title: 24_blood_pre

scan_protocol: Scanner: Axon4000B-2. Voltage: 500,325. Resolution (micrometers): 10.

source_name: 24_blood_pre(Blood taken pre treatment, ES-285 dose 256mg/2.)


title: 25_blood_pre_

status: Public on Apr 01 2009

type: RNA

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

description: 5ug of Cy3 labelled amplified sample was mixed with Cy5 labelled amplified human reference RNA, concentrated & amersham hyb buffer added. Slides were incubated at 42C for 3 days

hyb_protocol: Corresponding control and treated samples labelled with different fluorophores were combined in a 50 μl hybridisation mix (19 μl Microarray Hybridisation Solution purchased from GE Healthcare and 50% deionised formamide) and heated at 70°C for 2 min and then at 37°C for 10 min. Sample was pipetted onto a microarray slide and covered with a glass cover slip. A 150μl aliquot of 6 X SSPE was pipetted underneath the slide to prevent dehydration. The hybridisation chamber was sealed and incubated at 42°C for 72 h. Type 7* slides were washed three times in 4 X SSPE, 10 mM EDTA pH 8.0 as above, followed by a 10 s wash in 50% deionised formamide, 6 X SSPE, before a brief rinse in HPLC grade water and drying with nitrogen gas.

data_processing: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.

molecule: total RNA

organism: Homo sapiens

source_name: 25_blood_pre(Blood taken pre treatment, ES-285 dose 256mg/2.)

label_protocol: Total RNA (5 ug) was reversed transcribed into cDNA and fluorescently labelled with Cy3 or Cy5 mono-reactive dyes (GE, UK) using the Cyscribe Indirect cDNA Labelling Kit protocol (GE, UK) according to the manufacturer's instructions. After labelling, repetitive sequences within the cDNA samples were blocked with 16 ug Human Cot-1 DNA (Invitrogen, UK) to prevent non-specific sequences binding to the cDNA probes.

extract_protocol: RNA was extracted from whole blood using the PreAnalytiX PAXGene system according to the manufacturers instructions. The total RNA samples were then further purified using Qiagen RNeasy Cleanup, as manufacturers instructions.

tag: treatment

value: pre treatment

tag: sample tissue type

value: blood

source_name: Amplified Stratagene Human Reference(Stratagene Human Reference RNA amplified with Ambion MessageAmp II kit.)

extract_protocol: Universal Human total RNA Supplied By Stratagene    Centrifuge @ 12000g for 20min at 4C, Pipette out supernatant, add 200ul of 70% Ethanol, vortex and centrifuge @ 12000g for 20min. Pipette out supernatant and leave to air dry for 30 min. Add 200ul of RNAse free water.

value: Mixed Pool of Human Cell Lines


title: SF268_PI103_A_30min

status: Public on Apr 21 2009

description: 5ug of Cy5 labelled sample was mixed with Cy5 labelled control totalRNA,concentrated & amersham hyb buffer added. Slides were incubated at 42C for 3 days

scan_protocol: Scanner: Axon4000B-2. Voltage:550, 470. Resolution (micrometers): 10.

data_processing: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

source_name: SF268_PI103_A_30min(Brain Cancer Cell Line Treated with PI103)

extract_protocol: Total RNA was extracted from cells with the ABI PRISM™ 6100 Nucleic Acid PrepStation, using the RNA Cell method according to instructions from the manufacturer

tag: Cell Line

tag: Time Course

value: 30 minute

source_name: SF268_Control(Untreated tumour cell line SF268)


title: 22_skin_pre__

scan_protocol: Scanner: Axon4000B-2. Voltage: 475,350. Resolution (micrometers): 10.

source_name: 22_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 256mg/2.)

extract_protocol: Total RNA was isolated and purified from the Trizol fraction with the RNeasy Mini Kit (Qiagen Westburg bv., Leusden, The Netherlands).

value: skin


title: 24_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 515,325. Resolution (micrometers): 10.

source_name: 24_blood_post(Blood taken post treatment, ES-285 dose 256mg/2.)

value: post treatment


title: 26_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 490,330. Resolution (micrometers): 10.

source_name: 26_blood_post(Blood taken post treatment, ES-285 dose 256mg/2.)


title: 22_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 500,350. Resolution (micrometers): 10.

source_name: 22_skin_post(Skin Biopsy taken post treatment, ES-285 dose 256mg/2.)


title: HRCE-DS10666

status: Public on Nov 19 2009

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

hyb_protocol: Hybridizations were carried out according the manufacturer (Affymetrix) protocol

scan_protocol: Affymterix Gene Chip Scanner 3000

data_processing:
Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
Probe group file used for analysis: HuEx-1_0-st-v2.r2.pgf

label: biotin

source_name: human renal cortical epithelial cells

label_protocol: A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.

growth_protocol: Followed vendor recommendations for growth protocol/media

extract_protocol: At cell harvest, a subset of cells was stored at -20oC in RNALater. Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent).

treatment_protocol: not applicable

tag: cell type

value: human renal cortical epithelial cells

tag: term


title: 21_blood_pre_

scan_protocol: Scanner: Axon4000B-2. Voltage: 460,325. Resolution (micrometers): 10.

source_name: 21_blood_pre(Blood taken pre treatment, ES-285 dose 128mg/2.)


title: 20_blood_pre

description: 5ug of Cy3 labelled amplified sample was mixed with Cy5 labelled amplified human reference RNA, concentrated & amersham hyb buffer added. Slides were incubated at 42C for 3 days.

scan_protocol: Scanner: Axon4000B-2. Voltage: 480, 300. Resolution (micrometers): 10.

source_name: 20_blood_pre(Blood taken pre treatment, ES-285 dose 128mg/2.)


title: 05_blood_post

description: 5ug of Cy3 labelled amplified sample was mixed with Cy5 labelled amplified human reference RNA, concentrated & amersham hyb buffer added. Slides were left at 42C for 3 days.

scan_protocol: Scanner: Axon4000B-2. Voltage: 490, 360. Resolution (micrometers): 10.

source_name: 05_blood_post(Blood taken post treatment, ES-285 dose 8mg/2.)


title: 20_skin_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 450,325. Resolution (micrometers): 10.

source_name: 20_skin_post(skin biopsy taken post treatment, ES-285 dose 128mg/2.)


title: 21_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 400,350. Resolution (micrometers): 10.

source_name: 21_skin_post(Skin Biopsy taken post treatment, ES-285 dose 128mg/2.)


title: 20_skin_pre

scan_protocol: Scanner: Axon4000B-2. Voltage: 400,310. Resolution (micrometers): 10.

source_name: 20_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 128mg/2.)


title: 05_blood_pre_

source_name: 05_blood_pre(Blood taken pre treatment, ES-285 dose 8mg/2.)


title: 09_skin-pre__

scan_protocol: Scanner: Axon4000B-2. Voltage: 490, 380. Resolution (micrometers): 10.

source_name: 09_skin-pre(Skin Biopsy taken pre treatment, ES-285 dose 16mg/2.)


title: 11_skin_pre__

scan_protocol: Scanner: Axon4000B-2. Voltage: 500, 370. Resolution (micrometers): 10.

source_name: 11_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 16mg/2.)


title: 17_skin_pre__

scan_protocol: Scanner: Axon4000B-2. Voltage: 500, 390. Resolution (micrometers): 10.

source_name: 17_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 64mg/2.)

source_name: Amplified Stratagene Human Reference(Stratagene Human Reference RNA amplified with Ambion MessageAmp II kit.)


title: 21_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 460, 325. Resolution (micrometers): 10.

source_name: 21_blood_post(Blood taken post treatment, ES-285 dose 128mg/2.)


title: 09_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 530, 410. Resolution (micrometers): 10.

source_name: 09_skin_post(Skin Biopsy taken post treatment, ES-285 dose 816mg/2.)


title: 29_skin_post_

source_name: 29_skin_post(Skin Biopsy taken post treatment, ES-285 dose 200mg/2.)


title: 29_skin_pre__

scan_protocol: Scanner: Axon4000B-2. Voltage: 470, 360. Resolution (micrometers): 10.

source_name: 29_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 200mg/2.)


title: 27_skin_pre__

scan_protocol: Scanner: Axon4000B-2. Voltage: 470, 370. Resolution (micrometers): 10.

source_name: 27_skin_pre(Skin biopsy taken pre-treatment, ES-285 dose 200mg/m2)


title: 20_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 490, 325. Resolution (micrometers): 10.

source_name: 20_blood_post(Blood taken post treatment, ES-285 dose 128mg/2.)


title: 28_skin_pre__

source_name: 28_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 200mg/2.)


title: 15_blood_pre_

scan_protocol: Scanner: Axon4000B-2. Voltage: 500, 350. Resolution (micrometers): 10.

source_name: 15_blood_pre(Blood taken pre treatment, ES-285 dose 32mg/2.)


title: 29_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 500, 340. Resolution (micrometers): 10.

source_name: 29_blood_post(Blood taken post treatment, ES-285 dose 200mg/2.)


title: 15_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 500, 360. Resolution (micrometers): 10.

source_name: 15_blood_post(Blood taken post treatment, ES-285 dose 32mg/2.)


title: 11_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 500, 380. Resolution (micrometers): 10.

source_name: 11_skin_post(Skin Biopsy taken post treatment, ES-285 dose 16mg/2.)


title: 27_skin_post_

source_name: 27_skin_post(Skin biopsy taken post treatment, ES285 dose 200mg/m2)


title: 19_skin_pre__

scan_protocol: Scanner: Axon4000B-2. Voltage: 510, 357. Resolution (micrometers): 10.

source_name: 19_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 128mg/2.)


title: 17_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 490, 390. Resolution (micrometers): 10.

source_name: 17_skin_post(Skin Biopsy taken post treatment, ES-285 dose 64mg/2.)


title: 29_blood_pre_

source_name: 29_blood_pre(Blood taken pre treatment, ES-285 dose 200mg/2.)


title: 19_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 510, 420. Resolution (micrometers): 10.

source_name: 19_skin_post(Skin Biopsy taken post treatment, ES-285 dose 128mg/2.)


title: HeLa-S3-DS7930

scan_protocol: Affymterix Gene Chip Scanner 3000

source_name: cervical carcinoma

value: cervical carcinoma


title: 22_blood_pre

scan_protocol: Scanner: Axon4000B-2. Voltage: 450,350. Resolution (micrometers): 10.

source_name: 22_blood_pre(Blood taken pre treatment, ES-285 dose 256mg/2.)

source_name: Amplified Stratagene Human Reference(Stratagene Human Reference RNA amplified with Ambion MessageAmp II kit.)


title: 28_skin_post_

source_name: 28_skin_post(Skin Biopsy taken post treatment, ES-285 dose 200mg/2.)


title: 19_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 450, 330. Resolution (micrometers): 10.

source_name: 19_blood_post(Blood taken post treatment, ES-285 dose 128mg/2.)


title: 18_blood_pre_

scan_protocol: Scanner: Axon4000B-2. Voltage: 450, 320. Resolution (micrometers): 10.

source_name: 18_blood_pre(Blood taken pre treatment, ES-285 dose 64mg/2.)


title: 18_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 420, 310. Resolution (micrometers): 10.

source_name: 18_skin_post(Skin Biopsy taken post treatment, ES-285 dose 64mg/2.)


title: 17_blood_pre_

scan_protocol: Scanner: Axon4000B-2. Voltage: 460, 340. Resolution (micrometers): 10.

source_name: 17_blood_pre(Blood taken pre treatment, ES-285 dose 64mg/2.)


title: 27_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 460, 330. Resolution (micrometers): 10.

source_name: 27_blood_post(Blood taken post treatment, ES-285 dose 200mg/2.)


title: 21_skin_pre__

scan_protocol: Scanner: Axon4000B-2. Voltage: 475,325. Resolution (micrometers): 10.

source_name: 21_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 128mg/2.)


title: 17_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 490, 350. Resolution (micrometers): 10.

source_name: 17_blood_post(Blood taken post treatment, ES-285 dose 64mg/2)


title: 16_skin_pre__

scan_protocol: Scanner: Axon4000B-2. Voltage: 475, 375. Resolution (micrometers): 10.

source_name: 16_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 64mg/2.)


title: Caco-2-DS8235

source_name: colorectal adenocarcinoma

value: colorectal adenocarcinoma


title: 28_blood_pre_

scan_protocol: Scanner: Axon4000B-2. Voltage: 470, 330. Resolution (micrometers): 10.

source_name: 28_blood_pre(Blood taken pre treatment, ES-285 dose 200mg/2)


title: 14_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 625, 375. Resolution (micrometers): 10.

source_name: 14_skin_post(Skin Biopsy taken post treatment, ES-285 dose 32mg/2.)


title: 16_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 450, 360. Resolution (micrometers): 10.

source_name: 16_skin_post(Skin Biopsy taken post treatment, ES-285 dose 64mg/2.)


title: 19_blood_pre

scan_protocol: Scanner: Axon4000B-2. Voltage: 500, 380. Resolution (micrometers): 10.

source_name: 19_blood_pre(Blood taken pre treatment, ES-285 dose 128mg/2.)


title: 16_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 425, 325. Resolution (micrometers): 10.

source_name: 16_blood_post(Blood taken post treatment, ES-285 dose 64mg/2.)


title: 13_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 480, 370. Resolution (micrometers): 10.

source_name: 13_skin_post(Skin Biopsy taken post treatment, ES-285 dose 32mg/2.)


title: 14_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 500, 350. Resolution (micrometers): 10.

source_name: 14_blood_post(Blood taken post treatment, ES-285 dose 32mg/2.)

source_name: Amplified Stratagene Human Reference(Stratagene Human Reference RNA amplified with Ambion MessageAmp II kit.)


title: 15_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 550, 400. Resolution (micrometers): 10.

source_name: 15_skin_post(Skin Biopsy taken post treatment, ES-285 dose 32mg/2.)


title: 13_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 430, 320. Resolution (micrometers): 10.

source_name: 13_blood_post(Blood taken post treatment, ES-285 dose 32mg/2.)


title: 18_blood_post

source_name: 18_blood_post(Blood taken post treatment, ES-285 dose 64mg/2.)


title: 12_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 550, 375. Resolution (micrometers): 10.

source_name: 12_skin_post(Skin Biopsy taken post treatment, ES-285 dose 32mg/2.)


title: 16_blood_pre_

source_name: 16_blood_pre(Blood taken pre treatment, ES-285 dose 64mg/2.)


title: 14_blood_pre_

scan_protocol: Scanner: Axon4000B-2. Voltage: 450, 350. Resolution (micrometers): 10.

source_name: 14_blood_pre(Blood taken pre treatment, ES-285 dose 32mg/2.)


title: 15_skin_pre__

scan_protocol: Scanner: Axon4000B-2. Voltage: 470, 390. Resolution (micrometers): 10.

source_name: 15_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 32mg/2.)


title: 13_skin_pre__

scan_protocol: Scanner: Axon4000B-2. Voltage: 500, 425. Resolution (micrometers): 10.

source_name: 13_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 32mg/2.)


title: 18_skin_pre__

scan_protocol: Scanner: Axon4000B-2. Voltage: 480, 310. Resolution (micrometers): 10.

source_name: 18_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 64mg/2.)


title: 10_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 470, 350. Resolution (micrometers): 10.

source_name: 10_skin_post(Skin Biopsy taken post treatment, ES-285 dose 16mg/2.)


title: 12_skin_pre__

source_name: 12_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 32mg/2.)


title: 13_blood_pre_

source_name: 13_blood_pre(Blood taken pre treatment, ES-285 dose 32mg/2.)


title: 11_blood_pre_

source_name: 11_blood_pre(Blood taken pre treatment, ES-285 dose 16mg/2.)


title: 14_skin_pre__

source_name: 14_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 32mg/2.)


title: 12_blood_pre

source_name: 12_blood_pre(Blood taken pre treatment, ES-285 dose 32mg/2.)


title: 11_blood_post

source_name: 11_blood_post(Blood taken post treatment, ES-285 dose 16mg/2.)


title: 04_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 575, 300. Resolution (micrometers): 10.

source_name: 04_skin_post(Skin Biopsy taken post treatment, ES-285 dose 4mg/2.)

source_name: Amplified Stratagene Human Reference(Stratagene Human Reference RNA amplified with Ambion MessageAmp II kit.)


title: 07_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 485, 355. Resolution (micrometers): 10.

source_name: 07_skin_post(Skin Biopsy taken post treatment, ES-285 dose 8mg/2.)


title: 06_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 450, 320. Resolution (micrometers): 10.

source_name: 06_blood_post(Blood taken post treatment, ES-285 dose 8mg/2.)


title: 04_skin_pre__

scan_protocol: Scanner: Axon4000B-2. Voltage: 525, 310. Resolution (micrometers): 10.

source_name: 04_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 4mg/2.)


title: 06_blood_pre_

source_name: 06_blood_pre(Blood taken pre treatment, ES-285 dose 8mg/2.)


title: 05_skin_pre__

scan_protocol: Scanner: Axon4000B-2. Voltage: 500, 400. Resolution (micrometers): 10.

source_name: 05_skin_pre(Skin Biopsy taken post treatment, ES-285 dose 8mg/2.)


title: 27_blood_pre_

scan_protocol: Scanner: Axon4000B-2. Voltage: 450, 320. Resolution (micrometers): ?.

source_name: 27_blood_pre(Skin Biopsy taken pre treatment, ES-285 dose 200mg/2.)


title: 03_skin_pre__

scan_protocol: Scanner: Axon4000B-2. Voltage: 640, 440. Resolution (micrometers): 10.

source_name: 03_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 4mg/2.)


title: 09_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 460, 350. Resolution (micrometers): 10.

source_name: 09_blood_post(Blood taken post treatment, ES-285 dose 16mg/2.)


title: 04_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 460, 340. Resolution (micrometers): ?.

source_name: 04_blood_post(Blood taken post treatment, ES-285 dose 4mg/2.)


title: 04_blood_pre_

scan_protocol: Scanner: Axon4000B-2. Voltage: 500, 350. Resolution (micrometers): 10.

source_name: 04_blood_pre(Blood taken pre treatment, ES-285 dose 4mg/2.)


title: 09_blood_pre_

scan_protocol: Scanner: Axon4000B-2. Voltage: 470, 330. Resolution (micrometers): 10.

source_name: 09_blood_pre(Blood taken pre treatment, ES-285 dose 16mg/2.)


title: 08_blood_pre_

scan_protocol: Scanner: Axon4000B-2. Voltage: 480, 360. Resolution (micrometers): 10.

source_name: 08_blood_pre(Blood taken pre treatment, ES-285 dose 16mg/2.)


title: 07_skin_pre__

source_name: 07_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 8mg/2.)


title: 08_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 500, 360. Resolution (micrometers): 10.

source_name: 08_blood_post(Blood taken post treatment, ES-285 dose 16mg/2.)


title: 06_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 500, 325. Resolution (micrometers): 10.

source_name: 06_skin_post(Skin Biopsy taken post treatment, ES-285 dose 8mg/2.)


title: 07_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 480, 350. Resolution (micrometers): 10.

source_name: 07_blood_post(Blood taken post treatment, ES-285 dose 8mg/2.)


title: 05_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 425, 360. Resolution (micrometers): 10.

source_name: 05_skin_post(Skin Biopsy taken post treatment, ES-285 dose 8mg/2.)

source_name: Amplified Stratagene Human Reference(Stratagene Human Reference RNA amplified with Ambion MessageAmp II kit.)


title: 01_blood_pre_

scan_protocol: Scanner: Axon4000B-2. Voltage: 490, 340. Resolution (micrometers): 10.

source_name: 01_blood_pre(Blood taken pre treatment, ES-285 dose 4mg/2.)


title: 10_skin_pre__

scan_protocol: Scanner: Axon4000B-2. Voltage:550, 340. Resolution (micrometers): ?.

source_name: 10_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 16mg/2.)


title: 28_blood_post

source_name: 28_blood_post(Blood taken post treatment, ES-285 dose 200mg/2.)


title: 03_skin_post_

scan_protocol: Scanner: Axon4000B-2. Voltage: 650, 380. Resolution (micrometers): 10.

source_name: 03_skin_post(Skin Biopsy taken post treatment, ES-285 dose 4mg/2.)


title: 03_blood_post

scan_protocol: Scanner: Axon4000B-2. Voltage: 470, 340. Resolution (micrometers): 10.

source_name: 03_blood_post(Blood taken post treatment, ES-285 dose 4mg/2.)


title: 07_blood_pre_

source_name: 07_blood_pre(Blood taken pre treatment, ES-285 dose 8mg/2.)


title: 03_blood_pre_

scan_protocol: Scanner: Axon4000B-2. Voltage: 500, 340. Resolution (micrometers): 10.

source_name: 03_blood_pre(Blood taken pre treatment, ES-285 dose 4mg/2.)


title: 01_skin_pre__

scan_protocol: Scanner: Axon4000B-2. Voltage: 450, 375. Resolution (micrometers): 10.

source_name: 01_skin_pre(Skin Biopsy taken pre treatment, ES-285 dose 4mg/2.)


title: Mel CL 624.38 - mAdbID:64420

status: Public on Jul 22 2008

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 64420

hyb_protocol: Sample Hybrization Protocol Wash procedure: Washing: 1. Wash with 2x SSC + 0.1% SDS to remove coverslip. 2. Wash with 1x SSC for 1 min. 3. Wash with 0.2x SSC for 1 min. 4. Wash with 0.05x SSC for 10-20 seconds. 5. Centrifuge slide at 80-100 g for 3 min. Other: Hybridization: Combine Cy3 and Cy5 labeled target (adjust the color to purple) and complete dry the sample by speed vacuum . Add 37ul of the following mixture to the dried target (for 20x40mm slide): 1ul 50x Denhardt’s blocking solution (Sigma Cat# 2532) 1ul poly dA (8mg/ml Pharmacia Cat# 27-7988-01) 1ul yeast tRNA (4mg/ml Sigma Cat# R8759) 10ul Human Cot I DNA (1mg/ml Gibco BRL Cat# 15279-011) 3ul 20X SSC 1ul 10% SDS 20ul of DEPC H2O Heat for 2 min at 99oC and Cool to RT. Apply target mixture to array slide, add coverslip, place in humidified hyb chamber, and hybridize at 65oC over night.

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.04;; 4.84 Temperature: 27.7

data_processing:
BRBArrayTools
Calculation Method: Fluorescence intensities generated by Cy5 and Cy3 probes hybridized onto the microarray slides were scanned were scanned on a GenePix 4000 (Axon Instruments, Union City, CA) at variable PMT voltage to obtain maximal signal intensities with < 1% probe saturation. Data were uploaded to National Institute of Health, NCI/CCR µArray database (http://nciarray.nci.nih.gov). Raw data were retrieved in BRB-ArrayTools(http://linus.nci.nih.gov/BRBArrayTools.html) format for analysis and normalization. Following filter criteria was applied to the data set: 1. spots were excluded if intensity < 100, and spot size less than 25µm 2. genes were filtered out if >50% of experiment with missing data values. 3. log2 transformed data were normalized using lowess smoother, and intensity ratios were truncated if greater than 64. Transcriptional data were process by averaging results in replicate experiments for the same genes.Hierchical clustering analysis was performed on BRBArray tools using centered correlation as similarity metric and centroid linkage method: Cluster 3:0. Heat maps were generated using Eisen’s TreView Software.

label_protocol:
Cy5 Sample Labeling Protocol
Other: Target labeling by reverse transcription: 4ul First strand buffer 1ul dN6 primer (8ug/ul; Boehringer Mannheim Cat# 1034731 resuspended in 250ul DEPC H2O) 2ul 10X low T - dNTP (5mM A, C and GTP, 2mM dTTP) 2ul Cy-dUTP (1mM Cy5) 2ul 0.1 M DTT 1ul RNasin 3-6ug amplified mRNA in 7 ul DEPC H2O Mix well and heat to 65C for 5min then cool down to 42C. Add 1.5ul SSII and Incubate for 90 min at 42C. Add 2.5ul 500mM EDTA and heat to 65C for 1min. Add 5ul 1M NaOH and incubate at 65C for 15min to hydrolyze RNA. Add 12.5ul 1M Tris immediately to neutralize the pH. Add 35ul of 1xTE. Target clean up: Prepare Bio-6 column and run target solution through it. Collect flow through and add 200ul 1xTE. Concentrate target to ~20ul using a microcon YM-30 column (Millipore Cat# 42410).

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was isolated with RNeasy minikits (Qiagen, Germantown, MD) and amplified into anti-sense RNA as previously described (Wang,E., Miller,L., Ohnmacht,G.A., Liu,E. & Marincola,F.M.). High fidelity mRNA amplification for gene profiling using cDNA microarrays. Nature Biotech 17, 457-459; 2000).Quality of RNA was tested by Agilent technologies and spectophotometry (OD). For microarray analysis test samples were labeled with Cy5-dUTP (Amersham, Piscataway, NJ) while the reference sample (pooled normal donor PBMC) was labeled with Cy3-dUTP. Test-reference sample pairs were mixed and co-hybridized to 17K-cDNA microarrays generated in our lab (gal file http://nciarray.nci.nih.gov/gal_files/gal_custom_current.shtml, Hs-CCDTM17.5k-1px.gal

tag: Tissue

value: Skin

tag: Cell type

value: Allogeneic melanoma

tag: Disease state

value: Melanoma metastases

source_name: PBMC Pooled Donor Reference Sample

label_protocol:
Cy3 Sample Labeling Protocol
Other: Target labeling by reverse transcription: 4ul First strand buffer 1ul dN6 primer (8ug/ul; Boehringer Mannheim Cat# 1034731 resuspended in 250ul DEPC H2O) 2ul 10X low T - dNTP (5mM A, C and GTP, 2mM dTTP) 2ul Cy-dUTP (1mM Cy3) 2ul 0.1 M DTT 1ul RNasin 3-6ug amplified mRNA in 7 ul DEPC H2O Mix well and heat to 65C for 5min then cool down to 42C. Add 1.5ul SSII and Incubate for 90 min at 42C. Add 2.5ul 500mM EDTA and heat to 65C for 1min. Add 5ul 1M NaOH and incubate at 65C for 15min to hydrolyze RNA. Add 12.5ul 1M Tris immediately to neutralize the pH. Add 35ul of 1xTE. Target clean up: Prepare Bio-6 column and run target solution through it. Collect flow through and add 200ul 1xTE. Concentrate target to ~20ul using a microcon YM-30 column (Millipore Cat# 42410).

value: peripheral blood mononuclear cells


title: 01_skin_post_

source_name: 01_skin_post(Skin Biopsy taken post treatment, ES-285 dose 4mg/2.)


title: Mel CL 624.28 - repeat 1 - mAdbID:64416

description: mAdb experiment ID: 64416

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.1;; 5.31 Temperature: 29.96

source_name: Mel CL 624.28 - repeat 1


title: Mel 1858 Medi repeat 1 - mAdbID:64413

description: mAdb experiment ID: 64413

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.04;; 4.93 Temperature: 27.82

source_name: Mel 1858 Medi - repeat 1

value: MG melanoma


title: Mel 888 - repeat 1 - mAdbID:64417

description: mAdb experiment ID: 64417

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.09;; 5.4 Temperature: 29.44

source_name: Mel 888 - repeat 1


title: Mel CL 1195 - mAdbID:64419

description: mAdb experiment ID: 64419

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.03;; 5.22 Temperature: 27.36

source_name: Mel CL 1195


title: Mel 1858 Wash - repeat 1 - mAdbID:64414

description: mAdb experiment ID: 64414

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.1;; 5.34 Temperature: 29.87

source_name: Mel 1858 Wash - repeat 1


title: Mel 1290 p14 - mAdbID:64410

description: mAdb experiment ID: 64410

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.1;; 5.35 Temperature: 29.74


title: Mel 1290 p54 - mAdbID:64411

description: mAdb experiment ID: 64411

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.09;; 5.38 Temperature: 29.62


title: Mel 1858 Frag - repeat 1 - mAdbID:64412

description: mAdb experiment ID: 64412

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.04;; 5.02 Temperature: 28.37

source_name: Mel 1858 Frag - repeat 1


title: Mel 1858 Wash - repeat 2 - mAdbID:40506

description: mAdb experiment ID: 40506

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 100;; 100 LaserPower: 3.38;; 3.72 Temperature: 24.4

source_name: Mel 1858 Wash - repeat 2


title: Mel 888 - repeat 2 - mAdbID:40446

description: mAdb experiment ID: 40446

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 100;; 100 LaserPower: 3.39;; 3.73 Temperature: 25.69

source_name: Mel 888 - repeat 2


title: Mel CL 624.28 - repeat 2 - mAdbID:40436

description: mAdb experiment ID: 40436

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 100;; 100 LaserPower: 3.52;; 3.57 Temperature: 30.2

source_name: Mel CL 624.28 - repeat 2


title: Mel 1858 Frag - repeat 2 - mAdbID:40424

description: mAdb experiment ID: 40424

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 100;; 100 LaserPower: 3.53;; 3.57 Temperature: 30.29

source_name: Mel 1858 Frag - repeat 2


title: Mel 1936 Medi - mAdbID:64415

description: mAdb experiment ID: 64415

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.05;; 5.51 Temperature: 29.44

source_name: Mel 1936 Medi


title: Mel CL 526 - mAdbID:40433

description: mAdb experiment ID: 40433

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 100;; 100 LaserPower: 3.52;; 3.56 Temperature: 28.86

source_name: Mel CL 526


title: Mel 1858 Medi - repeat 2 - mAdbID:40427

description: mAdb experiment ID: 40427

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 100;; 100 LaserPower: 3.53;; 3.57 Temperature: 30.29

source_name: Mel 1858 Medi - repeat 2


title: Mel CL 1962 - mAdbID:64790

description: mAdb experiment ID: 64790

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.04;; 5.08 Temperature: 26.24

source_name: Mel Cl 1962


title: Mel 938 - mAdbID:64418

description: mAdb experiment ID: 64418

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.1;; 5.29 Temperature: 30.05

source_name: Mel 938


title: Mel CL 1182 - mAdbID:40422

description: mAdb experiment ID: 40422

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 100;; 100 LaserPower: 3.53;; 3.57 Temperature: 30.17

source_name: Mel CL 1182

source_name: PBMC Pooled Donor Reference Sample


title: Mel 1858 tumor digest - mAdbID:40425

description: mAdb experiment ID: 40425

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 100;; 100 LaserPower: 3.52;; 3.58 Temperature: 30.08

source_name: Mel 1858 tumor digest


title: Mel CL 036 - repeat 2 - mAdbID:40404

description: mAdb experiment ID: 40404

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 100;; 100 LaserPower: 3.52;; 3.61 Temperature: 29.81

source_name: Mel CL 036 - repeat 2


title: Mel CL 036 - repeat 1 - mAdbID:40296

description: mAdb experiment ID: 40296

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 100;; 100 LaserPower: 3.53;; 3.65 Temperature: 30.36

source_name: Mel CL 036 - repeat 1


title: 624.38 vs normal female 20 - mAdbID:72272

type: genomic

description: mAdb experiment ID: 72272

hyb_protocol: Sample Hybridization Protocol Wash procedure: Washing: 1. 2x SSC, 0.03% SDS at 65C for 5 minutes; 2. Wash with 2x SSC for 5 min at room temperature. 3 Wash with 1x SSC for 5 min at room temperature 4. 0.2x SSC at room temperature for 5 minutes 5. Centrifuge slide at 80-100 g for 3 min to dry. Other: Combine Cy3 and Cy5 Add 400µl of TE (pH=8.0) to each probe Apply labeled probe to Microcon YM 30 Spin 12000 xg for 11 minutes (make volume less than 20 µl) Discard flow-through, wash with 500 µl TE (pH=8.0) and spin 12000 xg for 11 minutes. Add Hybridization buffer mixing:Human Cot1 50 µl (1mg/ml)(Invitrogen, Cat# 15279-011);Yeast t-RNA 25 µl(4µg/µl)(4mg/ml Sigma- Aldrich Cat# R8759); Poly dT-dA 2.5µl (8 µg/µl)(8mg/ml Pharmacia Cat# 27-7988-01);TE (pH=8.0)450µl Mix well add to the filter Spin 12000 xg for 12 minutes Invert the filter to a new tube, spin for 2 minutes, Adjust volume by water up to 32 µl or dry samples if volume more than 32 microl; Make:Probe 32 µl,20 x SSC 6.8 µl,10% SDS 1.2 µl.Mix to minimize bubbles Denature by heating 99ºC for 3-4 minutes Incubate at 37ºC for 30 minutes Pre warm Hyb Chamber at 65 ºC Spin DNA probe for 5 minutes at max rcf Apply target mixture to array slide, add coverslip, place in humidified hyb chamber.Hybridization were conducted at 65oC for 16-18 hours.

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.33;; 3.28 Temperature: 30.84

data_processing:
BRB ArrayTool Data Processing
Calculation Method: Fluorescence intensities generated by Cy5 and Cy3 probes hybridized onto the microarray slides were scanned at 10-ìm resolution on a GenePix 4000 scanner (Axon Instruments, Union City,CA) at variable PMT voltage to obtain maximal signal intensities with < 1% probe saturation. The fluorescence intensity and ratio data for Cy5 and Cy3 were initially analyzed using GenePix 4.3 software. Raw data were retrieved in BRB-ArrayTools format for analysis and normalization(http://linus.nci.nih.gov/BRBArrayTools.html).. Following filter criteria was applied to the data set: 1. spots were excluded if intensity < 100, and spot size less than 25µm 2. genes were filtered out if >50% of experiment with missing data values. 3. log2 transformed data were normalized using lowess smoother, and intensity ratios were truncated if greater than 64 Further data preprocessing was done using webtool preP (http://prep.bioinfo.cnio.es/). Missing data were imputed using KNN imputation method with K=15. Gene location was extracted according to UniGene Cluster IDs from Ensemble and UCSC using IDconverter (http://idconverter.bioinfor.cnio.es/).The pre-processed aCGH data was then segmented using the circular binary segmentation method implemented in ADaCGH (http://adacgh.bioinfo.cnio.es/) to detect regions with abnormal DNA copy number. The smooth parameters were set as defaults.

molecule: genomic DNA

source_name: Normal donor - female 20

label_protocol:
Cy3 Labeling Protocol
Other: Four μg of genomic DNA were digested for 2 hours with Dpn II (New England Biolabs, Beverly, MA), followed by phenol-chloroform extraction. the labeling reaction was performed according to ARRAY CGH GENOMIC LABELING PROTOCOL (Invitrogen Cat# 18095-011. Digested DNA was mixed with 15 μg of random octamers (provided by kit) in a total volume of 41 μl reaction buffer and heated at 95ºC for 5 min. After chilling on ice, 5μl of 10x-dUTP Nucleotide Mix (provided by Kit, Cy3-dUTP (Amersham, Piscataway, NJ), and 1 μl of Exo-Klenow were added. The labeling reaction was completed at 37 ºC for 2 hours. Reactions were terminated by adding 5 μl of 0.5 M EDTA, pH 8.0. Target clean up: Add 45 µl of TE (pH= 8.0) to each tube Add 400 µl of purification buffer A (provided by kit) to each tube and vortex for 30 seconds Place the purification column(provided by kit) in a 2-ml collection tube, and load the sample into the column. Centrifuge at 11 000 xg for 1 minute at room temperature, discard the flow-through, place the column back in the tube. Add 600 µl of purification buffer B (provided by kit). Centrifuge at 11 000 xg for 1 minute at room temperature, discard the flow-through, place the column back in the tube Add 200 µl of purification buffer B (provided by kit) prepared to the column. Centrifuge at 11 000 xg for 1 minute at room temperature, discard the flow-through. Place the purification column in a new 1.5 ml collection tube Add 50 µl of sterile water and incubate at room temperature for 1 minute. Centrifuge at 11 000 xg for 1 minute at room temperature. The flow-through contains your purified labeled DNA probes.

extract_protocol:
Sample Extraction Protocol
Other: Genomic DNA was extracted from a short-term cultured tumor cells or PBMC using Qiagen Mini genomic kit (Qiagen, Valencia, CA). PROTEINASE K (Qiagen)was added to a solution containing 5x106 cells,PBS and AL buffer and mixed thoroughly by pipetting. The homogenate was then incubated at 56C for 10 minutes and centrifuged for 1 min at 13000 rpm at room temp. The mixture (approximately 400 microl) was then combined and mixed well with one volume of ethanol (96-100%) and transferred into a QIamp spin column placed in a 2ml collection tube. Genomic Dna was than isolated according to the manufacturer protocol.

tag: Gender

value: female

value: PBMC

label_protocol:
Cy5 Labeling Protocol
Other: Four μg of genomic DNA were digested for 2 hours with Dpn II (New England Biolabs, Beverly, MA), followed by phenol-chloroform extraction. the labeling reaction was performed according to ARRAY CGH GENOMIC LABELING PROTOCOL (Invitrogen Cat# 18095-011. Digested DNA was mixed with 15 μg of random octamers (provided by kit) in a total volume of 41 μl reaction buffer and heated at 95ºC for 5 min. After chilling on ice, 5μl of 10x-dUTP Nucleotide Mix (provided by Kit, Cy5-dUTP(Amersham, Piscataway, NJ), and 1 μl of Exo-Klenow were added. The labeling reaction was completed at 37 ºC for 2 hours. Reactions were terminated by adding 5 μl of 0.5 M EDTA, pH 8.0. Target clean up: Add 45 µl of TE (pH= 8.0) to each tube Add 400 µl of purification buffer A (provided by kit) to each tube and vortex for 30 seconds Place the purification column(provided by kit) in a 2-ml collection tube, and load the sample into the column. Centrifuge at 11 000 xg for 1 minute at room temperature, discard the flow-through, place the column back in the tube. Add 600 µl of purification buffer B (provided by kit). Centrifuge at 11 000 xg for 1 minute at room temperature, discard the flow-through, place the column back in the tube Add 200 µl of purification buffer B (provided by kit) prepared to the column. Centrifuge at 11 000 xg for 1 minute at room temperature, discard the flow-through. Place the purification column in a new 1.5 ml collection tube Add 50 µl of sterile water and incubate at room temperature for 1 minute. Centrifuge at 11 000 xg for 1 minute at room temperature. The flow-through contains your purified labeled DNA probes.

tag: Cell line


title: MG - 1858 Wash vs normal female 20 - mAdbID:79646

description: mAdb experiment ID: 79646

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.24;; 3.57 Temperature: 28.74

source_name: MG - 1858 Wash

value: 1858 Wash


title: Mel CL 1102 - mAdbID:40405

description: mAdb experiment ID: 40405

scan_protocol: Creator: GenePix Pro 4.0.1.14 Scanner: GenePix 4000B [84945] ScanPower: 100;; 100 LaserPower: 3.53;; 3.57 Temperature: 30.23

source_name: Mel CL 1102


title: 1195 vs normal female 20 - mAdbID:72273

description: mAdb experiment ID: 72273

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.35;; 3.25 Temperature: 31.21


title: 1102 vs normal female 20 - mAdbID:72270

description: mAdb experiment ID: 72270

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.33;; 3.26 Temperature: 31


title: 1182 vs normal female 20 - mAdbID:72274

description: mAdb experiment ID: 72274

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.33;; 3.47 Temperature: 30.29


title: A375 vs normal female 20 - mAdbID:72267

description: mAdb experiment ID: 72267

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.34;; 3.36 Temperature: 30.17


title: MG - 1290p54 vs normal female 20 - mAdbID:72264

description: mAdb experiment ID: 72264

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33;; n/a;; n/a LaserPower: 3.34;; 3.3;; n/a;; n/a Temperature: 30.66


title: 938 vs normal female 20 - mAdbID:72271

description: mAdb experiment ID: 72271

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.36;; 3.24 Temperature: 31.36


title: MG - 1858 Frag vs normal female 20 - mAdbID:79647

description: mAdb experiment ID: 79647

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.24;; 3.56 Temperature: 28.92

source_name: MG - 1858 Frag

value: 1858 Frag


title: 624.28 vs normal female 20 - mAdbID:72269

description: mAdb experiment ID: 72269

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.34;; 3.31 Temperature: 30.63

value: blood


title: MG - 1936 vs normal female 20 - mAdbID:72265

description: mAdb experiment ID: 72265

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.32;; 3.25 Temperature: 31.15


title: MG- 888 vs normal female 20 - mAdbID:72253

description: mAdb experiment ID: 72253

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33;; n/a;; n/a LaserPower: 3.34;; 3.3;; n/a;; n/a Temperature: 30.14


title: MG - 1290p14 vs normal female 20 - mAdbID:72256

description: mAdb experiment ID: 72256

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33;; n/a;; n/a LaserPower: 3.33;; 3.35;; n/a;; n/a Temperature: 30.36


title: 526 vs normal female 20 - mAdbID:72268

description: mAdb experiment ID: 72268

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.34;; 3.33 Temperature: 30.51


title: MG - 1962 vs normal female 20 - mAdbID:72250

description: mAdb experiment ID: 72250

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.34;; 3.38 Temperature: 30.08


title: MG - 1858 Medi vs normal female 20 - mAdbID:72266

description: mAdb experiment ID: 72266

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.33;; 3.34 Temperature: 30.14

source_name: MG - 1858 Medi

value: 1858 Medi


title: 06_skin_pre__

scan_protocol: Scanner: Axon4000B-2. Voltage: 450, 350. Resolution (micrometers): 10.

source_name: 06_skin_pre(Skin Biopsy taken post treatment, ES-285 dose 8mg/2.)

value: pre treatment

source_name: Amplified Stratagene Human Reference(Stratagene Human Reference RNA amplified with Ambion MessageAmp II kit.)

value: Mixed Pool of Human Cell Lines


title: Stage_5b_vs_Stage1b

status: Public on Feb 13 2008

city: Rockville

first: Jia

last: Liu

state: MD

address: 9712 Medical Center Drive

institute: Plant Genomics

description: Dormant/sprouting bud or eye tissue was collected from field grown Russet Burbank tubers using melon baler. These tubers after harvest washed with 5% Clorox, dried and stored at room temperature and allowed to sprout. Tissue samples were collected from dormant and sprouting eye at different physiological stages (based on length of the sprout) of sprouting. RNA was extracted using a hot phenol method and treated with DNAse. RNA extracted from different stages of sprouting potato tubers was used as query samples. RNA collected from non-sprouting eyes of potato tubers was used as reference samples  Information on RNA samples. Plant species: S. tuberosum CV Russet Burbank. Tissue harvested: Tissue was harvested from the dormant/sprouting bud/eye using ½ inch melon baler. Time points:  Dormant eyes –Stage 1 Initiating buds/sprouts – Stage 2 Sprouts (1/8 inch) – Stage 3 Sprouts (1/4 inch) – Stage 4 Sprout callus (1/4 inch) – Stage 5 Sprouts (1/2 inch) – Stage 6. Growth conditions: Field grown. Replicate information:  Biological replicates; A, B and C

hyb_protocol: Hybridization with indirectly labeled mRNA (SGED_SOP_6.1.1, SGED_SOP_6.2.1-4)

scan_protocol: Axon 4000B scanner. Both the 635nm (red, Cy5) and 532nm (green, Cy3) channels are scanned simultaneously at 100% laser power, the PMT set between 600 and 950. Slides are scanned at a resolution of 10micron

data_processing: The TIFF images were quantified using Genepix 5.0. Local background was subtracted from the signal value and the data was normalized using the quantile method in the limma package of bioconductor.

organism: Solanum tuberosum

label_protocol: Amino allyl labeling and direct labeling (SGED_SOP_5.1.1 + SGED_SOP_6.1.1)

growth_protocol: Field grown samples

extract_protocol: Phenol method with carbohydrate-enriched tissue such as tubers and trizol for other tissues such as leaves (SGED_SOP_3.1.1 + SGED_SOP_3.3.1)

treatment_protocol: Allowed to sprout at room temperature

tag: Solanum tuberosum, Tuber bud, Development


title: Stage_3b_vs_Stage1b


title: Stage_3a_vs_Stage1a


title: Stage_5a_vs_Stage1a


title: Stage_4c_vs_Stage1c


title: Stage_2c_vs_Stage1c


title: Stage_2b_vs_Stage1b


title: Stage_4a_vs_Stage1a


title: Stage_6a_vs_Stage1a


title: Stage_4b_vs_Stage1b


title: Stage_6c_vs_Stage1c


title: shma-p53null 24h 1 BPDE B

status: Public on Nov 13 2007

description: Labelled sample was reduced down to 3 µl using Microcon YM-30 centifugal filters (Millipore, UK). Corresponding control and treated samples labelled with different fluorophores were combined in a 50 µl hybridisation mix (19 µl Microarray Hybridisation Solution purchased from GE Healthcare and 50% deionised formamide) and heated at 70degC for 2 min and then at 37degC for 10 min. Sample was pipetted onto a microarray slide and covered with a glass cover slip. A 150µl aliquot of 6 X SSPE was pipetted underneath the slide to prevent dehydration. The hybridisation chamber was sealed and incubated at 42degC for 72 h.

hyb_protocol: Corresponding control and treated samples labelled with different fluorophores were combined in a 50 ul hybridisation mix (19 ul Microarray Hybridisation Solution purchased from GE Healthcare and 50% deionised formamide) and heated at 70°C for 2 min and then at 37°C for 10 min. Sample was pipetted onto a microarray slide and covered with a glass cover slip. A 150ul aliquot of 6 X SSPE was pipetted underneath the slide to prevent dehydration. The hybridisation chamber was sealed and incubated at 42°C for 72 h. Type 7* slides were washed three times in 4 X SSPE, 10 mM EDTA pH 8.0 as above, followed by a 10 s wash in 50% deionised formamide, 6 X SSPE, before a brief rinse in HPLC grade water and drying with nitrogen gas.

scan_protocol: Scanner: Axon4000A. Voltage: 3.76 3.06. Resolution (micrometers): 10.

data_processing: Regions were used for normalizing samples 1-24. A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

source_name: sh241005-p53null 24h DMSO B(sh241005-p53null 24h DMSO B  )

label_protocol: Total RNA (4 ug) was reversed transcribed into cDNA and fluorescently labelled with Cy3 or Cy5 mono-reactive dyes (Amersham Biosciences, UK) using the Invitrogen Indirect cDNA Labelling Kit protocol (Invitrogen, UK) according to the manufacturer's instructions. After labelling, repetitive sequences within the cDNA samples were blocked with 16 ug Human Cot-1 DNA (Invitrogen, UK) to prevent non-specific sequences binding to the cDNA probes.

extract_protocol: Cell pellets were collected and total RNA extracted using the Qiagen RNeasy Mini Kit protocol (RNeasy Mini Handbook, Qiagen, UK). After addition of lysis buffer (RLT, Qiagen) samples were homogenized using QIAshredders (Qiagen).

tag: tissue type

value: tumor

source_name: sh241005-p53null 24h 1 BPDE B(sh241005-p53null 24h 1 BPDE B  )


title: shma-p53null 6h 0.5 BPDE A

scan_protocol: Scanner: Axon4000A. Voltage: 3.73 3.26. Resolution (micrometers): 10.

source_name: sh241005-p53null 6h DMSO A(sh241005-p53null 6h DMSO A  )


title: shma-p53null 6h 1 BPDE A

scan_protocol: Scanner: Axon4000A. Voltage: 3.54 3.36. Resolution (micrometers): 10.

source_name: sh241005-p53null 6h 1 BPDE A(sh241005-p53null 6h 1 BPDE A  )


title: shma-p53null 24h 0.5 BPDE B

scan_protocol: Scanner: Axon4000A. Voltage: 3.66 3.21. Resolution (micrometers): 10.


title: shma-p53null 6h 0.5 BPDE B

scan_protocol: Scanner: Axon4000A. Voltage: 3.66 3.53. Resolution (micrometers): 10.

source_name: sh241005-p53null 6h DMSO B(sh241005-p53null 6h DMSO B  )


title: shma-p53null 24h 1 BPDE C

scan_protocol: Scanner: Axon4000A. Voltage: 3.69 3.07. Resolution (micrometers): 10.

source_name: sh241005-p53null 24h DMSO C(sh241005-p53null 24h DMSO C  )

source_name: sh241005-p53null 24h 1 BPDE C(sh241005-p53null 24h 1 BPDE C  )


title: shma-p53null 24h 1 BPDE A

scan_protocol: Scanner: Axon4000A. Voltage: 3.66 3.5. Resolution (micrometers): 10.

source_name: sh241005-p53null 24h DMSO A(sh241005-p53null 24h DMSO A  )

source_name: sh241005-p53null 24h 1 BPDE A(sh241005-p53null 24h 1 BPDE A  )


title: Stage_6b_vs_Stage1b


title: shma-p53null 6h 1 BPDE C

scan_protocol: Scanner: Axon4000A. Voltage: 3.62 3.28. Resolution (micrometers): 10.

source_name: sh241005-p53null 6h DMSO C(sh241005-p53null 6h DMSO C  )

source_name: sh241005-p53null 6h 1 BPDE C(sh241005-p53null 6h 1 BPDE C  )


title: shma-p53null 24h 0.5 BPDE C

scan_protocol: Scanner: Axon4000A. Voltage: 3.67 3.28. Resolution (micrometers): 10.


title: shma-p53null 6h 1 BPDE B

scan_protocol: Scanner: Axon4000A. Voltage: 3.57 3.35. Resolution (micrometers): 10.

source_name: sh241005-p53null 6h 1 BPDE B(sh241005-p53null 6h 1 BPDE B  )


title: shma-p53WT 24h 1 BPDE B

scan_protocol: Scanner: Axon4000A. Voltage: 3.65 3.26. Resolution (micrometers): 10.


title: Stage_2a_vs_Stage1a


title: shma-p53null 24h 0.5 BPDE A

scan_protocol: Scanner: Axon4000A. Voltage: 4.09 3.62. Resolution (micrometers): 10.


title: shma-p53null 6h 0.5 BPDE C

scan_protocol: Scanner: Axon4000A. Voltage: 3.79 3.68. Resolution (micrometers): 10.


title: shma-p53WT 24h 0.5 BPDE C

scan_protocol: Scanner: Axon4000A. Voltage: 3.68 3.03. Resolution (micrometers): 10.


title: Stage_5c_vs_Stage1c


title: shma-p53WT 24h 1 BPDE A

scan_protocol: Scanner: Axon4000A. Voltage: 3.69 3.24. Resolution (micrometers): 10.


title: Stage_3c_vs_Stage1c


title: shma-p53WT 6h 0.5 BPDE B

scan_protocol: Scanner: Axon4000A. Voltage: 3.65 3.45. Resolution (micrometers): 10.

source_name: sh241005-p53WT 6h DMSO B(sh241005-p53WT 6h DMSO B  )


title: shma-p53null 48h 5 BaP C

scan_protocol: Scanner: Axon4000A. Voltage: 4.05 3.67. Resolution (micrometers): 10.

data_processing: Regions were used for normalizing samples 1-23. A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

source_name: sh251005-p53null 48h DMSO C(sh251005-p53null 48h DMSO C  )


title: shma-p53WT 6h 1 BPDE A

scan_protocol: Scanner: Axon4000A. Voltage: 3.47 3.36. Resolution (micrometers): 10.

source_name: sh241005-p53WT 6h DMSO A(sh241005-p53WT 6h DMSO A  )


title: shma-p53WT 6h 0.5 BPDE C

scan_protocol: Scanner: Axon4000A. Voltage: 3.72 3.23. Resolution (micrometers): 10.

source_name: sh241005-p53WT 6h DMSO C(sh241005-p53WT 6h DMSO C  )


title: shma-p53null 48h 5 BaP B

scan_protocol: Scanner: Axon4000A. Voltage: 4.12 3.67. Resolution (micrometers): 10.

source_name: sh251005-p53null 48h DMSO B(sh251005-p53null 48h DMSO B  )


title: shma-p53WT 6h 1 BPDE C

scan_protocol: Scanner: Axon4000A. Voltage: 3.52 3.37. Resolution (micrometers): 10.


title: shma-p53WT 24h 0.5 BPDE B

scan_protocol: Scanner: Axon4000A. Voltage: 3.89 3.7. Resolution (micrometers): 10.


title: shma-p53null 24h 2.5 BaP B

scan_protocol: Scanner: Axon4000A. Voltage: 3.48 3.39. Resolution (micrometers): 10.

source_name: sh241005-p53null 24h DMSO B(sh241005-p53null 24h DMSO B  )


title: shma-p53WT 48h 5 BaP C

description: Labelled sample was reduced down to 3 µl using Microcon YM-30 centifugal filters (Millipore, UK). Corresponding control and treated samples labelled with different fluorophores were combined in a 50 µl hybridisation mix (19 µl Microarray Hybridisation Solution purchased from GE Healthcare and 50% deionised formamide) and heated at 70degC for 2 min and then at 37degC for 10 min. Sample was pipetted onto a microarray slide and covered with a glass cover slip. A 150µl aliquot of 6 X SSPE was pipetted underneath the slide to prevent dehydration. The hybridisation chamber was sealed and incubated at 42degC for 72 h

scan_protocol: Scanner: Axon4000A. Voltage: 4.03 3.72. Resolution (micrometers): 10.


title: shma-p53null 48h 2.5 BaP C

scan_protocol: Scanner: Axon4000A. Voltage: 4.12 3.97. Resolution (micrometers): 10.


title: shma-p53null 24h 5 BaP B

scan_protocol: Scanner: Axon4000A. Voltage: 3.7 3.52. Resolution (micrometers): 10.


title: shma-p53WT 6h 1 BPDE B

scan_protocol: Scanner: Axon4000A. Voltage: 3.54 3.35. Resolution (micrometers): 10.


title: shma-p53WT 24h 0.5 BPDE A

scan_protocol: Scanner: Axon4000A. Voltage: 3.52 3.26. Resolution (micrometers): 10.


title: shma-p53null 24h 2.5 BaP A

scan_protocol: Scanner: Axon4000A. Voltage: 3.59 3.29. Resolution (micrometers): 10.


title: shma-p53null 24h 2.5 BaP C

scan_protocol: Scanner: Axon4000A. Voltage: 3.67 3.23. Resolution (micrometers): 10.


title: shma-p53null 48h 2.5 BaP B

scan_protocol: Scanner: Axon4000A. Voltage: 3.6 3.53. Resolution (micrometers): 10.


title: shma-p53WT 6h 0.5 BPDE A

scan_protocol: Scanner: Axon4000A. Voltage: 3.72 3.27. Resolution (micrometers): 10.


title: shma-p53WT 48h 5 BaP A

scan_protocol: Scanner: Axon4000A. Voltage: 3.73 3.56. Resolution (micrometers): 10.

tag: gender

value: unknown


title: shma-p53null 48h 2.5 BaP A

scan_protocol: Scanner: Axon4000A. Voltage: 3.67 3.6. Resolution (micrometers): 10.

source_name: sh251005-p53null 48h DMSO A(sh251005-p53null 48h DMSO A  )


title: shma-p53null 24h 5 BaP A

scan_protocol: Scanner: Axon4000A. Voltage: 4.02 3.98. Resolution (micrometers): 10.


title: shma-p53WT 48h 2.5 BaP C

scan_protocol: Scanner: Axon4000A. Voltage: 3.94 4.03. Resolution (micrometers): 10.


title: shma-p53null 24h 5 BaP C


title: shma-p53WT 24h 1 BPDE C

scan_protocol: Scanner: Axon4000A. Voltage: 3.62 3.33. Resolution (micrometers): 10.


title: shma-p53null 48h 5 BaP A

scan_protocol: Scanner: Axon4000A. Voltage: 4.06 3.7. Resolution (micrometers): 10.


title: shma-p53WT 48h 5 BaP B

scan_protocol: Scanner: Axon4000A. Voltage: 3.98 3.74. Resolution (micrometers): 10.


title: Sprague-Dawley Male HighSalt Cortex rat710 sd_cortexr_k_710c_020802

status: Public on Jul 01 2007

city: West Point

first: David

middle: Lee

last: Gerhold

state: PA

address: Broad St & Sumneytown Pk

department: Mol Invest Toxicol

institute: Merck & Co.

description: Rat kidney samples (cortex and outer medulla) were analyzed. Separate experiments were done using 1) Dahl-Iwai salt-sensitive rats, 2) Sprague-Dawley w.t. rats, and 3) Gonadectomized Dahl-Iwai salt-sensitive rats. FOr each strain males vs females, and high salt vs low salt diets for 14 weeks.

hyb_protocol: Five-microgram mRNA samples typically yielded between 30 and 150 mg purified cRNA. 15 microgram cRNA samples were fragmented at 95°C for 35 min in 10 mM MgCl2 to a mean size of ;50–100 nucleotides, added to hybridization buffer, and hybridized to the microarray for 16 h at 45°C. GeneChips were washed, stained with streptavidin-R-phycoerythrin, and scanned with a dedicated instrument to capture a fluorescence image (Molecular Dynamics).

scan_protocol: (per Affymetrix)

data_processing: SAFER: Proc American Stat Assoc. Holder 2002

label: streptavidin-phycoerythrin

organism: Rattus norvegicus

label_protocol:
(per Affymetrix technical manual P/N 700220) A primer encoding the T7 RNA polymerase promoter linked to oligo-dT17 was used to prime doublestranded
cDNA synthesis from each mRNA sample using Superscript II RNase H2 reverse transcriptase (Life Technologies, Rockville, MD). Each double-stranded cDNA sample
was purified by adsorption to silica (Qiaquick kit, Qiagen) according to manufacturer’s instructions, then in vitro transcribed using T7 RNA polymerase (MEGAscript T7 kit; Ambion,
Austin, TX), incorporating biotin-UTP and biotin-CTP (Enzo Biochemicals, New York, NY) into the resulting copy RNA (cRNA). These cRNA transcripts were purified using RNEasy (Qiagen).

extract_protocol:
Trizol(r) phenol-guanidinium extract
sup. to Qiaquick spin column

treatment_protocol: 14 weeks salt-controlled diet


title: shma-p53WT 48h 2.5 BaP A

scan_protocol: Scanner: Axon4000A. Voltage: 4.14 3.65. Resolution (micrometers): 10.


title: shma-p53WT 48h 2.5 BaP B

scan_protocol: Scanner: Axon4000A. Voltage: 4 4.01. Resolution (micrometers): 10.


title: Dahl-Iwai  Male LowSalt Cortex rat110 dahl_cortexr_k_110c_072001

scan_protocol: per Affymetrix

label: strpetavidin-phycoerythrin

source_name: Dahl-Iwai _Male_LowSalt_Cortex_rat110

tag: Dahl-Iwai _Male_LowSalt_Cortex_rat110


title: shma-p53WT 24h 5 BaP C #2

scan_protocol: Scanner: Axon4000A. Voltage: 3.89 3.7. Resolution (micrometers): 10.


title: shma-p53WT 24h 2.5 BaP B

scan_protocol: Scanner: Axon4000A. Voltage: 3.6 3.06. Resolution (micrometers): 10.


title: shma-p53WT 24h 2.5 BaP C

scan_protocol: Scanner: Axon4000A. Voltage: 3.61 3.23. Resolution (micrometers): 10.


title: shma-p53WT 24h 5 BaP B

scan_protocol: Scanner: Axon4000A. Voltage: 3.99 3.73. Resolution (micrometers): 10.


title: RTS II cell line stimulation 12 (SsamcellINF12a)

status: Public on Jun 16 2007

city: Aberdeen

first: Sam

middle: A

last: Martin

state: Scotland

address: Tillydrone Avenue

department: Zoology

institute: University of Aberdeen

description: Rainbow trout cell line RTS II stimulated with recombinant Interleukin 1 beta for 6 hours

hyb_protocol: Prior to hybridization 1.5mL d(A)80 (1mg ml-1), 110mL formamide, 55ul hybridization buffer (Amersham Biosciences) and water was added to give a final volume of 220 ml.  The cDNA was heated to 95°C for 2 min before being added to the hybridization chamber.  The hybridization was performed for 16 h at 42°C on an Amersham Lucidea hybridization station. Prior to hybridization slides were pretreated by heating in water at 95°C for 5 min, then washed with isopropanol and air dried.  Washes were as follows:  1X SSC 10 min, 1X SSC +0.2% SDS 10 min, 0.1 X SSC + 0.2% SDS 10 min.  Slides were then dried before being scanned.

scan_protocol: Images were scanned using Axon 4100B scanner.  Resolution was at 10mM.  Gel images were edited using GenePix Version 5.1.

data_processing: Initial image analysis was performed with the GenPix (version 5.1, Axon instruments) program; the array images were edited to ensure that the GAL (Gene Associated List) file was correctly orientated and that any abnormal hybridization signals were flagged as bad.  Edited images were imported into Acuity (version 5.1, Axon instruments) and analysis performed.  All arrays were background corrected using local background correction and normalized using Lowess normalization. The data was filtered to remove bad signal and signal that did not reach a predetermined threshold (signal to noise ratio >1.5 for either Cy3 or Cy5).  Data in VALUE column is RAW data and not normalized

organism: Oncorhynchus mykiss

source_name: RTS II cells Non stimulated

label_protocol: Labelled cDNA was generated using Amersham Pharmacia post labelling kit.  Total RNA (20mg) was used as template for each labelling.

extract_protocol: RNAstat (TEL_TEST INC.)  According to manufacturers instructions.

tag: RTS II cells Non stimulated

source_name: RTS II cells stimulated with recombinant interferon gamma


title: RTS II cell line stimulation 11 (SsamcellINF11a)

tag: RTS II cells stimulated with recombinant interferon gamma


title: Unwinged 4th Instar Females Replicate 3

status: Public on Jun 05 2007

city: Princeton

first: Gregory

middle: K.

last: Davis

state: NJ

address: 106A Guyot Hall, Washington Road

department: Ecology and Evolutionary Biology

institute: Princeton University

description: Unwinged 4th Instar Females Replicate 3

hyb_protocol: Description : Slides were UV-crosslinked with 6000μJ and prehybridized for one hour in 3xSSC, 0.1% SDS and 1% blocking agent (Roche). Slides were boiled for two minutes prior to drying. Labeled cDNA was hybridized to slides under lifter slips (Erie Glass) overnight at 65?C in a hybridization buffer containing 3xSSC, 0.1% SDS, 20mM Hepes, 13.6 micrograms tRNA and 40 micrograms polyA RNA. All dye handling and hybridizations were conducted in an ozone free room.

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2006-01-30 Scan Temperature : 0.00 Scan Time : 09:53:09 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.1.24
Datafile type : GenePix Results 3
Image Origin : 0, 0

label: Alexa Fluor 555

organism: Acyrthosiphon pisum

source_name: Universal RNA

label_protocol: Description : 20 micrograms of total RNA was used to produce Alexa Fluor 555-labeled cDNA with the SuperScript Plus Direct cDNA Labeling System (Invitrogen).

extract_protocol: Description : Total RNA was isolated using the SV Total RNA Isolation Kit (Promega).

tag: Description

value: Single large-scale collection of parthenogenetic aphids at all stages of development.

label: Alexa Fluor 647

source_name: UW 4th Females

label_protocol: Description : 20 micrograms of total RNA was used to produce Alexa Fluor 647-labeled cDNA with the SuperScript Plus Direct cDNA Labeling System (Invitrogen).

value: Second-Day Unwinged 4th Instar Females were collected in groups of 15 and immediately frozen in liguid nitrogen.


title: Unwinged 4th Instar Males Replicate 3

description: Unwinged 4th Instar Males Replicate 3

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2006-01-30 Scan Temperature : 0.00 Scan Time : 09:52:43 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0

source_name: UW 4th Males

value: Second-Day Unwinged 4th Instar Males were collected in groups of 15 and immediately frozen in liquid nitrogen.


title: RTS II cell line stimulation 6 (SsamcellB6b)

source_name: RTS II cells stimulated with recombinant interleukin 1 beta


title: Unwinged 5th Instar Males Replicate 3

description: Unwinged 5th Instar Males Replicate 3

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2006-01-30 Scan Temperature : 0.00 Scan Time : 09:53:22 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0

source_name: UW 5th Males

value: Second-Day Unwinged 5th Instar (Adult) Males were collected in groups of 15 and immediately frozen in liquid nitrogen.


title: Winged 4th Instar Males Replicate 3

description: Winged 4th Instar Males Replicate 3

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2006-01-30 Scan Temperature : 0.00 Scan Time : 09:52:56 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0

source_name: W 4th F1 Males

value: Second-Day Winged 4th Instar Males were collected in groups of 15 and immediately frozen in liquid nitrogen.


title: RTS II cell line stimulation 9 (SsamcellINF9a)


title: RTS II cell line stimulation 7 (SsamcellINF7a)


title: RTS II cell line stimulation 10 (SsamcellINF10b)


title: Gonadectomized Dahl-Iwai Male LowSalt Cortex rat9 gdahl_cortexr_k_GX_9c_051702

scan_protocol: see manuscript (per Affymetrix)


title: RTS II cell line stimulation 5 (SsamcellB5a)

tag: RTS II cells stimulated with recombinant interleukin 1 beta


title: Unwinged 4th Instar Males Replicate 2

description: Unwinged 4th Instar Males Replicate 2

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2006-01-06 Scan Temperature : 0.00 Scan Time : 10:46:17 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0


title: Winged 5th Instar Females Replicate 3

description: Winged 5th Instar Females Replicate 3

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2006-01-06 Scan Temperature : 0.00 Scan Time : 10:45:50 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0

source_name: W 5th Females

value: Second-Day Winged 5th Instar (Adult) Females were collected in groups of 15 and immediately frozen in liquid nitrogen.


title: RTS II cell line stimulation 3 (SsamcellB3b)


title: Mo17 11-day seedling aerial tissue biological replicate 1

status: Public on Jun 21 2007

city: Saint Paul

first: Nathan

middle: M

last: Springer

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

description: refer to PMID: 16702414

hyb_protocol: Hybridization was performed according to the recommended Affymetrix protocols at the University of Minnesota Microarray facility.

scan_protocol: The Genechip 3000 scanner was used to scan each array

data_processing: MAS5.0 values are reported; the .cel file is also available

organism: Zea mays

source_name: Zea mays 11-day seedling aerial tissue genotype Mo17

label_protocol: Eight ug of total RNA was labeled for each hybridization using the One-Cycle cDNA Synthesis Kit, according to the manufacturer’s instructions (Affymetrix, Santa Clara CA).

growth_protocol:
Seeds for inbreds Mo17 and B73 and hybrids Mo17 3 B73
and B73 3 Mo17 were sown and grown under greenhouse conditions for 11 days and then sampled for gene expression
analysis. Three biological replicates were planted and grown sequentially over an 5-week period during May 2005. Seeds
were planted such that one seed of each genotype was present
in every pot. Twelve pots were selected for tissue collection;
thus 12 plants were sampled per genotype. All plants were
sampled between 9 am and 10 am and plants were cut immediately
above the highest root; thus all aboveground tissues
and meristems were sampled. The sampled tissues were flash
frozen in liquid nitrogen and stored at -80 C prior to RNA isolation.

extract_protocol:
For seedling RNA isolation, tissues from 12
seedlings/genotype/biological replicate were pooled and
ground in liquid nitrogen. RNAs were extracted using
Trizol reagent according to the manufacturer’s instructions
(Invitrogen, Carlsbad, CA). All RNAs were subsequently subjected
to DNAse treatment and phenol:chloroform extraction.
RNAs were precipitated with 0.13 volume sodium acetate
(pH 5.5) and 2.53 volume ethanol. Resuspended RNAs were
purified further using the RNeasy system, according to the
manufacturer’s instructions (QIAGEN, Valencia, CA).

tag: Genotype

tag: Stage

value: 11-day old seedling, all aerial tissue


title: Unwinged 5th Instar Males Replicate 2

description: Unwinged 5th Instar Males Replicate 2

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2006-01-06 Scan Temperature : 0.00 Scan Time : 10:46:04 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0


title: RTS II cell line stimulation 4 (SsamcellB4a)


title: RTS II cell line stimulation 2 (SsamcellB2)


title: Winged 5th Instar Females Replicate 2

description: Winged 5th Instar Females Replicate 2

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2005-12-20 Scan Temperature : 0.00 Scan Time : 16:03:03 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0


title: Winged 4th Instar Males Replicate 2

description: Winged 4th Instar Males Replicate 2

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2006-01-06 Scan Temperature : 0.00 Scan Time : 10:45:37 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0

source_name: W 4th Males


title: Winged 5th Instar Males Replicate 3

description: Winged 5th Instar Males Replicate 3

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2005-12-20 Scan Temperature : 0.00 Scan Time : 16:02:52 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0

source_name: W 5th Males

value: Second-Day Winged 5th Instar (Adult) Males were collected in groups of 15 and immediately frozen in liquid nitrogen.


title: Mo17xB73 11-day seedling aerial tissue biological replicate 1

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype Mo17xB73

growth_protocol:
Seeds for inbreds Mo17 and B73 and hybrids Mo17 x B73
and B73 x Mo17 were sown and grown under greenhouse conditions for 11 days and then sampled for gene expression analysis. Three biological replicates were planted and grown sequentially over an 5-week period during May 2005. Seeds
were planted such that one seed of each genotype was present
in every pot. Twelve pots were selected for tissue collection;
thus 12 plants were sampled per genotype. All plants were
sampled between 9 am and 10 am and plants were cut immediately
above the highest root; thus all aboveground tissues
and meristems were sampled. The sampled tissues were flash
frozen in liquid nitrogen and stored at -80 C prior to RNA isolation.

value: Mo17xB73 Stage:11-day old seedling, all aerial tissue


title: Winged 5th Instar Males Replicate 2

description: Winged 5th Instar Males Replicate 2

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2005-12-15 Scan Temperature : 0.00 Scan Time : 14:56:15 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0


title: Winged 4th Instar Females Replicate 3

description: Winged 4th Instar Females Replicate 3

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2005-12-20 Scan Temperature : 0.00 Scan Time : 16:03:30 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0

source_name: W 4th Females

value: Second-Day Winged 4th Instar Females were collected in groups of 15 and immediately frozen in liquid nitrogen.


title: Winged 4th Instar Females Replicate 2

description: Winged 4th Instar Females Replicate 2

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2005-12-15 Scan Temperature : 0.00 Scan Time : 14:56:30 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0

source_name: W 4th F1 Females


title: shma-p53WT 24h 2.5 BaP A

scan_protocol: Scanner: Axon4000A. Voltage: 3.5 2.79. Resolution (micrometers): 10.


title: RTS II cell line stimulation 8 (SsamcellINF8a)

scan_protocol: Images were scanned using Axon 4100B scanner.  Resolution was at 10mM.  Gel images were edited using GenePix Version 5.1.


title: Unwinged 5th Instar Females Replicate 3

description: Unwinged 5th Instar Females Replicate 3

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2005-12-20 Scan Temperature : 0.00 Scan Time : 16:03:16 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0

source_name: UW 5th Females

value: Second-Day Unwinged 5th Instar (Adult) Females were collected in groups of 15 and immediately frozen in liquid nitrogen.


title: Unwinged 4th Instar Females Replicate 2

description: Unwinged 4th Instar Females Replicate 2

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2005-12-20 Scan Temperature : 0.00 Scan Time : 16:02:38 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0


title: Winged 4th Instar Males Replicate 1

description: Winged 4th Instar Males Replicate 1

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2005-10-17 Scan Temperature : 0.00 Scan Time : 08:58:48 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0


title: Unwinged 4th Instar Females Replicate 1

description: Unwinged 4th Instar Females Replicate 1

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2005-09-22 Scan Temperature : 0.00 Scan Time : 11:43:47 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0


title: Unwinged 4th Instar Males Replicate 1

description: Unwinged 4th Instar Males Replicate 1

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2005-10-17 Scan Temperature : 0.00 Scan Time : 08:58:34 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0


title: Winged 4th Instar Females Replicate 1

description: Winged 4th Instar Females Replicate 1

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2005-09-22 Scan Temperature : 0.00 Scan Time : 14:00:30 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0


title: Unwinged 5th Instar Males Replicate 1

description: Unwinged 5th Instar Males Replicate 1

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2005-09-22 Scan Temperature : 0.00 Scan Time : 14:00:45 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0


title: Unwinged 5th Instar Females Replicate 2

description: Unwinged 5th Instar Females Replicate 2

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2005-12-15 Scan Temperature : 0.00 Scan Time : 14:56:03 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0


title: Winged 5th Instar Females Replicate 1

description: Winged 5th Instar Females Replicate 1

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2005-09-13 Scan Temperature : 0.00 Scan Time : 12:51:31 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0


title: Winged 5th Instar Males Replicate 1

description: Winged 5th Instar Males Replicate 1

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2005-09-22 Scan Temperature : 0.00 Scan Time : 14:00:00 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0


title: Unwinged 5th Instar Females Replicate 1

description: Unwinged 5th Instar Females Replicate 1

scan_protocol: Scan Power : 100 PMT Volts : 0 Pixel Size : 10 Laser on time : 0 Laser Power : 0.00 Scan Date : 2005-09-13 Scan Temperature : 0.00 Scan Time : 12:51:49 Scanner Make : Agilent Technologies Scanner Model : G2505B Scanning software : Agilent Scan Control Scanning software version : A.7.0.1 Focus Position : 0


title: B73 11-day seedling aerial tissue biological replicate 1

description: refer to PMID: 16702414

scan_protocol: The Genechip 3000 scanner was used to scan each array

source_name: Zea mays 11-day seedling aerial tissue genotype B73

value: B73 Stage:11-day old seedling, all aerial tissue


title: genotype A77 developing seed at 5 days after anthesis, biological rep1

status: Public on Mar 25 2007

city: Winnipeg

first: Mark

last: Jordan

state: Manitoba

address: 195 Dafoe Rd.

department: Cereal research Centre

country: Canada

institute: Agriculture and Agri-Food Canada

description: Gene expression data from field grown developing seeds 5 days after anthesis

hyb_protocol: Following fragmentation, the labelled samples were mixed with 0.1 mg/ml sonicated herring sperm DNA in hybridization buffer (100mM 2-N-morpholino-ethane-sulphonic acid (MES), 1 M NaCL, 20mM EDTA, 0.01% Tween 20, 0.5 mg/ml BSA, 10% DMSO), denatured at 99°C for 5 min then added to GeneChip Wheat Genome Array (Affymetrix) according to manufacturer instructions and hybridized for 16 h at 45°C in a rotisserie oven at 60 rpm. Following hybridization the arrays were washed and stained in the Affymetrix fluidics station 450 according to standard protocol (Section 2.3.3 of the Expression Analysis Technical Manual (http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

scan_protocol: GeneChips were scanned using the Affymetrix scanner 3000.

data_processing: The raw data in the Affymetrix CEL files of all 78 arrays representing two biological replicates of each of 39 genotypes were subjected to quantile normalization using Robust Multi-Array Average (RMA) (Bolstad, B.M., Irizarry, R.A., Astrand, M., Speed, T.P. 2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185-193) followed by normalization to the median.

molecule: polyA RNA

organism: Triticum aestivum

source_name: developing seed collected from field grown material 5 days after anthesis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, Affymetrix). mRNA was used for first and second strand cDNA synthesis using the One Cycle cDNA Synthesis Kit (Affymetrix, http://www.affymetrix.com) following the manufacturers instructions. The resulting cDNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) according to instructions and then used to make purified biotin labelled cRNA using the GeneChip IVT labelling kit and the GeneChip Sample Cleanup Module (Affymetrix). The resulting labelled cRNA was quantified and the yield and size distribution of labelled fragments checked by electrophoresis using the Agilent Bioanalyzer. The labelled cRNA was fragmented using the GeneChip Sample Cleanup Module (Affymetrix) and stored at -20°C.

growth_protocol: The 39 lines and parental lines were grown as 1.47 m rows in three replications in a 7x7 (49 entry) lattice design at Winnipeg, Manitoba in 2004. Each replicate had a unique randomization

extract_protocol: Total RNA was extracted from frozen seed using a modification of the protocol described atMontana State University Plant Sciences website. The content of a 2 mL tube full of frozen seeds was ground to a fine powder in liquid nitrogen using a mortar and pestle. Ground seed was transferred to 50 mL Oak Ridge tubes and 7.5 mL of extraction buffer was added. [50 mL Extraction Buffer contained 35 mL nuclease-free water, 2.5 mL 1M Tris, pH 9.0. 5 mL 2M NaCl, 5 mL 10% Sarcosyl, 2 mL 0.5M EDTA,  pH 8.0, 250 ?L 1M DTT]. After vortexing well, 3.75 mL phenol and 3.75 mL chloroform/isoamyl alcohol (49:2) were added and samples vortexed again. Samples were centrifuged 10 min at 13,000 rpm in a Sorvall model RC5C at 4°C using an SS-34 rotor. A total of 7.5 mL of the upper aqueous phase was transferred to a clean Oak Ridge tube, 15 mL Trizol was added and the sample was vortexed. A volume of 3 mL of choloroform was added and the sample was vortexed again. Samples were centrifuged 10 min at 13,000 rpm in the Sorvall at 4°C. A volume of 15 mL of the upper aqueous phase was transferred to a fresh Oak Ridge tube and 10 mL of chloroform was added and the sample was vortexed. Samples were centrifuged again in the Sorvall at 13,000 rpm for 10 min at 4°C. A volume of 12 mL of the upper phase was transferred to a fresh Oak Ridge tube and the RNA precipitated by adding 1,200 uL of 3M sodium acetate and 24 mL of absolute ethanol. Samples were left at -80°C overnight then centrifuged at 14,000 rpm at 4°C in the Sorvall for 20-30 minutes to precipitate the RNA. The pellet was rinsed with 70% ethanol, lightly dried and re-suspended in 1 mL of nuclease-free water. RNA concentration was quantified using a spectrophotometer. All solutions and equipment used in this procedure were RNAse-free. Messenger RNA was enriched from total RNA using the Poly(A) Purist MAG kit  (Ambion) according to the protocol provided by the manufacturer. Messenger RNA was checked for quality and quantified by micro-chromatography using an Agilent 2000 Bioanalyzer and the RNA 6000 Nano Assay Kit both purchased from Agilent Technologies. Quantification was carried out according to the instructions provided with the kit.

treatment_protocol: spikes were tagged when anthers were visible, enough developing seeds to fill a 2mL tube were isolated from each spike 5 days after tagging and flash frozen in liquid nitrogen

value: A77 from RL4452 x AC Domain mapping population

tag: Age

value: developing seed 5 days after anthesis


title: genotype H8 developing seed at 5 days after anthesis, biological rep3

value: H8 from RL4452 x AC Domain mapping population


title: genotype H9 developing seed at 5 days after anthesis, biological rep2

value: H9 from RL4452 x AC Domain mapping population


title: genotype B11 developing seed at 5 days after anthesis, biological rep3

value: B11 from RL4452 x AC Domain mapping population


title: genotype H23 developing seed at 5 days after anthesis, biological rep3

value: H23 from RL4452 x AC Domain mapping population


title: genotype C10 developing seed at 5 days after anthesis, biological rep1

value: C10 from RL4452 x AC Domain mapping population


title: genotype H8 developing seed at 5 days after anthesis, biological rep1


title: genotype F44 developing seed at 5 days after anthesis, biological rep1

value: F44 from RL4452 x AC Domain mapping population


title: genotype F44 developing seed at 5 days after anthesis, biological rep3


title: genotype B65 developing seed at 5 days after anthesis, biological rep1

value: B65 from RL4452 x AC Domain mapping population


title: genotype B65 developing seed at 5 days after anthesis, biological rep3


title: genotype F48 developing seed at 5 days after anthesis, biological rep3

value: F48 from RL4452 x AC Domain mapping population


title: genotype C22 developing seed at 5 days after anthesis, biological rep3

value: C22 from RL4452 x AC Domain mapping population


title: genotype C10 developing seed at 5 days after anthesis, biological rep3


title: genotype H23 developing seed at 5 days after anthesis, biological rep1


title: genotype H9 developing seed at 5 days after anthesis, biological rep3


title: genotype F82 developing seed at 5 days after anthesis, biological rep3

value: F82 from RL4452 x AC Domain mapping population


title: genotype B11 developing seed at 5 days after anthesis, biological rep1


title: genotype F48 developing seed at 5 days after anthesis, biological rep1


title: genotype D39 developing seed at 5 days after anthesis, biological rep3

value: D39 from RL4452 x AC Domain mapping population


title: genotype A77 developing seed at 5 days after anthesis, biological rep3


title: genotype C22 developing seed at 5 days after anthesis, biological rep1


title: genotype J15 developing seed at 5 days after anthesis, biological rep1

value: J15 from RL4452 x AC Domain mapping population


title: genotype J15 developing seed at 5 days after anthesis, biological rep3


title: genotype D39 developing seed at 5 days after anthesis, biological rep1


title: genotype F82 developing seed at 5 days after anthesis, biological rep1


title: genotype B33 developing seed at 5 days after anthesis, biological rep1

value: B33 from RL4452 x AC Domain mapping population


title: genotype F38a developing seed at 5 days after anthesis, biological rep3

value: F38a from RL4452 x AC Domain mapping population


title: genotype B33 developing seed at 5 days after anthesis, biological rep3


title: genotype C25 developing seed at 5 days after anthesis, biological rep3

value: C25 from RL4452 x AC Domain mapping population


title: genotype F38b developing seed at 5 days after anthesis, biological rep3

value: F38b from RL4452 x AC Domain mapping population


title: genotype F38a developing seed at 5 days after anthesis, biological rep1

value: developing seed 5 days after anthesis


title: genotype A35 developing seed at 5 days after anthesis, biological rep3

value: A35 from RL4452 x AC Domain mapping population


title: genotype A40 developing seed at 5 days after anthesis, biological rep1

value: A40 from RL4452 x AC Domain mapping population


title: genotype A35 developing seed at 5 days after anthesis, biological rep1


title: genotype C25 developing seed at 5 days after anthesis, biological rep1


title: genotype C31 developing seed at 5 days after anthesis, biological rep3

value: C31 from RL4452 x AC Domain mapping population


title: genotype G30 developing seed at 5 days after anthesis, biological rep3

value: G30 from RL4452 x AC Domain mapping population


title: genotype A88 developing seed at 5 days after anthesis, biological rep3

value: A88 from RL4452 x AC Domain mapping population


title: genotype B68 developing seed at 5 days after anthesis, biological rep1

value: B68 from RL4452 x AC Domain mapping population


title: genotype A81 developing seed at 5 days after anthesis, biological rep1

value: A81 from RL4452 x AC Domain mapping population


title: genotype A88 developing seed at 5 days after anthesis, biological rep1


title: genotype F38b developing seed at 5 days after anthesis, biological rep1


title: genotype A10 developing seed at 5 days after anthesis, biological rep3

value: A10 from RL4452 x AC Domain mapping population


title: genotype E5 developing seed at 5 days after anthesis, biological rep1

value: E5 from RL4452 x AC Domain mapping population


title: genotype A40 developing seed at 5 days after anthesis, biological rep3


title: genotype A10 developing seed at 5 days after anthesis, biological rep1


title: genotype A81 developing seed at 5 days after anthesis, biological rep3


title: genotype D15 developing seed at 5 days after anthesis, biological rep3

value: D15 from RL4452 x AC Domain mapping population


title: genotype D15 developing seed at 5 days after anthesis, biological rep1


title: genotype B68 developing seed at 5 days after anthesis, biological rep3


title: genotype G30 developing seed at 5 days after anthesis, biological rep1


title: genotype C31 developing seed at 5 days after anthesis, biological rep1


title: genotype DH95 developing seed at 5 days after anthesis, biological rep1

value: DH95 from RL4452 x AC Domain mapping population


title: genotype A91 developing seed at 5 days after anthesis, biological rep3

value: A91 from RL4452 x AC Domain mapping population


title: genotype E5 developing seed at 5 days after anthesis, biological rep3


title: genotype A91 developing seed at 5 days after anthesis, biological rep1


title: genotype F36 developing seed at 5 days after anthesis, biological rep1

value: F36 from RL4452 x AC Domain mapping population


title: genotype DH91 developing seed at 5 days after anthesis, biological rep3

value: DH91 from RL4452 x AC Domain mapping population


title: genotype F29 developing seed at 5 days after anthesis, biological rep3

value: F29 from RL4452 x AC Domain mapping population


title: genotype H5 developing seed at 5 days after anthesis, biological rep1

value: H5 from RL4452 x AC Domain mapping population


title: genotype DH91 developing seed at 5 days after anthesis, biological rep1

value: developing seed 5 days after anthesis


title: genotype H10 developing seed at 5 days after anthesis, biological rep3

value: H10 from RL4452 x AC Domain mapping population


title: genotype G32 developing seed at 5 days after anthesis, biological rep3

tag: Genotype:G32 from RL4452 x AC Domain mapping population


title: genotype F36 developing seed at 5 days after anthesis, biological rep3


title: genotype F29 developing seed at 5 days after anthesis, biological rep1


title: genotype G13 developing seed at 5 days after anthesis, biological rep1

value: G13 from RL4452 x AC Domain mapping population


title: genotype G32 developing seed at 5 days after anthesis, biological rep1

value: G32 from RL4452 x AC Domain mapping population


title: genotype H5 developing seed at 5 days after anthesis, biological rep3


title: genotype DH95 developing seed at 5 days after anthesis, biological rep3


title: Ok2: Hippocampus_NT-A_rep7

status: Public on Mar 15 2007

city: Lexington

first: Veronique

last: Thibault

state: KY

address: 800 Rose Street

department: Pharmacology

institute: University of Kentucky

description: Gene expression data from Young and Aged behaviorally characterized F344 rats

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Rattus Norvegus. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 7G scan.

data_processing: Microarray Data Filtering: Procedures employed were similar to those used previously (Blalock et al., 2003; Blalock et al., 2004). Briefly, the Microarray Analysis Suite 5 (MAS5) algorithm was applied using Affymetrix’ Gene Chip Operating System software (GCOS v1.1). All-probe-set scaling normalization (target intensity 500) was applied, and presence-call and signal intensity values were copied to Excel for further analysis. Annotations were downloaded from the Affymetrix website (July, 2005; augmented by a rat genome database search). For gene symbols represented by > 1 probe set (repeats), the probe set with the smallest test statistic was used. Within group outliers (> 2 SD from the group mean) (Blalock et al., 2004) were treated as missing values.

source_name: Non-Trained Aged Hippocampus (NT-A)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA (GCOS manual, 2005, Affymetrix).

growth_protocol: The animals were left undisturbed for a minimum of 1 month in our facility until the beginning of behavioral testing. Rats were housed in pairs in polycarbonate cages (45 x 30 x 18 cm) with corncob bedding and maintained on a 12 h light/dark schedule (lights off at 7:00 P.M.). Food (LabDiet 5001 rodent diet; LabDiet, Brentwood, MO) and water were available ad libitum. Animal health was monitored by a veterinarian; animals showing overt signs of morbidity were removed from the study.

extract_protocol: Immediately after euthanasia, the dorsal half of the left hippocampus was dissected free and frozen. Subsequently, mRNA was extracted, generating ~11micrograms total RNA per hippocampal sample, labeled and hybridized to RAE-230A (Affymetrix) GeneChips according to standard protocols

treatment_protocol: Young and aged rats were separated into home cage (Non-Trained, NT) and behaviorally-characterized groups. Aged animals in the behaviorally-characterized groups were separated into two categories, aged cognitively impaired (AI) and aged cognitively unimpaired (AU) based on their relative performance in the Morris Water Maze task as previously described (Tombaugh et al., 2005)

tag: Strain:F344 Gender:Male Age

value: 24-26 Months old tissue:brain-hippocampus


title: Ok4: Hippocampus_NT-A_rep9


title: Oj9: Hippocampus_5T-AI_rep10

source_name: Behaviorally-characterized Aged Impaired Hippocampus at Day5 (5T-AI)


title: Ok5: Hippocampus_NT-A_rep10


title: genotype G13 developing seed at 5 days after anthesis, biological rep3


title: Oj3: Hippocampus_5T-AI_rep9


title: Oi6: Hippocampus_5T-Y_rep10

source_name: Behaviorally-characterized Young Unimpaired Hippocampus at Day5 (5T-Y)

value: 4-6 Months old tissue:brain-hippocampus


title: Ok3: Hippocampus_NT-A_rep8


title: genotype H10 developing seed at 5 days after anthesis, biological rep1


title: Oi2: Hippocampus_5T-Y_rep6


title: Oj16: Hippocampus_5T-AI_rep8


title: Oj11: Hippocampus_5T-AI_rep6


title: Oi5: Hippocampus_5T-Y_rep9


title: Oi3: Hippocampus_5T-Y_rep7


title: Oj5: Hippocampus_21PT-AI_rep9

source_name: Behaviorally-characterized Aged Impaired Hippocampus at Day21 (21PT-AI)


title: Ok1: Hippocampus_NT-A_rep6


title: Oj19: Hippocampus_21PT-AI_rep8


title: Ny9: Hippocampus_5T-AI_rep5


title: Ny7: Hippocampus_21PT-AU_rep10

source_name: Behaviorally-characterized Aged Unimpaired Hippocampus at Day21 (21PT-AU)


title: Nz1: Hippocampus_21PT-Y_rep9

source_name: Behaviorally-characterized Young Unimpaired Hippocampus at Day21 (21PT-Y)


title: Oi4: Hippocampus_5T-Y_rep8


title: Ny6: Hippocampus_5T-AU_rep10

source_name: Behaviorally-characterized Aged Unimpaired Hippocampus at Day5 (5T-AU)


title: Nj20: Hippocampus_21PT-AU_rep9


title: Nj13: Hippocampus_21PT-AI_rep5


title: Oi1: Hippocampus_5T-Y_rep5


title: Nj18: Hippocampus_21PT-AI_rep7


title: Oj15: Hippocampus_5T-AI_rep7


title: Ny13: Hippocampus_5T-AU_rep8


title: Ng4: Hippocampus_NT-Y_rep10

source_name: Non-trained Young Hippocampus (NT-Y)


title: Ny5: Hippocampus_5T-AU_rep9


title: Nj14: Hippocampus_21PT-AU_rep8


title: Nj15: Hippocampus_21PT-AI_rep6


title: Nj10: Hippocampus_21PT-AI_rep4


title: Ny16: Hippocampus_5T-AI_rep4


title: Ng11: Hippocampus_NT-Y_rep6


title: Ng12: Hippocampus_NT-Y_rep7


title: Ng3: Hippocampus_NT-Y_rep9


title: Nd4: Hippocampus_5T-AU_rep7


title: Nd8: Hippocampus_21PT-AU_rep7


title: Nf1: Hippocampus_NT-A_rep4


title: Nf2: Hippocampus_NT-A_rep5


title: Mq2: Hippocampus_NT-A_rep3


title: Ng1: Hippocampus_NT-Y_rep5


title: Mq1: Hippocampus_NT-A_rep2


title: Ng2: Hippocampus_NT-Y_rep8


title: Mk2: Hippocampus_21PT-AI_rep2


title: Mk14: Hippocampus_5T-AI_rep3


title: Mk13: Hippocampus_21PT-AI_rep1


title: Mk12: Hippocampus_21PT-AU_rep5


title: Nd14: Hippocampus_21PT-AU_rep6


title: Mk8: Hippocampus_21PT-AI_rep3


title: Me1: Hippocampus_NT-Y_rep2


title: Me2: Hippocampus_NT-Y_rep3


title: Mk1: Hippocampus_21PT-AU_rep4


title: Lv1: Hippocampus_21PT-Y_rep6


title: Mc1: Hippocampus_5T-Y_rep2


title: Md4: Hippocampus_5T-AI_rep2


title: Mc3: Hippocampus_5T-Y_rep4


title: Mc2: Hippocampus_5T-Y_rep3


title: Lv3: Hippocampus_21PT-Y_rep8


title: Me3: Hippocampus_NT-Y_rep4


title: Lg19: Hippocampus_5T-AU_rep6


title: Ln2: Hippocampus_NT-Y_rep1


title: Lg11: Hippocampus_5T-AU_rep5


title: Lv2: Hippocampus_21PT-Y_rep7


title: Ln1: Hippocampus_NT-A_rep1


title: Lb1: Hippocampus_5T-AU_rep2


title: Ky3: Hippocampus_21PT-Y_rep3


title: Lb19: Hippocampus_5T-AU_rep4


title: Kr5: Hippocampus_5T-AU_rep1


title: Kg15: Hippocampus_21PT-AU_rep2


title: Ky6: Hippocampus_21PT-Y_rep5


title: Kg12: Hippocampus_21PT-AU_rep1


title: Ky5: Hippocampus_21PT-Y_rep4


title: Kp6: Hippocampus_5T-Y_rep1


title: Kz13: Hippocampus_21PT-AU_rep3


title: Lb16: Hippocampus_5T-AU_rep3


title: Kr10: Hippocampus_5T-AI_rep1