title: K5_1:K5 OD600 = 0.7

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: K5 OD600 = 0.7

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

scan_protocol: GeneChips were scanned using an array WoRx biochip reader (Applied Precision, LLC, Washington, USA).

data_processing: The data were analyzed with ImaGene 5.0 (BioDiscovery, Inc. Los Angeles, CA, USA) and  Array Assist 4.0 Software package (Stratagene Europe, Amsterdam, The Netherlands. Before normalization, each individual array data has been pruned to exclude bad and empty spots flagged by Imagene software. Normalization was performed using the LOWESS algorithm

organism: Streptococcus mutans

source_name: WT

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

growth_protocol: S. mutans UA159 wild type was cultured anaerobically in BM medium containing 0.5% sucrose at 37°C, and the samples were collected at the following optical densities of the culture: 0.05, 0.1, 0.2, 0.3, 0.5, 0.7, 0.9 and 1.2. To obtain the same amount of RNA from each growth stage, the volumes of the samples withdrawn ranged from 200 ml (OD600 = 0.05) to 2.5 ml (OD600 = 1.2). The samples were fixed using RNA Protect Bacterial Reagent (Qiagen, Hilden, Germany).

extract_protocol: Rneasy

tag: genetic modification:

tag: tissue:


title: C8_2_2:C8 OD 600 = 1.2

status: Public on Sep 01 2006

type: RNA

country: Germany

description: C8 OD 600 = 1.2

label: biotin

molecule: total RNA


title: D0_1:D0 OD600 = 0.05

description: D0 OD600 = 0.05


title: C8_1:C8 OD 600 = 1.2

description: C8 OD 600 = 1.2


title: C8_2:C8 OD 600 = 1.2

description: C8 OD 600 = 1.2


title: D1_2_2:D1 OD600 = 0.1

description: D1 OD600 = 0.1


title: K2_2:K2 OD600 = 0.2

description: K2 OD600 = 0.2


title: Ago2 knock down replicate 2

city: Basel

first: Daniela

last: Schmitter

address: Maulbeerstrasse 66

department: Epigenetics

country: Switzerland

institute: Friedrich Miescher Institut

description: 293 cells expressing the tet-repressor protein_ date of analysis_01062005

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix and Expressionist

organism: Homo sapiens

source_name: T-REx-293 cells

label_protocol: 15 micrograms of biotinylated fragmented cRNA was hybridized to each chip.

extract_protocol: RNA was extracted from cells in a confluent 6-well dish using Absolutely RNA Miniprep Kit (Stratagene)

tag: embryonic kidney cells

tag: 293 cells stably expressing the tet-repressor and a hairpin against Ago2 after induction, female, induced for 48 hrs with 10ug/ml of Tetracycline


title: K3_1_2:K3 OD600 = 0.3

description: K3 OD600 = 0.3


title: D1_2:D1 OD600 = 0.1

description: D1 OD600 = 0.1


title: Ago2 knock down replicate 1


title: shRNA ctrl replicate 1

tag: 293 cells stably expressing the tet-repressor and a scrambled hairpin after induction, female, induced for 48 hrs with 10ug/ml of Tetracycline


title: K2_1:K2 OD600 = 0.2

description: K2 OD600 = 0.2


title: K5_2_2:K5 OD600 = 0.7

description: K5 OD600 = 0.7


title: K2_1_2:K2 OD600 = 0.2

description: K2 OD600 = 0.2


title: J5_2:J5 OD600 = 0.7

description: J5 OD600 = 0.7


title: D0_1_2:D0 OD600 = 0.05

description: D0 OD600 = 0.05


title: J7_1_2:J7 OD600 = 1.0

description: J7 OD600 = 1.0


title: K2_2_2:K2 OD600 = 0.2

description: K2 OD600 = 0.2


title: J5_2_2:J5 OD600 = 0.7

description: J5 OD600 = 0.7


title: Androgen-starved LNCaP cells, treated with 1nM R1881 and DMSO for 6h, biol repl 2 (celastrol)

city: CAMBRIDGE

first: Haley

last: Hieronymus

state: MA

address: 7 Cambridge Center

country: USA

institute: Broad Institute of Harvard and MIT

description: Gene expression data from androgen-starved LNCaP cells treated with 1nM R1881 and DMSO for 24h

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained on a Affymetrix High-throughput array platform

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner

data_processing: The data were processed by RMA (GenePattern)

source_name: LNCaP cell line

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

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

treatment_protocol: LNCaP cells were grown in RPMI and charcol-stripped 10%FBS for 2d and then treated with 1nM R1881 and DMSO for 24h

tag: androgen-starved LNCaP cells, treated with 1nM R1881 and DMSO for 6h


title: K3_2:K3 OD600 = 0.3

description: K3 OD600 = 0.3


title: Androgen-starved LNCaP cells, treated with ethanol and DMSO for 24h, biol repl 3 (celastrol control)

description: Gene expression data from androgen-starved LNCaP cells treated with ethanol and DMSO for 24h

treatment_protocol: LNCaP cells were grown in RPMI and charcol-stripped 10%FBS for 2d and then treated with ethanol and DMSO for 24h

tag: androgen-starved LNCaP cells, treated with ethanol and DMSO for 24h


title: Androgen-starved LNCaP cells, treated with 1nM R1881 and DMSO for 6h, biol repl 1 (celastrol)


title: J5_1:J5 OD600 = 0.7

description: J5 OD600 = 0.7


title: Androgen-starved LNCaP cells, treated with ethanol and DMSO for 24h, biol repl 1 (celastrol control)

description: Gene expression data from androgen-starved LNCaP cells treated with ethanol and DMSO for 24h	!Sample_description = Gene expression data from androgen-starved LNCaP cells treated with ethanol and DMSO for 24h


title: LNCaP cells treated with 1nM R1881 and 1.25uM celastrol for 24h, biol repl 3

description: Gene expression data from androgen-starved LNCaP cells treated with 1with 1nM R1881 and 1.25uM celastrol for 24h

treatment_protocol: LNCaP cells were grown in RPMI and charcol-stripped 10%FBS for 2d and then treated with 1.25uM celastrol plus 1nM R1881 (synthetic, non-metabolizable androgen) for 24h


title: D8_1_2:D8 OD600 = 1.2

description: D8 OD600 = 1.2


title: LNCaP cells treated with 1nM R1881 and 1.25uM celastrol for 24h, biol repl 2


title: LNCaP cells treated with 1nM R1881 and 1.25uM celastrol for 24h, biol repl 1


title: C6_2:C6 OD600 = 0.9

description: C6 OD600 = 0.9


title: J7_2:J7 OD600 = 1.0

description: J7 OD600 = 1.0


title: C6_2_2:C6 OD600 = 0.9

description: C6 OD600 = 0.9


title: LNCaP cells, treated with DMSO for 6h, biol repl 1 (gedunin control)

description: Gene expression data from LNCaP cells treated with DMSO for 6h

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained on the Affymetrix High-throughput array platform

treatment_protocol: LNCaP cells grown in RPMI and 10%FBS were treated with DMSO for 6h

tag: LNCaP cells, treated with DMSO for 6h


title: LNCaP cells, treated with DMSO for 6h, biol repl 2 (gedunin control)


title: J7_1:J7 OD600 = 1.0

description: J7 OD600 = 1.0


title: LNCaP cells, treated with 20uM gedunin for 6h, biol repl 3

description: Gene expression data from LNCaP cells treated with 20uM gedunin for 6h

treatment_protocol: LNCaP cells grown in RPMI and 10%FBS were treated with 20uM gedunin for 6h

tag: = LNCaP cells, treated with 20uM gedunin for 6h


title: J7_2_2:J7 OD600 = 1.0

description: J7 OD600 = 1.0


title: C6_1:C6 OD600 = 0.9

description: C6 OD600 = 0.9


title: LNCaP cells, treated with 20uM gedunin for 6h, biol repl 1


title: LNCaP cells, treated with DMSO for 6h, biol repl 3 (celastrol control)

description: Gene expression data from LNCaP cells treated with 1.25uM celastrol for 6h


title: C6_1_2:C6 OD600 = 0.9

description: C6 OD600 = 0.9


title: Androgen-starved LNCaP cells, treated with 1nM R1881 and DMSO for 6h, biol repl 3 (celastrol)


title: LNCaP cells, treated with DMSO for 6h, biol repl 1 (celastrol control)


title: J4_2:J4 OD600 = 0.5

description: J4 OD600 = 0.5


title: J5_1_2:J5 OD600 = 0.7

description: J5 OD600 = 0.7


title: Androgen-starved LNCaP cells, treated with ethanol and DMSO for 24h, biol repl 2 (celastrol control)


title: LNCaP cells, treated with 1.25uM celastrol for 6h, biol repl 2

treatment_protocol: LNCaP cells grown in RPMI and 10%FBS were treated with 1.25uM celastrol for 6h


title: D8_1:D8 OD600 = 1.2

description: D8 OD600 = 1.2


title: LNCaP cells, treated with 1.25uM celastrol for 6h, biol repl 1


title: N_B_511_201

type: genomic

city: Leiden

first: Jan

last: Oosting

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

description: Genotype and allele specfic intensity of leukocyte DNA

data_processing: GenCall 6.0.0.7

molecule: genomic DNA

source_name: Leukocyte DNA from patient 511

label_protocol: DNA was prepared according to the standard Illumina protocol from 4 x 250 ng of DNA

extract_protocol: DNA isolation was performed by salting out precipitation.

tag: Colorectal cancer

tag: Low intensity replicate


title: T_F_108_201

source_name: Fresh frozen Tumor DNA from patient 108


title: J3_3:J3 OD600 = 0.3

description: J3 OD600 = 0.3


title: LNCaP cells, treated with DMSO for 6h, biol repl 3 (gedunin control)


title: J3_2_2:J3 OD600 = 0.3

description: J3 OD600 = 0.3


title: N_B_56_201

source_name: Leukocyte DNA from patient 56


title: J3_1:J3 OD600 = 0.3

description: J3 OD600 = 0.3


title: LNCaP cells, treated with 20uM gedunin for 6h, biol repl 2


title: N_B_44_201

source_name: Leukocyte DNA from patient 44


title: J3_1_2:J3 OD600 = 0.3

description: J3 OD600 = 0.3


title: T_P_40_201

source_name: Paraffin Tumor DNA from patient 40


title: J2_1:J2 OD600 = 0.2

description: J2 OD600 = 0.2


title: T_P_124_201

source_name: Paraffin Tumor DNA from patient 124


title: Small intestine_LPO-administered_rep3

city: Zama

first: Hiroyuki

last: Wakabayashi

state: Kanagawa

address: 5-1-83 Higashihara

department: Nutritional Science Laboratory

country: Japan

institute: Morinaga Milk Industry Co., Ltd.

description: No additional information

data_processing: GCOS5.0, normalized against "small intestine_water-administered_rep1" array

organism: Mus musculus

source_name: Small intestine 3 h after LPO administration

treatment_protocol: Mice were orally administered 200 microL of bovine lactoperoxidase (LPO; 2.5 g/kg body weight) solution.

tag: Strain

value: BALB/cByJ Jcl;

tag: Gender

value: female;

tag: Age

value: 8-9 weeks;

tag: Tissue

value: jejunum detached Payer's patch


title: LNCaP cells, treated with DMSO for 6h, biol repl 2 (celastrol control)


title: Small intestine_LPO-administered_rep2

description: No additional information


title: Small intestine_LPO-administered_rep1

description: No additional information

value: 8-9 weeks


title: N_B_108_201

source_name: Leukocyte DNA from patient 108


title: J1_2:J1 OD600 = 0.2

description: J1 OD600 = 0.2


title: J4_2_2:J4 OD600 = 0.5

description: J4 OD600 = 0.5


title: J1_1:J1 OD600 = 0.2

description: J1 OD600 = 0.2


title: N_B_40_201

source_name: Leukocyte DNA from patient 40


title: J4_1:J4 OD600 = 0.5

description: J4 OD600 = 0.5


title: T_P_56_201

source_name: Paraffin Tumor DNA from patient 56


title: T_F_44_201

source_name: Fresh frozen Tumor DNA from patient 44


title: K3_2_2:K3 OD600 = 0.3

description: K3 OD600 = 0.3


title: T_F_514_201

source_name: Fresh frozen Tumor DNA from patient 514


title: T_P_514_201

source_name: Paraffin Tumor DNA from patient 514


title: CO_1:C0  OD600 = 0.05

description: C0  OD600 = 0.05


title: Small intestine_water-administered_rep3

description: No additional information

source_name: Small intestine 3 h after water administration

treatment_protocol: Mice were orally administered 200 microL of water.

tag: Tissue jejunum detached Payer's patch


title: Small intestine_water-administered_rep2

description: No additional information


title: J1_1_2:J1 OD600 = 0.1

description: J1 OD600 = 0.1

source_name: WT


title: Small intestine_BSA-administered_rep3

description: No additional information

source_name: Small intestine 3 h after BSA administration

treatment_protocol: Mice were orally administered 200 microL of bovine serum albumin (BSA; 2.5 g/kg body weight) solution.


title: C0_2:C0  OD600 = 0.05

description: C0  OD600 = 0.05


title: Small intestine_BSA-administered_rep2

description: No additional information


title: N_P_124_201

source_name: Paraffin Normal DNA from patient 124


title: T_F_106_201

source_name: Fresh frozen Tumor DNA from patient 106


title: N_B_514_201

source_name: Leukocyte DNA from patient 514


title: J2_1_2:J2 OD600 = 0.2

description: J2 OD600 = 0.2


title: T_P_106_201

source_name: Paraffin Tumor DNA from patient 106


title: T_P_511_201

source_name: Paraffin Tumor DNA from patient 511


title: N_B_124_201

source_name: Leukocyte DNA from patient 124


title: N_B_106_201

source_name: Leukocyte DNA from patient 106


title: T_P_44_201

source_name: Paraffin Tumor DNA from patient 44


title: T_P_108_201

source_name: Paraffin Tumor DNA from patient 108


title: N_P_514_201

source_name: Paraffin Normal DNA from patient 514


title: T_F_511_201

source_name: Fresh frozen Tumor DNA from patient 511


title: T_F_44_260

source_name: Fresh frozen Tumor DNA from patient 44


title: T_F_124_201

source_name: Fresh frozen Tumor DNA from patient 124


title: T_P_56_260

source_name: Paraffin Tumor DNA from patient 56


title: N_B_56_260

source_name: Leukocyte DNA from patient 56


title: T_P_514_260

source_name: Paraffin Tumor DNA from patient 514


title: N_B_44_260

source_name: Leukocyte DNA from patient 44


title: T_F_124_260


title: N_B_40_260

source_name: Leukocyte DNA from patient 40


title: T_F_108_260

source_name: Fresh frozen Tumor DNA from patient 108


title: Small intestine_water-administered_rep1

description: No additional information

source_name: Small intestine 3 h after water administration


title: T_P_106_260

source_name: Paraffin Tumor DNA from patient 106


title: Small intestine_BSA-administered_rep1

description: No additional information

source_name: Small intestine 3 h after BSA administration


title: N_B_514_260

source_name: Leukocyte DNA from patient 514


title: T_P_124_260

source_name: Paraffin Tumor DNA from patient 124


title: T_F_106_260

source_name: Fresh frozen Tumor DNA from patient 106


title: T_P_40_260

source_name: Paraffin Tumor DNA from patient 40


title: N_P_124_260

source_name: Paraffin Normal DNA from patient 124


title: N_P_D02_260

source_name: Paraffin Normal DNA from patient D02


title: N_B_106_260

source_name: Leukocyte DNA from patient 106


title: N_B_124_260

source_name: Leukocyte DNA from patient 124


title: N_P_514_260

source_name: Paraffin Normal DNA from patient 514


title: Androgen-starved LNCaP cells, treated with 1nM R1881 and DMSO for 6h, biol repl 3 (gedunin)

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained on a Affymetrix Fluidics station

source_name: LNCaP cell line


title: Androgen-starved LNCaP cells, treated with 1nM R1881 and DMSO for 6h, biol repl 2 (gedunin)


title: T_F_511_260

source_name: Fresh frozen Tumor DNA from patient 511


title: T_P_108_260

source_name: Paraffin Tumor DNA from patient 108


title: T_P_44_260

source_name: Paraffin Tumor DNA from patient 44


title: N_B_511_260

source_name: Leukocyte DNA from patient 511


title: Androgen-starved LNCaP cells, treated with ethanol and DMSO for 24h, biol repl 2 (gedunin control)


title: Androgen-starved LNCaP cells, treated with 1nM R1881 and DMSO for 6h, biol repl 1 (gedunin)


title: Androgen-starved LNCaP cells, treated with ethanol and DMSO for 24h, biol repl 1 (gedunin control)


title: Androgen-starved LNCaP cells, treated with ethanol and DMSO for 24h, biol repl 3 (gedunin control)


title: LNCaP cells treated with 1nM R1881 and 20uM gedunin for 24h, biol repl 3

description: Gene expression data from androgen-starved LNCaP cells treated with 1with 1nM R1881 and 20uM gedunin for 24h

treatment_protocol: LNCaP cells were grown in RPMI and charcol-stripped 10%FBS for 2d and then treated with 20uM gedunin plus 1nM R1881 (synthetic, non-metabolizable androgen) for 24h


title: T_F_514_260

source_name: Fresh frozen Tumor DNA from patient 514


title: LNCaP cells treated with 1nM R1881 and 20uM gedunin for 24h, biol repl 2


title: N_B_108_260

source_name: Leukocyte DNA from patient 108


title: R99_eye_L19_S6

status: Public on Aug 31 2006

city: Iowa City

first: Bartley

middle: Joseph

last: Brown

state: IA

institute: The University of Iowa

description: Eye tissue from a twelve-week-old adult male F2 rat from two differemt inbred strains (SHR/SP and SR/jrHSD).

hyb_protocol: The resultant biotinylated cRNA was fragmented then hybridized to the GeneChip Rat Genome 230 2.0 Array (31,042 probe sets including over 28,000 rat genes; Affymetrix, Inc.).  The arrays were washed, stained, and scanned using the Affymetrix Model 450 Fluidics Station by the University of Iowa DNA Core Facility.

scan_protocol: The arrays were scanned with the Affymetrix Model 3000 using the manufacturer's recommended protocols by the University of Iowa DNA Core Facility.

data_processing: The hybridizations were normalized using the RMA (robust multi-chip averaging) method from Bioconductor to obtain summary expression values for each probe set.

organism: Rattus norvegicus

source_name: rat R99 12 week old eye tissue

label_protocol: Ten micrograms of total RNA was processed for use on the microarray by using the Affymetrix GeneChip one-cycle target labeling kit according to the manufacturer's recommended protocols.

extract_protocol: Total RNA was extracted from both eyes of each animal using the guanidinium isothiocynate method (TRIzol reagent), followed by purification using an RNeasy column. RNA quality was assessed using the Agilent Model 2100 Bioanalyzer.

tag: F2 rat, derived from two different inbred strains of rat


title: R9_eye_L2_S5_9.16.04

source_name: rat R9 12 week old eye tissue


title: LNCaP cells treated with 1nM R1881 and 20uM gedunin for 24h, biol repl 1


title: R96_eye_L18_S10

source_name: rat R96 12 week old eye tissue


title: R95_eye_L18_S10

source_name: rat R95 12 week old eye tissue


title: R98_eye_L18_S10

source_name: rat R98 12 week old eye tissue


title: R97_eye_L18_S10

source_name: rat R97 12 week old eye tissue


title: R93_eye_L18_S9

source_name: rat R93 12 week old eye tissue


title: R94_eye_L18_S9

source_name: rat R94 12 week old eye tissue


title: R90_eye_L18_S7.Re.scan

source_name: rat R90 12 week old eye tissue


title: R92_eye_L18_S8

source_name: rat R92 12 week old eye tissue


title: R91_eye_L18_S8

source_name: rat R91 12 week old eye tissue


title: R8_eye_L2_S4_9.02.04

source_name: rat R8 12 week old eye tissue


title: R88_eye_L18_S5_9.16.04

source_name: rat R88 12 week old eye tissue


title: R86_eye_L17_S8

source_name: rat R86 12 week old eye tissue


title: R87_eye_L17_S9

source_name: rat R87 12 week old eye tissue


title: R83_eye_L17_S6

source_name: rat R83 12 week old eye tissue


title: R80_eye_L16_S9

source_name: rat R80 12 week old eye tissue


title: R84_eye_L17_S7

source_name: rat R84 12 week old eye tissue


title: R7_eye_L2_S3_8.18.04

source_name: rat R7 12 week old eye tissue


title: R79_eye_L16_S8

source_name: rat R79 12 week old eye tissue


title: R89_eye_L18_S6

source_name: rat R89 12 week old eye tissue


title: R82_eye_L17_S5_9.16.04

source_name: rat R82 12 week old eye tissue


title: R76_eye_L16_S6

source_name: rat R76 12 week old eye tissue


title: R81_eye_L16_S9

source_name: rat R81 12 week old eye tissue


title: R85_eye_L17_S8

source_name: rat R85 12 week old eye tissue


title: R78_eye_L16_S8

source_name: rat R78 12 week old eye tissue


title: R70_eye_L14_S8

source_name: rat R70 12 week old eye tissue


title: R65_eye_L13_S6

source_name: rat R65 12 week old eye tissue


title: R69_eye_L14_S7

source_name: rat R69 12 week old eye tissue


title: R66_eye_L14_S4_9.02.04

source_name: rat R66 12 week old eye tissue


title: R75_eye_L16_S5_9.16.04

source_name: rat R75 12 week old eye tissue


title: R68_eye_L14_S6

source_name: rat R68 12 week old eye tissue


title: R71_eye_L15_S4_9.02.04

source_name: rat R71 12 week old eye tissue


title: R6_eye_L2_S2_8.13.04

source_name: rat R6 12 week old eye tissue


title: R72_eye_L15_S5_9.16.04

source_name: rat R72 12 week old eye tissue


title: R61_eye_L12_S3_8.18.04

source_name: rat R61 12 week old eye tissue


title: R63_eye_L13_S3_Re.Scan_8.18.04

source_name: rat R63 12 week old eye tissue


title: R62_eye_L12_S4_9.02.04

source_name: rat R62 12 week old eye tissue


title: R73_eye_L15_S6

source_name: rat R73 12 week old eye tissue


title: R64_eye_L13_S4_9.02.04

source_name: rat R64 12 week old eye tissue


title: R5_eye_L2_S1_8.12.04

source_name: rat R5 12 week old eye tissue


title: R60_eye_L12_S2_8.13.04

source_name: rat R60 12 week old eye tissue


title: R58_eye_L11_S5_9.16.04

source_name: rat R58 12 week old eye tissue


title: R74_eye_L15_S7

source_name: rat R74 12 week old eye tissue


title: R57_eye_L11_S4_9.02.04

source_name: rat R57 12 week old eye tissue


title: R56_eye_L11_S3_8.18.04

source_name: rat R56 12 week old eye tissue


title: R55_eye_L11_S2_8.13.04

source_name: rat R55 12 week old eye tissue


title: R53_eye_L10_S5_9.16.04

source_name: rat R53 12 week old eye tissue


title: R51_eye_L10_S3_8.18.04

source_name: rat R51 12 week old eye tissue


title: R52_eye_L10_S4_9.02.04

source_name: rat R52 12 week old eye tissue


title: R50_eye_L10_S2_8.13.04

source_name: rat R50 12 week old eye tissue


title: R49_eye_L10_S1_8.12.04

source_name: rat R49 12 week old eye tissue


title: R54_eye_L11_S1_8.12.04

source_name: rat R54 12 week old eye tissue


title: R47_eye_L9_S6

source_name: rat R47 12 week old eye tissue


title: R77_eye_L16_S7

source_name: rat R77 12 week old eye tissue


title: R43_eye_L9_S2_8.13.04

source_name: rat R43 12 week old eye tissue


title: R46_eye_L9_S5_9.16.04

source_name: rat R46 12 week old eye tissue


title: R45_eye_L9_S4_9.02.04

source_name: rat R45 12 week old eye tissue


title: R40_eye_L8_S6

source_name: rat R40 12 week old eye tissue


title: R35_eye_L8_S1_8.12.04

source_name: rat R35 12 week old eye tissue


title: R39_eye_L8_S5_9.16.04

source_name: rat R39 12 week old eye tissue


title: R42_eye_L9_S1_8.12.04

source_name: rat R42 12 week old eye tissue


title: R37_eye_L8_S3_8.18.04

source_name: rat R37 12 week old eye tissue


title: R44_eye_L9_S3_8.18.04

source_name: rat R44 12 week old eye tissue


title: R34_eye_L7_S4_9.02.04

source_name: rat R34 12 week old eye tissue


title: R3_eye_L1_S3_8.18.04

source_name: rat R3 12 week old eye tissue


title: R38_eye_L8_S4_9.02.04

source_name: rat R38 12 week old eye tissue


title: R33_eye_L7_S3_8.18.04

source_name: rat R33 12 week old eye tissue


title: R32_eye_L7_S2_8.13.04

source_name: rat R32 12 week old eye tissue


title: R2_eye_L1_S2_8.13.04

source_name: rat R2 12 week old eye tissue


title: R31_eye_L7_S1_8.12.04

source_name: rat R31 12 week old eye tissue


title: R36_eye_L8_S2_8.13.04

source_name: rat R36 12 week old eye tissue


title: R29_eye_L6_S5_9.16.04

source_name: rat R29 12 week old eye tissue


title: R27_eye_L6_S3_8.18.04

source_name: rat R27 12 week old eye tissue


title: R26_eye_L6_S2_8.13.04

source_name: rat R26 12 week old eye tissue


title: R25_eye_L6_S1_8.12.04

source_name: rat R25 12 week old eye tissue


title: R28_eye_L6_S4_9.02.04

source_name: rat R28 12 week old eye tissue


title: R21_eye_L5_S4_9.02.04

source_name: rat R21 12 week old eye tissue


title: R24_eye_L5_S7

source_name: rat R24 12 week old eye tissue


title: R23_eye_L5_S6

source_name: rat R23 12 week old eye tissue


title: R22_eye_L5_S5_9.16.04

source_name: rat R22 12 week old eye tissue


title: R20_eye_L5_S3_8.18.04

source_name: rat R20 12 week old eye tissue


title: R18_eye_L5_S1_8.12.04

source_name: rat R18 12 week old eye tissue


title: R1_eye_L1_S1_8.12.04

source_name: rat R1 12 week old eye tissue


title: R13_eye_L3_S1_8.12.04

source_name: rat R13 12 week old eye tissue


title: R19_eye_L5_S2_8.13.04

source_name: rat R19 12 week old eye tissue


title: R17_eye_L4_S3_8.18.04

source_name: rat R17 12 week old eye tissue


title: R12_eye_L2_S8

source_name: rat R12 12 week old eye tissue


title: R14_eye_L3_S2_8.13.04

source_name: rat R14 12 week old eye tissue


title: R125_eye_L22_S10

source_name: rat R125 12 week old eye tissue


title: R123_eye_L22_S10

source_name: rat R123 12 week old eye tissue


title: R16_eye_L4_S2_8.13.04

source_name: rat R16 12 week old eye tissue


title: R122_eye_L22_S10

source_name: rat R122 12 week old eye tissue


title: R15_eye_L4_S1_8.12.04

source_name: rat R15 12 week old eye tissue


title: R124_eye_L22_S10

source_name: rat R124 12 week old eye tissue


title: R11_eye_L2_S7

source_name: rat R11 12 week old eye tissue


title: R120_eye_L22_S10

source_name: rat R120 12 week old eye tissue


title: R119_eye_L21_S7

source_name: rat R119 12 week old eye tissue


title: R121_eye_L22_S10

source_name: rat R121 12 week old eye tissue


title: R117_eye_L21_S10

source_name: rat R117 12 week old eye tissue


title: R116_eye_L21_S10

source_name: rat R116 12 week old eye tissue


title: R118_eye_L21_S7.Re.scan

source_name: rat R118 12 week old eye tissue


title: R114_eye_L21_S9

source_name: rat R114 12 week old eye tissue


title: R115_eye_L21_S9

source_name: rat R115 12 week old eye tissue


title: R112_eye_L21_S7

source_name: rat R112 12 week old eye tissue


title: R110_eye_L20_S9

source_name: rat R110 12 week old eye tissue


title: R111_eye_L20_S10

source_name: rat R111 12 week old eye tissue


title: R10_eye_L2_S6

source_name: rat R10 12 week old eye tissue


title: R108_eye_L20_S8

source_name: rat R108 12 week old eye tissue


title: R109_eye_L20_S9

source_name: rat R109 12 week old eye tissue


title: R113_eye_L21_S9

source_name: rat R113 12 week old eye tissue


title: R107_eye_L20_S8

source_name: rat R107 12 week old eye tissue


title: R106_eye_L20_S7

source_name: rat R106 12 week old eye tissue


title: R105_eye_L20_S6

source_name: rat R105 12 week old eye tissue


title: R103_eye_L19_S9

source_name: rat R103 12 week old eye tissue


title: R100_eye_L19_S7

source_name: rat R100 12 week old eye tissue


title: R101_eye_L19_S8

source_name: rat R101 12 week old eye tissue


title: R102_eye_L19_S8

source_name: rat R102 12 week old eye tissue


title: R104_eye_L19_S9

source_name: rat R104 12 week old eye tissue


title: R67_eye_L14_S5_9.16.04

source_name: rat R67 12 week old eye tissue


title: Exp. #01, Neutral. S288C Genomic DNA, 03/20/00 vs S288C Genomic DNA 03/20/00 #2

status: Public on Aug 30 2006

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 203 Fordham Hall

department: Biology

institute: University of North Carolina at Chapel Hill

description: 03/20/00 Amplified Reference Versus 03/20/00 Amplified Reference #2

data_processing: Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Saccharomyces cerevisiae

source_name: Sonicated s288C Genomic DNA, Amplified 03-20-00


description: Full Name: Exp. #24, ORF+Int enr. Fixed Nuclear Extract (1% 30 min) *IP #2* REVERSED BEFORE P/C vs Fixed Nuclear Extract (1% 30 min) Input was DNA from nuclei that had been salt extracted. Crosslinks in the INPUT DNA were NOT REVERSED prior to Phenol Chloroform prep The crosslinks in the IP-DNA were reversed prior to Phenol Chloroform prep. *THESE RESULTS DO NOT REFLECT THE SPECIFICITY OF THE ANTI-H3 ANTIBODY.*

source_name: DNA prepared from IP Input, Amplified NOTE: NOT REVERSED prior to P/C Prep.

value: NOT REVERSED prior to P/C Prep.

source_name: "IP" DNA, Amplified THESE RESULTS DO NOT REFLECT THE SPECIFICITY OF THE ANTIBODY.


title: Exp. #15, Intergenic enrichment. Fixed Whole Extract (1% 60 min, break, 30 mins @ 37, then P/C) ...

description: Full Name: Exp. #15, Intergenic enrichment. Fixed Whole Extract (1% 60 min, break, 30 mins @ 37, then P/C) vs Whole, Unfixed. Nagy 4-25-02 Old Name: Extract: Whole Fixed Yeast (1% 60 min, break, 30 mins @ 37, then P/C) vs Whole, Unfixed. Nagy 4-25

source_name: S288C yeast OD 1, No Fix, CSH prep (P/C), Amplified

source_name: Extract: Whl Fixed Yst (1% 60 min, break, 30 mins @ 37, then P/C) CSH Prp (P/C), Amped

tag: Extract


title: Exp. #04, Neutral. Whole Extract vs 50 ng S288C Genomic DNA JDL 2-28-02

description: The sample DNA was never crosslinked. The reference DNA was never crosslinked. After P/C prep, samples were treated with 100 ng/uL RNAse A for 1 hour at 37 degrees.

source_name: Original S288C DNA (Derisi), 50 ng, Amplified

source_name: Whole S288C yeast OD .75, No Fix, Beadbeat, P/C, Amplified


title: Bovine LD Muscle low rep3

city: St Lucia

first: Yonghong

last: Wang

state: Queensland

address: 306 Carmody Road

department: Livestock Industries

country: Australia

institute: CSIRO

description: Bovine Longissumus dorsi muscle tissue rockhampton low diet replicate 3

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were mean centered and linear transformed to obtain the log and linear values given in the data table.

organism: Bos taurus

source_name: LD muscle tissue low diet

tag: Bovine Longissumus dorsi muscle tissue low diet

source_name: LD muscle tissue high diet pool

tag: Bovine Longissumus dorsi muscle tissue high diet pool


title: Bovine LD Muscle low pool rep2

description: Bovine Longissumus dorsi muscle tissue rockhampton low diet pool replicate2

source_name: LD muscle tissue low diet pool

tag: Bovine Longissumus dorsi muscle tissue low diet pool


title: Exp. #16, Intergenic enrichment. Fixed Whole Extract  (1% 60 min, 30 mins @ 37 w/ProtK, P/C) vs ...

description: Full Experiment Name: Exp. #16, Intergenic enrichment. Fixed Whole Extract (1% 60 min, 30 mins @ 37 w/ProtK, P/C) vs Whole Extract. Nagy 4-25-02

tag: S288C yeast OD 1, No Fix, CSH prep (P/C), Amplified

source_name: Extract: Whl Fixed Yst (1% 60min, break, 30mins @37 ProtK, then CSH P/C), Amped Nagy 4-25


title: Exp. #10, Intergenic enrichment. Fixed Whole Extract (1% 15 min) vs Whole Extract  Nagy 4-25-02

description: Extract: Whole Fixed Yeast (1% 15 min)  CSH Prep (P/C), Amplified Nagy 4-25 vs. S288C yeast OD 1, No Fix, CSH prep (P/C), Amplified


title: Bovine LD Muscle low pool rep1

description: Bovine Longissumus dorsi muscle tissue rockhampton low diet pool replicate1


title: Bovine LD Muscle low rep4

description: Bovine Longissumus dorsi muscle tissue rockhampton low diet replicate 4


title: Bovine LD Muscle medium rep4

description: Bovine Longissumus dorsi muscle tissue rockhampton medium diet replicate 4

source_name: LD muscle tissue medium diet

tag: Bovine Longissumus dorsi muscle tissue medium diet


title: Bovine LD Muscle medium rep2

description: Bovine Longissumus dorsi muscle tissue rockhampton medium diet replicate 2


title: Exp. #14, Intergenic enrichment. Fixed Whole Extract (1% 60 min) vs Whole Extract  Nagy 4-25-02

description: Extract: Whole Fixed Yeast (1% 60 min, break then P/C) CSH Prep (P/C), Amplified Nagy 4-25 vs. S288C yeast OD 1, No Fix, CSH prep (P/C), Amplified


title: Bovine LD Muscle JB vs HOL T2 rep4

description: Bovine Longissumus dorsi muscle tissue Japanese Black vs Holstein T2 replicate 4

source_name: LD muscle tissue Japanese Black

source_name: LD muscle tissue Holstein

tag: Bovine Longissumus dorsi muscle tissue Holstein


title: Bovine LD Muscle medium rep3

description: Bovine Longissumus dorsi muscle tissue rockhampton medium diet replicate 3


title: Bovine LD Muscle low rep2

description: Bovine Longissumus dorsi muscle tissue rockhampton low diet replicate 2


title: Exp. #17, Intergenic enrichment. Fixed Whole Extract  (5% 15 min) vs Whole Extract. Nagy 4-25-02

description: Extract: Whole Fixed Yeast (5% 15 min)  CSH Prep (P/C), Amplified Nagy 4-25 vs. S288C yeast OD 1, No Fix, CSH prep (P/C), Amplified


title: Bovine LD Muscle JB vs HOL T3 rep1

description: Bovine Longissumus dorsi muscle tissue Japanese Black vs Holstein T3 replicate 1


title: Bovine LD Muscle medium rep1

description: Bovine Longissumus dorsi muscle tissue rockhampton medium diet replicate 1


title: Bovine LD Muscle JB vs HOL T2 rep1

description: Bovine Longissumus dorsi muscle tissue Japanese Black vs Holstein T2 replicate 1


title: Bovine LD Muscle low rep1

description: Bovine Longissumus dorsi muscle tissue rockhampton low diet replicate 1


title: Bovine LD Muscle JB vs HOL T3 rep4

description: Bovine Longissumus dorsi muscle tissue Japanese Black vs Holstein T3 replicate 4


title: Bovine LD Muscle JB vs HOL T1 rep2

description: Bovine Longissumus dorsi muscle tissue Japanese Black vs Holstein T1 replicate 2


title: Bovine LD Muscle JB vs HOL T1 rep4

description: Bovine Longissumus dorsi muscle tissue Japanese Black vs Holstein T1 replicate 4


title: Bovine LD Muscle JB vs HOL T3 rep2

description: Bovine Longissumus dorsi muscle tissue Japanese Black vs Holstein T3 replicate 2


title: Bovine LD Muscle HOL T3 vs T2

description: Bovine Longissumus dorsi muscle tissue Holstein T3 vs T2

source_name: LD muscle tissue Holstein T3

source_name: LD muscle tissue Holstein T2

tag: Bovine Longissumus dorsi muscle tissue Holstein T2


title: Bovine LD Muscle HOL T1 vs T3

description: Bovine Longissumus dorsi muscle tissue Holstein T1 vs T3

source_name: LD muscle tissue Holstein T1

tag: Bovine Longissumus dorsi muscle tissue Holstein T3


title: Bovine LD Muscle JB vs HOL T1 rep1

description: Bovine Longissumus dorsi muscle tissue Japanese Black vs Holstein T1 replicate 1


title: Bovine LD Muscle JB vs HOL T1 rep3

description: Bovine Longissumus dorsi muscle tissue Japanese Black vs Holstein T1 replicate 3


title: Bovine LD Muscle JB T3 vs T2

description: Bovine Longissumus dorsi muscle tissue Japanese Black T3 vs T2

source_name: LD muscle tissue Japanese Black T3

source_name: LD muscle tissue Japanese Black T2

tag: Bovine Longissumus dorsi muscle tissue Japanese Black T2


title: Diffuse large B-cell lymphoma  VUMC_L94_b32_s73

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

institute: Vrije Universiteit Medical Center

description: protocols available via the VUMC MACF website

hyb_protocol: Hybridization protocol available via the VUMC MACF website Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

scan_protocol: Microarray Scanner G2505B (Agilent Technologies), default settings

data_processing: Using ImaGene as described in Carvalho et al (2004) J.Clin.Path., vol. 57, 644-646. Normalization was done to the mode value of the log2ratio's.

source_name: Lymph node

label_protocol:
DNA labeling protocol available via the VUMC MACF website
Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

extract_protocol:
DNA isolation protocol available via the VUMC MACF website
Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

tag: Diffuse large B-cell lymphoma

value: male

source_name: Female reference DNA

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol

tag: Pooled DNA from the blood of 10 normal individuals

value: female


title: Hyperplastic  VUMC_L92_b32_s68

source_name: Tonsil

tag: Hyperplastic

tag: Gender


title: Diffuse large B-cell lymphoma  VUMC_L95_b32_s74

source_name: Male reference DNA


title: Bovine LD Muscle JB T2 vs T1

description: Bovine Longissumus dorsi muscle tissue Japanese Black T2 vs T1

source_name: LD muscle tissue Japanese Black T1

tag: Bovine Longissumus dorsi muscle tissue Japanese Black T1


title: Bovine LD Muscle JB T1 vs T3

description: Bovine Longissumus dorsi muscle tissue Japanese Black T1 vs T3

tag: Bovine Longissumus dorsi muscle tissue Japanese Black T3


title: Bovine LD Muscle JB vs HOL T3 rep3

description: Bovine Longissumus dorsi muscle tissue Japanese Black vs Holstein T3 replicate 3


title: Diffuse large B-cell lymphoma  VUMC_L90_b32_s66

source_name: tonsil


title: Bovine LD Muscle PH low vs WH low rep2

description: Bovine Longissumus dorsi muscle tissue piedmontese x hereford low diet vs wagyu x hereford low diet replicate 2

source_name: LD muscle tissue piedmontese x hereford low diet

source_name: LD muscle tissue wagyu x hereford low diet

tag: Bovine Longissumus dorsi muscle tissue wagyu x hereford low diet


title: Bovine LD Muscle PH hig vs low rep1

description: Bovine Longissumus dorsi muscle tissue piedmontese x hereford high vs low diet replicate 1

source_name: LD muscle tissue piedmontese x hereford high diet

tag: Bovine Longissumus dorsi muscle tissue piedmontese x hereford high diet

tag: Bovine Longissumus dorsi muscle tissue piedmontese x hereford low diet


title: Diffuse large B-cell lymphoma  VUMC_L89_b32_s65

source_name: lymphnode


title: Bovine LD Muscle WH high vs low rep2

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford high vs low diet replicate 2

source_name: LD muscle tissue wagyu x hereford high diet

tag: Bovine Longissumus dorsi muscle tissue wagyu x hereford high diet


title: Diffuse large B-cell lymphoma  VUMC_L81_b32_s57

source_name: lymph node


title: Bovine LD Muscle PH low vs WH low rep1

description: Bovine Longissumus dorsi muscle tissue piedmontese x hereford low diet vs wagyu x hereford low diet replicate 1


title: Bovine LD Muscle JB vs HOL T2 rep2

description: Bovine Longissumus dorsi muscle tissue Japanese Black vs Holstein T2 replicate 2

source_name: LD muscle tissue Japanese Black

source_name: LD muscle tissue Holstein


title: Bovine LD Muscle PH hig vs low rep2

description: Bovine Longissumus dorsi muscle tissue piedmontese x hereford high vs low diet replicate 2


title: Diffuse large B-cell lymphoma  VUMC_L75_b32_s71


title: Bovine LD Muscle WH high vs PH high rep1

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford high diet vs piedmontese x hereford high diet replicate 1

source_name: LD muscle tissue wagyu x hereford high  diet

tag: Bovine Longissumus dorsi muscle tissue wagyu x hereford high diet diet


title: Bovine bone marrow stromal cells 0h T vs 3d C

description: Bovine bone marrow stromal cells 0h control vs 3d control

source_name: bone marrow stromal cells 0h control

tag: Bovine bone marrow stromal cells 0H control

source_name: bone marrow stromal cells 3d control

tag: Bovine bone marrow stromal cells 3d control


title: Diffuse large B-cell lymphoma  VUMC_L72_b32_s50


title: Diffuse large B-cell lymphoma  VUMC_L55_b32_s42


title: Diffuse large B-cell lymphoma  VUMC_L53_b32_s40


title: Bovine subcutaneous adipose tissue Angus steers treatment pool 3 vs control pool 3 at day 0

description: Bovine subcutaneous adipose tissue from Angus steers treatment pool 3 vs control pool 3 at day 0

tag: Bovine subcutaneous adipose tissue control pool 3 day0

tag: Bovine subcutaneous adipose tissue treated pool 3 day0


title: Diffuse large B-cell lymphoma  VUMC_L45_b32_s32


title: Bovine LD Muscle HOL T2 vs T1

description: Bovine Longissumus dorsi muscle tissue Holstein T2 vs T1

source_name: LD muscle tissue Holstein T2

source_name: LD muscle tissue Holstein T1

tag: Bovine Longissumus dorsi muscle tissue Holstein T1


title: Hyperplastic  VUMC_L91_b32_s67

source_name: Tonsil

source_name: Female reference DNA


title: Bovine LD Muscle JB vs HOL T2 rep3

description: Bovine Longissumus dorsi muscle tissue Japanese Black vs Holstein T2 replicate 3

tag: Bovine Longissumus dorsi muscle tissue Holstein


title: Diffuse large B-cell lymphoma  VUMC_L76_b32_s54

tag: Diffuse large B-cell lymphoma

source_name: Male reference DNA


title: Bovine subcutaneous adipose tissue steers JJJL pA vs LLLJ pA rep2

description: Bovine subcutaneous adipose tissue steers Jersey (JJJL) pool A vs Limousine (LLLJ) pool A replicate 2

source_name: subcutaneous adipose tissue JJJL pool A

tag: Bovine subcutaneous adipose tissue JJJL pool A

source_name: subcutaneous adipose tissue LLLJ pool A

tag: Bovine subcutaneous adipose tissue LLLJ pool A


title: Bovine LD Muscle WH high vs low rep1

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford high vs low diet replicate 1

source_name: LD muscle tissue wagyu x hereford low diet


title: Diffuse large B-cell lymphoma  VUMC_L14_b32_s86

description: protocols available via the VUMC MACF website

tag: Gender

tag: Pooled DNA from the blood of 10 normal individuals


title: Carcinoma  VUMC_C017_b21_s72

source_name: colon

tag: carcinoma

source_name: reference DNA


title: Bovine subcutaneous adipose tissue heifers JJJL pC vs LLLJ pC rep1

description: Bovine subcutaneous adipose tissue heifers Jersey (JJJL) pool C vs Limousine (LLLJ) pool C replicate 1

source_name: subcutaneous adipose tissue LLLJ pool C

tag: Bovine subcutaneous adipose tissue LLLJ pool C

source_name: subcutaneous adipose tissue JJJL pool C

tag: Bovine subcutaneous adipose tissue JJJL pool C


title: Carcinoma  VUMC_C016_b21_s69


title: Diffuse large B-cell lymphoma  VUMC_L87_b32_s63

source_name: lymph node


title: Bovine subcutaneous adipose tissue Angus steers treatment pool 2 vs control pool 2 at day 0

description: Bovine subcutaneous adipose tissue from Angus steers treatment pool 2 vs control pool 2 at day 0

tag: Bovine subcutaneous adipose tissue treatment pool 2 day0

tag: Bovine subcutaneous adipose tissue control pool 2 day0


title: Bovine subcutaneous adipose tissue steers JJJL pD vs LLLJ Pd

description: Bovine subcutaneous adipose tissue steers Jersey (JJJL) pool D vs Limousine (LLLJ) pool D

source_name: subcutaneous adipose tissue LLLJ pool D

tag: Bovine subcutaneous adipose tissue LLLJ pool D

source_name: subcutaneous adipose tissue JJJL pool D

tag: Bovine subcutaneous adipose tissue JJJL pool D


title: Bovine subcutaneous adipose tissue heifers JJJL pB vs LLLJ pB rep2

description: Bovine subcutaneous adipose tissue heifers Jersey (JJJL) pool B vs Limousine (LLLJ) pool B replicate 2

source_name: subcutaneous adipose tissue JJJL pool B

tag: Bovine subcutaneous adipose tissue JJJL pool B

source_name: subcutaneous adipose tissue LLLJ pool B

tag: Bovine subcutaneous adipose tissue LLLJ pool B


title: Bovine subcutaneous adipose tissue heifers JJJL pC vs LLLJ pC rep2

description: Bovine subcutaneous adipose tissue heifers Jersey (JJJL) pool C vs Limousine (LLLJ) pool C replicate 2


title: Bovine subcutaneous adipose tissue heifers JJJL pB vs LLLJ pB rep1

description: Bovine subcutaneous adipose tissue heifers Jersey (JJJL) pool B vs Limousine (LLLJ) pool B replicate 1


title: Carcinoma  VUMC_C014_b21_s71


title: Carcinoma  VUMC_C015_b21_s70


title: Carcinoma  VUMC_C013_b21_s74


title: Carcinoma  VUMC_C012_b21_s73


title: Diffuse large B-cell lymphoma  VUMC_L12_b32_s85


title: Bovine subcutaneous adipose tissue Angus steers treatment pool 4 vs control pool 4 at day 300

description: Bovine subcutaneous adipose tissue from Angus steers treatment pool 4 vs control pool 4 at day 300

tag: Bovine subcutaneous adipose tissue treatment pool 4 day300

tag: Bovine subcutaneous adipose tissue control pool 4 day300


title: Thermal Injury Day 7 Sample 3

city: Piscataway

first: Tim

middle: J

last: Maguire

state: NJ

address: 98 Brett Road, Engineering C252

department: BME

institute: Rutgers University

description: Both channels were processed simultaneously with the Affymetrix Rat RAE230A array (GPL341).

data_processing: The value column is a log base two of the ratio of burn to sham intensity values.

source_name: Sham Control Sample

tag: Liver tissue sample

source_name: Thermal Injury Sample


title: Bovine subcutaneous adipose tissue steers JJJL pA vs LLLJ pA rep1

description: Bovine subcutaneous adipose tissue steers Jersey (JJJL) pool A vs Limousine (LLLJ) pool A replicate 1


title: Bovine subcutaneous adipose tissue Angus steers treatment pool 3 vs control pool 3 at day 300

description: Bovine subcutaneous adipose tissue from Angus steers treatment pool 3 vs control pool 3 at day 300

tag: Bovine subcutaneous adipose tissue treatment pool 3 day300

tag: Bovine subcutaneous adipose tissue control pool 3 day300


title: Bovine subcutaneous adipose tissue heifers JJJL pA vs LLLJ Pa

description: Bovine subcutaneous adipose tissue heifers Jersey (JJJL) pool A vs Limousine (LLLJ) pool A

tag: Bovine subcutaneous adipose tissue JJJL pool A

tag: Bovine subcutaneous adipose tissue LLLJ pool A


title: Bovine subcutaneous adipose tissue heifers JJJL pD vs LLLJ pD

description: Bovine subcutaneous adipose tissue heifers Jersey (JJJL) pool D vs Limousine (LLLJ) pool D


title: Bovine LD Muscle Belmont Red T3 L pool 2 vs G pool 1

description: Bovine Longissumus dorsi muscle tissue Belmont Red T3 low diet pool 2 vs growth diet pool 1

source_name: LD muscle tissue Belmont Red T3 low diet pool 2

source_name: LD muscle tissue Belmont Red T3 growth diet pool 1

tag: Bovine Longissumus dorsi muscle tissue Belmont Red T3 growth diet pool 1


title: Bovine LD Muscle Belmont Red T2 L pool 2 vs T3 L pool 2

description: Bovine Longissumus dorsi muscle tissue Belmont Red T2 low diet pool 2 vs T3 low diet pool 2

tag: Bovine Longissumus dorsi muscle tissue Belmont Red T3 low diet pool 2

source_name: LD muscle tissue Belmont Red T2 low diet pool 2


title: Bovine subcutaneous adipose tissue Angus steers treatment pool 2 vs control pool 2 at day 300

description: Bovine subcutaneous adipose tissue from Angus steers treatment pool 2 vs control pool 2 at day 300

tag: Bovine subcutaneous adipose tissue control pool 2 day300

tag: Bovine subcutaneous adipose tissue treated pool 2 day300


title: Thermal Injury Day 7 Sample 2


title: Bovine subcutaneous adipose tissue steers JJJL pC vs LLLJ pC

description: Bovine subcutaneous adipose tissue steers Jersey (JJJL) pool C vs Limousine (LLLJ) pool C

tag: Bovine subcutaneous adipose tissue LLLJ pool C

tag: Bovine subcutaneous adipose tissue JJJL pool C


title: Bovine subcutaneous adipose tissue Angus steers treatment pool 1 vs control pool 1 at day 300

description: Bovine subcutaneous adipose tissue from Angus steers treatment pool 1 vs control pool 1 at day 300

tag: Bovine subcutaneous adipose tissue control pool 1 day300

tag: Bovine subcutaneous adipose tissue treated pool 1 day300


title: Bovine LD Muscle Belmont Red T1 L pool 1 vs T3 L pool 1

description: Bovine Longissumus dorsi muscle tissue Belmont Red T1 low diet pool 1 vs T3 low diet pool 1

source_name: LD muscle tissue Belmont Red T3 low diet pool 1

tag: Bovine Longissumus dorsi muscle tissue Belmont Red T3 low diet pool 1

source_name: LD muscle tissue Belmont Red T1 low diet pool 1


title: Thermal Injury Day 7 Sample 1


title: Thermal Injury Day 4 Sample 3


title: Bovine LD Muscle Belmont Red T3 L pool 1 vs G pool 2

description: Bovine Longissumus dorsi muscle tissue Belmont Red T3 low diet pool 1 vs growth diet pool 2

source_name: LD muscle tissue Belmont Red T3 growth diet pool 2

tag: Bovine Longissumus dorsi muscle tissue Belmont Red T3 growth diet pool 2


title: Bovine subcutaneous adipose tissue Angus steers treatment pool 4 vs control pool 4 at day 150

description: Bovine subcutaneous adipose tissue from Angus steers treatment pool 4 vs control pool 4 at day 150

tag: Bovine subcutaneous adipose tissue treatment pool 4 day150

tag: Bovine subcutaneous adipose tissue control pool 4 day150


title: Carcinoma  VUMC_C010_b21_s76

description: protocols available via the VUMC MACF website

source_name: colon

tag: carcinoma

tag: Pooled DNA from the blood of 10 normal individuals


title: Bovine LD Muscle Belmont Red T3 G pool 2 vs T2 G pool 2

description: Bovine Longissumus dorsi muscle tissue Belmont Red T3 growth diet pool 2 vs T2 growth diet pool 2

source_name: LD muscle tissue Belmont Red T2 growth diet pool 2

tag: Bovine Longissumus dorsi muscle tissue Belmont Red T2 growth diet pool 2


title: Bovine LD Muscle Belmont Red T1 G pool 1 vs T2 G pool 1

description: Bovine Longissumus dorsi muscle tissue Belmont Red T1 growth diet pool 1 vs T2 growth diet pool 1

source_name: LD muscle tissue Belmont Red T1 growth diet pool 1

source_name: LD muscle tissue Belmont Red T2 growth diet pool 1

tag: Bovine Longissumus dorsi muscle tissue Belmont Red T2 growth diet pool 1


title: Bovine LD Muscle Belmont Red T3 G pool 1 vs T1 G pool 1

description: Bovine Longissumus dorsi muscle tissue Belmont Red T3 growth diet pool 1 vs T1 growth diet pool 1

tag: Bovine Longissumus dorsi muscle tissue Belmont Red T1 growth diet pool 1


title: Bovine LD Muscle Belmont Red T3 G pool 2 vs L pool 2

description: Bovine Longissumus dorsi muscle tissue Belmont Red T3 growth diet pool 1 vs low diet pool 2


title: Thermal Injury Day 4 Sample 2

description: Both channels were processed simultaneously with the Affymetrix Rat RAE230A array (GPL341).

tag: Liver tissue sample


title: Bovine LD Muscle Belmont Red T1 L pool 2 vs T2 L pool 2

description: Bovine Longissumus dorsi muscle tissue Belmont Red T1 low diet pool 2 vs T2 low diet pool 2

tag: Bovine Longissumus dorsi muscle tissue Belmont Red T2 low diet pool 2

source_name: LD muscle tissue Belmont Red T1 low diet pool 2


title: Bovine LD Muscle Belmont Red T1 G pool 2 vs T2 G pool 2

description: Bovine Longissumus dorsi muscle tissue Belmont Red T1 growth diet pool 2 vs T2 growth diet pool 2

source_name: LD muscle tissue Belmont Red T1 growth diet pool 2


title: Bovine subcutaneous adipose tissue Angus steers treatment pool 1 vs control pool 1 at day 150

description: Bovine subcutaneous adipose tissue from Angus steers treatment pool 1 vs control pool 1 at day 150

tag: Bovine subcutaneous adipose tissue control pool 1 day150

tag: Bovine subcutaneous adipose tissue treated pool 1 day150


title: Thermal Injury Day 4 Sample 1


title: Bovine subcutaneous adipose tissue Angus steers treatment pool 3 vs control pool 3 at day 150

description: Bovine subcutaneous adipose tissue from Angus steers treatment pool 3 vs control pool 3 at day 150

tag: Bovine subcutaneous adipose tissue treatment pool 3 day150

tag: Bovine subcutaneous adipose tissue control pool 3 day150


title: Bovine LD Muscle Belmont Red T3 G pool 1 vs L pool 1

description: Bovine Longissumus dorsi muscle tissue Belmont Red T3 growth diet pool 1 vs low diet pool 1


title: Bovine subcutaneous adipose tissue Angus steers treatment pool 2 vs control pool 2 at day 150

description: Bovine subcutaneous adipose tissue from Angus steers treatment pool 2 vs control pool 2 at day 150

tag: Bovine subcutaneous adipose tissue control pool 2 day150

tag: Bovine subcutaneous adipose tissue treated pool 2 day150


title: Bovine LD Muscle Belmont Red T2 L pool 2 vs G pool 1

description: Bovine Longissumus dorsi muscle tissue Belmont Red T2 low diet pool 2 vs growth diet pool 1


title: Bovine LD Muscle Belmont Red T1 L pool 1 vs G pool 2

description: Bovine Longissumus dorsi muscle tissue Belmont Red T1 low diet pool 1 vs growh diet pool 2

source_name: LD muscle tissue Belmont Red T1 growh diet pool 2

tag: Bovine Longissumus dorsi muscle tissue Belmont Red T1 growh diet pool 2


title: Bovine LD Muscle Belmont Red T1 G pool 2 vs L pool 2

description: Bovine Longissumus dorsi muscle tissue Belmont Red T1 growth diet pool 2 vs low diet pool 2

tag: Bovine Longissumus dorsi muscle tissue Belmont Red T1 low diet pool 2


title: Thermal Injury Day 2 Sample 2


title: Thermal Injury Day 2 Sample 1


title: Bovine subcutaneous adipose tissue Angus steers treatment pool 1 vs control pool 1 at day 0

description: Bovine subcutaneous adipose tissue from Angus steers treatment pool 1 vs control pool 1 at day 0

tag: Bovine subcutaneous adipose tissue treatment pool 1 day0

tag: Bovine subcutaneous adipose tissue control pool 1 day0


title: Bovine LD Muscle Belmont Red T2 G pool 2 vs L pool 2

description: Bovine Longissumus dorsi muscle tissue Belmont Red T2 growth diet pool 2 vs low diet pool 2


title: Bovine bone marrow stromal cells 0H T vs C rep1

description: Bovine bone marrow stromal cells 0H treated vs control replicate 1

source_name: bone marrow stromal cells 0H treated

source_name: bone marrow stromal cells 0H control

tag: Bovine bone marrow stromal cells 0H control


title: Bovine LD Muscle Belmont Red T2 L pool 1 vs G pool 2

description: Bovine Longissumus dorsi muscle tissue Belmont Red T2 low diet pool 1 vs growth diet pool 2

source_name: LD muscle tissue Belmont Red T2 low diet pool 1


title: Bovine subcutaneous adipose tissue Angus steers treatment pool 4 vs control pool 4 at day 0

description: Bovine subcutaneous adipose tissue from Angus steers treatment pool 4 vs control pool 4 at day 0

tag: Bovine subcutaneous adipose tissue control pool 4 day0

tag: Bovine subcutaneous adipose tissue treated pool 4 day0


title: Bovine LD Muscle Belmont Red T2 L pool 1 vs T3 L pool 1

description: Bovine Longissumus dorsi muscle tissue Belmont Red T2 low diet pool 1 vs T3 low diet pool 1

tag: Bovine Longissumus dorsi muscle tissue Belmont Red T3 low diet pool 1


title: Bovine bone marrow stromal cells 0H T self hyb

description: Bovine bone marrow stromal cells 0H treated self hybridization


title: Thermal Injury Day 1 Sample 2

description: Both channels were processed simultaneously with the Affymetrix Rat RAE230A array (GPL341).

source_name: Sham Control Sample

source_name: Thermal Injury Sample


title: Bovine LD Muscle Belmont Red T3 G pool 1 vs T2 G pool 1

description: Bovine Longissumus dorsi muscle tissue Belmont Red T3 growth diet pool 1 vs T2 growth diet pool 1

tag: Bovine Longissumus dorsi muscle tissue Belmont Red T2 growth diet pool 1

source_name: LD muscle tissue Belmont Red T3 growth diet pool 1


title: Thermal Injury Day 2 Sample 3

tag: Liver tissue sample


title: Bovine LD Muscle Belmont Red T1 L pool 1 vs T2 L pool 1

description: Bovine Longissumus dorsi muscle tissue Belmont Red T1 low diet pool 1 vs T2 low diet pool 1

tag: Bovine Longissumus dorsi muscle tissue Belmont Red T2 low diet pool 1


title: Bovine LD Muscle Belmont Red T1 L pool 2 vs G pool 1

description: Bovine Longissumus dorsi muscle tissue Belmont Red T1 low diet pool 2 vs growh diet pool 1

source_name: LD muscle tissue Belmont Red T1 growh diet pool 1

tag: Bovine Longissumus dorsi muscle tissue Belmont Red T1 growh diet pool 1


title: Bovine bone marrow stromal cells 14d T vs C rep1

description: Bovine bone marrow stromal cells 14d treated vs control replicate 1

source_name: bone marrow stromal cells 14d treated

tag: Bovine bone marrow stromal cells 14dH treated

source_name: bone marrow stromal cells 14d control

tag: Bovine bone marrow stromal cells 14d control


title: Bovine bone marrow stromal cells 24H T vs C rep2

description: Bovine bone marrow stromal cells 24H treated vs control replicate 2

source_name: bone marrow stromal cells 24H control

tag: Bovine bone marrow stromal cells 24H control

source_name: bone marrow stromal cells 24H treated


title: Bovine LD Muscle Belmont Red T1 L pool 2 vs T3 L pool 2

description: Bovine Longissumus dorsi muscle tissue Belmont Red T1 low diet pool 2 vs T3 low diet pool 2

source_name: LD muscle tissue Belmont Red T3 low diet pool 2

tag: Bovine Longissumus dorsi muscle tissue Belmont Red T3 low diet pool 2


title: Thermal Injury Day 1 Sample 3


title: Diffuse large B-cell lymphoma  VUMC_L47_b32_s33

description: protocols available via the VUMC MACF website

source_name: lymph node

tag: Diffuse large B-cell lymphoma

tag: Gender

source_name: Male reference DNA

tag: Pooled DNA from the blood of 10 normal individuals


title: Thermal Injury Day 1 Sample 1


title: Bovine LD Muscle Belmont Red T3 G pool 2 vs T1 G pool 2

description: Bovine Longissumus dorsi muscle tissue Belmont Red T3 growth diet pool 2 vs T1 growth diet pool 2

tag: Bovine Longissumus dorsi muscle tissue Belmont Red T1 growth diet pool 2

source_name: LD muscle tissue Belmont Red T3 growth diet pool 2


title: Bovine LD Muscle Belmont Red T1 G pool 1 vs L pool 1

description: Bovine Longissumus dorsi muscle tissue Belmont Red T1 growth diet pool 1 vs low diet pool 1

source_name: LD muscle tissue Belmont Red T1 growth diet pool1

tag: Bovine Longissumus dorsi muscle tissue Belmont Red T1 growth diet pool1

source_name: LD muscle tissue Belmont Red T1 low diet pool1

tag: Bovine Longissumus dorsi muscle tissue Belmont Red T1 low diet pool1


title: Bovine LD Muscle PH T1 vs T2 rep2

description: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford T1 vs T2 replicate 2

source_name: LD muscle tissue Piedmontese x hereford T1

source_name: LD muscle tissue Piedmontese x hereford T2

tag: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford T2


title: Bovine bone marrow stromal cells 6d T vs C rep1

description: Bovine bone marrow stromal cells 6d treated vs control replicate 1

source_name: bone marrow stromal cells 6d treated

tag: Bovine bone marrow stromal cells 6dH treated

source_name: bone marrow stromal cells 6d control

tag: Bovine bone marrow stromal cells 6d control


title: Bovine LD Muscle Belmont Red T2 G pool 1 vs L pool 1

description: Bovine Longissumus dorsi muscle tissue Belmont Red T2 growth diet pool 1 vs low diet pool 1

source_name: LD muscle tissue Belmont Red T2 growth diet pool 1

source_name: LD muscle tissue Belmont Red T2 low diet pool 1


title: Bovine LD Muscle PH T1 vs T2 rep1

description: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford T1 vs T2 replicate 1


title: Bovine bone marrow stromal cells 3d T vs C rep1

description: Bovine bone marrow stromal cells 3d treated vs control replicate 1

source_name: bone marrow stromal cells 3d treated

tag: Bovine bone marrow stromal cells 3dH treated

source_name: bone marrow stromal cells 3d control

tag: Bovine bone marrow stromal cells 3d control


title: Carcinoma  VUMC_C011_b21_s75

source_name: colon

tag: carcinoma

source_name: reference DNA


title: Exp. #31, ORF enr. Fixed Nuclear Extract (1% 30 min, same as jdl_g_112J sample but REVERSED ...

description: Full Name: Exp. #31, ORF enr. Fixed Nuclear Extract (1% 30 min, same as jdl_g_112J sample but REVERSED BEFORE P/C, bs) vs S288C Genomic DNA Compare to unreversed samples in jdl_g_112J, jdl_g_050J and jdl_g_052J. The S288C reference DNA (Green Channel)was sonicated, but was never subjected to crosslinking or reversal conditions. S288C reference DNA was derived from the large Derisi Prep. Input was DNA from nuclei that had been salt extracted. Crosslinks in the INPUT DNA WERE REVERSED prior to Phenol Chloroform prep Old Name: REVERSED Input from HH3 Lys4meth WT IP #2+3 before debris clearing spin

source_name: Sonicated s288C Genomic DNA, Amplified Date of Experiment


title: Bovine LD Muscle WH T2 vs T3 rep2

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford T2 vs T3 replicate 2

source_name: LD muscle tissue wagyu x hereford T3

tag: Bovine Longissumus dorsi muscle tissue wagyu x hereford T3

source_name: LD muscle tissue wagyu x hereford T2


title: Bovine bone marrow stromal cells 24H T vs C rep1

description: Bovine bone marrow stromal cells 24H treated vs control replicate 1

source_name: bone marrow stromal cells 24H treated

source_name: bone marrow stromal cells 24H control


title: Bovine bone marrow stromal cells 3d T vs C rep2

description: Bovine bone marrow stromal cells 3d treated vs control replicate 2

tag: Bovine bone marrow stromal cells 3dH control


title: Bovine LD Muscle WH vs PH T3 rep4

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford vs piedmontese x hereford T3 replicate 4

source_name: LD muscle tissue piedmontese x hereford T3

tag: Bovine Longissumus dorsi muscle tissue piedmontese x hereford T3


title: Bovine subcutaneous adipose tissue steers JJJL pB vs LLLJ pB

description: Bovine subcutaneous adipose tissue steers Jersey (JJJL) pool B vs Limousine (LLLJ) pool B

source_name: subcutaneous adipose tissue JJJL pool B

tag: Bovine subcutaneous adipose tissue JJJL pool B

source_name: subcutaneous adipose tissue LLLJ pool B

tag: Bovine subcutaneous adipose tissue LLLJ pool B


title: Exp. #32, ORF enr. Fixed Nuclear Extract (1% 30 min, same as jdl_g_112J sample but REVERSED ...

description: Full Experiment Name: Exp. #32, ORF enr. Fixed Nuclear Extract (1% 30 min, same as jdl_g_112J sample but REVERSED BEFORE P/C, as) vs S288C Genomic DNA The S288C reference DNA (Green Channel)was sonicated, but was never subjected to crosslinking or reversal conditions. S288C reference DNA was derived from the large Derisi Prep. Input was DNA from nuclei that had been salt extracted. Crosslinks in the INPUT DNA WERE REVERSED prior to Phenol Chloroform prep Old Chan2 desc.: REVERSED Input from HH3 Lys4meth WT IP #2+3 after debris clearing spin

tag: Sonicated s288C Genomic DNA, Amplified Date of Experiment


description: Full Name: Exp. #30, ORF enr. Fixed Nuclear Extract (1% 30 min) *IP #4* REVERSED BEFORE P/C vs S288C Genomic DNA The crosslinks in the IP-DNA were reversed prior to Phenol Chloroform prep. *THESE RESULTS DO NOT REFLECT THE SPECIFICITY OF THE ANTI-H3 ANTIBODY.* The S288C reference DNA (Green Channel)was sonicated, but was never subjected to crosslinking or reversal conditions. S288C reference DNA was derived from the large Derisi Prep. Old Name: Histone H3 lysine 4 methylated, WT IP #4, Old style Nuc. Prep

source_name: "IP" DNA, Amplified THESE RESULTS DO NOT REFLECT THE SPECIFICITY OF THE ANTIBODY.


description: Full Name: Exp. #29, ORF enr. Fixed Nuclear Extract (1% 30 min) *IP #2* REVERSED BEFORE P/C vs S288C Genomic DNA The crosslinks in the IP-DNA were reversed prior to Phenol Chloroform prep. The S288C reference DNA (Green Channel)was sonicated, but was never subjected to crosslinking or reversal conditions. DNA was derived from the large Derisi Prep. *THESE RESULTS DO NOT REFLECT THE SPECIFICITY OF THE ANTI-H3 ANTIBODY.*.

source_name: IP-enriched DNA, Amplified

tag: IP-enriched DNA, Amplified


title: Bovine LD Muscle WH T1 vs T2 rep2

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford T1 vs T2 replicate 2

tag: Bovine Longissumus dorsi muscle tissue wagyu x hereford T2

source_name: LD muscle tissue wagyu x hereford T1


title: Bovine LD Muscle WH vs PH T3 rep2

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford vs piedmontese x hereford T3 replicate 2


title: Bovine bone marrow stromal cells 6H T vs C rep1

description: Bovine bone marrow stromal cells 6H treated vs control replicate 1

source_name: bone marrow stromal cells 6H treated

source_name: bone marrow stromal cells 6H control

tag: Bovine bone marrow stromal cells 6H control


description: Full Name: Exp. #27, ORF+Int enr. Fixed Nuclear Extract (1% 30 min) *Mock IP, No Ab* REVERSED BEFORE P/C vs Fixed Nuclear Extract (1% 30 min) Old Name: Mock #1, No Histone H3 lysine 4 methylated Ab, wild-type vs unreversed input DNA No Antibody Mock for Anti-Histone H3 lysine 4 methylated, wild-type #1 Input was DNA from nuclei that had been salt extracted. Crosslinks in the INPUT DNA were NOT REVERSED prior to Phenol Chloroform prep The crosslinks in the IP-DNA were reversed prior to Phenol Chloroform prep.

source_name: DNA prepared from mock IP Input, Amplified NOTE: NOT REVERSED prior to P/C Prep

value: NOT REVERSED prior to P/C Prep

source_name: Mock IP-enriched DNA, Amplified (Results not dependent on IP procedure)


title: Bovine LD Muscle PH T2 vs T3 rep2

description: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford T2 vs T3 replicate 2

source_name: LD muscle tissue Piedmontese x hereford T2

source_name: LD muscle tissue Piedmontese x hereford T3

tag: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford T3


title: Bovine LD Muscle WH T2 vs T3 rep1

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford T2 vs T3 replicate 1


title: Bovine LD Muscle PH T2 vs T3 rep1

description: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford T2 vs T3 replicate 1


title: Bovine bone marrow stromal cells 6H T vs C rep2

description: Bovine bone marrow stromal cells 6H treated vs control replicate 2


title: Bovine LD Muscle WH vs PH T2 rep4

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford vs piedmontese x hereford T2 replicate 4

source_name: LD muscle tissue piedmontese x hereford T2

tag: Bovine Longissumus dorsi muscle tissue piedmontese x hereford T2


title: Bovine LD Muscle WH vs PH T3 rep1

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford vs piedmontese x hereford T3 replicate 1

source_name: LD muscle tissue Wagyu x hereford T3

tag: Bovine Longissumus dorsi muscle tissue Wagyu x hereford T3


title: Bovine bone marrow stromal cells 0H T vs C rep2

description: Bovine bone marrow stromal cells 0H treated vs control replicate 2

source_name: bone marrow stromal cells 0H control

tag: Bovine bone marrow stromal cells 0H control

source_name: bone marrow stromal cells 0H treated


title: Bovine LD Muscle WH T1 vs T2 rep1

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford T1 vs T2 replicate 1

source_name: LD muscle tissue wagyu x hereford T2


title: Bovine LD Muscle WH vs PH T2 rep2

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford vs piedmontese x hereford T2 replicate 2


title: Bovine LD Muscle WH vs PH T3 rep3

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford vs piedmontese x hereford T3 replicate 3

source_name: LD muscle tissue piedmontese x hereford T3


title: Bovine bone marrow stromal cells 14d T vs 6H C

description: Bovine bone marrow stromal cells 14d treated vs 6H control

source_name: bone marrow stromal cells 14d treated

tag: Bovine bone marrow stromal cells 14dH treated


title: Bovine LD Muscle WH vs PH T2 rep3

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford vs piedmontese x hereford T2 replicate 3

source_name: LD muscle tissue Wagyu x hereford T2

tag: Bovine Longissumus dorsi muscle tissue Wagyu x hereford T2


title: Exp. #11, Intergenic enrichment. Fixed Whole Extract (1% 30 min) vs Whole Extract  JDL 2-28-02

description: Crosslinks in the sample DNA were NOT REVERSED prior to Phenol Chloroform prep The reference DNA was never crosslinked. After P/C prep, samples were treated with 100 ng/uL RNAse A for 1 hour at 37 degrees.

source_name: S288C yeast OD .75, No Fix, Beadbeat, P/C, Amplified

source_name: Whole S288C yeast OD .75, Fixed, Beadbeat, P/C, Amplified


title: Bovine bone marrow stromal cells 14d T vs C rep2

description: Bovine bone marrow stromal cells 14d treated vs control replicate 2

source_name: bone marrow stromal cells 14d control

tag: Bovine bone marrow stromal cells 14dH control


title: Bovine LD Muscle WH vs PH T2 rep1

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford vs piedmontese x hereford T2 replicate 1


title: Bovine LD Muscle WH vs PH T1 rep3

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford vs piedmontese x hereford T1 replicate 3

source_name: LD muscle tissue piedmontese x hereford T1

tag: Bovine Longissumus dorsi muscle tissue piedmontese x hereford T1

source_name: LD muscle tissue Wagyu x hereford T1

tag: Bovine Longissumus dorsi muscle tissue Wagyu x hereford T1


description: Full Name: Exp. #26, ORF+Int enr. Fixed Nuclear Extract (1% 30 min) *IP #3* REVERSED BEFORE P/C vs Fixed Nuclear Extract (1% 30 min) Input was DNA from nuclei that had been salt extracted. Crosslinks in the INPUT DNA were NOT REVERSED prior to Phenol Chloroform prep The crosslinks in the IP-DNA were reversed prior to Phenol Chloroform prep. *THESE RESULTS DO NOT REFLECT THE SPECIFICITY OF THE ANTI-H3 ANTIBODY.*

source_name: DNA prepared from IP Input, Amplified NOTE: NOT REVERSED prior to P/C Prep.

source_name: "IP" DNA, Amplified THESE RESULTS DO NOT REFLECT THE SPECIFICITY OF THE ANTIBODY.


title: Bovine bone marrow stromal cells 6d T vs C rep2

description: Bovine bone marrow stromal cells 6d treated vs control replicate 2

source_name: bone marrow stromal cells 6d control

tag: Bovine bone marrow stromal cells 6dH control

source_name: bone marrow stromal cells 6d treated


title: Bovine LD Muscle WH vs PH T1 rep2

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford vs piedmontese x hereford T1 replicate 2

source_name: LD muscle tissue wagyu x hereford T1

tag: Bovine Longissumus dorsi muscle tissue wagyu x hereford T1


description: Full Name: Exp. #28, ORF enr. Fixed Nuclear Extract (1% 30 min) *IP #1* REVERSED BEFORE P/C vs S288C Genomic DNA Input was DNA from nuclei that had been salt extracted. The crosslinks in the IP-DNA were reversed prior to Phenol Chloroform prep. After P/C prep, samples were treated with 100 ng/uL RNAse A for 1 hour. The S288C reference DNA (Green Channel)was sonicated, but was never subjected to crosslinking or reversal conditions. S288C reference DNA was derived from the large Derisi Prep. *THESE RESULTS DO NOT REFLECT THE SPECIFICITY OF THE ANTI-H3 ANTIBODY.* Old NAME: Histone H3 lysine 4 NON-methylated, WT IP #1, Old style Nuc. Prep

source_name: Sonicated s288C Genomic DNA, Amplified Date of Experiment

source_name: *IP #1* REVERSED BEFORE P/C

tag: *IP #1* REVERSED BEFORE P/C


title: Bovine LD Muscle WH vs PH T1 rep4

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford vs piedmontese x hereford T1 replicate 4


title: Bovine LD Muscle WH 135 days vs WH 60 days rep2

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford 135 days vs wagyu x hereford 60 days replicate 2

source_name: LD muscle tissue wagyu x hereford 135 days

source_name: LD muscle tissue wagyu x hereford 60 days

tag: Bovine Longissumus dorsi muscle tissue wagyu x hereford 60 days


title: Bovine LD Muscle WH 195 days vs WH 135 days rep2

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford 195 days vs wagyu x hereford 135 days replicate 2

source_name: LD muscle tissue wagyu x hereford 195 days

tag: Bovine Longissumus dorsi muscle tissue wagyu x hereford 135 days


title: Exp. #22, Intergenic enrichment. Fixed Nuclear Extract (1% 30 min, samples from jdl_g_50J and 52J...

description: Full Name: Exp. #22, Intergenic enrichment. Fixed Nuclear Extract (1% 30 min, samples from jdl_g_50J and 52J) vs S288C Genomic DNA This array is the same as jdl_g_061k, except the crosslinks were not reversed. The same as jdl_g_050J and jdl_g_052J, but an independent amplification and hyb for both sample and reference. The S288C reference DNA (Green Channel)was sonicated, but was never subjected to crosslinking or reversal conditions. S288C reference DNA was derived from the large Derisi Prep. Input was DNA from nuclei that had been salt extracted. Crosslinks in the INPUT DNA were NOT REVERSED prior to Phenol Chloroform prep

tag: Sonicated s288C Genomic DNA, Amplified Date of Experiment

source_name: Unreversed  Input from WT IP #2+3 before debris clearing spin


description: Full Exp. Name: Exp. #23, ORF+Int enr. Fixed Nuclear Extract (1% 30 min) *IP #1* REVERSED BEFORE P/C vs Fixed Nuclear Extract (1% 30 min) Anti-H3 lys4 meth, wild type 100% methylation Input was DNA from nuclei that had been salt extracted. Crosslinks in the INPUT DNA were NOT REVERSED prior to Phenol Chloroform prep The crosslinks in the IP-DNA were reversed prior to Phenol Chloroform prep. *THESE RESULTS DO NOT REFLECT THE SPECIFICITY OF THE ANTI-H3 ANTIBODY.*

source_name: DNA prepared from IP Input, Amplified NOTE: NOT REVERSED. set1 deletion Ref and wt Ref mixed

tag: "IP" DNA, Amplified THESE RESULTS DO NOT REFLECT THE SPECIFICITY OF THE ANTIBODY.


title: Bovine LD Muscle medium pool rep2

description: Bovine Longissumus dorsi muscle tissue rockhampton medium diet pool replicate2

source_name: LD muscle tissue high diet pool

tag: Bovine Longissumus dorsi muscle tissue high diet pool

source_name: LD muscle tissue medium diet pool

tag: Bovine Longissumus dorsi muscle tissue medium diet pool


title: Exp. #25, ORF+Int enr. Channel Swap for jdl_g_111E

description: Input was DNA (Red Channel) from nuclei that had been salt extracted. Crosslinks in the INPUT DNA were NOT REVERSED prior to Phenol Chloroform prep The crosslinks in the IP-DNA were reversed prior to Phenol Chloroform prep. *THESE RESULTS DO NOT REFLECT THE SPECIFICITY OF THE ANTI-H3 ANTIBODY.*

tag: DNA prepared from IP Input, Amplified NOTE


title: Bovine LD Muscle PH newborn vs WH newbornb rep2

description: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford newborn vs wagyu x hereford newborn replicate 2

source_name: LD muscle tissue Piedmontese x hereford newbore

source_name: LD muscle tissue wagyu x hereford newborn

tag: Bovine Longissumus dorsi muscle tissue wagyu x hereford newborn


title: Bovine LD Muscle PH 135d vs 195d rep2

description: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford 135 days vs 195 days replicate 2

source_name: LD muscle tissue Piedmontese x hereford 135 days

source_name: LD muscle tissue Piedmontese x hereford 195 days

tag: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford 195 days


title: Bovine LD Muscle WH newborn vs WH 195 days rep2

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford newborn vs wagyu x hereford 195 days replicate 2

source_name: LD muscle tissue wagyu x hereford newbore

tag: Bovine Longissumus dorsi muscle tissue wagyu x hereford 195 days


title: Exp. #20, Intergenic enrichment. Fixed Nuclear Extract (1% 30 min), used as ref in jdl_g_111E vs ...

description: Full Name: Exp. #20, Intergenic enrichment. Fixed Nuclear Extract (1% 30 min), used as ref in jdl_g_111E vs S288C Genomic DNA Input (RED CHANNEL) was DNA from nuclei that had been salt extracted. Crosslinks in the INPUT DNA were NOT REVERSED prior to Phenol Chloroform prep. The S288C reference DNA was sonicated, but was never subjected to crosslinking or reversal conditions.

source_name: Sonicated s288C Genomic DNA, Freshly Amplified

source_name: Input for Histone H3 WT IP #2 see note

tag: Input for Histone H3 WT IP #2 see note


title: Bovine LD Muscle medium vs low rep1

description: Bovine Longissumus dorsi muscle tissue rockhampton medium diet pool vs low diet pool replicate1

source_name: LD muscle tissue low diet pool

tag: Bovine Longissumus dorsi muscle tissue low diet pool


title: Carcinoma  VUMC_GTL9_b22_s52

description: protocols available via the VUMC MACF website

source_name: stomach

tag: carcinoma

source_name: reference DNA

tag: Pooled DNA from the blood of 10 normal individuals


title: Bovine LD Muscle medium vs low rep2

description: Bovine Longissumus dorsi muscle tissue rockhampton medium diet pool vs low diet pool replicate 2


title: Exp. #21, Intergenic enrichment. Fixed Nuclear Extract (1% 30 min), used as ref for jdl_g_099K vs...

description: Full Experiment Name: Exp. #21, Intergenic enrichment. Fixed Nuclear Extract (1% 30 min), used as ref for jdl_g_099K vs S288C Genomic DNA Input (RED Channel) was DNA from nuclei that had been salt extracted. Crosslinks in the INPUT DNA were NOT REVERSED prior to Phenol Chloroform prep The S288C reference DNA (Green Channel)was sonicated, but was never subjected to crosslinking or reversal conditions.S288C reference DNA was derived from the large Derisi Prep.

source_name: Sonicated s288C Genomic DNA, Amplified day of hyb

source_name: Input for IP #3, Amplified. See note below.


title: Bovine LD Muscle medium pool rep1

description: Bovine Longissumus dorsi muscle tissue rockhampton medium diet pool replicate 1


title: Bovine LD Muscle WH 135 days vs WH 60 days rep3

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford 135 days vs wagyu x hereford 60 days replicate 3

source_name: LD muscle tissue wagyu x hereford 135 days

source_name: LD muscle tissue wagyu x hereford 60 days


title: Bovine LD Muscle WH vs PH T1 rep1

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford vs piedmontese x hereford T1 replicate 1

source_name: LD muscle tissue piedmontese x hereford T1

tag: Bovine Longissumus dorsi muscle tissue piedmontese x hereford T1

source_name: LD muscle tissue Wagyu x hereford T1

tag: Bovine Longissumus dorsi muscle tissue Wagyu x hereford T1


title: Exp. #18, Intergenic enrichment. Fixed Spheroplasts Extract vs Whole Extract. Nagy 2-05

description: Crosslinks in the sample DNA were NOT REVERSED prior to Phenol Chloroform prep The reference DNA was never fixed. After P/C prep, samples were treated with 100 ng/uL RNAse A for 1 hour at 37 degrees.

source_name: S288C yeast OD 1, No Fix, CSH Prep (P/C), Amplified

source_name: S288C Spheroplasts OD 1, Fixed, Beadbeat, P/C, Amplified


title: Carcinoma  VUMC_GTL15_b22_s64


title: Exp. #19, Intergenic enrichment. Fixed Spheroplasts Extract (Incubted in NIB on ice o/n) vs ...

description: Full Exp Name: Exp. #19, Intergenic enrichment. Fixed Spheroplasts Extract (Incubted in NIB on ice o/n) vs Whole Extract. Nagy 2-05-02 Crosslinks in the sample DNA were NOT REVERSED prior to Phenol Chloroform prep The reference DNA was never crosslinked. After P/C prep, samples were treated with 100 ng/uL RNAse A for 1 hour at 37 degrees.

tag: S288C yeast OD 1, No Fix, CSH Prep (P/C), Amplified

source_name: S288C Spheros OD 1, Fixed, Incubated in NIB 20 mins on ice, o/n ice, Beadbeat, P/C, Amplified


title: Bovine LD Muscle WH 195 days vs WH 135 days rep3

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford 195 days vs wagyu x hereford 135 days replicate 3

source_name: LD muscle tissue wagyu x hereford 195 days


title: Bovine LD Muscle PH 60d vs 135d rep2

description: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford 60 days vs 135 days replicate 2

source_name: LD muscle tissue Piedmontese x hereford 60 days

source_name: LD muscle tissue Piedmontese x hereford 135 days

tag: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford 135 days


title: Exp. #13, Intergenic enrichment. Fixed Whole Extract (1% 30 min) REVERSED AFTER P/C prep vs ...

description: Full Experiment Name: Exp. #13, Intergenic enrichment. Fixed Whole Extract (1% 30 min) REVERSED AFTER P/C prep vs Whole Extract, Nagy 02-05-02 Crosslinks in the sample DNA were NOT REVERSED prior to Phenol Chloroform prep The reference DNA was never crosslinked. After P/C prep, samples were treated with 100 ng/uL RNAse A for 1 hour at 37 degrees.

source_name: S288C yeast OD 1, Fixed, CSH Prep (P/C), Amplified


title: Bovine LD Muscle WH newborn vs WH 195 days rep3

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford newborn vs wagyu x hereford 195 days replicate 3

source_name: LD muscle tissue wagyu x hereford newbore


title: Bovine LD Muscle WH 60 days vs PH 60 days rep1

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford 60 days vs Pidemontese x hereford 60 days replicate 1

source_name: LD muscle tissue Pidemontese x hereford 60 days

tag: Bovine Longissumus dorsi muscle tissue Pidemontese x hereford 60 days


title: Bovine LD Muscle PH 195d vs newborn rep1

description: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford 195 days vs newborn replicate 1

source_name: LD muscle tissue Piedmontese x hereford 195 days

source_name: LD muscle tissue Piedmontese x hereford newborn

tag: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford newborn


title: Bovine LD Muscle PH 195d vs newbornb rep2

description: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford 195 days vs newborn replicate 2


title: Bovine LD Muscle PH newborn vs WH newbornb rep1

description: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford newborn vs wagyu x hereford newborn replicate 1

source_name: LD muscle tissue Piedmontese x hereford newbore

source_name: LD muscle tissue wagyu x hereford newborn


title: Carcinoma  VUMC_GTL8_b22_s50

source_name: stomach

source_name: reference DNA


title: Bovine LD Muscle PH 135d vs 195d rep1

description: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford 135 days vs 195 days replicate 1


title: Exp. #12, Intergenic enrichment. Fixed Whole Extract (1% 15 min) vs Whole Extract  Nagy 2-05-02

description: Crosslinks in the sample DNA were NOT REVERSED prior to Phenol Chloroform prep The reference DNA was never crosslinked. After P/C prep, samples were treated with 100 ng/uL RNAse A for 1 hour at 37 degrees.

source_name: S288C yeast OD 1, No Fix, CSH prep (P/C), Amplified

source_name: S288C yeast OD 1, Fixed, CSH prep (P/C), not reversed, Amplified


title: Bovine LD Muscle PH 60d vs 135d rep1

description: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford 60 days vs 135 days replicate 1


title: Carcinoma  VUMC_GTL13_b22_s62

description: protocols available via the VUMC MACF website


title: Bovine LD Muscle WH 60 days vs PH 60 days rep3

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford 60 days vs Pidemontese x hereford 60 days replicate 3

source_name: LD muscle tissue wagyu x hereford 60 days


title: Carcinoma  VUMC_GTL12_b22_s61


title: Carcinoma  VUMC_GTL4_b22_s34


title: Bovine LD Muscle WH 195 days vs WH 135 days rep1

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford 195 days vs wagyu x hereford 135 days replicate 1

source_name: LD muscle tissue wagyu x hereford 135 days

tag: Bovine Longissumus dorsi muscle tissue wagyu x hereford 135 days


title: Exp. #09, Intergenic enrichment. Fixed Whole Extract (1% 15 min, High Phenol/Aq) vs Whole Extract

description: Full Name: Exp. #9, Intergenic enrichment. Fixed Whole Extract (1% 15 min, High Phenol/Aq) vs Whole Extract Nagy 4-25-02

tag: S288C yeast OD 1, No Fix, CSH prep (P/C), Amplified

source_name: Extract: Whole Fixed Yeast (1% 15 min) CSH Prep (P/C) High Phenol/Aq, Amplified  Nagy 4-25

tag: Extract


title: Bovine LD Muscle WH 135 days vs WH 60 days rep1

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford 135 days vs wagyu x hereford 60 days replicate 1

tag: Bovine Longissumus dorsi muscle tissue wagyu x hereford 60 days


title: Carcinoma  VUMC_GTL20_b22_s69


title: Bovine LD Muscle WH newborn vs WH 195 days rep1

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford newborn vs wagyu x hereford 195 days replicate 1

source_name: LD muscle tissue wagyu x hereford 195 days


title: Bovine LD Muscle WH 195 days vs WH 135 days rep4

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford 195 days vs wagyu x hereford 135 days replicate 4


title: Exp. #08, Neutral. Fixed Whole Extract, Reversed before P/C vs Whole Extract, Nagy 2-05-02

description: Crosslinks in the sample DNA were REVERSED prior to Phenol Chloroform prep. The reference DNA was never crosslinked. After P/C prep, samples were treated with 100 ng/uL RNAse A for 1 hour at 37 degrees. CSH= Cold Spring Harbor

source_name: S288C yeast OD 1, Fixed, Reversed, CSH prep (P/C), Amplified


title: Exp. #07, Neutral. Whole Extract FIXED AFTER P/C Prep vs Whole Extract, Nagy 2-05-02

description: The sample DNA was not crosslinked until after the P/C Prep. The crosslinkes were not reversed prior to labeling. The reference DNA was never crosslinked. After P/C prep, samples were treated with 100 ng/uL RNAse A for 1 hour at 37 degrees. Extract: Whole Unfixed, P/C, THEN FIXED vs Whole, Unfixed. Nagy 2-05-02

source_name: S288C yeast OD 1, No Fix, CSH prep (P/C), THEN FIXED, Amplified


title: Carcinoma  VUMC_GTL19_b22_s68


title: Bovine LD Muscle PH newborn vs WH newbornb rep3

description: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford newborn vs wagyu x hereford newborn replicate 3

tag: Bovine Longissumus dorsi muscle tissue wagyu x hereford newborn


title: Carcinoma  VUMC_GT037_bUCSF1.14_s36

description: protocols according to Snijders,A.M. et al. (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat.Genet., 29, 263-264.

data_processing: Described in Snijders,A.M. et al. (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat.Genet., 29, 263-264.


title: Carcinoma  VUMC_GT036_bUCSF1.14_s35


title: Bovine LD Muscle PH 135d vs 195d rep3

description: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford 135 days vs 195 days replicate 3

source_name: LD muscle tissue Piedmontese x hereford 135 days

tag: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford 195 days


title: Bovine LD Muscle self hyb

description: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford self hybridization

source_name: LD muscle tissue Piedmontese x hereford T1

tag: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford T1


title: Bovine LD Muscle PH 60d vs 135d rep3

description: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford 60 days vs 135 days replicate 3

source_name: LD muscle tissue Piedmontese x hereford 60 days


title: Exp. #06, Neutral. DNA prepared from Nuclear Extract vs Whole Extract, Nagy 2-05-02

description: The sample DNA was never crosslinked. The reference DNA was never crosslinked. After P/C prep, samples were treated with 100 ng/uL RNAse A for 1 hour at 37 degrees. Old Description: S288C Spheros prepped "old method" OD 1, Amplified

source_name: S288C DNA prepared from Nuclear Extract , OD 1, Amplified


title: Bovine LD Muscle WH 60 days vs PH 60 days rep2

description: Bovine Longissumus dorsi muscle tissue wagyu x hereford 60 days vs Pidemontese x hereford 60 days replicate 2

source_name: LD muscle tissue Pidemontese x hereford 60 days


title: Carcinoma  VUMC_GTL7_b22_s48


title: Carcinoma  VUMC_GT034_bUCSF1.14_s33


title: Carcinoma  VUMC_GT033_bUCSF1.14_s32


title: Carcinoma  VUMC_GT035_bUCSF1.14_s34


title: Carcinoma  VUMC_GTL3_b22_s33


title: Carcinoma  VUMC_GTL10_b22_s53


title: Carcinoma  VUMC_GT032_bUCSF1.14_s31


title: Carcinoma  VUMC_GT031_bUCSF1.14_s30


title: Exp. #05, Neutral. 0.1 ng S288C Genomic DNA, amplified vs 50ng of same DNA, amplified

description: The purpose of this array was to rule out any amplification bias linked to concentration of input DNA. 0.1 ng of input genomic DNA was the lowest amount for which we could achieve robust amplification.

source_name: Original S288C DNA (Derisi), 50 ng, Amplified

source_name: Original S288C DNA (Derisi), 0.1 ng, Amplified


title: Carcinoma  VUMC_GT029_bUCSF1.14_s28

source_name: stomach


title: Carcinoma  VUMC_GT030_bUCSF1.14_s29

source_name: reference DNA


title: Carcinoma  VUMC_GTL5_b22_s35

description: protocols available via the VUMC MACF website


title: Carcinoma  VUMC_GT028_bUCSF1.14_s27


title: Carcinoma  VUMC_GT027_bUCSF1.14_s26


title: Carcinoma  VUMC_GTL16_b22_s65


title: Carcinoma  VUMC_GTL11_b22_s60


title: Carcinoma  VUMC_GT026_bUCSF1.14_s25


title: Carcinoma  VUMC_GT025_bUCSF1.14_s24


title: Carcinoma  VUMC_GT024_bUCSF1.14_s23


title: Carcinoma  VUMC_GT023_bUCSF1.14_s22


title: Carcinoma  VUMC_GT022_bUCSF1.14_s21


title: Carcinoma  VUMC_GT021_bUCSF1.14_s20


title: Exp. #02, Neutral. Whole Extract vs Whole Extract Nagy 2-05-02

description: The DNA was never crosslinked. After P/C prep, samples were treated with 100 ng/uL RNAse A for 1 hour at 37 degrees. Extract: Whole Unfixed vs Whole, Unfixed. Int Enr Nagy 2-05-02

source_name: S288C yeast OD 1, No Fix, CSH prep (P/C), Amplified


title: Carcinoma  VUMC_GTL14_b22_s63


title: Carcinoma  VUMC_GTL17_b22_s66


title: Carcinoma  VUMC_GT018_bUCSF1.14_s17


title: Bovine LD Muscle PH 195d vs newbornb rep3

description: Bovine Longissumus dorsi muscle tissue Piedmontese x hereford 195 days vs newborn replicate 3

source_name: LD muscle tissue Piedmontese x hereford 195 days

source_name: LD muscle tissue Piedmontese x hereford newborn


title: Carcinoma  VUMC_GT017_bUCSF1.14_s16


title: Carcinoma  VUMC_GTL2_b22_s32


title: Carcinoma  VUMC_GT016_bUCSF1.14_s15


title: Carcinoma  VUMC_GT014_bUCSF1.14_s13


title: Carcinoma  VUMC_GTL18_b22_s67


title: Carcinoma  VUMC_GT019_bUCSF1.14_s18


title: Adenoma  VUMC_C020_b16_s30

source_name: colon

tag: adenoma


title: Exp. #03, Neutral. Whole Extract CSH Prep vs S288C Genomic DNA

description: The sample (red) DNA was sonicated, but was never subjected to crosslinking or reversal conditions. The S288C reference DNA (Green Channel) was sonicated, but was never subjected to crosslinking or reversal conditions. S288C reference DNA was derived from the large Derisi Prep.

source_name: Sonicated s288C Genomic DNA, Amplified Date of Experiment

source_name: TOTAL DNA Prep, before crosslinking or any treatment, Amplified


title: Carcinoma  VUMC_GTL6_b22_s36


title: Carcinoma  VUMC_GT013_bUCSF1.14_s12


title: Breast tumor cell line  VUMC_BT474_b28_s21

source_name: breast

tag: breast tumor cell line


title: Carcinoma  VUMC_GT012_bUCSF1.14_s11

tag: carcinoma


title: Adenoma  VUMC_C019_b16_s31

tag: Pooled DNA from the blood of 10 normal individuals


title: Carcinoma  VUMC_GTL1_b22_s31


title: Carcinoma  VUMC_GT011_bUCSF1.14_s10


title: Adenoma  VUMC_C018_b16_s32


title: Carcinoma  VUMC_GT015_bUCSF1.14_s14


title: Carcinoma  VUMC_C008_b17_s34


title: Adenoma  VUMC_C009_b17_s35


title: Carcinoma  VUMC_GT009_bUCSF1.14_s8


title: Carcinoma  VUMC_GT007_bUCSF1.14_s6


title: Carcinoma  VUMC_C005_b16_s48


title: Carcinoma  VUMC_C003_b16_s50


title: Carcinoma  VUMC_GT006_bUCSF1.14_s5


title: Carcinoma  VUMC_GT010_bUCSF1.14_s9


title: Carcinoma  VUMC_GT005_bUCSF1.14_s4


title: Carcinoma  VUMC_GT020_bUCSF1.14_s19


title: Carcinoma  VUMC_C002_b16_s51


title: Carcinoma  VUMC_GT004_bUCSF1.14_s3


title: Adenoma  VUMC_C001_b16_s52


title: XZ_tripleWhole_mCIPUB_03_F0132_07022005.CEL

city: Los Angeles

first: Steve

middle: E

last: Jacobsen

state: CA

address: 621 Charles E. Young Dr. South

department: Molecular Cell and Developmental Biology

institute: University of California, Los Angeles

description: Depleted for methylated DNA at all sequenced contexts

hyb_protocol: Whole Genome Tiling Array  was hybridized for 16 hrs, washed and stained with a streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 400 according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned on Affymetrix scanner G7

data_processing: Gene chip data files were processed using TileMap and KS method.

organism: Arabidopsis thaliana

source_name: whole palnt tissue w/o root, 40 days

label_protocol: The genomic DNA in the samples was 3'-end-labelled with dd-UTP (Roche) by the terminal transferase (TdT, Roche) reaction for 1 h at 37 degrees C.

growth_protocol: Plants were grown on soil under continuous illumination for 40 days at 25 degrees C

extract_protocol: genomic DNA was isolated from whole plant tissues using DNAeasy kit following instructions from the manufacturer (QIAGEN) instruction

treatment_protocol: Untreated


title: XZ_tripleWhole_mCIPUB_02_F0130_07022005.CEL

tag: Depleted for methylated DNA at all sequenced contexts


title: Carcinoma  VUMC_GT008_bUCSF1.14_s7


title: Carcinoma  VUMC_GT003_bUCSF1.14_s2


title: Carcinoma  VUMC_C004_b16_s49


title: Carcinoma  VUMC_C006_b14_s25


title: Carcinoma  VUMC_GT002_bUCSF1.14_s1


title: Carcinoma  VUMC_C007_b14_s24


title: Myotubes_rep2, chip HG-U133B

status: Public on Aug 29 2006

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description: The goal is to study the genome-wide mapping of histone modifications in differentiating human primary myoblasts.

scan_protocol: GeneArray 2500 scanner

data_processing: MicroArray Suite 5.0

label: Biotin

source_name: myotubes

growth_protocol: Cultured in SKGM-2 media

extract_protocol: RNA prep method: RNeasy

tag: Fetal skeletal myoblasts


title: Myotubes_rep3, chip HG-U133B


title: Myoblasts_rep3, chip HG-U133B

source_name: Getal skeletal myoblasts


title: Myobalsts_rep2, chip HG-U133B

source_name: myoblasts


title: XZ_tripleWhole_mCIPUB_01_F0110_07022005.CEL


title: XZ_met1Whole_mCIPUB_03_F0128_07022005.CEL


title: Myotubes_rep1, chip HG-U133B

molecule: nuclear RNA


title: Patient4

city: St. Louis

first: J

middle: Perren

last: Cobb

state: MO

address: Campus Box 8109, 660 South Euclid Avenue

institute: Washington University in St. Louis

description: Gene expression data (Affy Chip Hu6800)

data_processing: The data were analyzed (including normalization and modelling) with dChip

tag: Tissue

value: Spleen

tag: Type

value: Septic

tag: Replicate


title: XZ_tripleWhole_mCIPE_01_F0111_07022005.CEL

description: Enriched for methylated DNA at all sequenced contexts


title: Patient3

description: Gene expression data (Affy Chip Hu6800)


title: Myoblasts_rep1,chip HG-U133B


title: XZ_tripleWhole_mCIPE_03_F0133_07022005.CEL

tag: Enriched for methylated DNA at all sequenced contexts


title: Patient8

description: Gene expression data (Affy Chip Hu6800)


title: Patient1

description: Gene expression data (Affy Chip Hu6800)


title: Patient12

description: Gene expression data (Affy Chip Hu6800)

value: Injury


title: Patient10

description: Gene expression data (Affy Chip Hu6800)


title: Patient11

description: Gene expression data (Affy Chip Hu6800)


title: Patient5

description: Gene expression data (Affy Chip Hu6800)


title: XZ_met1Whole_mCIPUB_01_F0108_07022005.CEL


title: Patient13

description: Gene expression data (Affy Chip Hu6800)


title: MouseSpleenSham7

description:
UNKOWN
Gene expression data

data_processing: The data were analyzed with dChip

value: Sham


title: Patient2

description: Gene expression data (Affy Chip Hu6800)


title: XZ_met1Whole_mCIPE_02_F0127_07022005.CEL


title: MouseSpleenSham8

description:
UNKOWN
Gene expression data


title: MouseSpleenSham6

description:
UNKOWN
Gene expression data


title: XZ_met1Whole_mCIPUB_02_F0126_07022005.CEL


title: XZ_colWhole_mCIPE_04_F0441_12222005.CEL


title: MouseSpleenSham2

description:
UNKOWN
Gene expression data


title: MouseSpleenSham3

description:
UNKOWN
Gene expression data


title: XZ_colWhole_mCIPUB_05_F0442_12222005.CEL


title: XZ_colWhole_mCIPUB_04_F0440_12222005.CEL


title: MouseSpleenCLP6

description:
UNKOWN
Gene expression data

value: CLP


title: XZ_colWhole_mCIPUB_06_F0444_12222005.CEL


title: Patient6

description: Gene expression data (Affy Chip Hu6800)


title: MouseSpleenCLP8

description:
UNKOWN
Gene expression data


title: XZ_colWhole_HMBDL_03_F0114_06242005.CEL

description: Depleted for CG-methylated DNA

tag: Depleted for CG-methylated DNA


title: MouseSpleenSham4

description:
UNKOWN
Gene expression data


title: MouseSpleenCLP7

description:
UNKOWN
Gene expression data


title: MouseSpleenCLP5

description:
UNKOWN
Gene expression data


title: MouseSpleenSham1

description:
UNKOWN
Gene expression data


title: MouseSpleenCLP4

description:
UNKOWN
Gene expression data


title: Patient9

description: Gene expression data (Affy Chip Hu6800)


title: XZ_tripleWhole_mCIPE_02_F0131_07022005.CEL


title: XZ_met1Whole_mCIPE_03_F0129_07022005.CEL


title: XZ_colWhole_mCIPE_05_F0443_12222005.CEL


title: XZ_met1Whole_mCIPE_01_F0109_07022005.CEL


title: MouseSpleenCLP3

description:
UNKOWN
Gene expression data


title: MouseSpleenSham5

description:
UNKOWN
Gene expression data


title: MouseSpleenCLP1

description:
UNKOWN
Gene expression data


title: MouseBloodNotInfected2ShamControl

description:
UNKOWN
Gene expression data

value: Blood

value: NotInfected

tag: Batch

tag: Group

tag: Phenotype

value: Control


title: E. coli K-12 W3110 #3

city: Kgs. Lyngby

first: Hanni

last: Willenbrock

address: Kemikalievej, bygning 208

department: Center for Biological Sequence Analysis

country: Denmark

institute: DTU

description: Hybridization of genomic DNA from E. coli strain K-12 isolate W3110

data_processing: Standard Affymetrix procedure

label: terminal labeling with biotinylated Affymetrix GeneChip DNA Labeling Reagent

organism: Escherichia coli

label_protocol: see section 3 (Prokaryotic Sample and Array Processing) of the Affymetrix GeneChip Expression Analysis manual

growth_protocol: overnight in Luria-Bertani (LB) broth with continuous agitation

extract_protocol: Qiagen Genomic Tip 500/G (Qiagen, Hilden, Germany) and the Genomic DNA Buffer set (Qiagen)

tag: Isolate W3110 of K-12 strain


title: MouseBloodNotInfected1ShamControl

description:
UNKOWN
Gene expression data


title: MouseBloodNotInfected3SalineControl

description:
UNKOWN
Gene expression data

value: Saline


title: MouseBloodNotInfected1SalineControl

description:
UNKOWN
Gene expression data


title: MouseBloodNotInfected3NormalControl

description:
UNKOWN
Gene expression data

value: Normal


title: MouseSpleenCLP2

description:
UNKOWN
Gene expression data


title: E. coli K-12 W3110 #2


title: MouseBloodInfected3CLPMildSeptic

description:
UNKOWN
Gene expression data

value: Infected

value: CLPMild


title: MouseBloodNotInfected1NormalControl

description:
UNKOWN
Gene expression data


title: MouseBloodInfected2CLPMildSeptic

description:
UNKOWN
Gene expression data


title: E. coli D1 #2

description: Hybridization of genomic DNA from E. coli strain D1

tag: serotype O175:H16


title: E. coli EDL933 #3

description: Hybridization of genomic DNA from E. coli EDL933

tag: serotype O157:H7


title: MouseBloodNotInfected2NormalControl

description:
UNKOWN
Gene expression data


title: E. coli EDL933 #1