title: Bladder tumor 539-1 (30g1)


title: Bladder tumor 532-8 (52g1)

status: Public on Jun 15 2007

type: RNA

city: Aarhus N

first: Lars

last: Dyrskjot

address: Brendstrupgaardsvej

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University Hospital, Skejby

description: Gene expression data from a bladder tumor compared to a common reference sample

hyb_protocol: Described in: Dyrskjot L, Zieger K, Kruhoffer M, Thykjaer T, Jensen JL, Primdahl H, Aziz N, Marcussen N, Moller K, Orntoft TF. A molecular signature in superficial bladder carcinoma predicts clinical outcome. Clin Cancer Res. 2005 Jun 1;11(11):4029-36. PMID: 15930337

scan_protocol: Arrays were scanned using a ScanArray4000 scanner - settings: Cy5: 54% PMT, 100% laser power and Cy3: 78% PMT, 100% laser power

data_processing: Raw data were generated using TIGR Spotfinder 2.23 and raw data were lowess print-group normalized using TIGR MIDAS 2.19

molecule: total RNA

organism: Homo sapiens

source_name: Bladder tumor biopsy

extract_protocol: Total RNA extraction using standard protocols

tag: Bladder tumor

tag: Patient clinical information can be found in a Series supplementary file

source_name: Universal human reference RNA (Stratagene)

extract_protocol: Total RNA from Stratagene Universal human reference RNA

tag: reference sample


title: Bladder tumor 525_UK (12g2)

label_protocol: Described in: Dyrskjot L, Zieger K, Kruhoffer M, Thykjaer T, Jensen JL, Primdahl H, Aziz N, Marcussen N, Moller K, Orntoft TF. A molecular signature in superficial bladder carcinoma predicts clinical outcome. Clin Cancer Res. 2005 Jun 1;11(11):4029-36. PMID: 15930337


title: Bladder tumor 532-8 (51g1)


title: Bladder tumor 635_S (28g1)


title: Bladder tumor 518 (38g1) F


title: Bladder tumor 508 (17g2) F


title: Bladder tumor 506 (32g1) F


title: Bladder tumor 519_UK (12g1)


title: Bladder tumor 525_UK (13g2)


title: Bladder tumor 506 (17g1) F


title: Bladder tumor 490_UK (11g2)


title: Bladder tumor 521-1 (32g2)


title: Bladder tumor 505 (27g2) F


title: Bladder tumor 508 (32g2) F


title: Bladder tumor 441-1 (32g1)


title: Bladder tumor 448 (75g1) F


title: Bladder tumor 521-1 (31g2)


title: Bladder tumor 519_UK (13g1)


title: Bladder tumor 441-1 (31g1)


title: Bladder tumor 448 (6g1) F


title: Bladder tumor 490_UK (10g2)


title: Bladder tumor 431 (64g1) F


title: Bladder tumor 478-2 (6g2) F


title: Bladder tumor 413 (36g2) F


title: Bladder tumor 413 (35g2) F


title: Bladder tumor 505 (26g2) F


title: Bladder tumor 18970_S (60g2)


title: Bladder tumor 431 (63g1) F


title: Bladder tumor 518 (37g1) F


title: Bladder tumor 478-2 (75g2) F


title: Bladder tumor 18970_S (59g2)


title: Bladder tumor 18877_S (46g2)


title: Bladder tumor 18877_S (72g2)


title: Bladder tumor 18775_S (23g2)


title: Bladder tumor 18757_S (48g1)


title: Bladder tumor 18757_S (47g1)


title: Bladder tumor 18600_S (50g1)


title: Bladder tumor 18775_S (24g2)


title: Bladder tumor 18600_S (72g1)


title: Bladder tumor 18318_S (61g1)


title: Bladder tumor 18404_S (47g2)


title: Bladder tumor 17798_S (61g2)


title: Bladder tumor 17932_S (10g2)


title: Bladder tumor 18318_S (60g1)


title: Bladder tumor 18404_S (48g2)


title: Bladder tumor 17932_S (11g2)


title: Bladder tumor 17754_S (54g2)


title: Bladder tumor 18410_S (14g1)


title: Bladder tumor 18410_S (15g1)


title: Bladder tumor 17753_S (35g1)


title: Bladder tumor 17753_S (34g1)


title: Bladder tumor 17640_S (35g2)


title: Bladder tumor 17640_S (34g2)


title: Bladder tumor 17266_S (50g2)


title: Bladder tumor 17601_S (14g2)


title: Bladder tumor 17798_S (60g2)


title: Bladder tumor 17089_S (28g1)


title: Bladder tumor 17089_S (29g1)


title: Bladder tumor 16805_S (16g1)


title: Bladder tumor 17601_S (15g2)


title: Bladder tumor 16805_S (17g1)


title: Bladder tumor 16766_S (15g1)


title: Bladder tumor 17266_S (49g2)


title: Bladder tumor 17754_S (53g2)


title: Bladder tumor 16766_S (11g1)


title: Bladder tumor 16520_S (23g1)


title: Bladder tumor 16520_S (24g1)


title: Bladder tumor 16458_S (13g1)


title: Bladder tumor 16667_S (36g1)


title: Bladder tumor 16667_S (37g1)


title: Bladder tumor 16429_S (29g2)


title: Bladder tumor 16429_S (28g2)


title: Bladder tumor 16458_S (12g1)


title: Bladder tumor 16162_S (4g1)


title: Bladder tumor 15901_S (34g2)


title: Bladder tumor 16162_S (5g1)


title: Bladder tumor 15901_S (33g2)


title: Bladder tumor 15152_S (15g2)


title: Bladder tumor 15152_S (11g2)


title: Bladder tumor 13853_S (37g2)


title: Bladder tumor 13781_S (5g2)


title: Bladder tumor 13467_S (21g1)


title: Bladder tumor 14406_S (21g1)


title: Bladder tumor 14406_S (20g1)


title: Bladder tumor 13853_S (36g2)


title: Bladder tumor 13467_S (22g1)


title: Bladder tumor 13964_S (22g2)


title: Bladder tumor 14226_S (23g1)


title: Bladder tumor 13964_S (21g2)


title: Bladder tumor 14226_S (22g1)


title: Bladder tumor 13781_S (4g2)


title: Bladder tumor 13419_S (23g2)


title: Bladder tumor 13207_S (17g2)


title: Bladder tumor 13240_S (7g1)


title: Bladder tumor 13076_S (25g1)


title: Bladder tumor 13076_S (24g1)


title: Bladder tumor 13419_S (22g2)


title: Bladder tumor 13207_S (16g2)


title: Bladder tumor 13240_S (6g1)


title: Bladder tumor 12944_S (18g1)


title: Bladder tumor 11624_S (6g2)


title: Bladder tumor 11678_S (61g1)


title: Bladder tumor 10530_S (20g2)


title: Bladder tumor 12324_S (63g1)


title: Bladder tumor 11678_S (62g1)


title: Bladder tumor 12944_S (19g1)


title: Bladder tumor 11624_S (7g2)


title: Bladder tumor 12324_S (62g1)


title: Bladder tumor 10386_S (16g2)


title: Bladder tumor 10395_S (44g1)


title: Bladder tumor 10386_S (14g1)


title: Bladder tumor Esp9_E (8g1)


title: Bladder tumor 10054_S (62g2)


title: Bladder tumor 10395_S (43g1)


title: Bladder tumor 10530_S (19g2)


title: Bladder tumor Esp95_E (44g1)


title: Bladder tumor Esp95_E (43g1)


title: Bladder tumor Esp86_E (36g1)


title: Bladder tumor 10054_S (63g2)


title: Bladder tumor Esp9_E (7g1)


title: Bladder tumor Esp86_E (35g1)


title: Bladder tumor Esp80_E (34g1)


title: Bladder tumor Esp80_E (33g1)


title: Bladder tumor Esp69_E (31g2)


title: Bladder tumor Esp7_E (19g1)


title: Bladder tumor Esp69_E (32g2)


title: Bladder tumor Esp7_E (6g1)


title: Bladder tumor Esp66_E (32g1)


title: Bladder tumor Esp64_E (30g2)


title: Bladder tumor Esp66_E (31g1)


title: Bladder tumor Esp55_E (42g2)


title: Bladder tumor Esp55_E (41g2)


title: Bladder tumor Esp49_E (21g2)


title: Bladder tumor Esp52_E (22g1)


title: Bladder tumor Esp64_E (24g2)


title: Bladder tumor Esp49_E (20g2)


title: Bladder tumor Esp61_E (30g1)


title: Bladder tumor Esp58_E (23g2)


title: Bladder tumor Esp52_E (23g1)


title: Bladder tumor Esp58_E (22g2)


title: Bladder tumor Esp61_E (24g1)


title: Bladder tumor Esp46_E (20g1)


title: Bladder tumor Esp46_E (21g1)


title: Bladder tumor Esp40_E (18g2)


title: Bladder tumor Esp40_E (17g2)


title: Bladder tumor Esp38_E (18g1)


title: Bladder tumor Esp38_E (17g1)


title: Bladder tumor Esp37_E (16g2)


title: Bladder tumor Esp34_E (15g1)


title: Bladder tumor Esp37_E (15g2)


title: Bladder tumor Esp27_E (12g2)


title: Bladder tumor Esp30_ E (14g1)


title: Bladder tumor Esp21_E (9g2)


title: Bladder tumor Esp33_E (13g2)


title: Bladder tumor Esp27_E (11g2)


title: Bladder tumor Esp34_E (16g1)


title: Bladder tumor Esp21_E (10g2)


title: Bladder tumor Esp33_E (14g2)


title: Bladder tumor Esp112_E (44g2)


title: Bladder tumor Esp15_E (10g1)


title: Bladder tumor Esp12_E (8g2)


title: Bladder tumor Esp104_E (37g1)


title: Bladder tumor Esp12_E (7g2)


title: Bladder tumor 99_UK (39g1)


title: Bladder tumor Esp30_ E (13g1)


title: Bladder tumor Esp101_E (36g2)


title: Bladder tumor Esp101_E (35g2)


title: Bladder tumor Esp112_E (43g2)


title: Bladder tumor Esp15_E (9g1)


title: Bladder tumor Esp104_E (38g1)


title: Bladder tumor 74_UK (37g2)


title: Bladder tumor 58-11 (15g2)


title: Bladder tumor 62-9 (37g1)


title: Bladder tumor 62-9 (38g1)


title: Bladder tumor 74_UK (36g2)


title: Bladder tumor 99_UK (38g1)


title: Bladder tumor 58-11 (14g2)


title: Bladder tumor 407-1 (30g2)


title: Bladder tumor 402 (16g1) F


title: Bladder tumor 407 (15g2) F


title: Bladder tumor 407 (16g2) F


title: Bladder tumor 391 (14g2) F


title: Bladder tumor 368-4 (39g1)


title: Bladder tumor 368-4 (40g1)


title: Bladder tumor 361_UK (10g1)


title: Bladder tumor 407-1 (29g2)


title: Bladder tumor 37_UK (36g1)


title: Bladder tumor 342 (74g2) F


title: Bladder tumor 361_UK (11g1)


title: Bladder tumor 402 (15g1) F


title: Bladder tumor 37_UK (37g1)


title: Bladder tumor 391 (13g2) F


title: Bladder tumor 342 (73g2) F


title: Bladder tumor 338 (73g1) F


title: Bladder tumor 347-5 (25g2)


title: Bladder tumor 341_UK (9g2)


title: Bladder tumor 341_UK (8g2)


title: Bladder tumor 338 (74g1)


title: Bladder tumor 335-6 (38g2)


title: Bladder tumor 332-1 (29g1)


title: Bladder tumor 347-5 (24g2)


title: Bladder tumor 332-1 (30g1)


title: Bladder tumor 335-6 (37g2)


title: Bladder tumor 334_UK (9g1)


title: Bladder tumor 324 (62g2) F


title: Bladder tumor 334_UK (8g1)


title: Bladder tumor 324 (61g2) F


title: Bladder tumor 31999_S (5g2)


title: Bladder tumor 320-7 (24g1)


title: Bladder tumor 319 (61g1) F


title: Bladder tumor 31999_S (45g2)


title: Bladder tumor 320-7 (25g1)


title: Bladder tumor 319 (62g1) F


title: Bladder tumor 31373_S (45g1)


title: Bladder tumor 29600_S (43g2)


title: Bladder tumor 295_UK (4g2)


title: Bladder tumor 304_UK (6g1)


title: Bladder tumor 311_UK (7g2)


title: Bladder tumor 311_UK (6g2)


title: Bladder tumor 29600_S (44g2)


title: Bladder tumor 304_UK (7g1)


title: Bladder tumor 31373_S (5g1)


title: Bladder tumor 290_UK (4g1)


title: Bladder tumor 290_UK (5g1)


title: Bladder tumor 288-2 (34g2) F


title: Bladder tumor 289-3 (35g1) F


title: Bladder tumor 288-2 (33g2) F


title: Bladder tumor 281 (34g1) F


title: Bladder tumor 295_UK (5g2)


title: Bladder tumor 281 (33g1) F


title: Bladder tumor 276_UK (3g1)


title: Bladder tumor 277_UK (3g2)


title: Bladder tumor 276_UK (2g1)


title: Bladder tumor 277_UK (2g2)


title: Bladder tumor 289-3 (36g1) F


title: Bladder tumor 27386_S (22g1)


title: Bladder tumor 27386_S (23g1)


title: Bladder tumor 259 (27g1) F


title: Bladder tumor 263-1 (13g1) F


title: Bladder tumor 248_UK (44g2)


title: Bladder tumor 248_UK (45g2)


title: Bladder tumor 259 (26g1) F


title: Bladder tumor 247-9 (23g1)


title: Bladder tumor 242-3 (20g2)


title: Bladder tumor 24745_S (12g2)


title: Bladder tumor 225_UK (14g1)


title: Bladder tumor 22562_S (7g1)


title: Bladder tumor 240-12 (20g1)


title: Bladder tumor 217-11 (19g2)


title: Bladder tumor 266_UK (15g2)


title: Bladder tumor 266_UK (14g2)


title: Bladder tumor 22562_S (8g1)


title: Bladder tumor 225_UK (15g1)


title: Bladder tumor 21512_S (9g1)


title: Bladder tumor 21077_S (56g2)


title: Bladder tumor 263-1 (14g1) F


title: Bladder tumor 217-11 (18g2)


title: Bladder tumor 21077_S (55g2)


title: Bladder tumor 242-3 (21g2)


title: Bladder tumor 24745_S (13g2)


title: Bladder tumor 21512_S (10g1)


title: Bladder tumor 20803_S (3g1)


title: Bladder tumor 20975_S (9g2)


title: Bladder tumor 240-12 (21g1)


title: Bladder tumor 21040_S (20g2)


title: Bladder tumor 247-9 (22g1)


title: Bladder tumor 21040_S (21g2)


title: Bladder tumor 20750_S (56g1)


title: Bladder tumor 20975_S (10g2)


title: Bladder tumor 20724_S (58g1)


title: Bladder tumor 20724_S (57g1)


title: Bladder tumor 20803_S (2g1)


title: Bladder tumor 20750_S (55g1)


title: Bladder tumor 20421_S (26g1)


title: Bladder tumor 20577_S (20g1)


title: Bladder tumor 19992_S (58g2)


title: Bladder tumor 19783_S (2g2)


title: Bladder tumor 19992_S (57g2)


title: Bladder tumor 20421_S (25g1)


title: Bladder tumor 19783_S (3g2)


title: Bladder tumor 20577_S (21g1)


title: Bladder tumor 195 (51g1) F


title: Bladder tumor 195 (52g1) F


title: Bladder tumor 19134_S (60g1)


title: Bladder tumor 19292_S (45g1)


title: Bladder tumor 19292_S (46g1)


title: Bladder tumor 168_UK (42g2)


title: Bladder tumor 187_UK (44g1)


title: Bladder tumor 19134_S (59g1)


title: Bladder tumor 19700_S (11g1)


title: Bladder tumor 187_UK (45g1)


title: Bladder tumor 177-1 (18g1)


title: Hybridization time experiment: Sample 2: Scan 2

city: Los Angeles

first: Diana

last: Abdueva

state: CA

address: 443 S San Pedro St, STE 403

country: USA

institute: USC

description: Raw probe intensity data (PM) corresponding to spiked targets post stringent wash.

hyb_protocol: According to standard Affymetrix protocol, following the synthesis and purification of labeled cRNAs the product is fragmented and hybridized to the GeneChip  for 40 hours, after which the array is subject to a standard washing and staining steps prior to being scanned to obtain hybridization intensities.

scan_protocol: GeneChips were scanned using the GeneArray Scanner.

data_processing: No processing, i.e. raw probe intensities.

label: biotin

organism: Drosophila melanogaster

source_name: Drosophila cRNA transcripts spiked into complex backgrounds (total RNA from mouse cerebellum) at known concentrations.

label_protocol: Selective labeling of target antisense cRNA was achieved by pooling PCR products for direct use as templates for in vitro transcription (IVT) with T7 polymerase to generate biotinylated (GeneChip One-Cycle Target Labeling Kit) spiked target and  unlabeled (MEGAscript T7 Kit, Ambion) complex background cRNA.

extract_protocol: 20 cDNAs from the Drosophila Gene Collection adult testes (AT) library were PCR amplified, pooled, and used directly as targets for in vitro transcription (IVT). Biotin labeled and unlabeled antisense cRNAs were generated using either the GeneChip IVT Labeling Kit or Ambion’s MEGAscript  T7 Kit, respectively. Standard protocol, as described in the Affymetrix GeneChip  Expression Analysis manual, was followed for IVT, purification, and fragmentation of cRNA, with the exception that the volumes of reagents used to generate unlabeled cRNA transcripts were in accordance with Ambion’s MEGAscript  protocol.

tag: Wash Condition

value: 1 cycle of stringent wash

tag: Hybridization Time

value: 40 hrs

tag: Labeling Condition

value: 0.5 nM labeled spikes, 15 µg unlabeled background


title: Bladder tumor 19700_S (10g1)


title: Bladder tumor 168_UK (43g2)


title: Hybridization time experiment: Sample 2: Scan 1

description: Raw probe intensity data (PM) corresponding to spiked targets prior to stringent wash.

hyb_protocol: According to standard Affymetrix protocol, following the synthesis and purification of labeled cRNAs the product is fragmented and hybridized to the GeneChip  for 40 hours, after which the array is subject to a modified non-stringent washing and staining steps prior to being scanned to obtain hybridization intensities.

data_processing: Raw probe intensities.

extract_protocol: 20 cDNAs from the Drosophila Gene Collection adult testes (AT) library were PCR amplified, pooled, and used directly as targets for in vitro transcription (IVT). Biotin labeled and unlabeled antisense cRNAs were generated using either the GeneChip IVT Labeling Kit or Ambion’s MEGAscript  T7 Kit, respectively. Standard protocol, as described in the Affymetrix GeneChip  Expression Analysis manual, was followed for IVT, purification, and fragmentation of cRNA, with the exception that the volumes of reagents used to generate unlabeled cRNA transcripts were in accordance with Ambion’s MEGAscript  protocol. .

value: 1 cycle of non-stringent wash


title: Bladder tumor 167_UK (42g1)


title: Bladder tumor 177-1 (19g1)


title: Bladder tumor 167_UK (43g1)


title: Bladder tumor 154-5 (17g2)


title: Hybridization time experiment: Sample 1: Scan 1

hyb_protocol: According to standard Affymetrix protocol, following the synthesis and purification of labeled cRNAs the product is fragmented and hybridized to the GeneChip  for 16 hours, after which the array is subject to a modified non-stringent washing and staining steps prior to being scanned to obtain hybridization intensities.

value: 16 hrs


title: Hybridization time experiment: Sample 1: Scan 2

hyb_protocol: According to standard Affymetrix protocol, following the synthesis and purification of labeled cRNAs the product is fragmented and hybridized to the GeneChip  for 16 hours, after which the array is subject to a standard washing and staining steps prior to being scanned to obtain hybridization intensities.


title: Clone concentration experiment: Sample 1: Scan 1

description: Raw probe intensity data (PM) corresponding to spiked targets.

source_name: Drosophila cRNA transcripts at known concentrations hybridized to the array in the absense of complex background.

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

extract_protocol: 4 cDNAs from the Drosophila Gene Collection adult testes (AT) library were PCR amplified, pooled, and used directly as targets for in vitro transcription (IVT).

value: 10 nM labeled spikes, no background


title: Dahl Salt Sensitive Rat Lung- Hypoxia with SU-5416 rep2

city: Chicago

first: Ankit

middle: A

last: Desai

state: IL

address: 929 East 57th Street, Room W403R

department: Medicine

institute: The University of Chicago

description: Gene expression data from rat lungs exposed to FiO2 of ~9.5% and SU-5416 (hypoxia-SU-5416).

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GC Robust Multichip Average (RMA) module of Bioconductor package and the arrays were normalized against all of the 15 chips including those from normoxia, hypoxia, hypoxia-SU5416, and hypoxia-SU5416-so

organism: Rattus norvegicus

source_name: Rat Lung

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

growth_protocol: Not Applicable

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

treatment_protocol: At the termination of each experiment, all animals were euthanized by exsanguination under anesthesia in accordance with institutional guidelines. The pulmonary vasculature was perfused via the pulmonary artery with sterile ph

tag: Genotype

value: Dahl Salt Sensitive Rats with Hypoxia and SU-5416

tag: Weights


title: Dahl Salt Sensitive Rat Lung- Hypoxia alone rep4

description: Gene expression data from rat lungs exposed to FiO2 of ~9.5% (hypoxia).

value: Dahl Salt Sensitive Rats with Hypoxia alone


title: Clone concentration experiment: Sample 2: Scan 1

value: 1 nM labeled spikes, no background


title: Clone concentration experiment: Sample 1: Scan 2

hyb_protocol: According to standard Affymetrix protocol, following the synthesis and purification of labeled cRNAs the product is fragmented and hybridized to the GeneChip  for 16 hours, after which the array is subject to a standard stringent washing and staining steps prior to being scanned to obtain hybridization intensities.

value: standard stringent wash


title: Dahl Salt Sensitive Rat Lung- Hypoxia with SU-5416 rep1


title: Dahl Salt Sensitive Rat Lung- Hypoxia alone rep2


title: Washing cycle experiment: Sample 3 : Scan 3

hyb_protocol: According to standard Affymetrix protocol, following the synthesis and purification of labeled cRNAs the product is fragmented and hybridized to the GeneChip  for 16 hours, after which the array is subject to a standard washing and staining steps, followed by another stringent wash prior to being scanned to obtain hybridization intensities.

extract_protocol: 18 cDNAs from the Drosophila Gene Collection adult testes (AT) library were PCR amplified, pooled, and used directly as targets for in vitro transcription (IVT). Biotin labeled and unlabeled antisense cRNAs were generated using either the GeneChip IVT Labeling Kit or Ambion’s MEGAscript  T7 Kit, respectively. Standard protocol, as described in the Affymetrix GeneChip  Expression Analysis manual, was followed for IVT, purification, and fragmentation of cRNA, with the exception that the volumes of reagents used to generate unlabeled cRNA transcripts were in accordance with Ambion’s MEGAscript  protocol.

value: 2 cycles of stringent wash


title: Washing cycle experiment: Sample 3 : Scan 1

extract_protocol: 18 cDNAs from the Drosophila Gene Collection adult testes (AT) library were PCR amplified, pooled, and used directly as targets for in vitro transcription (IVT). Biotin labeled and unlabeled antisense cRNAs were generated using either the GeneChip IVT Labeling Kit or Ambion’s MEGAscript  T7 Kit, respectively. Standard protocol, as described in the Affymetrix GeneChip  Expression Analysis manual, was followed for IVT, purification, and fragmentation of cRNA, with the exception that the volumes of reagents used to generate unlabeled cRNA transcripts were in accordance with Ambion’s MEGAscript  protocol. .


title: Dahl Salt Sensitive Rat Lung- Hypoxia with SU-5416 rep3


title: Dahl Salt Sensitive Rat Lung- Hypoxia alone rep3


title: Bladder tumor 132_UK (41g1)


title: Bladder tumor 140-16 (16g1)


title: Dahl Salt Sensitive Rat Lung- Hypoxia alone rep1


title: Bladder tumor 154-5 (16g2)


title: Washing cycle experiment: Sample 2 : Scan 3

extract_protocol: 19 cDNAs from the Drosophila Gene Collection adult testes (AT) library were PCR amplified, pooled, and used directly as targets for in vitro transcription (IVT). Biotin labeled and unlabeled antisense cRNAs were generated using either the GeneChip IVT Labeling Kit or Ambion’s MEGAscript  T7 Kit, respectively. Standard protocol, as described in the Affymetrix GeneChip  Expression Analysis manual, was followed for IVT, purification, and fragmentation of cRNA, with the exception that the volumes of reagents used to generate unlabeled cRNA transcripts were in accordance with Ambion’s MEGAscript  protocol.


title: Washing cycle experiment: Sample 3: Scan 2


title: Clone concentration experiment: Sample 2: Scan 2


title: Dahl Salt Sensitive Rat Lung- Control 4

description: Gene expression data from rat lungs exposed to Normoxia (room air).

value: Control Dahl Salt Sensitive Rats


title: Dahl Salt Sensitive Rat Lung- Control 3


title: Washing cycle experiment: Sample 2: Scan 2


title: SARD Profile of Soil Sample WP45

type: genomic

city: Tiburon

first: Matthew

last: Ashby

address: 3152 Paradise Drive

institute: Taxon Biosciences, Inc.

description: Agricultural soil sample SARD tags.

data_processing: SARD tags extracted from Sanger DNA sequence data.

molecule: genomic DNA

organism: uncultured bacterium

source_name: soil sample

growth_protocol: Culture independent analysis

extract_protocol: Mechanical glass bead lysis procedure.

tag: Soil sample collected from asparagus field (~16" depth) from Victoria Is. of the Sacramento River Delta region of California.


title: Washing cycle experiment: Sample 2.Scan 1

extract_protocol: 19 cDNAs from the Drosophila Gene Collection adult testes (AT) library were PCR amplified, pooled, and used directly as targets for in vitro transcription (IVT). Biotin labeled and unlabeled antisense cRNAs were generated using either the GeneChip IVT Labeling Kit or Ambion’s MEGAscript  T7 Kit, respectively. Standard protocol, as described in the Affymetrix GeneChip  Expression Analysis manual, was followed for IVT, purification, and fragmentation of cRNA, with the exception that the volumes of reagents used to generate unlabeled cRNA transcripts were in accordance with Ambion’s MEGAscript  protocol. .


title: Bladder tumor 140-16 (17g1)


title: Dahl Salt Sensitive Rat Lung- Control 1


title: Bladder tumor 132_UK (40g1)


title: Bladder tumor 129_UK (39g2)


title: Washing cycle experiment: Sample 1 : Scan 3


title: Dahl Salt Sensitive Rat Lung- Control 2


title: SARD Profile of Soil Sample Pol-W

description: Agricultural soil sample SARD tags.

tag: Soil sample collected from alfalfa field (~16" depth) from Union Is. of the Sacramento River Delta region of California.


title: Bladder tumor 129_UK (38g2)


title: SARD Profile of Soil Sample Pol-NE

description: Agricultural soil sample SARD tags.


title: Bladder tumor 112-10 (45g1)


title: Bladder tumor 112-10 (46g1)


title: SARD Profile of Soil Sample WP43

description: Agricultural soil sample SARD tags.


title: Washing cycle experiment: Sample 1 : Scan 1


title: Washing cycle experiment: Sample 1: Scan 2


title: Control 1 vs. DES 1

status: Public on Jun 14 2007

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.    For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.    Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software (v7.4).

data_processing: Rosetta Resolver Error Model, values are Cy5/Cy3 in fold change

organism: Mus musculus

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 1µg of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.

growth_protocol: After birth, pups were separated by sex and female pups were standardized to 8 female pups per litter.  Mice were housed in polysulfone ventilated cages and provided NIH-31 laboratory mouse chow and fresh water ad libitum.  Mouse chow was tested for estrogenic activity and found to be negative.

extract_protocol: Uteri were snap frozen in liquid nitrogen.  Frozen tissues were pulverized and RA was prepared using RNeasy Mini kits according to the manufacturer's protocol.  The quality of the RNA was assessed by 1% agarose gel with ethidium bromide.  RNA was pooled from 10 mice and assayed again for quality using the Agilent 2100 Bioanalyzer.

treatment_protocol: Pooled RNA prepared from uteri of 19 day old female CD-1 mice treated on days1-5 with corn oil

tag: Control

treatment_protocol: Pooled RNA prepared from uteri of 19 day old female CD-1 mice treated on days1-5 with 1 µg/kg/day DES dissolved in corn oil

tag: DES treated


title: DES 10 vs. Control 10

hyb_protocol: For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.

scan_protocol: Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software (v7.4).

data_processing: Rosetta Resolver Error Model, values are Cy3/Cy5 in fold change

treatment_protocol: Pooled RNA prepared from uteri of 19 day old female CD-1 mice treated on days1-5 with 10 µg/kg/day DES dissolved in corn oil


title: DES 1000 vs. Control 1000

treatment_protocol: Pooled RNA prepared from uteri of 19 day old female CD-1 mice treated on days1-5 with 1000 µg/kg/day DES dissolved in corn oil


title: Control 10 vs. DES 10

source_name: RNA prepared from uteri of 19 day old female CD-1 mice


title: Control 1000 vs. DES 1000


title: DES 1 vs. Control 1


title: Blood Pool vs Blood_Sample_1021

status: Public on Jun 13 2007

city: Seattle

first: Valur

last: Emilsson

state: WA

address: 401 Terry Avenue N

department: Genetics

institute: Merck

description: The genetics of human gene expression from population based tissue sampling

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: Blood

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: Blood Pool


title: Blood Pool vs Blood_Sample_1015


title: Blood Pool vs Blood_Sample_1020


title: Blood Pool vs Blood_Sample_1008


title: Blood Pool vs Blood_Sample_1013


title: Blood Pool vs Blood_Sample_1019


title: Blood Pool vs Blood_Sample_1011


title: Blood Pool vs Blood_Sample_1010


title: Blood Pool vs Blood_Sample_1009


title: Blood Pool vs Blood_Sample_1003


title: Blood Pool vs Blood_Sample_1006


title: Blood Pool vs Blood_Sample_1007


title: Blood Pool vs Blood_Sample_1018


title: Blood Pool vs Blood_Sample_1004


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title: Blood Pool vs Blood_Sample_1016


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title: Blood Pool vs Blood_Sample_998


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title: Blood Pool vs Blood_Sample_999


title: Blood Pool vs Blood_Sample_996


title: Blood Pool vs Blood_Sample_1000


title: Blood Pool vs Blood_Sample_997


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title: Blood Pool vs Blood_Sample_988


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title: Blood Pool vs Blood_Sample_773


title: Blood Pool vs Blood_Sample_771


title: Blood Pool vs Blood_Sample_785


title: Blood Pool vs Blood_Sample_770


title: Blood Pool vs Blood_Sample_777


title: Blood Pool vs Blood_Sample_765


title: Blood Pool vs Blood_Sample_754


title: Blood Pool vs Blood_Sample_769


title: Blood Pool vs Blood_Sample_750


title: Blood Pool vs Blood_Sample_753


title: Blood Pool vs Blood_Sample_768


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title: Blood Pool vs Blood_Sample_756


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title: Blood Pool vs Blood_Sample_761


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title: Blood Pool vs Blood_Sample_751


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title: Blood Pool vs Blood_Sample_719


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title: Blood Pool vs Blood_Sample_452


title: Blood Pool vs Blood_Sample_458


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title: Adipose Pool vs Adipose_Sample_700

source_name: Adipose

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