title: RP 1-60-3

city: Beijing

first: Hua

last: Fu

address: 6#, Rongjing East Street

institute: Institute of pathogen biology

hyb_protocol: he pairs of the labeled cDNA samples were hybridized to the DNA microarrays following the protocol published at http://www.ifr.ac.uk/safety/micro arrays/protocols.html#Hybridisations.

scan_protocol: The slides were scanned by using a GenePix 4100A scanner.

data_processing: Fluorescent spots and local background intensities were quantified using GenePix Pro 6.0 software (Axon). Signal intensities were corrected by subtracting the local background value. The data set was filtered so that spots designated as “not found” flagged features; “bad” and “empty” features were excluded from further analysis. Moreover, spots either with signal-to-noise ratio below the detection limit of 3 or containing less than 55% of pixels, which were two standard deviations above background in both channels, were discarded from the data set. Lowess normalizations were performed with the fluorescent signal ratios (Cy5/Cy3) by using MIDAS software (http://www.tigr.org/software/tm4), with a 0.33 smooth parameter.

organism: Shigella flexneri

source_name: shigella flexneri strain 301 plus refampin

label_protocol: According to the manufacturer’s instructions, the cDNA was labeled with incorporation of fluorescent dyes (Amersham). Cy5-dCTP was used.

extract_protocol: Total RNA was extracted by using SV RNA Isolation System (Promega). Reverse transcription of RNA from the test sample treated with 1Xmic refampin for 60 min was performed with Superscript II system (Invitrogen) to prepare cDNA.

value: 1Xmic refampin for 60 min

source_name: shigella flexneri strain 301

label_protocol: According to the manufacturer’s instructions, the cDNA was labeled with incorporation of fluorescent dyes (Amersham). Cy3-dCTP was used.

extract_protocol: Total RNA was extracted by using SV RNA Isolation System (Promega). Reverse transcription of RNA from the control sample for 60 min was performed with Superscript II system (Invitrogen) to prepare cDNA.


title: SSD patient 22 after treatment with Venlafaxine

status: Public on Mar 21 2012

type: RNA

city: Shanghai

first: Zezhi

last: Li

address: 600 South Wan Ping Road Shanghai 200030, China

department: Division of Mood Disorders

country: China

institute: Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China

description:
CB2007224-D22B.CEL
MDD patient 22 after treatment with Venlafaxine

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by RMA method, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US). The values were log2 transformed.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Venous peripheral blood from fasting patients and healthy controls were collected during 7am to 9am.Peripheral blood lymphocytes were separated by Ficoll gradient centrifugation using Ficoll-PlaqueTM Plus (GE, Sweden) according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from lymphocytes using Trizol reagent (Invitrogen) according to the manufacturer's protocol. RNA concentrations were determined by Nanodrop ND-1000 (Nanodrop Technologies, Wilmington, DE). RNA quality was assessed on an Agilent 2100 Bioanalyzer

tag: tissue

value: peripheral blood

tag: cell type

value: lymphocytes

tag: disease status

value: SSD patient

tag: treatment

value: after treatment with Venlafaxine


title: SSD patient 22 before treatment

description:
CB2007224-D22A.CEL
MDD patient 22 before treatment with venlafaxine

source_name: SSD patient 22 before treatment

value: before treatment


title: heart_non diabetic_failure_sample_25

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

description: MALE, 59 years

hyb_protocol: Following fragmentation, 30 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST array. 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: Summarized signal intensities were generated in BRB ArrayTools using justRMA

source_name: LEFT VENTRICLE, NON DIABETIC, HEART FAILURE

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA Ambion WT Expression Kit (Life Technologies Co.)

extract_protocol: Trizol (Invitrogen) extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy mini kit following standard RNA cleanup protocol

value: left ventricle cardiac biopsy taken from the vital, non-infarcted zone

tag: gender

value: MALE

tag: age

value: 59 years

tag: disease state

value: NON DIABETIC, HEART FAILURE


title: Control Diet Supplemented  Mouse 6

city: Seoul

first: Jong-Doo

last: Lee

address: 250 seonsan-ro seodaemum-gu

country: South Korea

institute: Yonsei University

description: control replicate 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Raw data were extracted using the Illumina GenomeStudio. Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected gene signal value was divided by Actb signal value.
AVG signal divided by Actb AVG signal

organism: Mus musculus

source_name: C57BL/6 male mouse

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Five- week- old male C57BL6 mice were randomly divided into two groups and fed control diet (control group, LabDiet, Brentwood, MO, USA) or moderate restriced carbohydrate diet formula (MCD, Treat group) in a specific pathogen free zone. All procedures were approved by the institutional animal use and care committee.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Following a preliminary feeding of each diet formula for one week, 1 × 106 B16F10 cells (suspended with 100 μl of PBS) were subcutaneously injected into the back of the mice. After 2 weeks of diet supplementation, all mice were sacrificed.

tag: strain

value: 5 weeks old

value: male

value: B16F10 mouse melanoma cells

tag: diet

value: control diet


title: RP 1-60-2


title: heart_diabetic_failure_sample_42

description: MALE, 63 years

source_name: LEFT VENTRICLE, DIABETIC, HEART FAILURE

value: 63 years

value: DIABETIC, HEART FAILURE


title: Control Diet Supplemented  Mouse 5

description: control replicate 5


title: RP 1-60-1


title: SSD patient 21 after treatment with Venlafaxine

description:
CB2007224-D21B.CEL
MDD patient 21 after treatment with Venlafaxine


description:
CB2007224-D1B.CEL
MDD patient 1 after treatment with Venlafaxine

value: MDD patient


title: SSD patient 21 before treatment

description:
CB2007224-D21A.CEL
MDD patient 21 before treatment with venlafaxine

source_name: SSD patient 21 before treatment


title: RP 1-30-3

extract_protocol: Total RNA was extracted by using SV RNA Isolation System (Promega). Reverse transcription of RNA from the test sample treated with 1Xmic refampin for 30 min was performed with Superscript II system (Invitrogen) to prepare cDNA.

value: 1Xmic refampin for 30 min

extract_protocol: Total RNA was extracted by using SV RNA Isolation System (Promega). Reverse transcription of RNA from the control sample for 30 min was performed with Superscript II system (Invitrogen) to prepare cDNA.


title: Control Diet Supplemented  Mouse 1

description: control replicate 1


title: Lung adenocarcinoma 05L19_T (expression)

city: Los Angeles

first: Ite

last: Laird-Offringa

state: CA

address: 1441 Eastlake Avenue, Suite 6420

department: Biochemistry

country: USA

institute: University of Southern California

hyb_protocol: Standard illumina protocol performed at UT Southwestern Genomics Core

data_processing: Data was processed by log2-transformation and Robust Spline Normalization (RSN) using the lumi package in R (Du et al 2008).

source_name: Lung adenocarcinoma

extract_protocol: RNA was obtained by Trizol extraction from microdissected alternate sections of frozen tissue

tag: type

value: Lung adenocarcinoma

tag: batch

value: Batch 2

tag: sample id

tag: tissue source

value: nci-edrn

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: C

tag: bisulfite alu

value: Lung tumor

value: Female

tag: ethnicity

value: White

tag: pack years

tag: smoking status

value: Current

tag: Stage

value: Stage IV

tag: recurrence

value: Yes

tag: kras mutation status

value: WT

tag: egfr mutation status

tag: lkb1 mutation status

tag: kras mutation type

tag: subject


title: heart_diabetic_failure_sample_34

description: MALE, 65 years

tag: tissue

value: left ventricle cardiac biopsy taken from the vital, non-infarcted zone

tag: gender

value: MALE

tag: age

value: 65 years

tag: disease state


title: heart_diabetic_failure_sample_31

description: MALE, 61 years

value: 61 years

value: DIABETIC, HEART FAILURE


title: Control Diet Supplemented  Mouse 2

description: control replicate 2

tag: strain

value: 5 weeks old

value: male

value: B16F10 mouse melanoma cells

tag: diet

value: control diet


description:
CB2007224-D19B.CEL
MDD patient 19 after treatment with Venlafaxine

value: peripheral blood

tag: cell type

value: lymphocytes

tag: disease status

value: MDD patient

tag: treatment

value: after treatment with Venlafaxine


title: heart_diabetic_failure_sample_29

description: FEMALE, 72 years

value: FEMALE

value: 72 years


title: MDD patient 19 before treatment

description:
CB2007224-D19A.CEL
MDD patient 19 before treatment with venlafaxine

source_name: MDD patient 19 before treatment

value: before treatment


title: RP 1-30-2

value: 1Xmic refampin for 30 min


title: RP 1-30-1


title: heart_diabetic_failure_sample_27

description: MALE, 60 years

value: left ventricle cardiac biopsy taken from the vital, non-infarcted zone

value: 60 years


title: heart_diabetic_failure_sample_6

description: MALE, 65 years

value: MALE

value: 65 years


description:
CB2007224-D14B.CEL
MDD patient 14 after treatment with Venlafaxine


title: RP 1-10-2

extract_protocol: Total RNA was extracted by using SV RNA Isolation System (Promega). Reverse transcription of RNA from the test sample treated with 1Xmic refampin for 10 min was performed with Superscript II system (Invitrogen) to prepare cDNA.

value: 1Xmic refampin for 10 min

extract_protocol: Total RNA was extracted by using SV RNA Isolation System (Promega). Reverse transcription of RNA from the control sample for 10 min was performed with Superscript II system (Invitrogen) to prepare cDNA.


title: RP 1-10-1


title: RP 1-10-3


description:
CB2007224-D13B.CEL
MDD patient 13 after treatment with Venlafaxine


title: RP 0.5-60-1

extract_protocol: Total RNA was extracted by using SV RNA Isolation System (Promega). Reverse transcription of RNA from the test sample treated with 0.5Xmic refampin for 60 min was performed with Superscript II system (Invitrogen) to prepare cDNA.

value: 0.5Xmic refampin for 60 min


title: heart_control_sample_11

description: FEMALE, 44 years

source_name: LEFT VENTRICLE, CONTROL

value: 44 years

value: CONTROL


title: RP 0.5-60-3


title: Control Diet Supplemented  Mouse 3

description: control replicate 3

value: 5 weeks old

value: male

value: B16F10 mouse melanoma cells

value: control diet


title: heart_diabetic_failure_sample_5

description: MALE,70 years

value: 70 years

value: DIABETIC, HEART FAILURE


title: SSD patient 11 after treatment with Venlafaxine

description:
CB2007224-D11B.CEL
MDD patient 11 after treatment with Venlafaxine

value: peripheral blood

value: lymphocytes

value: SSD patient

value: after treatment with Venlafaxine


title: RP 0.5-30-2

extract_protocol: Total RNA was extracted by using SV RNA Isolation System (Promega). Reverse transcription of RNA from the test sample treated with 0.5Xmic refampin for 30 min was performed with Superscript II system (Invitrogen) to prepare cDNA.

value: 0.5Xmic refampin for 30 min


title: heart_control_sample_10

description: MALE, 49 years

value: left ventricle cardiac biopsy taken from the vital, non-infarcted zone

value: MALE

value: 49 years


title: SSD patient 10 before treatment

description:
CB2007224-D10A.CEL
MDD patient 10 before treatment with venlafaxine

source_name: SSD patient 10 before treatment

value: before treatment


title: MDD patient 13 before treatment

description:
CB2007224-D13A.CEL
MDD patient 13 before treatment with venlafaxine

source_name: MDD patient 13 before treatment

value: MDD patient


title: RP 0.5-60-2

value: 0.5Xmic refampin for 60 min


title: SSD patient 11 before treatment

description:
CB2007224-D11A.CEL
MDD patient 11 before treatment with venlafaxine

source_name: SSD patient 11 before treatment


title: heart_control_sample_3

description: MALE, 49 years

value: CONTROL


title: health control 8

description:
CB2007224-C8.CEL
health control 8

source_name: health control 8

value: healthy control


title: RP 0.5-30-3


title: RP 0.5-30-1


title: health control 6

description:
CB2007224-C6.CEL
health control 6

source_name: health control 6


title: RP 0.5-10-2

extract_protocol: Total RNA was extracted by using SV RNA Isolation System (Promega). Reverse transcription of RNA from the test sample treated with 0.5Xmic refampin for 10 min was performed with Superscript II system (Invitrogen) to prepare cDNA.

value: 0.5Xmic refampin for 10 min


title: RP 0.5-10-3


title: health control 7

description:
CB2007224-C7.CEL
health control 7

source_name: health control 7


title: RP 0.5-10-1


title: RX 1-60-3

source_name: shigella flexneri strain 301 plus rifaximin

extract_protocol: Total RNA was extracted by using SV RNA Isolation System (Promega). Reverse transcription of RNA from the test sample treated with 1Xmic rifaximin for 60 min was performed with Superscript II system (Invitrogen) to prepare cDNA.

value: 1Xmic rifaximin for 60 min


title: heart_control_sample_9

description: FEMALE, 49 years

value: FEMALE


title: health control 3

description:
CB2007224-C3.CEL
health control 3

source_name: health control 3


title: health control 2

description:
CB2007224-C2.CEL
health control 2

source_name: health control 2


title: health control 1

description:
CB2007224-C1.CEL
health control 1

source_name: health control 1


title: health control 5

description:
CB2007224-C5.CEL
health control 5

source_name: health control 5


title: health control 4

description:
CB2007224-C4.CEL
health control 4

source_name: health control 4


title: 13561261 - dcl2/dcl3/dcl4 Mock vs Col0 Mock

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Which genes (including miRNA genes) are differentially regulated by CaMV? Requirement of 21nt, 22nt, 24nt virus-derived siRNAs in this differential gene regulation?

hyb_protocol: Col0 Mock Cy5 / dcl2/dcl3/dcl4 Mock Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 520V,laser power 100%

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: Col0 Mock

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

growth_protocol: rosette - Media=Soil  Temperature=22°C Light=short day (8h)  After treatment : Media=Soil Temperature=24°C  Light=long day (12h)

treatment_protocol: Name:Mock Treatment - control buffer - control buffer,water:time 21day . Infection of 4/5 week old plant using CaMV SAP (mecanical infection of virions upon 2 leaves). Mock inoculation using H2O as control.

tag: ecotype

value: columbia

tag: harvest date

value: mock treatment

tag: genotype/variation

value: wild type

source_name: dcl2/dcl3/dcl4 Mock

value: mutant (dcl2/dcl3/dcl4)


title: RX 1-60-1

source_name: shigella flexneri strain 301


title: 13485535 - dcl2/dcl4 CaMV vs Col0 CaMV

hyb_protocol: Col0 CaMV Cy5 / dcl2/dcl4 CaMV Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

source_name: Col0 CaMV

treatment_protocol: Name:CaMV Infection - pathogen - pathogen infection,camv:time 21day . Infection of 4/5 week old plant using CaMV SAP (mecanical infection of virions upon 2 leaves). Mock inoculation using H2O as control.

value: CaMV Infection

source_name: dcl2/dcl4 CaMV

value: mutant (dcl2/dcl4)


title: 13561258 - Col0 Mock vs dcl2/dcl3/dcl4 Mock

hyb_protocol: dcl2/dcl3/dcl4 Mock Cy5 / Col0 Mock Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13415182 - Col0 CaMV vs dcl3/dcl4 CaMV

hyb_protocol: dcl3/dcl4 CaMV Cy5 / Col0 CaMV Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: dcl3/dcl4 CaMV

value: mutant (dcl3/dcl4)


title: 13415191 - Col0 CaMV vs dcl2/dcl4 CaMV

hyb_protocol: dcl2/dcl4 CaMV Cy5 / Col0 CaMV Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13485521 - dcl2/dcl3/dcl4 CaMV vs Col0 CaMV

hyb_protocol: Col0 CaMV Cy5 / dcl2/dcl3/dcl4 CaMV Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: dcl2/dcl3/dcl4 CaMV


title: 13485525 - dcl2/dcl3/dcl4 CaMV vs dcl2/dcl3/dcl4 Mock

hyb_protocol: dcl2/dcl3/dcl4 Mock Cy5 / dcl2/dcl3/dcl4 CaMV Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13485534 - dcl3/dcl4 CaMV vs Col0 CaMV

hyb_protocol: Col0 CaMV Cy5 / dcl3/dcl4 CaMV Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MDD patient 5 before treatment

description:
CB2007224-D5A.CEL
MDD patient 5 before treatment with venlafaxine

source_name: MDD patient 5 before treatment

value: peripheral blood

value: lymphocytes


title: 13485522 - dcl2/dcl3/dcl4 Mock vs dcl2/dcl3/dcl4 CaMV

hyb_protocol: dcl2/dcl3/dcl4 CaMV Cy5 / dcl2/dcl3/dcl4 Mock Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: SSD patient 15 before treatment

description:
CB2007224-D15A.CEL
MDD patient 15 before treatment with venlafaxine

source_name: SSD patient 15 before treatment

value: SSD patient

value: before treatment


title: 13485519 - Col0 CaMV vs dcl2/dcl3/dcl4 CaMV

hyb_protocol: dcl2/dcl3/dcl4 CaMV Cy5 / Col0 CaMV Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: RX 1-60-2


title: SSD patient 29 after treatment with Venlafaxine

description:
CB2007224-D29-2.CEL
MDD patient 29 after treatment with Venlafaxine

value: after treatment with Venlafaxine


title: RX 1-30-3

extract_protocol: Total RNA was extracted by using SV RNA Isolation System (Promega). Reverse transcription of RNA from the test sample treated with 1Xmic rifaximin for 30 min was performed with Superscript II system (Invitrogen) to prepare cDNA.

value: 1Xmic rifaximin for 30 min


title: MDD patient 2 before treatment

description:
CB2007224-D2A.CEL
MDD patient 2 before treatment with venlafaxine

source_name: MDD patient 2 before treatment

value: MDD patient


title: RX 1-30-2


title: RX 1-30-1

source_name: RX 1-30-1 test


title: RX 1-10-3

source_name: shigella flexneri strain 301 plus rifaximin

extract_protocol: Total RNA was extracted by using SV RNA Isolation System (Promega). Reverse transcription of RNA from the test sample treated with 1Xmic rifaximin for 10 min was performed with Superscript II system (Invitrogen) to prepare cDNA.

value: 1Xmic rifaximin for 10 min


title: 13420241 - Col0 CaMV vs Col0 Mock

hyb_protocol: Col0 Mock Cy5 / Col0 CaMV Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13485518 - dcl2/dcl3 CaMV vs Col0 CaMV

hyb_protocol: Col0 CaMV Cy5 / dcl2/dcl3 CaMV Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: dcl2/dcl3 CaMV

value: mutant (dcl2/dcl3)


title: RX 1-10-2

hyb_protocol: he pairs of the labeled cDNA samples were hybridized to the DNA microarrays following the protocol published at http://www.ifr.ac.uk/safety/micro arrays/protocols.html#Hybridisations.


title: RX 1-10-1


title: RX 0.5-60-3

extract_protocol: Total RNA was extracted by using SV RNA Isolation System (Promega). Reverse transcription of RNA from the test sample treated with 0.5Xmic rifaximin for 60 min was performed with Superscript II system (Invitrogen) to prepare cDNA.

value: 0.5Xmic rifaximin for 60 min


title: MDD patient 4 before treatment

description:
CB2007224-D4A.CEL
MDD patient 4 before treatment with venlafaxine

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

source_name: MDD patient 4 before treatment


title: 13485517 - Col0 CaMV vs dcl2/dcl3 CaMV

hyb_protocol: dcl2/dcl3 CaMV Cy5 / Col0 CaMV Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: columbia


title: Control Diet Supplemented  Mouse 3

type: genomic

description: Xenografted Melanoma

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

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

source_name: Control Diet Supplemented  Mouse 3

label_protocol: The enriched DNA and input DNA were amplified with WGA2 kit and then labeled using Bioprime kit as following manufacturer's instructions

growth_protocol: Five- week- old male C57BL6 mice were randomly divided into two groups (n=3/group) and fed control diet (control group, LabDiet, Brentwood, MO, USA) or moderate restriced carbohydrate diet formula (MCD, Treat group) in a specific pathogen free zone. All procedures were approved by the institutional animal use and care committee.

extract_protocol: Tumor tissue was excised for Chip-on-chip microarray. Chromatin immunoprecipitation was performed using the EpiQuik Tissue Chromatin Immunoprecipitation Kit from Epignetek (USA) (Cat# P-2003) as per manufacturer's instructions. Antibody used: Diagnode, anti-H3K4me3 polyclonal antibody, Catalogue No; PAB-003-050, Lot # A3152-003P.

value: B16F10 mouse melanoma cells

value: male

source_name: gDNA from pooled whole control diet supplemented  Mouse

tag: reference


title: 14249207 - Col0 OCS 3 vs Col0 3

city: Evry

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

description: We have tools to estimate this modification for the bacterial part. On the other hand, concerning the plant part, we know plants produce opines compounds but we dont know if this expression can modify the transcriptional state of the plant.

hyb_protocol: Col0 3 Cy5 / Col0 OCS 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

source_name: Col0 3

growth_protocol: whole plant - Media : nutritive solution (soluplant N/P/K 18/6/26)  hygrometry : 60%  Temperature : 24°C  Light : 200µmole photon.m.s-1 (8h day / 16h night)

extract_protocol: Col0 3:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

value: Columbia

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

source_name: Col0 OCS 3

extract_protocol: Col0 OCS 3:10ug. (Qiagen_RNeasy.pdf)


title: RX 0.5-60-1

extract_protocol: Total RNA was extracted by using SV RNA Isolation System (Promega). Reverse transcription of RNA from the control sample for 60 min was performed with Superscript II system (Invitrogen) to prepare cDNA.


title: MDD patient 1 before treatment

description:
CB2007224-D1A.CEL
MDD patient 1 before treatment with venlafaxine

source_name: MDD patient 1 before treatment

extract_protocol: Total RNA was extracted from lymphocytes using Trizol reagent (Invitrogen) according to the manufacturer's protocol. RNA concentrations were determined by Nanodrop ND-1000 (Nanodrop Technologies, Wilmington, DE). RNA quality was assessed on an Agilent 2100 Bioanalyzer


title: heart_non diabetic_failure_sample_2

description: MALE, 78 years

hyb_protocol: Following fragmentation, 30 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

source_name: LEFT VENTRICLE, NON DIABETIC, HEART FAILURE

extract_protocol: Trizol (Invitrogen) extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy mini kit following standard RNA cleanup protocol

value: left ventricle cardiac biopsy taken from the vital, non-infarcted zone

value: MALE

value: 78 years

value: NON DIABETIC, HEART FAILURE


title: RX 0.5-60-2

source_name: shigella flexneri strain 301


title: 14249204 - Col0 3 vs Col0 MAS 3

hyb_protocol: Col0 MAS 3 Cy5 / Col0 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 MAS 3

extract_protocol: Col0 MAS 3:10ug. (Qiagen_RNeasy.pdf)


title: 13420239 - Col0 Mock vs Col0 CaMV

hyb_protocol: Col0 CaMV Cy5 / Col0 Mock Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 CaMV

value: CaMV Infection

value: wild type

source_name: Col0 Mock

value: mock treatment


title: 14249205 - Col0 MAS 3 vs Col0 3

hyb_protocol: Col0 3 Cy5 / Col0 MAS 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14249206 - Col0 3 vs Col0 OCS 3

hyb_protocol: Col0 OCS 3 Cy5 / Col0 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14249203 - Col0 OCS 2 vs Col0 2

hyb_protocol: Col0 2 Cy5 / Col0 OCS 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 2

extract_protocol: Col0 2:10ug. (Qiagen_RNeasy.pdf)

source_name: Col0 OCS 2

extract_protocol: Col0 OCS 2:10ug. (Qiagen_RNeasy.pdf)


title: DAC Treated Kasumi CD34+ [mRNA profiling]

city: Ghent

first: Leander

last: Van Neste

address: Coupure Links 653

department: Molecular Biotechnology

country: Belgium

institute: Ghent University

description: Characterization of gene expression changes after treatment with the DNA methylation inhibitor DAC

hyb_protocol: Samples were amplified and labeled using Quick Amp Labeling Kit (Cat# 5190-0447, Agilent Technologies), Full Spectrum Primers (Cat# RA300A-2, System Bioscience), Cynine-3-CTP and Cynine-5-CTP (Perkin Elmer), and hybridized using Gene Expression Hybridization Kit by following manufacturer's protocol (G4140-90050, Agilent Technologies)

scan_protocol: Microarrays were scanned with Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for gene expression microarrays with 100% PMT and 5 micrometer resolutions. Data were extracted using Feature Extraction Software v9.5.3.1 (Agilent Technologies) and protocol for gene expression microarrays.

data_processing: Log ratio of red signal to green signal was calculated after loess normalization as implemented in the Limma package from Bioconductor

source_name: Mock treated Kasumi-1 CD34+ cells

label_protocol: Agilent low RNA input linear amplification kit

growth_protocol: McCoy's 5A medium with 10% BCS and 1x PBS

extract_protocol: TriZol extraction followed by RNeasy kit (Qiagen) clean-up with on-column DNase treatment

treatment_protocol: 10nM DAC for 72 hours

value: 1XPBS for 72 hours

value: Leukemia Cell Line

tag: cell line

value: Kasumi CD34+

source_name: DAC treated Kasumi-1 CD34+ cells

value: 10nM DAC


title: MDD patient 3 before treatment

description:
CB2007224-D3A.CEL
MDD patient 3 before treatment with venlafaxine

source_name: MDD patient 3 before treatment

value: peripheral blood

value: lymphocytes

value: MDD patient

value: before treatment


title: RX 0.5-30-2

source_name: shigella flexneri strain 301 plus rifaximin

extract_protocol: Total RNA was extracted by using SV RNA Isolation System (Promega). Reverse transcription of RNA from the test sample treated with 0.5Xmic rifaximin for 30 min was performed with Superscript II system (Invitrogen) to prepare cDNA.

value: 0.5Xmic rifaximin for 30 min

extract_protocol: Total RNA was extracted by using SV RNA Isolation System (Promega). Reverse transcription of RNA from the control sample for 30 min was performed with Superscript II system (Invitrogen) to prepare cDNA.


title: RX 0.5-30-1


title: 14249202 - Col0 2 vs Col0 OCS 2

hyb_protocol: Col0 OCS 2 Cy5 / Col0 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Columbia


title: DAC Treated Kasumi [mRNA profiling]

source_name: Mock treated Kasumi-1 cell line

value: Kasumi

source_name: DAC treated Kasumi-1 cell line


title: heart_control_sample_13

description: FEMALE, 51 years

source_name: LEFT VENTRICLE, CONTROL

value: left ventricle cardiac biopsy taken from the vital, non-infarcted zone

value: FEMALE

value: 51 years

value: CONTROL


title: DAC Treated Kasumi CD34- [mRNA profiling]

source_name: Mock treated Kasumi-1 CD34- cells

value: Kasumi CD34-

source_name: DAC treated Kasumi-1 CD34- cells


title: RX 0.5-30-3


title: RX 0.5-10-3

extract_protocol: Total RNA was extracted by using SV RNA Isolation System (Promega). Reverse transcription of RNA from the test sample treated with 0.5Xmic rifaximin for 10 min was performed with Superscript II system (Invitrogen) to prepare cDNA.

value: 0.5Xmic rifaximin for 10 min

extract_protocol: Total RNA was extracted by using SV RNA Isolation System (Promega). Reverse transcription of RNA from the control sample for 10 min was performed with Superscript II system (Invitrogen) to prepare cDNA.


title: DAC Treated 104 Day 3 [mRNA profiling]

source_name: Mock treated primary leukemia 104 at day 3

value: 1XPBS for 72 hours

value: Breast Cancer

source_name: DAC treated primary leukemia 104 at day 3

tag: time

value: day 3


title: RX 0.5-10-1

source_name: shigella flexneri strain 301


title: RX 0.5-10-2


title: 14249197 - Col0 2 vs Col0 MAS 2

hyb_protocol: Col0 MAS 2 Cy5 / Col0 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 MAS 2

extract_protocol: Col0 MAS 2:10ug. (Qiagen_RNeasy.pdf)


title: DAC Treated 104 Day 7 [mRNA profiling]

source_name: Mock treated primary leukemia 104 at day 7

source_name: DAC treated primary leukemia 104 at day 7

value: 10nM DAC

value: day 7


title: DAC Treated 104 Day 14 [mRNA profiling]

source_name: Mock treated primary leukemia 104 at day 14

source_name: DAC treated primary leukemia 104 at day 14

value: day 14


title: DAC Treated 103 Day 7 [mRNA profiling]

source_name: Mock treated primary leukemia 103 at day 7

source_name: DAC treated primary leukemia 103 at day 7


title: 14249199 - Col0 MAS 2 vs Col0 2

hyb_protocol: Col0 2 Cy5 / Col0 MAS 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 2


title: 14249195 - Col0 OCS 1 vs Col0 1

hyb_protocol: Col0 1 Cy5 / Col0 OCS 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 1

extract_protocol: Col0 1:10ug. (Qiagen_RNeasy.pdf)

source_name: Col0 OCS 1

extract_protocol: Col0 OCS 1:10ug. (Qiagen_RNeasy.pdf)


title: 14249193 - Col0 1 vs Col0 OCS 1

hyb_protocol: Col0 OCS 1 Cy5 / Col0 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: DAC Treated 1307 Day 14 [mRNA profiling]

source_name: Mock treated primary leukemia 1307 at day 14

value: Leukemia

source_name: DAC treated primary leukemia 1307 at day 14


title: DAC Treated 1307 Day 3 [mRNA profiling]

source_name: Mock treated primary leukemia 1307 at day 3

source_name: DAC treated primary leukemia 1307 at day 3


title: DAC Treated 1107 Day 7 [mRNA profiling]

source_name: Mock treated primary leukemia 1107 at day 7

source_name: DAC treated primary leukemia 1107 at day 7


title: 14249191 - Col0 MAS 1 vs Col0 1

hyb_protocol: Col0 1 Cy5 / Col0 MAS 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 MAS 1

extract_protocol: Col0 MAS 1:10ug. (Qiagen_RNeasy.pdf)


title: 14249190 - Col0 1 vs Col0 MAS 1

hyb_protocol: Col0 MAS 1 Cy5 / Col0 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: P. pacificus: Xenorhabdus nematophila vs. E. coli OP50 exposure; 4hours, Biological Replicate 1

status: Public on Mar 20 2012

city: Ipswich

first: Amit

last: Sinha

state: MA

address: 240 County Road

institute: New England Biolabs

description: Biological replicate 1 of 4.

hyb_protocol: The labelled and fragmented cRNAs were hybridized to Agilent P. pacificus oligonucleotide microarrays as per manufacturer's instructions.

scan_protocol: Scanned on a GenePix 4000B Microarray Scanner Images were quantified using GenePix Pro software  (version 6).

data_processing: The data was analyzed using the Bioconductor (Gentleman et al., 2004) package limma (Smyth, 397). Briefly, the array quality was assessed by checking for uniform background and foreground intensities over the entire array. The signal was background corrected using the "normexp" method (Ritchie et al., 2007). The arrays were lowess normalized individually ("normalizeWithinArrays" option), with differential weights assigned to probes and to positive control spike-ins which are expected to show no fold change (Smyth and Speed, 2003). This differential weighing of probes is particularly necessary to account for changes in the relative proportion of mRNA vs. total RNA. Without this differential weighing scheme, the fold change calculations can be erroneous (van de Peppel et al., 2003). The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function (Smyth, 2004). Control of FDR was used employed as the multiple testing correction.

organism: Pristionchus pacificus

source_name: P. pacificus young adults, fed Xenorhabdus nematophila, 4 hours

label_protocol: Equal amounts of total RNA (500ng to 1000ng) for 4 biological replicates from each stage was used to prepare Cy5- or Cy3- labelled cRNA using Quick Amp Labelling Kit (Agilent Technologies, Inc, Santa Clara, CA, USA), as per manufacturer's instructions. Based on the starting amounts of total RNA, appropriate dilutions of positive controls (Spike Mix-A and Spike-Mix B from Agilent) had been added to the reaction-mix before the RT reaction, as per manufacturer instructions.

growth_protocol: Synchronized populations of P. pacificus were obtained by hypochlorite treatment and allowed to grow to young adult stage on E. coli OP50 plates at 20C. For each biological replicate, about 200 young adult hermaphrodites were picked onto pathogen Xenorhabdus nematophila plates for 4 hours of exposure, after which they were collected into 1mL of TRIzol (Invitrogen), and stored at -80C till RNA extraction.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions, and was purified further by Phenol:Chloroform:Isoamyl Alcohol precipitation.

tag: developmental stage

value: young adults

value: exposed to Xenorhabdus nematophila

tag: timepoint

value: 4 hour feeding / exposure

source_name: P. pacificus young adults, fed E.coli OP50, 4 hours

growth_protocol: Synchronized populations of P. pacificus were obtained by hypochlorite treatment and allowed to grow to young adult stage on E. coli OP50 plates at 20C. For each biological replicate, about 200 young adult hermaphrodites were picked onto control E. coli OP50 plates for 4 hours of exposure, after which they were collected into 1mL of TRIzol (Invitrogen), and stored at -80C till RNA extraction.

value: exposed to E. coli OP50


title: P. pacificus: Xenorhabdus nematophila vs. E. coli OP50 exposure; 4hours, Biological Replicate 4 (Dye-swap)

description: Biological replicate 3 of 4. This is also a dye-swap


title: MDD patient 14 before treatment

description:
CB2007224-D14A.CEL
MDD patient 14 before treatment with venlafaxine

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

source_name: MDD patient 14 before treatment

tag: tissue

value: peripheral blood

value: lymphocytes

value: MDD patient

value: before treatment


title: P. pacificus: Xenorhabdus nematophila vs. E. coli OP50 exposure; 4hours, Biological Replicate 3 (Dye-swap)


title: P. pacificus: Serratia marcescens vs. E. coli OP50 exposure; 4hours, Biological Replicate 1

description: Biological replicate 1 of 4.

source_name: P. pacificus young adults, fed Serratia marcescens, 4 hours

growth_protocol: Synchronized populations of P. pacificus were obtained by hypochlorite treatment and allowed to grow to young adult stage on E. coli OP50 plates at 20C. For each biological replicate, about 200 young adult hermaphrodites were picked onto pathogen Serratia marcescens plates for 4 hours of exposure, after which they were collected into 1mL of TRIzol (Invitrogen), and stored at -80C till RNA extraction.

value: exposed to Serratia marcescens


title: P. pacificus: Staphylococcus aureus vs. E. coli OP50 exposure; 4hours, Biological Replicate 2 (Dye-swap)

description: Biological replicate 2 of 3. This is also a dye-swap.

source_name: P. pacificus young adults, fed Staphylococcus aureus, 4 hours

growth_protocol: Synchronized populations of P. pacificus were obtained by hypochlorite treatment and allowed to grow to young adult stage on E. coli OP50 plates at 20C. For each biological replicate, about 200 young adult hermaphrodites were picked onto pathogen Staphylococcus aureus plates for 4 hours of exposure, after which they were collected into 1mL of TRIzol (Invitrogen), and stored at -80C till RNA extraction.

value: exposed to Staphylococcus aureus


title: WSU-DLCL2

city: Cambridge

first: Nicolas

last: Stransky

address: 7 Cambridge center

department: Cancer Program

institute: Broad Institute

description: Gene expression data from the CCLE

hyb_protocol: Fragmentation of the biotin-labeled cRNA prepared the sample for hybridization on the GeneChip Human U133 2.0 (PN 900467). The washing and staining was performed on the GeneChip Fluidics station using standard Affymetrix protocols outlined in the Expression Analysis Technical Manual, 2001, Affymetrix.

scan_protocol: The GeneChip® Scanner 3000 was used for scanning the arrays.

data_processing: The data were analyzed with 2.14.0, using the packages affyio_1.22.0 and affy_1.32.0, and RMA as normalization method. rma() was used with default options (normalize=TRUE, background=TRUE) and with the package hgu133plus2hsentrezgcdf_15.0.0 from Brainarray for the CDF file.

label: Biotin

source_name: DSMZ

label_protocol: The Affymetrix One-Cycle Target labeling assay was used to synthesize hybridization target using 1 mg of total RNA. Labeled cRNA hybridization target was produced using a 3-day, semi-automated workflow

growth_protocol: Cells lines were cultured following growth recommendations from the cell line source vendors. Cells were incubated at 37 ºC at 5% CO2 until 70% confluency was reached.  Pellets were harvested 48 hours post media change, flash frozen, and stored at -80 ºC until nucleic acid extraction.

extract_protocol: RNA was isolated from frozen cell pellets, containing an average cell count of 4.5 million cells, via Trizol (Invitrogen) extraction following the manufacturers instructions. Samples were quantified using both the Nanodrop 8000 spectrophotometer (ThermoScientific) and via Agilent 2100 Bioanalyzer.

tag: primary site

tag: histology

tag: histology subtype1


title: Toledo

description: Gene expression data from the CCLE

source_name: ATCC


title: U-937

description: Gene expression data from the CCLE


title: TF-1

description: Gene expression data from the CCLE


title: P. pacificus: B. thuringiensis DB27 vs. E. coli OP50 exposure; 4hours, Biological Replicate 3 (Dye-swap)

description: Biological replicate 3 of 4. This is also a dye-swap.

tag: strain

tag: hybridization

value: Test sample

source_name: P. pacificus young adults, fed Bacillus thuringiensis DB27, 4 hours

growth_protocol: Synchronized populations of P. pacificus were obtained by hypochlorite treatment and allowed to grow to young adult stage on E. coli OP50 plates at 20C. For each biological replicate, about 200 young adult hermaphrodites were picked onto pathogen Bacillus thuringiensis DB27 plates for 4 hours of exposure, after which they were collected into 1mL of TRIzol (Invitrogen), and stored at -80C till RNA extraction.

value: exposed to Bacillus thuringiensis DB27

value: Reference sample


title: YD-15

description: Gene expression data from the CCLE

source_name: KCLB

value: carcinoma


title: SUP-T1

description: Gene expression data from the CCLE


title: TO 175.T

description: Gene expression data from the CCLE


title: TALL-1

description: Gene expression data from the CCLE


title: U266B1

description: Gene expression data from the CCLE


title: THP-1

description: Gene expression data from the CCLE


title: P. pacificus: Xenorhabdus nematophila vs. E. coli OP50 exposure; 4hours, Biological Replicate 2

description: Biological replicate 2 of 4.


title: SUP-T11

description: Gene expression data from the CCLE


title: UT-7

description: Gene expression data from the CCLE


title: P. pacificus: B. thuringiensis DB27 vs. E. coli OP50 exposure; 4hours, Biological Replicate 4 (Dye-swap)

description: Biological replicate 4 of 4. This is also a dye-swap.


title: P. pacificus: Serratia marcescens vs. E. coli OP50 exposure; 4hours, Biological Replicate 2

description: Biological replicate 2 of 4.


title: P. pacificus: Serratia marcescens vs. E. coli OP50 exposure; 4hours, Biological Replicate 3 (Dye-swap).

description: Biological replicate 3 of 4. This is also as dye-swap


title: P. pacificus: Serratia marcescens vs. E. coli OP50 exposure; 4hours, Biological Replicate 4 (Dye-swap).

description: Biological replicate 4 of 4. This is also as dye-swap


title: SUP-M2

description: Gene expression data from the CCLE


title: P. pacificus: Staphylococcus aureus vs. E. coli OP50 exposure; 4hours, Biological Replicate 1

description: Biological replicate 1 of 3.


title: P. pacificus: B. thuringiensis DB27 vs. E. coli OP50 exposure; 4hours, Biological Replicate 1

description: Biological replicate 1 of 4.


title: P. pacificus: B. thuringiensis DB27 vs. E. coli OP50 exposure; 4hours, Biological Replicate 2

description: Biological replicate 2 of 4.


title: P. pacificus: Staphylococcus aureus vs. E. coli OP50 exposure; 4hours, Biological Replicate 3 (Dye-swap)

description: Biological replicate 3 of 3.  This is also a dye-swap.


title: SU-DHL-8

description: Gene expression data from the CCLE


title: SU-DHL-10

description: Gene expression data from the CCLE


title: SU-DHL-5

description: Gene expression data from the CCLE


title: PL-21

description: Gene expression data from the CCLE


title: RPMI 6666

description: Gene expression data from the CCLE


title: SU-DHL-6

description: Gene expression data from the CCLE


title: RI-1

description: Gene expression data from the CCLE


title: RL

description: Gene expression data from the CCLE


title: Raji

description: Gene expression data from the CCLE


title: SEM

description: Gene expression data from the CCLE


title: SUP-B15

description: Gene expression data from the CCLE


title: SNU-324

description: Gene expression data from the CCLE

value: pancreas


title: SR-786

description: Gene expression data from the CCLE


title: RPMI-8402

description: Gene expression data from the CCLE


title: RPMI 8226

description: Gene expression data from the CCLE


title: SK-MM-2

description: Gene expression data from the CCLE


title: SKM-1

description: Gene expression data from the CCLE

source_name: HSRRB


title: SIG-M5

description: Gene expression data from the CCLE


title: REC-1

description: Gene expression data from the CCLE


title: SU-DHL-4

description: Gene expression data from the CCLE


title: SU-DHL-1

description: Gene expression data from the CCLE


title: SUP-HD1

description: Gene expression data from the CCLE


title: RCH-ACV

description: Gene expression data from the CCLE


title: PF-382

description: Gene expression data from the CCLE


title: Pfeiffer

description: Gene expression data from the CCLE


title: Reh

description: Gene expression data from the CCLE


title: Set-2

description: Gene expression data from the CCLE


title: RS4;11

description: Gene expression data from the CCLE


title: ST486

description: Gene expression data from the CCLE


title: P3HR-1

description: Gene expression data from the CCLE


title: OCI-AML3

description: Gene expression data from the CCLE


title: PEER

description: Gene expression data from the CCLE


title: P12-ICHIKAWA

description: Gene expression data from the CCLE


title: OCI-AML5

description: Gene expression data from the CCLE


title: NCO2

description: Gene expression data from the CCLE


title: OAW28

description: Gene expression data from the CCLE

source_name: ECACC

value: ovary


title: PCM6

description: Gene expression data from the CCLE

source_name: RIKEN


title: OPM-2

description: Gene expression data from the CCLE


title: P31/FUJ

description: Gene expression data from the CCLE


title: NU-DUL-1

description: Gene expression data from the CCLE


title: NCI-H929

description: Gene expression data from the CCLE


title: OCI-LY3

description: Gene expression data from the CCLE

source_name: Academic Lab


title: OCI-LY-19

description: Gene expression data from the CCLE


title: OCI-AML2

description: Gene expression data from the CCLE


title: OCI-M1

description: Gene expression data from the CCLE


title: NALM-6

description: Gene expression data from the CCLE


title: NCI-H1876

description: Gene expression data from the CCLE

value: lung


title: NOMO-1

description: Gene expression data from the CCLE


title: NALM-19

description: Gene expression data from the CCLE


title: NALM-1

description: Gene expression data from the CCLE


title: MOTN-1

description: Gene expression data from the CCLE


title: MUTZ-5

description: Gene expression data from the CCLE


title: NU-DHL-1

description: Gene expression data from the CCLE


title: DAC Treated 103 Day 3 [mRNA profiling]

source_name: Mock treated primary leukemia 103 at day 3

value: 1XPBS for 72 hours

tag: cell type

value: Breast Cancer

source_name: DAC treated primary leukemia 103 at day 3

value: 10nM DAC

value: day 3


title: MV-4-11

description: Gene expression data from the CCLE


title: NCI-H209

description: Gene expression data from the CCLE


title: NCI-H1930

description: Gene expression data from the CCLE


title: NCI-H1915

description: Gene expression data from the CCLE


title: NB-4

description: Gene expression data from the CCLE


title: MM1-S

description: Gene expression data from the CCLE


title: MOLM-13

description: Gene expression data from the CCLE


title: MOLP-8

description: Gene expression data from the CCLE


title: MONO-MAC-1

description: Gene expression data from the CCLE


title: MOLT-4

description: Gene expression data from the CCLE


title: MOLP-2

description: Gene expression data from the CCLE


title: MHH-CALL-4

description: Gene expression data from the CCLE


title: MOLT-16

description: Gene expression data from the CCLE


title: MJ

description: Gene expression data from the CCLE


title: MOLM-6

description: Gene expression data from the CCLE


title: MHH-CALL-3

description: Gene expression data from the CCLE


title: MEC-2

description: Gene expression data from the CCLE


title: MEC-1

description: Gene expression data from the CCLE


title: MOLM-16

description: Gene expression data from the CCLE


title: Mino

description: Gene expression data from the CCLE


title: MOLT-13

description: Gene expression data from the CCLE


title: MEG-01

description: Gene expression data from the CCLE


title: MHH-CALL-2

description: Gene expression data from the CCLE


title: MC116

description: Gene expression data from the CCLE


title: MONO-MAC-6

description: Gene expression data from the CCLE


title: Loucy

description: Gene expression data from the CCLE


title: M-07e

description: Gene expression data from the CCLE


title: LAMA-84

description: Gene expression data from the CCLE


title: L-428

description: Gene expression data from the CCLE


title: L-540

description: Gene expression data from the CCLE


title: ME-1

description: Gene expression data from the CCLE


title: L-363

description: Gene expression data from the CCLE


title: LP-1

description: Gene expression data from the CCLE


title: KMS-20

description: Gene expression data from the CCLE


title: KMS-18

description: Gene expression data from the CCLE


title: KMS-34

description: Gene expression data from the CCLE


title: KU812

description: Gene expression data from the CCLE


title: KMM-1

description: Gene expression data from the CCLE


title: KMS-21BM

description: Gene expression data from the CCLE


title: KOPN-8

description: Gene expression data from the CCLE


title: Ki-JK

description: Gene expression data from the CCLE


title: KM-H2

description: Gene expression data from the CCLE


title: KMS-27

description: Gene expression data from the CCLE


title: KG-1

description: Gene expression data from the CCLE


title: KHM-1B

description: Gene expression data from the CCLE


title: KYO-1

description: Gene expression data from the CCLE


title: Kasumi-6

description: Gene expression data from the CCLE


title: KARPAS-620

description: Gene expression data from the CCLE


title: KMS-12-BM

description: Gene expression data from the CCLE


title: KMS-26

description: Gene expression data from the CCLE


title: KMS-28BM

description: Gene expression data from the CCLE


title: KASUMI-2

description: Gene expression data from the CCLE


title: KASUMI-1

description: Gene expression data from the CCLE


title: KMS-11

description: Gene expression data from the CCLE


title: KCL-22

description: Gene expression data from the CCLE


title: KE-97

description: Gene expression data from the CCLE


title: K-562

description: Gene expression data from the CCLE


title: KE-37

description: Gene expression data from the CCLE


title: JVM-2

description: Gene expression data from the CCLE


title: JVM-3

description: Gene expression data from the CCLE


title: KARPAS-299

description: Gene expression data from the CCLE


title: L-1236

description: Gene expression data from the CCLE


title: JURL-MK1

description: Gene expression data from the CCLE


title: JM1

description: Gene expression data from the CCLE


title: JK-1

description: Gene expression data from the CCLE


title: HuNS1

description: Gene expression data from the CCLE


title: HuT 78

description: Gene expression data from the CCLE


title: JeKo-1

description: Gene expression data from the CCLE


title: HuTu 80

description: Gene expression data from the CCLE

value: adenocarcinoma


title: JURKAT

description: Gene expression data from the CCLE


title: Hs 751.T

description: Gene expression data from the CCLE


title: Hs 616.T

description: Gene expression data from the CCLE


title: Hs 611.T

description: Gene expression data from the CCLE


title: HuT 102

description: Gene expression data from the CCLE


title: HCI-005_original_tumor_without_hMSCs_[expression]

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

description: ILC Stage 2B

hyb_protocol: Agilent one-color heterologous gene expression hybridization and wash protocol.

scan_protocol: Microarray slides were scanned on an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.

data_processing:
TIFF images from the scanned microarrays were processed using Agilent Feature Extraction software version 10.5.1.1.
gProcessedSignal values were filtered to remove control features,  non-uniform outliers and feature population outliers. Remaining values were average to yield a single value for each unique probe.
Probe intensities were log transformed (log base 2) and quantile normalized.

source_name: HCI-005 original tumor grown without hMSCs [expression]

label_protocol: Agilent one-color quick-amp labeling protocol.

growth_protocol: Flash frozen tumor tissue from human subject or mouse xenograft

extract_protocol: Total RNA isolated using Trizol

tag: tumor type

value: metastatic

tag: er status

tag: pr status

tag: her2 status

tag: Stage

value: ILC Stage 2B

tag: tumor id

tag: sample type

value: original tumor

value: metastatic breast cancer tumor

tag: grown with hmscs


title: HT

description: Gene expression data from the CCLE


title: PD sample # I

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

description: Transcriptomic profiling of peripheral blood mononuclear cells from patients with Parkinson’s disease and control subjects.

hyb_protocol: Scanned on an Agilent G2505B scanner and Agilent-014850 whole Human genome microarrays 4x44K (Probe Name version).

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (Grid: 014850_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: PD sample # I

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1650 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Blood from control and PD subjects was collected in Vacutainer® CPT Cell Preparation Tubes (Becton Dickinson, Le Pont-de-Claix, France) and PBMC from human samples were isolated on a ficoll gradient. Total RNA from 5 x 106 cells was isolated using RNeasy mini-columns (Qiagen, Courtaboeuf, France). RNA concentration was measured by  absorbance at 260nm using a NanoDrop ND-1000 spectrophotometer. RNA quality and integrity were checked using the RNA 6000 NanoChip kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Massy, France). All samples included in the study had a RIN>9.

tag: patient group

value: Parkinson’s disease

value: peripheral blood mononuclear cells


title: PD sample # J

source_name: PD sample # J


title: PD sample # B

source_name: PD sample # B


title: Hs 604.T

description: Gene expression data from the CCLE


title: HCI-001_original_tumor_without_hMSCs_[expression]

description: IDC Stage 4

source_name: HCI-001 original tumor grown without hMSCs [expression]

value: primary breast tumor

value: IDC Stage 4


title: PD sample # C

source_name: PD sample # C


title: PD sample # H

source_name: PD sample # H


title: HCI-005_original_tumor_with_hMSCs_[expression]

description: ILC Stage 2B

source_name: HCI-005 original tumor grown with hMSCs [expression]


title: PD sample # E

source_name: PD sample # E


title: PD sample # F

source_name: PD sample # F


title: PD sample # A

source_name: PD sample # A


title: Control sample N°8

source_name: Control sample N°8

value: control


title: PD sample # G

source_name: PD sample # G


title: PD sample # D

source_name: PD sample # D


title: HCI-001_original_tumor_with_hMSCs_[expression]

description: IDC Stage 4

source_name: HCI-001 original tumor grown with hMSCs [expression]


title: Control sample N°7

source_name: Control sample N°7


title: Control sample N°6

source_name: Control sample N°6


title: Control sample N°3

source_name: Control sample N°3


title: n2

city: Hangzhou

first: Yang

last: Liu

state: Zhejiang

address: 388 Yu Hang Tang Road

department: Institute of Immunology

institute: Zhejiang University School of Medicine

hyb_protocol: Step 1: Combine the labeled sample(s). Step 2: Add 25 μL Hybridization buffer. Step 3: Denature at 95°C for 2 min. Step 4: Incubate 2 min. on ice. Step 5: Preparation of Tecan. Step 6: Flush hyb chamber with 1x Hybridization buffer. Step 7: Inject reaction mixture. Step 8: Incubate at 56°C for 16 h. Step 9: Two runs of wash at 56°C for 1 min. using Wash buffer A. Step 10: Two runs of wash at 23°C for 1 min. using Wash buffer B. Step 11: Two runs of wash at 23°C for 1 min. using Wash buffer C. Step 12: Wash at 23°C for 30 sec using Wash buffer C. Step 13: Dry slides.

scan_protocol: We are using an Agilent G2505B Microarray Scanner System. The scanning is normally performed with 10 μm. The sensitivity should be adjusted to 100% PMT. To avoid ozone bleaching, we scan the microarrays in an ozone-free environment (less than 2 ppb ozone). Before starting any analysis, confirm that the tiff image is in the correct orientation (two landing lights in lower right corner). Depending on the scanner, the image may need to be flipped from upper left to lower right.

data_processing: The intensity of green signal is calculated after background subtraction and replicated spots on the same slide have been averaged by getting a median intensity. We use Median Normalization Method to obtain “Normalized Data”, Normalized Data=(Foreground-Background)/median, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction.

source_name: Myeloid-derived suppressor cells

label_protocol: Step 1: Thaw all kit components. Place all kit components on ice and thaw for 15-20 min. Mix thoroughly by vortexing followed by brief centrifugation. Do not thaw or vortex the enzymes. Flick these tubes followed by brief centrifugation.  Step 2: Total RNA 2 ul; Spike-in miRNA kit v2  1ul; CIP buffer 0.5 ul; CIP enzyme 0.5 ul. Mix reagents on ice. Reagents should be combined in an RNase-free microcentrifuge tube and should be mixed by pipetting up and down to ensure that all reagents are mixed thoroughly.  Step 3: Incubate 30 min. at 37°C, using a PCR cycler with heated lid.  Step 4: Stop the enzyme reaction and denaturate the RNA by incubation at 95°C followed by snap cooling on ice.  Step 5: Incubate 2 min on ice.  Step 6: Mix reagents on ice. CIP reaction from step 5 4 ul; Labeling buffer 3 ul; Fluorescent label (Hy3™ or Hy5™) 1.5 ul; DMSO 2 ul; Labeling enzyme 2 ul.  Step 7: Mix and centrifuge the reagents briefly.  Step 8: Incubate for 1 hour at 16°C, using a PCR cycler with heated lid. Protect the reaction from light.  Step 9: After stopping the labeling procedure, briefly spin the reaction and leave it at 4°C. The labeled sample is now ready for hybridization on the array. Hybridization should preferably occur within 1-2 h.

extract_protocol: Total RNA was harvested using TRIzol (Invitrogen) and the RNeasy mini kit (QIAGEN).

value: BALB/c

tag: gender

value: female

tag: age

value: 6-8 wk old

tag: tumor stage

value: tumor-free mice


title: n1


title: t1

value: tumor-bearing mice


title: t2


title: n3


title: t3


title: Control sample N°5

source_name: Control sample N°5


title: HH

description: Gene expression data from the CCLE

source_name: ATCC

tag: primary site

tag: histology


title: HL-60

description: Gene expression data from the CCLE

tag: histology subtype1


title: HDLM-2

description: Gene expression data from the CCLE

source_name: DSMZ


title: HD-MY-Z

description: Gene expression data from the CCLE


title: HPB-ALL

description: Gene expression data from the CCLE


title: GDM-1

description: Gene expression data from the CCLE


title: HEL

description: Gene expression data from the CCLE


title: HCC1428

description: Gene expression data from the CCLE

value: breast

value: carcinoma


title: HEL 92.1.7

description: Gene expression data from the CCLE


title: GRANTA-519

description: Gene expression data from the CCLE


title: F-36P

description: Gene expression data from the CCLE


title: GA-10

description: Gene expression data from the CCLE


title: HCC-1171

description: Gene expression data from the CCLE

source_name: KCLB

value: lung


title: EM-2

description: Gene expression data from the CCLE


title: EOL-1

description: Gene expression data from the CCLE


title: Control sample N°1

source_name: Control sample N°1


title: EHEB

description: Gene expression data from the CCLE


title: KO52

description: Gene expression data from the CCLE

source_name: HSRRB


title: Control sample N°2

source_name: Control sample N°2


title: EJM

description: Gene expression data from the CCLE


title: Control sample N°4

source_name: Control sample N°4


title: DOHH-2

description: Gene expression data from the CCLE


title: DB

description: Gene expression data from the CCLE


title: Daudi

description: Gene expression data from the CCLE


title: DEL

description: Gene expression data from the CCLE


title: BL-70

description: Gene expression data from the CCLE


title: CML-T1

description: Gene expression data from the CCLE


title: CA46

description: Gene expression data from the CCLE


title: BHY

description: Gene expression data from the CCLE


title: CMK

description: Gene expression data from the CCLE


title: DND-41

description: Gene expression data from the CCLE


title: BL-41

description: Gene expression data from the CCLE


title: EB2

description: Gene expression data from the CCLE


title: CI-1

description: Gene expression data from the CCLE


title: EB1

description: Gene expression data from the CCLE


title: BV-173

description: Gene expression data from the CCLE


title: CMK-11-5

description: Gene expression data from the CCLE


title: BCP-1

description: Gene expression data from the CCLE


title: AMO-1

description: Gene expression data from the CCLE


title: BDCM

description: Gene expression data from the CCLE


title: AML-193

description: Gene expression data from the CCLE


title: 14178727 - col3 vs cdk3

description: difference in global transcript in mutants with an affected cell cycle progression

hyb_protocol: cdk3 Cy5 / col3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: aerial - media : 1/2 MS 0.5% Sucrose  temperature : 20 degrees C

tag: ecotype

tag: genotype/variation

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

value: wild type


title: 14178764 - de3 vs col3

hyb_protocol: col3 Cy5 / de3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14178697 - cdk3 vs col3

hyb_protocol: col3 Cy5 / cdk3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14178758 - d1 vs col1

hyb_protocol: col1 Cy5 / d1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.