title: 33_VP9.I1W2.CEL, Experimental replicate 2

description:
VP-RIL9 - P.sojae inoculated; 24 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 34_CON.I2W1.CEL, Experimental replicate 1

status: Public on Nov 26 2007

type: RNA

city: Blacksburg

first: sucheta

last: Tripathy

state: VA

address: 1, Washington street

department: Virginia  Bioinformatics Institute

country: USA

institute: Virginia Tech

description:
CONRAD - P.sojae inoculated; 48 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

hyb_protocol: hybridization cocktail is prepared, including the fragmented target, probe array controls, BSA, and herring sperm DNA. It is then hybridized to the probe array during a 16-hour incubation(Affymetrix technical manual - 2004)

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000

data_processing: The data were analyzed with RMA suite from R package version 2.4.0. Background correction was using RMA followed by quantile normalization and data was summarized using median polish method

label: biotin

molecule: total RNA

organism: Glycine max

source_name: Soybean cultivar CONRAD - pathogen(P.sojae) Inoculated: 48 hours post inoculation

label_protocol: The RNA samples isolated from each of the two inoculation replications were pooled in equal amounts before subjecting to microarray assay. RNA samples from mock inoculated tissue contain 0.03125-4% spike-in RNA from Phytophthora sojae mycellium grown in liquid sucrose-salts medium , depending upon resistance level and sampling time. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA. RNA is is first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction is carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling. The biotinylated cRNA targets are then cleaned up, fragmented, and hybridized to GeneChip expression arrays(Affymetrix Technical manual - 2004)

growth_protocol: Soybean plants were grown in growth chambers and later transferred to trays with clothes soaked in water

extract_protocol: QIAGEN RNeasy Kit : As recommended by manufacturer

treatment_protocol: Inoculation assays were performed using the slant board technique (Olah and Schmitthenner, 1985).[ Briefly, 7-day-old soybean seedlings were thoroughly rinsed under tap water and placed in an inoculation tray (10 plants per tray, 3 trays per inoculation replication). The plants were wounded at 2 cm below the beginning of the root zone by scraping the epidermis with a scalpel and then inoculated with a mycelial slurry from a 7-day-old culture or agar alone. Samples of root tissues were collected at 3 and 5 days post inoculation (dpi) from 7.5 mm below and above the lesion margin from each seedling with characteristic lesions. For the mock-inoculated plants, tissue sections were taken 7.5 mm below and above the position corresponding to the average lesion length measured from the inoculated samples. The lesion length (mm) from the inoculation point up to the edge of the lesion margin was also measured 3 and 5 dpi. For each experimental replication, 2 replicates of 30 seedlings per condition were inoculated and harvested separately. All the plants for an experiment were grown in the same environmental growth chamber (Chagrin Falls, Ohio; Model M-48 with TC2 microcontroller unit) with day and night temperatures settings of 27C and 21C and relative humidity averaging 75 to 90%.

tag: cultivar - CONRAD

tag: Tissue/Cell Type

value: Soybean root/hypocotyls - P.sojae mycelium from minimal medium

tag: total Soybean RNA


title: 35_V71.I5U1.CEL, Experimental replicate 1

description:
V71-370 - P.sojae inoculated; 120 hrs (upper); ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the upper side of the inoculation

tag: cultivar - V71-370


title: 37_VP9.M3W4.CEL, Experimental replicate 4

description:
VP-RIL9 - Mock inoculated; 72 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - Mock Inoculated (Inoculated with water + agar): 72 hours post inoculation

tag: cultivar - VP-RIL9

tag: total Soybean RNA Plus 2 % P.sojae RNA added


title: 32_SLO.M2W1.CEL, Experimental replicate 1

description:
SLOAN - Mock inoculated; 48 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - Mock Inoculated (Inoculated with water + agar): 48 hours post inoculation

tag: cultivar - SLOAN

tag: total Soybean RNA Plus 1 % P.sojae RNA added


title: 32_CON.M1W3.CEL, Experimental replicate 3

description:
CONRAD - Mock inoculated; 24 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - Mock Inoculated (Inoculated with water + agar): 24 hours post inoculation

tag: total Soybean RNA Plus 0.03125 % P.sojae RNA added


title: 32_VP9.I5U2.CEL, Experimental replicate 2

description:
VP-RIL9 - P.sojae inoculated; 120 hrs (upper); ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 31_SLO.I2W3.CEL, Experimental replicate 3

description:
SLOAN - P.sojae inoculated; 48 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 48 hours post inoculation


title: 31_SLO.I3U2.CEL, Experimental replicate 2

description:
SLOAN - P.sojae inoculated; 72 hrs (upper); ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 30_V71.M3W4.CEL, Experimental replicate 4

description:
V71-370 - Mock inoculated; 72 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - Mock Inoculated (Inoculated with water + agar): 72 hours post inoculation

tag: total Soybean RNA Plus 0.125 % P.sojae RNA added


title: 32_CON.I2W4.CEL, Experimental replicate 4

description:
CONRAD - P.sojae inoculated; 48 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 30_VP9.I3L3.CEL, Experimental replicate 3

description:
VP-RIL9 - P.sojae inoculated; 72 hrs (lower); ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 39_SLO.M2W4.CEL, Experimental replicate 4

description:
SLOAN - Mock inoculated; 48 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 30_V71.I3U1.CEL, Experimental replicate 1

description:
V71-370 - P.sojae inoculated; 72 hrs (upper); ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 31_VP9.I3L4.CEL, Experimental replicate 4

description:
VP-RIL9 - P.sojae inoculated; 72 hrs (lower); ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 2_CON.I5U1.CEL, Experimental replicate 1

description:
CONRAD - P.sojae inoculated; 120 hrs (upper); ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 28_VP9.M3W1.CEL, Experimental replicate 1

description:
VP-RIL9 - Mock inoculated; 72 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 29_V71.I5U3.CEL, Experimental replicate 3

description:
V71-370 - P.sojae inoculated; 120 hrs (upper); ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 2_CON.M3W2.CEL, Experimental replicate 2

description:
CONRAD - Mock inoculated; 72 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - Mock Inoculated (Inoculated with water + agar): 72 hours post inoculation


title: 2_V71.I2W3.CEL, Experimental replicate 3

description:
V71-370 - P.sojae inoculated; 48 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 48 hours post inoculation


title: 31_SLO.I5U1.CEL, Experimental replicate 1

description:
SLOAN - P.sojae inoculated; 120 hrs (upper); ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 29_CON.I1W1.CEL, Experimental replicate 1

description:
CONRAD - P.sojae inoculated; 24 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - pathogen(P.sojae) Inoculated: 24 hours post inoculation


title: 27_CON.I3L2.CEL, Experimental replicate 2

description:
CONRAD - P.sojae inoculated; 72 hrs (lower); ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 30_SLO.M1W2.CEL, Experimental replicate 2

description:
SLOAN - Mock inoculated; 24 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - Mock Inoculated (Inoculated with water + agar): 24 hours post inoculation

tag: total Soybean RNA Plus 0.5 % P.sojae RNA added


title: 2_V71.I3L4.CEL, Experimental replicate 4

description:
V71-370 - P.sojae inoculated; 72 hrs (lower); ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 27_VP9.I1W1.CEL, Experimental replicate 1

description:
VP-RIL9 - P.sojae inoculated; 24 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - pathogen(P.sojae) Inoculated: 24 hours post inoculation


title: 29_V71.I5U4.CEL, Experimental replicate 4

description:
V71-370 - P.sojae inoculated; 120 hrs (upper); ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 27_SLO.M5W4.CEL, Experimental replicate 4

description:
SLOAN - Mock inoculated; 120 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - Mock Inoculated (Inoculated with water + agar): 120 hours post inoculation

tag: total Soybean RNA Plus 4 % P.sojae RNA added


title: 29_CON.I5L2.CEL, Experimental replicate 2

description:
CONRAD - P.sojae inoculated; 120 hrs (lower); ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 28_V71.I1W2.CEL, Experimental replicate 2

description:
V71-370 - P.sojae inoculated; 24 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 24 hours post inoculation


title: 28_SLO.I3U4.CEL, Experimental replicate 4

description:
SLOAN - P.sojae inoculated; 72 hrs (upper); ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 26_VP9.M5W2.CEL, Experimental replicate 2

description:
VP-RIL9 - Mock inoculated; 120 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - Mock Inoculated (Inoculated with water + agar): 120 hours post inoculation


title: 28_SLO.I5L3.CEL, Experimental replicate 3

description:
SLOAN - P.sojae inoculated; 120 hrs (lower); ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 25_VP9.M2W3.CEL, Experimental replicate 3

description:
VP-RIL9 - Mock inoculated; 48 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - Mock Inoculated (Inoculated with water + agar): 48 hours post inoculation


title: 26_CON.I1W3.CEL, Experimental replicate 3

description:
CONRAD - P.sojae inoculated; 24 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 26_CON.M2W1.CEL, Experimental replicate 1

description:
CONRAD - Mock inoculated; 48 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - Mock Inoculated (Inoculated with water + agar): 48 hours post inoculation

tag: total Soybean RNA Plus 0.0625 % P.sojae RNA added


title: 27_V71.M5W3.CEL, Experimental replicate 3

description:
V71-370 - Mock inoculated; 120 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - Mock Inoculated (Inoculated with water + agar): 120 hours post inoculation

tag: total Soybean RNA Plus 0.25 % P.sojae RNA added


title: 25_V71.M5W1.CEL, Experimental replicate 1

description:
V71-370 - Mock inoculated; 120 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 25_V71.M3W2.CEL, Experimental replicate 2

description:
V71-370 - Mock inoculated; 72 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - Mock Inoculated (Inoculated with water + agar): 72 hours post inoculation


title: 26_VP9.M2W4.CEL, Experimental replicate 4

description:
VP-RIL9 - Mock inoculated; 48 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 24_VP9.M1W4.CEL, Experimental replicate 4

description:
VP-RIL9 - Mock inoculated; 24 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - Mock Inoculated (Inoculated with water + agar): 24 hours post inoculation


title: 25_CON.I5L4.CEL, Experimental replicate 4

description:
CONRAD - P.sojae inoculated; 120 hrs (lower); ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 24_VP9.M2W2.CEL, Experimental replicate 2

description:
VP-RIL9 - Mock inoculated; 48 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 24_CON.I5L1.CEL, Experimental replicate 1

description:
CONRAD - P.sojae inoculated; 120 hrs (lower); ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 24_CON.I3U3.CEL, Experimental replicate 3

description:
CONRAD - P.sojae inoculated; 72 hrs (upper); ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 23_VP9.M1W3.CEL, Experimental replicate 3

description:
VP-RIL9 - Mock inoculated; 24 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 23_V71.M5W2.CEL, Experimental replicate 2

description:
V71-370 - Mock inoculated; 120 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 22_SLO.M5W3.CEL, Experimental replicate 3

description:
SLOAN - Mock inoculated; 120 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 23_CON.M2W4.CEL, Experimental replicate 4

description:
CONRAD - Mock inoculated; 48 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 20_CON.M2W2.CEL, Experimental replicate 2

description:
CONRAD - Mock inoculated; 48 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 1_VP9.I3U3.CEL, Experimental replicate 3

description:
VP-RIL9 - P.sojae inoculated; 72 hrs (upper); ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 23_V71.M2W1.CEL, Experimental replicate 1

description:
V71-370 - Mock inoculated; 48 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - Mock Inoculated (Inoculated with water + agar): 48 hours post inoculation


title: 21_CON.I1W2.CEL, Experimental replicate 2

description:
CONRAD - P.sojae inoculated; 24 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - pathogen(P.sojae) Inoculated: 24 hours post inoculation


title: 1_V71.I3L1.CEL, Experimental replicate 1

description:
V71-370 - P.sojae inoculated; 72 hrs (lower); ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 20_V71.I3U3.CEL, Experimental replicate 3

description:
V71-370 - P.sojae inoculated; 72 hrs (upper); ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 21_SLO.M3W4.CEL, Experimental replicate 4

description:
SLOAN - Mock inoculated; 72 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - Mock Inoculated (Inoculated with water + agar): 72 hours post inoculation


title: 20_CON.I3L1.CEL, Experimental replicate 1

description:
CONRAD - P.sojae inoculated; 72 hrs (lower); ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 20_V71.I1W4.CEL, Experimental replicate 4

description:
V71-370 - P.sojae inoculated; 24 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 24 hours post inoculation


title: 19_VP9.I1W3.CEL, Experimental replicate 3

description:
VP-RIL9 - P.sojae inoculated; 24 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - pathogen(P.sojae) Inoculated: 24 hours post inoculation


title: 22_SLO.I5U4.CEL, Experimental replicate 4

description:
SLOAN - P.sojae inoculated; 120 hrs (upper); ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 22_VP9.M1W1.CEL, Experimental replicate 1

description:
VP-RIL9 - Mock inoculated; 24 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 1_SLO.M2W2.CEL, Experimental replicate 2

description:
SLOAN - Mock inoculated; 48 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - Mock Inoculated (Inoculated with water + agar): 48 hours post inoculation


title: 21_V71.I5L3.CEL, Experimental replicate 3

description:
V71-370 - P.sojae inoculated; 120 hrs (lower); ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 19_V71.M2W4.CEL, Experimental replicate 4

description:
V71-370 - Mock inoculated; 48 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 21_VP9.I3U1.CEL, Experimental replicate 1

description:
VP-RIL9 - P.sojae inoculated; 72 hrs (upper); ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 22_V71.I3L2.CEL, Experimental replicate 2

description:
V71-370 - P.sojae inoculated; 72 hrs (lower); ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 19_SLO.M5W2.CEL, Experimental replicate 2

description:
SLOAN - Mock inoculated; 120 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - Mock Inoculated (Inoculated with water + agar): 120 hours post inoculation


title: 19_V71.I2W1.CEL, Experimental replicate 1

description:
V71-370 - P.sojae inoculated; 48 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 48 hours post inoculation


title: 1_V71.M1W4.CEL, Experimental replicate 4

description:
V71-370 - Mock inoculated; 24 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - Mock Inoculated (Inoculated with water + agar): 24 hours post inoculation


title: 18_VP9.I5U4.CEL, Experimental replicate 4

description:
VP-RIL9 - P.sojae inoculated; 120 hrs (upper); ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 17_VP9.I3U2.CEL, Experimental replicate 2

description:
VP-RIL9 - P.sojae inoculated; 72 hrs (upper); ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 18_SLO.I5U3.CEL, Experimental replicate 3

description:
SLOAN - P.sojae inoculated; 120 hrs (upper); ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 18_SLO.I1W1.CEL, Experimental replicate 1

description:
SLOAN - P.sojae inoculated; 24 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 24 hours post inoculation


title: 17_SLO.M5W1.CEL, Experimental replicate 1

description:
SLOAN - Mock inoculated; 120 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 16_V71.I1W1.CEL, Experimental replicate 1

description:
V71-370 - P.sojae inoculated; 24 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 16_VP9.I5U3.CEL, Experimental replicate 3

description:
VP-RIL9 - P.sojae inoculated; 120 hrs (upper); ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 18_SLO.I3L2.CEL, Experimental replicate 2

description:
SLOAN - P.sojae inoculated; 72 hrs (lower); ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 15_CON.I3U1.CEL, Experimental replicate 1

description:
CONRAD - P.sojae inoculated; 72 hrs (upper); ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 17_CON.I3L4.CEL, Experimental replicate 4

description:
CONRAD - P.sojae inoculated; 72 hrs (lower); ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 16_SLO.I5L2.CEL, Experimental replicate 2

description:
SLOAN - P.sojae inoculated; 120 hrs (lower); ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 16_V71.M5W4.CEL, Experimental replicate 4

description:
V71-370 - Mock inoculated; 120 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - Mock Inoculated (Inoculated with water + agar): 120 hours post inoculation


title: 14_CON.M3W3.CEL, Experimental replicate 3

description:
CONRAD - Mock inoculated; 72 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - Mock Inoculated (Inoculated with water + agar): 72 hours post inoculation


title: 15_CON.M1W2.CEL, Experimental replicate 2

description:
CONRAD - Mock inoculated; 24 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - Mock Inoculated (Inoculated with water + agar): 24 hours post inoculation


title: 12_V71.M1W1.CEL, Experimental replicate 1

description:
V71-370 - Mock inoculated; 24 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 14_SLO.I5L1.CEL, Experimental replicate 1

description:
SLOAN - P.sojae inoculated; 120 hrs (lower); ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 14_VP9.I2W2.CEL, Experimental replicate 2

description:
VP-RIL9 - P.sojae inoculated; 48 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - pathogen(P.sojae) Inoculated: 48 hours post inoculation


title: 12_VP9.M5W3.CEL, Experimental replicate 3

description:
VP-RIL9 - Mock inoculated; 120 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - Mock Inoculated (Inoculated with water + agar): 120 hours post inoculation


title: 17_CON.M2W3.CEL, Experimental replicate 3

description:
CONRAD - Mock inoculated; 48 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - Mock Inoculated (Inoculated with water + agar): 48 hours post inoculation


title: 15_V71.I3U4.CEL, Experimental replicate 4

description:
V71-370 - P.sojae inoculated; 72 hrs (upper); ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 13_SLO.I2W1.CEL, Experimental replicate 1

description:
SLOAN - P.sojae inoculated; 48 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 48 hours post inoculation


title: 11_VP9.I5L4.CEL, Experimental replicate 4

description:
VP-RIL9 - P.sojae inoculated; 120 hrs (lower); ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 15_V71.I3L3.CEL, Experimental replicate 3

description:
V71-370 - P.sojae inoculated; 72 hrs (lower); ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 12_V71.I5L2.CEL, Experimental replicate 2

description:
V71-370 - P.sojae inoculated; 120 hrs (lower); ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 13_SLO.I1W3.CEL, Experimental replicate 3

description:
SLOAN - P.sojae inoculated; 24 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 11_VP9.M3W2.CEL, Experimental replicate 2

description:
VP-RIL9 - Mock inoculated; 72 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - Mock Inoculated (Inoculated with water + agar): 72 hours post inoculation


title: 12_CON.M5W4.CEL, Experimental replicate 4

description:
CONRAD - Mock inoculated; 120 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - Mock Inoculated (Inoculated with water + agar): 120 hours post inoculation


title: 13_SLO.I5U2.CEL, Experimental replicate 2

description:
SLOAN - P.sojae inoculated; 120 hrs (upper); ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 13_VP9.I2W4.CEL, Experimental replicate 4

description:
VP-RIL9 - P.sojae inoculated; 48 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 14_CON.I1W4.CEL, Experimental replicate 4

description:
CONRAD - P.sojae inoculated; 24 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - pathogen(P.sojae) Inoculated: 24 hours post inoculation


title: 11_CON.M5W1.CEL, Experimental replicate 1

description:
CONRAD - Mock inoculated; 120 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 10_VP9.I3L1.CEL, Experimental replicate 1

description:
VP-RIL9 - P.sojae inoculated; 72 hrs (lower); ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 11_CON.I2W3.CEL, Experimental replicate 3

description:
CONRAD - P.sojae inoculated; 48 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - pathogen(P.sojae) Inoculated: 48 hours post inoculation


title: head and neck squamous cell carcinoma (HNSCC) sampleNo.05

status: Public on Nov 24 2007

city: Chiba

first: Satoya

last: Shimizu

address: 1-8-1 Inohana, Chuo-ku

country: Japan

institute: Chiba university

hyb_protocol: Hybridized for 20 h at 50 C. Hybridization buffer and washing protocol was followed by the protocol supplied by Hitach Software Engineering Co., Ltd. http://www.dna-chip.co.jp/thesis/AceGeneProtocol.pdf

scan_protocol: ScanArray HT (PerkinElmer Japan Co., Ltd.) was used for scanning. Array images were analyzed with DNASIS Array (Hitachi Software Engineering Co., Ltd.).

data_processing: This data were analyzed by DNASIS array software(Hitachi Software Engineering), which converted the signal intensity of each spot into text format. Log2-ratios of the median subtracted background intensity levels were analyzed. Data from each microarray were normalized by LOWESS normalization.

organism: Homo sapiens

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp™  aRNA Amplification Kit (Ambion). CyeDye Coupling and fragmentation were performed as the protocol supplied by Hitach Software Engineering Co., Ltd. http://www.dna-chip.co.jp/thesis/AceGeneProtocol.pdf

extract_protocol: TriZol procedure

tag: Non-tumorus tissue

tag: Tumor tissue

tag: Histlogical Type:moderately differentiated squamous cell carcinoma

tag: Stage:Ⅲ (T2N1)


title: 10_CON.I2W2.CEL, Experimental replicate 2

description:
CONRAD - P.sojae inoculated; 48 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

tag: cultivar - CONRAD

tag: Tissue/Cell Type


title: head and neck squamous cell carcinoma (HNSCC) sampleNo.12

tag: Stage:Ⅰ (T1N0)


title: head and neck squamous cell carcinoma (HNSCC) sampleNo.16

tag: Histlogical Type:well differentiated squamous cell carcinoma

tag: Stage:ⅣA (T4N2b)


title: JMV449-treated HSC2 cell line

description: HSC2 cell line

source_name: Control HSC2 cell line

tag: HSC2 cells 2 hours after vehicle (PBS; control) treatment.

tag: HSC2 cell line is derived from human head and neck squamous cell carcinoma.

source_name: JMV449-treated HSC2 cell line

tag: HSC2 cells 2 hours after JMV449 (10-7M) treatment.


title: head and neck squamous cell carcinoma (HNSCC) sampleNo.17

tag: Stage:ⅣA (T2N2c)


title: head and neck squamous cell carcinoma (HNSCC) sampleNo.13

tag: Stage:ⅣA (T3N2c)


title: head and neck squamous cell carcinoma (HNSCC) sampleNo.02

tag: Histlogical Type:poorly differentiated squamous cell carcinoma


title: head and neck squamous cell carcinoma (HNSCC) sampleNo.11

tag: Stage:Ⅱ (T2N0)


title: JMV449-treated HSC3 cell line

description: HSC3 cell line

source_name: Control HSC3 cell line

tag: HSC3 cells 2 hours after vehicle (PBS; control) treatment.

tag: HSC3 cell line is derived from human head and neck squamous cell carcinoma.

source_name: JMV449-treated HSC3 cell line

tag: HSC3 cells 2 hours after JMV449 (10-7M) treatment.


title: head and neck squamous cell carcinoma (HNSCC) sampleNo.14

tag: Non-tumorus tissue

tag: Tumor tissue

tag: Histlogical Type:moderately differentiated squamous cell carcinoma


title: head and neck squamous cell carcinoma (HNSCC) sampleNo.04

tag: Stage:ⅣA (T4N2c)


title: head and neck squamous cell carcinoma (HNSCC) sampleNo.03


title: head and neck squamous cell carcinoma (HNSCC) sampleNo.01

tag: Stage:ⅣA (T3N2b)


title: head and neck squamous cell carcinoma (HNSCC) sampleNo.06

tag: Stage:Ⅲ (T2N1)


title: head and neck squamous cell carcinoma (HNSCC) sampleNo.15


title: head and neck squamous cell carcinoma (HNSCC) sampleNo.20


title: head and neck squamous cell carcinoma (HNSCC) sampleNo.21

tag: Stage:ⅣA (T4N2b)


title: head and neck squamous cell carcinoma (HNSCC) sampleNo.18


title: Female 67.9 yr after antibody enrichment scan 2 (U133B)

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

hyb_protocol: Hybridization, washing, and staining with phycoerythrin-streptavidin were done with an Affymetrix hybridization oven and fluidics station as recommended by Affymetrix

scan_protocol: Arrays were scanned with an Affymetrix scanner after signal enhancement with biotinylated anti-streptavidin antibody

data_processing: GCRMA normalization was done using ArrayAssist Lite (Stratagene)

source_name: vastus lateralis muscle

label_protocol: Biotinylated cRNA was prepared from 5 ug total RNA using the BioArray kit (Enzo Life Sciences) according to manufacturer's instructions

growth_protocol: not applicable

extract_protocol: RNA was extracted from frozen biopsy specimens in Tri-Reagent according to the manufacturer's recommended protocol

treatment_protocol: not applicable

tag: older female


title: Female 67.3 yr after antibody enrichment scan 2 (U133B)


title: head and neck squamous cell carcinoma (HNSCC) sampleNo.07

tag: Stage:ⅣA (T2N2b)


title: head and neck squamous cell carcinoma (HNSCC) sampleNo.19


title: Female 65.9 yr after antibody enrichment scan 2 (U133B)


title: Female 67.3 yr after antibody enrichment scan 2 (U133A)


title: Female 67.9 yr after antibody enrichment scan 2 (U133A)


title: Female 65.1 yr after antibody enrichment scan 2 (U133B)


title: Female 65.1 yr after antibody enrichment scan 2 (U133A)


title: Female 65.9 yr after antibody enrichment scan 2 (U133A)


title: Female 71.4 yr after antibody enrichment scan 2 (U133B)


title: Female 66.6 yr after antibody enrichment scan 2 (U133B)


title: Female 68.4 yr after antibody enrichment scan 2 (U133A)


title: Female 70.7 yr after antibody enrichment scan 2 (U133B)


title: Female 66.6 yr after antibody enrichment scan 2 (U133A)


title: Female 29.8 yr after antibody enrichment scan 2 (U133A)

tag: young female


title: Female 68.4 yr after antibody enrichment scan 2 (U133B)


title: Female 20.1 yr after antibody enrichment scan 2 (U133B)


title: Female 29.8 yr after antibody enrichment scan 2 (U133B)


title: Female 71.4 yr after antibody enrichment scan 2 (U133A)


title: Female 70.7 yr after antibody enrichment scan 2 (U133A)


title: Female 22.5 yr after antibody enrichment scan 2 (U133A)


title: Female 26.5 yr after antibody enrichment scan 2 (U133A)


title: Female 26.5 yr after antibody enrichment scan 2 (U133B)


title: Female 21.5 yr after antibody enrichment scan 2 (U133A)


title: Female 21.5 yr after antibody enrichment scan 2 (U133B)


title: Female 24.4 yr after antibody enrichment scan 2 (U133A)


title: Female 20.1 yr after antibody enrichment scan 2 (U133A)


title: Female 24.4 yr after antibody enrichment scan 2 (U133B)


title: Female 23.5 yr after antibody enrichment scan 2 (U133B)


title: Female 22.5 yr after antibody enrichment scan 2 (U133B)


title: Female 23.5 yr after antibody enrichment scan 2 (U133A)


title: Male 75.1 yr after antibody enrichment scan 2 (U133B)

tag: older male


title: Male 75.1 yr after antibody enrichment scan 2 (U133A)


title: Male 71.2 yr after antibody enrichment scan 2 (U133A)


title: Male 73.5 yr after antibody enrichment scan 2 (U133B)


title: Male 67.2 yr after antibody enrichment scan 2 (U133B)


title: Male 68.4 yr after antibody enrichment scan 2 (U133B)


title: Male 73.5 yr after antibody enrichment scan 2 (U133A)


title: Male 71.2 yr after antibody enrichment scan 2 (U133B)


title: Male 21.5 yr after antibody enrichment scan 2 (U133A)

tag: young male


title: Male 25.1 yr after antibody enrichment scan 2 (U133B)


title: Male 27.1 yr after antibody enrichment scan 2 (U133A)


title: Male 69.6 yr after antibody enrichment scan 2 (U133A)


title: Male 69.6 yr after antibody enrichment scan 2 (U133B)


title: Male 24.2 yr after antibody enrichment scan 2 (U133A)


title: Male 69.2 yr after antibody enrichment scan 2 (U133B)


title: Male 26.2 yr after antibody enrichment scan 2 (U133B)


title: Male 74.5 yr after antibody enrichment scan 2 (U133A)


title: Male 21.5 yr after antibody enrichment scan 2 (U133B)


title: Male 69.2 yr after antibody enrichment scan 2 (U133A)


title: Male 68.4 yr after antibody enrichment scan 2 (U133A)


title: Male 24.2 yr after antibody enrichment scan 2 (U133B)


title: Male 67.2 yr after antibody enrichment scan 2 (U133A)


title: Male 74.5 yr after antibody enrichment scan 2 (U133B)


title: Male 25.1 yr after antibody enrichment scan 2 (U133A)


title: Male 23.4 yr after antibody enrichment scan 2 (U133B)


title: Male 26.2 yr after antibody enrichment scan 2 (U133A)


title: Male 27.1 yr after antibody enrichment scan 2 (U133B)


title: Male 23.4 yr after antibody enrichment scan 2 (U133A)


title: Male 25.2 yr after antibody enrichment scan 2 (U133B)


title: 10_V71.M3W3.CEL, Experimental replicate 3

description:
V71-370 - Mock inoculated; 72 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - Mock Inoculated (Inoculated with water + agar): 72 hours post inoculation

tag: cultivar - V71-370

tag: Tissue/Cell Type

tag: total Soybean RNA Plus 0.125 % P.sojae RNA added


title: 10_SLO.M1W4.CEL, Experimental replicate 4

description:
SLOAN - Mock inoculated; 24 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - Mock Inoculated (Inoculated with water + agar): 24 hours post inoculation

tag: cultivar - SLOAN

tag: total Soybean RNA Plus 0.5 % P.sojae RNA added


title: Female 68.4 yr before antibody enrichment scan 1 (U133A)

scan_protocol: Arrays were scanned with an Affymetrix scanner after first stain (before signal enhancement with biotinylated anti-streptavidin antibody)


title: Female 29.8 yr before antibody enrichment scan 1 (U133B)


title: Male 25.2 yr after antibody enrichment scan 2 (U133A)


title: Female 68.4 yr before antibody enrichment scan 1 (U133B)


title: Female 65.1 yr before antibody enrichment scan 1 (U133B)


title: Female 65.1 yr before antibody enrichment scan 1 (U133A)


title: Female 66.6 yr before antibody enrichment scan 1 (U133B)


title: Female 67.9 yr before antibody enrichment scan 1 (U133B)


title: Female 67.3 yr before antibody enrichment scan 1 (U133B)


title: Female 70.7 yr before antibody enrichment scan 1 (U133A)


title: Female 23.5 yr before antibody enrichment scan 1 (U133B)


title: Female 20.1 yr before antibody enrichment scan 1 (U133B)


title: Female 71.4 yr before antibody enrichment scan 1 (U133B)


title: Female 24.4 yr before antibody enrichment scan 1 (U133B)


title: Female 29.8 yr before antibody enrichment scan 1 (U133A)


title: Female 22.5 yr before antibody enrichment scan 1 (U133B)


title: Female 67.9 yr before antibody enrichment scan 1 (U133A)


title: Female 26.5 yr before antibody enrichment scan 1 (U133B)


title: Female 26.5 yr before antibody enrichment scan 1 (U133A)


title: Female 70.7 yr before antibody enrichment scan 1 (U133B)


title: Female 71.4 yr before antibody enrichment scan 1 (U133A)


title: Female 24.4 yr before antibody enrichment scan 1 (U133A)


title: Female 22.5 yr before antibody enrichment scan 1 (U133A)


title: Female 65.9 yr before antibody enrichment scan 1 (U133A)


title: Female 67.3 yr before antibody enrichment scan 1 (U133A)


title: Female 20.1 yr before antibody enrichment scan 1 (U133A)


title: Female 66.6 yr before antibody enrichment scan 1 (U133A)


title: Female 21.5 yr before antibody enrichment scan 1 (U133B)


title: Female 21.5 yr before antibody enrichment scan 1 (U133A)


title: Female 65.9 yr before antibody enrichment scan 1 (U133B)


title: Female 23.5 yr before antibody enrichment scan 1 (U133A)


title: Male 71.2 yr before antibody enrichment scan 1 (U133B)


title: Male 75.1 yr before antibody enrichment scan 1 (U133A)


title: Male 74.5 yr before antibody enrichment scan 1 (U133B)


title: Male 67.2 yr before antibody enrichment scan 1 (U133B)


title: Male 71.2 yr before antibody enrichment scan 1 (U133A)


title: Male 73.5 yr before antibody enrichment scan 1 (U133B)


title: Male 75.1 yr before antibody enrichment scan 1 (U133B)


title: Male 69.2 yr before antibody enrichment scan 1 (U133B)


title: Male 68.4 yr before antibody enrichment scan 1 (U133B)


title: Male 69.6 yr before antibody enrichment scan 1 (U133B)


title: Male 21.5 yr before antibody enrichment scan 1 (U133B)


title: Male 73.5 yr before antibody enrichment scan 1 (U133A)


title: Male 68.4 yr before antibody enrichment scan 1 (U133A)


title: Male 74.5 yr before antibody enrichment scan 1 (U133A)


title: Male 25.1 yr before antibody enrichment scan 1 (U133B)


title: Male 25.1 yr before antibody enrichment scan 1 (U133A)


title: Pseudomonas aeruginosa (pMMB-PA0149) (1)

city: Amsterdam

first: Marian

last: Llamas

address: van der Boechorststraat 7

department: Medical Microbiology

country: Netherlands

institute: VU Medical Center

data_processing: Target hybridization, washing, staining and scanning were performed by the Affymetrix Core Facility using a GeneChip® hybridization oven, a Fluidics station and MICROARRAY SUITE software (Affymetrix). Genes were considered differentially regulated if the relative change (n-fold) was >2.5 and the P value was <0.05.

label: biotin-ddUTP

organism: Pseudomonas aeruginosa

label_protocol: Enzo BioArrayTM Terminal Labeling kit (Affymetrix)

extract_protocol: Total RNA was isolated by the hot phenol method using the Tri Reagent® LS (Molecular Research Center, Inc.). Contaminating DNA was eliminated by Dnase I (Amersham) treatment, and RNA was isolated by phenol-chloroform extraction and precipitation with 2.5 x volume 100% (vol/vol) ethanol and 0.1 x volume 3 M sodium acetate pH 4.8. An additional RNA purification step was performed using the RNeasy columns (Qiagen). RNA quantity was assessed by UV absorption at 260 nm in a ND-1000 Spectrophotometer (NanoDrop Technologies, USA). RNA quality was monitored by 1.5% (wt/vol) agarose gel electrophoresis containing 2,2 M formaldehyde as denaturing agent.

tag: P. aeruginosa PAO25 (pMMB67EH) was grown in 300 mL Erlenmeyer flask with 30 mL LB and 25 µg/ml piperacillin at 37°C and 200 revolutions per min.


title: Male 26.2 yr before antibody enrichment scan 1 (U133B)


title: Pseudomonas aeruginosa (pMMB-PA0149) (2)

description: Target hybridization, washing, staining and scanning were performed by the Affymetrix Core Facility using a GeneChip® hybridization oven, a Fluidics station and MICROARRAY SUITE software (Affymetrix)

tag: P. aeruginosa PAO25 (pMMB-PA0149) was grown in 300 mL Erlenmeyer flask with 30 mL LB and 25 µg/ml piperacillin at 37°C and 200 revolutions per min.


title: Male 69.2 yr before antibody enrichment scan 1 (U133A)


title: Pseudomonas aeruginosa (pMMB-PA2050)

hyb_protocol: Target hybridization, washing, staining and scanning were performed by the Affymetrix Core Facility using a GeneChip® hybridization oven, a Fluidics station and MICROARRAY SUITE software (Affymetrix)

source_name: Pseudomonas aeruginosa (pMMB-PA2050)

tag: P. aeruginosa PAO25 (pMMB-PA2050) was grown in 300 mL Erlenmeyer flask with 30 mL LB and 25 µg/ml piperacillin at 37°C and 200 revolutions per min.


title: Male 23.4 yr before antibody enrichment scan 1 (U133B)


title: Male 21.5 yr before antibody enrichment scan 1 (U133A)


title: Pseudomonas aeruginosa (pMMB-PA2093)

scan_protocol: Target hybridization, washing, staining and scanning were performed by the Affymetrix Core Facility using a GeneChip® hybridization oven, a Fluidics station and MICROARRAY SUITE software (Affymetrix)

source_name: Pseudomonas aeruginosa (pMMB-PA2093)

tag: P. aeruginosa PAO25 (pMMB-PA2093) was grown in 300 mL Erlenmeyer flask with 30 mL LB and 25 Âµg/ml piperacillin at 37Â°C and 200 revolutions per min.


title: Male 26.2 yr before antibody enrichment scan 1 (U133A)


title: Male 23.4 yr before antibody enrichment scan 1 (U133A)


title: Male 69.6 yr before antibody enrichment scan 1 (U133A)


title: Male 67.2 yr before antibody enrichment scan 1 (U133A)


title: Male 24.2 yr before antibody enrichment scan 1 (U133B)


title: Pseudomonas aeruginosa (pMMB-PA4896) (2)

tag: P. aeruginosa PAO25 (pMMB-PA4896) was grown in 300 mL Erlenmeyer flask with 30 mL LB and 25 µg/ml piperacillin at 37°C and 200 revolutions per min.


title: Male 24.2 yr before antibody enrichment scan 1 (U133A)


title: Male 27.1 yr before antibody enrichment scan 1 (U133A)


title: Pseudomonas aeruginosa (pMMB-PA4896) (1)


title: Male 27.1 yr before antibody enrichment scan 1 (U133B)


title: Male 25.2 yr before antibody enrichment scan 1 (U133B)


title: NHBE_Chip 11 rep1_rep2_rep3

status: Public on Nov 22 2007

first: Damon

middle: Scott

last: Perez

state: MN

address: 200 Fist Street SW

department: Experimental Pathology & Lab Medicine

institute: Mayo Clinic

description:
Ribominus untreated: rep1, rep2
Ribominus treated: rep3

hyb_protocol: Used GeneChip® Hybridization, Wash, and Stain Kit. Followed the procedure from the GeneChip® WT Double-Stranded  Target Assay Manual.

scan_protocol: Each array was scanned using the Affymetrix GeneChip® 300 G7 scanner.

data_processing: Data was analyzed using Tiling Analysis Software (TAS) and Integrated Genome Browser (IGB). Tiling Analysis Software v1.1 User Guide (Affymetrix) provides detailed description of its analysis capabilities including various uses of quality control measures. Briefly, the analyses provided within the TAS application included analyzing feature intensity data stored in CEL files to produce signal and p-values for each genomic position, computation of genomic intervals based on those computed signal and p-values, and computation of summary statistics and visualizations for assessing the quality of the array data. The results of this analysis were imported into applications such as IGB or the UCSC Human Genome Browser. With IGB, annotation variations were compared in different data sets as described in the User's Guide. Specifically, our data was normalized using quantile normalization plus scaling (scaled to the default target intensity of 500 for each ship). Array types were verified against library files. Replicates were not normalized together. BAR files were created in TAS and opened in IGB for signal visualization. Once a threshold of 99.5th percentile was selected, a "track" was made (which mark regions over the threshold level). Annotations from these "tracks" were saved into a bed file that can be opened in Excel for further analysis.

source_name: normal human bronchial/tracheal epithelial cells

label_protocol: GeneChip® Whole Transcript (WT) Double-Stranded DNA Terminal Labeling Kit and GeneChip® WT Amplified Double-Stranded cDNA Synthesis Kit from Affymetrix (Santa Clara, CA). This protocol entails first and second strand cDNA synthesis using random hexamers, RNA removal and cDNA purification, a quality control cDNA step, a cDNA fragmentation step, TdT labeling, prehybridization of the chips, and the final hybridization of the labeled cDNA onto the GeneChip® Human 35 bp Tiling Array 1.0R Set. Detailed procedure is found in the GeneChip® WT Double-Stranded Target Assay Manual.

extract_protocol: Total RNA was isolated using Gentra Systems Versagene Total RNA Cell Kit (included their DNAse Kit) was carried out according to manufacture's instructions


title: NHBE_Chip 10 rep1_rep2_rep3

tag: normal human bronchial/tracheal epithelial cells


title: NHBE_Chip 08 rep1_rep2_rep3


title: NHBE_Chip 09 rep1_rep2_rep3


title: Pseudomonas aeruginosa (pMMB67EH) (1)

source_name: Pseudomonas aeruginosa (pMMB67EH) (1)

growth_protocol: Grown in 300 mL Erlenmeyer flask with 30 mL LB and 25 µg/ml piperacillin at 37°C and 200 revolutions per min.

tag: strain

value: Pseudomonas aeruginosa PAO25 containing the plasmid pMMB67EH


title: NHBE_Chip 03 rep1_rep2_rep3


title: Pseudomonas aeruginosa (pMMB67EH) (2)

source_name: Pseudomonas aeruginosa (pMMB67EH) (2)


title: NHBE_Chip 01 rep1_rep2_rep3


title: NHBE_Chip 14 rep1_rep2_rep3


title: NHBE_Chip 02 rep1_rep2_rep3


title: NHBE_Chip 13 rep1_rep2_rep3


title: NHBE_Chip 12 rep1_rep2_rep3


title: NHBE_Chip 06 rep1_rep2_rep3


title: Foreskin Microarray data set (Sample 4)

type: mixed

city: Madison

first: Victor

last: Ruotti

state: WI

address: 425 Henry Mall

department: Biotechnology

institute: UW Madison

description: Total RNA from iPS clone was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's recommendations.

hyb_protocol: Hybridizations were performed in 3.6X SSC buffer with 35% formamide and 0.07% SDS at 42 °C overnight.

scan_protocol: Arrays were washed, dried and scanned with the GenePix 4000B Scanner

data_processing: Gene Expression data was extracted using NimbleScan Software v2.3

molecule: genomic DNA

source_name: Genomic DNA extracted from H1 Human Embryonic Stem Cells

label_protocol: Sonicated genomic DNA was primed with random octamers and labeled using Klenow in the present of 5-(3-aminoallyl)-dUTP

extract_protocol: Phenol/Chloroform Extraction

tag: Genomic DNA was extracted from H1 Human ES cells

source_name: Foreskin Cells Sample 4

label_protocol: Total RNA was enriched for the polyA fraction using Oligotex mRNA Mini Kit (Qiagen). Enriched mRNA (250 ng) was primed using random hexamers and reversed transcribed using Superscript III (Invitrogen) in the presence of 5-(3-aminoallyl)-dUTP (Ambion).

extract_protocol: Qiagen on column kit

tag: Foreskin Cells Sample 4


title: H7 Human Embryonic Stem cell (H7 ESC)

hyb_protocol: Hybridizations were performed in 3.6X SSC buffer with 35% formamide and 0.07% SDS at 42% C overnight.

tag: DNA was extracted from H1 ES cells

source_name: H7 Human Embryonic Stem Cell line

tag: RNA extracted from h7 hES cell


title: H9 Human Embryonic Stem cell (H9 ESC)

tag: DNA extracted from h1 ES cells

source_name: H9 Human Embryonic Stem Cell line

tag: RNA extracted from h9 hES cell


title: Foreskin Microarray data set (Sample 2)

source_name: Foreskin Cells Sample 2

tag: Foreskin Cells Sample 2


title: H13B Human Embryonic Stem cell (H13B ESC)

source_name: H13B Human Embryonic Stem Cell line

tag: RNA extracted from H13B cells


title: IMR90 from the ES(IMR90)-3 sample

source_name: IMR90 from the ES(IMR90)-3 sample

tag: Total RNA from IMR90 cells were extracted


title: Male 25.2 yr before antibody enrichment scan 1 (U133A)

tag: young male


title: IMR90 from the ES(IMR90)-2 sample

tag: DNA was extracted from h1 ES cells

source_name: IMR90 from the ES(IMR90)-2 sample


title: IMR90 from the ES(IMR90)-1 sample

source_name: IMR90 from the ES(IMR90)-1 sample


title: Foreskin Microarray data set (Sample 5) Non iPS Sample

source_name: Foreskin Cells Sample 5

tag: Foreskin Cells Sample 5


title: Foreskin Microarray data set (Sample 3)

source_name: Foreskin Cells Sample 3

tag: Foreskin Cells Sample 3


title: Foreskin Microarray data set (Sample 1)

source_name: Foreskin Cells Sample 1

tag: Foreskin Cells Sample 1


title: IMR90 from the ES(IMR90)-4 sample

source_name: IMR90 from the ES(IMR90)-4 sample


title: H14A Human Embryonic Stem cell (H14A ESC)

source_name: H14A Human Embryonic Stem Cell line

tag: RNA extracted from H14A ES cells


title: H1 Human Embryonic Stem cell (H1LESC)

tag: Genomic DNA extracted from H1 ES cells

source_name: H1 Human Embryonic Stem Cell line

tag: RNA extracted from h1 hES cell


title: NHBE_Chip 05 rep1_rep2_rep3

source_name: normal human bronchial/tracheal epithelial cells


title: NHBE_Chip 07 rep1_rep2_rep3

tag: normal human bronchial/tracheal epithelial cells


title: NHBE_Chip 04 rep1_rep2_rep3


title: Strain 383, biological rep2

status: Public on Nov 20 2007

city: Charlottesville

first: Jayasimha

last: Rao

address: 1300 Jefferson Park Avenue

department: Microbiology

institute: University of Virginia

description: Gene expression from mid-log phase cultures

hyb_protocol: Protocol and conditions used during hybridization, blocking and washing were from the Standard affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)

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

data_processing: GeneChip data analysis was performed using a combination of the Affymetrix Microarray Analysis Suite 5.0 (MAS 5.0, Affymetrix, Santa Clara, CA) and the dChip software (Li & Wong, 2001/www.dchip.org)..  Detection of a particular gene, called "present", "absent", or "marginal", was made using the nonparametric Wilcoxon ranked score algorithm as provided in MAS 5.0.  These detection calls were then imported into and utilized by the Dchip program.  To determine the reproducibility of the replicates as well as the degree of variations of the samples under comparison, scatter plots were generated using this software.  Quantification of the genes was performed using Dchip, which applied a model-based approach to derive the probe sensitivity and expression indices.  Linear regression was then applied to the two indices to quantify a particular gene.  When certain probes or transcripts deviated significantly from the modeled pattern, they were identified as outliers and thus excluded from the quantification process.  Normalization of the arrays was performed using the invariant set approach.  Comparative analysis of the samples using Dchip generated fold changes and paired sample t-test p-values.  A p<= 0.05 and a fold change >= 1.5 in combination with a percentage of "present" >= 50% was applied as an indication of significant change of gene expression for up- or down-regulation.  Hierarchical clustering of the genes was performed after an appropriate filtration of the data.  In addition, Significance Analysis of Microarray (SAM) software was used to select the transcripts with significant variations for comparison studies.

source_name: Pseudomonas aeruginosa strain 383 isolated from the sputum of a cystic fibrosis patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were grown overnight at 200 rpm in LB broth at 37°C.  Cultures were diluted 1:100 in 30 ml of fresh LB medium and grown to mid-log phase to an optical density (OD600) of 0.5

extract_protocol: Total RNA was isolated using the RiboPureTM Bacterial (RNAwiz) kit (Ambion, Austin, Texas) and contaminating DNA was removed with the DNA-free kit (Ambion) following the manufacturer's specification.

tag: Non-mucoid

tag: Mid-log phase (0.5 at OD600) in the culture


title: Strain 2192, biological rep2

source_name: Pseudomonas aeruginosa strain 2192 isolated from the sputum of a cystic fibrosis patient

tag: Mucoid


title: Strain 383, biological rep1


title: OS5

status: Public on Nov 21 2007

type: genomic

city: Toronto

first: Shamini

last: Selvarajah

state: Ontario

address: 555 University Ave

department: Cancer Institute

country: Canada

institute: Hospital for Sick Children

description: The identification of tumor-specific genomic profiles using array CGH.

hyb_protocol: Probe mixture of Cy3 labelled sample DNA, Cy5 labelled reference DNA, 50 μl of 1.0mg/ ml of human Cot-1 DNA (Invitrogen, USA), 50 μl of Agilent 10X Blocking Agent and 250 μl of Agilent 2X Hybridization Buffer (Agilent Technologies, Inc.) was denatured at 100C for 1 minute 30 s and incubated at 37C for 30 minutes.  The probe was applied to the array using an Agilent microarray hybridization chamber, and hybridized for 40 hours at 65C in a rotating oven (Robbins Scientific, Sunnyvale, USA) at 20 rpm. Dye swaps were carried out routinely.

scan_protocol: Arrays were washed according to the manufacturer’s recommendations, air dried, and scanned using an Agilent 2565AA DNA microarray scanner (Agilent Technologies, Inc).

data_processing:
Normalization strategy involved averaging the dye-flip Cy5/Cy3 and Cy3/Cy5 ratios for a sample; algorithm used was the ADM-1 proivded by Agilent analytics 3.4 with a threshold of 10.0.
Raw data and normalized data files for the individual dye-swap hybridizations are linked as supplementary files at the foot of the Sample record.

label: cy3 and cy5 (dye-flip)

source_name: pediatric osteosarcoma

label_protocol: Labelling reactions were performed using the BioPrime Array CGH Genomic Labelling System (Invitrogen, CA, USA) according to the manufacturer’s directions. Briefly, the reference and sample DNA were labelled with 3 μl  of 1.0 mM Cy5-dUTP or Cy3-dUTP (Perkin-Elmer Life and Analytical Sciences, Woodbridge, Canada),  in a 10 x dUTP nucleotide mix of 1.2 mM each of dATP, dGTP, dCTP and 0.6 mM dTTP (Invitrogen) and purified using a Centricon YM-30 filter (Millipore, Billerica, USA).

growth_protocol: tumor samples used were frozen prior to extraction

extract_protocol: The version 2.0 protocol (August 2005) for Oligonucleotide Array-Based CGH for Genomic DNA Analysis was used.  Three μg of Human Genomic DNA from multiple anonymous male donors (Promega Corporation, Madison, USA) and 3 μg of tumor genomic DNA samples were digested with AluI (50 units) and RsaI (50 units) (Promega) for a minimum of 2 hours at 37C.  Digestion quality was assessed by the DNA 1000 LabChip Kit (Agilent 2100 Bioanalyzer, Agilent Technologies), and the products purified using the Qiaquick PCR Cleanup Kit (Qiagen Inc., Cologne, Germany).

treatment_protocol: no treatment was performed

tag: female; age 12; femur

source_name: normal male DNA (reference sample)

tag: Human Genomic DNA from multiple anonymous male donors. Purchased from Promega Corporation, Madison, USA. Cat# G1471.


title: OS13

tag: male; age 9; leg


title: OS15

tag: female; age 14; femur


title: OS17

tag: male; age 15; tibia


title: OS7

tag: male; age 7; femur


title: OS9

tag: female; age 13; humerus


title: OS11

tag: male; age 13; femur


title: OS1

tag: female; age 9; tibia


title: OS18

tag: male; age 15; femur


title: Strain 2192, biological rep1


title: day 4 vs day 0 comparison 1

city: Beaverton

first: Valerie

last: Matagne

state: OR

address: 505 nw 185th Ave

department: Neuroscience

institute: OHSU

description: day 4 vs day 0, Biological replicate 1 of 3, experimental replicate 1-4 of 12

hyb_protocol: See Information on GPL5369 platform

scan_protocol: The slides were scanned at five micron resolution on a PerkinElmer ScanArray 4000XL array scanner.  The arrays were scanned sequentially, with Cy5 scanned first with a 633 nm laser, followed by Cy3 with a 543 nm laser.  Cy5 and Cy3 images were saved in 16-bit TIF files

data_processing: Signal values were generated from TIF images using ImaGene software (BioDiscovery, El Segundo, CA).   For each probe there is a “Flag” information (0=good, 1=bad) that will be used to determine the validity of the data. Every probe with a Flag value of 1 is discarded and the signal mean has a value of “NaN” in the raw data file. Normalization is performed using the marrayNorm module in BioConductor using R version 1.7.1. (www.bioconductor.org) . marrayNorm implements the loess functions of R. Following loess normalization, t-tests are run on each probe to see if the log ratio (Cy5/Cy3) is different than zero and a significance cutoff of p = 0.01 was used. In addition, only signal levels for either Cy5 or Cy3 above the 90 percentile of the negative controls were used in further analysis (with cut-off - absolute value of M > 0.8, M being log2(Cy5/Cy3)).  The data table generated contains log2 values for each replicate (1 to 4), the average mean, aveA (average mean intensity), and pvalue.   To identify genes that are differentially expressed in the mouse ovary at 48 and 96h after birth in comparison to <24 h post partum, genes showing a fold-change less than 1.8 times in either direction were removed from further analysis.  Thereafter, the data (average mean obtained after Loess normalization) were merged using OmniViz software (Maynard, MA), and genes showing a similar expression temporal pattern of expression were clustered and visualized via a K-means clustering algorithm using J-Express 2.0 software (De Nova, Vancouver, BC, Canada).

organism: Mus musculus

source_name: Total RNA from <24h day-old mouse ovaries labeled with cy3

label_protocol: See Information on GPL5369 platform

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Valencia, CA) using a modified protocol. Briefly, the tissue was homogenized in TRI Reagent (Molecular Research Center, Cincinnati, OH), and the aqueous and organic phases were separated by addition of 1 vol bromo-3-chloropropane (Sigma Chemicals, St. Louis, MO), followed by centrifugation at 13,000 rpm for 15 min at 4ºC. Thereafter, 350 μl of 70% ethanol (Sigma) were added to all samples, and each sample was applied to an RNeasy mini-column, followed by washing by centrifugation with buffers containing guanidine and ethanol. To elute the RNA, 30 μl of RNAse-free water were added directly onto the silica-gel membrane of the columns, which were then centrifuged for 1 min at 13,000 rpm. RNA was quantitated by measuring absorbance at 260 nm and stored at –85ºC until used. The quality of each RNA sample was assessed on 2% formaldehyde denaturing agarose gels.

tag: C57Bl/6J female

tag: age <24h

tag: ovaries

source_name: Total RNA from 4 day-old mouse ovaries labeled with cy5

tag: 4 day-old


title: OS4

tag: male; age 7; humerus


title: day 4 vs day 0 comparison 2

description: day 4 vs day 0, Biological replicate 2 of 3, experimental replicate 5-8 of 12


title: day 2 vs day 0 comparison 2

description: day 2 vs day 0, Biological replicate 2 of 3, experimental replicate 5-8 of 12

source_name: Total RNA from 2 day-old mouse ovaries labeled with cy5

tag: 2 day-old


title: day 2 vs day 0 comparison 3

description: day 2 vs day 0, Biological replicate 3 of 3, experimental replicate 9-12 of 12


title: day 2 vs day 0 comparison 1

description: day 2 vs day 0, Biological replicate 1 of 3, experimental replicate 1-4 of 12


title: day 4 vs day 0 comparison 3

description: day 4 vs day 0, Biological replicate 3 of 3, experimental replicate 9-12 of 12


title: HGF + PD, biological rep 2

city: philadelphia

first: Xiaofeng

last: Zuo

state: PA

address: 380 S. University Ave.

institute: University of Pennsylvania

description: Gene expression data from MDCK cells grown on a Transwell filter and exposed to HGF + PD

hyb_protocol: Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45C on Canine Genome 2.0 Array (Affymetrix).

scan_protocol: GeneChips were scanned at 3-nm resolution after excitation at 570 nm.

data_processing: GCRMA-calculated Signal Intensity and Affymetrix flags using ArrayAssist Lite v3.4, Stratagene

organism: Canis lupus familiaris

source_name: Madin Darby canine kidney (MDCK) cells, exposed to HGF + PD

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

growth_protocol: MDCK cells grown on a Transwell filter in a 37 °C 5% CO2 incubator and fed MEM + 5% FBS

extract_protocol: Qiagen extraction of total RNA according to the manufacturer's instructions.

treatment_protocol: MDCK cells grown on a Transwell filter for 7 days exposed to 24 hours of hepatocyte growth factor at 100 ng/ml and PD09859 at a concentration of 50 uM

tag: MDCK type II cells


title: HGF + PD, biological rep 1


title: HGF + UO, biological rep 2

description: Gene expression data from MDCK cells grown on a Transwell filter and exposed to HGF + UO

source_name: Madin Darby canine kidney (MDCK) cells, exposed to HGF + UO

treatment_protocol: MDCK cells grown on a Transwell filter for 7 days exposed to 24 hours of hepatocyte growth factor at 100 ng/ml and UO126 at a concentration of 10 uM


title: HGF + PD, biological rep 3


title: HGF + UO, biological rep 1


title: HGF, biological rep 4

description: Gene expression data from MDCK cells grown on a Transwell filter and exposed to HGF

source_name: Madin Darby canine kidney (MDCK) cells, exposed to HGF

treatment_protocol: MDCK cells grown on a Transwell filter for 7 days exposed to 24 hours of hepatocyte growth factor at 100 ng/ml


title: HGF + UO, biological rep 3


title: HGF + PD, biological rep 4


title: HGF, biological rep 3


title: HGF, biological rep 2


title: Control, biological rep 3

description: Gene expression data from MDCK cells grown on a Transwell filter

source_name: Madin Darby canine kidney (MDCK) cells, control

treatment_protocol: MDCK cells grown on a Transwell filter for 7 days exposed only to medium


title: HGF, biological rep 1


title: Control, biological rep 4


title: Control, biological rep 1


title: NSCB_expression_380K_108015

first: Melodee

last: Patterson

address: 510 Charmany Dr Ste 58 & 59

institute: WiCell

description: Gene expression chip experiments are used to detect the expression level of hESC and differentiation markers in hESC cell lines.

hyb_protocol: 1. Incubate at 95°C (in heat block), 5 min., spin briefly 2. Place at 42°C (in Maui machine), 5-15 min. 3. Prepare microarray: A)pre-heat array on Maui station B) put array into array-holder (with number facing up going in first) carefully remove glue-sticker from lid and put lid onto array C) take array w/ lid out of array-holder thoroughly attach lid using thick slide place array onto Maui station, approx. 2 min. make sure lid is completely attached D) Add 40 µl hyb solution onto microarray and allow to settle (approx. 15 sec.), dry lid thoroughly 4. Place stickers onto lid, press down on both at the same time, make sure are thoroughly attached 5. Squeeze bubbles away from center of array 6. Wet humid cover and place on Maui station 7. Incubate on Maui at 42°C overnight (17 hours) 8. Remove microarray w/lid from Maui and put in array-holder in Wash 1 (at 42°C) 9. Peel lid off chip while submerged 10. Incubate 10-15 sec. w/ gentle agitation 11. Transfer slide into a slide rack in a new container of Wash 1 (r.t.) Incubate 2 min. w/ gentle agitation 12. Transfer to Wash 2 13. Incubate 1 min. w/ gentle agitation 14. Transfer to Wash 3 15. Incubate 15 sec. w/ gentle agitation 16. Spin approx. 1 min. in Array-Go-Round (place arrays such that numbers are facing to the right when rack is placed in front part of wheel) (the rod on slide holder should be on the inside) 17. Blow off any residual liquid 18. Keep slides protected from light and scan as soon as possible

scan_protocol: 1. Turn on the scanner and allow it to warm up for at least 15 minutes before scanning. 2. Open the Gene Pix Scan 6.0 program. 3. Place the chip in the scanner, with the label facing down and outward. 4. Open hardware settings and make sure the pixel size is 5 and the power is 100% for both channels. 5. Do a Preview Scan to adjust the scan frame for the array. Use levels 750 for the 635 (Cy5) channel and 550 for the 532 (Cy3) channel. 6. Perform Data Scans until the PMT levels for the 635 and 532 channels have been adjusted. 7. Adjust the PMT level of the 635 channel so the histogram is leveling off at 1e-5. 8. Adjust the PMT level of the 532 channel so the median (found by the rectangular region measuring tool) is equal to or no more than 30 points higher than the median of the 635 channel. 9. Save image as Single-image TIFF File (*.tif) and make sure both channels are checked. The image files are named chipID_635.tif and chipID_532.tif and stored on the WiCell Iceland server under the scan date (yyyymmdd). 10. The image files are ready for analysis with the NimbleScan software.

data_processing:
1. Image extraction:
NimbleScan provided by NimbleGen is used to extract signal data from image files
(*.TFF). Signals from the scan for Cy3 (green channel) are saved in a file named as chipID_532.pair while signals from the scan for Cy5 (red channel) are saved in a file named as chipID_635.pair.
2. Normalization:
Signal intensities from RNA and gDNA samples are normalized with Robust Multiple-chip Analysis (RMA) algorithm (Irizarry et al., 2003) separately. A median-adjusted ratio is calculated for each gene by dividing its signal intensity from the RNA sample by the sum of the corresponding signal intensity from the gDNA sample and median signal intensity of all genes from the gDNA channel.

source_name: hESC H1 mRNA

label_protocol:
1. Dry the sample in the Speed Vac set at 30°C.
2. Resuspend the sample in 4.5μl 0.1M Na2CO3, pH 9.0.
3. Resuspend the Cy5 NHS ester in 4.5μl DMSO
4. Add Cy5 NHS ester to sample
5. Incubate at 22°C in a heat block for 1 hour. Protect the heat block and sample from light.
6. Purify the sample using a Qiaquick PCR purification Kit:
6.1. Add 35μl 100mM NaOAc, pH 5.2 to the sample.
6.2. Add 250μl PB buffer to the sample and load the sample on the column.
6.3. Spin at 13.000 rpm for 1 minute and remove the flow through.
6.4. Add 750μl PE buffer to the column.
6.5. Spin at 13.000 rpm for 1 minute and remove the flow through.
6.6. Spin at 13.000 rpm for 1 minute.
6.7. Transfer the column to new tube.
6.8. Add 30μl EB buffer and incubate for 1 minute on the column.
6.9. Elute once by centrifuging at 13.000 rpm for 1 minute.

extract_protocol:
1. In a hood equipped with an aspirator, remove spent media from the wells of hES cells.
2. Wash each well once with 1ml of PBS. Aspirate the PBS.
3. In the fume hood, add 1 ml of Trizol per well using a 1ml pipetman. Use the pipet tip to scrape the cells into solution and make sure no cells are left behind.
4. Transfer the cells from each well into a separate 1.5ml eppendorf tube.
5. Add 200μl of chloroform into each tube and mix by pipetting up and down. Use a 1ml Pipetman.
6. Spin the tubes at 16000 RCF for 20 minutes at 4°C.
7. Transfer the upper 500μl of the aqueous phase into a new 1.5ml eppendorf tube.
8. Add 500μl of isopropanol to the new tube, and it mix by pipetting up and down.
9. Let the samples sit at room temperature for 15 minutes.
10. Pellet the RNA by spining the tubes at 16000 RCF for 20 minutes at 4°C.
11. Wash the pelleted RNA using 70% ethanol. Slowly add 1ml of 70% ethanol to the RNA, cap the tube, and wash the pellet by flipping the tube twice. If the pellet is dislodged, perform a quick spin and then carefully decant the ethanol.
12. Dry the RNA in a vacuum; however, take care not to over dry it as that makes RNA resuspension difficult.
13. Resuspend the RNA in 25μl of nuclease free water.
14. Use a nanodrop spectrophotometer to measure the concentration and purity of RNA (A260/A280). Record these values for the gene expression submission form.

tag: cell type

value: human embryonic stem cell (hESC)

tag: cell line

value: Human embryonic stem cell line H1 mRNA

source_name: hESC H1 DNA

label_protocol:
1. Dry the sample in the Speed Vac set at 30°C.
2. Resuspend the sample in 4.5μl 0.1 M Na2CO3, pH 9.0.
3. Resuspend the Cy3 NHS ester in 4.5μl DMSO
4. Add Cy3 NHS ester to sample
5. Incubate at 22°C in a heat block for 1 hour. Protect the heat block and sample from light.
6. Purify the sample using a Qiaquick PCR purification Kit:
A) Add 35μl 100 mM NaOAc, pH 5.2 to the sample.
B) Add 250μl PB buffer to the sample and load the sample on the column.
C) Spin at 13.000 rpm for 1 minute and remove the flow through.
D) Add 750μl PE buffer to the column.
E) Spin at 13.000 rpm for 1 minute and remove the flow through.
F) Spin at 13.000 rpm for 1 minute.
G) Transfer the column to new tube.
H) Add 30μl H20 and incubate for 1 minute on the column.
I) Elute once by centrifuging at 13.000 rpm for 1 minute.

extract_protocol:
1. Determine When to Harvest hES cells for DNA Extraction
A) At least 1x10^6 hES cells should be harvested for DNA extraction, depending on the quantity
required.
B) Yields of genomic DNA will vary from sample to sample depending on the amount and type of cells processed. In addition, the quality of starting material will affect DNA yield.
C) Estimated yield for hES cells: 5pg of DNA per cell (5μg DNA per 10^6 cells). One well of a 6-well plate will normally have between 1-4x106 hES cells by day 5 after passage.
2. Trypsinize the Cells
A) The following steps should be performed in a sterile biosafety cabinet while wearing personal protective equipment.
B) Add 1.5ml of 1X trypsin-EDTA working solution (pre-warmed to 37oC) to each well of a 6- well plate.
C) Return the plate to the 37C incubator for 2-3 minutes.
D) Remove the plate from the incubator and observe cell detachment with an inverted phase contrast microscope. Proceed to next step when colony edges begin to lift off the plate.
E) Using a sterile glass serological pipet, gently pipet up and down to detach the cells and break up the cell clumps.
F) Pool the detached cells in a 15ml centrifuge tube containing 5ml of trypsin stop solution within 5-7 minutes of adding the trypsin-EDTA solution.
G) Gently pipet the solution up and down to mix thoroughly.
H) Centrifuge the tube for 5 minutes at 1000 RPM.
3. RNA Digestion
A) Aspirate the supernatant and gently flick the tube until the pellet is resuspended.
B) Slowly add 200μl PBS to the cells while tapping gently on the tube to ensure good mixing.
C) Add 4μl RNase A (100mg/ml) and incubate at room temperature (RT) for 2 minutes.
4. Protein Digestion
A) Add 20μl Proteinase K and 200μl Buffer AL to the sample, mixing thoroughly by
vortexing. It is important that the solution is immediately and thoroughly mixed by
vortexing and pipetting to yield a homogenous solution.
NOTE: Do not add proteinase K directly to buffer AL.
B) Incubate the cell solution in a 70°C waterbath for 10 minutes.
5. DNA Precipitation and Separation of Cellular Components
A) Add 200μl ethanol (96-100%) to the sample, and mix thoroughly by vortexing.
B) A white precipitate may form on addition of ethanol. This precipitate does not interfere with the DNeasy procedure.
C) Pipet the mixture (including all of the precipitate) into the DNeasy Mini spin column placed in a 2ml collection tube. Centrifuge at ≥6000 x g (8000 rpm) for 1 minute. Discard flowthrough and collection tube.
NOTE: In order to obtain optimum DNA yield and quality, it is important not to overload
the spin column. The maximum number of hES cells that should be used in a DNA
extraction is 5x106 (normally, 2 wells of a 6-well plate). For larger amounts of starting material use multiple spin columns.
6. Wash the DNA
A) Place the DNeasy spin column in a new collection tube and add 500μl of Buffer AW1.
B) Centrifuge at ≥6000 x g (8000rpm) for 1 minute. Discard flow-through and collection tube.
C)Place the DNeasy spin column in a new collection tube and add 500μl of buffer AW2.
D) Centrifuge at 20,000 x g (14,000 rpm) for 3 minutes to dry the DNeasy membrane. Discard flow-through and collection tube.
NOTE: It is important to dry the membrane of the DNeasy Mini spin column, since
residual ethanol may interfere with subsequent reactions. This centrifugation step ensures that no residual ethanol will be carried over during the following elution.
E) Following the centrifugation step, remove the DNeasy Mini spin column carefully so the column does not come into contact with the flow-through, since this will result in carryover of ethanol. If carryover of ethanol occurs, place the spin column in a new collection tube and centrifuge again for 1 minute at 20,000 x g (14,000 rpm). Again discard the flow-through and collection tube.
7. Elution
A) Place the DNeasy Mini spin column in a clean 1.5ml or 2ml microcentrifuge tube and pipet 50-200μl Buffer AE directly onto the DNeasy membrane. Incubate the column at room temperature for 1 minute and then centrifuge for 1 minute at ≥6000 x g (8000rpm) to elute.
NOTE: Elution with less than 200μl of Buffer AE increases the final DNA concentration in the elute, but also decreases the overall DNA yield.
B) Repeat elution step as described in 7 A).
NOTE: A new microcentrifuge tube can be used for the second elution step to prevent dilution of the first elute. Alternatively, to combine the two elutes, the microcentrifuge tube from step 4.7.1 can be reused for the second elution step.
NOTE: More than 200μl should not be eluted into a 1.5 ml microcentrifuge tube because the DNeasy spin column will come into contact with the elute.


title: NSCB_expression_380K_HSF1_2

value: HSF1 human embryonic stem cell mRNA


title: NSCB_expression_380K_ES03_68

value: ES03 human embryonic stem cell line mRNA


title: NSCB_expression_380K_H9

value: H9 human embryonic stem cell mRNA


title: Control, biological rep 2


title: NSCB_expression_380K_HSF1_1

value: HSF1 human embryonic stem cell line mRNA


title: NSCB_CGH_390K_WA01_37

description: This CGH experiment is designed to detect deletion, insertation, amplication, etc. in the sample relative to the reference.

scan_protocol: NimbleGen scan protocol

data_processing:
1. Image extraction:
NimbleScan provided by NimbleGen is used to extract signal data from image files
(*.TFF). Signals from the scan for Cy3 (green channel) are saved in a file named as chipID_532.pair while signals from the scan for Cy5 (red channel) are saved in a file named as chipID_635.pair.
2. Normalization:
Signals from Cy3/Cy5 channels are transformed by logarithms to base 2 and normalized with loess or qspline (Workman et al., 2002) algorithms by R to resolve the systematic errors and bias introduced by the microarray experimental platform. The log ratios of the signals are obtained by subtracting the log transformed signals from one channel by the corresponding ones from another channel.
3. Data smoothing and break-points identification:
Ratios of the normalized data are plotted by the corresponding genome locations. The data are smoothed by an adaptive weights smoothing algorithm (GLAD R-package, Wang et al., 2005), break-points are identified by a binary segmentation algorithm (DNAcopy R-package, Olshen et al., 2004) or by the segmentation algorithm available within Nimbelgen’s Nimblescan software.
4. Data visualization:
CGH results can be saved as SignalMap GFF files and can be visualized by SignalMap provided by NimbleGen. CGH results can also be visualized by other software, such as aCGHViewer (Shankar et al., 2006), CHARMView (Myers et al., 2005), etc. However, different software requires different input format.

value: embryonic stem cell line WA01_37


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set36_2

status: Public on Nov 19 2007

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

hyb_protocol: Sample was hybridized by Nimblegen according to their established protocol.

scan_protocol: Sample was scanned by Nimblegen according to their established protocol.

data_processing: Data were normalized to have median log2 ratio of zero and median absolute deviation (MAD) of one.

source_name: CD4+ DNAse-treated genomic DNA, replicate #2

label_protocol: Sample was labeled by Nimblegen according to their established protocol.

extract_protocol: DNAse treated DNA was extracted and amplified.

treatment_protocol: DNAse digestion

tag: Treatment:DNAse digested

source_name: CD4+ input genomic DNA, replicate #2

extract_protocol: Input DNA was extracted.

tag: Treatment:No DNAse


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set19_2


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set03_2


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set37_1

source_name: CD4+ DNAse-treated genomic DNA, replicate #1

source_name: CD4+ input genomic DNA, replicate #1


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set32_1


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set20_2


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set02_2


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set14_1


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set26_1


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set16_1


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set35_2


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set30_1


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set19_1


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set13_1


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set28_1


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set18_2


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set01_2


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set31_1


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set26_2


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set28_2


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set35_1


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set27_2


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set15_1


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set34_2


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set29_2


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set37_2


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set33_1


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set17_2


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set25_2


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set17_1


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set12_1


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set11_2


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set12_2


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set10_1


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set32_2


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set30_2


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set38_1


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set10_2


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set01_1


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set09_2


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set24_2


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set07_1


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set14_2


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set33_2


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set23_1


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set08_1


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set07_2


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set22_1


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set05_1


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set21_1


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set24_1


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set38_2


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set31_2


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set23_2


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set06_1


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set03_1


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set16_2


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set21_2


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set05_2


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set13_2


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set22_2


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set15_2


title: CO_sham_med_4

status: Public on Nov 16 2007

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

hyb_protocol: Following fragmentation, 4 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430A 2.0 Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000

data_processing: The raw intensity data (cel files) were analyzed with dChip2005 using invariant-set normalization and the PM-MM model

source_name: medulla

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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


title: CO_NP_med_4


title: CO_sham_mid_3

source_name: midbrain


title: CO_sham_med_3


title: CO_sham_mid_4


title: CO_NP_med_3


title: KO_sham_mid_4


title: KO_sham_mid_3


title: KO_sham_med_4


title: CO_NP_mid_4

description: 430A2_2045_78_control_neuropath_midbrain


title: CO_NP_mid_3

description: 430A2_2045_74_control_neuropath_midbrain


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set06_2


title: Patient 5 tumor vs. normal

status: Public on Nov 17 2007

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: patient 5

hyb_protocol: According to Agilent aCGH protocol (http://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=52010 )

scan_protocol: An Axon GenePix4000B sacnner was used with the following settings: 100% power, 5 µm 2 lines to average and PMT gain for each channel adjusted for each array.

data_processing: No Background correction, Lowess Normalization within each array, no between array normalization

label_protocol: Agilent aCGH protocol was followed and 2 µg of amplified MIRA-enriched fragments were labeled for each sample; tumor: cy5; matching normal: cy3.

extract_protocol: Standard phenol/chloroform method was used for DNA extraction. The MIRA procedure was as described in Rauch et al., 2006. Cancer Research 66:7939–7947

tag: Matching normal from patient 5

tag: stage 1 squamous cell carcinoma of lung


title: Patient 3 tumor vs. normal

description: patient 3

tag: Matching normal from patient 3


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set08_2


title: Patient 1 tumor vs. normal

description: patient 1

tag: Matching normal from patient 1


title: KO_NP_mid_4


title: KO_NP_mid_3


title: KO_sham_med_3


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set18_1


title: Patient 4 tumor vs. normal

description: patient 4

tag: Matching normal from patient 4


title: CO_NP_med_2


title: CO_sham_med_2


title: CO_NP_mid_1

description: 430A2_1945_60_control_neuropath_midbrain


title: CO_NP_mid_2

description: 430A2_1945_64_control_neuropath_midbrain


title: CO_NP_med_1


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set29_1


title: KO_sham_med_2


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set11_1


title: Patient 2 tumor vs. normal

description: patient 2

tag: Matching normal from patient 2


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set36_1


title: KO_NP_med_3


title: Fkbp8 wildtype_2007f

city: Houston

first: Rebecca

middle: Lee Yean

last: Wong

state: TX

address: 2121 W Holcombe Blvd

department: Center for Environmental and Genetic Medicine

institute: IBT Texas A&M University System HSC

hyb_protocol: CodeLink Expression Assay protocol

scan_protocol: CodeLink Expression Assay protocol

data_processing: CodeLink Expression Analysis Software version 4.1

label: CodeLink Expression Assay protocol

source_name: Wildtype embryo

label_protocol: CodeLink Expression Assay protocol

extract_protocol: Target tissue was dissected and solubilized in trizol. Total RNA was extracted and purified using PureLink Total RNA Purification System following manufacturer's protocol.

tag: embryonic day 9.5 posterior tissue


title: CD4+ DNAse hypersitivity_2006-02-27_Crawford_HG17_Set04_2


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set27_1


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set20_1


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set04_1


title: KO_sham_mid_1


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set25_1


title: KO_NP_med_2


title: KO_NP_mid_2


title: KO_NP_med_4


title: Fkbp8 wildtype_2007d


title: Fkbp8 wildtype_2007e


title: KO_NP_mid_1


title: CO_sham_mid_2


title: Fkbp8 mutant_2007b

label: Biotin

source_name: Fkbp8 mutant embryo

extract_protocol: Target tissue was dissected and solubilized in trizol. Total RNA was extracted and purified using PureLink Total RNA Purification System following manufacterer's protocol.


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set34_1


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set02_1


title: CO_sham_mid_1


title: CO_sham_med_1


title: KO_NP_med_1


title: Germ Cell Tumor 590A

status: Public on Nov 15 2007

city: New York

first: James

last: Korkola

address: 1275 York Ave

department: Cell Biology

institute: Memorial Sloan-Kettering

description: abbreviations: EC- embryonal carcinoma; CC- choriocarcinoma; Sem- Seminoma; YST- yolk sac tumor; Ter- teratoma; Ter(I)- immature teratoma; Ter(M)- mature teratoma; TMT- teratoma with malignant transfomation; trophs- trophoblast cells; rplnd- retroperitoneal lymph node; LN- lymph node

hyb_protocol: Labeled test and reference DNA were mixed and hybridized overnight in Spectral Hybridization buffer (Spectral Genomics) at 37C under lifter slips (Erie Scientific); following morning slides were washed sequentially according to array manufacturer's recommendations (Spectral Genomics)

scan_protocol: Slides were scanned on an Axon 4000B scanner Images were quantified using Genepix Pro v.3

data_processing: Utilized difference between log2 median Cy3 and Cy5 values as raw data for analysis; Subarray (block) median normalization and global loess correction was performed and duplicates were averaged; Changes in copy number were identified by CBS algorithm (see Chen W. et al., Blood 107(6):2477-85, 2006)

label: Cy5 & Cy3

source_name: Genomic DNA from germ cell tumor 590A labeled with Cy3 and Cy5 (dye swap)

label_protocol: DPNII digested DNA was labeled using a Bioprime Labeling Kit (Invitrogen) incorporating fluorescent dye (either dCTP-Cy3 or dCTP-Cy5) and mixed with differentially labeled reference DNA

extract_protocol: DNA was extracted using previously described protocols (see Chen W. et al., Blood 107(6):2477-85, 2006)

tag: germ cell tumor

tag: Histology

value: Ter(I),YST

tag: Site

value: Supraclavicular LN

label: Cy3 & Cy5

source_name: placenta reference DNA

tag: karyotypically normal female placental DNA


title: Germ Cell Tumor 587A

source_name: Genomic DNA from germ cell tumor 587A labeled with Cy5

value: Sem

value: testis


title: Germ Cell Tumor 593A

source_name: Genomic DNA from germ cell tumor 593A labeled with Cy5

value: Ter

value: Neck LN


title: Fkbp8 mutant_2007a

source_name: Fkbp8 mutant embryos


title: Fkbp8 mutant_2007c


title: Germ Cell Tumor 586A

source_name: Genomic DNA from germ cell tumor 586A labeled with Cy3 and Cy5 (dye swap)

value: Sem,EC


title: Germ Cell Tumor 594A

source_name: Genomic DNA from germ cell tumor 594A labeled with Cy3

value: Ter(I)

value: rplnd


title: Germ Cell Tumor 596A

source_name: Genomic DNA from germ cell tumor 596A labeled with Cy3


title: Germ Cell Tumor 583A

source_name: Genomic DNA from germ cell tumor 583A labeled with Cy3

value: EC,Sem

value: Testes


title: Germ Cell Tumor 585A

source_name: Genomic DNA from germ cell tumor 585A labeled with Cy3


title: Germ Cell Tumor 584A

source_name: Genomic DNA from germ cell tumor 584A labeled with Cy3

value: EC


title: CD4+ DNAse hypersitivity_2005-09-28_Crawford_HG17_Set09_1

source_name: CD4+ DNAse-treated genomic DNA, replicate #1


title: Germ Cell Tumor 582A

source_name: Genomic DNA from germ cell tumor 582A labeled with Cy3


title: Germ Cell Tumor 573A

source_name: Genomic DNA from germ cell tumor 573A labeled with Cy3

value: YST

value: Mediastinum


title: Germ Cell Tumor 570A

source_name: Genomic DNA from germ cell tumor 570A labeled with Cy3

value: Ter,TMT

value: Lung


title: Germ Cell Tumor 513A

source_name: Genomic DNA from germ cell tumor 513A labeled with Cy5


title: Germ Cell Tumor 539A

source_name: Genomic DNA from germ cell tumor 539A labeled with Cy5


title: Germ Cell Tumor 521A

source_name: Genomic DNA from germ cell tumor 521A labeled with Cy3


title: Germ Cell Tumor 562A

source_name: Genomic DNA from germ cell tumor 562A labeled with Cy5

source_name: placenta reference DNA


title: Germ Cell Tumor 532A

source_name: Genomic DNA from germ cell tumor 532A labeled with Cy3

value: YST,Ter(I)


title: Germ Cell Tumor 532B

source_name: Genomic DNA from germ cell tumor 532B labeled with Cy3

value: lung


title: Germ Cell Tumor 526A

source_name: Genomic DNA from germ cell tumor 526A labeled with Cy3

value: Ter(M)

value: Sm Bowel & mesentery


title: Germ Cell Tumor 512A

source_name: Genomic DNA from germ cell tumor 512A labeled with Cy3

value: YST,Ter(I,M),EC

value: testis


title: Germ Cell Tumor 493A

source_name: Genomic DNA from germ cell tumor 493A labeled with Cy3


title: Germ Cell Tumor 503A

source_name: Genomic DNA from germ cell tumor 503A labeled with Cy3

value: Sem,trophs


title: Germ Cell Tumor 497A

source_name: Genomic DNA from germ cell tumor 497A labeled with Cy3


title: Germ Cell Tumor 472A

source_name: Genomic DNA from germ cell tumor 472A labeled with Cy3


title: Germ Cell Tumor 465A

source_name: Genomic DNA from germ cell tumor 465A labeled with Cy3

value: YST,Ter(M)


title: Germ Cell Tumor 430A

source_name: Genomic DNA from germ cell tumor 430A labeled with Cy3


title: Germ Cell Tumor 429A

source_name: Genomic DNA from germ cell tumor 429A labeled with Cy3

value: Sem


title: Germ Cell Tumor 413A

source_name: Genomic DNA from germ cell tumor 413A labeled with Cy3

value: EC,YST,T(I)


title: Germ Cell Tumor 428A

source_name: Genomic DNA from germ cell tumor 428A labeled with Cy3


title: Germ Cell Tumor 500A

source_name: Genomic DNA from germ cell tumor 500A labeled with Cy3

value: EC,YST,Ter


title: Germ Cell Tumor 411A

source_name: Genomic DNA from germ cell tumor 411A labeled with Cy3

value: rplnd