title: H1hESC 120h 20%O2

status: Public on May 10 2009

city: Columbia

first: Toshihiko

last: Ezashi

state: MO

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

description: The cRNA target was hybridized to Agilent-014850 Whole Human Genome Microarrays 4x44K (G4112F). Slides were washed and scanned on an Agilent G2565 Microarray scanner, and data analyzed with Agilent Feature Extraction and GeneSpring GX v7.3.1 softwares.

hyb_protocol: cRNA was fragmented to uniform size and verified on the Bioanalyzer. Agilent Whole Genome arrays were hybridized with the cRNA target

scan_protocol: Slides were washed and scanned on an Agilent G2565 Microarray Scanner.

data_processing: Data was analyzed with Agilent Feature Extraction and GeneSpring GX v7.3.1 softwares.

source_name: human embryonic stem cells, BMP4 120h, 20% O2

label_protocol: Biotin labeling

growth_protocol: Human ESC H1 (WA01) at passage 23 was purchased from WiCell Research Institute (Madison, WI) and cultured in six-well tissue culture plates on a monolayer of γ-irradiated (8,000 cGy) mouse embryonic fibroblast (MEF) feeder cells until passage number 35. Thereafter, cells were cultured on a substratum of 1:30 dilutions of Matrigel™ in medium conditioned by MEF. The cells were used in the experiemts at passage number 37.

extract_protocol: RNA was isolated from hESCs by using RNA STAT-60 reagent (Tel-Test Inc, Friendswood, TX) according to the manufacturer's instructions. Isopropanol precipitated RNA pellets were dissolved in 35 ul of nuclease-free water and purified with spin columns of RNeasy Mini Kit (Qiagen).

treatment_protocol: hESC were cultured in either a standard humidified tissue culture CO2 incubator, set at 5% CO2 in air, or a sealed chamber (MIC-101, Billups-Rothenberg, Del Mar, CA) filled with the humidified physiological O2 mixture (~4 % O2/5 % CO2/92-90 % N2) in a standard tissue culture incubator at 37°C. Oxygen levels, measured by using a Bacharach CO2/O2 Analyzer (Bacharach, Model 2830), were ~19% in the standard incubator and 3.5–4.5% in the physiological O2 chamber. To minimize temporal ‘oxygen surge’ at each media change and at passage of the cells cultured under physiological O2 condition, the medium was pre-equilibrated for 24 h under physiological gas mixture. Processing cells while outside the incubator is generally completed within 30 min to minimize periodic reperfusion effects. The H1 hESC lines had been maintained in a physiological O2 atmosphere since passage 26. Total RNA was isolated after 0, 3, 12, 24, 72, and 120 h of BMP4 exposure at passage number 37 and had been maintained on Matrigel™ for 2 passages.

tag: human embronic stem cell, NIH code:WA01


title: H1hESC 72h 20%O2

type: RNA

country: USA

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: human embryonic stem cells, BMP4 72h, 20% O2


title: H1hESC 0h 20%O2

source_name: human embryonic stem cells, BMP4 0h, 20% O2


title: HBE_PBS24_code2

status: Public on May 19 2009

city: Chapel Hill

first: Wanda

middle: K.

last: O'Neal

state: NC

department: Cystic Fibrosis/Pulmonary Research and Treatment Center

institute: University of North Carolina at Chapel Hill

description: Gene expression data from human airway epithelium treated as described.

hyb_protocol: 15 mug of fragmented cRNA were hybridized for 16 hrs on Genechip Fluidics Station using Affymetrix HU133 plus 2.0 arrays (GPL570).

scan_protocol: Genechips were scanned using Hewlett-packard GeneArray scanner.

data_processing: Expressions were computed using the Bioconductor GCRMA package with default parameters.

source_name: well-differentiated primary airway bronchial culture

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 mug total RNA (Expression analysis technical manual, Affymetrix).

growth_protocol: Human bronchial epithelium harvested from normal lung donors. primary cells are placed on T-col membranes approximately 30 days until well-differentiated. Cells are grown at air-liquid interface which is established in 10-14 days.

extract_protocol: RNAzol followed by Qiagen RNeasy columns with DNAase treatment according to publisher and manufacturers protocols.

treatment_protocol: Well-differentiated human airway epithelium grown at air-liquid interface exposed to 30mul mucosal PBS for 24 hours. Samples were placed in RNAlater until RNA harvest.


title: H1hESC 24h 20%O2

source_name: human embryonic stem cells, BMP4 24h, 20% O2


title: H1hESC 12h 20%O2

source_name: human embryonic stem cells, BMP4 12h, 20% O2


title: H1hESC 3h 20%O2

source_name: human embryonic stem cells, BMP4 3h, 20% O2


title: H1hESC 72h 4%O2

source_name: human embryonic stem cells, BMP4 72h, 4% O2


title: H1hESC 12h 4%O2

source_name: human embryonic stem cells, BMP4 12h, 4% O2


title: HBE_AZIT72SMM24-code4

treatment_protocol: Well-differentiated human airway epithelium grown at air-liquid interface exposed to 30mug/ml serosal Azithromycin for 48 hours + 30mul mucosal SMM during last 24 hrs before harvested. Samples were placed in RNAlater until RNA harvest.


title: H1hESC 120h 4%O2

source_name: human embryonic stem cells, BMP4 120h, 4% O2


title: H1hESC 0h 4%O2

source_name: human embryonic stem cells, BMP4 0h, 4% O2


title: H1hESC 24h 4%O2

source_name: human embryonic stem cells, BMP4 24h, 4% O2


title: product 2 after 15 days (repeat I 15-2)

status: Public on May 01 2009

city: Beijing

first: Yeshi

last: Yin

address: NO.1 West Beichen Road, Chaoyang District

country: China

institute: Institute of Microbiology

description: It's the first time to design expression microarray of chicken's all genes which contain know genes and predict genes

hyb_protocol: Hybridization of cy5 labeled DNA was operated on MAUI Hybridization System (BioMicro Systems, Inc, USA) according to the NimbleGen’s protocols. (NimbleChipTM Arrays User’s Guide Gene Expression Analysis, http://www.nimblegen.com)

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.tiff file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, GenePixTM  4000B Microarray Scanner.

organism: Gallus gallus

source_name: Ileum of chickens which inoculated product 2 after 15 day

label_protocol: The first strand cDNA were synthesized by using SuperScriptTM III Reverse Transcriptase (Invitrogen, USA), and the second strand cDNA were synthesized by using M-MLV RTase cDNA Synthesis kit (TaKaRa, Japan) according to the manufacturer’s protocol. The double-strand cDNA were labeled by cy5. And labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

extract_protocol: Total RNA was extracted using AxyPrepTM Multisource Total RNA Miniprep Kit (Axygen, USA) according to the instructions and DNA was removed by on-column DNase digestion with the  Dnase I (TaKaRa, Japan). RNA quality and concentration was determined by analysis with a  spectrophotometer (NanoDrop, USA).

treatment_protocol: The ileum were immediately frozened in liquid nitrogen after dissection and then store at -80.

tag: developmental stage

value: 15 day

tag: tissue

value: Ileum


title: product 1 after 15 days (I 15-1)

source_name: Ileum of chickens which inoculated product1 after 15 day


title: water  after 7 days (repeat I 7-3)

source_name: Ileum of chickens which inoculated wate  after 7 day

value: 7 day


title: product 1 after 15 days (repeat I 15-1)


title: water  after 7 days (I 7-3)


title: water after 15 days (I 15-3)

source_name: Ileum of chickens which inoculated water after 15 day


title: product 1 after 7 days (repeat I 7-1)

source_name: Ileum of chickens which inoculated product1 after 7 day


title: product 2 after 7 days (repeat I 7-2)

source_name: Ileum of chickens which inoculated product 2 after 7 day


title: water after 15 days (repeat I 15-3)


title: water  after 1 day (I 1-3)

source_name: Ileum of chickens which inoculated wate  after 1 day

value: 1 day


title: product 2 after 15 days (I 15-2)


title: product 1 after 7 days (I 7-1)


title: Yr01_Mock_3_48h

city: Raleigh

first: Tristan

last: Coram

address: 4118 Williams Hall, NC State University

institute: USDA-ARS, NC State University

hyb_protocol: Labeled (biotinylated) cDNA targets were prepared for hybridization by re-suspending in 105 µL 1X hybridization buffer (4X SSC, 5X Denhardt’s reagent) for 1-2 hours in a 55ºC water bath, followed by rapid boiling for 3 min and immediately chilling on ice. Each 105 uL sample was individually applied sample to one slide well to cover the entire surface of the well. Slides were inserted into a hybridization chamber (50 mL tube) containing wetted thick filter paper and placed into a rack that was submerged in a pre-warmed 45 ºC water bath overnight (~16 h). Following hybridization, the washing detection steps were carried out with use of the Tyramide Signal Amplification (TSA) Biotin system (Perkin Elmer, Waltham, MA), which amplifies the fluorescent signal in a biotin-streptavidin system. Slides removed from the hybridization chambers were firstly washed in wash buffer (0.1 M Tris-HCl pH 7.5, 0.005% Tween-20) 3 times for 1 min each with agitation (80 rpm) followed by briefly spinning dry for 3-5 s. Slides were incubated with 100 µL per well of 1:100 Streptavidin-Horseradish Peroxidase (SA-HRP) in blocking buffer (for 200 mL combine 20 mL 1.0 M Tris-HCl pH 7.5, 6.0 mL 5 M NaCl, 1.0 g blocking reagent from TSA kit, 160 mL sterile water) for 30 min at room temperature to conjugate with the biotin present on the hybridized cDNA. Slides were then washed again as described above and then blocked with 100 µL per well of 10% Fetal Equine Serum (FES) in 2X SSC for 30 min at room temperature. After washing again, slides were incubated with 100 µL per well of Biotinyl Tyramide (from TSA kit) working solution for 10 min at room temperature to add additional biotin molecules to the already bound streptavidin. After another wash the slides were incubated with 100 µL per well of 1:500 SA-AlexaFluor®555 conjugate (Invitrogen, Carlsbad, CA) in 1X SSC, 5X Denhardt’s for 1 h in the dark at room temperature, which added the fluorophore needed for fluorescent detection.

scan_protocol: Slides were kept in the dark until scanned at 540 nm and 10 µm resolution with an Applied Precision arrayWoRx scanner (Applied Precision, Issaquah, WA). Images were saved as TIFF files for analysis.

data_processing: Image files segmented and quantified using Spot version 3.1 (Buckley 2002), which is an image analysis program designed for microarray analysis. TIFF files were loaded into Spot, a grid was defined, and an annotation file linked. The images were then segmented and intensity values for each spot were calculated along with quality data that was used to eliminate poor quality spots. Quantified spot data was pre-processed using R (R Development Core Team 2006). Firstly, the background median was subtracted from mean intensity values, values <1.0 were floored up to 1.0, and the data was log2 scaled. All arrays were then quantile-normalized using the Bioconductor (Gentleman et al. 2004) package affy (Gautier et al. 2004).

organism: Triticum aestivum

label_protocol: Microarray targets were synthesized and labeled by i. Combining 5.0 µg biotinylated oligo(dT)18 primer (Sigma Genosys, St. Louis, MO) and 10-20 µg of total RNA in a final volume of 21.0 µL and heating to 65ºC for 10 min followed by immediately chilling on ice, ii. Adding first strand cDNA synthesis reagents (Invitrogen, Carlsbad, CA) including 8.0 µL 5X first-strand buffer, 4.0 µL 100 mM DTT, 2.0 µL 10mM dNTP mix, 1.0 µL RNase-OUT and 800 U Superscript III in a final volume of 40 µL and incubating at 42ºC for 16 h, iii. Hydrolysis of RNA template by adding 1/3 volume 0.5 M EDTA (pH 8.0) and 1/3 volume 1 M NaOH and heating to 65ºC for 15 min, followed by neutralization by adding 1/2 volume 1 M Tris-HCl (pH 7.0), v. Precipitating cDNA by adding 1/10 volume 3 M sodium acetate and 2 volumes of 100% ethanol, followed by centrifugation at maximum speed for 30 min, removal of supernatant and washing with 70% ethanol, and centrifugation at maximum speed for 5 min, and vi. Drying of cDNA pellets in a vacuum dryer.

extract_protocol: Shoot tissue from the six seedlings corresponding to each experimental condition were quickly cut, pooled, and frozen in liquid nitrogen. Total RNA was extracted from 1.0 g of pooled tissue using the Trizol® Plus RNA Purification Kit (Invitrogen, Carlsbad, CA) with an on-column DNase treatment. Purified total RNA samples were quantified with a NanoDrop® ND-1000 (NanoDrop, Wilmington, DE) spectrophotometer, and satisfactory purity was indicated by A260:280 ratios of 1.9-2.1 in 10 mM Tris-Hcl (pH 7.5). Integrity of total RNA samples was assessed by denaturing formaldehyde gel electrophoresis, where the presence of sharp 28S and 18S ribosomal RNA bands at an intensity ratio of ~2:1 (28S:18S) indicated good integrity.

tag: Growth stage:SEEDLING

tag: Tissue

value: SHOOT


title: Yr05_Avr78_1_48h


title: Yr05_Avr78_1_24h


title: Yr01_Mock_3_24h


title: Yr01_Mock_2_48h


title: H1hESC 3h 4%O2

source_name: human embryonic stem cells, BMP4 3h, 4% O2


title: Yr01_Mock_2_24h


title: product 2 after 1 day (I 1-2)

source_name: Ileum of chickens which inoculated product 2 after 1 day


title: Yr01_Mock_1_48h


title: Yr01_Mock_1_24h


title: Yr01_Avr45_3_48h


title: product 1 after 1 day (I 1-1)

source_name: Ileum of chickens which inoculated product1 after 1 day


title: Yr01_Avr45_3_24h


title: Yr01_Avr45_2_48h


title: MCF7 cells E2 Stimulated 3hr replicate 3

city: London

first: geraint

last: barton

address: South Kensington Campus

department: Bioinformatics Support Service

country: United Kingdom

institute: Imperial College

hyb_protocol: Agilent standard protocol

scan_protocol: Microarrays were scanned with Agilent scanner G2565BA using Agilent Feature Extraction software

data_processing: Raw data from the Agilent feature extraction software.

source_name: MCF7 cells

label_protocol: Isolated RNA was labelled using the Agilent labelling kit following the manufacturer’s instruction (Agilent Technologies)

extract_protocol: Total RNA was collected using Trizol (Invitrogen, Paisley, UK). After extraction the quality and levels of RNA was determined using an Agilent Bioanalyzer (Agilent Technologies, Edinburgh, UK) and a NanoDrop® ND-1000 Spectrophotometer (Thermo Scientific, Horsham, UK)


title: MCF7-TO replicate 3

tag: MCF7-Tet-Off cells not treated with tetracycline replicate 3


title: product 2 after 7 days (I 7-2)


title: MCF7 cells E2 Stimulated 0hr replicate 2

extract_protocol: Total RNA was collected using Trizol (Invitrogen, Paisley, UK). For separation of small (< 200 nt) and large (> 200 nt) RNA fraction the miRNeasy mini kit was used for obtaining the larger fraction, followed by the RNeasy MinElute Cleanup kit to isolate the smaller fraction, according to the manufacturer’s instructions (Qiagen, Crawley, UK). Separation of RNA between the large and small fractions was confirmed by gel eletrophoresis. After extraction the quality and levels of RNA was determined using an Agilent Bioanalyzer (Agilent Technologies, Edinburgh, UK) and a NanoDrop® ND-1000 Spectrophotometer (Thermo Scientific, Horsham, UK)


title: MCF7 cells E2 Stimulated 0hr replicate 1


title: MCF7 cells E2 Stimulated 12hr replicate 2


title: MCF7 cells E2 Stimulated 3hr replicate 2


title: MCF7 cells E2 Stimulated 0hr replicate 3


title: Yr01_Avr45_2_24h


title: MCF7-TO replicate 1

description:
see Agilent feature extraction reference guide:
none

source_name: MCF7-Tet-Off cells

tag: MCF7-Tet-Off cells not treated with tetracycline replicate 1


title: MCF7 cells E2 Stimulated 12hr replicate 1


title: JP13 replicate1

tag: MCF7-Tet-Off cells stably transfected with PLZF-ERalpha (JP13) not treated with tetracycline replicate 1


title: MCF7-TO+TET replicate 3

scan_protocol: microarrays were scanned with Agilent scanner G2565BA using Agilent Feature Extraction software

tag: MCF7-Tet-Off cells treated with tetracycline replicate 3


title: JP13+TET replicate 2

tag: MCF7-Tet-Off cells stably transfected with PLZF-ERalpha (JP13) treated with tetracycline replicate 2


title: MCF7 cells E2 Stimulated 6hr replicate 3


title: MCF7 cells E2 Stimulated 6hr replicate 1


title: AVS_Vir78_3_48h


title: Yr01_Avr45_1_48h


title: AVS_Vir78_2_48h


title: AVS_Vir78_3_24h


title: AVS_Vir78_2_24h


title: Yr01_Avr45_1_24h


title: JP13 replicate 2

tag: MCF7-Tet-Off cells stably transfected with PLZF-ERalpha (JP13) not treated with tetracycline replicate 2


title: MCF7-TO+TET replicate 2

tag: MCF7 cells TO-TET MCF7-Tet-Off cells treated with tetracycline replicate 2


title: AVS_Mock_3_48h


title: AVS_Vir78_1_48h


title: AVS_Mock_1_24h


title: AVS_Mock_2_24h


title: AVS_Mock_1_48h


title: AVS_Mock_2_48h


title: AVS_Vir78_1_24h


title: Yr17_Mock_2_48h


title: Yr17_Mock_3_48h


title: Yr17_Mock_2_24h


title: JP13+TET replicate 1

tag: MCF7-Tet-Off cells stably transfected with PLZF-ERalpha (JP13) treated with tetracycline replicate 1


title: MCF7 cells E2 Stimulated 12hr replicate 3


title: Yr17_Mock_1_48h


title: JP13 replicate 3

tag: MCF7-Tet-Off cells stably transfected with PLZF-ERalpha (JP13) not treated with tetracycline replicate 3


title: Yr17_Avr21_3_24h


title: MCF7-TO replicate 2

tag: MCF7-Tet-Off cells not treated with tetracycline replicate 2


title: MCF7-TO+TET replicate 1

tag: MCF7-Tet-Off cells treated with tetracycline replicate 1


title: MCF7 cells E2 Stimulated 6hr replicate 2


title: MCF7 cells E2 Stimulated 3hr replicate 1


title: Yr17_Avr21_2_48h


title: JP13+TET replicate 3

tag: MCF7-Tet-Off cells stably transfected with PLZF-ERalpha (JP13) treated with tetracycline replicate 3


title: Yr17_Mock_1_24h


title: Yr17_Mock_3_24h


title: Yr15_Mock_2_24h


title: Yr15_Mock_2_48h


title: Yr15_Mock_3_48h


title: Yr15_Mock_3_24h


title: Yr17_Avr21_1_24h


title: Yr15_Mock_1_24h


title: Yr15_Mock_1_48h


title: Yr15_Avr78_3_24h


title: Yr17_Avr21_2_24h


title: Yr15_Avr78_3_48h


title: Yr15_Avr78_2_24h


title: Yr15_Avr78_2_48h


title: Yr10_Mock_3_48h


title: Yr15_Avr78_1_24h


title: Yr15_Avr78_1_48h


title: Yr17_Avr21_3_48h


title: Yr10_Mock_2_48h


title: Yr10_Mock_2_24h


title: Yr10_Mock_1_24h


title: Yr10_Mock_1_48h


title: Yr10_Mock_3_24h


title: Yr10_Avr21_3_48h


title: Yr10_Avr21_3_24h


title: Yr17_Avr21_1_48h


title: Yr10_Avr21_2_48h


title: Yr10_Avr21_2_24h


title: Yr09_Avr21_3_48h


title: Yr09_Avr21_3_24h


title: Yr10_Avr21_1_48h


title: Yr09_Mock_2_24h


title: Yr09_Mock_3_24h


title: Yr09_Mock_3_48h


title: Yr09_Mock_2_48h


title: Yr09_Avr21_1_24h


title: Yr09_Avr21_2_24h


title: Yr08_Mock_3_48h


title: Yr09_Mock_1_48h


title: Yr09_Mock_1_24h


title: Yr08_Mock_2_24h


title: Yr08_Avr21_1_48h


title: Yr08_Mock_1_48h


title: Yr08_Mock_3_24h


title: Yr09_Avr21_1_48h


title: Yr08_Avr21_2_48h


title: Yr09_Avr21_2_48h


title: Yr08_Avr21_3_48h


title: Yr08_Avr21_2_24h


title: Yr08_Avr21_3_24h


title: Yr08_Avr21_1_24h


title: Yr07_Mock_3_48h


title: Yr07_Mock_2_48h


title: Yr08_Mock_2_48h


title: Yr08_Mock_1_24h


title: Yr07_Mock_3_24h


title: Yr07_Mock_2_24h


title: Yr07_Avr45_2_48h


title: Yr07_Avr45_3_48h


title: Yr07_Avr45_1_48h


title: Yr07_Avr45_2_24h


title: Yr05_Mock_3_48h


title: Yr07_Mock_1_24h


title: Yr05_Mock_2_48h


title: Yr07_Avr45_3_24h


title: Yr07_Mock_1_48h


title: Yr07_Avr45_1_24h


title: Yr10_Avr21_1_24h


title: Yr05_Mock_3_24h


title: Yr05_Avr78_2_48h


title: Yr05_Avr78_3_24h


title: Yr05_Mock_1_48h


title: Yr05_Avr78_2_24h


title: Yr05_Mock_2_24h


title: Yr05_Avr78_3_48h


title: time31-211-2

status: Public on Apr 30 2009

city: Zurich

first: Valeria

last: Mozzetti

address: Schmelzbergstrasse 7

department: D-AGRL

country: Switzerland

institute: ETH

description: technical replicate 31-211 h

hyb_protocol: The hybridization conditions and the washing of the slide were performed as follows. To the 20 ul of cDNA (obtained with the Genisphere kit), 25 ul of control target Agilent, 60 ul of H2O and 105 ul of Agilent buffer were added. After 10 minutes of incubation at 80°C and 15 minutes at 65°C, the reaction was loaded on a pre-warmed slide in the hybridization chamber and incubated for 16 hours at 65°C, at four rpm in an Agilent oven. The cDNA hybridization was washed 10 min at 42°C in 6x SSC, 0.005% Triton x-100 and 10 min at RT in 0.2x SSC, 0.00016% Triton x-100. The 3DNA hybridization was carried out as described in the Genisphere protocol except for the hybridization volume which was increased to 204 ul and the washing modified as follows : 10 min at 65°C in 2x SSC, 0.0016% Triton x-100, 5 min at RT in 2x SSC, 0.0016% Triton x-100 and 10 min at RT in 0.2x SSC, 0.00016% Triton x-100.

scan_protocol: The slides were scanned at 10 um with a Scanarray 4000 (Packard Biochip Technologies, Billerica, MA, USA)

data_processing: Data were extracted with Imagene 5.6 (Biodiscovery, El Segundo, CA, USA). Data were treated with homemade scripts in Python language (www.python.org) and a local installation of the ArrayPipe web server (15). Probes showing a signal smaller than twice the standard deviation of the local background were considered without signal. Probes showing no signal or saturated signals in both channels were discarded from the analysis. Assuming an intensity-dependent variation in dye signal, (limma) loess global normalization was applied on signal ratios.

organism: Bifidobacterium longum

label_protocol: RNA labelling and cDNA synthesis were carried out using the 3DNA Array 900 MPX Genisphere kit (Genisphere Inc., Hatfield, PA, USA) combined with the In situ Hybridization Kit Plus.

growth_protocol: in MRS cystein medium

extract_protocol: Total RNA extraction as described in Parche et al. 2006. J.Bacteriol. 188:1260-1265.

tag: strain

tag: treatment

value: 211 h continuous culture

value: 31 h continuous culture


title: time31-211-1

description: technical replicate31-211 h


title: Yr05_Mock_1_24h


title: time31-134-2

description: technical replicate 31-134 h

value: 134 h continuous culture


title: Chondrosarcoma_case_64

status: Public on Apr 01 2009

type: genomic

city: Lund

first: Karolin

middle: H

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

description: 32k BAC array CGH data on chondrosarcoma

hyb_protocol: Arrays were hybridized and washed as described in Heidenblad et al. (Oncogene 2006;25:7106-16)

scan_protocol: Arrays were scanned in Agilent Microarray scanner

data_processing: Primary data were collected using the GenePix Pro 4.0 software, and the quantified data matrix was deposited into the web-based database BioArray Software Environment (BASE), where filtering and lowess normalization were performed.

molecule: genomic DNA

source_name: Case 64

label_protocol: BioPrime array CGH labeling module (Invitrogen, Carlsbad, CA, USA)

extract_protocol: DNeasy Tissue Kit (Qiagen, Valencia, CA, USA)

tag: Genomic DNA from fresh frozen chondrosarcoma biopsy

source_name: Promega reference male DNA (Promega, Madison, WI, USA)

tag: Pooled lymphoblastoid genomic DNA from ten male individuals


title: Chondrosarcoma_case_63

source_name: Case 63


title: time31-134-1

description: technical replicate 31-134 h


title: Chondrosarcoma_case_66

source_name: Case 66


title: Chondrosarcoma_case_59

source_name: Case 59


title: Chondrosarcoma_case_60

source_name: Case 60


title: Chondrosarcoma_case_48

source_name: Case 48


title: Chondrosarcoma_case_65

source_name: Case 65


title: Chondrosarcoma_case_50

source_name: Case 50


title: Chondrosarcoma_case_54

source_name: Case 54


title: Chondrosarcoma_case_49

source_name: Case 49


title: Chondrosarcoma_case_56

source_name: Case 56


title: Chondrosarcoma_case_61

source_name: Case 61


title: Chondrosarcoma_case_51

source_name: Case 51


title: Chondrosarcoma_case_52

source_name: Case 52


title: Chondrosarcoma_case_55

source_name: Case 55


title: Chondrosarcoma_case_62

source_name: Case 62


title: Chondrosarcoma_case_57

source_name: Case 57


title: Chondrosarcoma_case_43

source_name: Case 43

source_name: Promega reference male DNA (Promega, Madison, WI, USA)


title: Chondrosarcoma_case_58

source_name: Case 58


title: Chondrosarcoma_case_47

source_name: Case 47


title: Chondrosarcoma_case_53

source_name: Case 53


title: Chondrosarcoma_case_45

source_name: Case 45


title: Chondrosarcoma_case_46

source_name: Case 46


title: Chondrosarcoma_case_44

source_name: Case 44


title: Chondrosarcoma_case_40

source_name: Case 40


title: Chondrosarcoma_case_33

source_name: Case 33


title: Chondrosarcoma_case_38

source_name: Case 38


title: Chondrosarcoma_case_42

source_name: Case 42


title: Chondrosarcoma_case_39

source_name: Case 39


title: Chondrosarcoma_case_35

source_name: Case 35


title: Chondrosarcoma_case_37

source_name: Case 37


title: Chondrosarcoma_case_26

source_name: Case 26


title: Chondrosarcoma_case_32

source_name: Case 32


title: Chondrosarcoma_case_29

source_name: Case 29


title: Chondrosarcoma_case_24

source_name: Case 24

source_name: Promega reference male DNA (Promega, Madison, WI, USA)


title: Chondrosarcoma_case_41

source_name: Case 41


title: Chondrosarcoma_case_30

source_name: Case 30


title: Chondrosarcoma_case_28

source_name: Case 28


title: Chondrosarcoma_case_27

source_name: Case 27


title: Chondrosarcoma_case_20

source_name: Case 20


title: Chondrosarcoma_case_19

source_name: Case 19


title: Chondrosarcoma_case_25

source_name: Case 25


title: Chondrosarcoma_case_22

source_name: Case 22


title: Chondrosarcoma_case_21

source_name: Case 21


title: Chondrosarcoma_case_17

source_name: Case 17


title: Chondrosarcoma_case_23

source_name: Case 23


title: Chondrosarcoma_case_12

source_name: Case 12


title: Chondrosarcoma_case_13

source_name: Case 13


title: Chondrosarcoma_case_16

source_name: Case 16


title: Chondrosarcoma_case_15

source_name: Case 15


title: Chondrosarcoma_case_14

source_name: Case 14


title: Chondrosarcoma_case_7

source_name: Case 7

source_name: Promega reference male DNA (Promega, Madison, WI, USA)


title: Chondrosarcoma_case_18

source_name: Case 18


title: Chondrosarcoma_case_8

source_name: Case 8


title: Chondrosarcoma_case_9

source_name: Case 9


title: Chondrosarcoma_case_31

source_name: Case 31


title: Chondrosarcoma_case_10

source_name: Case 10


title: Chondrosarcoma_case_11

source_name: Case 11


title: Chondrosarcoma_case_6

source_name: Case 6


title: Chondrosarcoma_case_1

source_name: Case 1


title: S.cerevisiae and S.paradoxus at glycerol repeat #1 Cy3

city: Rehovot

first: Itay

last: Tirosh

address: herzl

department: Molecular genetics

country: Israel

institute: Weizmann Institute of Science

description:
Comparative analysis of gene expression in two yeast species and their interspecific hybrid
the S.cerevisiae sample was diluted to OD(600)=0.2 and harvested after 8 hours  due to very low growth rate

hyb_protocol: Agilent Gene Expression Hybridization Kit p/n 5188-5242

scan_protocol: Arrays were scanned using Agilent Microarray Scanner (p/n G2565BA) with a 5 micron resolution and photomultiplier tube (PMT) set to 100 and then rescanned with PMT=10. The images analyzed were from the PMT=100 unless data has reached saturation. The raw images  were analyzed and quantified using Spotreader software (Niles scientific).

data_processing: Raw hybridization intensities were background subtracted and log2-transformed. Results of different samples from the same condition were converted into the same distribution using percentile normalization. Probes were then sorted into 10 bins of similar %GC and the log-intensities of each bin were renormalized to the mean and Std of all probes. Finally, the normalized expression was averaged over the technical repeats of each probe (each probe was placed at 3-4 different positions on the array).

molecule: polyA RNA

organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus

source_name: S. cerevisiae (BY4741 ho::kanMX4  MATa), S. paradoxus (CBS432 ho::nat1 MATα)

label_protocol: Agilent Low RNA Input Amplificarion Kit (LRIAK) plus, two color p/n 5188-5340

growth_protocol:
glycerol (YPglycerol at 30°C)
All samples were collected at log-phase growth. Starters were grown over night, dluted to OD(600)=0.1 in 10ml medium and harvested ~5 hours after dilution when OD(600)=~0.5

extract_protocol: Total RNA was extracted using MasterPure™ Yeast RNA purification Kit (EPICENTRE).

value: S. cerevisiae (BY4741), S. paradoxus (CBS432)


title: Tumor in the mice bred with high fat diet No.3

city: Tokyo

first: Hidewaki

last: Nakaagwa

state: Tokyo

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

department: Institute of Medical Science

country: Japan

institute: The University of Tokyo

description: Synthesized siRNA duplexes to ELOVL7 (siELOVL7) or siCONTROL-oligo (Dharmacon) was transfected to C4-2B cells, and total RNAs were extracted 48 hour after the transfection.

hyb_protocol: Labeled cDNAs were mixed with microarray hybridization solution version 2 (Amersham) and formamide (Sigma) to a final concentration of 50%. After hybridization for 14-16 hours at 42 oC in Automated Slide Processor, the slides were washed in 2xSSC and 1% SDS for 10min at 55 oC, washed in 0.2xSSC and 0.1% SDS for 10min at 55 oC, and washed in 0.1xSSC for 1 min at room temperature in Automated Slide Processor.

scan_protocol: Microarray slides were scanned using the Array Scanner Generation III (Amersham) after hybridization.

data_processing: Images were gridded and the fluorescent intensity of each spot (Cy5/Cy3) was evaluated photometrically by the ArrayVision computer program (Imaging Research, Inc., St. Catharines, Ontario, Canada) . The fluorescent intensities of Cy5 (tumor) and Cy3 (control) for each target spot were adjusted so that the mean Cy3/Cy5 ratio of the 52 housekeeping genes was equal to one. Because data derived from low signal intensities are less reliable, we determined a cut-off value on each slide and excluded genes from further analysis when both Cy3 and Cy5 dyes yielded signal intensities lower than the cut-off value. For other genes, we calculated the Cy5/Cy3 ratio using the raw data of each sample.

source_name: Tumor in the mice bred with high fat diet (HFD)

label_protocol: 2.5 ug aliquots of aRNA from tumor cells or normal cells were annealed with random primer for 10 min at 70oC. They were labeled in a 50ul volume by reverse transcription reaction for 2 hours at 37oC using Superscript II reverse transcriptase (Invitrogen) with 1mM Cy5-dCTP for tumor cells or Cy3-dCTP for normal cells (Amersham) and 25mM each dATP, dGTP, and dTTP. The labeling reaction was stopped by adding 6ul 2.5 N NaOH and incubation for 30 min at 65oC and neutralized by 20ul 1M Tris-HCl (pH7.4) and 7ul 2.5N HCl. The labeled cDNAs were purified by QIAquick PCR Purification Kit (QIAGEN).

extract_protocol:
ELOVL7-overexpressing tumors of the mice bred with HFD or ND in vivo
Total RNAs were isolated from captured cells with QIAGNE RNAeasy Kit (QIAGEN). After DNAse I treatment, total RNAs were subjected to two rounds of T7-based amplification using Ampliscribe T7 Transcription Kit (Epicentre Technologies), or MEGAscript High Yield Transcription Kit (Ambion), which yielded 50–100 ug of amplified RNA (aRNA) from each sample.

tag: cell type

value: tumor cells

source_name: Tumor in the mice bred with normal diet (ND)


title: S.cerevisiae and S.paradoxus at rich media (SC) repeat #4 Cy5

description: Comparative analysis of gene expression in two yeast species and their interspecific hybrid

growth_protocol:
Synthetic Complete (SC) medium at 30°C
All samples were collected at log-phase growth. Starters were grown over night, dluted to OD(600)=0.1 in 10ml medium and harvested ~5 hours after dilution when OD(600)=~0.5


title: hybrid at with TSA repeat #1 Cy5

organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

source_name: S. cerevisiae BY4741 X  S. paradoxus CBS432 (ho::kanMX4/ho::nat1 MATa/MATα)

growth_protocol:
RPD3 inhibition (SC with 30µM trichostatin A)
All samples were collected at log-phase growth. Starters were grown over night, dluted to OD(600)=0.1 in 10ml medium and harvested ~5 hours after dilution when OD(600)=~0.5


title: S.cerevisiae and S.paradoxus at glycerol repeat #2 Cy5


title: hybrid at heatshock (35C) repeat #1 Cy5

description:
Comparative analysis of gene expression in two yeast species and their interspecific hybrid
cells were grown to log-phase at 30° and then transferred to 35° for three hours

growth_protocol:
heat-shock (YPD at 35°C)
All samples were collected at log-phase growth. Starters were grown over night, dluted to OD(600)=0.1 in 10ml medium and harvested ~5 hours after dilution when OD(600)=~0.5

value: S. cerevisiae BY4741 X  S. paradoxus CBS432


title: hybrid at rich media (SC) repeat #1 Cy5


title: Chondrosarcoma_case_5

source_name: Case 5


title: hybrid at glycerol repeat #1 Cy5


title: S.cerevisiae and S.paradoxus with TSA repeat #1 Cy3


title: hybrid at heatshock (35C) repeat #2 Cy3


title: hybrid at with TSA repeat #2 Cy3


title: ELOVL7 knockdown in C4-2B No.1

source_name: ELOVl7 siRNA_1

extract_protocol:
Synthesized siRNA duplexes to ELOVL7 (siELOVL7) or siCONTROL-oligo (Dharmacon) was transfected to C4-2B cells , and total RNAs were extracted 48 hour after the transfection.
Total RNAs were isolated from captured cells with QIAGNE RNAeasy Kit (QIAGEN). After DNAse I treatment, total RNAs were subjected to two rounds of T7-based amplification using Ampliscribe T7 Transcription Kit (Epicentre Technologies), or MEGAscript High Yield Transcription Kit (Ambion), which yielded 50–100 ug of amplified RNA (aRNA) from each sample.

value: prostate cancer cells

tag: cell line

value: C4-2B cells

source_name: Control siRNA_1


title: Tumor in the mice bred with high fat diet No.1


title: hybrid at rich media (SC) repeat #3 Cy5


title: S.cerevisiae and S.paradoxus at rich media (SC) repeat #2 Cy5


title: hybrid at rich media (SC) repeat #2 Cy3


title: ELOVL7 knockdown in C4-2B No.3

source_name: ELOVL7 siRNA_3

extract_protocol:
Synthesized siRNA duplexes to ELOVL7 (siELOVL7) or siCONTROL-oligo (Dharmacon) was transfected to C4-2B cells, and total RNAs were extracted 48 hour after the transfection.
Total RNAs were isolated from captured cells with QIAGNE RNAeasy Kit (QIAGEN). After DNAse I treatment, total RNAs were subjected to two rounds of T7-based amplification using Ampliscribe T7 Transcription Kit (Epicentre Technologies), or MEGAscript High Yield Transcription Kit (Ambion), which yielded 50–100 ug of amplified RNA (aRNA) from each sample.

source_name: Control siRNA_2


title: ELOVL7 knockdown in C4-2B No.2

source_name: ELOVL7 siRNA_2


title: S.cerevisiae and S.paradoxus at rich media (SC) repeat #1 Cy3


title: Tumor in the mice bred with high fat diet No.2


title: Chondrosarcoma_case_62

description: Genome-wide gene expression profiling of chondrosarcoma using the Human-6 v2 Expression BeadChip (Illumina Inc., San Diego, CA, USA)

hyb_protocol: Arrays were hybridized and washed according to the manufacturer's specifications (Illumina Inc., San Diego, CA, USA)

scan_protocol: Arrays were scanned in the Illumina BeadArray Reader

data_processing: Image analysis was performed using the Illumina® BeadStudio Application Software. Gene expression data were normalized using Rank Invariant Normalization and analyzed with the Illumina BeadStudio Gene Expression Module (Illumina).

source_name: Case 62

label_protocol: TotalPrep RNA Amplification Kit (Ambion Inc., Austin, TX, USA)

extract_protocol: Phenol-Chloroform followed by RNeasy mini column (Qiagen, Hilden, Germany)

tag: RNA from fresh frozen chondrosarcoma biopsy


title: hybrid at glycerol repeat #2 Cy3


title: Chondrosarcoma_case_63

source_name: Case 63


title: Chondrosarcoma_case_34

source_name: Case 34


title: Chondrosarcoma_case_37

source_name: Case 37


title: Chondrosarcoma_case_3

source_name: Case 3

source_name: Promega reference male DNA (Promega, Madison, WI, USA)


title: Chondrosarcoma_case_50

source_name: Case 50


title: S.cerevisiae and S.paradoxus at heatshock (35C) repeat #2 Cy5

source_name: S. cerevisiae (BY4741 ho::kanMX4  MATa), S. paradoxus (CBS432 ho::nat1 MATα)


title: S.cerevisiae and S.paradoxus at heatshock (35C) repeat #1 Cy3


title: S.cerevisiae and S.paradoxus with TSA repeat #2 Cy5


title: Chondrosarcoma_case_26

source_name: Case 26


title: Chondrosarcoma_case_29

source_name: Case 29


title: Chondrosarcoma_case_21

source_name: Case 21


title: Chondrosarcoma_case_14

source_name: Case 14


title: S.cerevisiae and S.paradoxus at rich media (SC) repeat #3 Cy3


title: hybrid at rich media (SC) repeat #4 Cy3

source_name: S. cerevisiae BY4741 X  S. paradoxus CBS432 (ho::kanMX4/ho::nat1 MATa/MATα)


title: Chondrosarcoma_case_55

source_name: Case 55


title: Chondrosarcoma_case_20

source_name: Case 20


title: Chondrosarcoma_case_28

source_name: Case 28


title: Chondrosarcoma_case_38

source_name: Case 38


title: Chondrosarcoma_case_4

source_name: Case 4


title: Chondrosarcoma_case_15

source_name: Case 15


title: Chondrosarcoma_case_2

source_name: Case 2


title: Chondrosarcoma_case_11

source_name: Case 11


title: 271 late rep5

status: Public on Mar 31 2009

city: Huntsville

first: Leland

middle: J.

last: Cseke

state: AL

address: 301 Sparkman Dr.

department: Biological Sciences

institute: The University of Alabama Huntsville

description: Ring 3.1 vs. 3.2

hyb_protocol: All microarray slides were checked using a dissecting microscope for uniformity of spots. Slides were prehybridized for 30 min on a slow rotary shaker in 5X SSC, 0.1% SDS, and 1% BSA, and rinsed 20 times in ddH2O.  DNA was denatured by incubating slides in 95°C ddH2O for 1 min, followed by washing in 100% ice-cold ethanol for 15 s.  Slides were dried by centrifugation (4°C, 2500 rpm, 2 min) and stored at 4°C.  Hybridization was performed within 1 h of prehybridization. Targets were resuspended in 55 µl hybridization solution (50% formamide, 5X SSC, 0.1% SDS, and 0.1% BSA) and centrifuged at 14,000 × g for 1 min before denaturation at 45°C for 5-10 min.  Hybridization was performed in Corning hybridization chambers (Corning Inc., Acton, MA) with Lifter slips (Erie Scientific Co., Portsmouth, NH) and incubated in a 43°C water bath in a hybridization oven for 36 h. Slides were rinsed in wash solution I (1X SSC, 0.2% SDS), prewarmed to 45°C, to remove the lifter slips.  Slides were washed once in wash solution I for 15 min at 45°C with gentle agitation, once in wash solution II (0.1X SSC, 0.2% SDS) for 10 min, and twice in wash solution III (0.1X SSC) for 2 min each.  Finally, slides were immersed in ddH2O for 10 seconds, 100% ethanol for 10 seconds, then dried by centrifugation (4°C, 2500 rpm, 2 min) and stored in darkness at room temperature.

scan_protocol: Slides were scanned using a VersArray ChipReader™ scanner (BioRad, Hercules, CA) at 5 µm resolution. Cy3 and Cy5 images were aligned and spots flagged using VersArray Analyzer 5.0 (BioRad, CA).

data_processing: After local background subtraction and exclusion of flagged spots, signal intensity was log(2) transformed and normalized by the LOWESS algorithm with a smoothing parameter of 0.2, using GeneGazer software (Bio-Rad, CA). Spots having intensities below 20 in both channels were excluded.

organism: Populus tremuloides

source_name: Clone 271, late season, ambient

label_protocol: RNA (13.5 µg of each sample) was reverse transcribed using a SuperscriptTM Indirect cDNA Labeling System (Invitrogen, Carlsbad, CA), with oligo-dT primers.  cDNA was purified using S.N.A.P. Columns (Invitrogen, Carlsbad, CA) and resuspended in 10 µl Coupling Buffer following the manufacturer’s instructions.  Individual aliquots of Cy3 and Cy5 (RPN 5661, GE Healthcare, Piscataway, NJ) were resuspended in 5 µl DMSO, mixed with 5 µl of the cDNA in Coupling Buffer and incubated at room temperature for 1 h in the dark. The labeled cDNAs were purified using S.N.A.P. purification columns, and the yield and dye incorporation were evaluated using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE). Targets were prepared by combining 40 pmol of each labeled sample in an amber microfuge tube.  This was flash frozen in liquid nitrogen and dried in a vacuum centrifuge before storage at -20°C.

growth_protocol: The study was performed on leaf tissues collected near Rhinelander, WI, U.S.A. (89.5° W, 45.7° N) at the Aspen FACE experimental site, which has been operating since 1997. Twelve, 30m diameter, plots are contained within a 32 ha site in a full factorial design. Plots are exposed to ambient air (control) and air enriched with CO2, ozone, or CO2 and ozone in combination. Due to their significant differences in growth response to e[CO2], this study utilized two trembling aspen (P. tremuloides Michx.) genotypes, clone 216 and clone 271. Since bud-break in this region occurred on May 19 and bud-set occurred in late August (for clone 216) and early September (for clone 271), harvest dates of June 15th (early) and August 17th (late), 2005 were chosen to assure recently mature early-season leaf collections and mature but not yet senescing leaf collections in the late season time point.

extract_protocol: Total RNA was extracted as described by Cseke et al. (2004), and treated with the TURBO DNA-free kit (Ambion Inc, Austin, TX) to remove genomic DNA contamination.    • Handbook of Molecular and Cellular Methods in Biology and Medicine-2nd ed., L.J. Cseke, P.B. Kaufman, G.K. Podila, and C.J. Tsai: CRC Press, Boca Raton, Florida, 2004.

treatment_protocol: In this study, only plots receiving ambient air ([CO2] = 372 µL L-1) and air enriched with CO2 (target [CO2] = 560 µL L-1) were used. The site is divided into three blocks, each containing a CO2 and a control plot. Elevated CO2 plots were fumigated from sunrise to sunset for the length of the growing season (May-September), and one-minute averages of [CO2] in the e[CO2] plots were within 20% of the target concentration. Upper canopy sun lit leaves were harvested between 10:00 and 11:00 am on each date.  Tissues were frozen in liquid nitrogen within 20 seconds of harvesting and stored at -80 oC until analyzed. To avoid potential variation derived from time-of-day effects, all pairs of control vs. e[CO2] samples were collected with 10 minutes of one another.

tag: phenotype

value: Responsive to e[CO2]

tag: genotype

value: Clone 271

source_name: Clone 271, late season, e[CO2]


title: 271 late rep2

description: Ring 1.1 vs. 1.2


title: Chondrosarcoma_case_36

description: 244k oligo array CGH data on chondrosarcoma

hyb_protocol: Arrays were hybridized and washed as described in Savola et al. (Cytogenet Genome Res 2007;119:21-26)

data_processing: Primary data were collected using the Feature Extraction 9.1 software (Agilent), and the quantified data matrix was deposited into the web-based database BioArray Software Environment (BASE), where filtering and lowess normalization were performed.

source_name: Case 36

label_protocol: Genomic DNA Labeling Kit (Agilent Technologies, CA, USA)

source_name: Gender-matched reference DNA

tag: Pooled lymphoblastoid genomic DNA from four male/female individuals


title: 271 late rep1

description: Ring 1.1 vs. 1.2


title: 271 late rep3

description: Ring 2.1 vs. 2.2


title: 271 late rep4

description: Ring 2.1 vs. 2.2


title: 271 early rep3

description: Ring 2.1 vs. 2.2

source_name: Clone 271, early season, ambient

source_name: Clone 271, early season, e[CO2]


title: Chondrosarcoma_case_67

source_name: Case 67


title: Chondrosarcoma_case_4


title: 216 late rep6

description: Ring 3.1 vs. 3.2

source_name: Clone 216, late season, e[CO2]

value: Not responsive to e[CO2]

value: Clone 216

source_name: Clone 216, late season, ambient


title: 216 late rep3

description: Ring 2.1 vs. 2.2


title: 271 early rep1

description: Ring 1.1 vs. 1.2


title: 216 late rep4

description: Ring 2.1 vs. 2.2


title: 216 early rep5

description: Ring 3.1 vs. 3.2

source_name: Clone 216, early season, ambient

source_name: Clone 216, early season, e[CO2]


title: 216 late rep1

description: Ring 1.1 vs. 1.2


title: 271 early rep4

description: Ring 2.1 vs. 2.2


title: 271 early rep6

description: Ring 3.1 vs. 3.2


title: 271 late rep6

description: Ring 3.1 vs. 3.2


title: Chondrosarcoma_case_34

source_name: Case 34


title: 216 early rep4

description: Ring 2.1 vs. 2.2


title: 216 early rep6

description: Ring 3.1 vs. 3.2


title: 216 early rep2

description: Ring 1.1 vs. 1.2


title: Chondrosarcoma_case_2


title: 216 late rep5

description: Ring 3.1 vs. 3.2


title: 216 early rep1

description: Ring 1.1 vs. 1.2


title: 216 early rep3

description: Ring 2.1 vs. 2.2


title: 271 early rep2

description: Ring 1.1 vs. 1.2


title: Nitrogen limited repC 11019602_532

status: Public on Mar 30 2009

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL

description: Nitrogen limited repC 11019602_532

hyb_protocol: Hybridization was carried out with 6ug of labeled cDNA suspended in NimbleGen hybridization solution for 17 hours at 42°C

scan_protocol: Arrays were scanned on the Axon4000B Scanner (Molecular Dynamics) and data was extracted from the scanned image using NimbleScan v2.4.

data_processing: Quantile normalization and robust multi-array averaging (RMA) applied

organism: Phanerodontia chrysosporium

source_name: mycelium

label_protocol: One ug of each cDNA sample was amplified and labeled with 1 unit per ul of Klenow Fragment (New England BioLabs) and 1 O.D unit of Cy3 fluorophore (TriLink Biotechnologies, Inc.) for 2 hours at 37°C

growth_protocol: Shake flasks at 37C

extract_protocol: RNA was converted to double-strand cDNA and labeled with the Cy3 fluorophore sample for hybridization to the array by Roche NimbleGen (Iceland).  In brief, 10ug of total RNA was incubated with 1X first strand buffer, 10 mM DTT, 0.5mM dNTPs, 100 pM oligo T7 d(T)24  primer, and 200 units of SuperScript II (Invitrogen) for 60 min at 42°C. Second strand cDNA was synthesized by incubation with 1X second strand buffer, 0.2mM dNTPs, 0.07 units per ul DNA ligase (Invitrogen), 0.27 units per ul DNA polymerase I (Invitrogen), 0.013 units per ul RNase H (Invitrogen), at 16°C for 2 hours.  Immediately following, 10 units T4 DNA polymerase (Invitrogen) was added for additional 5 minute incubation at 16°C.  Double-stranded cDNA was treated with 27ng/ul of RNase A (EpiCenter Technologies)  for 10 minutes at 37°C.  Treated cDNA was purified using an equal volume of phenol:chloroform:isoamyl alcohol (Ambion), ethanol precipitated, washed with 80% ethanol, and resuspended in 20ul water.


title: Nitrogen limited repB 10730202_532

description: Nitrogen limited repB 10730202_532


title: Carbon limited repC 10391702_532

description: Carbon limited repC 10391702_532


title: Carbon limited repA 10390502_532

description: Carbon limited repA 10390502_532


title: 216 late rep2

description: Ring 1.1 vs. 1.2


title: Nitrogen limited repA 10730002_532

description: Nitrogen limited repA 10730002_532


title: Differentially expressed genes in the Arabidopsis Ler-Waco9 interaction - Biological replicate 1

status: Public on Mar 17 2009

type: other

city: Amsterdam

first: Mark

middle: de

last: Jong

address: Kruislaan 318

country: Netherlands

institute: University of Amsterdam

description: The complete array procedure can be found in: de Jong, M., van Breukelen, B., Wittink, F.R., Menke, F.L., Weisbeek, P.J. and Van den Ackerveken, G. 2006. Membrane-associated transcripts in Arabidopsis; their isolation and characterization by DNA microarray analysis and bioinformatics. Plant J. 46:708-21.

hyb_protocol: The probes were hybridised overnight on CATMA arrays (de Jong et al., 2006)

scan_protocol: Scans were made using a ScanArray Express HT (PerkinElmer, Wellesley, MA, USA).

data_processing: Spot intensities of the scans were determined by ImaGene software version 6.5.1 (BioDiscovery, El Segundo, CA, USA). Analysis of spot intensities from the CATMA arrays and applied statistics were performed as described before (de Jong et al., 2006). Printtip LOESS & Scaling between arrays (median absolute deviation). VALUE represents log2(channel 1/channel 2). Data presented here is the average of 4 dyeswapped technical replicates.

molecule: other

organism: Arabidopsis thaliana

label_protocol: The complete microarray procedure used in this article is extensively described before (de Jong et al., 2006). Briefly, mRNA from isolated RNA was amplified with the MessageAmp II aRNA kit (Ambion, Austin, TX, USA). Amplified mRNA was used as template to synthesize modified cDNA with SuperScript III reverse transcriptase (Invitrogen, Carlsbad, CA, USA) and random nonamers (Gene Link, Westchester County, NY, USA) with incorporation of 5-(3-aminoallyl)-dUTP (Ambion). Obtained cDNA was labelled with either Cy3 or Cy5 mono-reactive dye (Amersham, Buckinghamshire, UK) and incorporation was determined using an UVmini-1240 spectrophotometer at 550 or 650 nm, respectively.

extract_protocol: RNA was extracted with a RNeasy kit (Qiagen, Venlo, The Netherlands) and treated with the RNase-free DNase set (Qiagen) yielding approximately 50 μg RNA per isolation. The quantity of RNA was measured using an UVmini-1240 spectrophotometer (Shimadzu, Kyoto, Japan) and the quality with the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA) using the RNA 6000 Nano Assay kit (Agilent Technologies).

tag: Arabidopsis accession Ler inoculated with H. arabidopsidis isolate Waco9. Material harvested after 3 dpi.

source_name: Ler-mock

tag: Arabidopsis accession Ler mock-inoculated. Material harvested after 3 dpi.


title: Carbon limited repB 10391002_532

description: Carbon limited repB 10391002_532


title: Replete medium repB 10482902_532

description: Replete medium repB 10482902_532


title: cells at 240 minutes after MBC treatment and growth in HU after G2/M arrest; biol rep 3

status: Public on Mar 06 2009

city: New York

first: Pei-Yun

middle: Jenny

last: Wu

state: NY

address: 1230 York Avenue

institute: Rockefeller University

description: MBC_3: Cells were synchronized at G2/M at 36.5ºC for 3h 30min; MBC was added for 10 minutes before shifting cells to 25ºC;l cells were grown at 25ºC for 65 minutes, then washed and grown in medium containing hydroxyurea until 240 minutes post-G2/M release.

hyb_protocol: Labeled DNA was hybridized to Affymetrix GeneChip S. pombe Tiling 1.0FR Arrays using standard protocols (20 hours at 45 ºC).  After hybridization, GeneChips were stained with streptavidin-phycoerythrin, followed by an antibody solution (anti-streptavidin) and a second streptavidin-phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 3000.

data_processing:
The data were analyzed using the Affymetrix Tiling Array Software using default settings with linear output.
Chromosomal datasets were obtained by taking a ratio to the "0" dataset for normalization; all probes which returned a value of "1" were discarded.  After averaging by the geometric mean for a sliding windows of 200 adjacent probes, we determined extrapolated values for every 500 bp.  Data were then normalized to the median value of the dataset for each chromosome.

organism: Schizosaccharomyces pombe

source_name: cells in S phase, after 65 min MBC treatment followed by hydroxyurea treament

label_protocol: Prior to labeling, IP DNA was amplified by blunting using T4 DNA polymerase, followed by linker ligation and PCR amplification for 22 cycles and purification on a Qiagen PCR purification column.).  2 µg of DNA was fragmented to 50-100 bp in One-Phor-All Buffer Plus (GE Healthcare) using Genechip fragmentation reagent (Affymetrix) and biotin labeled using the BioArray Terminal Labeling Kit (Enzo Life Sciences).

growth_protocol: cdc25-22 cells were synchronized by growing in minimal medium plus supplements (EMM4S) at 25ºC to 1-2x106 cells/ml, shifting to 36.5ºC to block cells in late G2, followed by release at 25ºC. Treatments for specific samples are indicated.

extract_protocol: Genomic DNA was prepared according to Hoffman and Winston, 1987 and purified using the Qiagen Genomic DNA kit. After sonication to 300-400 bp average length, 4-5 µg DNA was mixed with 40 µl BrdU antibody (anti-mouse, BD Biosciences) followed Protein G beads (GE Healthcare). Washes and elution were performed according to Martens and Winston, 2002.

treatment_protocol: Cells were treated with 0.01% sodium azide and harvested by centrifugation, followed by washing with 50 mM EDTA and TE buffer.

value: h- [Msmt-0] cdc25-22 leu1-32 his7-366 leu1::pFS181(leu1 adh1:hENT1) pJL218 (his7 adh1:tk)

source_name: non-replicating control_051007

tag: dataset


title: Differentially expressed genes in the Arabidopsis Ler-Waco9 interaction - Biological replicate 3


title: Differentially expressed genes in the Arabidopsis Ler-Waco9 interaction - Biological replicate 2


title: cells at 90 minutes in HU after G2/M arrest; biol rep 2

description: 90_2: Cells synchronized at G2/M for 3h 45min were released into medium containing hydroxyurea at 25ºC for 90 minutes.

source_name: cells in S phase, after 90 minutes in hydroxyurea

source_name: non-replicating control_071306


title: cells at 90 minutes in HU after G2/M arrest; biol rep 3

description: 90_3: Cells synchronized at G2/M for 3h 45min were released into medium containing hydroxyurea at 25ºC for 90 minutes.


title: Differentially expressed genes in the Arabidopsis Ler-Cala2 interaction - Biological replicate 2

tag: Arabidopsis accession Ler inoculated with H. arabidopsidis isolate Cala2. Material harvested after 3 dpi.


title: Differentially expressed genes in the Arabidopsis Ler-Cala2 interaction - Biological replicate 1


title: Replete medium repA 10480502_532

description: Replete medium repA 10480502_532


title: Differentially expressed genes in the Arabidopsis Ler-Cala2 interaction - Biological replicate 3


title: parentmix vs 6400

status: Public on Mar 11 2009

first: Robert

middle: Thomas

last: Gaeta

address: 117 Tucker Hall, Department of Biological Sciences, University of Missouri

institute: University of Missouri

description: Note:  We employed 2 dye swaps for each of 2 biological replicates (see 8 raw data files for each comparison), and therefore the analyzed data in matrix is based on 2 reps and 2 dye swaps for each comparison.  The matrix also shows the standard deviation, common variance, per-gene ANOVA p-value, and common variance ANOVA p-value.

scan_protocol: Microarrays were scanned using the GenePix 4000B scanner (Axon Instruments, Inc., Union City, CA) and GPR files were generated for data analysis according to protocols described in Wang er al., 2005.  Specific Scan settings can be found in the raw data files.

data_processing: The raw data were background corrected by subtracting the background median from the foreground median intensity for both red and green intensities; negative results were set to 1.  A transformation was performed on background-corrected intensities by taking the natural logarithm.  MA plots [41] were employed to investigate dye effects.  Data were normalized using a robust local regression (loess function).  Consistency and density plots were also used to investigate data quality.  To identify differentially expressed genes between any two samples, two Analysis of Variance (ANOVA) models were used: The first model used a common variance ANOVA  and the second model used per-gene variance ANOVA (See Wang et al., 2005 and Zhao et al., 2007).  To accommodate the multiple testing issues that arise from testing differential expression of 26,107 genes for differential expression, Benjamini-Hochberg’s FDR was employed to control the significance level at 0.05 (Benjamini and Hochberg 1995).  Among 26,107 genes, some genes were replicated 6, 48, 49, or 382 times on an array.  Genes with large number of replication have more degree of freedom so they have more statistical power when testing for differential expression.  To eliminate the replication imbalance and to put all genes on the same replication level, genes with replicates on the array were averaged and the average was considered as one feature for the analysis.

organism: Brassica napus

source_name: True leaves 2, 3, and 4 from 10 pooled plants per replicate

label_protocol: For labeling mRNA, 500 ng of mRNA (in 15 µl) was combined with 1 µl of oligo (dT) (2 µg/µl), and 1 µl of random nonamer (2 µg/µl, Gene Link, Hawthorne, NY) in a 1.5 ml microcentrifuge tube on ice.  Reactions were mixed and incubated at 65 °C for 5 minutes.  Samples were placed at room temperature for 10 minutes and briefly centrifuged.  Six microliters of reverse-transcriptase buffer (5 X), 3 µl of DTT (0.1 M), 1 µl of dNTP (10 mM dATP, dTTP, dGTP, 2.5 mM dCTP), 1.5 µl of Cy5- or Cy3-dCTP, and 1 µl of Superscript II Reverse Transcriptase (Amersham Biosciences, Piscataway, NJ; Invitrogen, Carlsbad, CA) were added to the reactions and mixed in a total volume of 30 µl.  Reverse transcription reactions were incubated at 42 °C for 2 hours under dark conditions.  Three microliters of 2.5 M NaOH was added to each reaction, samples were mixed, and incubated at 37 °C for 15 minutes in the dark.  Fifteen microliters of 2 M HEPES was added and mixed.  Labeled samples were then purified using the Qiagen PCR purification kit (Valencia, CA) and eluted in 30 µl of Buffer EB.  For any given hybridization-comparison, reciprocally labeled samples (one Cy3 labeled, the other Cy5 labeled) were mixed and heated at 95 °C for 2 minutes.  Then 12 µl of 20 X SSC, 2 µl of 10 % SDS, and 7.5 µl of 10 % BSA were added for a total hybridization volume of ~ 75 µl.  Hybridization to microarray slides and washing steps were performed as described by Wang et. al., 2005, except that hybridization was conducted at 55 °C.

growth_protocol: Two biological replicates were planted as separate blocks in an environmentally controlled growth chamber (Percival Scientific, Perry Iowa).  Plants were watered daily and fertilized every other day as needed with dilute (1 tblsp/20 liters) Peters Professional Peat Lite Special 20-10-20.  Temperature was maintained at 21 ºC and lighting was maintained at ~ 258 and 280 micromoles/m2/s-1 in each replicate growth chamber, respectively, for 16 hrs each day.  The two biological replicates of the parental genotypes was composed of pooled leaf tissue from 40 plants, and was arranged in flats of 10 plants.  The two biological replicates for each polyploid genotype were composed of bulked leaf tissue from 10 plants (S1 and S6 plants from each line were bulked to represent the S0 and S5, respectively), and the 10 plants were grown in a single flat.  Flat locations within each replicate were randomized weekly.  All plants were harvested at the same developmental stage, when the third and fourth true leaves were outstretched from the meristem.  Plants were harvested at the same time of day (11:00am to 12:00pm CST).  Leaves two, three, and four from individual plants were bulked (as described above) comprising a given line replicate, and were flash frozen and homogenized in liquid N2 and stored at –80 °C.

extract_protocol: Total RNA was extracted from each biological replicate using Tri-Reagent (Molecular Research Center Inc., Cincinnati, OH) according to manufacturer protocols, and was quantified using a NanoDrop ND-1000 (Wilmington, DE).  Messenger-RNA was purified from total RNA using the Invitrogen FastTrack Micro mRNA Isolation Kit according to manufacturer protocols (Carlsbad, CA).  The quality of extracted RNAs was confirmed by 1% agarose electrophoresis and 260/280 ratios.

treatment_protocol: Treatments were different genotypes:  Brassica oleracea line TO1000, Brassica rapa line IMB218, 1:1 mix of rapa and oleracea RNA, and 3 independently resythesized Brassica napus polploid lines at the S0 generation (1200, 5200, and 5250) , and the S5 generation (1250, 5250, and 6450).

tag: Resynthesized B.napus line 6400

organism: Brassica sp.

tag: 1:1 mix of rapa and oleracea mRNA

tag: mix of IMB218 and TO1000


title: cells at 240 minutes after MBC treatment and growth in HU after G2/M arrest; biol rep 2

description: MBC_2: Cells were synchronized at G2/M at 36.5ºC for 3h 30min; MBC was added for 10 minutes before shifting cells to 25ºC;l cells were grown at 25ºC for 65 minutes, then washed and grown in medium containing hydroxyurea until 240 minutes post-G2/M release.


title: parentmix vs 5250

hyb_protocol: Hybridization to microarray slides and washing steps were performed as described by Wang et. al., 2005, except that hybridization was conducted at 55 °C.

tag: Resynthesized B.napus line 5250


title: parentmix vs 5200

tag: Resynthesized B.napus line 5200


title: parentmix vs 1200

tag: Resynthesized B.napus line 1200


title: parentmix vs 6450

tag: Resynthesized B.napus line 6450


title: cells at 240 minutes after MBC treatment and growth in HU after G2/M arrest; biol rep 1

description: MBC_1: Cells were synchronized at G2/M at 36.5ºC for 3h 30min; MBC was added for 10 minutes before shifting cells to 25ºC;l cells were grown at 25ºC for 65 minutes, then washed and grown in medium containing hydroxyurea until 240 minutes post-G2/M release.


title: parentmix vs 1250

tag: Resynthesized B.napus line 1250


title: cells at 90 minutes in HU after G2/M arrest; biol rep 1

description: 90_1: Cells synchronized at G2/M for 3h 45min were released into medium containing hydroxyurea at 25ºC for 90 minutes.


title: rapa vs oleracea

organism: Brassica rapa

source_name: True leaves 2, 3, and 4 from 40 pooled plants per replicate

tag: strain IMB218

organism: Brassica oleracea

tag: strain TO1000


title: CRL-2335 breast cancer treated with Eicosapentanoic acid for 6 hr (13702992-T6-EPACRL-2335)

status: Public on Mar 05 2009

city: Silver Spring

first: Rasha

last: Hammamieh

state: MD

address: 503 Robert Grant Ave

department: Molecular Pathology

institute: Walter Reed Army Institute of Research

hyb_protocol: custom oligo-nucleotide glass array slide were used for hybridization over night at 55 degree celius

scan_protocol: images were scanned using Genepix 4000B (Axon Instruments)

data_processing: Intensities were extracted using Genepix PRO 6, and Lowess normalization and statistical analysis were performed using GeneSpring GX

source_name: Human: breast cancer cell-line

label_protocol: dual channel labling were used: human reference RNA was labled with Cy3 and isolated RNA with Cy5

growth_protocol: Cell lines were cultured in the recommended media

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Breast cancer cells were treated with 10 µM fatty acids added to fresh media and continued incubating for 6hrs and 24 hrs respectively. Control cells were incubated in fresh media in the absence of fatty acids.

tag: treatment

value: Eicosapentanoic acid

tag: status

value: ER N

tag: cell line

source_name: universal reference RNA

tag: sample

value: universal reference RNA from Stratagen


title: HTB-132 breast cancer treated with Eicosapentanoic acid for 24 hr (13702760-T24-EPA-HTB-132)


title: HTB30SIBR breast cancer treated with Eicosapentanoic acid for 6 hr (13702756-T6EPA-HTB30SIBR-3)


title: HTB-30SKBR breast cancer treated with Eicosapentanoic acid for 24 hr (13702633-T24-EPAHTB-30SKBR-3)


title: HTB-132 breast cancer treated with Eicosapentanoic acid for 6 hr (13703107-27-T6EPAHTB-132)


title: HCC-1500 breast cancer treated with Eicosapentanoic acid for 24 hr (13702990.T24EPA-HCC-1500(+AA))

value: ER P


title: HCC1500 breast cabcer treated with Eicosapentanoic acid for 6 hr (13702757 T6EPA-HCC1500)


title: McF-7 breast cancer treated with Eicosapentanoic acid for 24 hr (13693643.T24-EPA-McF-7(+Cau.))


title: HCC70 breast cancer treated with Eicosapentanoic acid for 24 hr (13689074-T24EPA-HCC70)


title: HCC70 breast cancer treated with Eicosapentanoic acid for 6 hr (13696302-T6EPAHCC70)


title: HTB-21CAMA1 breast cancer treated with Eicosapentanoic acid for 24 hr (13696301T6EPA-HTB-21CAMA1)


title: HTB-21CAMA1 breast cancer cells 6 hr control (13702991-C6-HTB-21CAMA1)

value: Control


title: HTB-132 breast cancer cells 24 hr control (13702876.C24-HTB-132)


title: HTB126 breast cancer treated with Eicosapentanoic acid for 24 hr (13688841-T24EPA-HTB126)


title: HTB-126 breast cancer treated with Eicosapentanoic acid for 24 hr (13691422-T6EPAHTB-126)


title: HTB-21CAMA1 breast cancer treated with Eicosapentanoic acid for 24 hr (13702636-T24-EPA-HTB-21CAMA1)


title: McF-7 breast cancer treated with Eicosapentanoic acid for 6 hr (13685793-T6EPAMcF-7)


title: CRL-2335 breast cancer treated with Eicosapentanoic acid for 24 hr (13691536-T24-EPACRL-2335)


title: HTB-30SKBR breast cancer cells 24 hr control (13703347-C24HTB-30SKBR-3)


title: HCC-1500 breast cancer cells 24 hr control (13703349.C24-HCC-1500(+AA))


title: MCF-7 breast cancer cells for 24 hr control (13694226-C24MCF-7)


title: CRL-2335 breast cancer cells 6 hr control (13693996-C6 CRL-2335(-AA))


title: HTB-126 breast cancer cells 6 hr control (13693994-C6-HTB-126)


title: HTB-30SKBR breast cancer cells for 6 hr control (13702874-C6HTB-30SKBR-3)


title: CRL-2335 breast cancer cells 24 hr control (13691420-C24-CRL-2335)


title: HTB-126 breast cancer cells 24 hr control (13689423-C24-HTB-126)


title: HCC70 breast cancer cells 6 hr control (13689514-C6HCC70)


title: HTB-132 breast cancer cells 6 hr control (13689190-C6HTB-132)


title: CRL-2335 breast cancer cells treated with AA for 24 hrs (13693761-T24-AA-CRL-2335(-AA))

value: arachidonic acid


title: HTB-21CAMA1 breast cancer cells 24 hr control (13685680c24-HTB-21CAMA1)


title: HTB-21CAMA1 breast cancer cells treated with AA for 6 hrs (13702170-T6AA-HTB-21CAMA1)


title: HCC70 breast cancer cells 6 hr control (13685795-C24HCC70)


title: HTB-30SKBR breast cancer cells treated with AA for 24 hrs (13703348-T24AA-HTB-30SKBR-3)


title: HCC70 breast cancer cells treated with AA for 6 hrs (13689465-T6AAHCC70)


title: HCC-1500 breast cancer cells treated with AA for 6 hrs (13702282-T6-AA-HCC-1500)


title: HCC-1500 breast cancer cells treated with AA for 24 hrs (13703350.T24AA-HCC-1500)


title: 271 early rep5

description: Ring 3.1 vs. 3.2

source_name: Clone 271, early season, ambient

tag: phenotype

tag: genotype

source_name: Clone 271, early season, e[CO2]


title: HCC70 breast cancer cells treated with AA for 24 hrs (13691421-T24AAHCC70)


title: HCC-1500 breast cancer cells 6 hr control (13688840-C6HCC-1500)


title: MCF-7 breast cancer cells 6hr control (13685794-C6MCF-7)


title: MCF-7 breast cancer cells treated with AA for 6 hrs (13702993-T6AAMCF-7)


title: HTB126 breast cancer cells treated with AA for 6 hrs (13694227-T6AA-HTB126)


title: P. syringae pv.phaseolicola NPS3121 responses to bean leaf extract (technical replicate 2)

status: Public on Mar 03 2009

city: Irapuato

first: Jose Luis

last: Hernandez-Flores

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León

department: Ingeniería Genética

country: Mexico

institute: Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional

description: Overnight culture of strain NPS3121 was used to inoculate the fresh minimal medium M9, and it was allowed to grow at 18 °C to the mid exponential growth phase (A600 = 0.6).  After reaching this stage, bean leaf extract was added.

hyb_protocol: Labeled probes dried and resuspended in 40 µl of hybridization solution (25% hybridization buffer supplied in the CyScribe kit, 25% nuclease free water and 50% formamide). The probe was immediately applied onto the array and covered with a cover slip (Hybri-slips, Sigma-Aldrich Co. St Louis U.S.A.), hybridized 16 hours at 45°C in a humid hybridization chamber (Corning Incorporated, N.Y., U.S.A). After hybridization, the slides were washed once in solutions 1–4 (wash solution 1: 2% SSC, 0.1% SDS at 45 ºC; wash solution 2: 0.1% SSC, 0.1% SDS; wash solution 3: 0.1% SSC; wash solution 4: 0.01% SSC) for 5 min with gentle stirring/agitation. Washed slides were dried by centrifugation at 1600 r.p.m

scan_protocol: Slides were scanned with an Axon GenePix 4000 B scanner at a resolution of 10 µm adjusting the laser and gain parameters to obtain similar levels of fluorescence intensity in both channels

data_processing: Spot intensities were quantified using Axon GenePix Pro 6.0 image analysis software. The mean of the signals and the median of backgrounds were used for further analysis. Raw data were imported into the R 2.2.1 software (http://www.R-project.org). Background correction was done using the method Robust Multichip Analysis "RMA" (Irizarry et al., 2003) whereas normalization of the signal intensities within slides was carried out using the "printtiploess" method (Yang et al., 2002) using the LIMMA package (Smyth et al., 2003, www.bioconductor.org). Normalized data were log2 transformed and then fitted into mixed model ANOVAs (Gibson and Wolfinger, 2004; Wolfinger et al., 2001) using the Mixed procedure. The p-values of the extract effects were adjusted for by the False Discovery Rate method “FDR” (Benjamini and Hochberg, 1995). Estimates of the expression differences were calculated using the mixed model. Based on these statistical analyses, the spots with tests with an FDR less or equal to 5% and with changes in signal intensity between cultures with extract and culture control without extract of 1.5 fold or higher difference were considered as differentially expressed

organism: Pseudomonas savastanoi pv. phaseolicola

source_name: P. syringae pv. phaseolicola NPS3121 whith bean leaf extract

label_protocol: Purified total RNA (30 ug) was mixed with 3 uL of random nonamer primers and was incubated at 70ºC for 5 min. Reactions were held at room temperature for 10 min to allow the primers and the RNA template to anneal. To each reaction, the following were added: 1 uL of Cy5/Cy3-dCTP (1 mM) (Amersham Biosciences, Piscataway, NJ, U.S.A.), 2 uL of 0.1 M dithiothreitol, 4 uL of 5X Cyscript buffer, 1 uL of dNTP mixture (15 mM dATP, dTTP, and dGTP; 5 mM dCTP), 1uL of Cy3/Cy5 labeled dUTP and 200 U of CyScript reverse transcriptase. Reactions were incubated at 42ºC for 2 h. CyDye labelled single strand cDNA using the CyScribe GFX Purification Kit (Amersham Biosciences, Piscataway, NJ, U.S.A.) and according to the protocol recommended by the supplier. The purified labeled cDNA was then quantified to have with a Nanodrop equipment to final amount of 150 pg of each labeled cDNA.

treatment_protocol: For microarray experiments, P. syringae pv. phaseolicola NPS3121 was inoculated and grown on M9 medium at 18 oC to an optical density of 0.6 (OD 600nm). The culture was then divided into two equal parts; to one culture bean leaf extract  was added, while the other culture was used without extract additions. Both cultures were grown under the same conditions. Test culture for 6 hours, and control culture to reach a optical density similar to control culture.

tag: strain

source_name: Pseudomonas syringae pv. phaseolicola NPS3121 whithout bean leaf extract

extract_protocol: Total RNA was isolated using Trizol reagent as recommended by the manufacturer (Invitrogen). A second step of purification was performed using RNeasy MinElute spin columns (Qiagen) to remove contaminating DNA. RNAs were eluted in 50 µl of diethylpyrocarbonate (DEPC)-treated water and the concentration was determined using the NanoDrop equipment. RNA integrity was checked by analytical agarose gel electrophoresis.

treatment_protocol: P. syringae pv. phaseolicola NPS3121 was inoculated and grown on M9 medium at 18o C to an optical density of 0.6 (OD 600nm). This culture are considered as positive control of experiment, this was not supplemented with any extract.


title: MCF7 breast cancer cells treated with AA for 24 hrs (13689189-T24AAMCF7)


title: HTB-126 breast cancer cells treated with AA for 24 hrs (13693760-T24AAHTB-126)


title: CRL-2335 breast cancer cells treated with AA for 6 hrs (13693995-14-T6-AACRL-2335)


title: HTB-30SKBR breast cancer cells treated with AA for 6 hrs (13685682T6AA-HTB-30SKBR-3)


title: HTM-STRETCHING-3

status: Public on Mar 04 2009

city: Durham

first: Pedro

last: Gonzalez

address: Erwin Road Box 3802

department: Ophthalmology

institute: Duke University

description: No treatment

data_processing: Data was analysed using GeneSpring 7.2 (Silicon Genetics). Genes were filtered to their intensities in the control channel (control used was Universal Reference Human RNA from Stratagene).  Intensity-dependent normalization was performed per spot and per chip (LOWESS)

source_name: Human Trabecular Meshwork cells, subjected to mechanical stress

growth_protocol: Cell cultures were maintained at 37oC in 5% CO2 low glucose Dulbecco’s Modified Eagle Medium. Cell cultures were used in passage 3

extract_protocol: Total RNA was then isolated using a RNeasy kit (Qiagen Inc. Valencia, CA) and treated with DNase.

treatment_protocol: No treatment

tag: cell type

value: HTM cell cultures were obtained from cadaver eyes, 48 hs post-mortem, with no history of eye diseases.

source_name: Stratagene Universal Human Reference

growth_protocol: No growth protocol

value: Stratagene Universal Human Reference http:/www.stratagene.com/manuals/74100.pdf


title: HTM-CONTROL-2

description: No treatment

source_name: Human Trabecular Meshwork cells, no subjected to mechanical stress


title: HTM-CONTROL-1

description: No treatment


title: HTM-STRETCHING-2

description: No treatment


title: HTM-STRETCHING-1

description: No treatment


title: HTB-21CAMA1 breast cancer cells treated with AA for 24 hrs (13702635-T24AA-HTB-21CAMA1)


title: P. syringae pv. phaseolicola NPS3121 responses to bean leaf extract (biological replicate 3)

description: Overnight culture of strain NPS3121 was used to inoculate the fresh minimal medium M9, and it was allowed to grow at 18 °C to the mid exponential growth phase (A600 = 0.6). After reaching this stage, bean leaf extract was added.

source_name: P. syringae pv. phaseolicola NPS3121 with bean leaf extract

extract_protocol: Total RNA was isolated using Trizol reagent as recommended by the manufacturer (Invitrogen). A second step of purification was performed using RNeasy MinElute spin columns (Qiagen) to remove contaminating DNA. RNAs were eluted in 50 µl of diethylpyrocarbonate (DEPC)-treated water and the concentration was determined using the NanoDrop equipment. RNA integrity was checked by analytical agarose gel electrophoresis

source_name: P. syringae pv. phaseolicola NPS3121 without bean leaf extract


title: P. syringae pv.phaseolicola NPS3121 responses to bean leaf extract (biological replicate 2)

growth_protocol: Overnight culture of strain NPS3121 was used to inoculate the fresh minimal medium M9, and it was allowed to grow at 18 °C to the mid exponential growth phase (A600 = 0.6).


title: HTM-CONTROL-3

description: No treatment


title: Replete medium repC 10492602_532

description: Replete medium repC 10492602_532

source_name: mycelium


title: P. syringae pv.phaseolicola NPS3121 responses to bean pod extract technical replicate 2

description: The bacterium P. syringae pv. phaseolicola is the causal agent of the “halo blight” disease of beans (Phaseolus vulgaris L.). The disease attack both foliage and pods. Overnight culture of strain NPS3121 was used to inoculate the fresh minimal medium M9, and it was allowed to grow at 18 °C to the mid exponential growth phase (A600 = 0.6).

hyb_protocol: Labeled probes dried and resuspended in 40 µl of hybridization solution (25% hybridization buffer supplied in the CyScribe kit, 25% nuclease free water and 50% formamide). The probe was immediately applied onto the array and covered with a cover slip (Hybri-slips, Sigma-Aldrich Co. St Louis U.S.A.), hybridized 16 hours at 45°C in a humid hybridization chamber (Corning Incorporated, N.Y., U.S.A). After hybridization, the slides were washed once in solutions 1–4 (wash solution 1: 2% SSC, 0.1% SDS at 45 ºC; wash solution 2: 0.1% SSC, 0.1% SDS; wash solution 3: 0.1% SSC; wash solution 4: 0.01% SSC) for 5 min with gentle stirring/agitation. Washed slides were dried by centrifugation at 1600 r.p.m.

data_processing: Spot intensities were quantified using Axon GenePix Pro 6.0 image analysis software. The mean of the signals and the median of backgrounds were used for further analysis. Raw data were imported into the R 2.2.1 software (http://www.R-project.org). Background correction was done using the method Robust Multichip Analysis "RMA" (Irizarry et al., 2003) whereas normalization of the signal intensities within slides was carried out using the "printtiploess" method (Yang et al., 2002) using the LIMMA package (Smyth et al., 2003, www.bioconductor.org). Normalized data were log2 transformed and then fitted into mixed model ANOVAs (Gibson and Wolfinger, 2004; Wolfinger et al., 2001) using the Mixed procedure. The p-values of the extract effects were adjusted for by the False Discovery Rate method “FDR” (Benjamini and Hochberg, 1995). Estimates of the expression differences were calculated using the mixed model. Based on these statistical analyses, the spots with tests with an FDR less or equal to 5% and with changes in signal intensity between cultures with extract and culture control without extract of 1.5 fold or higher difference were considered as differentially expressed.

source_name: P. syringae pv. phaseolicola NPS3121 with bean pod extract

treatment_protocol: For microarray experiments, P. syringae pv. phaseolicola NPS3121 was inoculated and grown on M9 medium at 18o C to an optical density of 0.6 (OD 600nm). Bean pod extract was added and the culture was grown for 6 more hours under the same conditions.

source_name: Pseudomonas syringae pv. phaseolicola NPS3121 whitout bean pod extract

treatment_protocol: P. syringae pv. phaseolicola NPS3121 was inoculated and grown on M9 medium at 18o C to an optical density of 0.6 (OD 600nm). In this treatment culture was not supplemented with any extract.


title: P. syringae pv.phaseolicola NPS3121 responses to bean pod extract biological replicate 1

label_protocol: Purified total RNA (30 ug) was mixed with 3 uL of random nonamer primers and was incubated at 70ºC for 5 min. Reactions were held at room temperature for 10 min to allow the primers and the RNA template to anneal. To each reaction, the following were added: 1 uL of Cy5/Cy3-dCTP (1 mM) (Amersham Biosciences, Piscataway, NJ, U.S.A.), 2 uL of 0.1 M dithiothreitol, 4 uL of 5X Cyscript buffer, 1 uL of dNTP mixture (15 mM dATP, dTTP, and dGTP; 5 mM dCTP), 1uL of Cy3/Cy5 labeled dUTP and 200 U of CyScript reverse transcriptase. Reactions were incubated at 42ºC for 2 h.  CyDye labelled single strand cDNA using the CyScribe GFX Purification Kit (Amersham Biosciences, Piscataway, NJ, U.S.A.) and according to the protocol recommended by the supplier. The purified labeled cDNA was then quantified to have with a Nanodrop equipment to final amount of 150 pg of each labeled cDNA.

source_name: Pseudomonas syringae pv. phaseolicola NPS3121


title: P. syringae pv.phaseolicola NPS3121 responses to bean pod extract technical replicate 3


title: P. syringae pv. phaseolicola NPS3121 responses to bean leaf extract (technical replicate 3)

source_name: P. syringae pv. phaseolicola with bean leaf extract


title: P. syringae pv.phaseolicola NPS3121 responses to bean pod extract biological replicate 2


title: P. syringae pv. phaseolicola NPS3121 with bean leaf extract (technical replicate 1)

treatment_protocol: For microarray experiments, P. syringae pv. phaseolicola NPS3121 was inoculated and grown on M9 medium at 18 oC to an optical density of 0.6 (OD 600nm). The culture was then divided into two equal parts; to one culture bean leaf extract was added, while the other culture was used without extract additions. Both cultures were grown under the same conditions. Test culture for 6 hours, and control culture to reach a optical density similar to control culture.

treatment_protocol: P. syringae pv. phaseolicola NPS3121 was inoculated and grown on M9 medium at 18o C to an optical density of 0.6 (OD 600nm). This culture are considered as positive control of experiment, this was not supplemented with any extract


title: P. syringae pv.phaseolicola NPS3121 responses to bean pod extract technical replicate 1


title: P. syringae pv. phaseolicola NPS3121 responses to apoplastic fluid technical replicate 2

description: P. syringae pv. phaseolicola NPS3121 were inoculated and grown on M9 medium at 18o C to an optical density of 0.6 (OD 600nm). The culture was then divided into two equal parts; to one culture apoplastic fluid of bean pod was added, while the other culture was used without extract additions. Both cultures were grown under the same conditions. Test culture for 6 hours, and control culture to reach a optical density similar to control culture.

source_name: P. syringae pv. phaseolicola NPS3121 with apoplastic fluid

treatment_protocol: For microarray experiments, P. syringae pv. phaseolicola NPS3121 was inoculated and grown on M9 medium at 18 oC to an optical density of 0.6 (OD 600nm). The culture was then divided into two equal parts; to one culture apoplastic fluid of bean leaf was added, while the other culture was used without extract additions. Both cultures were grown  under the same conditions. Test culture for 6 hours, and control culture to reach a optical density similar to control culture.

source_name: Pseudomonas syringae pv. phaseolicola NPS3121 whitout apoplastic fluid

treatment_protocol: P. syringae pv. phaseolicola NPS3121 was inoculated and grown on M9 medium at 18o C to an optical density of 0.6 (OD 600nm). This culture are considered as positive control of experiment,  this was not supplemented with any extract.


title: liver from animals lacking apolipoprotein E with cis9,trans11CLA

status: Public on Mar 01 2009

city: Zaragoza

first: Jesus

last: Osada

address: Miguel Servet, 177

country: Spain

institute: Universidad de Zaragoza

description: Gene expression data from liver apolipoprotein E-deficient male mice on a western diet for 12 weeks

hyb_protocol: Following fragmentation, 8 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Murine Genome U74A version 2

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Mus musculus

source_name: liver RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA

extract_protocol: Tri reagent extraction of total RNA was performed according to the manufacturer's instructions. RNA was extracted using a Quiagen RNeasy kit.

tag: three-month old Male Animals with a C57BL/6JxOLA129 genetic background were fed a high fat (30% of calories), high cholesterol diet(0.15%, w/w).The control diet also contained 1.0 % (wt/wt) cis9,trans11CLA


title: P. syringae pv. phaseolicola NPS3121 responses to apoplastic fluid biological replicate 3


title: P. syringae pv. phaseolicola NPS3121 responses to bean leaf extract (biological replicate 1)

source_name: Pseudomonas syringae pv. phaseolicola NPS3121 whitout bean leaf extract


title: P. syringae pv. phaseolicola NPS3121 responses to apoplastic fluid biological replicate 2


title: P. syringae pv. phaseolicola NPS3121 responses to apoplastic fluid, technical replicate 1


title: P. syringae pv.phaseolicola NPS3121 responses to bean pod extract biological replicate 3


title: liver from animals lacking apolipoprotein E with trans10,cis12CLA

source_name: Liver RNA

tag: three-month old Male Animals with a C57BL/6JxOLA129 genetic background were fed a high fat (30% of calories), high cholesterol diet(0.15%, w/w).The control diet also contained 1.0 % (wt/wt) trans10,cis12CLA


title: liver from animals lacking apolipoprotein E

description: Gene expression data from liver apolipoprotein E-deficient male  mice on a western diet for 12 weeks

tag: three-month old Male Animals with a C57BL/6JxOLA129 genetic background were fed a high fat (30% of calories), high cholesterol diet(0.15%, w/w).The control diet also contained 1.0 % (wt/wt) linoleic acid


title: E.rectale_in vitro_T-G media_#3

city: St Louis

first: Federico

middle: E

last: Rey

address: 4444 Forest Park Blvd

department: Pathology

institute: Washington University

description: Eubacterium rectale growing in vitro. Anaerobic. Tryptone-Glucose media (exponential phase of growth).

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Expression analyses were performed using the MAS5 algorithm implemented in BioConductor’s ‘Affy package’, following masking of GeneChip imperfections with Harshlight - in both cases using the default parameters.

label: Biotin

organism: Agathobacter rectalis

source_name: E.rectale growing anaerobically in tryptone-glucose media

label_protocol: Enzo Biochemicals Bioarray terminal labeling kit

extract_protocol: Qiagen RNeasy mini column extraction; Ambion DNA free treatment

tag: media

value: Tryptone-Glucose


title: E.rectale_in vitro_T-G media_#2


title: P. syringae pv. phaseolicola NPS3121 responses to apoplastic fluid, biological replicate 1

source_name: P. syringae pv. phaseolicola NPS3121 with bean apoplastic fluid, biological replicate 1

source_name: Pseudomonas syringae pv. phaseolicola NPS3121 whitout extract


title: E.rectale_in vitro_T-G media_#4


title: B.thetaiotaomicron-E.rectale_Bi-association_High polysaccharide diet_#3

description: Bacteroides thetaiotaomicron and Eubacterium rectale growing in the cecum of a mouse.

organism:
Bacteroides thetaiotaomicron
Agathobacter rectalis

source_name: B.thetaiotaomicron and E.rectale (Bi-association) growing in the cecum of mice fed a high polysaccharide diet

tag: host

value: mouse

value: NMRI

tag: gender

value: male

tag: age

value: 12-14 weeks

tag: diet

value: high polysaccharide


title: P. syringae pv. phaseolicola NPS3121 responses to apoplastic fluid technical replicate 3


title: E.rectale_in vitro_T-G media_#1


title: B.thetaiotaomicron-E.rectale_Bi-association_High polysaccharide diet_#2


title: E.rectale_monoassociation_High polysaccharide diet_#4

description: Eubacterium rectale growing in the cecum of a mouse.

source_name: E. rectale growing in the cecum of mice fed a high polysaccharide diet


title: E.rectale_monoassociation_High polysaccharide diet_#1


title: E.rectale_monoassociation_High polysaccharide diet_#2


title: B.thetaiotaomicron-E.rectale_Bi-association_High polysaccharide diet_#1


title: E.rectale_monoassociation_High polysaccharide diet_#3


title: B.thetaiotaomicron_monoassociation_High polysaccharide diet_#3

description: Bacteroides thetaiotaomicron growing in the cecum of a mouse.

organism: Bacteroides thetaiotaomicron

source_name: B.thetaiotaomicron growing in the cecum of mice fed a high polysaccharide diet


title: B.thetaiotaomicron_monoassociation_High polysaccharide diet_#2


title: B.thetaiotaomicron_monoassociation_High polysaccharide diet_#1


title: N2_MIX-1_IP1

city: Berkeley

first: Barbara

last: Meyer

state: CA

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

hyb_protocol: Hybridization protocol provided and performed by NimbleGen (http://www.nimblegen.com/products/chip/index.html)

scan_protocol: Sample scan protocol provided and performed by NimbleGen (http://www.nimblegen.com/products/chip/index.html)

data_processing: performed at Nimblegen using their standard protocol producing gff files with log2 ratios of experimental/input (http://www.nimblegen.com/products/chip/index.html).

organism: Caenorhabditis elegans

source_name: N2 embryo input

label_protocol: Sample labeling protocol provided and performed by Nimblegen using standard NimbleGen protocol

growth_protocol: Wild type, N2, Caenorhabditis elegans were grown on egg pates seeded with E. coli OP50

extract_protocol: see PDF linked to GSE14640

treatment_protocol: Embryos used for microarray analysis were obtained from bleached gravid adults.

tag: N2 XX embryo

tag: nonselected input

source_name: N2 embryo MIX-1 IP

tag: MIX-1 IP


title: B.thetaiotaomicron_monoassociation_High polysaccharide diet_#4


title: N2_DPY-27_IP1

source_name: N2 embryo DPY-27 IP

tag: DPY27 IP


title: B.theta-E.rectale-simple sugar, high fat diet_#4

description: Bacteroides thetaiotaomicron and Eubacterium rectale growing in the cecum of mice

data_processing: Expression analyses were performed using the MAS5 algorithm implemented in BioConductor’s ‘Affy package’, following masking of GeneChip  imperfections with Harshlight - in both cases using the default parameters.

source_name: B.theta and E.rectale growing in the cecum of mice fed a simple sugar, high fat diet

value: 14 weeks

value: simple sugar, high fat


title: B.theta-E.rectale-simple sugar, high fat diet_#5


title: B.thetaiotaomicron-E.rectale_Bi-association_High polysaccharide diet_#4


title: N2_mock-IP2

source_name: N2 embryo nonspecific-IgG  IP

tag: mock IP


title: B.theta-E.rectale-simple sugar, high fat diet_#3


title: N2_mock-IP1


title: N2_SDC-3_IP2

source_name: N2 embryo SDC-3 IP

tag: SDC-3 IP


title: N2_SDC-3_IP1


title: B.theta-E.rectale-simple sugar, high fat diet_#1


title: B.theta-E.rectale-simple sugar, high fat diet_#2


title: B.theta-E.rectale-simple sugar, low fat diet_#5

source_name: B.theta and E.rectale growing in the cecum of mice fed a simple sugar, low fat diet

value: simple sugar, low fat


title: B.theta-E.rectale-simple sugar, low fat diet_#3


title: B.theta-E.rectale-simple sugar, low fat diet_#4


title: N2_mock-IP3


title: B.theta-E.rectale-High polysaccharide diet_#5

description: B. thetaiotaomicron and Eubacterium rectale, grown in vivo in the cecum of NMRI inbred mouse fed a plant polysaccharide diet.

source_name: B.theta and E.rectale growing in the cecum of mice fed a high polysaccharide diet

extract_protocol: Qiagen RNAeasy column and Ambion DNAfree DNAseI treatment


title: B.theta-E.rectale-simple sugar, low fat diet_#1


title: B.theta-E.rectale-High polysaccharide diet_#2


title: B.theta-E.rectale-High polysaccharide diet_#4


title: B.theta-E.rectale-High polysaccharide diet_#1


title: Gnotobiotic_proximal_colon_germ_free_#4

description: Here we compare patterns of gene expression in the proximal colons of mice that were either germ-free, monoassociated with E.rectale or B. thetaiotaomicron, or  co-colonized with both organisms

hyb_protocol: Following fragmentation of 20 ug of the labeled cRNA, a hybridization cocktail containing Affymetrix spike-in controls and fragmented labeled cRNA was loaded onto a GeneChip array. The array was hybridized 16 hours at 45 degrees C with rotation at 60 rpm, then washed with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated antistreptavidin.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data was normalized using PLIER

source_name: proximal colon of germ-free mouse

label_protocol: Total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for the in vitro transcription reaction, producing biotin-labeled cRNA(ENZO labeling kit).

extract_protocol: Proximal colon was homgenized in RLT buffer. RNA was extracted using RNeasy mini kit (Qiagen)

tag: NMRI mice, males, 10-14 weeks old


title: N2_MIX-1_IP2


title: Gnotobiotic_proximal_colon_B_thetaiotaomicron_#4

source_name: proximal colon of mouse colonized with Bacteroides thetaiotaomicron


title: Gnotobiotic_proximal_colon_B_thetaiotaomicron_#1


title: Gnotobiotic_proximal_colon_B_thetaiotaomicron_#3


title: Gnotobiotic_proximal_colon_B_thetaiotaomicron_#2


title: Gnotobiotic_proximal_colon_germ_free_#3


title: Gnotobiotic_proximal_colon_germ_free_#2


title: Gnotobiotic_proximal_colon_E_rectale_#1

source_name: proximal colon of mouse colonized with Eubacterium rectale


title: Gnotobiotic_proximal_colon_E_rectale_#4


title: Gnotobiotic_proximal_colon_E_rectale_B_thetaiotaomicron_#4

source_name: proximal colon of mouse colonized with Eubacterium rectale and Bacteroides thetaiotaomicron


title: Gnotobiotic_proximal_colon_E_rectale_B_thetaiotaomicron_#3


title: B.theta-E.rectale-simple sugar, low fat diet_#2

tag: strain


title: Gnotobiotic_proximal_colon_E_rectale_#2


title: HeLa DMSO Vs HeLa SGR Experiment_2

status: Public on Feb 28 2009

city: Bangalore

first: Tapas

middle: Kumar

last: Kundu

state: Karnataka

address: Jakkur

department: Molecular Biology and Genetics Unit

country: India

institute: Jawaharlal Nehru Centre for Advanced scientific Research

description: Microarrays were scanned on an Agilent scanner (G2565AA) at 100% laser power, 30% PMT.Data extraction was carried out with Agilent Feature Extraction software (version 9.1), and normalization was done using linear per array algorithm according to the manufacturer’s protocol.

hyb_protocol: 1. Carefully pipette entire 40 ul sample mixture onto the middle of the array surface. Do not allow direct contact of the array surface with pipette tip, as this may scratch the array surface. Avoid creation of air bubbles in the hybridization buffer. 2. Gently overlay the cover slip onto the solution on the array by positioning the cover slip at one end of the array and lowering it down until it is in contact with the hybridization solution. Be sure the solution covers the entire array footprint. Small bubbles will not to lose hybridization. 3. Pipet 500 ul of 2X SSC onto a flat, folded dust free tissue. This is sufficient to maintain the humidity inside the hybridization chamber. 4. Very carefully, place the microarray slide over the damp tissue and seal the cap tightly. Be very careful that the cover slip does not slip off. Be sure that the array does not touch the tissue as this may remove hybridization solution from the array surface through capillary action. 5. Place the tube in a 650 C incubator. Ensure the microarray, now enclosed in the tube, is level and stable in the incubator. Allow the hybridization to proceed overnight (18 hours) at this temperature.

scan_protocol: Laser detection of Cyanine 3 and Cyanine 5 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.

data_processing: Scan data (Raw data) is analyzed using GeneSpring GX v7.3. Per spot per chip lowess normalization was done.A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead. Biological analysis was done using Genotypic's Biointerpreter software.

organism: Homo sapiens

source_name: HeLa cell line treated with SGR

label_protocol: Labeling of cDNA was carried out using the MICROMAXTM Direct Labeling Kit (PerkinElmer Life Sciences) according to the manufacturer’s instructions. Typically, 40 µg total RNA was used in each of the labeling reactions

extract_protocol: Trizol Method

tag: HeLa cell line derived from human cervical cancer tissues treated with SGR

source_name: HeLa cell line treated with DMSO

label_protocol: Labeling of cDNA was carried out using the MICROMAXTM Direct Labeling Kit (PerkinElmer Life Sciences) according to the manufacturer’s instructions. Typically, 50 µg total RNA was used in each of the labeling reactions.

tag: HeLa cell line derived from human cervical cancer tissues treated with DMSO


title: Gnotobiotic_proximal_colon_E_rectale_B_thetaiotaomicron_#1


title: Gnotobiotic_proximal_colon_E_rectale_#3


title: HeLa SGR Vs HeLa DMSO Experiment_1

source_name: HeLa cell line treated with p300-HAT inhibitor

tag: HeLa cell line derived from human cervical cancer tissues treated with p300-HAT inhibitor


title: Gnotobiotic_proximal_colon_germ_free_#1