title: T4373B3

description: Location: Left; DukesStage: C; Age_Diag: 26; Gender: M; DFS_Time: 50.43; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:26; Gender:M; DFS_Time:50.43; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T3254B

status: Public on Jan 08 2010

type: RNA

city: Parkville

first: Oliver

last: Sieber

state: Victoria

address: 6th floor, Centre for Medical Research,  Royal Melbourne Hospital,  Royal Parade

department: Melbourne Tumour Biology Branch

country: Australia

institute: Ludwig Institute for Cancer Research

description: Location: Left; DukesStage: C; Age_Diag: 83; Gender: F; DFS_Time: 54.9; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Use the simpleaffy package in R/Bioconductor to calculate MAS5.0 calls. These values were subsequently normalized using quantile normalization.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: primary colorectal adenocarcinoma

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Surgically isolated colorectal cancers were immediately frozen in liquid nitrogen. Total RNA was extracted from cancer tissue using Trizol reagent (Invitrogen).

tag: Location

value: Left; DukesStage:C; Age_Diag:83; Gender:F; DFS_Time:54.9; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T2916A

description: Location: Left; DukesStage: C; Age_Diag: 69; Gender: M; DFS_Time: 41.06; DFS_Cens: 0; AdjXRT: Y; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:69; Gender:M; DFS_Time:41.06; DFS_Cens:0; AdjXRT:Y; AdjCTX:Y


title: T3216A

description: Location: Right; DukesStage: C; Age_Diag: 73; Gender: F; DFS_Time: 38.72; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:73; Gender:F; DFS_Time:38.72; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T4174A

description: Location: Left; DukesStage: C; Age_Diag: 67; Gender: M; DFS_Time: 36.92; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:67; Gender:M; DFS_Time:36.92; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T4550B

description: Location: Right; DukesStage: C; Age_Diag: 41; Gender: M; DFS_Time: 34.19; DFS_Cens: 0; AdjXRT: Y; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:41; Gender:M; DFS_Time:34.19; DFS_Cens:0; AdjXRT:Y; AdjCTX:Y


title: T3804A

description: Location: Right; DukesStage: C; Age_Diag: 71; Gender: F; DFS_Time: 26.92; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:71; Gender:F; DFS_Time:26.92; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T1430C

description: Location: Left; DukesStage: C; Age_Diag: 58; Gender: M; DFS_Time: 27.58; DFS_Cens: 0; AdjXRT: Y; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:58; Gender:M; DFS_Time:27.58; DFS_Cens:0; AdjXRT:Y; AdjCTX:Y


title: T372A

description: Location: Left; DukesStage: C; Age_Diag: 26; Gender: M; DFS_Time: 29.39; DFS_Cens: 0; AdjXRT: Y; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:26; Gender:M; DFS_Time:29.39; DFS_Cens:0; AdjXRT:Y; AdjCTX:Y


title: T5139A1

description: Location: Left; DukesStage: C; Age_Diag: 79; Gender: F; DFS_Time: 31.92; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:79; Gender:F; DFS_Time:31.92; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T1600A

description: Location: Left; DukesStage: C; Age_Diag: 63; Gender: M; DFS_Time: 23.34; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:C; Age_Diag:63; Gender:M; DFS_Time:23.34; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: T4920A1

description: Location: Right; DukesStage: C; Age_Diag: 78; Gender: F; DFS_Time: 31.36; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:C; Age_Diag:78; Gender:F; DFS_Time:31.36; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T2307A1

description: Location: Right; DukesStage: C; Age_Diag: 87; Gender: F; DFS_Time: 22.25; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:87; Gender:F; DFS_Time:22.25; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T625A

description: Location: Left; DukesStage: C; Age_Diag: 53; Gender: M; DFS_Time: 21.27; DFS_Cens: 0; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:53; Gender:M; DFS_Time:21.27; DFS_Cens:0; AdjXRT:N; AdjCTX:Y


title: T2875A1

description: Location: Left; DukesStage: C; Age_Diag: 66; Gender: M; DFS_Time: 24.85; DFS_Cens: 0; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:66; Gender:M; DFS_Time:24.85; DFS_Cens:0; AdjXRT:N; AdjCTX:Y


title: T4080A

description: Location: Right; DukesStage: C; Age_Diag: 78; Gender: F; DFS_Time: 26.26; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:C; Age_Diag:78; Gender:F; DFS_Time:26.26; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T4110A

description: Location: Left; DukesStage: C; Age_Diag: 46; Gender: M; DFS_Time: 21.04; DFS_Cens: 0; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:46; Gender:M; DFS_Time:21.04; DFS_Cens:0; AdjXRT:N; AdjCTX:Y


title: T771A

description: Location: Left; DukesStage: C; Age_Diag: 90; Gender: F; DFS_Time: 27.74; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:C; Age_Diag:90; Gender:F; DFS_Time:27.74; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: T5565A1

description: Location: Right; DukesStage: C; Age_Diag: 81; Gender: F; DFS_Time: 19.98; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:81; Gender:F; DFS_Time:19.98; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T2926B

description: Location: Right; DukesStage: C; Age_Diag: 64; Gender: F; DFS_Time: 36.92; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:C; Age_Diag:64; Gender:F; DFS_Time:36.92; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: T4948A2

description: Location: Left; DukesStage: C; Age_Diag: 61; Gender: F; DFS_Time: 18.96; DFS_Cens: 1; AdjXRT: Y; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:61; Gender:F; DFS_Time:18.96; DFS_Cens:1; AdjXRT:Y; AdjCTX:Y


title: T672A

description: Location: Left; DukesStage: C; Age_Diag: 53; Gender: F; DFS_Time: 16.07; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:C; Age_Diag:53; Gender:F; DFS_Time:16.07; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: T223B

description: Location: Left; DukesStage: C; Age_Diag: 46; Gender: M; DFS_Time: 11.9; DFS_Cens: 0; AdjXRT: Y; AdjCTX: N

value: Left; DukesStage:C; Age_Diag:46; Gender:M; DFS_Time:11.9; DFS_Cens:0; AdjXRT:Y; AdjCTX:N


title: T801A1

description: Location: Left; DukesStage: C; Age_Diag: 67; Gender: F; DFS_Time: 8.31; DFS_Cens: 0; AdjXRT: Y; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:67; Gender:F; DFS_Time:8.31; DFS_Cens:0; AdjXRT:Y; AdjCTX:Y


title: T1213A

description: Location: Right; DukesStage: C; Age_Diag: 63; Gender: M; DFS_Time: 20.44; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:63; Gender:M; DFS_Time:20.44; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T4060A

description: Location: Left; DukesStage: C; Age_Diag: 51; Gender: F; DFS_Time: 8.58; DFS_Cens: 0; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:51; Gender:F; DFS_Time:8.58; DFS_Cens:0; AdjXRT:N; AdjCTX:Y


title: T2638B

description: Location: Rectum; DukesStage: C; Age_Diag: 50; Gender: F; DFS_Time: 18.93; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:C; Age_Diag:50; Gender:F; DFS_Time:18.93; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: T324A

description: Location: Right; DukesStage: C; Age_Diag: 38; Gender: M; DFS_Time: 8.21; DFS_Cens: 0; AdjXRT: Y; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:38; Gender:M; DFS_Time:8.21; DFS_Cens:0; AdjXRT:Y; AdjCTX:Y


title: T4644B1

description: Location: Left; DukesStage: C; Age_Diag: 75; Gender: F; DFS_Time: 24.13; DFS_Cens: 0; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:75; Gender:F; DFS_Time:24.13; DFS_Cens:0; AdjXRT:N; AdjCTX:Y


title: T1102A

description: Location: Right; DukesStage: C; Age_Diag: 74; Gender: M; DFS_Time: 5.35; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:C; Age_Diag:74; Gender:M; DFS_Time:5.35; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: T1479A

description: Location: Left; DukesStage: C; Age_Diag: 75; Gender: M; DFS_Time: 9.56; DFS_Cens: 0; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:75; Gender:M; DFS_Time:9.56; DFS_Cens:0; AdjXRT:N; AdjCTX:Y


title: T4448A

description: Location: Right; DukesStage: C; Age_Diag: 78; Gender: F; DFS_Time: 4.24; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:78; Gender:F; DFS_Time:4.24; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T949B

description: Location: Right; DukesStage: C; Age_Diag: 60; Gender: M; DFS_Time: 14.72; DFS_Cens: 0; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:60; Gender:M; DFS_Time:14.72; DFS_Cens:0; AdjXRT:N; AdjCTX:Y


title: T5811A1

description: Location: Right; DukesStage: C; Age_Diag: 62; Gender: F; DFS_Time: 5.22; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:62; Gender:F; DFS_Time:5.22; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T2567B1

description: Location: Right; DukesStage: C; Age_Diag: 83; Gender: F; DFS_Time: 3.32; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:C; Age_Diag:83; Gender:F; DFS_Time:3.32; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: 02-1140-P1840

description: Location: Colon; DukesStage: B; Age_Diag: 78; Gender: F; DFS_Time: 45.4; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Colon; DukesStage:B; Age_Diag:78; Gender:F; DFS_Time:45.4; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 02-47-P1097

description: Location: Right; DukesStage: B; Age_Diag: 81; Gender: F; DFS_Time: 55.9; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:81; Gender:F; DFS_Time:55.9; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 99-113-P447

description: Location: Right; DukesStage: B; Age_Diag: 48; Gender: F; DFS_Time: 74.2; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:B; Age_Diag:48; Gender:F; DFS_Time:74.2; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: 99-2-P2

description: Location: Right; DukesStage: B; Age_Diag: 72; Gender: M; DFS_Time: 84.9; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:72; Gender:M; DFS_Time:84.9; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T4695A1

description: Location: Right; DukesStage: C; Age_Diag: 54; Gender: M; DFS_Time: 0.92; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:C; Age_Diag:54; Gender:M; DFS_Time:0.92; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 03-1142-P2740

description: Location: Left; DukesStage: B; Age_Diag: 63; Gender: F; DFS_Time: 33.8; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:63; Gender:F; DFS_Time:33.8; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 01-28-P617

description: Location: Right; DukesStage: B; Age_Diag: 53; Gender: F; DFS_Time: 58.4; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:B; Age_Diag:53; Gender:F; DFS_Time:58.4; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: 04-TB-026-1A

description: Location: Left; DukesStage: B; Age_Diag: 74; Gender: M; DFS_Time: 5.2; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:74; Gender:M; DFS_Time:5.2; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 03-512-P2225

description: Location: Left; DukesStage: B; Age_Diag: 63; Gender: M; DFS_Time: 38; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:63; Gender:M; DFS_Time:38; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 02-1005-P1757

description: Location: Right; DukesStage: B; Age_Diag: 78; Gender: F; DFS_Time: 36.2; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:78; Gender:F; DFS_Time:36.2; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 03-TB-054-1C

description: Location: Rectum; DukesStage: B; Age_Diag: 64.6; Gender: M; DFS_Time: 11.6; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:B; Age_Diag:64.6; Gender:M; DFS_Time:11.6; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 04-TB-014-1A

description: Location: Left; DukesStage: B; Age_Diag: 63; Gender: F; DFS_Time: 44.4; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:63; Gender:F; DFS_Time:44.4; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 00-TB-010-1A

description: Location: Right; DukesStage: B; Age_Diag: 92; Gender: M; DFS_Time: 13.5; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:92; Gender:M; DFS_Time:13.5; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 03-TB-042-1B

description: Location: Right; DukesStage: B; Age_Diag: 44; Gender: M; DFS_Time: 31.3; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:44; Gender:M; DFS_Time:31.3; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T402B

description: Location: Left; DukesStage: B; Age_Diag: 43; Gender: F; DFS_Time: 110.79; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:43; Gender:F; DFS_Time:110.79; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T74A

description: Location: Rectum; DukesStage: B; Age_Diag: 74; Gender: F; DFS_Time: 118.58; DFS_Cens: 1; AdjXRT: Y; AdjCTX: Y

value: Rectum; DukesStage:B; Age_Diag:74; Gender:F; DFS_Time:118.58; DFS_Cens:1; AdjXRT:Y; AdjCTX:Y


title: T740A

description: Location: Left; DukesStage: B; Age_Diag: 70; Gender: M; DFS_Time: 106.94; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:70; Gender:M; DFS_Time:106.94; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 03-TB-052-1D

description: Location: Right; DukesStage: B; Age_Diag: 66; Gender: F; DFS_Time: 33.9; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:66; Gender:F; DFS_Time:33.9; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 02-470-P1392

description: Location: Left; DukesStage: B; Age_Diag: 70; Gender: M; DFS_Time: 50.9; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:70; Gender:M; DFS_Time:50.9; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 03-TB-084-1A

description: Location: Left; DukesStage: B; Age_Diag: 64; Gender: M; DFS_Time: 47.7; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:64; Gender:M; DFS_Time:47.7; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T1621B

description: Location: Left; DukesStage: B; Age_Diag: 71; Gender: F; DFS_Time: 85.28; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:71; Gender:F; DFS_Time:85.28; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T1979A

description: Location: Left; DukesStage: B; Age_Diag: 74; Gender: F; DFS_Time: 86.43; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:74; Gender:F; DFS_Time:86.43; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 03-TB-087-1A

description: Location: Rectum; DukesStage: B; Age_Diag: 72; Gender: M; DFS_Time: 38.2; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:B; Age_Diag:72; Gender:M; DFS_Time:38.2; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T2551A

description: Location: Right; DukesStage: B; Age_Diag: 86; Gender: F; DFS_Time: 80.25; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:86; Gender:F; DFS_Time:80.25; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 02-627-P1492

description: Location: Rectum; DukesStage: B; Age_Diag: 75; Gender: M; DFS_Time: 14.3; DFS_Cens: 0; AdjXRT: Y; AdjCTX: Y

value: Rectum; DukesStage:B; Age_Diag:75; Gender:M; DFS_Time:14.3; DFS_Cens:0; AdjXRT:Y; AdjCTX:Y


title: T2367A

description: Location: Right; DukesStage: B; Age_Diag: 57; Gender: F; DFS_Time: 79.13; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:B; Age_Diag:57; Gender:F; DFS_Time:79.13; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T1369A

description: Location: Right; DukesStage: B; Age_Diag: 74; Gender: M; DFS_Time: 88.99; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:B; Age_Diag:74; Gender:M; DFS_Time:88.99; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T379D

description: Location: Rectum; DukesStage: B; Age_Diag: 41; Gender: M; DFS_Time: 93.66; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:B; Age_Diag:41; Gender:M; DFS_Time:93.66; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: T2004A

description: Location: Left; DukesStage: B; Age_Diag: 83; Gender: F; DFS_Time: 70.65; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:83; Gender:F; DFS_Time:70.65; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T1403D

description: Location: Right; DukesStage: B; Age_Diag: 49; Gender: M; DFS_Time: 64.86; DFS_Cens: 1; AdjXRT: Y; AdjCTX: Y

value: Right; DukesStage:B; Age_Diag:49; Gender:M; DFS_Time:64.86; DFS_Cens:1; AdjXRT:Y; AdjCTX:Y


title: T2466A

description: Location: Left; DukesStage: B; Age_Diag: 75; Gender: M; DFS_Time: 58.02; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:75; Gender:M; DFS_Time:58.02; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T3258A

description: Location: Left; DukesStage: B; Age_Diag: 76; Gender: M; DFS_Time: 63.25; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:B; Age_Diag:76; Gender:M; DFS_Time:63.25; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T1249A

description: Location: Right; DukesStage: B; Age_Diag: 76; Gender: F; DFS_Time: 52.5; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:76; Gender:F; DFS_Time:52.5; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T2002B

description: Location: Left; DukesStage: B; Age_Diag: 74; Gender: F; DFS_Time: 55.92; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:74; Gender:F; DFS_Time:55.92; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T165A

description: Location: Right; DukesStage: B; Age_Diag: 77; Gender: F; DFS_Time: 55.33; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:77; Gender:F; DFS_Time:55.33; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T3688A

description: Location: Right; DukesStage: B; Age_Diag: 67; Gender: M; DFS_Time: 59.96; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:67; Gender:M; DFS_Time:59.96; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T3884A

description: Location: Right; DukesStage: B; Age_Diag: 71; Gender: M; DFS_Time: 49.84; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:71; Gender:M; DFS_Time:49.84; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T4555A1

description: Location: Left; DukesStage: B; Age_Diag: 60; Gender: M; DFS_Time: 35.9; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:60; Gender:M; DFS_Time:35.9; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T2746A

description: Location: Right; DukesStage: B; Age_Diag: 86; Gender: F; DFS_Time: 31.06; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:86; Gender:F; DFS_Time:31.06; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T2631A

description: Location: Left; DukesStage: B; Age_Diag: 89; Gender: F; DFS_Time: 28.86; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:89; Gender:F; DFS_Time:28.86; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T4257A

description: Location: Right; DukesStage: B; Age_Diag: 59; Gender: F; DFS_Time: 39.25; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:B; Age_Diag:59; Gender:F; DFS_Time:39.25; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T433A

description: Location: Left; DukesStage: B; Age_Diag: 51; Gender: F; DFS_Time: 27.64; DFS_Cens: 0; AdjXRT: Y; AdjCTX: Y

value: Left; DukesStage:B; Age_Diag:51; Gender:F; DFS_Time:27.64; DFS_Cens:0; AdjXRT:Y; AdjCTX:Y


title: T3541A

description: Location: Left; DukesStage: B; Age_Diag: 65; Gender: F; DFS_Time: 52.14; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:65; Gender:F; DFS_Time:52.14; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T1923A

description: Location: Right; DukesStage: B; Age_Diag: 75; Gender: F; DFS_Time: 37.31; DFS_Cens: 0; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:B; Age_Diag:75; Gender:F; DFS_Time:37.31; DFS_Cens:0; AdjXRT:N; AdjCTX:Y


title: T4491A1

description: Location: Right; DukesStage: B; Age_Diag: 76; Gender: F; DFS_Time: 36.75; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:B; Age_Diag:76; Gender:F; DFS_Time:36.75; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T4660A1

description: Location: Right; DukesStage: B; Age_Diag: 64; Gender: F; DFS_Time: 29.22; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:64; Gender:F; DFS_Time:29.22; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T4980A1

description: Location: Left; DukesStage: B; Age_Diag: 51; Gender: M; DFS_Time: 33.2; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:51; Gender:M; DFS_Time:33.2; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T4701A1

description: Location: Right; DukesStage: B; Age_Diag: 84; Gender: F; DFS_Time: 28.63; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:84; Gender:F; DFS_Time:28.63; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T3702A

description: Location: Left; DukesStage: B; Age_Diag: 56; Gender: M; DFS_Time: 47.86; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:B; Age_Diag:56; Gender:M; DFS_Time:47.86; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T3764A

description: Location: Left; DukesStage: B; Age_Diag: 48; Gender: F; DFS_Time: 46.71; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:B; Age_Diag:48; Gender:F; DFS_Time:46.71; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T5024A1

description: Location: Right; DukesStage: B; Age_Diag: 69; Gender: M; DFS_Time: 33.69; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:69; Gender:M; DFS_Time:33.69; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T932B1

description: Location: Right; DukesStage: C; Age_Diag: 71; Gender: F; DFS_Time: 1.57; DFS_Cens: 0; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:71; Gender:F; DFS_Time:1.57; DFS_Cens:0; AdjXRT:N; AdjCTX:Y


title: T4612A1

description: Location: Right; DukesStage: B; Age_Diag: 71; Gender: M; DFS_Time: 26.66; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:71; Gender:M; DFS_Time:26.66; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T1150A

description: Location: Right; DukesStage: B; Age_Diag: 66; Gender: M; DFS_Time: 26.82; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:66; Gender:M; DFS_Time:26.82; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T5107B1

description: Location: Left; DukesStage: B; Age_Diag: 78; Gender: M; DFS_Time: 25.61; DFS_Cens: 1; AdjXRT: Y; AdjCTX: Y

value: Left; DukesStage:B; Age_Diag:78; Gender:M; DFS_Time:25.61; DFS_Cens:1; AdjXRT:Y; AdjCTX:Y


title: T3463A

description: Location: Right; DukesStage: B; Age_Diag: 66; Gender: F; DFS_Time: 24.19; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:66; Gender:F; DFS_Time:24.19; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T5389A1

description: Location: Right; DukesStage: B; Age_Diag: 52; Gender: F; DFS_Time: 27.15; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:52; Gender:F; DFS_Time:27.15; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T3912A

description: Location: Right; DukesStage: B; Age_Diag: 38; Gender: F; DFS_Time: 17.95; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:B; Age_Diag:38; Gender:F; DFS_Time:17.95; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T4091A

description: Location: Left; DukesStage: B; Age_Diag: 73; Gender: M; DFS_Time: 15.71; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:73; Gender:M; DFS_Time:15.71; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T2511B

description: Location: Left; DukesStage: B; Age_Diag: 65; Gender: F; DFS_Time: 22.38; DFS_Cens: 0; AdjXRT: Y; AdjCTX: Y

value: Left; DukesStage:B; Age_Diag:65; Gender:F; DFS_Time:22.38; DFS_Cens:0; AdjXRT:Y; AdjCTX:Y


title: T4541A1

description: Location: Left; DukesStage: B; Age_Diag: 58; Gender: M; DFS_Time: 44.97; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:58; Gender:M; DFS_Time:44.97; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T1662A

description: Location: Left; DukesStage: B; Age_Diag: 79; Gender: F; DFS_Time: 26.53; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:79; Gender:F; DFS_Time:26.53; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T4508A1

description: Location: Right; DukesStage: B; Age_Diag: 71; Gender: M; DFS_Time: 25.24; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:71; Gender:M; DFS_Time:25.24; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T5162A1


title: T5376A1

description: Location: Right; DukesStage: B; Age_Diag: 68; Gender: M; DFS_Time: 18.18; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:68; Gender:M; DFS_Time:18.18; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T2965B

description: Location: Left; DukesStage: B; Age_Diag: 71; Gender: M; DFS_Time: 37.31; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:71; Gender:M; DFS_Time:37.31; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T1053B

description: Location: Rectum; DukesStage: B; Age_Diag: 54; Gender: M; DFS_Time: 9.96; DFS_Cens: 0; AdjXRT: Y; AdjCTX: Y

value: Rectum; DukesStage:B; Age_Diag:54; Gender:M; DFS_Time:9.96; DFS_Cens:0; AdjXRT:Y; AdjCTX:Y


title: T4376A

description: Location: Left; DukesStage: B; Age_Diag: 30; Gender: M; DFS_Time: 6.01; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:30; Gender:M; DFS_Time:6.01; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: T2976A

description: Location: Right; DukesStage: B; Age_Diag: 78; Gender: F; DFS_Time: 22.02; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:B; Age_Diag:78; Gender:F; DFS_Time:22.02; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T5261B1

description: Location: Left; DukesStage: B; Age_Diag: 40; Gender: F; DFS_Time: 2.26; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:40; Gender:F; DFS_Time:2.26; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 03-1929-P3382

description: Location: Right; DukesStage: A; Age_Diag: 76; Gender: F; DFS_Time: 30; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:A; Age_Diag:76; Gender:F; DFS_Time:30; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 03-TB-103-1A

description: Location: Left; DukesStage: A; Age_Diag: 57; Gender: M; DFS_Time: 44.2; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:A; Age_Diag:57; Gender:M; DFS_Time:44.2; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T5164A1

description: Location: Left; DukesStage: B; Age_Diag: 54; Gender: M; DFS_Time: 15.05; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:54; Gender:M; DFS_Time:15.05; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T789A

description: Location: Rectum; DukesStage: B; Age_Diag: 83; Gender: M; DFS_Time: 14.26; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:B; Age_Diag:83; Gender:M; DFS_Time:14.26; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: 01-568-P991

description: Location: Colon; DukesStage: A; Age_Diag: 65; Gender: F; DFS_Time: 52.1; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Colon; DukesStage:A; Age_Diag:65; Gender:F; DFS_Time:52.1; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T1483C

description: Location: Right; DukesStage: B; Age_Diag: 54; Gender: F; DFS_Time: 14.13; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:54; Gender:F; DFS_Time:14.13; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: 03-35-P1905

description: Location: Left; DukesStage: A; Age_Diag: 58; Gender: F; DFS_Time: 43.9; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:A; Age_Diag:58; Gender:F; DFS_Time:43.9; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 99-30-P29

description: Location: Rectum; DukesStage: A; Age_Diag: 64; Gender: F; DFS_Time: 80.8; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:A; Age_Diag:64; Gender:F; DFS_Time:80.8; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 01-TB-023-1A

description: Location: Right; DukesStage: A; Age_Diag: 63; Gender: F; DFS_Time: 42; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:A; Age_Diag:63; Gender:F; DFS_Time:42; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T1418A

description: Location: Rectum; DukesStage: A; Age_Diag: 66; Gender: M; DFS_Time: 84.13; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:A; Age_Diag:66; Gender:M; DFS_Time:84.13; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T1407A

description: Location: Right; DukesStage: A; Age_Diag: 75; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:A; Age_Diag:75; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: 02-TB-051-1B

description: Location: Left; DukesStage: A; Age_Diag: 74; Gender: M; DFS_Time: 36.3; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:A; Age_Diag:74; Gender:M; DFS_Time:36.3; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 03-TB-041-1B

description: Location: Left; DukesStage: A; Age_Diag: 75; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:A; Age_Diag:75; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: T940A

description: Location: Left; DukesStage: A; Age_Diag: 66; Gender: M; DFS_Time: 82.29; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:A; Age_Diag:66; Gender:M; DFS_Time:82.29; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T1129A

description: Location: Left; DukesStage: B; Age_Diag: 80; Gender: M; DFS_Time: 19.36; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:80; Gender:M; DFS_Time:19.36; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: T2011A

description: Location: Right; DukesStage: A; Age_Diag: 62; Gender: M; DFS_Time: 83.6; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:A; Age_Diag:62; Gender:M; DFS_Time:83.6; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T1498A

description: Location: Rectum; DukesStage: A; Age_Diag: 70; Gender: M; DFS_Time: 83.73; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:A; Age_Diag:70; Gender:M; DFS_Time:83.73; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T129A

description: Location: Right; DukesStage: A; Age_Diag: 73; Gender: M; DFS_Time: 142.55; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:A; Age_Diag:73; Gender:M; DFS_Time:142.55; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T309A

description: Location: Left; DukesStage: A; Age_Diag: 63; Gender: M; DFS_Time: 122.72; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:A; Age_Diag:63; Gender:M; DFS_Time:122.72; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T3123A

description: Location: Rectum; DukesStage: A; Age_Diag: 78; Gender: F; DFS_Time: 67.82; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:A; Age_Diag:78; Gender:F; DFS_Time:67.82; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T981A

description: Location: Left; DukesStage: A; Age_Diag: 63; Gender: M; DFS_Time: 109.21; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:A; Age_Diag:63; Gender:M; DFS_Time:109.21; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T2688A

description: Location: Right; DukesStage: A; Age_Diag: 82; Gender: M; DFS_Time: 76.07; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:A; Age_Diag:82; Gender:M; DFS_Time:76.07; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T3599A

description: Location: Right; DukesStage: B; Age_Diag: 74; Gender: F; DFS_Time: 59.6; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:74; Gender:F; DFS_Time:59.6; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T1239A

description: Location: Right; DukesStage: A; Age_Diag: 88; Gender: M; DFS_Time: 65.88; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:A; Age_Diag:88; Gender:M; DFS_Time:65.88; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T462A

description: Location: Rectum; DukesStage: A; Age_Diag: 61; Gender: M; DFS_Time: 68.51; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:A; Age_Diag:61; Gender:M; DFS_Time:68.51; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T2183A1

description: Location: Left; DukesStage: B; Age_Diag: 73; Gender: M; DFS_Time: 76.04; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:73; Gender:M; DFS_Time:76.04; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 02-TB-011-1B

description: Location: Right; DukesStage: A; Age_Diag: 77; Gender: F; DFS_Time: 56.5; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:A; Age_Diag:77; Gender:F; DFS_Time:56.5; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T1558A

description: Location: Left; DukesStage: A; Age_Diag: 61; Gender: F; DFS_Time: 64.37; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:A; Age_Diag:61; Gender:F; DFS_Time:64.37; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: arp6-10  2h at 27 ºC  rep4

city: Norwich

first: Vinod

last: Kumar

address: Norwich Research Park

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

description: Gene expression data from arp6-10 seedlings at 27 ºC for 2 h

hyb_protocol: Following fragmentation, 1µ ug of cRNA were hybridized for 16 hr at 45 ºC Arabidopsis ATH1 microarray. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000

data_processing: Quality checks and data analyses were carried out using Affymetrix GeneChip® Operating Software(GCOS) and quality reporter

organism: Arabidopsis thaliana

source_name: arp6-10 seedlings at 27 ºC for 2 h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix GeneChip® protocol (Affymetrix) from 1µg total RNA.

growth_protocol: Sterilized wild type Arabidopsis Col-0 as well as the arp6-10 mutant seeds were plated on half-strength MS plates without sugar. Plates were incubated at 4 ºC in dark  for 48 hours before transfering to 20 ºC  with light. 5 day old seedlings were transfered to 12 ºC incubaor with continuous light for 3 days befroe shifting to 27 ºC.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: A set of seedlings incubated at 12 ºC were shifted to 27 ºC. Samples (Whole seedlings) were collected before shifting (0 h) and 2 h and 24 h after shifting to 27 ºC by immediately freezing in liquid nitrogen.

tag: tissue

value: whole seedlings

tag: genotype

tag: age

value: 8-day old


title: T3566A

description: Location: Right; DukesStage: A; Age_Diag: 87; Gender: F; DFS_Time: 64.1; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:A; Age_Diag:87; Gender:F; DFS_Time:64.1; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: arp6-10  2h at 27 ºC  rep3


title: T519A

description: Location: Left; DukesStage: A; Age_Diag: 68; Gender: F; DFS_Time: 67.19; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:A; Age_Diag:68; Gender:F; DFS_Time:67.19; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: arp6-10  24h at 27 ºC  rep3

description: Gene expression data from arp6-10 seedlings at 27 ºC for 24 h

source_name: arp6-10 seedlings at 27 ºC for 24 h


title: arp6-10  24h at 27 ºC  rep2


title: T773A1

description: Location: Left; DukesStage: A; Age_Diag: 50; Gender: M; DFS_Time: 59.53; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:A; Age_Diag:50; Gender:M; DFS_Time:59.53; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T3737A

description: Location: Right; DukesStage: A; Age_Diag: 55; Gender: M; DFS_Time: 57.79; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:A; Age_Diag:55; Gender:M; DFS_Time:57.79; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: arp6-10  24h at 27 ºC  rep1


title: arp6-10  2h at 27 ºC  rep1


title: arp6-10  24h at 27 ºC  rep4


title: T4573A1

description: Location: Right; DukesStage: A; Age_Diag: 86; Gender: F; DFS_Time: 43.79; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:A; Age_Diag:86; Gender:F; DFS_Time:43.79; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: arp6-10 12 ºC rep4

description: gene expression data from arp6-10 seedlings at 12 ºC

source_name: arp6-10 seedlings at 12 ºC


title: T3201B

description: Location: Right; DukesStage: A; Age_Diag: 76; Gender: M; DFS_Time: 52.24; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:A; Age_Diag:76; Gender:M; DFS_Time:52.24; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: arp6-10  2h at 27 ºC  rep2


title: arp6-10 12 ºC rep3


title: T3686A

description: Location: Right; DukesStage: A; Age_Diag: 74; Gender: F; DFS_Time: 55.13; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:A; Age_Diag:74; Gender:F; DFS_Time:55.13; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T552G

description: Location: Left; DukesStage: A; Age_Diag: 51; Gender: M; DFS_Time: 28.96; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:A; Age_Diag:51; Gender:M; DFS_Time:28.96; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: arp6-10 12 ºC rep2


title: T5287A1

description: Location: Right; DukesStage: A; Age_Diag: 57; Gender: M; DFS_Time: 23.96; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:A; Age_Diag:57; Gender:M; DFS_Time:23.96; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T5589B1

description: Location: Left; DukesStage: A; Age_Diag: 81; Gender: M; DFS_Time: 20.02; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:A; Age_Diag:81; Gender:M; DFS_Time:20.02; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: arp6-10 12 ºC rep1


title: T2725C

description: Location: Left; DukesStage: B; Age_Diag: 56; Gender: F; DFS_Time: 25.21; DFS_Cens: 0; AdjXRT: Y; AdjCTX: Y

value: Left; DukesStage:B; Age_Diag:56; Gender:F; DFS_Time:25.21; DFS_Cens:0; AdjXRT:Y; AdjCTX:Y


title: T4919A1

description: Location: Left; DukesStage: A; Age_Diag: 58; Gender: M; DFS_Time: 19.75; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:A; Age_Diag:58; Gender:M; DFS_Time:19.75; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: Col-0  24h at 27 ºC  rep2

description: Gene expression data from Col-0 seedlings at 27 ºC for 24 h

source_name: Col-0 seedlings at 27 ºC for 24 h


title: T1856A

description: Location: Left; DukesStage: A; Age_Diag: 80; Gender: F; DFS_Time: 16.47; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:A; Age_Diag:80; Gender:F; DFS_Time:16.47; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: Col-0  2h at 27 ºC  rep2

description: Gene expression data from Col-0 seedlings at 27 ºC for 2 h

source_name: Col-0 seedlings at 27 ºC for 2 h


title: Col-0 12 ºC rep2

description: Gene expression data from Col-0 seedlings at 12 ºC

source_name: Col-0 seedlings at 12 ºC


title: Col-0 12 ºC rep1


title: Col-0  2h at 27 ºC  rep1


title: Col-0  24h at 27 ºC  rep1


title: T866D

description: Location: Left; DukesStage: A; Age_Diag: 63; Gender: F; DFS_Time: 27.02; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:A; Age_Diag:63; Gender:F; DFS_Time:27.02; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: T5266A1

description: Location: Right; DukesStage: A; Age_Diag: 78; Gender: M; DFS_Time: 3.64; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:A; Age_Diag:78; Gender:M; DFS_Time:3.64; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T521B

description: Location: Rectum; DukesStage: A; Age_Diag: 53; Gender: F; DFS_Time: 14.53; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:A; Age_Diag:53; Gender:F; DFS_Time:14.53; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: T656A

description: Location: Left; DukesStage: A; Age_Diag: 56; Gender: F; DFS_Time: 119.21; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:A; Age_Diag:56; Gender:F; DFS_Time:119.21; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: Human Cord Blood CD34+ Cells_1

status: Public on Jan 05 2010

city: New York

first: Shahin

last: Rafii

state: NY

address: 1300 York Avenue

country: USA

institute: Weill Cornell Medical College

hyb_protocol: Fragmented cRNA was hybridized to the gene chips, washed, and stained with streptavidin phycoerythrin.

scan_protocol: The probe arrays were scanned with the Genechip System confocal scanner.

data_processing: Affymetrix Microarray suite 5.0 was used to analyze the data using default settings. Raw values with standard error between biological duplicates; cutoff = minimal expression 100 in at least one group.

label: Biotin

source_name: isolated and Human Cord Blood CD34+ Cells

label_protocol: The Superscript choice kit (Invitrogen, Carlsbad,CA) was used to make cDNA with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. The biotin labeled cRNA was made by in vitro transcription (Enzo Diagnostics).

extract_protocol: The protocol used to extract RNA was according to Manufacturers specifications QIAGEN RNeasy kit.

tag: developmental stage

value: mature

tag: cell type

value: Cord Blood CD34+ Cells


title: Day 24 hESC ECs_2

description: Phase 2 VPrGFP+SB_2

source_name: purified hESC-derived ECs isolated at day 14 of differentiation and cultured for an additional 10 days in the presence of TGFbeta inhibition

value: embroynic

value: hESC-derived Endothelial Cells

tag: genome/variation

value: EC-specific VE-cadherin promoter driving GFP (hVPr-GFP)


title: Human Umbilical Vein ECs_1

source_name: Human Umbilical Vein ECs cultured in serum free conditions for 48 hours

value: Umbilical Vein Endothelial Cells


title: Day 14 hESC ECs_1

description: Phase 1 VPrGFP_1

source_name: purified hESC-derived ECs isolated at day 14 of differentiation in the presence of TGFbeta inhibition


title: Human Umbilical Vein ECs_2


title: Day 14 hESC Ebs_2

description: d14 EB_2

source_name: hESC Ebs differentiated for 14 days in pro-angiogenic cytokines

value: Embryonic Stem Cells (hESCs)


title: astrocytomas at T3, biological rep5

city: Luoyang

first: Zhiqiang

last: Yao

state: Henan

address: No.288, Zhongzhou Road

department: Neurosurgery

country: China

institute: No.150 Military Central Hospital

description: gene expression data from WHO grade  Ⅲ astrocytomas pathological resected tissues

hyb_protocol: Carry out the hybridization process in a affymetrix  hybridazaiton Oven 640 ,P/N28320.

scan_protocol: Use Affymetrix GeneChip  Scaner 3000 controlled by Affymetrix Microarray Suit or GCOS to aquire the hybridization image.

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.

source_name: anaplastic astrocytomas (WHO grade Ⅲ)

label_protocol: Use One-Cycle Target Labeling and Control Reagents, Affymetrix, P/N 900493 to label the 3' termini of the fragmentation products.

tag: sex

value: M

value: anaplastic astrocytomas

tag: grade

value: WHO grade Ⅲ


title: Day 14 hESC ECs_2

description: Phase 1 VPrGFP_2


title: Human Umbilical Vein Smooth Muscle Cells_1

source_name: Human Umbilical Vein Smooth Muscle Cells cultured in serum free conditions for 48 hours


title: Day 24 hESC ECs_1

description: Phase 2 VPrGFP+SB_1


title: Human Umbilical Vein Smooth Muscle Cells_2


title: astrocytomas at T4, biological rep1

description: gene expression data from WHO grade  Ⅳ astrocytomas pathological resected tissues

source_name: Glioblastoma multiforme (GBM) glioblastomas (WHO grade Ⅳ)

value: Glioblastoma multiforme (GBM glioblastomas)

value: WHO grade Ⅳ


title: Human Cord Blood CD34+ Cells_2


title: Day 14 hESC Ebs_1

description: d14 EB_1


title: astrocytomas at T4, biological rep5


title: astrocytomas at T4, biological rep2


title: astrocytomas at T4, biological rep3


title: astrocytomas at T3, biological rep3


title: astrocytomas at T3, biological rep2

value: F


title: astrocytomas at T2, biological rep2

description: gene expression data from WHO grade Ⅱ astrocytomas pathological resected tissues

source_name: diffusely infiltrating astrocytic gliomas (WHO grade Ⅱ)

value: WHO grade Ⅱ


title: astrocytomas at T4, biological rep4


title: astrocytomas at T3, biological rep1


title: astrocytomas at T3, biological rep4


title: astrocytomas at T2, biological rep4

value: diffusely infiltrating astrocytic gliomas


title: astrocytomas at T2, biological rep1


title: astrocytomas at T2, biological rep3


title: astrocytomas at T1, biological rep2

description: gene expression data from WHO grade Ⅰ astrocytomas pathological resected tissues

source_name: Apilocytic astrocytoma (WHO grade Ⅰ), juvenile pilocytic astrocytoma, or cystic cerebellar astrocytoma

value: Apilocytic astrocytoma, juvenile pilocytic astrocytoma, or cystic cerebellar astrocytoma

value: WHO grade Ⅰ


title: astrocytomas at T1, biological rep1


title: normal tissue,biological rep1

description: gene expression data from normal brain tissue

source_name: pooled normal brain tissue

value: pooled normal brain tissue


title: astrocytomas at T2, biological rep5


title: NZM15_siPAX3_30hrs_rep1

city: Dunedin

first: Aaron

last: Jeffs

address: PO Box 56

country: New Zealand

institute: University of Otago

description: Gene expression data from NZM15 metastatic melanoma cells treated with siRNA targeting PAX3

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45°C on U133 Plus 2.0 GeneChip arrays. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

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

data_processing: The data was processed with the ExpressionFileCreator module of GenePattern by using the RMA method with quantile normalization and background correction.

source_name: NZM15 metastatic melanoma cells treated with PAX3 siRNA

label_protocol: Biotinylated cRNA were prepared from 200 ng total RNA by using an Ambion MessageAmp Premiere kit according to the manufacturer's instructions.

extract_protocol: Trizol extraction and Qiagen RNeasy column purification according to the manufacturer's instructions.

treatment_protocol: Reverse transfection of siRNA with a final concentration of 10 nM was performed in a 24-well plate with 30,000 cells/well by using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer's instructions. PAX3 siRNA, Ambion ID#215907, sense, GCCGCAUCCUGAGAAGUAAtt, antisense, UUACUUCUCAGGAUGCGGCtg; MITF siRNA, Ambion ID#3816, sense,GGACAAUCACAACCUGAUUtt, antisense, AAUCAGGUUGUGAUUGUCCtt; GL2 luciferase siRNA, Dharmacon Research Inc, target sequence 5'-AACGUACGCGGAAUACUUCGA-3'. Transfection efficiency determined by using the fluorescently labelled luciferase control siRNA was >90%. RNA was isolated from siRNA-treated cells and media-only controls 30 hours post-transfection.

value: skin

tag: cell line

tag: tumour stage

value: metastatic melanoma

tag: tumour site

value: neck nodule

tag: treatment

value: PAX3 siRNA


title: FetalColon

city: Meguro-ku

first: Atsushi

last: Kaneda

state: Tokyo

address: 4-6-1 Komaba

department: RCAST

country: Japan

institute: The University of Tokyo

description: Stratagene, cat#738009, lot#0610532

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix GCOS was used with target intensity=100.

source_name: fetal colon

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Total RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).

value: fetal colon


title: NZM15_media_control_30hrs_rep1

status: Public on Jan 02 2010

description: Gene expression data from untreated NZM15 metastatic melanoma cells

source_name: NZM15 metastatic melanoma cells media-only control

value: media-only control


title: HCT116_aza3_tsa300

description: Treated with 3uM 5-aza-2-deoxycytidine and 300 nM trichostatin A

source_name: Colon cancer cell line


title: SW480_aza3_tsa300


title: NZM15_siMITF_30hrs_rep1

description: Gene expression data from NZM15 metastatic melanoma cells treated with siRNA targeting MITF

source_name: NZM15 metastatic melanoma cells treated with MITF siRNA

value: MITF siRNA


title: NZM12_siMITF_30hrs_rep1

description: Gene expression data from NZM12 metastatic melanoma cells treated with siRNA targeting MITF

source_name: NZM12 metastatic melanoma cells treated with MITF siRNA

value: small intestine


title: NZM12_negative_control_30hrs_rep1

description: Gene expression data from NZM12 metastatic melanoma cells treated with non-targeting negative control siRNA (luciferase)

source_name: NZM12 metastatic melanoma cells treated with luciferase negative control siRNA

value: luciferase siRNA negative control


title: HCT116_aza0_tsa0

description: No treatment with 5-aza-2-deoxycytidine and trichostatin A


title: Drosophila OSS cells_1

status: Public on Jan 04 2010

first: Nicolas

last: Robine

address: 430, East 67th Street, RRL 517

department: Developmental Biology

institute: Sloan-Kettering Institute

description:
OSS cells are a stable cell line derived from follicular stem cells of the Drosophila ovary. The cells express the Fas III gene as a marker of follicle cells, and are described in Niki et. al., Proc Natl Acad Sci USA 2006 Oct 31;103(44): 16325-30.
CEL and DAT files were outputed from scanning and utilized in custom analysis scripts

hyb_protocol: Hybridization on the Affymetrix Fluidics 450 system was performed with the standard protocol #FS450_0002 as detailed in the program software.

scan_protocol: Scanning was performed on the GeneChip ® Scanner 3000 using the preset pixel value and resolution parameters defined in the scanner.

data_processing: Array files were processed with Bioconductor scripts in the R statistical and graphing package.

organism: Drosophila melanogaster

source_name: OSS cells

label_protocol: 10 ug of total RNA from each sample was converted to cDNA and then to biotinylated cRNA with the One-Cycle Target Labeling protocol as detailed in the Affymetrix manual for GeneChip® Eukaryotic Labeling Assays for Expression Analysis.

growth_protocol: Cells were cultured in 6 well plates, split every 3 days 1:3,  and were cultured in Shield and Sang's M3 media supplemented with 10% fetal bovine serum, 1ug/ml insulin, 60ug/ml glutathione, and 5% fly extract.

extract_protocol: Near-confluent wells washed once with 1XPBS, then subject to Trizol extraction to obtain total RNA.

treatment_protocol: Cells grown in exponential phase in standard medium, no additional treatment

value: OSS

value: follicular stem cell


title: Drosophila OSS cells_2


title: PCSC-2 sphere biol repl 1

status: Public on Jan 01 2010

city: Frederick

first: Maria

middle: Ana

last: Duhagon

state: MD

address: 1050 Boyles St.

department: Laboratory of Cancer Prevention

institute: NCI-Frederick

description: Gene expression data from parental-adherent considered as cells commited to differentiation

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Array; Affymetrix (p/n 900467). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip scanner 3000.

data_processing: Data were collected using Affymetrix GCOS software, normalized using the GC-RMA algorithm and log 2 transformed.

source_name: PCSC-2 spheres 7 days in SCM-1% KO

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA using Affymetrix 3' One Cycle Target Labeling kit following manufacturer’s instructions.

growth_protocol: Spheres were grown in SCM medium (DMEM:F12 plus 10 ng/mL bFGF, 20 ng/mL EGF, 5 mg/mL insulin, and 0.4% BSA) supplemented with 1% KO serum replacement (Invitrogen/Gibco, p/n 10828-028) at a density of 2500 cells/mL. Parental cell line was grown in RPMI-1640-10% FBS. Regular tissue culture flask treated to improve cell attachment were used in both cases.

extract_protocol: Total RNA extracted using RNeasy kit from Qiagen

treatment_protocol: Spheres were grown from a single cell suspension of bulk PCSCS adherent cultures, washed three times in PBS and plated at low density in SCM-1%KO. The cultures were grown for 7 days and floating spheres were then isolated.

value: prostate cancer stem cell primary lines

tag: culture type

value: sphere


title: HCT116_aza3_tsa0

description: Treated with 3uM 5-aza-2-deoxycytidine and no trichostatin A


title: Drosophila OSS cells_3


title: NZM12_media_control_30hrs_rep1

description: Gene expression data from untreated NZM12 metastatic melanoma cells

source_name: NZM12 metastatic melanoma cells media-only control


title: NormalColon

description: Ambion, cat#7986, lot#071P10B

source_name: normal colon

value: adult normal colon


title: NZM15_negative_control_30hrs_rep1

description: Gene expression data from NZM15 metastatic melanoma cells treated with non-targeting negative control siRNA (luciferase)

source_name: NZM15 metastatic melanoma cells treated with luciferase negative control siRNA


title: PCSC-3 sphere biol repl 2

source_name: PCSC-3 spheres 7 days in SCM-1% KO


title: PCSC-3 sphere biol repl 1


title: NZM12_siPAX3_30hrs_rep1

description: Gene expression data from NZM12 metastatic melanoma cells treated with siRNA targeting PAX3

source_name: NZM12 metastatic melanoma cells treated with PAX3 siRNA


title: PCSC-2 sphere biol repl 2


title: SW480_aza3_tsa0


title: SW480_aza0_tsa0


title: PCSC-1 sphere biol repl 1

source_name: PCSC-1 spheres 7 days in SCM-1% KO


title: PCSC-2 parental biol repl 2

source_name: PCSC-2 parental cultures in PCSCs medium

value: adherent


title: PCSC-1 sphere biol repl 2


title: PCSC-3 parental biol repl 2

source_name: PCSC-3 parental cultures in PCSCs medium


title: PCSC-3 parental biol repl 1


title: WI-38 cells, at 24 h after exposure to 0.1 uM BPDE, biological rep1

city: Stockholm

first: Kristian

last: Dreij

address: Nobels väg 13

department: Environmental Medicine

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from WI-38 cells exposed to DMSO vehicle control

hyb_protocol: Standard Affymetrix Protocols

scan_protocol: The microarrays were scanned using a GeneChip® Scanner 3000 (Affymetrix) and subsequent image analysis was performed using Affymetrix GCOS software using standard Affymetrix protocols.

data_processing: The resulting .cel files were normalized with the robust multichip average (RMA) method.

source_name: WI-38 cells exposed to 0.1 uM BPDE for 24 h

label_protocol: Standard Affymetrix Protocols

extract_protocol: Total cellular RNA was prepared using the RNeasy Mini Kit from (Qiagen), treated with TURBO DNA-freeTM (Ambion) and RNA integrity analyzed using Agilent Bioanalyzer 2100.

value: Normal human diploid WI-38 lung fibroblasts, CCL-75(TM), passage 7-12.


title: WI-38 cells, at 24 h after exposure to DMSO vehicle control, biological rep1

source_name: WI-38 cells exposed to DMSO vehicle control for 24 h


title: WI-38 cells, at 24 h after exposure to DMSO vehicle control, biological rep4


title: PCSC-1 parental biol repl 2

source_name: PCSC-1 parental cultures in PCSCs medium


title: PCSC-2 parental biol repl 1


title: WI-38 cells, at 24 h after exposure to 0.1 uM BPDE, biological rep3


title: WI-38 cells, at 24 h after exposure to 1 uM BPDE, biological rep1

description: Gene expression data from WI-38 cells exposed to BPDE

source_name: WI-38 cells exposed to 1 uM BPDE for 24 h


title: WI-38 cells, at 24 h after exposure to 0.5 uM BPDE, biological rep2

source_name: WI-38 cells exposed to 0.5 uM BPDE for 24 h


title: WI-38 cells, at 24 h after exposure to 0.5 uM BPDE, biological rep3


title: WI-38 cells, at 24 h after exposure to DMSO vehicle control, biological rep2


title: WI-38 cells, at 24 h after exposure to 1 uM BPDE, biological rep3


title: WI-38 cells, at 24 h after exposure to DMSO vehicle control, biological rep3


title: WI-38 cells, at 24 h after exposure to 1 uM BPDE, biological rep2


title: PCSC-1 parental biol repl 1


title: WI-38 cells, at 24 h after exposure to 1 uM BPDE, biological rep4


title: WI-38 cells, at 24 h after exposure to 0.5 uM BPDE, biological rep1


title: WI-38 cells, at 24 h after exposure to 0.1 uM BPDE, biological rep2


title: PMN_control_4_STAT60

city: Hamilton

first: Addie

last: Whitney

state: MT

address: 903 S 4th St

department: LHBP

institute: NIH/NIAID/RML

description: control PMNs

hyb_protocol: cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix).  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix scanner.

data_processing: Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips.  All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files.  A pivot table with all samples was created including calls, call p-value and signal intensity for each gene.  Statistical and quality filters were applied as follows.  The average scaled expression must be at least 100 in at least one group.

source_name: polymorphonuclear leukocytes, control, patient 4, STAT60 RNA isolation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.

treatment_protocol: Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.

tag: disease state

value: control

tag: patient

value: polymorphonuclear leukocytes

tag: rna isolation method


title: PMN_test_5_STAT60

description: test PMNs

source_name: polymorphonuclear leukocytes, test, patient 5, STAT60 RNA isolation

value: autosomal dominant monocytopenia


title: PMN_control_3_STAT60

description: control PMNs

source_name: polymorphonuclear leukocytes, control, patient 3, STAT60 RNA isolation


title: PMN_test_3_STAT60

description: test PMNs

source_name: polymorphonuclear leukocytes, test, patient 3, STAT60 RNA isolation


title: PMN_test_1_STAT60

description: test PMNs

source_name: polymorphonuclear leukocytes, test, patient 1, STAT60 RNA isolation


title: PMN_test_4_STAT60

description: test PMNs

source_name: polymorphonuclear leukocytes, test, patient 4, STAT60 RNA isolation


title: PMN_test_2_STAT60

description: test PMNs

source_name: polymorphonuclear leukocytes, test, patient 2, STAT60 RNA isolation


title: PMN_control_5_STAT60

description: control PMNs

source_name: polymorphonuclear leukocytes, control, patient 5, STAT60 RNA isolation


title: PMN_control_7_RNeasy

description: control PMNs

data_processing: Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips.  All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files.  A pivot table with all samples was created including calls, call p-value and signal intensity for each gene.  Statistical and quality filters were applied as follows.  The average scaled expression must be at least 100 in at least one group.  For probe sets more highly expressed in healthy control samples, the call must be present/marginal in at least 5 of 7 samples; for probe sets more highly expressed in test samples, the call must be present/marginal in at least 2 of 3 samples.  At least a 1.5-fold change and a T test p-value of less than 0.05 are required.

source_name: polymorphonuclear leukocytes, control, patient 7, RNeasy RNA isolation

value: RNeasy


title: PMN_control_1_STAT60

description: control PMNs

source_name: polymorphonuclear leukocytes, control, patient 1, STAT60 RNA isolation


title: PMN_control_4_RNeasy

description: control PMNs

source_name: polymorphonuclear leukocytes, control, patient 4, RNeasy RNA isolation


title: PMN_test_2_RNeasy

description: test PMNs

source_name: polymorphonuclear leukocytes, test, patient 2, RNeasy RNA isolation


title: PMN_control_5_RNeasy

description: control PMNs

source_name: polymorphonuclear leukocytes, control, patient 5, RNeasy RNA isolation


title: PMN_control_2_STAT60

description: control PMNs

source_name: polymorphonuclear leukocytes, control, patient 2, STAT60 RNA isolation


title: PMN_test_1_RNeasy

description: test PMNs

source_name: polymorphonuclear leukocytes, test, patient 1, RNeasy RNA isolation


title: PMN_control_2_RNeasy

description: control PMNs

source_name: polymorphonuclear leukocytes, control, patient 2, RNeasy RNA isolation


title: PMN_test_3_RNeasy

description: test PMNs

source_name: polymorphonuclear leukocytes, test, patient 3, RNeasy RNA isolation


title: PMN_control_6_RNeasy

description: control PMNs

source_name: polymorphonuclear leukocytes, control, patient 6, RNeasy RNA isolation


title: PMN_control_1_RNeasy

description: control PMNs

source_name: polymorphonuclear leukocytes, control, patient 1, RNeasy RNA isolation


title: PMN_control_3_RNeasy

description: control PMNs

source_name: polymorphonuclear leukocytes, control, patient 3, RNeasy RNA isolation


title: AML with normal karyotype #169

first: Hans-Ulrich

last: Klein

department: Neurology

institute: Columbia University Medical Center

description: MUC

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.20.2) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)

source_name: mononuclear cells from bone marrow

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

extract_protocol: The total RNA was purified either with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) or with TRIzol-based protocols.

treatment_protocol: Samples are from untreated patients (de novo AML)

value: positive

value: negative

tag: cebpa

tag: diagnosis

value: AML with normal karyotype

tag: gender

value: female

tag: specimen type

value: Bone Marrow

tag: blast cell percentage

value: de novo AML


title: AML with normal karyotype #174

description: MUC

tag: age


title: AML with normal karyotype #172

description: MUC

value: male


title: AML with normal karyotype #171

description: MUC


title: AML with normal karyotype #159

description: MUC

value: t-AML


title: AML with normal karyotype #164

description: MUC


title: AML with normal karyotype #161

description: MUC


title: AML with normal karyotype #160

description: MUC


title: AML with normal karyotype #150

description: MUC


title: AML with normal karyotype #173

description: MUC


title: AML with normal karyotype #154

description: MUC


title: AML with normal karyotype #155

description: MUC


title: AML with normal karyotype #168

description: MUC


title: AML with normal karyotype #170

description: MUC

value: S-AML


title: AML with normal karyotype #156

description: MUC


title: AML with normal karyotype #158

description: MUC


title: AML with normal karyotype #151

description: MUC


title: AML with normal karyotype #149

description: MUC


title: AML with normal karyotype #167

description: MUC


title: AML with normal karyotype #165

description: MUC


title: AML with normal karyotype #148

description: MUC


title: AML with normal karyotype #153

description: MUC


title: AML with normal karyotype #157

description: MUC


title: AML with normal karyotype #163

description: MUC


title: AML with normal karyotype #162

description: MUC


title: AML with normal karyotype #166

description: MUC


title: AML with normal karyotype #152

description: MUC


title: AML with normal karyotype #147

description: MUC


title: AML with normal karyotype #146

description: MUC


title: AML with normal karyotype #141

description: MUC


title: AML with normal karyotype #139

description: MUC


title: AML with normal karyotype #143

description: MUC


title: AML with normal karyotype #138

description: MUC


title: AML with normal karyotype #142

description: MUC


title: AML with normal karyotype #140

description: MUC

value: Peripheral Blood


title: AML with normal karyotype #144

description: MUC


title: AML with normal karyotype #127

description: MUC


title: AML with normal karyotype #145

description: MUC


title: AML with normal karyotype #135

description: MUC


title: AML with normal karyotype #132

description: MUC


title: AML with normal karyotype #90

description: MUC


title: Sample 40 - not-AML-like

city: Padova

first: Andrea

last: Zangrando

address: Via Giustiniani, 3

department: Woman and Child's Health

country: Italy

institute: University of Padova

description: Gene expression data from juvenile myelomonocytic leukemia samples at diagnosis

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.

scan_protocol: GeneChips were scanned using the Scan GCS3000Dx.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org]

source_name: stored and frozen Bone Marrow cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA purification using selective binding columns

treatment_protocol: stored, frozen Bone Marrow or Peripheral Blood cells

tag: disease

value: JMML

tag: tissue


title: Sample 30 - not-AML-like


title: Sample 39 - not-AML-like


title: Sample 33 - not-AML-like


title: Sample 32 - AML-like


title: Sample 38 - AML-like


title: Sample 37 - not-AML-like


title: Sample 28 - AML-like


title: Sample 29 - AML-like

source_name: stored and frozen Peripheral Blood cells


title: Sample 26 - AML-like


title: Sample 31 - AML-like


title: Sample 36 - not-AML-like


title: Sample 27 - AML-like


title: Sample 35 - AML-like


title: Sample 24 - AML-like


title: Sample 23 - not-AML-like


title: Sample 34 - AML-like


title: Sample 20 - not-AML-like


title: Sample 15 - not-AML-like


title: Sample 16 - not-AML-like


title: Sample 18 - not-AML-like


title: Sample 22 - not-AML-like


title: Sample 11 - AML-like


title: Sample 13 - not-AML-like


title: Sample 14 - not-AML-like


title: Sample 17 - not-AML-like


title: Sample 12 - AML-like


title: Sample 19 - not-AML-like


title: Sample 25 - AML-like


title: Sample 9 - not-AML-like


title: Sample 7 - AML-like


title: Sample 4 - AML-like


title: Sample 10 - not-AML-like


title: Sample 3 - AML-like


title: Sample 5 - AML-like


title: Sample 1 - AML-like


title: Sample 2 - AML-like


title: Sample 6 - AML-like


title: Sample 8 - not-AML-like


title: Sample 21 - not-AML-like


title: Validation Set Responder 15

city: Portland

first: Michael

last: Deininger

state: OR

address: 3181 SW Sam Jackson Park Rd

institute: OHSU

description: Validation Set Responder 15

hyb_protocol: Following successful amplification, 5μg of labelled target cRNA was hybridized to HG-U133 Plus 2.0 GeneChip arrays (Affymetrix).

scan_protocol: Arrays were scanned using a laser confocal scanner (Agilent) and the image processing and expression analysis were performed using Affymetrix GCOS v1.2 software.

data_processing: QA/QC was performed in the R/Bioconductor Framework. Normalization was done using the RMA algorithm (PM only, model-based background, quantile normalization and median polish)

source_name: CML patient with a complete cytogenetic response (CCyR)  after 12 months of imatinib therapy

label_protocol: To generate sufficient RNA for microarrray hybridization we used the GeneChip® Eukaryotic Small Sample Target Labeling Assay Version II (Affymetrix, Santa Clara, CA), with adjustments for the lower than recommended input of starting RNA (5 to 10ng instead of 20-100 ng).

growth_protocol: Not applicable

extract_protocol: CD34+ cells were separated from mononuclear cells (MNC). RNA extraction was performed with the PicoPure™ RNA Isolation Kit (Arcturus) once all cell sorting had been completed. Samples were quantified using the NanoDrop® ND-1000 UV-Vis spectrophotometer (NanoDrop Technologies,Wilmington, DE) and the quality of the RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Samples were collected prior to starting imatinib therapy

tag: CD34+ cells were separated from freshly isolated MNC using MiniMACS columns (Miltenyi Biotec, Bergisch-Gladbach, Germany), following the instructions of the manufacturer.


title: Validation Set Responder 16

description: Validation Set Responder 16


title: Validation Set Responder 14

description: Validation Set Responder 14


title: Validation Set Responder 17

description: Validation Set Responder 17


title: Validation Set Responder 12

description: Validation Set Responder 12


title: Validation Set Responder 13

description: Validation Set Responder 13


title: Validation Set Responder 9

description: Validation Set Responder 9


title: Validation Set Responder 10

description: Validation Set Responder 10


title: Validation Set Responder 5

description: Validation Set Responder 5


title: Validation Set Responder 6

description: Validation Set Responder 6


title: Validation Set Responder 8

description: Validation Set Responder 8


title: Validation Set Responder 11

description: Validation Set Responder 11


title: Validation Set Responder 7

description: Validation Set Responder 7


title: Validation Set Responder 1

description: Validation Set Responder 1


title: Validation Set NonResponder 2

description: Validation Set NonResponder 2

source_name: CML patient with >65% Ph-positive metaphases after 12 months of imatinib therapy


title: Validation Set NonResponder 4

description: Validation Set NonResponder 4


title: Validation Set NonResponder 5

description: Validation Set NonResponder 5


title: Training Set Responder 21

description: Traiing Set Responder 21

tag: CD34+ cells were sorted from cryopreserved MNC by a BD FACSAria™ (BD Biosciences).


title: Validation Set NonResponder 3

description: Validation Set NonResponder 3


title: Validation Set Responder 3

description: Validation Set Responder 3


title: Validation Set Responder 2

description: Validation Set Responder 2


title: Validation Set NonResponder 1

description: Validation Set NonResponder 1


title: Training Set Responder 22

description: Traiing Set Responder 22


title: AML with normal karyotype #123

description: MUC


title: Validation Set Responder 4

description: Validation Set Responder 4


title: Training Set Responder 19

description: Traiing Set Responder 19


title: Training Set Responder 23

description: Traiing Set Responder 23


title: Training Set Responder 24

description: Traiing Set Responder 24


title: Training Set Responder 17

description: Traiing Set Responder 17


title: Training Set Responder 16

description: Traiing Set Responder 16


title: Training Set Responder 18

description: Traiing Set Responder 18


title: Training Set Responder 13

description: Traiing Set Responder 13


title: Training Set Responder 11

description: Traiing Set Responder 11


title: Training Set Responder 15

description: Traiing Set Responder 15


title: Training Set Responder 6

description: Traiing Set Responder 6


title: Training Set Responder 10

description: Traiing Set Responder 10


title: Training Set Responder 9

description: Traiing Set Responder 9


title: Training Set Responder 8

description: Traiing Set Responder 8


title: Training Set Responder 4

description: Traiing Set Responder 4


title: Training Set Responder 14

description: Traiing Set Responder 14


title: Training Set Responder 3

description: Traiing Set Responder 3


title: Training Set Responder 1

description: Traiing Set Responder 1


title: Validation Set NonResponder 6

description: Validation Set NonResponder 6


title: Training Set NonResponder 10

description: Training Set NonResponder 10


title: Training Set Responder 5

description: Traiing Set Responder 5


title: Training Set NonResponder 5

description: Training Set NonResponder 5


title: Training Set NonResponder 8

description: Training Set NonResponder 8


title: Training Set NonResponder 3

description: Training Set NonResponder 3


title: Training Set NonResponder 6

description: Training Set NonResponder 6


title: Training Set NonResponder 7

description: Training Set NonResponder 7


title: Training Set NonResponder 4

description: Training Set NonResponder 4


title: Training Set NonResponder 9

description: Training Set NonResponder 9


title: Training Set NonResponder 12

description: Training Set NonResponder 12


title: Training Set Responder 7

description: Traiing Set Responder 7


title: Training Set Responder 12

description: Traiing Set Responder 12


title: Training Set NonResponder 2

description: Training Set NonResponder 2


title: M07_anti-miR-125b_exp2

status: Public on Dec 29 2009

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

country: Germany

institute: Goehte University Frankfurt

description: Gene expression data from anti-miR-125b transfected M07 cells

hyb_protocol: The fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to MOE 430.2 chips overnight at 45°C. The chips were then transferred to a fluidics instrument that performs washes to remove cRNA that had not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured.

data_processing: The raw CEL files were imported into dChip and invariant-set normalized with dChip as described in the user's manual (http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm). After normalization, the model-based expression values were calculated by dChip and exported.

source_name: M07 cell line, anti-miR-125b, experiment 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: M07 and CMK cells were grown in RPMI +10%FCS +1%P/S. HSPCs were grown in StemSpan +IL3 +IL6 +FLT3 +SCF +TPO.

extract_protocol: Trizol extraction of total RNA followed by cleaning up using columns from the Promega SV total RNA isolation kit.

treatment_protocol: M07 and CMK cells were transfected with Cy3-labelled non-silencing olignucleotides or anti-miR-125b and sorted. HSPCs were retrovirally transduced on retronectin coated plates and sorted for GFP positive cells.

tag: cell line

tag: cell type

value: Megakaryoblastic leukemia cell line

tag: sirna

value: anti-miR-125b (Cy3 labelled)


title: CMK_anti-miR-125b_exp2

description: Gene expression data from anti-miR-125b transfected CMK cells

source_name: CMK cell line, anti-miR-125b, experiment 2

value: CMK

value: Down Syndrome megakaryoblastic leukemia cell line


title: Training Set Responder 2

description: Traiing Set Responder 2


title: CD34+-HSPCs_empty-vector-transduced

description: Gene expression data from empty vector transduced CD34+-HSPCs

source_name: CD34+-HSPCs, empty vector-transduced

value: CD34+/- Hematopoietic stem and progenitor cells

tag: genome/variation

value: transduced with empty MIGR1 retrovirus


title: CD34+-HSPCs_miR-125b-2-transduced

description: Gene expression data from miR-125b-2 transduced CD34+-HSPCs

source_name: CD34+-HSPCs, miR-125b-2-transduced

value: transduced with miR-125b-2 expressing retrovirus


title: M07_non-silencing_control_exp1

description: Gene expression data from non-silencing oligonucleotides transfected M07 cells

source_name: M07 cell line, non-silencing control, experiment 1

value: non-silencing control (Cy3 labelled)


title: Training Set NonResponder 1

description: Training Set NonResponder 1


title: M07_anti-miR-125b_exp1


title: M07_non-silencing_control_exp2


title: CMK_non-silencing_control_exp1

description: Gene expression data from non-silencing oligonucleotides transfected CMK cells

source_name: CMK cell line, non-silencing control, experiment 1


title: CMK_anti-miR-125b_exp1

source_name: CMK cell line, anti-miR-125b, experiment 1


title: Training Set NonResponder 11

description: Training Set NonResponder 11


title: SKBR3 p53i biological rep1

city: Rehovot

first: Perry

last: Stambolsky

address: Herzel 200

department: MCB

country: Israel

institute: Weizmann institute of science

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Hu133 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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 100.

source_name: SKBR3 cells knocked down for mutp53 expression

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

growth_protocol: SKBR3 breast cancer cells were maintained in RPMI-1640 medium supplemented with 10% charcoal stripped fetal calf serum (FCS) and antibiotics.

treatment_protocol: SKBR3  cells were transfected with siRNA oligonucleotides  ("Invitrogen") specific for p53  (p53i) or LacZ (LacZi) as negative control, using darmafect protocol. After 24h, 1alpha25(OH)2D3 (D3, 100nM) was added for for the time points indicated. Cells were harvested and RNA was extracted.

value: Breast carcinoma

tag: treatment group

value: untreated


title: SKBR3 LacZi nt biological rep2

source_name: SKBR3 control cells

value: LacZi


title: SKBR3 LacZi D3 50h

source_name: SKBR3 control treated with vitamin D3 for 50h

value: 1a25-vitamin D3 50 hrs


title: SKBR3 p53i D3 20h

source_name: SKBR3 cells knocked down for mutp53 expression, treated with vitamin D3 for 20h

value: 1a25-vitamin D3 20 hrs


title: SKBR3 p53i D3 50h

source_name: SKBR3 cells knocked down for mutp53 expression, treated with vitamin D3 for50h


title: SKBR3 p53Zi D3 8h

source_name: SKBR3 cells knocked down for mutp53 expression, treated with vitamin D3 for 8h

value: 1a25-vitamin D3 8 hrs


title: SKBR3 p53i biological rep2


title: SKBR3 LacZi D3 8h

source_name: SKBR3 control treated with vitamin D3 for 8h


title: SKBR3 LacZi D3 20h

source_name: SKBR3 control treated with vitamin D3 for 20h


status: Public on Dec 27 2009

city: Yokohama

first: Miyako

last: Kusano

state: Kanagawa

address: 1-7-22, Suehiro, Tsurumi

institute: RIKEN CSRS

description: Gene expression data from aerial parts of rice LBD37 FOX Arabidopsis plants.

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

source_name: Aerial parts of rice-Arabidopsis FOX line K19624, replicate 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 μg of total RNA.

extract_protocol: Total RNA was prepared using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: Homozygous line K19624, aerial parts, T3 generation, 18-day-old sample grown on solid MS- medium, one plant per batch was analyzed.


source_name: Aerial parts of the empty vector control (T3) for rice-Arabidopsis FOX lines, replicate 1

tag: Homozygous empty vector control (BIG), aerial parts, T3 generation, 18-day-old sample grown on solid MS- medium, one plant per batch was analyzed and taken as a control for K19624.


source_name: Aerial parts of the empty vector control (T3) for rice-Arabidopsis FOX lines, replicate 3


title: Training Set Responder 20

description: Traiing Set Responder 20

source_name: CML patient with a complete cytogenetic response (CCyR)  after 12 months of imatinib therapy


source_name: Aerial parts of the empty vector control for rice-Arabidopsis FOX lines, replicate 3

tag: The empty vector control (BIG), aerial parts, T2 generation, 18-day-old sample grown on solid MS- medium supplemented with 20 mg/l Hygromycin, one plant per batch was analyzed  and taken as a control for K16331.


source_name: Aerial parts of rice-Arabidopsis FOX line K19624, replicate 3


source_name: Aerial parts of rice-Arabidopsis FOX line K19624, replicate 1


source_name: Aerial parts of rice-Arabidopsis FOX line K16331, replicate 2

tag: Line K16331, aerial parts, T2 generation, 18-day-old sample grown on solid MS- medium supplemented with 20 mg/l Hygromycin, two plants were bulked as one batch.


title: CMK_non-silencing_control_exp2

source_name: CMK cell line, non-silencing control, experiment 2


title: SKBR3 LacZi nt biological rep1


title: NP cells neural sphere rep3

status: Public on Dec 23 2009

city: Athens

first: William

last: Kisaalita

state: GA

address: Dritmier Engineering Center

institute: University of Georgia

description: Gene expression data from cultured human neural progenitor cells

hyb_protocol: The standard hybridization protocol from Affymetrix was followed

scan_protocol: Arrays were scanned at high resolution using an Affymetrix GeneChip Scanner 3000 located at Medical College of Georgia Microarray Core Facility (Augusta, GA)

data_processing: The data were analyzed with Gene Expression Console using Affymetrix default Plier analysis settings and global scaling as normalization method.

source_name: Neural progenitor cells cultured as neural spheres

growth_protocol: Human Progenitor cells were cultured as standard protocol from Millipore

extract_protocol: Total RNA was extracted by RNAeasy mini kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: Differentiation Medium was used to replace ordinary growth medium to induce differentiation. The composition of both media can be found in millipore standard protocol

tag: Neural sphere cultured NP cells as in vivo surrogate


source_name: Aerial parts of rice-Arabidopsis FOX line K16331, replicate 3


title: NP cells neural sphere rep2


source_name: Aerial parts of the empty vector control (T3) for rice-Arabidopsis FOX lines, replicate 2


title: NP cells 2D after differentiation rep2

source_name: Neural progenitor cells 7 days into differentiation cultured on 2D petri dishes

tag: Neural progenitor cells cultured on 2D


title: NP cells 2D after differentiation rep3


title: NP cells 3D after differentiation rep1

source_name: Neural progenitor cells 7 days into differentiation cultured in 3D polystyrene scaffolds

tag: Neural progenitor cells cultured in 3D scaffolds


title: NP cells neural sphere rep4


source_name: Aerial parts of the empty vector control for rice-Arabidopsis FOX lines, replicate 2

tag: The empty vector control (BIG), aerial parts, 18-day-old sample grown on solid MS- medium supplemented with 20 mg/l Hygromycin, one plant per batch was analyzed and taken as a control for K16331.


title: NP cells 3D after differentiation rep2


title: NP cells 3D after differentiation rep4


source_name: Aerial parts of the empty vector control for rice-Arabidopsis FOX lines, replicate 1


source_name: Aerial parts of rice-Arabidopsis FOX line K16331, replicate 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 µg of total RNA.


title: NP cells 2D before differentiation rep4

source_name: Neural progenitor cells without differentiation cultured on 2D petri dishes


title: NP cells 2D after differentiation rep1


title: NP cells 3D before differentiation rep2

source_name: Neural progenitor cells without differentiation cultured in 3D polystyrene scaffolds


title: NP cells 3D before differentiation rep1


title: NP cells 2D after differentiation rep4


title: NP cells 2D before differentiation rep3


title: NP cells 2D before differentiation rep1


title: NP cells 2D before differentiation rep2


title: NP cells neural sphere rep1


title: Sample 2 from patient 131, Affected site

status: Public on Dec 22 2009

first: Ryan

middle: T

last: Demmer

department: Epidemiology

institute: Columbia University

description: A total of 120 patients undergoing periodontal surgery contributed with a minimum of two interproximal gingival papillae (range 2-4) from a maxillary posterior. Prior to tissue harvesting, subgingival plaque samples were collected from the mesial and distal aspects of each papilla. Gingival tissue RNA was extracted, reverse-transcribed, labeled, and hybridized with whole-genome microarrays (310 in total)

hyb_protocol: According to the manufacturer's instructions.

data_processing: All CEL files in the series were processed using RMA in R using justRMA with default parameters.

source_name: Patient 131 gingival tissue sample collected as Affected

label_protocol: Synthesis of Biotin-Labeled cRNA was performed using the GeneChip Expression 3'-Amplification Reagents for IVT labeling kit (Affymetrix). The cRNA yield was determined spectrophotometrically at 260 nm. Finally, the cRNA was fragmented by incubation in fragmentation buffer  at 94 0C for 35 min and stored at ?80 0C until hybridizations.

extract_protocol: Gingival tissue specimens were homogenized in Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA collected in the upper aqueous phase was precipitated by mixing with isopropyl alcohol and additional centrifugation and washed in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions. The purified RNA was quantitated spectrophotometrically, and 7.5 micrograms of total RNA was reverse transcribed using GeneChip Expression 3' amplification one-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer's instructions.

treatment_protocol: After collection gingival tissue specimens were thoroughly rinsed with sterile normal saline solution and transferred into Eppendorf tubes containing 5 volumes of a RNA stabilization reagent (RNAlater, Ambion, Austin, TX, USA).  Specimens were stored in RNAlater overnight at 4.0 C and thereafter snap-frozen and stored in liquid nitrogen. All further processing occurred simultaneously for gingival biopsies originating from the same donor.

tag: gingival tissue phenotype

value: Diseased (BoP + interproximal PPD of>3 mm + concomitant CAL of>2 mm)

value: Gingival


title: Sample 2 from patient 123, Affected site

scan_protocol: According to the manufacturer's instructions.

source_name: Patient 123 gingival tissue sample collected as Affected

tag: tissue


title: Sample 2 from patient 125, Affected site

source_name: Patient 125 gingival tissue sample collected as Affected


title: Sample 1 from patient 131, Affected site


title: Sample 1 from patient 130, Affected site

source_name: Patient 130 gingival tissue sample collected as Affected


title: Sample 2 from patient 124, Affected site

source_name: Patient 124 gingival tissue sample collected as Affected


title: Sample 1 from patient 125, Affected site


title: Sample 2 from patient 126, Affected site

source_name: Patient 126 gingival tissue sample collected as Affected


title: Sample 1 from patient 121, Affected site

source_name: Patient 121 gingival tissue sample collected as Affected


title: Sample 2 from patient 121, Affected site


title: Sample 2 from patient 118, Affected site

source_name: Patient 118 gingival tissue sample collected as Affected


title: Sample 2 from patient 119, Affected site

source_name: Patient 119 gingival tissue sample collected as Affected


title: Sample 1 from patient 127, Affected site

source_name: Patient 127 gingival tissue sample collected as Affected


title: Sample 2 from patient 129, Affected site

source_name: Patient 129 gingival tissue sample collected as Affected


title: Sample 1 from patient 126, Affected site


title: Sample 1 from patient 120, Affected site

source_name: Patient 120 gingival tissue sample collected as Affected


title: Sample 1 from patient 124, Affected site


title: Sample 1 from patient 118, Affected site


title: Sample 2 from patient 127, Affected site


title: Sample 1 from patient 129, Affected site


title: Sample 2 from patient 120, Affected site


title: Sample 1 from patient 119, Affected site


title: Sample 1 from patient 123, Affected site


title: Sample 2 from patient 115, Affected site

source_name: Patient 115 gingival tissue sample collected as Affected


title: Sample 2 from patient 117, Affected site

source_name: Patient 117 gingival tissue sample collected as Affected


title: Sample 1 from patient 116, Affected site

source_name: Patient 116 gingival tissue sample collected as Affected


title: Sample 2 from patient 130, Affected site


title: Sample 2 from patient 116, Affected site


title: Sample 2 from patient 109, Affected site

source_name: Patient 109 gingival tissue sample collected as Affected


title: Sample 2 from patient 112, Affected site

source_name: Patient 112 gingival tissue sample collected as Affected


title: Sample 3 from patient 113, Unaffected site

source_name: Patient 113 gingival tissue sample collected as Unaffected

value: Healthy (no BoP + PPD of<5 mm + CAL of<3 2 mm


title: Sample 1 from patient 113, Affected site

source_name: Patient 113 gingival tissue sample collected as Affected


title: Sample 2 from patient 113, Affected site


title: Sample 1 from patient 112, Affected site


title: Sample 1 from patient 111, Affected site

source_name: Patient 111 gingival tissue sample collected as Affected


title: Sample 2 from patient 106, Affected site

source_name: Patient 106 gingival tissue sample collected as Affected


title: Sample 2 from patient 107, Affected site

source_name: Patient 107 gingival tissue sample collected as Affected


title: Sample 2 from patient 110, Affected site

source_name: Patient 110 gingival tissue sample collected as Affected


title: Sample 3 from patient 107, Unaffected site

source_name: Patient 107 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 115, Affected site


title: Sample 1 from patient 109, Affected site


title: Sample 2 from patient 111, Affected site


title: Sample 2 from patient 108, Affected site

source_name: Patient 108 gingival tissue sample collected as Affected


title: Sample 1 from patient 110, Affected site


title: Sample 1 from patient 108, Affected site


title: Sample 3 from patient 106, Unaffected site

source_name: Patient 106 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 107, Affected site


title: Sample 1 from patient 117, Affected site


title: Sample 2 from patient 104, Affected site

source_name: Patient 104 gingival tissue sample collected as Affected


title: Sample 1 from patient 105, Affected site

source_name: Patient 105 gingival tissue sample collected as Affected


title: Sample 1 from patient 106, Affected site


title: Sample 2 from patient 105, Affected site


title: Sample 1 from patient 104, Affected site


title: Sample 3 from patient 108, Unaffected site

source_name: Patient 108 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 102, Affected site

source_name: Patient 102 gingival tissue sample collected as Affected


title: Sample 1 from patient 102, Affected site


title: Sample 3 from patient 102, Unaffected site

source_name: Patient 102 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 100, Affected site

source_name: Patient 100 gingival tissue sample collected as Affected


title: Sample 3 from patient 98, Unaffected site

source_name: Patient 98 gingival tissue sample collected as Unaffected


title: Sample 3 from patient 101, Affected site

source_name: Patient 101 gingival tissue sample collected as Affected


title: Sample 2 from patient 100, Affected site


title: Sample 1 from patient 99, Affected site

source_name: Patient 99 gingival tissue sample collected as Affected


title: Sample 2 from patient 98, Affected site

source_name: Patient 98 gingival tissue sample collected as Affected


title: Sample 2 from patient 101, Affected site


title: Sample 2 from patient 92, Affected site

source_name: Patient 92 gingival tissue sample collected as Affected


title: Sample 1 from patient 92, Affected site


title: Sample 3 from patient 93, Unaffected site

source_name: Patient 93 gingival tissue sample collected as Unaffected


title: Sample 3 from patient 92, Unaffected site

source_name: Patient 92 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 93, Affected site

source_name: Patient 93 gingival tissue sample collected as Affected


title: Sample 3 from patient 91, Unaffected site

source_name: Patient 91 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 99, Affected site


title: Sample 3 from patient 95, Unaffected site

source_name: Patient 95 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 94, Affected site

source_name: Patient 94 gingival tissue sample collected as Affected


title: Sample 2 from patient 91, Affected site

source_name: Patient 91 gingival tissue sample collected as Affected


title: Sample 3 from patient 94, Unaffected site

source_name: Patient 94 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 95, Affected site

source_name: Patient 95 gingival tissue sample collected as Affected


title: Sample 1 from patient 95, Affected site


title: Sample 1 from patient 98, Affected site


title: Sample 2 from patient 93, Affected site


title: Sample 2 from patient 94, Affected site


title: Sample 2 from patient 90, Affected site

source_name: Patient 90 gingival tissue sample collected as Affected


title: NP cells 3D before differentiation rep4

source_name: Neural progenitor cells without differentiation cultured in 3D polystyrene scaffolds


title: Sample 3 from patient 90, Unaffected site

source_name: Patient 90 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 90, Affected site


title: Sample 1 from patient 91, Affected site


title: Sample 1 from patient 89, Affected site

source_name: Patient 89 gingival tissue sample collected as Affected


title: Sample 3 from patient 88, Unaffected site

source_name: Patient 88 gingival tissue sample collected as Unaffected


title: Sample 3 from patient 87, Unaffected site

source_name: Patient 87 gingival tissue sample collected as Unaffected


title: Sample 3 from patient 86, Unaffected site

source_name: Patient 86 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 89, Affected site


title: Sample 1 from patient 88, Affected site

source_name: Patient 88 gingival tissue sample collected as Affected


title: Sample 2 from patient 87, Affected site

source_name: Patient 87 gingival tissue sample collected as Affected


title: Sample 1 from patient 86, Affected site

source_name: Patient 86 gingival tissue sample collected as Affected


title: Sample 2 from patient 88, Affected site


title: Sample 1 from patient 84, Affected site

source_name: Patient 84 gingival tissue sample collected as Affected


title: Sample 1 from patient 83, Affected site

source_name: Patient 83 gingival tissue sample collected as Affected


title: Sample 2 from patient 85, Affected site

source_name: Patient 85 gingival tissue sample collected as Affected


title: Sample 2 from patient 83, Affected site


title: Sample 1 from patient 85, Affected site


title: Sample 1 from patient 87, Affected site


title: Sample 2 from patient 81, Affected site

source_name: Patient 81 gingival tissue sample collected as Affected


title: Sample 1 from patient 77, Affected site

source_name: Patient 77 gingival tissue sample collected as Affected


title: Sample 1 from patient 78, Affected site

source_name: Patient 78 gingival tissue sample collected as Affected


title: Sample 1 from patient 82, Affected site

source_name: Patient 82 gingival tissue sample collected as Affected


title: Sample 3 from patient 83, Unaffected site

source_name: Patient 83 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 80, Affected site

source_name: Patient 80 gingival tissue sample collected as Affected


title: Sample 1 from patient 80, Affected site


title: Sample 2 from patient 78, Affected site


title: Sample 2 from patient 77, Affected site


title: Sample 3 from patient 77, Unaffected site

source_name: Patient 77 gingival tissue sample collected as Unaffected


title: Sample 1 from patient 81, Affected site


title: Sample 3 from patient 76, Unaffected site

source_name: Patient 76 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 86, Affected site


title: Sample 3 from patient 78, Unaffected site

source_name: Patient 78 gingival tissue sample collected as Unaffected


title: Sample 2 from patient 75, Affected site

source_name: Patient 75 gingival tissue sample collected as Affected


title: Sample 1 from patient 76, Affected site

source_name: Patient 76 gingival tissue sample collected as Affected


title: Sample 2 from patient 71, Affected site

source_name: Patient 71 gingival tissue sample collected as Affected