title: FFPE19 - mAdbID:81359

description: mAdb experiment ID: 81359

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.26;; 3.26 Temperature: 31.94


title: FFPE20 - mAdbID:81503

status: Public on Mar 11 2010

type: RNA

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 81503

hyb_protocol: microRNA Hybridization Protocol Other: Resuspend Cy3 and Cy5 labeled miR in 10ul and combine them together (20ul total) and add the following reagents: 1ul 50x Denhardt’s blocking solution ,1ul poly dA (8ug/), 1ul yeast tRNA (4mg/ml), 10ul Human Cot I DNA (10mg/ml), 3ul 20X SSC and 1ul 10% SDS. Heat sample at 70C for 3min and immediately hybridize after spin at 10,000g for 30 sec. Start hybridization at RT over night in the dark.

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.28;; 3.23 Temperature: 32.09

data_processing:
BRB-ArrayTools Data Processing Protocol
Calculation Method: Included duplicate spots per each miR, whose intensity was averaged. A spot with signal intensity <100 in both channels was filtered out. If the signal intensity was <100 in one channel only, it was set to 100 in computing the log-ratio value. A spot size smaller than 25 pixels was also filtered out. The normalization method used is ratio median over entire array method.

molecule: total RNA

organism:
Homo sapiens
human gammaherpesvirus 4

source_name: EBV Control Sample

label_protocol:
Cy3 Labeling Protocol
Other: Small RNA, equivalent to 10 ug of the total RNA from FFPE and EBV reference samples, was labeled with Cy3 using mirVana™ miRNA Labeling Kit (Ambion, Austin, TX USA).

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was isolated from 20um sections from FFPE tissue blocks using RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE Tissues (Ambion, Austin, TX USA). Small RNA was enriched and purified by flashPAGE Fractionator (Ambion, Austin, TX USA) according to the manufacturer’s instruction.

tag: strain

tag: cell line

value: Epstein-Barr virus (EBV)-transformed lymphoblastoid cell line

tag: cell type

value: lymphoblastoid

organism: Homo sapiens

label_protocol:
Cy5 Labeling Protocol
Other: Small RNA, equivalent to 10 ug of the total RNA from FFPE and EBV reference samples, was labeled with Cy5 using mirVana™ miRNA Labeling Kit (Ambion, Austin, TX USA).

tag: gender

value: female

tag: age

tag: tissue

value: Lung

tag: disease state

value: None Small Cell Carcinoma

tag: clinical info

value: Final pathology diagnosis:Squamous Cell Carcinoma


title: FFPE38 - mAdbID:81517

description: mAdb experiment ID: 81517

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.27;; 3.25 Temperature: 32.13

value: male

value: Histology of male smoker:male adenocarcinoma smoker


title: FFPE6 - mAdbID:80953

description: mAdb experiment ID: 80953

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.24;; 3.99 Temperature: 28.77


title: FFPE22 - mAdbID:81360

description: mAdb experiment ID: 81360

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 5.14 Temperature: 28.46


title: FFPE17 - mAdbID:80950

description: mAdb experiment ID: 80950

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 3.97 Temperature: 29.53


title: FFPE14 - mAdbID:80944

description: mAdb experiment ID: 80944

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.27;; 4.19 Temperature: 30.75


title: FFPE15 - mAdbID:80945

description: mAdb experiment ID: 80945

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.24;; 4.09 Temperature: 28.68


title: FFPE18 - mAdbID:80951

description: mAdb experiment ID: 80951

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.26;; 3.98 Temperature: 30.17


title: FFPE13 - mAdbID:80943

description: mAdb experiment ID: 80943

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 33 LaserPower: 3.27;; 3.25 Temperature: 30.57


title: FFPE16 - mAdbID:80948

description: mAdb experiment ID: 80948

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 3.99 Temperature: 29.32


title: FFPE187 - mAdbID:81489

description: mAdb experiment ID: 81489

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.27;; 4.06 Temperature: 31.27


title: FFPE11 - mAdbID:80941

description: mAdb experiment ID: 80941

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.27;; 4.19 Temperature: 30.32


title: FFPE10 - mAdbID:80938

description: mAdb experiment ID: 80938

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.24;; 4.13 Temperature: 28.55


title: FFPE12 - mAdbID:80942

description: mAdb experiment ID: 80942

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.28;; 4.28 Temperature: 31.15


title: FFPE9 - mAdbID:80937

description: mAdb experiment ID: 80937

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.24;; 3.96 Temperature: 28.4


title: FFPE7 - mAdbID:80935

description: mAdb experiment ID: 80935

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.24;; 4.04 Temperature: 28.37


title: FFPE5 - mAdbID:80932

description: mAdb experiment ID: 80932

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.22;; 4.93 Temperature: 26.78


title: FFPE8 - mAdbID:80936

description: mAdb experiment ID: 80936

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 4.04 Temperature: 27.79


title: FFPE1 - mAdbID:80922

description: mAdb experiment ID: 80922

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.22;; 4.79 Temperature: 27.27


title: FFPE3 - mAdbID:80927

description: mAdb experiment ID: 80927

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.24;; 3.95 Temperature: 28.68


title: FFPE4 - mAdbID:80931

description: mAdb experiment ID: 80931

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.24;; 4.15 Temperature: 28.46


title: FFPE2 - mAdbID:80924

description: mAdb experiment ID: 80924

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.26;; 3.97 Temperature: 30.02


title: GEK_RA_time2_3replicate_Filter9

status: Public on Mar 06 2010

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description:
After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times.
Filters were stripped by pouring 3X150 ml boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane. The first time, the stripping buffer was immediately changed while after the second and third washes the filters were left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager.

hyb_protocol: Hybridization Solution was: 5XSSC, 5XDenhart’s, 0.5% SDS and 100 µg herring sperm DNA/ml. The hybridization protocol used was as follows. Filters were inserted in 12.5X2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X10exp6 dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1h at 65ºC for 20 min in 2X SSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2XSSC, 0.1% SDS.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager.

data_processing: Raw image quantization background subtracted. The data were normalized using a gDNA hybridization for each filter.

organism: Saccharomyces cerevisiae

source_name: YPD exponentially growing yeast strain, RA_time2_3replicate_Filter9

label_protocol: About 30-40 µg of total RNA were reverse transcribed into cDNA by adding 200 us of RT polymerase SuperScript II and random hexamers (Invitrogen), 1 µL RNaseOUT (Invitrogen), 6 µL 5X First Strand Buffer (Invitrogen), 1.5 µL dNTP mix (16 mM dATP, dTTP, dGTP, and 100 µM dCTP) and 5 µL [α-33P]dCTP (3000 Ci/mmol, 10 µCi/microL) in a final reaction volume of 30 µL. The labeling reaction was incubated for 1 h at 43ºC. 1 µL of EDTA 0.5 M was added to stop the reaction. The labeled cDNAs were purified by a S300-HR MicroSpin column (Amersham BioSciences).

growth_protocol: Exponential growth in YPD medium

extract_protocol: Total RNA from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York

tag: Total RNA from FY1679 yeast strain . Time 2 (OD600 =0.38) 3rd replicate. Filter 9.


title: GEK_RA_time5_2replicate_Filter10

source_name: YPD exponentially growing yeast strain, RA_time5_2replicate_Filter10

tag: Total RNA from FY1679 yeast strain . Time 5 (OD600 =0.47) 2nd replicate. Filter 10.


title: GEK_RA_time4_1replicate_Filter4

source_name: YPD exponentially growing yeast strain, RA_time4_1replicate_Filter4

tag: Total RNA from FY1679 yeast strain . Time 4 (OD600 =0.44) 1st replicate. Filter 4.


title: GEK_RA_time1_3replicate_Filter8

source_name: YPD exponentially growing yeast strain, RA_time1_3replicate_Filter8

tag: Total RNA from FY1679 yeast strain . Time 1 (OD600 =0.36) 3rd replicate. Filter 8.


title: GEK_RA_time3_1replicate_Filter3

source_name: YPD exponentially growing yeast strain, RA_time3_1replicate_Filter3

tag: Total RNA from FY1679 yeast strain . Time 3 (OD600 =0.41) 1st replicate. Filter 3.


title: GEK_RA_time4_3replicate_Filter6

source_name: YPD exponentially growing yeast strain, RA_time4_3replicate_Filter6

tag: Total RNA from FY1679 yeast strain . Time 4 (OD600 =0.44) 3rd replicate. Filter 6.


title: GEK_RA_time4_2replicate_Filter9

source_name: YPD exponentially growing yeast strain, RA_time4_2replicate_Filter9

tag: Total RNA from FY1679 yeast strain . Time 5 (OD600 =0.44) 2nd replicate. Filter 9.


title: GEK_RA_time3_3replicate_Filter10

source_name: YPD exponentially growing yeast strain, RA_time3_3replicate_Filter10

tag: Total RNA from FY1679 yeast strain . Time 3 (OD600 =0.41) 3rd replicate. Filter 10.


title: GEK_RA_time5_3replicate_Filter7

source_name: YPD exponentially growing yeast strain, RA_time5_3replicate_Filter7

tag: Total RNA from FY1679 yeast strain . Time 5 (OD600 =0.47) 3rd replicate. Filter 7.


title: GEK_RA_time5_1replicate_Filter5

source_name: YPD exponentially growing yeast strain, RA_time5_1replicate_Filter5

tag: Total RNA from FY1679 yeast strain . Time 5 (OD600 =0.47) 1st replicate. Filter 5.


title: GEK_RA_time2_2replicate_Filter7

source_name: YPD exponentially growing yeast strain, RA_time2_2replicate_Filter7

tag: Total RNA from FY1679 yeast strain . Time 2 (OD600 =0.38) 2nd replicate. Filter 7.


title: GEK_RA_time2_1replicate_Filter2

source_name: YPD exponentially growing yeast strain, RA_time2_1replicate_Filter2

tag: Total RNA from FY1679 yeast strain . Time 2 (OD600 =0.38) 1nd replicate. Filter 2.


title: GEK_RA_time1_1replicate_Filter1

source_name: YPD exponentially growing yeast strain, RA_time1_1replicate_Filter1

tag: Total RNA from FY1679 yeast strain . Time 1 (OD600 =0.36) 1st replicate. Filter 1.


title: GEK_GRO_time2_3replicate_Filter9

description:
After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times.
Filters were stripped by washing them once with 50 mM NaOH at 45ºC, once with 50 mM Tris-HCl, pH 7.5, 0.1x SSC, 0.1% SDS and once pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager.

data_processing: Raw image quantification background subtracted. The data were normalized using a gDNA hybridization for each filter.

source_name: YPD exponentially growing yeast strain, GRO_time2_3replicate_Filter9

label_protocol:
In vivo labeling by run-on (GRO) using 33P-UTP.
Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were washed in cold water and the cell pellet was resuspended in 900 µl of sterile cold water (final volume 950 µl). Then, the cell suspension was transferred to a fresh micro centrifuge tube, 50 µl of 10% sarkosyl were added and cells were incubated for 20 minutes on ice. After the permeabilization step, cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 120 µl of 2.5x transcription buffer (50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2), 16 µl of AGC mix (10 mM each of CTP, ATP and GTP), 6 µl of DTT (0.1 M) and 13 µl of [α-33P]UTP (3000 Ci/mmol, 10 μCi/µL). Cells were maintained on ice at all times. The final volume was adjusted to 300 µl with distilled water and the mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York

tag: In vivo labeled RNA from FY1679 yeast strain . Time 2 (OD600 =0.38) 3rd replicate. Filter 9.


title: GEK_RA_time1_2replicate_Filter6

source_name: YPD exponentially growing yeast strain, RA_time1_2replicate_Filter6

tag: Total RNA from FY1679 yeast strain . Time 1 (OD600 =0.36) 2nd replicate. Filter 6.


title: GEK_GRO_time3_3replicate_Filter10

source_name: YPD exponentially growing yeast strain, GRO_time3_3replicate_Filter10

tag: In vivo labeled RNA from FY1679 yeast strain . Time 3 (OD600 =0.41) 3rd replicate. Filter 10.


title: GEK_GRO_time1_3replicate_Filter8

data_processing: Raw image quantitation background subtracted. The data were normalized using a gDNA hybridization for each filter.

source_name: YPD exponentially growing yeast strain, GRO_time1_3replicate_Filter8

tag: In vivo labeled RNA from FY1679 yeast strain . Time 1 (OD600 =0.36) 3rd replicate. Filter 8.


title: GEK_GRO_time3_2replicate_Filter8

source_name: YPD exponentially growing yeast strain, GRO_time3_2replicate_Filter8

tag: In vivo labeled RNA from FY1679 yeast strain . Time 3 (OD600 =0.41) 2nd replicate. Filter 8.


title: GEK_RA_time3_2replicate_Filter8

source_name: YPD exponentially growing yeast strain, RA_time3_2replicate_Filter8

tag: Total RNA from FY1679 yeast strain . Time 3 (OD600 =0.41) 2nd replicate. Filter 8.


title: GEK_GRO_time5_3replicate_Filter7

source_name: YPD exponentially growing yeast strain, GRO_time5_3replicate_Filter7

tag: In vivo labeled RNA from FY1679 yeast strain . Time 5 (OD600 =0.47) 3rd replicate. Filter 7.


title: GEK_GRO_time4_3replicate_Filter6

source_name: YPD exponentially growing yeast strain, GRO_time4_3replicate_Filter6

tag: In vivo labeled RNA from FY1679 yeast strain . Time 4 (OD600 =0.44) 3rd replicate. Filter 6.


title: GEK_GRO_time4_2replicate_Filter9

source_name: YPD exponentially growing yeast strain, GRO_time4_2replicate_Filter9

tag: In vivo labeled RNA from FY1679 yeast strain . Time 4 (OD600 =0.44) 2nd replicate. Filter 9.


title: GEK_GRO_time5_2replicate_Filter10

source_name: YPD exponentially growing yeast strain, GRO_time5_2replicate_Filter10

tag: In vivo labeled RNA from FY1679 yeast strain . Time 5 (OD600 =0.47) 2nd replicate. Filter 10.


title: GEK_GRO_time2_2replicate_Filter7

source_name: YPD exponentially growing yeast strain, GRO_time2_2replicate_Filter7

tag: In vivo labeled RNA from FY1679 yeast strain . Time 2 (OD600 =0.38) 2nd replicate. Filter 7.


title: GEK_GRO_time3_1replicate_Filter3

source_name: YPD exponentially growing yeast strain, GRO_time3_1replicate_Filter3

tag: In vivo labeled RNA from FY1679 yeast strain . Time 3 (OD600 =0.41) 1st replicate. Filter 3.


title: GEK_GRO_time4_1replicate_Filter4

source_name: YPD exponentially growing yeast strain, GRO_time4_1replicate_Filter4

tag: In vivo labeled RNA from FY1679 yeast strain . Time 4 (OD600 =0.44) 1st replicate. Filter 4.


title: GEK_GRO_time5_1replicate_Filter5

source_name: YPD exponentially growing yeast strain, GRO_time5_1replicate_Filter5

tag: In vivo labeled RNA from FY1679 yeast strain . Time 5 (OD600 =0.47) 1st replicate. Filter 5.


title: GEK_GRO_time1_2replicate_Filter6

source_name: YPD exponentially growing yeast strain, GRO_time1_2replicate_Filter6

tag: In vivo labeled RNA from FY1679 yeast strain . Time 1 (OD600 =0.36) 2nd replicate. Filter 6.


title: GEK_gDNA_Filter 1

type: genomic

description: Filters were stripped by pouring 3X150 ml boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane. The first time, the stripping buffer was immediately changed while after the second and third washes the filters were left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with a Phosphorimager.

hyb_protocol: Hybridization Solution was: 5XSSC, 5XDenhart’s, 0.5% SDS and 100 µg herring sperm DNA/ml. The hybridization protocol used was as follows. New macroarrays were pre-treated for 30 min at 80ºC with 0.5% SDS to remove particles deposited during array printing. This step was not necessary in subsequent hybridizations. Filters were  inserted in 12.5X2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X106dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1at 65ºC for 20 min in 2SSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2SSC, 0.1% SDS. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times.

molecule: genomic DNA

source_name: Yeast genomic DNA

label_protocol:
Yeast genomic DNA was labeled following a random priming procedure. 800 ng genomic DNA in 45 ul distilled water was denatured for 5 minutes by boiling, added to a microcentrifuge tube of Ready-To-Go DNA labeling beads (Amersham Biosciences) and mixed with 50 uCi [α-33P] dCTP (2500 Ci/mmol).
The mixture was incubated at 37C for 1–2 h. In order to eliminate non-incorporated components, Probe Quant G–50 columns (Amersham Biosciences) were used.

extract_protocol: Genomic DNA was isolated from yeast cells by phenol extraction with glass beads, essentially as described by Hoffman CS, Winston F (1987) A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 57:267–272

tag: Total genomic DNA from FY1679 yeast strain


title: GEK_GRO_time1_1replicate_Filter1

source_name: YPD exponentially growing yeast strain, GRO_time1_1replicate_Filter1

tag: In vivo labeled RNA from FY1679 yeast strain . Time 1 (OD600 =0.36) 1st replicate. Filter 1.


title: GEK_gDNA_Filter 3


title: GEK_gDNA_Filter 2


title: GEK_gDNA_Filter 5


title: GEK_gDNA_Filter 4


title: Staphylococcus aureus Newman treated with cathelicidin LL-37 - Replicate #2

status: Public on Mar 02 2010

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description: Staphylococcus aureus Newman treated/untreated with cathelicidin LL-37 - Replicate #2

hyb_protocol: A mixture of control (without peptide) and test conditions (with peptide) was diluted in 250 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven

data_processing: Local background-subtracted signals were corrected for unequal dye incorporation or unequal load of labelled product. The algorithm consisted of a rank consistency filter and a curve fit using the default LOWESS (locally weighted linear regression) method

organism: Staphylococcus aureus

source_name: Total RNA from Staphylococcus aureus Newman incubated with cathelicidin LL-37

label_protocol: Samples of 8 µg total S. aureus RNA were labelled by Cy-3 or Cy-5 dCTP using the SuperScript II (Invitrogen, Basel, Switzerland) following manufacturer's instructions

extract_protocol: Total RNA was purified with Qiagen RNeasy mini kit and treated with DNAse following manufacturer’s recommendations

tag: strain

value: Staphylococcus aureus Newman

tag: treatment

value: incubated with cathelicidin LL-37

source_name: Total RNA from Staphylococcus aureus Newman untreated

value: untreated


title: Staphylococcus aureus Newman treated with cathelicidin LL-37 - Replicate #1

description: Staphylococcus aureus Newman treated/untreated with cathelicidin LL-37 - Replicate #1


title: Staphylococcus aureus Newman treated with dermaseptin - Replicate #2

description: Staphylococcus aureus Newman treated/untreated with dermaseptin - Replicate #2

source_name: Total RNA from Staphylococcus aureus Newman incubated with Dermaseptin

value: incubated with Dermaseptin


title: Staphylococcus aureus Newman treated with Temporin-L  - Replicate #2

description: Staphylococcus aureus Newman treated/untreated with Temporin-L  - Replicate #2

source_name: Total RNA from Staphylococcus aureus Newman incubated with Temporin-L

value: incubated with Temporin-L


title: Staphylococcus aureus Newman treated with cathelicidin LL-37 - Replicate #3

description: Staphylococcus aureus Newman treated/untreated with cathelicidin LL-37 - Replicate #3


title: Staphylococcus aureus Newman treated with Ovispirin-1  - Replicate #3

description: Staphylococcus aureus Newman treated/untreated with Ovispirin-1  - Replicate #3

source_name: Total RNA from Staphylococcus aureus Newman incubated with Ovispirin-1

value: incubated with Ovispirin-1


title: Staphylococcus aureus Newman treated with Ovispirin-1  - Replicate #2

description: Staphylococcus aureus Newman treated/untreated with Ovispirin-1  - Replicate #2


title: Staphylococcus aureus Newman treated with Ovispirin-1  - Replicate #1

description: Staphylococcus aureus Newman treated/untreated with Ovispirin-1  - Replicate #1


title: Staphylococcus aureus Newman treated with Temporin-L  - Replicate #1

description: Staphylococcus aureus Newman treated/untreated with Temporin-L  - Replicate #1


title: Staphylococcus aureus Newman treated with Temporin-L  - Replicate #3

description: Staphylococcus aureus Newman treated/untreated with Temporin-L  - Replicate #3


title: Staphylococcus aureus Newman treated with dermaseptin - Replicate #1

description: Staphylococcus aureus Newman treated/untreated with dermaseptin - Replicate #1


title: Staphylococcus aureus Newman treated with dermaseptin - Replicate #3

description: Staphylococcus aureus Newman treated/untreated with dermaseptin - Replicate #3


title: Liver_animal_2066_sham_90min

status: Public on Mar 01 2010

city: Aarhus

first: Lene

middle: Nagstrup

last: Conley

state: Denmark

address: Langelandsgade 140

department: Department of Chemistry

country: Denmark

institute: University of Aarhus

description: The differential expression of genes in the liver was studied under two predefined situations; portal arterialization of segments II, III and IV ( by aortoportal shunting) and sham. Gene expression profiles were obtained from biopsies sampled from the arterialized segments and from the same segments in sham animals. Sampling points were 1, 5, 10, 30, 60, 90 minutes and 2, 3, 4 and 6 hours after shunt opening

hyb_protocol: The slides were hybridized in a Discovery XT hybridization station (Ventana Discovery Systems, Tucson, AZ, USA). Transfer Chip Prep-2 from 4 ºC to room temperature 1 hour before use. Prepare ChipSpread by mixing equal volumes of ChipSpread A (20 mg/mL BSA, 4x SSC, 0.5 mg/mL sodium azide) and B (formamide; 2 mg/mL SDS) and incubate at room temperature for 1 hour before use. A total of 2.5 mL is needed per slide. Print labels, trim them and place them on the slides. Mix the Chip Map reagents (Chip Prep-1, -2 and - 3) by inversion, remove the cap and place the reagents in the Discovery. Place the slides in the machine and initiate the run. Cover slide with 2.5 mL ChipSpread when the message appears (after few minutes). The machine now runs for app. 1.5 hours to pre-hybridize the slides. Heat a waterbath to 90°C or use a PCR machine. Mix the Chiphybe80, add 200 µL to the sample (<20 µL) and mix carefully. Heat the sample mixture at 90°C for 3 minutes and mix carefully by pipetting. Press button on the machine which then prepares the slides for hybridization. When the message appears apply the samples onto the slides and press button and the machine hybridizes at 48 ºC for 6 hours. Wipe oil from backside of slides using a clean-room napkin and place slides in the slide-holder from the High Throughput Wash Station (Telechem, cat.no. HTW) placed in a mTub filled with RiboWash. If processing more than 20 slides, place equal number of slides in two slide-holders and continue in parallel. Transfer the slide-holder to a HTW filled with RiboWash and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with RiboWash and repeat the wash. Dip the slide-holder in 2x SSC filled in a mTub (200 mL 20x SSC, Elga H2O + 1800 mL water). Transfer the slide-holder to a HTW filled with 2x SSC and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with 2x SSC and repeat the wash. Dip the slide-holder 10 times in 0.1x SSC filled in a mTub (5 mL 20x SSC, Elga H2O + 995 mL water) and leave the holder submerged in 0.1x SSC. Transfer the slides to a mBox slide holder placed in a mTub filled with Elga H2O. Dry arrays by centrifugation (at 300 x g for 4 min placed in a mBox)

scan_protocol: Scanner: ScanArray Express HT system (Perkin Elmer), 5 µm resolution, 100 % laser power and PMT adjusted individually for each channel. Image analysis software: GenePix Pro (version 6.0.1.22, Molecular Devices) using FeatureType = Irregular Filled and LocalFeature as background measurement.

data_processing: Statistical analysis was carried out in the R computing environment (version 2.3.1 for Windows) using the package Linear Models for Microarray Analysis (Limma, version 2.7.10) which is part of the Bioconductor project. The median intensities were background corrected by using the normexp function on the median background intensities. Following background correction, the log2-transformed ratios of Alexa-594 to Alexa-488 were normalized within-slide using printtip-loess with default parameters as implemented in Limma. The set of normalized log-ratios were then analyzed in Limma to identify genes being significantly differentially expressed between time points within treatment as well as between treatments. Time point contrasts were formed referring to the sample taken at time point 1 min. followed by multiple testing across genes and contrasts with p-values below 0.001 considered as significant. The features of the arrays were mapped to a LocusLink identifier and an annotation package was built using the Bioconductor package AnnBuilder (version 1.9.14). Tests for significantly (P < 0.05) overrepresentation of gene ontology (GO) terms were conducted using the GOHyperG function of the Bioconductor package GOstats (ver 1.5.5). The sets of overrepresented GO terms were further analysed by utilising information from Online Mendelian Inheritance in Man (OMIM) to group the genes by function.

organism: Sus scrofa

label_protocol: 20 µg total RNA was labelled by using the Superscript Indirect cDNA Labeling System (Invitrogen) in combination with ARES cDNA labeling kits (Molecular Probes/Invitrogen) following the enclosed protocols. Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the cDNA reactions. Green spike-in RNA was added to the common reference samples and red spike-in RNA was added to the test samples.

growth_protocol: Eighteen castrate sus scrofa domesticus pigs were used for all experiments, conducted in compliance with the institutional animal care guidelines and the National Institute of Health’s Guide for the Care and Use of Laboratory Animals [DHHS Publication No. (NIH) 85-23, Revised 1985]. In the acute series, we followed the same anesthesia protocol as previously described (Mortensen et al. Am J Physiol Gastrointest Liver Physiol 294: G819–G830, 2008). In the chronic series, anesthesia was maintained with Isoflurane 1.5-2% mixed with 55% oxygen. Respiratory rate was adjusted to achieve an Et CO2 between 35 and 40 mmHg. Mean alveolar concentration of Isoflurane was maintained at 1.3 using a Capnomac (Nycomed Jean Mette). Analgesia was induced and maintained with Fentanyl 0.01 mg/kg. Before surgery, all animals received a single i.m. shot of antibiotic prophylaxis (Enrofloxacin, 2.5 mg/kg).

extract_protocol: RNeasy Maxi Kit with DNase treatment following the enclosed protocol (Qiagen)

treatment_protocol: Catheters: In the acute series, a 16G central venous catheter  (CVK, Secalon® T) was placed in the left external jugular vein for administration of anesthesia and infusions. A 5 French Swan-Ganz catheter (Edwards Lifesciences™) was floated via the right external jugular vein to the pulmonary artery for cardiac output (CO) measurements. A 16G CVK (Secalon® T) was placed in the left femoral artery for continuous arterial blood pressure monitoring. A 7 French 110 cm angiographic catheter (Cordis®, Johnson&Johnson™) was placed in the right hepatic vein draining segments V, VI, VII and VIII via the right internal jugular vein for blood pressure monitoring and blood sampling. A 5 French Swan-Ganz catheter (Edwards Lifesciences™) was placed in the hepatic vein draining segments II and III by direct transhepatic placement for pressure monitoring and blood sampling. Inflation of the balloon allowed wedged hepatic pressure measurement. A pediatric CVK (Arrow® International) was placed in the portal vein for blood pressure monitoring and blood sampling. No catheters were placed in the pigs in the chronic series, as the main objective here was to anastomose the shunt from the aorta to the left portal vein branch with minimal damage to the hepatic hilus. Measurements: In the acute series, calibrated transducers  (Transact 3™, Abbott Critical Care Systems, Chicago, IL, USA) were used for continuous pressure registration and signals were stored electronically (Macintosh Quadra 950, Apple Computers, CA, USA). Perivascular ultrasonic flow probes (CardioMed Systems, Medistim A/S, Oslo, Norway) were placed around the portal vein, right hepatic artery, left hepatic artery and around the aortoportal shunt. Cardiac output was measured by thermo dilution (Vigilance™ Volumetrics, Edwards Lifesciences™). Measurements were made in triplicate and averaged. The heart rate was monitored with an electrocardiogram (ECG). In the chronic series, the heart rate was monitored with an electrocardiogram (ECG). Flow in the aortoportal shunt was measured using an 8 mm perivascular ultrasonic flow probe (CardioMed Systems, Medistim A/S, Oslo, Norway). Surgery: In the acute series, after a midline laparotomy and placement of all catheters and flow probes as described above, we isolated and recorded the flow in the left portal vein branch (LPVB). When the activated clotting time (ACT) was above 250 seconds a 5mm Propaten Gore-Tex™ graft was anastomosed end-to-side from the aorta (between truncus coeliacus (TC) and the superior mesenteric artery (SMA)) to the LPVB. The LPVB was then ligated proximal to the bifurcation to prevent backflow to the main portal vein trunk (MPVT). The Bulldog was removed and time = 0 noted. Flow in the shunt was standardized to 1000 mL/minute by shunt constriction using a ligature and flow probe (fig. 1). In the chronic series, after a midline laparotomy, a similar shunt was placed from the aorta to the LPVB once the animal had received 5000 IE Heparin i.v. Only this time we used an interposed aorta graft from a donor pig (as the Gore-Tex grafts™ tended to become occluded). The LPVB was ligated proximal to the portal bifurcation to prevent backflow to the MPVT. Flow was standardized to 100mL/minute. Upon relaparatomy three weeks later, the shunt was isolated and flow measured. The flow in the MPVT (now supplying the right liver only) was recorded. Sampling: In the acute series, sequential biopsies were taken from the shunted segments II, III and IV at time points 1, 5, 10, 30, 60, 90 minutes and 2, 3, 4 and 6 hours after shunt opening (t = 0). Biopsies were placed immediately in RNAlater (Ambion®). In the chronic series, only peroperative arterial blood gas samples were taken (directly from the aorta) to monitor respiratory status.

tag: Breed

value: landrace

tag: gender

value: male-castrates

tag: age

value: 3 months

tag: weight

value: 30 Kg

tag: tissue

value: liver

source_name: common liver reference

value: DLY X Hampshire

tag: animal

tag: project

value: RN


title: Liver_animal_2069_sham_5min

value: female


title: Liver_animal_2019_shunt_10min


title: Liver_animal_2033_shunt_5min


title: Liver_animal_2060_sham_3h


title: Liver_animal_2033_shunt_4h


title: Liver_animal_2032_shunt_6h


title: Liver_animal_2060_sham_6h


title: Liver_animal_2033_shunt_30min


title: Liver_animal_2060_sham_30min


title: Liver_animal_2066_sham_2h


title: Liver_animal_2060_sham_5min


title: Liver_animal_2069_sham_3h


title: Liver_animal_2060_sham_10min


title: Liver_animal_2032_shunt_1min


title: Liver_animal_2019_shunt_4h


title: Liver_animal_2066_sham_6h


title: Liver_animal_2033_shunt_6h


title: Liver_animal_2032_shunt_2h


title: Liver_animal_2066_sham_10min


title: Liver_animal_2019_shunt_6h


title: Liver_animal_2019_shunt_1min


title: Liver_animal_2069_sham_30min


title: Liver_animal_2033_shunt_90min


title: Liver_animal_2069_sham_6h


title: Liver_animal_2069_sham_4h


title: Liver_animal_2032_shunt_30min


title: Liver_animal_2019_shunt_5min


title: Liver_animal_2032_shunt_90min


title: Liver_animal_2032_shunt_10min


title: Liver_animal_2019_shunt_3h


title: Liver_animal_2019_shunt_30min


title: Liver_animal_2019_shunt_2h


title: Liver_animal_2069_sham_1min


title: Liver_animal_2033_shunt_2h


title: Liver_animal_2066_sham_1min


title: Liver_animal_2069_sham_2h


title: Liver_animal_2060_sham_90min


title: Liver_animal_2019_shunt_90min


title: Liver_animal_2033_shunt_1min


title: Liver_animal_2032_shunt_5min


title: Liver_animal_2033_shunt_3h


title: Liver_animal_2032_shunt_4h


title: Liver_animal_2060_sham_4h


title: Liver_animal_2032_shunt_3h


title: Liver_animal_2060_sham_2h


title: Liver_animal_2066_sham_30min


title: Liver_animal_2069_sham_90min


title: Liver_animal_2066_sham_5min


title: Liver_animal_2066_sham_4h


title: Liver_animal_2066_sham_3h


title: Liver_animal_2060_sham_1min


title: Liver_animal_2033_shunt_10min


title: Liver_animal_2069_sham_10min


title: D9 T72_BCL

status: Public on Jan 08 2010

city: La Jolla

first: Sunil

last: Kurian

state: CA

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

country: USA

institute: The Scripps Research Institute

hyb_protocol: Standard Affymetrix 49 Format Hybridization with 15mg of fragmented cRNA

scan_protocol: Affymetrix EukGE-WS2v4

data_processing: Xray (Biotique Systems)

label: biotin

source_name: B-lymphocytes at time 72

label_protocol: Whole Transcript sense target labeling

growth_protocol: T and B Cells in RPMI-1640 ( See study Design)

extract_protocol: Total RNA was extracted using the Mirvana kit

treatment_protocol: CD3/28 and anti-CD40 + rIL2, rIL10

tag: Purified B cells from healthy human donor


title: D7 T72_BCL


title: D1 T72_BCL


title: D6 T72_BCL


title: D8 T72_BCL


title: D2 T72_BCL


title: D3 T72_BCL


title: D5 T72_BCL


title: D4 T72_BCL


title: D10 T48_BCL

source_name: B-lymphocytes at time 48


title: D7 T48_BCL


title: D9 T48_BCL


title: D4 T48_BCL


title: D10 T72_BCL


title: D6 T48_BCL


title: D2 T48_BCL


title: D3 T24_BCL

source_name: B-lymphocytes at time 24


title: D4 T24_BCL


title: D8 T24_BCL


title: D5 T48_BCL


title: D4 T0_BCL

source_name: B-lymphocytes at time 0


title: D1 T24_BCL


title: D10 T24_BCL


title: D7 T24_BCL


title: D1 T48_BCL


title: D6 T24_BCL


title: D3 T0_BCL


title: D9 T24_BCL


title: D3 T48_BCL


title: D8 T48_BCL


title: D2 T24_BCL

source_name: B-lymphocyte at time 24


title: D6 T0_BCL


title: D7 T0_BCL


title: D9 T0_BCL


title: D8 T0_BCL


title: D1 T0_BCL


title: D2 T0_BCL


title: D10 T0_BCL

source_name: B-lymphocyte at time 0


title: D7 T72_TCL

source_name: T-lymphocytes at time 72

tag: Purified T cells from healthy human donor


title: D5 T0_BCL


title: D8 T72_TCL


title: D9 T72_TCL


title: D6 T72_TCL


title: D3 T72_TCL


title: D1 T72_TCL


title: D2 T72_TCL


title: D5 T72_TCL


title: D10 T72_TCL


title: D4 T72_TCL


title: D5 T24_BCL


title: D10 T48_TCL

source_name: T-lymphocytes at time 48


title: D6 T48_TCL


title: D3 T48_TCL


title: D2 T48_TCL


title: D5 T48_TCL


title: D7 T48_TCL


title: D9 T48_TCL


title: D4 T48_TCL


title: D7 T24_TCL

source_name: T-lymphocytes at time 24


title: D6 T24_TCL


title: D5 T24_TCL


title: D9 T24_TCL


title: D4 T24_TCL


title: D1 T24_TCL


title: D10 T24_TCL


title: D8 T48_TCL


title: HBx versus Control Biological repeat 1

status: Public on Dec 31 2009

type: other

city: Singapore

first: Yu

last: Wang

address: 11 Hospital Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

description: Biological repeat 1

hyb_protocol: The Cy-5 and Cy-3 labeled samples were then mixed in equal amount and hybridized onto the mirVana™ bioarrays at 42 °C overnight.

scan_protocol: Scanned on an Axon 4000B scanner and signal quantified with GenePix Pro 6.0.

data_processing:
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.
This study focuses only on human sequences.  Only those human miRNAs with foreground signal more than 3X background signal are considered significant.

molecule: other

source_name: Control HepG2_1

label_protocol: Small RNA from 20ug of total RNA from HBx cells were labelled with Cy-5 and that from control cells were labelled Cy-3 with Kreatech ULS™ Small RNA Labeling Kit

growth_protocol: The human hepatocellular carcinoma HepG2 cells were cultured in Dulbecco’s modified Eagle’s media (DMEM) supplemented with 10% fetal calf serumand 25mM HEPES. The cells were incubated at 37 °C in a humidified atmosphere with 5% CO2

extract_protocol: Total RNA including low molecular weight RNA (LMW RNA) were extracted with Ambion MirVana™  MiRNA Isolation Kit and small RNA of <40 nt were enriched with FlashPage Fractionator

treatment_protocol: HepG2 cells were transduced with either HBx-expressing recombinant adenovirus (HBx) or control adenovirus (Control). 48 hours post transduction, the treated cells were exposed to UV irradiation for 30 seconds with a germicidal lamp calibrated to deliver ~20 J/m2. Cells were harvested 24 hours post UV irradiation for microarray analysis.

tag: cell line

value: Control adenovirus transduced and UV treated

source_name: HBx-expressing HepG2_1

value: HBx adenovirus transduced and UV treated


title: HBx versus Control Biological repeat 2

description: Biological repeat 2

source_name: Control HepG2_2

source_name: HBx-expressing HepG2_2


title: HBx versus Control Biological repeat 3

description: Biological repeat 3

source_name: Control HepG2_3

source_name: HBx-expressing HepG2_3


title: D2 T24_TCL


title: Total blood mRNA profile from 14 pooled individuals (7 males + 7 females) before EPO treatment

status: Public on Jan 01 2010

type: SAGE

anchor: NlaIII

city: Montpellier

first: David

last: Piquemal

address: 1682, rue de la Valsière

country: France

institute: ACOBIOM

description: unpurified blood cells from 7 males + 7 females, pooled after RNA extraction

data_processing: Skuld-Tech (Montpellier, France) platform

molecule: polyA RNA

source_name: total blood - control

extract_protocol: TRIzol

treatment_protocol: no

tag: tissue = unpurified blood cells


title: D6 T0_TCL

source_name: T-lymphocytes at time 0


title: D2 T0_TCL


title: D3 T24_TCL


title: Total blood mRNA profile from 14 pooled individuals (7 males + 7 females) during EPO treatment

description:
The SAGE librairies were constructed by pooling blood samples from 14 athletes (7 males, 7 females) injected with darbepoetin alpha (Amgen Europe B.V., Holland, 0.72 ± 0.01 g/kg injections per week, 4 weeks).
unpurified blood cells from 7 males + 7 females, pooled after RNA extraction

source_name: total blood - during EPO treatment


title: D8 T24_TCL


title: D7 T0_TCL


title: D8 T0_TCL


title: Maize-Petit-RR-2005-2

city: Wageningen

first: Jeroen

last: van Dijk

address: Bornsesteeg 45

country: Netherlands

institute: RIKILT, institute of food safety

hyb_protocol: The slides were prehybridized according to the protocol described by Hedge et al, (2000).The hybridization mixture was equally dispersed over the two slides. The hybridization was performed in a hybridization chamber and gasket (Agilent, Amstelveen, Netherlands). Slides were hybridized overnight at 60°C in a rotating hybridization oven in darkness (Agilent, Amstelveen, Netherlands). After hybridization the slides were washed with wash buffer 1, 2 and stabilization and drying solution, according to the manufacturer’s instructions (Agilent, Amstelveen, Netherlands). The slides were stored at room temperature in darkness until scanning.

scan_protocol: Microarrays were scanned after excitation of Cy3 dye with 543 nm laser using scanner ScanArray® Express HT (Perkin Elmer, USA). The microarrays were scanned at constant laser power (90 %) and 10 μm resolution settings.Tiff images were imported into the ArrayVision software (Imaging Research, Waalwijk, The Netherlands) and the fluorescent intensity and background were determined for each spot.

data_processing: Quality checked visually; control spots removed; Filtering of rows of spots with 17 out of 18 samples having a value lower than 2X background, Median normalized (array-wise, separately for the two platforms).

organism: Zea mays

source_name: maize kernels, dried

label_protocol: RNA (100μg) was labeled by incorporation of Cy3-dCTP during a cDNA synthesis reaction using 21-mer oligo-dT primers according to the method described by Boeuf et al (2001) and Franssen-van Hal et al (2002). Labeled cDNA was first dissolved in MiliQ treated water (500 μl) to which later 2X hybridization buffer was added (500 μl), pre-warmed to 60°C

growth_protocol: The Bt F1 hybrids (DKC 78-15Bt), the RR F1 hybrid (DKC 78-35RR) and the isoline (CRN 3505) were grown in 2 different Monsanto sites, namely, Petit and Lichtenburg (South Africa) under high-input system; these lines were planted in Petit over three growing seasons (2004, 2005 and 2006) and in Lichtenburg over one growing season (2004). At planting the plants were fertilized with 300kg/Ha 4:3:4 (33), Topdressing 300kg/Ha KAN (28) and treated with herbicide 1.8L/Ha Guardian + 200M1/Ha Sumi Alpha. Two months after planting the plants were treated with herbicide, 2.2L/Ha A-maizing + 1L/Ha Harness + 220Ml/Ha alphacypermytrin. Three months after planting the material was treated with pesticide, 750Ml/Ha Endosulfan against stalkborer. The plant material was harvested 8 months after planting; the kernels were removed from the cobs on site by machine and packed in plastic bags. The moisture content was 11-13%. The Bt F1 hybrid (DKC 78-15Bt) and the control conventional line (CRN 3505) were also grown in Potchefstroom (South Africa) under low-input system which means that no fertilizer, no fungicide and no herbicide were applied throughout the growth of the plants. The plant material was also harvested after the cobs were dry around 8 months after planting.

extract_protocol: Total RNA extraction following a protocol for extraction of RNA from polysaccharide rich tissues  (Chang et al.,2003,Plant Molecular Biology Reporter, 11: 113–116)

treatment_protocol: Maize kernels from all samples were couriered to Technische Universität München, Germany for milling and distribution. The maize kernels were milled using a cyclone mill (Cyclotec, Foss, Germany) equipped with a 500-µm sieve and freeze-dried (ALPHA 1-4 LSC, Christ, Osterode, Germany) for 48 hours. Aliquots of maize powders (2g) were prepared and couriered to the different laboratories for specific analysis. Upon arrival the maize powders were kept at -20 degrees Celcius and used as needed.

value: maize kernels

tag: name

value: DKC 78-35 RR

tag: common name

tag: trait

value: Glyphosate herbicide tolerance

tag: growing year

tag: location

value: Petit

tag: input

value: high input


title: D4 T0_TCL


title: D3 T0_TCL


title: D1 T0_TCL


title: Maize-Petit-Bt-2005-3

value: DKC 78-15 Bt

value: MON 810

value: Resistance to European corn borer (Ostrinia nubilalis).


title: D9 T0_TCL


title: D10 T0_TCL


title: D5 T0_TCL


title: Maize-Lichtenburg-RR-2004-1

value: Lichtenburg


title: Maize-Petit-WT-2005-2

value: conventional

value: wild-type


title: Maize-Petit-WT-2005-1


title: Maize-Lichtenburg-WT-2004-1


title: Maize-Petit-RR-2005-1


title: Maize-Lichtenburg-Bt-2004-1


title: Maize-Petit-Bt-2005-2


title: Maize-Petit-WT-2006-1


title: Maize-Potchefstroom-WT-2004-1

value: Potchefstroom

value: low input


title: Maize-Petit-Bt-2004-1


title: Maize-Petit-RR-2004-1


title: Maize-Petit-Bt-2005-1


title: Maize-Petit-RR-2006-1


title: Maize-Potchefstroom-Bt-2004-1


title: Maize-Petit-Bt-2006-1


title: Maize-Petit-WT-2004-1


title: D3-ES 7d without LIF& 50 nM Li, biological rep2

city: Sevilla

first: Patricia

last: Ruiz-Ontañón

address: Av Américo Vespucio

department: TErapia CElular y Medicina Regenerativa

institute: CABIMER

description: Gene expression data from D3-ES cultivated without LIF and treated with 50 nM lithium for 7 days

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 420 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The data were realized with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings from GeneChip® Operating System 1.4.0.036 and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

organism: Mus musculus

source_name: D3-ES cultivated without LIF and treated with 50 nM lithum for 7 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA One-Cycle Target Labeling Assays (GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004).

growth_protocol: 7 days of treatment with standard ESC medium (15% serum) with or without 1000 unit/ml LIF and 50 nM of lithium

extract_protocol: Rneasy mini kit (Qiagen) of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were trypsinized (10%, Gibco) and washed twice with PBS 1X and placed on ice. Total RNA was extracted with the Rneasy kit protocol (Qiagen).

tag: mice embryonic stem cells.

tag: D3-ES cell line


title: D3-ES 7d without LIF, biological rep3

description: Gene expression data from D3-ES cultivated without LIF for 7 days

source_name: D3-ES cultivated without LIF for 7 days


title: D3-ES 7d without LIF& 50 nM Li, biological rep1


title: D3-ES 7d without LIF& 50 nM Li, biological rep3


title: D3-ES 7d without LIF, biological rep2


title: D3-ES 7d with LIF& 50 nM Li, biological rep3

description: Gene expression data from D3-ES cultivated with LIF and treated with 50 nM lithium for 7 days


title: D3-ES 7d without LIF, biological rep1


title: Hunk WT rep5

city: Philadelphia

first: Lewis

middle: A.

last: Chodosh

state: PA

address: 421 curie blvd, BRB II/III 616

department: Cancer Biology

institute: University of Pennsylvania

description: Myc tumors with Hunk WT genotype

hyb_protocol: Affymetrix Generic Hybrdization

scan_protocol: Arrays were scanned using the Affymetrix GeneArray Scanner

data_processing: The data were analyzed with GCRMA using R and quantile normalized

source_name: Hunk WT, Mammary gland

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: A 129/Sv mouse genomic library (Stratagene, La Jolla, CA) was screened with a Hunk cDNA fragment (nt 1-706) (Gardner et al., 2000b).  The Hunk gene was disrupted by replacement of a 1.1 kb fragment containing the putative promoter and exon 1 of Hunk with a pGKneo cassette flanked by LoxP sites.  25 µg of linearized vector was electroporated into 1x107 E14 ES cells (kindly provided by Marisa Bartolomei, University of Pennsylvania) and selected in 300 µg /ml G418.  Properly target clones, as well as the resulting mice, were screened by Southern hybridization using a 3’ Xho I/Xmn I flanking probe.  Lung protein lysates (7 mg) were subjected to immunoprecipitation and immunoblotting with Hunk-specific C-terminal antisera as previously described (Gardner et al., 2000a).

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

treatment_protocol: Hunk-deficient animals were crossed to mice harboring an MMTV-c-myc transgene (Leder et al., 1986).  Hunk heterozygous, MMTV-c-myc mice were backcrossed to Hunk heterozygous animals.  MMTV-c-myc female animals of each Hunk genotype were mated twice, then monitored twice weekly for mammary tumors.  Mice possessing tumors with a maximum diameter of 20 mm were sacrificed and organs were examined at necropsy.  Tumor nodules were identified by examination of organs through a Leica Wild MZ8 dissection microscope.

tag: Genotype

value: MMTV-c-myc/Hunk WT; Gender:Female; Tissue:Mammary gland tumors; Strain:FVB


title: Hunk WT rep1

description: Myc tumors with Hunk WT genotype


title: D3-ES 7d with LIF, biological rep2

description: Gene expression data from D3-ES cultivated with LIF for 7 days

source_name: D3-ES cultivated with LIF for 7 days


title: D3-ES 7d with LIF, biological rep1

tag: mice embryonic stem cells


title: Hunk Knock-Out rep 6

description: Myc tumors with Hunk KO genotype

source_name: Hunk Knock-Out, Mammary gland

value: MMTV-c-myc/Hunk KO; Gender:Female; Tissue:Mammary gland tumors; Strain:FVB


title: Hunk Knock-Out rep 5

description: Myc tumors with Hunk KO genotype


title: Hunk WT rep4

description: Myc tumors with Hunk WT genotype


title: Hunk WT rep6

description: Myc tumors with Hunk WT genotype


title: Hunk Knock-Out rep 4

description: Myc tumors with Hunk KO genotype


title: Hunk WT rep2

description: Myc tumors with Hunk WT genotype


title: D3-ES 7d with LIF& 50 nM Li, biological rep2

source_name: D3-ES cultivated with LIF and treated with 50 nM lithium for 7 days


title: Hunk WT rep3

description: Myc tumors with Hunk WT genotype


title: Hunk Knock-Out rep 2

description: Myc tumors with Hunk KO genotype


title: Maize-Petit-RR-2005-1

tag: tissue


title: Maize-Petit-Bt-2005-2


title: Maize-Petit-WT-2005-2


title: Maize-Petit-RR-2005-2


title: Hunk Knock-Out rep 3

description: Myc tumors with Hunk KO genotype


title: Maize-Petit-WT-2005-1


title: Maize-Petit-WT-2006-1


title: Maize-Petit-Bt-2005-3


title: Hunk Knock-Out rep 1

description: Myc tumors with Hunk KO genotype


title: Maize-Petit-Bt-2006-1


title: Maize-Lichtenburg-WT-2004-1


title: Maize-Potchefstroom-Bt-2004-1


title: Maize-Petit-RR-2004-1


title: Maize-Potchefstroom-WT-2004-1


title: Maize-Petit-WT-2004-1


title: Maize-Lichtenburg-Bt-2004-1


title: Maize-Petit-RR-2006-1


title: Maize-Lichtenburg-RR-2004-1


title: D3-ES 7d with LIF, biological rep3


title: Maize-Petit-Bt-2005-1


title: Maize-Petit-Bt-2004-1


title: Control siRNA_rep2

city: Tokyo

first: Hidewaki

last: Nakaagwa

state: Tokyo

address: 4-6-1 Shirokanedai, Minato-ku,

department: Institute of Medical Science

country: Japan

institute: The University of Tokyo

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Probe signal intensities were normalized by RMA and Quantile normalization methods (using R and Bioconductor).

source_name: LNCaP cells treated with siRNA to EGFP_2

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

extract_protocol: Total RNA was extracted uisng Trizol (Invitrogen) according to the manufacturer's protocol and then purified with Qiagne's Rneasy column.

value: Prostate cancer cell line LNCaP

tag: treatment

value: siEGFP


title: PCARNEQ siRNA_rep3

source_name: LNCaP cells treated with siRNA to PCARNEQ_3

value: siPCARNEQ


title: PCARNEQ siRNA_rep2

source_name: LNCaP cells treated with siRNA to PCARNEQ_2


title: PCARNEQ siRNA_rep1

source_name: LNCaP cells treated with siRNA to PCARNEQ_1


title: D3-ES 7d with LIF& 50 nM Li, biological rep1


title: Control siRNA_rep1

source_name: LNCaP cells treated with siRNA to EGFP_1


title: STyphi_viaB_vs_tviBvexE_lowsalt_rep2

status: Public on Dec 11 2009

city: Davis

first: Sebastian

last: Winter

address: One Shields Ave

department: MMI

institute: UC Davis

description: Comparison between viaB mutant and tviB-vexE mutant to assess effect of regulatory gene tviA on global gene expression

hyb_protocol: Seo YS, Sriariyanun M, Wang L, Pfeiff J, Phetsom J, Lin Y, Jung KH, Chou HH, Bogdanove A, Ronald P. A two-genome microarray for the rice pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola and its use in the discovery of a difference in their regulation of hrp genes. BMC Microbiol. 2008 Jun 18;8:99. PMID 18564427

data_processing:
For raw data processing and analysis, the TM4 Microarray Software Suite was used. Local background intensity was substracted from each itensity value. Raw expression data were normalized using a global Locfit/LOWESS algorithm.  Replicates on each replicate were combined by averaging the fold change of each gene.
Photomultiplier setting (HI: high intensity, LI low intensity): Data from both scans was processed (local background subtraction, normalization, in-slide replicates averaged). Then HI and LI were compared. If the intensity value of any channel (Ch1 or Ch2) in the high intensity scan was higher than 32000 (half of the maximum value), all information was replaced with that from the low intensity scan (values <32000).

label: Alexa Fluor 555

organism: Salmonella enterica subsp. enterica serovar Typhi

source_name: S. Typhi Ty2 viaB mutant low salt

growth_protocol: S. Typhi viaB mutant was grown in SOB broth to mid-log phase (OD600 = 0.4-0.5) statically at 37C

extract_protocol: S. Typhi strains were grown in 5 ml broth. 0.8 ml stop solution (5 % water saturated phenol in ethanol) was added and the suspension centrifuged at 7,700 g for 5 min at 4°C. The bacterial pellet was resuspended in 0.4 ml lysis solution (0.1 mg/ml lysozyme, 1mM EDTA 10mM, Tris/Cl pH = 8.0) and the suspension incubated at 25°C for 1 h. Next, 40 μl 10 % SDS was added and the solution heated to 65°C. After 2 min, 0.44 ml 1 M sodium acetate and 0.9 ml hot (65°C) phenol was added to the sample. The emulsion was incubated at 65°C for 6 min, chilled on ice for 10 min and centrifuged at 20,000 g for 10 min at 4°C. The aqueous phase was transferred to a new tube, extracted with 0.9 ml chloroform. Phases were separated by centrifugation at 20,000 g for 5 min at 4°C. After transferring the upper aqueous phase to a new tube, the RNA was precipitated by adding 80 μl 1 mM EDTA 3 M sodium acetate pH = 5.2 and 1 ml isopropanol. The samples were centrifuged for 30 min at 20,000 g at 4°C and the supernatant discarded. The RNA pellet was washed with 1 ml 80 % Ethanol and the samples were centrifuged for 5 min at 20,000 g at 4°C. RNA was air-dried and resuspended in RNase-free water. Traces of DNA in the RNA preparation were removed by DNase treatment (DNA-free DNase treatment, Applied Biosystems).

tag: genotype/variation

value: viaB mutant

label: Alexa Fluor 647

source_name: S. Typhi Ty2 tviB-vexE mutant low salt

label_protocol: modifications: cDNA was synthesized and differentially labeled using the SuperScript Plus Indirect cDNA Labeling System (Invitrogen)

growth_protocol: S. Typhi tviB-vexE mutant was grown in SOB broth to mid-log phase (OD600 = 0.4-0.5) statically at 37C

value: tviB-vexE mutant


title: Control siRNA_rep3

source_name: LNCaP cells treated with siRNA to EGFP_3


title: Quail20-Cy3_Quail25-Cy5_2

status: Public on Dec 03 2009

city: Saint Louis

first: Kara

last: Powder

state: MO

address: 4566 Scott Ave

department: Genetics

institute: Washington University in St Louis

description: Quail Stage 20 Cy3 versus Quail Stage 25 Cy5, technical replicate number 2

hyb_protocol: Labeled cDNA populations were resuspended in 40ul hybridization buffer (0.25M NaPo4, 0.5% SDS, 1mM EDTA, 1x SSC, 2X Denharts). Microarray slides were hybridized at 42 degrees C for 12h.

scan_protocol: Microarray chips were scanned using a GMS 418 Scanner (Affymetrix, Santa Clara, CA).  Original TIFF image files available upon request.

data_processing: Microarray images were analyzed with the BioDiscovery Imagene software package to generate raw intensity data.

organism: Coturnix japonica

source_name: Frontonasal prominence mesenchyme

label_protocol: Purified run-off RNAs from each sample were labeled using Genisphere 3DNA kits as directed.

extract_protocol: Isolation of RNA, cDNA synthesis and amplification were carried out as described in Hawkins et al, 2007 (PMID: 17565378).

tag: Frontonasal prominence mesenchyme microdissected at Hamburger-Hamilton stage 25

tag: Frontonasal prominence mesenchyme microdissected at Hamburger-Hamilton stage 20


title: Quail20-Cy5_Quail25-Cy3_2

description: Quail Stage 20 Cy5 versus Quail Stage 25 Cy3, technical replicate number 2


title: Duck20-Cy5_Duck25-Cy3_2

description: Duck Stage 20 Cy5 versus Duck Stage 25 Cy3, technical replicate number 2

organism: Anas platyrhynchos


title: Quail20-Cy5_Quail25-Cy3_1

description: Quail Stage 20 Cy5 versus Quail Stage 25 Cy3, technical replicate number 1


title: STyphi_viaB_vs_tviB-vexE_lowsalt_rep1

scan_protocol: Seo YS, Sriariyanun M, Wang L, Pfeiff J, Phetsom J, Lin Y, Jung KH, Chou HH, Bogdanove A, Ronald P. A two-genome microarray for the rice pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola and its use in the discovery of a difference in their regulation of hrp genes. BMC Microbiol. 2008 Jun 18;8:99. PMID 18564427

label_protocol: cDNA was synthesized and differentially labeled using the SuperScript Plus Indirect cDNA Labeling System (Invitrogen)


title: STyphi_Ty2_vs_rcsB_lowsalt_rep2

description: Comparison between the S. Typhi wild-type strain and a rcsB mutant to assess effect of the regulatory gene rcsB on global gene expression

source_name: S. Typhi Ty2 wild-type low salt

growth_protocol: S. Typhi was grown in SOB broth to mid-log phase (OD600 = 0.4-0.5) statically at 37C

source_name: S. Typhi Ty2 rcsB mutant low salt

value: rcsB mutant


title: Duck20-Cy3_Duck25-Cy5_2

description: Duck Stage 20 Cy3 versus Duck Stage 25 Cy5, technical replicate number 2


title: STyphi_Ty2_vs_rcsB_lowsalt_rep1


title: Duck20-Cy3_Duck25-Cy5_1

description: Duck Stage 20 Cy3 versus Duck Stage 25 Cy5, technical replicate number 1


title: Quail20-Cy3_Quail25-Cy5_1

description: Quail Stage 20 Cy3 versus Quail Stage 25 Cy5, technical replicate number 1


title: Chicken20-Cy3_Chicken25-Cy5_2

description: Chicken Stage 20 Cy3 versus Chicken Stage 25 Cy5, technical replicate number 2

organism: Gallus gallus


title: Duck20-Cy5_Duck25-Cy3_1

description: Duck Stage 20 Cy5 versus Duck Stage 25 Cy3, technical replicate number 1


title: Chicken20-Cy3_Chicken25-Cy5_1

description: Chicken Stage 20 Cy3 versus Chicken Stage 25 Cy5, technical replicate number 1


title: Chicken20-Cy5_Chicken25-Cy3_1

description: Chicken Stage 20 Cy5 versus Chicken Stage 25 Cy3, technical replicate number 1


title: Duck25-Cy5_Quail25-Cy3_4

description: Duck Stage 25 Cy5 versus Quail Stage 25 Cy3, technical replicate number 4


title: Chicken20-Cy5_Chicken25-Cy3_2

description: Chicken Stage 20 Cy5 versus Chicken Stage 25 Cy3, technical replicate number 2


title: Duck25-Cy5_Quail25-Cy3_2

description: Duck Stage 25 Cy5 versus Quail Stage 25 Cy3, technical replicate number 2


title: Duck25-Cy5_Quail25-Cy3_3

description: Duck Stage 25 Cy5 versus Quail Stage 25 Cy3, technical replicate number 3


title: Duck25-Cy5_Quail25-Cy3_1

description: Duck Stage 25 Cy5 versus Quail Stage 25 Cy3, technical replicate number 1


title: Duck25-Cy3_Quail25-Cy5_4

description: Duck Stage 25 Cy3 versus Quail Stage 25 Cy5, technical replicate number 4


title: Duck20-Cy5_Quail20-Cy3_5

description: Duck Stage 20 Cy5 versus Quail Stage 20 Cy3, technical replicate number 5


title: Duck25-Cy3_Quail25-Cy5_1

description: Duck Stage 25 Cy3 versus Quail Stage 25 Cy5, technical replicate number 1


title: Duck20-Cy3_Quail20-Cy5_3

description: Duck Stage 20 Cy3 versus Quail Stage 20 Cy5, technical replicate number 3


title: Duck20-Cy5_Quail20-Cy3_4

description: Duck Stage 20 Cy5 versus Quail Stage 20 Cy3, technical replicate number 4


title: Duck25-Cy3_Quail25-Cy5_2

description: Duck Stage 25 Cy3 versus Quail Stage 25 Cy5, technical replicate number 2


title: Duck20-Cy3_Quail20-Cy5_1

description: Duck Stage 20 Cy3 versus Quail Stage 20 Cy5, technical replicate number 1


title: Duck20-Cy5_Quail20-Cy3_2

description: Duck Stage 20 Cy5 versus Quail Stage 20 Cy3, technical replicate number 2


title: Duck20-Cy5_Quail20-Cy3_3

description: Duck Stage 20 Cy5 versus Quail Stage 20 Cy3, technical replicate number 3


title: Duck20-Cy3_Quail20-Cy5_4

description: Duck Stage 20 Cy3 versus Quail Stage 20 Cy5, technical replicate number 4


title: Duck25-Cy5_Chicken25-Cy3_5

description: Duck Stage 25 Cy-5 versus Chicken Stage 25 Cy-3, technical replicate number 5


title: Duck25-Cy3_Quail25-Cy5_3

description: Duck Stage 25 Cy3 versus Quail Stage 25 Cy5, technical replicate number 3


title: Duck25-Cy5_Chicken25-Cy3_2

description: Duck Stage 25 Cy-5 versus Chicken Stage 25 Cy-3, technical replicate number 2


title: Duck25-Cy5_Chicken25-Cy3_4

description: Duck Stage 25 Cy-5 versus Chicken Stage 25 Cy-3, technical replicate number 4


title: Duck20-Cy3_Quail20-Cy5_2

description: Duck Stage 20 Cy3 versus Quail Stage 20 Cy5, technical replicate number 2


title: Duck25-Cy3_Chicken25-Cy5_3

description: Duck Stage 25 Cy-3 versus Chicken Stage 25 Cy-5, technical replicate number 3


title: Duck20-Cy5_Chicken20-Cy3_1

description: Duck Stage 20 Cy-5 versus Chicken Stage 20 Cy-3, technical replicate number 1


title: Duck20-Cy3_Chicken20-Cy5_3

description: Duck Stage 20 Cy-3 versus Chicken Stage 20 Cy-5, technical replicate number 3


title: Duck25-Cy3_Chicken25-Cy5_2

description: Duck Stage 25 Cy-3 versus Chicken Stage 25 Cy-5, technical replicate number 2


title: Duck25-Cy5_Chicken25-Cy3_3

description: Duck Stage 25 Cy-5 versus Chicken Stage 25 Cy-3, technical replicate number 3


title: Duck20-Cy3_Chicken20-Cy5_1

description: Duck Stage 20 Cy-3 versus Chicken Stage 20 Cy-5, technical replicate number 1


title: Duck20-Cy5_Chicken20-Cy3_3

description: Duck Stage 20 Cy-5 versus Chicken Stage 20 Cy-3, technical replicate number 3


title: Duck20-Cy5_Quail20-Cy3_1

description: Duck Stage 20 Cy5 versus Quail Stage 20 Cy3, technical replicate number 1


title: Duck25-Cy3_Chicken25-Cy5_1

description: Duck Stage 25 Cy-3 versus Chicken Stage 25 Cy-5, technical replicate number 1


title: Duck20-Cy3_Chicken20-Cy5_2

description: Duck Stage 20 Cy-3 versus Chicken Stage 20 Cy-5, technical replicate number 2


title: Chicken25-Cy5_Quail25-Cy3_3

description: Chicken Stage 25 Cy5 versus Quail Stage 25 Cy3, technical replicate number 3


title: Chicken25-Cy5_Quail25-Cy3_2

description: Chicken Stage 25 Cy5 versus Quail Stage 25 Cy3, technical replicate number 2


title: Duck20-Cy5_Chicken20-Cy3_2

description: Duck Stage 20 Cy-5 versus Chicken Stage 20 Cy-3, technical replicate number 2


title: Duck25-Cy5_Chicken25-Cy3_1

description: Duck Stage 25 Cy-5 versus Chicken Stage 25 Cy-3, technical replicate number 1


title: Chicken25-Cy5_Quail25-Cy3_1

description: Chicken Stage 25 Cy5 versus Quail Stage 25 Cy3, technical replicate number 1


title: Chicken25-Cy3_Quail25-Cy5_2

description: Chicken Stage 25 Cy3 versus Quail Stage 25 Cy5, technical replicate number 2


title: Chicken25-Cy3_Quail25-Cy5_3

description: Chicken Stage 25 Cy3 versus Quail Stage 25 Cy5, technical replicate number 3


title: Chicken20-Cy3_Quail20-Cy5_1

description: Chicken Stage 20 Cy3 versus Quail Stage 20 Cy5, technical replicate number 1


title: Chicken20-Cy5_Quail20-Cy3_2

description: Chicken Stage 20 Cy5 versus Quail Stage 20 Cy3, technical replicate number 2


title: Chicken20-Cy5_Quail20-Cy3_1

description: Chicken Stage 20 Cy5 versus Quail Stage 20 Cy3, technical replicate number 1


title: Chicken25-Cy3_Quail25-Cy5_1

description: Chicken Stage 25 Cy3 versus Quail Stage 25 Cy5, technical replicate number 1


title: Chicken20-Cy3_Quail20-Cy5_3

description: Chicken Stage 20 Cy3 versus Quail Stage 20 Cy5, technical replicate number 3


title: liver-HW-cornoil-19h rep3

status: Public on Nov 24 2009

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: liver, HW, COil, 19 hours

hyb_protocol: Manufacturer's protocol

scan_protocol: Manufacturer's protocol

data_processing: Array data were loaded into the R statistical environment (v2.6.1) using the affy package (v1.12.0) of the BioConductor open-source library (Gentleman et al., 2004).  The array data were pre-processed with the GCRMA algorithm (v2.10.0, (Irizarry et al., 2003)).

organism: Rattus norvegicus

source_name: liver, HW, COil, 19 hours

label_protocol: Manufacturer's protocol

growth_protocol: Three rat strains/lines harbouring wildtype AHR were selected: Sprague-Dawley (SD), Long-Evans (LE), and Line-C (LnC). Two rat strains/lines harbouring mutant AHR were selected: Han/Wistar(Kuopio) (HW) and Line-A (LnA). Four animals of each strain were obtained from the breeding colonies of the National Public Health Institute, Division of Environmental Health, Kuopio, Finland; they were fed and housed under identical conditions in this facility. All animals were males 10-12 weeks old.

extract_protocol: Total RNA was extracted using Qiagen RNeasy kits according to the manufacturer's instructions (Qiagen, Mississauga, Canada). Total RNA yield was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Liver was harvested between 8:30 and 11:00 from rats treated by gavage with corn oil vehicle for 19 hours.


title: liver-LnC-cornoil-19h rep1

description: liver, LnC, COil, 19 hours

source_name: liver, LnC, COil, 19 hours


title: liver-LnC-cornoil-19h rep4

description: liver, LnC, COil, 19 hours


title: liver-LnA-cornoil-19h rep3

description: liver, LnA, COil, 19 hours

source_name: liver, LnA, COil, 19 hours


title: Chicken20-Cy3_Quail20-Cy5_2

description: Chicken Stage 20 Cy3 versus Quail Stage 20 Cy5, technical replicate number 2


title: liver-LnA-cornoil-19h rep2

description: liver, LnA, COil, 19 hours


title: liver-LnC-cornoil-19h rep2

description: liver, LnC, COil, 19 hours


title: liver-HW-cornoil-19h rep4

description: liver, HW, COil, 19 hours


title: Chicken20-Cy5_Quail20-Cy3_3

description: Chicken Stage 20 Cy5 versus Quail Stage 20 Cy3, technical replicate number 3


title: liver-HW-cornoil-19h rep2

description: liver, HW, COil, 19 hours


title: liver-LE-cornoil-19h rep4

description: liver, LE, COil, 19 hours

source_name: liver, LE, COil, 19 hours


title: liver-HW-cornoil-19h rep1

description: liver, HW, COil, 19 hours


title: liver-LE-cornoil-19h rep3

description: liver, LE, COil, 19 hours


title: liver-LE-cornoil-19h rep2

description: liver, LE, COil, 19 hours


title: liver-LnC-cornoil-19h rep3

description: liver, LnC, COil, 19 hours


title: liver-LnA-cornoil-19h rep4

description: liver, LnA, COil, 19 hours


title: liver-LE-cornoil-19h rep1

description: liver, LE, COil, 19 hours


title: liver-SpragueDawley-control rep4

description: liver, SpragueDawley, control

source_name: liver, SpragueDawley, control

value: liver, Gender:Male


title: liver-SpragueDawley-control rep2

description: liver, SpragueDawley, control


title: liver-LnC-TCDD-19h-rep2

description: liver, LnC, TCDD, 19 hours

data_processing: Array data were loaded into the R statistical environment (v2.3.1) using the affy package (v1.10.0) of the BioConductor open-source library (Gentleman et al., 2004).  The array data were pre-processed with the GCRMA algorithm (v2.4.1, (Irizarry et al., 2003)).

source_name: liver, LnC, TCDD, 19 hours

growth_protocol: Two dioxin-sensitive rat strains/lines, L-E and LnC (which express wildtype AHR), and two dioxin-resistant rat strains/lines, H/W and LnA, (that have a deletion in the AHR transactivation domain, (Pohjanvirta et al., 1998)) were from breeding colonies of the National Public Health Institute, Division of Environmental Health, Kuopio, Finland.  All animals were males 10-12 weeks old.

treatment_protocol: Liver was harvested between 8:30 and 11:00 from rats treated by gavage with a single 100 µg/kg dose of TCDD or with corn oil vehicle for 3 or 19 h.


title: liver-SpragueDawley-control rep3

description: liver, SpragueDawley, control


title: liver-LnC-cornoil-19h-rep1

description: liver, LnC, COil, 19 hours


title: liver-LnC-cornoil-19h-rep4

description: liver, LnC, COil, 19 hours


title: liver-LnA-TCDD-19h-rep4

description: liver, LnA, TCDD, 19 hours

source_name: liver, LnA, TCDD, 19 hours


title: liver-LnC-TCDD-19h-rep3

description: liver, LnC, TCDD, 19 hours


title: liver-LnC-cornoil-19h-rep3

description: liver, LnC, COil, 19 hours


title: liver-SpragueDawley-control rep1

description: liver, SpragueDawley, control


title: liver-LnA-cornoil-19h-rep3

description: liver, LnA, COil, 19 hours


title: liver-LnA-TCDD-19h-rep2

description: liver, LnA, TCDD, 19 hours


title: liver-LnA-TCDD-19h-rep1

description: liver, LnA, TCDD, 19 hours


title: liver-LnA-cornoil-19h-rep4

description: liver, LnA, COil, 19 hours


title: liver-LnC-TCDD-19h-rep1

description: liver, LnC, TCDD, 19 hours


title: liver-LnC-TCDD-19h-rep4

description: liver, LnC, TCDD, 19 hours


title: liver-LE-TCDD-19h-rep4

description: liver, LE, TCDD, 19 hours

source_name: liver, LE, TCDD, 19 hours


title: liver-LnA-cornoil-19h-rep1

description: liver, LnA, COil, 19 hours


title: liver-LnA-TCDD-19h-rep3

description: liver, LnA, TCDD, 19 hours


title: liver-LnC-cornoil-19h-rep2

description: liver, LnC, COil, 19 hours


title: liver-LE-TCDD-19h-rep2

description: liver, LE, TCDD, 19 hours


title: liver-HW-TCDD-19h-rep3

description: liver, HW, TCDD, 19 hours

source_name: liver, HW, TCDD, 19 hours


title: liver-LnA-cornoil-19h-rep2

description: liver, LnA, COil, 19 hours


title: liver-HW-TCDD-19h-rep2

description: liver, HW, TCDD, 19 hours


title: liver-HW-cornoil-19h-rep4

description: liver, HW, COil, 19 hours


title: liver-HW-TCDD-19h-rep4

description: liver, HW, TCDD, 19 hours


title: liver-HW-cornoil-19h-rep3

description: liver, HW, COil, 19 hours


title: liver-LE-TCDD-19h-rep3

description: liver, LE, TCDD, 19 hours


title: liver-HW-cornoil-19h-rep1

description: liver, HW, COil, 19 hours


title: liver-LE-cornoil-19h-rep4

description: liver, LE, COil, 19 hours


title: liver-LE-cornoil-19h-rep2

description: liver, LE, COil, 19 hours


title: liver-LE-TCDD-19h-rep1

description: liver, LE, TCDD, 19 hours


title: liver-LE-TCDD-3h-rep3

description: liver, LE, TCDD, 3 hours

source_name: liver, LE, TCDD, 3 hours


title: liver-LE-cornoil-19h-rep1

description: liver, LE, COil, 19 hours


title: liver-HW-cornoil-19h-rep2

description: liver, HW, COil, 19 hours


title: liver-LE-cornoil-19h-rep3

description: liver, LE, COil, 19 hours


title: liver-LE-TCDD-3h-rep4

description: liver, LE, TCDD, 3 hours


title: liver-LE-TCDD-3h-rep2

description: liver, LE, TCDD, 3 hours


title: liver-HW-TCDD-3h-rep2

description: liver, HW, TCDD, 3 hours

source_name: liver, HW, TCDD, 3 hours


title: liver-HW-TCDD-3h-rep4

description: liver, HW, TCDD, 3 hours


title: liver-HW-TCDD-19h-rep1

description: liver, HW, TCDD, 19 hours


title: liver-HW-TCDD-3h-rep3

description: liver, HW, TCDD, 3 hours


title: liver-LE-TCDD-3h-rep1

description: liver, LE, TCDD, 3 hours


title: 13832717 - Ctrl light 2 vs NadC 4.11 light 2

status: Public on Nov 01 2009

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: Establish which transcripts are affected by changes in NAD concentration, and whether this depends on light/dark.

hyb_protocol: NadC 4.11 light 2 Cy5 / Ctrl light 2 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,460V,laser power 35%, Cy5:635nm,pmt voltage 460V,laser power 30%

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

organism: Arabidopsis thaliana

source_name: NadC 4.11, light

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 - light intensity: 100 µmol/m2/s temperature: 20/18°C day/night media : soil with nutritive solution twice a week humidité : 65%

extract_protocol: NadC 4.11 light 2:5.09ug.

treatment_protocol: Name:quinolinate, light - compound based treatment - light,quinolinate:quantity 0.1mM time 24hour . 16h light period

tag: condition

value: light

value: quinolinate

tag: ecotype

value: Columbia

tag: age

value: 5 weeks

source_name: Ctrl, light

extract_protocol: Ctrl light 2:11.38ug.

treatment_protocol: Name:MOPS, light - compound based treatment - light,mops:quantity 50mM time 24hour . 24h with 16h light period


title: 13832711 - Ctrl dark 2 vs NadC 15.3 dark 2

hyb_protocol: NadC 15.3 dark 2 Cy5 / Ctrl dark 2 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.

source_name: NadC 15.3, dark

treatment_protocol: Name:quinolinate, dark - compound based treatment - light,quinolinate:quantity 0.1mM time 48hour . 48h in the dark

value: dark

source_name: Ctrl, dark

extract_protocol: Ctrl dark 2:10.4ug.

treatment_protocol: Name:MOPS, dark - compound based treatment - compound addition,mops:quantity 50mM time 48hour . 48h in the dark


title: 13832713 - Ctrl light 1 vs NadC 4.11 light 1

hyb_protocol: NadC 4.11 light 1 Cy5 / Ctrl light 1 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.

extract_protocol: NadC 4.11 light 1:6.57ug.

extract_protocol: Ctrl light 1:7.88ug.


title: 13832714 - NadC 4.11 light 1 vs Ctrl light 1

hyb_protocol: Ctrl light 1 Cy5 / NadC 4.11 light 1 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: 13832722 - NadC 15.3 light 2 vs Ctrl light 2

hyb_protocol: Ctrl light 2 Cy5 / NadC 15.3 light 2 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.

source_name: NadC 15.3, light


title: 13832712 - NadC 15.3 dark 2 vs Ctrl dark 2

hyb_protocol: Ctrl dark 2 Cy5 / NadC 15.3 dark 2 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: 13832721 - Ctrl light 2 vs NadC 15.3 light 2

hyb_protocol: NadC 15.3 light 2 Cy5 / Ctrl light 2 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: 13832715 - Ctrl light 1 vs NadC 15.3 light 1

hyb_protocol: NadC 15.3 light 1 Cy5 / Ctrl light 1 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.

extract_protocol: NadC 15.3 light 1:8.93ug.


title: 13832716 - NadC 15.3 light 1 vs Ctrl light 1

hyb_protocol: Ctrl light 1 Cy5 / NadC 15.3 light 1 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: 13832706 - NadC 4.11 dark 1 vs Ctrl dark 1

hyb_protocol: Ctrl dark 1 Cy5 / NadC 4.11 dark 1 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.

extract_protocol: Ctrl dark 1:6.96ug.

source_name: NadC 4.11, dark


title: liver-HW-TCDD-3h-rep1

description: liver, HW, TCDD, 3 hours


title: 13832709 - NadC 4.11 dark 2 vs Ctrl dark 2

hyb_protocol: Ctrl dark 2 Cy5 / NadC 4.11 dark 2 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: 13832708 - NadC 15.3 dark 1 vs Ctrl dark 1

hyb_protocol: Ctrl dark 1 Cy5 / NadC 15.3 dark 1 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: 13832707 - Ctrl dark 1 vs NadC 15.3 dark 1

hyb_protocol: NadC 15.3 dark 1 Cy5 / Ctrl dark 1 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: 13832704 - Ctrl dark 1 vs NadC 4.11 dark 1

hyb_protocol: NadC 4.11 dark 1 Cy5 / Ctrl dark 1 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: 309360: control fibroblast L7 vs fibroblast PMA L1

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description:
control fibroblast L7 vs fibroblast PMA L1
Date:2007/04/05

hyb_protocol: Agilent : 750.0 ng at 48 degree_C during 18 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : printtiploess, Background norm. : none, Software used : limmagui --> VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: control fibroblast L7

label_protocol: Invitrogen - Ulysis

extract_protocol: MirVana

value: control fibroblast

value: Control fibroblast

tag: Tissue

value: Normal human lung fibroblasts

value: CCL-153 (normal human lung fibroblasts)

source_name: fibroblast PMA L1

tag: Labeling_reference:fibroblast PMA L1

value: fibroblast PMA


title: 309362: fibroblast IL-1beta L2 vs control fibroblast L4

description:
fibroblast IL-1beta L2 vs control fibroblast L4
Date:2007/04/05

hyb_protocol: Agilent : 700.0 ng at 48 degree_C during 18 hours

source_name: fibroblast IL-1beta L2

value: fibroblast IL-1beta

value: 10ng/ml IL-1beta treated fibroblasts (24 hours)

source_name: control fibroblast L4


title: 309365: fibroblast PMA L2 vs control fibroblast L8

description:
fibroblast PMA L2 vs control fibroblast L8
Date:2007/04/05

source_name: fibroblast PMA L2

tag: Labeling_reference:fibroblast PMA L2

source_name: control fibroblast L8


title: 309357: fibroblast TNFalpha L2 vs control fibroblast L10

description:
fibroblast TNFalpha L2 vs control fibroblast L10
Date:2007/04/05

source_name: fibroblast TNFalpha L2

value: fibroblast TNFalpha

value: 10ng/ml TNFalpha treated fibroblasts (24 hours)

source_name: control fibroblast L10


title: 040879

description:
A549 L2 vs control fibroblast L6
Date:2007/04/05

tag: Labeling_reference:A549 L2

value: Human lung adenocarcinoma cell line

value: Human adenocarcinoma of the lung

source_name: control fibroblast L6


title: 309356: control fibroblast L9 vs fibroblast TNFalpha L1

description:
control fibroblast L9 vs fibroblast TNFalpha L1
Date:2007/04/05

source_name: control fibroblast L9

source_name: fibroblast TNFalpha L1


title: 040878

description:
control fibroblast L5 vs A549 L1
Date:2007/04/05

source_name: control fibroblast L5

tag: Labeling_reference:A549 L1


title: 309285: fibroblast TGFbeta L2 vs control fibroblast L2

description:
fibroblast TGFbeta L2 vs control fibroblast L2
Date:2007/04/05

source_name: fibroblast TGFbeta L2

value: fibroblast TGFbeta

value: 10ng/ml TGFbeta treated fibroblasts (24 hours)

source_name: control fibroblast L2


title: 309364: control fibroblast L1 vs fibroblast TGFbeta L1

description:
control fibroblast L1 vs fibroblast TGFbeta L1
Date:2007/04/05

source_name: control fibroblast L1

source_name: fibroblast TGFbeta L1


title: 309363: control fibroblast L3 vs fibroblast IL-1beta L1

description:
control fibroblast L3 vs fibroblast IL-1beta L1
Date:2007/04/05

source_name: control fibroblast L3

extract_protocol: Other

source_name: fibroblast IL-1beta L1