title: OTA_bAH_biological rep3

status: Public on Feb 20 2010

type: RNA

city: Konstanz

first: Daniel

middle: R.

last: Dietrich

address: Jakob-Burckhardt-Str. 25

department: Environmental Toxicology

country: Germany

institute: University of Konstanz

description: OTA_bAH_biological rep3

hyb_protocol: According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.

scan_protocol: The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)

data_processing: Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Renal basophilic hyperplasia, OTA treated Eker rat 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).

growth_protocol: Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)

treatment_protocol: Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.

tag: Strain

value: Tsc2 mutant Long Evans rats (Eker rats).

tag: Gender

value: male.

tag: Age

value: 6-8 weeks

tag: Tissue

value: Kidney

tag: Sample

value: microdissected renal basophilic atypical hyperplasia


title: OTA_HT_biological rep2

description: OTA_HT_biological rep2

source_name: Healthy renal tissue, OTA treated Eker rat 2

value: Tsc2 mutant Long Evans rats (Eker rats)

value: microdissected healthy tubule


title: OTA_bAH_biological rep1

description: OTA_bAH_biological rep1

source_name: Renal basophilic hyperplasia, OTA treated Eker rat 1


title: AA_bAH_biological rep1

description: AA_bAH_biological rep1

source_name: Renal basophilic hyperplasia, AA treated Eker rat 1


title: OTA_HT_biological rep3

description: OTA_HT_biological rep3

source_name: Healthy renal tissue, OTA treated Eker rat 3


title: C(OTA)_HT_biological rep1

description: C(OTA)_HT_biological rep1

source_name: Healthy renal tissue, vehicle control 1


title: OTA_bAT_biological rep1

description: OTA_bAT_biological rep1

source_name: Renal basophilic atypical tubule, OTA treated Eker rat 1

value: microdissected renal basophilic atypical tubules


title: OTA_bAT_biological rep3

description: OTA_bAT_biological rep3

source_name: Renal basophilic atypical tubule, OTA treated Eker rat 2


title: OTA_bAH_biological rep2

description: OTA_bAH_biological rep2

source_name: Renal basophilic hyperplasia, OTA treated Eker rat 2


title: AA_bAH_biological rep2

description: AA_bAH_biological rep2

source_name: Renal basophilic hyperplasia, AA treated Eker rat 2


title: OTA_HT_biological rep1

description: OTA_HT_biological rep1

source_name: Healthy renal tissue, OTA treated Eker rat 1


title: OTA_bAT_biological rep2

description: OTA_bAT_biological rep2


title: AA_bAT_biological rep1

description: AA_bAT_biological rep1

source_name: Renal basophilic atypical tubule, AA treated Eker rat 1


title: AA_bAH_biological rep3

description: AA_bAH_biological rep3

source_name: Renal basophilic hyperplasia, AA treated Eker rat 3


title: C(OTA)_HT_biological rep2

description: C(OTA)_HT_biological rep2

source_name: Healthy renal tissue, vehicle control 2


title: AA_bAT_biological rep3

description: AA_bAT_biological rep3

source_name: Renal basophilic atypical tubule, AA treated Eker rat 2


title: AA_bAT_biological rep2

description: AA_bAT_biological rep2


title: AA_HT_biological rep1

description: AA_HT_biological rep1

source_name: Healthy renal tissue, AA treated Eker rat 1


title: AA_HT_biological rep2

description: AA_HT_biological rep2

source_name: Healthy renal tissue, AA treated Eker rat 2


title: C(AA)_bAH_biological rep2

description: C(AA)_bAH_biological rep2

source_name: Renal basophilic hyperplasia, vehicle control 2


title: C(AA)_bAH_biological rep3

description: C(AA)_bAH_biological rep3

source_name: Renal basophilic hyperplasia, vehicle control 3


title: C(AA)_bAT_biological rep2

description: C(AA)_bAT_biological rep2

source_name: Renal basophilic atypical tubule, vehicle control 2


title: C(AA)_bAT_biological rep1

description: C(AA)_bAT_biological rep1

source_name: Renal basophilic atypical tubule, vehicle control 1


title: AA_HT_biological rep3

description: AA_HT_biological rep3

source_name: Healthy renal tissue, AA treated Eker rat 3


title: C(AA)_bAH_biological rep1

description: C(AA)_bAH_biological rep1

source_name: Renal basophilic hyperplasia, vehicle control 1


title: C(AA)_bAT_biological rep3

description: C(AA)_bAT_biological rep3

source_name: Renal basophilic atypical tubule, vehicle control 3


title: C(AA,OTA)_HT_biological rep3

description: C(AA,OTA)_HT_biological rep3

source_name: Healthy renal tissue, vehicle control 3


title: Thoracic Duct / Vena Cava normal 4

status: Public on Jan 27 2010

city: Temple

first: David

middle: C.

last: Zawieja

state: TX

address: 702 SW HK Dodgen Loop

department: Dept. of Systems Biology and Translational Medicine

country: USA

institute: Texas A&M Health Science Center

description: Thoracic duct samples were paired with vena cava samples acquired from the same donor animal. Hybridization and scanning was performed by the Department of Systems Biology and Translational Medicine Microarray Core Facility, Texas A&M Health Science Center, Temple, TX.

hyb_protocol: Spotted arrays were incubated 45 min @48ºC with 35 rpm orbital agitation in prehybridization buffer (5X SSC , 0.1% SDS, 0.2% BSA) and then gently agitated 2 x 5 min in nuclease-free water followed by 2 x 5 min in isopropanol before being spun dry and maintained at 48ºC until hybridization. Equal mass, dye-coupled amplified RNA samples were mixed, column purified, and fragmented by hydrolysis (Fragmentation Reagents, Ambion) prior to hybridization. The sample was then diluted to at least 0.5X with Slidehyb Glass Hybridization buffer (Ambion) and applied directly to the array surface. The sample was then covered with a Hybrislip (Grace Biolabs) and incubated for 16hrs @48ºC. Following hybridization, the arrays were gently agitated in 48ºC 1X SSC, 0.1% SDS for 6 min followed by room temperature 1X SSC, 0.1% SDS for 6 min followed room temperature 0.1X SSC for 3 x 6 min. The slides were then scanned immediately.

scan_protocol: The array is scanned at 635 nm and 532 nm wavelengths with a 10 µm resolution using Genepix 4000A scanner (Axon instruments). The two individual wavelength scans are then integrated and superimposed into a false color ratio image from which fluorescence data is collected using Genepix pro 6.0 (Axon instruments). All data is acquired in a tabular form and exported for analysis by other software.

data_processing: Unprocessed fluorescence intensity data was exported to Microsoft Excel 11.2 software for quality control evaluation. Data points were flagged if both dye channels failed any of the following requirements: at least 40% of feature pixels exhibiting fluorescent intensity greater than local mean background+2SD, feature intensity greater than local background intensity by at least 10 units, ratio of feature intensity to local background intensity greater than 2.5. The flagged raw feature and background intensity values for both dye channels were then imported into GeneSpring GX 7.3 software (Agilent Technologies), transformed to accomodate dye swap (the Cy3 values were interpreted as Cy5 values and vice versa), and normalized by subtracting the local background intensity from the feature intensity for each channel, setting all Cy5 measurements less than 1 to 1, and applying a per-gene and per-array, intensity-dependent (LOWESS) normalization utilizing 20% of data for smoothing and a Cy3 channel cutoff of 1. Values obtained from replicate oligos on the same array were averaged.

source_name: Vena cava, normal

label_protocol: Total cellular RNA was subjected to two rounds of linear amplification using the Amino Allyl MessageAmp aRNA Kit (Ambion). Briefly, mRNA is reverse transcribed to form cDNA containing a T7 promoter. After conversion of the cDNA to double-stranded DNA, T7 RNA Polymerase is used to generate numerous antisense copies of each mRNA. During the second round of in vitro transcription, 5-(3-aminoallyl)-UTP is incorporated into the amplified RNA, which is then chemically coupled to NHS esters of Cy dye (Amersham Biosciences).

growth_protocol: The animal was housed in facilities accredited by the Association for the Assessment and Accreditation of Laboratory Animal Care (AAALAC International) and that adhere to the regulations, policies and principles detailed in the Public Health Service Policy for the Humane Care and Use of Laboratory Animals (PHS Policy, 1996) and the United States Department of Agriculture's (USDA) Animal Welfare Regulations (Animal Welfare Act, AWA, 9CFR, 1985, 1992).  Animal was exposed to a 12 hr light/dark cycle and given open access to food and water.  All animal procedures performed for this study were reviewed and approved by the Texas A&M University Laboratory Animal Care Committee before the activity was initiated.

extract_protocol: The tissue of interest was rapidly isolated by microdisection and transferred to RNAlater (Ambion) to stop endogenous RNase activity. The tissue was then cleaned of all extraneous tissue prior to RNA extraction.  Total vessel RNA was isolated using a rotor-stator homogenizer and TRIzol Reagent (Invitrogen) according to the manufacturers protocol. The RNA was subsequently DNase-treated with DNA-free (Ambion) and analyzed for integrity and quantity using the Agilent 2100 Bioanalyzer and RNA6000 Pico LabChip Kit (Agilent).

tag: Weight

tag: Sex

value: male

value: Sprague-Dawley

tag: Anesthesia

value: fentanyl/droperidol solution (droperidol 20 mg/ml, fentanyl 0.4 mg/ml; 0.3 ml/kg I.M.) and diazepam (2.5 mg/kg I.M.)

value: Vena cava

tag: Treatment

source_name: Thoracic duct, normal

value: Thoracic duct


title: C(AA)_HT_biological rep2

description: C(AA)_HT_biological rep2


title: Thoracic Duct / Vena Cava normal 1

description: Thoracic duct samples were paired with vena cava samples acquired from the same donor animal.  Hybridization and scanning was performed by the Department of Systems Biology and Translational Medicine Microarray Core Facility, Texas A&M Health Science Center, Temple, TX.

hyb_protocol: Spotted arrays were incubated 45 min @48ºC with 35 rpm orbital agitation in prehybridization buffer (5X SSC , 0.1% SDS, 0.2% BSA) and then gently agitated 2 x 5 min in nuclease-free water followed by 2 x 5 min in isopropanol before being spun dry and maintained at 48ºC until hybridization.  Equal mass, dye-coupled amplified RNA samples were mixed, column purified, and fragmented by hydrolysis (Fragmentation Reagents, Ambion) prior to hybridization.  The sample was then diluted to at least 0.5X with Slidehyb Glass Hybridization buffer (Ambion) and applied directly to the array surface.  The sample was then covered with a Hybrislip (Grace Biolabs) and incubated for 16hrs @48ºC.  Following hybridization, the arrays were gently agitated in 48ºC 1X SSC, 0.1% SDS for 6 min followed by room temperature 1X SSC, 0.1% SDS for 6 min followed room temperature 0.1X SSC for 3 x 6 min.  The slides were then scanned immediately.

scan_protocol: The array is scanned at 635 nm and 532 nm wavelengths with a 10 µm resolution using Genepix 4000A scanner (Axon instruments).  The two individual wavelength scans are then integrated and superimposed into a false color ratio image from which fluorescence data is collected using Genepix pro 6.0 (Axon instruments).  All data is acquired in a tabular form and exported for analysis by other software.

data_processing: Unprocessed fluorescence intensity data was exported to Microsoft Excel 11.2 software for quality control evaluation.  Data points were flagged if both dye channels failed any of the following requirements:  at least 40% of feature pixels exhibiting fluorescent intensity greater than local mean background+2SD, feature intensity greater than local background intensity by at least 10 units, ratio of feature intensity to local background intensity greater than 2.5.  The flagged raw feature and background intensity values for both dye channels were then imported into GeneSpring GX 7.3 software (Agilent Technologies) and normalized by subtracting the local background intensity from the feature intensity for each channel, setting all Cy5 measurements less than 1 to 1, and applying a per-gene and per-array, intensity-dependent (LOWESS) normalization utilizing 20% of data for smoothing and a Cy3 channel cutoff of 1. Values obtained from replicate oligos on the same array were averaged.

label_protocol: Total cellular RNA was subjected to two rounds of linear amplification using the Amino Allyl MessageAmp aRNA Kit (Ambion).  Briefly, mRNA is reverse transcribed to form cDNA containing a T7 promoter.  After conversion of the cDNA to double-stranded DNA, T7 RNA Polymerase is used to generate numerous antisense copies of each mRNA.  During the second round of in vitro transcription, 5-(3-aminoallyl)-UTP is incorporated into the amplified RNA, which is then chemically coupled to NHS esters of Cy dye (Amersham Biosciences).

extract_protocol: The tissue of interest was rapidly isolated by microdisection and transferred to RNAlater (Ambion) to stop endogenous RNase activity. The tissue was then cleaned of all extraneous tissue prior to RNA extraction.  Total vessel RNA was isolated using a rotor-stator homogenizer and TRIzol Reagent (Invitrogen) according to the manufacturers protocol.  The RNA was subsequently DNase-treated with DNA-free (Ambion) and analyzed for integrity and quantity using the Agilent 2100 Bioanalyzer and RNA6000 Pico LabChip Kit (Agilent).


title: Thoracic Duct / Vena Cava normal 3

data_processing: Unprocessed fluorescence intensity data was exported to Microsoft Excel 11.2 software for quality control evaluation. Data points were flagged if both dye channels failed any of the following requirements: at least 40% of feature pixels exhibiting fluorescent intensity greater than local mean background+2SD, feature intensity greater than local background intensity by at least 10 units, ratio of feature intensity to local background intensity greater than 2.5. The flagged raw feature and background intensity values for both dye channels were then imported into GeneSpring GX 7.3 software (Agilent Technologies) and normalized by subtracting the local background intensity from the feature intensity for each channel, setting all Cy5 measurements less than 1 to 1, and applying a per-gene and per-array, intensity-dependent (LOWESS) normalization utilizing 20% of data for smoothing and a Cy3 channel cutoff of 1. Values obtained from replicate oligos on the same array were averaged.


title: Thoracic Duct / Vena Cava normal 2


title: hEBD LVEC_continuous magnetic field exposure_one day recovery_rep2

status: Public on Jan 18 2010

city: baltimore

first: zhiyun

last: wang

state: MD

address: 3400 N Charles St

department: Biomedical Engineering

institute: Johns Hopkins Univesity

description: Embryoid body derived LVEC cells continuous exposure to magnetic field for 4 days followed by 1 day recovery

hyb_protocol: According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array)

data_processing: Affymetrix U133 Plus 2.0 GCRMA DATA

organism: Homo sapiens

source_name: Embryoid body derived LVEC cells continuous exposure to magnetic field with one day recovery

treatment_protocol:
1) Plate hEBD LVEC cells (p11) at 500k per 100mm collagen coated dish (day 0);
2) Culture for 24 hr in normal conditions (day 1);
3) Expose cells to the magnetic flux density of 0.249 T (day 2- day 5) follow by one day recovery in normal conditions (day 6);
4) Extract RNA on day 7;
5) Send for Microarray Analysis.

tag: hEBD LVEC

tag: Passage 11


title: hEBD LVEC_one day magnetic field exposure_rep2

description: Embryoid body derived LVEC cells with one day magnetic field exposure

scan_protocol: According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array)

source_name: Embryoid body derived LVEC cells exposed to magnetic field on day 6

treatment_protocol:
1) Plate hEBD LVEC cells (p11) at 500k per 100mm collagen coated dish (day 0);
2) Culture in normal conditions with no magnetic field exposure (day 1 – day 5);
3) Expose cells to the magnetic flux density of 0.249 T (day 6)
4) Extract RNA on day 7;
5) Send for Microarray Analysis.


title: C(AA)_HT_biological rep1

description: C(AA)_HT_biological rep1

source_name: Healthy renal tissue, vehicle control 1


title: hEBD LVEC_control_rep2

description: Embryoid body derived LVEC cells cultured in normal conditions with no magnetic field exposure

source_name: Embryoid body derived LVEC cells at constant temperature 37 degree Celsius with no exposure to magnetic field

label_protocol: According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array)

treatment_protocol:
1) Plate hEBD LVEC cells (p11) at 500k per 100mm collagen coated dish (day 0);
2) Culture in normal conditions with no magnetic field exposure (day 1 – day 6);
3) Extract RNA on day 7;
4) Send for Microarray Analysis.


title: hEBD LVEC_continuous magnetic field exposure_no recovery_rep2

description: Embryoid body derived LVEC cells continuous exposure to magnetic field for 5 days with no recovery

source_name: Embryoid body derived LVEC cells continuous exposure to magnetic field with no recovery

extract_protocol: According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array)

treatment_protocol:
1) Plate hEBD LVEC cells (p11) at 500k per 100mm collagen coated dish (day 0);
2) Culture for 24 hr in normal conditions (day 1);
3) Expose cells with magnetic flux density of 0.249 T (day 2- day 6);
4) Extract RNA on day 7;
5) Send for Microarray Analysis.


title: Caco2, untreated

status: Public on Jan 23 2010

city: MODENA

first: Alexis

last: Grande

address: via Campi n 287

department: Department of Biomedical Sciences

country: Italy

institute: University of Modena and Reggio Emilia

description: Synthesis of biotinylated cRNA targets, arrays hybridization (Human HG-U133 Plus 2 GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 3µg of total RNA.

hyb_protocol: The fragmented cRNA was then hybridized to an identical lot of Affymetrix Human HG-U133 Plus 2 GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard FS450_0001 protocol, using antibody-mediated signal amplification.

scan_protocol: GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.

data_processing: Scaling to TGT value=150. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples.

source_name: Caco2 cells, untreated

label_protocol: Total RNA (3 µg) of Caco2 cells untreated and treated for 96 hours with 20 mM 5-ASA were converted in biotinylated cRNA according to the one-cycle target labeling protocol advised by Affymetrix (Affymetrix, Santa Clara,CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.

growth_protocol: The Caco2 cell line was obtained from ATCC (Rockville, MD) and cultured in DMEM medium (Euroclone, Devon, UK), supplemented with 10% heat inactivated fetal bovine serum (Lonza, Walkersvillle, MD) and 1mM L-Glutamine (Euroclone).

extract_protocol: Total cellular RNA was extracted from 5-10x105 cells of each sample using RNeasy Mini Kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer.

treatment_protocol: Untreated cells.

tag: Colon cancer cell line


title: hEBD LVEC_continuous magnetic field exposure_one day recovery

label_protocol: According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array


title: hEBD LVEC_one day magnetic field exposure

extract_protocol: According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array


title: hEBD LVEC_continuous magnetic field exposure_no recovery

extract_protocol: According to the Affymetrix standard progocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array)


title: Caco2, 20 mM 5-ASA 96h

source_name: Caco2 cells, treated with mesalazine

treatment_protocol: 5-ASA (SofarFarm S.p.A., Milano, Italy) was dissolved in cell culture medium at concentrations 20 mM. Caco2 cell line was treated with 5-ASA 20mM for 96h.


title: hEBD LVEC_control


title: 02-TB-059-1B

status: Public on Jan 08 2010

city: Parkville

first: Oliver

last: Sieber

state: Victoria

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

department: Melbourne Tumour Biology Branch

country: Australia

institute: Ludwig Institute for Cancer Research

description: Location: Right; DukesStage: C; Age_Diag: 77; Gender: F; DFS_Time: 68.7; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

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

source_name: primary colorectal adenocarcinoma

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

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

tag: Location

value: Right; DukesStage:C; Age_Diag:77; Gender:F; DFS_Time:68.7; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: 04-TB-061-1A

description: Location: Left; DukesStage: C; Age_Diag: 59; Gender: M; DFS_Time: 18.7; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:59; Gender:M; DFS_Time:18.7; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: 03-TB-030-1B

description: Location: Right; DukesStage: C; Age_Diag: 77; Gender: M; DFS_Time: 59.5; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:C; Age_Diag:77; Gender:M; DFS_Time:59.5; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 04-TB-015-1B

description: Location: Rectum; DukesStage: D; Age_Diag: 59; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:D; Age_Diag:59; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: 00-TB-005-1B

description: Location: Rectum; DukesStage: C; Age_Diag: 77; Gender: F; DFS_Time: 16.9; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:C; Age_Diag:77; Gender:F; DFS_Time:16.9; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 02-TB-087-1G

description: Location: Rectum; DukesStage: D; Age_Diag: 62; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:D; Age_Diag:62; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: 01-TB-030-1B

description: Location: Left; DukesStage: C; Age_Diag: 49; Gender: F; DFS_Time: 9.5; DFS_Cens: 0; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:49; Gender:F; DFS_Time:9.5; DFS_Cens:0; AdjXRT:N; AdjCTX:Y


title: 02-TB-018-1D

description: Location: Rectum; DukesStage: D; Age_Diag: 84; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:D; Age_Diag:84; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: 03-TB-019-1B

description: Location: Rectum; DukesStage: D; Age_Diag: 65; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:D; Age_Diag:65; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: 00-TB-002-1A

description: Location: Right; DukesStage: C; Age_Diag: 75; Gender: M; DFS_Time: 84.7; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:75; Gender:M; DFS_Time:84.7; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: ATH6_ChIP_3 replicate 2

status: Public on Jan 12 2010

type: genomic

city: Daejeon

first: Giltsu

last: Choi

address: 335 Gwahangno

department: Biological Sciences

country: South Korea

institute: KAIST

description: Biological replicate 2 of 3. PIL5 ChIP-chip analysis

hyb_protocol: CY5- or CY3-labeled probes were hybridized with the Arabidopsis whole genome tiling array chip (NimbleGen, Inc)

scan_protocol: The arrays were scanned using NimbleScan and image files were processed using NimbleGen's data extraction software

data_processing: The log2-ratio is centered to zero by scaling with the bi-weight mean method. Performed by Nimblegen: http://www.nimblegen.com/products/lit/lit.html

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Input DNA

label_protocol: 500ng of amplified DNA was labeled by CY5 or CY3.

growth_protocol: PIL5OX3 seeds were incubated in the dark for 6 hours after far-red light irradiation.

extract_protocol: The Chromatin-DNA complex was extracted as previously described. (Oh et al. Plant Cell 19, 1192-1208)

treatment_protocol: Far-red light treatment (3.2 μmol m-2 s-1, 5 mins)

tag: PIL5OX3 seeds

source_name: precipitated DNA


title: ATH6_ChIP_3 replicate 3

description: Biological replicate 3 of 3. PIL5 ChIP-chip analysis


title: ATH6_ChIP_3 replicate 1

description: Biological replicate 1 of 3. PIL5 ChIP-chip analysis


title: 03-TB-108-1B

description: Location: Right; DukesStage: C; Age_Diag: 69; Gender: M; DFS_Time: 40.4; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:69; Gender:M; DFS_Time:40.4; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: 03-TB-031-1D

description: Location: Rectum; DukesStage: C; Age_Diag: 83; Gender: M; DFS_Time: 38.1; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:C; Age_Diag:83; Gender:M; DFS_Time:38.1; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: 04-TB-138A

description: Location: Rectum; DukesStage: C; Age_Diag: 66; Gender: M; DFS_Time: 10.2; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Rectum; DukesStage:C; Age_Diag:66; Gender:M; DFS_Time:10.2; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: 02-TB-060-1G

description: Location: Rectum; DukesStage: C; Age_Diag: 73; Gender: M; DFS_Time: 61.4; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:C; Age_Diag:73; Gender:M; DFS_Time:61.4; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 03-TB-022-1I

description: Location: Right; DukesStage: C; Age_Diag: 79; Gender: F; DFS_Time: 4.5; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:C; Age_Diag:79; Gender:F; DFS_Time:4.5; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: 01-TB-024-1B

description: Location: Left; DukesStage: C; Age_Diag: 59; Gender: M; DFS_Time: 69.1; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:59; Gender:M; DFS_Time:69.1; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: 03-TB-003-1G

description: Location: Rectum; DukesStage: C; Age_Diag: 77; Gender: F; DFS_Time: 18.8; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:C; Age_Diag:77; Gender:F; DFS_Time:18.8; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 04-TB-077-1C

description: Location: Right; DukesStage: C; Age_Diag: 69; Gender: M; DFS_Time: 49.6; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:69; Gender:M; DFS_Time:49.6; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: 05-WH-057-1A

description: Location: Right; DukesStage: C; Age_Diag: 51; Gender: M; DFS_Time: 31.6; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:51; Gender:M; DFS_Time:31.6; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: 02-TB-056-1F

description: Location: Rectum; DukesStage: C; Age_Diag: 56; Gender: F; DFS_Time: 59.2; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Rectum; DukesStage:C; Age_Diag:56; Gender:F; DFS_Time:59.2; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: 02-TB-084-1D

description: Location: Right; DukesStage: C; Age_Diag: 72; Gender: F; DFS_Time: 15; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:C; Age_Diag:72; Gender:F; DFS_Time:15; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 02-TB-085-1E

description: Location: Right; DukesStage: C; Age_Diag: 60; Gender: F; DFS_Time: 57.8; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:60; Gender:F; DFS_Time:57.8; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: 05-WH-018-1A

description: Location: Rectum; DukesStage: C; Age_Diag: 75; Gender: M; DFS_Time: 30.9; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Rectum; DukesStage:C; Age_Diag:75; Gender:M; DFS_Time:30.9; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: 02-TB-052-1D

description: Location: Right; DukesStage: C; Age_Diag: 62; Gender: M; DFS_Time: 10.3; DFS_Cens: 0; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:62; Gender:M; DFS_Time:10.3; DFS_Cens:0; AdjXRT:N; AdjCTX:Y


title: 03-TB-096-1B

description: Location: Right; DukesStage: C; Age_Diag: 73; Gender: M; DFS_Time: 5.7; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:C; Age_Diag:73; Gender:M; DFS_Time:5.7; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: CZQ_2C/S-H/Y_8HU_120min_R1

city: Singapore

first: Zhaoqing

last: Chu

address: 60, Biopolis Streat

country: Singapore

institute: Genome Institute of Singapore

description: Schizosaccharomyces pombe ployg mutant cells growing in YES medium at 30 degree centigrade vs Schizosaccharomyces pombe asynchronized mid log phase WT cells (OD600 was around 0.3).

hyb_protocol: Hybridization was performed using EasyHyb solution (Roche) in a MUAI mixer (BioMicro systems).  Hybridized slides were washed in a series of buffers containing various concentration of SSC (2x - 0.2x) with or without 1% SDS.

data_processing: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software. After background correction and removal of flagged values, features with low intensity (F/B<2 at either 635 or 532 channel) were removed. Medians of log base 2 expression ratios were given in the data table.

organism: Schizosaccharomyces pombe

source_name: Fission yeast cells, CZQ_2C/S-H/Y_8HU_120min_R1

label_protocol: For fluorescence labeling of cDNAs, ~30 micro gram total RNA was used to synthesize cDNA coupled with amino allyl-dUTP (aa-dUTP) by reverse transcriptase (Superscript-II, Invitrogen, Carlsbad, CA). cDNA was subsequently washed with Milli-Q water using microcon-YM30 (Millipore, Billerica,MA). ~1.5 micro gram cDNA was used to couple with Cy5-fluorescence dye for 1 h in dark and purified through a spin column (Qiagen, Hilden, Germany) followed by washing on a micorcon YM-30.

growth_protocol: Schizosaccharomyces pombe rep2 truncations and a site mutation cells indicated growing in YES medium to mid log phase treated with 8 mM HU for various time points with two repeat. Yeast cells were cultured at 30 degree centigrade.

extract_protocol: Total RNA of tissue samples were extracted using hot phenol methold described in materials and methods.

tag: CZQ_2C/S-H/Y, 8 mM HU treated, 120min

source_name: Fission yeast wildtype cells, reference

label_protocol: For fluorescence labeling of cDNAs, ~30 micro gram total RNA was used to synthesize cDNA coupled with amino allyl-dUTP (aa-dUTP) by reverse transcriptase (Superscript-II, Invitrogen, Carlsbad, CA) according to manufacturer's instruction. cDNA was subsequently washed with Milli-Q water using microcon-YM30 (Millipore, Billerica,MA). ~1.5 micro gram cDNA was used to couple with Cy3-fluorescence dye for 1 h in dark and purified through a spin column (Qiagen, Hilden, Germany) followed by washing on a micorcon YM-30.

growth_protocol: Reference RNA was obtained by pooling equal amount of total RNA extracted from Schizosaccharomyces pombe mid-log phase cells (OD600 was around 0.3) growing at 30 degree centigrade.


title: 01-TB-019-1A

description: Location: Left; DukesStage: C; Age_Diag: 84; Gender: F; DFS_Time: 24.2; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:C; Age_Diag:84; Gender:F; DFS_Time:24.2; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: CZQ_2C/S-H/Y_8HU_060min_R1

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.

source_name: Fission yeast cells, CZQ_2C/S-H/Y_8HU_060min_R1

tag: CZQ_2C/S-H/Y, 8 mM HU treated, 060min

tag: Reference RNA was obtained by pooling equal amount of total RNA extracted from Schizosaccharomyces pombe mid-log phase cells (OD600 was around 0.3) growing at 30 degree centigrade.


title: CZQ_2C/S-H/Y_8HU_030min_R2

source_name: Fission yeast cells, CZQ_2C/S-H/Y_8HU_030min_R2

tag: CZQ_2C/S-H/Y, 8 mM HU treated, 030min


title: CZQ_2C/S-H/Y_8HU_010min_R2

source_name: Fission yeast cells, CZQ_2C/S-H/Y_8HU_010min_R2

tag: CZQ_2C/S-H/Y, 8 mM HU treated, 010min


title: 02-TB-050-1G

description: Location: Left; DukesStage: C; Age_Diag: 74; Gender: M; DFS_Time: 68.1; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:74; Gender:M; DFS_Time:68.1; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: CZQ_2C/S-H/Y_8HU_010min_R1

source_name: Fission yeast cells, CZQ_2C/S-H/Y_8HU_010min_R1


title: 01-TB-008-1B

description: Location: Left; DukesStage: C; Age_Diag: 69; Gender: M; DFS_Time: 15.2; DFS_Cens: 0; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:69; Gender:M; DFS_Time:15.2; DFS_Cens:0; AdjXRT:N; AdjCTX:Y


title: 05-WH-027

description: Location: Left; DukesStage: C; Age_Diag: 64; Gender: F; DFS_Time: 24; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:64; Gender:F; DFS_Time:24; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: CZQ_2C/S-H/Y_8HU_060min_R2

source_name: Fission yeast cells, CZQ_2C/S-H/Y_8HU_060min_R2


title: CZQ_2C/S-H/Y_8HU_120min_R2

source_name: Fission yeast cells, CZQ_2C/S-H/Y_8HU_120min_R2


title: CZQ_C delta94_8HU_120min_R1

source_name: Fission yeast cells, CZQ_C delta94_8HU_120min_R1

tag: CZQ_C delta94, 8 mM HU treated, 120min


title: CZQ_2C/S-H/Y_8HU_030min_R1

source_name: Fission yeast cells, CZQ_2C/S-H/Y_8HU_030min_R1


title: CZQ_C delta94_8HU_120min_R2

source_name: Fission yeast cells, CZQ_C delta94_8HU_120min_R2


title: CZQ_C delta94_8HU_010min_R2

source_name: Fission yeast cells, CZQ_C delta94_8HU_010min_R2

tag: CZQ_C delta94, 8 mM HU treated, 010min


title: CZQ_2C/S-H/Y_8HU_000min_R2

source_name: Fission yeast cells, CZQ_2C/S-H/Y_8HU_000min_R2

tag: CZQ_2C/S-H/Y, 8 mM HU treated, 000min


title: CZQ_2C/S-H/Y_8HU_000min_R1

source_name: Fission yeast cells, CZQ_2C/S-H/Y_8HU_000min_R1


title: CZQ_C delta53_8HU_010min_R1

source_name: Fission yeast cells, CZQ_C delta53_8HU_010min_R1

tag: CZQ_C delta53, 8 mM HU treated, 010min


title: CZQ_C delta94_8HU_060min_R2

source_name: Fission yeast cells, CZQ_C delta94_8HU_060min_R2

tag: CZQ_C delta94, 8 mM HU treated, 060min


title: CZQ_C delta53_8HU_060min_R2

source_name: Fission yeast cells, CZQ_C delta53_8HU_060min_R2

tag: CZQ_C delta53, 8 mM HU treated, 060min


title: CZQ_C delta53_8HU_030min_R1

source_name: Fission yeast cells, CZQ_C delta53_8HU_030min_R1

tag: CZQ_C delta53, 8 mM HU treated, 030min


title: CZQ_C delta94_8HU_030min_R1

source_name: Fission yeast cells, CZQ_C delta94_8HU_030min_R1

tag: CZQ_C delta94, 8 mM HU treated, 030min

source_name: Fission yeast wildtype cells, reference


title: CZQ_C delta94_8HU_060min_R1

source_name: Fission yeast cells, CZQ_C delta94_8HU_060min_R1


title: CZQ_C delta53_8HU_000min_R1

source_name: Fission yeast cells, CZQ_C delta53_8HU_000min_R1

tag: CZQ_C delta53, 8 mM HU treated, 000min


title: CZQ_C delta94_8HU_030min_R2

source_name: Fission yeast cells, CZQ_C delta94_8HU_030min_R2


title: CZQ_C delta53_8HU_000min_R2

source_name: Fission yeast cells, CZQ_C delta53_8HU_000min_R2


title: CZQ_C delta94_8HU_010min_R1

source_name: Fission yeast cells, CZQ_C delta94_8HU_010min_R1


title: CZQ_C delta94_8HU_000min_R1

source_name: Fission yeast cells, CZQ_C delta94_8HU_000min_R1

tag: CZQ_C delta94, 8 mM HU treated, 000min


title: CZQ_C delta21_8HU_060min_R2

source_name: Fission yeast cells, CZQ_C delta21_8HU_060min_R2

tag: CZQ_C delta21, 8 mM HU treated, 060min


title: CZQ_C delta53_8HU_120min_R1

source_name: Fission yeast cells, CZQ_C delta53_8HU_120min_R1

tag: CZQ_C delta53, 8 mM HU treated, 120min


title: CZQ_C delta53_8HU_120min_R2

source_name: Fission yeast cells, CZQ_C delta53_8HU_120min_R2


title: CZQ_C delta21_8HU_060min_R1

source_name: Fission yeast cells, CZQ_C delta21_8HU_060min_R1


title: CZQ_C delta94_8HU_000min_R2

source_name: Fission yeast cells, CZQ_C delta94_8HU_000min_R2


title: CZQ_C delta21_8HU_010min_R2

source_name: Fission yeast cells, CZQ_C delta21_8HU_010min_R2

tag: CZQ_C delta21, 8 mM HU treated, 010min


title: SGBS_adipocytes_RPMI media_4h_rep6

status: Public on Jan 07 2010

city: Sharnbrook

first: Fei Ling

last: Lim

state: Bedfordshire

address: Colworth Science Park

country: United Kingdom

institute: Unilever

hyb_protocol: The Agilent Hybridisation Kit (catalogue number 5188-5242) was used in conjunction with Agilent Mouse Oligo Arrays (catalogue number G4122F).  2μg of the labelled sample RNA were used for hybridisation according to the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol The hybridisation was performed for 17 h at 65 ºC at 10 rpm. Slides were them washed for 1 min at 22 ºC in Wash Solution 1 (catalogue number 5188-5325) and 1 min at 22 ºC in Wash Solution 2, pre-warmed to 37 ºC (catalogue number 5188-5326). Slides were incubated for 30s in Agilent Stabilisation and Drying Solution (catalogue number 5185-5979).

scan_protocol: Microarrays were scanned using the Agilent Technologies Scanner G2505B US45102871 (ChipScan software version A.7.0.1), scan region 61 X 21.6mm, scan resolution 5 micron single pass, extended dynamic range selected (XDR Hi 100%; XDR Lo 10%).

data_processing: Data was extracted from the scanned image using the Agilent Feature Extraction Software version. 9.1.3.1 (protocol GE1-v5_91_0806). The VALUE column came from the gProcessedSignal column of the result table.

source_name: Human SGBS adipocytes differentiated in culture, unconditioned RPMI media 4h

label_protocol: 200 ng RNA and 2.0µl (1:5000 dilution) Agilent One-Color RNA Spike-In RNA were labelled with the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color according to Manufacture’s instructions as follows:  1.2 µl T7 Promoter Primer was added to 600 ng RNA and 3 µl spike in control and denatured at 65 ºC. First Strand Buffer, DTT, dNTP MMLV and RNaseOut was added. The cDNA was synthesised during the following incubation step (2h at 40 ºC). After 10 min denaturation at 65 ºC and the addition of Cy-labelled CTP, Transcription Buffer, DTT, NTP, PEG, RNaseOUT, Inorganic Phosphatase, and T7 RNA Polymerase the synthesis of the fluorescent labelled cRNA was performed during the second incubation step (2 h at 40 ºC).  The labelled cRNA was purified with the Qiagen RNeasy Mini Kit according to Manufacturer’s protocol.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit (Qiagen).  The integrity of the RNA was confirmed with analysis by the Agilent 2100 bioanalyser using the RNA 6000 LabChip kit.

treatment_protocol: SGBS cells were grown to confluence, plated in 12 well plates at 20,000 cells per well (per ml).  The cells were treated with differentiation media for four days, after which feeding media was used.  After 10 days, differentiated adipocytes were then treated for 4h or 24h with 150µl conditioned media from U937 macrophage cells.  Control SGBS cells were treated with unconditioned media (control) or RPMI media alone to control for differences in media used to culture U937 cells.  U937 cells were grown to confluence then plated in 12 well plates at 2 x105 cells per well.  Once 25-30% confluent, PMA was  added to the media (30nM) to differentiate the cells.  Cells differentiated for seven days prior to collection of conditioned media for treatment of SGBS cells.

tag: SGBS cells were obtained from the Laboratory of Dr Wabitsch, University of Ulm.  U937 were purchased from the ATCC.


title: CZQ_C delta53_8HU_010min_R2

source_name: Fission yeast cells, CZQ_C delta53_8HU_010min_R2

tag: Reference RNA was obtained by pooling equal amount of total RNA extracted from Schizosaccharomyces pombe mid-log phase cells (OD600 was around 0.3) growing at 30 degree centigrade.


title: CZQ_C delta21_8HU_010min_R1

source_name: Fission yeast cells, CZQ_C delta21_8HU_010min_R1


title: CZQ_C delta53_8HU_030min_R2

source_name: Fission yeast cells, CZQ_C delta53_8HU_030min_R2


title: SGBS_adipocytes_U937 media_4h_rep6

source_name: Human SGBS adipocytes differentiated in culture, U937 macrophage conditioned RPMI media 4h


title: SGBS_adipocytes_RPMI media_24h_rep6

source_name: Human SGBS adipocytes differentiated in culture, unconditioned RPMI media 24h


title: CZQ_C delta21_8HU_120min_R2

source_name: Fission yeast cells, CZQ_C delta21_8HU_120min_R2

tag: CZQ_C delta21, 8 mM HU treated, 120min

source_name: Fission yeast wildtype cells, reference


title: SGBS_adipocytes_U937 media_24h_rep6

source_name: Human SGBS adipocytes differentiated in culture, U937 macrophage conditioned RPMI media 24h


title: CZQ_C delta21_8HU_120min_R1

source_name: Fission yeast cells, CZQ_C delta21_8HU_120min_R1


title: SGBS_adipocytes_control media_4h_rep5

source_name: Human SGBS adipocytes differentiated in culture


title: SGBS_adipocytes_U937 media_4h_rep5


title: CZQ_C delta21_8HU_000min_R2

source_name: Fission yeast cells, CZQ_C delta21_8HU_000min_R2

tag: CZQ_C delta21, 8 mM HU treated, 000min


title: SGBS_adipocytes_RPMI media_24h_rep5


title: CZQ_C delta21_8HU_030min_R1

source_name: Fission yeast cells, CZQ_C delta21_8HU_030min_R1

tag: CZQ_C delta21, 8 mM HU treated, 030min


title: CZQ_C delta21_8HU_000min_R1

source_name: Fission yeast cells, CZQ_C delta21_8HU_000min_R1


title: SGBS_adipocytes_control media_4h_rep6


title: CZQ_C delta21_8HU_030min_R2

source_name: Fission yeast cells, CZQ_C delta21_8HU_030min_R2


title: CZQ_C delta53_8HU_060min_R1

source_name: Fission yeast cells, CZQ_C delta53_8HU_060min_R1


title: SGBS_adipocytes_control media_24h_rep6


title: SGBS_adipocytes_U937 media_4h_rep4


title: SGBS_adipocytes_control media_24h_rep5


title: SGBS_adipocytes_U937 media_24h_rep5


title: SGBS_adipocytes_RPMI media_4h_rep5

tag: SGBS cells were obtained from the Laboratory of Dr Wabitsch, University of Ulm.  U937 were purchased from the ATCC


title: SGBS_adipocytes_control media_4h_rep4


title: SGBS_adipocytes_U937 media_24h_rep4


title: SGBS_adipocytes_RPMI media_4h_rep4


title: SGBS_adipocytes_RPMI media_4h_rep2


title: SGBS_adipocytes_U937 media_4h_rep3


title: SGBS_adipocytes_control media_4h_rep2


title: SGBS_adipocytes_U937 media_24h_rep3


title: SGBS_adipocytes_RPMI media_24h_rep2


title: SGBS_adipocytes_RPMI media_4h_rep1


title: SGBS_adipocytes_control media_24h_rep3


title: SGBS_adipocytes_U937 media_4h_rep1


title: SGBS_adipocytes_control media_24h_rep4


title: SGBS_adipocytes_RPMI media_24h_rep1


title: SGBS_adipocytes_RPMI media_4h_rep3


title: SGBS_adipocytes_RPMI media_24h_rep4

source_name: SGBS_adipocytes_RPMI media_24h_rep4


title: 213-CRT

status: Public on Jan 05 2010

city: Baltimore

first: Andreas

middle: Sebastian

last: Barth

address: 720 Rutland Ave.

department: Medicine, Division of Cardiology

institute: Johns Hopkins University

description: Gene expression of 213-CRT

hyb_protocol: Using Agilent hybridization chambers and oven following manufacturer's protocol (65oC for 17h).

scan_protocol: Microarrays were scanned using an Agilent G2565AA Scanner controlled by Agilent Scan Control 7.0 software. Data were extracted with Agilent Feature Extraction 8.5.1.1 software.

data_processing:
gMedianSignal and rMedianSignal were loess-normalized using limmaGUI (R/Bioconductor) without background correction. Differentially expressed transcripts were identified with Significance Analysis of Microarrays (SAM).

The VALUEs in the data tables represent loess-normalized log2 (lateral/anterior) ratios.

organism: Canis lupus familiaris

source_name: Myocardium, subendocardial sample, left ventricle, lateral wall

label_protocol: 0.4 ug total RNA was reverse-transcribed into cDNA by MMLV-RT using an oligo dT primer (System Biosciences) that incorporates a T7 promoter sequence. The cDNA was then used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine-3 labeled CTP (Perkin Elmer). The labeled cRNA was purified using RNeasy mini kit (Qiagen). RNA spike-in controls (Agilent Technologies) were added to RNA samples before amplification and labeling according to manufacturer’s protocol.

growth_protocol: After sacrificing the animal, myocardial tissue was transported to the lab in ice-cold saline, snap-frozen in liquid nitrogen and stored at -80 degrees Celsius. RNA was isolated from frozen tissue.

extract_protocol: Total RNA was isolated with TRIzol reagent from the subendocardium of the anterior and lateral LV walls in the distribution of the LAD and left circumflex artery, respectively. RNA was quantified with NanoDrop ND-1000 followed by quality assessment with 2100 Bioanalyzer (Agilent Technologies) according to manufacturer’s protocol.

treatment_protocol: Cardiac Resynchronization Therapy (CRT): One week after ablation of the left bundle branch, animals were paced at 200 beats per minute for 3 weeks from the right atrium (via epicardial pacing leads). Then, bi-ventricular rapid pacing at the same rate was instituted for the following 3 weeks (200 beats per minute via epicardial pacing leads from the right ventricular free wall and the lateral left ventricular wall).

tag: Adult male dogs

source_name: Myocardium, subendocardial sample, left ventricle, anterior wall

label_protocol: 0.4 ug total RNA was reverse-transcribed into cDNA by MMLV-RT using an oligo dT primer (System Biosciences) that incorporates a T7 promoter sequence. The cDNA was then used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine-5 labeled CTP (Perkin Elmer). The labeled cRNA was purified using RNeasy mini kit (Qiagen). RNA spike-in controls (Agilent Technologies) were added to RNA samples before amplification and labeling according to manufacturer’s protocol.


title: SGBS_adipocytes_control media_24h_rep1


title: 104-CRT

description: Gene expression of 104-CRT


title: SGBS_adipocytes_control media_4h_rep1


title: SGBS_adipocytes_U937 media_24h_rep1


title: SGBS_adipocytes_control media_4h_rep3


title: 289-NF

description: Gene expression of 289-NF

treatment_protocol: non-failing control


title: SGBS_adipocytes_control media_24h_rep2


title: SGBS_adipocytes_U937 media_24h_rep2


title: SGBS_adipocytes_U937 media_4h_rep2


title: 105-CRT

description: Gene expression of 105-CRT


title: 283-NF

description: Gene expression of 283-NF


title: 338-CRT

description: Gene expression of 338-CRT


title: 103-CRT

description: Gene expression of 103-CRT


title: 425-DHF

description: Gene expression of 425-DHF

treatment_protocol: Dyssynchronous heart failure (DHF): One week after ablation of the left bundle branch, animals were paced at 200 beats per minute for 6 weeks from the right atrium (via epicardial pacing leads).


title: 424-DHF

description: Gene expression of 424-DHF


title: CRT_lateral_332

description: Gene expression of CRT_lateral_332

hyb_protocol: 0.825 ug of each Cy3-labeled sample was used for hybridization on Agilent 44K whole canine genome microarray at 65ºC for 17 hours in a hybridization oven with rotation. After hybridization, microarrays are washed and dried according to Agilent microarray processing protocol using stabilization and drying solution.

scan_protocol: Microarrays were scanned using an Agilent G2565AA Scanner controlled by Agilent Scan Control 7.0 software. Data were extracted with Agilent Feature Extraction 9.5.3.1 software.

data_processing: gMedianSignal (raw values) after quantile normalization, without pos. and neg. control probes. Differentially expressed transcripts were identified with Significance Analysis of Microarrays (SAM).


title: CRT_anterior_294

description: Gene expression of CRT_anterior_294


title: 53-DHF

description: Gene expression of 53-DHF


title: CRT_lateral_294

description: Gene expression of CRT_lateral_294


title: CRT_anterior_332

description: Gene expression of CRT_anterior_332


title: 101-DHF

description: Gene expression of 101-DHF


title: CRT_anterior_338

description: Gene expression of CRT_anterior_338


title: 2-DHF

description: Gene expression of 2-DHF


title: CRT_anterior_29

description: Gene expression of CRT_anterior_29


title: CRT_anterior_213

description: Gene expression of CRT_anterior_213


title: CRT_lateral_104

description: Gene expression of CRT_lateral_104


title: 281-NF

description: Gene expression of 281-NF


title: CRT_anterior_92

description: Gene expression of CRT_anterior_92


title: CRT_lateral_213

description: Gene expression of CRT_lateral_213


title: DHF_anterior_152

description: Gene expression of DHF_anterior_152


title: DHF_anterior_16

description: Gene expression of DHF_anterior_16


title: 273-NF

description: Gene expression of 273-NF


title: 267-NF

description: Gene expression of 267-NF


title: DHF_lateral_16

description: Gene expression of DHF_lateral_16


title: CRT_anterior_104

description: Gene expression of CRT_anterior_104


title: 06-29-NF

description: Gene expression of 06-29-NF


title: CRT_lateral_338

description: Gene expression of CRT_lateral_338


title: CRT_anterior_124

description: Gene expression of CRT_anterior_124


title: CRT_lateral_124

description: Gene expression of CRT_lateral_124


title: DHF_anterior_101

description: Gene expression of DHF_anterior_101


title: DHF_lateral_101

description: Gene expression of DHF_lateral_101


title: DHF_anterior_424

description: Gene expression of DHF_anterior_424


title: DHF_anterior_169

description: Gene expression of DHF_anterior_169


title: CRT_lateral_29

description: Gene expression of CRT_lateral_29


title: CRT_lateral_105

description: Gene expression of CRT_lateral_105


title: DHF_anterior_151

description: Gene expression of DHF_anterior_151


title: CRT_lateral_92

description: Gene expression of CRT_lateral_92


title: CRT_anterior_105

description: Gene expression of CRT_anterior_105


title: DHF_lateral_152

description: Gene expression of DHF_lateral_152


title: DHF_lateral_424

description: Gene expression of DHF_lateral_424


title: DHF_lateral_169

description: Gene expression of DHF_lateral_169


title: DHF_anterior_76

description: Gene expression of DHF_anterior_76


title: DHF_anterior_53

description: Gene expression of DHF_anterior_53


title: DHF_lateral_151

description: Gene expression of DHF_lateral_151


title: DHF_lateral_76

description: Gene expression of DHF_lateral_76


title: non-failing_anterior_07-017

description: Gene expression of non-failing_anterior_07-017

treatment_protocol: Non-failing control


title: DHF_lateral_136

description: Gene expression of DHF_lateral_136


title: non-failing_anterior_12

description: Gene expression of non-failing_anterior_12


title: non-failing_anterior_281

description: Gene expression of non-failing_anterior_281


title: DHF_anterior_32

description: Gene expression of DHF_anterior_32


title: DHF_lateral_53

description: Gene expression of DHF_lateral_53


title: non-failing_lateral_269

description: Gene expression of non-failing_lateral_269


title: non-failing_lateral_12

description: Gene expression of non-failing_lateral_12


title: non-failing_lateral_281

description: Gene expression of non-failing_lateral_281


title: non-failing_anterior_289

description: Gene expression of non-failing_anterior_289


title: non-failing_lateral_07-017

description: Gene expression of non-failing_lateral_07-017


title: non-failing_anterior_105

description: Gene expression of non-failing_anterior_105


title: non-failing_anterior_07-034

description: Gene expression of non-failing_anterior_07-034


title: non-failing_lateral_105

description: Gene expression of non-failing_lateral_105


title: non-failing_anterior_269

description: Gene expression of non-failing_anterior_269


title: non-failing_lateral_07-034

description: Gene expression of non-failing_lateral_07-034


title: SGBS_adipocytes_RPMI media_24h_rep3


title: non-failing_lateral_289

description: Gene expression of non-failing_lateral_289


title: non-failing_anterior_283

description: Gene expression of non-failing_anterior_283


title: DHF_anterior_136

description: Gene expression of DHF_anterior_136


title: High Salt-acclimated Cell Replicate 2

status: Public on Jan 01 2010

city: Seoul

first: MinJung

last: Kim

address: 17 Haengdang-dong, Seongdong-gu

department: Life Science

institute: Hanyang University

description: Biological replicate 2 of 2. Two-condition experiment, normal condition (1.5M NaCl) cells vs. high salt-acclimated (4.5M NaCl) cells.             One replicate per array.

hyb_protocol: A slide was pre-incubated with a pre-hybridization solution (25% Formamide, 5x SSC, 0.1% SDS, 10mg/ml BSA), which was pre-warmed to 58℃ in a slide box for one hour at 42℃. The slide was then washed by being dipped five times into distilled water and was dried by centrifugation at 650 rpm for five minutes. The Cy3- and Cy5-labeled cDNA target samples were dissolved in a reasonable volume of hybridization buffer by heating for five minutes at 95℃. The Cy3- and Cy5-labeled cDNA target samples were mixed together and hybridized to microarrays for more than 16 hours at 65℃ in humidified incubation chambers. The array’s cover slip was removed by immersing the slide in 2X SSC/0.1% SDS for 10 minutes at 58℃. The slide was then washed two times for five minutes each in 0.1X SSC/0.1% SDS and rinsed for one minute in 0.1X SSC at 25℃.

scan_protocol: Scanned on an Scan Array Lite (Packard Bioscience, Boston, MA, USA) scanner.  Images were quantified using GenePix Pro 3.0 software (Axon Instrument, Union City, CA, USA).

data_processing: 1. log2(Cy5/Cy3) 2. Normalization using LOWESS(f=0.2)

organism: Dunaliella salina

source_name: cDNA from high salt(4.5M NaCl)-acclimated cells labeled with Cyanine-5 (red).

label_protocol: Fluorescent-labeled cDNA was produced with 50μg of total RNA (or 2μg of poly(A)+ RNA), 1μg oligo (dT) primer (Ambion, U.S.A.), 10μl of 5X First Strand Buffer, and 400 units of Superscript III reverse transcriptase (Invitrogen, U.S.A.) in the presence of aminoallyl-dUTP (Sigma, U.S.A.). According to the method suggested by the manufacturer, the coupling of Cy5 dye (Amersham Pharmacia Biotech, U.S.A.) were performed with a reaction volume of 20 μl. After the cDNA probes were incubated with the appropriate NHS-ester Cy dye (prepared in DMSO) for 1 hour in the dark, at room temperature, unincorporated fluorescent nucleotides were cleaned up using a QIAquick PCR purification kit (Qiagen, U.S.A.) followed by a Micron YM-30 column (Millipore, Bedford, MA., U.S.A.).

growth_protocol: Cells were harvested by centrifugation from 1.5M NaCl medium and re-suspended in a medium with 3M NaCl medium for 1week. Following cells were harvested by centrifugation and re-suspended in medium containing 4.5M NaCl (hypersaline medium).

extract_protocol: Total RNA was extracted using the TRI regent (Moleacular Research Center, Inc., USA).

tag: Acclimated cells in 4.5M NaCl medium for a week

source_name: cDNA from normal condition(1.5M NaCl) cells labeled with Cyanine-3 (green).

label_protocol: Fluorescent-labeled cDNA was produced with 50μg of total RNA (or 2μg of poly(A)+ RNA), 1μg oligo (dT) primer (Ambion, U.S.A.), 10μl of 5X First Strand Buffer, and 400 units of Superscript III reverse transcriptase (Invitrogen, U.S.A.) in the presence of aminoallyl-dUTP (Sigma, U.S.A.). According to the method suggested by the manufacturer, the coupling of Cy3 dye (Amersham Pharmacia Biotech, U.S.A.) were performed with a reaction volume of 20 μl. After the cDNA probes were incubated with the appropriate NHS-ester Cy dye (prepared in DMSO) for 1 hour in the dark, at room temperature, unincorporated fluorescent nucleotides were cleaned up using a QIAquick PCR purification kit (Qiagen, U.S.A.) followed by a Micron YM-30 column (Millipore, Bedford, MA., U.S.A.).

tag: Dunaliella sp. was grown in modified, artificial seawater medium (Pick et al. 1986) at a normal condition(1.5M D medium). Carbon was supplied as NaHCO3 at an initial concentration of 20mM. First, cells were grown photoautotrophically to the mid-exponential phase (about 2-2.5 x 106 cells/ml) in 100ml of D media at 24 Degree Celsius with agitation under continuous low cool, white fluorescent light (45 μmol of photons m-2s-1).


title: DHF_lateral_32

description: Gene expression of DHF_lateral_32


title: non-failing_lateral_125

description: Gene expression of non-failing_lateral_125


title: non-failing_anterior_125

description: Gene expression of non-failing_anterior_125


title: Low Salt-acclimated Cell Replicate 2

description: Two-condition experiment, normal condition (1.5M NaCl) cells vs. low salt-acclimated (0.08M NaCl) cells.One replicate per array.

scan_protocol: Scanned on an Scan Array Lite (Packard Bioscience, Boston, MA, USA) scanner. Images were quantified using GenePix Pro 3.0 software (Axon Instrument, Union City, CA, USA).

data_processing:
1. log2(Cy5/Cy3)
2. Normalization using LOWESS(f=0.2)

source_name: cDNA from low salt(0.08M NaCl)-acclimated cells labeled with Cyanine-5 (red).

growth_protocol: Cells were harvested by centrifugation from 1.5M NaCl medium and re-suspended in a medium with 0.5M NaCl medium for 1week. Following cells were harvested by centrifugation and re-suspended in medium containing 0.08M NaCl (hyposaline medium).

tag: Acclimated cells in 0.08M NaCl medium for a week


title: non-failing_anterior_07-097

description: Gene expression of non-failing_anterior_07-097


title: Low Salt-acclimated Cell Replicate 1

source_name: Normal condition(1.5M NaCl) cells labeled with Cyanine-3 (green).


title: non-failing_lateral_07-097

description: Gene expression of non-failing_lateral_07-097


title: non-failing_lateral_283

description: Gene expression of non-failing_lateral_283


title: High Salt-acclimated Cell Replicate 1

description:
Biological replicate 1 of 2. Two-condition experiment, normal condition (1.5M NaCl) cells vs. high salt-acclimated (4.5M NaCl) cells.
One replicate per array.


title: 13832962 - gdh3_b-leaf vs WT_c-leaf

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

description: Identification of the function and regulation of the GDH enzyme in plants

hyb_protocol: WT_c-leaf Cy5 / gdh3_b-leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,500V,laser power 35%, Cy5:635nm,pmt voltage 500V,laser power 30%

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

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. 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: leaf - Media Hydropony NO3 6mM hygrometry 75% Temperature 21°C Light 120mE

treatment_protocol: no treatment

tag: Arabidopsis thaliana (col-0)  - dev.stage (Boyes et al. Plant Cell 2001):boyes

tag: Arabidopsis thaliana (col-0)  mutant (gdh3-) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: 13697198 - WT_b-leaf vs gdh3_a-leaf

hyb_protocol: gdh3_a-leaf Cy5 / WT_b-leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (col-0)  - age:2monthdev.stage (Boyes et al. Plant Cell 2001):boyes


title: 13832642 - WT_c-leaf vs gdh3_b-leaf

hyb_protocol: gdh3_b-leaf Cy5 / WT_c-leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13832964 - WT_c-stem vs gdh3_b-stem

hyb_protocol: gdh3_b-stem Cy5 / WT_c-stem Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: stem - Media Hydropony NO3 6mM hygrometry 75% Temperature 21°C Light 120mE


title: 13697199 - gdh3_a-leaf vs WT_b-leaf

hyb_protocol: WT_b-leaf Cy5 / gdh3_a-leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13697196 - WT_b-stem vs gdh3_a-stem

hyb_protocol: gdh3_a-stem Cy5 / WT_b-stem Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13697197 - gdh3_a-stem vs WT_b-stem

hyb_protocol: WT_b-stem Cy5 / gdh3_a-stem Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13833026 - gdh3_b-root vs WT_c-root

hyb_protocol: WT_c-root Cy5 / gdh3_b-root Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: root - Media Hydropony NO3 6mM hygrometry 75% Temperature 21°C Light 120mE


title: 13833024 - gdh3_b-stem vs WT_c-stem

hyb_protocol: WT_c-stem Cy5 / gdh3_b-stem Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13833025 - WT_c-root vs gdh3_b-root

hyb_protocol: gdh3_b-root Cy5 / WT_c-root Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: non-failing_anterior_273

description: Gene expression of non-failing_anterior_273


title: 13697194 - WT_b-root vs gdh3_a-root

hyb_protocol: gdh3_a-root Cy5 / WT_b-root Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13697192 - WT_b-leaf vs gdh123_b-leaf

hyb_protocol: gdh123_b-leaf Cy5 / WT_b-leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (col-0)  mutant (gdh1-2-3-) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: 13697193 - gdh123_b-leaf vs WT_b-leaf

hyb_protocol: WT_b-leaf Cy5 / gdh123_b-leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: non-failing_lateral_273

description: Gene expression of non-failing_lateral_273


title: 13697191 - gdh123_b-stem vs WT_b-stem

hyb_protocol: WT_b-stem Cy5 / gdh123_b-stem Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13697190 - WT_b-stem vs gdh123_b-stem

hyb_protocol: gdh123_b-stem Cy5 / WT_b-stem Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690759 - gdh123_a-leaf vs WT_a-leaf

hyb_protocol: WT_a-leaf Cy5 / gdh123_a-leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (col-0)  mutant (gdh1-2-3-) - age:2monthdev.stage (Boyes et al. Plant Cell 2001):boyes


title: 13697195 - gdh3_a-root vs WT_b-root

hyb_protocol: WT_b-root Cy5 / gdh3_a-root Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13697186 - WT_b-root vs gdh123_b-root

hyb_protocol: gdh123_b-root Cy5 / WT_b-root Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688119 - WT_a-stem vs gdh123_a-stem

hyb_protocol: gdh123_a-stem Cy5 / WT_a-stem Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690760 - WT_a-leaf vs gdh123_a-leaf

hyb_protocol: gdh123_a-leaf Cy5 / WT_a-leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688118 - WT_a-root vs gdh123_a-root

hyb_protocol: gdh123_a-root Cy5 / WT_a-root Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688121 - gdh123_a-stem vs WT_a-stem

hyb_protocol: WT_a-stem Cy5 / gdh123_a-stem Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688115 - gdh123_a-root vs WT_a-root

hyb_protocol: WT_a-root Cy5 / gdh123_a-root Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: pIC 10h

city: Madrid

first: Maria

middle: S

last: Soengas

address: Melchor Fernandez Almagro, 3

department: Molecular Pathology

country: Spain

institute: Spanish National Cancer Research Institute

description: SK-Mel-103 treated 10 hours with 1ug/ml of polyinosine-polycytidylic acid

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

scan_protocol: Images were quantified using Agilent Feature Extraction Software

data_processing: Background substraction were carried out using normexp. Lowess method for within array normalization and quantiles method  for between array normalization were performed. Differentially expressed genes were obtained by using R limma package (Smyth et al., 2005) from Bioconductor project (http://www.bioconductor.org).    Smyth GK, Michaud J and Scott HS. (2005). Use of within-array replicate spots for assessing differential expression in microarray experiments.   Bioinformatics 21: 2067-2075.

source_name: SK-Mel-103 Control 10h

label_protocol: Cy3 NT Cy5 treated (pIC/PEI-pIC)

growth_protocol: Dulbecco’s modified Eagle’s medium (Life Technologies, Rockville, MD, USA) supplemented with 10% fetal bovine serum (Nova-Tech Inc., Grand Island, NY, USA) penicillin (100 U/ml), streptomycin (100 U/ml)

extract_protocol: Total RNA extracted using Qiagen Rneasy mini kit following manufacturer's instructions

treatment_protocol: 1ug/ml of pIC or 1ug/ml pIC coupled with PEI

tag: SK-Mel-103 Time

source_name: pIC treated SK-Mel-103 10h

tag: SK-Mel-103 treated with 1ug/ml of polyinosine-polycytidylic acid Age

value: 10 hours


title: pIC+PEI 10h

description: SK-Mel-103 treated 10 hours with 1ug/ml of polyinosine-polycytidylic acid with polyethyleneimine

source_name: pIC+PEI treated SK-Mel-103 10h

tag: SK-Mel-103 treated with 1ug/ml of polyinosine-polycytidylic acid with polyethyleneimine Age