title: CRC141 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC141

value: CRC Patient CRC141


title: Caco-2 [50K_Hind]

status: Public on Aug 06 2010

type: genomic

city: Abbott Park

first: Xin

last: Lu

state: IL

address: 100 Abbott Park Rd

department: Cancer Research

country: USA

institute: Abbott Laboratories

description: Hybridized to Hind240

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 G7.

data_processing: Feature data were collected and extracted from the scanner using the Affymetrix GeneChip® Operating Software (GCOS). Affymetrix 100K Mapping Array intensity signal CEL files were processed by Partek software (Build 6.08.0623) using the PM/MM difference model. Ninety normal samples were previously downloaded from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=100k) and averaged to establish the reference for calculating the copy numbers.

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: CRC CellLine Caco-2

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: As per manufacturer (Affymetrix)

tag: cell type

value: CRC

tag: cell line

value: CRC CellLine Caco-2


title: LS513 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Cell Line LS513

value: CRC Cell Line LS513


title: CRC138 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC138

value: CRC Patient CRC138


title: CRC133 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC133

value: CRC Patient CRC133


title: CRC135 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC135

value: CRC Patient CRC135


title: CRC131 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC131

value: CRC Patient CRC131


title: CRC136 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC136

value: CRC Patient CRC136


title: CRC123 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC123

value: CRC Patient CRC123


title: CRC137 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC137

value: CRC Patient CRC137


title: CRC127 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC127

value: CRC Patient CRC127


title: CRC122 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC122

value: CRC Patient CRC122


title: CRC121 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC121

value: CRC Patient CRC121


title: CRC120 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC120

value: CRC Patient CRC120


title: CRC128 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC128

value: CRC Patient CRC128


title: CRC111 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC111

value: CRC Patient CRC111


title: CRC117 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC117

value: CRC Patient CRC117


title: CRC118 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC118

value: CRC

value: CRC Patient CRC118


title: CRC110 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC110

value: CRC Patient CRC110


title: CRC80 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC80

value: CRC Patient CRC80


title: CRC125 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC125

value: CRC Patient CRC125


title: CRC106 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC106

value: CRC Patient CRC106


title: CRC105 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC105

value: CRC Patient CRC105


title: CRC108 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC108

value: CRC Patient CRC108


title: CRC119 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC119

value: CRC Patient CRC119


title: NCI-H1975 [50K_Hind]

description: Hybridized to Hind240

source_name: NSCLC Cell Line NCI-H1975

value: NSCLC

value: NSCLC Cell Line NCI-H1975


title: CRC103 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC103

value: CRC Patient CRC103


title: CRC102 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC102

value: CRC Patient CRC102


title: CRC101 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC101

value: CRC Patient CRC101


title: CRC114 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC114

value: CRC Patient CRC114


title: CRC104 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC104

value: CRC Patient CRC104


title: CRC115 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC115

value: CRC Patient CRC115


title: CRC113 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC113

value: CRC

value: CRC Patient CRC113


title: SW620rep2 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Cell Line SW620, rep2

value: CRC Cell Line SW620


title: CRC100 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC100

value: CRC Patient CRC100


title: CRC97 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC97

value: CRC Patient CRC97


title: CRC94 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC94

value: CRC Patient CRC94


title: CRC83 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC83

value: CRC Patient CRC83


title: CRC85 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC85

value: CRC Patient CRC85


title: CRC84 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC84

value: CRC Patient CRC84


title: CRC65 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC65

value: CRC Patient CRC65


title: CRC95 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC95

value: CRC Patient CRC95


title: CRC77 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC77

value: CRC Patient CRC77


title: CRC91 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC91

value: CRC Patient CRC91


title: CRC73 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC73

value: CRC Patient CRC73


title: CRC79 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC79

value: CRC Patient CRC79


title: CRC66 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC66

value: CRC Patient CRC66


title: CRC72 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC72

value: CRC Patient CRC72


title: CRC59 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC59

value: CRC

value: CRC Patient CRC59


title: CRC58 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC58

value: CRC Patient CRC58


title: CRC92 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC92

value: CRC Patient CRC92


title: CRC81 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC81

value: CRC Patient CRC81


title: CRC96 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC96

value: CRC Patient CRC96


title: CRC54 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC54

value: CRC Patient CRC54


title: CRC68 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC68

value: CRC Patient CRC68


title: CRC51 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC51

value: CRC Patient CRC51


title: CRC57 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC57

value: CRC Patient CRC57


title: CRC49 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC49

value: CRC Patient CRC49


title: CRC48 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC48

value: CRC Patient CRC48


title: CRC50 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC50

value: CRC Patient CRC50


title: CRC42 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC42

value: CRC Patient CRC42


title: CRC45 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC45

value: CRC Patient CRC45


title: CRC43 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC43

value: CRC Patient CRC43


title: CRC38 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC38

value: CRC Patient CRC38


title: CRC46 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC46

value: CRC

value: CRC Patient CRC46


title: CRC87 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC87

value: CRC Patient CRC87


title: CRC26 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC26

value: CRC Patient CRC26


title: CRC32 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC32

value: CRC Patient CRC32


title: CRC29 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC29

value: CRC Patient CRC29


title: CRC40 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC40

value: CRC Patient CRC40


title: CRC30 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC30

value: CRC Patient CRC30


title: CRC36 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC36

value: CRC Patient CRC36


title: CRC24 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC24

value: CRC Patient CRC24


title: CRC21 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC21

value: CRC Patient CRC21


title: CRC34 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC34

value: CRC Patient CRC34


title: CRC35 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC35

value: CRC Patient CRC35


title: CRC22 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC22

value: CRC Patient CRC22


title: CRC31 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC31

value: CRC Patient CRC31


title: CRC27 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC27

value: CRC Patient CRC27


title: LoVo (ATCC) [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Cell Line LoVo (ATCC)

value: CRC Cell Line LoVo (ATCC)


title: HCT-15 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Cell Line HCT-15

value: CRC

value: CRC Cell Line HCT-15


title: SW620rep1 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Cell Line SW620, rep1

value: CRC Cell Line SW620


title: CRC41 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC41

value: CRC Patient CRC41


title: HCT116 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Cell Line HCT116

value: CRC Cell Line HCT116


title: CRC69 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC69

value: CRC Patient CRC69


title: DLD-1 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Cell Line DLD-1

value: CRC Cell Line DLD-1


title: HT-29 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Cell Line HT-29

value: CRC Cell Line HT-29


title: CRC25 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC25

value: CRC Patient CRC25


title: CRC20 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC20

value: CRC Patient CRC20


title: CRC16 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC16

value: CRC Patient CRC16


title: CRC116 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC116

value: CRC Patient CRC116


title: CRC63 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC63

value: CRC Patient CRC63


title: CRC13 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC13

value: CRC Patient CRC13


title: CRC11 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC11

value: CRC Patient CRC11


title: CRC6 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC6

value: CRC Patient CRC6


title: CRC18 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC18

value: CRC Patient CRC18


title: CRC14 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC14

value: CRC

value: CRC Patient CRC14


title: CRC17 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC17

value: CRC Patient CRC17


title: CRC5 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC5

value: CRC Patient CRC5


title: CRC2 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC2

value: CRC Patient CRC2


title: CRC15 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC15

value: CRC Patient CRC15


title: CRC1 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC1

value: CRC Patient CRC1


title: CRC3 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC3

value: CRC Patient CRC3


title: CRC7 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC7

value: CRC Patient CRC7


title: CRC88 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC88

value: CRC Patient CRC88


title: CRC12 [50K_Hind]

description: Hybridized to Hind240

source_name: CRC Patient CRC12

value: CRC Patient CRC12


title: MEF ToR G1 phase vs. S phase DNA rep2

status: Public on May 25 2010

city: Jerusalem

first: Itamar

last: Simon

address: Ein Karem Campus

department: Molecular Biology

country: Israel

institute: The Hebrew university

description: G1/S MEF rep2 LogRatio

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent  scanner. Images were quantified using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software, Data obtained from log10 of processed Red signal/processed Green signal.

organism: Mus musculus

source_name: MEF cells, G1 phase DNA, replicate 2

label_protocol: 250-1000 ng DNA was labeled with either dUTP-cy3 or dUTP-cy5 by direct labeling using Agilent labeling kit

extract_protocol: DNA was extracted using a strandard protocol - incubation with lysis buffer that included ProteinaseK, that was followed by phenol-chlorophorm extraction, sonication of the DNA to smaller fragments (300-1000bp) and Ethanol precipitationand purification using QIAGEN PCR purification kit.

value: MEF (mouse embryonic fibroblasts)

source_name: MEF cells, Sphase DNA, replicate 2


title: L1210 ToR G1 phase vs. S phase DNA rep2

description: G1/S L1210 rep2 LogRatio

source_name: L1210 cells, S phase DNA, replicate 2

value: L1210 cell line

source_name: L1210 cells, G1 phase DNA, replicate 2


title: MEF ToR G1 phase vs. S phase DNA rep1

description: G1/S MEF rep1 LogRatio

source_name: MEF cells, G1 phase DNA, replicate 1

source_name: MEF cells, S phase DNA, replicate 1


title: L1210 ToR G1 phase vs. S phase DNA rep1

description: G1/S L1210 rep1 LogRatio

source_name: L1210 cells, S phase DNA, replicate 1

source_name: L1210 cells, G1 phase DNA, replicate 1


title: Male PANIYA South Asia  PNYD1 Human610-Quad v1.0

status: Public on Jun 10 2010

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

description: Genomic DNA extracted from blood was genotyped using Human610-Quad v1.0  Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Genomic DNA extracted from blood was genotyped using Infinium Human610-Quad v1.0  Genotyping BeadChips (Illumina).
Genomestudio v2009.2 with GT module 1.5.16 (Illumina).

label: C-Bio and A-DNP

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: gender

value: Male

tag: population

value: PANIYA

tag: region

value: South Asia

tag: tissue

value: blood


title: Male Bene Israel Jews South Asia  Indian_Jew_6 Human610-Quad v1.0

value: Bene Israel Jews


title: Male Bene Israel Jews South Asia  Indian_Jew_8 Human610-Quad v1.0


title: Female PANIYA South Asia  PNYD3 Human610-Quad v1.0

value: Female


title: SH39 Chinese prostate cancer

status: Public on May 15 2010

city: London

first: Xueying

last: Mao

address: Charterhouse Square

country: United Kingdom

institute: Queen Mary

description: Hybridized to human SNP 6.0 array

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: CEL files and CHP files generated by Affymetrix Genechip Operating Software. Very weakly hybridized SNPs were filtered by the same software. The signal intensity data from SNP array were analyzed by in-house software- GOLF and commerical software-Partek.

source_name: Chinese prostate cancer

extract_protocol: Fresh frozen samples were digested by Proteinase K  and RNaseA. DNA was extracted from these samples using phenol/chroloform.

value: Prostate cancer


title: SH35 Chinese normal prostate

description: Hybridized to human SNP 6.0 array

source_name: Chinese normal prostate

value: Normal prostate


title: SH34 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: Male Bene Israel Jews South Asia  Indian_Jew_7 Human610-Quad v1.0


title: SH37 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: SH36 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: SH36 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: SH31 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: SH29 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: SH33 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: SH38 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: SH27 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: SH26 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: SH30 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: SH28 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: SH34 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: SH37 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: Male PANIYA South Asia  PNYD9 Human610-Quad v1.0


title: SH27 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: serous tumor (11888)

status: Public on Feb 25 2010

type: RNA

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: serous tumor (11888)

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: The image data were compiled into a project using  Beadstudio software gene expression module version 3.2.7.  No normalization was used. The data was exported as txt files using the build-in function of export to GeneSpring GX format. The option of sample probe profile was chosen. Data were subsequently quantile normalized for the analysis.

label: biotin

molecule: total RNA

source_name: serous ovarian adenocarcinoma

label_protocol: According to Illumina protocol.

growth_protocol: Primary cultures of normal ovarian surface epithelium (NOSE) were performed as previously described. Briefly, brushings of the ovarian surface were performed in pre- and postmenopausal women undergoing clinically indicated surgery. NOSE cells were cultured in 1:1 MCDB105/M199 (Sigma). The epithelial origin of cultured cells was confirmed using immunohistochemistry to examine the expression of vimentin and cytokeratins, and only cultures containing >90% epithelial cells were used.  NOSE and cancer cell lines were cultured with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin solution (Invitrogen).

extract_protocol: Total RNA was extracted using the mirVana miRNA Isolation Kit (ABI). RNA quality were inspected on a 2100 Bioanalyzer (Agilent).

tag: disease state

value: Ovarian tumor (serous)


title: serous tumor (9510)

description: serous tumor (9510)


title: serous tumor (9418)

description: serous tumor (9418)


title: serous tumor (human_15_b)

description: serous tumor (human_15_b)


title: serous tumor (16399)

description: serous tumor (16399)


title: SH30 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: serous tumor (39395)

description: serous tumor (39395)


title: SH29 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: Pancreas of E15.5 KO_rep3

status: Public on Jan 01 2010

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: RNA sample was purified from embryo stage at 15.5 day from Glis3 mutant

hyb_protocol: 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

scan_protocol: Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the GenechipÆ Operating Software (Version 1.4.0.036).

data_processing: The resulting files (.dat, .cel and .chp) were imported into the Rosetta Resolver system (Version 7.2).  This system performs data pre-processing and error modeling as described in Weng (2006).  Resolver generated fold-changes and p values, based on ratios built in the system, were exported for further analysis.

source_name: Glis3 mutant pancreas, E15.5 embryo

label_protocol: Starting with 100ng of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3í Amplification Two-Cycle Target labeling kit according to manufacturerís protocol.

extract_protocol: PicoPure RNA Isolation kit with DNAseI treatment

tag: strain

tag: age

value: pancreas


title: SH35 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: Pancreas of E15.5 KO_rep4


title: serous tumor (39245)

description: serous tumor (39245)


title: SH38 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: Pancreas of E15.5 WT_rep2

description: RNA sample was purified from WT embryo stage at 15.5 day

source_name: WT Pancreas, E15.5 embryo


title: Pancreas of E15.5 WT_rep1


title: SH24 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: Ad libitum feeding in Liver of Cry1,Cry2 KO mice_CT42

status: Public on Nov 12 2009

city: La Jolla

first: Christopher

last: Vollmers

state: CA

address: 10010 North Torrey Pines Road

department: Regulatory Biology Laboratory

institute: The Salk Institute for Biological Studies

description: Food was made available ad libitum for two weeks to Cry1,Cry2 double KO mice. Mice were then released into constant darkness and tissue was collected during the second day of constant darkness

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix scan protocol

data_processing: Data from CEL files were normalized in R using the 'affy' package and the gcRMA algorithm.  Log transformation of values was reversed and all values of a series of arrays were median normalized to 100

source_name: Cry1,Cry2 KO mouse Liver under ad libitum feeding at circadian time 42

label_protocol: Standard Affymetrix protocol

extract_protocol: Trizol extraction followed by Qiagen RNeasy columns

tag: Strain

value: Cry1,Cry2 double KO mice, Gender:female, Age:8-16 weeks, Condition:ad libitum food availability


title: Ad libitum feeding in Liver of Cry1,Cry2 KO mice_CT46

source_name: Cry1,Cry2 KO mouse Liver under ad libitum feeding at circadian time 46


title: SH26 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: Pancreas of E15.5 KO_rep5


title: Pancreas of E15.5 WT_rep3


title: Ad libitum feeding in Liver of Cry1,Cry2 KO mice_CT36

source_name: Cry1,Cry2 KO mouse Liver under ad libitum feeding at circadian time 36

value: Cry1,Cry2 double KO mice, Gender:male, Age:8-16 weeks, Condition:ad libitum food availability


title: Ad libitum feeding in Liver of Cry1,Cry2 KO mice_CT40

source_name: Cry1,Cry2 KO mouse Liver under ad libitum feeding at circadian time 40


title: Ad libitum feeding in Liver of Cry1,Cry2 KO mice_CT38

source_name: Cry1,Cry2 KO mouse Liver under ad libitum feeding at circadian time 38


title: SH24 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: serous tumor (39513)

description: serous tumor (39513)


title: Male Bene Israel Jews South Asia  Indian_Jew_5 Human610-Quad v1.0


title: SH13 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: Ad libitum feeding in Liver of Cry1,Cry2 KO mice_CT34

source_name: Cry1,Cry2 KO mouse Liver under ad libitum feeding at circadian time 34


title: Ad libitum feeding in Liver of Cry1,Cry2 KO mice_CT32

source_name: Cry1,Cry2 KO mouse Liver under ad libitum feeding at circadian time 32


title: SH23 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: Wildtype-mouse-liver-TCDD-rep6

status: Public on Sep 18 2009

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: Manufacturer's protocol.

scan_protocol: Manufacturer's protocol.

data_processing: Array data were loaded into the R statistical environment (v2.8.1) using the affy package (v1.20.2) of the BioConductor open-source library. Array data was investigated for spatial and distributional homogeneity; all arrays were included in subsequent analyses. Liver and kidney data were separately pre-processed using the GCRMA algorithm (Irizarry et al. Nucleic Acids Research 2003 and Wu et al. Jeans Hopkins University Department of Biostatistics Working Papers 2004) as implemented in the gcrma package (v2.14.1) of BioConductor. Array data were associated with updated sequence-annotation using the mouse4302mmentrezg package (v11.0.1), which remaps each probe to a unique Entrez Gene ID (Dai et al. Nucleic Acids Research 2005).

source_name: Wildtype mouse liver, TCDD treated, 19 hours

label_protocol: Manufacturer's protocol.

growth_protocol: Male Ahr–/– mice (15 weeks old) in a C57BL/6J background were obtained from The Jackson Laboratory (Bar Harbor, ME). Wild-type (Ahr+/+) male C57BL/6J mice (15 weeks old) were bred at the National Public Health Institute (Kuopio, Finland) from stock originally obtained from The Jackson Laboratory.

extract_protocol: Liver was harvested 19 h after treatment, sliced, snap-frozen, and stored in liquid nitrogen until homogenization. Total RNA was extracted using RNeasy kits (QIAGEN, Valencia, CA) according to the manufacturer's instructions. DNase (QIAGEN) was added to the RNeasy elution column as recommended by the manufacturer. RNA yield was quantified by UV spectrophotometry, and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Mice were given a single dose of 1000 µg/kg TCDD or corn oil vehicle by gavage. TCDD initially was dissolved in ether and added to corn oil; the ether subsequently was evaporated off. TCDD was purchased from the UFA-Oil Institute (Ufa, Russia) and was >99% pure as determined by gas chromatography-mass spectrometry.

tag: background

value: male

tag: ahr

value: wildtype

value: 15 weeks

tag: treatment

value: TCDD

value: liver


title: Ad libitum feeding in Liver of Cry1,Cry2 KO mice_CT28

source_name: Cry1,Cry2 KO mouse Liver under ad libitum feeding at circadian time 28


title: Wildtype-mouse-liver-CornOil-rep4

source_name: Wildtype mouse liver, corn oil treated, 19 hours

value: Corn oil


title: Ad libitum feeding in Liver of Cry1,Cry2 KO mice_CT26

source_name: Cry1,Cry2 KO mouse Liver under ad libitum feeding at circadian time 26


title: Wildtype-mouse-liver-TCDD-rep5


title: SH25 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: SH12 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: SH25 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: SH33 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: Pancreas of E15.5 KO_rep2


title: Ad libitum feeding in Liver of Cry1,Cry2 KO mice_CT30

source_name: Cry1,Cry2 KO mouse Liver under ad libitum feeding at circadian time 30


title: Wildtype-mouse-liver-CornOil-rep3


title: Ad libitum feeding in Liver of Cry1,Cry2 KO mice_CT24

source_name: Cry1,Cry2 KO mouse Liver under ad libitum feeding at circadian time 24


title: Ad libitum feeding in Liver of Cry1,Cry2 KO mice_CT44

source_name: Cry1,Cry2 KO mouse Liver under ad libitum feeding at circadian time 44


title: Wildtype-mouse-liver-CornOil-rep2


title: Wildtype-mouse-liver-TCDD-rep4


title: Wildtype-mouse-liver-TCDD-rep3


title: AHRnull-mouse-liver-TCDD-rep3

source_name: AHR knockout mouse liver, TCDD treated, 19 hours

value: knockout


title: Wildtype-mouse-liver-CornOil-rep5


title: AHRnull-mouse-liver-CornOil-rep3

source_name: AHR knockout mouse liver, corn oil treated, 19 hours


title: AHRnull-mouse-liver-TCDD-rep2


title: SH28 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array

source_name: Chinese prostate cancer


title: Wildtype-mouse-liver-TCDD-rep2


title: AHRnull-mouse-liver-TCDD-rep1


title: SH9 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: SH11 Chinese normal prostate

description: Hybridized to human SNP 6.0 array

source_name: Chinese normal prostate


title: SH10 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: AHRnull-mouse-liver-CornOil-rep2


title: Wildtype-mouse-liver-CornOil-rep1


title: Wildtype-mouse-kidney-CornOil-rep6

source_name: Wildtype mouse kidney, corn oil treated, 19 hours

extract_protocol: Kidney was harvested 19 h after treatment, sliced, snap-frozen, and stored in liquid nitrogen until homogenization. Total RNA was extracted using RNeasy kits (QIAGEN, Valencia, CA) according to the manufacturer's instructions. DNase (QIAGEN) was added to the RNeasy elution column as recommended by the manufacturer. RNA yield was quantified by UV spectrophotometry, and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: kidney


title: Wildtype-mouse-kidney-TCDD-rep6

source_name: Wildtype mouse kidney, TCDD treated, 19 hours


title: Wildtype-mouse-kidney-TCDD-rep5


title: Wildtype-mouse-liver-TCDD-rep1


title: Wildtype-mouse-kidney-TCDD-rep2


title: Wildtype-mouse-kidney-TCDD-rep3


title: Wildtype-mouse-kidney-TCDD-rep1


title: Wildtype-mouse-kidney-CornOil-rep4


title: Wildtype-mouse-kidney-CornOil-rep1


title: SH11 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: SH10 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: Wildtype-mouse-kidney-CornOil-rep5


title: AHRnull-mouse-kidney-TCDD-rep3

source_name: AHR knockout mouse kidney, TCDD treated, 19 hours


title: Wildtype-mouse-kidney-CornOil-rep2


title: AHRnull-mouse-liver-CornOil-rep1


title: Wildtype-mouse-kidney-CornOil-rep3


title: AHRnull-mouse-kidney-CornOil-rep2

source_name: AHR knockout mouse kidney, corn oil treated, 19 hours


title: AHRnull-mouse-kidney-TCDD-rep1


title: SH23 Chinese prostate cancer

description: Hybridized to human SNP 6.0 array


title: AHRnull-mouse-kidney-CornOil-rep1


title: AHRnull-mouse-kidney-CornOil-rep3


title: AHRnull-mouse-kidney-TCDD-rep2


title: PAO1 in MMP supplemented with glutamate and agmatine by Han Ting Chou

status: Public on Apr 07 2008

city: Atlanta

first: Han Ting

last: Chou

state: GA

address: 1 University Park Drive

department: Biology

institute: Georgia State University

description: wild type PAO1

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0. Chip target intensity is normalized to 500.

organism: Pseudomonas aeruginosa

source_name: Aerobic batch cultures of P. aeruginosa wild type PAO1

label_protocol: standard Affymetrix procedures

growth_protocol: P. aeruginosa PAO1 was grown aerobically in minimal medium P with 350 rpm shaking at 37C.  Cells were harvested when the optical density at 600 nm reached 0.5~0.6 by centrifugation for 5 minutes at 4C.

extract_protocol: Total RNA samples were isolated by RNeasy purification kit following instructions of the manufacturer (Qiagen). Reverse transcription for cDNA synthesis and fragmentation by DNase I treatment were performed according to the instructions of GeneChip manufacturer (Affymetrix).

treatment_protocol: P. aeruginosa PAO1 was grown in minimal medium P in the presence of L-glutamate with the addition of agmatine at 20 mM.

tag: Wild type PAO1 strain cultured in MMP supplemented with glutamate and agmatine by Han Ting Chou


title: PAO1 in MMP supplemented with glutamate by Lu

description: wild type PAO1

treatment_protocol: P. aeruginosa PAO1 was grown in minimal medium P in the presence of L-glutamate at 20 mM.

tag: Wild type PAO1 strain cultured in MMP supplemented with glutamate by Lu


title: PAO1 in MMP supplemented with glutamate and putrescine by Lu

description: wild type PAO1

treatment_protocol: P. aeruginosa PAO1 was grown in minimal medium P in the presence of L-glutamate with the addition of putrescine at 20 mM.

tag: Wild type PAO1 strain cultured in MMP supplemented with glutamate and putrescine by Lu


title: PAO1 in MMP supplemented with glutamate and agmatine by Lu

description: wild type PAO1

tag: Wild type PAO1 strain cultured in MMP supplemented with glutamate and agmatine by Lu


title: SLE myeloid cells 14

status: Public on Mar 01 2008

city: Dallas

first: Laurie

middle: S

last: Davis

address: 5323 Harry Hines Blvd

department: Internal Medicine

institute: UT Southwestern Medical Center

description: Gene expression data from freshly sorted cells

hyb_protocol: Following fragmentation, hybridization was carried out according to the Affymetrix Expression Analysis Technical Manual; only samples passing stringent quality control guidelines were assessed

scan_protocol: Affymetrix arrays were scanned using the Affymetrix GeneChip Scanner 3000 System

data_processing: Data was analyzed with Microarray Suite version 5.0 (MAS 5.0) software using the Affymetrix default analysis settings and global scaling normalization methods.

source_name: Peripheral blood from individuals with systemic lupus erythematosus

label_protocol: Biotinylated cRNA was prepared according to the Affymetrix protocol from at least 5 ug of high quality RNA

extract_protocol: Qiagen Rneasy mini column; only high quality RNA samples as assessed by BioAnalyzer were hybridized to the GeneChips

treatment_protocol: PBMC were isolated, tagged with fluorochrome-conjugated antibodies to CD3, CD4, CD19 and CD33 for 30 min. PBMC were sorted into subsets on a Cytomation MoFlo cytometer into individual subsets. Purity of the populations was confirmed after sorting.

tag: SLE patient


title: PAO1 in MMP supplemented with Glutamate and GABA by Han Ting Chou

description: wild type PAO1

treatment_protocol: P. aeruginosa PAO1 was grown in minimal medium P in the presence of L-glutamate and GABA at 20 mM.

value: Wild type P. aeruginosa PAO1


title: SLE CD4 T cells 14


title: SLE CD19 B cells 12


title: SLE myeloid cells 12


title: SH9 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: SLE CD19 B cells 11


title: SLE CD19 B cells 14


title: SLE CD19 B cells 10


title: SLE CD4 T cells 11


title: SLE CD19 B cells 13


title: SLE myeloid cells 10


title: SLE CD19 B cells 9


title: SLE CD19 B cells 8


title: SLE CD4 T cells 8


title: SLE myeloid cells 8


title: SLE myeloid cells 9


title: SLE CD19 B cells 6


title: SLE myeloid cells 7


title: SLE myeloid cells 6


title: SLE myeloid cells 11


title: SLE CD4 T cells 9


title: SH12 Chinese normal prostate

description: Hybridized to human SNP 6.0 array


title: SLE CD4 T cells 7


title: SLE CD19 B cells 7


title: SLE CD4 T cells 6


title: SLE CD19 B cells 5


title: SLE CD19 B cells 4


title: SLE CD4 T cells 2


title: SLE myeloid cells 3


title: SLE CD19 B cells 3


title: SLE CD4 T cells 5


title: healthy myeloid cells 9

source_name: Peripheral blood from healthy individuals

tag: healthy donor


title: SLE CD4 T cells 10


title: SLE CD4 T cells 3


title: healthy myeloid cells 11


title: SLE myeloid cells 2


title: Wildtype-mouse-kidney-TCDD-rep4

tag: gender


title: PAO1 in MMP supplemented with glutamate and putrescine by Han Ting Chou

description: wild type PAO1

treatment_protocol: P. aeruginosa PAO1 was grown in minimal medium P in the presence of L-glutamate and putrescine at 20 mM.

tag: Wild type PAO1 strain cultured in MMP supplemented with glutamate and putrescine by Han Ting Chou


title: SLE CD4 T cells 1


title: healthy myeloid cells 7


title: healthy CD4 T cells 8


title: SLE myeloid cells 4


title: healthy CD19 B cells 5


title: healthy CD4 T cells 3


title: healthy myeloid cells 10


title: healthy CD19 B cells 8


title: healthy myeloid cells 6


title: SLE CD4 T cells 4


title: healthy myeloid cells 5


title: healthy CD4 T cells 6


title: healthy myeloid cells 3


title: SLE CD19 B cells 1


title: healthy CD19 B cells 3


title: healthy CD19 B cells 7


title: healthy CD19 B cells 4


title: healthy CD4 T cells 5


title: SLE CD19 B cells 2


title: healthy myeloid cells 8


title: healthy CD19 B cells 9


title: healthy CD19 B cells 6


title: healthy CD4 T cells 9


title: healthy CD4 T cells 4


title: SLE CD4 T cells 12


title: healthy CD4 T cells 7


title: healthy CD19 B cells 1


title: healthy myeloid cells 4


title: healthy CD4 T cells 2


title: healthy myeloid cells 1


title: healthy CD4 T cells 1


title: healthy CD19 B cells 2


title: KIT_82A83 (HG-U133B)

status: Public on Mar 01 2007

first: Benjamin

last: Haibe-Kains

address: 610 University Avenue

department: Princess Margaret Research

institute: Princess Margaret Cancer Centre

description: Tumor samples from tamoxifen treated primary breast cancer patients.

data_processing: RMA Bioconductor

source_name: breast

label_protocol: Approximately 1 microgram of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Isolation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturers instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc)olation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturers instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc)

tag: samplename

tag: ID

tag: series

value: KIT

tag: grade

tag: size

tag: er

tag: pgr

tag: node


title: KIT_41C65 (HG-U133B)

tag: age


title: KIT_7B96 (HG-U133B)


title: KIT_6B85 (HG-U133B)


title: KIT_85A03 (HG-U133B)


title: KIT_64A59 (HG-U133B)


title: KIT_56A94 (HG-U133B)


title: KIT_71A50 (HG-U133B)


title: KIT_63A62 (HG-U133B)


title: KIT_96A21 (HG-U133B)


title: KIT_69A93 (HG-U133B)


title: KIT_53A06 (HG-U133B)


title: KIT_84A44 (HG-U133B)


title: KIT_46A25 (HG-U133B)


title: KIT_311A27 (HG-U133B)


title: KIT_79A35 (HG-U133B)


title: KIT_76A44 (HG-U133B)


title: KIT_48A46 (HG-U133B)


title: KIT_72A92 (HG-U133B)


title: KIT_77A50 (HG-U133B)


title: KIT_67A43 (HG-U133B)


title: KIT_313A87 (HG-U133B)


title: KIT_307C50 (HG-U133B)


title: KIT_51A98 (HG-U133B)


title: KIT_40C57 (HG-U133B)


title: KIT_35C29 (HG-U133B)


title: KIT_301C66 (HG-U133B)


title: KIT_55A79 (HG-U133B)


title: KIT_8B87 (HG-U133B)


title: KIT_256C45 (HG-U133B)


title: KIT_39C24 (HG-U133B)


title: KIT_298C47 (HG-U133B)


title: KIT_271C71 (HG-U133B)


title: KIT_289C75 (HG-U133B)


title: KIT_230C47 (HG-U133B)


title: KIT_288C57 (HG-U133B)


title: KIT_239C32 (HG-U133B)


title: KIT_191B79 (HG-U133B)


title: KIT_216C61 (HG-U133B)


title: KIT_238C87 (HG-U133B)


title: KIT_291C17 (HG-U133B)


title: KIT_27C82 (HG-U133B)


title: KIT_189B83 (HG-U133B)


title: KIT_203B49 (HG-U133B)


title: KIT_183B75 (HG-U133B)


title: KIT_194B60 (HG-U133B)


title: KIT_193B72 (HG-U133B)


title: KIT_245C22 (HG-U133B)


title: KIT_17C40 (HG-U133B)


title: KIT_252C64 (HG-U133B)


title: KIT_244C89 (HG-U133B)


title: KIT_202B44 (HG-U133B)


title: KIT_254C80 (HG-U133B)


title: KIT_207C08 (HG-U133B)


title: KIT_235C20 (HG-U133B)


title: KIT_186B22 (HG-U133B)


title: KIT_225C52 (HG-U133B)


title: KIT_212C21 (HG-U133B)


title: KIT_171B77 (HG-U133B)


title: KIT_170B15 (HG-U133B)


title: KIT_173B43 (HG-U133B)


title: KIT_169B79 (HG-U133B)


title: KIT_154B42 (HG-U133B)


title: KIT_162B98 (HG-U133B)


title: KIT_166B79 (HG-U133B)


title: KIT_138B34 (HG-U133B)


title: KIT_148B49 (HG-U133B)


title: KIT_159B47 (HG-U133B)


title: KIT_135B40 (HG-U133B)


title: KIT_150B81 (HG-U133B)


title: KIT_165B72 (HG-U133B)


title: KIT_103B41 (HG-U133B)


title: KIT_131B79 (HG-U133B)


title: KIT_139B03 (HG-U133B)


title: KIT_112B55 (HG-U133B)


title: KIT_14B98 (HG-U133B)


title: OXFT_894 (HG-U133B)

value: OXFT


title: OXFT_890 (HG-U133B)


title: OXFT_944 (HG-U133B)


title: OXFT_887 (HG-U133B)


title: KIT_147B19 (HG-U133B)


title: KIT_15C94 (HG-U133B)


title: KIT_104B91 (HG-U133B)


title: OXFT_837 (HG-U133B)


title: KIT_114B68 (HG-U133B)


title: OXFT_876 (HG-U133B)


title: KIT_130B92 (HG-U133B)


title: OXFT_928 (HG-U133B)


title: OXFT_848 (HG-U133B)


title: OXFT_913 (HG-U133B)


title: OXFT_829 (HG-U133B)


title: OXFT_779 (HG-U133B)


title: OXFT_849 (HG-U133B)


title: OXFT_742 (HG-U133B)


title: OXFT_738 (HG-U133B)


title: OXFT_771 (HG-U133B)


title: OXFT_711 (HG-U133B)


title: OXFT_676 (HG-U133B)


title: OXFT_729 (HG-U133B)


title: OXFT_680 (HG-U133B)


title: OXFT_638 (HG-U133B)


title: OXFT_706 (HG-U133B)


title: OXFT_669 (HG-U133B)


title: OXFT_705 (HG-U133B)


title: OXFT_736 (HG-U133B)


title: OXFT_697 (HG-U133B)


title: OXFT_550 (HG-U133B)


title: OXFT_619 (HG-U133B)


title: OXFT_630 (HG-U133B)


title: OXFT_555 (HG-U133B)


title: OXFT_588 (HG-U133B)


title: OXFT_511 (HG-U133B)


title: OXFT_429 (HG-U133B)


title: OXFT_380 (HG-U133B)


title: OXFT_412 (HG-U133B)


title: OXFT_5210 (HG-U133B)


title: OXFT_443 (HG-U133B)


title: OXFT_3597 (HG-U133B)


title: OXFT_5428 (HG-U133B)


title: OXFT_55 (HG-U133B)


title: OXFT_427 (HG-U133B)


title: OXFT_4904 (HG-U133B)


title: OXFT_596 (HG-U133B)


title: OXFT_375 (HG-U133B)


title: OXFT_2340 (HG-U133B)


title: OXFT_2341 (HG-U133B)


title: OXFT_700 (HG-U133B)


title: OXFT_2227 (HG-U133B)


title: OXFT_2190 (HG-U133B)


title: OXFT_2338 (HG-U133B)


title: OXFT_2175 (HG-U133B)


title: OXFT_2188 (HG-U133B)


title: OXFT_595 (HG-U133B)


title: OXFT_2092 (HG-U133B)


title: OXFT_1982 (HG-U133B)


title: OXFT_2069 (HG-U133B)


title: OXFT_2221 (HG-U133B)


title: OXFT_209 (HG-U133B)


title: OXFT_2027 (HG-U133B)


title: OXFT_192 (HG-U133B)


title: OXFT_2005 (HG-U133B)


title: OXFT_1821 (HG-U133B)


title: OXFT_2093 (HG-U133B)


title: OXFT_2002 (HG-U133B)


title: OXFT_1902 (HG-U133B)


title: OXFT_1981 (HG-U133B)


title: OXFT_2220 (HG-U133B)


title: OXFT_1301 (HG-U133B)


title: OXFT_1800 (HG-U133B)


title: OXFT_1525 (HG-U133B)


title: OXFT_2152 (HG-U133B)


title: OXFT_1770 (HG-U133B)


title: OXFT_1397 (HG-U133B)


title: OXFT_1320 (HG-U133B)


title: OXFT_1441 (HG-U133B)


title: OXFT_1766 (HG-U133B)


title: OXFT_1889 (HG-U133B)


title: OXFT_1769 (HG-U133B)


title: OXFT_1432 (HG-U133B)


title: OXFT_1939 (HG-U133B)


title: OXFT_1804 (HG-U133B)


title: OXFT_1962 (HG-U133B)


title: OXFT_2057 (HG-U133B)


title: OXFT_124 (HG-U133B)


title: OXFT_1662 (HG-U133B)


title: OXFT_1342 (HG-U133B)


title: OXFT_1818 (HG-U133B)


title: OXFT_1331 (HG-U133B)


title: OXFT_1200 (HG-U133B)


title: OXFT_1579 (HG-U133B)


title: OXFT_1193 (HG-U133B)


title: OXFT_1177 (HG-U133B)


title: OXFT_116 (HG-U133B)


title: OXFT_1142 (HG-U133B)


title: OXFT_1097 (HG-U133B)


title: OXFT_1168 (HG-U133B)


title: OXFT_1103 (HG-U133B)


title: OXFT_1167 (HG-U133B)


title: OXFT_1127 (HG-U133B)


title: OXFT_1181 (HG-U133B)


title: OXFT_1157 (HG-U133B)


title: OXFT_1125 (HG-U133B)


title: OXFT_1089 (HG-U133B)


title: OXFT_114 (HG-U133B)


title: OXFT_1173 (HG-U133B)


title: OXFT_1156 (HG-U133B)


title: OXFT_1120 (HG-U133B)


title: OXFT_1107 (HG-U133B)


title: OXFT_1070 (HG-U133B)


title: KIU_87A79 (HG-U133B)

description: Tumor samples from untreated primary breast cancer patients.

value: KIU


title: KIU_43C47 (HG-U133B)


title: KIU_89A64 (HG-U133B)


title: KIU_42C67 (HG-U133B)


title: KIU_38C94 (HG-U133B)


title: KIU_74A63 (HG-U133B)


title: KIU_86A40 (HG-U133B)


title: KIU_5B97 (HG-U133B)


title: KIU_88A67 (HG-U133B)


title: KIU_292C66 (HG-U133B)


title: KIU_52A90 (HG-U133B)


title: KIU_314B55 (HG-U133B)


title: KIU_284C63 (HG-U133B)


title: KIU_36C17 (HG-U133B)


title: KIU_279C61 (HG-U133B)


title: KIU_304C89 (HG-U133B)


title: KIU_65A68 (HG-U133B)


title: KIU_28C76 (HG-U133B)


title: KIU_280C43 (HG-U133B)


title: KIU_308C93 (HG-U133B)


title: KIU_303C36 (HG-U133B)


title: KIU_286C91 (HG-U133B)


title: KIU_309C49 (HG-U133B)


title: KIU_316C64 (HG-U133B)


title: KIU_266C51 (HG-U133B)


title: KIU_282C51 (HG-U133B)


title: KIU_272C88 (HG-U133B)


title: KIU_268C87 (HG-U133B)


title: KIU_248C91 (HG-U133B)


title: KIU_243C70 (HG-U133B)


title: KIU_247C76 (HG-U133B)


title: KIU_227C50 (HG-U133B)


title: KIU_229C44 (HG-U133B)


title: KIU_259C74 (HG-U133B)


title: KIU_197B95 (HG-U133B)


title: KIU_233C91 (HG-U133B)


title: KIU_260C91 (HG-U133B)


title: KIU_196B81 (HG-U133B)


title: KIU_151B84 (HG-U133B)


title: KIU_144B49 (HG-U133B)


title: KIU_172B19 (HG-U133B)


title: KIU_199B55 (HG-U133B)


title: KIU_205B99 (HG-U133B)


title: KIU_214C35 (HG-U133B)


title: KIU_140B91 (HG-U133B)


title: KIU_184B38 (HG-U133B)


title: KIU_231C80 (HG-U133B)


title: KIU_220C70 (HG-U133B)


title: KIU_164B81 (HG-U133B)


title: KIU_24C30 (HG-U133B)


title: KIU_177B67 (HG-U133B)


title: KIU_242C21 (HG-U133B)


title: KIU_155B52 (HG-U133B)


title: KIU_163B27 (HG-U133B)


title: KIU_219C42 (HG-U133B)


title: KIU_188B13 (HG-U133B)


title: KIU_136B04 (HG-U133B)


title: KIU_120B73 (HG-U133B)


title: OXFU_93 (HG-U133B)

value: OXFU


title: KIU_124B25 (HG-U133B)


title: KIU_101B88 (HG-U133B)


title: OXFU_662 (HG-U133B)


title: KIU_111B51 (HG-U133B)


title: KIU_134B33 (HG-U133B)


title: KIU_127B00 (HG-U133B)


title: OXFU_885 (HG-U133B)


title: OXFU_557 (HG-U133B)


title: KIU_125B43 (HG-U133B)


title: KIU_105B13 (HG-U133B)


title: KIU_106B55 (HG-U133B)


title: KIU_113B11 (HG-U133B)


title: OXFU_869 (HG-U133B)


title: OXFU_88 (HG-U133B)


title: OXFU_90 (HG-U133B)


title: OXFU_598 (HG-U133B)


title: OXFU_547 (HG-U133B)


title: OXFU_559 (HG-U133B)


title: OXFU_573 (HG-U133B)


title: OXFU_57 (HG-U133B)


title: OXFU_543 (HG-U133B)


title: OXFU_53 (HG-U133B)


title: OXFU_549 (HG-U133B)


title: OXFU_608 (HG-U133B)


title: OXFU_535 (HG-U133B)


title: OXFU_544 (HG-U133B)


title: OXFU_530 (HG-U133B)


title: OXFU_533 (HG-U133B)


title: OXFU_522 (HG-U133B)


title: OXFU_484 (HG-U133B)


title: OXFU_489 (HG-U133B)


title: OXFU_531 (HG-U133B)


title: OXFU_471 (HG-U133B)


title: OXFU_513 (HG-U133B)


title: OXFU_485 (HG-U133B)


title: OXFU_37 (HG-U133B)


title: KIU_278C80 (HG-U133B)


title: OXFU_476 (HG-U133B)


title: OXFU_382 (HG-U133B)


title: OXFU_449 (HG-U133B)


title: OXFU_491 (HG-U133B)


title: OXFU_419 (HG-U133B)


title: OXFU_348 (HG-U133B)


title: OXFU_360 (HG-U133B)


title: OXFU_373 (HG-U133B)


title: OXFU_320 (HG-U133B)


title: OXFU_316 (HG-U133B)


title: OXFU_247 (HG-U133B)


title: OXFU_337 (HG-U133B)


title: OXFU_281 (HG-U133B)


title: OXFU_366 (HG-U133B)


title: OXFU_446 (HG-U133B)


title: OXFU_359 (HG-U133B)


title: OXFU_397 (HG-U133B)


title: OXFU_254 (HG-U133B)


title: OXFU_220 (HG-U133B)


title: OXFU_138 (HG-U133B)


title: OXFU_157 (HG-U133B)


title: OXFU_16 (HG-U133B)


title: OXFU_245 (HG-U133B)


title: OXFU_145 (HG-U133B)


title: OXFU_1373 (HG-U133B)


title: OXFU_217 (HG-U133B)


title: OXFU_23 (HG-U133B)


title: OXFU_1415 (HG-U133B)


title: OXFT_1133 (HG-U133B)


title: OXFU_1328 (HG-U133B)


title: OXFU_1286 (HG-U133B)


title: OXFU_1210 (HG-U133B)


title: OXFU_1065 (HG-U133B)


title: OXFU_126 (HG-U133B)


title: OXFU_127 (HG-U133B)


title: OXFU_223 (HG-U133B)


title: OXFU_104 (HG-U133B)


title: OXFU_12 (HG-U133B)


title: OXFU_1248 (HG-U133B)


title: OXFU_1183 (HG-U133B)


title: J1 EB 6 hr 3, chip MOE430A

status: Public on Dec 06 2005

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E201
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201
SCGP Sample ID:				S243
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201#SAMPLE_210
Short description:			6 hours of an 11-point time course study on differentiating embryoid bodies from a murine J1 embryonic stem cell line. The time course includes 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 4 days, 7 days, 9 days and 14 days.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Undetermined
Sample volume:				15 uL

data_processing: Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpla2=0.06

source_name: J1, Fetal cells

growth_protocol:
Growth medium:				ES Cell Medium - DMEM (high glucose)
Media supplements:			Hyclone FCS, non-essential amino acids, Glutamax, Penicillin/Streptomycin, sodium pyruvate, beta-mercaptoethanol
Culture conditions:			37 C, 5% CO2

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			Culturing
Contaminating cell type:			None
Method for estimating purity:		By eye

treatment_protocol: Assays to confirm viability:		Stratagene mycoplasma PCR test

tag: Strain:					129/Sv

tag: Gender:					Male


title: J1 EB 6 hr 1, chip MOE430A


title: J1 EB 6 hr 2, chip MOE430A


title: Family10_TE3

status: Public on Mar 31 2006

first: Helen

middle: Rose

last: Jensen

address: 30 Marie-Curie street

department: Ottawa-Carleton Institute of Biology

institute: University of Ottawa

description: A hybridization with reversed fluorescent labeling of identical biological samples.  This hybridization compared gene expression profiles of Drosophila treated with an insecticidal extract of Piper nigrum seeds to a control group of Drosophila treated with the carrier solvent ethanol.

hyb_protocol: Hybridization protocol as specified in Neal et al. (2003), Genome 46: 879-892. 80 μg of total RNA from the control and treated samples were hybridized.

scan_protocol: Scan protocol using the ScanArray 4000 XL (GSI Lumonics/Packard Biochips) as specified in Neal et al. (2003), Genome 46: 879-892.

data_processing: Quantarray Microarray Analysis Software version 3.0 (Packard BioScience, copyright 2001) was used to quantify image data. Spot and background intensity were measured using the adaptive circle quantification method. Gene TrafficTM Duo, version 2.8 (Iobion Informatics, copyright 2002) was used for further analysis. Data normalization was performed on background subtracted spots on a subgrid basis using the Locally Weighted Scatter Plot Smoother (LOWESS) algorithm with a smoothing factor of 20. Spots with intensity values less than 100 units and spots with intensity values below the average background intensity value and/or below the local background intensity value were excluded from normalization and analysis. Data was filtered so as to exclude all genes with less than two-thirds of spots being usable as defined by quality filters and by a mean differential expression ratio with a coefficient of variance higher than 100%.

organism: Drosophila melanogaster

label_protocol: 80 μg of total RNA was labeled using the direct labeling protocol as specified in Neal et al. (2003), Genome 46: 879-892.

extract_protocol: Total RNA from approximately 240 adult female Drosophila was isolated using the acid guanidium thiocyanate-phenol-choloroform extraction method (Chomczynski and Sacchi, 1987). Samples were homogenized in 200 μL of solution D using a Kontes pestle and further homogenized with 3 short sonicator pulses after adding an additional 800 μL of solution D. Insoluble material was removed from samples by centrifuging at 16 000 x g for 3 minutes and transferring the supernatant to new microtubes. Three washes with cold 80% EtOH were performed to ensure the removal of red coloured eye pigments and organic contaminants from the RNA pellet. RNA samples with (A260/A280) values between 1.8 and 2.0 were considered suitable for microarray analysis.

treatment_protocol: Treatment: 2 mL of 99% ethanol

tag: Strain

value: Oregon-R

tag: Sex

value: Female

tag: Age

value: 4-10 days (after adult emergence)

tag: Temperature:23 degrees Celsius

tag: Relative Humidity

tag: Label type

value: Reverse

treatment_protocol: Treatment: 2 mL of 0.2 mg/mL Piper nigrum seed ethylacetate extract formulated in 99% ethanol


title: Family10_TE4

treatment_protocol:
Treatment: 2 mL of 99% ethanol
Type: topical mist application using a Potter's tower
Time elapsed between application and sampling: 6 hours

treatment_protocol:
Treatment: 2 mL of 0.2 mg/mL Piper nigrum seed ethylacetate extract formulated in 99% ethanol
Type: topical mist application using a Potter's tower
Time elapsed between application and sampling: 6 hours


title: CPGSC#23, chip MOE430A

status: Public on Sep 01 2005

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S154
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_114
Short description:			6 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.3 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				30 ul

source_name: V6.5 (P18), Embryonic

growth_protocol:
Growth medium:				ES Cell Medium - DMEM(high glucose)
Media supplements:			Hyclone FCS (heat inactivated), non-essential amino acids, Glutamax, Penicillin/Streptomycin, beta-mercaptoethanol
Culture conditions:			37 C, 5% CO2

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			Cultured
Contaminating cell type:			none

tag: Strain:					129SV x C57Bl/6


title: CPGSC#25, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S154
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_114
Short description:			6 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			1.45 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15 ul


title: OXFU_1605 (HG-U133B)

tag: samplename

tag: ID


title: R1 EB 7d 2, chip MOE430A

status: Public on Jul 22 2005

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S215
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_173
Short description:			7 days of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15.0 uL

source_name: R1, Fetal cells

growth_protocol:
Growth medium:				ES Cell Medium - DMEM (high glucose)
Media supplements:			Hyclone FCS (heat inactivated), non-essential amino acids, Glutamax, Penicillin/Streptomycin, sodium pyruvate, beta-mercaptoethanol
Culture conditions:			37 C, 5% CO2

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			Culturing
Contaminating cell type:			none

tag: Strain:					129/Sv x 129/Sv-CP


title: R1 EB 9d 3, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S216
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_174
Short description:			9 days of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15.0 uL


title: R1 EB 4d 1, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S213
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_172
Short description:			4 days of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15.0 uL


title: R1 EB 14d 1, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S217
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_175
Short description:			14 days of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15.0 uL


title: R1 EB 14d 3, chip MOE430A


title: R1 EB 24h 2, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S210
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_169
Short description:			24 hours of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15.0 uL


title: R1 EB 48h 2, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S212
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_171
Short description:			48 hours of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15.0 uL


title: CPGSC#24, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S154
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_114
Short description:			6 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.5 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15 ul


title: R1 EB 9d 2, chip MOE430A


title: R1 EB 36h 3, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S211
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_170
Short description:			36 hours of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15.0 uL


title: R1 EB 4d 2, chip MOE430A


title: R1 EB 36h 2, chip MOE430A


title: R1 EB 14d 2, chip MOE430A


title: R1 EB 7d 3, chip MOE430A


title: R1 EB 36h 1, chip MOE430A


title: R1 EB 24h 3, chip MOE430A


title: R1 EB 48h 1, chip MOE430A


title: R1 EB 7d 1, chip MOE430A


title: R1 EB 48h 3, chip MOE430A


title: R1 EB 9d 1, chip MOE430A


title: R1 EB 18h 2, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S209
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_168
Short description:			18 hours of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15.0 uL


title: R1 EB 18h 1, chip MOE430A


title: OXFU_181 (HG-U133B)

tag: series

tag: grade

tag: size


title: R1 EB 18h 3, chip MOE430A


title: R1 EB 12h 3, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S208
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_167
Short description:			12 hours of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15 uL


title: R1 EB 6h 2, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S207
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_166
Short description:			6 hours of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15 uL


title: R1 EB 6h 1, chip MOE430A


title: R1 EB 6h 3, chip MOE430A


title: R1 ES 0h 3, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S206
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_165
Short description:			0 hours of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryoid bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15.0 uL

growth_protocol:
Growth medium:				ES Cell Medium - DMEM (high glucose)
Media supplements:			Hyclone FCS (heat inactivated), non-essential amino acids, Glutamax, Penicillin/Streptomycin, sodium pyruvate, beta-mercaptoethanol, LIF
Culture conditions:			37 C, 5% CO2

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			Culturing
Contaminating cell type:			None


title: R1 ES 0h 2, chip MOE430A


title: R1 EB 24h 1, chip MOE430A


title: R1 ES 0h 1, chip MOE430A


title: R1 EB 12h 1, chip MOE430A


title: R1 EB 4d 3, chip MOE430A


title: R1 EB 12h 2, chip MOE430A