-off_24h_rep3


title: Erbb2 transfected NIH3T3_tet-off_3d_rep2


title: Erbb2 transfected NIH3T3_tet-off_3d_rep3


title: Erbb2 transfected NIH3T3_tet-off_12h_rep2


title: Erbb2 transfected NIH3T3_tet-off_4h_rep3

source_name: Erbb2 transfected NIH3T3_tet-off_4h

tag: Erbb2 transfected NIH3T3 cell line 4h after tetracycline treatment (tet-off) to stop Erbb2 overexpression


title: Erbb2 transfected NIH3T3_tet-off_12h_rep1

tag: Erbb2 transfected NIH3T3 cell line before tetracycline treatment


title: Erbb2 transfected NIH3T3_tet-off_4h_rep2


title: Erbb2 transfected NIH3T3_tet-off_4h_rep4


title: Erbb2 transfected NIH3T3_tet-off_24h_rep1


title: Erbb2 transfected NIH3T3_untreated_rep2


title: Erbb2 transfected NIH3T3_tet-off_24h_rep2


title: Erbb2 transfected NIH3T3_untreated_rep1


title: Erbb2 transfected NIH3T3_tet-off_2h_rep4

source_name: Erbb2 transfected NIH3T3_tet-off_2h

tag: Erbb2 transfected NIH3T3 cell line 2h after tetracycline treatment (tet-off) to stop Erbb2 overexpression


title: Erbb2 transfected NIH3T3_tet-off_4h_rep1


title: Erbb2 transfected NIH3T3_tet-off_12h_rep3


title: Erbb2 transfected NIH3T3_tet-off_2h_rep3


title: Erbb2 transfected NIH3T3_tet-off_2h_rep2


title: Erbb2 transfected NIH3T3_tet-off_1h_rep1

source_name: Erbb2 transfected NIH3T3_tet-off_1h

tag: Erbb2 transfected NIH3T3 cell line 1h after tetracycline treatment (tet-off) to stop Erbb2 overexpression

tag: Erbb2 transfected NIH3T3 cells – untreated


title: Erbb2 transfected NIH3T3_tet-off_1h_rep3


title: Erbb2 transfected NIH3T3_tet-off_1h_rep2


title: Erbb2 transfected NIH3T3_tet-off_2h_rep1


title: Erbb2 transfected NIH3T3_tet-off_1h_rep4


title: SK-N-SH_RA_0h_rep2

city: Yokohama

first: Tadayuki

last: Takeda

state: Kanagawa

address: 1-7-22, Suehiro-cho, Tsurumi-ku

department: Computatinal and Experimental Systems Biology Group

country: Japan

institute: RIKEN GSC

description: Sampling of RNA was performed at six different time points (0h, 6h, 1d, 2d, 3d, and 5d, respectively) under RA inducible conditions and at five different time points (0h, 6h, 1d, 2d and 3d, respectively) after the cells were transferred to serum-free medium containing BDNF.

hyb_protocol: Biotin-labeled cRNA was applied on the Human Genome U133 Plus 2.0 Array (Affymetrix, Inc.) and then hybridized at 45oC for 17 h in a GeneChip Hybridization Oven (Affymetrix, Inc.).

scan_protocol: Washing, staining and scanning of the array were performed using the GeneChip Wash and Stain Kit and a GeneChip Scanner 3000 (Affymetrix, Inc.), respectively.

data_processing: The average signal intensity for all probes was initially tuned to 500 as global scaling and individual signal intensities were evaluated by detection call (present/marginal/absent) using the Affymetrix Micro Array Suite 5.0 (MAS 5.0) software (Affymetrix, Inc.).

source_name: neuroblastoma cell, retinoic acid (RA), 0hour

label_protocol: First-strand cDNA was synthesized using 5 μg of total RNA and the GeneChip One-cycle cDNA Synthesis Kit (Affymetrix, Inc.). Biotin-labeled cRNA was generated by the GeneChip IVT labeling Kit (Affymetrix, Inc.)

growth_protocol: Tissue culture cells were maintained in D-MEM/F12 1:1 mixture supplemented with 15% FBS (Fetal Bovine Serum) and 1% NEAA (Non-essential amino acid) in a 5% CO2 humidified incubator at 37oC. The culture medium was changed twice a week.

extract_protocol: Total cellular RNA was extracted from the cells at specific intervals using the RiboPure Kit (Ambion, An Applied Biosystems Business, Austin, TX, USA) according to the manufacturer’s instructions.

treatment_protocol: SK-N-SH cells were seeded in laminin coated culture dishes (BioCoat Laminin Cellware; BD Biosciences) for 1 day and then transferred to a medium containing 10 μM of RA for five days.

tag: Cell line

value: SH-SY5Y (HTB-11, obtained from ATCC (American Type Culture Collection Cultures))


title: SK-N-SH_RA_1d_rep2

source_name: neuroblastoma cell, retinoic acid (RA), 1day


title: SK-N-SH_RA_3d_rep2

source_name: neuroblastoma cell, retinoic acid (RA), 3day


title: SK-N-SH_RA_2d_rep2

source_name: neuroblastoma cell, retinoic acid (RA), 2day


title: SK-N-SH_BDNF_3d_rep1

source_name: neuroblastoma cell, brain-derived neurotrophic factor (BDNF), 3day

treatment_protocol: SK-N-SH cells were washed with D-MEM/F12 twice after five days in the presence of RA and then incubated with 50 ng/ml of BDNF in D-MEM/F12 without serum for three days.


title: SK-N-SH_RA_5d_rep2

source_name: neuroblastoma cell, retinoic acid (RA), 5day


title: SK-N-SH_BDNF_6h_rep2

source_name: neuroblastoma cell, brain-derived neurotrophic factor (BDNF), 6hour


title: SK-N-SH_BDNF_2d_rep2

source_name: neuroblastoma cell, brain-derived neurotrophic factor (BDNF), 2day


title: SK-N-SH_RA_3d_rep1


title: SK-N-SH_RA_5d_rep1


title: SH-SY5Y(ECACC)_BDNF_2d_rep3

treatment_protocol: SH-SY5Y-E cells were washed with D-MEM/F12 twice after five days in the presence of RA and then incubated with 50 ng/ml of BDNF in D-MEM/F12 without serum for three days.

value: SH-SY5Y (EC94030304, obtained from ECACC (European Collection of Cell Cultures))


title: SK-N-SH_RA_2d_rep1


title: SK-N-SH_BDNF_6h_rep1


title: SH-SY5Y(ECACC)_BDNF_6h_rep3


title: SK-N-SH_BDNF_3d_rep2


title: SK-N-SH_BDNF_2d_rep1


title: SK-N-SH_RA_0h_rep1


title: SH-SY5Y(ECACC)_BDNF_3d_rep3


title: SK-N-SH_RA_6h_rep1

source_name: neuroblastoma cell, retinoic acid (RA), 6hour


title: SK-N-SH_BDNF_1d_rep2

source_name: neuroblastoma cell, brain-derived neurotrophic factor (BDNF), 1day


title: SH-SY5Y(ECACC)_BDNF_1d_rep3


title: SH-SY5Y(ECACC)_RA_3d_rep3

treatment_protocol: SH-SY5Y-E cells were seeded in laminin coated culture dishes (BioCoat Laminin Cellware; BD Biosciences) for 1 day and then transferred to a medium containing 10 μM of RA  for five days.


title: SK-N-SH_RA_6h_rep2


title: SK-N-SH_BDNF_1d_rep1


title: SH-SY5Y(ECACC)_RA_1d_rep3


title: SH-SY5Y(ECACC)_RA_6h_rep3


title: SK-N-SH_RA_1d_rep1


title: SH-SY5Y(ECACC)_RA_0h_rep3


title: SH-SY5Y(ECACC)_RA_5d_rep3


title: SH-SY5Y(ECACC)_BDNF_1d_rep2


title: SH-SY5Y(ECACC)_BDNF_2d_rep2


title: SH-SY5Y(ECACC)_BDNF_6h_rep2


title: SH-SY5Y(ECACC)_BDNF_3d_rep2


title: SH-SY5Y(ECACC)_RA_1d_rep2


title: SH-SY5Y(ECACC)_RA_5d_rep1


title: SH-SY5Y(ECACC)_RA_2d_rep1


title: SH-SY5Y(ECACC)_RA_3d_rep2


title: SH-SY5Y(ECACC)_BDNF_1d_rep1


title: SH-SY5Y(ECACC)_RA_2d_rep2


title: SH-SY5Y(ECACC)_RA_1d_rep1


title: SH-SY5Y(ECACC)_BDNF_3d_rep1


title: SH-SY5Y(ECACC)_RA_inhibiter_LY294002_2d_rep2

description: Sampling of RNA was performed at six different time points (0h, 6h, 1d, 2d, 3d, and 5d, respectively) under RA inducible conditions in the presence of LY294002.

source_name: neuroblastoma cell, retinoic acid (RA), LY294002, 2day

treatment_protocol: SH-SY5Y-E cells were seeded in laminin coated culture dishes (BioCoat Laminin Cellware; BD Biosciences) for 1 day and then transferred to a medium containing 10 μM of RA in the presence of LY294002 (10 μM) for five days.


title: SH-SY5Y(ECACC)_RA_0h_rep2


title: SH-SY5Y(ECACC)_RA_inhibiter_LY294002_0h_rep2

source_name: neuroblastoma cell, retinoic acid (RA), LY294002, 0hour


title: SH-SY5Y(ECACC)_RA_inhibiter_LY294002_3d_rep1

source_name: neuroblastoma cell, retinoic acid (RA), LY294002, 3day


title: SH-SY5Y(ECACC)_RA_inhibiter_LY294002_5d_rep1

source_name: neuroblastoma cell, retinoic acid (RA), LY294002, 5day


title: SH-SY5Y(ECACC)_RA_3d_rep1


title: SH-SY5Y(ECACC)_RA_6h_rep2


title: SH-SY5Y(ECACC)_RA_inhibiter_LY294002_6h_rep2

source_name: neuroblastoma cell, retinoic acid (RA), LY294002, 6hour


title: SH-SY5Y(ECACC)_RA_5d_rep2


title: SH-SY5Y(ECACC)_BDNF_2d_rep1


title: SH-SY5Y(ECACC)_RA_6h_rep1


title: SH-SY5Y(ECACC)_RA_inhibiter_LY294002_1d_rep2

source_name: neuroblastoma cell, retinoic acid (RA), LY294002, 1day


title: SH-SY5Y(ECACC)_RA_inhibiter_LY294002_2d_rep1


title: SH-SY5Y(ECACC)_RA_inhibiter_LY294002_3d_rep2


title: SH-SY5Y(ECACC)_BDNF_6h_rep1


title: SH-SY5Y(ECACC)_RA_inhibiter_LY294002_5d_rep2


title: SH-SY5Y(ECACC)_RA_0h_rep1


title: SH-SY5Y(ATCC)_RA_2d_rep2

description: Sampling of RNA was performed at six different time points (0h, 6h, 1d, 2d, 3d, and 5d, respectively) under RA inducible conditions.

treatment_protocol: SH-SY5Y-A cells were seeded in laminin coated culture dishes (BioCoat Laminin Cellware; BD Biosciences) for 1 day and then transferred to a medium containing 10 μM of RA for five days.

value: SH-SY5Y (CRL-2266, obtained from ATCC (American Type Culture Collection Cultures))


title: SH-SY5Y(ECACC)_RA_inhibiter_LY294002_0h_rep1


title: SH-SY5Y(ECACC)_RA_inhibiter_LY294002_1d_rep1


title: SH-SY5Y(ECACC)_RA_inhibiter_LY294002_6h_rep1


title: SH-SY5Y(ATCC)_RA_3d_rep1


title: SH-SY5Y(ATCC)_RA_3d_rep2


title: SH-SY5Y(ATCC)_RA_0h_rep1


title: SH-SY5Y(ATCC)_RA_0h_rep2


title: SH-SY5Y(ATCC)_RA_6h_rep1


title: SH-SY5Y(ATCC)_RA_inhibiter_LY294002_3d_rep2

description: Sampling of RNA was performed at six different time points (0h, 6h, 1d, 2d, 3d, and 5d, respectively) under RA inducible conditions in the presence of Ly294002.

treatment_protocol: SH-SY5Y-A cells were seeded in laminin coated culture dishes (BioCoat Laminin Cellware; BD Biosciences) for 1 day and then transferred to a medium containing 10 μM of RA in the presence of LY294002 (10 μM) for five days.


title: SH-SY5Y(ATCC)_RA_1d_rep1


title: SH-SY5Y(ATCC)_RA_inhibiter_LY294002_6h_rep2


title: SH-SY5Y(ATCC)_RA_inhibiter_LY294002_2d_rep2


title: SH-SY5Y(ATCC)_RA_1d_rep2


title: SH-SY5Y(ATCC)_RA_5d_rep2


title: SH-SY5Y(ATCC)_RA_6h_rep2


title: SH-SY5Y(ATCC)_RA_5d_rep1


title: SH-SY5Y(ATCC)_RA_inhibiter_LY294002_5d_rep2


title: SH-SY5Y(ATCC)_RA_inhibiter_LY294002_0h_rep1


title: SH-SY5Y(ATCC)_RA_inhibiter_LY294002_1d_rep1


title: SH-SY5Y(ATCC)_RA_inhibiter_LY294002_6h_rep1


title: SH-SY5Y(ATCC)_RA_2d_rep1


title: SH-SY5Y(ATCC)_RA_inhibiter_LY294002_2d_rep1


title: SH-SY5Y(ATCC)_RA_inhibiter_LY294002_0h_rep2


title: SH-SY5Y(ECACC)_RA_2d_rep3


title: SH-SY5Y(ATCC)_RA_inhibiter_LY294002_5d_rep1


title: DelCu60T12_Rep2

status: Public on Aug 26 2009

city: Talca

first: Fernando

last: Guerra

state: Talca

address: 2 Norte 685

department: Instituto de Biologia Vegetal y Biotecnologia

country: Chile

institute: Universidad de Talca

description: Spots positions in the 5x5 grid within the 384 blocks generated by the arrayer were retrieved in scanned 16-bits TIFF images by using the XDotsReader spot finder software (COSE, Paris France). In the raw file generated by XDotsReader, the spot position (1 to 23, odd numbers) is followed by block position (A to P; 1 to 24) in the 'def.coord' column and the raw signal intensity is given in the 'sel' column

hyb_protocol: Nylon arrays were preincubated in 30 ml of a hybridization solution (5XSSC, 5XDenhardt’s solution, 0.5% SDS, 50µg/ml shared salmon sperm DNA) for 4 h at 65°C in a rotating hybridization incubator. The arrays were then incubated in 10 ml of fresh hybridization solution containing the 33P-labeled probe at 65°C for 22 h. The hybridized arrays were washed successively for 3 x 5 min in 2X SSC at room temperature; 2 x 20 min in 2X SSC, 0.05% SDS (65°C); 2 X 20 min in 1X SSC, 0.1% SDS (65°C); and 2 x 20 min in 0.1X SSC, 0.1% SDS (65°C).

scan_protocol: Arrays were exposed to phosphorimaging screen (Eastman Kodak Company) and cDNA spots intensities were visualized by scanning at a resolution of 50 µm per pixel in a Personal Molecular Imager FX (Bio-Rad).

data_processing: Data were processed as follow: the mean value of all empty spots positions was calculated and then a flag-limit corresponding to 2 x this value was set; all spots that showed raw intensities below this flag-limit in all treatments were removed from the analysis; remaining spots intensities were centered-normalized to mean intensity value within each experiment. The statistical analysis was implemented using the MIXED procedure of the SAS system utilizing an approach based on linear mixed models

label: [33P]dCTP, [33P]dATP

organism: Populus deltoides

source_name: Populus deltoides roots from plants grown in basal nutrient solution supplemented with copper 60 µM, after 12 hours of incubation (Cu60, T12)

label_protocol: Total RNA were treated with DNase and cDNA were aplified with SMART-PCR cDNA Synthesis Kit (BD BioSciences). cDNA probes were labelled with 30 μCi [33P]dCTP and 30 μCi [33P]dATP using the Prime-a-Gene Kit (Promega). The unincorporated labeled nucleotides were removed using QIAquick columns (QIAGEN)

extract_protocol: Roots were ground in liquid nitrogen, bead beat in QIAgen buffer RLC and then RNA were isolated with QIAgen RNeasy Plant kit

tag: Plants of a Populus deltoides clone grown in a hydroponic system during 4 weeks were incubated in basal nutrient solution (Hoagland’s modiefied salt, ¼ strength) supplemented with copper 60 µM and maintained during 12 h before root harvest.


title: DelCu60T24_Rep3

source_name: Populus deltoides roots from plants grown in basal nutrient solution supplemented with copper 60 µM, after 24 hours of incubation (Cu60, T24)

tag: Plants of a Populus deltoides clone grown in a hydroponic system during 4 weeks were incubated in basal nutrient solution (Hoagland’s modiefied salt, ¼ strength) supplemented with copper 60 µM and maintained during 24 h before root harvest.


title: DelCu60T12_Rep3


title: DelCu30T12_Rep2

source_name: Populus deltoides roots from plants grown in basal nutrient solution supplemented with copper 30 µM, after 12 hours of incubation (Cu30, T12)

tag: Plants of a Populus deltoides clone grown in a hydroponic system during 4 weeks were incubated in basal nutrient solution (Hoagland’s modiefied salt, ¼ strength) supplemented with copper 30 µM and maintained during 12 h before root harvest.


title: SH-SY5Y(ATCC)_RA_inhibiter_LY294002_1d_rep2


title: DelCu30T12_Rep3


title: DelCu60T24_Rep1


title: DelCu60T12_Rep1


title: DelCu60T24_Rep2


title: SH-SY5Y(ATCC)_RA_inhibiter_LY294002_3d_rep1


title: DelCu30T24_Rep1

source_name: Populus deltoides roots from plants grown in basal nutrient solution supplemented with copper 30 µM, after 24 hours of incubation (Cu30, T24)

tag: Plants of a Populus deltoides clone grown in a hydroponic system during 4 weeks were incubated in basal nutrient solution (Hoagland’s modiefied salt, ¼ strength) supplemented with copper 30 µM and maintained during 24 h before root harvest.


title: DelCu30T24_Rep2


title: DelCu30T24_Rep3


title: DelCu0T24_Rep3

description: Spots positions in the 5x5 grid within the 384 blocks generated by the arrayer were retrieved in scanned 16-bits TIFF images by using the XDotsReader spot finder software (COSE, Paris France). In the raw file generated by XDotsReader, the spot position (1 to 23, odd numbers) is followed by block position (A to P; 1 to 24) in the 'def.coord' column and the raw signal intensity is given in the 'sel' column.

data_processing: Data were processed as follow: the mean value of all empty spots positions was calculated and then a flag-limit corresponding to 2 x this value was set; all spots that showed raw intensities below this flag-limit in all treatments were removed from the analysis; remaining spots intensities were centered-normalized to mean intensity value within each experiment. The statistical analysis was implemented using the MIXED procedure of the SAS system utilizing an approach based on linear mixed models.

source_name: Populus deltoides roots from plants grown in basal nutrient solution after 24 hours of incubation (control, T24)

extract_protocol: Roots were ground in liquid nitrogen, bead beat in QIAgen buffer RLC and then RNA were isolated with QIAgen RNeasy Plant kit.

tag: Plants of a Populus deltoides clone grown in a hydroponic system during 4 weeks were incubated in basal nutrient solution (Hoagland’s modified salt, ¼ strength) and maintained during 24 h before root harvest.


title: DelCu0T12_Rep3

source_name: Populus deltoides roots from plants grown in basal nutrient solution after 12 hours of incubation (control, T12)

tag: Plants of a Populus deltoides clone grown in a hydroponic system during 4 weeks were incubated in basal nutrient solution (Hoagland’s modified salt, ¼ strength) and maintained during 12 h before root harvest.


title: DelCu0T24_Rep1


title: DelCu30T12_Rep1


title: DelCu0T12_Rep2

label_protocol: Total RNA were treated with DNase and cDNA were aplified with SMART-PCR cDNA Synthesis Kit (BD BioSciences). cDNA probes were labelled with 30 μCi [33P]dCTP and 30 μCi [33P]dATP using the Prime-a-Gene Kit (Promega). The unincorporated labeled nucleotides were removed using QIAquick columns (QIAGEN).

tag: Plants of a Populus deltoides clone grown in a hydroponic system during 4 week were incubated in basal nutrient solution (Hoaglands’s modified salt, ¼ strength) and maintained during 12 h before root harvest.


title: DelCu0T12_Rep1

tag: Plants of a Populus deltoides clone grown in a hydroponic system during 4 weeks were incubated in basal nutrient solution (Hoagland’s modified salt, ¼ strength) and maintained during 12 h before root collect.


title: DelCu0T24_Rep2


title: Periodontal ligament cells

status: Public on Aug 30 2009

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: periodontal ligament cells

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: Periodontal ligament cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNeasy mini Kit (Qiagen, Hilden, Germany)

tag: genetic modification:

tag: tissue

value: periodontal ligament cells


title: Dye swap 2

status: Public on Aug 24 2009

city: Caen

first: Benoit

middle: Denis

last: Roussel

address: Bd Becquerel

department: GIP Cyceron

institute: INSERM

description: The level of expression of each gene was evaluated by calculating the mean ratio “signal/background” for each corresponding spot from the 2 dye-swap experiments. Genes were considered to be expressed if their mean ratio was higher or equal to 1.2. Genes with mean ratio <1.2 in the 2 conditions were not used for further analysis.

hyb_protocol: RNG-MRC_MM25k_EVRY microarrays (Le brigand et al., NAR, 2006) were first incubated in a humid chamber for 2 hours to rehydrate the spots then placed for 1 hour in a dessicator and blocked for 1 hour at room temperature in 50mM Sodium Borate pH 9, 0.003% ethanolamine. Slides were then washed 5 minutes with water and dried by centrifugation. Hybridizations were performed in 50% formamide, 5X Denhardt’s, 4x SSC and 0.1% SDS solution at 42°C for 16 hours. Microarrays were then washed at room temperature 5 minutes in 2X SSC, 0.1% SDS, 5 minutes in 1X SSC, 5 minutes in 0.2X SSC and 5 minutes in 0.05X SSC. Slides were finally dried by centrifugation 4 minutes at 900rpm.

scan_protocol: Microarray images were obtained using a ScanArray Gx scanner (Perkin Elmer). Median signal and median local background intensities were extracted from the images using Genepix 4.1 software (Axon Instruments).

data_processing: Filtered data were submitted to VARAN (http//:www. bionet. espci.fr) for lowess fit normalization and differential expression analysis (Golfier et al.,2004). Normalized log2ratio 21 months/4 months were then used for further statistical analysis by SAM software (Tusher et al., 2001) and t-test with a p-value equal to 5% using TIGR Multiexperiment Viewer (TM4:MeV, http://www.tm4.org/mev.html).

source_name: Cortex 21 months old

label_protocol: 5µg of total RNA were reverse-transcribed in the presence of 7.5µM random hexamers (GE Healthcare), 75µM aa-dUTP (Sigma-Aldrich) and 100U Rtases Reverse-iT Blend (Thermo scientific) overnight at 37°C. Aminoallyl cDNAs were labelled with Cy5 mono-Reactive Dye (GE Healthcare) according to the manusfacturer’s instructions. Labelled cDNAs were then purified on Qiaquick PCR prurification kit (Qiagen)

extract_protocol: Using Nucleospin® by Macherey-Nagel

tag: Strain

value: C57BL6/J, Stage :21 months, Tissue :cortex

source_name: Cortex 4 months old

label_protocol: 5µg of total RNA were reverse-transcribed in the presence of 7.5µM random hexamers (GE Healthcare), 75µM aa-dUTP (Sigma-Aldrich) and 100U Rtases Reverse-iT Blend (Thermo scientific) overnight at 37°C. Aminoallyl cDNAs were labelled with Cy3 mono-Reactive Dye (GE Healthcare) according to the manusfacturer’s instructions. Labelled cDNAs were then purified on Qiaquick PCR prurification kit (Qiagen)

value: C57BL6/J, Stage :4 months, Tissue :cortex


title: Embryo ethanol EXP1 rep1

city: Indianapolis

first: Feng

last: Zhou

state: IN

address: 635 Barnhill Dr.

department: Anatomy & Cell Biology

institute: Indiana University School of Medicine

description: Gene expression data from whole embryo

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on RGU34A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

source_name: embryo, gestational day 8.25

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: The gravid uterus was removed and placed in a sterile PBS (0.1 M phosphate buffer containing saline) at 37°C. The embryo in the visceral yolk sac along with a small piece of the ectoplacental cone (hereafter called embryo, unless otherwise stated) was carefully removed from the deciduas tissues and the Reichert’s membrane and immediately immersed in PBS containing 4% fetal bovine serum (Sigma, St Louise. MO). Three embryos bearing 3-5 somites (E8.25) were placed in a culture bottle (20 mL, B.T.C. Precision Incubator Unit, B.T.C. engineering, Cambridge, England, 36 rpm) containing the culture medium which consisted of 70% immediately centrifuged heat-inactivated rat serum (Harlan Sprague-Dawley, Inc, Indianapolis, IN) and 30% phosphate buffered saline (137 mM NaCl, 2.7 mM KCl, 0.5 mM MgCl2, 8 mM Na2HPO4, 1.47 mM KH2PO4, 0.9 mM CaCl2, 5.6 mM glucose, 0.33 mM sodium pyruvate, pH7.4) supplemented with 20 units/ml penicillin and 20 units/ml streptomycin (Sigma, St. Louis, MO). Bottles were gassed between 0 and 22 h with 5% O2, 5% CO2, and 90% N2, and between 22 and 44 h with 20% O2, 5% CO2, and 75% N2 in a rotating culture system (B.T.C. Precision Incubator Unit, B.T.C. engineering, Cambridge, England, 36 rpm) at 37 °C. After the pre-culture period (4 hours), alcohol exposure was started by transferring the embryos into medium containing 6 µL/mL of 95% ethanol (400 mg/dL in culture). The dose of alcohol exposure was previously determined decline from this initial peak concentration over the day to ~44mM (200mg/dL).

extract_protocol: Each embryo was immediately lysed in 1 ml RNeasy solution (TelTest, Houston, TX) and passed through a 18 gauge hypodermic needle 4 times. RNA was isolated according to the manufacturer’s directions.

tag: C57bl embryo

tag: exposed to ethanol 46 hours

tag: Open Neural tube


title: Embryo control EXP1 rep1

description: Gene expression data from whole embryo

tag: no ethanol


title: Embryo ethanol open EXP2 rep4

description: Gene expression data from whole embryo


title: Embryo ethanol EXP1 rep4

description: Gene expression data from whole embryo


title: Embryo control EXP1 rep3

description: Gene expression data from whole embryo


title: Experiment_1


title: Chronically inflamed peri-implant

description: chronically inflamed peri-implant

source_name: Chronically inflamed peri-implant

value: Peri-implant cells


title: Embryo ethanol closed EXP2 rep3

description: Gene expression data from whole embryo

tag: Closed Neural tube


title: Dye swap 1


title: Embryo ethanol open EXP2 rep1

description: Gene expression data from whole embryo


title: Embryo control EXP2 rep2

description: Gene expression data from whole embryo


title: Embryo ethanol open EXP2 rep3

description: Gene expression data from whole embryo


title: Embryo ethanol EXP1 rep2

description: Gene expression data from whole embryo


title: Whole embryo 3

status: Public on Aug 19 2009

city: Syracuse

first: Michael

middle: E

last: Zuber

state: NY

address: 766 Irving Ave

department: Ophthalmology

institute: SUNY Upstate Medical University

description:
Carried out at SUNY-MAC (Syracuse, NY) per manufacturers
protocol (Affymetrix).

data_processing:
GeneSpring GX, ver. 7.3.1 (Agilent Technologies) was used for analysis. Cel file
data was pre-processed using RMA method with the average signal intensity normalized to stage 15 whole embryos when analyzing EP, PNP and LE samples.

label: Biotin labelling

molecule: polyA RNA

organism: Xenopus laevis

source_name: Xenopus Laevis Stage 15 whole embryo

tag: Xenopus Laevis Stage 15 whole embryo


title: Embryo ethanol EXP1 rep3

description: Gene expression data from whole embryo


title: Embryo ethanol closed EXP2 rep1

description: Gene expression data from whole embryo


title: Embryo control EXP1 rep2

description: Gene expression data from whole embryo


title: Embryo control EXP2 rep4

description: Gene expression data from whole embryo


title: Embryo ethanol closed EXP2 rep2

description: Gene expression data from whole embryo


title: Embryo control EXP1 rep4

description: Gene expression data from whole embryo


title: Posterior neural plate 2

hyb_protocol: Carried out at SUNY-MAC (Syracuse, NY) per manufacturers protocol (Affymetrix).

source_name: Xenopus Laevis Stage 15 posterior neural plate


title: Experiment_2


title: Embryo ethanol open EXP2 rep2

description: Gene expression data from whole embryo


title: Embryo control EXP2 rep3

description: Gene expression data from whole embryo


title: Whole embryo 2

scan_protocol: Carried out at SUNY-MAC (Syracuse, NY) per manufacturers protocol (Affymetrix).


title: Whole embryo 1

label_protocol:
Carried out at SUNY-MAC (Syracuse, NY) per manufacturers
protocol (Affymetrix).


title: Posterior neural plate 1

extract_protocol:
Carried out at SUNY-MAC (Syracuse, NY) per manufacturers
protocol (Affymetrix).

tag: Xenopus Laevis Stage 15 posterior neural plate


title: Embryo control EXP2 rep1

description: Gene expression data from whole embryo


title: GFP injected stage 15 Xenopus Laevis animal cap 3

data_processing:
GeneSpring GX, ver. 7.3.1 (Agilent Technologies) was used for analysis. Cel file
data was pre-processed using RMA method with the average signal intensity normalized to primitive ectoderm isolated from Venus YFP RNA injected embryos in the case of EFTF-injected caps.

label: Biotin Labelling

source_name: GFPinjected animal cap


title: Lateral endoderm 1

source_name: Stage 15 Xenopus Laevis lateral endoderm


title: GFP injected stage 15 Xenopus Laevis animal cap 2

source_name: GFP injected animal cap


title: Lateral endoderm 2

tag: Stage 15 Xenopus Laevis lateral endoderm


title: GFP injected stage 15 Xenopus Laevis animal cap 4

tag: GFP injected stage 15 Xenopus Laevis animal cap.


title: GFP injected stage 15 Xenopus Laevis animal cap 1

source_name: EFTF injected animal cap


title: Eye primordia 1

source_name: Stage 15 Xenopus Laevis Eye Primordia

tag: Stage 15 Xenopus Laevis Eye Primordia


title: Eye primordia 3

source_name: Xenopus Laevis Stage 15 eye primordia

tag: Xenopus Laevis Stage 15 eye primordia


title: Posterior neural plate 3


title: Eye primordia 2


title: EFTF injected stage 15 Xenopus Laevis animal cap 2

description:
Carried out at SUNY-MAC (Syracuse, NY) per manufacturers
protocol (Affymetrix).
Label


title: Testis_control untreated_rep5

status: Public on Aug 18 2009

city: Oxford

first: Dilair

last: Baban

address: Roosevelt Drive

department: Wellcome Trust Centre Human Genetics

country: United Kingdom

institute: University of Oxford

description: Here we have addressed important question of changes in the global gene expression profile of testicular tissue following hormone stimulation (rFSH) for 12, 24 and 72h following injections compared to control untreated hpg males of the same age.

hyb_protocol: Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.

scan_protocol: Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)

data_processing: We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these chips

label: Biotin

source_name: Testis

label_protocol: 8 µg of RNA was converted to double-stranded cDNA using one-cycle cDNA synthesis kit (Affymetrix), followed by in vitro transcription (IVT) to generate biotin-labelled cRNA probes.

growth_protocol: male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by cervical dislocation, testes dissected out, weighed and snap frozen in liquid nitrogen. Tissue was stored at -70oC until RNA extraction.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Lipid Tissue Mini kit (Qiagen, Valencia, CA) according to the the manufacturer’s instructions manufacturer’s instructions.

treatment_protocol: Control untreated

tag: 10 week old hpg males were killed by cervical dislocation; testes dissected out, weighed and snap frozen in liquid nitrogen. Tissue was stored at -70oC until use. RNA was extracted using Qiagen RNeasy Lipid Tissue Mini kit (Qiagen, Valencia, CA) according to the the manufacturer’s instructions manufacturer’s instructions. Biological Replicate 5


title: EFTF injected stage 15 Xenopus Laevis animal cap 4


title: EFTF injected stage 15 Xenopus Laevis animal cap 3

source_name: EfTF injected animal cap