title: jacob-00182: 323

value: ALL MARGINS PATHOLOGICALLY NEGATIVE


title: jacob-00182: 322

status: Public on May 02 2015

type: RNA

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

country: USA

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: DFCI

value: Lung Adenocarcinoma

tag: Sex

value: Male

tag: age

tag: race

value: White

value: Alive

value: No

value: Smoked in the past

value: Lung

value: POORLY DIFFERENTIATED


title: jacob-00182: 319

scan_protocol: See mage-tab files linked to series entry for additional details

value: Unknown

value: Dead

value: Yes

value: Moderate Differentiation


title: jacob-00182: 320

data_processing: See mage-tab files linked to series entry for additional details

value: Female

value: WELL DIFFERENTIATED


title: jacob-00182: 317

label_protocol: See mage-tab files linked to series entry for additional details


title: jacob-00182: 321

extract_protocol: See mage-tab files linked to series entry for additional details


title: jacob-00182: 316


title: jacob-00182: 314


title: jacob-00182: 315


title: jacob-00182: 313


title: jacob-00182: 312

value: Never smoked


title: jacob-00182: 306


title: jacob-00182: 310


title: jacob-00182: 311


title: jacob-00182: 318


title: jacob-00182: 309


title: jacob-00182: 308


title: jacob-00182: 324


title: jacob-00182: 302


title: jacob-00182: 255

source_name: MSKCC


title: jacob-00182: 305

value: Currently smoking


title: jacob-00182: 256

value: ALL MARGINS PATHOLOGICALLY NEGATIVE


title: jacob-00182: 457

source_name: HLM

value: Lung Adenocarcinoma


title: jacob-00182: 307

value: Male


title: jacob-00182: 257

value: White


title: jacob-00182: 301

value: Alive


title: jacob-00182: 249

value: No


title: jacob-00182: 303

value: Smoked in the past


title: jacob-00182: 250

value: Lung


title: jacob-00182: 251


title: jacob-00182: 248

value: POORLY DIFFERENTIATED


title: jacob-00182: 304

value: Unknown


title: jacob-00182: 244

value: Dead


title: jacob-00182: 247

value: Yes


title: jacob-00182: 242


title: jacob-00182: 239


title: jacob-00182: 237


title: jacob-00182: 246

value: Moderate Differentiation


title: jacob-00182: 230

value: Female


title: jacob-00182: 224


title: jacob-00182: 233


title: jacob-00182: 236


title: jacob-00182: 226


title: jacob-00182: 238

value: WELL DIFFERENTIATED


title: jacob-00182: 228


title: jacob-00182: 235


title: jacob-00182: 232


title: jacob-00182: 241


title: jacob-00182: 220


title: jacob-00182: 219


title: jacob-00182: 229


title: jacob-00182: 496


title: jacob-00182: 225


title: jacob-00182: 222


title: jacob-00182: 223

value: Black or African American


title: jacob-00182: 231

value: Never smoked


title: jacob-00182: 234

value: ALL MARGINS PATHOLOGICALLY NEGATIVE


title: jacob-00182: 252

value: Lung Adenocarcinoma


title: jacob-00182: 227


title: jacob-00182: 221


title: jacob-00182: 240


title: jacob-00182: 217


title: jacob-00182: 218

value: Male


title: jacob-00182: 214

value: White


title: jacob-00182: 210

value: Alive


title: jacob-00182: 216

value: No


title: jacob-00182: 207

value: Smoked in the past


title: jacob-00182: 206

value: Lung


title: jacob-00182: 215


title: jacob-00182: 213

value: POORLY DIFFERENTIATED


title: jacob-00182: 212


title: jacob-00182: 209


title: jacob-00182: 208

value: Currently smoking


title: jacob-00182: 211


title: jacob-00182: 203

value: Asian

value: Dead


title: jacob-00182: 202

value: Moderate Differentiation


title: jacob-00182: 197


title: jacob-00182: 194

value: Female


title: jacob-00182: 193

value: Yes


title: jacob-00182: 198


title: jacob-00182: 200


title: jacob-00182: 199


title: jacob-00182: 201

value: WELL DIFFERENTIATED


title: jacob-00182: 196


title: jacob-00182: 189


title: jacob-00182: 195


title: jacob-00182: 205


title: jacob-00182: 192


title: jacob-00182: 182


title: jacob-00182: 188

value: Never smoked


title: jacob-00182: 179

value: ALL MARGINS PATHOLOGICALLY NEGATIVE


title: jacob-00182: 180

value: Lung Adenocarcinoma


title: jacob-00182: 190

value: Male


title: jacob-00182: 181

value: White


title: jacob-00182: 184


title: jacob-00182: 185

value: Alive


title: jacob-00182: 187

value: No


title: jacob-00182: 178

value: Smoked in the past


title: jacob-00182: 183

value: Lung


title: jacob-00182: 191


title: jacob-00182: 176

value: POORLY DIFFERENTIATED


title: jacob-00182: 177


title: jacob-00182: 174

value: Black or African American


title: jacob-00182: 170


title: jacob-00182: 172


title: jacob-00182: 173

value: Currently smoking


title: jacob-00182: 243


title: jacob-00182: 245

value: Dead


title: jacob-00182: 167


title: jacob-00182: 168


title: jacob-00182: 165


title: jacob-00182: 166


title: jacob-00182: 169

value: MICROSCOPICALLY POSITIVE MARGINS OR MICROSCOPIC RESIDUAL DISEASE


title: jacob-00182: 175

value: Female

value: Moderate Differentiation


title: jacob-00182: 163


title: jacob-00182: 164

value: Yes


title: jacob-00182: 160


title: jacob-00182: 159

value: Never smoked


title: jacob-00182: 156

value: ALL MARGINS PATHOLOGICALLY NEGATIVE


title: jacob-00182: 155

value: Lung Adenocarcinoma


title: jacob-00182: 154

value: Male


title: jacob-00182: 150

source_name: MI

value: Unknown


title: jacob-00182: 162

value: White

value: Alive


title: jacob-00182: 153

value: No

value: Smoked in the past


title: jacob-00182: 171

value: Lung

value: POORLY DIFFERENTIATED


title: jacob-00182: 151

value: Currently smoking


title: jacob-00182: 158

value: WELL DIFFERENTIATED


title: jacob-00182: 149

value: Dead


title: jacob-00182: 146


title: jacob-00182: 152


title: jacob-00182: 161


title: jacob-00182: 128

value: Female


title: jacob-00182: 132

value: Moderate Differentiation


title: jacob-00182: 134


title: jacob-00182: 142

value: Not Reported

value: Yes


title: jacob-00182: 135

value: ALL MARGINS PATHOLOGICALLY NEGATIVE


title: jacob-00182: 129

value: Lung Adenocarcinoma


title: jacob-00182: 123


title: jacob-00182: 144

value: Male


title: jacob-00182: 143

value: Unknown


title: jacob-00182: 147


title: jacob-00182: 130

value: White


title: jacob-00182: 141

value: Alive


title: jacob-00182: 127

value: No


title: jacob-00182: 140


title: jacob-00182: 157

value: Never smoked


title: jacob-00182: 122

value: Lung


title: jacob-00182: 145

value: POORLY DIFFERENTIATED


title: jacob-00182: 148


title: jacob-00182: 126


title: jacob-00182: 124


title: jacob-00182: 137


title: jacob-00182: 120


title: jacob-00182: 121


title: jacob-00182: 131


title: jacob-00182: 204


title: jacob-00182: 117


title: jacob-00182: 109


title: jacob-00182: 116


title: jacob-00182: 112

value: MICROSCOPICALLY POSITIVE MARGINS OR MICROSCOPIC RESIDUAL DISEASE


title: jacob-00182: 103


title: jacob-00182: 107

value: Black or African American


title: jacob-00182: 118

value: WELL DIFFERENTIATED


title: jacob-00182: 101


title: jacob-00182: 110

value: Female

value: Dead


title: jacob-00182: 111

value: Moderate Differentiation


title: jacob-00182: 119


title: jacob-00182: 97

value: Yes


title: jacob-00182: 106

value: ALL MARGINS PATHOLOGICALLY NEGATIVE


title: jacob-00182: 105

value: Lung Adenocarcinoma


title: jacob-00182: 115


title: jacob-00182: 102


title: jacob-00182: 108

value: Male


title: jacob-00182: 114

value: Unknown


title: jacob-00182: 93

value: White

value: Smoked in the past


title: jacob-00182: 91

value: No


title: jacob-00182: 113

value: Alive


title: jacob-00182: 90

value: Lung


title: jacob-00182: 96

value: Never smoked


title: jacob-00182: 98


title: jacob-00182: 100


title: jacob-00182: 99

value: POORLY DIFFERENTIATED


title: jacob-00182: 95


title: jacob-00182: 104


title: jacob-00182: 94


title: jacob-00182: 89


title: jacob-00182: 85

value: Not Reported


title: jacob-00182: 83


title: jacob-00182: 74

value: WELL DIFFERENTIATED


title: jacob-00182: 88


title: jacob-00182: 79

value: Female


title: jacob-00182: 72


title: jacob-00182: 73

value: Black or African American


title: jacob-00182: 68

value: Asian


title: jacob-00182: 61

value: Moderate Differentiation


title: jacob-00182: 69

value: Dead

value: ALL MARGINS PATHOLOGICALLY NEGATIVE


title: jacob-00182: 66

value: Lung Adenocarcinoma

value: Yes


title: jacob-00182: 65

value: Male

value: White


title: jacob-00182: 81


title: jacob-00182: 70

value: No

value: Smoked in the past


title: jacob-00182: 84

value: Lung


title: jacob-00182: 82


title: jacob-00182: 78


title: jacob-00182: 75


title: jacob-00182: 63


title: jacob-00182: 80

value: Alive

value: Never smoked


title: jacob-00182: 76


title: jacob-00182: 87

value: POORLY DIFFERENTIATED


title: jacob-00182: 77


title: jacob-00182: 71


title: jacob-00182: 62


title: jacob-00182: 64


title: jacob-00182: 60


title: jacob-00182: 59


title: jacob-00182: 67


title: jacob-00182: 58


title: jacob-00182: 55

value: WELL DIFFERENTIATED


title: jacob-00182: 51


title: jacob-00182: 42


title: jacob-00182: 47

value: Female


title: jacob-00182: 56


title: jacob-00182: 53


title: jacob-00182: 54

value: Unknown


title: jacob-00182: 57


title: jacob-00182: 52


title: jacob-00182: 49


title: jacob-00182: 50


title: jacob-00182: 37

value: Black or African American


title: jacob-00182: 40

value: Moderate Differentiation


title: jacob-00182: 32

value: Dead


title: jacob-00182: 39

value: ALL MARGINS PATHOLOGICALLY NEGATIVE


title: jacob-00182: 35

value: Lung Adenocarcinoma


title: jacob-00182: 33

value: Yes


title: jacob-00182: 44


title: jacob-00182: 43

value: Male


title: jacob-00182: 48


title: jacob-00182: 45

value: Asian

value: MICROSCOPICALLY POSITIVE MARGINS OR MICROSCOPIC RESIDUAL DISEASE


title: 12_10T_-TI_-N

city: Wuerzburg

first: Ellen

last: Leich

department: Institute of Pathology

country: Germany

institute: University of Wuerzburg

description: mRNA

hyb_protocol: Following fragmentation, 20 micrograms of cRNA were hybridized for 16 hours at 45C on U133 Plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning was performed by the Affymetrix 3000 Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: human blood samples, healthy, stimulated minus natalizumab, not restimulated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg mRNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Synchronized human CD4+ T cells were grown on irradiated feeder cells and stimulated with OKT-3 (30 ng/ml) and recombinant IL-2 (50 U/ml) either in the absence or presence of natalizumab (30 ug/ml).

extract_protocol: RNA was isolated using Trizol from Life Technologies.

treatment_protocol: After 10 days, cells were restimulated or not with 10 ng/ml TPA and 2 μM ionomycin plus/minus fresh natalizumab for 8 h.

tag: tissue

value: blood

tag: cell type

value: CD4+ T cells

tag: disease state

value: healthy

value: median 32 yrs (range 23-46)

tag: treatment


title: jacob-00182: 38

value: White

value: No

value: Smoked in the past

value: Lung


title: jacob-00182: 36

value: Alive

value: POORLY DIFFERENTIATED


title: jacob-00182: 46

value: Black or African American

value: Dead

value: Moderate Differentiation


title: jacob-00182: 34

value: Lung Adenocarcinoma

value: ALL MARGINS PATHOLOGICALLY NEGATIVE


title: 11_10T_-TI_-N

description: mRNA

value: stimulated minus natalizumab, not restimulated


title: 10_10T_-TI_-N

description: mRNA


title: jacob-00182: 41

value: Male


title: jacob-00182: 31


title: 8_10T_-TI_+N

description: mRNA

source_name: human blood samples, healthy, stimulated plus natalizumab, not restimulated

value: blood


title: 9_10T_-TI_+N

description: mRNA

value: CD4+ T cells

value: stimulated plus natalizumab, not restimulated


title: jacob-00182: 29

value: Yes


title: jacob-00182: 21

value: Female

value: White


title: jacob-00182: 28

value: Smoked in the past


title: jacob-00182: 26

value: Lung


title: jacob-00182: 24

value: No


title: jacob-00182: 25

value: Unknown


title: 5_10T_+TI_-N

description: mRNA

source_name: human blood samples, healthy, stimulated minus natalizumab, restimulated minus natalizumab

value: healthy

value: median 32 yrs (range 23-46)


title: 1_10T_+TI_+N

description: mRNA

source_name: human blood samples, healthy, stimulated plus natalizumab, restimulated plus natalizumab


title: jacob-00182: 15

value: Dead

value: POORLY DIFFERENTIATED


title: 4_10T_+TI_-N

description: mRNA

value: stimulated minus natalizumab, restimulated minus natalizumab


title: 2_10T_+TI_+N

description: mRNA

value: stimulated plus natalizumab, restimulated plus natalizumab


title: jacob-00182: 17

value: Lung Adenocarcinoma

value: ALL MARGINS PATHOLOGICALLY NEGATIVE

value: Moderate Differentiation


title: jacob-00182: 20

value: Alive


title: jacob-00182: 30

value: Male


title: 7_10T_-TI_+N

description: mRNA

value: blood

value: CD4+ T cells

value: stimulated plus natalizumab, not restimulated


title: jacob-00182: 18

value: Female

value: White

value: Yes

value: Smoked in the past

value: Lung


title: jacob-00182: 27

value: Unknown

value: Dead


title: Des-/- rep2

city: Athens

first: Yassemi

last: Capetanaki

state: Attiki

address: Soranou Ephessiou 4

department: Basic Research

country: Greece

institute: Biomedical Research Foundation of Academy of Athens

description: Gene expression data of myocardium from 3-mo-old Des-/- mice

hyb_protocol: cRNA were hybridized in triplicate to Affymetrix 430 2.0 microarrays at the MIT BioMicrocenter facility (Boston, MA, USA). GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the facility infrastucture of the MIT BioMicrocenter facility (Boston, MA, USA).

data_processing: Data analysis were performed using the “GeneSpring GX” software (Genespring GX9 and GX12.5; Agilent). Background correction and normalization was performed by RMA algorithm. The cutoff filter of the probesets based on their signal intensity values was set at 20%.

organism: Mus musculus

source_name: hearts of 3-mo-old mice

label_protocol: Pooled RNA from 3 hearts of each genotype were converted into biotin-labeled cRNA

extract_protocol: Hearts were quickly excised, flushed with ice-cold PBS to remove excess blood and kept in ‘RNAlater’ (Ambion) until homogenized in ‘Trizol’ (Invitrogen) to isolate total RNA according to the manufacturer’s instructions.

tag: strain

value: heart

tag: genotype

value: Des-/-

value: 3 months old


title: TNFαDes-/- rep1

description: Gene expression data of myocardium from 3-mo-old TNFαDes-/- mice

value: mixed 129SV/C57

value: TNFαDes-/-


title: jacob-00182: 16

value: Lung Adenocarcinoma

value: Asian

value: Alive

value: Never smoked

value: ALL MARGINS PATHOLOGICALLY NEGATIVE

value: Moderate Differentiation


title: Des-/- rep3


title: jacob-00182: 13

value: Female

value: White

value: No

value: POORLY DIFFERENTIATED


title: jacob-00182: 12

value: Unknown

value: Yes

value: Smoked in the past

value: Lung


title: TNFαDes-/- rep3

value: heart

value: 3 months old


title: jacob-00182: 19

value: Dead


title: jacob-00182: 14

value: Lung Adenocarcinoma

value: Male


title: 3_10T_+TI_+N

description: mRNA

value: blood

value: CD4+ T cells

value: healthy

value: median 32 yrs (range 23-46)

value: stimulated plus natalizumab, restimulated plus natalizumab


title: jacob-00182: 11

value: White

value: ALL MARGINS PATHOLOGICALLY NEGATIVE

value: Moderate Differentiation


title: TNFαDes-/- rep2

value: mixed 129SV/C57

value: TNFαDes-/-


title: jacob-00182: 22

value: Female

value: No

value: Yes

value: Smoked in the past

value: WELL DIFFERENTIATED


title: jacob-00182: 6

value: Lung Adenocarcinoma

value: Alive

value: Lung


title: NFS 03 [RT-PCR]

status: Public on May 01 2015

city: Miami

first: Horacio

middle: Adrian

last: Ramirez

state: Florida

address: 1600 NW10th Avenue RMSB room 2029A

department: Dermatology

institute: University of Miami

description: non-Diabetic Foot Skin 03 epidermis miR profile

data_processing:
Raw CT values were imported and processed in Exiqon GenEX software.  Processing of the data involved, interplate calibration, elimination of very low expression microRNAs (ct > 35) and microRNAs with incomplete data (>25% missing data). Normalization was done using SNORD49 as a reference gene and the ΔCt method.
The 'normalized_data.txt' contains the relative quantities obtained after interplate calibration, elimination of very low expression microRNAs (ct > 35) and microRNAs with incomplete data (>25% missing data). Normalization was done using SNORD49 as a reference gene and the ΔCt method.  The 'fold_change.txt' includes the fold change (Avg relative quantity of DFS/avg relative quantity of NFS) with the corresponding ttest p-values and p-values after multiple testing corrections.

label: Sybr green

source_name: non-Diabetic Foot skin

label_protocol: cDNA was synthesized using EXIQON universal cDNA synthesis kit following the manufacturer's instructions. PCR reactions were done using the EXIQON ExiLENT SYBR® Green master mix following the manufacturer's instructions.

extract_protocol: total RNA was extracted from Laser captured epidermis (see overall design) using the FFPE miRNeasy kit (QIAGEN Inc.) following to the manufacturer’s instructions

value: healthy non-diabetic foot skin (NFS)


title: NFS 02 [RT-PCR]

description: non-Diabetic Foot Skin 02 epidermis miR profile


title: jacob-00182: 10

value: Dead


title: DFS 03 [RT-PCR]

description: Diabetic Foot Skin 03 epidermis miR profile

source_name: Diabetic Foot skin

value: non-ulcerated non-neuropathic diabetic foot skin (DFS)


title: DFS 02 [RT-PCR]

description: Diabetic Foot Skin 02 epidermis miR profile


title: NFS 01 [RT-PCR]

description: non-Diabetic Foot Skin 01 epidermis miR profile


title: 6_10T_+TI_-N

description: mRNA

value: blood

value: CD4+ T cells

value: healthy

value: median 32 yrs (range 23-46)

value: stimulated minus natalizumab, restimulated minus natalizumab


title: Mature-Auxin-12days_rep3

city: Rishon Le-Zion

first: Ron

last: Ophir

address: Hamacabim St.

department: Fruit Tree Sciences

country: Israel

institute: Agricultural Research Organization - the Volcani Center

description: Raw data - Cy5: ES_253014210004_S01_GE2_107_Sep09_2_2.txt

hyb_protocol: Agilent protocol

scan_protocol: Agilent Technologies Scanner G2505C US22502692

data_processing: Robust Quantile Normalization using R preprocessCore package.

molecule: polyA RNA

organism: Eucalyptus grandis

source_name: stem sections pruned at 10-15 cm. Auxin treated. 12 days after pruning

label_protocol: Agilent labeling kit

growth_protocol: Seeds of E. grandis were grown for one month after germination in small pots and then transplanted into15 liter pots containing peat and TUFF (70:30) and 2 g/l Osmokot. Six-month-old seedlings grown in a net-house were pruned at 10-15 cm and 150-200 cm above the ground to enhance cutting production in these specific stem sections (juvenile and mature respectively).  Cuttings, consisting of 4-6 leaves with 60% of the leaf blade removed were used.

extract_protocol: RNA extraction was carried out as previously described (Southerton et al. 1998), with some modifications. Three g of tissue were ground in liquid nitrogen to a fine powder using a mortar and pestle, and then 10 ml of extraction buffer pre-heated to 65°C were added, and the tubes were shaken thoroughly and incubated for 5 min at 65°C. The extraction buffer contained 2% cetyl-trimethyl-ammonium bromide (CTAB), 2% polyvinyl pyrrolidone (PVP) 40, 100 mM Tris-HCl, pH 8.0, 25 mM EDTA, 2 M NaCl, 0.5 g/l spermidine, and 2% beta-mercaptoethanol. All reagents were freshly prepared. Two steps of chloroform extraction were employed, followed by centrifugation at 10,000g for 15 min after each step. The upper phase was mixed with 0.25 volume of 10 M LiCl, and the RNA was precipitated overnight at 4°C. Following centrifugation at 10,000g for 20 min, the RNA pellet was dissolved in 500 ul of SSTE buffer, and then extracted with an equal volume of chloroform.  The SSTE buffer contained 0.5% SDS, 1 M NaCl, 10 mM Tris-HCl, pH 8.0, and 1 mM EDTA. The RNA was then precipitated by the addition of 2 volumes of ethanol, placed at -70°C for 1 h, and then pelleted by centrifugation at 10,000g in a microcentrifuge at 4°C. The pellet was dried and then dissolved in RNAse free water. The RNA sample was further purified by using Qiagen RNeasy mini kit and DNAse treatment using RNAse free DNAse1 from Qiagen

treatment_protocol: After excision, the base of the cuttings was dipped for 20 sec in a solution containing 6000 ppm K-IBA (Sigma). Cuttings were rooted in a rooting table heated to 24 0C under relative humidity of ≥90% for a period up to of 14-42 days.

value: Mature

tag: time

value: 12 days


title: jacob-00182: 7

value: Female

value: White

value: No

value: ALL MARGINS PATHOLOGICALLY NEGATIVE


title: jacob-00182: 2

value: Lung Adenocarcinoma

value: Smoked in the past

value: WELL DIFFERENTIATED


title: DFS 01 [RT-PCR]

description: Diabetic Foot Skin 01 epidermis miR profile


title: jacob-00182: 1

value: Alive

value: Lung

value: Moderate Differentiation


title: jacob-00182: 3

value: Dead

value: Yes


title: Mature-Auxin-1day_rep3

description: Raw data - Cy3: ES_253014210004_S01_GE2_107_Sep09_2_1.txt

source_name: stem sections pruned at 10-15 cm. Auxin treated. 1 day after pruning

value: 1 day


title: Mature-Auxin-3days_rep3

description: Raw data - Cy5: ES_253014210004_S01_GE2_107_Sep09_2_1.txt

source_name: stem sections pruned at 10-15 cm. Auxin treated. 3 days after pruning

value: 3 days


title: jacob-00182: 9


title: jacob-00182: 4

value: Unknown

value: Never smoked


title: jacob-00182: 5


title: Juvenile-untreated-1day_rep3

description: Raw data - Cy3: ES_253014210003_S01_GE2_107_Sep09_2_1.txt

source_name: stem sections pruned at 150-200 cm. 1 day after pruning

value: Juvenile


title: Juvenile-untreated-time0_rep3

description: Raw data - Cy5: ES_253014210003_S01_GE2_107_Sep09_2_1.txt

source_name: stem sections pruned at 150-200 cm. right after after pruning

value: stem sections pruned at 150-200 cm. right after pruning


title: Mature-untreated-12days_rep3

description: Raw data - Cy5: ES_253014210004_S01_GE2_107_Sep09_2_3.txt

source_name: stem sections pruned at 10-15 cm. 12 days after pruning

value: Mature

value: 12 days


title: Juvenile-untreated-3days_rep3

description: Raw data - Cy5: ES_253014210003_S01_GE2_107_Sep09_2_2.txt

source_name: stem sections pruned at 150-200 cm. 3 days after pruning


title: Juvenile-Auxin-9days_rep3

description: Raw data - Cy5: ES_253014210004_S01_GE2_107_Sep09_2_4.txt

source_name: stem sections pruned at 150-200 cm. Auxin treated. 9 days after pruning

value: 9 days


title: Mature-untreated-9days_rep3

description: Raw data - Cy3: ES_253014210004_S01_GE2_107_Sep09_2_3.txt

source_name: stem sections pruned at 10-15 cm. 9 days after pruning


title: Juvenile-untreated-12days_rep3

description: Raw data - Cy3: ES_253014210004_S01_GE2_107_Sep09_2_4.txt

source_name: stem sections pruned at 150-200 cm. 12 days after pruning


title: Juvenile-untreated-time0_rep1

description: Raw data - Cy5: ES_253014210003_S01_GE2_107_Sep09_2_3.txt


title: Mature-Auxin-6days_rep3

description: Raw data - Cy3: ES_253014210004_S01_GE2_107_Sep09_2_2.txt

source_name: stem sections pruned at 10-15 cm. Auxin treated. 6 days after pruning

value: 6 days


title: Juvenile-untreated-time0_rep2

description: Raw data - Cy3: ES_253014210003_S01_GE2_107_Sep09_2_2.txt


title: Juvenile-Auxin-9days_rep2

description: Raw data - Cy3: ES_253014210002_S01_GE2_107_Sep09_2_1.txt

value: stem sections pruned at 150-200 cm. Auxin treated. 9 days after pruning


title: Juvenile-untreated-9days_rep3

description: Raw data - Cy3: ES_253014210003_S01_GE2_107_Sep09_2_3.txt

source_name: stem sections pruned at 150-200 cm. 9 days after pruning


title: Des-/- rep1

description: Gene expression data of myocardium from 3-mo-old Des-/- mice

value: heart

value: Des-/-

value: 3 months old


title: Mature-untreated-1day_rep4

description: Raw data - Cy3: ES_253014210003_S01_GE2_107_Sep09_2_4.txt

source_name: stem sections pruned at 10-15 cm. 1 day after pruning


title: Juvenile-Auxin-3days_rep3

description: Raw data - Cy5: ES_253014210003_S01_GE2_107_Sep09_2_4.txt

source_name: stem sections pruned at 150-200 cm. Auxin treated. 3 days after pruning


title: Mature-Auxin-9days_rep2

description: Raw data - Cy3: ES_253014210002_S01_GE2_107_Sep09_2_2.txt

source_name: stem sections pruned at 10-15 cm. Auxin treated. 9 days after pruning


title: Juvenile-untreated-9days_rep2

description: Raw data - Cy5: ES_253014210002_S01_GE2_107_Sep09_2_1.txt

value: stem sections pruned at 150-200 cm. 9 days after pruning


title: Juvenile-Auxin-9days_rep1

description: Raw data - Cy5: ES_253014210002_S01_GE2_107_Sep09_2_2.txt


title: Mature-untreated-9days_rep2

description: Raw data - Cy3: ES_253014210002_S01_GE2_107_Sep09_2_3.txt

value: stem sections pruned at 10-15 cm. 9 days after pruning


title: 254706910034_b1 - col_heart_BR1 vs gso1/gso2_heart_BR1

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Analyse a signalling pathway necessary for embryonic cuticle reinforcement during seed development in Arabidopsis

hyb_protocol: gso1/gso2_heart_BR1 Cy5 / col_heart_BR1 Cy3 : 20pmol.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seed,seedling - Media=MS sucrose 0.5% hygrometry=50-60%;Temperature=22°C;Light=16h

treatment_protocol: no treatment

tag: ecotype

value: arabidopsis thaliana (columbia)

tag: dev.stage (boyes et al. plant cell 2001)

growth_protocol: seed,seedling - Media=MS sucrose 0.5%;Temperature=22°C;Light=16h

value: col


title: Juvenile-untreated-3days_rep2

description: Raw data - Cy5: ES_253014210001_S01_GE2_107_Sep09_2_1.txt

value: stem sections pruned at 150-200 cm. 3 days after pruning

value: 3 days


title: Mature-untreated-9days_rep1

description: Raw data - Cy5: ES_253014210002_S01_GE2_107_Sep09_2_4.txt


title: 254706910015_b4 - ale-1_glob_BR3 vs col_glob_BR3

hyb_protocol: col_glob_BR3 Cy5 / ale-1_glob_BR3 Cy3 : 20pmol.

value: glob

growth_protocol: seed,seedling - Media=MS sucrose 0.5% hygrometry=50-60%;Temperature=19°C;Light=8h


title: Juvenile-untreated-9days_rep1

description: Raw data - Cy3: ES_253014210002_S01_GE2_107_Sep09_2_4.txt

value: Juvenile


title: 254706910013_b4 - ale-1_glob_BR1 vs col_glob_BR1

hyb_protocol: col_glob_BR1 Cy5 / ale-1_glob_BR1 Cy3 : 20pmol.


title: Juvenile-Auxin-3days_rep1

description: Raw data - Cy5: ES_253014210001_S01_GE2_107_Sep09_2_2.txt

value: stem sections pruned at 150-200 cm. Auxin treated. 3 days after pruning


title: 254706910034_b4 - gso1/gso2_glob_BR1 vs col_glob_BR1

hyb_protocol: col_glob_BR1 Cy5 / gso1/gso2_glob_BR1 Cy3 : 20pmol.


title: Mature-Auxin-9days_rep1

description: Raw data - Cy5: ES_253014210002_S01_GE2_107_Sep09_2_3.txt

value: Mature

value: stem sections pruned at 10-15 cm. Auxin treated. 9 days after pruning


title: 254706910015_b2 - ale-1_heart_BR3 vs col_heart_BR3

hyb_protocol: col_heart_BR3 Cy5 / ale-1_heart_BR3 Cy3 : 20pmol.


title: Mature-Auxin-3days_rep2

description: Raw data - Cy3: ES_253014210001_S01_GE2_107_Sep09_2_2.txt

value: stem sections pruned at 10-15 cm. Auxin treated. 3 days after pruning


title: 254706910014_b1 - col_heart_BR2 vs ale-1_heart_BR2

hyb_protocol: ale-1_heart_BR2 Cy5 / col_heart_BR2 Cy3 : 20pmol.


title: 254706910034_b2 - gso1/gso2_heart_BR1 vs col_heart_BR1

hyb_protocol: col_heart_BR1 Cy5 / gso1/gso2_heart_BR1 Cy3 : 20pmol.


title: 254706910034_b3 - col_glob_BR1 vs gso1/gso2_glob_BR1

hyb_protocol: gso1/gso2_glob_BR1 Cy5 / col_glob_BR1 Cy3 : 20pmol.


title: 254706910014_b2 - ale-1_heart_BR2 vs col_heart_BR2

hyb_protocol: col_heart_BR2 Cy5 / ale-1_heart_BR2 Cy3 : 20pmol.


title: 254706910015_b1 - col_heart_BR3 vs ale-1_heart_BR3

hyb_protocol: ale-1_heart_BR3 Cy5 / col_heart_BR3 Cy3 : 20pmol.


title: 254706910013_b1 - col_heart_BR1 vs ale-1_heart_BR1

hyb_protocol: ale-1_heart_BR1 Cy5 / col_heart_BR1 Cy3 : 20pmol.


title: Mature-untreated-3days_rep3

description: Raw data - Cy3: ES_253014210001_S01_GE2_107_Sep09_2_3.txt

source_name: stem sections pruned at 10-15 cm. 3 days after pruning


title: 254706910013_b2 - ale-1_heart_BR1 vs col_heart_BR1

hyb_protocol: col_heart_BR1 Cy5 / ale-1_heart_BR1 Cy3 : 20pmol.


title: 254706910014_b3 - col_glob_BR2 vs ale-1_glob_BR2

hyb_protocol: ale-1_glob_BR2 Cy5 / col_glob_BR2 Cy3 : 20pmol.


title: 254706910013_b3 - col_glob_BR1 vs ale-1_glob_BR1

hyb_protocol: ale-1_glob_BR1 Cy5 / col_glob_BR1 Cy3 : 20pmol.


title: Juvenile-Auxin-3days_rep2

description: Raw data - Cy3: ES_253014210001_S01_GE2_107_Sep09_2_1.txt


title: 254706910015_b3 - col_glob_BR3 vs ale-1_glob_BR3

hyb_protocol: ale-1_glob_BR3 Cy5 / col_glob_BR3 Cy3 : 20pmol.


title: 254706910014_b4 - ale-1_glob_BR2 vs col_glob_BR2

hyb_protocol: col_glob_BR2 Cy5 / ale-1_glob_BR2 Cy3 : 20pmol.


title: Mature-Auxin-3days_rep1

description: Raw data - Cy5: ES_253014210001_S01_GE2_107_Sep09_2_3.txt

hyb_protocol: Agilent protocol


title: 254706910012_b4 - gso1/gso2_glob_BR3 vs col_glob_BR3

hyb_protocol: col_glob_BR3 Cy5 / gso1/gso2_glob_BR3 Cy3 : 20pmol.


title: A45

type: genomic

city: Chongqing

first: Ting

middle: huan

last: zhang

address: Rongchang

country: China

institute: Chongqing Academy of Animal Science

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

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

data_processing: BeadStudio (Illumina Inc.) software were used to genotyped the SNPs .

molecule: genomic DNA

organism: Sus scrofa

source_name: blood

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37℃ using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Genomic DNA for each individuals was extracted from the blood using Qiagen DNeasy blood kit (Qiagen, Germany).

tag: breed

value: Chinese Rongchang

tag: gender

value: Male

value: blood

value: normal


title: 254706910012_b3 - col_glob_BR3 vs gso1/gso2_glob_BR3

hyb_protocol: gso1/gso2_glob_BR3 Cy5 / col_glob_BR3 Cy3 : 30pmol.


title: A44


title: A43

value: Female


title: Mature-untreated-3days_rep1

description: Raw data - Cy5: ES_253014210004_S01_GE2_107_Sep09_1_3.txt

value: stem sections pruned at 10-15 cm. 3 days after pruning


title: Mature-untreated-1day_rep3

description: Raw data - Cy3: ES_253014210004_S01_GE2_107_Sep09_1_2.txt

value: stem sections pruned at 10-15 cm. 1 day after pruning

value: 1 day


title: Juvenile-Auxin-6days_rep3

description: Raw data - Cy3: ES_253014210004_S01_GE2_107_Sep09_1_1.txt

source_name: stem sections pruned at 150-200 cm. Auxin treated. 6 days after pruning

value: 6 days


title: A42


title: A41


title: 254706910011_b3 - col_glob_BR2 vs gso1/gso2_glob_BR2

hyb_protocol: gso1/gso2_glob_BR2 Cy5 / col_glob_BR2 Cy3 : 20pmol.

value: arabidopsis thaliana (columbia)

value: col


title: 254706910012_b2 - gso1/gso2_heart_BR3 vs col_heart_BR3

hyb_protocol: col_heart_BR3 Cy5 / gso1/gso2_heart_BR3 Cy3 : 20pmol.

value: heart


title: Mature-untreated-time0_rep3

description: Raw data - Cy5: ES_253014210004_S01_GE2_107_Sep09_1_2.txt

source_name: stem sections pruned at 10-15 cm. right after after pruning

value: stem sections pruned at 10-15 cm. right after pruning


title: Juvenile-Auxin-12days_rep3

description: Raw data - Cy5: ES_253014210004_S01_GE2_107_Sep09_1_1.txt

source_name: stem sections pruned at 150-200 cm. Auxin treated. 12 days after pruning

value: Juvenile

value: 12 days


title: 254706910011_b2 - gso1/gso2_heart_BR2 vs col_heart_BR2

hyb_protocol: col_heart_BR2 Cy5 / gso1/gso2_heart_BR2 Cy3 : 20pmol.


title: 254706910032_b4 - 12_mkk3ABA_3 vs 11_mkk3mock_3

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Identification of the miss-regulated genes in mkk3 under ABA treatment

hyb_protocol: 11_mkk3mock_3 Cy5 / 12_mkk3ABA_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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.

growth_protocol: seedling - 1/2MS (SIGMA M6899)+1% Sucrose+0,05%MES pH 5.7 adjusted with HCL 25 mL in medium petri dish

extract_protocol: 11_mkk3mock_3:30ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:MOCK_treatment - environmental treatment - compound addition,ethanol:quantity 0.1percent time 4hour .

tag: cultivar

value: columbia

value: mkk3 mutant t-dna

tag: developmental stage (boyes et al plant cell 2001)

value: boyes 1.03

extract_protocol: 12_mkk3ABA_3:30ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:ABA_treatment - environmental treatment - compound addition,abscissic acid:quantity 50uM time 4hour .


title: Mature-untreated-3days_rep2

description: Raw data - Cy5: ES_253014210001_S01_GE2_107_Sep09_2_4.txt

value: Mature

value: 3 days


title: 254706910012_b1 - col_heart_BR3 vs gso1/gso2_heart_BR3

description: Analyse a signalling pathway necessary for embryonic cuticle reinforcement during seed development in Arabidopsis

hyb_protocol: gso1/gso2_heart_BR3 Cy5 / col_heart_BR3 Cy3 : 20pmol.


title: 254706910011_b4 - gso1/gso2_glob_BR2 vs col_glob_BR2

hyb_protocol: col_glob_BR2 Cy5 / gso1/gso2_glob_BR2 Cy3 : 20pmol.

value: glob


title: A40

value: Chinese Rongchang

value: Male

value: blood

value: normal


title: Mature-untreated-time0_rep2

description: Raw data - Cy3: ES_253014210004_S01_GE2_107_Sep09_1_3.txt


title: Juvenile-untreated-3days_rep1

description: Raw data - Cy3: ES_253014210001_S01_GE2_107_Sep09_2_4.txt

value: stem sections pruned at 150-200 cm. 3 days after pruning


title: 254706910011_b1 - col_heart_BR2 vs gso1/gso2_heart_BR2

hyb_protocol: gso1/gso2_heart_BR2 Cy5 / col_heart_BR2 Cy3 : 20pmol.

value: arabidopsis thaliana (columbia)


title: A37

value: Female


title: A31


title: A29


title: A33


title: A46


title: A32


title: A35


title: A36


title: A34


title: Mature-untreated-6days_rep3

description: Raw data - Cy3: ES_253014210004_S01_GE2_107_Sep09_1_4.txt

source_name: stem sections pruned at 10-15 cm. 6 days after pruning

value: 6 days


title: A30


title: 254706910032_b3 - 11_mkk3mock_3 vs 12_mkk3ABA_3

hyb_protocol: 12_mkk3ABA_3 Cy5 / 11_mkk3mock_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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-untreated-time0_rep1

description: Raw data - Cy5: ES_253014210004_S01_GE2_107_Sep09_1_4.txt

value: stem sections pruned at 10-15 cm. right after pruning


title: Juvenile-Auxin-12days_rep2

description: Raw data - Cy5: ES_253014210003_S01_GE2_107_Sep09_1_1.txt

value: Juvenile

value: stem sections pruned at 150-200 cm. Auxin treated. 12 days after pruning


title: Juvenile-untreated-12days_rep2

description: Raw data - Cy3: ES_253014210003_S01_GE2_107_Sep09_1_1.txt

value: stem sections pruned at 150-200 cm. 12 days after pruning

value: 12 days


title: A28


title: A39


title: A38


title: Mature-Auxin-12days_rep2

description: Raw data - Cy5: ES_253014210003_S01_GE2_107_Sep09_1_2.txt

source_name: stem sections pruned at 10-15 cm. Auxin treated. 12 days after pruning


title: 254706910031_b4 - 8_mkk3ABA_2 vs 7_mkk3mock_2

hyb_protocol: 7_mkk3mock_2 Cy5 / 8_mkk3ABA_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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.

extract_protocol: 7_mkk3mock_2:30ug. (Qiagen_RNeasy.pdf)

value: columbia

value: mkk3 mutant t-dna

value: boyes 1.03

extract_protocol: 8_mkk3ABA_2:30ug. (Qiagen_RNeasy.pdf)


title: A27


title: A25


title: A21


title: A20


title: A26


title: Juvenile-Auxin-12days_rep1

description: Raw data - Cy3: ES_253014210003_S01_GE2_107_Sep09_1_2.txt


title: 254706910032_b2 - 10_colABA_3 vs 9_colmock_3

hyb_protocol: 9_colmock_3 Cy5 / 10_colABA_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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.

extract_protocol: 9_colmock_3:30ug. (Qiagen_RNeasy.pdf)

extract_protocol: 10_colABA_3:30ug. (Qiagen_RNeasy.pdf)


title: 254706910032_b1 - 9_colmock_3 vs 10_colABA_3

hyb_protocol: 10_colABA_3 Cy5 / 9_colmock_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: A22


title: A24


title: Mature-untreated-12days_rep2

description: Raw data - Cy5: ES_253014210003_S01_GE2_107_Sep09_1_3.txt

source_name: stem sections pruned at 10-15 cm. 12 days after pruning

value: Mature


title: 254706910031_b1 - 3_mkk3mock_1 vs 4_mkk3ABA_1

hyb_protocol: 4_mkk3ABA_1 Cy5 / 3_mkk3mock_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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.

growth_protocol: seedling - 1/2MS (SIGMA M6899)+1% Sucrose+0,05%MES. pH 5.7 adjusted with HCl. 25 mL in medium petri dish.

extract_protocol: 4_mkk3ABA_1:30ug. (Qiagen_RNeasy.pdf)

extract_protocol: 3_mkk3mock_1:30ug. (Qiagen_RNeasy.pdf)


title: Mature-Auxin-12days_rep1

description: Raw data - Cy3: ES_253014210003_S01_GE2_107_Sep09_1_3.txt

value: stem sections pruned at 10-15 cm. Auxin treated. 12 days after pruning


title: Juvenile-untreated-12days_rep1

description: Raw data - Cy5: ES_253014210003_S01_GE2_107_Sep09_1_4.txt


title: A18

value: Chinese Rongchang

value: Male


title: A17

value: blood

value: normal


title: Mature-untreated-12days_rep1

description: Raw data - Cy3: ES_253014210003_S01_GE2_107_Sep09_1_4.txt

value: stem sections pruned at 10-15 cm. 12 days after pruning


title: 254706910031_b2 - 4_mkk3ABA_1 vs 3_mkk3mock_1

hyb_protocol: 3_mkk3mock_1 Cy5 / 4_mkk3ABA_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 254706910030_b4 - 6_colABA_2 vs 5_colmock_2

hyb_protocol: 5_colmock_2 Cy5 / 6_colABA_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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.

extract_protocol: 5_colmock_2:30ug. (Qiagen_RNeasy.pdf)

extract_protocol: 6_colABA_2:30ug. (Qiagen_RNeasy.pdf)


title: A16

value: Female


title: A19


title: A15


title: 254706910030_b3 - 5_colmock_2 vs 6_colABA_2

hyb_protocol: 6_colABA_2 Cy5 / 5_colmock_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: A14

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


title: 254706910030_b2 - 2_colABA_1 vs 1_colmock_1

hyb_protocol: 1_colmock_1 Cy5 / 2_colABA_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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.

extract_protocol: 1_colmock_1:30ug. (Qiagen_RNeasy.pdf)

extract_protocol: 2_colABA_1:30ug. (Qiagen_RNeasy.pdf)


title: 254706910031_b3 - 7_mkk3mock_2 vs 8_mkk3ABA_2

hyb_protocol: 8_mkk3ABA_2 Cy5 / 7_mkk3mock_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: A23


title: A12


title: 254706910030_b1 - 1_colmock_1 vs 2_colABA_1

hyb_protocol: 2_colABA_1 Cy5 / 1_colmock_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: Juvenile-untreated-6days_rep2

description: Raw data - Cy3: ES_253014210002_S01_GE2_107_Sep09_1_1.txt

hyb_protocol: Agilent protocol

source_name: stem sections pruned at 150-200 cm. 6 days after pruning

value: 6 days


title: A13


title: Mature-Auxin-6days_rep2

description: Raw data - Cy5: ES_253014210002_S01_GE2_107_Sep09_1_2.txt

value: stem sections pruned at 10-15 cm. Auxin treated. 6 days after pruning


title: Juvenile-Auxin-6days_rep1

description: Raw data - Cy3: ES_253014210002_S01_GE2_107_Sep09_1_2.txt

value: Juvenile

value: stem sections pruned at 150-200 cm. Auxin treated. 6 days after pruning


title: A11


title: Mature-untreated-6days_rep2

description: Raw data - Cy5: ES_253014210002_S01_GE2_107_Sep09_1_3.txt

value: stem sections pruned at 10-15 cm. 6 days after pruning


title: 254706910027_b4 - 12_mkk3ABA_3 vs 10_colABA_3

description: Identification of the miss-regulated genes in mkk3 under ABA treatment

hyb_protocol: 10_colABA_3 Cy5 / 12_mkk3ABA_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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-Auxin-6days_rep1

description: Raw data - Cy3: ES_253014210002_S01_GE2_107_Sep09_1_3.txt


title: A8


title: A6


title: A9


title: 254706910027_b1 - 9_colmock_3 vs 11_mkk3mock_3

hyb_protocol: 11_mkk3mock_3 Cy5 / 9_colmock_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 254706910027_b3 - 10_colABA_3 vs 12_mkk3ABA_3

hyb_protocol: 12_mkk3ABA_3 Cy5 / 10_colABA_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: A10


title: Juvenile-Auxin-1day_rep2

description: Raw data - Cy5: ES_253014210001_S01_GE2_107_Sep09_1_1.txt

source_name: stem sections pruned at 150-200 cm. Auxin treated. 1 day after pruning

value: 1 day


title: Mature-untreated-6days_rep1

description: Raw data - Cy3: ES_253014210002_S01_GE2_107_Sep09_1_4.txt


title: Juvenile-untreated-6days_rep1

description: Raw data - Cy5: ES_253014210002_S01_GE2_107_Sep09_1_4.txt

value: stem sections pruned at 150-200 cm. 6 days after pruning


title: 254706910027_b2 - 11_mkk3mock_3 vs 9_colmock_3

hyb_protocol: 9_colmock_3 Cy5 / 11_mkk3mock_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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.

value: columbia

value: mkk3 mutant t-dna


title: Mature-Auxin-1day_rep2

description: Raw data - Cy5: ES_253014210001_S01_GE2_107_Sep09_1_2.txt

source_name: stem sections pruned at 10-15 cm. Auxin treated. 1 day after pruning

value: Mature


title: 254706910026_b4 - 8_mkk3ABA_2 vs 6_colABA_2

hyb_protocol: 6_colABA_2 Cy5 / 8_mkk3ABA_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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.

value: boyes 1.03


title: A5

value: Chinese Rongchang


title: fruit

city: Hang zhou

first: Jie

last: Wang

state: Zhe jiang province

address: Yu hangtang road 388 of West Lake District

department: Horticulture

institute: Zhejiang university

description: Test

data_processing:
For the normalization it uses the housekeeping gene: EF1a (accession number EF446145).
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]

label: SYBR Green

organism: Cucumis sativus

source_name: ‘Jinyan No.4’cultivar

label_protocol: PCR assays were performed using the Bio-rad laboratories, lnc. PCR assay panel following the Manufacturer’s instructions. Reverse transcription was performed from 1 ug total RNA using the Reverse Transcription System ( Takara, Japan). Quantitative real-time PCR were performed in a final volume of 20 µl containing 3 pmol specific primers and 12.5 µl SYBR Green.

extract_protocol: Total RNA was extracted with with TRIZOL reagent (Invitrogen, USA) according to the manufacturer’s instructions.

tag: developmental stage

value: 10 d after pollination

value: fruit


title: 254706910026_b2 - 4_mkk3ABA_1 vs 2_colABA_1

hyb_protocol: 2_colABA_1 Cy5 / 4_mkk3ABA_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: Juvenile-untreated-1day_rep2

description: Raw data - Cy3: ES_253014210001_S01_GE2_107_Sep09_1_1.txt

source_name: stem sections pruned at 150-200 cm. 1 day after pruning


title: Juvenile-Auxin-1day_rep1

description: Raw data - Cy3: ES_253014210001_S01_GE2_107_Sep09_1_2.txt

value: stem sections pruned at 150-200 cm. Auxin treated. 1 day after pruning


title: male flower bud

description: Test

value: approximately 1.0 cm in length

value: male flower bud


title: 254706910025_b4 - 7_mkk3mock_2 vs 5_colmock_2

hyb_protocol: 5_colmock_2 Cy5 / 7_mkk3mock_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 254706910026_b3 - 6_colABA_2 vs 8_mkk3ABA_2

hyb_protocol: 8_mkk3ABA_2 Cy5 / 6_colABA_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 254706910026_b1 - 2_colABA_1 vs 4_mkk3ABA_1

hyb_protocol: 4_mkk3ABA_1 Cy5 / 2_colABA_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 254706910025_b3 - 5_colmock_2 vs 7_mkk3mock_2

hyb_protocol: 7_mkk3mock_2 Cy5 / 5_colmock_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 254706910025_b2 - 3_mkk3mock_1 vs 1_colmock_1

hyb_protocol: 1_colmock_1 Cy5 / 3_mkk3mock_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: A1

value: Female

value: blood

value: normal


title: female flower bud

description: Test

value: 3 d before anthesis

value: female flower bud


title: A3

value: Male


title: A2


title: stem

description: Test

value: stem


title: leaf

description: Test

value: leaf


title: 254706910025_b1 - 1_colmock_1 vs 3_mkk3mock_1

hyb_protocol: 3_mkk3mock_1 Cy5 / 1_colmock_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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.

value: columbia

value: mkk3 mutant t-dna


title: A4

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


title: root

description: Test

value: root


title: B84

value: Chinese Rongchang


title: Mature-Auxin-1day_rep1

description: Raw data - Cy3: ES_253014210001_S01_GE2_107_Sep09_1_3.txt

value: Mature

value: stem sections pruned at 10-15 cm. Auxin treated. 1 day after pruning

value: 1 day


title: ABA-8h

description: Test

data_processing:
For the normalization it uses the housekeeping gene: EF1a (accession number EF446145).
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Fold Change  reports test/control  ratios. One of the gene which has the lowest expression  was treated as a control.

source_name: ‘Jinyan No.26’cultivar

value: leaves of three weeks seedings

value: ABA


title: B85


title: Juvenile-Auxin-6days_rep2

description: Raw data - Cy5: ES_253014210002_S01_GE2_107_Sep09_1_1.txt

value: Juvenile

value: stem sections pruned at 150-200 cm. Auxin treated. 6 days after pruning

value: 6 days


title: B81

value: Female

value: blood

value: normal


title: Juvenile-untreated-1day_rep1

description: Raw data - Cy5: ES_253014210001_S01_GE2_107_Sep09_1_4.txt

value: stem sections pruned at 150-200 cm. 1 day after pruning


title: ABA-4h

description: Test

source_name: ‘Jinyan No.25’cultivar


title: Mature-untreated-1day_rep1

description: Raw data - Cy3: ES_253014210001_S01_GE2_107_Sep09_1_4.txt

source_name: stem sections pruned at 10-15 cm. 1 day after pruning


title: B82


title: Mature-untreated-1day_rep2

description: Raw data - Cy5: ES_253014210001_S01_GE2_107_Sep09_1_3.txt

value: stem sections pruned at 10-15 cm. 1 day after pruning


title: B83

value: Male


title: ABA-1h

description: Test

source_name: ‘Jinyan No.23’cultivar


title: ABA-2h

description: Test

source_name: ‘Jinyan No.24’cultivar


title: B77

source_name: blood


title: B76


title: B80


title: B78


title: PD-L1_Pos_rep5

city: Baltimore

first: Alan

middle: E.

last: Berger

address: 5501 Hopkins Bayview Circle Room 3B.74C

department: School of Medicine

institute: Johns Hopkins University

description: PD-L1 Positive melanoma

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Signal intensity quantification was performed using an Illumina BeadStation 500GX Genetic Analysis Systems scanner, using the standard Illumina scanning protocol.

data_processing:
For each sample, a single intensity (expression) value for each Illumina probe on the array was obtained using
Illumina GenomeStudio software with standard settings and no background correction.
For the sample data tables, the ID_REF is the Illumina Probe_ID, and the Detection Pval is as provided by the Illumina software.
Detection Pvalues near 0 indicate Present  (above background).
Based on the appearance of the histogram of the Illumina expression values (signal intensities) for each of the samples (see Histograms.pdf linked as a supplementary file on the Series record),
we considered expression values at or above 1024 (log base 2 of expression value at or above 10) to be Present.
Also based on the appearance of the histograms, no normalization (such as scaling or quantile) was done as the assumptions underlying
these methods do not appear to be valid. Analysis was done on log base 2 of the scanned Illumina signal intensities.

source_name: metastasis, lymph node

label_protocol: Total RNA was biotin labeled with the WG-DASL pre 1 MCS4 w/UDG Kit according to the manufacturers suggested protocol.

extract_protocol:
Laser capture microdissection (LCM) and RNA isolation from FFPE melanoma specimens were performed as described
in the reference above and in  Taube JM, Anders RA, Young GD, Xu H, Sharma R, McMiller TL, et al.  Co-localization of inflammatory
response with B7-H1 expression in human melanocytic lesions supports an adaptive resistance mechanism
of immune escape.  Science Transl Med 2012; 4:127ra37.
Total RNA was isolated from LCM specimens using the High Pure RNA Paraffin Kit (Roche) as described in the reference given in the three lines above.

tag: specimen

value: melanoma

tag: pd-l1 status

value: PD-L1 positive

value: M


title: PD-L1_Pos_rep3

description: PD-L1 Positive melanoma


title: PD-L1_Pos_rep4

description: PD-L1 Positive melanoma

value: F


title: MeJA-4h

description: Test

source_name: ‘Jinyan No.20’cultivar

value: MeJA


title: MeJA-8h

description: Test

source_name: ‘Jinyan No.21’cultivar


title: B75

value: Chinese Rongchang


title: MeJA-2h

description: Test

source_name: ‘Jinyan No.19’cultivar

value: leaves of three weeks seedings


title: MeJA-1h

description: Test

source_name: ‘Jinyan No.18’cultivar


title: B74


title: PD-L1_Pos_rep2

description: PD-L1 Positive melanoma

source_name: primary lesion, skin (scalp)


title: MeJA-0h

description: Control

source_name: ‘Jinyan No.17’cultivar


title: B73


title: ABA-0h

description: Control

source_name: ‘Jinyan No.22’cultivar

value: ABA


title: P.cubensis-3d

description: Test

source_name: ‘Jinyan No.16’cultivar


title: P.cubensis-2d

description: Test

source_name: ‘Jinyan No.15’cultivar


title: B70


title: PD-L1_Pos_rep1

description: PD-L1 Positive melanoma

source_name: metastasis, lung


title: PD-L1_Neg_rep4

description: PD-L1 Negative melanoma

value: PD-L1 negative


title: P.cubensis-0d

description: Control

source_name: ‘Jinyan No.13’cultivar


title: PD-L1_Neg_rep6

description: PD-L1 Negative melanoma

source_name: primary lesion, skin (foot)


title: PD-L1_Neg_rep3

description: PD-L1 Negative melanoma

source_name: metastasis, small bowel


title: drought-6d

description: Test

source_name: ‘Jinyan No.12’cultivar

value: drought


title: PD-L1_Neg_rep5

description: PD-L1 Negative melanoma


title: B69


title: B68


title: B66


title: drought-4d

description: Test

source_name: ‘Jinyan No.11’cultivar


title: P.cubensis-1d

description: Test

source_name: ‘Jinyan No.14’cultivar


title: drought-2d

description: Test

source_name: ‘Jinyan No.10’cultivar


title: PD-L1_Neg_rep1

description: PD-L1 Negative melanoma

source_name: metastasis, lymph node


title: B67

source_name: blood


title: B65


title: drought-0d

description: Control

source_name: ‘Jinyan No.9’cultivar


title: 564018A12 - MYB1_BR2 vs CONTROLpJRpFAST_BR2

description: Transcription modification produced by transgenes

hyb_protocol: CONTROLpJRpFAST_BR2 Cy5 / MYB1_BR2 Cy3 : 30pmol.

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

growth_protocol: stem - Media= hygrometry=70% Temperature=22 Light=short day conditions 8h/16h

value: arabidopsis thaliana (wassilewskija)  mutant (ws) -  dev.stage (boyes et al. plant cell 2001):boyes:6.90


title: 564018A11 - CONTROLpJRpFAST_BR2 vs MYB1_BR2

hyb_protocol: MYB1_BR2 Cy5 / CONTROLpJRpFAST_BR2 Cy3 : 30pmol.

value: arabidopsis thaliana (wassilewskija)  mutant (ws)


title: B60

value: blood


title: B58

value: normal


title: B63

value: Female


title: B64


title: heat-4h

description: Test

source_name: ‘Jinyan No.7’cultivar

value: heat


title: 564018A07 - CONTROLpJRpFAST_BR2 vs HISTONE-MYB1_BR2

hyb_protocol: HISTONE-MYB1_BR2 Cy5 / CONTROLpJRpFAST_BR2 Cy3 : 30pmol.


title: heat-2h

description: Test

source_name: ‘Jinyan No.6’cultivar


title: B59

value: Male


title: 564018A10 - MYB1_BR1 vs CONTROLpJRpFAST_BR1

hyb_protocol: CONTROLpJRpFAST_BR1 Cy5 / MYB1_BR1 Cy3 : 30pmol.


title: heat-1h

description: Test

source_name: ‘Jinyan No.5’cultivar


title: B56


title: 564018A09 - CONTROLpJRpFAST_BR1 vs MYB1_BR1

hyb_protocol: MYB1_BR1 Cy5 / CONTROLpJRpFAST_BR1 Cy3 : 30pmol.


title: B72


title: B57


title: B55


title: heat-0h

description: Control

source_name: ‘Jinyan No.4’cultivar


title: 564018A06 - HISTONE-MYB1_BR1 vs CONTROLpJRpFAST_BR1

hyb_protocol: CONTROLpJRpFAST_BR1 Cy5 / HISTONE-MYB1_BR1 Cy3 : 30pmol.


title: cold-4h

description: Test

value: cold


title: B50


title: cold-8h

description: Test


title: heat-8h

description: Test

source_name: ‘Jinyan No.8’cultivar


title: B48


title: cold-2h

description: Test


title: 564018A08 - HISTONE-MYB1_BR2 vs CONTROLpJRpFAST_BR2

hyb_protocol: CONTROLpJRpFAST_BR2 Cy5 / HISTONE-MYB1_BR2 Cy3 : 30pmol.


title: 564018A05 - CONTROLpJRpFAST_BR1 vs HISTONE-MYB1_BR1

hyb_protocol: HISTONE-MYB1_BR1 Cy5 / CONTROLpJRpFAST_BR1 Cy3 : 30pmol.


title: B46


title: cold-0h

description: Control


title: 564018A03 - CONTROLpJRpFAST_BR2 vs HISTONE_BR2

hyb_protocol: HISTONE_BR2 Cy5 / CONTROLpJRpFAST_BR2 Cy3 : 30pmol.


title: B45


title: B42


title: cold-1h

description: Test


title: 564018A04 - HISTONE_BR2 vs CONTROLpJRpFAST_BR2

hyb_protocol: CONTROLpJRpFAST_BR2 Cy5 / HISTONE_BR2 Cy3 : 30pmol.


title: B43


title: 564018A02 - HISTONE_BR1 vs CONTROLpJRpFAST_BR1

hyb_protocol: CONTROLpJRpFAST_BR1 Cy5 / HISTONE_BR1 Cy3 : 30pmol.


title: B44


title: 564014A08 - OVATE_BR2 vs CONTROLpJRpFAST_BR2

hyb_protocol: CONTROLpJRpFAST_BR2 Cy5 / OVATE_BR2 Cy3 : 30pmol.


title: 564014A07 - CONTROLpJRpFAST_BR2 vs OVATE_BR2

hyb_protocol: OVATE_BR2 Cy5 / CONTROLpJRpFAST_BR2 Cy3 : 30pmol.


title: Non diabetic foot fibroblasts sample 23

description:
20140717_olivera-071714_NFF23_05.RCC
nanostring data generated from RNA isolated from fibroblasts generated from a non-diabetic skin biopsy

data_processing:
The miRNA data were all normalized to housekeeping genes included in the assays
The fold change values [fold_change.txt] are expressed as Fold change(DFS/NFS)

source_name: non-Diabetic Foot skin

label_protocol: 100ng of total RNA was used for sample preparation for the nanoString nCounter assay according to the Nanostring protocols.

growth_protocol: foot skin biopsies obtained from diabetic and non-diabetic people were thoroughly washed in DMEM supplemented with 2× Penicillin/Streptomycin/Fungizone, and gentamicin (50mg/L). After, the epidermis was removed from specimens, the dermis was finely minced and placed in 12-well plates. For the establishment of fibroblast cultures, DMEM (Life Technologies) supplemented with 10% FBS, HEPES (1.9mg/ml), streptomycin (100 μg/ml), penicillin (100 U/ml), and Fungizone Antimycotic (0.25 µg/mL) was used

extract_protocol: Total RNA was isolated from cells (passage 1 or 2) using miRNeasy Mini Kit (QIAGEN)

value: healthy non-diabetic foot skin (NFS)

value: fibroblast


title: Non diabetic foot fibroblasts sample 14

description:
20140717_olivera-071714_NFF14_12.RCC
nanostring data generated from RNA isolated from fibroblasts generated from a non-diabetic skin biopsy


title: B35


title: 564018A01 - CONTROLpJRpFAST_BR1 vs HISTONE_BR1

hyb_protocol: HISTONE_BR1 Cy5 / CONTROLpJRpFAST_BR1 Cy3 : 30pmol.


title: B34


title: B36


title: 564014A06 - OVATE_BR1 vs CONTROLpJRpFAST_BR1

hyb_protocol: CONTROLpJRpFAST_BR1 Cy5 / OVATE_BR1 Cy3 : 30pmol.


title: Non diabetic foot fibroblasts sample 11

description:
20140717_olivera-071714_NFF11_11.RCC
nanostring data generated from RNA isolated from fibroblasts generated from a non-diabetic skin biopsy


title: Diabetic foot fibroblasts sample 09

description:
20140717_olivera-071714_DFF9_08.RCC
nanostring data generated from RNA isolated from fibroblasts generated from a diabetic skin biopsy

source_name: Diabetic Foot skin

value: non-ulcerated non-neuropathic diabetic foot skin (DFS)


title: Diabetic foot fibroblasts sample 05

description:
20140717_olivera-071714_DFF5_09.RCC
nanostring data generated from RNA isolated from fibroblasts generated from a diabetic skin biopsy


title: B41

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


title: Non diabetic foot fibroblasts sample 12

description:
20140717_olivera-071714_NFF12_10.RCC
nanostring data generated from RNA isolated from fibroblasts generated from a non-diabetic skin biopsy


title: BT549_pcDNA3_flag_ERβ2_rep2

city: Stockholm

first: Li

last: Xu

address: Hälsovägen 7-9

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

hyb_protocol: Hybridization was performed according to Affymetyrix standard protocols

scan_protocol: Sanning was performed using an Affymetrix GeneTitan scanner

data_processing: Raw data was processed in Affymetrix Expression Console using the RMA method

source_name: BT549 cells_pcDNA3-flag-ERβ2_24h

label_protocol: Labeling was performed from 150 ng of starting material according to standard Affymetrix protocols

growth_protocol: The human breast cancer cell line BT549 was maintained in RPMI 1640 medium  supplemented with 10% fetal bovine serum (FBS) (Invitrogen) at 37°C, under a humidified atmosphere of 5% carbon dioxide.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: BT549 cells were transfected with a control siRNA or with the of siRNAs targeting ERβ2 and total RNA was extracted 48h after transfection. BT549 cells were transfected with a control pcDNA3 empty vector or with the of flag tagged ERβ2 cDNA and total RNA was extracted 24h after transfection.

tag: cell line

value: breast cancer cell line

tag: transfected with

value: ERβ2 cDNA (pcDNA3-flag-ERβ2)

tag: time point

value: 24h after transfection


title: 564014A05 - CONTROLpJRpFAST_BR1 vs OVATE_BR1

hyb_protocol: OVATE_BR1 Cy5 / CONTROLpJRpFAST_BR1 Cy3 : 30pmol.


title: 564014A04 - CONTROLpJRpFAST_BR2 vs OVATE-MYB1_BR2

hyb_protocol: OVATE-MYB1_BR2 Cy5 / CONTROLpJRpFAST_BR2 Cy3 : 30pmol.


title: B33

extract_protocol: Genomic DNA for each individuals was extracted from the blood using Qiagen DNeasy blood kit (Qiagen, Germany).

value: Chinese Rongchang

tag: tissue

tag: disease state


title: PD-L1_Neg_rep2

description: PD-L1 Negative melanoma

hyb_protocol: Standard Illumina hybridization protocol

source_name: primary lesion, skin (scalp)

value: melanoma

value: PD-L1 negative

value: M


title: B30


title: BT549_pcDNA3_flag_ERβ2_rep3

tag: cell type


title: Diabetic foot fibroblasts sample 24

description:
20140717_olivera-071714_DFF24_01.RCC
nanostring data generated from RNA isolated from fibroblasts generated from a diabetic skin biopsy


title: 564014A01 - CONTROLpJRpFAST_BR1 vs OVATE-MYB1_BR1

hyb_protocol: OVATE-MYB1_BR1 Cy5 / CONTROLpJRpFAST_BR1 Cy3 : 30pmol.

tag: genotype

value: arabidopsis thaliana (wassilewskija)  mutant (ws)


title: 564014A02 - OVATE-MYB1_BR1 vs CONTROLpJRpFAST_BR1

hyb_protocol: CONTROLpJRpFAST_BR1 Cy5 / OVATE-MYB1_BR1 Cy3 : 30pmol.


title: 564014A03 - OVATE-MYB1_BR2 vs CONTROLpJRpFAST_BR2

hyb_protocol: CONTROLpJRpFAST_BR2 Cy5 / OVATE-MYB1_BR2 Cy3 : 30pmol.


title: Diabetic foot fibroblasts sample 20

description:
20140717_olivera-071714_DFF20_04.RCC
nanostring data generated from RNA isolated from fibroblasts generated from a diabetic skin biopsy


title: BT549_pcDNA3_EV_rep3

source_name: BT549 cells_pcDNA3-EV_24h

value: empty vector control (pcDNA3-EV)


title: B25

value: blood

value: normal


title: B29


title: B24


title: BT549_pcDNA3_flag_ERβ2_rep1


title: B28

value: Female


title: B21

value: Male


title: B19


title: BT549_pcDNA3_EV_rep2


title: CP70-DDB2-3

city: Columbus

first: Qi-En

state: OH

address: 420 W.12th Avenue

department: Radiation Oncology

institute: The Ohio State University

description: Gene expression data from CP70 cells transfected with DDB2-expressing vector

hyb_protocol: Following fragment and label, 5.2 g of single-strand DNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human transcriptome array 2.0. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0

source_name: CP70 cells transfected with DDB2-expressing vector, clone-3

label_protocol: Amplified and biotinylated sense-strand DNA were prepared according to the standard Affymetrix protocol from 100ng total RNA

growth_protocol: Cells were grown in RPMI 1640 medium supplemented with 10% (v/v) fetal bovine serum (FBS), and maintained in a humidified atmosphere with 5% CO2 at 37°C.

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

value: ovarian cancer cell line A2780-CP70

tag: protocol


title: mature_hepatocyte_3

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

country: United Kingdom

institute: University of Stirling

hyb_protocol: The samples were briefly spun down and then loaded onto a MAUI hybridization station (BioMicro Inc., USA). The arrays were incubated at 56C for 16 hours, then washed briefly at 60C using buffer A, rinsed in buffer B, followed by a 2-minute wash in buffer B, a 2-minute wash in buffer C with a final brief fixing rinse in 99% ethanol. The arrays were dried by centrifugation (1000rpm for 5 minutes).

scan_protocol: Arrays were scanned using a GenePix 4200A microarray scanner.

data_processing: Raw scan data were analysed using GenePix Pro 6 software.

source_name: RNA from mature human hepatocytes

label_protocol: 1ug of total RNA was labelled with Hy3 dye according to the manufacturer's protocol. Briefly, RNA was incubated with the Hy3 dye, labelling enzyme, and spike-in miRNAs, in a total volume of 12.5ul for 1 hour at 16C. The enzyme was then heat-inactivated at 65C for 15 minutes. The samples were incubated at 95C for 2 minutes protected from light. Labelled samples were made up to 50ul by addition of 37.5ul of hybridization buffer.

extract_protocol: Total RNA was extracted from foetal cells using TriZol (Invitrogen) according to the manufacturer's protocol. Total RNA from adult hepatocytes was purchased from 3H Biomedical, Uppsala, Sweden. The Nanodrop instrument (Labtech UK) was used to quantify RNA and assess 260/280 and 260/230 ratios. RNA integrity was examined using a 2100 Bioanalyzer (Agilent UK). All samples used had RIN scores > 9, 260/280 ratios > 2, and 260/230 ratios > 1.9.

tag: cell

value: mature hepatocyte


title: BT549_pcDNA3_EV_rep1


title: BT549_siERβ2_rep1

source_name: BT549 cells_siERβ2l_48h

value: siRNA targeting ERβ2

value: 48h after transfection


title: foetal_liver_progenitor_1

source_name: RNA from foetal liver progenitor cells at week 14 of development

value: Foetal liver progenitor


title: foetal_liver_progenitor_3


title: foetal_liver_progenitor_2


title: B13


title: CP70-DDB2-2

source_name: CP70 cells transfected with DDB2-expressing vector, clone-2


title: mature_hepatocyte_2


title: B17

source_name: blood


title: B16


title: BT549_sicontrol_rep3

source_name: BT549 cells_siControl_48h

value: breast cancer cell line

value: control siRNA


title: CP70-DDB2-1

source_name: CP70 cells transfected with DDB2-expressing vector, clone-1


title: B8

value: Chinese Rongchang


title: BT549_siERβ2_rep2


title: BT549_sicontrol_rep2


title: B14


title: CP70-Vector-3

description: Gene expression data from CP70 cells transfected with empty vector

source_name: CP70 cells transfected with empty vector, clone-2

value: control


title: CP70-Vector-1

source_name: CP70 cells transfected with empty vector, clone-1


title: BT549_sicontrol_rep1


title: B6


title: mature_hepatocyte_1


title: controll mouse wildtype C57Bl6 (rep3)

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

institute: Technische Universität München

description:
Gene expression data from CD19+ sIgM- bone marrow cells of wildtype C57BL/6 control mouse
S2250_WT3

hyb_protocol: The amplified and fragmented biotinylated cRNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays using standard procedures.

scan_protocol: Affymetrix scanner 3000 7g.

data_processing: Raw data analysis was performed with R and Bioconductor (Gentleman et al. 2004; R Development Core Team 2007). Arrays were assessed for quality and  GCRMA -normalized. “Quality assessment” consisted of RNA degradation plots, Affymetrix quality control metrics, sample cross-correlation, data distributions, and probe-level visualizations.  The data were analyzed for differential gene expression using an empirical Bayes moderated t-test (Smyth 2004), implemented in the Bioconductor package Linear Models for Microarray Data (LIMMA).  The results were sorted by the false discovery rate and exported in tab-delimited format.

source_name: CD19+ CD25+ sIGM-  bone marrow cell sort of  wildtype C57Bl6 control mouse

label_protocol: Total RNA (1.5 μg) and newly transcribed RNA (280 ng) were amplified and labeled using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's recommendations. As newly transcribed RNA mainly consists of mRNA, it was amplified and labeled according to the manufacturer's protocol for mRNA.

extract_protocol: Total RNA extraktion was performed with the RNeasy Mini Kit (Quiagen) according to the manufacturer's instructions.

tag: strain background

tag: genotype/variation

value: wild type

value: CD19+ CD25+ sIGM-  bone marrow cells


title: B5

tag: breed

tag: gender


title: controll mouse wildtype C57Bl6 (rep2)

description:
Gene expression data from CD19+ sIgM- bone marrow cells of wildtype C57BL/6 control mouse
S2249_WT2

value: CD19+ CD25+ sIGM- bone marrow cells


title: B4


title: B3


title: controll mouse wildtype C57Bl6 (rep1)

description:
Gene expression data from CD19+ sIgM- bone marrow cells of wildtype C57BL/6 control mouse
S2248_WT1


title: B1


title: controll mouse IRF4 Knockout (rep1)

description:
Gene expression data from CD19+ sIgM- bone marrow cells of IRF4 knockout mouse
S2245_KO1_KM_IRF4

source_name: CD19+ sIgM-  bone marrow cell sort from  IRF4 Knockout control mouse

value: IRF4 Knockout

value: CD19+ sIgM-  bone marrow cells