title: HUVEC_CA-STAT6-Ad #1

status: Public on May 01 2011

city: Tokyo

first: Yasuharu

last: Kanki

address: 4-6-1 Komaba, Meguro-ku

institute: The University of Tokyo

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix GeneChip Operating Software (GCOS) Version 1.0. with target intensity=100.

source_name: HUVEC, CA-STAT6-Adenovirus 48h #1

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Total RNAs were extracted using Trizol (Invitrogen). 2 micrograms of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix.

tag: cell

value: HUVEC

tag: infection

value: Constitutive Active STAT6 Adenovirus for 48h #1

tag: treatment

value: Ad-CA-STAT6 #1


title: HUVEC_CA-STAT6-Ad #2

type: RNA

country: Japan

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: HUVEC, CA-STAT6-Adenovirus 48h #2

value: Constitutive Active STAT6 Adenovirus for 48h #2

value: Ad-CA-STAT6 #2


title: Clear-cell renal cell carcinoma AV D

status: Public on May 28 2011

city: Rennes

first: Julien

last: Edeline

address: Av prof leon Bernard

country: France

institute: CNRS-Université Rennes1

hyb_protocol: 750 ng of the two cDNA labelled Cyanine 3 and Cyanine 5 were hybridizated using the kit In-Situ Hybridization Kit Plus - PN 5184-3568  - Agilent Technologies

scan_protocol: Agilent Technologies Scanner G2505B US22502565  Agilent Technologies Scanner G2505B US22502565 Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Clear-cell renal cell carcinoma AV D

label_protocol: cRNA were amplified from 350 ng of total RNA were amplified and fluorescent cDNA were synthesis from cRNA using the kit Agilent Low RNA Input Fluorescent Linear Amplification Kit - PN 5184-3523 - Agilent Technologies

extract_protocol: Total RNA was extracted from snap-frozen tumours using the Qiamp total RNA kit - PN 74104 -QIAGEN, Hilden, Germany after histological control.

treatment_protocol: Immediately after nephrectomy, a sample was taken from the tumor and frozen in liquid nitrogen

tag: age at diagnosis (y)

tag: t (tnm stage)

tag: n (tnm stage)

tag: m (tnm stage)

tag: fuhrman grade

tag: renal vein involvement

tag: inferior vena cava involvement

tag: peri-nephric fat involvement

tag: sarcomatoid component

tag: tumor necrosis

tag: microvascular invasion

tag: microvascular density (mvd)

tag: progression (1=yes, 0=no)

tag: death (1=yes, 0=no)

tag: death from cancer (1=yes, 0=no)

tag: tissue

value: Clear-cell renal cell carcinoma

tag: survival time

source_name: Total RNA from pooled tumor RNA samples

tag: sample type

value: Total RNA from pooled tumor RNA samples


title: Clear-cell renal cell carcinoma MO R

source_name: Clear-cell renal cell carcinoma MO R

tag: age at diagnosis (y)

tag: t (tnm stage)


title: Clear-cell renal cell carcinoma BO M

source_name: Clear-cell renal cell carcinoma BO M

tag: n (tnm stage)

tag: m (tnm stage)


title: Clear-cell renal cell carcinoma BO G

source_name: Clear-cell renal cell carcinoma BO G

tag: fuhrman grade

tag: renal vein involvement


title: Clear-cell renal cell carcinoma BR M

source_name: Clear-cell renal cell carcinoma BR M

tag: inferior vena cava involvement

tag: peri-nephric fat involvement


title: Clear-cell renal cell carcinoma DU B

source_name: Clear-cell renal cell carcinoma DU B

tag: sarcomatoid component

tag: tumor necrosis


title: HUVEC_si-STAT6 Oligo1,IL-4_4h

source_name: HUVEC, IL-4 4h, si-STAT6 Oligo1

tag: cell

tag: stimulation

value: IL-4 treatment for 4h

tag: treatment

value: si-STAT6 Oligo1


title: Clear-cell renal cell carcinoma GI F

source_name: Clear-cell renal cell carcinoma GI F

tag: microvascular invasion

tag: progression (1=yes, 0=no)

tag: death (1=yes, 0=no)

tag: death from cancer (1=yes, 0=no)


title: HUVEC_IL-4,4h

source_name: HUVEC, IL-4 4h


title: HUVEC_si-STAT6 Oligo2,IL-4_4h

source_name: HUVEC, IL-4 4h, si-STAT6 Oligo2

value: si-STAT6 Oligo2


title: C_AN07176_T

city: Los Angeles

first: Irina

last: Voineagu

state: CA

address: 695 Chrles E Young Dr

country: USA

institute: UCLA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Log2 transformation and Quantile normalization uzing the R Lumi package.
The normalized data file contains log2 transformed and quantile normalized data for all probes that fulfilled the robust expression criteria (i.e detection pvalue<0.05 for at least half of the samples). Expression data for cortex and cerebellum are listed separately as the two datasets were normalized separately and contain different number of probes that fulfilled the expression criteria.

label: Biotin

source_name: postmortem brain tissue

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total RNA was isolated using the RNeasy Mini kit  according to the protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: disease status

value: controls

tag: tissue (brain region)

value: Temporal cortex


title: HUVEC_control-Adenovirus

source_name: HUVEC, Control-Adenovirus 48h

tag: infection

value: Control-Adenovirus for 48h

value: Ad-Ctrl


title: Clear-cell renal cell carcinoma CO A

source_name: Clear-cell renal cell carcinoma CO A

tag: age at diagnosis (y)

tag: t (tnm stage)

tag: n (tnm stage)

tag: m (tnm stage)

tag: survival time

tag: tissue

tag: sample type


title: Clear-cell renal cell carcinoma BA G

source_name: Clear-cell renal cell carcinoma BA G

tag: fuhrman grade

tag: renal vein involvement

tag: peri-nephric fat involvement

tag: sarcomatoid component

tag: tumor necrosis


title: C_AN00142_T


title: HUVEC_si-control IL-4_0h

source_name: HUVEC, IL-4 0h, si-control #1

tag: cell

tag: stimulation

value: IL-4 treatment for 0h

tag: treatment

value: si-control #1


title: HUVEC_IL-4,8h

source_name: HUVEC, IL-4 8h

value: IL-4 treatment for 8h


title: HUVEC_IL-4,1h

source_name: HUVEC, IL-4 1h

value: HUVEC

value: IL-4 treatment for 1h


title: Clear-cell renal cell carcinoma BA B

source_name: Clear-cell renal cell carcinoma BA B

tag: inferior vena cava involvement

tag: microvascular invasion

tag: microvascular density (mvd)

tag: progression (1=yes, 0=no)

tag: death (1=yes, 0=no)

tag: death from cancer (1=yes, 0=no)

source_name: Total RNA from pooled tumor RNA samples


title: HUVEC_IL-4,0h

source_name: HUVEC, IL-4 0h


title: HUVEC_IL-4,2h

source_name: HUVEC, IL-4 2h

value: IL-4 treatment for 2h


title: C_AN19760_T

tag: disease status

tag: tissue (brain region)


title: C_AN01125_T


title: C_AN00544_T


title: HUVEC_si-control IL-4_4h

source_name: HUVEC, IL-4 4h, si-control #1


title: C_AN12240_T


title: C_AN04479_T


title: C_AN14757_T


title: A_AN00764_T

value: autism


title: C_AN17425_T


title: A_AN08873_T


title: C_AN10028_T


title: C_AN19442_T


title: C_AN10833_T


title: A_AN09730_T


title: A_AN08792_T


title: A_AN06420_T


title: C_AN15566_T


title: A_AN17777_T


title: HUVEC_IL-4,16h

source_name: HUVEC, IL-4 16h

value: IL-4 treatment for 16h


title: A_AN17138_T


title: A_AN19511_T


title: A_AN01570_T


title: A_AN16641_T


title: A_AN12457_T


title: A_AN08166_T


title: C_AN00142_F

value: Frontal cortex


title: C_AN00544_F


title: C_AN01410_F


title: C_AN19760_F


title: C_AN01125_F


title: C_AN03217_F


title: C_AN15566_F


title: C_AN14757_F


title: C_AN19442_F


title: A_AN11989_T


title: C_AN10028_F


title: C_AN10833_F


title: A_AN00764_F


title: C_AN12137_F


title: C_AN12240_F


title: C_AN04479_F


title: C_AN07176_F


title: A_AN00493_F


title: A_AN08166_F


title: A_AN06420_F


title: A_AN01570_F


title: A_AN08873_F


title: A_AN17777_F


title: A_AN08792_F


title: A_AN19511_F


title: A_AN11989_F


title: A_AN17138_F


title: A_AN16641_F


title: C_AN19442_C

value: Cerebellum


title: A_AN12457_F


title: A_AN17254_F


title: C_AN00142_C


title: A_AN16115_F


title: C_AN01125_C


title: C_AN19760_C


title: C_AN10028_C


title: C_AN13295_C


title: C_AN17425_C


title: C_AN03217_C


title: C_AN14757_C


title: C_AN15566_C


title: A_AN08873_C


title: C_AN12240_C


title: A_AN06420_C


title: A_AN01570_C


title: A_AN17254_C


title: A_AN08166_C


title: A_AN16641_C


title: C_AN17425_F


title: A_AN00764_C


title: A_AN19511_C


title: A_AN16115_C


title: A_AN11989_C


title: 160

status: Public on Apr 27 2011

city: Edmonton

first: Kathryn

last: Graham

state: Alberta

address: 11560 University Ave

department: Oncology

country: Canada

institute: University of Alberta

description: gene expression in breast cancer

hyb_protocol: 1.5 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) 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 immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities.  The data was them imported into GeneSpring 7.3.1 and default normalization procedures were used.

source_name: primary breast cancer

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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.

extract_protocol: A polytron was used to disrupt tissue in the pressence of Trizol (SigmaAldrich). The sample was then phenol/chloroform extracted, the aquaous layer was adjusted to 30% ethanol and applied to an RNeasy column (Qiagen) according to the manufacturer's instructions.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: disease state

value: primary breast tumor


title: 161

description: gene expression in breast cancer


title: 173

description: gene expression in breast cancer


title: 172

description: gene expression in breast cancer


title: 174

description: gene expression in breast cancer


title: 169

description: gene expression in breast cancer


title: 176

description: gene expression in breast cancer


title: 170

description: gene expression in breast cancer


title: 167

description: gene expression in breast cancer


title: 168

description: gene expression in breast cancer


title: 164

description: gene expression in breast cancer


title: 171

description: gene expression in breast cancer


title: 166

description: gene expression in breast cancer


title: 156

description: gene expression in breast cancer


title: 163

description: gene expression in breast cancer


title: 162

description: gene expression in breast cancer


title: 165

description: gene expression in breast cancer


title: 158

description: gene expression in breast cancer


title: 157

description: gene expression in breast cancer


title: 175

description: gene expression in breast cancer


title: 159

description: gene expression in breast cancer


title: 154

description: gene expression in breast cancer


title: 153

description: gene expression in breast cancer


title: 152

description: gene expression in breast cancer


title: 149

description: gene expression in breast cancer


title: 148

description: gene expression in breast cancer


title: 150

description: gene expression in breast cancer


title: 155

description: gene expression in breast cancer


title: 151

description: gene expression in breast cancer


title: 144

description: gene expression in breast cancer


title: 147

description: gene expression in breast cancer


title: 145

description: gene expression in breast cancer


title: 140

description: gene expression in breast cancer


title: 143

description: gene expression in breast cancer


title: 136

description: gene expression in breast cancer


title: 137

description: gene expression in breast cancer


title: 139

description: gene expression in breast cancer


title: 141

description: gene expression in breast cancer


title: 146

description: gene expression in breast cancer


title: A_AN09730_F


title: 142

description: gene expression in breast cancer


title: 133

description: gene expression in breast cancer


title: 132

description: gene expression in breast cancer


title: 138

description: gene expression in breast cancer


title: 134

description: gene expression in breast cancer


title: 135

description: gene expression in breast cancer


title: 129

description: gene expression in breast cancer


title: 130

description: gene expression in breast cancer


title: 131

description: gene expression in breast cancer


title: 127

description: gene expression in breast cancer


title: 126

description: gene expression in breast cancer


title: 128

description: gene expression in breast cancer


title: 123

description: gene expression in breast cancer


title: 120

description: gene expression in breast cancer


title: 116

description: gene expression in breast cancer


title: 122

description: gene expression in breast cancer


title: 125

description: gene expression in breast cancer


title: 121

description: gene expression in breast cancer


title: 124

description: gene expression in breast cancer


title: 118

description: gene expression in breast cancer


title: 119

description: gene expression in breast cancer


title: 109

description: gene expression in breast cancer


title: 111

description: gene expression in breast cancer


title: 107

description: gene expression in breast cancer


title: 112

description: gene expression in breast cancer


title: 105

description: gene expression in breast cancer


title: 115

description: gene expression in breast cancer


title: 103

description: gene expression in breast cancer


title: 114

description: gene expression in breast cancer


title: 108

description: gene expression in breast cancer


title: 101

description: gene expression in breast cancer


title: 113

description: gene expression in breast cancer


title: 110

description: gene expression in breast cancer


title: 104

description: gene expression in breast cancer


title: 117

description: gene expression in breast cancer


title: 99

description: gene expression in breast cancer


title: 100

description: gene expression in breast cancer


title: 106

description: gene expression in breast cancer


title: 102

description: gene expression in breast cancer


title: 98

description: gene expression in breast cancer


title: 95

description: gene expression in breast cancer


title: 91

description: gene expression in breast cancer


title: 84

description: gene expression in breast cancer


title: 93

description: gene expression in breast cancer


title: 92

description: gene expression in breast cancer


title: 86

description: gene expression in breast cancer


title: 90

description: gene expression in breast cancer


title: 97

description: gene expression in breast cancer


title: 82

description: gene expression in breast cancer


title: 83

description: gene expression in breast cancer


title: 89

description: gene expression in breast cancer


title: 87

description: gene expression in breast cancer


title: 94

description: gene expression in breast cancer


title: 78

description: gene expression in breast cancer


title: 80

description: gene expression in breast cancer


title: 88

description: gene expression in breast cancer


title: 85

description: gene expression in breast cancer


title: 76

description: gene expression in breast cancer


title: 81

description: gene expression in breast cancer


title: 75

description: gene expression in breast cancer


title: 79

description: gene expression in breast cancer


title: 72

description: gene expression in breast cancer


title: 96

description: gene expression in breast cancer


title: 77

description: gene expression in breast cancer


title: 73

description: gene expression in breast cancer


title: 74

description: gene expression in breast cancer


title: 70

description: gene expression in breast cancer


title: 71

description: gene expression in breast cancer


title: 69

description: gene expression in breast cancer


title: 67

description: gene expression in breast cancer


title: 68

description: gene expression in breast cancer


title: 64

description: gene expression in breast cancer


title: 61

description: gene expression in breast cancer


title: 62

description: gene expression in breast cancer


title: 60

description: gene expression in breast cancer


title: 59

description: gene expression in breast cancer


title: 66

description: gene expression in breast cancer


title: 56

description: gene expression in breast cancer


title: 65

description: gene expression in breast cancer


title: 55

description: gene expression in breast cancer


title: 63

description: gene expression in breast cancer


title: 57

description: gene expression in breast cancer


title: 58

description: gene expression in breast cancer


title: 53

description: gene expression in breast cancer


title: 54

description: gene expression in breast cancer


title: 49

description: gene expression in breast cancer


title: 47

description: gene expression in breast cancer


title: 50

description: gene expression in breast cancer


title: 46

description: gene expression in breast cancer


title: 52

description: gene expression in breast cancer


title: 48

description: gene expression in breast cancer


title: 44

description: gene expression in breast cancer


title: 51

description: gene expression in breast cancer


title: 45

description: gene expression in breast cancer


title: 41

description: gene expression in breast cancer


title: 42

description: gene expression in breast cancer


title: 37

description: gene expression in breast cancer


title: 38

description: gene expression in breast cancer


title: 34

description: gene expression in breast cancer


title: 40

description: gene expression in breast cancer


title: 43

description: gene expression in breast cancer


title: 39

description: gene expression in breast cancer


title: 35

description: gene expression in breast cancer


title: 36

description: gene expression in breast cancer


title: 31

description: gene expression in breast cancer


title: 28

description: gene expression in breast cancer


title: 22

description: gene expression in breast cancer


title: 27

description: gene expression in breast cancer


title: 24

description: gene expression in breast cancer


title: 20

description: gene expression in breast cancer


title: 29

description: gene expression in breast cancer


title: 32

description: gene expression in breast cancer


title: 23

description: gene expression in breast cancer


title: 25

description: gene expression in breast cancer


title: 16

description: gene expression in breast cancer


title: 19

description: gene expression in breast cancer


title: 30

description: gene expression in breast cancer


title: 26

description: gene expression in breast cancer


title: 17

description: gene expression in breast cancer


title: 13

description: gene expression in breast cancer


title: 14

description: gene expression in breast cancer


title: 18

description: gene expression in breast cancer


title: 21

description: gene expression in breast cancer


title: 9

description: gene expression in breast cancer


title: 7

description: gene expression in breast cancer


title: 6

description: gene expression in breast cancer


title: 5

description: gene expression in breast cancer


title: 15

description: gene expression in breast cancer


title: 12

description: gene expression in breast cancer


title: 33

description: gene expression in breast cancer


title: 10

description: gene expression in breast cancer


title: 4

description: gene expression in breast cancer


title: 3

description: gene expression in breast cancer


title: 1

description: gene expression in breast cancer


title: 11

description: gene expression in breast cancer


title: P164M

status: Public on Mar 11 2011

city: Goettingen

first: Marian

last: Grade

address: Robert-Koch-Str. 40

department: Surgery

country: Germany

institute: University Medical Center Goettingen, Georg-August-University

description: Human pretherapeutic rectal cancer patient biopsy sample P164M

hyb_protocol: 1.5 mg of Cy3-labeled cRNA was hybridized to an oligonucleotide-based Whole Human Genome Microarray (4x44K, Agilent Technologies) and incubated at 65˚C for 17 hours.

scan_protocol: Slides were washed and scanned using an Agilent G2565BA scanner.

data_processing: Raw data were extracted using the Feature Extraction software version 9.1 (Agilent Technologies). Median signal intensities from the Feature Extraction Software were converted to log2 and quantile normalized using the R package “limma”.

source_name: Pretherapeutic rectal cancer patient biopsy

label_protocol: 1 µg of total RNA was labeled with Cy3 using the Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's recommendations (Agilent Technologies, Santa Clara, CA). Quantity and efficiency of the labeled amplified cRNA were determined using the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.

growth_protocol: Biospies from patients not cell lines were used for analyses

extract_protocol: Biopsies were immediately stored in RNAlater (Qiagen, Hilden, Germany). Subsequently, RNA and DNA was isolated using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer´s instructions.  Nucleic acid quantity, quality and purity were determined using a spectrophotometer (Nanodrop, Rockland, DE) and a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: No treatment prior to expression profiling analysis was performed.

tag: patient id

value: rectal cancer

tag: age

tag: gender

value: male

tag: tissue

value: mucosa

tag: genome/variation

value: mutated KRAS


title: P160M

description: Human pretherapeutic rectal cancer patient biopsy sample P160M

value: wild type KRAS


title: P138M

description: Human pretherapeutic rectal cancer patient biopsy sample P138M


title: P161M

description: Human pretherapeutic rectal cancer patient biopsy sample P161M

value: female


title: P131M

description: Human pretherapeutic rectal cancer patient biopsy sample P131M


title: P152M

description: Human pretherapeutic rectal cancer patient biopsy sample P152M


title: P136M

description: Human pretherapeutic rectal cancer patient biopsy sample P136M


title: P158M

description: Human pretherapeutic rectal cancer patient biopsy sample P158M


title: P159M

description: Human pretherapeutic rectal cancer patient biopsy sample P159M


title: P125M

description: Human pretherapeutic rectal cancer patient biopsy sample P125M


title: P165M

description: Human pretherapeutic rectal cancer patient biopsy sample P165M


title: P119M

description: Human pretherapeutic rectal cancer patient biopsy sample P119M


title: P151M

description: Human pretherapeutic rectal cancer patient biopsy sample P151M


title: P139M

description: Human pretherapeutic rectal cancer patient biopsy sample P139M


title: 8

description: gene expression in breast cancer


title: P167M

description: Human pretherapeutic rectal cancer patient biopsy sample P167M


title: P143M

description: Human pretherapeutic rectal cancer patient biopsy sample P143M


title: P132M

description: Human pretherapeutic rectal cancer patient biopsy sample P132M


title: P128M

description: Human pretherapeutic rectal cancer patient biopsy sample P128M


title: 2

description: gene expression in breast cancer


title: P149M

description: Human pretherapeutic rectal cancer patient biopsy sample P149M


title: P123M

description: Human pretherapeutic rectal cancer patient biopsy sample P123M


title: P115M

description: Human pretherapeutic rectal cancer patient biopsy sample P115M


title: P130M

description: Human pretherapeutic rectal cancer patient biopsy sample P130M


title: P124M

description: Human pretherapeutic rectal cancer patient biopsy sample P124M


title: P112M

description: Human pretherapeutic rectal cancer patient biopsy sample P112M


title: P110M

description: Human pretherapeutic rectal cancer patient biopsy sample P110M


title: P090M

description: Human pretherapeutic rectal cancer patient biopsy sample P090M


title: P104M

description: Human pretherapeutic rectal cancer patient biopsy sample P104M


title: P092M

description: Human pretherapeutic rectal cancer patient biopsy sample P092M


title: P108M

description: Human pretherapeutic rectal cancer patient biopsy sample P108M


title: P103M

description: Human pretherapeutic rectal cancer patient biopsy sample P103M


title: P083M

description: Human pretherapeutic rectal cancer patient biopsy sample P083M


title: P106M

description: Human pretherapeutic rectal cancer patient biopsy sample P106M


title: P102M

description: Human pretherapeutic rectal cancer patient biopsy sample P102M


title: P071M

description: Human pretherapeutic rectal cancer patient biopsy sample P071M


title: P107M

description: Human pretherapeutic rectal cancer patient biopsy sample P107M


title: P070M

description: Human pretherapeutic rectal cancer patient biopsy sample P070M


title: P081M

description: Human pretherapeutic rectal cancer patient biopsy sample P081M


title: P114M

description: Human pretherapeutic rectal cancer patient biopsy sample P114M


title: P100M

description: Human pretherapeutic rectal cancer patient biopsy sample P100M


title: P066M

description: Human pretherapeutic rectal cancer patient biopsy sample P066M


title: P089M

description: Human pretherapeutic rectal cancer patient biopsy sample P089M


title: P118M

description: Human pretherapeutic rectal cancer patient biopsy sample P118M


title: P116M

description: Human pretherapeutic rectal cancer patient biopsy sample P116M


title: P062M

description: Human pretherapeutic rectal cancer patient biopsy sample P062M


title: P057M

description: Human pretherapeutic rectal cancer patient biopsy sample P057M


title: P073M

description: Human pretherapeutic rectal cancer patient biopsy sample P073M


title: P093M

description: Human pretherapeutic rectal cancer patient biopsy sample P093M


title: P055M

description: Human pretherapeutic rectal cancer patient biopsy sample P055M


title: P052M

description: Human pretherapeutic rectal cancer patient biopsy sample P052M


title: P056M

description: Human pretherapeutic rectal cancer patient biopsy sample P056M


title: P050M

description: Human pretherapeutic rectal cancer patient biopsy sample P050M


title: P051M

description: Human pretherapeutic rectal cancer patient biopsy sample P051M


title: P007M

description: Human pretherapeutic rectal cancer patient biopsy sample P007M


title: P165T

description: Human pretherapeutic rectal cancer patient biopsy sample P165T

value: tumor


title: P160T

description: Human pretherapeutic rectal cancer patient biopsy sample P160T


title: P036M

description: Human pretherapeutic rectal cancer patient biopsy sample P036M


title: P043M

description: Human pretherapeutic rectal cancer patient biopsy sample P043M


title: P158T

description: Human pretherapeutic rectal cancer patient biopsy sample P158T


title: P161T

description: Human pretherapeutic rectal cancer patient biopsy sample P161T


title: P049M

description: Human pretherapeutic rectal cancer patient biopsy sample P049M


title: P048M

description: Human pretherapeutic rectal cancer patient biopsy sample P048M


title: P045M

description: Human pretherapeutic rectal cancer patient biopsy sample P045M


title: P152T

description: Human pretherapeutic rectal cancer patient biopsy sample P152T


title: P038M

description: Human pretherapeutic rectal cancer patient biopsy sample P038M


title: P031M

description: Human pretherapeutic rectal cancer patient biopsy sample P031M


title: P159T

description: Human pretherapeutic rectal cancer patient biopsy sample P159T


title: P167T

description: Human pretherapeutic rectal cancer patient biopsy sample P167T


title: P006M

description: Human pretherapeutic rectal cancer patient biopsy sample P006M


title: P151T

description: Human pretherapeutic rectal cancer patient biopsy sample P151T


title: P164T

description: Human pretherapeutic rectal cancer patient biopsy sample P164T


title: P139T

description: Human pretherapeutic rectal cancer patient biopsy sample P139T


title: P128T

description: Human pretherapeutic rectal cancer patient biopsy sample P128T


title: P030M

description: Human pretherapeutic rectal cancer patient biopsy sample P030M


title: P149T

description: Human pretherapeutic rectal cancer patient biopsy sample P149T


title: P116T

description: Human pretherapeutic rectal cancer patient biopsy sample P116T


title: P143T

description: Human pretherapeutic rectal cancer patient biopsy sample P143T


title: P130T

description: Human pretherapeutic rectal cancer patient biopsy sample P130T


title: P123T

description: Human pretherapeutic rectal cancer patient biopsy sample P123T


title: P136T

description: Human pretherapeutic rectal cancer patient biopsy sample P136T


title: P108T

description: Human pretherapeutic rectal cancer patient biopsy sample P108T


title: P132T

description: Human pretherapeutic rectal cancer patient biopsy sample P132T


title: P124T

description: Human pretherapeutic rectal cancer patient biopsy sample P124T


title: P118T

description: Human pretherapeutic rectal cancer patient biopsy sample P118T


title: P112T

description: Human pretherapeutic rectal cancer patient biopsy sample P112T


title: P138T

description: Human pretherapeutic rectal cancer patient biopsy sample P138T


title: P115T

description: Human pretherapeutic rectal cancer patient biopsy sample P115T


title: P033M

description: Human pretherapeutic rectal cancer patient biopsy sample P033M


title: P110T

description: Human pretherapeutic rectal cancer patient biopsy sample P110T


title: P125T

description: Human pretherapeutic rectal cancer patient biopsy sample P125T


title: P131T

description: Human pretherapeutic rectal cancer patient biopsy sample P131T


title: P114T

description: Human pretherapeutic rectal cancer patient biopsy sample P114T


title: P113T

description: Human pretherapeutic rectal cancer patient biopsy sample P113T


title: P119T

description: Human pretherapeutic rectal cancer patient biopsy sample P119T


title: P111M

description: Human pretherapeutic rectal cancer patient biopsy sample P111M


title: P106T

description: Human pretherapeutic rectal cancer patient biopsy sample P106T


title: P111T

description: Human pretherapeutic rectal cancer patient biopsy sample P111T


title: P104T

description: Human pretherapeutic rectal cancer patient biopsy sample P104T


title: P113M

description: Human pretherapeutic rectal cancer patient biopsy sample P113M


title: P103T

description: Human pretherapeutic rectal cancer patient biopsy sample P103T


title: P107T

description: Human pretherapeutic rectal cancer patient biopsy sample P107T


title: P102T

description: Human pretherapeutic rectal cancer patient biopsy sample P102T


title: P100T

description: Human pretherapeutic rectal cancer patient biopsy sample P100T


title: P083T

description: Human pretherapeutic rectal cancer patient biopsy sample P083T


title: P073T

description: Human pretherapeutic rectal cancer patient biopsy sample P073T


title: P071T

description: Human pretherapeutic rectal cancer patient biopsy sample P071T


title: P090T

description: Human pretherapeutic rectal cancer patient biopsy sample P090T


title: P093T

description: Human pretherapeutic rectal cancer patient biopsy sample P093T


title: P055T

description: Human pretherapeutic rectal cancer patient biopsy sample P055T


title: P056T

description: Human pretherapeutic rectal cancer patient biopsy sample P056T


title: P081T

description: Human pretherapeutic rectal cancer patient biopsy sample P081T


title: P070T

description: Human pretherapeutic rectal cancer patient biopsy sample P070T


title: P057T

description: Human pretherapeutic rectal cancer patient biopsy sample P057T


title: P062T

description: Human pretherapeutic rectal cancer patient biopsy sample P062T


title: P052T

description: Human pretherapeutic rectal cancer patient biopsy sample P052T


title: P050T

description: Human pretherapeutic rectal cancer patient biopsy sample P050T


title: P051T

description: Human pretherapeutic rectal cancer patient biopsy sample P051T


title: P048T

description: Human pretherapeutic rectal cancer patient biopsy sample P048T


title: P049T

description: Human pretherapeutic rectal cancer patient biopsy sample P049T


title: P045T

description: Human pretherapeutic rectal cancer patient biopsy sample P045T


title: P033T

description: Human pretherapeutic rectal cancer patient biopsy sample P033T


title: P043T

description: Human pretherapeutic rectal cancer patient biopsy sample P043T


title: P089T

description: Human pretherapeutic rectal cancer patient biopsy sample P089T


title: P007T

description: Human pretherapeutic rectal cancer patient biopsy sample P007T


title: P038T

description: Human pretherapeutic rectal cancer patient biopsy sample P038T


title: P036T

description: Human pretherapeutic rectal cancer patient biopsy sample P036T


title: P006T

description: Human pretherapeutic rectal cancer patient biopsy sample P006T


title: P092T

description: Human pretherapeutic rectal cancer patient biopsy sample P092T


title: P030T

description: Human pretherapeutic rectal cancer patient biopsy sample P030T


title: P031T

description: Human pretherapeutic rectal cancer patient biopsy sample P031T


title: P066T

description: Human pretherapeutic rectal cancer patient biopsy sample P066T


title: Abcb4 knockout mouse treated with norUDCA for 4 weeks 2

status: Public on Feb 02 2011

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

hyb_protocol: Microarrays were hybridized in a volume of 1.5 ml at 55°C for 16 hours. After hybridization, arrays were washed with hybridization wash buffer and chemiluminescence rinse buffer. Enhanced chemiluminescent signals were generated by incubating arrays with alkaline phosphatase conjugated anti-digoxigenin antibody followed by incubation with chemiluminescence enhancing solution and a final addition of chemiluminescence substrate.

scan_protocol: Four images were collected for each microarray using the ABI 1700 Chemiluminescent Microarray Analyzer.

data_processing:
Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background and spot, and spatially normalized.
Expression values were imported into GeneSpring 6.2.1 (Silicon Genetics, Redwood, CA, USA) and processed according to Applied Biosystems standard procedure ("per chip" and "per gene" normalization). Data were filtered using the Cross-Gene Error Model (CEM); S/N >3 and Flag = 0.

label: Applied Biosystems Chemiluminescent RT Labeling Kit

organism: Mus musculus

source_name: mouse liver RNA

label_protocol: Each microarray was first pre-hybridized at 55°C for 1 hour in hybridization buffer with blocking reagent. Oligo(dT)-primed, DIG-labeled cDNA targets were fragmented, mixed with internal control target.

extract_protocol: Tissues were immediately snap-frozen in pre-chilled 2-methylbutane after excision and stored in liquid nitrogen. RNA was isolated using TrizolTM reagent according to the manufacturer’s protocol. RNA samples were analyzed using Agilent Bioanalyzer Lab-on-chip Nano 6000 to determine integrity, quality, and concentration of the samples. Only samples fulfilling the quality criteria (Ratio of 28S to 18S rRNA of >2.0) were used for further microarray analysis.

tag: strain

value: FVB/N

value: 3 months

value: liver

tag: genotype

value: Abcb4 KO

value: side-chain modified bile acid "norUDCA" for 4weeks


title: Normal Adult Brain (Methylation)

status: Public on Mar 07 2011

type: genomic

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

description: brain.adult

hyb_protocol: Standard Illumina Hybridisation Protocols

scan_protocol: Standard Illuminina Scanning Protocols

data_processing: Data were exported from Illumina Genome Studio (BeadStudio Methylation Analysis Module) and analysed using R.  Submitted data are those exported from Genome Studio.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Commercial Normal Tissue Sample

label_protocol: Genomic DNA (500 ng) from each sample was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo research Corporation, Orange, US) before being amplified and enzymatically fragmented (standard Illumina protocols)

extract_protocol: Genomic DNA was extracted using standard molecular biology protocols (pK digestion, phenol-chloroform extraction and ethanol precipitation)

value: Normal Adult Brain


title: Abcb4 knockout mouse treated with norUDCA for 4 weeks 1

tag: treatment


title: 02-TB-079-1C

status: Public on Jan 08 2010

city: Parkville

first: Oliver

last: Sieber

state: Victoria

address: 6th floor, Centre for Medical Research,  Royal Melbourne Hospital,  Royal Parade

department: Melbourne Tumour Biology Branch

country: Australia

institute: Ludwig Institute for Cancer Research

description: Location: Right; DukesStage: B; Age_Diag: 80; Gender: M; DFS_Time: 4.1; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Use the simpleaffy package in R/Bioconductor to calculate MAS5.0 calls. These values were subsequently normalized using quantile normalization.

source_name: primary colorectal adenocarcinoma

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Surgically isolated colorectal cancers were immediately frozen in liquid nitrogen. Total RNA was extracted from cancer tissue using Trizol reagent (Invitrogen).

tag: Location

value: Right; DukesStage:B; Age_Diag:80; Gender:M; DFS_Time:4.1; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 03-TB-040-1G

description: Location: Right; DukesStage: B; Age_Diag: 54; Gender: F; DFS_Time: 32.6; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:54; Gender:F; DFS_Time:32.6; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: 02-TB-064-1N

description: Location: Right; DukesStage: B; Age_Diag: 62; Gender: M; DFS_Time: 40; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:62; Gender:M; DFS_Time:40; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: spinal cord Olig2cre/DA-Cat at 4 days, biological replicate 1

status: Public on Dec 10 2009

city: SAN FRANCISCO

first: David

last: Rowitch

address: 513 Parnassus Ave, Medical Science Building

department: Neurology

institute: University of California San Francisco

description: ventrolateral spinal cord white matter was injected with 1% lysolecithin

hyb_protocol: Affymetrix 3' IVT

scan_protocol: Affymetrix 3' IVT

data_processing: BRB array Tools

source_name: ventrolateral spinal cord white matter, Olig2cre/DA-Cat at 4 days

label_protocol: Affymetrix 3' IVT

extract_protocol: RNA was extracted using the RNAqueous-Micro kit (Ambion), and RNA quality was checked on an Agilent Bioanalyser.

treatment_protocol: Demyelinated lesions were produced in the ventrolateral spinal cord white matter of 8- to 10-wk-old Olig2cre/DA-Cat, and wild-type littermate mice. Anesthesia was induced and maintained with inhalational isoflurane/oxygen, supplemented with 0.05 mL of buprenorphine (Vetergesic 0.05 mg/mL) given subcutaneously. Having exposed the spinal vertebrae at the level of T12/T13, tissue was cleared overlying the intervertebral space, and the dura was pierced with a dental needle just lateral to midline. A Hamilton needle was advanced through the pierced dura at an angle of 45° and 0.5 μL of 1% lysolecithin (L-α-lysophosphatidylcholine) was injected into the ventrolateral white matter. Unlesioned spinal cords or 14-dpl lesioned cords were removed fresh and snap-frozen in iso-pentane and stored at −80°C. Cords were subsequently cut as 50-μm-thick cryosections, and unlesioned white matter or 14-dpl lesions were manually isolated from the sections using a micro-scalpel (Fine Science Tools 10318-14). Approximately 80 sections were cut from each spinal cord to obtain 1 μg of RNA.

tag: developmental stage

value: Day 4


title: 04-TB-124-1B

description: Location: Rectum; DukesStage: B; Age_Diag: 66; Gender: M; DFS_Time: 44.8; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:B; Age_Diag:66; Gender:M; DFS_Time:44.8; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 03-TB-009-1I

description: Location: Left; DukesStage: B; Age_Diag: 30; Gender: F; DFS_Time: 59.5; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:30; Gender:F; DFS_Time:59.5; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 05-WH-067-1A

description: Location: Right; DukesStage: B; Age_Diag: 74; Gender: F; DFS_Time: 29.6; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:74; Gender:F; DFS_Time:29.6; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 03-TB-036-1B

description: Location: Rectum; DukesStage: B; Age_Diag: 63; Gender: M; DFS_Time: 57; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:B; Age_Diag:63; Gender:M; DFS_Time:57; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 01-TB-034-1C

description: Location: Left; DukesStage: B; Age_Diag: 70; Gender: M; DFS_Time: 52.8; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:70; Gender:M; DFS_Time:52.8; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 04-TB-075-1A

description: Location: Right; DukesStage: B; Age_Diag: 82; Gender: M; DFS_Time: 56.3; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:82; Gender:M; DFS_Time:56.3; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: spinal cord Olig2cre/DA-Cat at 4 days, biological replicate 2


title: 04-TB-076-1B

description: Location: Right; DukesStage: B; Age_Diag: 53; Gender: M; DFS_Time: 47.4; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:B; Age_Diag:53; Gender:M; DFS_Time:47.4; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: spinal cord Olig2cre/DA-Cat at 4 days, biological replicate 3


title: 03-TB-078-1B

description: Location: Right; DukesStage: B; Age_Diag: 60; Gender: M; DFS_Time: 28.5; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:60; Gender:M; DFS_Time:28.5; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 04-TB-021-1B

description: Location: Rectum; DukesStage: B; Age_Diag: 78; Gender: M; DFS_Time: 40.4; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:B; Age_Diag:78; Gender:M; DFS_Time:40.4; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 01-TB-032-1B

description: Location: Left; DukesStage: B; Age_Diag: 72; Gender: M; DFS_Time: 56.8; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:B; Age_Diag:72; Gender:M; DFS_Time:56.8; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 03-TB-061-1C

description: Location: Rectum; DukesStage: B; Age_Diag: 82; Gender: M; DFS_Time: 37; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:B; Age_Diag:82; Gender:M; DFS_Time:37; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 02-TB-074-1C

description: Location: Right; DukesStage: B; Age_Diag: 78; Gender: M; DFS_Time: 14.2; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:78; Gender:M; DFS_Time:14.2; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: spinal cord wild type at 4 days, biological replicate 3

source_name: ventrolateral spinal cord white matter, wild type at 4 days

value: Wild type


title: 02-TB-045-1I

description: Location: Rectum; DukesStage: B; Age_Diag: 61; Gender: M; DFS_Time: 55.7; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:B; Age_Diag:61; Gender:M; DFS_Time:55.7; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 03-TB-021-1B

description: Location: Right; DukesStage: B; Age_Diag: 79; Gender: F; DFS_Time: 42.9; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:79; Gender:F; DFS_Time:42.9; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 05-WH-052-1A

description: Location: Right; DukesStage: B; Age_Diag: 92; Gender: F; DFS_Time: 12.1; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:92; Gender:F; DFS_Time:12.1; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: spinal cord wild type at 4 days, biological replicate 2

value: Day 4


title: spinal cord wild type at 4 days, biological replicate 1


title: 02-TB-035-1F

description: Location: Right; DukesStage: B; Age_Diag: 68; Gender: F; DFS_Time: 45.3; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:B; Age_Diag:68; Gender:F; DFS_Time:45.3; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: spinal cord Olig2cre/DA-Cat at 15 days, biological replicate 3

description: ventrolateral spinal cord white matter was injected with 1% lysolecithin

source_name: ventrolateral spinal cord white matter, Olig2cre/DA-Cat at 15 days

value: Day 15


title: spinal cord Olig2cre/DA-Cat at 15 days, biological replicate 1


title: spinal cord Olig2cre/DA-Cat at 15 days, biological replicate 2


title: 01-TB-020-1B

description: Location: Rectum; DukesStage: A; Age_Diag: 67; Gender: F; DFS_Time: 22.8; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:A; Age_Diag:67; Gender:F; DFS_Time:22.8; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 03-TB-008-1I

description: Location: Rectum; DukesStage: A; Age_Diag: 74; Gender: M; DFS_Time: 54.4; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:A; Age_Diag:74; Gender:M; DFS_Time:54.4; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: spinal cord wild type at 15 days, biological replicate 1

source_name: ventrolateral spinal cord white matter, wild type at 15 days


title: spinal cord wild type at 15 days, biological replicate 2


title: spinal cord wild type at 15 days, biological replicate 3


title: 13688410 - Anther L.erecta set2 vs Anther SPL set2

status: Public on Dec 07 2008

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: What are the gene expressed during meiosis pathway in Arabidopsis thalina.

hyb_protocol: Anther SPL set2 Cy5 / Anther L.erecta set2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 6.0, Cy3:pmt voltage 532nm,500V,laser power 30%, Cy5:635nm,pmt voltage 500V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: Anther L.erecta set2

label_protocol: labelling  , amplification=,   .

growth_protocol: stamen - Media=soil   hygrometry=70  Temperature=18  Light=11h

extract_protocol: Anther L.erecta set2:38.8ug.

tag: arabidopsis thaliana (landsberg erecta)  - harvest date

source_name: Anther SPL set2

extract_protocol: Anther SPL set2:1ug.

tag: arabidopsis thaliana (landsberg erecta)  mutant (spl1-1) - harvest date


title: Mature_stem_rep_5

status: Public on Nov 19 2006

city: St Lucia

first: Rosanne

middle: Elena

last: Casu

state: QLD

address: Queensland Bioscience Precinct, 306 Carmody Rd

institute: CSIRO Agriculture Flagship

description: Three tissue samples were harvested from four biological replicates of field-grown Q117 sugarcane plants. The plants were grown as a commercial crop and were harvested in late March, 2005, 11 months after planting at Kalamia Mill estate in the Burdekin River region (North Queensland, Australia, Lat.: 19° 32’ S; Long.: 147° 25’ E). The tissue samples comprised (i) young stem (meristem and internodes 1-3; M,I1-3); (ii) maturing stem (internode 8; I8) and mature stem (internode 20; I20). Internodes were numbered from the apex down according to the method of Moore (1987). All samples were immediately frozen in liquid nitrogen and stored at -80ºC until required, then ground to a fine powder in liquid nitrogen using a coffee grinder followed by a mortar and pestle, and then stored again at -80ºC. Total RNA was isolated from each tissue using a modification of the method devised by Chomczynski and Sacchi (1987). Each RNA sample was subjected to DNase digestion (QIAGEN) to remove any remaining DNA and purified through an RNeasy column according to the manufacturer’s directions (QIAGEN). Labelled cRNA target for use in hybridisations was generated from 15 µg of total RNA using the One-Cycle Eukaryotic Target Labeling Assay, and hybridized to an Affymetrix Sugarcane Genome Array with washing, staining and scanning beingperformed as specified in the manufacturer’s protocol (Affymetrix, Inc.). The scanner operating software, GCOS, converted the signal on each array into a DAT file, which was then used to generate CEL and CHP files for analysis. GeneSpring 7.3 (Agilent Technologies) was used for data analysis. A “Sugarcane Genome” text file describing the probe sets present on the array was developed from the Sugar_Cane.gin file provided by Affymetrix as part of the GeneChip Sugarcane Genome Array Library Files.  The CHP file was imported into GeneSpring running the Sugarcane Genome. A final normalised ratio was obtained by applying an additional “per probe set” normalisation. This was achieved by dividing the raw value for each probe set by the median value for that probe set in the whole experiment. This centred the data near a value of 1 and ensured ease of identification of differentially expressed probe sets.

data_processing: The VALUE for each probe set identifier was generated in GCOS, and a NORMALIZED_VALUE (also supplied) was determined using Genespring 7.3

label: biotinylated cRNA

organism: Saccharum hybrid cultivar Q117

source_name: Mature stem (internode 20)

growth_protocol: Field-grown in North Queensland, Australia

tag: variety

value: Q117; Age:11 months; Biological replicate:5


title: 13688409 - Anther SPL set2 vs Anther L.erecta set2

hyb_protocol: Anther L.erecta set2 Cy5 / Anther SPL set2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Mature_stem_rep_3

value: Q117; Age:11 months; Biological replicate:3


title: Mature_stem_rep_2

value: Q117; Age:11 months; Biological replicate:2


title: Young_stem_rep_3

source_name: Young stem (meristem, internodes 1-3)


title: Adult_mouse_heart_infarcted_rep3

status: Public on Oct 24 2009

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Determine the transcriptomic alteration induced in a murine model of post ischemic heart failure

hyb_protocol: Alexa Fluor®_647-labeled cDNA was co-hybridized with Alexa Fluor®_555-labeled universal mouse reference prepared in our lab from ten adult mouse tissues (aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from males and females) overnight at 50°C on a MO3 AECOM mouse oligonucleotide array spotted with 32k Operon 70-mer oligonucleotides V3.0 (GPL5371).

scan_protocol: After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNAs, each array was scanned WITH A 4000B scanner (MDS, Toronto, Canada)) and images were primarily analyzed with GenePixPro 6.0 (Axon Instruments, CA).

data_processing: Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al. Physiol Genomics 2005.

label: Alexa Fluor®_647

label_protocol: 30ug total RNA extracted from each heart was reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_647–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).

growth_protocol: Mice were housed at controlled temperature (23ºC) with 12:12-hour light-dark cycle and received standard mouse chow and water ad libitum.

extract_protocol: total RNA was extracted using the TRIzol® protocol (Invitrogen, CA). RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: Permanent myocardial infarcts were produced by ligation of the descending branch of the left coronary artery. Animals were anesthetized by an intraperitoneal injection with ketamine (40mg/kg) and xylazine (80mg/kg), placed in a supine position and intubated. Mice were ventilated with a volume-cycled ventilator (100 cycles/min, Harvard Apparatus; Holliston, MA) with volume sufficient to adequately expand but not overexpand the lungs. After a left anterior thoracotomy, the heart was exposed and the suture (8-0 mononylon) was passed under the artery at a position ~1mm from the tip of the normally positioned left auricle. The chest was then closed and the skin sutured with 5-0 nylon. Sham operations were created by the same method but without tying the suture in LAD.

value: heart infarcted

value: 8-10 weeks

value: Ischemic heart failure induced by ligation of the descending branch of the left coronary artery

label: Alexa Fluor®_555

source_name: Universal mouse RNA reference

label_protocol: 30ug total RNA extracted from each heart was reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_555–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).

tag: reference

value: universal mouse RNA reference prepared from ten adult mouse tissues (aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from males and females)


title: Young_stem_rep_1

value: Q117; Age:11 months; Biological replicate:1


title: Adult_mouse_heart_control_rep1

value: heart control


title: Maturing_stem_rep_1

source_name: Maturing stem (internode 8)


title: Adult_mouse_heart_infarcted_rep1


title: Maturing_stem_rep_3


title: Adult_mouse_heart_infarcted_rep4


title: Adult_mouse_heart_control_rep3


title: Mature_stem_rep_1


title: Young_stem_rep_5


title: Adult_mouse_heart_control_rep2


title: Adult_mouse_heart_infarcted_rep2


title: Young_stem_rep_2


title: Maturing_stem_rep_2


title: Adult_mouse_heart_control_rep4


title: 3 dpa con c

status: Public on Mar 20 2006

city: Corvallis

first: Robert

middle: L

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

description: Adult male zebrafish were i.p. injected with 50 ng/g TCDD or vehicle and caudal fins were amputated. Regenerating fin tissue was collected at 1, 3 and 5 days post amputation for mRNA abundance analysis.

hyb_protocol: Hybridization was conducted as stipulated by Affymetrix GeneChip Expression Analysis Technical Manual (701021 Rev. 5).

scan_protocol: Affymetrix fluidics station 400 was used to wash the arrays. Arrays were scanned with an Affymetrix scanner 3000.

data_processing: Data was GC-RMA preprocessed and each gene was normalized to the median using Gene Spring 7.1 software.

label: Labeling and probe processing was conducted under manufactures recommendations.

organism: Danio rerio

source_name: Adult Male Zebrafish Caudal Fin 3 Day Post Amputation, Vehicle Exposed Replicate C

label_protocol: 2.5 µg of total RNA was used to generate biotinylated complementary RNA (cRNA) for each treatment group using the One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA). RNA was reverse transcribed using a T7-(dT)24 primer and Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA).

growth_protocol: Fish were matained at 27oC until under standard conditions.

extract_protocol: Amputated tissue was stored in RNAlater (Qiagen, Valencia, CA) and frozen at -80oC. RNAlater was removed from the samples and total RNA was purified with TRI reagent (Molecular Research Laboratories, Cincinnati, OH) according to the manufacturer’s instructions. Total RNA was DNase treated with RQ1 DNase (Promega, Madison, WI) according to the manufacture’s protocol and RNA quantity and quality was determined by UV absorbance. Ribosomal RNA abundance and degree of degradation was determined in electropherogram patterns using the 2100 Bioanalyzer and RNA 6000 Nano chips (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Adult male zebrafish (Danio rerio) (AB strain, Eugene, OR) were anesthetized with tricaine methanesulfonate (MS-222) and their caudal fins were amputated at the bifurcation of the fin rays. Fish were then injected with phosphatidylcholine liposomes (vehicle control) alone or liposomes incorporated with TCDD (>99% pure, Chemsyn, Lenexa, KS) resulting in a final dose of 50 ng TCDD/g fish. At the indicated dpa, fish were euthanized with an over dose of MS-222. Regenerated fin tissue was then isolated by amputation within two ray segments anterior to the original amputation plane. Amputated tissue was then stored in RNAlater (Qiagen, Valencia, CA) and frozen at -80oC until RNA was isolated from the tissue. Tissues from 10 fish were combined to comprise a single experimental group (replicate). Three groups of tissue were obtained from vehicle control or TCDD exposed fish at 1, 3, and 5 dpa.

value: AB Zebrafish

value: Adult

value: Male

tag: time point

value: 3 day post amputation of caudal fin

tag: exposure

value: vehicle


title: 5 dpa tcdd a

source_name: Adult Male Zebrafish Caudal Fin 5 Day Post Amputation, TCDD Exposed Replicate A

value: 5 day post amputation of caudal fin

value: TCDD


title: 5 dpa con b

source_name: Adult Male Zebrafish Caudal Fin 5 Day Post Amputation, Vehicle Exposed Replicate B


title: 1 dpa con d

source_name: Adult Male Zebrafish Caudal Fin 1 day Post Amputation, Vehicle Exposed Replicate D

extract_protocol: Amputated tissue was stored in RNAlater (Qiagen, Valencia, CA) and frozen at -80oC.  RNAlater was removed from the samples and total RNA was purified with TRI reagent (Molecular Research Laboratories, Cincinnati, OH) according to the manufacturer’s instructions. Total RNA was DNase treated with RQ1 DNase (Promega, Madison, WI) according to the manufacture’s protocol and RNA quantity and quality was determined by UV absorbance. Ribosomal RNA abundance and degree of degradation was determined in electropherogram patterns using the 2100 Bioanalyzer and RNA 6000 Nano chips (Agilent Technologies, Palo Alto, CA).

value: 1 day post amputation of caudal fin


title: 5 dpa tcdd b

source_name: Adult Male Zebrafish Caudal Fin 5 Day Post Amputation, TCDD Exposed Replicate B


title: 1 dpa con b

source_name: Adult Male Zebrafish Caudal Fin 1 day Post Amputation, Vehicle Exposed Replicate B


title: Maturing_stem_rep_5

value: Q117; Age:11 months; Biological replicate:5


title: 3 dpa con a

source_name: Adult Male Zebrafish Caudal Fin 3 Day Post Amputation, Vehicle Exposed Replicate A


title: 5 dpa tcdd d

source_name: Adult Male Zebrafish Caudal Fin 5 Day Post Amputation, TCDD Exposed Replicate D


title: 3 dpa tcdd a

source_name: Adult Male Zebrafish Caudal Fin 3 Day Post Amputation, TCDD Exposed Replicate A


title: 3 dpa tcdd b

source_name: Adult Male Zebrafish Caudal Fin 3 Day Post Amputation, TCDD Exposed Replicate B


title: 3 dpa tcdd c

source_name: Adult Male Zebrafish Caudal Fin 3 Day Post Amputation, TCDD Exposed Replicate C


title: 3 dpa con b

source_name: Adult Male Zebrafish Caudal Fin 3 Day Post Amputation, Vehicle Exposed Replicate B


title: 1 dpa con e

source_name: Adult Male Zebrafish Caudal Fin 1 Day Post Amputation, Vehicle Exposed Replicate E


title: 5 dpa con c

source_name: Adult Male Zebrafish Caudal Fin 5 Day Post Amputation, Vehicle Exposed Replicate C


title: 1 dpa tcdd b

source_name: Adult Male Zebrafish Caudal Fin 1 Day Post Amputation, TCDD Exposed Replicate B


title: 1 dpa tcdd a

source_name: Adult Male Zebrafish Caudal Fin 1 Day Post Amputation, TCDD Exposed Replicate A

growth_protocol: Fish were maintained at 27oC until under standard conditions.


title: 5 dpa con a

source_name: Adult Male Zebrafish Caudal Fin 5 Day Post Amputation, Vehicle Exposed Replicate A


title: 1 dpa tcdd d

source_name: Adult Male Zebrafish Caudal Fin 1 Day Post Amputation, TCDD Exposed Replicate D