title: DFL 12 wild-type vs. delta-luxI1 pDP1 OD600 0.2 Rep 2

status: Public on Nov 03 2012

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

description: wild-type compared with delta-luxI1 pDP1 overexpressing the luxI1 gene exponential growth phase

hyb_protocol: Hybridization was performerd according to the Agilent two-color microarray protocol

scan_protocol: Microarays were scanned using the Agilent DNA microarray scanner. Raw data was collected using the Agilent feature extraction software v10.7.

data_processing: Median values of Cy3 and Cy5 channel were processed in the R environment using the limma package. Backround correction was performed using the normexp method, Cy3 and Cy5 channels were loess normalized, Quantil-normalization was used for seperate microarrays.

organism: Dinoroseobacter shibae DFL 12 = DSM 16493

source_name: wild-type OD600 0.2

label_protocol: total RNA was labelled using the Universal Linker System (Kreatech) according to the manufacturers  protocol

growth_protocol: DFL 12 was grown in a defined minimal medium with succinate as sole carbon source. Growth temperature was 30°C, cells were kept in the dark

extract_protocol: Samples were collected in RNAprotect (Qiagen). RNA was extracted using the Rneasy Mini kit (Qiagen) with on column DNA digestion according to the manufacturers protocol followed by a second DNA digestion step in solution using DnaseI (Quiagen) and RNA purification using the RNeasy mini kit.

treatment_protocol: no special treatment

tag: strain

value: wild-type

tag: growth phase (od600)

source_name: delta-luxI1 pDP1 OD600 0.2

value: delta-luxI1 pDP1


title: DFL 12 wild-type vs. delta-luxI1 pDP1 OD600 0.8 Rep 2

type: RNA

molecule: total RNA

source_name: wild-type OD600 0.8

source_name: delta-luxI1 pDP1 OD600 0.8


title: DFL 12 wild-type vs. delta-luxI1 pDP1 OD600 0.6 Rep 2

source_name: wild-type OD600 0.6

source_name: delta-luxI1 pDP1 OD600 0.6


title: DFL 12 wild-type vs. delta-luxI1 pDP1 stationary Rep 2

description: wild-type compared with delta-luxI1 pDP1 overexpressing the luxI1 gene stationary phase

source_name: wild-type stationary

value: stationary

source_name: delta-luxI1 pDP1 stationary


title: DFL 12 wild-type vs. delta-luxI1 pDP1 stationary Rep 1


title: DFL 12 wild-type vs. delta-luxI1 pDP1 OD600 0.8 Rep 1


title: DFL 12 wild-type vs. delta-luxI1 pDP1 OD600 0.1 Rep 1

source_name: wild-type OD600 0.1

source_name: delta-luxI1 pDP1 OD600 0.1


title: DFL 12 wild-type vs. delta-luxI1 pDP1 OD600 0.4 Rep 2

source_name: wild-type OD600 0.4

source_name: delta-luxI1 pDP1 OD600 0.4


title: DFL 12 wild-type vs. delta-luxI1 pDP1 OD600 0.4 Rep 1


title: DFL 12 wild-type vs. delta-luxI1 pDP1 OD600 0.1 Rep 2


title: DFL 12 wild-type vs. delta-luxI1 pDP1 OD600 0.2 Rep 1


title: DFL 12 wild-type vs. delta-luxI1 OD600 0.2 Rep 1

description: wild-type compared with quorum sensing null mutant exponential growth phase

source_name: delta-luxI1 OD600 0.2


title: DFL 12 wild-type vs. delta-luxI1 OD600 0.6 Rep 2

source_name: delta-luxI1 OD600 0.6


title: DFL 12 wild-type vs. delta-luxI1 OD600 0.1 Rep 2

source_name: delta-luxI1 OD600 0.1


title: DFL 12 delta-luxI1 vs. delta-luxI1 + C18-HSL OD600 0.4

source_name: delta-luxI1 OD600 0.4

treatment_protocol: DFL 12 delta-luxI1 was supplemented with 500 nM AHL at cultivation start

tag: treatment

source_name: delta-luxI1 + C18-HSL OD600 0.4


title: DFL 12 wild-type vs. delta-luxI1 OD600 0.8 Rep 1

source_name: delta-luxI1 OD600 0.8


title: DFL 12 wild-type vs. delta-luxI1 OD600 0.4 Rep 1


title: DFL 12 wild-type vs. delta-luxI1 OD600 0.2 Rep 2

source_name: wild-type OD600 0.2


title: DFL 12 wild-type vs. delta-luxI1 stationary Rep 1

description: wild-type compared with quorum sensing null mutant stationary phase

source_name: delta-luxI1 stationary


title: DFL 12 wild-type vs. delta-luxI1 stationary Rep 2


title: DFL 12 wild-type vs. delta-luxI1 OD600 0.4 Rep 2


title: DFL 12 wild-type vs. delta-luxI1 OD600 0.8 Rep 2

source_name: wild-type OD600 0.8


title: gastric cancer tissue sample 64

status: Public on Nov 05 2012

type: genomic

city: San Francisco

first: Xin

last: Chen

state: CA

country: USA

institute: UCSF

hyb_protocol: The hybridization solution was denatured for 10 min at 72°C and then incubated for 1 h at 37°C. Hybridization was performed for 48-72 h in a moist chamber on a slow rocking table. Next, Arrays were washed for 10 min in 50% formamide and 2 × SSC at 45°C, and 10 min in phosphate buffer at room temperature. Slides were mounted in mounting solutions containing 0.3 microgram/ml DAPI.

scan_protocol: Three single-color intensity images (DAPI, Cy3 and Cy5) were collected for each array using a charge coupled device camera.

data_processing: The UCSF SPOT software [PMID: 11827952] was used to automatically segment the spots based on the DAPI images, perform local background correction and calculate various measurement parameters, including log2 ratios of the total integrated Cy3 and Cy5 intensities for each spot.

molecule: genomic DNA

organism: Homo sapiens

label_protocol: For hybridization, 1 microgram of tumor DNA and 1 microgram of gender matched reference DNA was labeled by random priming using Cy3-dCTP and Cy5- dCTP, respectively, using Bioprime Kit (Invitrogen).

extract_protocol: Genomic DNA was extracted using the Genomic DNA purification Kit (Qiagen, Valencia, CA).

tag: tissue

value: gastric cancer tissue sample 64

source_name: Three mixed normal blood sample

tag: reference

value: Three mixed normal blood sample


title: DFL 12 wild-type vs. delta-luxI1 pDP1 OD600 0.6 Rep 1

source_name: wild-type OD600 0.6

source_name: delta-luxI1 pDP1 OD600 0.6


title: DFL 12 wild-type vs. delta-luxI1 OD600 0.6 Rep 1


title: DFL 12  delta-luxI1 + C18dien-HSL vs. wild-type OD600 0.4

source_name: delta-luxI1 + C18dien-HSL OD600 0.4


title: DFL 12 delta-luxI1 + C18-HSL vs. delta-luxI1 + C18en-HSL OD600 0.4

source_name: delta-luxI1 + C18en-HSL OD600 0.4


title: DFL 12 delta-luxI1 + C18en-HSL vs. delta-luxI1 + C18dien-HSL OD600 0.4

source_name: delta-luxI1 + C18en-HSLOD600 0.4


title: DFL 12 wild-type vs. delta-luxI1 OD600 0.1 Rep 1

source_name: wild-type OD600 0.1


title: DFL 12 delta-luxI1 vs. delta-luxI1 + C18dien-HSL OD600 0.4

source_name: delta-luxI1 + C18di-HSL OD600 0.4


title: rs1360780 AA/AG trauma subject 129

city: Munich

first: Divya

last: Mehta

country: Germany

institute: MPI

description: AA/AG

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Microarray expression analysis was performed in R, using beadarray (providing routines to handle Illumina BeadStudio data) , limma (for statistical routines) and vsn (for normalization) packages. Raw microarray scan files were exported using the Illumina Beadstudio program and loaded into R for downstream analysis. The data were transformed and normalized using the variance stabilizing normalization method.

label: biotin

source_name: whole blood

label_protocol: standard Illumina protocol

extract_protocol: TempusTM Spin RNA Isolation Kit

tag: genotype

tag: condition

value: trauma

value: whole blood


title: DFL 12 wild-type vs. delta-luxI1 OD600 0.4

source_name: wild-type OD600 0.4


title: rs1360780 AA/AG control subject 128

description: AA/AG

value: control


title: rs1360780 AA/AG control subject 127

description: AA/AG


title: rs1360780 AA/AG control subject 123

description: AA/AG


title: rs1360780 AA/AG trauma subject 124

description: AA/AG


title: rs1360780 GG trauma subject 122

description: GG


title: rs1360780 AA/AG control subject 125

description: AA/AG


title: rs1360780 AA/AG control subject 121

description: AA/AG


title: rs1360780 GG trauma subject 126

description: GG


title: rs1360780 AA/AG trauma subject 120

description: AA/AG


title: rs1360780 GG trauma subject 119

description: GG


title: rs1360780 AA/AG trauma subject 117

description: AA/AG


title: rs1360780 GG control subject 118

description: GG


title: rs1360780 AA/AG control subject 114

description: AA/AG


title: rs1360780 AA/AG trauma subject 112

description: AA/AG


title: rs1360780 AA/AG trauma subject 116

description: AA/AG


title: rs1360780 GG trauma subject 113

description: GG


title: rs1360780 AA/AG trauma subject 115

description: AA/AG


title: rs1360780 AA/AG control subject 111

description: AA/AG


title: rs1360780 AA/AG control subject 110

description: AA/AG


title: rs1360780 AA/AG trauma subject 108

description: AA/AG


title: rs1360780 GG control subject 107

description: GG


title: rs1360780 AA/AG control subject 96

description: AA/AG


title: rs1360780 AA/AG control subject 104

description: AA/AG


title: rs1360780 AA/AG trauma subject 90

description: AA/AG


title: rs1360780 GG trauma subject 100

description: GG


title: rs1360780 GG trauma subject 105

description: GG


title: rs1360780 AA/AG trauma subject 109

description: AA/AG


title: rs1360780 AA/AG control subject 106

description: AA/AG


title: rs1360780 AA/AG control subject 88

description: AA/AG


title: rs1360780 AA/AG control subject 89

description: AA/AG


title: rs1360780 AA/AG control subject 94

description: AA/AG


title: rs1360780 GG control subject 98

description: GG


title: rs1360780 AA/AG control subject 102

description: AA/AG


title: rs1360780 AA/AG control subject 87

description: AA/AG


title: rs1360780 GG trauma subject 85

description: GG


title: rs1360780 AA/AG trauma subject 101

description: AA/AG


title: rs1360780 AA/AG control subject 86

description: AA/AG


title: rs1360780 AA/AG trauma subject 99

description: AA/AG


title: rs1360780 GG control subject 95

description: GG


title: rs1360780 AA/AG control subject 84

description: AA/AG


title: rs1360780 AA/AG control subject 91

description: AA/AG


title: rs1360780 AA/AG control subject 97

description: AA/AG


title: rs1360780 AA/AG control subject 92

description: AA/AG


title: rs1360780 AA/AG trauma subject 82

description: AA/AG


title: rs1360780 AA/AG trauma subject 83

description: AA/AG


title: rs1360780 AA/AG trauma subject 71

description: AA/AG


title: rs1360780 GG trauma subject 93

description: GG


title: rs1360780 AA/AG control subject 70

description: AA/AG


title: rs1360780 GG trauma subject 72

description: GG


title: rs1360780 AA/AG trauma subject 73

description: AA/AG


title: rs1360780 AA/AG control subject 77

description: AA/AG


title: rs1360780 AA/AG trauma subject 81

description: AA/AG


title: rs1360780 AA/AG control subject 79

description: AA/AG


title: rs1360780 GG control subject 80

description: GG


title: rs1360780 AA/AG control subject 75

description: AA/AG


title: rs1360780 GG trauma subject 74

description: GG


title: rs1360780 AA/AG trauma subject 78

description: AA/AG


title: rs1360780 GG trauma subject 67

description: GG


title: rs1360780 AA/AG control subject 103

description: AA/AG


title: rs1360780 AA/AG trauma subject 69

description: AA/AG


title: rs1360780 AA/AG control subject 61

description: AA/AG


title: rs1360780 AA/AG control subject 65

description: AA/AG


title: rs1360780 AA/AG trauma subject 66

description: AA/AG


title: rs1360780 AA/AG control subject 63

description: AA/AG


title: rs1360780 AA/AG control subject 58

description: AA/AG


title: rs1360780 AA/AG control subject 64

description: AA/AG


title: rs1360780 AA/AG control subject 76

description: AA/AG


title: rs1360780 AA/AG control subject 56

description: AA/AG


title: rs1360780 AA/AG trauma subject 62

description: AA/AG


title: rs1360780 GG control subject 68

description: GG


title: rs1360780 AA/AG control subject 60

description: AA/AG


title: rs1360780 AA/AG control subject 57

description: AA/AG


title: rs1360780 AA/AG control subject 59

description: AA/AG


title: rs1360780 AA/AG control subject 51

description: AA/AG


title: rs1360780 AA/AG control subject 47

description: AA/AG


title: rs1360780 GG control subject 53

description: GG


title: rs1360780 GG control subject 50

description: GG


title: rs1360780 AA/AG trauma subject 44

description: AA/AG


title: rs1360780 AA/AG control subject 52

description: AA/AG


title: rs1360780 AA/AG control subject 42

description: AA/AG


title: rs1360780 GG control subject 46

description: GG


title: rs1360780 GG control subject 55

description: GG


title: rs1360780 AA/AG trauma subject 40

description: AA/AG


title: rs1360780 AA/AG trauma subject 49

description: AA/AG


title: rs1360780 AA/AG trauma subject 48

description: AA/AG


title: rs1360780 AA/AG trauma subject 43

description: AA/AG


title: rs1360780 AA/AG trauma subject 38

description: AA/AG


title: rs1360780 AA/AG trauma subject 39

description: AA/AG


title: rs1360780 AA/AG control subject 31

description: AA/AG


title: rs1360780 AA/AG control subject 36

description: AA/AG


title: rs1360780 AA/AG control subject 32

description: AA/AG


title: rs1360780 GG control subject 34

description: GG


title: rs1360780 AA/AG trauma subject 29

description: AA/AG


title: rs1360780 AA/AG trauma subject 41

description: AA/AG


title: rs1360780 AA/AG control subject 33

description: AA/AG


title: rs1360780 AA/AG control subject 30

description: AA/AG


title: rs1360780 AA/AG control subject 45

description: AA/AG


title: rs1360780 AA/AG control subject 35

description: AA/AG


title: rs1360780 AA/AG control subject 27

description: AA/AG


title: rs1360780 GG control subject 26

description: GG


title: rs1360780 AA/AG control subject 28

description: AA/AG


title: rs1360780 AA/AG control subject 25

description: AA/AG


title: rs1360780 AA/AG trauma subject 37

description: AA/AG


title: rs1360780 AA/AG trauma subject 24

description: AA/AG


title: rs1360780 AA/AG trauma subject 22

description: AA/AG


title: rs1360780 GG trauma subject 23

description: GG


title: rs1360780 AA/AG trauma subject 21

description: AA/AG


title: BV2_E19

city: Münster

first: Susanne

last: Höing

address: Röntgenstraße 20

department: Cell and Developmental Biology

institute: Max Planck Institute for Molecular Biomedicine

hyb_protocol: According to manufacturer's instructions. Hybridization time: 18h

scan_protocol: Illumina iScan system using default settings

data_processing: Cubic Spline normalization with background subtraction in Illumina GenomeStudio V2010.3 with the module GeneExpression 1.8.0. Signal intensities below 10 were arbitrarily trimmed to the value of 10.

organism: Mus musculus

source_name: 4h culture of activated BV2 cells treated with E19

label_protocol: Ambion TotalPrep RNA Amplification Kit. RNA in put: 400ng, IVT: 12h

growth_protocol: Microglial cells were cultured on uncoated plastic tissue culture plates and grown in microglia medium.

extract_protocol: Qiagen RNeasy kit with on-column DNA digestion

treatment_protocol: Cells were resuspended in DK10 medium, seeded at a density of 1.5 x 1,000,000 cells/cm2 and activated with 1 µg/ml LPS and 10 ng/ml IFN-γ. Following activation, cells were treated with the indicated hit compound for 4 h. Cells were harvested directly on the culture dish.

tag: cell line

tag: cell type

value: microglia cells

tag: activated with

value: 1 µg/ml LPS and 10 ng/ml IFN-γ

tag: treated with

value: hit compound E19 for 4hr


title: rs1360780 AA/AG control subject 20

description: AA/AG


title: rs1360780 AA/AG control subject 19

description: AA/AG


title: BV2_E23

source_name: 4h culture of activated BV2 cells treated with E23

value: hit compound E23 for 4hr


title: rs1360780 AA/AG control subject 16

description: AA/AG


title: BV2_E21

source_name: 4h culture of activated BV2 cells treated with E21

value: hit compound E21 for 4hr


title: BV2_E33

source_name: 4h culture of activated BV2 cells treated with E33

value: hit compound E33 for 4hr


title: BV2_E14

source_name: 4h culture of activated BV2 cells treated with E14

value: hit compound E14 for 4hr


title: rs1360780 GG control subject 15

description: GG


title: rs1360780 GG control subject 18

description: GG


title: rs1360780 AA/AG control subject 14

description: AA/AG


title: BV2_E20

source_name: 4h culture of activated BV2 cells treated with E20

value: hit compound E20 for 4hr


title: rs1360780 GG trauma subject 17

description: GG


title: BV2_E18

source_name: 4h culture of activated BV2 cells treated with E18

value: hit compound E18 for 4hr


title: rs1360780 AA/AG trauma subject 12

description: AA/AG


title: BV2_E5

source_name: 4h culture of activated BV2 cells treated with E5

value: hit compound E5 for 4hr


title: rs1360780 AA/AG trauma subject 11

description: AA/AG


title: BV2_activated control

source_name: 4h culture of activated BV2 cells without compound treatment


title: BV2_non-activated control

source_name: 4h culture of BV2 cells without activation stimuli and compound treatment


title: rs1360780 GG trauma subject 10

description: GG


title: AC_E33

source_name: 4h culture of activated AC treated with E33

growth_protocol: Astrocytes were differentiated from NSCs on gelatine in medium containing 10% FCS for 4 days and replated at a density of 1.5 x 1,000,000 cells/cm2 on Matrigel-coated cell culture dishes and matured for 14 days before treatment.

treatment_protocol: Medium was switched to DK10 and cells were activated with 1 µg/ml LPS and 10 ng/ml IFN-γ, followed by treatment with the indicated hit compound for 4 h. Cells were harvested directly on the culture dish.

value: Neural stem cell (NSC)-derived astrocytes (AC)


title: AC_E29

source_name: 4h culture of activated AC treated with E29

value: hit compound E29 for 4hr


title: rs1360780 AA/AG trauma subject 9

description: AA/AG


title: BV2_E4

source_name: 4h culture of activated BV2 cells treated with E4

value: hit compound E4 for 4hr


title: rs1360780 AA/AG trauma subject 8

description: AA/AG


title: AC_E23

source_name: 4h culture of activated AC treated with E23


title: AC_E21

source_name: 4h culture of activated AC treated with E21


title: AC_E18

source_name: 4h culture of activated AC treated with E18


title: rs1360780 AA/AG control subject 6

description: AA/AG

source_name: whole blood


title: rs1360780 AA/AG trauma subject 7

description: AA/AG


title: rs1360780 AA/AG control subject 5

description: AA/AG


title: AC_E20

source_name: 4h culture of activated AC treated with E20


title: AC_E14

source_name: 4h culture of activated AC treated with E14


title: rs1360780 GG trauma subject 4

description: GG


title: rs1360780 AA/AG control subject 3

description: AA/AG


title: AC_E5

source_name: 4h culture of activated AC treated with E5


title: rs1360780 AA/AG control subject 2

description: AA/AG


title: Trichosporon asahii infected THP-1 Cells Replicate 2

city: Beijing

first: Lin

last: Cong

address: 5 Nanmencang, Dongcheng District

country: China

institute: General Hospital of Beijing Military Command

description: 1 × 10^7 PMA-stimulated THP-1 cells, untreated

hyb_protocol: Arrays were hybridized was preformed in a CapitalBio BioMixerTM II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: confocal LuxScanTM scanner and the images obtained were then analyzed using LuxScanTM 3.0 software (Both from CapitalBio)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: THP-1 monocytic cell line

label_protocol: 2 μg amplified RNA was mixed with 4 μg random nanomer, denatured at 65℃ for 5min, and cooled on ice. Then, 5 μL of 4×first-strand buffer, 2 μL of 0.1M DTT, and 1.5 μL CbcScript Ⅱ reverse transcriptase were added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14 μL. The cDNA was mixed with 4 μg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 5 μL Klenow buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (GE Healthcare) were added to final concentrations of 240 μM dATP, 240 μM dGTP, 240 μM dTTP, 120 μM dCTP, and 40 μM Cy-dCTP. 1.2 μL Klenow enzyme was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in 80 μl hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray

growth_protocol: The cells were grown in a 5% humidified CO2 incubator at 37°C in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum,2 mM L-Glutamine, penicillin (100 units/ml) and streptomycin (100 μg/ml).Cells were resuspended at a concentration of 1 × 106 cells/ml. Cell differentiation was induced by treatment with 10ng/ml phorbol myristate acetate (PMA) at 37°C for 6 h. Cells were then washed twice with Hanks’ balanced salt solution without Ca2+ and Mg2+ and incubated without PMA at 37°C for a further 22 h

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: 1 × 10^7 PMA-stimulated THP-1 cells were infected with T. asahii (5 × 107 cells) at the multiplicity of infection (MOI) of 5 (5 fungi/1 cell) for 3 h at 37°C.

value: Trichosporon asahii infected

source_name: Control THP-1 Cells


title: Trichosporon asahii infected THP-1 Cells Replicate 1


title: rs1360780 AA/AG trauma subject 1

description: AA/AG

value: trauma


title: AC_activated control

source_name: 4h culture of activated AC without compound treatment


title: AC_E19

source_name: 4h culture of activated AC treated with E19


title: Trichosporon asahii infected THP-1 Cells Replicate 3


title: AC_E4

source_name: 4h culture of activated AC treated with E4


title: not infected dex 0h 4859453024_G

status: Public on Nov 02 2012

city: Los Angeles

first: Dai-Ying

last: Wu

address: 1441 Eastlake Ave, NOR 6314

department: Biochemistry

institute: University of Southern California

description:
NI_0h
4859453024_G

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Spatial artifacts removed with BASH, data normalized using neqc with limma in R

source_name: not infected dex 0h

label_protocol: Labeling, hybridization and scanning was performed by Epigenome Center Core Facility at USC as per their standard protocol.

growth_protocol: Cells were maintained in DMEM and hormone treated cells were plated and grown in phenol red-free medium supplemented with 5% charcoal stripped serum for 3 days prior to hormone treatment

extract_protocol: RNA was extracted using the TRIzol method as per the manufacturer's instructions

treatment_protocol: Cells were treated with 100nM dexamethasone for 24 hours

value: 100nM dexamethasone

tag: time

tag: knockdown


title: shG9a dex 24h 4859453024_F

description:
shG9a_24h
4859453024_F

source_name: shG9a dex 24h


title: not infected dex 24h 4859453027_A

description:
NI_24h
4859453027_A

source_name: not infected dex 24h


title: shG9a dex 24h 4859453023_F

description:
shG9a_24h
4859453023_F


title: not infected dex 0h 4859453023_G

description:
NI_0h
4859453023_G


title: shNS dex 0h 4859453023_A

description:
shNS_0h
4859453023_A

source_name: shNS dex 0h

value: shNS


title: not infected dex 24h 4859453027_E

description:
NI_24h
4859453027_E


title: shNS dex 24h 4859453023_C

description:
shNS_24h
4859453023_C

source_name: shNS dex 24h


title: shNS dex 0h 4859453024_A

description:
shNS_0h
4859453024_A


title: not infected dex 0h 4859453004_G

description:
NI_0h
4859453004_G


title: rs1360780 AA/AG control subject 54

description: AA/AG

value: control

value: whole blood


title: shNS dex 24h 4859453024_C

description:
shNS_24h
4859453024_C


title: shG9a dex 24h 4859453004_F

description:
shG9a_24h
4859453004_F


title: shG9a dex 0h 4859453004_D

description:
shG9a_0h
4859453004_D

source_name: shG9a dex 0h


title: shG9a dex 0h 4859453024_D

description:
shG9a_0h
4859453024_D


title: shNS dex 24h 4859453004_C

description:
shNS_24h
4859453004_C


title: shG9a dex 0h 4859453023_D

description:
shG9a_0h
4859453023_D


title: not infected dex 24h 4849554032_E

description:
NI_24h
4849554032_E


title: AC_non-activated control

source_name: 4h culture of NSC-derived astrocytes without activation stimuli and compound treatment


title: shNS dex 0h 4859453004_A

description:
shNS_0h
4859453004_A


title: not infected dex 24h 4849554032_A

description:
NI_24h
4849554032_A


title: BV2_E29

source_name: 4h culture of activated BV2 cells treated with E29

value: microglia cells

value: 1 µg/ml LPS and 10 ng/ml IFN-γ


title: COLO320 CDX2 siRNA #8 24hr

city: Boston

first: Keyan

last: Salari

state: MA

address: Gray/Bigelow Rm 1102, 55 Fruit Street

institute: Massachusetts General Hospital

hyb_protocol: Oligoarray hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slide was washed following manufacturer's instructions.

scan_protocol: Scanned on an Agilent G2505C Microarray Scanner System Images were quantified using Agilent Feature Extraction Software (version 9.5.3).

data_processing: Agilent Feature Extraction Software (v 9.5.3) was used for background subtraction and LOWESS normalization.

source_name: COLO320 CDX2 siRNA #8 24hr

label_protocol: Time-matched RNA from cells transfected with siCDX2 and non-targeting control constructs were reverse-transcribed, fluorescently-labeled, and co-hybridized to Agilent Whole Human Genome 44K gene expression arrays according to manufacturer protocols.

growth_protocol: COLO320 cells were grown in RPMI-1640 media + 10% FBS.

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen) according to manufacturer's protocol

treatment_protocol: Cells were transfected with 100 nM of either of two CDX2-targeting siRNA constructs or a non-targeting control siRNA construct. Cell culture media was changed the following morning, and cells were then harvested for RNA 24 hrs later (coinciding with the time of maximal CDX2 protein knockdown)

source_name: COLO320 Non-targeting control siRNA 24hr

value: Non-targeting control siRNA


title: small intestine, compost, replicate1

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

country: Japan

institute: Kanazawa University

description: Gene Expression in small intestine of rats given  1% (v/v) compost extracts in drinking water.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Microarray 4x44K (G4131F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green. Scan mode is eXtended Dynamic range Scan mode and PMT is set to 10% and 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE1-v5_91_0806 and Grid: 014879_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: RNA from small intestine of rat administered the compost extract

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the Low RNA Input Fluorescent Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Three-weeks old rats were fed compost extract during 12 weeks or left untreated. The compost extract were described in the below treatment protocol. The body weights of them did not differ from each other.

extract_protocol: The genomic DNA was removed with TurboDNA-free kit (Life Technologies Corporation, Carlsbad, CA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: In 3 week old Male Wistar rats, tap water was supplemented with 1.0% (v/v) compost extract for the experimental rats, whereas water only was given to the control rats. The rats received water ad libitum for 12 weeks. Fresh gut samples were collected from individual rats at the end of the feeding test and stored at -80°C. Compost was produced using an aerobic repeated batch-fed fermentation system, as previously described (Niisawa et al., J. Gen. Appl. Microbiol., 54, 149-158 (2008).). This compost has been marketed as an organic fertilizer or as fermentation feed for fishes, pigs and chickens (Miroku Co. Ltd. and Keiyo Plant Engineering Co. Ltd., Japan). The compost was diluted 1/100 (v/v) with potable water and incubated under aerobic conditions at 60°C for at least 10 h; this diluted compost solution was used as the compost extract in this experiment. The compost extract (pH 7.5 to 8.5) contained < 99.9% H2O, < 0.1% protein, < 0.1% lipid, < 0.1% fiber, < 0.1% ash, < 50 ppm lactate, and < 50 ppm butyrate, indicating that the compost extract itself included few valuable nutrients, such as carbohydrates, lipids, and amino acids. When the number of bacteria in the compost extract was tested by cultivation, there were < 5.0 x 106 CFU/ml thermophiles.

value: Wistar

value: small intestine excluding Peyer’s patches

tag: gender

value: male


title: HDA18Genome_at

first: Linchen

last: Li

address: 5 Yiheyuan Road

department: College of Life Sciences

institute: Peking University

description: HDA18 ChIP in Arabidopsis root tips.

hyb_protocol: The Whole Genome Tiling Array was hybridized for 16 hrs, washed, and stained with the GeneChip® Hybridization, Wash, and Stain Kit on the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol.

scan_protocol: The GeneChips were scanned on an Affymetrix Scanner 3000 7G.

data_processing:
The data were analyzed with Tiling Analysis Software (TAS) using Affymetrix default analysis settings.
The results files represent the putative HDA18 protein-binding sites, which were significantly enriched in HDA18 ChIPed DNAs compared with DNA ChIPed with pre-immune mouse serum. Genome coordinates are based on the Arabidopsis genome build TIGRv5.

organism: Arabidopsis thaliana

source_name: ChIPed DNA with anti-HDA18 mouse serum from Arabidopsis root tips

label_protocol: The samples were labeled with the GeneChip® WT Double-Stranded DNA Terminal Labeling Kit.

growth_protocol: Arabidopsis plants were grown on Petri dishes with Murashigi-Skoog (MS) agar medium, vertically oriented at 22℃ under a 16 h light/8 h dark light regime.

extract_protocol: The samples were prepared by ChIP using an antibody against HDA18 or pre-immune mouse serum (antibody was raised in mouse at the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences).

treatment_protocol: No treatment.

tag: ecotype

tag: genotype/variation

value: root tips

tag: chip antibody

value: anti-HDA18 mouse serum

source_name: ChIPed DNA with pre-immune mouse serum from Arabidopsis root tips

value: pre-immune mouse serum


title: small intestine, control, replicate2

description: Gene Expression in small intestine of rats given water only

source_name: RNA from small intestine of control rat

tag: strain


title: COLO320 CDX2 siRNA #6 24hr

source_name: COLO320 CDX2 siRNA #6 24hr


title: small intestine, control, replicate1


title: shfc42|LOVO

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68858.gif

hyb_protocol: not provided

scan_protocol: model: GenePix 4000A

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

source_name: Normal human male genomic DNA

label_protocol: not provided

extract_protocol: not provided

value: Normal human male genomic DNA

source_name: LOVO genomic DNA

value: colorectal cancer

value: LOVO


title: rs1360780 AA/AG control subject 13

description: AA/AG

source_name: whole blood


title: WT_yw_ZT16

city: Waltham

first: Stefan

last: Pescatore

address: 415 South Street

department: Biology

institute: Brandeis University / HHMI

hyb_protocol: RNA was hybrized to Drosophila Genome 2.0 arrays following manufacturers recommendations.  Arrays were washed and stained on a Fluidics 450 Station running protocol Midi_euk2 v3.

scan_protocol: Drosophila Genome 2.0 arrays were scanned using a Affymetrix GeneChip Scanner 3000 and GCOS version 1.4.

data_processing: Normalized log2 values were computed from the CEL files using the GC-RMA algorithm in the Bioconductor analysis package for R software (http://www.r-project.org)

organism: Drosophila melanogaster

label_protocol: RNA was labeled for hybridization to Drosophila Genome 2.0 arrays (Affymetrix) using the IVT Express Kit (Affymetrix).

growth_protocol: Adult flies were kept in constant 12 hr:12 hr light:dark conditions for 3 days before collection

extract_protocol: Total RNA was extracted from fly heads using TRIzol reagent (Invitrogen) as suggested by the supplier

treatment_protocol: Flies were collected at specified time point and frozen on dry ice, heads were removed

value: Fly heads

value: yw ; tim-gal4/CyO


title: small intestine, compost, replicate2


title: shfc108|HCT116

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68860.gif

scan_protocol: model: GenePix 4000B

source_name: HCT116 genomic DNA


title: CLUSTER-OE_ZT4

value: yw ; tim-gal4, UAS-mir-cluster/CyO


title: rd1_P8_rep4

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MOE430A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetric GeneArray 2500 scanner.

data_processing: Expression scores were obtained using Robust Multichip Average to do background correction, quantile normalization and summarization. Normalized data  was subjected to a two-stage analysis based on FDR-CI.

source_name: rd1 mouse retina at age postnatal day 8

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

growth_protocol: Animals were grown to postnatal day 2, 4, 6 or 8 where eyes were enucleaded and retinas isolated.  8-14 retinas were combined per sample.

extract_protocol: Total RNA was isolated from retinas using TRIzol reagent according to manufacture's protocol.

value: retina

tag: age

value: postnatal day 8


title: rd1_P8_rep3


title: WT_yw_ZT4


title: rd1_P8_rep2


title: shfc21|SW620

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69151.gif

source_name: SW620 genomic DNA


title: rd1_P8_rep1


title: shfc40|SW837

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68863.gif

source_name: SW837 genomic DNA


title: shfc78|SW403

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69148.gif

source_name: Normal human genomic DNA

value: Normal human genomic DNA

source_name: SW403 genomic DNA


title: shfc80|RKO

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69146.gif

source_name: RKO genomic DNA

value: RKO


title: shfc39|SW480

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68862.gif

source_name: SW480 genomic DNA


title: CLUSTER-NULL_ZT16


title: CLUSTER-NULL_ZT4


title: rd1_P6_rep4

source_name: rd1 mouse retina at age postnatal day 6

value: postnatal day 6


title: shfc38|SKCO1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69145.gif

source_name: SKCO1 genomic DNA


title: WT_w1118_ZT16


title: rd1_P6_rep3


title: shfc77|NCIH747

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69149.gif

source_name: NCIH747 genomic DNA


title: shfc41|HCT15

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68857.gif

source_name: HCT15 genomic DNA


title: rd1_P6_rep2


title: shfc20|CACO2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68865.gif

source_name: CACO2 genomic DNA


title: shfc76|NCIH508

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69150.gif

source_name: NCIH508 genomic DNA


title: shfc109|HT29

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68861.gif

source_name: Normal human female genomic DNA

value: Normal human female genomic DNA

source_name: HT29 genomic DNA


title: shfc110|DLD1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68859.gif

source_name: Normal human male genomic DNA

source_name: DLD1 genomic DNA


title: rd1_P6_rep1


title: shfc22|SW48

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68864.gif

source_name: SW48 genomic DNA


title: rd1_P4_rep1

source_name: rd1 mouse retina at age postnatal day 4

value: postnatal day 4


title: WT_w1118_ZT4


title: dctp-2 MCF7-72h

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

description: Gene expression data from MCF7 cells treated with control drug

hyb_protocol: See Affymetrix protocol.

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

data_processing: The data were analyzed with RMA.

source_name: MCF7 cells treated with control drug

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

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

treatment_protocol: MCF7 cells were treated with the control drug or AS1411 aptamer. After 72hours total RNA was collected and analyzed by Affymetrix U133 plus.


title: dctp-1 MCF7-72h


title: as1411 MCF7-72h-3

description: Gene expression data from MCF7 cells treated with AS1411 aptamer

source_name: MCF7 cells treated with AS1411 aptamer


title: dctp-3 MCF7-72h


title: as1411 MCF7-72h-2


title: rd1_P4_rep4


title: CLUSTER-OE_ZT16


title: rd1_P4_rep2


title: rd1_P2_rep4

source_name: rd1 mouse retina at age postnatal day 2

value: postnatal day 2


title: rd1_P2_rep2


title: rd1_P2_rep3


title: as1411 MCF7-72h-4


title: wt_P8_rep3

source_name: wild type mouse retina at age postnatal day 8

value: wild type


title: shfc79|SW1116

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69147.gif

source_name: Normal human genomic DNA

source_name: SW1116 genomic DNA


title: rd1_P2_rep1


title: rd1_P4_rep3


title: wt_P6_rep4

source_name: wild type mouse retina at age postnatal day 6


title: wt_P8_rep2


title: wt_P8_rep4


title: COLO320 DNA copy number

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.

data_processing:
CEL files were processed by Affymetrix Genotyping Console and copy number analysis performed using the Birdseed algorithm
log2 copy number ratio

source_name: COLO320 genomic DNA

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: COLO320 cells were grown in RPMI-1640 + 10% FBS

extract_protocol: Genomic DNA was extracted from cells using the Qiagen Genomic DNA Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.


title: wt_P6_rep2


title: cbf12-HA Overexpression Replicate 1

city: Calgary

first: Gordon

last: Chua

state: Alberta

address: 2500 University Drive NW

department: Biological Sciences

country: Canada

institute: University of Calgary

description:
cbf12 OE-rep1
Untreated strains.
PolyA RNA.

hyb_protocol: Hybridization was performed according to the manufacturer's instructions (Agilent Technology). Microarray was washed in 6X SSPE/0.005% sodium N-lauroylsarcosine at room temperature for 5 min, followed by a second wash in pre-heated 42°C 0.6X SSPE for 2 min.

scan_protocol: Microarrays were scanned on a GenePix 4200A instrument with GenePix 3.0 software.

data_processing: The raw data was lowess normalized and the average log2 ratios with the corresponding t-test p values from the dye-swap experiments were obtained using the R Bioconductor Limma package.

organism: Schizosaccharomyces pombe

source_name: cbf12 overexpression strain

label_protocol: 2 ug of mRNA were converted into cDNA using 140 nmol of Oligo-dT(25) anchored primer (Sigma), 20 nmol of aminoallyl dUTP dNTP (Sigma) mixture, and 200 units of SuperScript II reverse transcriptase (Invitrogen). 1 ug of cDNA each from the overexpression or deletion strain and the empty vector control strain were labeled with Cy3 or Cy5 (GE Healthcare) and were combined for QIAquick purification (QIAGEN).

growth_protocol: S. pombe yeast cells were inoculated in EMM+AU minimal media with no thiamine or in YES+ALU media and cultured for 20-24hr.

extract_protocol: Total RNA was extracted using the hot phenol-chloroform method, followed by mRNA isolation using gravity-flow Oligo-dT cellulose beads.

value: cbf12 overexpression

source_name: empty vector


title: cbf11 Deletion

description:
cbf11 del
Untreated strains.
PolyA RNA.

source_name: cbf11 deletion

source_name: wild type strain


title: cbf12-HA Overexpression Replicate 2

description:
cbf12 OE-rep2
Untreated strains.
PolyA RNA.


title: wt_P6_rep3


title: wt_P6_rep1


title: MCF7 cells 12 hr doxorubicin treatment rep3

first: Shannon

middle: Terrell

last: Bailey

address: 450 Brookline Avenue, D728

department: Medical Oncology

institute: Dana-Farber Cancer Institute

hyb_protocol: The biotinylated complementary RNA (cRNA) was purified from the IVT reaction mixture using magnetic particles, and it was quantified spectrophotometrically. The purity of the cRNA was also assessed by spectrophometric measurements.  The purified cRNA was first fragmented to facilitate hybridization, and the fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control) and hybridized to a microarray chip overnight at 45°C after which the hybridization solution was removed. The chips were transferred to a fluidics instrument that washed away and cRNA that did not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluorophores were then added using a biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured.

data_processing: The expression data were normalized using the robust multichip average (RMA) method and processed using linear models for microarray data (Limma) using R.

source_name: MCF7 breast cancer cell line 12 hr treatment

label_protocol: RNA was converted into cDNA using a T7 promoter-tailed oligo-dT primer to synthesize the first cDNA strand and a second strand cDNA synthesis was then performed.  The double-stranded cDNA was used as a template for an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.

extract_protocol: A hybrid Trizol/Qiagen Rneasy protocol was used to isolate total RNA

tag: treatment

value: 10 uM doxorubicin


title: wt_P4_rep4

source_name: wild type mouse retina at age postnatal day 4

tag: tissue


title: wt_P4_rep2


title: MCF7 cells 12 hr doxorubicin treatment rep1


title: wt_P4_rep1


title: MCF7 cells 12 hr doxorubicin treatment rep2


title: yox1 Deletion

description:
yox1 del
Untreated strains.
PolyA RNA.

source_name: yox1 deletion strain

value: yox1 deletion


title: sre2 Deletion

description:
sre2 del
Untreated strains.
PolyA RNA.

source_name: sre2 deletion strain

value: sre2 deletion


title: wt_P2_rep4

source_name: wild type mouse retina at age postnatal day 2


title: MCF7 cells vehicle treatment rep2

value: vehicle


title: MCF7 cells vehicle treatment rep3


title: adn2 Overexpression

description:
adn2 OE
Untreated strains.
PolyA RNA.

source_name: adn2 overexpression strain

value: adn2 overexpression


title: wt_P2_rep3


title: Wild-type revertant female TS cells H3K27me3 ChIP DNA rep2

city: Paris

first: Celine

last: Morey

address: 35 rue Hélène Brion

department: University Paris 7

country: France

institute: UMR7216-Epigenetics and stem cell

hyb_protocol: Hybridisation was performed by NimbleGen (http://www.nimblegen.com/products/chip/)

scan_protocol: Scanning was performed by NimbleGen (http://www.nimblegen.com/products/chip/)

data_processing: Reproducibility and quality control of the data were assessed using the “R” package combined with an algorithm especially developed for ChIP-on-Chip data analysis of histone modifications (http://www.epigenome-noe.net/WWW/researchtools/protocol.php?protid=43). Briefly, the global hybridisation patterns across each array were controlled by MA-plotting of all the probe signals on the array and by calculating the Pearson correlation coefficients between pairs of replicates (all the coefficients were > 0.8). The two replicates showing the highest Pearson correlation coefficient were used for further analysis. We applied a Lowess normalisation to each dataset and the “SAM” algorithms to determined statistically enriched probe (Tusher et al., PNAS, 2001). A VSN (variance stabilization) normalisation of each array was also performed independently, then a SAM algorithm and a lfdr > 0,2 (local false discovery rate probability test) to determine the significance of enrichment of each probel were applied (data not included in this submission but available upon request).

source_name: wildtype revertant female TS cells H3K27me3 ChIP DNA rep2

label_protocol: Labelling was performed by NimbleGen using 4 ug of ChIP DNA and 4 ug of Input DNA (http://www.nimblegen.com/products/chip/tutorial.html)

extract_protocol: Chromatin was fixed in 1% formaldehyde for 10 min, sheared to 200-700 bp using a Bioruptor (Diagenode). It was immunoprecipitated using the indicated antibody. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input by phenol extraction and ethanol precipitation. The ChIP material was amplified using whole genome amplification (WGA-2, SIGMA). For detailed protocol see (Navarro et al., Genes Dev, 2005).

treatment_protocol: FACS sorted for GFP fluorescence

value: Hprt-/XGFP

value: Trophoblast Stem cells isolated from E3.5 blastocysts

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #

value: female

source_name: Input DNA from wildtype revertant female TS cells rep2

value: none, input DNA


title: Eed-/- female TS cells H3K27me3 ChIP DNA

description:
specimen described in Kalantry S. et al., Nat Cell Biol, 2006
EED_XX_H3K27me3

treatment_protocol: No treatment

tag: genotype

value: XWT/XGFP

source_name: Input DNA from Eed-/- female TS cells


title: BMN_8

city: Bochum

first: Michael

last: Sand

state: NRW

address: Gudrunstr. 56

department: Depatment of Dermatology, Venereology and Allergology

institute: Ruhr-University Bochum

hyb_protocol: Labeled miRNA samples  were  hybridized  at  55°C  for  20  hrs  on  separate  Human  miRNA  Microarrays Release 16.0 (8x60K format, (Agilent Technologies, Santa Clara, USA). Afterwards, microarrays  were  washed  with  increasing  stringency  using  Gene  Expression Wash Buffers  (Agilent Technologies, Santa Clara, USA) followed by drying with acetonitrile  (Sigma-Aldich, St.Louis, USA).

scan_protocol: Fluorescent signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies, Santa Clara, USA) on the Agilent DNA Microarray Scanner.

data_processing: Fluorescent signal intensities were extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies, Santa Clara, USA). All the steps described were carried out according to the manufacturer´s instructions.

source_name: nevi biopsy

label_protocol: For assessment of labeling and hybridization efficiencies total RNA samples were spiked with in-vitro synthesized oligonucleotides by using the MicroRNA Spike-In Kit (Agilent Technologies, Santa Clara, USA). A total of 100 ng total RNA per sample were introduced into a labeling reaction. The  spiked  total  RNA  was  treated  with  alkaline  calf  intestine  phosphatase  (CIP).  The dephosphorylated RNA was labeled with the miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, USA) according to the manufacturer´s instructions using T4 RNA ligase, incorporating Cyanine 3-Cytidine biphosphate (pCp). The Cyanine-3-labeled miRNA samples were prepared for One-Color based hybridization with Complete miRNA Labeling and Hyb Kit (Agilent Technologies, Santa Clara, USA) according to the manufacturer´s instructions.

extract_protocol: Total RNA including miRNAs was isolated using the miRNeasy Mini Kit (Quiagen, Hilden, Germany) according to the manufacturer’s protocol. RNA concentration and purity was determined by NanoDrop ND-1000 spectral photometer (Peqlab, Erlangen, Germany). RNA integrity control (RIN) was determined by means of capillary electrophoresis with the 2100 Bioanalyzer and the RNA 6000 NanoLabCHip Kits (both Agilent Technologies, Santa Clara, USA).

treatment_protocol: All cutaneous specimens were harvested in the operating room, immediately stored in RNAlater (Quiagen, Hilden, Germany) and kept at - 80 °C until RNA isolation.

value: skin

value: male


title: rfl1 Deletion Replicate 2

description:
rfl1 del-rep2
Untreated strains.
PolyA RNA.

source_name: rfl1 deletion strain

value: rfl1 deletion


title: mbx2-HA Overexpression Replicate 2

description:
mbx2 OE-rep2
Untreated strains.
PolyA RNA.

source_name: mbx2 overexpression strain

value: mbx2 overexpression


title: MCF7 cells vehicle treatment rep1

tag: cell line


title: wt_P2_rep1

value: retina

value: postnatal day 2

value: wild type


title: Eed-/- male TS cells H3K27me3 ChIP DNA

description:
specimen described in Kalantry S. et al., Nat Cell Biol, 2006
EED_XY_H3K27me3

source_name: Eed-/- male TS cells H3K27me3 ChIP DNA

tag: cell type

source_name: Input DNA from Eed-/- male TS cells


title: rfl1 Deletion Replicate 1

description:
rfl1 del-rep1
Untreated strains.
PolyA RNA.


title: BMN_7


title: wt_P2_rep2


title: Wild-type female TS cells H3K27me3 ChIP DNA rep3

source_name: wildtype female TS cells H3K27me3 ChIP DNA rep3

source_name: Input DNA from wildtype female TS cells rep3


title: mbx2-HA Overexpression Replicate 1

description:
mbx2 OE-rep1
Untreated strains.
PolyA RNA.

source_name: empty vector


title: Wild-type revertant female TS cells H3K27me3 ChIP DNA rep1

source_name: wildtype revertant female TS cells H3K27me3 ChIP DNA rep1

source_name: Input DNA from wildtype revertant female TS cells rep1


title: wt_P8_rep1

source_name: wild type mouse retina at age postnatal day 8

value: postnatal day 8


title: wt_P4_rep3

source_name: wild type mouse retina at age postnatal day 4

value: postnatal day 4


title: Wild-type revertant female TS cells H3K27me3 ChIP DNA rep3

source_name: wildtype revertant female TS cells H3K27me3 ChIP DNA rep3

source_name: Input DNA from wildtype revertant female TS cells rep3


title: BMN_5


title: BMN_3


title: BMN_4


title: BMN_2


title: Wild-type female TS cells H3K27me3 ChIP DNA rep2

source_name: wildtype female TS cells H3K27me3 ChIP DNA rep2

source_name: Input DNA from wildtype female TS cells rep2


title: CMMM_4

source_name: melanoma metastasis biopsy


title: BMN_1

source_name: nevi biopsy


title: Wild-type female TS cells H3K27me3 ChIP DNA rep1

source_name: wildtype female TS cells H3K27me3 ChIP DNA rep1

source_name: Input DNA from wildtype female TS cells rep1


title: adn3 Overexpression

description:
adn3 OE
Untreated strains.
PolyA RNA.

source_name: adn3 overexpression strain

value: adn3 overexpression


title: Wild-type male TS cells H3K27me3 ChIP DNA rep2

source_name: wildtype male TS cells H3K27me3 ChIP DNA rep2

value: XWT/Y

source_name: Input DNA from wildtype male TS cells rep2


title: Wild-type male TS cells H3K27me3 ChIP DNA rep1

source_name: wildtype male TS cells H3K27me3 ChIP DNA rep1

source_name: Input DNA from wildtype male TS cells rep1


title: CMMM_2


title: shgu239|SNUC2B

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69475.gif

source_name: Normal human female genomic DNA

tag: reference

value: Norma human female genomic DNA

source_name: SNUC2B genomic DNA

value: colorectal cancer


title: SHGU225|COLO320

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69937.gif

value: Normal human female genomic DNA

source_name: COLO320 genomic DNA


title: CMMM_3

value: female


title: PCMM_9

source_name: melanoma biopsy


title: CMMM_1


title: P5.SS1NN3_Smo/Smo mutant

city: West Point

first: Michele

last: Cleary

state: PA

address: 770 Sumneytown Pike

department: Genetics and Pharmacogenomics

institute: Merck and Co., Inc.

description: Affymetrix gene expression profiling of mouse Smoothened mutant and wild type samples

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45'C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver' system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez'cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

source_name: Brain

label_protocol:
Biotin is incorporated during the amplification.  This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.
The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

value: brain

value: P5.SS1NN3_Smo/Smo mutant


title: P5.SS1NN2_Smo/Smo mutant

value: P5.SS1NN2_Smo/Smo mutant


title: PCMM_8

value: skin

value: male


title: shgu235|LS174T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69655.gif

source_name: LS174T genomic DNA


title: P5.221EA3_SmoA2 mutant

value: P5.221EA3_SmoA2 mutant


title: PCMM_7


title: shgu230|T84

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69846.gif

source_name: Normal human male genomic DNA

value: Normal human male genomic DNA

source_name: T84 genomic DNA


title: P5.SS1NN1_Smo/Smo mutant

value: P5.SS1NN1_Smo/Smo mutant


title: P5.221EA6_Wildtype


title: shgu236|LS180

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69478.gif

source_name: LS180 genomic DNA


title: PCMM_6


title: C23_3

description: HeLa transfected with nucleolin siRNA

hyb_protocol: Hybrdization reactions were performed according to the manufacturer's instructions (NanoString.com) with 5 Āµl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 65Ā°C for a minimum of 18 h.

scan_protocol: Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturerās instructions.  For each assay, a high-density scan (600 fields of view) was performed

data_processing: The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using code count normalization according to manufacturer's protocol (Nanostring). We then applied Variance Stabilization algorithm (vsn). In the normalized table we removed the control probes (Positive and Negative Controls, Housekeeping genes and viral microRNAs).

label_protocol: RNA was not labeled; instead, RNA (33 ng/ul) was pre-processed following the NanoString manufacturer's protocol by the Ohio State Microarray Core Facility

extract_protocol: Trizol according to manufacture's instructions

value: HeLa

value: transfected with nucleolin siRNA


title: P5.221EA5_SmoA2 mutant

value: P5.221EA5_SmoA2 mutant


title: shgu228|LIM1215

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69844.gif

source_name: LIM1215 genomic DNA


title: C23_2

description: HeLa transfected with nucleolin siRNA


title: C23_1

description: HeLa transfected with nucleolin siRNA


title: P5.221EA1_Wildtype


title: shgu237|SW1417

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69477.gif

source_name: SW1417 genomic DNA


title: PCMM_4


title: PCMM_3


title: shgu227|LIM2412

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69843.gif

source_name: LIM2412 genomic DNA


title: Ctrl_3

description: HeLa transfected with control siRNA

source_name: Control

value: transfected with control siRNA


title: PCMM_2


title: Ctrl_2

description: HeLa transfected with control siRNA


title: PCMM_1


title: Ctrl_1

description: HeLa transfected with control siRNA


title: shgu233|COLO741

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69651.gif

source_name: COLO741 genomic DNA


title: PCMM_5


title: shgu234|COLO205

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69652.gif

source_name: COLO205 genomic DNA


title: P5.221EA2_SmoA2 mutant

value: P5.221EA2_SmoA2 mutant


title: BMN_6

source_name: nevi biopsy


title: rfl1-HA Overexpression ChIP-chip

description:
rfl1 del chIP-chip
Untreated strains.

data_processing: The raw data was normalized using global linear normalization and significant spots were selected with chIPOTle.

source_name: rfl1 HA tagged strain, HA ChIP

label_protocol: The linker-ligated DNA was PCR-amplified by adding 15 µl of labeling mix (2 µl aa-dUTP dNTP mix containing 5 mM each dATP, dCTP and dGTP, 3 mM dTTP, and 2 mM aminoallyl-dUTP (Sigma)), 1.25 µl 40 µM Oligo #1 (5'-GCGGTGACCCGGGAGATCTGAATTC-3'), and 5 and 0.001 units of GoTaq DNA polymerase (Promega) and Pfu Turbo DNA polymerase (Stratagene), respectively, and using the following program: one cycle of 55°C (4 min); 72°C (5 min); 95°C (2 min) and 30 cycles of 95°C (30 sec); 55°C (30 sec); 72°C (1 min), followed by a final extension at 72°C (4 min). Equal amounts of PCR product (3-5 mg) from immunoprecipitated and corresponding input samples were coupled to Cy3 and Cy5 dyes (GE Healthcare), and combined for QIAquick purification (QIAGEN).

extract_protocol: Cells were fixed and quenched in 1% formaldehyde and 125 mM glycine, respectively, followed by 30 minute room temperature agitation and lysis by bead-beating. The cell lysate was sonicated to generate 100 bp-1 kb DNA fragments. The chromatin-bound transcription factor was immunoprecipitated with 100-200 µl of Dynabeads® conjugated with sheep anti-mouse IgG (Invitrogen) and 5 µg of anti-HA F-7 antibody (Santa Cruz Biotechnology, catalog # sc-7392, lot E0610). Both immunoprecipitated and input cell lysates were incubated at 65°C overnight to reverse the DNA-protein cross-linking, and DNA was then extracted by phenol-chloroform. Blunt ends were generated in the entire immunoprecipitate and input DNA samples with 1 unit of T4 DNA Polymerase (Invitrogen), and 200 pmol of annealed linker (linker generated with Oligo #1: 5'-GCGGTGACCCGGGAGATCTGAATTC-3' and Oligo #2: 5'-GAATTCAGATC-3') was ligated with 1000 units of T4 DNA Ligase (NEB).

value: rfl1 HA tagged

value: anti-HA F-7 antibody

source_name: rfl1 HA tagged strain, input

value: strain:MBY192 (leu1 - 32, ura4-D18)


title: shgu238|SW948

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69476.gif

source_name: Normal human female genomic DNA

value: Normal human female genomic DNA

source_name: SW948 genomic DNA

value: colorectal cancer


title: SHGU226|LS411

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69938.gif

source_name: LS411 genomic DNA


title: mbx2-HA Overexpression ChIP-chip

description:
mbx2 OE chIP-chip
Untreated strains.

source_name: mbx2 HA tagged overexpression strain, HA ChIP

value: mbx2 HA tagged overexpression

source_name: mbx2 HA tagged overexpression strain, input


title: RCC-HS

status: Public on Nov 01 2012

city: Groningen

first: Klaas

last: Kok

department: Genetics

country: Netherlands

institute: UMCG

description: Raw data file: RCCHS_027730.txt

hyb_protocol: According to protocols recommendated by AGILENT

scan_protocol: Agilent scanner at 2 um resolution

data_processing: AGILENT feature extraction software

source_name: RCC-HS

growth_protocol: See publication by Duns et al, Cancer Research 2010

treatment_protocol: untreated

tag: name

value: RCC-HS

value: ccRCC derived cell line

value: Female

value: clear cell renal cell carcinoma primary tumour

tag: tumor stage

tag: age of diagnosis

source_name: Reference pool

value: This pool consists of healthy individuals, either  50 males or 50 females. The persons were selected randomly, and blind from a large pool of anonymous "in house" control DNA samples. The reference pool was home-made.


title: RCC-4

description: Raw data file: RCC4_027730.txt

label_protocol: According to protocols recommendated by AGILENT

extract_protocol: See publication by Duns et al, Cancer Research 2010


title: RCC-5

description: Raw data file: RCC5_027730.txt


title: Wildtype_Mm_4d_3

city: Leiden

first: Michiel

last: van der Vaart

address: Einsteinweg 55

department: IBL

institute: University of Leiden

description:
Biological replicate 3 of 3: control embryos M.marinum infected 4d
252823310046_3u20b_S01_GE2_107_Sep09_1_1.txt

hyb_protocol: The dual colour hybridization of the microarray chips was performed at the Microarray Department (MAD) of the University of Amsterdam (Amsterdam, The Netherlands) using the standard Agilent protocol.

scan_protocol: The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies. The arrays were scanned twice with 10% PMT and 100% PMT laser power.

data_processing: Microarray data was processed from raw data image files with Feature Extraction Software 9.5.3.1 (Agilent Technologies). The XDR function was used to extend the dynamic range. Processed data were subsequently imported into Rosetta Resolver 7.0 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. The Agilent Feature Extraction files contain the final log ratio data. The algorithms that were used to normalize the feature signal and calculate the log ratios are described in the Reference Guide for Agilent Feature Extraction Software v9.5. The standard settings as described for the GE2-v5_95 protocol in the Reference Guide were used. In order to calculate the normalized signal, the Rank Consistency Probes method was used and the Linear&LOWESSDyeNormFactor (= DyeNormalSignal/(BGSubSignal x LinearDyeNormFactor) was calculated as described on page 231 of the Reference Guide. The dye normalized signal was calculated as follows (page 232): DyeNormSignal = BGSubSignal x DyeNormFactor. The log10 ratio was subsequently calculated as follows (page 232): LogRatio = Log(rProcessedSignal/gProcessedSignal), where rProcessedSignal and gProcessedSignal are signals post dye normalization and post surrogate processing in the red and green channels, respectively. The surrogate values are calculated and used as the lowest limit of detection to replace the dye normalized signal when either the mean feature signal is less than the background signal or not significant when compared to the background signal, or when the mean signal is less than its background standard deviation (page 226).

organism: Danio rerio

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 ug of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 or Cy5 dye (GE Healthcare) and column purified.

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: Single embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro-injected into the caudal vein with (1) 200 CFU of S. typhimurium SL1027 bacteria suspended in PBS (phosphate-buffered saline), (2)  mock-injected with PBS as a control for S. typhimurium infection, (3) 200 CFU of M. marinum Mma20 bacteria suspended in PBS/2%PVP (polyvinylpyrrolidone), (4) mock-injected with PBS/2%PVP as a control for M. marinum infection, (5) 200 CFU of E. tarda bacteria suspended in PBS/2%PVP, (6) mock-injected with PBS/2%PVP as a control for E. tarda . At 36 hpf (8 h post infection)  three single embryos per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.Additionally, for the M. marinum infection and its control group samples were also taken at 5 dpf (4 d post infection)

tag: common reference

value: The CR was a mixture of all RNA samples from  the M. marinum infection experiment

tag: injection

value: M. marinum

tag: injection site

value: caudal vein

tag: developmental stage

value: 28 hpf

tag: time

value: 4d post injection


title: wildtype_male_mouse_colon_litter1

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: log2 RMA

source_name: Colon

label_protocol: Standard Affymetrix

extract_protocol: Standard Affymetrix

tag: genetic background

value: colon

value: wild type

tag: gender

value: M

tag: litter

tag: age


title: Wildtype_PBS-PVP_4d_2

description:
Biological replicate 2 of 3: control embryos PBS/PVP control 4d
252823310045_3u20b_S01_GE2_107_Sep09_1_4.txt

value: PBS/PVP buffer (mock-injected)_control for M. marinum


title: Wildtype_PBS-PVP_4d_3

description:
Biological replicate 3 of 3: control embryos PBS/PVP control 4d
252823310075_3u20b_S01_GE2_107_Sep09_1_2.txt


title: Wildtype_Mm_8h_2

description:
Biological replicate 2 of 3: control embryos M.marinum infected 8h
252823310086_3u20b_S01_GE2_107_Sep09_1_3.txt

value: 8 h post injection


title: B73_lowN_d20_3

city: Erlangen

first: Urte

last: Schluter

address: Staudtstr. 5

institute: FA University Erlangen

hyb_protocol: An aliquot of 1.65 mg of RNA was loaded on one-color microarrays with custom-designed oligonucleotide probes (Agilent 025271).

scan_protocol: Slides were scanned immediately after washing on the Agilent G2565B Microarray Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software v9.5.3.1 (Agilent) using default parameters (protocol GE-v5_95_Feb07). The processed signals were log2 transformed and normalised to the 75th percentile within each array followed by median base line correction using the Agilent GeneSpring GX 11.0 software.

organism: Zea mays

source_name: lamina fifth leaf

label_protocol: The cDNA and following antisense cRNA synthesis was performed according to the one-color microarray-based gene expression analysis protocol (Agilent).

growth_protocol: Zea mays seeds of genotypes A188 and B73 were germinated on wet filter paper and transferred into pots of 1.5L volume containing nutrient poor peat soil (Basissubstrat 2, Klasmann& Deilmann, Germany). Plants were either fertilized with high N (15mM nitrate) or low N (0.15mM nitrate) supplied Hoagland solution. Growth conditions in the plant climate chamber (PlantMaster PGR 3045, CLF Plant Climatics GmbH, Germany) were set at diurnal rhythm of 14h light (ca. 200 µmol m-2 s-1 at level of the soil surface and ca. 650 µmol m-2 s-1 just under the light source which was adjusted according to plant height to give maximal possible irradiance) at 28°C and 80% humidity, and 10h night at 20°C and 50% humidity. Harvest of plant material always started two hours after start of the light period and was always completed before midday.

extract_protocol: RNA was extracted from four biological replicates per genotype, growth stage and treatment after the method described by Logemann et al. (1987) using 100mg of frozen leaf material. The isolated RNA was purified with the RNeasy purification kit according to the manufacturer’s instructions (Qiagen, Germany). The quality was checked with the Agilent 2100 Bioanalyzer using the RNA 6000 Nano kit.

treatment_protocol: Fertilization started at day seven after germination with a modified Hoagland solution (5mM CaCl2, 2mM MgSO4, 2mg/L Fe, 0.5mM KH2PO4, 50µM H3BO4, 10µM MnCl2, 1µM ZnSO4, 0.3µM CuSO4, 0.5µM Na2MoO4). Depending on N treatment scheme, the nutrient solution contained 15mM for high N treatment or 0.15mM KNO3 for low N treatment. The differences in potassium supply were balanced with KCl. Plants received 100ml of nutrient solution every third day, between the fertilisation supply, plants were watered with distilled water depending on water status in the pot. The last watering with nutrient solution always happened two days before the harvest.

tag: inbred line

tag: treatment

value: 0.15mM nitrate supply

tag: plant age

value: 20 days


title: myc335_null_male_mouse_colon_litter1

tag: tissue

tag: genotype

value: Myc-335 null


title: B73_lowN_d30_4

source_name: lamina sixth leaf

value: 30 days


title: B73_lowN_d20_1


title: RCC-JW

description: Raw data file: RCCJW_027730.txt

source_name: RCC-JW

tag: name

value: RCC-JW

tag: cell line

value: ccRCC derived cell line

value: Male

tag: reference


title: B73_lowN_d30_1


title: Wildtype_Mm_4d_1

description:
Biological replicate 1 of 3: control embryos M.marinum infected 4d
252823310075_3u20b_S01_GE2_107_Sep09_1_3.txt

tag: common reference

value: The CR was a mixture of all RNA samples from  the M. marinum infection experiment


title: Wildtype_Mm_4d_2

description:
Biological replicate 2 of 3: control embryos M.marinum infected 4d
252823310076_3u20b_S01_GE2_107_Sep09_1_4.txt

tag: injection

value: M. marinum


title: Wildtype_Mm_8h_3

description:
Biological replicate 3 of 3: control embryos M.marinum infected 8h
252823310085_3u20b_S01_GE2_107_Sep09_1_4.txt

tag: injection site

value: caudal vein


title: B73_lowN_d30_3


title: B73_lowN_d20_4


title: cbf12-HA Overexpression ChIP-chip

description:
cbf12 OE chIP-chip
Untreated strains.

source_name: cbf12 HA tagged overexpression strain, HA ChIP

tag: strain

tag: genotype/variation

value: cbf12 HA tagged overexpression

tag: chip antibody

value: anti-HA F-7 antibody

source_name: cbf12 HA tagged overexpression strain, input


title: Wildtype_PBS-PVP_8h_3

description:
Biological replicate 3 of 3: control embryos PBS/PVP control 8h
252823310046_3u20b_S01_GE2_107_Sep09_1_2.txt

tag: developmental stage

value: 28 hpf

tag: time


title: B73_lowN_d20_2


title: B73_highN_d30_3

value: 15mM nitrate supply


title: Wildtype_PBS-PVP_4d_1

description:
Biological replicate 1 of 3: control embryos PBS/PVP control 4d
252823310085_3u20b_S01_GE2_107_Sep09_1_3.txt

value: 4d post injection


title: B73_highN_d30_2


title: Wildtype_Mm_8h_1

description:
Biological replicate 1 of 3: control embryos M.marinum infected 8h
252823310045_3u20b_S01_GE2_107_Sep09_1_2.txt


title: B73_lowN_d30_2


title: P5.221EA4_Wildtype

description: Affymetrix gene expression profiling of mouse Smoothened mutant and wild type samples

source_name: Brain

value: brain


title: Wildtype_PBS-PVP_8h_1

description:
Biological replicate 1 of 3: control embryos PBS/PVP control 8h
252823310076_3u20b_S01_GE2_107_Sep09_1_3.txt

value: PBS/PVP buffer (mock-injected)_control for M. marinum

value: 8 h post injection


title: B73_highN_d30_1


title: B73_highN_d20_2

value: 20 days


title: B73_highN_d20_4


title: A188_lowN_d30_3

value: 0.15mM nitrate supply


title: B73_highN_d20_1


title: B73_highN_d20_3


title: Wildtype_PBS-PVP_8h_2

description:
Biological replicate 2 of 3: control embryos PBS/PVP control 8h
252823310086_3u20b_S01_GE2_107_Sep09_1_4.txt


title: A188_highN_d30_3

value: 30 days


title: A188_highN_d30_4


title: A188_lowN_d30_1


title: A188_lowN_d20_2


title: A188_lowN_d30_4


title: A188_lowN_d20_3


title: A188_lowN_d30_2


title: A188_highN_d20_2


title: A188_lowN_d20_1


title: RCC-MF

description:
Raw data file(s):
US45102948_251911811402_S01_miRNA-v1_10_Apr08_1_4.txt

hyb_protocol: Hybridization was performed following the manufacturer's protocols

scan_protocol: Slides were scanned using the G25052C DNA microarray scanner (Agilent) following the manufacturer's protocol

data_processing: Array images were analyzed using Agilent feature extraction software (v10.5.1.1) and GeneSpring GX (Agilent). Data were normalized using a 75% percentile shift (Gibcus et al., 2009). MicroRNAs that were assigned flags present (P) or marginal (M) by the Agilent Feature Extraction software in four or more of the samples were used in the subsequent analyses.

source_name: clear cell renal cell carcinoma- derived cell line

label_protocol: RNA was Cy3 labeled following the manufacturer's protocols

growth_protocol: All clear cell renal cell carcinoma-derived cell lines were maintained in RPMI 1640 (Sigma) supplemented with 10% fetal calf serum (Gibco), penicillin (1.0 U/l) (Gibco), streptomycin (1µg/µl) (Gibco), glutamin (2.0 mM) (Gibco). Cells were grown in an incubator at 37 °C, 5% CO2.  PTECs were grown in renal epithelial cell basal medium supplied with renal epithelial cell growth kit (ATCC, PCS-400-030, PCS-400-040) grown at 37 °C, 5% CO2..

extract_protocol: Cells were grown to 70% confluence. Total RNA fractions were isolated using the Trizol reagent (Invitrogen, Carlsbad, CA, USA). RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Cells were not treated

value: RCC-MF (KTCTL-1M )

tag: gender

value: clear cell renal cell carcinoma (lung metastasis)

tag: tumor stage

value: pT2,N1,Mx/GII-III (lung-metastasis)

tag: age of diagnosis


title: RCC-JW

description:
Raw data file(s):
US45102948_251911811405_S01_miRNA-v1_10_Apr08_2_1.txt

value: RCC-JW (KTCTL-195)

value: ccRCC derived cell line

value: Male

value: clear cell renal cell carcinoma primary tumour


title: A188_highN_d20_1

tag: inbred line

tag: treatment

tag: plant age


title: A188_highN_d20_4


title: A188_highN_d20_3


title: RCC-HS

description:
Raw data file(s):
US45102948_251911811402_S01_miRNA-v1_10_Apr08_1_3.txt

tag: name

value: RCC-HS (KTCTL-30)

value: Female

tag: tissue


title: RCC-FG2

description:
Raw data file(s):
US45102948_251911811405_S01_miRNA-v1_10_Apr08_1_2.txt

value: RCC-FG2 (KTCTL-26A)

tag: cell line


title: A188_highN_d30_1

value: 15mM nitrate supply


title: RCC-ER

description:
Raw data file(s):
US45102948_251911811402_S01_miRNA-v1_10_Apr08_2_1.txt

value: RCC-ER (KTCTL-13)

value: pT3a, N1,Mx/GIII


title: RCC-AB

description:
Raw data file(s):
US45102948_251911811413_S01_miRNA-v1_95_May07_2_2.txt

value: RCC-AB (KTCTL-21)

value: pT2, N0, MX/GII


title: PTEC_reps 1 and 2

description:
Raw data file(s):
US45102948_251911811405_S01_miRNA-v1_10_Apr08_2_3.txt
US45102948_251911811402_S01_miRNA-v1_10_Apr08_2_3.txt

source_name: proximal tubular epithelial cell sample

value: PTEC

value: primary culture derived from proximal tubular epithelial cells


title: RCC-4

description:
Raw data file(s):
US45102948_251911811405_S01_miRNA-v1_10_Apr08_1_1.txt


title: RCC-JF_reps 1 and 2

description:
Raw data file(s):
US45102948_251911811405_S01_miRNA-v1_10_Apr08_1_3.txt
US45102948_251911811405_S01_miRNA-v1_10_Apr08_1_4.txt

value: RCC-JF (KTCTL-140 )


title: MN-160_reps 1 and 2

description:
Raw data file(s):
US45102948_251911811405_S01_miRNA-v1_10_Apr08_2_4.txt
US45102948_251911811402_S01_miRNA-v1_10_Apr08_2_4.txt


title: shgu229|HCA7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69845.gif

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

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Normal human female genomic DNA

source_name: HCA7 genomic DNA

tag: cell type

value: colorectal cancer


title: RCC-5

description:
Raw data file(s):
US45102948_251911811402_S01_miRNA-v1_10_Apr08_1_1.txt


title: A188_lowN_d20_4

value: 0.15mM nitrate supply

value: 20 days


title: ISO control D

city: Aachen

first: Viktoria

last: Schiller

address: Forckenbeckstrasse 6

department: UNIFISH

institute: Fraunhofer IME

description: Gene expression of ISO water control embryos after 48hpf

hyb_protocol: Hybridization was carried out according to the Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies)

scan_protocol: Microarrays were scanned immediately after wahsing with the Agilent Microarray Scanner (Agilent Technologies)

data_processing: Data were extracted and processed using Agilent Feature Extraction Software applying default parameters (protocol GE1-v5_95_Feb07, QC metric set GE1_QCMT_Feb07)

source_name: 48 hpf embryos

label_protocol: We carried out cDNA synthesis, cRNA Cy3 labeling, amplification and hybridization according to the manufacturer’s protocols (Quick Amp Labeling Kit; Agilent Technologies), using 500ng RNA as starting material.

extract_protocol: Total RNA was isolated from frozen, pooled embryos by homogenization in TRIreagent (Sigma-Aldrich, T9424) followed by extraction with chloroform and ethanol and final purification using RNeasy Mini Spin Columns (QIAGEN, Hilden, Germany) according to the manufacturers’ protocols. RNA concentration was measured using a NanoDrop 1000 (Thermo Fisher Scientific, Schwerte, Germany) and RNA quality was verified on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA).

treatment_protocol: Per concentration and replicate, 24 newly fertilized embryos (<2hpf) were exposed to 2.2 mg/l (EC10) and 2.4 mg/l (EC20) genistein for 48 hours in 96 well plates. After exposure, each group of 24 fish embryos was pooled together, snap-frozen over dry ice and stored at –80°C.

value: whole embryo

tag: age

value: 48 hours post fertilization

value: ISO water control


title: RCC-1

description:
Raw data file(s):
US45102948_251911811400_S01_miRNA-v1_10_Apr08_2_3.txt

value: ccRCC derived cell line


title: ISO control C


title: Genistein EC20 D

description: Gene expression of embryos exposed to 2.4mg/l genistein after 48hpf

value: 2.4mg/l genistein


title: Solvent Control D

description: Gene expression of solvent control (acetone) embryos after 48hpf

value: solvent control


title: Genistein EC10 D

description: Gene expression of embryos exposed to 2.2mg/l genistein after 48hpf

value: 2.2mg/l genistein


title: Genistein EC20 B


title: ISO control A


title: Genistein EC20 C


title: Genistein EC10 B


title: Genistein EC20 A


title: Genistein EC10 A


title: Solvent Control C


title: Solvent Control B


title: Genistein EC10 C


title: daf-10 vs wt  replicate 1

city: Madison

first: Marta

middle: Maria

last: Gaglia

state: WI

address: 1525 Linden Dr

institute: University of Wisconsin Madison

description: Biological replicate 1 of 3

hyb_protocol: Oligoarray control targets and hybridization buffer (3XSSC, 20mM HEPES pH 7.0, 0.2% SDS) were added, and samples were applied to microarrays enclosed in hybridization chambers. After hybridization for at least 6 hours at 63 centidegree, slides were washed sequentially

scan_protocol: scanned on GenePix 4000B scanner,

data_processing: initial quality control and spot identification using Genepix 6.0 software. Linear normalization was carried out using Acuity v4.0 (Molecular Devices).

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: day 1 adult daf-10(m79) animals

label_protocol: 5 ug of polyA+ RNA were retrotranscribed with Superscript II (Invitrogen) for 2 hrs at 42°C in the presence of dATP, dTTP, dGTP, dCTP, and aa-dUTP. It was then coupled too Cy3 or Cy5 dyes, quenched and cleaned up.

growth_protocol: Synchronized with L1 arrest, grown at 20°C until day 1 of adulthood

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions; poly A+ RNA was purified using Oligotex kit

tag: Stage

value: day 1 adult

source_name: day 1 adult wild-type N2 animals

value: wild-type N2


title: Solvent Control A


title: daf-10 vs wt  replicate 3

description: Biological replicate 3 of 3

tag: genotype/variation


title: daf-10 vs wt  replicate 2

description: Biological replicate 2 of 3


title: genomic DNA from whole blood_1848345023_541

city: Detroit

middle: A.

last: Tainsky

state: MI

address: 110 E. Warren

department: Department of Oncology, Molecular Biology and Genetics

institute: Wayne State University School Of Medicine

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software V3.1.0  (Illumina)

label: Biotin

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA samples were extracted from blood specimens and  bisulfite treated with EZ DNA Methylation Kit (Zymo Research)

tag: study id number

tag: classification for analysis

value: Case_Mutation Neg

value: Female

tag: race

value: White

tag: age at blood sample collection

tag: 1st diagnosis

value: Breast

tag: age at 1st diagnosis

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).

tag: number of relatives in the family dignosed with breast cancers before age 50

tag: number of the members of the same family (1st degree relatives) on the arrays.

tag: relatives on the array.


title: chronic-pancreatitis_sample1

city: Heidelberg

last: Dutruel

address: Im Neuenheimer Feld 280

institute: DKFZ

description: chronic pancreatitis sample 1 of 2

hyb_protocol: Each test sample was cohybridized with the reference on a 244K Human CpG Island microarray using the Oligo aCGH/ChIP-on-chip Hybridization Kit (Agilent technologies, Palo Alto, USA), following the instructions of the manufacturer.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.10.5.1.1).

data_processing: Scanned raw data were processed using the R statistical environment. Background correction and log 2-ratio transformation were performed according to the NormExp method with offset = 50 [Ritchie, Bioinformatics, 2007]. To reduce variations between co-hybridized samples, intensity-based LOESS normalization on rank-invariant probes and negative controls was applied [Tseng, Nucleic Acids Res, 2001]. For between-array normalization, log-intensity ratios (M-values) and log-intensity averages (A-values) were scaled to have the same median-absolute-value across the arrays.

label: Alexa Fluor 5

source_name: chronic pancreatitis tissue

label_protocol: Highly methylated sample and reference (pool of DNAs from 11 NP tissues including male and female patients) DNAs were labeled with Alexa Fluor® 5 and 3 (BioPrime Total Genomic Labeling System, Invitrogen, Karlsruhe, Germany), respectively, following the instructions of the manufacturer.

extract_protocol: High-molecular weight DNA was isolated from fresh-frozen normal, CP and PDAC tissue samples using the QIAamp DNA Mini kit (Qiagen, Hilden, Germany). Methyl-CpG binding domain (MBD)-Fc protein was produced and MCIp performed as described previously [Schilling, Genomics, 2007] with minor modifications. Briefly, 60 µg of MBD-Fc protein was coupled to 150 µl nProtein A Sepharose beads (GE Healthcare, Neu Isenburg, Germany) at 4°C overnight. After binding of 2 µg sonicated DNA mixed with 2 pg of a mixture of in-vitro methylated and unmethylated synthetic DNA of 630 bp containing 47 CpGs, DNA elution was performed with increasing NaCl concentrations (300-1000 mM) using Ultra-free-CL centrifugal filter devices (Merck-Millipore, Billerica, USA). Low and high salt concentrations were used to enrich for lowly and highly methylated DNA, respectively.

tag: tissue

value: chronic pancreatitis tissue

tag: gender

value: male

label: Alexa Fluor 3

source_name: pooled of 11 normal pancreatic tissues

value: pooled of 11 normal pancreatic tissues

value: mixed


title: chronic-pancreatitis_sample2

description: chronic pancreatitis sample 2 of 2


title: normal-pancreas_sample5

description: normal sample 5 of 5

source_name: normal pancreatic tissue

value: normal pancreatic tissue


title: genomic DNA from whole blood_1848345023_73155

value: Control_Mutation Pos


title: genomic DNA from whole blood_1848345023_73135

value: Control_Mutation Neg

tag: breast and ovarian cancer in same person in the family

value: yes


title: genomic DNA from whole blood_1848345023_73138

value: breast


title: genomic DNA from whole blood_1848345023_73082


title: genomic DNA from whole blood_1848345023_73146


title: genomic DNA from whole blood_1848345023_73153


title: genomic DNA from whole blood_1848345023_73109

value: Ovary


title: normal-pancreas_sample2

description: normal sample 2 of 5


title: PDAC_sample7

description: PDAC sample 7 of 7

source_name: PDAC tissue

value: PDAC tissue


title: ISO control B

value: whole embryo

tag: age

value: 48 hours post fertilization

tag: treatment

value: ISO water control


title: PDAC_sample6

description: PDAC sample 6 of 7


title: genomic DNA from whole blood_1848345023_73166

tag: study id number

tag: classification for analysis

value: Female


title: PDAC_sample2

description: PDAC sample 2 of 7


title: normal-pancreas_sample3

description: normal sample 3 of 5


title: normal-pancreas_sample1

description: normal sample 1 of 5


title: PDAC_sample4

description: PDAC sample 4 of 7


title: B73_highN_d30_4

tag: inbred line

value: 15mM nitrate supply

tag: plant age

value: 30 days


title: genomic DNA from whole blood_1848345023_73154

tag: race

value: White

tag: age at blood sample collection


title: genomic DNA from whole blood_1848345023_72186

value: Case_Mutation Pos

tag: 1st diagnosis

value: BREAST

tag: age at 1st diagnosis

tag: 2nd diagnosis

tag: age at 2nd diagnosis

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).


title: genomic DNA from whole blood_1848345023_73129

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).

tag: number of relatives in the family dignosed with breast cancers before age 50


title: PDAC_sample3

description: PDAC sample 3 of 7

tag: tissue

tag: gender

value: male

value: pooled of 11 normal pancreatic tissues

value: mixed


title: normal-pancreas_sample4

description: normal sample 4 of 5

value: normal pancreatic tissue


title: genomic DNA from whole blood_1848345023_73130

tag: study id number

value: Breast

value: Bone


title: genomic DNA from whole blood_1848345023_73124

tag: classification for analysis

value: breast


title: genomic DNA from whole blood_1848345023_73125

value: Case_Mutation Neg


title: genomic DNA from whole blood_1848345023_73115

tag: number of the members of the same family (1st degree relatives) on the arrays.

tag: relatives on the array.


title: genomic DNA from whole blood_1848345023_73121

tag: race


title: genomic DNA from whole blood_1848345023_73113

value: Native American/African American

tag: age at blood sample collection


title: genomic DNA from whole blood_1848345023_1852

tag: 1st diagnosis

value: Ovary


title: genomic DNA from whole blood_1848345023_73106

value: Black, African American

tag: age at 1st diagnosis


title: genomic DNA from whole blood_1848345023_73103

value: Control_Mutation Neg

value: Female


title: genomic DNA from whole blood_1848345023_73102

value: breast (DCIS)


title: PDAC_sample1

description: PDAC sample 1 of 7

value: PDAC tissue


title: genomic DNA from whole blood_1848345023_73101

value: White


title: A188_highN_d30_2

tag: inbred line

tag: treatment

value: 15mM nitrate supply

tag: plant age

value: 30 days


title: genomic DNA from whole blood_1848345023_3504

value: Case_Mutation Pos

tag: 2nd diagnosis

tag: age at 2nd diagnosis

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).


title: genomic DNA from whole blood_1848345023_73095

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).

tag: breast and ovarian cancer in same person in the family

value: yes

tag: number of relatives in the family dignosed with breast cancers before age 50


title: genomic DNA from whole blood_1848345023_73131

tag: study id number

tag: classification for analysis

tag: gender


title: genomic DNA from whole blood_1848345023_73090

tag: race

tag: age at blood sample collection


title: genomic DNA from whole blood_1848345023_73123

tag: 1st diagnosis

value: ALL

tag: age at 1st diagnosis


title: genomic DNA from whole blood_1848345023_73099

value: Breast

value: Skin


title: genomic DNA from whole blood_1848345023_73081

tag: number of the members of the same family (1st degree relatives) on the arrays.

tag: relatives on the array.


title: genomic DNA from whole blood_1848345023_73083


title: genomic DNA from whole blood_1848345023_73147

tag: 2nd diagnosis


title: genomic DNA from whole blood_1848345023_73026


title: genomic DNA from whole blood_1848345023_73060

value: Breast (DCIS)


title: genomic DNA from whole blood_1848345023_73080

value: Case_Mutation Neg

tag: age at 2nd diagnosis


title: PDAC_sample5

description: PDAC sample 5 of 7

tag: tissue

value: male

value: pooled of 11 normal pancreatic tissues

value: mixed


title: genomic DNA from whole blood_1848345023_73021

value: breast

tag: number of 1st degree relatives with breast cancer (sister, mother, daughter).

tag: number of 1st degree relatives with ovarian cancer (sister, mother, daughter).


title: genomic DNA from whole blood_1848345023_73030

value: Female

value: Melanoma

tag: number of 2nd degree relatives with breast cancer (grandmother, aunt, niece)

tag: number of 2nd degree relatives with ovarian cancer (grandmother, aunt, niece).


title: genomic DNA from whole blood_1848345023_1049

value: Ovary

tag: number of relatives in the family dignosed with breast cancers before age 50


title: genomic DNA from whole blood_1848345023_72082

tag: study id number

value: White

value: DCIS


title: genomic DNA from whole blood_1848345023_73112

tag: classification for analysis

value: Control_Mutation Pos

value: Native American/African American


title: genomic DNA from whole blood_1848345023_73058

value: Control_Mutation Neg

tag: gender


title: genomic DNA from whole blood_1848345023_73116

tag: race


title: genomic DNA from whole blood_1848345023_73009

value: Black, African American

tag: age at blood sample collection


title: genomic DNA from whole blood_1848345023_72981

tag: 1st diagnosis


title: genomic DNA from whole blood_1848345023_72979


title: genomic DNA from whole blood_1848345023_72976

value: Case_Mutation Pos

value: Breast

tag: age at 1st diagnosis


title: genomic DNA from whole blood_1848345023_612

tag: number of the members of the same family (1st degree relatives) on the arrays.


title: genomic DNA from whole blood_1848345023_73057

tag: relatives on the array.


title: Colorectal carcinoma CRC19 [MCIp]

city: Regensburg

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

institute: University Hospital Regensburg

description: Comparative MCIp-on-Chip for colorectal carcinoma and normal human colon

hyb_protocol: Comparative MCIp hybridizations on CpG island oligonucleotide microarrays (Agilent) were performed using the recommended, stringent protocol (Agilent).

scan_protocol: Scanned on an Agilent scanner at 5 µm resolution. Images were analysed and data extracted using Agilent Feature Extraction Software (version 9.5.1).

data_processing: Linear normalized, background subtracted VALUE data were obtained from log10 transformed, processed Red signal/processed Green signal values derived from image analysis with Agilent Feature Extraction Software (version 9.5.1).  Processed signal intensities were further normalized using GC-dependent regression and imported into Microsoft Office Excel 2007 for further analysis.

label: Alexa Fluor 5–dCTP

source_name: colorectal carcinoma

label_protocol: Enriched methylated DNA fragments of the high-salt MCIp fractions were labeled with Alexa Fluor 5–dCTP (cancer cells) and Alexa Fluor 3–dCTP (normal cells) using the BioPrime Total Genomic Labeling System (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

growth_protocol: Colorectal cancer samples were collected from 9 patients who underwent colon resection for biopsy-proven invasive colorectal adenocarcinoma at the University of Regensburg. The study was performed in agreement with the Institutional ethical review board of the University of Regensburg (05/003). DNA from frozen colon tissues was isolated using the PUREGENE™ DNA Purification Kit (Gentra, Minneapolis, USA) according to the supplier’s recommendation. Three normal colon DNAs (male, age 50-63) were purchased from BioChain Institute Inc. (Hayward, CA)

extract_protocol: MCIp enrichment of methylated DNA was performed essentially as described (Gebhard et al. 2006, Cancer Research). In brief, genomic DNA was sonicated to a mean fragment size of 350-400 bp. Two µg of each sample were incubated with 150 µl Protein A-Sepharose 4 Fast Flow beads (GE Healthcare) coated with 60 µg purified MBD-Fc protein in 2 ml Ultrafree-MC centrifugal filter devices (Amicon/Millipore) for 3 h at 4°C in buffer containing 300 mM NaCl. Beads were centrifuged to recover unbound DNA fragments (300 mM fraction) and subsequently washed with buffers containing increasing NaCl concentrations (400, 500, 550 mM). Densely CpG-methylated DNA was eluted with a high-salt buffer (1000 mM NaCl) and all fractions were desalted using the MinElute PCR purification kit (Qiagen). The separation of CpG methylation densities of individual MCIp fractions was controlled by qPCR using primers covering the imprinted SNRPN

value: female

tag: age

tag: crc location

value: Sigma-Ca

tag: ms status

value: microsatellite stable (MSS)

tag: kras- and braf mutational status

value: KRAS-wt; BRAF-wt

label: Alexa Fluor 3–dCTP

source_name: normal colon

tag: sample

value: normal colon; mixture of three samples (age 50-63)


title: Colorectal carcinoma CRC15 [MCIp]

value: male

value: KRAS-mut; BRAF-wt


title: Colorectal carcinoma CRC21 [MCIp]

value: Colon-Ca

value: not available


title: Colorectal carcinoma CRC17 [MCIp]